[{"doi":"10.1145/2933575.2935304","main_file_link":[{"url":"https://arxiv.org/abs/1602.02670","open_access":"1"}],"publication":"Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science","oa_version":"Preprint","date_created":"2018-12-11T11:50:22Z","day":"05","status":"public","page":"197 - 206","external_id":{"arxiv":["1602.02670"]},"conference":{"name":"LICS: Logic in Computer Science","start_date":"2016-07-05","end_date":"2016-07-08","location":"New York, NY, USA"},"year":"2016","month":"07","date_published":"2016-07-05T00:00:00Z","alternative_title":["Proceedings Symposium on Logic in Computer Science"],"acknowledgement":"K.  C.,  M.  H.,  and  W.  D.  are  partially  supported  by  the  Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003.\r\nK. C. is partially supported by the Austrian Science Fund (FWF)\r\nNFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant\r\n(279307: Graph Games). For W. D., M. H., and V. L. the research\r\nleading to these results has received funding from the European\r\nResearch Council under the European Union’s Seventh Framework\r\nProgramme (FP/2007-2013) / ERC Grant Agreement no. 340506.","date_updated":"2025-06-02T08:53:44Z","oa":1,"project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"publication_status":"published","citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvoák, Monika H Henzinger, and Veronika Loitzenbauer. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 197–206. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2935304\">https://doi.org/10.1145/2933575.2935304</a>.","ama":"Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>. IEEE; 2016:197-206. doi:<a href=\"https://doi.org/10.1145/2933575.2935304\">10.1145/2933575.2935304</a>","ieee":"K. Chatterjee, W. Dvoák, M. H. Henzinger, and V. Loitzenbauer, “Model and objective separation with conditional lower bounds: disjunction is harder than conjunction,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, New York, NY, USA, 2016, pp. 197–206.","ista":"Chatterjee K, Dvoák W, Henzinger MH, Loitzenbauer V. 2016. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science, , 197–206.","short":"K. Chatterjee, W. Dvoák, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206.","mla":"Chatterjee, Krishnendu, et al. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, IEEE, 2016, pp. 197–206, doi:<a href=\"https://doi.org/10.1145/2933575.2935304\">10.1145/2933575.2935304</a>.","apa":"Chatterjee, K., Dvoák, W., Henzinger, M. H., &#38; Loitzenbauer, V. (2016). Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i> (pp. 197–206). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2935304\">https://doi.org/10.1145/2933575.2935304</a>"},"type":"conference","abstract":[{"text":"Given a model of a system and an objective, the model-checking question asks whether the model satisfies the objective. We study polynomial-time problems in two classical models, graphs and Markov Decision Processes (MDPs), with respect to several fundamental -regular objectives, e.g., Rabin and Streett objectives. For many of these problems the best-known upper bounds are quadratic or cubic, yet no super-linear lower bounds are known. In this work our contributions are two-fold: First, we present several improved algorithms, and second, we present the first conditional super-linear lower bounds based on widely believed assumptions about the complexity of CNF-SAT and combinatorial Boolean matrix multiplication. A separation result for two models with respect to an objective means a conditional lower bound for one model that is strictly higher than the existing upper bound for the other model, and similarly for two objectives with respect to a model. Our results establish the following separation results: (1) A separation of models (graphs and MDPs) for disjunctive queries of reachability and Büchi objectives. (2) Two kinds of separations of objectives, both for graphs and MDPs, namely, (2a) the separation of dual objectives such as Streett/Rabin objectives, and (2b) the separation of conjunction and disjunction of multiple objectives of the same type such as safety, Büchi, and coBüchi. In summary, our results establish the first model and objective separation results for graphs and MDPs for various classical -regular objectives. Quite strikingly, we establish conditional lower bounds for the disjunction of objectives that are strictly higher than the existing upper bounds for the conjunction of the same objectives. © 2016 ACM.","lang":"eng"}],"arxiv":1,"scopus_import":"1","_id":"1140","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"KrCh"}],"publist_id":"6219","language":[{"iso":"eng"}],"publisher":"IEEE","title":"Model and objective separation with conditional lower bounds: disjunction is harder than conjunction","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Wolfgang","last_name":"Dvoák","full_name":"Dvoák, Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"full_name":"Loitzenbauer, Veronika","first_name":"Veronika","last_name":"Loitzenbauer"}]},{"page":"249 - 260","department":[{"_id":"ChWo"}],"publist_id":"6217","language":[{"iso":"eng"}],"year":"2016","date_published":"2016-11-01T00:00:00Z","intvolume":"        17","month":"11","acknowledgement":"The work presented in this paper was partially supported by Polish National Science Centre grant nos. DEC-2012/05/N/ST6/03433 and DEC-2011/03/B/ST6/01393. Radosław Łazarz was supported by Polish National Science Centre grant no. DEC-2013/10/M/ST6/00531.","publisher":"Elsevier","date_updated":"2021-01-12T06:48:35Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization","author":[{"full_name":"Łazarz, Radosław","first_name":"Radosław","last_name":"Łazarz"},{"last_name":"Idzik","first_name":"Michał","full_name":"Idzik, Michał"},{"last_name":"Gądek","first_name":"Konrad","full_name":"Gądek, Konrad"},{"last_name":"Gajda-Zagorska","first_name":"Ewa P","id":"47794CF0-F248-11E8-B48F-1D18A9856A87","full_name":"Gajda-Zagorska, Ewa P"}],"issue":"1","publication":"Journal of Computational Science","doi":"10.1016/j.jocs.2016.03.004","publication_status":"published","oa_version":"None","volume":17,"citation":{"apa":"Łazarz, R., Idzik, M., Gądek, K., &#38; Gajda-Zagorska, E. P. (2016). Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. <i>Journal of Computational Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">https://doi.org/10.1016/j.jocs.2016.03.004</a>","mla":"Łazarz, Radosław, et al. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” <i>Journal of Computational Science</i>, vol. 17, no. 1, Elsevier, 2016, pp. 249–60, doi:<a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">10.1016/j.jocs.2016.03.004</a>.","ama":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. <i>Journal of Computational Science</i>. 2016;17(1):249-260. doi:<a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">10.1016/j.jocs.2016.03.004</a>","ista":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. 2016. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. Journal of Computational Science. 17(1), 249–260.","short":"R. Łazarz, M. Idzik, K. Gądek, E.P. Gajda-Zagorska, Journal of Computational Science 17 (2016) 249–260.","ieee":"R. Łazarz, M. Idzik, K. Gądek, and E. P. Gajda-Zagorska, “Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization,” <i>Journal of Computational Science</i>, vol. 17, no. 1. Elsevier, pp. 249–260, 2016.","chicago":"Łazarz, Radosław, Michał Idzik, Konrad Gądek, and Ewa P Gajda-Zagorska. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” <i>Journal of Computational Science</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">https://doi.org/10.1016/j.jocs.2016.03.004</a>."},"scopus_import":1,"abstract":[{"lang":"eng","text":"In this paper we introduce the Multiobjective Optimization Hierarchic Genetic Strategy with maturing (MO-mHGS), a meta-algorithm that performs evolutionary optimization in a hierarchy of populations. The maturing mechanism improves growth and reduces redundancy. The performance of MO-mHGS with selected state-of-the-art multiobjective evolutionary algorithms as internal algorithms is analysed on benchmark problems and their modifications for which single fitness evaluation time depends on the solution accuracy. We compare the proposed algorithm with the Island Model Genetic Algorithm as well as with single-deme methods, and discuss the impact of internal algorithms on the MO-mHGS meta-algorithm. © 2016 Elsevier B.V."}],"type":"journal_article","_id":"1141","date_created":"2018-12-11T11:50:22Z","day":"01","status":"public","quality_controlled":"1"},{"author":[{"last_name":"Martins","first_name":"Rui","full_name":"Martins, Rui"},{"full_name":"Maier, Julia","last_name":"Maier","first_name":"Julia"},{"full_name":"Gorki, Anna","first_name":"Anna","last_name":"Gorki"},{"full_name":"Huber, Kilian","first_name":"Kilian","last_name":"Huber"},{"first_name":"Omar","last_name":"Sharif","full_name":"Sharif, Omar"},{"last_name":"Starkl","first_name":"Philipp","full_name":"Starkl, Philipp"},{"full_name":"Saluzzo, Simona","last_name":"Saluzzo","first_name":"Simona"},{"full_name":"Quattrone, Federica","first_name":"Federica","last_name":"Quattrone"},{"first_name":"Riem","last_name":"Gawish","full_name":"Gawish, Riem"},{"first_name":"Karin","last_name":"Lakovits","full_name":"Lakovits, Karin"},{"first_name":"Michael","last_name":"Aichinger","full_name":"Aichinger, Michael"},{"first_name":"Branka","last_name":"Radic Sarikas","full_name":"Radic Sarikas, Branka"},{"last_name":"Lardeau","first_name":"Charles","full_name":"Lardeau, Charles"},{"full_name":"Hladik, Anastasiya","first_name":"Anastasiya","last_name":"Hladik"},{"first_name":"Ana","last_name":"Korosec","full_name":"Korosec, Ana"},{"last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","full_name":"Brown, Markus"},{"full_name":"Vaahtomeri, Kari","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari"},{"last_name":"Duggan","first_name":"Michelle","id":"2EDEA62C-F248-11E8-B48F-1D18A9856A87","full_name":"Duggan, Michelle"},{"first_name":"Dontscho","last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho"},{"last_name":"Esterbauer","first_name":"Harald","full_name":"Esterbauer, Harald"},{"first_name":"Jacques","last_name":"Colinge","full_name":"Colinge, Jacques"},{"last_name":"Eisenbarth","first_name":"Stephanie","full_name":"Eisenbarth, Stephanie"},{"full_name":"Decker, Thomas","first_name":"Thomas","last_name":"Decker"},{"last_name":"Bennett","first_name":"Keiryn","full_name":"Bennett, Keiryn"},{"first_name":"Stefan","last_name":"Kubicek","full_name":"Kubicek, Stefan"},{"full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"full_name":"Superti Furga, Giulio","first_name":"Giulio","last_name":"Superti Furga"},{"full_name":"Knapp, Sylvia","first_name":"Sylvia","last_name":"Knapp"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions","publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"publist_id":"6216","department":[{"_id":"MiSi"},{"_id":"PeJo"}],"quality_controlled":"1","_id":"1142","type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"Hemolysis drives susceptibility to bacterial infections and predicts poor outcome from sepsis. These detrimental effects are commonly considered to be a consequence of heme-iron serving as a nutrient for bacteria. We employed a Gram-negative sepsis model and found that elevated heme levels impaired the control of bacterial proliferation independently of heme-iron acquisition by pathogens. Heme strongly inhibited phagocytosis and the migration of human and mouse phagocytes by disrupting actin cytoskeletal dynamics via activation of the GTP-binding Rho family protein Cdc42 by the guanine nucleotide exchange factor DOCK8. A chemical screening approach revealed that quinine effectively prevented heme effects on the cytoskeleton, restored phagocytosis and improved survival in sepsis. These mechanistic insights provide potential therapeutic targets for patients with sepsis or hemolytic disorders."}],"citation":{"apa":"Martins, R., Maier, J., Gorki, A., Huber, K., Sharif, O., Starkl, P., … Knapp, S. (2016). Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3590\">https://doi.org/10.1038/ni.3590</a>","mla":"Martins, Rui, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” <i>Nature Immunology</i>, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1361–72, doi:<a href=\"https://doi.org/10.1038/ni.3590\">10.1038/ni.3590</a>.","ama":"Martins R, Maier J, Gorki A, et al. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. <i>Nature Immunology</i>. 2016;17(12):1361-1372. doi:<a href=\"https://doi.org/10.1038/ni.3590\">10.1038/ni.3590</a>","short":"R. Martins, J. Maier, A. Gorki, K. Huber, O. Sharif, P. Starkl, S. Saluzzo, F. Quattrone, R. Gawish, K. Lakovits, M. Aichinger, B. Radic Sarikas, C. Lardeau, A. Hladik, A. Korosec, M. Brown, K. Vaahtomeri, M. Duggan, D. Kerjaschki, H. Esterbauer, J. Colinge, S. Eisenbarth, T. Decker, K. Bennett, S. Kubicek, M.K. Sixt, G. Superti Furga, S. Knapp, Nature Immunology 17 (2016) 1361–1372.","ista":"Martins R, Maier J, Gorki A, Huber K, Sharif O, Starkl P, Saluzzo S, Quattrone F, Gawish R, Lakovits K, Aichinger M, Radic Sarikas B, Lardeau C, Hladik A, Korosec A, Brown M, Vaahtomeri K, Duggan M, Kerjaschki D, Esterbauer H, Colinge J, Eisenbarth S, Decker T, Bennett K, Kubicek S, Sixt MK, Superti Furga G, Knapp S. 2016. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology. 17(12), 1361–1372.","ieee":"R. Martins <i>et al.</i>, “Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions,” <i>Nature Immunology</i>, vol. 17, no. 12. Nature Publishing Group, pp. 1361–1372, 2016.","chicago":"Martins, Rui, Julia Maier, Anna Gorki, Kilian Huber, Omar Sharif, Philipp Starkl, Simona Saluzzo, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” <i>Nature Immunology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ni.3590\">https://doi.org/10.1038/ni.3590</a>."},"publication_status":"published","issue":"12","oa":1,"date_updated":"2021-01-12T06:48:36Z","acknowledgement":"Y. Fukui (Medical Institute of Bioregulation, Kyushu University) and J. Stein (Theodor Kocher Institute, University of Bern) are acknowledged for providing the DOCK8 deficient bone marrow. and H. Häcker (St. Judes Children's Research Hospital) for providing the ERHBD-HoxB8-encoding retroviral construct. pSpCas9(BB)-2a-Puro (PX459) was a gift from F. Zhang (Massachusetts Institute of Technology) (Addgene plasmid # 48139) and pGRG36 was a gift from N. Craig (Johns Hopkins University School of Medicine) (Addgene plasmid # 16666). LifeAct-GFP-encoding retrovirus was kindly provided by A. Leithner (Institute of Science and Technology Austria). pSIM8 and TKC E. coli were gifts from D.L. Court (Center for Cancer Research, National Cancer Institute). We acknowledge M. Gröger and S. Rauscher for excellent technical support (Core imaging facility, Medical University of Vienna). We thank D.P. Barlow and L.R. Cheever for critical reading of the manuscript. This work was supported by the Austrian Academy of Sciences, the Science Fund of the Austrian National Bank (14107) and the Austrian Science Fund FWF (I1620-B22) in the Infect-ERA framework (to S.Knapp).","intvolume":"        17","month":"12","date_published":"2016-12-01T00:00:00Z","year":"2016","page":"1361 - 1372","status":"public","day":"01","date_created":"2018-12-11T11:50:22Z","volume":17,"oa_version":"Submitted Version","main_file_link":[{"url":"https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d","open_access":"1"}],"doi":"10.1038/ni.3590","publication":"Nature Immunology"},{"quality_controlled":"1","_id":"1143","abstract":[{"text":"We study the ground state of a dilute Bose gas in a scaling limit where the Gross-Pitaevskii functional emerges. This is a repulsive nonlinear Schrödinger functional whose quartic term is proportional to the scattering length of the interparticle interaction potential. We propose a new derivation of this limit problem, with a method that bypasses some of the technical difficulties that previous derivations had to face. The new method is based on a combination of Dyson\\'s lemma, the quantum de Finetti theorem and a second moment estimate for ground states of the effective Dyson Hamiltonian. It applies equally well to the case where magnetic fields or rotation are present.","lang":"eng"}],"scopus_import":1,"type":"journal_article","citation":{"mla":"Nam, Phan, et al. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” <i>Analysis and PDE</i>, vol. 9, no. 2, Mathematical Sciences Publishers, 2016, pp. 459–85, doi:<a href=\"https://doi.org/10.2140/apde.2016.9.459\">10.2140/apde.2016.9.459</a>.","apa":"Nam, P., Rougerie, N., &#38; Seiringer, R. (2016). Ground states of large bosonic systems: The gross Pitaevskii limit revisited. <i>Analysis and PDE</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/apde.2016.9.459\">https://doi.org/10.2140/apde.2016.9.459</a>","chicago":"Nam, Phan, Nicolas Rougerie, and Robert Seiringer. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” <i>Analysis and PDE</i>. Mathematical Sciences Publishers, 2016. <a href=\"https://doi.org/10.2140/apde.2016.9.459\">https://doi.org/10.2140/apde.2016.9.459</a>.","ama":"Nam P, Rougerie N, Seiringer R. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. <i>Analysis and PDE</i>. 2016;9(2):459-485. doi:<a href=\"https://doi.org/10.2140/apde.2016.9.459\">10.2140/apde.2016.9.459</a>","short":"P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.","ista":"Nam P, Rougerie N, Seiringer R. 2016. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE. 9(2), 459–485.","ieee":"P. Nam, N. Rougerie, and R. Seiringer, “Ground states of large bosonic systems: The gross Pitaevskii limit revisited,” <i>Analysis and PDE</i>, vol. 9, no. 2. Mathematical Sciences Publishers, pp. 459–485, 2016."},"publication_status":"published","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"author":[{"full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam"},{"full_name":"Rougerie, Nicolas","first_name":"Nicolas","last_name":"Rougerie"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"title":"Ground states of large bosonic systems: The gross Pitaevskii limit revisited","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Mathematical Sciences Publishers","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"publist_id":"6215","status":"public","day":"24","date_created":"2018-12-11T11:50:23Z","volume":9,"ec_funded":1,"oa_version":"Preprint","publication":"Analysis and PDE","main_file_link":[{"url":"https://arxiv.org/abs/1503.07061","open_access":"1"}],"doi":"10.2140/apde.2016.9.459","oa":1,"issue":"2","date_updated":"2021-01-12T06:48:36Z","date_published":"2016-03-24T00:00:00Z","intvolume":"         9","month":"03","year":"2016","page":"459 - 485"},{"publication":"Molecular Plant","doi":"10.1016/j.molp.2016.08.010","oa_version":"Published Version","ec_funded":1,"volume":9,"day":"07","status":"public","ddc":["581"],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2018-12-11T11:50:23Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"1504 - 1519","year":"2016","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.","date_published":"2016-11-07T00:00:00Z","intvolume":"         9","month":"11","oa":1,"issue":"11","date_updated":"2021-01-12T06:48:37Z","publication_status":"published","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"scopus_import":1,"abstract":[{"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","lang":"eng"}],"file_date_updated":"2018-12-12T10:13:22Z","type":"journal_article","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.","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>","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>.","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","_id":"1145","department":[{"_id":"JiFr"}],"publist_id":"6213","pubrep_id":"746","language":[{"iso":"eng"}],"publisher":"Cell Press","has_accepted_license":"1","title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components","author":[{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"first_name":"Jan","last_name":"Hejátko","full_name":"Hejátko, Jan"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"5004","content_type":"application/pdf","creator":"system","file_size":5005876,"relation":"main_file","access_level":"open_access","file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf","date_updated":"2018-12-12T10:13:22Z","date_created":"2018-12-12T10:13:22Z"}]},{"day":"08","status":"public","date_created":"2018-12-11T11:50:24Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["581"],"volume":6,"oa_version":"Published Version","doi":"10.1038/srep35955","publication":"Scientific Reports","oa":1,"date_updated":"2021-01-12T06:48:38Z","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).","article_number":"35955","intvolume":"         6","month":"11","date_published":"2016-11-08T00:00:00Z","year":"2016","license":"https://creativecommons.org/licenses/by/4.0/","quality_controlled":"1","_id":"1147","file_date_updated":"2018-12-12T10:09:28Z","type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","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."}],"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>.","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.","short":"J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl, S. Procházka, Scientific Reports 6 (2016).","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>"},"publication_status":"published","file":[{"file_name":"IST-2017-745-v1+1_srep35955.pdf","date_created":"2018-12-12T10:09:28Z","date_updated":"2018-12-12T10:09:28Z","file_size":1587544,"creator":"system","content_type":"application/pdf","file_id":"4752","relation":"main_file","access_level":"open_access"}],"title":"Auxin flow mediated competition between axillary buds to restore apical dominance","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Balla, Jozef","first_name":"Jozef","last_name":"Balla"},{"last_name":"Medved'Ová","first_name":"Zuzana","full_name":"Medved'Ová, Zuzana"},{"full_name":"Kalousek, Petr","last_name":"Kalousek","first_name":"Petr"},{"first_name":"Natálie","last_name":"Matiješčuková","full_name":"Matiješčuková, Natálie"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí"},{"last_name":"Reinöhl","first_name":"Vilém","full_name":"Reinöhl, Vilém"},{"first_name":"Stanislav","last_name":"Procházka","full_name":"Procházka, Stanislav"}],"publisher":"Nature Publishing Group","has_accepted_license":"1","pubrep_id":"745","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publist_id":"6211"},{"citation":{"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.","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.","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>","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>.","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>"},"scopus_import":1,"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"}],"type":"journal_article","_id":"1148","quality_controlled":"1","project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"publication_status":"published","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Schilling","first_name":"Christian","full_name":"Schilling, Christian"},{"full_name":"Bogomolov, Sergiy","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","last_name":"Bogomolov"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Podelski, Andreas","first_name":"Andreas","last_name":"Podelski"},{"first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282","last_name":"Ruess","full_name":"Ruess, Jakob"}],"title":"Adaptive moment closure for parameter inference of biochemical reaction networks","publist_id":"6210","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"language":[{"iso":"eng"}],"volume":149,"date_created":"2018-12-11T11:50:24Z","day":"01","status":"public","publication":"Biosystems","doi":"10.1016/j.biosystems.2016.07.005","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1658"}]},"ec_funded":1,"oa_version":"None","date_published":"2016-11-01T00:00:00Z","month":"11","intvolume":"       149","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.","date_updated":"2023-02-23T10:08:46Z","page":"15 - 25","year":"2016"},{"department":[{"_id":"HeEd"}],"publist_id":"6209","page":"34 - 47","year":"2016","language":[{"iso":"eng"}],"publisher":"Elsevier","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.","month":"09","intvolume":"       107","date_published":"2016-09-01T00:00:00Z","author":[{"first_name":"Tomoyuki","last_name":"Miyaji","full_name":"Miyaji, Tomoyuki"},{"last_name":"Pilarczyk","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","full_name":"Pilarczyk, Pawel"},{"first_name":"Marcio","last_name":"Gameiro","full_name":"Gameiro, Marcio"},{"full_name":"Kokubu, Hiroshi","last_name":"Kokubu","first_name":"Hiroshi"},{"full_name":"Mischaikow, Konstantin","last_name":"Mischaikow","first_name":"Konstantin"}],"title":"A study of rigorous ODE integrators for multi scale set oriented computations","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:48:38Z","doi":"10.1016/j.apnum.2016.04.005","publication_status":"published","publication":"Applied Numerical Mathematics","project":[{"name":"Persistent Homology - Images, Data and Maps","_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033","call_identifier":"FP7"}],"oa_version":"None","ec_funded":1,"type":"journal_article","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"}],"scopus_import":1,"citation":{"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>.","short":"T. Miyaji, P. Pilarczyk, M. Gameiro, H. Kokubu, K. Mischaikow, Applied Numerical Mathematics 107 (2016) 34–47.","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.","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>","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>"},"volume":107,"status":"public","quality_controlled":"1","day":"01","_id":"1149","date_created":"2018-12-11T11:50:25Z"},{"oa_version":"None","publication":"Developmental Cell","publication_status":"published","doi":"10.1016/j.devcel.2016.08.017","day":"12","status":"public","quality_controlled":"1","_id":"1150","date_created":"2018-12-11T11:50:25Z","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."}],"scopus_import":1,"type":"journal_article","volume":38,"citation":{"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>.","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.","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.","short":"J. Renkawitz, M.K. Sixt, Developmental Cell 38 (2016) 448–450.","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>"},"year":"2016","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"}],"publist_id":"6208","page":"448 - 450","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"A Radical Break Restraining Neutrophil Migration","author":[{"first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg"},{"orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"issue":"5","date_updated":"2021-01-12T06:48:39Z","publisher":"Cell Press","date_published":"2016-09-12T00:00:00Z","month":"09","intvolume":"        38"},{"publication":"Genes and Development","doi":"10.1101/gad.285361.116","oa_version":"Published Version","volume":30,"pmid":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:50:25Z","ddc":["570"],"day":"15","status":"public","external_id":{"pmid":["27898393"]},"page":"2286 - 2296","year":"2016","date_published":"2016-10-15T00:00:00Z","month":"10","intvolume":"        30","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. ","date_updated":"2021-01-12T06:48:39Z","oa":1,"issue":"20","publication_status":"published","citation":{"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>","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>.","short":"S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30 (2016) 2286–2296.","ieee":"S. Simonini <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.","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>"},"abstract":[{"lang":"eng","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."}],"scopus_import":1,"type":"journal_article","file_date_updated":"2019-01-25T09:32:55Z","_id":"1151","quality_controlled":"1","department":[{"_id":"JiFr"}],"publist_id":"6207","language":[{"iso":"eng"}],"has_accepted_license":"1","publisher":"Cold Spring Harbor Laboratory Press","title":"A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis","author":[{"full_name":"Simonini, Sara","first_name":"Sara","last_name":"Simonini"},{"full_name":"Deb, Joyita","last_name":"Deb","first_name":"Joyita"},{"full_name":"Moubayidin, Laila","first_name":"Laila","last_name":"Moubayidin"},{"last_name":"Stephenson","first_name":"Pauline","full_name":"Stephenson, Pauline"},{"first_name":"Manoj","last_name":"Valluru","full_name":"Valluru, Manoj"},{"full_name":"Freire Rios, Alejandra","first_name":"Alejandra","last_name":"Freire Rios"},{"full_name":"Sorefan, Karim","first_name":"Karim","last_name":"Sorefan"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"full_name":"Östergaard, Lars","first_name":"Lars","last_name":"Östergaard"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2016_GeneDev_Simonini.pdf","success":1,"date_updated":"2019-01-25T09:32:55Z","date_created":"2019-01-25T09:32:55Z","creator":"dernst","file_size":1419263,"content_type":"application/pdf","file_id":"5882","relation":"main_file","access_level":"open_access"}]},{"publication_status":"published","project":[{"name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","call_identifier":"FP7"}],"quality_controlled":"1","_id":"1153","scopus_import":1,"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."}],"type":"journal_article","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>","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>.","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.","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.","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>"},"language":[{"iso":"eng"}],"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publist_id":"6205","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"A model of differential growth guided apical hook formation in plants","author":[{"full_name":"Žádníková, Petra","last_name":"Žádníková","first_name":"Petra"},{"full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","orcid":"0000-0001-7263-0560"},{"full_name":"Abuzeineh, Anas","first_name":"Anas","last_name":"Abuzeineh"},{"full_name":"Gallemí, Marçal","first_name":"Marçal","last_name":"Gallemí"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"},{"full_name":"Smith, Richard","first_name":"Richard","last_name":"Smith"},{"full_name":"Inze, Dirk","first_name":"Dirk","last_name":"Inze"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Prusinkiewicz, Przemysław","last_name":"Prusinkiewicz","first_name":"Przemysław"},{"full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"publisher":"American Society of Plant Biologists","oa_version":"Submitted Version","ec_funded":1,"publication":"Plant Cell","doi":"10.1105/tpc.15.00569","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/","open_access":"1"}],"day":"01","status":"public","date_created":"2018-12-11T11:50:26Z","volume":28,"year":"2016","page":"2464 - 2477","oa":1,"issue":"10","date_updated":"2021-01-12T06:48:40Z","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).","date_published":"2016-10-01T00:00:00Z","intvolume":"        28","month":"10"},{"has_accepted_license":"1","publisher":"Nature Publishing Group","author":[{"full_name":"Schwarz, Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","last_name":"Bierbaum","full_name":"Bierbaum, Veronika"},{"orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"full_name":"Frank, Tino","last_name":"Frank","first_name":"Tino"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"},{"last_name":"Tay","first_name":"Savaş","full_name":"Tay, Savaş"},{"full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8599-1226","last_name":"Mehling","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Mehling, Matthias"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients","file":[{"date_updated":"2018-12-12T10:09:32Z","date_created":"2018-12-12T10:09:32Z","file_name":"IST-2017-744-v1+1_srep36440.pdf","access_level":"open_access","relation":"main_file","file_size":2353456,"creator":"system","file_id":"4756","content_type":"application/pdf"}],"publist_id":"6204","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"ToBo"}],"language":[{"iso":"eng"}],"pubrep_id":"744","citation":{"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>.","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.","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.","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).","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>","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>.","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>"},"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"}],"scopus_import":1,"type":"journal_article","file_date_updated":"2018-12-12T10:09:32Z","_id":"1154","quality_controlled":"1","project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281556"},{"call_identifier":"FWF","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","date_published":"2016-11-07T00:00:00Z","month":"11","intvolume":"         6","article_number":"36440","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","date_updated":"2021-01-12T06:48:41Z","oa":1,"year":"2016","volume":6,"ddc":["579"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:50:27Z","day":"07","status":"public","publication":"Scientific Reports","doi":"10.1038/srep36440","oa_version":"Published Version","ec_funded":1},{"citation":{"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>","short":"J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.","ieee":"J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population,” <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.","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>.","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>","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>."},"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"}],"scopus_import":1,"type":"journal_article","_id":"1157","quality_controlled":"1","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7"}],"publication_status":"published","publisher":"Institute of Mathematical Statistics","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ji","last_name":"Lee","full_name":"Lee, Ji"},{"full_name":"Schnelli, Kevin","first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","orcid":"0000-0003-0954-3231"}],"title":"Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population","publist_id":"6201","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"volume":26,"date_created":"2018-12-11T11:50:27Z","status":"public","day":"15","publication":"Annals of Applied Probability","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1409.4979"}],"doi":"10.1214/16-AAP1193","oa_version":"Preprint","ec_funded":1,"date_published":"2016-12-15T00:00:00Z","intvolume":"        26","month":"12","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.","date_updated":"2021-01-12T06:48:43Z","oa":1,"issue":"6","page":"3786 - 3839","year":"2016"},{"title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"full_name":"Anciaux, Youann","last_name":"Anciaux","first_name":"Youann"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","date_updated":"2020-07-14T12:44:36Z","date_created":"2018-12-12T10:15:42Z","file_id":"5164","content_type":"application/pdf","creator":"system","file_size":2494348,"relation":"main_file","checksum":"2bab63b068a9840efd532b9ae583f9bb","access_level":"open_access"}],"publisher":"Public Library of Science","has_accepted_license":"1","pubrep_id":"742","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publist_id":"6200","quality_controlled":"1","_id":"1158","abstract":[{"lang":"eng","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."}],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:36Z","type":"journal_article","citation":{"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>.","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>","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>.","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.","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.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016)."},"publication_status":"published","oa":1,"issue":"12","date_updated":"2023-02-23T14:11:16Z","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.","article_number":"e2000234","date_published":"2016-12-27T00:00:00Z","intvolume":"        14","month":"12","year":"2016","status":"public","day":"27","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576"],"date_created":"2018-12-11T11:50:28Z","volume":14,"oa_version":"Published Version","related_material":{"record":[{"id":"9862","relation":"research_data","status":"public"},{"id":"9863","status":"public","relation":"research_data"}]},"publication":"PLoS Biology","doi":"10.1371/journal.pbio.2000234"},{"year":"2016","page":"468 - 481","external_id":{"arxiv":["1608.08662"]},"conference":{"location":"Athens, Greece","name":"GD: Graph Drawing and Network Visualization","start_date":"2016-09-19","end_date":"2016-09-21"},"date_updated":"2023-02-23T10:05:57Z","oa":1,"alternative_title":["LNCS"],"date_published":"2016-12-08T00:00:00Z","intvolume":"      9801","month":"12","related_material":{"record":[{"id":"1113","relation":"later_version","status":"public"},{"relation":"earlier_version","status":"public","id":"1595"}]},"oa_version":"Preprint","ec_funded":1,"doi":"10.1007/978-3-319-50106-2_36","main_file_link":[{"url":"https://arxiv.org/abs/1608.08662","open_access":"1"}],"date_created":"2018-12-11T11:50:29Z","status":"public","day":"08","volume":9801,"language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"UlWa"}],"publist_id":"6193","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"full_name":"Pelsmajer, Michael","last_name":"Pelsmajer","first_name":"Michael"},{"first_name":"Marcus","last_name":"Schaefer","full_name":"Schaefer, Marcus"}],"title":"Hanani-Tutte for radial planarity II","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"publication_status":"published","_id":"1164","quality_controlled":"1","citation":{"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>.","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.","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>","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>"},"scopus_import":1,"arxiv":1,"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."}],"type":"conference"},{"volume":"9801 ","status":"public","day":"08","date_created":"2018-12-11T11:50:30Z","doi":"10.1007/978-3-319-50106-2_8","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.01346"}],"oa_version":"Preprint","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"later_version","id":"794"}]},"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.","month":"12","alternative_title":["LNCS"],"date_published":"2016-12-08T00:00:00Z","oa":1,"date_updated":"2023-09-27T12:14:48Z","conference":{"location":"Athens, Greece","name":"GD: Graph Drawing and Network Visualization","end_date":"2016-09-21","start_date":"2016-09-19"},"page":"94 - 106","year":"2016","type":"conference","scopus_import":1,"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."}],"citation":{"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.","short":"R. Fulek, in:, Springer, 2016, pp. 94–106.","ista":"Fulek R. 2016. C-planarity of embedded cyclic c-graphs. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 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>","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>.","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>","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>."},"quality_controlled":"1","_id":"1165","publication_status":"published","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publisher":"Springer","author":[{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","last_name":"Fulek","orcid":"0000-0001-8485-1774"}],"title":"C-planarity of embedded cyclic c-graphs","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"UlWa"}],"publist_id":"6192","language":[{"iso":"eng"}]},{"status":"public","day":"02","quality_controlled":"1","date_created":"2018-12-11T11:50:30Z","_id":"1166","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"}],"type":"conference","volume":2016,"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.","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.","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."},"ec_funded":1,"oa_version":"None","related_material":{"link":[{"relation":"table_of_contents","url":"https://dl.acm.org/citation.cfm?id=3016355"}],"record":[{"relation":"earlier_version","status":"public","id":"5443"}]},"publication":"Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence","publication_status":"published","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"title":"A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"last_name":"Davies","first_name":"Jessica","id":"378E0060-F248-11E8-B48F-1D18A9856A87","full_name":"Davies, Jessica"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T12:26:41Z","publisher":"AAAI Press","date_published":"2016-12-02T00:00:00Z","month":"12","intvolume":"      2016","year":"2016","language":[{"iso":"eng"}],"conference":{"location":"Phoenix, AZ, USA","start_date":"2016-02-12","end_date":"2016-02-17","name":"AAAI: Conference on Artificial Intelligence"},"publist_id":"6191","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"page":"3225 - 3232"},{"year":"2016","article_number":"e1005218","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.","month":"12","intvolume":"        12","date_published":"2016-12-09T00:00:00Z","issue":"12","oa":1,"date_updated":"2023-02-23T14:11:22Z","doi":"10.1371/journal.pcbi.1005218","publication":"PLoS Computational Biology","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"9866"}]},"volume":12,"day":"09","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2018-12-11T11:50:30Z","department":[{"_id":"AnKi"}],"publist_id":"6190","article_processing_charge":"No","pubrep_id":"740","language":[{"iso":"eng"}],"publisher":"Public Library of Science","has_accepted_license":"1","file":[{"file_name":"IST-2017-740-v1+1_journal.pcbi.1005218.pdf","date_created":"2018-12-12T10:12:08Z","date_updated":"2020-07-14T12:44:37Z","file_id":"4926","content_type":"application/pdf","creator":"system","file_size":3822299,"access_level":"open_access","relation":"main_file","checksum":"84f44ae92866c52ff1ca8a574558dca7"}],"title":"Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","last_name":"Zagórski","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Burda, Zdzisław","last_name":"Burda","first_name":"Zdzisław"},{"full_name":"Wacław, Bartłomiej","first_name":"Bartłomiej","last_name":"Wacław"}],"publication_status":"published","file_date_updated":"2020-07-14T12:44:37Z","type":"journal_article","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."}],"scopus_import":"1","citation":{"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>.","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.","short":"M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (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.","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>","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>"},"quality_controlled":"1","_id":"1167"},{"year":"2016","page":"B988 - B1008","date_updated":"2021-01-12T06:48:49Z","issue":"6","date_published":"2016-11-15T00:00:00Z","month":"11","intvolume":"        38","oa_version":"Submitted Version","publication":"SIAM Journal on Scientific Computing","doi":"10.1137/15M103306X","date_created":"2018-12-11T11:50:31Z","ddc":["003","518","570","621"],"day":"15","status":"public","volume":38,"language":[{"iso":"eng"}],"pubrep_id":"811","publist_id":"6186","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Modular parameter identification of biomolecular networks","author":[{"full_name":"Lang, Moritz","last_name":"Lang","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jörg","last_name":"Stelling","full_name":"Stelling, Jörg"}],"file":[{"file_name":"IST-2017-811-v1+1_modular_parameter_identification.pdf","date_created":"2018-12-12T10:14:41Z","date_updated":"2020-07-14T12:44:37Z","content_type":"application/pdf","file_id":"5095","creator":"system","file_size":871964,"relation":"main_file","access_level":"local","checksum":"781bc3ffd30b2dd65b7727c5a285fc78"}],"has_accepted_license":"1","publisher":"Society for Industrial and Applied Mathematics ","publication_status":"published","_id":"1170","quality_controlled":"1","citation":{"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>","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>.","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.","ista":"Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.","short":"M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.","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>."},"scopus_import":1,"abstract":[{"lang":"eng","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."}],"file_date_updated":"2020-07-14T12:44:37Z","type":"journal_article"},{"year":"2016","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"publist_id":"6185","page":"166 - 167","author":[{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"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.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:48:50Z","publisher":"Elsevier","month":"07","intvolume":"        17","date_published":"2016-07-01T00:00:00Z","oa_version":"None","publication_status":"published","doi":"10.1016/j.plrev.2016.06.005","publication":"Physics of Life Reviews","status":"public","quality_controlled":"1","day":"01","_id":"1171","date_created":"2018-12-11T11:50:32Z","type":"journal_article","scopus_import":1,"citation":{"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>","short":"G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.","ieee":"G. Tkačik, “Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#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.","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.","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>.","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>."},"volume":17}]