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Here, we report that the Cyclin-dependent Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts and this in turn translates into differential CDKG1 protein expression coordinating the alternative splicing of ATU2AF65A. This article is protected by copyright. All rights reserved."}],"oa_version":"Published Version","department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:46:22Z","date_updated":"2023-09-19T10:07:08Z","ddc":["580"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"403","page":"1010 - 1022","date_created":"2018-12-11T11:46:17Z","date_published":"2018-06-01T00:00:00Z","doi":"10.1111/tpj.13914","year":"2018","has_accepted_license":"1","isi":1,"publication":"The Plant Journal","day":"01","oa":1,"publisher":"Wiley","quality_controlled":"1","acknowledgement":"CN, DD and JHD were funded by the BBSRC (grant number BB/M009459/1). NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna. AB and AF were supported by the Austrian Science Fund (FWF) [DK W1207; SFB RNAreg F43-P10]","article_processing_charge":"No","external_id":{"isi":["000434365500008"]},"author":[{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"last_name":"Nibau","full_name":"Nibau, Candida","first_name":"Candida"},{"first_name":"Armin","full_name":"Fuchs, Armin","last_name":"Fuchs"},{"full_name":"Dadarou, Despoina","last_name":"Dadarou","first_name":"Despoina"},{"last_name":"Barta","full_name":"Barta, Andrea","first_name":"Andrea"},{"full_name":"Doonan, John","last_name":"Doonan","first_name":"John"}],"publist_id":"7426","title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","citation":{"mla":"Cavallari, Nicola, et al. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal, vol. 94, no. 6, Wiley, 2018, pp. 1010–22, doi:10.1111/tpj.13914.","apa":"Cavallari, N., Nibau, C., Fuchs, A., Dadarou, D., Barta, A., & Doonan, J. (2018). The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.13914","ama":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 2018;94(6):1010-1022. doi:10.1111/tpj.13914","ieee":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, and J. Doonan, “The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A,” The Plant Journal, vol. 94, no. 6. Wiley, pp. 1010–1022, 2018.","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","chicago":"Cavallari, Nicola, Candida Nibau, Armin Fuchs, Despoina Dadarou, Andrea Barta, and John Doonan. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal. Wiley, 2018. https://doi.org/10.1111/tpj.13914.","ista":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. 2018. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 94(6), 1010–1022."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"title":"The compound interest in relaxing punctuality","author":[{"last_name":"Ferrere","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7765","article_processing_charge":"No","external_id":{"isi":["000489765800009"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.","chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. https://doi.org/10.1007/978-3-319-95582-7_9.","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: International Symposium on Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: International Symposium on Formal Methods, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-95582-7_9","ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:10.1007/978-3-319-95582-7_9","mla":"Ferrere, Thomas. The Compound Interest in Relaxing Punctuality. Vol. 10951, Springer, 2018, pp. 147–64, doi:10.1007/978-3-319-95582-7_9."},"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"doi":"10.1007/978-3-319-95582-7_9","date_published":"2018-07-12T00:00:00Z","date_created":"2018-12-11T11:44:55Z","page":"147 - 164","day":"12","isi":1,"has_accepted_license":"1","year":"2018","publisher":"Springer","quality_controlled":"1","oa":1,"file_date_updated":"2020-10-09T06:22:41Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-09-19T10:05:37Z","status":"public","type":"conference","conference":{"end_date":"2018-07-17","location":"Oxford, UK","start_date":"2018-07-15","name":"FM: International Symposium on Formal Methods"},"_id":"156","volume":10951,"file":[{"success":1,"checksum":"a045c213c42c445f1889326f8db82a0a","file_id":"8637","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_LNCS_Ferrere.pdf","date_created":"2020-10-09T06:22:41Z","creator":"dernst","file_size":485576,"date_updated":"2020-10-09T06:22:41Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 10951","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"text":"Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost.","lang":"eng"}]},{"abstract":[{"text":"The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 19","month":"10","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5740","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-18T09:46:00Z","file_name":"2018_MolecPlantPath_Seitner.pdf","date_updated":"2018-12-18T09:46:00Z","file_size":682335,"creator":"dernst"}],"issue":"10","volume":19,"_id":"104","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","date_updated":"2023-09-19T10:06:42Z","ddc":["580"],"file_date_updated":"2018-12-18T09:46:00Z","department":[{"_id":"GradSch"}],"acknowledgement":"the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).","oa":1,"quality_controlled":"1","publisher":"Wiley","year":"2018","isi":1,"has_accepted_license":"1","publication":"Molecular Plant Pathology","day":"01","page":"2277 - 2287","date_created":"2018-12-11T11:44:39Z","date_published":"2018-10-01T00:00:00Z","doi":"10.1111/mpp.12698","citation":{"chicago":"Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology. Wiley, 2018. https://doi.org/10.1111/mpp.12698.","ista":"Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10), 2277–2287.","mla":"Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology, vol. 19, no. 10, Wiley, 2018, pp. 2277–87, doi:10.1111/mpp.12698.","ama":"Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 2018;19(10):2277-2287. doi:10.1111/mpp.12698","apa":"Seitner, D., Uhse, S., Gallei, M. C., & Djamei, A. (2018). The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. Wiley. https://doi.org/10.1111/mpp.12698","short":"D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287.","ieee":"D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1 is required for early infection of maize by Ustilago maydis,” Molecular Plant Pathology, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000445624100006"]},"article_processing_charge":"No","publist_id":"7950","author":[{"full_name":"Seitner, Denise","last_name":"Seitner","first_name":"Denise"},{"full_name":"Uhse, Simon","last_name":"Uhse","first_name":"Simon"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei"},{"first_name":"Armin","last_name":"Djamei","full_name":"Djamei, Armin"}],"title":"The core effector Cce1 is required for early infection of maize by Ustilago maydis"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950.","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.","ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975."},"title":"The consequences of an introgression event","publist_id":"8014","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000454600500001"],"pmid":["30599087"]},"quality_controlled":"1","publisher":"Wiley","oa":1,"day":"31","publication":"Molecular Ecology","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1111/mec.14950","date_published":"2018-12-31T00:00:00Z","date_created":"2018-12-11T11:44:18Z","page":"4973-4975","_id":"40","status":"public","type":"journal_article","article_type":"letter_note","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576"],"date_updated":"2023-09-19T10:06:08Z","file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance."}],"month":"12","intvolume":" 27","scopus_import":"1","file":[{"file_id":"6652","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-07-19T06:54:46Z","file_name":"2018_MolecularEcology_BartonNick.pdf","date_updated":"2020-07-14T12:46:22Z","file_size":295452,"creator":"apreinsp"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1365294X"]},"publication_status":"published","volume":27,"issue":"24","related_material":{"record":[{"relation":"research_data","status":"public","id":"9805"}]}},{"article_number":"e37888","citation":{"chicago":"Alanko, Jonna H, and Michael K Sixt. “The Cell Sets the Tone.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.37888.","ista":"Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888.","mla":"Alanko, Jonna H., and Michael K. Sixt. “The Cell Sets the Tone.” ELife, vol. 7, e37888, eLife Sciences Publications, 2018, doi:10.7554/eLife.37888.","ama":"Alanko JH, Sixt MK. The cell sets the tone. eLife. 2018;7. doi:10.7554/eLife.37888","apa":"Alanko, J. H., & Sixt, M. K. (2018). The cell sets the tone. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.37888","ieee":"J. H. Alanko and M. K. Sixt, “The cell sets the tone,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"J.H. Alanko, M.K. Sixt, ELife 7 (2018)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","last_name":"Alanko"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"external_id":{"isi":["000434375000001"]},"article_processing_charge":"No","title":"The cell sets the tone","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"has_accepted_license":"1","isi":1,"year":"2018","day":"06","publication":"eLife","date_published":"2018-06-06T00:00:00Z","doi":"10.7554/eLife.37888","date_created":"2019-01-20T22:59:19Z","_id":"5861","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-19T10:01:39Z","ddc":["570"],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:13Z","abstract":[{"lang":"eng","text":"In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal."}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 7","publication_identifier":{"issn":["2050084X"]},"publication_status":"published","file":[{"file_id":"5973","checksum":"f1c7ec2a809408d763c4b529a98f9a3b","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_eLife_Alanko.pdf","date_created":"2019-02-13T10:52:11Z","creator":"dernst","file_size":358141,"date_updated":"2020-07-14T12:47:13Z"}],"language":[{"iso":"eng"}],"volume":7},{"acknowledgement":"We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.).","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","publication":"The Plant Cell","day":"12","year":"2018","isi":1,"date_created":"2018-12-11T11:44:52Z","doi":"10.1105/tpc.18.00127","date_published":"2018-11-12T00:00:00Z","page":"2553 - 2572","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell. Oxford University Press, 2018. https://doi.org/10.1105/tpc.18.00127.","ista":"Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572.","mla":"Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:10.1105/tpc.18.00127.","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572.","ieee":"U. Kania et al., “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” The Plant Cell, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018.","apa":"Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. Oxford University Press. https://doi.org/10.1105/tpc.18.00127","ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 2018;30(10):2553-2572. doi:10.1105/tpc.18.00127"},"title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","article_processing_charge":"No","external_id":{"isi":["000450000500023"],"pmid":["30018156"]},"author":[{"last_name":"Kania","full_name":"Kania, Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"first_name":"Qing","full_name":"Lu, Qing","last_name":"Lu"},{"first_name":"Glenn R","full_name":"Hicks, Glenn R","last_name":"Hicks"},{"first_name":"Wim","full_name":"Nerinckx, Wim","last_name":"Nerinckx"},{"full_name":"Mishev, Kiril","last_name":"Mishev","first_name":"Kiril"},{"first_name":"Francois","last_name":"Peurois","full_name":"Peurois, Francois"},{"last_name":"Cherfils","full_name":"Cherfils, Jacqueline","first_name":"Jacqueline"},{"first_name":"Rycke Riet Maria","full_name":"De, Rycke Riet Maria","last_name":"De"},{"full_name":"Grones, Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"last_name":"Russinova","full_name":"Russinova, Eugenia","first_name":"Eugenia"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7776","pmid":1,"oa_version":"Published Version","abstract":[{"text":"The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development.","lang":"eng"}],"intvolume":" 30","month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1105/tpc.18.00127"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1040-4651"]},"ec_funded":1,"volume":30,"issue":"10","_id":"147","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-09-19T10:09:12Z","department":[{"_id":"JiFr"}]},{"scopus_import":"1","intvolume":" 4","month":"07","abstract":[{"text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"issue":"8","volume":4,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/","description":"News on IST Homepage"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"7043","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-11-18T16:24:07Z","file_name":"2018_NaturePlants_Shi.pdf","creator":"dernst","date_updated":"2020-07-14T12:44:56Z","file_size":226829}],"type":"journal_article","article_type":"original","status":"public","_id":"146","file_date_updated":"2020-07-14T12:44:56Z","department":[{"_id":"JiFr"}],"date_updated":"2023-09-19T10:08:45Z","ddc":["580"],"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","page":"596 - 604","date_created":"2018-12-11T11:44:52Z","date_published":"2018-07-30T00:00:00Z","doi":"10.1038/s41477-018-0212-z","year":"2018","has_accepted_license":"1","isi":1,"publication":"Nature Plants","day":"30","external_id":{"isi":["000443861300016"],"pmid":["30061750"]},"article_processing_charge":"No","publist_id":"7777","author":[{"full_name":"Shi, Chun Lin","last_name":"Shi","first_name":"Chun Lin"},{"last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel","orcid":"0000-0002-6862-1247","first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ullrich","full_name":"Herrmann, Ullrich","last_name":"Herrmann"},{"first_name":"Mari","last_name":"Wildhagen","full_name":"Wildhagen, Mari"},{"last_name":"Kulik","full_name":"Kulik, Ivan","first_name":"Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB"},{"last_name":"Kopf","full_name":"Kopf, Andreas","first_name":"Andreas"},{"first_name":"Takashi","full_name":"Ishida, Takashi","last_name":"Ishida"},{"first_name":"Vilde","full_name":"Olsson, Vilde","last_name":"Olsson"},{"full_name":"Anker, Mari Kristine","last_name":"Anker","first_name":"Mari Kristine"},{"first_name":"Markus","last_name":"Albert","full_name":"Albert, Markus"},{"first_name":"Melinka A","last_name":"Butenko","full_name":"Butenko, Melinka A"},{"full_name":"Felix, Georg","last_name":"Felix","first_name":"Georg"},{"full_name":"Sawa, Shinichiro","last_name":"Sawa","first_name":"Shinichiro"},{"last_name":"Claassen","full_name":"Claassen, Manfred","first_name":"Manfred"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Reidunn B","last_name":"Aalen","full_name":"Aalen, Reidunn B"}],"title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","citation":{"mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:10.1038/s41477-018-0212-z.","ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 2018;4(8):596-604. doi:10.1038/s41477-018-0212-z","apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0212-z","ieee":"C. L. Shi et al., “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604.","chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0212-z.","ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication":"Nature Human Behaviour","day":"28","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:45:39Z","doi":"10.1038/s41562-018-0354-z","date_published":"2018-05-28T00:00:00Z","page":"397 - 404","acknowledgement":"This work was supported by a grant from the John Templeton Foundation and by the Office of Naval Research Grant N00014-16-1-2914 (M.A.N.). C.H. acknowledges generous support from the ISTFELLOW programme and by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Hoffman M, Hilbe C, Nowak M. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2018;2:397-404. doi:10.1038/s41562-018-0354-z","apa":"Hoffman, M., Hilbe, C., & Nowak, M. (2018). The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0354-z","ieee":"M. Hoffman, C. Hilbe, and M. Nowak, “The signal-burying game can explain why we obscure positive traits and good deeds,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 397–404, 2018.","short":"M. Hoffman, C. Hilbe, M. Nowak, Nature Human Behaviour 2 (2018) 397–404.","mla":"Hoffman, Moshe, et al. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 397–404, doi:10.1038/s41562-018-0354-z.","ista":"Hoffman M, Hilbe C, Nowak M. 2018. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2, 397–404.","chicago":"Hoffman, Moshe, Christian Hilbe, and Martin Nowak. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0354-z."},"title":"The signal-burying game can explain why we obscure positive traits and good deeds","article_processing_charge":"No","external_id":{"isi":["000435551300009"]},"publist_id":"7588","author":[{"full_name":"Hoffman, Moshe","last_name":"Hoffman","first_name":"Moshe"},{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-19T08:17:23Z","file_name":"2018_NatureHumanBeh_Hoffman.pdf","date_updated":"2020-07-14T12:45:54Z","file_size":194734,"creator":"dernst","checksum":"32efaf06a597495c184df91b3fbb19c0","file_id":"7051","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","ec_funded":1,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/the-logic-of-modesty-why-it-pays-to-be-humble/","relation":"press_release"}]},"volume":2,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"People sometimes make their admirable deeds and accomplishments hard to spot, such as by giving anonymously or avoiding bragging. Such ‘buried’ signals are hard to reconcile with standard models of signalling or indirect reciprocity, which motivate costly pro-social behaviour by reputational gains. To explain these phenomena, we design a simple game theory model, which we call the signal-burying game. This game has the feature that senders can bury their signal by deliberately reducing the probability of the signal being observed. If the signal is observed, however, it is identified as having been buried. We show under which conditions buried signals can be maintained, using static equilibrium concepts and calculations of the evolutionary dynamics. We apply our analysis to shed light on a number of otherwise puzzling social phenomena, including modesty, anonymous donations, subtlety in art and fashion, and overeagerness."}],"intvolume":" 2","month":"05","scopus_import":"1","ddc":["000"],"date_updated":"2023-09-19T10:12:03Z","file_date_updated":"2020-07-14T12:45:54Z","department":[{"_id":"KrCh"}],"_id":"293","status":"public","type":"journal_article","article_type":"original"},{"oa":1,"quality_controlled":"1","publisher":"Birkhäuser","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors acknowledge support by ERC Advanced Grant 321029 and by VILLUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059). The authors would like to thank Sébastien Breteaux, Enno Lenzmann, Mathieu Lewin and Jochen Schmid for comments and discussions about well-posedness of the Bogoliubov–de Gennes equations.","page":"1167 - 1214","date_created":"2018-12-11T11:46:34Z","doi":"10.1007/s00023-018-0644-z","date_published":"2018-04-01T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Annales Henri Poincare","day":"01","article_processing_charge":"No","external_id":{"isi":["000427578900006"]},"publist_id":"7367","author":[{"orcid":"0000-0002-1071-6091","full_name":"Benedikter, Niels P","last_name":"Benedikter","first_name":"Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jérémy","last_name":"Sok","full_name":"Sok, Jérémy"},{"full_name":"Solovej, Jan","last_name":"Solovej","first_name":"Jan"}],"title":"The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations","citation":{"mla":"Benedikter, Niels P., et al. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare, vol. 19, no. 4, Birkhäuser, 2018, pp. 1167–214, doi:10.1007/s00023-018-0644-z.","short":"N.P. Benedikter, J. Sok, J. Solovej, Annales Henri Poincare 19 (2018) 1167–1214.","ieee":"N. P. Benedikter, J. Sok, and J. Solovej, “The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations,” Annales Henri Poincare, vol. 19, no. 4. Birkhäuser, pp. 1167–1214, 2018.","ama":"Benedikter NP, Sok J, Solovej J. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 2018;19(4):1167-1214. doi:10.1007/s00023-018-0644-z","apa":"Benedikter, N. P., Sok, J., & Solovej, J. (2018). The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-018-0644-z","chicago":"Benedikter, Niels P, Jérémy Sok, and Jan Solovej. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare. Birkhäuser, 2018. https://doi.org/10.1007/s00023-018-0644-z.","ista":"Benedikter NP, Sok J, Solovej J. 2018. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 19(4), 1167–1214."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["Annales Henri Poincare"],"scopus_import":"1","intvolume":" 19","month":"04","abstract":[{"lang":"eng","text":"The derivation of effective evolution equations is central to the study of non-stationary quantum many-body systems, and widely used in contexts such as superconductivity, nuclear physics, Bose–Einstein condensation and quantum chemistry. We reformulate the Dirac–Frenkel approximation principle in terms of reduced density matrices and apply it to fermionic and bosonic many-body systems. We obtain the Bogoliubov–de Gennes and Hartree–Fock–Bogoliubov equations, respectively. While we do not prove quantitative error estimates, our formulation does show that the approximation is optimal within the class of quasifree states. Furthermore, we prove well-posedness of the Bogoliubov–de Gennes equations in energy space and discuss conserved quantities"}],"oa_version":"Published Version","volume":19,"issue":"4","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:46:31Z","file_size":923252,"creator":"system","date_created":"2018-12-12T10:11:57Z","file_name":"IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4914","checksum":"883eeccba8384ad7fcaa28761d99a0fa"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"993","status":"public","_id":"455","file_date_updated":"2020-07-14T12:46:31Z","department":[{"_id":"RoSe"}],"date_updated":"2023-09-19T10:07:41Z","ddc":["510","539"]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Bauer G, Fakhri N, Kicheva A, Kondev J, Kruse K, Noji H, Riveline D, Saunders T, Thatta M, Wieschaus E. 2018. The science of living matter for tomorrow. Cell Systems. 6(4), 400–402.","chicago":"Bauer, Guntram, Nikta Fakhri, Anna Kicheva, Jané Kondev, Karsten Kruse, Hiroyuki Noji, Daniel Riveline, Timothy Saunders, Mukund Thatta, and Eric Wieschaus. “The Science of Living Matter for Tomorrow.” Cell Systems. Cell Press, 2018. https://doi.org/10.1016/j.cels.2018.04.003.","ama":"Bauer G, Fakhri N, Kicheva A, et al. The science of living matter for tomorrow. Cell Systems. 2018;6(4):400-402. doi:10.1016/j.cels.2018.04.003","apa":"Bauer, G., Fakhri, N., Kicheva, A., Kondev, J., Kruse, K., Noji, H., … Wieschaus, E. (2018). The science of living matter for tomorrow. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2018.04.003","ieee":"G. Bauer et al., “The science of living matter for tomorrow,” Cell Systems, vol. 6, no. 4. Cell Press, pp. 400–402, 2018.","short":"G. Bauer, N. Fakhri, A. Kicheva, J. Kondev, K. Kruse, H. Noji, D. Riveline, T. Saunders, M. Thatta, E. Wieschaus, Cell Systems 6 (2018) 400–402.","mla":"Bauer, Guntram, et al. “The Science of Living Matter for Tomorrow.” Cell Systems, vol. 6, no. 4, Cell Press, 2018, pp. 400–02, doi:10.1016/j.cels.2018.04.003."},"title":"The science of living matter for tomorrow","external_id":{"pmid":["29698645"],"isi":["000432192100003"]},"article_processing_charge":"No","publist_id":"7551","author":[{"full_name":"Bauer, Guntram","last_name":"Bauer","first_name":"Guntram"},{"first_name":"Nikta","full_name":"Fakhri, Nikta","last_name":"Fakhri"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"},{"last_name":"Kondev","full_name":"Kondev, Jané","first_name":"Jané"},{"last_name":"Kruse","full_name":"Kruse, Karsten","first_name":"Karsten"},{"last_name":"Noji","full_name":"Noji, Hiroyuki","first_name":"Hiroyuki"},{"first_name":"Daniel","last_name":"Riveline","full_name":"Riveline, Daniel"},{"first_name":"Timothy","last_name":"Saunders","full_name":"Saunders, Timothy"},{"first_name":"Mukund","full_name":"Thatta, Mukund","last_name":"Thatta"},{"last_name":"Wieschaus","full_name":"Wieschaus, Eric","first_name":"Eric"}],"oa":1,"publisher":"Cell Press","quality_controlled":"1","publication":"Cell Systems","day":"25","year":"2018","isi":1,"date_created":"2018-12-11T11:45:46Z","date_published":"2018-04-25T00:00:00Z","doi":"10.1016/j.cels.2018.04.003","page":"400 - 402","_id":"314","status":"public","article_type":"letter_note","type":"journal_article","date_updated":"2023-09-19T10:11:25Z","department":[{"_id":"AnKi"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"The interface of physics and biology pro-vides a fruitful environment for generatingnew concepts and exciting ways forwardto understanding living matter. Examplesof successful studies include the estab-lishment and readout of morphogen gra-dients during development, signal pro-cessing in protein and genetic networks,the role of fluctuations in determining thefates of cells and tissues, and collectiveeffects in proteins and in tissues. It is nothard to envision that significant further ad-vances will translate to societal benefitsby initiating the development of new de-vices and strategies for curing disease.However, research at the interface posesvarious challenges, in particular for youngscientists, and current institutions arerarely designed to facilitate such scientificprograms. In this Letter, we propose aninternational initiative that addressesthese challenges through the establish-ment of a worldwide network of platformsfor cross-disciplinary training and incuba-tors for starting new collaborations.","lang":"eng"}],"intvolume":" 6","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cels.2018.04.003"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2405-4712"]},"issue":"4","volume":6},{"language":[{"iso":"eng"}],"publication_status":"published","volume":208,"issue":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. ","lang":"eng"}],"month":"01","intvolume":" 208","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/","open_access":"1"}],"date_updated":"2023-09-19T10:12:31Z","department":[{"_id":"NiBa"}],"_id":"565","status":"public","type":"journal_article","article_type":"original","day":"01","publication":"Genetics","isi":1,"year":"2018","doi":"10.1534/genetics.117.300426","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:47:12Z","page":"377 - 382","quality_controlled":"1","publisher":"Genetics ","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426","ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp. 377–82, doi:10.1534/genetics.117.300426.","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426."},"title":"The spread of an inversion with migration and selection","author":[{"first_name":"Brian","full_name":"Charlesworth, Brian","last_name":"Charlesworth"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publist_id":"7249","article_processing_charge":"No","external_id":{"isi":["000419356300025"],"pmid":["29158424"]}},{"issue":"3","volume":71,"language":[{"iso":"eng"}],"publication_status":"published","month":"03","intvolume":" 71","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.07355"}],"oa_version":"Preprint","abstract":[{"text":"We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z > 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential.","lang":"eng"}],"department":[{"_id":"RoSe"}],"date_updated":"2023-09-19T10:09:40Z","status":"public","article_type":"original","type":"journal_article","_id":"446","doi":"10.1002/cpa.21717","date_published":"2018-03-01T00:00:00Z","date_created":"2018-12-11T11:46:31Z","page":"577 - 614","day":"01","publication":"Communications on Pure and Applied Mathematics","isi":1,"year":"2018","publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"acknowledgement":"We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n","title":"The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory","author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"last_name":"Phan Thanh","full_name":"Phan Thanh, Nam","first_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hanne","full_name":"Van Den Bosch, Hanne","last_name":"Van Den Bosch"}],"publist_id":"7377","external_id":{"arxiv":["1606.07355"],"isi":["000422675800004"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2018. https://doi.org/10.1002/cpa.21717.","ista":"Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614.","mla":"Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:10.1002/cpa.21717.","ama":"Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 2018;71(3):577-614. doi:10.1002/cpa.21717","apa":"Frank, R., Nam, P., & Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21717","ieee":"R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” Communications on Pure and Applied Mathematics, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018.","short":"R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614."}},{"doi":"10.1534/genetics.118.300786","date_published":"2018-04-01T00:00:00Z","date_created":"2018-12-11T11:46:26Z","page":"1351 - 1355","day":"01","publication":"Genetics","has_accepted_license":"1","isi":1,"year":"2018","quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"title":"Tread lightly interpreting polygenic tests of selection","author":[{"first_name":"John","last_name":"Novembre","full_name":"Novembre, John"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publist_id":"7393","external_id":{"isi":["000429094400005"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786.","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786","apa":"Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786.","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355."},"issue":"4","volume":208,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"3d838dc285df394376555b794b6a5ad1","file_id":"4958","file_size":500129,"date_updated":"2020-07-14T12:46:26Z","creator":"system","file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","date_created":"2018-12-12T10:12:40Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"04","intvolume":" 208","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly."}],"file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"NiBa"}],"ddc":["576"],"date_updated":"2023-09-19T10:17:30Z","status":"public","pubrep_id":"1012","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"430"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9060294.","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","ieee":"W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” Genes, vol. 9, no. 6. MDPI AG, 2018.","ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., & Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. MDPI AG. https://doi.org/10.3390/genes9060294","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes, vol. 9, no. 6, 294, MDPI AG, 2018, doi:10.3390/genes9060294."},"title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","publist_id":"7714","author":[{"first_name":"Wen","full_name":"Ma, Wen","last_name":"Ma"},{"full_name":"Veltsos, Paris","last_name":"Veltsos","first_name":"Paris"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","last_name":"Toups"},{"first_name":"Nicolas","last_name":"Rodrigues","full_name":"Rodrigues, Nicolas"},{"last_name":"Sermier","full_name":"Sermier, Roberto","first_name":"Roberto"},{"full_name":"Jeffries, Daniel","last_name":"Jeffries","first_name":"Daniel"},{"first_name":"Nicolas","last_name":"Perrin","full_name":"Perrin, Nicolas"}],"article_processing_charge":"No","external_id":{"isi":["000436494200026"]},"article_number":"294","day":"12","publication":"Genes","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.3390/genes9060294","date_published":"2018-06-12T00:00:00Z","date_created":"2018-12-11T11:45:09Z","quality_controlled":"1","publisher":"MDPI AG","oa":1,"ddc":["570"],"date_updated":"2023-09-19T10:15:31Z","file_date_updated":"2020-07-14T12:45:22Z","department":[{"_id":"BeVi"}],"_id":"199","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2019-02-01T07:52:28Z","file_name":"2018_Genes_Ma.pdf","date_updated":"2020-07-14T12:45:22Z","file_size":3985796,"creator":"dernst","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","file_id":"5905","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":9,"issue":"6","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes."}],"month":"06","intvolume":" 9","scopus_import":"1"},{"department":[{"_id":"GaTk"}],"date_updated":"2023-09-19T10:16:35Z","status":"public","type":"journal_article","_id":"543","volume":115,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","month":"01","intvolume":" 115","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/152660 ","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits.","lang":"eng"}],"title":"Toward a unified theory of efficient, predictive, and sparse coding","publist_id":"7273","author":[{"last_name":"Chalk","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000419128700049"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115","apa":"Chalk, M. J., Marre, O., & Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1711114115","mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115.","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1711114115."},"project":[{"grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_published":"2018-01-02T00:00:00Z","doi":"10.1073/pnas.1711114115","date_created":"2018-12-11T11:47:04Z","page":"186 - 191","day":"02","publication":"PNAS","isi":1,"year":"2018","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1},{"date_published":"2018-02-27T00:00:00Z","doi":"10.1016/j.bpj.2017.12.022","date_created":"2018-12-11T11:46:23Z","page":"968 - 977","day":"27","publication":"Biophysical Journal","isi":1,"year":"2018","publisher":"Biophysical Society","quality_controlled":"1","oa":1,"title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","publist_id":"7403","author":[{"first_name":"Kinjal","last_name":"Dasbiswas","full_name":"Dasbiswas, Kinjal"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Claude-Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Claude-Edouard B"},{"first_name":"Nir","last_name":"Gov","full_name":"Gov, Nir"}],"article_processing_charge":"No","external_id":{"arxiv":["1709.01486"],"isi":["000428016700021"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022.","ista":"Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.","mla":"Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022.","ieee":"K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” Biophysical Journal, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","apa":"Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022","ama":"Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977. doi:10.1016/j.bpj.2017.12.022"},"volume":114,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","month":"02","intvolume":" 114","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1709.01486","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients.","lang":"eng"}],"department":[{"_id":"EdHa"}],"date_updated":"2023-09-19T10:13:55Z","status":"public","type":"journal_article","_id":"421"},{"article_number":"480","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480.","chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9100480.","short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” Genes, vol. 9, no. 10. MDPI AG, 2018.","ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480","apa":"Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. Genes. MDPI AG. https://doi.org/10.3390/genes9100480","mla":"Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI AG, 2018, doi:10.3390/genes9100480."},"title":"Unusual diversity of sex chromosomes in African cichlid fishes","article_processing_charge":"No","external_id":{"isi":["000448656700018"]},"author":[{"first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220","last_name":"Gammerdinger"},{"full_name":"Kocher, Thomas","last_name":"Kocher","first_name":"Thomas"}],"publist_id":"7991","acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","oa":1,"publisher":"MDPI AG","quality_controlled":"1","publication":"Genes","day":"04","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:26Z","doi":"10.3390/genes9100480","date_published":"2018-10-04T00:00:00Z","_id":"63","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2023-09-19T10:37:03Z","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:27Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade."}],"intvolume":" 9","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:27Z","file_size":1415791,"date_created":"2018-12-18T09:54:46Z","file_name":"2018_Genes_Gammerdinger.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"bec527692e2c9b56919c0429634ff337","file_id":"5743"}],"publication_status":"published","ec_funded":1,"issue":"10","volume":9},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Turner, C., Michailidis, A., Abanin, D., Serbyn, M., & Papić, Z. (2018). Weak ergodicity breaking from quantum many-body scars. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-018-0137-5","ama":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 2018;14:745-749. doi:10.1038/s41567-018-0137-5","short":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, Z. Papić, Nature Physics 14 (2018) 745–749.","ieee":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, and Z. Papić, “Weak ergodicity breaking from quantum many-body scars,” Nature Physics, vol. 14. Nature Publishing Group, pp. 745–749, 2018.","mla":"Turner, Christopher, et al. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 745–49, doi:10.1038/s41567-018-0137-5.","ista":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. 2018. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 14, 745–749.","chicago":"Turner, Christopher, Alexios Michailidis, Dmitry Abanin, Maksym Serbyn, and Zlatko Papić. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0137-5."},"title":"Weak ergodicity breaking from quantum many-body scars","article_processing_charge":"No","external_id":{"isi":["000438253600028"]},"author":[{"first_name":"Christopher","full_name":"Turner, Christopher","last_name":"Turner"},{"first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","last_name":"Michailidis"},{"last_name":"Abanin","full_name":"Abanin, Dmitry","first_name":"Dmitry"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"last_name":"Papić","full_name":"Papić, Zlatko","first_name":"Zlatko"}],"publist_id":"7585","acknowledgement":"C.J.T., A.M. and Z.P. acknowledge support from EPSRC grants EP/P009409/1 and EP/M50807X/1, and Royal Society Research Grant RG160635. D.A. acknowledges support from the Swiss National Science Foundation.","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","publication":"Nature Physics","day":"14","year":"2018","isi":1,"date_created":"2018-12-11T11:45:40Z","doi":"10.1038/s41567-018-0137-5","date_published":"2018-05-14T00:00:00Z","page":"745 - 749","_id":"296","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-19T10:37:55Z","department":[{"_id":"MaSe"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The thermodynamic description of many-particle systems rests on the assumption of ergodicity, the ability of a system to explore all allowed configurations in the phase space. Recent studies on many-body localization have revealed the existence of systems that strongly violate ergodicity in the presence of quenched disorder. Here, we demonstrate that ergodicity can be weakly broken by a different mechanism, arising from the presence of special eigenstates in the many-body spectrum that are reminiscent of quantum scars in chaotic non-interacting systems. In the single-particle case, quantum scars correspond to wavefunctions that concentrate in the vicinity of unstable periodic classical trajectories. We show that many-body scars appear in the Fibonacci chain, a model with a constrained local Hilbert space that has recently been experimentally realized in a Rydberg-atom quantum simulator. The quantum scarred eigenstates are embedded throughout the otherwise thermalizing many-body spectrum but lead to direct experimental signatures, as we show for periodic recurrences that reproduce those observed in the experiment. Our results suggest that scarred many-body bands give rise to a new universality class of quantum dynamics, opening up opportunities for the creation of novel states with long-lived coherence in systems that are now experimentally realizable."}],"intvolume":" 14","month":"05","main_file_link":[{"url":"http://eprints.whiterose.ac.uk/130860/","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","volume":14},{"oa_version":"Submitted Version","abstract":[{"text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one.","lang":"eng"}],"month":"08","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1704.08757","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":"376-377","_id":"607","status":"public","type":"journal_article","date_updated":"2023-09-19T10:38:34Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"01","publication":"Physica D: Nonlinear Phenomena","isi":1,"year":"2018","doi":"10.1016/j.physd.2017.10.015","date_published":"2018-08-01T00:00:00Z","date_created":"2018-12-11T11:47:28Z","page":"108-120","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.","apa":"Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015","ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015"},"title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","author":[{"last_name":"Bodova","full_name":"Bodova, Katarina","orcid":"0000-0002-7214-0171","first_name":"Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","full_name":"Haskovec, Jan","last_name":"Haskovec"},{"first_name":"Peter","full_name":"Markowich, Peter","last_name":"Markowich"}],"publist_id":"7198","external_id":{"isi":["000437962900012"],"arxiv":["1704.08757"]},"article_processing_charge":"No"},{"intvolume":" 97","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1801.06892"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"We developed a method to calculate two-photon processes in quantum mechanics that replaces the infinite summation over the intermediate states by a perturbation expansion. This latter consists of a series of commutators that involve position, momentum, and Hamiltonian quantum operators. We analyzed several single- and many-particle cases for which a closed-form solution to the perturbation expansion exists, as well as more complicated cases for which a solution is found by convergence. Throughout the article, Rayleigh and Raman scattering are taken as examples of two-photon processes. The present method provides a clear distinction between the Thomson scattering, regarded as classical scattering, and quantum contributions. Such a distinction lets us derive general results concerning light scattering. Finally, possible extensions to the developed formalism are discussed.","lang":"eng"}],"ec_funded":1,"volume":97,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"294","department":[{"_id":"MiLe"}],"date_updated":"2023-09-19T10:17:56Z","oa":1,"quality_controlled":"1","publisher":"American Physical Society","date_created":"2018-12-11T11:45:40Z","date_published":"2018-04-18T00:00:00Z","doi":"10.1103/PhysRevA.97.043842","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","day":"18","year":"2018","isi":1,"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Two-photon processes based on quantum commutators","article_processing_charge":"No","external_id":{"isi":["000430296800008"],"arxiv":["1801.06892"]},"publist_id":"7587","author":[{"first_name":"Filippo","full_name":"Fratini, Filippo","last_name":"Fratini"},{"full_name":"Safari, Laleh","last_name":"Safari","first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Amaro, Pedro","last_name":"Amaro","first_name":"Pedro"},{"last_name":"Santos","full_name":"Santos, José","first_name":"José"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Fratini, Filippo, et al. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043842.","apa":"Fratini, F., Safari, L., Amaro, P., & Santos, J. (2018). Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043842","ama":"Fratini F, Safari L, Amaro P, Santos J. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043842","short":"F. Fratini, L. Safari, P. Amaro, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","ieee":"F. Fratini, L. Safari, P. Amaro, and J. Santos, “Two-photon processes based on quantum commutators,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","chicago":"Fratini, Filippo, Laleh Safari, Pedro Amaro, and José Santos. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043842.","ista":"Fratini F, Safari L, Amaro P, Santos J. 2018. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4)."}}]