[{"day":"12","publication":"Developmental Cell","language":[{"iso":"eng"}],"publication_status":"published","year":"2016","volume":38,"date_published":"2016-09-12T00:00:00Z","issue":"5","doi":"10.1016/j.devcel.2016.08.017","date_created":"2018-12-11T11:50:25Z","page":"448 - 450","oa_version":"None","abstract":[{"text":"When neutrophils infiltrate a site of inflammation, they have to stop at the right place to exert their effector function. In this issue of Developmental Cell, Wang et al. (2016) show that neutrophils sense reactive oxygen species via the TRPM2 channel to arrest migration at their target site. © 2016 Elsevier Inc.","lang":"eng"}],"month":"09","intvolume":" 38","scopus_import":1,"publisher":"Cell Press","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:48:39Z","citation":{"mla":"Renkawitz, Jörg, and Michael K. Sixt. “A Radical Break Restraining Neutrophil Migration.” Developmental Cell, vol. 38, no. 5, Cell Press, 2016, pp. 448–50, doi:10.1016/j.devcel.2016.08.017.","short":"J. Renkawitz, M.K. Sixt, Developmental Cell 38 (2016) 448–450.","ieee":"J. Renkawitz and M. K. Sixt, “A Radical Break Restraining Neutrophil Migration,” Developmental Cell, vol. 38, no. 5. Cell Press, pp. 448–450, 2016.","ama":"Renkawitz J, Sixt MK. A Radical Break Restraining Neutrophil Migration. Developmental Cell. 2016;38(5):448-450. doi:10.1016/j.devcel.2016.08.017","apa":"Renkawitz, J., & Sixt, M. K. (2016). A Radical Break Restraining Neutrophil Migration. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.08.017","chicago":"Renkawitz, Jörg, and Michael K Sixt. “A Radical Break Restraining Neutrophil Migration.” Developmental Cell. Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.08.017.","ista":"Renkawitz J, Sixt MK. 2016. A Radical Break Restraining Neutrophil Migration. Developmental Cell. 38(5), 448–450."},"title":"A Radical Break Restraining Neutrophil Migration","department":[{"_id":"MiSi"}],"author":[{"first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","last_name":"Renkawitz"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"publist_id":"6208","_id":"1150","status":"public","type":"journal_article"},{"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)"},"status":"public","_id":"1151","file_date_updated":"2019-01-25T09:32:55Z","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:48:39Z","ddc":["570"],"scopus_import":1,"month":"10","intvolume":" 30","abstract":[{"text":"Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormonesensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants. © 2016 Simonini et al.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","issue":"20","volume":30,"publication_status":"published","file":[{"file_id":"5882","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-01-25T09:32:55Z","file_name":"2016_GeneDev_Simonini.pdf","date_updated":"2019-01-25T09:32:55Z","file_size":1419263,"creator":"dernst"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Simonini, Sara","last_name":"Simonini","first_name":"Sara"},{"first_name":"Joyita","full_name":"Deb, Joyita","last_name":"Deb"},{"last_name":"Moubayidin","full_name":"Moubayidin, Laila","first_name":"Laila"},{"last_name":"Stephenson","full_name":"Stephenson, Pauline","first_name":"Pauline"},{"full_name":"Valluru, Manoj","last_name":"Valluru","first_name":"Manoj"},{"full_name":"Freire Rios, Alejandra","last_name":"Freire Rios","first_name":"Alejandra"},{"last_name":"Sorefan","full_name":"Sorefan, Karim","first_name":"Karim"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Östergaard","full_name":"Östergaard, Lars","first_name":"Lars"}],"publist_id":"6207","external_id":{"pmid":["27898393"]},"title":"A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis","citation":{"mla":"Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” Genes and Development, vol. 30, no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:10.1101/gad.285361.116.","short":"S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30 (2016) 2286–2296.","ieee":"S. Simonini et al., “A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis,” Genes and Development, vol. 30, no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.","apa":"Simonini, S., Deb, J., Moubayidin, L., Stephenson, P., Valluru, M., Freire Rios, A., … Östergaard, L. (2016). A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.285361.116","ama":"Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 2016;30(20):2286-2296. doi:10.1101/gad.285361.116","chicago":"Simonini, Sara, Joyita Deb, Laila Moubayidin, Pauline Stephenson, Manoj Valluru, Alejandra Freire Rios, Karim Sorefan, Dolf Weijers, Jiří Friml, and Lars Östergaard. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” Genes and Development. Cold Spring Harbor Laboratory Press, 2016. https://doi.org/10.1101/gad.285361.116.","ista":"Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire Rios A, Sorefan K, Weijers D, Friml J, Östergaard L. 2016. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 30(20), 2286–2296."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Cold Spring Harbor Laboratory Press","oa":1,"acknowledgement":"We thank Norwich Research Park Bioimaging, Grant Calder, Roy\r\nDunford, Caroline Smith, Paul Thomas, and Mark Youles for\r\ntechnical support; Charlie Scutt, Alejandro Ferrando, and George\r\nLomonossoff for plasmids; Toshiro Ito for seeds; Brendan Davies\r\nand Barry Causier for the REGIA library; and Mark Buttner,\r\nSimona Masiero, Fabio Rossi, Doris Wagner, and Jun Xiao for\r\nhelp and material. We are also grateful to Stefano Bencivenga,\r\nMarie Brüser, Friederike Jantzen, Lukasz Langowski, Xinran Li,\r\nand Nicola Stacey for discussions and helpful comments on the\r\nmanuscript. This work was supported by grants BB/M004112/1\r\nand BB/I017232/1 (Crop Improvement Research Club) to L.Ø.\r\nfrom the Biotechnological and Biological Sciences Research\r\nCouncil, and Institute Strategic Programme grant (BB/J004553/\r\n1) to the John Innes Centre. S.S., J.D., and L.Ø conceived the ex-\r\nperiments. ","page":"2286 - 2296","doi":"10.1101/gad.285361.116","date_published":"2016-10-15T00:00:00Z","date_created":"2018-12-11T11:50:25Z","has_accepted_license":"1","year":"2016","day":"15","publication":"Genes and Development"},{"citation":{"chicago":"Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz, and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00569.","ista":"Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477.","mla":"Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” Plant Cell, vol. 28, no. 10, American Society of Plant Biologists, 2016, pp. 2464–77, doi:10.1105/tpc.15.00569.","ama":"Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth guided apical hook formation in plants. Plant Cell. 2016;28(10):2464-2477. doi:10.1105/tpc.15.00569","apa":"Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten, D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical hook formation in plants. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.15.00569","ieee":"P. Žádníková et al., “A model of differential growth guided apical hook formation in plants,” Plant Cell, vol. 28, no. 10. American Society of Plant Biologists, pp. 2464–2477, 2016.","short":"P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten, R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016) 2464–2477."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Žádníková","full_name":"Žádníková, Petra","first_name":"Petra"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","last_name":"Wabnik"},{"first_name":"Anas","last_name":"Abuzeineh","full_name":"Abuzeineh, Anas"},{"first_name":"Marçal","last_name":"Gallemí","full_name":"Gallemí, Marçal"},{"last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique","first_name":"Dominique"},{"last_name":"Smith","full_name":"Smith, Richard","first_name":"Richard"},{"first_name":"Dirk","full_name":"Inze, Dirk","last_name":"Inze"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"first_name":"Przemysław","full_name":"Prusinkiewicz, Przemysław","last_name":"Prusinkiewicz"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"}],"publist_id":"6205","title":"A model of differential growth guided apical hook formation in plants","project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis"}],"year":"2016","publication":"Plant Cell","day":"01","page":"2464 - 2477","date_created":"2018-12-11T11:50:26Z","doi":"10.1105/tpc.15.00569","date_published":"2016-10-01T00:00:00Z","acknowledgement":"We thank Martine De Cock and Annick Bleys for help in preparing the manuscript, Daniel Van Damme for sharing material and stimulating discussion, and Rudiger Simon for support during revision of the manuscript.\r\nThis work was supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship (LT-000209-2014).","oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","date_updated":"2021-01-12T06:48:40Z","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"_id":"1153","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"issue":"10","volume":28,"abstract":[{"text":"Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/"}],"scopus_import":1,"intvolume":" 28","month":"10"},{"file_date_updated":"2018-12-12T10:09:32Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"ToBo"}],"ddc":["579"],"date_updated":"2021-01-12T06:48:41Z","pubrep_id":"744","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","_id":"1154","ec_funded":1,"volume":6,"language":[{"iso":"eng"}],"file":[{"file_size":2353456,"date_updated":"2018-12-12T10:09:32Z","creator":"system","file_name":"IST-2017-744-v1+1_srep36440.pdf","date_created":"2018-12-12T10:09:32Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4756"}],"publication_status":"published","intvolume":" 6","month":"11","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cellular locomotion is a central hallmark of eukaryotic life. It is governed by cell-extrinsic molecular factors, which can either emerge in the soluble phase or as immobilized, often adhesive ligands. To encode for direction, every cue must be present as a spatial or temporal gradient. Here, we developed a microfluidic chamber that allows measurement of cell migration in combined response to surface immobilized and soluble molecular gradients. As a proof of principle we study the response of dendritic cells to their major guidance cues, chemokines. The majority of data on chemokine gradient sensing is based on in vitro studies employing soluble gradients. Despite evidence suggesting that in vivo chemokines are often immobilized to sugar residues, limited information is available how cells respond to immobilized chemokines. We tracked migration of dendritic cells towards immobilized gradients of the chemokine CCL21 and varying superimposed soluble gradients of CCL19. Differential migratory patterns illustrate the potential of our setup to quantitatively study the competitive response to both types of gradients. Beyond chemokines our approach is broadly applicable to alternative systems of chemo- and haptotaxis such as cells migrating along gradients of adhesion receptor ligands vs. any soluble cue. \r\n"}],"title":"A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients","publist_id":"6204","author":[{"full_name":"Schwarz, Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","full_name":"Bierbaum, Veronika","last_name":"Bierbaum"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"full_name":"Frank, Tino","last_name":"Frank","first_name":"Tino"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach"},{"first_name":"Savaş","full_name":"Tay, Savaş","last_name":"Tay"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"orcid":"0000-0001-8599-1226","full_name":"Mehling, Matthias","last_name":"Mehling","first_name":"Matthias","id":"3C23B994-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Schwarz J, Bierbaum V, Merrin J, Frank T, Hauschild R, Bollenbach MT, Tay S, Sixt MK, Mehling M. 2016. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 6, 36440.","chicago":"Schwarz, Jan, Veronika Bierbaum, Jack Merrin, Tino Frank, Robert Hauschild, Mark Tobias Bollenbach, Savaş Tay, Michael K Sixt, and Matthias Mehling. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep36440.","ama":"Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 2016;6. doi:10.1038/srep36440","apa":"Schwarz, J., Bierbaum, V., Merrin, J., Frank, T., Hauschild, R., Bollenbach, M. T., … Mehling, M. (2016). A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep36440","short":"J. Schwarz, V. Bierbaum, J. Merrin, T. Frank, R. Hauschild, M.T. Bollenbach, S. Tay, M.K. Sixt, M. Mehling, Scientific Reports 6 (2016).","ieee":"J. Schwarz et al., “A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","mla":"Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” Scientific Reports, vol. 6, 36440, Nature Publishing Group, 2016, doi:10.1038/srep36440."},"project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556"},{"name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"36440","date_created":"2018-12-11T11:50:27Z","date_published":"2016-11-07T00:00:00Z","doi":"10.1038/srep36440","publication":"Scientific Reports","day":"07","year":"2016","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"This work was supported by the Swiss National Science Foundation (Ambizione fellowship; PZ00P3-154733 to M.M.), the Swiss Multiple Sclerosis Society (research support to M.M.), a fellowship from the Boehringer Ingelheim Fonds (BIF) to J.S., the European Research Council (grant ERC GA 281556) and a START award from the Austrian Science Foundation (FWF) to M.S. #BioimagingFacility"},{"type":"journal_article","status":"public","_id":"1157","department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T06:48:43Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1409.4979"}],"scopus_import":1,"intvolume":" 26","month":"12","abstract":[{"lang":"eng","text":"We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where the sample X is an M ×N random matrix whose entries are real independent random variables with variance 1/N and whereσ is an M × M positive-definite deterministic matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class of populations σ in the sub-critical regime, we show that the distribution of the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians or (2) that σ is diagonal and that the entries of X have a sub-exponential decay."}],"oa_version":"Preprint","ec_funded":1,"volume":26,"issue":"6","publication_status":"published","language":[{"iso":"eng"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"author":[{"first_name":"Ji","full_name":"Lee, Ji","last_name":"Lee"},{"last_name":"Schnelli","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin"}],"publist_id":"6201","title":"Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population","citation":{"ista":"Lee J, Schnelli K. 2016. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. 26(6), 3786–3839.","chicago":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” Annals of Applied Probability. Institute of Mathematical Statistics, 2016. https://doi.org/10.1214/16-AAP1193.","short":"J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.","ieee":"J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population,” Annals of Applied Probability, vol. 26, no. 6. Institute of Mathematical Statistics, pp. 3786–3839, 2016.","apa":"Lee, J., & Schnelli, K. (2016). Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AAP1193","ama":"Lee J, Schnelli K. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. 2016;26(6):3786-3839. doi:10.1214/16-AAP1193","mla":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” Annals of Applied Probability, vol. 26, no. 6, Institute of Mathematical Statistics, 2016, pp. 3786–839, doi:10.1214/16-AAP1193."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","acknowledgement":"We thank Horng-Tzer Yau for numerous discussions and remarks. We are grateful to Ben Adlam, Jinho Baik, Zhigang Bao, Paul Bourgade, László Erd ̋os, Iain Johnstone and Antti Knowles for comments. We are also grate-\r\nful to the anonymous referee for carefully reading our manuscript and suggesting several improvements.","page":"3786 - 3839","date_created":"2018-12-11T11:50:27Z","date_published":"2016-12-15T00:00:00Z","doi":"10.1214/16-AAP1193","year":"2016","publication":"Annals of Applied Probability","day":"15"},{"pubrep_id":"811","status":"public","type":"journal_article","_id":"1170","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:44:37Z","ddc":["003","518","570","621"],"date_updated":"2021-01-12T06:48:49Z","intvolume":" 38","month":"11","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identification of model parameters. While modularization of the corresponding optimization problems could help reduce the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into subnetworks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we present here a modular parameter identification approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This definition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of different modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set---but not during earlier iterations---the intermodule communication as well as the individual modules\\' state dynamics agree with the dynamics of the nonmodularized network. Our modular parameter identification approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to suboptimal local minima. We demonstrate the algorithm\\'s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway.","lang":"eng"}],"issue":"6","volume":38,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"local","relation":"main_file","checksum":"781bc3ffd30b2dd65b7727c5a285fc78","file_id":"5095","date_updated":"2020-07-14T12:44:37Z","file_size":871964,"creator":"system","date_created":"2018-12-12T10:14:41Z","file_name":"IST-2017-811-v1+1_modular_parameter_identification.pdf"}],"publication_status":"published","title":"Modular parameter identification of biomolecular networks","author":[{"full_name":"Lang, Moritz","last_name":"Lang","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stelling","full_name":"Stelling, Jörg","first_name":"Jörg"}],"publist_id":"6186","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics , 2016. https://doi.org/10.1137/15M103306X.","ista":"Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.","mla":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing, vol. 38, no. 6, Society for Industrial and Applied Mathematics , 2016, pp. B988–1008, doi:10.1137/15M103306X.","short":"M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.","ieee":"M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” SIAM Journal on Scientific Computing, vol. 38, no. 6. Society for Industrial and Applied Mathematics , pp. B988–B1008, 2016.","ama":"Lang M, Stelling J. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 2016;38(6):B988-B1008. doi:10.1137/15M103306X","apa":"Lang, M., & Stelling, J. (2016). Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/15M103306X"},"publisher":"Society for Industrial and Applied Mathematics ","quality_controlled":"1","date_created":"2018-12-11T11:50:31Z","doi":"10.1137/15M103306X","date_published":"2016-11-15T00:00:00Z","page":"B988 - B1008","publication":"SIAM Journal on Scientific Computing","day":"15","year":"2016","has_accepted_license":"1"},{"publication":"Physics of Life Reviews","language":[{"iso":"eng"}],"day":"01","year":"2016","publication_status":"published","date_created":"2018-12-11T11:50:32Z","doi":"10.1016/j.plrev.2016.06.005","volume":17,"date_published":"2016-07-01T00:00:00Z","page":"166 - 167","oa_version":"None","intvolume":" 17","month":"07","publisher":"Elsevier","scopus_import":1,"quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:48:50Z","citation":{"chicago":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function" by O. C. Martin et Al.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.005.","ista":"Tkačik G. 2016. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al. Physics of Life Reviews. 17, 166–167.","mla":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function" by O. C. Martin et Al.” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 166–67, doi:10.1016/j.plrev.2016.06.005.","short":"G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.","ieee":"G. Tkačik, “Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.,” Physics of Life Reviews, vol. 17. Elsevier, pp. 166–167, 2016.","ama":"Tkačik G. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al. Physics of Life Reviews. 2016;17:166-167. doi:10.1016/j.plrev.2016.06.005","apa":"Tkačik, G. (2016). Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.005"},"title":"Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.","department":[{"_id":"GaTk"}],"publist_id":"6185","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"_id":"1171","status":"public","type":"journal_article"},{"file_date_updated":"2020-07-14T12:44:37Z","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:48:50Z","ddc":["576"],"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)"},"status":"public","pubrep_id":"737","_id":"1172","volume":6,"publication_status":"published","file":[{"file_id":"4977","checksum":"cb378732da885ea4959ec5b845fb6e52","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-737-v1+1_srep38840.pdf","date_created":"2018-12-12T10:12:56Z","creator":"system","file_size":760967,"date_updated":"2020-07-14T12:44:37Z"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"12","intvolume":" 6","abstract":[{"text":"A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.","lang":"eng"}],"oa_version":"Published Version","publist_id":"6183","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"last_name":"Barma","full_name":"Barma, Mustansir","first_name":"Mustansir"},{"last_name":"Rao","full_name":"Rao, Madan","first_name":"Madan"}],"title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","citation":{"mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6, 38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 2016;6. doi:10.1038/srep38840","apa":"Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38840","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840.","ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"38840","doi":"10.1038/srep38840","date_published":"2016-12-19T00:00:00Z","date_created":"2018-12-11T11:50:32Z","has_accepted_license":"1","year":"2016","day":"19","publication":"Scientific Reports","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions."},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"C. Kamath Hosdurg, S. Chatterjee, Algorithmica 74 (2016) 1321–1362.","ieee":"C. Kamath Hosdurg and S. Chatterjee, “A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound,” Algorithmica, vol. 74, no. 4. Springer, pp. 1321–1362, 2016.","ama":"Kamath Hosdurg C, Chatterjee S. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. 2016;74(4):1321-1362. doi:10.1007/s00453-015-9997-6","apa":"Kamath Hosdurg, C., & Chatterjee, S. (2016). A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. Springer. https://doi.org/10.1007/s00453-015-9997-6","mla":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” Algorithmica, vol. 74, no. 4, Springer, 2016, pp. 1321–62, doi:10.1007/s00453-015-9997-6.","ista":"Kamath Hosdurg C, Chatterjee S. 2016. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. 74(4), 1321–1362.","chicago":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” Algorithmica. Springer, 2016. https://doi.org/10.1007/s00453-015-9997-6."},"date_updated":"2021-01-12T06:48:52Z","department":[{"_id":"KrPi"}],"title":"A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound","publist_id":"6177","author":[{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Chatterjee, Sanjit","last_name":"Chatterjee","first_name":"Sanjit"}],"_id":"1177","status":"public","type":"journal_article","publication":"Algorithmica","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2016","date_created":"2018-12-11T11:50:33Z","date_published":"2016-04-01T00:00:00Z","doi":"10.1007/s00453-015-9997-6","volume":74,"issue":"4","page":"1321 - 1362","acknowledgement":"We are grateful to the anonymous reviewers for their insightful comments. The\r\ndetailed reports helped us a lot to address the technical mistakes as well as to improve the overall presentation of the paper.","oa_version":"Submitted Version","abstract":[{"text":"Boldyreva, Palacio and Warinschi introduced a multiple forking game as an extension of general forking. The notion of (multiple) forking is a useful abstraction from the actual simulation of cryptographic scheme to the adversary in a security reduction, and is achieved through the intermediary of a so-called wrapper algorithm. Multiple forking has turned out to be a useful tool in the security argument of several cryptographic protocols. However, a reduction employing multiple forking incurs a significant degradation of (Formula presented.) , where (Formula presented.) denotes the upper bound on the underlying random oracle calls and (Formula presented.) , the number of forkings. In this work we take a closer look at the reasons for the degradation with a tighter security bound in mind. We nail down the exact set of conditions for success in the multiple forking game. A careful analysis of the cryptographic schemes and corresponding security reduction employing multiple forking leads to the formulation of ‘dependence’ and ‘independence’ conditions pertaining to the output of the wrapper in different rounds. Based on the (in)dependence conditions we propose a general framework of multiple forking and a General Multiple Forking Lemma. Leveraging (in)dependence to the full allows us to improve the degradation factor in the multiple forking game by a factor of (Formula presented.). By implication, the cost of a single forking involving two random oracles (augmented forking) matches that involving a single random oracle (elementary forking). Finally, we study the effect of these observations on the concrete security of existing schemes employing multiple forking. We conclude that by careful design of the protocol (and the wrapper in the security reduction) it is possible to harness our observations to the full extent.","lang":"eng"}],"intvolume":" 74","month":"04","main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2013/651"}],"oa":1,"quality_controlled":"1","publisher":"Springer"},{"page":"183 - 203","date_created":"2018-12-11T11:50:34Z","doi":"10.1007/978-3-662-53641-4_8","date_published":"2016-10-22T00:00:00Z","year":"2016","day":"22","oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"K. Pietrzak—Supported by the European Research Council consolidator grant (682815-TOCNeT).\r\nM. Skórski—Supported by the National Science Center, Poland (2015/17/N/ST6/03564).","publist_id":"6175","author":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"},{"first_name":"Skorski","last_name":"Maciej","full_name":"Maciej, Skorski"}],"title":"Pseudoentropy: Lower-bounds for chain rules and transformations","citation":{"chicago":"Pietrzak, Krzysztof Z, and Skorski Maciej. “Pseudoentropy: Lower-Bounds for Chain Rules and Transformations,” 9985:183–203. Springer, 2016. https://doi.org/10.1007/978-3-662-53641-4_8.","ista":"Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985, 183–203.","mla":"Pietrzak, Krzysztof Z., and Skorski Maciej. Pseudoentropy: Lower-Bounds for Chain Rules and Transformations. Vol. 9985, Springer, 2016, pp. 183–203, doi:10.1007/978-3-662-53641-4_8.","short":"K.Z. Pietrzak, S. Maciej, in:, Springer, 2016, pp. 183–203.","ieee":"K. Z. Pietrzak and S. Maciej, “Pseudoentropy: Lower-bounds for chain rules and transformations,” presented at the TCC: Theory of Cryptography Conference, Beijing, China, 2016, vol. 9985, pp. 183–203.","apa":"Pietrzak, K. Z., & Maciej, S. (2016). Pseudoentropy: Lower-bounds for chain rules and transformations (Vol. 9985, pp. 183–203). Presented at the TCC: Theory of Cryptography Conference, Beijing, China: Springer. https://doi.org/10.1007/978-3-662-53641-4_8","ama":"Pietrzak KZ, Maciej S. Pseudoentropy: Lower-bounds for chain rules and transformations. In: Vol 9985. Springer; 2016:183-203. doi:10.1007/978-3-662-53641-4_8"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"ec_funded":1,"volume":9985,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://eprint.iacr.org/2016/159","open_access":"1"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 9985","month":"10","abstract":[{"lang":"eng","text":"Computational notions of entropy have recently found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The two main types of results which make computational notions so useful are (1) Chain rules, which quantify by how much the computational entropy of a variable decreases if conditioned on some other variable (2) Transformations, which quantify to which extend one type of entropy implies another.\r\n\r\nSuch chain rules and transformations typically lose a significant amount in quality of the entropy, and are the reason why applying these results one gets rather weak quantitative security bounds. In this paper we for the first time prove lower bounds in this context, showing that existing results for transformations are, unfortunately, basically optimal for non-adaptive black-box reductions (and it’s hard to imagine how non black-box reductions or adaptivity could be useful here.)\r\n\r\nA variable X has k bits of HILL entropy of quality (ϵ,s)\r\nif there exists a variable Y with k bits min-entropy which cannot be distinguished from X with advantage ϵ\r\n\r\nby distinguishing circuits of size s. A weaker notion is Metric entropy, where we switch quantifiers, and only require that for every distinguisher of size s, such a Y exists.\r\n\r\nWe first describe our result concerning transformations. By definition, HILL implies Metric without any loss in quality. Metric entropy often comes up in applications, but must be transformed to HILL for meaningful security guarantees. The best known result states that if a variable X has k bits of Metric entropy of quality (ϵ,s)\r\n, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2). We show that this loss of a factor Ω(ϵ−2)\r\n\r\nin circuit size is necessary. In fact, we show the stronger result that this loss is already necessary when transforming so called deterministic real valued Metric entropy to randomised boolean Metric (both these variants of Metric entropy are implied by HILL without loss in quality).\r\n\r\nThe chain rule for HILL entropy states that if X has k bits of HILL entropy of quality (ϵ,s)\r\n, then for any variable Z of length m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still leaves a gap of ϵ between the known bound and our lower bound."}],"oa_version":"Preprint","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T06:48:53Z","conference":{"name":"TCC: Theory of Cryptography Conference","start_date":"2016-10-31","location":"Beijing, China","end_date":"2016-11-03"},"type":"conference","status":"public","_id":"1179"},{"_id":"1181","project":[{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014"}],"status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. 2016. Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. Journal of Neuroscience. 36(45), 11394–11401.","chicago":"Dwyer, Noelle, Bin Chen, Shen Chou, Simon Hippenmeyer, Laurent Nguyen, and Troy Ghashghaei. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience. Society for Neuroscience, 2016. https://doi.org/10.1523/JNEUROSCI.2359-16.2016.","apa":"Dwyer, N., Chen, B., Chou, S., Hippenmeyer, S., Nguyen, L., & Ghashghaei, T. (2016). Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2359-16.2016","ama":"Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. Journal of Neuroscience. 2016;36(45):11394-11401. doi:10.1523/JNEUROSCI.2359-16.2016","short":"N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, T. Ghashghaei, Journal of Neuroscience 36 (2016) 11394–11401.","ieee":"N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, and T. Ghashghaei, “Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity,” Journal of Neuroscience, vol. 36, no. 45. Society for Neuroscience, pp. 11394–11401, 2016.","mla":"Dwyer, Noelle, et al. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience, vol. 36, no. 45, Society for Neuroscience, 2016, pp. 11394–401, doi:10.1523/JNEUROSCI.2359-16.2016."},"date_updated":"2021-01-12T06:48:54Z","title":"Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity","department":[{"_id":"SiHi"}],"publist_id":"6172","author":[{"last_name":"Dwyer","full_name":"Dwyer, Noelle","first_name":"Noelle"},{"last_name":"Chen","full_name":"Chen, Bin","first_name":"Bin"},{"full_name":"Chou, Shen","last_name":"Chou","first_name":"Shen"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"first_name":"Laurent","last_name":"Nguyen","full_name":"Nguyen, Laurent"},{"full_name":"Ghashghaei, Troy","last_name":"Ghashghaei","first_name":"Troy"}],"acknowledgement":"This work was supported by National Institutes of Health Grants R01NS089795 and R01NS098370 to H.T.G., R01NS076640 to N.D.D., and R01MH094589 and R01NS089777 to B.C., Academia Sinica AS-104-TPB09-2 to S.-J.C, European Union FP7-CIG618444 and Human Frontiers Science Program RGP0053 to S.H., and Fonds Léon Fredericq, from the Fondation Médicale Reine Elisabeth, and from the Fonation Simone et Pierre Clerdent to L.N. The authors apologize to colleagues whose work could not be cited due to space limitations.","oa_version":"None","abstract":[{"text":"This review accompanies a 2016 SFN mini-symposium presenting examples of current studies that address a central question: How do neural stem cells (NSCs) divide in different ways to produce heterogeneous daughter types at the right time and in proper numbers to build a cerebral cortex with the appropriate size and structure? We will focus on four aspects of corticogenesis: cytokinesis events that follow apical mitoses of NSCs; coordinating abscission with delamination from the apical membrane; timing of neurogenesis and its indirect regulation through emergence of intermediate progenitors; and capacity of single NSCs to generate the correct number and laminar fate of cortical neurons. Defects in these mechanisms can cause microcephaly and other brain malformations, and understanding them is critical to designing diagnostic tools and preventive and corrective therapies.","lang":"eng"}],"intvolume":" 36","month":"11","scopus_import":1,"quality_controlled":"1","publisher":"Society for Neuroscience","language":[{"iso":"eng"}],"publication":"Journal of Neuroscience","day":"09","publication_status":"published","year":"2016","date_created":"2018-12-11T11:50:35Z","doi":"10.1523/JNEUROSCI.2359-16.2016","volume":36,"issue":"45","date_published":"2016-11-09T00:00:00Z","page":"11394 - 11401"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.05090v1"}],"oa":1,"quality_controlled":"1","publisher":"AAAI Press","scopus_import":1,"month":"01","abstract":[{"text":"Balanced knockout tournaments are ubiquitous in sports competitions and are also used in decisionmaking and elections. The traditional computational question, that asks to compute a draw (optimal draw) that maximizes the winning probability for a distinguished player, has received a lot of attention. Previous works consider the problem where the pairwise winning probabilities are known precisely, while we study how robust is the winning probability with respect to small errors in the pairwise winning probabilities. First, we present several illuminating examples to establish: (a) there exist deterministic tournaments (where the pairwise winning probabilities are 0 or 1) where one optimal draw is much more robust than the other; and (b) in general, there exist tournaments with slightly suboptimal draws that are more robust than all the optimal draws. The above examples motivate the study of the computational problem of robust draws that guarantee a specified winning probability. Second, we present a polynomial-time algorithm for approximating the robustness of a draw for sufficiently small errors in pairwise winning probabilities, and obtain that the stated computational problem is NP-complete. We also show that two natural cases of deterministic tournaments where the optimal draw could be computed in polynomial time also admit polynomial-time algorithms to compute robust optimal draws.","lang":"eng"}],"oa_version":"Preprint","page":"172 - 179","date_created":"2018-12-11T11:50:35Z","ec_funded":1,"date_published":"2016-01-01T00:00:00Z","volume":"2016-January","related_material":{"link":[{"relation":"table_of_contents","url":"https://www.ijcai.org/proceedings/2016"}]},"year":"2016","publication_status":"published","language":[{"iso":"eng"}],"day":"01","conference":{"name":"IJCAI: International Joint Conference on Artificial Intelligence","end_date":"2016-07-15","location":"New York, NY, USA","start_date":"2016-07-09"},"type":"conference","status":"public","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"}],"_id":"1182","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec"}],"publist_id":"6171","department":[{"_id":"KrCh"}],"title":"Robust draws in balanced knockout tournaments","citation":{"ista":"Chatterjee K, Ibsen-Jensen R, Tkadlec J. 2016. Robust draws in balanced knockout tournaments. IJCAI: International Joint Conference on Artificial Intelligence vol. 2016–January, 172–179.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Josef Tkadlec. “Robust Draws in Balanced Knockout Tournaments,” 2016–January:172–79. AAAI Press, 2016.","short":"K. Chatterjee, R. Ibsen-Jensen, J. Tkadlec, in:, AAAI Press, 2016, pp. 172–179.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and J. Tkadlec, “Robust draws in balanced knockout tournaments,” presented at the IJCAI: International Joint Conference on Artificial Intelligence, New York, NY, USA, 2016, vol. 2016–January, pp. 172–179.","ama":"Chatterjee K, Ibsen-Jensen R, Tkadlec J. Robust draws in balanced knockout tournaments. In: Vol 2016-January. AAAI Press; 2016:172-179.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Tkadlec, J. (2016). Robust draws in balanced knockout tournaments (Vol. 2016–January, pp. 172–179). Presented at the IJCAI: International Joint Conference on Artificial Intelligence, New York, NY, USA: AAAI Press.","mla":"Chatterjee, Krishnendu, et al. Robust Draws in Balanced Knockout Tournaments. Vol. 2016–January, AAAI Press, 2016, pp. 172–79."},"date_updated":"2023-02-21T10:04:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"1184","pubrep_id":"736","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":["576","592"],"date_updated":"2021-01-12T06:48:55Z","file_date_updated":"2020-07-14T12:44:37Z","department":[{"_id":"SyCr"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Across multicellular organisms, the costs of reproduction and self-maintenance result in a life history trade-off between fecundity and longevity. Queens of perennial social Hymenoptera are both highly fertile and long-lived, and thus, this fundamental trade-off is lacking. Whether social insect males similarly evade the fecundity/longevity trade-off remains largely unstudied. Wingless males of the ant genus Cardiocondyla stay in their natal colonies throughout their relatively long lives and mate with multiple female sexuals. Here, we show that Cardiocondyla obscurior males that were allowed to mate with large numbers of female sexuals had a shortened life span compared to males that mated at a low frequency or virgin males. Although frequent mating negatively affects longevity, males clearly benefit from a “live fast, die young strategy” by inseminating as many female sexuals as possible at a cost to their own survival."}],"intvolume":" 6","month":"12","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-736-v1+1_Metzler_et_al-2016-Ecology_and_Evolution.pdf","date_created":"2018-12-12T10:14:12Z","file_size":328414,"date_updated":"2020-07-14T12:44:37Z","creator":"system","file_id":"5062","checksum":"789026eb9e1be2a0da08376f29f569cf","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","issue":"24","volume":6,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Metzler, Sina, et al. “Mating and Longevity in Ant Males.” Ecology and Evolution, vol. 6, no. 24, Wiley-Blackwell, 2016, pp. 8903–06, doi:10.1002/ece3.2474.","short":"S. Metzler, J. Heinze, A. Schrempf, Ecology and Evolution 6 (2016) 8903–8906.","ieee":"S. Metzler, J. Heinze, and A. Schrempf, “Mating and longevity in ant males,” Ecology and Evolution, vol. 6, no. 24. Wiley-Blackwell, pp. 8903–8906, 2016.","ama":"Metzler S, Heinze J, Schrempf A. Mating and longevity in ant males. Ecology and Evolution. 2016;6(24):8903-8906. doi:10.1002/ece3.2474","apa":"Metzler, S., Heinze, J., & Schrempf, A. (2016). Mating and longevity in ant males. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.2474","chicago":"Metzler, Sina, Jürgen Heinze, and Alexandra Schrempf. “Mating and Longevity in Ant Males.” Ecology and Evolution. Wiley-Blackwell, 2016. https://doi.org/10.1002/ece3.2474.","ista":"Metzler S, Heinze J, Schrempf A. 2016. Mating and longevity in ant males. Ecology and Evolution. 6(24), 8903–8906."},"title":"Mating and longevity in ant males","publist_id":"6169","author":[{"id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina","full_name":"Metzler, Sina","last_name":"Metzler"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"},{"full_name":"Schrempf, Alexandra","last_name":"Schrempf","first_name":"Alexandra"}],"acknowledgement":"German Science Foundation. Grant Number: SCHR 1135/2-1. We thank M. Adam for handling part of the setups and J. Zoellner for behavioral observations.","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","publication":"Ecology and Evolution","day":"01","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:50:36Z","date_published":"2016-12-01T00:00:00Z","doi":"10.1002/ece3.2474","page":"8903 - 8906"},{"publisher":"Company of Biologists","quality_controlled":"1","scopus_import":1,"month":"12","intvolume":" 143","abstract":[{"lang":"eng","text":"The developmental programme of the pistil is under the control of both auxin and cytokinin. Crosstalk between these factors converges on regulation of the auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length and ovule number were reduced. PIN1 expression was also lower in the triple mutant and the phenotypes could not be rescued by exogenous cytokinin application. pin1 complementation studies using genomic PIN1 constructs showed that the pistil phenotypes were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating the pivotal role of CRFs in auxin-cytokinin crosstalk."}],"oa_version":"None","acknowledgement":"M.C. was funded by a PhD fellowship from the Università degli Studi di Milano-Bicocca and from Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR) [MIUR-PRIN 2012]. L.C. is also supported by MIUR [MIUR-PRIN 2012]. We would like to thank Andrew MacCabe and Edward Kiegle for editing the paper.","page":"4419 - 4424","date_published":"2016-12-01T00:00:00Z","volume":143,"doi":"10.1242/dev.143545","issue":"23","date_created":"2018-12-11T11:50:36Z","publication_status":"published","year":"2016","day":"01","publication":"Development","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1185","publist_id":"6168","author":[{"last_name":"Cucinotta","full_name":"Cucinotta, Mara","first_name":"Mara"},{"first_name":"Silvia","full_name":"Manrique, Silvia","last_name":"Manrique"},{"first_name":"Andrea","full_name":"Guazzotti, Andrea","last_name":"Guazzotti"},{"full_name":"Quadrelli, Nadia","last_name":"Quadrelli","first_name":"Nadia"},{"full_name":"Mendes, Marta","last_name":"Mendes","first_name":"Marta"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"first_name":"Lucia","last_name":"Colombo","full_name":"Colombo, Lucia"}],"title":"Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development","department":[{"_id":"EvBe"}],"date_updated":"2021-01-12T06:48:56Z","citation":{"chicago":"Cucinotta, Mara, Silvia Manrique, Andrea Guazzotti, Nadia Quadrelli, Marta Mendes, Eva Benková, and Lucia Colombo. “Cytokinin Response Factors Integrate Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.143545.","ista":"Cucinotta M, Manrique S, Guazzotti A, Quadrelli N, Mendes M, Benková E, Colombo L. 2016. Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. 143(23), 4419–4424.","mla":"Cucinotta, Mara, et al. “Cytokinin Response Factors Integrate Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” Development, vol. 143, no. 23, Company of Biologists, 2016, pp. 4419–24, doi:10.1242/dev.143545.","ama":"Cucinotta M, Manrique S, Guazzotti A, et al. Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. 2016;143(23):4419-4424. doi:10.1242/dev.143545","apa":"Cucinotta, M., Manrique, S., Guazzotti, A., Quadrelli, N., Mendes, M., Benková, E., & Colombo, L. (2016). Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. Company of Biologists. https://doi.org/10.1242/dev.143545","ieee":"M. Cucinotta et al., “Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development,” Development, vol. 143, no. 23. Company of Biologists, pp. 4419–4424, 2016.","short":"M. Cucinotta, S. Manrique, A. Guazzotti, N. Quadrelli, M. Mendes, E. Benková, L. Colombo, Development 143 (2016) 4419–4424."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"The human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus."}],"oa_version":"Published Version","scopus_import":1,"month":"12","intvolume":" 6","publication_status":"published","file":[{"file_name":"IST-2017-735-v1+1_srep38094.pdf","date_created":"2018-12-12T10:10:18Z","creator":"system","file_size":2716045,"date_updated":"2020-07-14T12:44:37Z","checksum":"e007d78b483bc59bf5ab98e9d42a6ec1","file_id":"4804","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":6,"_id":"1186","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)"},"status":"public","pubrep_id":"735","date_updated":"2021-01-12T06:48:56Z","ddc":["576","610"],"department":[{"_id":"LeSa"}],"file_date_updated":"2020-07-14T12:44:37Z","acknowledgement":"We gratefully acknowledge Karsta Barnekow and Kristine Sievert-Giermann, for technical assistance and Lothar Petruschka for in silico analysis (all Dept. of Genetics, University of Greifswald). We are further grateful to the staff from SLS synchrotron beamline for help in data collection. This work was supported by grants from the Deutsche Forschungsgemeinschaft DFG GRK 1870 (to SH) and the Spanish Ministry of Economy and Competitiveness (BFU2014-59389-P to JAH, CTQ2014-52633-P to MB and SAF2012-39760-C02-02 to FG) and S2010/BMD-2457 (Community of Madrid to JAH and FG).","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2016","day":"05","publication":"Scientific Reports","doi":"10.1038/srep38094","date_published":"2016-12-05T00:00:00Z","date_created":"2018-12-11T11:50:36Z","article_number":"38094","citation":{"chicago":"Gutierrez-Fernandez, Javier, Malek Saleh, Martín Alcorlo, Alejandro Gómez Mejóa, David Pantoja Uceda, Miguel Treviño, Franziska Vob, et al. “Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal Pathogenesis.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38094.","ista":"Gutierrez-Fernandez J, Saleh M, Alcorlo M, Gómez Mejóa A, Pantoja Uceda D, Treviño M, Vob F, Abdullah M, Galán Bartual S, Seinen J, Sánchez Murcia P, Gago F, Bruix M, Hammerschmidt S, Hermoso J. 2016. Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. Scientific Reports. 6, 38094.","mla":"Gutierrez-Fernandez, Javier, et al. “Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal Pathogenesis.” Scientific Reports, vol. 6, 38094, Nature Publishing Group, 2016, doi:10.1038/srep38094.","ama":"Gutierrez-Fernandez J, Saleh M, Alcorlo M, et al. Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. Scientific Reports. 2016;6. doi:10.1038/srep38094","apa":"Gutierrez-Fernandez, J., Saleh, M., Alcorlo, M., Gómez Mejóa, A., Pantoja Uceda, D., Treviño, M., … Hermoso, J. (2016). Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38094","ieee":"J. Gutierrez-Fernandez et al., “Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","short":"J. Gutierrez-Fernandez, M. Saleh, M. Alcorlo, A. Gómez Mejóa, D. Pantoja Uceda, M. Treviño, F. Vob, M. Abdullah, S. Galán Bartual, J. Seinen, P. Sánchez Murcia, F. Gago, M. Bruix, S. Hammerschmidt, J. Hermoso, Scientific Reports 6 (2016)."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Gutierrez-Fernandez, Javier","last_name":"Gutierrez-Fernandez","first_name":"Javier","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Malek","last_name":"Saleh","full_name":"Saleh, Malek"},{"last_name":"Alcorlo","full_name":"Alcorlo, Martín","first_name":"Martín"},{"first_name":"Alejandro","full_name":"Gómez Mejóa, Alejandro","last_name":"Gómez Mejóa"},{"last_name":"Pantoja Uceda","full_name":"Pantoja Uceda, David","first_name":"David"},{"first_name":"Miguel","last_name":"Treviño","full_name":"Treviño, Miguel"},{"full_name":"Vob, Franziska","last_name":"Vob","first_name":"Franziska"},{"first_name":"Mohammed","last_name":"Abdullah","full_name":"Abdullah, Mohammed"},{"first_name":"Sergio","full_name":"Galán Bartual, Sergio","last_name":"Galán Bartual"},{"first_name":"Jolien","full_name":"Seinen, Jolien","last_name":"Seinen"},{"first_name":"Pedro","last_name":"Sánchez Murcia","full_name":"Sánchez Murcia, Pedro"},{"first_name":"Federico","last_name":"Gago","full_name":"Gago, Federico"},{"last_name":"Bruix","full_name":"Bruix, Marta","first_name":"Marta"},{"first_name":"Sven","last_name":"Hammerschmidt","full_name":"Hammerschmidt, Sven"},{"first_name":"Juan","last_name":"Hermoso","full_name":"Hermoso, Juan"}],"publist_id":"6167","title":"Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis"},{"citation":{"mla":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOPscience, 2016, doi:10.1088/1742-5468/aa4e8f.","ieee":"D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOPscience, 2016.","short":"D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).","apa":"De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa4e8f","ama":"De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f","chicago":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.","ista":"De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6165","author":[{"last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Davide","last_name":"Masoero","full_name":"Masoero, Davide"}],"title":"Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth","article_number":"123502","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"year":"2016","day":"30","publication":" Journal of Statistical Mechanics: Theory and Experiment","doi":"10.1088/1742-5468/aa4e8f","date_published":"2016-12-30T00:00:00Z","date_created":"2018-12-11T11:50:37Z","acknowledgement":"D De Martino is supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011. D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano and Vera Luz Masoero for useful discussions, also late at night.","publisher":"IOPscience","quality_controlled":"1","oa":1,"date_updated":"2021-01-12T06:48:57Z","department":[{"_id":"GaTk"}],"_id":"1188","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":2016,"issue":"12","ec_funded":1,"abstract":[{"lang":"eng","text":"We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation is solved for the steady state in the WKB\r\napproximation that maps it into the ground state of a quantum particle in an\r\nAiry potential plus a centrifugal term. We retrieve scaling laws for growth rate\r\nfluctuations and time response with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal populations can have a faster response\r\nto perturbations."}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1606.09048","open_access":"1"}],"month":"12","intvolume":" 2016"},{"oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"The authors thank all members of the Institute of Population\r\nGenetics for discussion and support on the project and par-\r\nticularly N. Barghi for helpful comments on earlier versions of\r\nthe manuscript. This work was supported by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”.","page":"174 - 184","date_created":"2018-12-11T11:50:39Z","date_published":"2016-10-03T00:00:00Z","doi":"10.1093/molbev/msw210","year":"2016","has_accepted_license":"1","publication":"Molecular Biology and Evolution","day":"03","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"author":[{"first_name":"Susan","last_name":"Franssen","full_name":"Franssen, Susan"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Christian","last_name":"Schlötterer","full_name":"Schlötterer, Christian"}],"publist_id":"6155","title":"Reconstruction of haplotype-blocks selected during experimental evolution.","citation":{"mla":"Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210.","apa":"Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210","ama":"Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184. doi:10.1093/molbev/msw210","short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.","ieee":"S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” Molecular Biology and Evolution, vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.","chicago":"Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210.","ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"intvolume":" 34","month":"10","abstract":[{"text":"The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. 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Hilbe and A. Traulsen, “Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on ‘Evolutionary game theory using agent-based methods’ by C. Adami, J. Schossau and A. Hintze,” Physics of Life Reviews, vol. 19. Elsevier, pp. 29–31, 2016.","short":"C. Hilbe, A. Traulsen, Physics of Life Reviews 19 (2016) 29–31.","apa":"Hilbe, C., & Traulsen, A. (2016). Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.10.004","ama":"Hilbe C, Traulsen A. Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze. 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Schossau and A. Hintze.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.10.004."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6150","author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X"},{"first_name":"Arne","last_name":"Traulsen","full_name":"Traulsen, Arne"}],"title":"Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze","acknowledgement":"C.H. acknowledges generous support from the ISTFELLOW program.","publisher":"Elsevier","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2016","day":"01","publication":"Physics of Life Reviews","page":"29 - 31","date_published":"2016-12-01T00:00:00Z","doi":"10.1016/j.plrev.2016.10.004","date_created":"2018-12-11T11:50:40Z","_id":"1200","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","pubrep_id":"798","date_updated":"2021-01-12T06:49:03Z","ddc":["530"],"file_date_updated":"2020-07-14T12:44:39Z","department":[{"_id":"KrCh"}],"oa_version":"Submitted Version","scopus_import":1,"month":"12","intvolume":" 19","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4855","checksum":"95e6dc78278334b99dacbf8822509364","creator":"system","file_size":171352,"date_updated":"2020-07-14T12:44:39Z","file_name":"IST-2017-798-v1+1_comment_adami.pdf","date_created":"2018-12-12T10:11:02Z"}],"language":[{"iso":"eng"}],"volume":19,"ec_funded":1},{"type":"journal_article","status":"public","_id":"1201","author":[{"first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"publist_id":"6149","department":[{"_id":"MiSi"}],"title":"Formin’ a nuclear protection","citation":{"chicago":"Renkawitz, Jörg, and Michael K Sixt. “Formin’ a Nuclear Protection.” Cell. Cell Press, 2016. https://doi.org/10.1016/j.cell.2016.11.024.","ista":"Renkawitz J, Sixt MK. 2016. Formin’ a nuclear protection. Cell. 167(6), 1448–1449.","mla":"Renkawitz, Jörg, and Michael K. Sixt. “Formin’ a Nuclear Protection.” Cell, vol. 167, no. 6, Cell Press, 2016, pp. 1448–49, doi:10.1016/j.cell.2016.11.024.","ama":"Renkawitz J, Sixt MK. Formin’ a nuclear protection. Cell. 2016;167(6):1448-1449. doi:10.1016/j.cell.2016.11.024","apa":"Renkawitz, J., & Sixt, M. K. (2016). Formin’ a nuclear protection. Cell. Cell Press. https://doi.org/10.1016/j.cell.2016.11.024","short":"J. Renkawitz, M.K. Sixt, Cell 167 (2016) 1448–1449.","ieee":"J. Renkawitz and M. K. Sixt, “Formin’ a nuclear protection,” Cell, vol. 167, no. 6. Cell Press, pp. 1448–1449, 2016."},"date_updated":"2021-01-12T06:49:03Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Cell Press","quality_controlled":"1","scopus_import":1,"intvolume":" 167","month":"12","abstract":[{"lang":"eng","text":"In this issue of Cell, Skau et al. show that the formin FMN2 organizes a perinuclear actin cytoskeleton that protects the nucleus and its genomic content of migrating cells squeezing through small spaces."}],"oa_version":"None","page":"1448 - 1449","date_created":"2018-12-11T11:50:41Z","doi":"10.1016/j.cell.2016.11.024","issue":"6","date_published":"2016-12-01T00:00:00Z","volume":167,"year":"2016","publication_status":"published","language":[{"iso":"eng"}],"publication":"Cell","day":"01"},{"_id":"1202","status":"public","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"ddc":["570"],"date_updated":"2021-01-12T06:49:03Z","file_date_updated":"2020-07-14T12:44:39Z","department":[{"_id":"SyCr"}],"oa_version":"Published Version","month":"08","intvolume":" 119","scopus_import":1,"file":[{"date_updated":"2020-07-14T12:44:39Z","file_size":1473211,"creator":"kschuh","date_created":"2019-01-25T13:00:20Z","file_name":"2016_Elsevier_Milutinovic.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5885","checksum":"8396d5bd95f9c4295857162f902afabf"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":119,"project":[{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Milutinovic, Barbara, et al. “Immune Priming in Arthropods: An Update Focusing on the Red Flour Beetle.” Zoology , vol. 119, no. 4, Elsevier, 2016, pp. 254–61, doi:10.1016/j.zool.2016.03.006.","ama":"Milutinovic B, Peuß R, Ferro K, Kurtz J. Immune priming in arthropods: an update focusing on the red flour beetle. Zoology . 2016;119(4):254-261. doi:10.1016/j.zool.2016.03.006","apa":"Milutinovic, B., Peuß, R., Ferro, K., & Kurtz, J. (2016). Immune priming in arthropods: an update focusing on the red flour beetle. Zoology . Elsevier. https://doi.org/10.1016/j.zool.2016.03.006","ieee":"B. Milutinovic, R. Peuß, K. Ferro, and J. Kurtz, “Immune priming in arthropods: an update focusing on the red flour beetle,” Zoology , vol. 119, no. 4. Elsevier, pp. 254–261, 2016.","short":"B. Milutinovic, R. Peuß, K. Ferro, J. Kurtz, Zoology 119 (2016) 254–261.","chicago":"Milutinovic, Barbara, Robert Peuß, Kevin Ferro, and Joachim Kurtz. “Immune Priming in Arthropods: An Update Focusing on the Red Flour Beetle.” Zoology . Elsevier, 2016. https://doi.org/10.1016/j.zool.2016.03.006.","ista":"Milutinovic B, Peuß R, Ferro K, Kurtz J. 2016. Immune priming in arthropods: an update focusing on the red flour beetle. Zoology . 119(4), 254–261."},"title":"Immune priming in arthropods: an update focusing on the red flour beetle","author":[{"last_name":"Milutinovic","full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara"},{"first_name":"Robert","full_name":"Peuß, Robert","last_name":"Peuß"},{"first_name":"Kevin","full_name":"Ferro, Kevin","last_name":"Ferro"},{"first_name":"Joachim","full_name":"Kurtz, Joachim","last_name":"Kurtz"}],"publist_id":"6147","acknowledgement":"The authors thank Sophie A.O. Armitage and Jan N. Offenborn for helpful comments on the figures, and two anonymous reviewers for their helpful comments. The project was funded by the Deutsche Forschungsgemeinschaft (DFG, KU 1929/4-2) within the priority programme SPP 1399 “Host–Parasite Coevolution”.","quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"01","publication":"Zoology ","has_accepted_license":"1","year":"2016","date_published":"2016-08-01T00:00:00Z","doi":"10.1016/j.zool.2016.03.006","date_created":"2018-12-11T11:50:41Z","page":"254 - 261"}]