[{"publist_id":"7729","ec_funded":1,"file_date_updated":"2020-07-14T12:45:20Z","article_number":"10279","related_material":{"record":[{"id":"8822","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Grones, Peter","first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","last_name":"Abas","first_name":"Melinda F","full_name":"Abas, Melinda F"},{"last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub"},{"full_name":"Jones, Angharad","first_name":"Angharad","last_name":"Jones"},{"first_name":"Sascha","last_name":"Waidmann","full_name":"Waidmann, Sascha"},{"full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"volume":8,"date_created":"2018-12-11T11:45:06Z","date_updated":"2024-03-28T23:30:38Z","year":"2018","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"Springer","publication_status":"published","month":"07","doi":"10.1038/s41598-018-28188-1","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000437673200053"]},"oa":1,"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"},{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"quality_controlled":"1","isi":1,"issue":"1","abstract":[{"text":"Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2018_ScientificReports_Grones.pdf","access_level":"open_access","creator":"dernst","file_size":2413876,"content_type":"application/pdf","file_id":"5714","relation":"main_file","date_created":"2018-12-17T15:38:56Z","date_updated":"2020-07-14T12:45:20Z","checksum":"266b03f4fb8198e83141617aaa99dcab"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"191","intvolume":" 8","title":"PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism","status":"public","ddc":["581"],"article_processing_charge":"No","has_accepted_license":"1","day":"06","scopus_import":"1","date_published":"2018-07-06T00:00:00Z","citation":{"ista":"Grones P, Abas MF, Hajny J, Jones A, Waidmann S, Kleine Vehn J, Friml J. 2018. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 8(1), 10279.","ieee":"P. Grones et al., “PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism,” Scientific Reports, vol. 8, no. 1. Springer, 2018.","apa":"Grones, P., Abas, M. F., Hajny, J., Jones, A., Waidmann, S., Kleine Vehn, J., & Friml, J. (2018). PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. Springer. https://doi.org/10.1038/s41598-018-28188-1","ama":"Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-28188-1","chicago":"Grones, Peter, Melinda F Abas, Jakub Hajny, Angharad Jones, Sascha Waidmann, Jürgen Kleine Vehn, and Jiří Friml. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports. Springer, 2018. https://doi.org/10.1038/s41598-018-28188-1.","mla":"Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports, vol. 8, no. 1, 10279, Springer, 2018, doi:10.1038/s41598-018-28188-1.","short":"P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018)."},"publication":"Scientific Reports"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Plant hormones as signalling molecules play an essential role in the control of plant growth and development. Typically, sites of hormonal action are usually distant from the site of biosynthesis thus relying on efficient transport mechanisms. Over the last decades, molecular identification of proteins and protein complexes involved in hormonal transport has started. Advanced screens for genes involved in hormonal transport in combination with transport assays using heterologous systems such as yeast, insect, or tobacco BY2 cells or Xenopus oocytes provided important insights into mechanisms underlying distribution of hormones in plant body and led to identification of principal transporters for each hormone. This review gives a short overview of the mechanisms of hormonal transport and transporters identified in Arabidopsis thaliana."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"47","status":"public","title":"Transporters and mechanisms of hormone transport in arabidopsis","intvolume":" 87","oa_version":"None","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Advances in Botanical Research","citation":{"ista":"Abualia R, Benková E, Lacombe B. 2018. Transporters and mechanisms of hormone transport in arabidopsis. Advances in Botanical Research. 87, 115–138.","ieee":"R. Abualia, E. Benková, and B. Lacombe, “Transporters and mechanisms of hormone transport in arabidopsis,” Advances in Botanical Research, vol. 87. Elsevier, pp. 115–138, 2018.","apa":"Abualia, R., Benková, E., & Lacombe, B. (2018). Transporters and mechanisms of hormone transport in arabidopsis. Advances in Botanical Research. Elsevier. https://doi.org/10.1016/bs.abr.2018.09.007","ama":"Abualia R, Benková E, Lacombe B. Transporters and mechanisms of hormone transport in arabidopsis. Advances in Botanical Research. 2018;87:115-138. doi:10.1016/bs.abr.2018.09.007","chicago":"Abualia, Rashed, Eva Benková, and Benoît Lacombe. “Transporters and Mechanisms of Hormone Transport in Arabidopsis.” Advances in Botanical Research. Elsevier, 2018. https://doi.org/10.1016/bs.abr.2018.09.007.","mla":"Abualia, Rashed, et al. “Transporters and Mechanisms of Hormone Transport in Arabidopsis.” Advances in Botanical Research, vol. 87, Elsevier, 2018, pp. 115–38, doi:10.1016/bs.abr.2018.09.007.","short":"R. Abualia, E. Benková, B. Lacombe, Advances in Botanical Research 87 (2018) 115–138."},"page":"115 - 138","date_published":"2018-01-01T00:00:00Z","publist_id":"8007","year":"2018","publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Elsevier","author":[{"full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","first_name":"Rashed"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"first_name":"Benoît","last_name":"Lacombe","full_name":"Lacombe, Benoît"}],"related_material":{"record":[{"id":"10303","status":"public","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:44:20Z","date_updated":"2024-03-28T23:30:40Z","volume":87,"month":"01","external_id":{"isi":["000453657800006"]},"isi":1,"quality_controlled":"1","doi":"10.1016/bs.abr.2018.09.007","language":[{"iso":"eng"}]},{"acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41590-018-0109-z","isi":1,"quality_controlled":"1","project":[{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients"},{"grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"},{"_id":"25A48D24-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1396-2014","name":"Molecular and system level view of immune cell migration"},{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"external_id":{"pmid":["29777221"],"isi":["000433041500026"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29777221"}],"month":"05","date_created":"2018-12-11T11:44:10Z","date_updated":"2024-03-28T23:30:40Z","volume":19,"author":[{"orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","last_name":"Hons","first_name":"Miroslav","full_name":"Hons, Miroslav"},{"first_name":"Aglaja","last_name":"Kopf","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja"},{"full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F","full_name":"Leithner, Alexander F"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","first_name":"Florian R","last_name":"Gärtner","full_name":"Gärtner, Florian R"},{"full_name":"Abe, Jun","last_name":"Abe","first_name":"Jun"},{"orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","first_name":"Jörg","full_name":"Renkawitz, Jörg"},{"full_name":"Stein, Jens","last_name":"Stein","first_name":"Jens"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6891"}]},"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"MiSi"},{"_id":"Bio"}],"year":"2018","acknowledgement":"This work was funded by grants from the European Research Council (ERC StG 281556 and CoG 724373) and the Austrian Science Foundation (FWF) to M.S. and by Swiss National Foundation (SNF) project grants 31003A_135649, 31003A_153457 and CR23I3_156234 to J.V.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687, and J.R. was funded by an EMBO long-term fellowship (ALTF 1396-2014).","pmid":1,"ec_funded":1,"publist_id":"8040","date_published":"2018-05-18T00:00:00Z","page":"606 - 616","publication":"Nature Immunology","citation":{"mla":"Hons, Miroslav, et al. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” Nature Immunology, vol. 19, no. 6, Nature Publishing Group, 2018, pp. 606–16, doi:10.1038/s41590-018-0109-z.","short":"M. Hons, A. Kopf, R. Hauschild, A.F. Leithner, F.R. Gärtner, J. Abe, J. Renkawitz, J. Stein, M.K. Sixt, Nature Immunology 19 (2018) 606–616.","chicago":"Hons, Miroslav, Aglaja Kopf, Robert Hauschild, Alexander F Leithner, Florian R Gärtner, Jun Abe, Jörg Renkawitz, Jens Stein, and Michael K Sixt. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” Nature Immunology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41590-018-0109-z.","ama":"Hons M, Kopf A, Hauschild R, et al. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 2018;19(6):606-616. doi:10.1038/s41590-018-0109-z","ista":"Hons M, Kopf A, Hauschild R, Leithner AF, Gärtner FR, Abe J, Renkawitz J, Stein J, Sixt MK. 2018. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 19(6), 606–616.","apa":"Hons, M., Kopf, A., Hauschild, R., Leithner, A. F., Gärtner, F. R., Abe, J., … Sixt, M. K. (2018). Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. Nature Publishing Group. https://doi.org/10.1038/s41590-018-0109-z","ieee":"M. Hons et al., “Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells,” Nature Immunology, vol. 19, no. 6. Nature Publishing Group, pp. 606–616, 2018."},"day":"18","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","title":"Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells","status":"public","intvolume":" 19","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"15","abstract":[{"lang":"eng","text":"Although much is known about the physiological framework of T cell motility, and numerous rate-limiting molecules have been identified through loss-of-function approaches, an integrated functional concept of T cell motility is lacking. Here, we used in vivo precision morphometry together with analysis of cytoskeletal dynamics in vitro to deconstruct the basic mechanisms of T cell migration within lymphatic organs. We show that the contributions of the integrin LFA-1 and the chemokine receptor CCR7 are complementary rather than positioned in a linear pathway, as they are during leukocyte extravasation from the blood vasculature. Our data demonstrate that CCR7 controls cortical actin flows, whereas integrins mediate substrate friction that is sufficient to drive locomotion in the absence of considerable surface adhesions and plasma membrane flux."}],"issue":"6","type":"journal_article"},{"page":"2542 - 2544","publication":"Brain a journal of neurology","citation":{"short":"X. Contreras, S. Hippenmeyer, Brain a Journal of Neurology 141 (2018) 2542–2544.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” Brain a Journal of Neurology, vol. 141, no. 9, Oxford University Press, 2018, pp. 2542–44, doi:10.1093/brain/awy218.","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” Brain a Journal of Neurology. Oxford University Press, 2018. https://doi.org/10.1093/brain/awy218.","ama":"Contreras X, Hippenmeyer S. Incorrect trafficking route leads to autism. Brain a journal of neurology. 2018;141(9):2542-2544. doi:10.1093/brain/awy218","apa":"Contreras, X., & Hippenmeyer, S. (2018). Incorrect trafficking route leads to autism. Brain a Journal of Neurology. Oxford University Press. https://doi.org/10.1093/brain/awy218","ieee":"X. Contreras and S. Hippenmeyer, “Incorrect trafficking route leads to autism,” Brain a journal of neurology, vol. 141, no. 9. Oxford University Press, pp. 2542–2544, 2018.","ista":"Contreras X, Hippenmeyer S. 2018. Incorrect trafficking route leads to autism. Brain a journal of neurology. 141(9), 2542–2544."},"date_published":"2018-09-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Incorrect trafficking route leads to autism","intvolume":" 141","_id":"28","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","type":"journal_article","abstract":[{"text":"This scientific commentary refers to ‘NEGR1 and FGFR2 cooperatively regulate cortical development and core behaviours related to autism disorders in mice’ by Szczurkowska et al. ","lang":"eng"}],"issue":"9","quality_controlled":"1","isi":1,"external_id":{"isi":["000446548100012"]},"language":[{"iso":"eng"}],"doi":"10.1093/brain/awy218","month":"09","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"SiHi"}],"year":"2018","date_created":"2018-12-11T11:44:14Z","date_updated":"2024-03-28T23:30:42Z","volume":141,"author":[{"first_name":"Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7902"}]}},{"intvolume":" 8","ddc":["576","581"],"status":"public","title":"Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls","_id":"442","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:29Z","date_created":"2018-12-12T10:17:43Z","checksum":"6644ba698206eda32b0abf09128e63e3","relation":"main_file","file_id":"5299","content_type":"application/pdf","file_size":11352389,"creator":"system","file_name":"IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf","access_level":"open_access"}],"pubrep_id":"970","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH."}],"article_type":"original","citation":{"short":"L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018).","mla":"Li, Lanxin, et al. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol, vol. 8, no. 1, Bio-protocol, 2018, doi:10.21769/BioProtoc.2685.","chicago":"Li, Lanxin, Gabriel Krens, Matyas Fendrych, and Jiří Friml. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol. Bio-protocol, 2018. https://doi.org/10.21769/BioProtoc.2685.","ama":"Li L, Krens G, Fendrych M, Friml J. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 2018;8(1). doi:10.21769/BioProtoc.2685","apa":"Li, L., Krens, G., Fendrych, M., & Friml, J. (2018). Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-Protocol. Bio-protocol. https://doi.org/10.21769/BioProtoc.2685","ieee":"L. Li, G. Krens, M. Fendrych, and J. Friml, “Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls,” Bio-protocol, vol. 8, no. 1. Bio-protocol, 2018.","ista":"Li L, Krens G, Fendrych M, Friml J. 2018. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 8(1)."},"publication":"Bio-protocol","date_published":"2018-01-05T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"05","department":[{"_id":"JiFr"},{"_id":"Bio"}],"publisher":"Bio-protocol","publication_status":"published","acknowledgement":"This protocol was adapted from Fendrych et al., 2016. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, and Austrian Science Fund (FWF) [M 2128-B21]. ","year":"2018","volume":8,"date_updated":"2024-03-28T23:30:43Z","date_created":"2018-12-11T11:46:30Z","related_material":{"record":[{"id":"10083","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li","full_name":"Li, Lanxin"},{"full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","first_name":"Gabriel"},{"orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas","full_name":"Fendrych, Matyas"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"ec_funded":1,"publist_id":"7381","file_date_updated":"2020-07-14T12:46:29Z","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.21769/BioProtoc.2685","publication_identifier":{"eissn":["2331-8325"]},"month":"01"},{"month":"11","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"}],"doi":"10.1038/s41593-018-0266-2","project":[{"name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425","grant_number":"401299"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000451324700010"]},"publist_id":"8054","file_date_updated":"2020-07-14T12:45:58Z","volume":21,"date_created":"2018-12-11T11:44:05Z","date_updated":"2024-03-28T23:30:45Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/mutation-that-causes-autism-and-intellectual-disability-makes-brain-less-flexible/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"6074","status":"public","relation":"popular_science"},{"id":"12364","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Deliu, Elena","first_name":"Elena","last_name":"Deliu","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5293"},{"full_name":"Arecco, Niccoló","first_name":"Niccoló","last_name":"Arecco"},{"full_name":"Morandell, Jasmin","last_name":"Morandell","first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dotter, Christoph","first_name":"Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096"},{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","first_name":"Ximena","full_name":"Contreras, Ximena"},{"last_name":"Girardot","first_name":"Charles","full_name":"Girardot, Charles"},{"last_name":"Käsper","first_name":"Eva","full_name":"Käsper, Eva"},{"id":"C50A9596-02D0-11E9-976E-E38CFE5CBC1D","last_name":"Kozlova","first_name":"Alena","full_name":"Kozlova, Alena"},{"last_name":"Kishi","first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi"},{"full_name":"Chiaradia, Ilaria","orcid":"0000-0002-9529-4464","id":"B6467F20-02D0-11E9-BDA5-E960C241894A","last_name":"Chiaradia","first_name":"Ilaria"},{"full_name":"Noh, Kyung","first_name":"Kyung","last_name":"Noh"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"department":[{"_id":"GaNo"},{"_id":"EdHa"}],"publisher":"Nature Publishing Group","publication_status":"published","acknowledgement":"This work was supported by the Simons Foundation Autism Research Initiative (grant 401299) to G.N. and the DFG (SPP1738 grant NO 1249) to K.-M.N.","year":"2018","has_accepted_license":"1","article_processing_charge":"No","day":"19","scopus_import":"1","date_published":"2018-11-19T00:00:00Z","page":"1717 - 1727","article_type":"original","citation":{"mla":"Deliu, Elena, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience, vol. 21, no. 12, Nature Publishing Group, 2018, pp. 1717–27, doi:10.1038/s41593-018-0266-2.","short":"E. Deliu, N. Arecco, J. Morandell, C. Dotter, X. Contreras, C. Girardot, E. Käsper, A. Kozlova, K. Kishi, I. Chiaradia, K. Noh, G. Novarino, Nature Neuroscience 21 (2018) 1717–1727.","chicago":"Deliu, Elena, Niccoló Arecco, Jasmin Morandell, Christoph Dotter, Ximena Contreras, Charles Girardot, Eva Käsper, et al. “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Nature Neuroscience. Nature Publishing Group, 2018. https://doi.org/10.1038/s41593-018-0266-2.","ama":"Deliu E, Arecco N, Morandell J, et al. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 2018;21(12):1717-1727. doi:10.1038/s41593-018-0266-2","ista":"Deliu E, Arecco N, Morandell J, Dotter C, Contreras X, Girardot C, Käsper E, Kozlova A, Kishi K, Chiaradia I, Noh K, Novarino G. 2018. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. 21(12), 1717–1727.","apa":"Deliu, E., Arecco, N., Morandell, J., Dotter, C., Contreras, X., Girardot, C., … Novarino, G. (2018). Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/s41593-018-0266-2","ieee":"E. Deliu et al., “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition,” Nature Neuroscience, vol. 21, no. 12. Nature Publishing Group, pp. 1717–1727, 2018."},"publication":"Nature Neuroscience","issue":"12","abstract":[{"lang":"eng","text":"SETD5 gene mutations have been identified as a frequent cause of idiopathic intellectual disability. Here we show that Setd5-haploinsufficient mice present developmental defects such as abnormal brain-to-body weight ratios and neural crest defect-associated phenotypes. Furthermore, Setd5-mutant mice show impairments in cognitive tasks, enhanced long-term potentiation, delayed ontogenetic profile of ultrasonic vocalization, and behavioral inflexibility. Behavioral issues are accompanied by abnormal expression of postsynaptic density proteins previously associated with cognition. Our data additionally indicate that Setd5 regulates RNA polymerase II dynamics and gene transcription via its interaction with the Hdac3 and Paf1 complexes, findings potentially explaining the gene expression defects observed in Setd5-haploinsufficient mice. Our results emphasize the decisive role of Setd5 in a biological pathway found to be disrupted in humans with intellectual disability and autism spectrum disorder."}],"type":"journal_article","file":[{"file_name":"2017_NatureNeuroscience_Deliu.pdf","access_level":"open_access","creator":"dernst","file_size":8167169,"content_type":"application/pdf","file_id":"6255","relation":"main_file","date_created":"2019-04-09T07:41:57Z","date_updated":"2020-07-14T12:45:58Z","checksum":"60abd0f05b7cdc08a6b0ec460884084f"}],"oa_version":"Submitted Version","pubrep_id":"1071","intvolume":" 21","status":"public","title":"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"3"},{"quality_controlled":"1","isi":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30429320"}],"oa":1,"external_id":{"isi":["000451351000063"],"pmid":["30429320"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1810565115","month":"11","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","year":"2018","pmid":1,"date_created":"2018-12-11T11:44:05Z","date_updated":"2024-03-28T23:30:45Z","volume":115,"author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian"},{"first_name":"Laura","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura"},{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/no-cooperation-without-open-communication/"}],"record":[{"id":"10293","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"page":"12241-12246","publication":"PNAS","citation":{"ama":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 2018;115(48):12241-12246. doi:10.1073/pnas.1810565115","ista":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. 2018. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 115(48), 12241–12246.","apa":"Hilbe, C., Schmid, L., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Indirect reciprocity with private, noisy, and incomplete information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1810565115","ieee":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, and M. Nowak, “Indirect reciprocity with private, noisy, and incomplete information,” PNAS, vol. 115, no. 48. National Academy of Sciences, pp. 12241–12246, 2018.","mla":"Hilbe, Christian, et al. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” PNAS, vol. 115, no. 48, National Academy of Sciences, 2018, pp. 12241–46, doi:10.1073/pnas.1810565115.","short":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, M. Nowak, PNAS 115 (2018) 12241–12246.","chicago":"Hilbe, Christian, Laura Schmid, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1810565115."},"date_published":"2018-11-27T00:00:00Z","scopus_import":"1","day":"27","article_processing_charge":"No","title":"Indirect reciprocity with private, noisy, and incomplete information","status":"public","intvolume":" 115","_id":"2","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Indirect reciprocity explores how humans act when their reputation is at stake, and which social norms they use to assess the actions of others. A crucial question in indirect reciprocity is which social norms can maintain stable cooperation in a society. Past research has highlighted eight such norms, called “leading-eight” strategies. This past research, however, is based on the assumption that all relevant information about other population members is publicly available and that everyone agrees on who is good or bad. Instead, here we explore the reputation dynamics when information is private and noisy. We show that under these conditions, most leading-eight strategies fail to evolve. Those leading-eight strategies that do evolve are unable to sustain full cooperation.Indirect reciprocity is a mechanism for cooperation based on shared moral systems and individual reputations. It assumes that members of a community routinely observe and assess each other and that they use this information to decide who is good or bad, and who deserves cooperation. When information is transmitted publicly, such that all community members agree on each other’s reputation, previous research has highlighted eight crucial moral systems. These “leading-eight” strategies can maintain cooperation and resist invasion by defectors. However, in real populations individuals often hold their own private views of others. Once two individuals disagree about their opinion of some third party, they may also see its subsequent actions in a different light. Their opinions may further diverge over time. Herein, we explore indirect reciprocity when information transmission is private and noisy. We find that in the presence of perception errors, most leading-eight strategies cease to be stable. Even if a leading-eight strategy evolves, cooperation rates may drop considerably when errors are common. Our research highlights the role of reliable information and synchronized reputations to maintain stable moral systems."}],"issue":"48"},{"title":"Evolutionary potential of transcription factors for gene regulatory rewiring","ddc":["570"],"status":"public","intvolume":" 2","_id":"67","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"383a2e2c944a856e2e821ec8e7bf71b6","date_created":"2020-05-14T11:28:52Z","date_updated":"2020-07-14T12:47:37Z","file_id":"7830","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1135973,"access_level":"open_access","file_name":"2018_NatureEcology_Igler.pdf"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Gene regulatory networks evolve through rewiring of individual components—that is, through changes in regulatory connections. However, the mechanistic basis of regulatory rewiring is poorly understood. Using a canonical gene regulatory system, we quantify the properties of transcription factors that determine the evolutionary potential for rewiring of regulatory connections: robustness, tunability and evolvability. In vivo repression measurements of two repressors at mutated operator sites reveal their contrasting evolutionary potential: while robustness and evolvability were positively correlated, both were in trade-off with tunability. Epistatic interactions between adjacent operators alleviated this trade-off. A thermodynamic model explains how the differences in robustness, tunability and evolvability arise from biophysical characteristics of repressor–DNA binding. The model also uncovers that the energy matrix, which describes how mutations affect repressor–DNA binding, encodes crucial information about the evolutionary potential of a repressor. The biophysical determinants of evolutionary potential for regulatory rewiring constitute a mechanistic framework for understanding network evolution."}],"issue":"10","article_type":"original","page":"1633 - 1643","publication":"Nature Ecology and Evolution","citation":{"short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.","mla":"Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution. Nature Publishing Group, 2018. https://doi.org/10.1038/s41559-018-0651-y.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2018;2(10):1633-1643. doi:10.1038/s41559-018-0651-y","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018.","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. Nature Publishing Group. https://doi.org/10.1038/s41559-018-0651-y","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2(10), 1633–1643."},"date_published":"2018-09-10T00:00:00Z","scopus_import":"1","day":"10","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"JoBo"}],"year":"2018","date_updated":"2024-03-28T23:30:49Z","date_created":"2018-12-11T11:44:27Z","volume":2,"author":[{"last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia"},{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato","full_name":"Lagator, Mato"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5585"},{"relation":"dissertation_contains","status":"public","id":"6371"}]},"file_date_updated":"2020-07-14T12:47:37Z","ec_funded":1,"publist_id":"7987","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"},{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573"}],"external_id":{"isi":["000447947600021"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41559-018-0651-y","month":"09"},{"article_processing_charge":"No","has_accepted_license":"1","month":"07","day":"20","doi":"10.15479/AT:ISTA:108","date_published":"2018-07-20T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:108","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, 10.15479/AT:ISTA:108.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:108.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","mla":"Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:108."},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"ec_funded":1,"abstract":[{"text":"Mean repression values and standard error of the mean are given for all operator mutant libraries.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:07Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data","datarep_id":"108","related_material":{"record":[{"id":"67","relation":"research_paper","status":"public"},{"relation":"research_paper","status":"public","id":"6371"}]},"author":[{"full_name":"Igler, Claudia","last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik"},{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"}],"oa_version":"Published Version","file":[{"date_created":"2018-12-12T13:02:45Z","date_updated":"2020-07-14T12:47:07Z","checksum":"1435781526c77413802adee0d4583cce","relation":"main_file","file_id":"5611","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_size":16507,"creator":"system","file_name":"IST-2018-108-v1+1_data_figures.xlsx","access_level":"open_access"}],"date_created":"2018-12-12T12:31:40Z","date_updated":"2024-03-28T23:30:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5585","year":"2018","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","status":"public","title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","ddc":["576"]},{"issue":"32","abstract":[{"lang":"eng","text":"From microwave ovens to satellite television to the GPS and data services on our mobile phones, microwave technology is everywhere today. But one technology that has so far failed to prove its worth in this wavelength regime is quantum communication that uses the states of single photons as information carriers. This is because single microwave photons, as opposed to classical microwave signals, are extremely vulnerable to noise from thermal excitations in the channels through which they travel. Two new independent studies, one by Ze-Liang Xiang at Technische Universität Wien (Vienna), Austria, and colleagues [1] and another by Benoît Vermersch at the University of Innsbruck, also in Austria, and colleagues [2] now describe a theoretical protocol for microwave quantum communication that is resilient to thermal and other types of noise. Their approach could become a powerful technique to establish fast links between superconducting data processors in a future all-microwave quantum network."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_size":193622,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_Physics_Fink.pdf","success":1,"date_updated":"2019-10-24T11:38:14Z","date_created":"2019-10-24T11:38:14Z","relation":"main_file","file_id":"6968"}],"intvolume":" 10","ddc":["530"],"status":"public","title":"Viewpoint: Microwave quantum states beat the heat","_id":"1013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","has_accepted_license":"1","day":"27","date_published":"2017-03-27T00:00:00Z","article_type":"review","citation":{"ama":"Fink JM. Viewpoint: Microwave quantum states beat the heat. Physics. 2017;10(32). doi:10.1103/Physics.10.32","ista":"Fink JM. 2017. Viewpoint: Microwave quantum states beat the heat. Physics. 10(32).","apa":"Fink, J. M. (2017). Viewpoint: Microwave quantum states beat the heat. Physics. American Physical Society. https://doi.org/10.1103/Physics.10.32","ieee":"J. M. Fink, “Viewpoint: Microwave quantum states beat the heat,” Physics, vol. 10, no. 32. American Physical Society, 2017.","mla":"Fink, Johannes M. “Viewpoint: Microwave Quantum States Beat the Heat.” Physics, vol. 10, no. 32, American Physical Society, 2017, doi:10.1103/Physics.10.32.","short":"J.M. Fink, Physics 10 (2017).","chicago":"Fink, Johannes M. “Viewpoint: Microwave Quantum States Beat the Heat.” Physics. American Physical Society, 2017. https://doi.org/10.1103/Physics.10.32."},"publication":"Physics","publist_id":"6382","file_date_updated":"2019-10-24T11:38:14Z","volume":10,"date_created":"2018-12-11T11:49:41Z","date_updated":"2022-06-07T10:58:31Z","author":[{"full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"publisher":"American Physical Society","department":[{"_id":"JoFi"}],"publication_status":"published","year":"2017","month":"03","language":[{"iso":"eng"}],"doi":"10.1103/Physics.10.32","quality_controlled":"1","oa":1},{"type":"journal_article","issue":"POPL","abstract":[{"text":"We present a new proof rule for proving almost-sure termination of probabilistic programs, including those that contain demonic non-determinism. An important question for a probabilistic program is whether the probability mass of all its diverging runs is zero, that is that it terminates \"almost surely\". Proving that can be hard, and this paper presents a new method for doing so. It applies directly to the program's source code, even if the program contains demonic choice. Like others, we use variant functions (a.k.a. \"super-martingales\") that are real-valued and decrease randomly on each loop iteration; but our key innovation is that the amount as well as the probability of the decrease are parametric. We prove the soundness of the new rule, indicate where its applicability goes beyond existing rules, and explain its connection to classical results on denumerable (non-demonic) Markov chains.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10418","intvolume":" 2","title":"A new proof rule for almost-sure termination","status":"public","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"07","citation":{"chicago":"Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost P Katoen. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158121.","short":"A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM on Programming Languages 2 (2017).","mla":"Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 33, Association for Computing Machinery, 2017, doi:10.1145/3158121.","ieee":"A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule for almost-sure termination,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","apa":"Mciver, A., Morgan, C., Kaminski, B. L., & Katoen, J. P. (2017). A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158121","ista":"Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33.","ama":"Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158121"},"publication":"Proceedings of the ACM on Programming Languages","article_type":"original","date_published":"2017-12-07T00:00:00Z","article_number":"33","acknowledgement":"McIver and Morgan are grateful to David Basin and the Information Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during part of which this work began. And thanks particularly to Andreas Lochbihler, who shared with us the probabilistic termination problem that led to it. They acknowledge the support of ARC grant DP140101119. Part of this work was carried out during the Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden. Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4.","year":"2017","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","author":[{"full_name":"Mciver, Annabelle","first_name":"Annabelle","last_name":"Mciver"},{"last_name":"Morgan","first_name":"Carroll","full_name":"Morgan, Carroll"},{"first_name":"Benjamin Lucien","last_name":"Kaminski","full_name":"Kaminski, Benjamin Lucien"},{"full_name":"Katoen, Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","last_name":"Katoen","first_name":"Joost P"}],"volume":2,"date_updated":"2021-12-07T08:04:14Z","date_created":"2021-12-05T23:01:49Z","publication_identifier":{"eissn":["2475-1421"]},"month":"12","external_id":{"arxiv":["1711.03588"]},"main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3158121","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1145/3158121","conference":{"name":"POPL: Programming Languages","end_date":"2018-01-13","location":"Los Angeles, CA, United States","start_date":"2018-01-07"},"language":[{"iso":"eng"}]},{"doi":"10.1145/3040718.3040729","date_published":"2017-01-12T00:00:00Z","conference":{"name":"FOGA: Foundations of Genetic Algorithms","end_date":"2017-01-15","start_date":"2017-01-12","location":"Copenhagen, Denmark"},"language":[{"iso":"eng"}],"citation":{"chicago":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729.","short":"T. Paixao, J. Pérez Heredia, in:, Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11.","mla":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729.","apa":"Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential equations to evolutionary algorithms. In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms (pp. 3–11). Copenhagen, Denmark: ACM. https://doi.org/10.1145/3040718.3040729","ieee":"T. Paixao and J. Pérez Heredia, “An application of stochastic differential equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017, pp. 3–11.","ista":"Paixao T, Pérez Heredia J. 2017. An application of stochastic differential equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms, 3–11.","ama":"Paixao T, Pérez Heredia J. An application of stochastic differential equations to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729"},"publication":"Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms","page":"3 - 11","quality_controlled":"1","publication_identifier":{"isbn":["978-145034651-1"]},"month":"01","day":"12","scopus_import":1,"author":[{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"last_name":"Pérez Heredia","first_name":"Jorge","full_name":"Pérez Heredia, Jorge"}],"oa_version":"None","date_updated":"2021-01-12T06:48:22Z","date_created":"2018-12-11T11:50:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1112","year":"2017","publisher":"ACM","department":[{"_id":"NiBa"}],"publication_status":"published","status":"public","title":"An application of stochastic differential equations to evolutionary algorithms","publist_id":"6255","abstract":[{"lang":"eng","text":"There has been renewed interest in modelling the behaviour of evolutionary algorithms by more traditional mathematical objects, such as ordinary differential equations or Markov chains. The advantage is that the analysis becomes greatly facilitated due to the existence of well established methods. However, this typically comes at the cost of disregarding information about the process. Here, we introduce the use of stochastic differential equations (SDEs) for the study of EAs. SDEs can produce simple analytical results for the dynamics of stochastic processes, unlike Markov chains which can produce rigorous but unwieldy expressions about the dynamics. On the other hand, unlike ordinary differential equations (ODEs), they do not discard information about the stochasticity of the process. We show that these are especially suitable for the analysis of fixed budget scenarios and present analogs of the additive and multiplicative drift theorems for SDEs. We exemplify the use of these methods for two model algorithms ((1+1) EA and RLS) on two canonical problems(OneMax and LeadingOnes)."}],"type":"conference"},{"month":"01","publication_identifier":{"issn":["18688969"]},"conference":{"name":"ITCS: Innovations in Theoretical Computer Science","end_date":"2017-01-11","location":"Berkeley, CA, United States","start_date":"2017-01-09"},"doi":"10.4230/LIPIcs.ITCS.2017.38","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","file_date_updated":"2020-07-14T12:44:37Z","publist_id":"6179","author":[{"full_name":"Alwen, Joel F","first_name":"Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Susanna","last_name":"De Rezende","full_name":"De Rezende, Susanna"},{"full_name":"Nordstrom, Jakob","last_name":"Nordstrom","first_name":"Jakob"},{"full_name":"Vinyals, Marc","first_name":"Marc","last_name":"Vinyals"}],"date_created":"2018-12-11T11:50:33Z","date_updated":"2021-01-12T06:48:51Z","volume":67,"year":"2017","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrPi"}],"editor":[{"full_name":"Papadimitriou, Christos","last_name":"Papadimitriou","first_name":"Christos"}],"day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2017-01-01T00:00:00Z","citation":{"chicago":"Alwen, Joel F, Susanna De Rezende, Jakob Nordstrom, and Marc Vinyals. “Cumulative Space in Black-White Pebbling and Resolution.” edited by Christos Papadimitriou, 67:38:1-38-21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ITCS.2017.38.","mla":"Alwen, Joel F., et al. Cumulative Space in Black-White Pebbling and Resolution. Edited by Christos Papadimitriou, vol. 67, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, p. 38:1-38-21, doi:10.4230/LIPIcs.ITCS.2017.38.","short":"J.F. Alwen, S. De Rezende, J. Nordstrom, M. Vinyals, in:, C. Papadimitriou (Ed.), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, p. 38:1-38-21.","ista":"Alwen JF, De Rezende S, Nordstrom J, Vinyals M. 2017. Cumulative space in black-white pebbling and resolution. ITCS: Innovations in Theoretical Computer Science, LIPIcs, vol. 67, 38:1-38-21.","apa":"Alwen, J. F., De Rezende, S., Nordstrom, J., & Vinyals, M. (2017). Cumulative space in black-white pebbling and resolution. In C. Papadimitriou (Ed.) (Vol. 67, p. 38:1-38-21). Presented at the ITCS: Innovations in Theoretical Computer Science, Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2017.38","ieee":"J. F. Alwen, S. De Rezende, J. Nordstrom, and M. Vinyals, “Cumulative space in black-white pebbling and resolution,” presented at the ITCS: Innovations in Theoretical Computer Science, Berkeley, CA, United States, 2017, vol. 67, p. 38:1-38-21.","ama":"Alwen JF, De Rezende S, Nordstrom J, Vinyals M. Cumulative space in black-white pebbling and resolution. In: Papadimitriou C, ed. Vol 67. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:38:1-38-21. doi:10.4230/LIPIcs.ITCS.2017.38"},"page":"38:1-38-21","abstract":[{"text":"We study space complexity and time-space trade-offs with a focus not on peak memory usage but on overall memory consumption throughout the computation. Such a cumulative space measure was introduced for the computational model of parallel black pebbling by [Alwen and Serbinenko ’15] as a tool for obtaining results in cryptography. We consider instead the non- deterministic black-white pebble game and prove optimal cumulative space lower bounds and trade-offs, where in order to minimize pebbling time the space has to remain large during a significant fraction of the pebbling. We also initiate the study of cumulative space in proof complexity, an area where other space complexity measures have been extensively studied during the last 10–15 years. Using and extending the connection between proof complexity and pebble games in [Ben-Sasson and Nordström ’08, ’11] we obtain several strong cumulative space results for (even parallel versions of) the resolution proof system, and outline some possible future directions of study of this, in our opinion, natural and interesting space measure.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"pubrep_id":"927","oa_version":"Published Version","file":[{"file_size":557769,"content_type":"application/pdf","creator":"system","file_name":"IST-2018-927-v1+1_LIPIcs-ITCS-2017-38.pdf","access_level":"open_access","date_created":"2018-12-12T10:17:11Z","date_updated":"2020-07-14T12:44:37Z","checksum":"dbc94810be07c2fb1945d5c2a6130e6c","relation":"main_file","file_id":"5263"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1175","ddc":["005","600"],"status":"public","title":"Cumulative space in black-white pebbling and resolution","intvolume":" 67"},{"scopus_import":1,"day":"01","publication":"Bulletin of Mathematical Biology","citation":{"chicago":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology. Springer, 2017. https://doi.org/10.1007/s11538-016-0244-3.","short":"R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559.","mla":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology, vol. 79, no. 3, Springer, 2017, pp. 525–59, doi:10.1007/s11538-016-0244-3.","ieee":"R. Kollár and S. Novak, “Existence of traveling waves for the generalized F–KPP equation,” Bulletin of Mathematical Biology, vol. 79, no. 3. Springer, pp. 525–559, 2017.","apa":"Kollár, R., & Novak, S. (2017). Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. Springer. https://doi.org/10.1007/s11538-016-0244-3","ista":"Kollár R, Novak S. 2017. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559.","ama":"Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 2017;79(3):525-559. doi:10.1007/s11538-016-0244-3"},"page":"525-559","date_published":"2017-03-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed."}],"issue":"3","_id":"1191","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Existence of traveling waves for the generalized F–KPP equation","status":"public","intvolume":" 79","oa_version":"Preprint","month":"03","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1607.00944","open_access":"1"}],"quality_controlled":"1","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"doi":"10.1007/s11538-016-0244-3","language":[{"iso":"eng"}],"publist_id":"6160","ec_funded":1,"acknowledgement":"We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas for constructive feed-\r\nback and support. Furthermore, we would like to express our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed comments and suggestions that significantly helped us to improve the manuscript. This project has\r\nreceived funding from the European Union’s Seventh Framework Programme for research, technological\r\ndevelopment and demonstration under Grant Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN), from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13 and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378 (RK). RK would also like to\r\nthank IST Austria for its hospitality during the work on this project.","year":"2017","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Springer","author":[{"full_name":"Kollár, Richard","first_name":"Richard","last_name":"Kollár"},{"first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"}],"date_updated":"2021-01-12T06:48:58Z","date_created":"2018-12-11T11:50:38Z","volume":79},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1211","ddc":["530"],"status":"public","title":"Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system","intvolume":" 167","pubrep_id":"782","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2017-782-v1+1_BudCvi15.pdf","creator":"system","content_type":"application/pdf","file_size":2820207,"file_id":"5319","relation":"main_file","checksum":"3e971d09eb167761aa0888ed415b0056","date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:18:01Z"}],"type":"journal_article","abstract":[{"text":"Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here.","lang":"eng"}],"issue":"3-4","publication":"Journal of Statistical Physics","citation":{"ama":"Budanur NB, Cvitanović P. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 2017;167(3-4):636-655. doi:10.1007/s10955-016-1672-z","ista":"Budanur NB, Cvitanović P. 2017. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 167(3–4), 636–655.","apa":"Budanur, N. B., & Cvitanović, P. (2017). Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-016-1672-z","ieee":"N. B. Budanur and P. Cvitanović, “Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system,” Journal of Statistical Physics, vol. 167, no. 3–4. Springer, pp. 636–655, 2017.","mla":"Budanur, Nazmi B., and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics, vol. 167, no. 3–4, Springer, 2017, pp. 636–55, doi:10.1007/s10955-016-1672-z.","short":"N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 636–655.","chicago":"Budanur, Nazmi B, and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics. Springer, 2017. https://doi.org/10.1007/s10955-016-1672-z."},"page":"636-655","date_published":"2017-05-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","year":"2017","acknowledgement":"This work was supported by the family of late G. Robinson, Jr. and NSF Grant DMS-1211827. ","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Springer","author":[{"full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cvitanović, Predrag","last_name":"Cvitanović","first_name":"Predrag"}],"date_created":"2018-12-11T11:50:44Z","date_updated":"2021-01-12T06:49:07Z","volume":167,"file_date_updated":"2020-07-14T12:44:39Z","publist_id":"6136","oa":1,"quality_controlled":"1","doi":"10.1007/s10955-016-1672-z","language":[{"iso":"eng"}],"month":"05"},{"doi":"10.7155/jgaa.00408","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1608.08662"]},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","month":"01","related_material":{"record":[{"id":"1164","relation":"earlier_version","status":"public"},{"relation":"earlier_version","status":"public","id":"1595"}]},"author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pelsmajer","first_name":"Michael","full_name":"Pelsmajer, Michael"},{"full_name":"Schaefer, Marcus","last_name":"Schaefer","first_name":"Marcus"}],"volume":21,"date_updated":"2023-02-23T10:05:57Z","date_created":"2018-12-11T11:50:13Z","year":"2017","department":[{"_id":"UlWa"}],"publisher":"Brown University","publication_status":"published","publist_id":"6254","ec_funded":1,"file_date_updated":"2019-10-24T10:54:37Z","date_published":"2017-01-01T00:00:00Z","citation":{"ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” Journal of Graph Algorithms and Applications, vol. 21, no. 1. Brown University, pp. 135–154, 2017.","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2017). Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00408","ista":"Fulek R, Pelsmajer M, Schaefer M. 2017. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 21(1), 135–154.","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 2017;21(1):135-154. doi:10.7155/jgaa.00408","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications. Brown University, 2017. https://doi.org/10.7155/jgaa.00408.","short":"R. Fulek, M. Pelsmajer, M. Schaefer, Journal of Graph Algorithms and Applications 21 (2017) 135–154.","mla":"Fulek, Radoslav, et al. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications, vol. 21, no. 1, Brown University, 2017, pp. 135–54, doi:10.7155/jgaa.00408."},"publication":"Journal of Graph Algorithms and Applications","page":"135 - 154","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":1,"file":[{"success":1,"date_created":"2019-10-24T10:54:37Z","date_updated":"2019-10-24T10:54:37Z","relation":"main_file","file_id":"6967","content_type":"application/pdf","file_size":573623,"creator":"dernst","access_level":"open_access","file_name":"2017_JournalGraphAlgorithms_Fulek.pdf"}],"oa_version":"Published Version","_id":"1113","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 21","status":"public","ddc":["510"],"title":"Hanani-Tutte for radial planarity","issue":"1","abstract":[{"text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C 1 , . . . , C k with common center c , and edges are drawn radially : every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Toth.","lang":"eng"}],"type":"journal_article"},{"day":"29","month":"11","publication_identifier":{"isbn":["978-1-78262-865-1"]},"series_title":"Mechanisms of Primary Energy Transduction in Biology ","language":[{"iso":"eng"}],"date_published":"2017-11-29T00:00:00Z","doi":"10.1039/9781788010405-00025","quality_controlled":"1","page":"25 - 59","publication":"Mechanisms of primary energy transduction in biology ","citation":{"short":"L.A. Sazanov, in:, M. Wikström (Ed.), Mechanisms of Primary Energy Transduction in Biology , Royal Society of Chemistry, 2017, pp. 25–59.","mla":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, Royal Society of Chemistry, 2017, pp. 25–59, doi:10.1039/9781788010405-00025.","chicago":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” In Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, 25–59. Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781788010405-00025.","ama":"Sazanov LA. Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Wikström M, ed. Mechanisms of Primary Energy Transduction in Biology . Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry; 2017:25-59. doi:10.1039/9781788010405-00025","ieee":"L. A. Sazanov, “Structure of respiratory complex I: ‘Minimal’ bacterial and ‘de luxe’ mammalian versions,” in Mechanisms of primary energy transduction in biology , M. Wikström, Ed. Royal Society of Chemistry, 2017, pp. 25–59.","apa":"Sazanov, L. A. (2017). Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In M. Wikström (Ed.), Mechanisms of primary energy transduction in biology (pp. 25–59). Royal Society of Chemistry. https://doi.org/10.1039/9781788010405-00025","ista":"Sazanov LA. 2017.Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Mechanisms of primary energy transduction in biology . , 25–59."},"abstract":[{"lang":"eng","text":"Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy generation, contributing to the proton motive force used to produce ATP. It couples the transfer of two electrons between NADH and quinone to translocation of four protons across the membrane. It is the largest protein assembly of bacterial and mitochondrial respiratory chains, composed, in mammals, of up to 45 subunits with a total molecular weight of ∼1 MDa. Bacterial enzyme is about half the size, providing the important “minimal” model of complex I. The l-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. Previously, we have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus and of the membrane domain from Escherichia coli, followed by the atomic structure of intact, entire complex I from T. thermophilus. Recently, we have solved by cryo-EM a first complete atomic structure of mammalian (ovine) mitochondrial complex I. Core subunits are well conserved from the bacterial version, whilst supernumerary subunits form an interlinked, stabilizing shell around the core. Subunits containing additional cofactors, including Zn ion, NADPH and phosphopantetheine, probably have regulatory roles. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The structure of mammalian enzyme provides many insights into complex I mechanism, assembly, maturation and dysfunction, allowing detailed molecular analysis of disease-causing mutations."}],"publist_id":"7379","type":"book_chapter","date_created":"2018-12-11T11:46:30Z","date_updated":"2021-01-12T07:56:59Z","oa_version":"None","author":[{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"publication_status":"published","status":"public","title":"Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions","department":[{"_id":"LeSa"}],"publisher":"Royal Society of Chemistry","editor":[{"last_name":"Wikström","first_name":"Mårten","full_name":"Wikström, Mårten"}],"_id":"444","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"07","article_processing_charge":"No","has_accepted_license":"1","date_published":"2017-11-07T00:00:00Z","publication":"Biophysical Journal","citation":{"ieee":"T. Fallesen, J. Roostalu, C. F. Düllberg, G. Pruessner, and T. Surrey, “Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement,” Biophysical Journal, vol. 113, no. 9. Biophysical Society, pp. 2055–2067, 2017.","apa":"Fallesen, T., Roostalu, J., Düllberg, C. F., Pruessner, G., & Surrey, T. (2017). Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.09.006","ista":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. 2017. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 113(9), 2055–2067.","ama":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 2017;113(9):2055-2067. doi:10.1016/j.bpj.2017.09.006","chicago":"Fallesen, Todd, Johanna Roostalu, Christian F Düllberg, Gunnar Pruessner, and Thomas Surrey. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal. Biophysical Society, 2017. https://doi.org/10.1016/j.bpj.2017.09.006.","short":"T. Fallesen, J. Roostalu, C.F. Düllberg, G. Pruessner, T. Surrey, Biophysical Journal 113 (2017) 2055–2067.","mla":"Fallesen, Todd, et al. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal, vol. 113, no. 9, Biophysical Society, 2017, pp. 2055–67, doi:10.1016/j.bpj.2017.09.006."},"article_type":"original","page":"2055 - 2067","abstract":[{"lang":"eng","text":"Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor."}],"issue":"9","type":"journal_article","pubrep_id":"965","file":[{"file_name":"IST-2018-965-v1+1_2017_Duellberg_Ensembles_of.pdf","access_level":"open_access","content_type":"application/pdf","file_size":977192,"creator":"system","relation":"main_file","file_id":"5052","date_created":"2018-12-12T10:14:03Z","date_updated":"2020-07-14T12:46:31Z","checksum":"99a2474088e20ac74b1882c4fbbb45b1"}],"oa_version":"Published Version","_id":"453","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement","ddc":["570"],"status":"public","intvolume":" 113","month":"11","doi":"10.1016/j.bpj.2017.09.006","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:31Z","publist_id":"7369","author":[{"full_name":"Fallesen, Todd","first_name":"Todd","last_name":"Fallesen"},{"full_name":"Roostalu, Johanna","first_name":"Johanna","last_name":"Roostalu"},{"full_name":"Düllberg, Christian F","first_name":"Christian F","last_name":"Düllberg","id":"459064DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6335-9748"},{"full_name":"Pruessner, Gunnar","first_name":"Gunnar","last_name":"Pruessner"},{"full_name":"Surrey, Thomas","first_name":"Thomas","last_name":"Surrey"}],"date_created":"2018-12-11T11:46:33Z","date_updated":"2021-01-12T07:59:28Z","volume":113,"year":"2017","acknowledgement":"The plasmid for full-length kinesin-1 was a gift from G. Holzwarth and J. Macosko with permission from J. Howard. We thank I. Lueke and N. I. Cade for technical assistance. G.P. thanks the Francis Crick Institute, and in particular the Surrey and Salbreux groups, for their hospitality during his sabbatical stay, as well as Imperial College London for making it possible. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001163), the United Kingdom Medical Research Council (FC001163), and the Wellcome Trust (FC001163), and by Imperial College London. J.R. was also supported by a Sir Henry Wellcome Postdoctoral Fellowship (100145/Z/12/Z) and T.S. by the European Research Council (Advanced Grant, project 323042). ","publication_status":"published","publisher":"Biophysical Society","department":[{"_id":"MaLo"}]},{"date_published":"2017-09-26T00:00:00Z","citation":{"short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, Logical Methods in Computer Science 13 (2017).","mla":"Chatterjee, Krishnendu, et al. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science, vol. 13, no. 3, 26, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:26)2017.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:26)2017.","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:26)2017","ieee":"K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms for parity and Streett objectives,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","apa":"Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:26)2017","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V. 2017. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 13(3), 26."},"publication":"Logical Methods in Computer Science","article_processing_charge":"No","has_accepted_license":"1","day":"26","scopus_import":"1","pubrep_id":"956","oa_version":"Published Version","file":[{"file_name":"IST-2018-956-v1+1_2017_Chatterjee_Improved_algorithms.pdf","access_level":"open_access","content_type":"application/pdf","file_size":582940,"creator":"system","relation":"main_file","file_id":"5010","date_updated":"2020-07-14T12:46:32Z","date_created":"2018-12-12T10:13:27Z","checksum":"12d469ae69b80361333d7dead965cf5d"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"464","intvolume":" 13","title":"Improved algorithms for parity and Streett objectives","ddc":["004"],"status":"public","issue":"3","abstract":[{"text":"The computation of the winning set for parity objectives and for Streett objectives in graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formedness of specifications, and the synthesis of reactive systems. We show how to compute the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs in time O(n2+nklogn). For both problems this gives faster algorithms for dense graphs and represents the first improvement in asymptotic running time in 15 years.","lang":"eng"}],"type":"journal_article","doi":"10.23638/LMCS-13(3:26)2017","language":[{"iso":"eng"}],"oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"external_id":{"arxiv":["1410.0833"]},"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","publication_identifier":{"issn":["1860-5974"]},"month":"09","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1661"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer","first_name":"Veronika"}],"volume":13,"date_updated":"2023-02-23T10:08:55Z","date_created":"2018-12-11T11:46:37Z","year":"2017","department":[{"_id":"KrCh"}],"publisher":"International Federation of Computational Logic","publication_status":"published","ec_funded":1,"publist_id":"7357","file_date_updated":"2020-07-14T12:46:32Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","article_number":"26"},{"issue":"4","abstract":[{"text":"This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"82a3b2bfeee4ddef16ecc21675d1a48a","date_created":"2020-01-24T09:32:35Z","date_updated":"2020-07-14T12:46:34Z","file_id":"7359","relation":"main_file","creator":"wojtan","content_type":"application/pdf","file_size":13131683,"access_level":"open_access","file_name":"wavepackets_final.pdf"}],"_id":"470","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 36","ddc":["006"],"status":"public","title":"Water wave packets","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","scopus_import":1,"date_published":"2017-07-01T00:00:00Z","citation":{"ama":"Jeschke S, Wojtan C. Water wave packets. ACM Transactions on Graphics. 2017;36(4). doi:10.1145/3072959.3073678","ieee":"S. Jeschke and C. Wojtan, “Water wave packets,” ACM Transactions on Graphics, vol. 36, no. 4. ACM, 2017.","apa":"Jeschke, S., & Wojtan, C. (2017). Water wave packets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3072959.3073678","ista":"Jeschke S, Wojtan C. 2017. Water wave packets. ACM Transactions on Graphics. 36(4), 103.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 36 (2017).","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics, vol. 36, no. 4, 103, ACM, 2017, doi:10.1145/3072959.3073678.","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics. 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The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds. ","lang":"eng"}],"type":"journal_article","date_published":"2017-05-01T00:00:00Z","citation":{"mla":"Daca, Przemyslaw, et al. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2, 12, ACM, 2017, doi:10.1145/3060139.","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, ACM Transactions on Computational Logic (TOCL) 18 (2017).","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3060139.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 2017;18(2). doi:10.1145/3060139","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2017. Faster statistical model checking for unbounded temporal properties. 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Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"4758","relation":"main_file","date_updated":"2020-07-14T12:46:35Z","date_created":"2018-12-12T10:09:34Z","checksum":"f79e8558bfe4b368dfefeb8eec2e3a5e","file_name":"IST-2018-949-v1+1_2016_huber_PLanar_matchings.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":769296}],"pubrep_id":"949","intvolume":" 26","title":"Planar matchings for weighted straight skeletons","status":"public","ddc":["004","514","516"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"481","has_accepted_license":"1","day":"13","scopus_import":1,"date_published":"2017-04-13T00:00:00Z","page":"211 - 229","citation":{"ieee":"T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight skeletons,” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4. World Scientific Publishing, pp. 211–229, 2017.","apa":"Biedl, T., Huber, S., & Palfrader, P. (2017). Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195916600050","ista":"Biedl T, Huber S, Palfrader P. 2017. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 26(3–4), 211–229.","ama":"Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons. 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Palfrader, International Journal of Computational Geometry and Applications 26 (2017) 211–229.","mla":"Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4, World Scientific Publishing, 2017, pp. 211–29, doi:10.1142/S0218195916600050."},"publication":"International Journal of Computational Geometry and Applications","publist_id":"7338","file_date_updated":"2020-07-14T12:46:35Z","volume":26,"date_created":"2018-12-11T11:46:43Z","date_updated":"2023-02-21T16:06:22Z","related_material":{"record":[{"id":"10892","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Biedl, Therese","first_name":"Therese","last_name":"Biedl"},{"last_name":"Huber","first_name":"Stefan","orcid":"0000-0002-8871-5814","id":"4700A070-F248-11E8-B48F-1D18A9856A87","full_name":"Huber, Stefan"},{"full_name":"Palfrader, Peter","last_name":"Palfrader","first_name":"Peter"}],"publisher":"World Scientific Publishing","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2017","acknowledgement":"Supported by NSERC and the Ross and Muriel Cheriton Fellowship. Research supported by Austrian Science Fund (FWF): P25816-N15.","month":"04","language":[{"iso":"eng"}],"doi":"10.1142/S0218195916600050","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"intvolume":" 21","title":"Bogoliubov correction to the mean-field dynamics of interacting bosons","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"484","oa_version":"Submitted Version","type":"journal_article","issue":"3","abstract":[{"text":"We consider the dynamics of a large quantum system of N identical bosons in 3D interacting via a two-body potential of the form N3β-1w(Nβ(x - y)). For fixed 0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution in the Nparticle Hilbert space. The leading order behaviour of the dynamics is determined by Hartree theory while the second order is given by Bogoliubov theory.","lang":"eng"}],"page":"683 - 738","citation":{"ama":"Nam P, Napiórkowski MM. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 2017;21(3):683-738. doi:10.4310/ATMP.2017.v21.n3.a4","apa":"Nam, P., & Napiórkowski, M. M. (2017). Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a4","ieee":"P. Nam and M. M. Napiórkowski, “Bogoliubov correction to the mean-field dynamics of interacting bosons,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 683–738, 2017.","ista":"Nam P, Napiórkowski MM. 2017. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 21(3), 683–738.","short":"P. Nam, M.M. Napiórkowski, Advances in Theoretical and Mathematical Physics 21 (2017) 683–738.","mla":"Nam, Phan, and Marcin M. Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 683–738, doi:10.4310/ATMP.2017.v21.n3.a4.","chicago":"Nam, Phan, and Marcin M Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a4."},"publication":"Advances in Theoretical and Mathematical Physics","date_published":"2017-01-01T00:00:00Z","scopus_import":1,"day":"01","department":[{"_id":"RoSe"}],"publisher":"International Press","publication_status":"published","year":"2017","volume":21,"date_updated":"2021-01-12T08:00:58Z","date_created":"2018-12-11T11:46:43Z","author":[{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam","full_name":"Nam, Phan"},{"id":"4197AD04-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin M","last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M"}],"ec_funded":1,"publist_id":"7336","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1509.04631","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.4310/ATMP.2017.v21.n3.a4","publication_identifier":{"issn":["10950761"]},"month":"01"},{"day":"25","scopus_import":1,"date_published":"2017-08-25T00:00:00Z","publication":"Advances in Theoretical and Mathematical Physics","citation":{"mla":"Bourgade, Paul, et al. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 739–800, doi:10.4310/ATMP.2017.v21.n3.a5.","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Advances in Theoretical and Mathematical Physics 21 (2017) 739–800.","chicago":"Bourgade, Paul, László Erdös, Horng Yau, and Jun Yin. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a5.","ama":"Bourgade P, Erdös L, Yau H, Yin J. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 2017;21(3):739-800. doi:10.4310/ATMP.2017.v21.n3.a5","ista":"Bourgade P, Erdös L, Yau H, Yin J. 2017. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 21(3), 739–800.","ieee":"P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Universality for a class of random band matrices,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 739–800, 2017.","apa":"Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2017). Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a5"},"page":"739 - 800","abstract":[{"text":"We prove the universality for the eigenvalue gap statistics in the bulk of the spectrum for band matrices, in the regime where the band width is comparable with the dimension of the matrix, W ~ N. All previous results concerning universality of non-Gaussian random matrices are for mean-field models. By relying on a new mean-field reduction technique, we deduce universality from quantum unique ergodicity for band matrices.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"483","status":"public","title":"Universality for a class of random band matrices","intvolume":" 21","month":"08","publication_identifier":{"issn":["10950761"]},"doi":"10.4310/ATMP.2017.v21.n3.a5","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.02312"}],"oa":1,"quality_controlled":"1","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"publist_id":"7337","ec_funded":1,"author":[{"full_name":"Bourgade, Paul","first_name":"Paul","last_name":"Bourgade"},{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yau, Horng","first_name":"Horng","last_name":"Yau"},{"last_name":"Yin","first_name":"Jun","full_name":"Yin, Jun"}],"date_updated":"2021-01-12T08:00:57Z","date_created":"2018-12-11T11:46:43Z","volume":21,"year":"2017","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"International Press"},{"abstract":[{"text":"In this paper we study network architecture for unlicensed cellular networking for outdoor coverage in TV white spaces. The main technology proposed for TV white spaces is 802.11af, a Wi-Fi variant adapted for TV frequencies. However, 802.11af is originally designed for improved indoor propagation. We show that long links, typical for outdoor use, exacerbate known Wi-Fi issues, such as hidden and exposed terminal, and significantly reduce its efficiency. Instead, we propose CellFi, an alternative architecture based on LTE. LTE is designed for long-range coverage and throughput efficiency, but it is also designed to operate in tightly controlled and centrally managed networks. CellFi overcomes these problems by designing an LTE-compatible spectrum database component, mandatory for TV white space networking, and introducing an interference management component for distributed coordination. CellFi interference management is compatible with existing LTE mechanisms, requires no explicit communication between base stations, and is more efficient than CSMA for long links. We evaluate our design through extensive real world evaluation on of-the-shelf LTE equipment and simulations. We show that, compared to 802.11af, it increases coverage by 40% and reduces median flow completion times by 2.3x.","lang":"eng"}],"publist_id":"7333","type":"conference","date_created":"2018-12-11T11:46:45Z","date_updated":"2023-02-23T12:21:11Z","oa_version":"None","author":[{"first_name":"Ghufran","last_name":"Baig","full_name":"Baig, Ghufran"},{"first_name":"Bozidar","last_name":"Radunovic","full_name":"Radunovic, Bozidar"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"last_name":"Balkwill","first_name":"Matthew","full_name":"Balkwill, Matthew"},{"first_name":"Thomas","last_name":"Karagiannis","full_name":"Karagiannis, Thomas"},{"first_name":"Lili","last_name":"Qiu","full_name":"Qiu, Lili"}],"publication_status":"published","title":"Towards unlicensed cellular networks in TV white spaces","status":"public","department":[{"_id":"DaAl"}],"publisher":"ACM","year":"2017","_id":"487","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"28","month":"11","publication_identifier":{"isbn":["978-145035422-6"]},"scopus_import":1,"language":[{"iso":"eng"}],"conference":{"name":"CoNEXT: Conference on emerging Networking EXperiments and Technologies","end_date":"2017-12-15","start_date":"2017-12-12","location":"Incheon, South Korea"},"date_published":"2017-11-28T00:00:00Z","doi":"10.1145/3143361.3143367","quality_controlled":"1","page":"2 - 14","publication":"Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies","citation":{"ieee":"G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, and L. Qiu, “Towards unlicensed cellular networks in TV white spaces,” in Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies, Incheon, South Korea, 2017, pp. 2–14.","apa":"Baig, G., Radunovic, B., Alistarh, D.-A., Balkwill, M., Karagiannis, T., & Qiu, L. (2017). Towards unlicensed cellular networks in TV white spaces. In Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies (pp. 2–14). Incheon, South Korea: ACM. https://doi.org/10.1145/3143361.3143367","ista":"Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. 2017. Towards unlicensed cellular networks in TV white spaces. Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies. CoNEXT: Conference on emerging Networking EXperiments and Technologies, 2–14.","ama":"Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. Towards unlicensed cellular networks in TV white spaces. In: Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies. ACM; 2017:2-14. doi:10.1145/3143361.3143367","chicago":"Baig, Ghufran, Bozidar Radunovic, Dan-Adrian Alistarh, Matthew Balkwill, Thomas Karagiannis, and Lili Qiu. “Towards Unlicensed Cellular Networks in TV White Spaces.” In Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, 2–14. ACM, 2017. https://doi.org/10.1145/3143361.3143367.","short":"G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, L. Qiu, in:, Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14.","mla":"Baig, Ghufran, et al. “Towards Unlicensed Cellular Networks in TV White Spaces.” Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14, doi:10.1145/3143361.3143367."}},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1038/ncomms16032","language":[{"iso":"eng"}],"publication_identifier":{"issn":["20411723"]},"month":"07","year":"2017","department":[{"_id":"JoCs"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"full_name":"Simonnet, Jean","last_name":"Simonnet","first_name":"Jean"},{"full_name":"Nassar, Mérie","last_name":"Nassar","first_name":"Mérie"},{"last_name":"Stella","first_name":"Federico","orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","full_name":"Stella, Federico"},{"full_name":"Cohen, Ivan","first_name":"Ivan","last_name":"Cohen"},{"first_name":"Bertrand","last_name":"Mathon","full_name":"Mathon, Bertrand"},{"id":"3FC06552-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7237-5109","first_name":"Charlotte","last_name":"Boccara","full_name":"Boccara, Charlotte"},{"last_name":"Miles","first_name":"Richard","full_name":"Miles, Richard"},{"full_name":"Fricker, Desdemona","first_name":"Desdemona","last_name":"Fricker"}],"volume":8,"date_created":"2018-12-11T11:46:54Z","date_updated":"2021-01-12T08:01:16Z","article_number":"16032","publist_id":"7305","file_date_updated":"2020-07-14T12:46:36Z","citation":{"apa":"Simonnet, J., Nassar, M., Stella, F., Cohen, I., Mathon, B., Boccara, C. N., … Fricker, D. (2017). Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms16032","ieee":"J. Simonnet et al., “Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","ista":"Simonnet J, Nassar M, Stella F, Cohen I, Mathon B, Boccara CN, Miles R, Fricker D. 2017. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 8, 16032.","ama":"Simonnet J, Nassar M, Stella F, et al. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 2017;8. doi:10.1038/ncomms16032","chicago":"Simonnet, Jean, Mérie Nassar, Federico Stella, Ivan Cohen, Bertrand Mathon, Charlotte N. Boccara, Richard Miles, and Desdemona Fricker. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms16032.","short":"J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R. Miles, D. Fricker, Nature Communications 8 (2017).","mla":"Simonnet, Jean, et al. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications, vol. 8, 16032, Nature Publishing Group, 2017, doi:10.1038/ncomms16032."},"publication":"Nature Communications","date_published":"2017-07-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","_id":"514","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8","status":"public","ddc":["571"],"title":"Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum","pubrep_id":"937","file":[{"checksum":"76d8a2b72a58e56adb410ec37dfa7eee","date_created":"2018-12-12T10:14:31Z","date_updated":"2020-07-14T12:46:36Z","file_id":"5083","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":2948357,"access_level":"open_access","file_name":"IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Orientation in space is represented in specialized brain circuits. Persistent head direction signals are transmitted from anterior thalamus to the presubiculum, but the identity of the presubicular target neurons, their connectivity and function in local microcircuits are unknown. Here, we examine how thalamic afferents recruit presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic interactions between these cells. Pyramidal neuron activation of Martinotti cells in superficial layers is strongly facilitating such that high-frequency head directional stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback plays a dual role: precisely timed spikes may not inhibit the firing of in-tune head direction cells, while exerting lateral inhibition. Autonomous attractor dynamics emerge from a modelled network implementing wiring motifs and timing sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop. This inhibitory microcircuit is therefore tuned to refine and maintain head direction information in the presubiculum.","lang":"eng"}]},{"file_date_updated":"2020-07-14T12:46:36Z","ec_funded":1,"publist_id":"7304","year":"2017","publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Nature Publishing Group","author":[{"last_name":"Letts","first_name":"James A","orcid":"0000-0002-9864-3586","id":"322DA418-F248-11E8-B48F-1D18A9856A87","full_name":"Letts, James A"},{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"date_updated":"2021-01-12T08:01:17Z","date_created":"2018-12-11T11:46:54Z","volume":24,"month":"10","publication_identifier":{"issn":["15459993"]},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","grant_number":"701309","_id":"2590DB08-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/nsmb.3460","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the inner mitochondrial membrane is composed of five large protein complexes, named CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome), as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the assembly and function of the SCs. Here we review and compare these recent studies and discuss how they have advanced our understanding of mitochondrial electron transport.","lang":"eng"}],"issue":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"515","title":"Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain","status":"public","ddc":["572"],"intvolume":" 24","oa_version":"Submitted Version","file":[{"file_id":"6993","relation":"main_file","date_created":"2019-11-07T12:51:07Z","date_updated":"2020-07-14T12:46:36Z","checksum":"9bc7e8c41b43636dd7566289e511f096","file_name":"29893_2_merged_1501257589_red.pdf","access_level":"open_access","creator":"lsazanov","file_size":4118385,"content_type":"application/pdf"}],"scopus_import":1,"day":"05","has_accepted_license":"1","publication":"Nature Structural and Molecular Biology","citation":{"ista":"Letts JA, Sazanov LA. 2017. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 24(10), 800–808.","ieee":"J. A. Letts and L. A. Sazanov, “Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain,” Nature Structural and Molecular Biology, vol. 24, no. 10. Nature Publishing Group, pp. 800–808, 2017.","apa":"Letts, J. A., & Sazanov, L. A. (2017). Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.3460","ama":"Letts JA, Sazanov LA. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 2017;24(10):800-808. doi:10.1038/nsmb.3460","chicago":"Letts, James A, and Leonid A Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/nsmb.3460.","mla":"Letts, James A., and Leonid A. Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 800–08, doi:10.1038/nsmb.3460.","short":"J.A. Letts, L.A. Sazanov, Nature Structural and Molecular Biology 24 (2017) 800–808."},"article_type":"original","page":"800 - 808","date_published":"2017-10-05T00:00:00Z"},{"publication_status":"published","status":"public","title":"Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence","department":[{"_id":"BjHo"}],"intvolume":" 2","publisher":"American Physical Society","_id":"513","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:16Z","date_created":"2018-12-11T11:46:54Z","volume":2,"oa_version":"Preprint","author":[{"orcid":"0000-0003-1740-7635","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","last_name":"Klotz","first_name":"Lukasz","full_name":"Klotz, Lukasz"},{"id":"4787FE80-F248-11E8-B48F-1D18A9856A87","first_name":"Grégoire M","last_name":"Lemoult","full_name":"Lemoult, Grégoire M"},{"last_name":"Frontczak","first_name":"Idalia","full_name":"Frontczak, Idalia"},{"full_name":"Tuckerman, Laurette","first_name":"Laurette","last_name":"Tuckerman"},{"last_name":"Wesfreid","first_name":"José","full_name":"Wesfreid, José"}],"article_number":"043904","type":"journal_article","abstract":[{"lang":"eng","text":"We present an experimental setup that creates a shear flow with zero mean advection velocity achieved by counterbalancing the nonzero streamwise pressure gradient by moving boundaries, which generates plane Couette-Poiseuille flow. We obtain experimental results in the transitional regime for this flow. Using flow visualization, we characterize the subcritical transition to turbulence in Couette-Poiseuille flow and show the existence of turbulent spots generated by a permanent perturbation. Due to the zero mean advection velocity of the base profile, these turbulent structures are nearly stationary. We distinguish two regions of the turbulent spot: the active turbulent core, which is characterized by waviness of the streaks similar to traveling waves, and the surrounding region, which includes in addition the weak undisturbed streaks and oblique waves at the laminar-turbulent interface. We also study the dependence of the size of these two regions on Reynolds number. Finally, we show that the traveling waves move in the downstream (Poiseuille) direction."}],"issue":"4","publist_id":"7306","quality_controlled":"1","publication":"Physical Review Fluids","main_file_link":[{"url":"https://arxiv.org/abs/1704.02619","open_access":"1"}],"citation":{"chicago":"Klotz, Lukasz, Grégoire M Lemoult, Idalia Frontczak, Laurette Tuckerman, and José Wesfreid. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids. American Physical Society, 2017. https://doi.org/10.1103/PhysRevFluids.2.043904.","short":"L. Klotz, G.M. Lemoult, I. Frontczak, L. Tuckerman, J. Wesfreid, Physical Review Fluids 2 (2017).","mla":"Klotz, Lukasz, et al. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids, vol. 2, no. 4, 043904, American Physical Society, 2017, doi:10.1103/PhysRevFluids.2.043904.","apa":"Klotz, L., Lemoult, G. M., Frontczak, I., Tuckerman, L., & Wesfreid, J. (2017). Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.2.043904","ieee":"L. Klotz, G. M. Lemoult, I. Frontczak, L. Tuckerman, and J. Wesfreid, “Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence,” Physical Review Fluids, vol. 2, no. 4. American Physical Society, 2017.","ista":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. 2017. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2(4), 043904.","ama":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2017;2(4). doi:10.1103/PhysRevFluids.2.043904"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevFluids.2.043904","date_published":"2017-04-01T00:00:00Z","scopus_import":1,"day":"01","month":"04"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"520","intvolume":" 6","title":"Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803","status":"public","oa_version":"None","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Cyanobacteria are mostly engineered to be sustainable cell-factories by genetic manipulations alone. Here, by modulating the concentration of allosteric effectors, we focus on increasing product formation without further burdening the cells with increased expression of enzymes. Resorting to a novel 96-well microplate cultivation system for cyanobacteria, and using lactate-producing strains of Synechocystis PCC6803 expressing different l-lactate dehydrogenases (LDH), we titrated the effect of 2,5-anhydro-mannitol supplementation. The latter acts in cells as a nonmetabolizable analogue of fructose 1,6-bisphosphate, a known allosteric regulator of one of the tested LDHs. In this strain (SAA023), we achieved over 2-fold increase of lactate productivity. Furthermore, we observed that as carbon is increasingly deviated during growth toward product formation, there is an increased fixation rate in the population of spontaneous mutants harboring an impaired production pathway. This is a challenge in the development of green cell factories, which may be countered by the incorporation in biotechnological processes of strategies such as the one pioneered here."}],"citation":{"ama":"Du W, Angermayr A, Jongbloets J, et al. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 2017;6(3):395-401. doi:10.1021/acssynbio.6b00235","apa":"Du, W., Angermayr, A., Jongbloets, J., Molenaar, D., Bachmann, H., Hellingwerf, K., & Branco Dos Santos, F. (2017). Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00235","ieee":"W. Du et al., “Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803,” ACS Synthetic Biology, vol. 6, no. 3. American Chemical Society, pp. 395–401, 2017.","ista":"Du W, Angermayr A, Jongbloets J, Molenaar D, Bachmann H, Hellingwerf K, Branco Dos Santos F. 2017. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 6(3), 395–401.","short":"W. Du, A. Angermayr, J. Jongbloets, D. Molenaar, H. Bachmann, K. Hellingwerf, F. Branco Dos Santos, ACS Synthetic Biology 6 (2017) 395–401.","mla":"Du, Wei, et al. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology, vol. 6, no. 3, American Chemical Society, 2017, pp. 395–401, doi:10.1021/acssynbio.6b00235.","chicago":"Du, Wei, Andreas Angermayr, Joeri Jongbloets, Douwe Molenaar, Herwig Bachmann, Klaas Hellingwerf, and Filipe Branco Dos Santos. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology. American Chemical Society, 2017. https://doi.org/10.1021/acssynbio.6b00235."},"publication":"ACS Synthetic Biology","page":"395 - 401","article_type":"letter_note","date_published":"2017-03-17T00:00:00Z","scopus_import":1,"day":"17","pmid":1,"year":"2017","publisher":"American Chemical Society","department":[{"_id":"ToBo"}],"publication_status":"published","author":[{"last_name":"Du","first_name":"Wei","full_name":"Du, Wei"},{"full_name":"Angermayr, Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8619-2223","first_name":"Andreas","last_name":"Angermayr"},{"last_name":"Jongbloets","first_name":"Joeri","full_name":"Jongbloets, Joeri"},{"full_name":"Molenaar, Douwe","last_name":"Molenaar","first_name":"Douwe"},{"last_name":"Bachmann","first_name":"Herwig","full_name":"Bachmann, Herwig"},{"last_name":"Hellingwerf","first_name":"Klaas","full_name":"Hellingwerf, Klaas"},{"first_name":"Filipe","last_name":"Branco Dos Santos","full_name":"Branco Dos Santos, Filipe"}],"volume":6,"date_updated":"2021-01-12T08:01:21Z","date_created":"2018-12-11T11:46:56Z","publist_id":"7298","external_id":{"pmid":["27936615"]},"quality_controlled":"1","doi":"10.1021/acssynbio.6b00235","language":[{"iso":"eng"}],"publication_identifier":{"issn":["21615063"]},"month":"03"},{"month":"01","day":"01","publication_identifier":{"issn":["01668641"]},"date_published":"2017-01-01T00:00:00Z","doi":"10.1016/j.topol.2016.10.005","language":[{"iso":"eng"}],"publication":"Topology and its Applications","main_file_link":[{"url":"https://arxiv.org/abs/1608.03954v1","open_access":"1"}],"citation":{"ama":"Austin K, Virk Z. Higson compactification and dimension raising. Topology and its Applications. 2017;215:45-57. doi:10.1016/j.topol.2016.10.005","ista":"Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology and its Applications. 215, 45–57.","ieee":"K. Austin and Z. Virk, “Higson compactification and dimension raising,” Topology and its Applications, vol. 215. Elsevier, pp. 45–57, 2017.","apa":"Austin, K., & Virk, Z. (2017). Higson compactification and dimension raising. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2016.10.005","mla":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications, vol. 215, Elsevier, 2017, pp. 45–57, doi:10.1016/j.topol.2016.10.005.","short":"K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57.","chicago":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2016.10.005."},"oa":1,"quality_controlled":"1","page":"45 - 57","abstract":[{"lang":"eng","text":"Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful in showing that the classical dimension raising theorems hold in large scale; that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely n-to-1 maps, which include the natural quotient maps via a finite group action, and prove that they preserve the asymptotic dimension."}],"publist_id":"7299","type":"journal_article","author":[{"last_name":"Austin","first_name":"Kyle","full_name":"Austin, Kyle"},{"full_name":"Virk, Ziga","id":"2E36B656-F248-11E8-B48F-1D18A9856A87","first_name":"Ziga","last_name":"Virk"}],"date_updated":"2021-01-12T08:01:21Z","date_created":"2018-12-11T11:46:56Z","oa_version":"Submitted Version","volume":215,"_id":"521","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Higson compactification and dimension raising","status":"public","publication_status":"published","publisher":"Elsevier","department":[{"_id":"HeEd"}],"intvolume":" 215"},{"issue":"4","abstract":[{"text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"534","intvolume":" 58","title":"Finding non-orientable surfaces in 3-Manifolds","status":"public","article_processing_charge":"No","day":"09","scopus_import":1,"date_published":"2017-06-09T00:00:00Z","citation":{"ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-Manifolds,” Discrete & Computational Geometry, vol. 58, no. 4. Springer, pp. 871–888, 2017.","apa":"Burton, B., de Mesmay, A. N., & Wagner, U. (2017). Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9900-0","ista":"Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 58(4), 871–888.","ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 2017;58(4):871-888. doi:10.1007/s00454-017-9900-0","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-017-9900-0.","short":"B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry 58 (2017) 871–888.","mla":"Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry, vol. 58, no. 4, Springer, 2017, pp. 871–88, doi:10.1007/s00454-017-9900-0."},"publication":"Discrete & Computational Geometry","page":"871 - 888","article_type":"original","publist_id":"7283","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1379"}]},"author":[{"full_name":"Burton, Benjamin","last_name":"Burton","first_name":"Benjamin"},{"id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","first_name":"Arnaud N","last_name":"De Mesmay","full_name":"De Mesmay, Arnaud N"},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"volume":58,"date_created":"2018-12-11T11:47:01Z","date_updated":"2023-02-21T17:01:34Z","year":"2017","publisher":"Springer","department":[{"_id":"UlWa"}],"publication_status":"published","publication_identifier":{"issn":["01795376"]},"month":"06","doi":"10.1007/s00454-017-9900-0","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.07907"}],"oa":1,"external_id":{"arxiv":["1602.07907"]},"quality_controlled":"1"},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf","file_size":1668557,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5007","checksum":"d66fee867e7cdbfa3fe276c2fb0778bb","date_created":"2018-12-12T10:13:24Z","date_updated":"2020-07-14T12:46:39Z"}],"pubrep_id":"932","title":"Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen","ddc":["571"],"status":"public","intvolume":" 129","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"538","abstract":[{"text":"Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung. ","lang":"ger"}],"issue":"16","type":"journal_article","date_published":"2017-05-20T00:00:00Z","page":"4679 - 4682","publication":"Angewandte Chemie","citation":{"chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682.","mla":"Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie, vol. 129, no. 16, Wiley, 2017, pp. 4679–82, doi:10.1002/ange.201611998.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201611998","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,” Angewandte Chemie, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 129(16), 4679–4682.","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 2017;129(16):4679-4682. doi:10.1002/ange.201611998"},"day":"20","has_accepted_license":"1","date_updated":"2021-01-12T08:01:33Z","date_created":"2018-12-11T11:47:02Z","volume":129,"author":[{"first_name":"Stephanie","last_name":"Kainrath","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","full_name":"Kainrath, Stephanie"},{"full_name":"Stadler, Manuela","first_name":"Manuela","last_name":"Stadler"},{"full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart","first_name":"Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Distel, Martin","last_name":"Distel","first_name":"Martin"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"year":"2017","file_date_updated":"2020-07-14T12:46:39Z","ec_funded":1,"publist_id":"7279","language":[{"iso":"eng"}],"doi":"10.1002/ange.201611998","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24","_id":"255A6082-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"05"},{"title":"Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein","status":"public","ddc":["576","616"],"intvolume":" 13","_id":"540","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:12:26Z","date_updated":"2020-07-14T12:46:44Z","checksum":"1aa20f19a1e90664fadce6e7d5284fdc","relation":"main_file","file_id":"4944","content_type":"application/pdf","file_size":4106772,"creator":"system","file_name":"IST-2018-931-v1+1_journal.ppat.1006758.pdf","access_level":"open_access"}],"pubrep_id":"931","type":"journal_article","abstract":[{"lang":"eng","text":"RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host."}],"issue":"12","publication":"PLoS Pathogens","citation":{"chicago":"Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe, Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens. Public Library of Science, 2017. https://doi.org/10.1371/journal.ppat.1006758.","mla":"Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens, vol. 13, no. 12, e1006758, Public Library of Science, 2017, doi:10.1371/journal.ppat.1006758.","short":"K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L. Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer, K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).","ista":"Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L, Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K, Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758.","apa":"Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M., … Bergthaler, A. (2017). Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1006758","ieee":"K. Khamina et al., “Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein,” PLoS Pathogens, vol. 13, no. 12. Public Library of Science, 2017.","ama":"Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 2017;13(12). doi:10.1371/journal.ppat.1006758"},"date_published":"2017-12-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","publication_status":"published","department":[{"_id":"GaNo"}],"publisher":"Public Library of Science","year":"2017","date_updated":"2021-01-12T08:01:48Z","date_created":"2018-12-11T11:47:03Z","volume":13,"author":[{"full_name":"Khamina, Kseniya","last_name":"Khamina","first_name":"Kseniya"},{"full_name":"Lercher, Alexander","last_name":"Lercher","first_name":"Alexander"},{"last_name":"Caldera","first_name":"Michael","full_name":"Caldera, Michael"},{"last_name":"Schliehe","first_name":"Christopher","full_name":"Schliehe, Christopher"},{"full_name":"Vilagos, Bojan","first_name":"Bojan","last_name":"Vilagos"},{"last_name":"Sahin","first_name":"Mehmet","full_name":"Sahin, Mehmet"},{"last_name":"Kosack","first_name":"Lindsay","full_name":"Kosack, Lindsay"},{"full_name":"Bhattacharya, Anannya","first_name":"Anannya","last_name":"Bhattacharya"},{"full_name":"Májek, Peter","last_name":"Májek","first_name":"Peter"},{"last_name":"Stukalov","first_name":"Alexey","full_name":"Stukalov, Alexey"},{"full_name":"Sacco, Roberto","last_name":"Sacco","first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Leo","last_name":"James","full_name":"James, Leo"},{"full_name":"Pinschewer, Daniel","last_name":"Pinschewer","first_name":"Daniel"},{"full_name":"Bennett, Keiryn","last_name":"Bennett","first_name":"Keiryn"},{"full_name":"Menche, Jörg","first_name":"Jörg","last_name":"Menche"},{"first_name":"Andreas","last_name":"Bergthaler","full_name":"Bergthaler, Andreas"}],"article_number":"e1006758","file_date_updated":"2020-07-14T12:46:44Z","publist_id":"7276","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.ppat.1006758","month":"12","publication_identifier":{"issn":["15537366"]}},{"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309"}],"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.23638/LMCS-13(2:15)2017","month":"07","publication_identifier":{"issn":["18605974"]},"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"International Federation of Computational Logic","year":"2017","date_created":"2018-12-11T11:46:38Z","date_updated":"2023-02-23T12:26:16Z","volume":13,"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Zuzana","last_name":"Křetínská","full_name":"Křetínská, Zuzana"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky","full_name":"Kretinsky, Jan"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1657"},{"relation":"earlier_version","status":"public","id":"5429"},{"relation":"earlier_version","status":"public","id":"5435"}]},"article_number":"15","file_date_updated":"2020-07-14T12:46:33Z","publist_id":"7355","ec_funded":1,"publication":"Logical Methods in Computer Science","citation":{"ieee":"K. Chatterjee, Z. Křetínská, and J. Kretinsky, “Unifying two views on multiple mean-payoff objectives in Markov decision processes,” Logical Methods in Computer Science, vol. 13, no. 2. International Federation of Computational Logic, 2017.","apa":"Chatterjee, K., Křetínská, Z., & Kretinsky, J. (2017). Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(2:15)2017","ista":"Chatterjee K, Křetínská Z, Kretinsky J. 2017. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 13(2), 15.","ama":"Chatterjee K, Křetínská Z, Kretinsky J. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 2017;13(2). doi:10.23638/LMCS-13(2:15)2017","chicago":"Chatterjee, Krishnendu, Zuzana Křetínská, and Jan Kretinsky. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(2:15)2017.","short":"K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science 13 (2017).","mla":"Chatterjee, Krishnendu, et al. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science, vol. 13, no. 2, 15, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(2:15)2017."},"date_published":"2017-07-03T00:00:00Z","scopus_import":1,"day":"03","has_accepted_license":"1","title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","status":"public","ddc":["004"],"intvolume":" 13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"466","file":[{"content_type":"application/pdf","file_size":511832,"creator":"system","file_name":"IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:33Z","date_created":"2018-12-12T10:18:32Z","checksum":"bfa405385ec6229ad5ead89ab5751639","relation":"main_file","file_id":"5354"}],"oa_version":"Published Version","pubrep_id":"957","type":"journal_article","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. "}],"issue":"2"},{"publication_identifier":{"issn":["15293785"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1145/3152769","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1606.03598"]},"main_file_link":[{"url":"https://arxiv.org/abs/1606.03598","open_access":"1"}],"ec_funded":1,"publist_id":"7354","article_number":"31","volume":18,"date_updated":"2023-02-23T12:26:19Z","date_created":"2018-12-11T11:46:38Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1656"},{"id":"5415","status":"public","relation":"earlier_version"},{"status":"public","relation":"earlier_version","id":"5436"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"ACM","publication_status":"published","year":"2017","day":"01","scopus_import":1,"date_published":"2017-12-01T00:00:00Z","citation":{"ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Nested weighted automata. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3152769","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 18(4), 31.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational Logic (TOCL) 18 (2017).","mla":"Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4, 31, ACM, 2017, doi:10.1145/3152769.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3152769."},"publication":"ACM Transactions on Computational Logic (TOCL)","issue":"4","abstract":[{"lang":"eng","text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 18","status":"public","title":"Nested weighted automata","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"467"},{"type":"journal_article","abstract":[{"lang":"eng","text":"The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. "}],"issue":"3","_id":"465","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"status":"public","title":"Edit distance for pushdown automata","intvolume":" 13","pubrep_id":"955","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5090","date_created":"2018-12-12T10:14:37Z","date_updated":"2020-07-14T12:46:33Z","checksum":"08041379ba408d40664f449eb5907a8f","file_name":"IST-2015-321-v1+1_main.pdf","access_level":"open_access","file_size":279071,"content_type":"application/pdf","creator":"system"},{"access_level":"open_access","file_name":"IST-2018-955-v1+1_2017_Chatterjee_Edit_distance.pdf","creator":"system","content_type":"application/pdf","file_size":279071,"file_id":"5091","relation":"main_file","checksum":"08041379ba408d40664f449eb5907a8f","date_updated":"2020-07-14T12:46:33Z","date_created":"2018-12-12T10:14:38Z"}],"scopus_import":1,"day":"13","has_accepted_license":"1","publication":"Logical Methods in Computer Science","citation":{"apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017). Edit distance for pushdown automata. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:23)2017","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for pushdown automata. Logical Methods in Computer Science. 13(3).","ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017.","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods in Computer Science 13 (2017).","mla":"Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science, vol. 13, no. 3, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:23)2017."},"date_published":"2017-09-13T00:00:00Z","file_date_updated":"2020-07-14T12:46:33Z","publist_id":"7356","ec_funded":1,"year":"2017","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"International Federation of Computational Logic","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Otop","first_name":"Jan","full_name":"Otop, Jan"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1610"},{"status":"public","relation":"earlier_version","id":"5438"}]},"date_created":"2018-12-11T11:46:37Z","date_updated":"2023-02-23T12:26:25Z","volume":13,"month":"09","publication_identifier":{"issn":["18605974"]},"oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"quality_controlled":"1","project":[{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"doi":"10.23638/LMCS-13(3:23)2017","language":[{"iso":"eng"}]},{"pubrep_id":"938","oa_version":"Published Version","file":[{"file_name":"IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1536783,"file_id":"5357","relation":"main_file","date_updated":"2020-07-14T12:46:36Z","date_created":"2018-12-12T10:18:35Z","checksum":"7d05cbdd914e194a019c0f91fb64e9a8"}],"_id":"512","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 7","title":"Amplification on undirected population structures: Comets beat stars","status":"public","ddc":["004"],"issue":"1","abstract":[{"text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Cometswarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively. ","lang":"eng"}],"type":"journal_article","date_published":"2017-03-06T00:00:00Z","citation":{"chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/s41598-017-00107-w.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports 7 (2017).","mla":"Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports, vol. 7, no. 1, 82, Nature Publishing Group, 2017, doi:10.1038/s41598-017-00107-w.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2017). Amplification on undirected population structures: Comets beat stars. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-017-00107-w","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification on undirected population structures: Comets beat stars,” Scientific Reports, vol. 7, no. 1. Nature Publishing Group, 2017.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 7(1), 82.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 2017;7(1). doi:10.1038/s41598-017-00107-w"},"publication":"Scientific Reports","has_accepted_license":"1","article_processing_charge":"No","day":"06","scopus_import":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5449"}]},"author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"},{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"volume":7,"date_created":"2018-12-11T11:46:53Z","date_updated":"2023-02-23T12:26:57Z","year":"2017","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","publication_status":"published","ec_funded":1,"publist_id":"7307","file_date_updated":"2020-07-14T12:46:36Z","article_number":"82","doi":"10.1038/s41598-017-00107-w","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"quality_controlled":"1","publication_identifier":{"issn":["20452322"]},"month":"03"},{"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n","year":"2017","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5455"}]},"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bhavya","last_name":"Choudhary","full_name":"Choudhary, Bhavya"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"}],"volume":2,"date_created":"2021-12-05T23:01:48Z","date_updated":"2023-02-23T12:27:13Z","article_number":"30","ec_funded":1,"file_date_updated":"2021-12-07T08:06:28Z","external_id":{"arxiv":["1910.00241"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","doi":"10.1145/3158118","conference":{"name":"POPL: Programming Languages","start_date":"2018-01-07","location":"Los Angeles, CA, United States","end_date":"2018-01-13"},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2475-1421"]},"month":"12","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10416","intvolume":" 2","status":"public","title":"Optimal Dyck reachability for data-dependence and Alias analysis","ddc":["000"],"oa_version":"Published Version","file":[{"date_created":"2021-12-07T08:06:28Z","date_updated":"2021-12-07T08:06:28Z","checksum":"faa3f7b3fe8aab84b50ed805c26a0ee5","success":1,"relation":"main_file","file_id":"10421","content_type":"application/pdf","file_size":460188,"creator":"cchlebak","file_name":"2017_ACMProgLang_Chatterjee.pdf","access_level":"open_access"}],"type":"journal_article","issue":"POPL","abstract":[{"lang":"eng","text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks."}],"citation":{"ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158118","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability for data-dependence and Alias analysis,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158118","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2(POPL), 30.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 2 (2017).","mla":"Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118.","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118."},"publication":"Proceedings of the ACM on Programming Languages","article_type":"original","date_published":"2017-12-27T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"27"},{"oa":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2017-870-v1-1","publication_identifier":{"issn":["2664-1690"]},"month":"10","publisher":"IST Austria","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2017","date_created":"2018-12-12T11:39:26Z","date_updated":"2023-02-21T15:54:10Z","related_material":{"record":[{"id":"10416","relation":"later_version","status":"public"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Choudhary","first_name":"Bhavya","full_name":"Choudhary, Bhavya"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"}],"file_date_updated":"2020-07-14T12:46:59Z","page":"37","citation":{"ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, Optimal Dyck reachability for data-dependence and alias analysis. IST Austria, 2017.","apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and alias analysis. IST Austria. https://doi.org/10.15479/AT:IST-2017-870-v1-1","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and alias analysis, IST Austria, 37p.","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria; 2017. doi:10.15479/AT:IST-2017-870-v1-1","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-870-v1-1.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Optimal Dyck Reachability for Data-Dependence and Alias Analysis, IST Austria, 2017.","mla":"Chatterjee, Krishnendu, et al. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017, doi:10.15479/AT:IST-2017-870-v1-1."},"date_published":"2017-10-23T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"23","title":"Optimal Dyck reachability for data-dependence and alias analysis","status":"public","ddc":["000"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"5455","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-870-v1+1_main.pdf","content_type":"application/pdf","file_size":960491,"creator":"system","relation":"main_file","file_id":"5524","checksum":"177a84a46e3ac17e87b31534ad16a4c9","date_created":"2018-12-12T11:54:02Z","date_updated":"2020-07-14T12:46:59Z"}],"pubrep_id":"870","alternative_title":["IST Austria Technical Report"],"type":"technical_report","abstract":[{"text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graphwhere the edges are labeled with different types of opening and closing parentheses, and the reachabilityinformation is computed via paths whose parentheses are properly matched. We present new results for Dyckreachability problems with applications to alias analysis and data-dependence analysis. Our main contributions,that include improved upper bounds as well as lower bounds that establish optimality guarantees, are asfollows:First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph withnnodes andmedges, we present: (i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching lower bound that shows that our algorithm is optimalwrt to worst-case complexity; and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtainanalysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almostlinear time, after which the contribution of the library in the complexity of the client analysis is only linear,and only wrt the number of call sites.Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean MatrixMultiplication, which is a long-standing open problem. Thus we establish that the existing combinatorialalgorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the samehardness holds for graphs of constant treewidth.Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependenceanalysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform allexisting methods on the two problems, over real-world benchmarks.","lang":"eng"}]},{"month":"06","day":"26","citation":{"apa":"Petritsch, B. (2017). Implementing the institutional data repository IST DataRep. IST Austria.","ieee":"B. Petritsch, Implementing the institutional data repository IST DataRep. IST Austria, 2017.","ista":"Petritsch B. 2017. Implementing the institutional data repository IST DataRep, IST Austria,p.","ama":"Petritsch B. Implementing the Institutional Data Repository IST DataRep. IST Austria; 2017.","chicago":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017.","short":"B. Petritsch, Implementing the Institutional Data Repository IST DataRep, IST Austria, 2017.","mla":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://repository.ist.ac.at/id/eprint/724."}],"publication_date":"2017-06-26","date_published":"2017-06-26T00:00:00Z","type":"report","file_date_updated":"2020-07-14T12:46:59Z","abstract":[{"text":"In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.","lang":"eng"}],"extern":0,"year":"2017","_id":"5450","publisher":"IST Austria","department":[{"_id":"E-Lib"}],"title":"Implementing the institutional data repository IST DataRep","status":"public","pubrep_id":"724","author":[{"last_name":"Petritsch","first_name":"Barbara","orcid":"0000-0003-2724-4614","id":"406048EC-F248-11E8-B48F-1D18A9856A87","full_name":"Barbara Petritsch"}],"file":[{"access_level":"open_access","file_name":"IST-2017-724-v1+1_DataRep_Project_Report_2017.pdf","file_size":3460985,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5483","checksum":"6321792dcfa82bf490f17615a9b22355","date_created":"2018-12-12T11:53:22Z","date_updated":"2020-07-14T12:46:59Z"}],"date_updated":"2020-07-14T23:05:03Z","date_created":"2018-12-12T11:39:24Z"},{"volume":2,"date_created":"2021-12-05T23:01:49Z","date_updated":"2023-02-23T12:27:16Z","related_material":{"record":[{"id":"5448","relation":"earlier_version","status":"public"},{"status":"public","relation":"earlier_version","id":"5456"}]},"author":[{"full_name":"Chalupa, Marek","first_name":"Marek","last_name":"Chalupa"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"full_name":"Sinha, Nishant","first_name":"Nishant","last_name":"Sinha"},{"full_name":"Vaidya, Kapil","last_name":"Vaidya","first_name":"Kapil"}],"department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","publication_status":"published","year":"2017","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","ec_funded":1,"article_number":"31","language":[{"iso":"eng"}],"doi":"10.1145/3158119","conference":{"end_date":"2018-01-13","start_date":"2018-01-07","location":"Los Angeles, CA, United States","name":"POPL: Programming Languages"},"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3158119"}],"oa":1,"external_id":{"arxiv":["1610.01188"]},"publication_identifier":{"eissn":["2475-1421"]},"month":"12","oa_version":"Published Version","intvolume":" 2","title":"Data-centric dynamic partial order reduction","status":"public","_id":"10417","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"POPL","abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence."}],"type":"journal_article","date_published":"2017-12-27T00:00:00Z","article_type":"original","citation":{"chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158119.","mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for Computing Machinery, 2017, doi:10.1145/3158119.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2017).","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158119","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158119"},"publication":"Proceedings of the ACM on Programming Languages","article_processing_charge":"No","day":"27","scopus_import":"1"},{"date_published":"2017-10-23T00:00:00Z","doi":"10.15479/AT:IST-2017-872-v1-1","language":[{"iso":"eng"}],"citation":{"mla":"Chalupa, Marek, et al. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017, doi:10.15479/AT:IST-2017-872-v1-1.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2017.","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-872-v1-1.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-Centric Dynamic Partial Order Reduction. IST Austria; 2017. doi:10.15479/AT:IST-2017-872-v1-1","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction, IST Austria, 36p.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. IST Austria. https://doi.org/10.15479/AT:IST-2017-872-v1-1","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, Data-centric dynamic partial order reduction. IST Austria, 2017."},"oa":1,"page":"36","day":"23","month":"10","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"author":[{"first_name":"Marek","last_name":"Chalupa","full_name":"Chalupa, Marek"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"},{"full_name":"Sinha, Nishant","last_name":"Sinha","first_name":"Nishant"},{"last_name":"Vaidya","first_name":"Kapil","full_name":"Vaidya, Kapil"}],"pubrep_id":"872","related_material":{"record":[{"id":"10417","relation":"later_version","status":"public"},{"status":"public","relation":"earlier_version","id":"5448"}]},"date_created":"2018-12-12T11:39:26Z","date_updated":"2023-02-23T12:26:54Z","file":[{"checksum":"d2635c4cf013000f0a1b09e80f9e4ab7","date_created":"2018-12-12T11:53:26Z","date_updated":"2020-07-14T12:46:59Z","relation":"main_file","file_id":"5487","content_type":"application/pdf","file_size":910347,"creator":"system","access_level":"open_access","file_name":"IST-2017-872-v1+1_main.pdf"}],"oa_version":"Published Version","year":"2017","_id":"5456","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["000"],"title":"Data-centric dynamic partial order reduction","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IST Austria","abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes."}],"file_date_updated":"2020-07-14T12:46:59Z","type":"technical_report","alternative_title":["IST Austria Technical Report"]},{"date_published":"2017-11-01T00:00:00Z","citation":{"ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2017. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 61.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2017). Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.61","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, “Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.61","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.61.","mla":"Chatterjee, Krishnendu, et al. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” Leibniz International Proceedings in Informatics, vol. 83, 61, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.61.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"publication":"Leibniz International Proceedings in Informatics","has_accepted_license":"1","day":"01","scopus_import":1,"file":[{"creator":"system","content_type":"application/pdf","file_size":535077,"file_name":"IST-2018-924-v1+1_LIPIcs-MFCS-2017-61.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T10:18:04Z","checksum":"2eed5224c0e4e259484a1d71acb8ba6a","file_id":"5322","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"924","intvolume":" 83","status":"public","ddc":["004"],"title":"Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs","_id":"551","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs. ","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.MFCS.2017.61","conference":{"location":"Aalborg, Denmark","start_date":"2017-08-21","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"isbn":["978-395977046-0"]},"month":"11","volume":83,"date_updated":"2021-01-12T08:02:34Z","date_created":"2018-12-11T11:47:08Z","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2017","publist_id":"7263","file_date_updated":"2020-07-14T12:47:00Z","article_number":"61"},{"doi":"10.4230/LIPIcs.MFCS.2017.39","conference":{"location":"Aalborg, Denmark","start_date":"2017-08-21","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"quality_controlled":"1","publication_identifier":{"isbn":["978-395977046-0"]},"month":"11","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"},{"full_name":"Svozil, Alexander","first_name":"Alexander","last_name":"Svozil"}],"volume":83,"date_created":"2018-12-11T11:47:08Z","date_updated":"2023-02-14T10:06:46Z","year":"2017","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","ec_funded":1,"publist_id":"7262","file_date_updated":"2020-07-14T12:47:00Z","license":"https://creativecommons.org/licenses/by/3.0/","article_number":"39","date_published":"2017-11-01T00:00:00Z","citation":{"chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Alexander Svozil. “Faster Algorithms for Mean-Payoff Parity Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.39.","short":"K. Chatterjee, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Mean-Payoff Parity Games.” Leibniz International Proceedings in Informatics, vol. 83, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.39.","ieee":"K. Chatterjee, M. H. Henzinger, and A. Svozil, “Faster algorithms for mean-payoff parity games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","apa":"Chatterjee, K., Henzinger, M. H., & Svozil, A. (2017). Faster algorithms for mean-payoff parity games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.39","ista":"Chatterjee K, Henzinger MH, Svozil A. 2017. Faster algorithms for mean-payoff parity games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 39.","ama":"Chatterjee K, Henzinger MH, Svozil A. Faster algorithms for mean-payoff parity games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.39"},"publication":"Leibniz International Proceedings in Informatics","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","pubrep_id":"923","file":[{"file_id":"5248","relation":"main_file","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T10:16:57Z","checksum":"c67f4866ddbfd555afef1f63ae9a8fc7","file_name":"IST-2018-923-v1+1_LIPIcs-MFCS-2017-39.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":610339}],"oa_version":"Published Version","_id":"552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 83","title":"Faster algorithms for mean-payoff parity games","ddc":["004"],"status":"public","abstract":[{"text":"Graph games provide the foundation for modeling and synthesis of reactive processes. Such games are played over graphs where the vertices are controlled by two adversarial players. We consider graph games where the objective of the first player is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a meanpayoff condition). There are two variants of the problem, namely, the threshold problem where the quantitative goal is to ensure that the mean-payoff value is above a threshold, and the value problem where the quantitative goal is to ensure the optimal mean-payoff value; in both cases ensuring the qualitative parity objective. The previous best-known algorithms for game graphs with n vertices, m edges, parity objectives with d priorities, and maximal absolute reward value W for mean-payoff objectives, are as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for the value problem. Our main contributions are faster algorithms, and the running times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem, and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives with two priorities, our algorithms match the best-known bounds of the algorithms for mean-payoff games (without conjunction with parity objectives). Our results are relevant in synthesis of reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective).","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"]},{"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.MFCS.2017.55","conference":{"name":"MFCS: Mathematical Foundations of Computer Science (SG)","location":"Aalborg, Denmark","start_date":"2017-08-21","end_date":"2017-08-25"},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1506.02434"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"isbn":["978-395977046-0"]},"month":"11","volume":83,"date_updated":"2021-01-12T08:02:35Z","date_created":"2018-12-11T11:47:08Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Hansen, Kristofer","first_name":"Kristofer","last_name":"Hansen"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus"}],"department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2017","publist_id":"7261","file_date_updated":"2020-07-14T12:47:00Z","article_number":"55","date_published":"2017-11-01T00:00:00Z","citation":{"chicago":"Chatterjee, Krishnendu, Kristofer Hansen, and Rasmus Ibsen-Jensen. “Strategy Complexity of Concurrent Safety Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.55.","short":"K. Chatterjee, K. Hansen, R. Ibsen-Jensen, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Chatterjee, Krishnendu, et al. “Strategy Complexity of Concurrent Safety Games.” Leibniz International Proceedings in Informatics, vol. 83, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.55.","ieee":"K. Chatterjee, K. Hansen, and R. Ibsen-Jensen, “Strategy complexity of concurrent safety games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","apa":"Chatterjee, K., Hansen, K., & Ibsen-Jensen, R. (2017). Strategy complexity of concurrent safety games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.55","ista":"Chatterjee K, Hansen K, Ibsen-Jensen R. 2017. Strategy complexity of concurrent safety games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 55.","ama":"Chatterjee K, Hansen K, Ibsen-Jensen R. Strategy complexity of concurrent safety games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.55"},"publication":"Leibniz International Proceedings in Informatics","has_accepted_license":"1","day":"01","scopus_import":1,"oa_version":"Published Version","file":[{"file_id":"4753","relation":"main_file","date_created":"2018-12-12T10:09:29Z","date_updated":"2020-07-14T12:47:00Z","checksum":"7101facb56ade363205c695d72dbd173","file_name":"IST-2018-922-v1+1_LIPIcs-MFCS-2017-55.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":549967}],"pubrep_id":"922","intvolume":" 83","ddc":["004"],"status":"public","title":"Strategy complexity of concurrent safety games","_id":"553","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. ","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference"},{"scopus_import":1,"day":"01","publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","citation":{"chicago":"Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London, 2017. https://doi.org/10.1098/rspa.2017.0104.","short":"M. Gerencser, A. Jentzen, D. Salimova, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 473 (2017).","mla":"Gerencser, Mate, et al. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207, 0104, Royal Society of London, 2017, doi:10.1098/rspa.2017.0104.","ieee":"M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207. Royal Society of London, 2017.","apa":"Gerencser, M., Jentzen, A., & Salimova, D. (2017). On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2017.0104","ista":"Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 473(2207), 0104.","ama":"Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2017;473(2207). doi:10.1098/rspa.2017.0104"},"date_published":"2017-11-01T00:00:00Z","type":"journal_article","abstract":[{"text":"In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions.","lang":"eng"}],"issue":"2207","status":"public","title":"On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions","intvolume":" 473","_id":"560","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","month":"11","publication_identifier":{"issn":["13645021"]},"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.03229"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rspa.2017.0104","article_number":"0104","publist_id":"7256","ec_funded":1,"publication_status":"published","publisher":"Royal Society of London","department":[{"_id":"JaMa"}],"year":"2017","date_updated":"2021-01-12T08:03:04Z","date_created":"2018-12-11T11:47:11Z","volume":473,"author":[{"first_name":"Mate","last_name":"Gerencser","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate"},{"last_name":"Jentzen","first_name":"Arnulf","full_name":"Jentzen, Arnulf"},{"last_name":"Salimova","first_name":"Diyora","full_name":"Salimova, Diyora"}]},{"year":"2017","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"American Mathematical Society","author":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"full_name":"Yau, Horng","first_name":"Horng","last_name":"Yau"}],"date_updated":"2022-05-24T06:57:28Z","date_created":"2018-12-11T11:47:13Z","volume":28,"ec_funded":1,"publist_id":"7247","quality_controlled":"1","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"doi":"10.1090/cln/028","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eisbn":["978-1-4704-4194-4"],"isbn":["9-781-4704-3648-3"]},"_id":"567","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A Dynamical Approach to Random Matrix Theory","status":"public","intvolume":" 28","oa_version":"None","type":"book","alternative_title":["Courant Lecture Notes"],"abstract":[{"text":"This book is a concise and self-contained introduction of recent techniques to prove local spectral universality for large random matrices. Random matrix theory is a fast expanding research area, and this book mainly focuses on the methods that the authors participated in developing over the past few years. Many other interesting topics are not included, and neither are several new developments within the framework of these methods. The authors have chosen instead to present key concepts that they believe are the core of these methods and should be relevant for future applications. They keep technicalities to a minimum to make the book accessible to graduate students. With this in mind, they include in this book the basic notions and tools for high-dimensional analysis, such as large deviation, entropy, Dirichlet form, and the logarithmic Sobolev inequality.\r\n","lang":"eng"}],"citation":{"ama":"Erdös L, Yau H. A Dynamical Approach to Random Matrix Theory. Vol 28. American Mathematical Society; 2017. doi:10.1090/cln/028","apa":"Erdös, L., & Yau, H. (2017). A Dynamical Approach to Random Matrix Theory (Vol. 28). American Mathematical Society. https://doi.org/10.1090/cln/028","ieee":"L. Erdös and H. Yau, A Dynamical Approach to Random Matrix Theory, vol. 28. American Mathematical Society, 2017.","ista":"Erdös L, Yau H. 2017. A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 226p.","short":"L. Erdös, H. Yau, A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 2017.","mla":"Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28, American Mathematical Society, 2017, doi:10.1090/cln/028.","chicago":"Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28. Courant Lecture Notes. American Mathematical Society, 2017. https://doi.org/10.1090/cln/028."},"page":"226","date_published":"2017-01-01T00:00:00Z","series_title":"Courant Lecture Notes","day":"01","article_processing_charge":"No"},{"author":[{"full_name":"Franek, Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Franek"},{"last_name":"Krcál","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek"}],"volume":19,"date_updated":"2021-01-12T08:03:12Z","date_created":"2018-12-11T11:47:14Z","year":"2017","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publisher":"International Press","publication_status":"published","publist_id":"7246","ec_funded":1,"doi":"10.4310/HHA.2017.v19.n2.a16","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.04310"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","call_identifier":"H2020","grant_number":"701309","_id":"2590DB08-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publication_identifier":{"issn":["15320073"]},"month":"01","oa_version":"Submitted Version","_id":"568","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 19","status":"public","title":"Persistence of zero sets","issue":"2","abstract":[{"text":"We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r > 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C).","lang":"eng"}],"type":"journal_article","date_published":"2017-01-01T00:00:00Z","citation":{"ieee":"P. Franek and M. Krcál, “Persistence of zero sets,” Homology, Homotopy and Applications, vol. 19, no. 2. International Press, pp. 313–342, 2017.","apa":"Franek, P., & Krcál, M. (2017). Persistence of zero sets. Homology, Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2017.v19.n2.a16","ista":"Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and Applications. 19(2), 313–342.","ama":"Franek P, Krcál M. Persistence of zero sets. Homology, Homotopy and Applications. 2017;19(2):313-342. doi:10.4310/HHA.2017.v19.n2.a16","chicago":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications. International Press, 2017. https://doi.org/10.4310/HHA.2017.v19.n2.a16.","short":"P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342.","mla":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:10.4310/HHA.2017.v19.n2.a16."},"publication":"Homology, Homotopy and Applications","page":"313 - 342","day":"01","scopus_import":1},{"scopus_import":1,"has_accepted_license":"1","day":"13","citation":{"short":"M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).","mla":"Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921.","chicago":"Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.","ama":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921","ieee":"M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921","ista":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921."},"publication":"eLife","date_published":"2017-11-13T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. "}],"intvolume":" 6","ddc":["576"],"title":"Regulatory network structure determines patterns of intermolecular epistasis","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"570","file":[{"access_level":"open_access","file_name":"IST-2017-918-v1+1_elife-28921-figures-v3.pdf","file_size":8453470,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5096","checksum":"273ab17f33305e4eaafd911ff88e7c5b","date_created":"2018-12-12T10:14:42Z","date_updated":"2020-07-14T12:47:10Z"},{"creator":"system","content_type":"application/pdf","file_size":1953221,"access_level":"open_access","file_name":"IST-2017-918-v1+2_elife-28921-v3.pdf","checksum":"b433f90576c7be597cd43367946f8e7f","date_created":"2018-12-12T10:14:43Z","date_updated":"2020-07-14T12:47:10Z","file_id":"5097","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"918","publication_identifier":{"issn":["2050084X"]},"month":"11","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.28921","article_number":"e28921","publist_id":"7244","ec_funded":1,"file_date_updated":"2020-07-14T12:47:10Z","department":[{"_id":"CaGu"},{"_id":"JoBo"},{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","publication_status":"published","year":"2017","volume":6,"date_created":"2018-12-11T11:47:14Z","date_updated":"2021-01-12T08:03:15Z","author":[{"first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","first_name":"Srdjan","last_name":"Sarikas","full_name":"Sarikas, Srdjan"},{"full_name":"Acar, Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1986-9753","first_name":"Hande","last_name":"Acar"},{"full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"}]},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.7554/eLife.30867","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2050084X"]},"month":"11","year":"2017","publisher":"eLife Sciences Publications","department":[{"_id":"MiSi"}],"publication_status":"published","author":[{"full_name":"Spira, Felix","first_name":"Felix","last_name":"Spira"},{"last_name":"Cuylen Haering","first_name":"Sara","full_name":"Cuylen Haering, Sara"},{"full_name":"Mehta, Shalin","last_name":"Mehta","first_name":"Shalin"},{"last_name":"Samwer","first_name":"Matthias","full_name":"Samwer, Matthias"},{"last_name":"Reversat","first_name":"Anne","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","full_name":"Reversat, Anne"},{"full_name":"Verma, Amitabh","first_name":"Amitabh","last_name":"Verma"},{"full_name":"Oldenbourg, Rudolf","first_name":"Rudolf","last_name":"Oldenbourg"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"first_name":"Daniel","last_name":"Gerlich","full_name":"Gerlich, Daniel"}],"volume":6,"date_updated":"2023-02-23T12:30:29Z","date_created":"2018-12-11T11:47:14Z","article_number":"e30867","publist_id":"7245","file_date_updated":"2020-07-14T12:47:10Z","citation":{"ama":"Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 2017;6. doi:10.7554/eLife.30867","ista":"Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 6, e30867.","apa":"Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma, A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.30867","ieee":"F. Spira et al., “Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments,” eLife, vol. 6. eLife Sciences Publications, 2017.","mla":"Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife, vol. 6, e30867, eLife Sciences Publications, 2017, doi:10.7554/eLife.30867.","short":"F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma, R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017).","chicago":"Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.30867."},"publication":"eLife","date_published":"2017-11-06T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"569","intvolume":" 6","ddc":["570"],"title":"Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments","status":"public","pubrep_id":"919","file":[{"file_size":9666973,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-919-v1+1_elife-30867-figures-v1.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:10:40Z","checksum":"ba09c1451153d39e4f4b7cee013e314c","relation":"main_file","file_id":"4829"},{"access_level":"open_access","file_name":"IST-2017-919-v1+2_elife-30867-v1.pdf","creator":"system","file_size":5951246,"content_type":"application/pdf","file_id":"4830","relation":"main_file","checksum":"01eb51f1d6ad679947415a51c988e137","date_created":"2018-12-12T10:10:41Z","date_updated":"2020-07-14T12:47:10Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings."}]}]