[{"doi":"10.1371/journal.pbio.2001894","publication":"PLoS Biology","isi":1,"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"9856"},{"relation":"research_data","status":"public","id":"9857"},{"id":"9858","status":"public","relation":"research_data"}]},"volume":15,"day":"30","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:49:22Z","ddc":["576"],"external_id":{"isi":["000402520000012"]},"year":"2017","article_number":"e2001894","intvolume":" 15","month":"05","date_published":"2017-05-30T00:00:00Z","issue":"5","oa":1,"date_updated":"2023-09-22T10:02:52Z","publication_status":"published","type":"journal_article","file_date_updated":"2020-07-14T12:48:16Z","abstract":[{"lang":"eng","text":"Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo"}],"scopus_import":"1","citation":{"apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894","mla":"Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.","ama":"Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 2017;15(5). doi:10.1371/journal.pbio.2001894","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 15(5), e2001894.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology 15 (2017).","ieee":"T. Schmidt et al., “Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,” PLoS Biology, vol. 15, no. 5. Public Library of Science, 2017.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894."},"publication_identifier":{"issn":["15449173"]},"quality_controlled":"1","_id":"951","department":[{"_id":"NiBa"}],"publist_id":"6464","article_processing_charge":"No","pubrep_id":"843","language":[{"iso":"eng"}],"publisher":"Public Library of Science","has_accepted_license":"1","file":[{"content_type":"application/pdf","file_id":"4691","creator":"system","file_size":5541206,"checksum":"107d290bd1159ec77b734eb2824b01c8","access_level":"open_access","relation":"main_file","file_name":"IST-2017-843-v1+1_journal.pbio.2001894.pdf","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:08:30Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Tom","last_name":"Schmidt","full_name":"Schmidt, Tom"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"},{"first_name":"Gordana","last_name":"Rasic","full_name":"Rasic, Gordana"},{"last_name":"Turley","first_name":"Andrew","full_name":"Turley, Andrew"},{"last_name":"Montgomery","first_name":"Brian","full_name":"Montgomery, Brian"},{"full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki","last_name":"Iturbe Ormaetxe"},{"first_name":"Peter","last_name":"Cook","full_name":"Cook, Peter"},{"last_name":"Ryan","first_name":"Peter","full_name":"Ryan, Peter"},{"last_name":"Ritchie","first_name":"Scott","full_name":"Ritchie, Scott"},{"full_name":"Hoffmann, Ary","last_name":"Hoffmann","first_name":"Ary"},{"full_name":"O’Neill, Scott","last_name":"O’Neill","first_name":"Scott"},{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"}],"title":"Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti"},{"date_published":"2017-06-01T00:00:00Z","month":"06","intvolume":" 115","oa":1,"date_updated":"2023-09-22T10:02:21Z","page":"45 - 60","external_id":{"pmid":["28411063"]},"year":"2017","volume":115,"pmid":1,"status":"public","day":"01","ddc":["576"],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2018-12-11T11:49:22Z","publication":"Theoretical Population Biology","doi":"10.1016/j.tpb.2017.03.003","oa_version":"Submitted Version","publisher":"Elsevier","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"title":"Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti","file":[{"file_name":"2017_TheoreticalPopulationBio_Turelli.pdf","date_updated":"2020-07-14T12:48:16Z","date_created":"2019-04-17T06:39:45Z","file_size":2073856,"creator":"dernst","content_type":"application/pdf","file_id":"6327","relation":"main_file","checksum":"9aeff86fa7de69f7a15cf4fc60d57d01","access_level":"open_access"}],"department":[{"_id":"NiBa"}],"publist_id":"6463","article_processing_charge":"No","pubrep_id":"972","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area."}],"file_date_updated":"2020-07-14T12:48:16Z","type":"journal_article","publication_identifier":{"issn":["00405809"]},"citation":{"ama":"Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003","ista":"Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 115, 45–60.","short":"M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.","ieee":"M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti,” Theoretical Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.","chicago":"Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.","apa":"Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003","mla":"Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003."},"quality_controlled":"1","_id":"952","publication_status":"published"},{"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"publist_id":"6462","article_processing_charge":"No","title":"The sources of adaptive evolution","author":[{"full_name":"Charlesworth, Deborah","last_name":"Charlesworth","first_name":"Deborah"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Royal Society, The","publication_status":"published","quality_controlled":"1","_id":"953","scopus_import":"1","abstract":[{"lang":"eng","text":"The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed."}],"type":"journal_article","citation":{"chicago":"Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2017. https://doi.org/10.1098/rspb.2016.2864.","ama":"Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 2017;284(1855). doi:10.1098/rspb.2016.2864","short":"D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society of London Series B Biological Sciences 284 (2017).","ieee":"D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive evolution,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855. Royal Society, The, 2017.","ista":"Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855), 20162864.","mla":"Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855, 20162864, Royal Society, The, 2017, doi:10.1098/rspb.2016.2864.","apa":"Charlesworth, D., Barton, N. H., & Charlesworth, B. (2017). The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.2864"},"year":"2017","external_id":{"isi":["000405148800021"],"pmid":["28566483"]},"oa":1,"issue":"1855","date_updated":"2023-09-22T10:01:48Z","article_number":"20162864","date_published":"2017-05-31T00:00:00Z","month":"05","intvolume":" 284","oa_version":"Submitted Version","isi":1,"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","doi":"10.1098/rspb.2016.2864","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/"}],"status":"public","day":"31","date_created":"2018-12-11T11:49:23Z","volume":284,"pmid":1},{"file":[{"checksum":"59cdd4400fb41280122d414fea971546","access_level":"open_access","relation":"main_file","creator":"system","file_size":2441529,"content_type":"application/pdf","file_id":"5306","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:17:49Z","file_name":"IST-2017-841-v1+1_elife-25192-v2.pdf"},{"file_name":"IST-2017-841-v1+2_elife-25192-figures-v2.pdf","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:17:50Z","content_type":"application/pdf","file_id":"5307","file_size":3752660,"creator":"system","checksum":"b69024880558b858eb8c5d47a92b6377","relation":"main_file","access_level":"open_access"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"On the mechanistic nature of epistasis in a canonical cis-regulatory element","author":[{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","full_name":"Lagator, Mato"},{"full_name":"Paixao, Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C"}],"has_accepted_license":"1","publisher":"eLife Sciences Publications","language":[{"iso":"eng"}],"pubrep_id":"841","article_processing_charge":"Yes","publist_id":"6460","department":[{"_id":"CaGu"},{"_id":"NiBa"},{"_id":"JoBo"}],"_id":"954","quality_controlled":"1","publication_identifier":{"issn":["2050084X"]},"citation":{"mla":"Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192.","apa":"Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192","chicago":"Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.","ama":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192","ieee":"M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6. eLife Sciences Publications, 2017.","short":"M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).","ista":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192."},"type":"journal_article","file_date_updated":"2020-07-14T12:48:16Z","abstract":[{"text":"Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for.","lang":"eng"}],"scopus_import":"1","project":[{"call_identifier":"FP7","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"},{"name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020"}],"publication_status":"published","date_updated":"2023-09-22T10:01:17Z","oa":1,"intvolume":" 6","month":"05","date_published":"2017-05-18T00:00:00Z","article_number":"e25192","year":"2017","external_id":{"isi":["000404024800001"]},"date_created":"2018-12-11T11:49:23Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576"],"day":"18","status":"public","volume":6,"isi":1,"ec_funded":1,"oa_version":"Published Version","doi":"10.7554/eLife.25192","publication":"eLife"},{"scopus_import":"1","abstract":[{"text":"Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:16Z","type":"journal_article","citation":{"chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","ista":"Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.","ama":"Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8","mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.","apa":"Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8"},"publication_identifier":{"issn":["20411723"]},"quality_controlled":"1","_id":"955","publication_status":"published","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27"}],"publisher":"Nature Publishing Group","has_accepted_license":"1","author":[{"last_name":"Friedlander","first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar"},{"last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2018-12-12T10:14:14Z","date_updated":"2020-07-14T12:48:16Z","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","access_level":"open_access","relation":"main_file","checksum":"29a1b5db458048d3bd5c67e0e2a56818","content_type":"application/pdf","file_id":"5064","creator":"system","file_size":998157},{"relation":"main_file","access_level":"open_access","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","file_size":9715993,"creator":"system","content_type":"application/pdf","file_id":"5065","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:14:15Z","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf"}],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publist_id":"6459","article_processing_charge":"Yes (in subscription journal)","pubrep_id":"864","language":[{"iso":"eng"}],"volume":8,"day":"09","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:49:23Z","ddc":["539","576"],"publication":"Nature Communications","doi":"10.1038/s41467-017-00238-8","ec_funded":1,"oa_version":"Published Version","isi":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6071"}]},"article_number":"216","date_published":"2017-08-09T00:00:00Z","intvolume":" 8","month":"08","oa":1,"issue":"1","date_updated":"2025-05-28T11:42:50Z","external_id":{"isi":["000407198800005"]},"year":"2017"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance","author":[{"last_name":"Carlen","first_name":"Eric","full_name":"Carlen, Eric"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Maas","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan"}],"publisher":"Academic Press","language":[{"iso":"eng"}],"department":[{"_id":"JaMa"}],"publist_id":"6452","article_processing_charge":"No","quality_controlled":"1","_id":"956","abstract":[{"text":"We study a class of ergodic quantum Markov semigroups on finite-dimensional unital C⁎-algebras. These semigroups have a unique stationary state σ, and we are concerned with those that satisfy a quantum detailed balance condition with respect to σ. We show that the evolution on the set of states that is given by such a quantum Markov semigroup is gradient flow for the relative entropy with respect to σ in a particular Riemannian metric on the set of states. This metric is a non-commutative analog of the 2-Wasserstein metric, and in several interesting cases we are able to show, in analogy with work of Otto on gradient flows with respect to the classical 2-Wasserstein metric, that the relative entropy is strictly and uniformly convex with respect to the Riemannian metric introduced here. As a consequence, we obtain a number of new inequalities for the decay of relative entropy for ergodic quantum Markov semigroups with detailed balance.","lang":"eng"}],"scopus_import":"1","type":"journal_article","citation":{"apa":"Carlen, E., & Maas, J. (2017). Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2017.05.003","mla":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis, vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:10.1016/j.jfa.2017.05.003.","ama":"Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 2017;273(5):1810-1869. doi:10.1016/j.jfa.2017.05.003","short":"E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869.","ista":"Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5), 1810–1869.","ieee":"E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance,” Journal of Functional Analysis, vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017.","chicago":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis. Academic Press, 2017. https://doi.org/10.1016/j.jfa.2017.05.003."},"publication_identifier":{"issn":["00221236"]},"publication_status":"published","oa":1,"issue":"5","date_updated":"2023-09-22T10:00:18Z","date_published":"2017-09-01T00:00:00Z","intvolume":" 273","month":"09","year":"2017","page":"1810 - 1869","external_id":{"isi":["000406082300005"]},"day":"01","status":"public","date_created":"2018-12-11T11:49:24Z","volume":273,"oa_version":"Submitted Version","isi":1,"publication":"Journal of Functional Analysis","doi":"10.1016/j.jfa.2017.05.003","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.01254"}]},{"page":"71 - 87","series_title":"Synthetic Protein Switches","year":"2017","alternative_title":["Methods in Molecular Biology"],"date_published":"2017-03-15T00:00:00Z","intvolume":" 1596","month":"03","date_updated":"2021-01-12T08:22:13Z","publication":"Synthetic Protein Switches","doi":"10.1007/978-1-4939-6940-1_5","oa_version":"None","volume":1596,"date_created":"2018-12-11T11:49:24Z","day":"15","status":"public","publist_id":"6451","department":[{"_id":"HaJa"}],"language":[{"iso":"eng"}],"publisher":"Springer","author":[{"full_name":"Clifton, Ben","last_name":"Clifton","first_name":"Ben"},{"full_name":"Whitfield, Jason","last_name":"Whitfield","first_name":"Jason"},{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada","last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada"},{"full_name":"Herde, Michel","first_name":"Michel","last_name":"Herde"},{"full_name":"Henneberger, Christian","first_name":"Christian","last_name":"Henneberger"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jackson, Colin","first_name":"Colin","last_name":"Jackson"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","project":[{"grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publication_identifier":{"issn":["10643745"]},"citation":{"mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5","chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.","short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87.","ieee":"B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.","ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87.","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5"},"scopus_import":1,"abstract":[{"lang":"eng","text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors."}],"type":"book_chapter","_id":"957","editor":[{"last_name":"Stein","first_name":"Viktor","full_name":"Stein, Viktor"}],"quality_controlled":"1"},{"extern":"1","publication_identifier":{"issn":["1571-0653"]},"citation":{"chicago":"Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for the Littlewood-Offord Problem.” Electronic Notes in Discrete Mathematics. Elsevier, 2017. https://doi.org/10.1016/j.endm.2017.06.025.","short":"A.S. Bandeira, A. Ferber, M.A. Kwan, Electronic Notes in Discrete Mathematics 61 (2017) 93–99.","ista":"Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood-Offord problem. Electronic Notes in Discrete Mathematics. 61, 93–99.","ieee":"A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood-Offord problem,” Electronic Notes in Discrete Mathematics, vol. 61. Elsevier, pp. 93–99, 2017.","ama":"Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood-Offord problem. Electronic Notes in Discrete Mathematics. 2017;61:93-99. doi:10.1016/j.endm.2017.06.025","mla":"Bandeira, Afonso S., et al. “Resilience for the Littlewood-Offord Problem.” Electronic Notes in Discrete Mathematics, vol. 61, Elsevier, 2017, pp. 93–99, doi:10.1016/j.endm.2017.06.025.","apa":"Bandeira, A. S., Ferber, A., & Kwan, M. A. (2017). Resilience for the Littlewood-Offord problem. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2017.06.025"},"arxiv":1,"abstract":[{"text":"Consider the sum X(ξ)=∑ni=1aiξi, where a=(ai)ni=1 is a sequence of non-zero reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that is, Pr[ξi=1]=Pr[ξi=−1]=1/2). The classical Littlewood-Offord problem asks for the best possible upper bound on the concentration probabilities Pr[X=x]. In this paper we study a resilience version of the Littlewood-Offord problem: how many of the ξi is an adversary typically allowed to change without being able to force concentration on a particular value? We solve this problem asymptotically, and present a few interesting open problems.","lang":"eng"}],"scopus_import":"1","type":"journal_article","_id":"9574","quality_controlled":"1","publication_status":"published","publisher":"Elsevier","author":[{"full_name":"Bandeira, Afonso S.","first_name":"Afonso S.","last_name":"Bandeira"},{"first_name":"Asaf","last_name":"Ferber","full_name":"Ferber, Asaf"},{"first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","last_name":"Kwan","full_name":"Kwan, Matthew Alan"}],"title":"Resilience for the Littlewood-Offord problem","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","volume":61,"date_created":"2021-06-21T06:31:10Z","day":"01","status":"public","publication":"Electronic Notes in Discrete Mathematics","main_file_link":[{"url":"https://arxiv.org/abs/1609.08136","open_access":"1"}],"doi":"10.1016/j.endm.2017.06.025","oa_version":"Preprint","date_published":"2017-08-01T00:00:00Z","month":"08","intvolume":" 61","date_updated":"2023-02-23T14:01:26Z","oa":1,"external_id":{"arxiv":["1609.08136"]},"page":"93-99","year":"2017"},{"scopus_import":1,"abstract":[{"lang":"eng","text":"Biosensors that exploit Forster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors."}],"type":"book_chapter","citation":{"ama":"Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6","ieee":"J. Mitchell et al., “Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 89–99.","short":"J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 89–99.","ista":"Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2017.Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 89–99.","chicago":"Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6.","apa":"Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara, M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer. https://doi.org/10.1007/978-1-4939-6940-1_6","mla":"Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6."},"publication_identifier":{"issn":["10643745"]},"quality_controlled":"1","_id":"958","editor":[{"last_name":"Stein","first_name":"Viktor","full_name":"Stein, Viktor"}],"publication_status":"published","publisher":"Springer","author":[{"full_name":"Mitchell, Joshua","first_name":"Joshua","last_name":"Mitchell"},{"full_name":"Zhang, William","first_name":"William","last_name":"Zhang"},{"last_name":"Herde","first_name":"Michel","full_name":"Herde, Michel"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"},{"full_name":"Janovjak, Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"},{"full_name":"O'Mara, Megan","last_name":"O'Mara","first_name":"Megan"},{"last_name":"Jackson","first_name":"Colin","full_name":"Jackson, Colin"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment","department":[{"_id":"HaJa"}],"publist_id":"6450","language":[{"iso":"eng"}],"volume":1596,"status":"public","day":"15","date_created":"2018-12-11T11:49:24Z","publication":"Synthetic Protein Switches","doi":"10.1007/978-1-4939-6940-1_6","oa_version":"None","alternative_title":["Methods in Molecular Biology"],"date_published":"2017-05-15T00:00:00Z","intvolume":" 1596","month":"05","date_updated":"2021-01-12T08:22:13Z","page":"89 - 99","series_title":"Synthetic Protein Switches","year":"2017"},{"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Elsevier","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Resilience for the Littlewood–Offord problem","author":[{"full_name":"Bandeira, Afonso S.","last_name":"Bandeira","first_name":"Afonso S."},{"first_name":"Asaf","last_name":"Ferber","full_name":"Ferber, Asaf"},{"first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan"}],"publication_status":"published","type":"journal_article","abstract":[{"text":"Consider the sum X(ξ)=∑ni=1aiξi , where a=(ai)ni=1 is a sequence of non-zero reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that is, Pr[ξi=1]=Pr[ξi=−1]=1/2 ). The classical Littlewood-Offord problem asks for the best possible upper bound on the concentration probabilities Pr[X=x] . In this paper we study a resilience version of the Littlewood-Offord problem: how many of the ξi is an adversary typically allowed to change without being able to force concentration on a particular value? We solve this problem asymptotically, and present a few interesting open problems.","lang":"eng"}],"scopus_import":"1","arxiv":1,"citation":{"chicago":"Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for the Littlewood–Offord Problem.” Advances in Mathematics. Elsevier, 2017. https://doi.org/10.1016/j.aim.2017.08.031.","ama":"Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood–Offord problem. Advances in Mathematics. 2017;319:292-312. doi:10.1016/j.aim.2017.08.031","ista":"Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood–Offord problem. Advances in Mathematics. 319, 292–312.","short":"A.S. Bandeira, A. Ferber, M.A. Kwan, Advances in Mathematics 319 (2017) 292–312.","ieee":"A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood–Offord problem,” Advances in Mathematics, vol. 319. Elsevier, pp. 292–312, 2017.","mla":"Bandeira, Afonso S., et al. “Resilience for the Littlewood–Offord Problem.” Advances in Mathematics, vol. 319, Elsevier, 2017, pp. 292–312, doi:10.1016/j.aim.2017.08.031.","apa":"Bandeira, A. S., Ferber, A., & Kwan, M. A. (2017). Resilience for the Littlewood–Offord problem. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2017.08.031"},"publication_identifier":{"issn":["0001-8708"]},"extern":"1","quality_controlled":"1","_id":"9588","external_id":{"arxiv":["1609.08136"]},"page":"292-312","year":"2017","intvolume":" 319","month":"10","date_published":"2017-10-15T00:00:00Z","oa":1,"date_updated":"2023-02-23T14:01:57Z","main_file_link":[{"url":"https://arxiv.org/abs/1609.08136","open_access":"1"}],"doi":"10.1016/j.aim.2017.08.031","publication":"Advances in Mathematics","oa_version":"Preprint","volume":319,"status":"public","day":"15","date_created":"2021-06-22T11:51:27Z"},{"status":"public","day":"01","date_created":"2021-06-22T12:18:59Z","volume":63,"oa_version":"Published Version","publication":"European Journal of Combinatorics","doi":"10.1016/j.ejc.2017.02.003","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ejc.2017.02.003"}],"oa":1,"date_updated":"2023-02-23T14:02:00Z","date_published":"2017-06-01T00:00:00Z","intvolume":" 63","month":"06","year":"2017","page":"6-25","external_id":{"arxiv":["1606.01586"]},"quality_controlled":"1","_id":"9589","arxiv":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"We give an asymptotic expression for the expected number of spanning trees in a random graph with a given degree sequence , provided that the number of edges is at least , where is the maximum degree. A key part of our argument involves establishing a concentration result for a certain family of functions over random trees with given degrees, using Prüfer codes."}],"type":"journal_article","publication_identifier":{"issn":["0195-6698"]},"citation":{"ista":"Greenhill C, Isaev M, Kwan MA, McKay BD. 2017. The average number of spanning trees in sparse graphs with given degrees. European Journal of Combinatorics. 63, 6–25.","short":"C. Greenhill, M. Isaev, M.A. Kwan, B.D. McKay, European Journal of Combinatorics 63 (2017) 6–25.","ieee":"C. Greenhill, M. Isaev, M. A. Kwan, and B. D. McKay, “The average number of spanning trees in sparse graphs with given degrees,” European Journal of Combinatorics, vol. 63. Elsevier, pp. 6–25, 2017.","ama":"Greenhill C, Isaev M, Kwan MA, McKay BD. The average number of spanning trees in sparse graphs with given degrees. European Journal of Combinatorics. 2017;63:6-25. doi:10.1016/j.ejc.2017.02.003","chicago":"Greenhill, Catherine, Mikhail Isaev, Matthew Alan Kwan, and Brendan D. McKay. “The Average Number of Spanning Trees in Sparse Graphs with given Degrees.” European Journal of Combinatorics. Elsevier, 2017. https://doi.org/10.1016/j.ejc.2017.02.003.","apa":"Greenhill, C., Isaev, M., Kwan, M. A., & McKay, B. D. (2017). The average number of spanning trees in sparse graphs with given degrees. European Journal of Combinatorics. Elsevier. https://doi.org/10.1016/j.ejc.2017.02.003","mla":"Greenhill, Catherine, et al. “The Average Number of Spanning Trees in Sparse Graphs with given Degrees.” European Journal of Combinatorics, vol. 63, Elsevier, 2017, pp. 6–25, doi:10.1016/j.ejc.2017.02.003."},"extern":"1","publication_status":"published","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Catherine","last_name":"Greenhill","full_name":"Greenhill, Catherine"},{"last_name":"Isaev","first_name":"Mikhail","full_name":"Isaev, Mikhail"},{"orcid":"0000-0002-4003-7567","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan"},{"last_name":"McKay","first_name":"Brendan D.","full_name":"McKay, Brendan D."}],"title":"The average number of spanning trees in sparse graphs with given degrees","publisher":"Elsevier","article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"}],"title":"Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics","publisher":"American Institute of Physics","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"publist_id":"6446","article_processing_charge":"No","quality_controlled":"1","_id":"959","abstract":[{"lang":"eng","text":"In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions."}],"scopus_import":"1","type":"journal_article","citation":{"ama":"De Martino D. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;95(6):062419. doi:10.1103/PhysRevE.95.062419","short":"D. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 95 (2017) 062419.","ieee":"D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6. American Institute of Physics, p. 062419, 2017.","ista":"De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . 95(6), 062419.","chicago":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.95.062419.","apa":"De Martino, D. (2017). Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.95.062419","mla":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6, American Institute of Physics, 2017, p. 062419, doi:10.1103/PhysRevE.95.062419."},"publication_identifier":{"issn":["24700045"]},"publication_status":"published","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"oa":1,"issue":"6","date_updated":"2023-09-22T09:59:01Z","date_published":"2017-06-28T00:00:00Z","intvolume":" 95","month":"06","year":"2017","external_id":{"isi":["000404546400004"]},"page":"062419","status":"public","day":"28","date_created":"2018-12-11T11:49:25Z","volume":95,"oa_version":"Submitted Version","ec_funded":1,"isi":1,"publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","main_file_link":[{"url":"https://arxiv.org/pdf/1703.00853.pdf","open_access":"1"}],"doi":"10.1103/PhysRevE.95.062419"},{"volume":31,"day":"12","status":"public","date_created":"2021-06-22T12:26:25Z","main_file_link":[{"url":"https://arxiv.org/abs/1507.07960","open_access":"1"}],"doi":"10.1137/15m1032910","publication":"SIAM Journal on Discrete Mathematics","oa_version":"Preprint","month":"01","intvolume":" 31","date_published":"2017-01-12T00:00:00Z","issue":"1","oa":1,"date_updated":"2023-02-23T14:02:05Z","page":"155-171","external_id":{"arxiv":["1507.07960"]},"year":"2017","type":"journal_article","arxiv":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"We show that for any fixed dense graph G and bounded-degree tree T on the same number of vertices, a modest random perturbation of G will typically contain a copy of T . This combines the viewpoints of the well-studied problems of embedding trees into fixed dense graphs and into random graphs, and extends a sizeable body of existing research on randomly perturbed graphs. Specifically, we show that there is c=c(α,Δ) such that if G is an n-vertex graph with minimum degree at least αn, and T is an n-vertex tree with maximum degree at most Δ , then if we add cn uniformly random edges to G, the resulting graph will contain T asymptotically almost surely (as n→∞ ). Our proof uses a lemma concerning the decomposition of a dense graph into super-regular pairs of comparable sizes, which may be of independent interest."}],"publication_identifier":{"issn":["0895-4801"],"eissn":["1095-7146"]},"extern":"1","citation":{"chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Bounded-Degree Spanning Trees in Randomly Perturbed Graphs.” SIAM Journal on Discrete Mathematics. Society for Industrial & Applied Mathematics, 2017. https://doi.org/10.1137/15m1032910.","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Bounded-degree spanning trees in randomly perturbed graphs,” SIAM Journal on Discrete Mathematics, vol. 31, no. 1. Society for Industrial & Applied Mathematics, pp. 155–171, 2017.","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, SIAM Journal on Discrete Mathematics 31 (2017) 155–171.","ista":"Krivelevich M, Kwan MA, Sudakov B. 2017. Bounded-degree spanning trees in randomly perturbed graphs. SIAM Journal on Discrete Mathematics. 31(1), 155–171.","ama":"Krivelevich M, Kwan MA, Sudakov B. Bounded-degree spanning trees in randomly perturbed graphs. SIAM Journal on Discrete Mathematics. 2017;31(1):155-171. doi:10.1137/15m1032910","mla":"Krivelevich, Michael, et al. “Bounded-Degree Spanning Trees in Randomly Perturbed Graphs.” SIAM Journal on Discrete Mathematics, vol. 31, no. 1, Society for Industrial & Applied Mathematics, 2017, pp. 155–71, doi:10.1137/15m1032910.","apa":"Krivelevich, M., Kwan, M. A., & Sudakov, B. (2017). Bounded-degree spanning trees in randomly perturbed graphs. SIAM Journal on Discrete Mathematics. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/15m1032910"},"quality_controlled":"1","_id":"9590","publication_status":"published","publisher":"Society for Industrial & Applied Mathematics","title":"Bounded-degree spanning trees in randomly perturbed graphs","author":[{"first_name":"Michael","last_name":"Krivelevich","full_name":"Krivelevich, Michael"},{"last_name":"Kwan","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan"},{"last_name":"Sudakov","first_name":"Benny","full_name":"Sudakov, Benny"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}]},{"external_id":{"isi":["000404486700001"]},"year":"2017","article_number":"176","date_published":"2017-06-28T00:00:00Z","intvolume":" 11","month":"06","oa":1,"date_updated":"2024-03-25T23:30:23Z","publication":"Frontiers in Cellular Neuroscience","doi":"10.3389/fncel.2017.00176","ec_funded":1,"oa_version":"Published Version","isi":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9962"}]},"volume":11,"day":"28","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:49:25Z","ddc":["570"],"publist_id":"6445","department":[{"_id":"SiHi"},{"_id":"MaLo"}],"article_processing_charge":"Yes","pubrep_id":"830","language":[{"iso":"eng"}],"publisher":"Frontiers Research Foundation","has_accepted_license":"1","title":"Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Hansen, Andi H","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen"},{"full_name":"Düllberg, Christian F","first_name":"Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87","last_name":"Düllberg","orcid":"0000-0001-6335-9748"},{"full_name":"Mieck, Christine","orcid":"0000-0003-1919-7416","last_name":"Mieck","id":"34CAE85C-F248-11E8-B48F-1D18A9856A87","first_name":"Christine"},{"full_name":"Loose, Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"file":[{"file_name":"IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:09:40Z","creator":"system","file_size":2153858,"content_type":"application/pdf","file_id":"4764","relation":"main_file","access_level":"open_access","checksum":"dc1f5a475b918d09a0f9f587400b1626"}],"publication_status":"published","project":[{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","grant_number":"618444"},{"grant_number":"RGP0053/2014","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"},{"name":"The biochemical basis of PAR polarization","_id":"25985A36-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"T00817-B21"}],"abstract":[{"lang":"eng","text":"The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases. In this review we discuss the role of cell polarity at sequential stages during cortex development. We first provide an overview of morphological cell polarity features in cortical neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual molecular and biochemical framework how cell polarity is established at the cellular level through a break in symmetry in nascent cortical projection neurons. Lastly we provide a perspective how the molecular mechanisms applying to single cells could be probed and integrated in an in vivo and tissue-wide context."}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-07-14T12:48:16Z","citation":{"mla":"Hansen, Andi H., et al. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience, vol. 11, 176, Frontiers Research Foundation, 2017, doi:10.3389/fncel.2017.00176.","apa":"Hansen, A. H., Düllberg, C. F., Mieck, C., Loose, M., & Hippenmeyer, S. (2017). Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncel.2017.00176","chicago":"Hansen, Andi H, Christian F Düllberg, Christine Mieck, Martin Loose, and Simon Hippenmeyer. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience. Frontiers Research Foundation, 2017. https://doi.org/10.3389/fncel.2017.00176.","ama":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 2017;11. doi:10.3389/fncel.2017.00176","ista":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. 2017. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 11, 176.","ieee":"A. H. Hansen, C. F. Düllberg, C. Mieck, M. Loose, and S. Hippenmeyer, “Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks,” Frontiers in Cellular Neuroscience, vol. 11. Frontiers Research Foundation, 2017.","short":"A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers in Cellular Neuroscience 11 (2017)."},"publication_identifier":{"issn":["16625102"]},"quality_controlled":"1","_id":"960"},{"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570","590"],"date_created":"2018-12-11T11:49:25Z","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"day":"01","status":"public","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_825","related_material":{"record":[{"id":"1100","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1537"},{"status":"public","relation":"part_of_dissertation","id":"1912"},{"status":"public","relation":"part_of_dissertation","id":"2926"},{"id":"3246","status":"public","relation":"part_of_dissertation"},{"id":"676","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"735"}]},"oa_version":"Published Version","month":"03","date_published":"2017-03-01T00:00:00Z","alternative_title":["ISTA Thesis"],"acknowledgement":"Many people accompanied me during this trip: I would not have reached my destination nor \r\nenjoyed the travelling without them. First of all, thanks to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting and incredibly competent people and thanks for \r\nall the good science I witnessed and participated in. It has been a \r\nblast, an incredibly \r\nexciting one! Thanks to JLo, for teaching me how to master my pipettes and showing me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching me basically everything \r\nabout zebrafish and being always there to advice, sugge\r\nst, support...and play fussball! \r\nThank you to Julien, for the critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing kicker matches, and Keisuke, for showing me the light, and to the three of them \r\ntogether for all the good laughs we\r\nhad. My start in Vienna would have been a lot more \r\ndifficult without you guys. Also it would not have been possible without Elena and Inês: \r\nthanks for helping setting up this lab and for the dinners in Gugging. Thanks to Martin, for \r\nhelping me understand \r\nthe physics behind biology. Thanks to Philipp, for the interest and \r\nadvice, and to Michael, for the Viennise take on things. Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel for the enthusiasm and the neverending energy and for all your \r\nhelp over the years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat. To Shayan, for being such a motivated student. To Matt, for helping out\r\nwith coding \r\nand for finding punk solutions to data analysis problems. Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla, Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza, for the wonderful atmosphere in the lab. Many than\r\nks to Koni and Deborah: doing \r\nexperiments would have been much more difficult without your help. Special thanks to Katjia \r\nfor setting up an amazing imaging facility and for building the best team, Robert, Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith all the late sortings and for helping with all \r\nthe technical problems. Thanks to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald Janovjak for being a present and helpful committee member over the years \r\nand to Patrick Lemaire f\r\nor the helpful insight and extremely interesting discussion we had \r\nabout the project. Also, this journey would not have been the same without all the friends \r\nthat I met in Dresden and then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne, Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph, \r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled my days with \r\nfun and support. A special thank to my family, always close even if they are \r\nkilometers away. \r\nGrazie ai miei fratelli, Nunzio e William, e alla mia mamma, per essermi sempre vicini pur \r\nvivendo a chilometri di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe crazy life of a scientist, the living apart for\r\nso long, never knowing when things are going \r\nto happen. Thanks for being a great partner and my number one fan!","date_updated":"2023-09-27T14:16:45Z","oa":1,"page":"109","year":"2017","publication_identifier":{"issn":["2663-337X"]},"citation":{"apa":"Barone, V. (2017). Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_825","mla":"Barone, Vanessa. Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_825.","ama":"Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. 2017. doi:10.15479/AT:ISTA:th_825","ista":"Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria.","short":"V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.","ieee":"V. Barone, “Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.","chicago":"Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_825."},"file_date_updated":"2020-07-14T12:48:16Z","type":"dissertation","abstract":[{"text":"Cell-cell contact formation constitutes the first step in the emergence of multicellularity in evolution, thereby allowing the differentiation of specialized cell types. In metazoan development, cell-cell contact formation is thought to influence cell fate specification, and cell fate specification has been implicated in cell-cell contact formation. However, remarkably little is yet known about whether and how the interaction and feedback between cell-cell contact formation and cell fate specification affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and mesendoderm cell fate specification during zebrafish gastrulation. We show that long lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an effective positive feedback loop between ppl cell-cell contact duration and cell fate specification. Finally, by using a combination of theoretical modeling and experimentation, we show that this feedback loop determines whether anterior axial mesendoderm cells become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal that the gene regulatory networks leading to cell fate diversification within the developing embryo are controlled by the interdependent activities of cell-cell signaling and contact formation.","lang":"eng"}],"_id":"961","publication_status":"published","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"access_level":"closed","checksum":"242f88c87f2cf267bf05049fa26a687b","relation":"source_file","file_id":"6205","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":14497822,"creator":"dernst","date_updated":"2020-07-14T12:48:16Z","date_created":"2019-04-05T08:36:52Z","file_name":"2017_Barone_thesis_final.docx"},{"date_updated":"2020-07-14T12:48:16Z","date_created":"2019-04-05T08:36:52Z","file_name":"2017_Barone_thesis_.pdf","access_level":"open_access","relation":"main_file","checksum":"ba5b0613ed8bade73a409acdd880fb8a","file_id":"6206","content_type":"application/pdf","creator":"dernst","file_size":14995941}],"title":"Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0003-2676-3367","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Barone, Vanessa"}],"article_processing_charge":"No","publist_id":"6444","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"pubrep_id":"825"},{"year":"2017","external_id":{"isi":["000431900900021"]},"page":"399 - 418","conference":{"location":"Heidelberg, Germany","end_date":"2017-07-28","start_date":"2017-07-24","name":"CAV: Computer Aided Verification"},"date_updated":"2023-09-22T09:58:02Z","month":"01","intvolume":" 10427","alternative_title":["LNCS"],"date_published":"2017-01-01T00:00:00Z","isi":1,"oa_version":"None","doi":"10.1007/978-3-319-63390-9_21","date_created":"2018-12-11T11:49:26Z","day":"01","status":"public","volume":10427,"language":[{"iso":"eng"}],"article_processing_charge":"No","publist_id":"6443","department":[{"_id":"ToHe"}],"author":[{"first_name":"Minh","last_name":"Trinh","full_name":"Trinh, Minh"},{"last_name":"Chu","id":"3598E630-F248-11E8-B48F-1D18A9856A87","first_name":"Duc Hiep","full_name":"Chu, Duc Hiep"},{"full_name":"Jaffar, Joxan","last_name":"Jaffar","first_name":"Joxan"}],"title":"Model counting for recursively-defined strings","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer","project":[{"name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"}],"publication_status":"published","editor":[{"full_name":"Majumdar, Rupak","last_name":"Majumdar","first_name":"Rupak"},{"first_name":"Viktor","last_name":"Kunčak","full_name":"Kunčak, Viktor"}],"_id":"962","quality_controlled":"1","citation":{"chicago":"Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer, 2017. https://doi.org/10.1007/978-3-319-63390-9_21.","ista":"Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings. CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418.","short":"M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 399–418.","ieee":"M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 399–418.","ama":"Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:10.1007/978-3-319-63390-9_21","mla":"Trinh, Minh, et al. Model Counting for Recursively-Defined Strings. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418, doi:10.1007/978-3-319-63390-9_21.","apa":"Trinh, M., Chu, D. H., & Jaffar, J. (2017). Model counting for recursively-defined strings. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_21"},"publication_identifier":{"issn":["03029743"]},"type":"conference","abstract":[{"lang":"eng","text":"We present a new algorithm for model counting of a class of string constraints. In addition to the classic operation of concatenation, our class includes some recursively defined operations such as Kleene closure, and replacement of substrings. Additionally, our class also includes length constraints on the string expressions, which means, by requiring reasoning about numbers, that we face a multi-sorted logic. In the end, our string constraints are motivated by their use in programming for web applications. Our algorithm comprises two novel features: the ability to use a technique of (1) partial derivatives for constraints that are already in a solved form, i.e. a form where its (string) satisfiability is clearly displayed, and (2) non-progression, where cyclic reasoning in the reduction process may be terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally compare our model counter with two recent works on model counting of similar constraints, SMC [18] and ABC [5], to demonstrate its superior performance."}],"scopus_import":"1"},{"oa_version":"Published Version","related_material":{"record":[{"relation":"later_version","status":"public","id":"6005"}]},"doi":"10.4230/LIPIcs.MFCS.2017.37","status":"public","day":"01","ddc":["004"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:49:26Z","volume":83,"year":"2017","conference":{"location":"Aalborg, Denmark","end_date":"2017-08-25","start_date":"2017-08-21","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"oa":1,"date_updated":"2023-02-23T12:35:50Z","article_number":"37","date_published":"2017-06-01T00:00:00Z","alternative_title":["LIPIcs"],"intvolume":" 83","month":"06","publication_status":"published","project":[{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"}],"quality_controlled":"1","_id":"963","scopus_import":1,"abstract":[{"text":"Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. ","lang":"eng"}],"type":"conference","file_date_updated":"2020-07-14T12:48:18Z","publication_identifier":{"issn":["18688969"]},"citation":{"apa":"Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37","ista":"Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark, 2017, vol. 83.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37."},"pubrep_id":"829","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"publist_id":"6438","title":"Timed network games with clocks","author":[{"orcid":"0000-0001-5588-8287","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","full_name":"Avni, Guy"},{"first_name":"Shibashis","last_name":"Guha","full_name":"Guha, Shibashis"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:48:18Z","date_created":"2018-12-12T10:14:10Z","file_name":"IST-2017-829-v1+1_mfcs-cr.pdf","checksum":"f55eaf7f3c36ea07801112acfedd17d5","access_level":"open_access","relation":"main_file","file_size":369730,"creator":"system","file_id":"5059","content_type":"application/pdf"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","has_accepted_license":"1"},{"month":"09","intvolume":" 147","date_published":"2017-09-14T00:00:00Z","article_number":"104707","date_updated":"2023-02-23T14:04:02Z","issue":"10","oa":1,"external_id":{"arxiv":["1703.06062"],"pmid":["28915742"]},"year":"2017","pmid":1,"volume":147,"date_created":"2021-07-15T08:13:29Z","day":"14","status":"public","main_file_link":[{"open_access":"1","url":"https://pure.qub.ac.uk/en/publications/the-gibbs-free-energy-of-homogeneous-nucleation-from-atomistic-nuclei-to-the-planar-limit(4599cdb4-dcc4-4522-8763-7b2a165ebf12).html"}],"doi":"10.1063/1.4997180","publication":"The Journal of Chemical Physics","oa_version":"Submitted Version","publisher":"AIP Publishing","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"},{"full_name":"Tribello, Gareth A.","last_name":"Tribello","first_name":"Gareth A."},{"last_name":"Ceriotti","first_name":"Michele","full_name":"Ceriotti, Michele"}],"title":"The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit","article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"citation":{"chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “The Gibbs Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.” The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4997180.","ista":"Cheng B, Tribello GA, Ceriotti M. 2017. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical Physics. 147(10), 104707.","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit,” The Journal of Chemical Physics, vol. 147, no. 10. AIP Publishing, 2017.","short":"B. Cheng, G.A. Tribello, M. Ceriotti, The Journal of Chemical Physics 147 (2017).","ama":"Cheng B, Tribello GA, Ceriotti M. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical Physics. 2017;147(10). doi:10.1063/1.4997180","mla":"Cheng, Bingqing, et al. “The Gibbs Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.” The Journal of Chemical Physics, vol. 147, no. 10, 104707, AIP Publishing, 2017, doi:10.1063/1.4997180.","apa":"Cheng, B., Tribello, G. A., & Ceriotti, M. (2017). The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4997180"},"extern":"1","type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable."}],"arxiv":1,"_id":"9660","quality_controlled":"1","publication_status":"published"},{"article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Bridging the gap between atomistic and macroscopic models of homogeneous nucleation","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"orcid":"0000-0002-3584-9632","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing"},{"first_name":"Michele","last_name":"Ceriotti","full_name":"Ceriotti, Michele"}],"publisher":"AIP Publishing","publication_status":"published","quality_controlled":"1","_id":"9661","type":"journal_article","abstract":[{"lang":"eng","text":"Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms, by capturing the microscopic configurations of all the atoms. In this paper, we introduce a thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework for testing the limits of classical nucleation theory."}],"scopus_import":"1","arxiv":1,"citation":{"ama":"Cheng B, Ceriotti M. Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. The Journal of Chemical Physics. 2017;146(3). doi:10.1063/1.4973883","ieee":"B. Cheng and M. Ceriotti, “Bridging the gap between atomistic and macroscopic models of homogeneous nucleation,” The Journal of Chemical Physics, vol. 146, no. 3. AIP Publishing, 2017.","ista":"Cheng B, Ceriotti M. 2017. Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. The Journal of Chemical Physics. 146(3), 034106.","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 146 (2017).","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation.” The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4973883.","apa":"Cheng, B., & Ceriotti, M. (2017). Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4973883","mla":"Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation.” The Journal of Chemical Physics, vol. 146, no. 3, 034106, AIP Publishing, 2017, doi:10.1063/1.4973883."},"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"extern":"1","year":"2017","external_id":{"pmid":["28109231"],"arxiv":["1610.01322"]},"issue":"3","oa":1,"date_updated":"2021-08-09T12:31:57Z","article_number":"034106","month":"01","intvolume":" 146","date_published":"2017-01-21T00:00:00Z","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1610.01322","open_access":"1"}],"doi":"10.1063/1.4973883","publication":"The Journal of Chemical Physics","status":"public","day":"21","date_created":"2021-07-15T08:27:31Z","pmid":1,"volume":146},{"year":"2017","conference":{"start_date":"2017-08-06","end_date":"2017-08-11","name":"ICML: International Conference on Machine Learning","location":"Sydney, Australia"},"external_id":{"arxiv":["1612.08185"],"isi":["000683309501102"]},"page":"1905 - 1914","oa":1,"date_updated":"2023-09-22T09:50:41Z","acknowledgement":"We thank Tim Salimans for spotting a mistake in our preliminary arXiv manuscript. This work was funded by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.","date_published":"2017-08-01T00:00:00Z","intvolume":" 70","month":"08","ec_funded":1,"oa_version":"Submitted Version","isi":1,"publication":"34th International Conference on Machine Learning","main_file_link":[{"url":"https://arxiv.org/abs/1612.08185","open_access":"1"}],"status":"public","day":"01","date_created":"2018-12-11T11:49:37Z","volume":70,"language":[{"iso":"eng"}],"publist_id":"6398","department":[{"_id":"ChLa"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","last_name":"Kolesnikov"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"title":"PixelCNN models with auxiliary variables for natural image modeling","publisher":"JMLR","has_accepted_license":"1","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","_id":"1000","arxiv":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"We study probabilistic models of natural images and extend the autoregressive family of PixelCNN models by incorporating latent variables. Subsequently, we describe two new generative image models that exploit different image transformations as latent variables: a quantized grayscale view of the image or a multi-resolution image pyramid. The proposed models tackle two known shortcomings of existing PixelCNN models: 1) their tendency to focus on low-level image details, while largely ignoring high-level image information, such as object shapes, and 2) their computationally costly procedure for image sampling. We experimentally demonstrate benefits of our LatentPixelCNN models, in particular showing that they produce much more realistically looking image samples than previous state-of-the-art probabilistic models. "}],"type":"conference","publication_identifier":{"isbn":["978-151085514-4"]},"citation":{"ieee":"A. Kolesnikov and C. Lampert, “PixelCNN models with auxiliary variables for natural image modeling,” in 34th International Conference on Machine Learning, Sydney, Australia, 2017, vol. 70, pp. 1905–1914.","ista":"Kolesnikov A, Lampert C. 2017. PixelCNN models with auxiliary variables for natural image modeling. 34th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 70, 1905–1914.","short":"A. Kolesnikov, C. Lampert, in:, 34th International Conference on Machine Learning, JMLR, 2017, pp. 1905–1914.","ama":"Kolesnikov A, Lampert C. PixelCNN models with auxiliary variables for natural image modeling. In: 34th International Conference on Machine Learning. Vol 70. JMLR; 2017:1905-1914.","chicago":"Kolesnikov, Alexander, and Christoph Lampert. “PixelCNN Models with Auxiliary Variables for Natural Image Modeling.” In 34th International Conference on Machine Learning, 70:1905–14. JMLR, 2017.","apa":"Kolesnikov, A., & Lampert, C. (2017). PixelCNN models with auxiliary variables for natural image modeling. In 34th International Conference on Machine Learning (Vol. 70, pp. 1905–1914). Sydney, Australia: JMLR.","mla":"Kolesnikov, Alexander, and Christoph Lampert. “PixelCNN Models with Auxiliary Variables for Natural Image Modeling.” 34th International Conference on Machine Learning, vol. 70, JMLR, 2017, pp. 1905–14."}}]