[{"scopus_import":1,"date_created":"2018-12-11T11:50:28Z","date_published":"2016-12-27T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6200","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","intvolume":" 14","publisher":"Public Library of Science","year":"2016","oa":1,"article_number":"e2000234","related_material":{"record":[{"id":"9862","status":"public","relation":"research_data"},{"id":"9863","status":"public","relation":"research_data"}]},"date_updated":"2023-02-23T14:11:16Z","publication":"PLoS Biology","oa_version":"Published Version","month":"12","file_date_updated":"2020-07-14T12:44:36Z","ddc":["576"],"day":"27","citation":{"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,” PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.","apa":"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. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.","mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234."},"pubrep_id":"742","volume":14,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"5164","date_created":"2018-12-12T10:15:42Z","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","relation":"main_file","creator":"system","file_size":2494348,"date_updated":"2020-07-14T12:44:36Z","access_level":"open_access","checksum":"2bab63b068a9840efd532b9ae583f9bb","content_type":"application/pdf"}],"doi":"10.1371/journal.pbio.2000234","issue":"12","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 "grey zone" 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."}],"_id":"1158","author":[{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"last_name":"Fraisse","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"first_name":"Youann","last_name":"Anciaux","full_name":"Anciaux, Youann"},{"first_name":"Nicolas","full_name":"Galtier, Nicolas","last_name":"Galtier"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","status":"public","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.","publication_status":"published"},{"publist_id":"6193","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"UlWa"}],"date_created":"2018-12-11T11:50:29Z","scopus_import":1,"date_published":"2016-12-08T00:00:00Z","external_id":{"arxiv":["1608.08662"]},"publisher":"Springer","intvolume":" 9801","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.08662"}],"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"oa":1,"year":"2016","alternative_title":["LNCS"],"date_updated":"2023-02-23T10:05:57Z","page":"468 - 481","related_material":{"record":[{"status":"public","relation":"later_version","id":"1113"},{"relation":"earlier_version","status":"public","id":"1595"}]},"month":"12","citation":{"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.","apa":"Fulek, R., Pelsmajer, M., & 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. https://doi.org/10.1007/978-3-319-50106-2_36","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:10.1007/978-3-319-50106-2_36","short":"R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2016, pp. 468–481.","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity II,” 9801:468–81. Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_36.","mla":"Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity II. Vol. 9801, Springer, 2016, pp. 468–81, doi:10.1007/978-3-319-50106-2_36."},"day":"08","oa_version":"Preprint","conference":{"start_date":"2016-09-19","location":"Athens, Greece","end_date":"2016-09-21","name":"GD: Graph Drawing and Network Visualization"},"arxiv":1,"article_processing_charge":"No","volume":9801,"_id":"1164","title":"Hanani-Tutte for radial planarity II","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"first_name":"Michael","full_name":"Pelsmajer, Michael","last_name":"Pelsmajer"},{"last_name":"Schaefer","full_name":"Schaefer, Marcus","first_name":"Marcus"}],"doi":"10.1007/978-3-319-50106-2_36","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."}],"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"status":"public","publication_status":"published"},{"conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2016-09-21","start_date":"2016-09-19","location":"Athens, Greece"},"oa_version":"Preprint","month":"12","day":"08","citation":{"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. https://doi.org/10.1007/978-3-319-50106-2_8","ieee":"R. Fulek, “C-planarity of embedded cyclic c-graphs,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp. 94–106.","ama":"Fulek R. C-planarity of embedded cyclic c-graphs. In: Vol 9801. Springer; 2016:94-106. doi:10.1007/978-3-319-50106-2_8","ista":"Fulek R. 2016. C-planarity of embedded cyclic c-graphs. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 94–106.","short":"R. Fulek, in:, Springer, 2016, pp. 94–106.","chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs,” 9801:94–106. Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_8.","mla":"Fulek, Radoslav. C-Planarity of Embedded Cyclic c-Graphs. Vol. 9801, Springer, 2016, pp. 94–106, doi:10.1007/978-3-319-50106-2_8."},"volume":"9801 ","doi":"10.1007/978-3-319-50106-2_8","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."}],"_id":"1165","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","full_name":"Fulek, Radoslav","last_name":"Fulek","orcid":"0000-0001-8485-1774"}],"title":"C-planarity of embedded cyclic c-graphs","ec_funded":1,"status":"public","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.","publication_status":"published","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"scopus_import":1,"date_created":"2018-12-11T11:50:30Z","date_published":"2016-12-08T00:00:00Z","publist_id":"6192","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"UlWa"}],"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1602.01346","open_access":"1"}],"publisher":"Springer","alternative_title":["LNCS"],"year":"2016","oa":1,"page":"94 - 106","related_material":{"record":[{"relation":"later_version","status":"public","id":"794"}]},"date_updated":"2023-09-27T12:14:48Z"},{"_id":"1166","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"full_name":"Davies, Jessica","last_name":"Davies","id":"378E0060-F248-11E8-B48F-1D18A9856A87","first_name":"Jessica"}],"title":"A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps","year":"2016","abstract":[{"text":"POMDPs are standard models for probabilistic planning problems, where an agent interacts with an uncertain environment. We study the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a policy to ensure that the target set is reached with probability 1 (almost-surely). While in general the problem is EXPTIMEcomplete, in many practical cases policies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. In this work, we first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach. © 2016, Association for the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved.","lang":"eng"}],"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"date_updated":"2023-02-23T12:26:41Z","publication":"Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence","ec_funded":1,"page":"3225 - 3232","publication_status":"published","status":"public","related_material":{"link":[{"url":"https://dl.acm.org/citation.cfm?id=3016355","relation":"table_of_contents"}],"record":[{"status":"public","relation":"earlier_version","id":"5443"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6191","month":"12","day":"02","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"citation":{"ieee":"K. Chatterjee, M. Chmelik, and J. Davies, “A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps,” in Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, Phoenix, AZ, USA, 2016, vol. 2016, pp. 3225–3232.","apa":"Chatterjee, K., Chmelik, M., & Davies, J. (2016). A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps. In Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence (Vol. 2016, pp. 3225–3232). Phoenix, AZ, USA: AAAI Press.","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.","ama":"Chatterjee K, Chmelik M, Davies J. A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps. In: Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence. Vol 2016. AAAI Press; 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 Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, 2016:3225–32. AAAI Press, 2016.","mla":"Chatterjee, Krishnendu, et al. “A Symbolic SAT Based Algorithm for Almost Sure Reachability with Small Strategies in Pomdps.” Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, vol. 2016, AAAI Press, 2016, pp. 3225–32."},"conference":{"name":"AAAI: Conference on Artificial Intelligence","start_date":"2016-02-12","location":"Phoenix, AZ, USA","end_date":"2016-02-17"},"oa_version":"None","date_created":"2018-12-11T11:50:30Z","date_published":"2016-12-02T00:00:00Z","intvolume":" 2016","publisher":"AAAI Press","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"volume":2016},{"year":"2016","oa":1,"article_number":"e1005218","related_material":{"record":[{"status":"public","relation":"research_data","id":"9866"}]},"date_updated":"2023-02-23T14:11:22Z","publication":"PLoS Computational Biology","date_created":"2018-12-11T11:50:30Z","scopus_import":"1","date_published":"2016-12-09T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publist_id":"6190","department":[{"_id":"AnKi"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Public Library of Science","intvolume":" 12","doi":"10.1371/journal.pcbi.1005218","abstract":[{"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 > 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.","lang":"eng"}],"issue":"12","_id":"1167","title":"Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks","author":[{"orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P"},{"full_name":"Burda, Zdzisław","last_name":"Burda","first_name":"Zdzisław"},{"first_name":"Bartłomiej","last_name":"Wacław","full_name":"Wacław, Bartłomiej"}],"status":"public","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.","publication_status":"published","oa_version":"Published Version","month":"12","ddc":["570"],"file_date_updated":"2020-07-14T12:44:37Z","pubrep_id":"740","citation":{"short":"M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016).","ama":"Zagórski MP, Burda Z, Wacław B. Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. 2016;12(12). doi:10.1371/journal.pcbi.1005218","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.","apa":"Zagórski, M. P., Burda, Z., & Wacław, B. (2016). Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218","ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks,” PLoS Computational Biology, vol. 12, no. 12. Public Library of Science, 2016.","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “Beyond the Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.” PLoS Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005218.","mla":"Zagórski, Marcin P., et al. “Beyond the Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.” PLoS Computational Biology, vol. 12, no. 12, e1005218, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218."},"day":"09","article_processing_charge":"No","volume":12,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2018-12-12T10:12:08Z","file_id":"4926","content_type":"application/pdf","checksum":"84f44ae92866c52ff1ca8a574558dca7","access_level":"open_access","date_updated":"2020-07-14T12:44:37Z","file_size":3822299,"relation":"main_file","creator":"system","file_name":"IST-2017-740-v1+1_journal.pcbi.1005218.pdf"}]},{"file":[{"date_created":"2018-12-12T10:14:41Z","file_id":"5095","checksum":"781bc3ffd30b2dd65b7727c5a285fc78","content_type":"application/pdf","access_level":"local","date_updated":"2020-07-14T12:44:37Z","relation":"main_file","creator":"system","file_size":871964,"file_name":"IST-2017-811-v1+1_modular_parameter_identification.pdf"}],"volume":38,"has_accepted_license":"1","month":"11","file_date_updated":"2020-07-14T12:44:37Z","ddc":["003","518","570","621"],"citation":{"chicago":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics , 2016. https://doi.org/10.1137/15M103306X.","mla":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing, vol. 38, no. 6, Society for Industrial and Applied Mathematics , 2016, pp. B988–1008, doi:10.1137/15M103306X.","ista":"Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.","ama":"Lang M, Stelling J. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 2016;38(6):B988-B1008. doi:10.1137/15M103306X","short":"M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.","ieee":"M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” SIAM Journal on Scientific Computing, vol. 38, no. 6. Society for Industrial and Applied Mathematics , pp. B988–B1008, 2016.","apa":"Lang, M., & Stelling, J. (2016). Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/15M103306X"},"pubrep_id":"811","day":"15","oa_version":"Submitted Version","publication_status":"published","status":"public","_id":"1170","title":"Modular parameter identification of biomolecular networks","author":[{"last_name":"Lang","full_name":"Lang, Moritz","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stelling","full_name":"Stelling, Jörg","first_name":"Jörg"}],"doi":"10.1137/15M103306X","abstract":[{"text":"The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identification of model parameters. While modularization of the corresponding optimization problems could help reduce the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into subnetworks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we present here a modular parameter identification approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This definition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of different modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set---but not during earlier iterations---the intermodule communication as well as the individual modules\\' state dynamics agree with the dynamics of the nonmodularized network. Our modular parameter identification approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to suboptimal local minima. We demonstrate the algorithm\\'s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway.","lang":"eng"}],"issue":"6","publisher":"Society for Industrial and Applied Mathematics ","intvolume":" 38","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publist_id":"6186","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_created":"2018-12-11T11:50:31Z","scopus_import":1,"date_published":"2016-11-15T00:00:00Z","date_updated":"2021-01-12T06:48:49Z","publication":"SIAM Journal on Scientific Computing","page":"B988 - B1008","year":"2016"},{"date_published":"2016-07-01T00:00:00Z","date_created":"2018-12-11T11:50:32Z","oa_version":"None","scopus_import":1,"citation":{"ama":"Tkačik G. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al. Physics of Life Reviews. 2016;17:166-167. doi:10.1016/j.plrev.2016.06.005","short":"G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.","ista":"Tkačik G. 2016. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al. Physics of Life Reviews. 17, 166–167.","ieee":"G. Tkačik, “Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.,” Physics of Life Reviews, vol. 17. Elsevier, pp. 166–167, 2016.","apa":"Tkačik, G. (2016). Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.005","mla":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function" by O. C. Martin et Al.” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 166–67, doi:10.1016/j.plrev.2016.06.005.","chicago":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function" by O. C. Martin et Al.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.005."},"day":"01","department":[{"_id":"GaTk"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6185","month":"07","volume":17,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Elsevier","intvolume":" 17","year":"2016","doi":"10.1016/j.plrev.2016.06.005","title":"Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.","author":[{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"_id":"1171","publication_status":"published","status":"public","page":"166 - 167","publication":"Physics of Life Reviews","date_updated":"2021-01-12T06:48:50Z"},{"publication_status":"published","status":"public","acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","author":[{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mustansir","last_name":"Barma","full_name":"Barma, Mustansir"},{"first_name":"Madan","last_name":"Rao","full_name":"Rao, Madan"}],"_id":"1172","abstract":[{"text":"A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.","lang":"eng"}],"doi":"10.1038/srep38840","file":[{"file_id":"4977","date_created":"2018-12-12T10:12:56Z","date_updated":"2020-07-14T12:44:37Z","access_level":"open_access","content_type":"application/pdf","checksum":"cb378732da885ea4959ec5b845fb6e52","file_name":"IST-2017-737-v1+1_srep38840.pdf","creator":"system","file_size":760967,"relation":"main_file"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","volume":6,"citation":{"apa":"Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38840","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 2016;6. doi:10.1038/srep38840","mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6, 38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840."},"pubrep_id":"737","day":"19","ddc":["576"],"file_date_updated":"2020-07-14T12:44:37Z","month":"12","oa_version":"Published Version","publication":"Scientific Reports","date_updated":"2021-01-12T06:48:50Z","article_number":"38840","oa":1,"year":"2016","publisher":"Nature Publishing Group","intvolume":" 6","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","department":[{"_id":"NiBa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6183","date_published":"2016-12-19T00:00:00Z","date_created":"2018-12-11T11:50:32Z","scopus_import":1},{"doi":"10.1007/s00453-015-9997-6","issue":"4","year":"2016","abstract":[{"lang":"eng","text":"Boldyreva, Palacio and Warinschi introduced a multiple forking game as an extension of general forking. The notion of (multiple) forking is a useful abstraction from the actual simulation of cryptographic scheme to the adversary in a security reduction, and is achieved through the intermediary of a so-called wrapper algorithm. Multiple forking has turned out to be a useful tool in the security argument of several cryptographic protocols. However, a reduction employing multiple forking incurs a significant degradation of (Formula presented.) , where (Formula presented.) denotes the upper bound on the underlying random oracle calls and (Formula presented.) , the number of forkings. In this work we take a closer look at the reasons for the degradation with a tighter security bound in mind. We nail down the exact set of conditions for success in the multiple forking game. A careful analysis of the cryptographic schemes and corresponding security reduction employing multiple forking leads to the formulation of ‘dependence’ and ‘independence’ conditions pertaining to the output of the wrapper in different rounds. Based on the (in)dependence conditions we propose a general framework of multiple forking and a General Multiple Forking Lemma. Leveraging (in)dependence to the full allows us to improve the degradation factor in the multiple forking game by a factor of (Formula presented.). By implication, the cost of a single forking involving two random oracles (augmented forking) matches that involving a single random oracle (elementary forking). Finally, we study the effect of these observations on the concrete security of existing schemes employing multiple forking. We conclude that by careful design of the protocol (and the wrapper in the security reduction) it is possible to harness our observations to the full extent."}],"_id":"1177","author":[{"last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Sanjit","last_name":"Chatterjee","first_name":"Sanjit"}],"oa":1,"title":"A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound","page":"1321 - 1362","acknowledgement":"We are grateful to the anonymous reviewers for their insightful comments. The\r\ndetailed reports helped us a lot to address the technical mistakes as well as to improve the overall presentation of the paper.","status":"public","publication_status":"published","date_updated":"2021-01-12T06:48:52Z","publication":"Algorithmica","date_created":"2018-12-11T11:50:33Z","oa_version":"Submitted Version","date_published":"2016-04-01T00:00:00Z","publist_id":"6177","month":"04","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","department":[{"_id":"KrPi"}],"citation":{"ama":"Kamath Hosdurg C, Chatterjee S. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. 2016;74(4):1321-1362. doi:10.1007/s00453-015-9997-6","short":"C. Kamath Hosdurg, S. Chatterjee, Algorithmica 74 (2016) 1321–1362.","ista":"Kamath Hosdurg C, Chatterjee S. 2016. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. 74(4), 1321–1362.","ieee":"C. Kamath Hosdurg and S. Chatterjee, “A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound,” Algorithmica, vol. 74, no. 4. Springer, pp. 1321–1362, 2016.","apa":"Kamath Hosdurg, C., & Chatterjee, S. (2016). A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. Springer. https://doi.org/10.1007/s00453-015-9997-6","mla":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” Algorithmica, vol. 74, no. 4, Springer, 2016, pp. 1321–62, doi:10.1007/s00453-015-9997-6.","chicago":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” Algorithmica. Springer, 2016. https://doi.org/10.1007/s00453-015-9997-6."},"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","volume":74,"intvolume":" 74","main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2013/651"}],"publisher":"Springer"},{"publisher":"Springer","intvolume":" 9985","main_file_link":[{"url":"https://eprint.iacr.org/2016/159","open_access":"1"}],"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6175","department":[{"_id":"KrPi"}],"date_created":"2018-12-11T11:50:34Z","scopus_import":1,"date_published":"2016-10-22T00:00:00Z","date_updated":"2021-01-12T06:48:53Z","page":"183 - 203","oa":1,"alternative_title":["LNCS"],"year":"2016","volume":9985,"month":"10","citation":{"ieee":"K. Z. Pietrzak and S. Maciej, “Pseudoentropy: Lower-bounds for chain rules and transformations,” presented at the TCC: Theory of Cryptography Conference, Beijing, China, 2016, vol. 9985, pp. 183–203.","apa":"Pietrzak, K. Z., & Maciej, S. (2016). Pseudoentropy: Lower-bounds for chain rules and transformations (Vol. 9985, pp. 183–203). Presented at the TCC: Theory of Cryptography Conference, Beijing, China: Springer. https://doi.org/10.1007/978-3-662-53641-4_8","short":"K.Z. Pietrzak, S. Maciej, in:, Springer, 2016, pp. 183–203.","ama":"Pietrzak KZ, Maciej S. Pseudoentropy: Lower-bounds for chain rules and transformations. In: Vol 9985. Springer; 2016:183-203. doi:10.1007/978-3-662-53641-4_8","ista":"Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985, 183–203.","chicago":"Pietrzak, Krzysztof Z, and Skorski Maciej. “Pseudoentropy: Lower-Bounds for Chain Rules and Transformations,” 9985:183–203. Springer, 2016. https://doi.org/10.1007/978-3-662-53641-4_8.","mla":"Pietrzak, Krzysztof Z., and Skorski Maciej. Pseudoentropy: Lower-Bounds for Chain Rules and Transformations. Vol. 9985, Springer, 2016, pp. 183–203, doi:10.1007/978-3-662-53641-4_8."},"day":"22","oa_version":"Preprint","conference":{"name":"TCC: Theory of Cryptography Conference","end_date":"2016-11-03","location":"Beijing, China","start_date":"2016-10-31"},"project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"K. Pietrzak—Supported by the European Research Council consolidator grant (682815-TOCNeT).\r\nM. Skórski—Supported by the National Science Center, Poland (2015/17/N/ST6/03564).","_id":"1179","title":"Pseudoentropy: Lower-bounds for chain rules and transformations","author":[{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"full_name":"Maciej, Skorski","last_name":"Maciej","first_name":"Skorski"}],"doi":"10.1007/978-3-662-53641-4_8","abstract":[{"lang":"eng","text":"Computational notions of entropy have recently found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The two main types of results which make computational notions so useful are (1) Chain rules, which quantify by how much the computational entropy of a variable decreases if conditioned on some other variable (2) Transformations, which quantify to which extend one type of entropy implies another.\r\n\r\nSuch chain rules and transformations typically lose a significant amount in quality of the entropy, and are the reason why applying these results one gets rather weak quantitative security bounds. In this paper we for the first time prove lower bounds in this context, showing that existing results for transformations are, unfortunately, basically optimal for non-adaptive black-box reductions (and it’s hard to imagine how non black-box reductions or adaptivity could be useful here.)\r\n\r\nA variable X has k bits of HILL entropy of quality (ϵ,s)\r\nif there exists a variable Y with k bits min-entropy which cannot be distinguished from X with advantage ϵ\r\n\r\nby distinguishing circuits of size s. A weaker notion is Metric entropy, where we switch quantifiers, and only require that for every distinguisher of size s, such a Y exists.\r\n\r\nWe first describe our result concerning transformations. By definition, HILL implies Metric without any loss in quality. Metric entropy often comes up in applications, but must be transformed to HILL for meaningful security guarantees. The best known result states that if a variable X has k bits of Metric entropy of quality (ϵ,s)\r\n, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2). We show that this loss of a factor Ω(ϵ−2)\r\n\r\nin circuit size is necessary. In fact, we show the stronger result that this loss is already necessary when transforming so called deterministic real valued Metric entropy to randomised boolean Metric (both these variants of Metric entropy are implied by HILL without loss in quality).\r\n\r\nThe chain rule for HILL entropy states that if X has k bits of HILL entropy of quality (ϵ,s)\r\n, then for any variable Z of length m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still leaves a gap of ϵ between the known bound and our lower bound."}]},{"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"MIT Press","intvolume":" 28","date_created":"2020-07-05T22:00:47Z","scopus_import":1,"date_published":"2016-09-01T00:00:00Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"page":"142-143","date_updated":"2021-01-12T08:16:53Z","publication":"Proceedings of the Artificial Life Conference 2016","year":"2016","oa":1,"article_processing_charge":"No","volume":28,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2020-07-06T12:59:09Z","file_id":"8096","date_updated":"2020-07-14T12:48:09Z","content_type":"application/pdf","checksum":"cff63e7a4b8ac466ba51a9c84153a940","access_level":"open_access","creator":"cziletti","file_size":678670,"relation":"main_file","file_name":"2016_ProcALIFE_Martius.pdf"}],"oa_version":"Published Version","conference":{"location":"Cancun, Mexico","start_date":"2016-07-04","end_date":"2016-07-08","name":"ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems"},"month":"09","file_date_updated":"2020-07-14T12:48:09Z","ddc":["610"],"citation":{"short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. Proceedings of the Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: Proceedings of the Artificial Life Conference 2016. Vol 28. MIT Press; 2016:142-143. doi:10.7551/978-0-262-33936-0-ch029","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in Proceedings of the Artificial Life Conference 2016, Cancun, Mexico, 2016, vol. 28, pp. 142–143.","apa":"Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In Proceedings of the Artificial Life Conference 2016 (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. https://doi.org/10.7551/978-0-262-33936-0-ch029","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In Proceedings of the Artificial Life Conference 2016, 28:142–43. MIT Press, 2016. https://doi.org/10.7551/978-0-262-33936-0-ch029.","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” Proceedings of the Artificial Life Conference 2016, vol. 28, MIT Press, 2016, pp. 142–43, doi:10.7551/978-0-262-33936-0-ch029."},"day":"01","ec_funded":1,"publication_status":"published","status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"publication_identifier":{"isbn":["9780262339360"]},"doi":"10.7551/978-0-262-33936-0-ch029","abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"_id":"8094","title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","author":[{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","full_name":"Martius, Georg S","last_name":"Martius"},{"first_name":"Rafael","full_name":"Hostettler, Rafael","last_name":"Hostettler"},{"first_name":"Alois","last_name":"Knoll","full_name":"Knoll, Alois"},{"full_name":"Der, Ralf","last_name":"Der","first_name":"Ralf"}]},{"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"content_type":"application/pdf","checksum":"284b72b12fbe15474833ed3d4549f86b","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","relation":"main_file","creator":"system","file_size":905348,"file_name":"IST-2016-469-v1+1_Kowalski_et_al-Hippocampus.pdf","date_created":"2018-12-12T10:13:47Z","file_id":"5033"}],"has_accepted_license":"1","volume":26,"article_processing_charge":"No","day":"01","citation":{"mla":"Kowalski, Janina, et al. “Intrinsic Membrane Properties Determine Hippocampal Differential Firing Pattern in Vivo in Anesthetized Rats.” Hippocampus, vol. 26, no. 5, Wiley, 2016, pp. 668–82, doi:10.1002/hipo.22550.","chicago":"Kowalski, Janina, Jian Gan, Peter M Jonas, and Alejandro Pernia-Andrade. “Intrinsic Membrane Properties Determine Hippocampal Differential Firing Pattern in Vivo in Anesthetized Rats.” Hippocampus. Wiley, 2016. https://doi.org/10.1002/hipo.22550.","ista":"Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. 2016. Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. Hippocampus. 26(5), 668–682.","ama":"Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. Hippocampus. 2016;26(5):668-682. doi:10.1002/hipo.22550","short":"J. Kowalski, J. Gan, P.M. Jonas, A. Pernia-Andrade, Hippocampus 26 (2016) 668–682.","ieee":"J. Kowalski, J. Gan, P. M. Jonas, and A. Pernia-Andrade, “Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats,” Hippocampus, vol. 26, no. 5. Wiley, pp. 668–682, 2016.","apa":"Kowalski, J., Gan, J., Jonas, P. M., & Pernia-Andrade, A. (2016). Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. Hippocampus. Wiley. https://doi.org/10.1002/hipo.22550"},"pubrep_id":"469","ddc":["570"],"file_date_updated":"2020-07-14T12:45:07Z","month":"05","oa_version":"Published Version","publication_identifier":{"eissn":["1098-1063"],"issn":["1050-9631"]},"status":"public","publication_status":"published","acknowledgement":"The authors thank Jose Guzman for critically reading prior versions of the manuscript. They also thank T. Asenov for\r\nengineering mechanical devices, A. Schlögl for efficient pro-gramming, F. Marr for technical assistance, and E. Kramberger for manuscript editing.","author":[{"first_name":"Janina","id":"3F3CA136-F248-11E8-B48F-1D18A9856A87","last_name":"Kowalski","full_name":"Kowalski, Janina"},{"full_name":"Gan, Jian","last_name":"Gan","id":"3614E438-F248-11E8-B48F-1D18A9856A87","first_name":"Jian"},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M"},{"id":"36963E98-F248-11E8-B48F-1D18A9856A87","first_name":"Alejandro","full_name":"Pernia-Andrade, Alejandro","last_name":"Pernia-Andrade"}],"title":"Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats","_id":"1616","issue":"5","abstract":[{"lang":"eng","text":"The hippocampus plays a key role in learning and memory. Previous studies suggested that the main types of principal neurons, dentate gyrus granule cells (GCs), CA3 pyramidal neurons, and CA1 pyramidal neurons, differ in their activity pattern, with sparse firing in GCs and more frequent firing in CA3 and CA1 pyramidal neurons. It has been assumed but never shown that such different activity may be caused by differential synaptic excitation. To test this hypothesis, we performed high-resolution whole-cell patch-clamp recordings in anesthetized rats in vivo. In contrast to previous in vitro data, both CA3 and CA1 pyramidal neurons fired action potentials spontaneously, with a frequency of ∼3–6 Hz, whereas GCs were silent. Furthermore, both CA3 and CA1 cells primarily fired in bursts. To determine the underlying mechanisms, we quantitatively assessed the frequency of spontaneous excitatory synaptic input, the passive membrane properties, and the active membrane characteristics. Surprisingly, GCs showed comparable synaptic excitation to CA3 and CA1 cells and the highest ratio of excitation versus hyperpolarizing inhibition. Thus, differential synaptic excitation is not responsible for differences in firing. Moreover, the three types of hippocampal neurons markedly differed in their passive properties. While GCs showed the most negative membrane potential, CA3 pyramidal neurons had the highest input resistance and the slowest membrane time constant. The three types of neurons also differed in the active membrane characteristics. GCs showed the highest action potential threshold, but displayed the largest gain of the input-output curves. In conclusion, our results reveal that differential firing of the three main types of hippocampal principal neurons in vivo is not primarily caused by differences in the characteristics of the synaptic input, but by the distinct properties of synaptic integration and input-output transformation."}],"doi":"10.1002/hipo.22550","intvolume":" 26","publisher":"Wiley","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5550","date_published":"2016-05-01T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:53:03Z","publication":"Hippocampus","date_updated":"2023-10-17T10:02:02Z","page":"668 - 682","oa":1,"year":"2016"},{"date_updated":"2021-01-12T06:52:02Z","publication":"Journal of Complexity","page":"199 - 216","acknowledgement":"We are grateful to the referee whose suggestions greatly improved the quality and clarity of the exposition.","publication_status":"published","status":"public","_id":"1617","author":[{"orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian","last_name":"Pausinger","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"full_name":"Steinerberger, Stefan","last_name":"Steinerberger","first_name":"Stefan"}],"title":"On the discrepancy of jittered sampling","oa":1,"doi":"10.1016/j.jco.2015.11.003","year":"2016","abstract":[{"text":"We study the discrepancy of jittered sampling sets: such a set P⊂ [0,1]d is generated for fixed m∈ℕ by partitioning [0,1]d into md axis aligned cubes of equal measure and placing a random point inside each of the N=md cubes. We prove that, for N sufficiently large, 1/10 d/N1/2+1/2d ≤EDN∗(P)≤ √d(log N) 1/2/N1/2+1/2d, where the upper bound with an unspecified constant Cd was proven earlier by Beck. Our proof makes crucial use of the sharp Dvoretzky-Kiefer-Wolfowitz inequality and a suitably taylored Bernstein inequality; we have reasons to believe that the upper bound has the sharp scaling in N. Additional heuristics suggest that jittered sampling should be able to improve known bounds on the inverse of the star-discrepancy in the regime N≳dd. We also prove a partition principle showing that every partition of [0,1]d combined with a jittered sampling construction gives rise to a set whose expected squared L2-discrepancy is smaller than that of purely random points.","lang":"eng"}],"intvolume":" 33","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.00251"}],"publisher":"Academic Press","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","volume":33,"publist_id":"5549","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"04","day":"01","department":[{"_id":"HeEd"}],"citation":{"mla":"Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered Sampling.” Journal of Complexity, vol. 33, Academic Press, 2016, pp. 199–216, doi:10.1016/j.jco.2015.11.003.","chicago":"Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered Sampling.” Journal of Complexity. Academic Press, 2016. https://doi.org/10.1016/j.jco.2015.11.003.","apa":"Pausinger, F., & Steinerberger, S. (2016). On the discrepancy of jittered sampling. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.11.003","ieee":"F. Pausinger and S. Steinerberger, “On the discrepancy of jittered sampling,” Journal of Complexity, vol. 33. Academic Press, pp. 199–216, 2016.","ama":"Pausinger F, Steinerberger S. On the discrepancy of jittered sampling. Journal of Complexity. 2016;33:199-216. doi:10.1016/j.jco.2015.11.003","short":"F. Pausinger, S. Steinerberger, Journal of Complexity 33 (2016) 199–216.","ista":"Pausinger F, Steinerberger S. 2016. On the discrepancy of jittered sampling. Journal of Complexity. 33, 199–216."},"scopus_import":1,"oa_version":"Submitted Version","date_created":"2018-12-11T11:53:03Z","date_published":"2016-04-01T00:00:00Z"},{"year":"2016","oa":1,"page":"189 - 216","date_updated":"2021-01-12T06:52:03Z","publication":"Communications in Mathematical Physics","date_created":"2018-12-11T11:53:04Z","scopus_import":1,"date_published":"2016-02-01T00:00:00Z","publist_id":"5546","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Springer","intvolume":" 342","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.2352"}],"doi":"10.1007/s00220-015-2526-2","abstract":[{"text":"We consider the Bardeen–Cooper–Schrieffer free energy functional for particles interacting via a two-body potential on a microscopic scale and in the presence of weak external fields varying on a macroscopic scale. We study the influence of the external fields on the critical temperature. We show that in the limit where the ratio between the microscopic and macroscopic scale tends to zero, the next to leading order of the critical temperature is determined by the lowest eigenvalue of the linearization of the Ginzburg–Landau equation.","lang":"eng"}],"issue":"1","_id":"1620","title":"The external field dependence of the BCS critical temperature","author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521"},{"full_name":"Solovej, Jan","last_name":"Solovej","first_name":"Jan"}],"acknowledgement":"The authors are grateful to I. M. Sigal for useful discussions. Financial support from the US National Science Foundation through Grants PHY-1347399 and DMS-1363432 (R.L.F.), from the Danish council for independent research and from ERC Advanced Grant 321029 (J.P.S.) is acknowledged.","publication_status":"published","status":"public","oa_version":"Submitted Version","month":"02","citation":{"mla":"Frank, Rupert, et al. “The External Field Dependence of the BCS Critical Temperature.” Communications in Mathematical Physics, vol. 342, no. 1, Springer, 2016, pp. 189–216, doi:10.1007/s00220-015-2526-2.","chicago":"Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “The External Field Dependence of the BCS Critical Temperature.” Communications in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-015-2526-2.","ista":"Frank R, Hainzl C, Seiringer R, Solovej J. 2016. The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. 342(1), 189–216.","ama":"Frank R, Hainzl C, Seiringer R, Solovej J. The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. 2016;342(1):189-216. doi:10.1007/s00220-015-2526-2","short":"R. Frank, C. Hainzl, R. Seiringer, J. Solovej, Communications in Mathematical Physics 342 (2016) 189–216.","ieee":"R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “The external field dependence of the BCS critical temperature,” Communications in Mathematical Physics, vol. 342, no. 1. Springer, pp. 189–216, 2016.","apa":"Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2016). The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2526-2"},"day":"01","volume":342},{"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Springer","intvolume":" 219","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.04570"}],"date_created":"2018-12-11T11:53:05Z","scopus_import":1,"date_published":"2016-03-01T00:00:00Z","publist_id":"5542","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"page":"1343 - 1382","date_updated":"2021-01-12T06:52:04Z","publication":"Archive for Rational Mechanics and Analysis","year":"2016","oa":1,"volume":219,"oa_version":"Submitted Version","month":"03","citation":{"mla":"Lundholm, Douglas, et al. “Fractional Hardy–Lieb–Thirring and Related Inequalities for Interacting Systems.” Archive for Rational Mechanics and Analysis, vol. 219, no. 3, Springer, 2016, pp. 1343–82, doi:10.1007/s00205-015-0923-5.","chicago":"Lundholm, Douglas, Phan Nam, and Fabian Portmann. “Fractional Hardy–Lieb–Thirring and Related Inequalities for Interacting Systems.” Archive for Rational Mechanics and Analysis. Springer, 2016. https://doi.org/10.1007/s00205-015-0923-5.","short":"D. Lundholm, P. Nam, F. Portmann, Archive for Rational Mechanics and Analysis 219 (2016) 1343–1382.","ama":"Lundholm D, Nam P, Portmann F. Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. 2016;219(3):1343-1382. doi:10.1007/s00205-015-0923-5","ista":"Lundholm D, Nam P, Portmann F. 2016. Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. 219(3), 1343–1382.","ieee":"D. Lundholm, P. Nam, and F. Portmann, “Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems,” Archive for Rational Mechanics and Analysis, vol. 219, no. 3. Springer, pp. 1343–1382, 2016.","apa":"Lundholm, D., Nam, P., & Portmann, F. (2016). Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-015-0923-5"},"day":"01","ec_funded":1,"acknowledgement":"We thank Jan Philip Solovej, Robert Seiringer and Vladimir Maz’ya for helpful discussions, as well as Rupert Frank\r\nand the anonymous referee for useful comments. Part of this work has been carried out during a visit at the Institut Mittag-Leffler (Stockholm). D.L. acknowledges financial support by the grant KAW 2010.0063 from the Knut and Alice Wallenberg Foundation and the Swedish Research Council grant no. 2013-4734. P.T.N. is supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. F.P. acknowledges support from the ERC project no. 321029 “The\r\nmathematics of the structure of matter”.","publication_status":"published","status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"doi":"10.1007/s00205-015-0923-5","abstract":[{"text":"We prove analogues of the Lieb–Thirring and Hardy–Lieb–Thirring inequalities for many-body quantum systems with fractional kinetic operators and homogeneous interaction potentials, where no anti-symmetry on the wave functions is assumed. These many-body inequalities imply interesting one-body interpolation inequalities, and we show that the corresponding one- and many-body inequalities are actually equivalent in certain cases.","lang":"eng"}],"issue":"3","_id":"1622","title":"Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems","author":[{"full_name":"Lundholm, Douglas","last_name":"Lundholm","first_name":"Douglas"},{"first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam","full_name":"Nam, Phan"},{"full_name":"Portmann, Fabian","last_name":"Portmann","first_name":"Fabian"}]},{"volume":108,"has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:45:07Z","content_type":"application/pdf","checksum":"6a65ba187994d4ad86c1c509e0ff482a","access_level":"open_access","relation":"main_file","creator":"system","file_size":1684043,"file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","date_created":"2018-12-12T10:11:12Z","file_id":"4865"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","month":"04","ddc":["576"],"file_date_updated":"2020-07-14T12:45:07Z","day":"01","pubrep_id":"465","citation":{"chicago":"Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology. Academic Press, 2016. https://doi.org/10.1016/j.tpb.2015.10.008.","mla":"Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology, vol. 108, Academic Press, 2016, pp. 1–12, doi:10.1016/j.tpb.2015.10.008.","short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12.","ama":"Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 2016;108:1-12. doi:10.1016/j.tpb.2015.10.008","ista":"Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 108, 1–12.","ieee":"J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree versus genetic ancestry in spatially distributed populations,” Theoretical Population Biology, vol. 108. Academic Press, pp. 1–12, 2016.","apa":"Kelleher, J., Etheridge, A., Véber, A., & Barton, N. H. (2016). Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2015.10.008"},"ec_funded":1,"publication_status":"published","status":"public","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"doi":"10.1016/j.tpb.2015.10.008","abstract":[{"text":"Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models.","lang":"eng"}],"_id":"1631","author":[{"first_name":"Jerome","last_name":"Kelleher","full_name":"Kelleher, Jerome"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","intvolume":" 108","publisher":"Academic Press","scopus_import":1,"date_created":"2018-12-11T11:53:08Z","date_published":"2016-04-01T00:00:00Z","publist_id":"5524","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"page":"1 - 12","date_updated":"2021-01-12T06:52:07Z","publication":"Theoretical Population Biology","year":"2016","oa":1},{"file":[{"date_created":"2018-12-12T10:08:34Z","file_id":"4695","checksum":"0dc6a300cde6536ceedd2bcdd2060efb","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:08Z","file_size":5637591,"creator":"system","relation":"main_file","file_name":"IST-2018-1001-v1+1_Zemova_JPlantGrowthRegul_2016_proofs.pdf"}],"has_accepted_license":"1","volume":35,"pubrep_id":"1001","citation":{"mla":"Zemová, Radka, et al. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation, vol. 35, no. 2, Springer, 2016, pp. 465–76, doi:10.1007/s00344-015-9553-2.","chicago":"Zemová, Radka, Marta Zwiewka, Agnieszka Bielach, Hélène Robert, and Jiří Friml. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation. Springer, 2016. https://doi.org/10.1007/s00344-015-9553-2.","apa":"Zemová, R., Zwiewka, M., Bielach, A., Robert, H., & Friml, J. (2016). A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. Springer. https://doi.org/10.1007/s00344-015-9553-2","ieee":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, and J. Friml, “A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana,” Journal of Plant Growth Regulation, vol. 35, no. 2. Springer, pp. 465–476, 2016.","ama":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 2016;35(2):465-476. doi:10.1007/s00344-015-9553-2","short":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, J. Friml, Journal of Plant Growth Regulation 35 (2016) 465–476.","ista":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. 2016. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 35(2), 465–476."},"day":"01","month":"06","ddc":["581"],"file_date_updated":"2020-07-14T12:45:08Z","oa_version":"Preprint","acknowledgement":"European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to JF. ","status":"public","publication_status":"published","title":"A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana","author":[{"full_name":"Zemová, Radka","last_name":"Zemová","first_name":"Radka"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"first_name":"Hélène","full_name":"Robert, Hélène","last_name":"Robert"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"_id":"1641","abstract":[{"text":"The plant hormone auxin (indole-3-acetic acid) is a major regulator of plant growth and development including embryo and root patterning, lateral organ formation and growth responses to environmental stimuli. Auxin is directionally transported from cell to cell by the action of specific auxin influx [AUXIN-RESISTANT1 (AUX1)] and efflux [PIN-FORMED (PIN)] transport regulators, whose polar, subcellular localizations are aligned with the direction of the auxin flow. Auxin itself regulates its own transport by modulation of the expression and subcellular localization of the auxin transporters. Increased auxin levels promote the transcription of PIN2 and AUX1 genes as well as stabilize PIN proteins at the plasma membrane, whereas prolonged auxin exposure increases the turnover of PIN proteins and their degradation in the vacuole. In this study, we applied a forward genetic approach, to identify molecular components playing a role in the auxin-mediated degradation. We generated EMS-mutagenized Arabidopsis PIN2::PIN2:GFP, AUX1::AUX1:YFP eir1aux1 populations and designed a screen for mutants with persistently strong fluorescent signals of the tagged PIN2 and AUX1 after prolonged treatment with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D). This approach yielded novel auxin degradation mutants defective in trafficking and degradation of PIN2 and AUX1 proteins and established a role for auxin-mediated degradation in plant development.","lang":"eng"}],"issue":"2","doi":"10.1007/s00344-015-9553-2","publisher":"Springer","intvolume":" 35","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"JiFr"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5512","date_published":"2016-06-01T00:00:00Z","date_created":"2018-12-11T11:53:12Z","scopus_import":1,"publication":"Journal of Plant Growth Regulation","date_updated":"2021-01-12T06:52:11Z","page":"465 - 476","oa":1,"year":"2016"},{"file":[{"creator":"system","file_size":580088,"relation":"main_file","file_name":"IST-2016-677-v1+1_869.pdf","date_updated":"2020-07-14T12:45:08Z","content_type":"application/pdf","checksum":"a57711cb660c5b17b42bb47275a00180","access_level":"open_access","date_created":"2018-12-12T10:12:05Z","file_id":"4923"}],"volume":9452,"has_accepted_license":"1","file_date_updated":"2020-07-14T12:45:08Z","ddc":["000"],"month":"01","citation":{"ista":"Okamoto T, Pietrzak KZ, Waters B, Wichs D. 2016. New realizations of somewhere statistically binding hashing and positional accumulators. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 9452, 121–145.","ama":"Okamoto T, Pietrzak KZ, Waters B, Wichs D. New realizations of somewhere statistically binding hashing and positional accumulators. In: Vol 9452. Springer; 2016:121-145. doi:10.1007/978-3-662-48797-6_6","short":"T. Okamoto, K.Z. Pietrzak, B. Waters, D. Wichs, in:, Springer, 2016, pp. 121–145.","apa":"Okamoto, T., Pietrzak, K. Z., Waters, B., & Wichs, D. (2016). New realizations of somewhere statistically binding hashing and positional accumulators (Vol. 9452, pp. 121–145). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand: Springer. https://doi.org/10.1007/978-3-662-48797-6_6","ieee":"T. Okamoto, K. Z. Pietrzak, B. Waters, and D. Wichs, “New realizations of somewhere statistically binding hashing and positional accumulators,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand, 2016, vol. 9452, pp. 121–145.","chicago":"Okamoto, Tatsuaki, Krzysztof Z Pietrzak, Brent Waters, and Daniel Wichs. “New Realizations of Somewhere Statistically Binding Hashing and Positional Accumulators,” 9452:121–45. Springer, 2016. https://doi.org/10.1007/978-3-662-48797-6_6.","mla":"Okamoto, Tatsuaki, et al. New Realizations of Somewhere Statistically Binding Hashing and Positional Accumulators. Vol. 9452, Springer, 2016, pp. 121–45, doi:10.1007/978-3-662-48797-6_6."},"pubrep_id":"677","day":"08","oa_version":"Submitted Version","conference":{"end_date":"2015-12-03","location":"Auckland, New Zealand","start_date":"2015-11-29","name":"ASIACRYPT: Theory and Application of Cryptology and Information Security"},"project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"ec_funded":1,"status":"public","publication_status":"published","_id":"1653","title":"New realizations of somewhere statistically binding hashing and positional accumulators","author":[{"first_name":"Tatsuaki","last_name":"Okamoto","full_name":"Okamoto, Tatsuaki"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"full_name":"Waters, Brent","last_name":"Waters","first_name":"Brent"},{"last_name":"Wichs","full_name":"Wichs, Daniel","first_name":"Daniel"}],"doi":"10.1007/978-3-662-48797-6_6","abstract":[{"lang":"eng","text":"A somewhere statistically binding (SSB) hash, introduced by Hubáček and Wichs (ITCS ’15), can be used to hash a long string x to a short digest y = H hk (x) using a public hashing-key hk. Furthermore, there is a way to set up the hash key hk to make it statistically binding on some arbitrary hidden position i, meaning that: (1) the digest y completely determines the i’th bit (or symbol) of x so that all pre-images of y have the same value in the i’th position, (2) it is computationally infeasible to distinguish the position i on which hk is statistically binding from any other position i’. Lastly, the hash should have a local opening property analogous to Merkle-Tree hashing, meaning that given x and y = H hk (x) it should be possible to create a short proof π that certifies the value of the i’th bit (or symbol) of x without having to provide the entire input x. A similar primitive called a positional accumulator, introduced by Koppula, Lewko and Waters (STOC ’15) further supports dynamic updates of the hashed value. These tools, which are interesting in their own right, also serve as one of the main technical components in several recent works building advanced applications from indistinguishability obfuscation (iO).\r\n\r\nThe prior constructions of SSB hashing and positional accumulators required fully homomorphic encryption (FHE) and iO respectively. In this work, we give new constructions of these tools based on well studied number-theoretic assumptions such as DDH, Phi-Hiding and DCR, as well as a general construction from lossy/injective functions."}],"publisher":"Springer","intvolume":" 9452","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","publist_id":"5497","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"date_created":"2018-12-11T11:53:16Z","scopus_import":1,"date_published":"2016-01-08T00:00:00Z","date_updated":"2021-01-12T06:52:16Z","page":"121 - 145","oa":1,"alternative_title":["LNCS"],"year":"2016"},{"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme.\r\nBoth authors thank Anne Marie Svane for her comments on an early version of this paper. The second author wishes to thank Eva B. Vedel Jensen and Markus Kiderlen from Aarhus University for enlightening discussions and their kind hospitality during a visit of their department in 2014.","project":[{"call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.aim.2015.10.004","abstract":[{"text":"We introduce a modification of the classic notion of intrinsic volume using persistence moments of height functions. Evaluating the modified first intrinsic volume on digital approximations of a compact body with smoothly embedded boundary in Rn, we prove convergence to the first intrinsic volume of the body as the resolution of the approximation improves. We have weaker results for the other modified intrinsic volumes, proving they converge to the corresponding intrinsic volumes of the n-dimensional unit ball.","lang":"eng"}],"_id":"1662","title":"Approximation and convergence of the intrinsic volume","author":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"orcid":"0000-0002-8379-3768","last_name":"Pausinger","full_name":"Pausinger, Florian","first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87"}],"volume":287,"has_accepted_license":"1","file":[{"file_id":"4928","date_created":"2018-12-12T10:12:10Z","file_name":"IST-2017-774-v1+1_2016-J-03-FirstIntVolume.pdf","file_size":248985,"relation":"main_file","creator":"system","access_level":"open_access","checksum":"f8869ec110c35c852ef6a37425374af7","content_type":"application/pdf","date_updated":"2020-07-14T12:45:10Z"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa_version":"Published Version","month":"01","ddc":["004"],"file_date_updated":"2020-07-14T12:45:10Z","citation":{"ieee":"H. Edelsbrunner and F. Pausinger, “Approximation and convergence of the intrinsic volume,” Advances in Mathematics, vol. 287. Academic Press, pp. 674–703, 2016.","apa":"Edelsbrunner, H., & Pausinger, F. (2016). Approximation and convergence of the intrinsic volume. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2015.10.004","ama":"Edelsbrunner H, Pausinger F. Approximation and convergence of the intrinsic volume. Advances in Mathematics. 2016;287:674-703. doi:10.1016/j.aim.2015.10.004","ista":"Edelsbrunner H, Pausinger F. 2016. Approximation and convergence of the intrinsic volume. Advances in Mathematics. 287, 674–703.","short":"H. Edelsbrunner, F. Pausinger, Advances in Mathematics 287 (2016) 674–703.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” Advances in Mathematics, vol. 287, Academic Press, 2016, pp. 674–703, doi:10.1016/j.aim.2015.10.004.","chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” Advances in Mathematics. Academic Press, 2016. https://doi.org/10.1016/j.aim.2015.10.004."},"pubrep_id":"774","day":"10","page":"674 - 703","related_material":{"record":[{"id":"1399","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-09-07T11:41:25Z","publication":"Advances in Mathematics","year":"2016","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"Academic Press","intvolume":" 287","date_created":"2018-12-11T11:53:20Z","scopus_import":1,"date_published":"2016-01-10T00:00:00Z","publist_id":"5488","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}]},{"year":"2016","oa":1,"page":"449 - 467","date_updated":"2021-01-12T06:52:38Z","publication":"International Journal on Software Tools for Technology Transfer","scopus_import":1,"date_created":"2018-12-11T11:53:34Z","date_published":"2016-08-01T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5431","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","intvolume":" 18","publisher":"Springer","doi":"10.1007/s10009-015-0393-y","issue":"4","abstract":[{"lang":"eng","text":"Hybrid systems represent an important and powerful formalism for modeling real-world applications such as embedded systems. A verification tool like SpaceEx is based on the exploration of a symbolic search space (the region space). As a verification tool, it is typically optimized towards proving the absence of errors. In some settings, e.g., when the verification tool is employed in a feedback-directed design cycle, one would like to have the option to call a version that is optimized towards finding an error trajectory in the region space. A recent approach in this direction is based on guided search. Guided search relies on a cost function that indicates which states are promising to be explored, and preferably explores more promising states first. In this paper, we propose an abstraction-based cost function based on coarse-grained space abstractions for guiding the reachability analysis. For this purpose, a suitable abstraction technique that exploits the flexible granularity of modern reachability analysis algorithms is introduced. The new cost function is an effective extension of pattern database approaches that have been successfully applied in other areas. The approach has been implemented in the SpaceEx model checker. The evaluation shows its practical potential."}],"_id":"1705","author":[{"full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","orcid":"0000-0002-0686-0365"},{"first_name":"Alexandre","full_name":"Donzé, Alexandre","last_name":"Donzé"},{"last_name":"Frehse","full_name":"Frehse, Goran","first_name":"Goran"},{"last_name":"Grosu","full_name":"Grosu, Radu","first_name":"Radu"},{"last_name":"Johnson","full_name":"Johnson, Taylor","first_name":"Taylor"},{"last_name":"Ladan","full_name":"Ladan, Hamed","first_name":"Hamed"},{"last_name":"Podelski","full_name":"Podelski, Andreas","first_name":"Andreas"},{"full_name":"Wehrle, Martin","last_name":"Wehrle","first_name":"Martin"}],"title":"Guided search for hybrid systems based on coarse-grained space abstractions","ec_funded":1,"status":"public","publication_status":"published","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:13Z","ddc":["000"],"month":"08","day":"01","pubrep_id":"457","citation":{"ieee":"S. Bogomolov et al., “Guided search for hybrid systems based on coarse-grained space abstractions,” International Journal on Software Tools for Technology Transfer, vol. 18, no. 4. Springer, pp. 449–467, 2016.","apa":"Bogomolov, S., Donzé, A., Frehse, G., Grosu, R., Johnson, T., Ladan, H., … Wehrle, M. (2016). Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. Springer. https://doi.org/10.1007/s10009-015-0393-y","ista":"Bogomolov S, Donzé A, Frehse G, Grosu R, Johnson T, Ladan H, Podelski A, Wehrle M. 2016. Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. 18(4), 449–467.","ama":"Bogomolov S, Donzé A, Frehse G, et al. Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. 2016;18(4):449-467. doi:10.1007/s10009-015-0393-y","short":"S. Bogomolov, A. Donzé, G. Frehse, R. Grosu, T. Johnson, H. Ladan, A. Podelski, M. Wehrle, International Journal on Software Tools for Technology Transfer 18 (2016) 449–467.","mla":"Bogomolov, Sergiy, et al. “Guided Search for Hybrid Systems Based on Coarse-Grained Space Abstractions.” International Journal on Software Tools for Technology Transfer, vol. 18, no. 4, Springer, 2016, pp. 449–67, doi:10.1007/s10009-015-0393-y.","chicago":"Bogomolov, Sergiy, Alexandre Donzé, Goran Frehse, Radu Grosu, Taylor Johnson, Hamed Ladan, Andreas Podelski, and Martin Wehrle. “Guided Search for Hybrid Systems Based on Coarse-Grained Space Abstractions.” International Journal on Software Tools for Technology Transfer. Springer, 2016. https://doi.org/10.1007/s10009-015-0393-y."},"volume":18,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file":[{"file_size":2296522,"creator":"system","relation":"main_file","file_name":"IST-2016-457-v1+1_s10009-015-0393-y.pdf","content_type":"application/pdf","checksum":"31561d7705599a9bd4ea816accc0752e","access_level":"open_access","date_updated":"2020-07-14T12:45:13Z","date_created":"2018-12-12T10:15:26Z","file_id":"5146"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}}]