[{"oa_version":"Preprint","fulldoi":"https://doi.org/10.1007/978-3-319-50106-2_8","isi":1,"ec_funded":1,"oa":1,"publist_id":"6192","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek"}],"date_updated":"2025-09-22T09:54:03Z","language":[{"iso":"eng"}],"conference":{"end_date":"2016-09-21","start_date":"2016-09-19","name":"GD: Graph Drawing and Network Visualization","location":"Athens, Greece"},"alternative_title":["LNCS"],"citation":{"chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs,” 9801:94–106. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_8\">https://doi.org/10.1007/978-3-319-50106-2_8</a>.","short":"R. Fulek, in:, Springer, 2016, pp. 94–106.","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>.","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.","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>","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>"},"doi":"10.1007/978-3-319-50106-2_8","arxiv":1,"scopus_import":"1","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.","year":"2016","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."}],"department":[{"_id":"UlWa"}],"volume":"9801 ","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.01346"}],"month":"12","quality_controlled":"1","status":"public","title":"C-planarity of embedded cyclic c-graphs","type":"conference","external_id":{"arxiv":["1602.01346"],"isi":["000405478500008"]},"_id":"1165","page":"94 - 106","day":"08","related_material":{"record":[{"id":"794","status":"public","relation":"later_version"}]},"publication_status":"published","publisher":"Springer","date_created":"2018-12-11T11:50:30Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2016-12-08T00:00:00Z"},{"external_id":{"arxiv":["1511.08456"]},"intvolume":"      2016","title":"A symbolic SAT based algorithm for almost sure reachability with small strategies in POMDPs","type":"conference","status":"public","quality_controlled":"1","month":"12","OA_type":"green","date_created":"2018-12-11T11:50:30Z","date_published":"2016-12-02T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"AAAI Press","day":"02","page":"3225 - 3232","related_material":{"link":[{"relation":"table_of_contents","url":"https://dl.acm.org/citation.cfm?id=3016355"}],"record":[{"status":"public","id":"5443","relation":"earlier_version"}]},"OA_place":"repository","publication":"Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence","_id":"1166","language":[{"iso":"eng"}],"conference":{"start_date":"2016-02-12","end_date":"2016-02-17","location":"Phoenix, AZ, United States","name":"AAAI: Conference on Artificial Intelligence"},"date_updated":"2025-06-25T11:52:14Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"first_name":"Jessica","last_name":"Davies","id":"378E0060-F248-11E8-B48F-1D18A9856A87","full_name":"Davies, Jessica"}],"oa":1,"publist_id":"6191","ec_funded":1,"fulldoi":"https://doi.org/10.1609/aaai.v30i1.10422","corr_author":"1","oa_version":"Preprint","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1511.08456"}],"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"volume":2016,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"arxiv":1,"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","abstract":[{"lang":"eng","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."}],"year":"2016","doi":"10.1609/aaai.v30i1.10422","citation":{"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, United States, 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.","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. doi:<a href=\"https://doi.org/10.1609/aaai.v30i1.10422\">10.1609/aaai.v30i1.10422</a>","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, United States: AAAI Press. <a href=\"https://doi.org/10.1609/aaai.v30i1.10422\">https://doi.org/10.1609/aaai.v30i1.10422</a>","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. <a href=\"https://doi.org/10.1609/aaai.v30i1.10422\">https://doi.org/10.1609/aaai.v30i1.10422</a>.","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, doi:<a href=\"https://doi.org/10.1609/aaai.v30i1.10422\">10.1609/aaai.v30i1.10422</a>.","short":"K. Chatterjee, M. Chmelik, J. Davies, in:, Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, AAAI Press, 2016, pp. 3225–3232."}},{"publist_id":"6190","oa":1,"language":[{"iso":"eng"}],"date_updated":"2025-09-22T09:53:16Z","author":[{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","first_name":"Marcin P","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P"},{"full_name":"Burda, Zdzisław","last_name":"Burda","first_name":"Zdzisław"},{"full_name":"Wacław, Bartłomiej","first_name":"Bartłomiej","last_name":"Wacław"}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.1371/journal.pcbi.1005218","file":[{"relation":"main_file","date_created":"2018-12-12T10:12:08Z","creator":"system","checksum":"84f44ae92866c52ff1ca8a574558dca7","access_level":"open_access","date_updated":"2020-07-14T12:44:37Z","file_size":3822299,"content_type":"application/pdf","file_id":"4926","file_name":"IST-2017-740-v1+1_journal.pcbi.1005218.pdf"}],"isi":1,"article_number":"e1005218","volume":12,"department":[{"_id":"AnKi"}],"issue":"12","article_processing_charge":"No","citation":{"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.","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>","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>","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.","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>.","short":"M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016).","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>."},"year":"2016","pubrep_id":"740","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."}],"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.","scopus_import":"1","doi":"10.1371/journal.pcbi.1005218","ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        12","has_accepted_license":"1","external_id":{"isi":["000392126000015"]},"license":"https://creativecommons.org/licenses/by/4.0/","month":"12","quality_controlled":"1","type":"journal_article","file_date_updated":"2020-07-14T12:44:37Z","title":"Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks","status":"public","publisher":"Public Library of Science","publication_status":"published","date_published":"2016-12-09T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:30Z","_id":"1167","publication":"PLoS Computational Biology","related_material":{"record":[{"status":"public","id":"9866","relation":"research_data"}]},"day":"09"},{"fulldoi":"https://doi.org/10.1016/j.plrev.2016.06.005","oa_version":"None","month":"07","quality_controlled":"1","status":"public","isi":1,"type":"journal_article","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.","intvolume":"        17","publist_id":"6185","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"date_updated":"2025-09-22T09:50:37Z","language":[{"iso":"eng"}],"external_id":{"isi":["000381544100033"]},"_id":"1171","publication":"Physics of Life Reviews","citation":{"apa":"Tkačik, G. (2016). Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. <i>Physics of Life Reviews</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">https://doi.org/10.1016/j.plrev.2016.06.005</a>","ista":"Tkačik G. 2016. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. Physics of Life Reviews. 17, 166–167.","ama":"Tkačik G. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. <i>Physics of Life Reviews</i>. 2016;17:166-167. doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">10.1016/j.plrev.2016.06.005</a>","ieee":"G. Tkačik, “Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al.,” <i>Physics of Life Reviews</i>, vol. 17. Elsevier, pp. 166–167, 2016.","short":"G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.","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>.","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>."},"page":"166 - 167","day":"01","doi":"10.1016/j.plrev.2016.06.005","year":"2016","scopus_import":"1","publisher":"Elsevier","publication_status":"published","department":[{"_id":"GaTk"}],"volume":17,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2016-07-01T00:00:00Z","date_created":"2018-12-11T11:50:32Z","article_processing_charge":"No"},{"volume":6,"department":[{"_id":"NiBa"}],"article_processing_charge":"No","citation":{"apa":"Sachdeva, H., Barma, M., &#38; Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>","ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>, vol. 6, 38840, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>.","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>."},"scopus_import":"1","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"}],"acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","pubrep_id":"737","year":"2016","ddc":["576"],"doi":"10.1038/srep38840","oa":1,"publist_id":"6183","language":[{"iso":"eng"}],"date_updated":"2025-09-22T09:49:53Z","author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani"},{"full_name":"Barma, Mustansir","first_name":"Mustansir","last_name":"Barma"},{"first_name":"Madan","last_name":"Rao","full_name":"Rao, Madan"}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.1038/srep38840","file":[{"content_type":"application/pdf","file_name":"IST-2017-737-v1+1_srep38840.pdf","file_id":"4977","file_size":760967,"checksum":"cb378732da885ea4959ec5b845fb6e52","access_level":"open_access","date_created":"2018-12-12T10:12:56Z","date_updated":"2020-07-14T12:44:37Z","creator":"system","relation":"main_file"}],"isi":1,"article_number":"38840","publication_status":"published","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:50:32Z","date_published":"2016-12-19T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Scientific Reports","_id":"1172","day":"19","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"         6","has_accepted_license":"1","external_id":{"isi":["000389885900001"]},"month":"12","quality_controlled":"1","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","file_date_updated":"2020-07-14T12:44:37Z","type":"journal_article","status":"public"},{"doi":"10.1007/s00453-015-9997-6","year":"2016","abstract":[{"text":"Boldyreva, Palacio and Warinschi introduced a multiple forking game as an extension of general forking. The notion of (multiple) forking is a useful abstraction from the actual simulation of cryptographic scheme to the adversary in a security reduction, and is achieved through the intermediary of a so-called wrapper algorithm. Multiple forking has turned out to be a useful tool in the security argument of several cryptographic protocols. However, a reduction employing multiple forking incurs a significant degradation of (Formula presented.) , where (Formula presented.) denotes the upper bound on the underlying random oracle calls and (Formula presented.) , the number of forkings. In this work we take a closer look at the reasons for the degradation with a tighter security bound in mind. We nail down the exact set of conditions for success in the multiple forking game. A careful analysis of the cryptographic schemes and corresponding security reduction employing multiple forking leads to the formulation of ‘dependence’ and ‘independence’ conditions pertaining to the output of the wrapper in different rounds. Based on the (in)dependence conditions we propose a general framework of multiple forking and a General Multiple Forking Lemma. Leveraging (in)dependence to the full allows us to improve the degradation factor in the multiple forking game by a factor of (Formula presented.). By implication, the cost of a single forking involving two random oracles (augmented forking) matches that involving a single random oracle (elementary forking). Finally, we study the effect of these observations on the concrete security of existing schemes employing multiple forking. We conclude that by careful design of the protocol (and the wrapper in the security reduction) it is possible to harness our observations to the full extent.","lang":"eng"}],"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.","cryptoeprintid":1,"citation":{"short":"C. Kamath Hosdurg, S. Chatterjee, Algorithmica 74 (2016) 1321–1362.","mla":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” <i>Algorithmica</i>, vol. 74, no. 4, Springer, 2016, pp. 1321–62, doi:<a href=\"https://doi.org/10.1007/s00453-015-9997-6\">10.1007/s00453-015-9997-6</a>.","chicago":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” <i>Algorithmica</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00453-015-9997-6\">https://doi.org/10.1007/s00453-015-9997-6</a>.","apa":"Kamath Hosdurg, C., &#38; Chatterjee, S. (2016). A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-015-9997-6\">https://doi.org/10.1007/s00453-015-9997-6</a>","ama":"Kamath Hosdurg C, Chatterjee S. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. <i>Algorithmica</i>. 2016;74(4):1321-1362. doi:<a href=\"https://doi.org/10.1007/s00453-015-9997-6\">10.1007/s00453-015-9997-6</a>","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,” <i>Algorithmica</i>, vol. 74, no. 4. Springer, pp. 1321–1362, 2016."},"main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2013/651"}],"article_processing_charge":"No","issue":"4","department":[{"_id":"KrPi"}],"volume":74,"isi":1,"fulldoi":"https://doi.org/10.1007/s00453-015-9997-6","oa_version":"Submitted Version","date_updated":"2026-06-22T14:07:33Z","author":[{"first_name":"Chethan","last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan","orcid":"0009-0006-6812-7317"},{"first_name":"Sanjit","last_name":"Chatterjee","full_name":"Chatterjee, Sanjit"}],"language":[{"iso":"eng"}],"publist_id":"6177","oa":1,"day":"01","page":"1321 - 1362","_id":"1177","publication":"Algorithmica","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2016-04-01T00:00:00Z","date_created":"2018-12-11T11:50:33Z","publisher":"Springer","publication_status":"published","status":"public","das_tickbox":"1","type":"journal_article","title":"A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound","month":"04","quality_controlled":"1","external_id":{"cryptoeprintid":["2013/651"],"isi":["000373640000005"]},"intvolume":"        74"},{"main_file_link":[{"url":"https://eprint.iacr.org/2016/159","open_access":"1"}],"article_processing_charge":"No","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"volume":9985,"department":[{"_id":"KrPi"}],"year":"2016","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).","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","doi":"10.1007/978-3-662-53641-4_8","citation":{"mla":"Pietrzak, Krzysztof Z., and Skorski Maciej. <i>Pseudoentropy: Lower-Bounds for Chain Rules and Transformations</i>. Vol. 9985, Springer, 2016, pp. 183–203, doi:<a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">10.1007/978-3-662-53641-4_8</a>.","short":"K.Z. Pietrzak, S. Maciej, in:, Springer, 2016, pp. 183–203.","chicago":"Pietrzak, Krzysztof Z, and Skorski Maciej. “Pseudoentropy: Lower-Bounds for Chain Rules and Transformations,” 9985:183–203. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">https://doi.org/10.1007/978-3-662-53641-4_8</a>.","ama":"Pietrzak KZ, Maciej S. Pseudoentropy: Lower-bounds for chain rules and transformations. In: Vol 9985. Springer; 2016:183-203. doi:<a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">10.1007/978-3-662-53641-4_8</a>","ista":"Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985, 183–203.","apa":"Pietrzak, K. Z., &#38; Maciej, S. (2016). Pseudoentropy: Lower-bounds for chain rules and transformations (Vol. 9985, pp. 183–203). Presented at the TCC: Theory of Cryptography Conference, Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">https://doi.org/10.1007/978-3-662-53641-4_8</a>","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."},"alternative_title":["LNCS"],"conference":{"end_date":"2016-11-03","start_date":"2016-10-31","name":"TCC: Theory of Cryptography Conference","location":"Beijing, China"},"language":[{"iso":"eng"}],"date_updated":"2025-09-22T09:48:49Z","author":[{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maciej, Skorski","first_name":"Skorski","last_name":"Maciej"}],"publist_id":"6175","oa":1,"ec_funded":1,"isi":1,"oa_version":"Preprint","fulldoi":"https://doi.org/10.1007/978-3-662-53641-4_8","date_published":"2016-10-22T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:34Z","publisher":"Springer","publication_status":"published","day":"22","page":"183 - 203","_id":"1179","external_id":{"isi":["000390176000008"]},"intvolume":"      9985","type":"conference","title":"Pseudoentropy: Lower-bounds for chain rules and transformations","status":"public","quality_controlled":"1","month":"10"},{"day":"09","page":"11394 - 11401","_id":"1181","publication":"Journal of Neuroscience","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2016-11-09T00:00:00Z","date_created":"2018-12-11T11:50:35Z","publisher":"Society for Neuroscience","publication_status":"published","type":"journal_article","title":"Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity","status":"public","month":"11","quality_controlled":"1","external_id":{"isi":["000391054300003"]},"intvolume":"        36","year":"2016","abstract":[{"lang":"eng","text":"This review accompanies a 2016 SFN mini-symposium presenting examples of current studies that address a central question: How do neural stem cells (NSCs) divide in different ways to produce heterogeneous daughter types at the right time and in proper numbers to build a cerebral cortex with the appropriate size and structure? We will focus on four aspects of corticogenesis: cytokinesis events that follow apical mitoses of NSCs; coordinating abscission with delamination from the apical membrane; timing of neurogenesis and its indirect regulation through emergence of intermediate progenitors; and capacity of single NSCs to generate the correct number and laminar fate of cortical neurons. Defects in these mechanisms can cause microcephaly and other brain malformations, and understanding them is critical to designing diagnostic tools and preventive and corrective therapies."}],"acknowledgement":"This work was supported by National Institutes of Health Grants R01NS089795 and R01NS098370 to H.T.G., R01NS076640 to N.D.D., and R01MH094589 and R01NS089777 to B.C., Academia Sinica AS-104-TPB09-2 to S.-J.C, European Union FP7-CIG618444 and Human Frontiers Science Program RGP0053 to S.H., and Fonds Léon Fredericq, from the Fondation Médicale Reine Elisabeth, and from the Fonation Simone et Pierre Clerdent to L.N. The authors apologize to colleagues whose work could not be cited due to space limitations.","scopus_import":"1","doi":"10.1523/JNEUROSCI.2359-16.2016","citation":{"chicago":"Dwyer, Noelle, Bin Chen, Shen Chou, Simon Hippenmeyer, Laurent Nguyen, and Troy Ghashghaei. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2016. <a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">https://doi.org/10.1523/JNEUROSCI.2359-16.2016</a>.","short":"N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, T. Ghashghaei, Journal of Neuroscience 36 (2016) 11394–11401.","mla":"Dwyer, Noelle, et al. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms Regulating Progenitor Behavior and Productivity.” <i>Journal of Neuroscience</i>, vol. 36, no. 45, Society for Neuroscience, 2016, pp. 11394–401, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">10.1523/JNEUROSCI.2359-16.2016</a>.","ieee":"N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, and T. Ghashghaei, “Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity,” <i>Journal of Neuroscience</i>, vol. 36, no. 45. Society for Neuroscience, pp. 11394–11401, 2016.","apa":"Dwyer, N., Chen, B., Chou, S., Hippenmeyer, S., Nguyen, L., &#38; Ghashghaei, T. (2016). Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">https://doi.org/10.1523/JNEUROSCI.2359-16.2016</a>","ama":"Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. <i>Journal of Neuroscience</i>. 2016;36(45):11394-11401. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">10.1523/JNEUROSCI.2359-16.2016</a>","ista":"Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. 2016. Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. Journal of Neuroscience. 36(45), 11394–11401."},"issue":"45","article_processing_charge":"No","project":[{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425"}],"volume":36,"department":[{"_id":"SiHi"}],"isi":1,"fulldoi":"https://doi.org/10.1523/JNEUROSCI.2359-16.2016","oa_version":"None","language":[{"iso":"eng"}],"author":[{"full_name":"Dwyer, Noelle","first_name":"Noelle","last_name":"Dwyer"},{"last_name":"Chen","first_name":"Bin","full_name":"Chen, Bin"},{"last_name":"Chou","first_name":"Shen","full_name":"Chou, Shen"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"full_name":"Nguyen, Laurent","first_name":"Laurent","last_name":"Nguyen"},{"last_name":"Ghashghaei","first_name":"Troy","full_name":"Ghashghaei, Troy"}],"date_updated":"2025-09-22T09:48:17Z","publist_id":"6172"},{"date_published":"2016-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:50:35Z","publisher":"AAAI Press","publication_status":"published","related_material":{"link":[{"relation":"table_of_contents","url":"https://www.ijcai.org/proceedings/2016"}]},"day":"01","page":"172 - 179","_id":"1182","external_id":{"arxiv":["1604.05090"]},"type":"conference","title":"Robust draws in balanced knockout tournaments","status":"public","quality_controlled":"1","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1604.05090","open_access":"1"}],"article_processing_charge":"No","volume":"2016-January","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"KrCh"}],"abstract":[{"text":"Balanced knockout tournaments are ubiquitous in sports competitions and are also used in decisionmaking and elections. The traditional computational question, that asks to compute a draw (optimal draw) that maximizes the winning probability for a distinguished player, has received a lot of attention. Previous works consider the problem where the pairwise winning probabilities are known precisely, while we study how robust is the winning probability with respect to small errors in the pairwise winning probabilities. First, we present several illuminating examples to establish: (a) there exist deterministic tournaments (where the pairwise winning probabilities are 0 or 1) where one optimal draw is much more robust than the other; and (b) in general, there exist tournaments with slightly suboptimal draws that are more robust than all the optimal draws. The above examples motivate the study of the computational problem of robust draws that guarantee a specified winning probability. Second, we present a polynomial-time algorithm for approximating the robustness of a draw for sufficiently small errors in pairwise winning probabilities, and obtain that the stated computational problem is NP-complete. We also show that two natural cases of deterministic tournaments where the optimal draw could be computed in polynomial time also admit polynomial-time algorithms to compute robust optimal draws.","lang":"eng"}],"year":"2016","scopus_import":"1","arxiv":1,"citation":{"apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Tkadlec, J. (2016). Robust draws in balanced knockout tournaments (Vol. 2016–January, pp. 172–179). Presented at the IJCAI: International Joint Conference on Artificial Intelligence, New York, NY, USA: AAAI Press.","ama":"Chatterjee K, Ibsen-Jensen R, Tkadlec J. Robust draws in balanced knockout tournaments. In: Vol 2016-January. AAAI Press; 2016:172-179.","ista":"Chatterjee K, Ibsen-Jensen R, Tkadlec J. 2016. Robust draws in balanced knockout tournaments. IJCAI: International Joint Conference on Artificial Intelligence vol. 2016–January, 172–179.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and J. Tkadlec, “Robust draws in balanced knockout tournaments,” presented at the IJCAI: International Joint Conference on Artificial Intelligence, New York, NY, USA, 2016, vol. 2016–January, pp. 172–179.","short":"K. Chatterjee, R. Ibsen-Jensen, J. Tkadlec, in:, AAAI Press, 2016, pp. 172–179.","mla":"Chatterjee, Krishnendu, et al. <i>Robust Draws in Balanced Knockout Tournaments</i>. Vol. 2016–January, AAAI Press, 2016, pp. 172–79.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Josef Tkadlec. “Robust Draws in Balanced Knockout Tournaments,” 2016–January:172–79. AAAI Press, 2016."},"conference":{"name":"IJCAI: International Joint Conference on Artificial Intelligence","location":"New York, NY, USA","end_date":"2016-07-15","start_date":"2016-07-09"},"language":[{"iso":"eng"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"}],"date_updated":"2025-04-22T13:42:22Z","publist_id":"6171","oa":1,"ec_funded":1,"corr_author":"1","oa_version":"Preprint"},{"article_processing_charge":"No","issue":"24","department":[{"_id":"SyCr"}],"volume":6,"ddc":["576","592"],"doi":"10.1002/ece3.2474","year":"2016","pubrep_id":"736","abstract":[{"text":"Across multicellular organisms, the costs of reproduction and self-maintenance result in a life history trade-off between fecundity and longevity. Queens of perennial social Hymenoptera are both highly fertile and long-lived, and thus, this fundamental trade-off is lacking. Whether social insect males similarly evade the fecundity/longevity trade-off remains largely unstudied. Wingless males of the ant genus Cardiocondyla stay in their natal colonies throughout their relatively long lives and mate with multiple female sexuals. Here, we show that Cardiocondyla obscurior males that were allowed to mate with large numbers of female sexuals had a shortened life span compared to males that mated at a low frequency or virgin males. Although frequent mating negatively affects longevity, males clearly benefit from a “live fast, die young strategy” by inseminating as many female sexuals as possible at a cost to their own survival.","lang":"eng"}],"acknowledgement":"German Science Foundation. Grant Number: SCHR 1135/2-1. We thank M. Adam for handling part of the setups and J. Zoellner for behavioral observations.","scopus_import":"1","citation":{"ieee":"S. Metzler, J. Heinze, and A. Schrempf, “Mating and longevity in ant males,” <i>Ecology and Evolution</i>, vol. 6, no. 24. Wiley-Blackwell, pp. 8903–8906, 2016.","ista":"Metzler S, Heinze J, Schrempf A. 2016. Mating and longevity in ant males. Ecology and Evolution. 6(24), 8903–8906.","ama":"Metzler S, Heinze J, Schrempf A. Mating and longevity in ant males. <i>Ecology and Evolution</i>. 2016;6(24):8903-8906. doi:<a href=\"https://doi.org/10.1002/ece3.2474\">10.1002/ece3.2474</a>","apa":"Metzler, S., Heinze, J., &#38; Schrempf, A. (2016). Mating and longevity in ant males. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.2474\">https://doi.org/10.1002/ece3.2474</a>","chicago":"Metzler, Sina, Jürgen Heinze, and Alexandra Schrempf. “Mating and Longevity in Ant Males.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1002/ece3.2474\">https://doi.org/10.1002/ece3.2474</a>.","mla":"Metzler, Sina, et al. “Mating and Longevity in Ant Males.” <i>Ecology and Evolution</i>, vol. 6, no. 24, Wiley-Blackwell, 2016, pp. 8903–06, doi:<a href=\"https://doi.org/10.1002/ece3.2474\">10.1002/ece3.2474</a>.","short":"S. Metzler, J. Heinze, A. Schrempf, Ecology and Evolution 6 (2016) 8903–8906."},"date_updated":"2025-09-22T09:47:16Z","author":[{"id":"48204546-F248-11E8-B48F-1D18A9856A87","last_name":"Metzler","first_name":"Sina","orcid":"0000-0002-9547-2494","full_name":"Metzler, Sina"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"full_name":"Schrempf, Alexandra","first_name":"Alexandra","last_name":"Schrempf"}],"language":[{"iso":"eng"}],"publist_id":"6169","oa":1,"isi":1,"file":[{"relation":"main_file","content_type":"application/pdf","file_id":"5062","file_name":"IST-2017-736-v1+1_Metzler_et_al-2016-Ecology_and_Evolution.pdf","date_updated":"2020-07-14T12:44:37Z","file_size":328414,"access_level":"open_access","checksum":"789026eb9e1be2a0da08376f29f569cf","date_created":"2018-12-12T10:14:12Z","creator":"system"}],"fulldoi":"https://doi.org/10.1002/ece3.2474","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2016-12-01T00:00:00Z","date_created":"2018-12-11T11:50:36Z","publisher":"Wiley-Blackwell","publication_status":"published","day":"01","page":"8903 - 8906","_id":"1184","publication":"Ecology and Evolution","external_id":{"isi":["000392063300022"]},"has_accepted_license":"1","intvolume":"         6","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","file_date_updated":"2020-07-14T12:44:37Z","type":"journal_article","title":"Mating and longevity in ant males","month":"12","quality_controlled":"1"},{"intvolume":"       143","external_id":{"isi":["000393454100012"]},"quality_controlled":"1","month":"12","type":"journal_article","title":"Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development","status":"public","publisher":"Company of Biologists","publication_status":"published","date_published":"2016-12-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:36Z","_id":"1185","publication":"Development","day":"01","page":"4419 - 4424","publist_id":"6168","language":[{"iso":"eng"}],"author":[{"first_name":"Mara","last_name":"Cucinotta","full_name":"Cucinotta, Mara"},{"first_name":"Silvia","last_name":"Manrique","full_name":"Manrique, Silvia"},{"first_name":"Andrea","last_name":"Guazzotti","full_name":"Guazzotti, Andrea"},{"full_name":"Quadrelli, Nadia","last_name":"Quadrelli","first_name":"Nadia"},{"full_name":"Mendes, Marta","last_name":"Mendes","first_name":"Marta"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"},{"full_name":"Colombo, Lucia","first_name":"Lucia","last_name":"Colombo"}],"date_updated":"2025-09-22T09:46:43Z","fulldoi":"https://doi.org/10.1242/dev.143545","oa_version":"None","isi":1,"volume":143,"department":[{"_id":"EvBe"}],"issue":"23","article_processing_charge":"No","citation":{"ieee":"M. Cucinotta <i>et al.</i>, “Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development,” <i>Development</i>, vol. 143, no. 23. Company of Biologists, pp. 4419–4424, 2016.","ista":"Cucinotta M, Manrique S, Guazzotti A, Quadrelli N, Mendes M, Benková E, Colombo L. 2016. Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. 143(23), 4419–4424.","ama":"Cucinotta M, Manrique S, Guazzotti A, et al. Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. <i>Development</i>. 2016;143(23):4419-4424. doi:<a href=\"https://doi.org/10.1242/dev.143545\">10.1242/dev.143545</a>","apa":"Cucinotta, M., Manrique, S., Guazzotti, A., Quadrelli, N., Mendes, M., Benková, E., &#38; Colombo, L. (2016). Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.143545\">https://doi.org/10.1242/dev.143545</a>","chicago":"Cucinotta, Mara, Silvia Manrique, Andrea Guazzotti, Nadia Quadrelli, Marta Mendes, Eva Benková, and Lucia Colombo. “Cytokinin Response Factors Integrate Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” <i>Development</i>. Company of Biologists, 2016. <a href=\"https://doi.org/10.1242/dev.143545\">https://doi.org/10.1242/dev.143545</a>.","mla":"Cucinotta, Mara, et al. “Cytokinin Response Factors Integrate Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” <i>Development</i>, vol. 143, no. 23, Company of Biologists, 2016, pp. 4419–24, doi:<a href=\"https://doi.org/10.1242/dev.143545\">10.1242/dev.143545</a>.","short":"M. Cucinotta, S. Manrique, A. Guazzotti, N. Quadrelli, M. Mendes, E. Benková, L. Colombo, Development 143 (2016) 4419–4424."},"abstract":[{"lang":"eng","text":"The developmental programme of the pistil is under the control of both auxin and cytokinin. Crosstalk between these factors converges on regulation of the auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length and ovule number were reduced. PIN1 expression was also lower in the triple mutant and the phenotypes could not be rescued by exogenous cytokinin application. pin1 complementation studies using genomic PIN1 constructs showed that the pistil phenotypes were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating the pivotal role of CRFs in auxin-cytokinin crosstalk."}],"year":"2016","acknowledgement":"M.C. was funded by a PhD fellowship from the Università degli Studi di Milano-Bicocca and from Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR) [MIUR-PRIN 2012]. L.C. is also supported by MIUR [MIUR-PRIN 2012]. We would like to thank Andrew MacCabe and Edward Kiegle for editing the paper.","scopus_import":"1","doi":"10.1242/dev.143545"},{"volume":6,"department":[{"_id":"LeSa"}],"article_processing_charge":"No","citation":{"mla":"Gutierrez-Fernandez, Javier, et al. “Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal Pathogenesis.” <i>Scientific Reports</i>, vol. 6, 38094, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep38094\">10.1038/srep38094</a>.","short":"J. Gutierrez-Fernandez, M. Saleh, M. Alcorlo, A. Gómez Mejóa, D. Pantoja Uceda, M. Treviño, F. Vob, M. Abdullah, S. Galán Bartual, J. Seinen, P. Sánchez Murcia, F. Gago, M. Bruix, S. Hammerschmidt, J. Hermoso, Scientific Reports 6 (2016).","chicago":"Gutierrez-Fernandez, Javier, Malek Saleh, Martín Alcorlo, Alejandro Gómez Mejóa, David Pantoja Uceda, Miguel Treviño, Franziska Vob, et al. “Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal Pathogenesis.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep38094\">https://doi.org/10.1038/srep38094</a>.","ama":"Gutierrez-Fernandez J, Saleh M, Alcorlo M, et al. Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep38094\">10.1038/srep38094</a>","ista":"Gutierrez-Fernandez J, Saleh M, Alcorlo M, Gómez Mejóa A, Pantoja Uceda D, Treviño M, Vob F, Abdullah M, Galán Bartual S, Seinen J, Sánchez Murcia P, Gago F, Bruix M, Hammerschmidt S, Hermoso J. 2016. Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. Scientific Reports. 6, 38094.","apa":"Gutierrez-Fernandez, J., Saleh, M., Alcorlo, M., Gómez Mejóa, A., Pantoja Uceda, D., Treviño, M., … Hermoso, J. (2016). Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep38094\">https://doi.org/10.1038/srep38094</a>","ieee":"J. Gutierrez-Fernandez <i>et al.</i>, “Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016."},"pubrep_id":"735","abstract":[{"text":"The human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus.","lang":"eng"}],"acknowledgement":"We gratefully acknowledge Karsta Barnekow and Kristine Sievert-Giermann, for technical assistance and Lothar Petruschka for in silico analysis (all Dept. of Genetics, University of Greifswald). We are further grateful to the staff from SLS synchrotron beamline for help in data collection. This work was supported by grants from the Deutsche Forschungsgemeinschaft DFG GRK 1870 (to SH) and the Spanish Ministry of Economy and Competitiveness (BFU2014-59389-P to JAH, CTQ2014-52633-P to MB and SAF2012-39760-C02-02 to FG) and S2010/BMD-2457 (Community of Madrid to JAH and FG).","year":"2016","scopus_import":"1","doi":"10.1038/srep38094","ddc":["576","610"],"publist_id":"6167","oa":1,"language":[{"iso":"eng"}],"author":[{"id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","last_name":"Gutierrez-Fernandez","first_name":"Javier","full_name":"Gutierrez-Fernandez, Javier"},{"full_name":"Saleh, Malek","first_name":"Malek","last_name":"Saleh"},{"full_name":"Alcorlo, Martín","last_name":"Alcorlo","first_name":"Martín"},{"full_name":"Gómez Mejóa, Alejandro","first_name":"Alejandro","last_name":"Gómez Mejóa"},{"last_name":"Pantoja Uceda","first_name":"David","full_name":"Pantoja Uceda, David"},{"last_name":"Treviño","first_name":"Miguel","full_name":"Treviño, Miguel"},{"last_name":"Vob","first_name":"Franziska","full_name":"Vob, Franziska"},{"full_name":"Abdullah, Mohammed","last_name":"Abdullah","first_name":"Mohammed"},{"first_name":"Sergio","last_name":"Galán Bartual","full_name":"Galán Bartual, Sergio"},{"first_name":"Jolien","last_name":"Seinen","full_name":"Seinen, Jolien"},{"last_name":"Sánchez Murcia","first_name":"Pedro","full_name":"Sánchez Murcia, Pedro"},{"last_name":"Gago","first_name":"Federico","full_name":"Gago, Federico"},{"full_name":"Bruix, Marta","first_name":"Marta","last_name":"Bruix"},{"full_name":"Hammerschmidt, Sven","last_name":"Hammerschmidt","first_name":"Sven"},{"last_name":"Hermoso","first_name":"Juan","full_name":"Hermoso, Juan"}],"date_updated":"2025-09-22T09:46:12Z","fulldoi":"https://doi.org/10.1038/srep38094","oa_version":"Published Version","file":[{"relation":"main_file","checksum":"e007d78b483bc59bf5ab98e9d42a6ec1","date_updated":"2020-07-14T12:44:37Z","access_level":"open_access","file_size":2716045,"date_created":"2018-12-12T10:10:18Z","creator":"system","content_type":"application/pdf","file_name":"IST-2017-735-v1+1_srep38094.pdf","file_id":"4804"}],"isi":1,"article_number":"38094","publisher":"Nature Publishing Group","publication_status":"published","date_published":"2016-12-05T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:36Z","_id":"1186","publication":"Scientific Reports","day":"05","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"         6","has_accepted_license":"1","external_id":{"isi":["000389129100001"]},"quality_controlled":"1","month":"12","type":"journal_article","file_date_updated":"2020-07-14T12:44:37Z","title":"Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis","status":"public"},{"oa_version":"Preprint","fulldoi":"https://doi.org/10.1109/FOCS.2016.88","isi":1,"article_number":"7782993","ec_funded":1,"oa":1,"publist_id":"6158","author":[{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir"}],"date_updated":"2025-09-22T09:44:20Z","conference":{"start_date":"2016-09-09","end_date":"2016-09-11","location":"New Brunswick, NJ, USA ","name":"FOCS: Foundations of Computer Science"},"language":[{"iso":"eng"}],"citation":{"ista":"Kolmogorov V. 2016. Commutativity in the algorithmic Lovasz local lemma. Proceedings - Annual IEEE Symposium on Foundations of Computer Science. FOCS: Foundations of Computer Science vol. 2016–December, 7782993.","ama":"Kolmogorov V. Commutativity in the algorithmic Lovasz local lemma. In: <i>Proceedings - Annual IEEE Symposium on Foundations of Computer Science</i>. Vol 2016-December. IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/FOCS.2016.88\">10.1109/FOCS.2016.88</a>","apa":"Kolmogorov, V. (2016). Commutativity in the algorithmic Lovasz local lemma. In <i>Proceedings - Annual IEEE Symposium on Foundations of Computer Science</i> (Vol. 2016–December). New Brunswick, NJ, USA : IEEE. <a href=\"https://doi.org/10.1109/FOCS.2016.88\">https://doi.org/10.1109/FOCS.2016.88</a>","ieee":"V. Kolmogorov, “Commutativity in the algorithmic Lovasz local lemma,” in <i>Proceedings - Annual IEEE Symposium on Foundations of Computer Science</i>, New Brunswick, NJ, USA , 2016, vol. 2016–December.","mla":"Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.” <i>Proceedings - Annual IEEE Symposium on Foundations of Computer Science</i>, vol. 2016–December, 7782993, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/FOCS.2016.88\">10.1109/FOCS.2016.88</a>.","short":"V. Kolmogorov, in:, Proceedings - Annual IEEE Symposium on Foundations of Computer Science, IEEE, 2016.","chicago":"Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.” In <i>Proceedings - Annual IEEE Symposium on Foundations of Computer Science</i>, Vol. 2016–December. IEEE, 2016. <a href=\"https://doi.org/10.1109/FOCS.2016.88\">https://doi.org/10.1109/FOCS.2016.88</a>."},"doi":"10.1109/FOCS.2016.88","acknowledgement":"European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 616160","abstract":[{"text":"We consider the recent formulation of the Algorithmic Lovász Local Lemma [1], [2] for finding objects that avoid &quot;bad features&quot;, or &quot;flaws&quot;. It extends the Moser-Tardos resampling algorithm [3] to more general discrete spaces. At each step the method picks a flaw present in the current state and &quot;resamples&quot; it using a &quot;resampling oracle&quot; provided by the user. However, it is less flexible than the Moser-Tardos method since [1], [2] require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and thus can potentially be implemented more efficiently). We formulate a new &quot;commutativity&quot; condition, and prove that it is sufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additional assumption. We then show that existing resampling oracles for perfect matchings and permutations do satisfy this condition. Finally, we generalize the precondition in [2] (in the case of symmetric potential causality graphs). This unifies special cases that previously were treated separately.","lang":"eng"}],"year":"2016","arxiv":1,"scopus_import":"1","department":[{"_id":"VlKo"}],"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"volume":"2016-December","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1506.08547v7"}],"article_processing_charge":"No","quality_controlled":"1","month":"12","status":"public","type":"conference","title":"Commutativity in the algorithmic Lovasz local lemma","external_id":{"isi":["000391198500082"],"arxiv":["1506.08547"]},"_id":"1193","publication":"Proceedings - Annual IEEE Symposium on Foundations of Computer Science","related_material":{"record":[{"relation":"later_version","status":"public","id":"5975"}]},"day":"15","publisher":"IEEE","publication_status":"published","date_published":"2016-12-15T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:38Z"},{"citation":{"ieee":"S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” <i>Molecular Biology and Evolution</i>, vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.","apa":"Franssen, S., Barton, N. H., &#38; Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msw210\">https://doi.org/10.1093/molbev/msw210</a>","ama":"Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. <i>Molecular Biology and Evolution</i>. 2016;34(1):174-184. doi:<a href=\"https://doi.org/10.1093/molbev/msw210\">10.1093/molbev/msw210</a>","ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184.","chicago":"Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msw210\">https://doi.org/10.1093/molbev/msw210</a>.","short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.","mla":"Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” <i>Molecular Biology and Evolution</i>, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:<a href=\"https://doi.org/10.1093/molbev/msw210\">10.1093/molbev/msw210</a>."},"doi":"10.1093/molbev/msw210","ddc":["576"],"pubrep_id":"770","abstract":[{"lang":"eng","text":"The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. "}],"acknowledgement":"The authors thank all members of the Institute of Population\r\nGenetics for discussion and support on the project and par-\r\nticularly N. Barghi for helpful comments on earlier versions of\r\nthe  manuscript.  This  work  was  supported  by  the  European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”.","year":"2016","scopus_import":"1","department":[{"_id":"NiBa"}],"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"volume":34,"article_processing_charge":"No","issue":"1","oa_version":"Submitted Version","fulldoi":"https://doi.org/10.1093/molbev/msw210","isi":1,"file":[{"checksum":"1e78d3aaffcb40dc8b02b7b4666019e0","date_created":"2018-12-12T10:16:35Z","access_level":"open_access","date_updated":"2020-07-14T12:44:38Z","file_size":295274,"creator":"system","file_id":"5223","file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf","content_type":"application/pdf","relation":"main_file"},{"relation":"main_file","file_name":"IST-2017-770-v1+2_Fig1.pdf","file_id":"5224","content_type":"application/pdf","creator":"system","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","date_created":"2018-12-12T10:16:36Z","checksum":"e13171843283774404c936c581b4543e","file_size":10902625},{"content_type":"application/pdf","file_id":"5225","file_name":"IST-2017-770-v1+3_Fig2.pdf","file_size":21437,"checksum":"63bc6e6e61f347594d8c00c37f874a0b","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","date_created":"2018-12-12T10:16:37Z","creator":"system","relation":"main_file"},{"relation":"main_file","content_type":"application/pdf","file_name":"IST-2017-770-v1+4_Fig3.pdf","file_id":"5226","date_created":"2018-12-12T10:16:38Z","file_size":1172194,"date_updated":"2020-07-14T12:44:38Z","checksum":"da87cc7c78808837f22a3dae1c8397f9","access_level":"open_access","creator":"system"},{"relation":"main_file","content_type":"application/pdf","file_name":"IST-2017-770-v1+5_Fig4.pdf","file_id":"5227","file_size":50045,"creator":"system","checksum":"e47b2a0c32142f423b3100150c0294f8","date_created":"2018-12-12T10:16:38Z","access_level":"open_access","date_updated":"2020-07-14T12:44:38Z"},{"access_level":"open_access","file_size":50705,"date_updated":"2020-07-14T12:44:38Z","checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9","date_created":"2018-12-12T10:16:39Z","creator":"system","content_type":"application/pdf","file_name":"IST-2017-770-v1+6_Fig5.pdf","file_id":"5228","relation":"main_file"}],"ec_funded":1,"publist_id":"6155","oa":1,"date_updated":"2025-09-22T09:43:41Z","author":[{"first_name":"Susan","last_name":"Franssen","full_name":"Franssen, Susan"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"full_name":"Schlötterer, Christian","last_name":"Schlötterer","first_name":"Christian"}],"language":[{"iso":"eng"}],"_id":"1195","publication":"Molecular Biology and Evolution","page":"174 - 184","day":"03","publisher":"Oxford University Press","publication_status":"published","date_published":"2016-10-03T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:39Z","month":"10","quality_controlled":"1","status":"public","file_date_updated":"2020-07-14T12:44:38Z","type":"journal_article","title":"Reconstruction of haplotype-blocks selected during experimental evolution.","intvolume":"        34","has_accepted_license":"1","external_id":{"isi":["000396772000009"]}},{"external_id":{"isi":["000391230900008"]},"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        12","file_date_updated":"2020-07-14T12:44:38Z","type":"journal_article","title":"Error-robust modes of the retinal population code","status":"public","month":"11","quality_controlled":"1","date_published":"2016-11-17T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:40Z","publisher":"Public Library of Science","publication_status":"published","related_material":{"record":[{"id":"9709","status":"public","relation":"research_data"}]},"day":"17","_id":"1197","publication":"PLoS Computational Biology","language":[{"iso":"eng"}],"date_updated":"2025-09-22T09:43:12Z","author":[{"first_name":"Jason","last_name":"Prentice","full_name":"Prentice, Jason"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"full_name":"Ioffe, Mark","last_name":"Ioffe","first_name":"Mark"},{"full_name":"Loback, Adrianna","first_name":"Adrianna","last_name":"Loback"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"full_name":"Berry, Michael","first_name":"Michael","last_name":"Berry"}],"oa":1,"publist_id":"6153","file":[{"date_updated":"2020-07-14T12:44:38Z","file_size":4492021,"checksum":"47b08cbd4dbf32b25ba161f5f4b262cc","access_level":"open_access","date_created":"2019-01-25T10:35:00Z","creator":"kschuh","file_id":"5884","file_name":"2016_PLOS_Prentice.pdf","content_type":"application/pdf","relation":"main_file"}],"article_number":"e1005855","isi":1,"fulldoi":"https://doi.org/10.1371/journal.pcbi.1005148","oa_version":"Published Version","issue":"11","article_processing_charge":"No","project":[{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"volume":12,"department":[{"_id":"GaTk"}],"acknowledgement":"JSP was supported by a C.V. Starr Fellowship from the Starr Foundation (http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation (https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler for helpful comments on the manuscript.","year":"2016","abstract":[{"lang":"eng","text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina."}],"scopus_import":"1","doi":"10.1371/journal.pcbi.1005148","ddc":["570"],"citation":{"apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., &#38; Berry, M. (2016). Error-robust modes of the retinal population code. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005148\">https://doi.org/10.1371/journal.pcbi.1005148</a>","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes of the retinal population code. <i>PLoS Computational Biology</i>. 2016;12(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005148\">10.1371/journal.pcbi.1005148</a>","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855.","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” <i>PLoS Computational Biology</i>, vol. 12, no. 11. Public Library of Science, 2016.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016).","mla":"Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.” <i>PLoS Computational Biology</i>, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005148\">10.1371/journal.pcbi.1005148</a>.","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” <i>PLoS Computational Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pcbi.1005148\">https://doi.org/10.1371/journal.pcbi.1005148</a>."}},{"external_id":{"isi":["000390640200003"]},"has_accepted_license":"1","intvolume":"        19","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","file_date_updated":"2020-07-14T12:44:39Z","type":"journal_article","title":"Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. 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The project was funded by the Deutsche Forschungsgemeinschaft (DFG, KU 1929/4-2) within the priority programme SPP 1399 “Host–Parasite Coevolution”.","publist_id":"6147","oa":1,"author":[{"full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","last_name":"Milutinovic","first_name":"Barbara"},{"last_name":"Peuß","first_name":"Robert","full_name":"Peuß, Robert"},{"last_name":"Ferro","first_name":"Kevin","full_name":"Ferro, Kevin"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"}],"date_updated":"2025-09-22T09:41:02Z","language":[{"iso":"eng"}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.1016/j.zool.2016.03.006","isi":1,"file":[{"checksum":"8396d5bd95f9c4295857162f902afabf","date_created":"2019-01-25T13:00:20Z","access_level":"open_access","date_updated":"2020-07-14T12:44:39Z","file_size":1473211,"creator":"kschuh","content_type":"application/pdf","file_id":"5885","file_name":"2016_Elsevier_Milutinovic.pdf","relation":"main_file"}]},{"fulldoi":"https://doi.org/10.1128/JCM.01511-16","oa_version":"Submitted Version","isi":1,"publist_id":"6146","oa":1,"language":[{"iso":"eng"}],"date_updated":"2025-09-22T09:40:28Z","author":[{"last_name":"Hu","first_name":"Fang","full_name":"Hu, Fang"},{"full_name":"Rishishwar, Lavanya","first_name":"Lavanya","last_name":"Rishishwar"},{"full_name":"Sivadas, Ambily","first_name":"Ambily","last_name":"Sivadas"},{"last_name":"Mitchell","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","full_name":"Mitchell, Gabriel"},{"full_name":"King, Jordan","first_name":"Jordan","last_name":"King"},{"last_name":"Murphy","first_name":"Timothy","full_name":"Murphy, Timothy"},{"full_name":"Gilsdorf, Janet","last_name":"Gilsdorf","first_name":"Janet"},{"first_name":"Leonard","last_name":"Mayer","full_name":"Mayer, Leonard"},{"last_name":"Wang","first_name":"Xin","full_name":"Wang, Xin"}],"citation":{"chicago":"Hu, Fang, Lavanya Rishishwar, Ambily Sivadas, Gabriel Mitchell, Jordan King, Timothy Murphy, Janet Gilsdorf, Leonard Mayer, and Xin Wang. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” <i>Journal of Clinical Microbiology</i>. American Society for Microbiology, 2016. <a href=\"https://doi.org/10.1128/JCM.01511-16\">https://doi.org/10.1128/JCM.01511-16</a>.","mla":"Hu, Fang, et al. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” <i>Journal of Clinical Microbiology</i>, vol. 54, no. 12, American Society for Microbiology, 2016, pp. 3010–17, doi:<a href=\"https://doi.org/10.1128/JCM.01511-16\">10.1128/JCM.01511-16</a>.","short":"F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf, L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.","ieee":"F. Hu <i>et al.</i>, “Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,” <i>Journal of Clinical Microbiology</i>, vol. 54, no. 12. American Society for Microbiology, pp. 3010–3017, 2016.","ama":"Hu F, Rishishwar L, Sivadas A, et al. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. <i>Journal of Clinical Microbiology</i>. 2016;54(12):3010-3017. doi:<a href=\"https://doi.org/10.1128/JCM.01511-16\">10.1128/JCM.01511-16</a>","ista":"Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 54(12), 3010–3017.","apa":"Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G., King, J., Murphy, T., … Wang, X. (2016). Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. <i>Journal of Clinical Microbiology</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/JCM.01511-16\">https://doi.org/10.1128/JCM.01511-16</a>"},"scopus_import":"1","abstract":[{"lang":"eng","text":"Haemophilus haemolyticus has been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae (NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified because none of the existing tests targeting the known phenotypes of H. haemolyticus are able to specifically identify H. haemolyticus. Through comparative genomic analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to H. haemolyticus that can be used as targets for the identification of H. haemolyticus. A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detecting H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets (H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification of H. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused by H. haemolyticus and NT H. influenzae."}],"year":"2016","acknowledgement":"We are grateful to ABCs for providing strains and the Bacterial Meningitis Laboratory for technical support.","doi":"10.1128/JCM.01511-16","volume":54,"department":[{"_id":"GaTk"}],"issue":"12","article_processing_charge":"No","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121393/","open_access":"1"}],"quality_controlled":"1","month":"12","title":"Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination","type":"journal_article","status":"public","intvolume":"        54","external_id":{"isi":["000389209600026"]},"publication":"Journal of Clinical Microbiology","_id":"1203","day":"01","page":"3010 - 3017","publication_status":"published","publisher":"American Society for Microbiology","date_created":"2018-12-11T11:50:41Z","date_published":"2016-12-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"page":"609 - 612","day":"01","_id":"1204","publication":"American Mathematical Monthly","date_published":"2016-06-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:42Z","publisher":"Mathematical Association of America","publication_status":"published","type":"journal_article","title":"Surprises in numerical expressions of physical constants","status":"public","month":"06","quality_controlled":"1","external_id":{"arxiv":["1603.00299"],"isi":["000381754900010"]},"intvolume":"       123","year":"2016","abstract":[{"text":"In science, as in life, &quot;surprises&quot; can be adequately appreciated only in the presence of a null model, what we expect a priori. In physics, theories sometimes express the values of dimensionless physical constants as combinations of mathematical constants like π or e. The inverse problem also arises, whereby the measured value of a physical constant admits a &quot;surprisingly&quot; simple approximation in terms of well-known mathematical constants. Can we estimate the probability for this to be a mere coincidence, rather than an inkling of some theory? We answer the question in the most naive form.","lang":"eng"}],"scopus_import":"1","arxiv":1,"doi":"10.4169/amer.math.monthly.123.6.609","citation":{"apa":"Amir, A., Lemeshko, M., &#38; Tokieda, T. (2016). Surprises in numerical expressions of physical constants. <i>American Mathematical Monthly</i>. Mathematical Association of America. <a href=\"https://doi.org/10.4169/amer.math.monthly.123.6.609\">https://doi.org/10.4169/amer.math.monthly.123.6.609</a>","ista":"Amir A, Lemeshko M, Tokieda T. 2016. Surprises in numerical expressions of physical constants. American Mathematical Monthly. 123(6), 609–612.","ama":"Amir A, Lemeshko M, Tokieda T. Surprises in numerical expressions of physical constants. <i>American Mathematical Monthly</i>. 2016;123(6):609-612. doi:<a href=\"https://doi.org/10.4169/amer.math.monthly.123.6.609\">10.4169/amer.math.monthly.123.6.609</a>","ieee":"A. Amir, M. Lemeshko, and T. Tokieda, “Surprises in numerical expressions of physical constants,” <i>American Mathematical Monthly</i>, vol. 123, no. 6. Mathematical Association of America, pp. 609–612, 2016.","short":"A. Amir, M. Lemeshko, T. Tokieda, American Mathematical Monthly 123 (2016) 609–612.","mla":"Amir, Ariel, et al. “Surprises in Numerical Expressions of Physical Constants.” <i>American Mathematical Monthly</i>, vol. 123, no. 6, Mathematical Association of America, 2016, pp. 609–12, doi:<a href=\"https://doi.org/10.4169/amer.math.monthly.123.6.609\">10.4169/amer.math.monthly.123.6.609</a>.","chicago":"Amir, Ariel, Mikhail Lemeshko, and Tadashi Tokieda. “Surprises in Numerical Expressions of Physical Constants.” <i>American Mathematical Monthly</i>. Mathematical Association of America, 2016. <a href=\"https://doi.org/10.4169/amer.math.monthly.123.6.609\">https://doi.org/10.4169/amer.math.monthly.123.6.609</a>."},"issue":"6","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.00299"}],"article_processing_charge":"No","volume":123,"department":[{"_id":"MiLe"}],"isi":1,"oa_version":"Preprint","fulldoi":"https://doi.org/10.4169/amer.math.monthly.123.6.609","language":[{"iso":"eng"}],"author":[{"last_name":"Amir","first_name":"Ariel","full_name":"Amir, Ariel"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tokieda, Tadashi","first_name":"Tadashi","last_name":"Tokieda"}],"date_updated":"2025-09-22T09:39:09Z","oa":1,"publist_id":"6143"}]