[{"volume":28,"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/"}],"citation":{"short":"P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten, R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016) 2464–2477.","ama":"Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth guided apical hook formation in plants. <i>Plant Cell</i>. 2016;28(10):2464-2477. doi:<a href=\"https://doi.org/10.1105/tpc.15.00569\">10.1105/tpc.15.00569</a>","apa":"Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten, D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical hook formation in plants. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.15.00569\">https://doi.org/10.1105/tpc.15.00569</a>","ieee":"P. Žádníková <i>et al.</i>, “A model of differential growth guided apical hook formation in plants,” <i>Plant Cell</i>, vol. 28, no. 10. American Society of Plant Biologists, pp. 2464–2477, 2016.","ista":"Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477.","chicago":"Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz, and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” <i>Plant Cell</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1105/tpc.15.00569\">https://doi.org/10.1105/tpc.15.00569</a>.","mla":"Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” <i>Plant Cell</i>, vol. 28, no. 10, American Society of Plant Biologists, 2016, pp. 2464–77, doi:<a href=\"https://doi.org/10.1105/tpc.15.00569\">10.1105/tpc.15.00569</a>."},"abstract":[{"lang":"eng","text":"Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved."}],"type":"journal_article","quality_controlled":"1","_id":"1153","month":"10","scopus_import":"1","issue":"10","publication_status":"published","date_created":"2018-12-11T11:50:26Z","external_id":{"isi":["000390135400013"]},"isi":1,"publication":"Plant Cell","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"call_identifier":"FP7","grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis"}],"oa":1,"day":"01","doi":"10.1105/tpc.15.00569","date_published":"2016-10-01T00:00:00Z","intvolume":"        28","year":"2016","acknowledgement":"We thank Martine De Cock and Annick Bleys for help in preparing the manuscript, Daniel Van Damme for sharing material and stimulating discussion, and Rudiger Simon for support during revision of the manuscript.\r\nThis work was supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship (LT-000209-2014).","ec_funded":1,"title":"A model of differential growth guided apical hook formation in plants","author":[{"first_name":"Petra","full_name":"Žádníková, Petra","last_name":"Žádníková"},{"first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560"},{"last_name":"Abuzeineh","full_name":"Abuzeineh, Anas","first_name":"Anas"},{"last_name":"Gallemí","full_name":"Gallemí, Marçal","first_name":"Marçal"},{"first_name":"Dominique","full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten"},{"last_name":"Smith","full_name":"Smith, Richard","first_name":"Richard"},{"full_name":"Inze, Dirk","last_name":"Inze","first_name":"Dirk"},{"full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí"},{"full_name":"Prusinkiewicz, Przemysław","last_name":"Prusinkiewicz","first_name":"Przemysław"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková"}],"page":"2464 - 2477","date_updated":"2025-09-22T09:56:45Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Submitted Version","publist_id":"6205"},{"doi":"10.1038/srep36440","day":"07","file":[{"file_id":"4756","date_updated":"2018-12-12T10:09:32Z","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:09:32Z","file_name":"IST-2017-744-v1+1_srep36440.pdf","file_size":2353456,"creator":"system","access_level":"open_access"}],"oa":1,"intvolume":"         6","date_published":"2016-11-07T00:00:00Z","article_number":"36440","ec_funded":1,"year":"2016","acknowledgement":"This work was supported by the Swiss National Science Foundation (Ambizione fellowship; PZ00P3-154733 to M.M.), the Swiss Multiple Sclerosis Society (research support to M.M.), a fellowship from the Boehringer Ingelheim Fonds (BIF) to J.S., the European Research Council (grant ERC GA 281556) and a START award from the Austrian Science Foundation (FWF) to M.S. #BioimagingFacility","publication":"Scientific Reports","isi":1,"project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"281556"},{"grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FWF"}],"license":"https://creativecommons.org/licenses/by/4.0/","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["579"],"oa_version":"Published Version","publist_id":"6204","author":[{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","last_name":"Schwarz","first_name":"Jan"},{"full_name":"Bierbaum, Veronika","last_name":"Bierbaum","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","first_name":"Veronika"},{"first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","last_name":"Merrin"},{"full_name":"Frank, Tino","last_name":"Frank","first_name":"Tino"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert"},{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias"},{"full_name":"Tay, Savaş","last_name":"Tay","first_name":"Savaş"},{"last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K"},{"orcid":"0000-0001-8599-1226","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","last_name":"Mehling","full_name":"Mehling, Matthias","first_name":"Matthias"}],"title":"A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients","date_updated":"2025-09-22T09:56:13Z","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2018-12-12T10:09:32Z","has_accepted_license":"1","article_processing_charge":"No","type":"journal_article","abstract":[{"lang":"eng","text":"Cellular locomotion is a central hallmark of eukaryotic life. It is governed by cell-extrinsic molecular factors, which can either emerge in the soluble phase or as immobilized, often adhesive ligands. To encode for direction, every cue must be present as a spatial or temporal gradient. Here, we developed a microfluidic chamber that allows measurement of cell migration in combined response to surface immobilized and soluble molecular gradients. As a proof of principle we study the response of dendritic cells to their major guidance cues, chemokines. The majority of data on chemokine gradient sensing is based on in vitro studies employing soluble gradients. Despite evidence suggesting that in vivo chemokines are often immobilized to sugar residues, limited information is available how cells respond to immobilized chemokines. We tracked migration of dendritic cells towards immobilized gradients of the chemokine CCL21 and varying superimposed soluble gradients of CCL19. Differential migratory patterns illustrate the potential of our setup to quantitatively study the competitive response to both types of gradients. Beyond chemokines our approach is broadly applicable to alternative systems of chemo- and haptotaxis such as cells migrating along gradients of adhesion receptor ligands vs. any soluble cue. \r\n"}],"citation":{"ama":"Schwarz J, Bierbaum V, Merrin J, et al. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep36440\">10.1038/srep36440</a>","apa":"Schwarz, J., Bierbaum, V., Merrin, J., Frank, T., Hauschild, R., Bollenbach, M. T., … Mehling, M. (2016). A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep36440\">https://doi.org/10.1038/srep36440</a>","ieee":"J. Schwarz <i>et al.</i>, “A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","mla":"Schwarz, Jan, et al. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” <i>Scientific Reports</i>, vol. 6, 36440, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep36440\">10.1038/srep36440</a>.","ista":"Schwarz J, Bierbaum V, Merrin J, Frank T, Hauschild R, Bollenbach MT, Tay S, Sixt MK, Mehling M. 2016. A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients. Scientific Reports. 6, 36440.","chicago":"Schwarz, Jan, Veronika Bierbaum, Jack Merrin, Tino Frank, Robert Hauschild, Mark Tobias Bollenbach, Savaş Tay, Michael K Sixt, and Matthias Mehling. “A Microfluidic Device for Measuring Cell Migration towards Substrate Bound and Soluble Chemokine Gradients.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep36440\">https://doi.org/10.1038/srep36440</a>.","short":"J. Schwarz, V. Bierbaum, J. Merrin, T. Frank, R. Hauschild, M.T. Bollenbach, S. Tay, M.K. Sixt, M. Mehling, Scientific Reports 6 (2016)."},"quality_controlled":"1","volume":6,"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"ToBo"}],"publisher":"Nature Publishing Group","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2018-12-11T11:50:27Z","external_id":{"isi":["000387118300001"]},"_id":"1154","pubrep_id":"744","month":"11","scopus_import":"1"},{"scopus_import":"1","issue":"6","month":"12","_id":"1157","external_id":{"arxiv":["1409.4979"],"isi":["000391240100016"]},"date_created":"2018-12-11T11:50:27Z","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1409.4979","open_access":"1"}],"publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"volume":26,"quality_controlled":"1","type":"journal_article","abstract":[{"lang":"eng","text":"We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where the sample X is an M ×N random matrix whose entries are real independent random variables with variance 1/N and whereσ is an M × M positive-definite deterministic matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class of populations σ in the sub-critical regime, we show that the distribution of the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians or (2) that σ is diagonal and that the entries of X have a sub-exponential decay."}],"citation":{"short":"J. Lee, K. Schnelli, Annals of Applied Probability 26 (2016) 3786–3839.","ieee":"J. Lee and K. Schnelli, “Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population,” <i>Annals of Applied Probability</i>, vol. 26, no. 6. Institute of Mathematical Statistics, pp. 3786–3839, 2016.","apa":"Lee, J., &#38; Schnelli, K. (2016). Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/16-AAP1193\">https://doi.org/10.1214/16-AAP1193</a>","ama":"Lee J, Schnelli K. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. <i>Annals of Applied Probability</i>. 2016;26(6):3786-3839. doi:<a href=\"https://doi.org/10.1214/16-AAP1193\">10.1214/16-AAP1193</a>","ista":"Lee J, Schnelli K. 2016. Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population. Annals of Applied Probability. 26(6), 3786–3839.","chicago":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2016. <a href=\"https://doi.org/10.1214/16-AAP1193\">https://doi.org/10.1214/16-AAP1193</a>.","mla":"Lee, Ji, and Kevin Schnelli. “Tracy-Widom Distribution for the Largest Eigenvalue of Real Sample Covariance Matrices with General Population.” <i>Annals of Applied Probability</i>, vol. 26, no. 6, Institute of Mathematical Statistics, 2016, pp. 3786–839, doi:<a href=\"https://doi.org/10.1214/16-AAP1193\">10.1214/16-AAP1193</a>."},"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","page":"3786 - 3839","date_updated":"2025-09-22T09:55:43Z","author":[{"last_name":"Lee","full_name":"Lee, Ji","first_name":"Ji"},{"orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","full_name":"Schnelli, Kevin","first_name":"Kevin"}],"title":"Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population","publist_id":"6201","oa_version":"Preprint","project":[{"call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"publication":"Annals of Applied Probability","isi":1,"ec_funded":1,"year":"2016","acknowledgement":"We thank Horng-Tzer Yau for numerous discussions and remarks. We are grateful to Ben Adlam, Jinho Baik, Zhigang Bao, Paul Bourgade, László Erd ̋os, Iain Johnstone and Antti Knowles for comments. We are also grate-\r\nful to the anonymous referee for carefully reading our manuscript and suggesting several improvements.","intvolume":"        26","date_published":"2016-12-15T00:00:00Z","day":"15","doi":"10.1214/16-AAP1193","oa":1},{"date_created":"2018-12-11T11:50:28Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000392120100008"]},"_id":"1158","pubrep_id":"742","scopus_import":"1","issue":"12","month":"12","quality_controlled":"1","abstract":[{"lang":"eng","text":"Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate &quot;grey zone&quot; of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation."}],"type":"journal_article","citation":{"chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234.","mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. 2016;14(12). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” <i>PLoS Biology</i>, vol. 14, no. 12. Public Library of Science, 2016.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016)."},"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"volume":14,"publisher":"Public Library of Science","publist_id":"6200","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"9862"},{"relation":"research_data","id":"9863","status":"public"}]},"date_updated":"2025-09-22T09:55:10Z","author":[{"last_name":"Roux","full_name":"Roux, Camille","first_name":"Camille"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"full_name":"Anciaux, Youann","last_name":"Anciaux","first_name":"Youann"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","file_date_updated":"2020-07-14T12:44:36Z","article_processing_charge":"No","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"intvolume":"        14","date_published":"2016-12-27T00:00:00Z","day":"27","doi":"10.1371/journal.pbio.2000234","file":[{"file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","date_created":"2018-12-12T10:15:42Z","creator":"system","file_size":2494348,"access_level":"open_access","date_updated":"2020-07-14T12:44:36Z","file_id":"5164","checksum":"2bab63b068a9840efd532b9ae583f9bb","content_type":"application/pdf","relation":"main_file"}],"oa":1,"acknowledgement":"European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité.","year":"2016","article_number":"e2000234","publication":"PLoS Biology","isi":1,"ddc":["576"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"month":"12","scopus_import":"1","_id":"1164","conference":{"name":"GD: Graph Drawing and Network Visualization","location":"Athens, Greece","start_date":"2016-09-19","end_date":"2016-09-21"},"alternative_title":["LNCS"],"external_id":{"isi":["000405478500036"],"arxiv":["1608.08662"]},"publication_status":"published","date_created":"2018-12-11T11:50:29Z","publisher":"Springer","main_file_link":[{"url":"https://arxiv.org/abs/1608.08662","open_access":"1"}],"volume":9801,"department":[{"_id":"UlWa"}],"citation":{"short":"R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2016, pp. 468–481.","mla":"Fulek, Radoslav, et al. <i>Hanani-Tutte for Radial Planarity II</i>. Vol. 9801, Springer, 2016, pp. 468–81, doi:<a href=\"https://doi.org/10.1007/978-3-319-50106-2_36\">10.1007/978-3-319-50106-2_36</a>.","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.","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity II,” 9801:468–81. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_36\">https://doi.org/10.1007/978-3-319-50106-2_36</a>.","apa":"Fulek, R., Pelsmajer, M., &#38; Schaefer, M. (2016). Hanani-Tutte for radial planarity II (Vol. 9801, pp. 468–481). Presented at the GD: Graph Drawing and Network Visualization, Athens, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_36\">https://doi.org/10.1007/978-3-319-50106-2_36</a>","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.","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity II. In: Vol 9801. Springer; 2016:468-481. doi:<a href=\"https://doi.org/10.1007/978-3-319-50106-2_36\">10.1007/978-3-319-50106-2_36</a>"},"type":"conference","abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"first_name":"Radoslav","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pelsmajer","full_name":"Pelsmajer, Michael","first_name":"Michael"},{"full_name":"Schaefer, Marcus","last_name":"Schaefer","first_name":"Marcus"}],"title":"Hanani-Tutte for radial planarity II","related_material":{"record":[{"status":"public","relation":"later_version","id":"1113"},{"relation":"earlier_version","id":"1595","status":"public"}]},"page":"468 - 481","date_updated":"2025-09-23T09:13:42Z","oa_version":"Preprint","publist_id":"6193","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"arxiv":1,"year":"2016","ec_funded":1,"oa":1,"doi":"10.1007/978-3-319-50106-2_36","day":"08","date_published":"2016-12-08T00:00:00Z","intvolume":"      9801"},{"ec_funded":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","day":"08","doi":"10.1007/978-3-319-50106-2_8","oa":1,"date_published":"2016-12-08T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"arxiv":1,"isi":1,"oa_version":"Preprint","publist_id":"6192","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","full_name":"Fulek, Radoslav","first_name":"Radoslav"}],"title":"C-planarity of embedded cyclic c-graphs","page":"94 - 106","related_material":{"record":[{"status":"public","relation":"later_version","id":"794"}]},"date_updated":"2025-09-22T09:54:03Z","type":"conference","abstract":[{"lang":"eng","text":"We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle."}],"citation":{"ieee":"R. Fulek, “C-planarity of embedded cyclic c-graphs,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp. 94–106.","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>","apa":"Fulek, R. (2016). C-planarity of embedded cyclic c-graphs (Vol. 9801, pp. 94–106). Presented at the GD: Graph Drawing and Network Visualization, Athens, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_8\">https://doi.org/10.1007/978-3-319-50106-2_8</a>","mla":"Fulek, Radoslav. <i>C-Planarity of Embedded Cyclic c-Graphs</i>. Vol. 9801, Springer, 2016, pp. 94–106, doi:<a href=\"https://doi.org/10.1007/978-3-319-50106-2_8\">10.1007/978-3-319-50106-2_8</a>.","ista":"Fulek R. 2016. C-planarity of embedded cyclic c-graphs. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 94–106.","chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs,” 9801:94–106. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-50106-2_8\">https://doi.org/10.1007/978-3-319-50106-2_8</a>.","short":"R. Fulek, in:, Springer, 2016, pp. 94–106."},"quality_controlled":"1","publisher":"Springer","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.01346"}],"volume":"9801 ","department":[{"_id":"UlWa"}],"conference":{"start_date":"2016-09-19","name":"GD: Graph Drawing and Network Visualization","location":"Athens, Greece","end_date":"2016-09-21"},"external_id":{"isi":["000405478500008"],"arxiv":["1602.01346"]},"alternative_title":["LNCS"],"publication_status":"published","date_created":"2018-12-11T11:50:30Z","month":"12","scopus_import":"1","_id":"1165"},{"publication_status":"published","date_created":"2018-12-11T11:50:30Z","conference":{"end_date":"2016-02-17","start_date":"2016-02-12","location":"Phoenix, AZ, United States","name":"AAAI: Conference on Artificial Intelligence"},"external_id":{"arxiv":["1511.08456"]},"_id":"1166","month":"12","citation":{"short":"K. Chatterjee, M. Chmelik, J. Davies, in:, Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, AAAI Press, 2016, pp. 3225–3232.","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>.","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.","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>.","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.","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>","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>"},"type":"conference","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"}],"quality_controlled":"1","volume":2016,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"OA_type":"green","publisher":"AAAI Press","corr_author":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1511.08456","open_access":"1"}],"oa_version":"Preprint","publist_id":"6191","title":"A symbolic SAT based algorithm for almost sure reachability with small strategies in POMDPs","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"first_name":"Jessica","id":"378E0060-F248-11E8-B48F-1D18A9856A87","full_name":"Davies, Jessica","last_name":"Davies"}],"date_updated":"2025-06-25T11:52:14Z","page":"3225 - 3232","related_material":{"link":[{"relation":"table_of_contents","url":"https://dl.acm.org/citation.cfm?id=3016355"}],"record":[{"relation":"earlier_version","id":"5443","status":"public"}]},"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"doi":"10.1609/aaai.v30i1.10422","day":"02","date_published":"2016-12-02T00:00:00Z","intvolume":"      2016","year":"2016","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.","ec_funded":1,"arxiv":1,"publication":"Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","date_created":"2018-12-11T11:50:30Z","external_id":{"isi":["000392126000015"]},"_id":"1167","pubrep_id":"740","month":"12","issue":"12","scopus_import":"1","citation":{"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>","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.","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>.","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>.","short":"M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016)."},"type":"journal_article","abstract":[{"lang":"eng","text":"Evolutionary pathways describe trajectories of biological evolution in the space of different variants of organisms (genotypes). The probability of existence and the number of evolutionary pathways that lead from a given genotype to a better-adapted genotype are important measures of accessibility of local fitness optima and the reproducibility of evolution. Both quantities have been studied in simple mathematical models where genotypes are represented as binary sequences of two types of basic units, and the network of permitted mutations between the genotypes is a hypercube graph. However, it is unclear how these results translate to the biologically relevant case in which genotypes are represented by sequences of more than two units, for example four nucleotides (DNA) or 20 amino acids (proteins), and the mutational graph is not the hypercube. Here we investigate accessibility of the best-adapted genotype in the general case of K &gt; 2 units. Using computer generated and experimental fitness landscapes we show that accessibility of the global fitness maximum increases with K and can be much higher than for binary sequences. The increase in accessibility comes from the increase in the number of indirect trajectories exploited by evolution for higher K. As one of the consequences, the fraction of genotypes that are accessible increases by three orders of magnitude when the number of units K increases from 2 to 16 for landscapes of size N ∼ 106genotypes. This suggests that evolution can follow many different trajectories on such landscapes and the reconstruction of evolutionary pathways from experimental data might be an extremely difficult task."}],"quality_controlled":"1","volume":12,"department":[{"_id":"AnKi"}],"publisher":"Public Library of Science","publist_id":"6190","oa_version":"Published Version","author":[{"first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P","last_name":"Zagórski","orcid":"0000-0001-7896-7762"},{"full_name":"Burda, Zdzisław","last_name":"Burda","first_name":"Zdzisław"},{"first_name":"Bartłomiej","last_name":"Wacław","full_name":"Wacław, Bartłomiej"}],"title":"Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks","related_material":{"record":[{"id":"9866","relation":"research_data","status":"public"}]},"date_updated":"2025-09-22T09:53:16Z","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2020-07-14T12:44:37Z","file":[{"checksum":"84f44ae92866c52ff1ca8a574558dca7","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:44:37Z","file_id":"4926","access_level":"open_access","creator":"system","file_size":3822299,"file_name":"IST-2017-740-v1+1_journal.pcbi.1005218.pdf","date_created":"2018-12-12T10:12:08Z"}],"oa":1,"doi":"10.1371/journal.pcbi.1005218","day":"09","date_published":"2016-12-09T00:00:00Z","intvolume":"        12","article_number":"e1005218","year":"2016","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.","isi":1,"publication":"PLoS Computational Biology","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"]},{"publisher":"Society for Industrial and Applied Mathematics ","corr_author":"1","volume":38,"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"OA_type":"green","citation":{"short":"M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.","ista":"Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.","chicago":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” <i>SIAM Journal on Scientific Computing</i>. Society for Industrial and Applied Mathematics , 2016. <a href=\"https://doi.org/10.1137/15M103306X\">https://doi.org/10.1137/15M103306X</a>.","mla":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” <i>SIAM Journal on Scientific Computing</i>, vol. 38, no. 6, Society for Industrial and Applied Mathematics , 2016, pp. B988–1008, doi:<a href=\"https://doi.org/10.1137/15M103306X\">10.1137/15M103306X</a>.","apa":"Lang, M., &#38; Stelling, J. (2016). Modular parameter identification of biomolecular networks. <i>SIAM Journal on Scientific Computing</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/15M103306X\">https://doi.org/10.1137/15M103306X</a>","ieee":"M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” <i>SIAM Journal on Scientific Computing</i>, vol. 38, no. 6. Society for Industrial and Applied Mathematics , pp. B988–B1008, 2016.","ama":"Lang M, Stelling J. Modular parameter identification of biomolecular networks. <i>SIAM Journal on Scientific Computing</i>. 2016;38(6):B988-B1008. doi:<a href=\"https://doi.org/10.1137/15M103306X\">10.1137/15M103306X</a>"},"abstract":[{"lang":"eng","text":"The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identification of model parameters. While modularization of the corresponding optimization problems could help reduce the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into subnetworks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we present here a modular parameter identification approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This definition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of different modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set---but not during earlier iterations---the intermodule communication as well as the individual modules\\' state dynamics agree with the dynamics of the nonmodularized network. Our modular parameter identification approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to suboptimal local minima. We demonstrate the algorithm\\'s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway."}],"type":"journal_article","quality_controlled":"1","month":"11","scopus_import":"1","issue":"6","_id":"1170","pubrep_id":"811","external_id":{"isi":["000391853100010"]},"publication_status":"published","date_created":"2018-12-11T11:50:31Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["003","518","570","621"],"OA_place":"repository","isi":1,"publication":"SIAM Journal on Scientific Computing","article_type":"original","year":"2016","file":[{"access_level":"open_access","date_created":"2018-12-12T10:14:41Z","file_name":"IST-2017-811-v1+1_modular_parameter_identification.pdf","file_size":871964,"creator":"system","relation":"main_file","checksum":"781bc3ffd30b2dd65b7727c5a285fc78","content_type":"application/pdf","file_id":"5095","date_updated":"2025-06-25T11:26:45Z"}],"oa":1,"doi":"10.1137/15M103306X","day":"15","date_published":"2016-11-15T00:00:00Z","intvolume":"        38","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2025-06-25T11:26:45Z","title":"Modular parameter identification of biomolecular networks","author":[{"first_name":"Moritz","full_name":"Lang, Moritz","last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jörg","full_name":"Stelling, Jörg","last_name":"Stelling"}],"page":"B988 - B1008","date_updated":"2025-09-22T09:51:45Z","oa_version":"Submitted Version","publist_id":"6186"},{"year":"2016","type":"journal_article","doi":"10.1016/j.plrev.2016.06.005","day":"01","citation":{"chicago":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot; by O. C. Martin et Al.” <i>Physics of Life Reviews</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">https://doi.org/10.1016/j.plrev.2016.06.005</a>.","ista":"Tkačik G. 2016. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. Physics of Life Reviews. 17, 166–167.","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>.","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.","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>","ama":"Tkačik G. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. <i>Physics of Life Reviews</i>. 2016;17:166-167. doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">10.1016/j.plrev.2016.06.005</a>","short":"G. Tkačik, Physics of Life Reviews 17 (2016) 166–167."},"quality_controlled":"1","intvolume":"        17","date_published":"2016-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Elsevier","volume":17,"publication":"Physics of Life Reviews","department":[{"_id":"GaTk"}],"isi":1,"external_id":{"isi":["000381544100033"]},"publication_status":"published","date_created":"2018-12-11T11:50:32Z","oa_version":"None","publist_id":"6185","status":"public","month":"07","language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","author":[{"first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"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.","_id":"1171","date_updated":"2025-09-22T09:50:37Z","page":"166 - 167"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["576"],"publication":"Scientific Reports","isi":1,"article_number":"38840","year":"2016","acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","doi":"10.1038/srep38840","day":"19","file":[{"creator":"system","file_size":760967,"file_name":"IST-2017-737-v1+1_srep38840.pdf","date_created":"2018-12-12T10:12:56Z","access_level":"open_access","date_updated":"2020-07-14T12:44:37Z","file_id":"4977","checksum":"cb378732da885ea4959ec5b845fb6e52","content_type":"application/pdf","relation":"main_file"}],"oa":1,"intvolume":"         6","date_published":"2016-12-19T00:00:00Z","status":"public","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:37Z","article_processing_charge":"No","has_accepted_license":"1","author":[{"first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barma","full_name":"Barma, Mustansir","first_name":"Mustansir"},{"first_name":"Madan","last_name":"Rao","full_name":"Rao, Madan"}],"title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","date_updated":"2025-09-22T09:49:53Z","oa_version":"Published Version","publist_id":"6183","publisher":"Nature Publishing Group","volume":6,"department":[{"_id":"NiBa"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"citation":{"short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>.","ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","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>.","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>","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>","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."},"quality_controlled":"1","month":"12","scopus_import":"1","pubrep_id":"737","_id":"1172","external_id":{"isi":["000389885900001"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2018-12-11T11:50:32Z"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"publication":"Algorithmica","year":"2016","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.","date_published":"2016-04-01T00:00:00Z","intvolume":"        74","oa":1,"day":"01","doi":"10.1007/s00453-015-9997-6","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-09-22T09:49:20Z","page":"1321 - 1362","title":"A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound","author":[{"first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"},{"first_name":"Sanjit","full_name":"Chatterjee, Sanjit","last_name":"Chatterjee"}],"publist_id":"6177","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2013/651"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"volume":74,"quality_controlled":"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>.","ista":"Kamath Hosdurg C, Chatterjee S. 2016. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. 74(4), 1321–1362.","chicago":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” <i>Algorithmica</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00453-015-9997-6\">https://doi.org/10.1007/s00453-015-9997-6</a>.","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>","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.","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>"},"type":"journal_article","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."}],"issue":"4","month":"04","_id":"1177","external_id":{"isi":["000373640000005"]},"date_created":"2018-12-11T11:50:33Z","publication_status":"published"},{"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"oa":1,"day":"22","doi":"10.1007/978-3-662-53641-4_8","date_published":"2016-10-22T00:00:00Z","intvolume":"      9985","acknowledgement":"K. Pietrzak—Supported by the European Research Council consolidator grant (682815-TOCNeT).\r\nM. Skórski—Supported by the National Science Center, Poland (2015/17/N/ST6/03564).","year":"2016","ec_funded":1,"title":"Pseudoentropy: Lower-bounds for chain rules and transformations","author":[{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z"},{"last_name":"Maciej","full_name":"Maciej, Skorski","first_name":"Skorski"}],"date_updated":"2025-09-22T09:48:49Z","page":"183 - 203","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","publist_id":"6175","oa_version":"Preprint","volume":9985,"department":[{"_id":"KrPi"}],"publisher":"Springer","main_file_link":[{"url":"https://eprint.iacr.org/2016/159","open_access":"1"}],"citation":{"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>.","ista":"Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985, 183–203.","mla":"Pietrzak, Krzysztof Z., and Skorski Maciej. <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>.","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., &#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>","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>"},"type":"conference","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."}],"quality_controlled":"1","_id":"1179","month":"10","scopus_import":"1","publication_status":"published","date_created":"2018-12-11T11:50:34Z","conference":{"end_date":"2016-11-03","name":"TCC: Theory of Cryptography Conference","location":"Beijing, China","start_date":"2016-10-31"},"external_id":{"isi":["000390176000008"]},"alternative_title":["LNCS"]},{"publication":"Journal of Neuroscience","isi":1,"project":[{"grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        36","date_published":"2016-11-09T00:00:00Z","day":"09","doi":"10.1523/JNEUROSCI.2359-16.2016","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.","year":"2016","date_updated":"2025-09-22T09:48:17Z","page":"11394 - 11401","author":[{"last_name":"Dwyer","full_name":"Dwyer, Noelle","first_name":"Noelle"},{"last_name":"Chen","full_name":"Chen, Bin","first_name":"Bin"},{"last_name":"Chou","full_name":"Chou, Shen","first_name":"Shen"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nguyen","full_name":"Nguyen, Laurent","first_name":"Laurent"},{"last_name":"Ghashghaei","full_name":"Ghashghaei, Troy","first_name":"Troy"}],"title":"Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","publist_id":"6172","oa_version":"None","department":[{"_id":"SiHi"}],"volume":36,"publisher":"Society for Neuroscience","quality_controlled":"1","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."}],"type":"journal_article","citation":{"apa":"Dwyer, N., Chen, B., Chou, S., Hippenmeyer, S., Nguyen, L., &#38; Ghashghaei, T. (2016). Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">https://doi.org/10.1523/JNEUROSCI.2359-16.2016</a>","ama":"Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity. <i>Journal of Neuroscience</i>. 2016;36(45):11394-11401. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2359-16.2016\">10.1523/JNEUROSCI.2359-16.2016</a>","ieee":"N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, and T. Ghashghaei, “Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity,” <i>Journal of Neuroscience</i>, vol. 36, no. 45. Society for Neuroscience, pp. 11394–11401, 2016.","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>.","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.","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>.","short":"N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, T. Ghashghaei, Journal of Neuroscience 36 (2016) 11394–11401."},"_id":"1181","scopus_import":"1","issue":"45","month":"11","date_created":"2018-12-11T11:50:35Z","publication_status":"published","external_id":{"isi":["000391054300003"]}},{"year":"2016","ec_funded":1,"date_published":"2016-01-01T00:00:00Z","oa":1,"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"}],"arxiv":1,"oa_version":"Preprint","publist_id":"6171","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-04-22T13:42:22Z","related_material":{"link":[{"relation":"table_of_contents","url":"https://www.ijcai.org/proceedings/2016"}]},"page":"172 - 179","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","full_name":"Tkadlec, Josef"}],"title":"Robust draws in balanced knockout tournaments","quality_controlled":"1","citation":{"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.","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.","ama":"Chatterjee K, Ibsen-Jensen R, Tkadlec J. Robust draws in balanced knockout tournaments. In: Vol 2016-January. AAAI Press; 2016:172-179.","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.","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."},"type":"conference","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"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.05090"}],"corr_author":"1","publisher":"AAAI Press","department":[{"_id":"KrCh"}],"volume":"2016-January","external_id":{"arxiv":["1604.05090"]},"conference":{"location":"New York, NY, USA","name":"IJCAI: International Joint Conference on Artificial Intelligence","start_date":"2016-07-09","end_date":"2016-07-15"},"date_created":"2018-12-11T11:50:35Z","publication_status":"published","scopus_import":"1","month":"01","_id":"1182"},{"publisher":"Wiley-Blackwell","volume":6,"department":[{"_id":"SyCr"}],"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"}],"type":"journal_article","citation":{"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>","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.","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>","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>.","ista":"Metzler S, Heinze J, Schrempf A. 2016. Mating and longevity in ant males. Ecology and Evolution. 6(24), 8903–8906.","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>.","short":"S. Metzler, J. Heinze, A. Schrempf, Ecology and Evolution 6 (2016) 8903–8906."},"quality_controlled":"1","month":"12","scopus_import":"1","issue":"24","pubrep_id":"736","_id":"1184","external_id":{"isi":["000392063300022"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2018-12-11T11:50:36Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["576","592"],"publication":"Ecology and Evolution","isi":1,"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.","year":"2016","day":"01","doi":"10.1002/ece3.2474","file":[{"access_level":"open_access","file_size":328414,"creator":"system","date_created":"2018-12-12T10:14:12Z","file_name":"IST-2017-736-v1+1_Metzler_et_al-2016-Ecology_and_Evolution.pdf","relation":"main_file","checksum":"789026eb9e1be2a0da08376f29f569cf","content_type":"application/pdf","file_id":"5062","date_updated":"2020-07-14T12:44:37Z"}],"oa":1,"intvolume":"         6","date_published":"2016-12-01T00:00:00Z","status":"public","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:37Z","article_processing_charge":"No","has_accepted_license":"1","title":"Mating and longevity in ant males","author":[{"first_name":"Sina","orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87","last_name":"Metzler","full_name":"Metzler, Sina"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"first_name":"Alexandra","last_name":"Schrempf","full_name":"Schrempf, Alexandra"}],"page":"8903 - 8906","date_updated":"2025-09-22T09:47:16Z","publist_id":"6169","oa_version":"Published Version"},{"citation":{"short":"M. Cucinotta, S. Manrique, A. Guazzotti, N. Quadrelli, M. Mendes, E. Benková, L. Colombo, Development 143 (2016) 4419–4424.","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>.","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>.","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.","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.","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>"},"type":"journal_article","abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","volume":143,"department":[{"_id":"EvBe"}],"publisher":"Company of Biologists","publication_status":"published","date_created":"2018-12-11T11:50:36Z","external_id":{"isi":["000393454100012"]},"_id":"1185","month":"12","scopus_import":"1","issue":"23","doi":"10.1242/dev.143545","day":"01","date_published":"2016-12-01T00:00:00Z","intvolume":"       143","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.","year":"2016","isi":1,"publication":"Development","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","publist_id":"6168","author":[{"full_name":"Cucinotta, Mara","last_name":"Cucinotta","first_name":"Mara"},{"last_name":"Manrique","full_name":"Manrique, Silvia","first_name":"Silvia"},{"full_name":"Guazzotti, Andrea","last_name":"Guazzotti","first_name":"Andrea"},{"full_name":"Quadrelli, Nadia","last_name":"Quadrelli","first_name":"Nadia"},{"first_name":"Marta","full_name":"Mendes, Marta","last_name":"Mendes"},{"full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva"},{"first_name":"Lucia","last_name":"Colombo","full_name":"Colombo, Lucia"}],"title":"Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development","date_updated":"2025-09-22T09:46:43Z","page":"4419 - 4424","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No"},{"quality_controlled":"1","type":"journal_article","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"}],"citation":{"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>.","ista":"Gutierrez-Fernandez J, Saleh M, Alcorlo M, Gómez Mejóa A, Pantoja Uceda D, Treviño M, Vob F, Abdullah M, Galán Bartual S, Seinen J, Sánchez Murcia P, Gago F, Bruix M, Hammerschmidt S, Hermoso J. 2016. Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis. Scientific Reports. 6, 38094.","mla":"Gutierrez-Fernandez, Javier, et al. “Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal Pathogenesis.” <i>Scientific Reports</i>, vol. 6, 38094, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep38094\">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.","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>","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>"},"publisher":"Nature Publishing Group","department":[{"_id":"LeSa"}],"volume":6,"external_id":{"isi":["000389129100001"]},"date_created":"2018-12-11T11:50:36Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"scopus_import":"1","month":"12","pubrep_id":"735","_id":"1186","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","article_number":"38094","intvolume":"         6","date_published":"2016-12-05T00:00:00Z","day":"05","doi":"10.1038/srep38094","file":[{"date_created":"2018-12-12T10:10:18Z","file_name":"IST-2017-735-v1+1_srep38094.pdf","creator":"system","file_size":2716045,"access_level":"open_access","date_updated":"2020-07-14T12:44:37Z","file_id":"4804","checksum":"e007d78b483bc59bf5ab98e9d42a6ec1","content_type":"application/pdf","relation":"main_file"}],"oa":1,"ddc":["576","610"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Scientific Reports","isi":1,"oa_version":"Published Version","publist_id":"6167","file_date_updated":"2020-07-14T12:44:37Z","article_processing_charge":"No","has_accepted_license":"1","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-09-22T09:46:12Z","title":"Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis","author":[{"first_name":"Javier","last_name":"Gutierrez-Fernandez","full_name":"Gutierrez-Fernandez, Javier","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Malek","last_name":"Saleh","full_name":"Saleh, Malek"},{"first_name":"Martín","full_name":"Alcorlo, Martín","last_name":"Alcorlo"},{"first_name":"Alejandro","last_name":"Gómez Mejóa","full_name":"Gómez Mejóa, Alejandro"},{"first_name":"David","full_name":"Pantoja Uceda, David","last_name":"Pantoja Uceda"},{"first_name":"Miguel","full_name":"Treviño, Miguel","last_name":"Treviño"},{"first_name":"Franziska","last_name":"Vob","full_name":"Vob, Franziska"},{"first_name":"Mohammed","last_name":"Abdullah","full_name":"Abdullah, Mohammed"},{"full_name":"Galán Bartual, Sergio","last_name":"Galán Bartual","first_name":"Sergio"},{"full_name":"Seinen, Jolien","last_name":"Seinen","first_name":"Jolien"},{"first_name":"Pedro","last_name":"Sánchez Murcia","full_name":"Sánchez Murcia, Pedro"},{"last_name":"Gago","full_name":"Gago, Federico","first_name":"Federico"},{"last_name":"Bruix","full_name":"Bruix, Marta","first_name":"Marta"},{"last_name":"Hammerschmidt","full_name":"Hammerschmidt, Sven","first_name":"Sven"},{"full_name":"Hermoso, Juan","last_name":"Hermoso","first_name":"Juan"}]},{"external_id":{"arxiv":["1606.09048"],"isi":["000391973900001"]},"date_created":"2018-12-11T11:50:37Z","publication_status":"published","scopus_import":"1","issue":"12","month":"12","_id":"1188","quality_controlled":"1","citation":{"short":"D. De Martino, D. Masoero,  Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).","ama":"De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. 2016;2016(12). doi:<a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">10.1088/1742-5468/aa4e8f</a>","ieee":"D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth,” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2016, no. 12. IOP Publishing, 2016.","apa":"De Martino, D., &#38; Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">https://doi.org/10.1088/1742-5468/aa4e8f</a>","mla":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &#38;amp; Growth.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2016, no. 12, 123502, IOP Publishing, 2016, doi:<a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">10.1088/1742-5468/aa4e8f</a>.","chicago":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &#38;amp; Growth.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing, 2016. <a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">https://doi.org/10.1088/1742-5468/aa4e8f</a>.","ista":"De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth.  Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502."},"abstract":[{"text":"We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation is solved for the steady state in the WKB\r\napproximation that maps it into the ground state of a quantum particle in an\r\nAiry potential plus a centrifugal term. We retrieve scaling laws for growth rate\r\nfluctuations and time response with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal populations can have a faster response\r\nto perturbations.","lang":"eng"}],"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.09048"}],"publisher":"IOP Publishing","department":[{"_id":"GaTk"}],"volume":2016,"publist_id":"6165","oa_version":"Preprint","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-09-22T09:45:38Z","author":[{"orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","full_name":"De Martino, Daniele","first_name":"Daniele"},{"last_name":"Masoero","full_name":"Masoero, Davide","first_name":"Davide"}],"title":"Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth","acknowledgement":"D De Martino is supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011. D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano and Vera Luz Masoero for useful discussions, also late at night.","year":"2016","ec_funded":1,"article_number":"123502","date_published":"2016-12-30T00:00:00Z","intvolume":"      2016","oa":1,"day":"30","doi":"10.1088/1742-5468/aa4e8f","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"isi":1,"publication":" Journal of Statistical Mechanics: Theory and Experiment","arxiv":1},{"publisher":"IEEE","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1506.08547v7"}],"volume":"2016-December","department":[{"_id":"VlKo"}],"citation":{"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>","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>","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.","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>.","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.","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."},"type":"conference","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","month":"12","scopus_import":"1","_id":"1193","conference":{"name":"FOCS: Foundations of Computer Science","location":"New Brunswick, NJ, USA ","start_date":"2016-09-09","end_date":"2016-09-11"},"external_id":{"arxiv":["1506.08547"],"isi":["000391198500082"]},"publication_status":"published","date_created":"2018-12-11T11:50:38Z","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"publication":"Proceedings - Annual IEEE Symposium on Foundations of Computer Science","arxiv":1,"article_number":"7782993","acknowledgement":"European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 616160","year":"2016","ec_funded":1,"oa":1,"day":"15","doi":"10.1109/FOCS.2016.88","date_published":"2016-12-15T00:00:00Z","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir"}],"title":"Commutativity in the algorithmic Lovasz local lemma","date_updated":"2025-09-22T09:44:20Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"5975"}]},"oa_version":"Preprint","publist_id":"6158"}]