[{"date_published":"2018-07-30T00:00:00Z","publication":"PeerJ","citation":{"ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438.","ieee":"C. Fraisse et al., “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., & Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7). doi:10.7717/peerj.5198","chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5198.","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:10.7717/peerj.5198.","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018)."},"day":"30","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"date_created":"2018-12-18T09:42:11Z","date_updated":"2020-07-14T12:44:48Z","checksum":"7d55ae22598a1c70759cd671600cff53","file_id":"5739","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1480792,"file_name":"2018_PeerJ_Fraisse.pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"139","ddc":["576"],"title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","status":"public","intvolume":" 2018","abstract":[{"lang":"eng","text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed."}],"issue":"7","type":"journal_article","doi":"10.7717/peerj.5198","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000440484800002"]},"isi":1,"quality_controlled":"1","month":"07","author":[{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"first_name":"Pierre","last_name":"Gagnaire","full_name":"Gagnaire, Pierre"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"full_name":"Faivre, Nicolas","last_name":"Faivre","first_name":"Nicolas"},{"full_name":"Welch, John","first_name":"John","last_name":"Welch"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"date_created":"2018-12-11T11:44:50Z","date_updated":"2023-10-17T12:25:28Z","volume":2018,"year":"2018","publication_status":"published","publisher":"PeerJ","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:48Z","publist_id":"7784","article_number":"30083438"},{"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"PeerJ","year":"2018","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","pmid":1,"date_updated":"2023-10-17T12:24:43Z","date_created":"2018-12-11T11:44:16Z","volume":2018,"author":[{"full_name":"Bertl, Johanna","last_name":"Bertl","first_name":"Johanna"},{"full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","first_name":"Harald"},{"full_name":"Blum, Michaël","first_name":"Michaël","last_name":"Blum"}],"article_number":"e5325","file_date_updated":"2020-07-14T12:46:06Z","publist_id":"8022","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000447204400001"],"pmid":["30294507"]},"language":[{"iso":"eng"}],"doi":"10.7717/peerj.5325","month":"10","ddc":["576"],"status":"public","title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","intvolume":" 2018","_id":"33","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"3334886c4b39678db4c4b74299ca14ba","date_created":"2018-12-17T10:46:06Z","date_updated":"2020-07-14T12:46:06Z","file_id":"5692","relation":"main_file","creator":"dernst","file_size":1328344,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_PeerJ_Bertl.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species."}],"issue":"10","publication":"PeerJ","citation":{"short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:10.7717/peerj.5325.","chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5325.","ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325","apa":"Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ. https://doi.org/10.7717/peerj.5325","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018, no. 10. PeerJ, 2018.","ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325."},"date_published":"2018-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1"},{"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Nature Research","year":"2018","pmid":1,"date_created":"2018-12-16T22:59:18Z","date_updated":"2023-10-17T12:19:28Z","volume":4,"author":[{"orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833"}],"external_id":{"pmid":["30518833"],"isi":["000454576600017"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41477-018-0318-3","month":"12","publication_identifier":{"issn":["2055-0278"]},"title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","status":"public","intvolume":" 4","_id":"5673","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate—a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2–5. Here, we provide mechanistic insights into post-cytokinetic re-establishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cell-intrinsic manner and that re-establishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2 polarity re-establishment.","lang":"eng"}],"issue":"12","page":"1082-1088","publication":"Nature Plants","citation":{"chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants. Nature Research, 2018. https://doi.org/10.1038/s41477-018-0318-3.","mla":"Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants, vol. 4, no. 12, Nature Research, 2018, pp. 1082–88, doi:10.1038/s41477-018-0318-3.","short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.","ista":"Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088.","ieee":"M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division,” Nature Plants, vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018.","apa":"Glanc, M., Fendrych, M., & Friml, J. (2018). Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. Nature Research. https://doi.org/10.1038/s41477-018-0318-3","ama":"Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 2018;4(12):1082-1088. doi:10.1038/s41477-018-0318-3"},"date_published":"2018-12-03T00:00:00Z","scopus_import":"1","day":"03","article_processing_charge":"No"},{"file":[{"file_size":219837,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_RS_IbsenJensen.pdf","checksum":"444e1a9d98eb0e780671be82b13025f3","date_updated":"2020-07-14T12:45:22Z","date_created":"2019-02-12T07:54:37Z","relation":"main_file","file_id":"5955"}],"oa_version":"Submitted Version","ddc":["000"],"title":"Language acquisition with communication between learners","status":"public","intvolume":" 15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"198","abstract":[{"text":"We consider a class of students learning a language from a teacher. The situation can be interpreted as a group of child learners receiving input from the linguistic environment. The teacher provides sample sentences. The students try to learn the grammar from the teacher. In addition to just listening to the teacher, the students can also communicate with each other. The students hold hypotheses about the grammar and change them if they receive counter evidence. The process stops when all students have converged to the correct grammar. We study how the time to convergence depends on the structure of the classroom by introducing and evaluating various complexity measures. We find that structured communication between students, although potentially introducing confusion, can greatly reduce some of the complexity measures. Our theory can also be interpreted as applying to the scientific process, where nature is the teacher and the scientists are the students.","lang":"eng"}],"issue":"140","type":"journal_article","date_published":"2018-03-01T00:00:00Z","article_type":"original","publication":"Journal of the Royal Society Interface","citation":{"ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with communication between learners. Journal of the Royal Society Interface. 2018;15(140). doi:10.1098/rsif.2018.0073","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition with communication between learners. Journal of the Royal Society Interface. 15(140), 20180073.","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition with communication between learners,” Journal of the Royal Society Interface, vol. 15, no. 140. The Royal Society, 2018.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2018). Language acquisition with communication between learners. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2018.0073","mla":"Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface, vol. 15, no. 140, 20180073, The Royal Society, 2018, doi:10.1098/rsif.2018.0073.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal Society Interface 15 (2018).","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Language Acquisition with Communication between Learners.” Journal of the Royal Society Interface. The Royal Society, 2018. https://doi.org/10.1098/rsif.2018.0073."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-10-18T06:36:00Z","date_created":"2018-12-11T11:45:09Z","volume":15,"author":[{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"related_material":{"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4028971"}],"record":[{"id":"9814","relation":"research_data","status":"public"}]},"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"The Royal Society","year":"2018","pmid":1,"file_date_updated":"2020-07-14T12:45:22Z","ec_funded":1,"publist_id":"7715","article_number":"20180073","language":[{"iso":"eng"}],"doi":"10.1098/rsif.2018.0073","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"oa":1,"external_id":{"isi":["000428576200023"],"pmid":["29593089"]},"month":"03","publication_identifier":{"eissn":["1742-5662"]}},{"article_type":"original","citation":{"ieee":"B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions in the emergence of syntax networks,” Royal Society Open Science, vol. 5, no. 12. The Royal Society, 2018.","apa":"Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.181286","ista":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.","ama":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 2018;5(12). doi:10.1098/rsos.181286","chicago":"Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.","short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018).","mla":"Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The Royal Society, 2018, doi:10.1098/rsos.181286."},"publication":"Royal Society Open Science","date_published":"2018-12-12T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"12","intvolume":" 5","ddc":["570"],"title":"Chromatic transitions in the emergence of syntax networks","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5859","file":[{"checksum":"9664d4417f6b792242e31eea77ce9501","date_updated":"2020-07-14T12:47:13Z","date_created":"2019-02-05T14:38:09Z","relation":"main_file","file_id":"5924","file_size":646732,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_RoyalSocOS_Corominas.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"12","abstract":[{"text":"The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.","lang":"eng"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000456566500027"],"pmid":["30662738"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rsos.181286","publication_identifier":{"issn":["2054-5703"]},"month":"12","department":[{"_id":"EdHa"}],"publisher":"The Royal Society","publication_status":"published","pmid":1,"acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","year":"2018","volume":5,"date_updated":"2023-10-18T06:41:12Z","date_created":"2019-01-20T22:59:18Z","author":[{"orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat"},{"first_name":"Martí Sànchez","last_name":"Fibla","full_name":"Fibla, Martí Sànchez"},{"last_name":"Valverde","first_name":"Sergi","full_name":"Valverde, Sergi"},{"last_name":"Solé","first_name":"Ricard","full_name":"Solé, Ricard"}],"article_number":"181286","file_date_updated":"2020-07-14T12:47:13Z"},{"article_processing_charge":"No","day":"20","month":"04","date_published":"2018-04-20T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["1804.07752"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.07752","open_access":"1"}],"citation":{"mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, 1804.07752.","short":"J. Alt, L. Erdös, T.H. Krüger, ArXiv (n.d.).","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, n.d.","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv.","ista":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv, 1804.07752.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” arXiv. .","apa":"Alt, J., Erdös, L., & Krüger, T. H. (n.d.). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv."},"publication":"arXiv","abstract":[{"text":"We study the unique solution $m$ of the Dyson equation \\[ -m(z)^{-1} = z - a\r\n+ S[m(z)] \\] on a von Neumann algebra $\\mathcal{A}$ with the constraint\r\n$\\mathrm{Im}\\,m\\geq 0$. Here, $z$ lies in the complex upper half-plane, $a$ is\r\na self-adjoint element of $\\mathcal{A}$ and $S$ is a positivity-preserving\r\nlinear operator on $\\mathcal{A}$. We show that $m$ is the Stieltjes transform\r\nof a compactly supported $\\mathcal{A}$-valued measure on $\\mathbb{R}$. Under\r\nsuitable assumptions, we establish that this measure has a uniformly\r\n$1/3$-H\\\"{o}lder continuous density with respect to the Lebesgue measure, which\r\nis supported on finitely many intervals, called bands. In fact, the density is\r\nanalytic inside the bands with a square-root growth at the edges and internal\r\ncubic root cusps whenever the gap between two bands vanishes. The shape of\r\nthese singularities is universal and no other singularity may occur. We give a\r\nprecise asymptotic description of $m$ near the singular points. These\r\nasymptotics generalize the analysis at the regular edges given in the companion\r\npaper on the Tracy-Widom universality for the edge eigenvalue statistics for\r\ncorrelated random matrices [arXiv:1804.07744] and they play a key role in the\r\nproof of the Pearcey universality at the cusp for Wigner-type matrices\r\n[arXiv:1809.03971,arXiv:1811.04055]. We also extend the finite dimensional band\r\nmass formula from [arXiv:1804.07744] to the von Neumann algebra setting by\r\nshowing that the spectral mass of the bands is topologically rigid under\r\ndeformations and we conclude that these masses are quantized in some important\r\ncases.","lang":"eng"}],"type":"preprint","article_number":"1804.07752","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"},{"status":"public","relation":"later_version","id":"14694"}]},"author":[{"first_name":"Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"Erdös, László"},{"first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"}],"oa_version":"Preprint","date_updated":"2023-12-18T10:46:08Z","date_created":"2019-03-28T09:20:06Z","_id":"6183","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LaEr"}],"status":"public","publication_status":"submitted","title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps"},{"author":[{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","first_name":"Sergey","full_name":"Avvakumov, Sergey"},{"last_name":"Karasev","first_name":"Roman","full_name":"Karasev, Roman"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8156"}]},"date_updated":"2023-12-18T10:51:02Z","date_created":"2018-12-11T11:44:30Z","oa_version":"Preprint","_id":"75","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Convex fair partitions into arbitrary number of pieces","publisher":"arXiv","department":[{"_id":"HeEd"},{"_id":"JaMa"}],"abstract":[{"lang":"eng","text":"We prove that any convex body in the plane can be partitioned into m convex parts of equal areas and perimeters for any integer m≥2; this result was previously known for prime powers m=pk. We also give a higher-dimensional generalization."}],"ec_funded":1,"article_number":"1804.03057","type":"preprint","date_published":"2018-09-13T00:00:00Z","doi":"10.48550/arXiv.1804.03057","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.03057"}],"oa":1,"external_id":{"arxiv":["1804.03057"]},"citation":{"ama":"Akopyan A, Avvakumov S, Karasev R. Convex fair partitions into arbitrary number of pieces. 2018. doi:10.48550/arXiv.1804.03057","ista":"Akopyan A, Avvakumov S, Karasev R. 2018. Convex fair partitions into arbitrary number of pieces. 1804.03057.","apa":"Akopyan, A., Avvakumov, S., & Karasev, R. (2018). Convex fair partitions into arbitrary number of pieces. arXiv. https://doi.org/10.48550/arXiv.1804.03057","ieee":"A. Akopyan, S. Avvakumov, and R. Karasev, “Convex fair partitions into arbitrary number of pieces.” arXiv, 2018.","mla":"Akopyan, Arseniy, et al. Convex Fair Partitions into Arbitrary Number of Pieces. 1804.03057, arXiv, 2018, doi:10.48550/arXiv.1804.03057.","short":"A. Akopyan, S. Avvakumov, R. Karasev, (2018).","chicago":"Akopyan, Arseniy, Sergey Avvakumov, and Roman Karasev. “Convex Fair Partitions into Arbitrary Number of Pieces.” arXiv, 2018. https://doi.org/10.48550/arXiv.1804.03057."},"project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"day":"13","month":"09","article_processing_charge":"No"},{"month":"11","publication_identifier":{"issn":["1424-0637"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00023-018-0723-1","quality_controlled":"1","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"}],"external_id":{"arxiv":["1704.05809"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:47:03Z","ec_funded":1,"publist_id":"7258","date_updated":"2024-02-20T10:48:17Z","date_created":"2018-12-11T11:47:09Z","volume":19,"author":[{"full_name":"Betea, Dan","last_name":"Betea","first_name":"Dan"},{"last_name":"Bouttier","first_name":"Jeremie","full_name":"Bouttier, Jeremie"},{"full_name":"Nejjar, Peter","last_name":"Nejjar","first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vuletic, Mirjana","first_name":"Mirjana","last_name":"Vuletic"}],"publication_status":"published","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"publisher":"Springer Nature","year":"2018","day":"13","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2018-11-13T00:00:00Z","article_type":"original","page":"3663-3742","publication":"Annales Henri Poincare","citation":{"apa":"Betea, D., Bouttier, J., Nejjar, P., & Vuletic, M. (2018). The free boundary Schur process and applications I. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-018-0723-1","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletic, “The free boundary Schur process and applications I,” Annales Henri Poincare, vol. 19, no. 12. Springer Nature, pp. 3663–3742, 2018.","ista":"Betea D, Bouttier J, Nejjar P, Vuletic M. 2018. The free boundary Schur process and applications I. Annales Henri Poincare. 19(12), 3663–3742.","ama":"Betea D, Bouttier J, Nejjar P, Vuletic M. The free boundary Schur process and applications I. Annales Henri Poincare. 2018;19(12):3663-3742. doi:10.1007/s00023-018-0723-1","chicago":"Betea, Dan, Jeremie Bouttier, Peter Nejjar, and Mirjana Vuletic. “The Free Boundary Schur Process and Applications I.” Annales Henri Poincare. Springer Nature, 2018. https://doi.org/10.1007/s00023-018-0723-1.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742.","mla":"Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” Annales Henri Poincare, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:10.1007/s00023-018-0723-1."},"abstract":[{"text":"We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions.","lang":"eng"}],"issue":"12","type":"journal_article","file":[{"relation":"main_file","file_id":"5866","date_updated":"2020-07-14T12:47:03Z","date_created":"2019-01-21T15:18:55Z","checksum":"0c38abe73569b7166b7487ad5d23cc68","file_name":"2018_Annales_Betea.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3084674,"creator":"dernst"}],"oa_version":"Published Version","ddc":["500"],"title":"The free boundary Schur process and applications I","status":"public","intvolume":" 19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"556"},{"citation":{"ista":"Alhaija H, Sellent A, Kondermann D, Rother C. 2018. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow, Institute of Science and Technology Austria, 10.15479/AT:ISTA:82.","apa":"Alhaija, H., Sellent, A., Kondermann, D., & Rother, C. (2018). Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:82","ieee":"H. Alhaija, A. Sellent, D. Kondermann, and C. Rother, “Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018.","ama":"Alhaija H, Sellent A, Kondermann D, Rother C. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. 2018. doi:10.15479/AT:ISTA:82","chicago":"Alhaija, Hassan, Anita Sellent, Daniel Kondermann, and Carsten Rother. “Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:82.","mla":"Alhaija, Hassan, et al. Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:82.","short":"H. Alhaija, A. Sellent, D. Kondermann, C. Rother, (2018)."},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"date_published":"2018-01-04T00:00:00Z","doi":"10.15479/AT:ISTA:82","keyword":["graph matching","quadratic assignment problem<"],"has_accepted_license":"1","article_processing_charge":"No","month":"01","day":"04","department":[{"_id":"VlKo"}],"publisher":"Institute of Science and Technology Austria","status":"public","title":"Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow","ddc":["001"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5573","year":"2018","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:05Z","date_created":"2018-12-12T13:02:34Z","checksum":"53c17082848e12f3c2e1b4185b578208","relation":"main_file","file_id":"5600","file_size":1737958,"content_type":"application/zip","creator":"system","file_name":"IST-2018-82-v1+1_GraphFlowMatchingProblems.zip","access_level":"open_access"}],"date_created":"2018-12-12T12:31:36Z","date_updated":"2024-02-21T13:41:17Z","contributor":[{"first_name":"Paul","last_name":"Swoboda","contributor_type":"researcher","id":"446560C6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"relation":"research_paper","url":"https://doi.org/10.1007/978-3-319-24947-6_23"}]},"author":[{"first_name":"Hassan","last_name":"Alhaija","full_name":"Alhaija, Hassan"},{"last_name":"Sellent","first_name":"Anita","full_name":"Sellent, Anita"},{"full_name":"Kondermann, Daniel","first_name":"Daniel","last_name":"Kondermann"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"}],"type":"research_data","datarep_id":"82","license":"https://creativecommons.org/publicdomain/zero/1.0/","file_date_updated":"2020-07-14T12:47:05Z","abstract":[{"text":"Graph matching problems for large displacement optical flow of RGB-D images.","lang":"eng"}]},{"article_number":"e1006057","file_date_updated":"2020-07-14T12:45:53Z","ec_funded":1,"year":"2018","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"author":[{"first_name":"Vicent","last_name":"Botella Soler","id":"421234E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8790-1914","full_name":"Botella Soler, Vicent"},{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"last_name":"Martius","first_name":"Georg S","full_name":"Martius, Georg S"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"}],"related_material":{"record":[{"id":"5584","status":"public","relation":"research_data"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/video-of-moving-discs-reconstructed-from-rat-retinal-neuron-signals/"}]},"date_updated":"2024-02-21T13:45:25Z","date_created":"2018-12-11T11:45:39Z","volume":14,"month":"05","external_id":{"isi":["000434012100002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270"},{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF"}],"doi":"10.1371/journal.pcbi.1006057","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Retina is a paradigmatic system for studying sensory encoding: the transformation of light into spiking activity of ganglion cells. The inverse problem, where stimulus is reconstructed from spikes, has received less attention, especially for complex stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred neurons from a dense patch in a rat retina and decoded movies of multiple small randomly-moving discs. We constructed nonlinear (kernelized and neural network) decoders that improved significantly over linear results. An important contribution to this was the ability of nonlinear decoders to reliably separate between neural responses driven by locally fluctuating light signals, and responses at locally constant light driven by spontaneous-like activity. This improvement crucially depended on the precise, non-Poisson temporal structure of individual spike trains, which originated in the spike-history dependence of neural responses. We propose a general principle by which downstream circuitry could discriminate between spontaneous and stimulus-driven activity based solely on higher-order statistical structure in the incoming spike trains."}],"issue":"5","_id":"292","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"title":"Nonlinear decoding of a complex movie from the mammalian retina","status":"public","intvolume":" 14","oa_version":"Published Version","file":[{"file_id":"5974","relation":"main_file","checksum":"3026f94d235219e15514505fdbadf34e","date_updated":"2020-07-14T12:45:53Z","date_created":"2019-02-13T11:07:15Z","access_level":"open_access","file_name":"2018_Plos_Botella_Soler.pdf","creator":"dernst","content_type":"application/pdf","file_size":3460786}],"scopus_import":"1","day":"10","article_processing_charge":"Yes","has_accepted_license":"1","publication":"PLoS Computational Biology","citation":{"short":"V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkačik, PLoS Computational Biology 14 (2018).","mla":"Botella Soler, Vicente, et al. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology, vol. 14, no. 5, e1006057, Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057.","chicago":"Botella Soler, Vicente, Stephane Deny, Georg S Martius, Olivier Marre, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pcbi.1006057.","ama":"Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 2018;14(5). doi:10.1371/journal.pcbi.1006057","apa":"Botella Soler, V., Deny, S., Martius, G. S., Marre, O., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1006057","ieee":"V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina,” PLoS Computational Biology, vol. 14, no. 5. Public Library of Science, 2018.","ista":"Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 14(5), e1006057."},"article_type":"original","date_published":"2018-05-10T00:00:00Z"}]