[{"acknowledgement":"This research has been financially supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N., M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]); Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G. Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E. Feraru for helpful discussions.","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.molp.2016.08.010","department":[{"_id":"JiFr"}],"has_accepted_license":"1","type":"journal_article","date_updated":"2021-01-12T06:48:37Z","oa_version":"Published Version","day":"07","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"date_published":"2016-11-07T00:00:00Z","file":[{"file_size":5005876,"creator":"system","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:13:22Z","file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf","access_level":"open_access","file_id":"5004","date_updated":"2018-12-12T10:13:22Z"}],"page":"1504 - 1519","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure–function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. © 2016 The Authors"}],"title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components","publication":"Molecular Plant","oa":1,"ddc":["581"],"_id":"1145","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2016","citation":{"ista":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 9(11), 1504–1519.","short":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml, Molecular Plant 9 (2016) 1504–1519.","chicago":"Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová, Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” <i>Molecular Plant</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">https://doi.org/10.1016/j.molp.2016.08.010</a>.","ieee":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml, “Enquiry into the topology of plasma membrane localized PIN auxin transport components,” <i>Molecular Plant</i>, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.","ama":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry into the topology of plasma membrane localized PIN auxin transport components. <i>Molecular Plant</i>. 2016;9(11):1504-1519. doi:<a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">10.1016/j.molp.2016.08.010</a>","apa":"Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., &#38; Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin transport components. <i>Molecular Plant</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">https://doi.org/10.1016/j.molp.2016.08.010</a>","mla":"Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” <i>Molecular Plant</i>, vol. 9, no. 11, Cell Press, 2016, pp. 1504–19, doi:<a href=\"https://doi.org/10.1016/j.molp.2016.08.010\">10.1016/j.molp.2016.08.010</a>."},"quality_controlled":"1","author":[{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"last_name":"Hejátko","first_name":"Jan","full_name":"Hejátko, Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí"}],"date_created":"2018-12-11T11:50:23Z","month":"11","status":"public","intvolume":"         9","publist_id":"6213","file_date_updated":"2018-12-12T10:13:22Z","publisher":"Cell Press","volume":9,"issue":"11","pubrep_id":"746"},{"volume":6,"pubrep_id":"745","publisher":"Nature Publishing Group","file_date_updated":"2018-12-12T10:09:28Z","publist_id":"6211","intvolume":"         6","article_number":"35955","status":"public","date_created":"2018-12-11T11:50:24Z","month":"11","author":[{"first_name":"Jozef","last_name":"Balla","full_name":"Balla, Jozef"},{"full_name":"Medved'Ová, Zuzana","last_name":"Medved'Ová","first_name":"Zuzana"},{"first_name":"Petr","last_name":"Kalousek","full_name":"Kalousek, Petr"},{"first_name":"Natálie","last_name":"Matiješčuková","full_name":"Matiješčuková, Natálie"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml"},{"last_name":"Reinöhl","first_name":"Vilém","full_name":"Reinöhl, Vilém"},{"last_name":"Procházka","first_name":"Stanislav","full_name":"Procházka, Stanislav"}],"quality_controlled":"1","citation":{"chicago":"Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková, Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep35955\">https://doi.org/10.1038/srep35955</a>.","short":"J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl, S. Procházka, Scientific Reports 6 (2016).","ista":"Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka S. 2016. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 6, 35955.","ieee":"J. Balla <i>et al.</i>, “Auxin flow mediated competition between axillary buds to restore apical dominance,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","ama":"Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between axillary buds to restore apical dominance. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep35955\">10.1038/srep35955</a>","mla":"Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” <i>Scientific Reports</i>, vol. 6, 35955, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep35955\">10.1038/srep35955</a>.","apa":"Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl, V., &#38; Procházka, S. (2016). Auxin flow mediated competition between axillary buds to restore apical dominance. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep35955\">https://doi.org/10.1038/srep35955</a>"},"year":"2016","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"ddc":["581"],"_id":"1147","publication":"Scientific Reports","title":"Auxin flow mediated competition between axillary buds to restore apical dominance","publication_status":"published","abstract":[{"text":"Apical dominance is one of the fundamental developmental phenomena in plant biology, which determines the overall architecture of aerial plant parts. Here we show apex decapitation activated competition for dominance in adjacent upper and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a model system to monitor and assess auxin flow, auxin transport channels, and dormancy and initiation status of axillary buds. Auxin flow was manipulated by lateral stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid (TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide (CHX) treatments, which served to interfere with axillary bud competition. Redirecting auxin flow to different points influenced which bud formed the outgrowing and dominant shoot. The obtained results proved that competition between upper and lower axillary buds as secondary auxin sources is based on the same auxin canalization principle that operates between the shoot apex and axillary bud. © The Author(s) 2016.","lang":"eng"}],"date_published":"2016-11-08T00:00:00Z","file":[{"relation":"main_file","date_created":"2018-12-12T10:09:28Z","content_type":"application/pdf","creator":"system","file_size":1587544,"date_updated":"2018-12-12T10:09:28Z","file_id":"4752","file_name":"IST-2017-745-v1+1_srep35955.pdf","access_level":"open_access"}],"scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"08","type":"journal_article","date_updated":"2021-01-12T06:48:38Z","oa_version":"Published Version","language":[{"iso":"eng"}],"doi":"10.1038/srep35955","has_accepted_license":"1","department":[{"_id":"JiFr"}],"acknowledgement":"This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II., supported by the project “CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013)."},{"scopus_import":1,"date_published":"2016-11-01T00:00:00Z","page":"15 - 25","acknowledgement":"This work is based on the CMSB 2015 paper “Adaptive moment closure for parameter inference of biochemical reaction networks” (Bogomolov et al., 2015). The work was partly supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS1), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award). J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.biosystems.2016.07.005","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"type":"journal_article","date_updated":"2023-02-23T10:08:46Z","oa_version":"None","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:50:24Z","month":"11","status":"public","intvolume":"       149","publist_id":"6210","publisher":"Elsevier","volume":149,"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd"}],"title":"Adaptive moment closure for parameter inference of biochemical reaction networks","publication":"Biosystems","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1658"}]},"_id":"1148","year":"2016","citation":{"apa":"Schilling, C., Bogomolov, S., Henzinger, T. A., Podelski, A., &#38; Ruess, J. (2016). Adaptive moment closure for parameter inference of biochemical reaction networks. <i>Biosystems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">https://doi.org/10.1016/j.biosystems.2016.07.005</a>","mla":"Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” <i>Biosystems</i>, vol. 149, Elsevier, 2016, pp. 15–25, doi:<a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">10.1016/j.biosystems.2016.07.005</a>.","ama":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment closure for parameter inference of biochemical reaction networks. <i>Biosystems</i>. 2016;149:15-25. doi:<a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">10.1016/j.biosystems.2016.07.005</a>","ieee":"C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive moment closure for parameter inference of biochemical reaction networks,” <i>Biosystems</i>, vol. 149. Elsevier, pp. 15–25, 2016.","ista":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 149, 15–25.","chicago":"Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski, and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” <i>Biosystems</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">https://doi.org/10.1016/j.biosystems.2016.07.005</a>.","short":"C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25."},"quality_controlled":"1","author":[{"full_name":"Schilling, Christian","last_name":"Schilling","first_name":"Christian"},{"first_name":"Sergiy","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Podelski, Andreas","first_name":"Andreas","last_name":"Podelski"},{"last_name":"Ruess","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282"}]},{"status":"public","month":"09","date_created":"2018-12-11T11:50:25Z","scopus_import":1,"publist_id":"6209","intvolume":"       107","publisher":"Elsevier","volume":107,"page":"34 - 47","date_published":"2016-09-01T00:00:00Z","abstract":[{"text":"We study the usefulness of two most prominent publicly available rigorous ODE integrators: one provided by the CAPD group (capd.ii.uj.edu.pl), the other based on the COSY Infinity project (cosyinfinity.org). Both integrators are capable of handling entire sets of initial conditions and provide tight rigorous outer enclosures of the images under a time-T map. We conduct extensive benchmark computations using the well-known Lorenz system, and compare the computation time against the final accuracy achieved. We also discuss the effect of a few technical parameters, such as the order of the numerical integration method, the value of T, and the phase space resolution. We conclude that COSY may provide more precise results due to its ability of avoiding the variable dependency problem. However, the overall cost of computations conducted using CAPD is typically lower, especially when intervals of parameters are involved. Moreover, access to COSY is limited (registration required) and the rigorous ODE integrators are not publicly available, while CAPD is an open source free software project. Therefore, we recommend the latter integrator for this kind of computations. Nevertheless, proper choice of the various integration parameters turns out to be of even greater importance than the choice of the integrator itself. © 2016 IMACS. Published by Elsevier B.V. All rights reserved.","lang":"eng"}],"publication_status":"published","project":[{"name":"Persistent Homology - Images, Data and Maps","grant_number":"622033","call_identifier":"FP7","_id":"255F06BE-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"MG was partially supported by FAPESP grants 2013/07460-7 and 2010/00875-9, and by CNPq grants 305860/2013-5 and 306453/2009-6, Brazil. The work of HK was partially supported by Grant-in-Aid for Scientific Research (Nos.24654022, 25287029), Ministry of Education, Science, Technology, Culture and Sports, Japan. KM was supported by NSF grants NSF-DMS-0835621, 0915019, 1125174, 1248071, and contracts from AFOSR and DARPA. TM was supported by Grant-in-Aid for JSPS Fellows No. 245312. A part of the research of TM and HK was also supported by JST, CREST.\r\n\r\nResearch conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE – Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (Ref. FCT PTDC/MAT/098871/2008); from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 622033; and from the same sources as HK.\r\n\r\nThe authors express their gratitude to the Department of Mathematics of Kyoto University for making their server available for conducting the computations described in the paper, and to the reviewers for helpful comments that contributed towards increasing the quality of the paper.","department":[{"_id":"HeEd"}],"_id":"1149","language":[{"iso":"eng"}],"doi":"10.1016/j.apnum.2016.04.005","ec_funded":1,"publication":"Applied Numerical Mathematics","title":"A study of rigorous ODE integrators for multi scale set oriented computations","year":"2016","day":"01","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T06:48:38Z","author":[{"last_name":"Miyaji","first_name":"Tomoyuki","full_name":"Miyaji, Tomoyuki"},{"first_name":"Pawel","last_name":"Pilarczyk","full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gameiro, Marcio","first_name":"Marcio","last_name":"Gameiro"},{"first_name":"Hiroshi","last_name":"Kokubu","full_name":"Kokubu, Hiroshi"},{"full_name":"Mischaikow, Konstantin","first_name":"Konstantin","last_name":"Mischaikow"}],"quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Miyaji, Tomoyuki, et al. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” <i>Applied Numerical Mathematics</i>, vol. 107, Elsevier, 2016, pp. 34–47, doi:<a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">10.1016/j.apnum.2016.04.005</a>.","apa":"Miyaji, T., Pilarczyk, P., Gameiro, M., Kokubu, H., &#38; Mischaikow, K. (2016). A study of rigorous ODE integrators for multi scale set oriented computations. <i>Applied Numerical Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">https://doi.org/10.1016/j.apnum.2016.04.005</a>","ieee":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, and K. Mischaikow, “A study of rigorous ODE integrators for multi scale set oriented computations,” <i>Applied Numerical Mathematics</i>, vol. 107. Elsevier, pp. 34–47, 2016.","ama":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. A study of rigorous ODE integrators for multi scale set oriented computations. <i>Applied Numerical Mathematics</i>. 2016;107:34-47. doi:<a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">10.1016/j.apnum.2016.04.005</a>","ista":"Miyaji T, Pilarczyk P, Gameiro M, Kokubu H, Mischaikow K. 2016. A study of rigorous ODE integrators for multi scale set oriented computations. Applied Numerical Mathematics. 107, 34–47.","short":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, K. Mischaikow, Applied Numerical Mathematics 107 (2016) 34–47.","chicago":"Miyaji, Tomoyuki, Pawel Pilarczyk, Marcio Gameiro, Hiroshi Kokubu, and Konstantin Mischaikow. “A Study of Rigorous ODE Integrators for Multi Scale Set Oriented Computations.” <i>Applied Numerical Mathematics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.apnum.2016.04.005\">https://doi.org/10.1016/j.apnum.2016.04.005</a>."}},{"year":"2016","day":"12","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T06:48:39Z","author":[{"first_name":"Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg"},{"last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Renkawitz and M. K. Sixt, “A Radical Break Restraining Neutrophil Migration,” <i>Developmental Cell</i>, vol. 38, no. 5. Cell Press, pp. 448–450, 2016.","ama":"Renkawitz J, Sixt MK. A Radical Break Restraining Neutrophil Migration. <i>Developmental Cell</i>. 2016;38(5):448-450. doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">10.1016/j.devcel.2016.08.017</a>","ista":"Renkawitz J, Sixt MK. 2016. A Radical Break Restraining Neutrophil Migration. Developmental Cell. 38(5), 448–450.","short":"J. Renkawitz, M.K. Sixt, Developmental Cell 38 (2016) 448–450.","chicago":"Renkawitz, Jörg, and Michael K Sixt. “A Radical Break Restraining Neutrophil Migration.” <i>Developmental Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">https://doi.org/10.1016/j.devcel.2016.08.017</a>.","mla":"Renkawitz, Jörg, and Michael K. Sixt. “A Radical Break Restraining Neutrophil Migration.” <i>Developmental Cell</i>, vol. 38, no. 5, Cell Press, 2016, pp. 448–50, doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">10.1016/j.devcel.2016.08.017</a>.","apa":"Renkawitz, J., &#38; Sixt, M. K. (2016). A Radical Break Restraining Neutrophil Migration. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2016.08.017\">https://doi.org/10.1016/j.devcel.2016.08.017</a>"},"abstract":[{"lang":"eng","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."}],"publication_status":"published","_id":"1150","department":[{"_id":"MiSi"}],"doi":"10.1016/j.devcel.2016.08.017","language":[{"iso":"eng"}],"title":"A Radical Break Restraining Neutrophil Migration","publication":"Developmental Cell","publisher":"Cell Press","volume":38,"issue":"5","page":"448 - 450","date_published":"2016-09-12T00:00:00Z","status":"public","month":"09","date_created":"2018-12-11T11:50:25Z","scopus_import":1,"publist_id":"6208","intvolume":"        38"},{"scopus_import":1,"date_published":"2016-10-15T00:00:00Z","external_id":{"pmid":["27898393"]},"file":[{"file_name":"2016_GeneDev_Simonini.pdf","access_level":"open_access","success":1,"file_id":"5882","date_updated":"2019-01-25T09:32:55Z","file_size":1419263,"content_type":"application/pdf","creator":"dernst","relation":"main_file","date_created":"2019-01-25T09:32:55Z"}],"page":"2286 - 2296","language":[{"iso":"eng"}],"doi":"10.1101/gad.285361.116","department":[{"_id":"JiFr"}],"has_accepted_license":"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. ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_updated":"2021-01-12T06:48:39Z","oa_version":"Published Version","day":"15","intvolume":"        30","publist_id":"6207","date_created":"2018-12-11T11:50:25Z","month":"10","status":"public","volume":30,"issue":"20","file_date_updated":"2019-01-25T09:32:55Z","publisher":"Cold Spring Harbor Laboratory Press","publication":"Genes and Development","title":"A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis","pmid":1,"oa":1,"ddc":["570"],"_id":"1151","publication_status":"published","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"}],"citation":{"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.","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.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2016. <a href=\"https://doi.org/10.1101/gad.285361.116\">https://doi.org/10.1101/gad.285361.116</a>.","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.","ama":"Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. <i>Genes and Development</i>. 2016;30(20):2286-2296. doi:<a href=\"https://doi.org/10.1101/gad.285361.116\">10.1101/gad.285361.116</a>","ieee":"S. Simonini <i>et al.</i>, “A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis,” <i>Genes and Development</i>, vol. 30, no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.","mla":"Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” <i>Genes and Development</i>, vol. 30, no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:<a href=\"https://doi.org/10.1101/gad.285361.116\">10.1101/gad.285361.116</a>.","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. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.285361.116\">https://doi.org/10.1101/gad.285361.116</a>"},"author":[{"full_name":"Simonini, Sara","first_name":"Sara","last_name":"Simonini"},{"last_name":"Deb","first_name":"Joyita","full_name":"Deb, Joyita"},{"last_name":"Moubayidin","first_name":"Laila","full_name":"Moubayidin, Laila"},{"full_name":"Stephenson, Pauline","last_name":"Stephenson","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"},{"first_name":"Karim","last_name":"Sorefan","full_name":"Sorefan, Karim"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml"},{"first_name":"Lars","last_name":"Östergaard","full_name":"Östergaard, Lars"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016"},{"quality_controlled":"1","author":[{"full_name":"Žádníková, Petra","last_name":"Žádníková","first_name":"Petra"},{"full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","last_name":"Wabnik"},{"full_name":"Abuzeineh, Anas","last_name":"Abuzeineh","first_name":"Anas"},{"full_name":"Gallemí, Marçal","first_name":"Marçal","last_name":"Gallemí"},{"full_name":"Van Der Straeten, Dominique","first_name":"Dominique","last_name":"Van Der Straeten"},{"full_name":"Smith, Richard","first_name":"Richard","last_name":"Smith"},{"last_name":"Inze","first_name":"Dirk","full_name":"Inze, Dirk"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prusinkiewicz","first_name":"Przemysław","full_name":"Prusinkiewicz, Przemysław"},{"first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"citation":{"mla":"Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” <i>Plant Cell</i>, vol. 28, no. 10, American Society of Plant Biologists, 2016, pp. 2464–77, doi:<a href=\"https://doi.org/10.1105/tpc.15.00569\">10.1105/tpc.15.00569</a>.","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. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.15.00569\">https://doi.org/10.1105/tpc.15.00569</a>","ieee":"P. Žádníková <i>et al.</i>, “A model of differential growth guided apical hook formation in plants,” <i>Plant Cell</i>, vol. 28, no. 10. American Society of Plant Biologists, pp. 2464–2477, 2016.","ama":"Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth guided apical hook formation in plants. <i>Plant Cell</i>. 2016;28(10):2464-2477. doi:<a href=\"https://doi.org/10.1105/tpc.15.00569\">10.1105/tpc.15.00569</a>","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.” <i>Plant Cell</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1105/tpc.15.00569\">https://doi.org/10.1105/tpc.15.00569</a>.","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.","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."},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/","open_access":"1"}],"year":"2016","oa":1,"_id":"1153","publication":"Plant Cell","title":"A model of differential growth guided apical hook formation in plants","publication_status":"published","abstract":[{"lang":"eng","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."}],"project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis"}],"volume":28,"issue":"10","publisher":"American Society of Plant Biologists","publist_id":"6205","intvolume":"        28","status":"public","date_created":"2018-12-11T11:50:26Z","month":"10","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","type":"journal_article","date_updated":"2021-01-12T06:48:40Z","oa_version":"Submitted Version","language":[{"iso":"eng"}],"doi":"10.1105/tpc.15.00569","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"ec_funded":1,"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).","page":"2464 - 2477","date_published":"2016-10-01T00:00:00Z","scopus_import":1},{"scopus_import":1,"date_published":"2016-11-07T00:00:00Z","file":[{"date_updated":"2018-12-12T10:09:32Z","file_id":"4756","access_level":"open_access","file_name":"IST-2017-744-v1+1_srep36440.pdf","date_created":"2018-12-12T10:09:32Z","relation":"main_file","file_size":2353456,"content_type":"application/pdf","creator":"system"}],"ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1038/srep36440","has_accepted_license":"1","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"ToBo"}],"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","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_updated":"2021-01-12T06:48:41Z","oa_version":"Published Version","day":"07","intvolume":"         6","publist_id":"6204","date_created":"2018-12-11T11:50:27Z","month":"11","article_number":"36440","status":"public","volume":6,"pubrep_id":"744","file_date_updated":"2018-12-12T10:09:32Z","publisher":"Nature Publishing Group","publication":"Scientific Reports","title":"A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients","oa":1,"ddc":["579"],"_id":"1154","project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556"},{"call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","grant_number":"Y 564-B12"}],"publication_status":"published","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"}],"citation":{"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. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep36440\">https://doi.org/10.1038/srep36440</a>","mla":"Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” <i>Scientific Reports</i>, vol. 6, 36440, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep36440\">10.1038/srep36440</a>.","ieee":"J. Schwarz <i>et al.</i>, “A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","ama":"Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep36440\">10.1038/srep36440</a>","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.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep36440\">https://doi.org/10.1038/srep36440</a>.","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).","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."},"quality_controlled":"1","author":[{"full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Jan"},{"full_name":"Bierbaum, Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","last_name":"Bierbaum","first_name":"Veronika"},{"first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"first_name":"Tino","last_name":"Frank","full_name":"Frank, Tino"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias"},{"last_name":"Tay","first_name":"Savaş","full_name":"Tay, Savaş"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K"},{"orcid":"0000-0001-8599-1226","full_name":"Mehling, Matthias","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","last_name":"Mehling","first_name":"Matthias"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016"},{"page":"3786 - 3839","date_published":"2016-12-15T00:00:00Z","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"15","oa_version":"Preprint","type":"journal_article","date_updated":"2021-01-12T06:48:43Z","department":[{"_id":"LaEr"}],"doi":"10.1214/16-AAP1193","language":[{"iso":"eng"}],"ec_funded":1,"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.","issue":"6","volume":26,"publisher":"Institute of Mathematical Statistics","publist_id":"6201","intvolume":"        26","status":"public","month":"12","date_created":"2018-12-11T11:50:27Z","author":[{"last_name":"Lee","first_name":"Ji","full_name":"Lee, Ji"},{"first_name":"Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1409.4979","open_access":"1"}],"citation":{"mla":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” <i>Annals of Applied Probability</i>, vol. 26, no. 6, Institute of Mathematical Statistics, 2016, pp. 3786–839, doi:<a href=\"https://doi.org/10.1214/16-AAP1193\">10.1214/16-AAP1193</a>.","apa":"Lee, J., &#38; Schnelli, K. (2016). Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/16-AAP1193\">https://doi.org/10.1214/16-AAP1193</a>","ama":"Lee J, Schnelli K. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. <i>Annals of Applied Probability</i>. 2016;26(6):3786-3839. doi:<a href=\"https://doi.org/10.1214/16-AAP1193\">10.1214/16-AAP1193</a>","ieee":"J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population,” <i>Annals of Applied Probability</i>, vol. 26, no. 6. Institute of Mathematical Statistics, pp. 3786–3839, 2016.","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.","short":"J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.","chicago":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2016. <a href=\"https://doi.org/10.1214/16-AAP1193\">https://doi.org/10.1214/16-AAP1193</a>."},"year":"2016","_id":"1157","oa":1,"title":"Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population","publication":"Annals of Applied Probability","abstract":[{"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.","lang":"eng"}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}]},{"doi":"10.1371/journal.pbio.2000234","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"has_accepted_license":"1","acknowledgement":"European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"27","date_updated":"2023-02-23T14:11:16Z","type":"journal_article","oa_version":"Published Version","scopus_import":1,"date_published":"2016-12-27T00:00:00Z","file":[{"file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","checksum":"2bab63b068a9840efd532b9ae583f9bb","access_level":"open_access","date_updated":"2020-07-14T12:44:36Z","file_id":"5164","file_size":2494348,"content_type":"application/pdf","creator":"system","relation":"main_file","date_created":"2018-12-12T10:15:42Z"}],"ddc":["576"],"oa":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9862"},{"relation":"research_data","status":"public","id":"9863"}]},"_id":"1158","publication":"PLoS Biology","title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","publication_status":"published","abstract":[{"text":"Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate &quot;grey zone&quot; of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.","lang":"eng"}],"author":[{"last_name":"Roux","first_name":"Camille","full_name":"Roux, Camille"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"full_name":"Anciaux, Youann","first_name":"Youann","last_name":"Anciaux"},{"full_name":"Galtier, Nicolas","first_name":"Nicolas","last_name":"Galtier"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"quality_controlled":"1","citation":{"short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. 2016;14(12). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” <i>PLoS Biology</i>, vol. 14, no. 12. Public Library of Science, 2016.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>","mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>."},"year":"2016","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publist_id":"6200","intvolume":"        14","status":"public","article_number":"e2000234","date_created":"2018-12-11T11:50:28Z","month":"12","issue":"12","volume":14,"pubrep_id":"742","publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:44:36Z"},{"title":"Hanani-Tutte for radial planarity II","related_material":{"record":[{"relation":"later_version","status":"public","id":"1113"},{"status":"public","relation":"earlier_version","id":"1595"}]},"oa":1,"_id":"1164","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","abstract":[{"lang":"eng","text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, … , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. A pair of edges e and f in a graph is independent if e and f do not share a vertex. We show that a graph G is radial planar if G has a radial drawing in which every two independent edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the strong Hanani-Tutte theorem for radial planarity. This characterization yields a very simple algorithm for radial planarity testing."}],"citation":{"mla":"Fulek, Radoslav, et al. <i>Hanani-Tutte for Radial Planarity II</i>. Vol. 9801, Springer, 2016, pp. 468–81, doi:<a href=\"https://doi.org/10.1007/978-3-319-50106-2_36\">10.1007/978-3-319-50106-2_36</a>.","apa":"Fulek, R., Pelsmajer, M., &#38; Schaefer, M. (2016). Hanani-Tutte for radial planarity II (Vol. 9801, pp. 468–481). Presented at the GD: Graph Drawing and Network Visualization, Athens, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_36\">https://doi.org/10.1007/978-3-319-50106-2_36</a>","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity II,” 9801:468–81. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_36\">https://doi.org/10.1007/978-3-319-50106-2_36</a>.","short":"R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2016, pp. 468–481.","ista":"Fulek R, Pelsmajer M, Schaefer M. 2016. Hanani-Tutte for radial planarity II. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 468–481.","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity II. In: Vol 9801. Springer; 2016:468-481. doi:<a href=\"https://doi.org/10.1007/978-3-319-50106-2_36\">10.1007/978-3-319-50106-2_36</a>","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity II,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp. 468–481."},"main_file_link":[{"url":"https://arxiv.org/abs/1608.08662","open_access":"1"}],"quality_controlled":"1","author":[{"first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"full_name":"Pelsmajer, Michael","first_name":"Michael","last_name":"Pelsmajer"},{"first_name":"Marcus","last_name":"Schaefer","full_name":"Schaefer, Marcus"}],"year":"2016","intvolume":"      9801","publist_id":"6193","date_created":"2018-12-11T11:50:29Z","month":"12","conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2016-09-21","location":"Athens, Greece","start_date":"2016-09-19"},"status":"public","volume":9801,"publisher":"Springer","ec_funded":1,"doi":"10.1007/978-3-319-50106-2_36","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","type":"conference","date_updated":"2023-02-23T10:05:57Z","oa_version":"Preprint","day":"08","alternative_title":["LNCS"],"scopus_import":1,"arxiv":1,"date_published":"2016-12-08T00:00:00Z","external_id":{"arxiv":["1608.08662"]},"page":"468 - 481"},{"scopus_import":1,"alternative_title":["LNCS"],"page":"94 - 106","date_published":"2016-12-08T00:00:00Z","acknowledgement":"R. Fulek—The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].\r\nI would like to thank Jan Kynčl and Dömötör Pálvölgyi for many comments and suggestions that helped to improve the presentation of the result.","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-50106-2_8","ec_funded":1,"day":"08","oa_version":"Preprint","type":"conference","date_updated":"2023-09-27T12:14:48Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","conference":{"end_date":"2016-09-21","name":"GD: Graph Drawing and Network Visualization","start_date":"2016-09-19","location":"Athens, Greece"},"month":"12","date_created":"2018-12-11T11:50:30Z","publist_id":"6192","publisher":"Springer","volume":"9801 ","abstract":[{"lang":"eng","text":"We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle."}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"_id":"1165","related_material":{"record":[{"id":"794","status":"public","relation":"later_version"}]},"oa":1,"title":"C-planarity of embedded cyclic c-graphs","year":"2016","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","last_name":"Fulek"}],"quality_controlled":"1","citation":{"mla":"Fulek, Radoslav. <i>C-Planarity of Embedded Cyclic c-Graphs</i>. Vol. 9801, Springer, 2016, pp. 94–106, doi:<a href=\"https://doi.org/10.1007/978-3-319-50106-2_8\">10.1007/978-3-319-50106-2_8</a>.","apa":"Fulek, R. (2016). C-planarity of embedded cyclic c-graphs (Vol. 9801, pp. 94–106). Presented at the GD: Graph Drawing and Network Visualization, Athens, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_8\">https://doi.org/10.1007/978-3-319-50106-2_8</a>","ieee":"R. Fulek, “C-planarity of embedded cyclic c-graphs,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp. 94–106.","ama":"Fulek R. C-planarity of embedded cyclic c-graphs. In: Vol 9801. Springer; 2016:94-106. doi:<a href=\"https://doi.org/10.1007/978-3-319-50106-2_8\">10.1007/978-3-319-50106-2_8</a>","ista":"Fulek R. 2016. C-planarity of embedded cyclic c-graphs. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 94–106.","chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs,” 9801:94–106. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_8\">https://doi.org/10.1007/978-3-319-50106-2_8</a>.","short":"R. Fulek, in:, Springer, 2016, pp. 94–106."},"main_file_link":[{"url":"https://arxiv.org/abs/1602.01346","open_access":"1"}]},{"related_material":{"link":[{"url":"https://dl.acm.org/citation.cfm?id=3016355","relation":"table_of_contents"}],"record":[{"relation":"earlier_version","status":"public","id":"5443"}]},"language":[{"iso":"eng"}],"_id":"1166","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ec_funded":1,"publication":"Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence","title":"A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps","publication_status":"published","abstract":[{"text":"POMDPs are standard models for probabilistic planning problems, where an agent interacts with an uncertain environment. We study the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a policy to ensure that the target set is reached with probability 1 (almost-surely). While in general the problem is EXPTIMEcomplete, in many practical cases policies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. In this work, we first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach. © 2016, Association for the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved.","lang":"eng"}],"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"last_name":"Davies","first_name":"Jessica","id":"378E0060-F248-11E8-B48F-1D18A9856A87","full_name":"Davies, Jessica"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","citation":{"apa":"Chatterjee, K., Chmelik, M., &#38; Davies, J. (2016). A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps. In <i>Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence</i> (Vol. 2016, pp. 3225–3232). Phoenix, AZ, USA: AAAI Press.","mla":"Chatterjee, Krishnendu, et al. “A Symbolic SAT Based Algorithm for Almost Sure Reachability with Small Strategies in Pomdps.” <i>Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence</i>, vol. 2016, AAAI Press, 2016, pp. 3225–32.","ista":"Chatterjee K, Chmelik M, Davies J. 2016. A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps. Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 2016, 3225–3232.","short":"K. Chatterjee, M. Chmelik, J. Davies, in:, Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, AAAI Press, 2016, pp. 3225–3232.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. “A Symbolic SAT Based Algorithm for Almost Sure Reachability with Small Strategies in Pomdps.” In <i>Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence</i>, 2016:3225–32. AAAI Press, 2016.","ama":"Chatterjee K, Chmelik M, Davies J. A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps. In: <i>Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence</i>. Vol 2016. AAAI Press; 2016:3225-3232.","ieee":"K. Chatterjee, M. Chmelik, and J. Davies, “A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps,” in <i>Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence</i>, Phoenix, AZ, USA, 2016, vol. 2016, pp. 3225–3232."},"day":"02","year":"2016","date_updated":"2023-02-23T12:26:41Z","type":"conference","oa_version":"None","publist_id":"6191","intvolume":"      2016","status":"public","date_created":"2018-12-11T11:50:30Z","month":"12","conference":{"end_date":"2016-02-17","name":"AAAI: Conference on Artificial Intelligence","location":"Phoenix, AZ, USA","start_date":"2016-02-12"},"volume":2016,"page":"3225 - 3232","date_published":"2016-12-02T00:00:00Z","publisher":"AAAI Press"},{"date_published":"2016-12-09T00:00:00Z","file":[{"file_id":"4926","date_updated":"2020-07-14T12:44:37Z","file_name":"IST-2017-740-v1+1_journal.pcbi.1005218.pdf","checksum":"84f44ae92866c52ff1ca8a574558dca7","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:12:08Z","file_size":3822299,"content_type":"application/pdf","creator":"system"}],"scopus_import":"1","type":"journal_article","date_updated":"2023-02-23T14:11:22Z","oa_version":"Published Version","day":"09","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","acknowledgement":"MZ acknowledges the Polish National Science Centre grant no. DEC-2012/07/N/NZ2/00107. BW was supported by the Scottish Government/Royal Society of Edinburgh Personal Research Fellowship. We thank Marjon de Vos and Oliver Martin for critically reading the manuscript.","language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1005218","department":[{"_id":"AnKi"}],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:44:37Z","publisher":"Public Library of Science","volume":12,"issue":"12","pubrep_id":"740","date_created":"2018-12-11T11:50:30Z","month":"12","article_number":"e1005218","status":"public","intvolume":"        12","publist_id":"6190","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016","citation":{"ama":"Zagórski MP, Burda Z, Wacław B. Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. <i>PLoS Computational Biology</i>. 2016;12(12). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218\">10.1371/journal.pcbi.1005218</a>","ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks,” <i>PLoS Computational Biology</i>, vol. 12, no. 12. Public Library of Science, 2016.","ista":"Zagórski MP, Burda Z, Wacław B. 2016. Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. 12(12), e1005218.","short":"M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016).","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “Beyond the Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.” <i>PLoS Computational Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218\">https://doi.org/10.1371/journal.pcbi.1005218</a>.","mla":"Zagórski, Marcin P., et al. “Beyond the Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.” <i>PLoS Computational Biology</i>, vol. 12, no. 12, e1005218, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218\">10.1371/journal.pcbi.1005218</a>.","apa":"Zagórski, M. P., Burda, Z., &#38; Wacław, B. (2016). Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218\">https://doi.org/10.1371/journal.pcbi.1005218</a>"},"author":[{"last_name":"Zagórski","first_name":"Marcin P","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Burda","first_name":"Zdzisław","full_name":"Burda, Zdzisław"},{"first_name":"Bartłomiej","last_name":"Wacław","full_name":"Wacław, Bartłomiej"}],"quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Evolutionary pathways describe trajectories of biological evolution in the space of different variants of organisms (genotypes). The probability of existence and the number of evolutionary pathways that lead from a given genotype to a better-adapted genotype are important measures of accessibility of local fitness optima and the reproducibility of evolution. Both quantities have been studied in simple mathematical models where genotypes are represented as binary sequences of two types of basic units, and the network of permitted mutations between the genotypes is a hypercube graph. However, it is unclear how these results translate to the biologically relevant case in which genotypes are represented by sequences of more than two units, for example four nucleotides (DNA) or 20 amino acids (proteins), and the mutational graph is not the hypercube. Here we investigate accessibility of the best-adapted genotype in the general case of K &gt; 2 units. Using computer generated and experimental fitness landscapes we show that accessibility of the global fitness maximum increases with K and can be much higher than for binary sequences. The increase in accessibility comes from the increase in the number of indirect trajectories exploited by evolution for higher K. As one of the consequences, the fraction of genotypes that are accessible increases by three orders of magnitude when the number of units K increases from 2 to 16 for landscapes of size N ∼ 106genotypes. This suggests that evolution can follow many different trajectories on such landscapes and the reconstruction of evolutionary pathways from experimental data might be an extremely difficult task."}],"publication":"PLoS Computational Biology","title":"Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks","related_material":{"record":[{"status":"public","relation":"research_data","id":"9866"}]},"ddc":["570"],"oa":1,"_id":"1167"},{"author":[{"first_name":"Moritz","last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz"},{"full_name":"Stelling, Jörg","last_name":"Stelling","first_name":"Jörg"}],"quality_controlled":"1","citation":{"ama":"Lang M, Stelling J. Modular parameter identification of biomolecular networks. <i>SIAM Journal on Scientific Computing</i>. 2016;38(6):B988-B1008. doi:<a href=\"https://doi.org/10.1137/15M103306X\">10.1137/15M103306X</a>","ieee":"M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” <i>SIAM Journal on Scientific Computing</i>, vol. 38, no. 6. Society for Industrial and Applied Mathematics , pp. B988–B1008, 2016.","chicago":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” <i>SIAM Journal on Scientific Computing</i>. Society for Industrial and Applied Mathematics , 2016. <a href=\"https://doi.org/10.1137/15M103306X\">https://doi.org/10.1137/15M103306X</a>.","short":"M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.","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.” <i>SIAM Journal on Scientific Computing</i>, vol. 38, no. 6, Society for Industrial and Applied Mathematics , 2016, pp. B988–1008, doi:<a href=\"https://doi.org/10.1137/15M103306X\">10.1137/15M103306X</a>.","apa":"Lang, M., &#38; Stelling, J. (2016). Modular parameter identification of biomolecular networks. <i>SIAM Journal on Scientific Computing</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/15M103306X\">https://doi.org/10.1137/15M103306X</a>"},"year":"2016","_id":"1170","ddc":["003","518","570","621"],"publication":"SIAM Journal on Scientific Computing","title":"Modular parameter identification of biomolecular networks","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"}],"publication_status":"published","pubrep_id":"811","issue":"6","volume":38,"publisher":"Society for Industrial and Applied Mathematics ","file_date_updated":"2020-07-14T12:44:37Z","publist_id":"6186","intvolume":"        38","status":"public","month":"11","date_created":"2018-12-11T11:50:31Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"15","oa_version":"Submitted Version","date_updated":"2021-01-12T06:48:49Z","type":"journal_article","has_accepted_license":"1","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"language":[{"iso":"eng"}],"doi":"10.1137/15M103306X","page":"B988 - B1008","file":[{"file_id":"5095","date_updated":"2020-07-14T12:44:37Z","access_level":"local","file_name":"IST-2017-811-v1+1_modular_parameter_identification.pdf","checksum":"781bc3ffd30b2dd65b7727c5a285fc78","date_created":"2018-12-12T10:14:41Z","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":871964}],"date_published":"2016-11-15T00:00:00Z","scopus_import":1},{"date_published":"2016-07-01T00:00:00Z","volume":17,"page":"166 - 167","publisher":"Elsevier","intvolume":"        17","publist_id":"6185","scopus_import":1,"date_created":"2018-12-11T11:50:32Z","month":"07","status":"public","citation":{"apa":"Tkačik, G. (2016). Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. <i>Physics of Life Reviews</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">https://doi.org/10.1016/j.plrev.2016.06.005</a>","mla":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot; by O. C. Martin et Al.” <i>Physics of Life Reviews</i>, vol. 17, Elsevier, 2016, pp. 166–67, doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">10.1016/j.plrev.2016.06.005</a>.","short":"G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.","chicago":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot; by O. C. Martin et Al.” <i>Physics of Life Reviews</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">https://doi.org/10.1016/j.plrev.2016.06.005</a>.","ista":"Tkačik G. 2016. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. Physics of Life Reviews. 17, 166–167.","ama":"Tkačik G. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. <i>Physics of Life Reviews</i>. 2016;17:166-167. doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">10.1016/j.plrev.2016.06.005</a>","ieee":"G. Tkačik, “Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al.,” <i>Physics of Life Reviews</i>, vol. 17. Elsevier, pp. 166–167, 2016."},"quality_controlled":"1","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:48:50Z","type":"journal_article","oa_version":"None","day":"01","year":"2016","title":"Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&quot; by O. C. Martin et al.","publication":"Physics of Life Reviews","language":[{"iso":"eng"}],"doi":"10.1016/j.plrev.2016.06.005","department":[{"_id":"GaTk"}],"_id":"1171","publication_status":"published"},{"oa":1,"ddc":["576"],"_id":"1172","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","publication":"Scientific Reports","publication_status":"published","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"}],"quality_controlled":"1","author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani"},{"full_name":"Barma, Mustansir","first_name":"Mustansir","last_name":"Barma"},{"full_name":"Rao, Madan","first_name":"Madan","last_name":"Rao"}],"citation":{"ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>.","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>, vol. 6, 38840, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>.","apa":"Sachdeva, H., Barma, M., &#38; Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>"},"year":"2016","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publist_id":"6183","intvolume":"         6","article_number":"38840","status":"public","date_created":"2018-12-11T11:50:32Z","month":"12","volume":6,"pubrep_id":"737","publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:44:37Z","language":[{"iso":"eng"}],"doi":"10.1038/srep38840","has_accepted_license":"1","department":[{"_id":"NiBa"}],"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","day":"19","date_updated":"2021-01-12T06:48:50Z","type":"journal_article","oa_version":"Published Version","scopus_import":1,"date_published":"2016-12-19T00:00:00Z","file":[{"file_id":"4977","date_updated":"2020-07-14T12:44:37Z","file_name":"IST-2017-737-v1+1_srep38840.pdf","checksum":"cb378732da885ea4959ec5b845fb6e52","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:12:56Z","content_type":"application/pdf","creator":"system","file_size":760967}]},{"intvolume":"        74","publist_id":"6177","month":"04","date_created":"2018-12-11T11:50:33Z","status":"public","date_published":"2016-04-01T00:00:00Z","page":"1321 - 1362","volume":74,"issue":"4","publisher":"Springer","publication":"Algorithmica","title":"A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound","_id":"1177","department":[{"_id":"KrPi"}],"oa":1,"doi":"10.1007/s00453-015-9997-6","language":[{"iso":"eng"}],"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.","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"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2013/651"}],"citation":{"mla":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” <i>Algorithmica</i>, vol. 74, no. 4, Springer, 2016, pp. 1321–62, doi:<a href=\"https://doi.org/10.1007/s00453-015-9997-6\">10.1007/s00453-015-9997-6</a>.","apa":"Kamath Hosdurg, C., &#38; Chatterjee, S. (2016). A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-015-9997-6\">https://doi.org/10.1007/s00453-015-9997-6</a>","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.” <i>Algorithmica</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00453-015-9997-6\">https://doi.org/10.1007/s00453-015-9997-6</a>.","short":"C. Kamath Hosdurg, S. Chatterjee, Algorithmica 74 (2016) 1321–1362.","ama":"Kamath Hosdurg C, Chatterjee S. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. <i>Algorithmica</i>. 2016;74(4):1321-1362. doi:<a href=\"https://doi.org/10.1007/s00453-015-9997-6\">10.1007/s00453-015-9997-6</a>","ieee":"C. Kamath Hosdurg and S. Chatterjee, “A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound,” <i>Algorithmica</i>, vol. 74, no. 4. Springer, pp. 1321–1362, 2016."},"author":[{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan"},{"last_name":"Chatterjee","first_name":"Sanjit","full_name":"Chatterjee, Sanjit"}],"quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","date_updated":"2021-01-12T06:48:52Z","year":"2016","day":"01"},{"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."}],"publication_status":"published","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"_id":"1179","oa":1,"title":"Pseudoentropy: Lower-bounds for chain rules and transformations","year":"2016","quality_controlled":"1","author":[{"last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Maciej, Skorski","last_name":"Maciej","first_name":"Skorski"}],"main_file_link":[{"url":"https://eprint.iacr.org/2016/159","open_access":"1"}],"citation":{"ama":"Pietrzak KZ, Maciej S. Pseudoentropy: Lower-bounds for chain rules and transformations. In: Vol 9985. Springer; 2016:183-203. doi:<a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">10.1007/978-3-662-53641-4_8</a>","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.","ista":"Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985, 183–203.","chicago":"Pietrzak, Krzysztof Z, and Skorski Maciej. “Pseudoentropy: Lower-Bounds for Chain Rules and Transformations,” 9985:183–203. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">https://doi.org/10.1007/978-3-662-53641-4_8</a>.","short":"K.Z. Pietrzak, S. Maciej, in:, Springer, 2016, pp. 183–203.","mla":"Pietrzak, Krzysztof Z., and Skorski Maciej. <i>Pseudoentropy: Lower-Bounds for Chain Rules and Transformations</i>. Vol. 9985, Springer, 2016, pp. 183–203, doi:<a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">10.1007/978-3-662-53641-4_8</a>.","apa":"Pietrzak, K. Z., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">https://doi.org/10.1007/978-3-662-53641-4_8</a>"},"status":"public","month":"10","conference":{"end_date":"2016-11-03","name":"TCC: Theory of Cryptography Conference","start_date":"2016-10-31","location":"Beijing, China"},"date_created":"2018-12-11T11:50:34Z","publist_id":"6175","intvolume":"      9985","publisher":"Springer","volume":9985,"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).","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-53641-4_8","ec_funded":1,"day":"22","oa_version":"Preprint","date_updated":"2021-01-12T06:48:53Z","type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"alternative_title":["LNCS"],"page":"183 - 203","date_published":"2016-10-22T00:00:00Z"},{"title":"Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity","publication":"Journal of Neuroscience","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.2359-16.2016","department":[{"_id":"SiHi"}],"_id":"1181","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.","project":[{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","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"}],"citation":{"apa":"Dwyer, N., Chen, B., Chou, S., Hippenmeyer, S., Nguyen, L., &#38; Ghashghaei, T. (2016). Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">https://doi.org/10.1523/JNEUROSCI.2359-16.2016</a>","mla":"Dwyer, Noelle, et al. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity.” <i>Journal of Neuroscience</i>, vol. 36, no. 45, Society for Neuroscience, 2016, pp. 11394–401, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">10.1523/JNEUROSCI.2359-16.2016</a>.","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.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2016. <a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">https://doi.org/10.1523/JNEUROSCI.2359-16.2016</a>.","short":"N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, T. Ghashghaei, Journal of Neuroscience 36 (2016) 11394–11401.","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.","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. <i>Journal of Neuroscience</i>. 2016;36(45):11394-11401. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">10.1523/JNEUROSCI.2359-16.2016</a>","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,” <i>Journal of Neuroscience</i>, vol. 36, no. 45. Society for Neuroscience, pp. 11394–11401, 2016."},"quality_controlled":"1","author":[{"full_name":"Dwyer, Noelle","last_name":"Dwyer","first_name":"Noelle"},{"full_name":"Chen, Bin","first_name":"Bin","last_name":"Chen"},{"last_name":"Chou","first_name":"Shen","full_name":"Chou, Shen"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer"},{"last_name":"Nguyen","first_name":"Laurent","full_name":"Nguyen, Laurent"},{"first_name":"Troy","last_name":"Ghashghaei","full_name":"Ghashghaei, Troy"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_updated":"2021-01-12T06:48:54Z","oa_version":"None","day":"09","year":"2016","intvolume":"        36","publist_id":"6172","scopus_import":1,"date_created":"2018-12-11T11:50:35Z","month":"11","status":"public","date_published":"2016-11-09T00:00:00Z","issue":"45","page":"11394 - 11401","volume":36,"publisher":"Society for Neuroscience"}]