[{"date_updated":"2023-12-18T10:46:08Z","external_id":{"arxiv":["1804.07752"]},"year":"2018","related_material":{"record":[{"relation":"dissertation_contains","id":"149","status":"public"},{"status":"public","relation":"later_version","id":"14694"}]},"day":"20","_id":"6183","department":[{"_id":"LaEr"}],"article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"article_number":"1804.07752","month":"04","date_published":"2018-04-20T00:00:00Z","citation":{"mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, 1804.07752.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, n.d.","ista":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv, 1804.07752.","ama":"Alt J, Erdös L, Krüger TH. 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.","short":"J. Alt, L. Erdös, T.H. Krüger, ArXiv (n.d.).","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” arXiv. ."},"main_file_link":[{"url":"https://arxiv.org/abs/1804.07752","open_access":"1"}],"oa_version":"Preprint","publication_status":"submitted","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","type":"preprint","oa":1,"language":[{"iso":"eng"}],"publication":"arXiv","author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt","full_name":"Alt, Johannes"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"}],"date_created":"2019-03-28T09:20:06Z"},{"main_file_link":[{"url":"https://arxiv.org/abs/1804.03057","open_access":"1"}],"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.","mla":"Akopyan, Arseniy, et al. Convex Fair Partitions into Arbitrary Number of Pieces. 1804.03057, arXiv, 2018, doi:10.48550/arXiv.1804.03057.","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.","ieee":"A. Akopyan, S. Avvakumov, and R. Karasev, “Convex fair partitions into arbitrary number of pieces.” arXiv, 2018.","short":"A. Akopyan, S. Avvakumov, R. Karasev, (2018).","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"},"title":"Convex fair partitions into arbitrary number of pieces","type":"preprint","status":"public","publisher":"arXiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa_version":"Preprint","doi":"10.48550/arXiv.1804.03057","language":[{"iso":"eng"}],"oa":1,"date_created":"2018-12-11T11:44:30Z","ec_funded":1,"author":[{"orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"},{"last_name":"Karasev","first_name":"Roman","full_name":"Karasev, Roman"}],"year":"2018","external_id":{"arxiv":["1804.03057"]},"date_updated":"2023-12-18T10:51:02Z","day":"13","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8156"}]},"abstract":[{"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.","lang":"eng"}],"department":[{"_id":"HeEd"},{"_id":"JaMa"}],"article_processing_charge":"No","_id":"75","project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"}],"date_published":"2018-09-13T00:00:00Z","month":"09","article_number":"1804.03057"},{"date_updated":"2024-02-20T10:48:17Z","year":"2018","day":"13","_id":"556","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"month":"11","date_published":"2018-11-13T00:00:00Z","citation":{"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.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742.","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","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","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.","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."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","status":"public","type":"journal_article","volume":19,"publication_identifier":{"issn":["1424-0637"]},"language":[{"iso":"eng"}],"intvolume":" 19","doi":"10.1007/s00023-018-0723-1","publication":"Annales Henri Poincare","author":[{"full_name":"Betea, Dan","last_name":"Betea","first_name":"Dan"},{"full_name":"Bouttier, Jeremie","first_name":"Jeremie","last_name":"Bouttier"},{"full_name":"Nejjar, Peter","first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","last_name":"Nejjar"},{"full_name":"Vuletic, Mirjana","first_name":"Mirjana","last_name":"Vuletic"}],"file_date_updated":"2020-07-14T12:47:03Z","publist_id":"7258","external_id":{"arxiv":["1704.05809"]},"scopus_import":"1","license":"https://creativecommons.org/licenses/by/4.0/","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"}],"article_processing_charge":"Yes (via OA deal)","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"}],"has_accepted_license":"1","page":"3663-3742","file":[{"date_updated":"2020-07-14T12:47:03Z","creator":"dernst","checksum":"0c38abe73569b7166b7487ad5d23cc68","file_size":3084674,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5866","date_created":"2019-01-21T15:18:55Z","file_name":"2018_Annales_Betea.pdf"}],"issue":"12","quality_controlled":"1","oa_version":"Published Version","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The free boundary Schur process and applications I","oa":1,"article_type":"original","ddc":["500"],"ec_funded":1,"date_created":"2018-12-11T11:47:09Z"},{"department":[{"_id":"VlKo"}],"article_processing_charge":"No","_id":"5573","file":[{"checksum":"53c17082848e12f3c2e1b4185b578208","creator":"system","date_updated":"2020-07-14T12:47:05Z","access_level":"open_access","relation":"main_file","file_size":1737958,"content_type":"application/zip","file_id":"5600","date_created":"2018-12-12T13:02:34Z","file_name":"IST-2018-82-v1+1_GraphFlowMatchingProblems.zip"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Graph matching problems for large displacement optical flow of RGB-D images."}],"datarep_id":"82","date_published":"2018-01-04T00:00:00Z","month":"01","date_updated":"2024-02-21T13:41:17Z","year":"2018","related_material":{"link":[{"url":"https://doi.org/10.1007/978-3-319-24947-6_23","relation":"research_paper"}]},"license":"https://creativecommons.org/publicdomain/zero/1.0/","day":"04","ddc":["001"],"oa":1,"doi":"10.15479/AT:ISTA:82","file_date_updated":"2020-07-14T12:47:05Z","author":[{"full_name":"Alhaija, Hassan","first_name":"Hassan","last_name":"Alhaija"},{"full_name":"Sellent, Anita","first_name":"Anita","last_name":"Sellent"},{"full_name":"Kondermann, Daniel","first_name":"Daniel","last_name":"Kondermann"},{"last_name":"Rother","first_name":"Carsten","full_name":"Rother, Carsten"}],"date_created":"2018-12-12T12:31:36Z","keyword":["graph matching","quadratic assignment problem<"],"contributor":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","contributor_type":"researcher","last_name":"Swoboda"}],"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"citation":{"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","short":"H. Alhaija, A. Sellent, D. Kondermann, C. Rother, (2018).","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.","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.","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.","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","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."},"oa_version":"Published Version","type":"research_data","title":"Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Institute of Science and Technology Austria"},{"date_created":"2018-12-11T11:45:39Z","ec_funded":1,"article_type":"original","ddc":["570"],"oa":1,"title":"Nonlinear decoding of a complex movie from the mammalian retina","publisher":"Public Library of Science","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","oa_version":"Published Version","issue":"5","has_accepted_license":"1","abstract":[{"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.","lang":"eng"}],"file":[{"file_name":"2018_Plos_Botella_Soler.pdf","date_created":"2019-02-13T11:07:15Z","file_id":"5974","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":3460786,"creator":"dernst","checksum":"3026f94d235219e15514505fdbadf34e","date_updated":"2020-07-14T12:45:53Z"}],"article_processing_charge":"Yes","project":[{"_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","call_identifier":"H2020"},{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF"}],"scopus_import":"1","external_id":{"isi":["000434012100002"]},"file_date_updated":"2020-07-14T12:45:53Z","author":[{"orcid":"0000-0002-8790-1914","full_name":"Botella Soler, Vicent","last_name":"Botella Soler","id":"421234E8-F248-11E8-B48F-1D18A9856A87","first_name":"Vicent"},{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"publication":"PLoS Computational Biology","doi":"10.1371/journal.pcbi.1006057","language":[{"iso":"eng"}],"intvolume":" 14","volume":14,"type":"journal_article","status":"public","publication_status":"published","citation":{"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.","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.","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","short":"V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkačik, PLoS Computational Biology 14 (2018).","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."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_published":"2018-05-10T00:00:00Z","month":"05","article_number":"e1006057","department":[{"_id":"GaTk"}],"isi":1,"_id":"292","day":"10","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/video-of-moving-discs-reconstructed-from-rat-retinal-neuron-signals/"}],"record":[{"status":"public","relation":"research_data","id":"5584"}]},"year":"2018","date_updated":"2024-02-21T13:45:25Z"},{"oa_version":"Published Version","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Oxford University Press","title":"Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations","issue":"6","date_created":"2018-12-11T11:46:29Z","oa":1,"ddc":["576"],"scopus_import":"1","external_id":{"isi":["000429009500021"]},"project":[{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","page":"2918-2931","file":[{"date_created":"2018-12-12T10:15:30Z","file_name":"IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf","file_id":"5151","content_type":"application/pdf","checksum":"3ff4f545c27e11a4cd20ccb30778793e","creator":"system","date_updated":"2020-07-14T12:46:27Z","relation":"main_file","access_level":"open_access","file_size":5027978}],"abstract":[{"text":"The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress.","lang":"eng"}],"pubrep_id":"971","publication_status":"published","status":"public","volume":46,"type":"journal_article","citation":{"ista":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 46(6), 2918–2931.","ama":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 2018;46(6):2918-2931. doi:10.1093/nar/gky079","chicago":"Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese, Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research. Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079.","mla":"Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research, vol. 46, no. 6, Oxford University Press, 2018, pp. 2918–31, doi:10.1093/nar/gky079.","ieee":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I. Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations,” Nucleic Acids Research, vol. 46, no. 6. Oxford University Press, pp. 2918–2931, 2018.","short":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll, Nucleic Acids Research 46 (2018) 2918–2931.","apa":"Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., & Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gky079"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"author":[{"orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller"},{"last_name":"Vandervelde","first_name":"Alexandra","full_name":"Vandervelde, Alexandra"},{"first_name":"Tanino","last_name":"Albanese","full_name":"Albanese, Tanino"},{"first_name":"Lendert","last_name":"Gelens","full_name":"Gelens, Lendert"},{"full_name":"Moll, Isabella","first_name":"Isabella","last_name":"Moll"}],"file_date_updated":"2020-07-14T12:46:27Z","language":[{"iso":"eng"}],"intvolume":" 46","doi":"10.1093/nar/gky079","publication":"Nucleic Acids Research","related_material":{"record":[{"id":"5569","relation":"popular_science","status":"public"}]},"day":"06","date_updated":"2024-02-21T13:44:45Z","year":"2018","month":"04","date_published":"2018-04-06T00:00:00Z","_id":"438","isi":1,"department":[{"_id":"CaGu"}]},{"scopus_import":"1","external_id":{"isi":["000441388200001"]},"has_accepted_license":"1","abstract":[{"text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. ","lang":"eng"}],"file":[{"content_type":"application/pdf","file_id":"5695","date_created":"2018-12-17T11:55:05Z","file_name":"2018_eLife_Picard.pdf","access_level":"open_access","relation":"main_file","file_size":3158125,"checksum":"d6331d4385b1fffd6b47b45d5949d841","creator":"dernst","date_updated":"2020-07-14T12:44:43Z"}],"article_processing_charge":"No","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","publisher":"eLife Sciences Publications","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","quality_controlled":"1","date_created":"2018-12-11T11:44:47Z","article_type":"original","ddc":["570"],"oa":1,"day":"13","related_material":{"record":[{"status":"public","id":"5586","relation":"popular_science"}]},"year":"2018","date_updated":"2024-02-21T13:45:12Z","date_published":"2018-08-13T00:00:00Z","month":"08","article_number":"e35684","isi":1,"department":[{"_id":"BeVi"}],"_id":"131","type":"journal_article","volume":7,"status":"public","publication_status":"published","citation":{"ieee":"M. A. L. Picard et al., “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” eLife, vol. 7. eLife Sciences Publications, 2018.","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., & Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.35684","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684.","ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 2018;7. doi:10.7554/eLife.35684","chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.35684.","mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife, vol. 7, e35684, eLife Sciences Publications, 2018, doi:10.7554/eLife.35684."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publist_id":"7792","file_date_updated":"2020-07-14T12:44:43Z","author":[{"orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A"},{"first_name":"Celine","last_name":"Cosseau","full_name":"Cosseau, Celine"},{"first_name":"Sabrina","last_name":"Ferré","full_name":"Ferré, Sabrina"},{"full_name":"Quack, Thomas","last_name":"Quack","first_name":"Thomas"},{"full_name":"Grevelding, Christoph","first_name":"Christoph","last_name":"Grevelding"},{"last_name":"Couté","first_name":"Yohann","full_name":"Couté, Yohann"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"publication":"eLife","acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","doi":"10.7554/eLife.35684","intvolume":" 7","language":[{"iso":"eng"}]},{"year":"2018","date_updated":"2024-02-21T13:45:26Z","day":"29","related_material":{"record":[{"relation":"used_in_publication","id":"292","status":"public"}]},"abstract":[{"text":"This package contains data for the publication \"Nonlinear decoding of a complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018). \r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. ","lang":"eng"}],"file":[{"checksum":"6808748837b9afbbbabc2a356ca2b88a","creator":"system","date_updated":"2020-07-14T12:47:07Z","access_level":"open_access","relation":"main_file","file_size":1142543971,"file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat","date_created":"2018-12-12T13:02:24Z","content_type":"application/octet-stream","file_id":"5590"},{"file_id":"5591","content_type":"application/pdf","file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf","date_created":"2018-12-12T13:02:25Z","date_updated":"2020-07-14T12:47:07Z","checksum":"d6d6cd07743038fe3a12352983fcf9dd","creator":"system","file_size":702336,"access_level":"open_access","relation":"main_file"},{"creator":"system","checksum":"0c9cfb4dab35bb3dc25a04395600b1c8","date_updated":"2020-07-14T12:47:07Z","access_level":"open_access","relation":"main_file","file_size":432,"file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat","date_created":"2018-12-12T13:02:26Z","content_type":"application/octet-stream","file_id":"5592"},{"checksum":"2a83b011012e21e934b4596285b1a183","creator":"system","date_updated":"2020-07-14T12:47:07Z","access_level":"open_access","relation":"main_file","file_size":986,"content_type":"text/plain","file_id":"5593","file_name":"IST-2018-98-v1+4_README.txt","date_created":"2018-12-12T13:02:26Z"}],"has_accepted_license":"1","_id":"5584","project":[{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"article_processing_charge":"No","month":"03","date_published":"2018-03-29T00:00:00Z","datarep_id":"98","citation":{"ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","apa":"Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98","ista":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, 10.15479/AT:ISTA:98.","mla":"Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98.","chicago":"Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98."},"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","status":"public","title":"Nonlinear decoding of a complex movie from the mammalian retina","type":"research_data","oa_version":"Published Version","doi":"10.15479/AT:ISTA:98","oa":1,"ddc":["570"],"keyword":["retina","decoding","regression","neural networks","complex stimulus"],"date_created":"2018-12-12T12:31:39Z","author":[{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"full_name":"Botella-Soler, Vicente","first_name":"Vicente","last_name":"Botella-Soler"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S"},{"last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"file_date_updated":"2020-07-14T12:47:07Z"},{"abstract":[{"lang":"eng","text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. "}],"page":"988 - 999","article_processing_charge":"No","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"external_id":{"isi":["000441753000007"]},"scopus_import":"1","date_created":"2018-12-11T11:45:37Z","ec_funded":1,"issue":"5","title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","oa_version":"None","quality_controlled":"1","isi":1,"department":[{"_id":"NiBa"}],"_id":"286","date_published":"2018-09-01T00:00:00Z","month":"09","year":"2018","date_updated":"2024-02-21T13:45:00Z","day":"01","related_material":{"record":[{"id":"5583","relation":"popular_science","status":"public"}]},"publication":"Molecular Ecology Resources","doi":"10.1111/1755-0998.12782","acknowledgement":"ERC, Grant/Award Number: 250152","intvolume":" 18","language":[{"iso":"eng"}],"author":[{"last_name":"Ellis","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"citation":{"ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” Molecular Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.","apa":"Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782","ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999.","ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 2018;18(5):988-999. doi:10.1111/1755-0998.12782","mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782."},"volume":18,"type":"journal_article","status":"public","publication_status":"published"},{"department":[{"_id":"BeVi"}],"article_processing_charge":"No","_id":"5586","project":[{"call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"file":[{"creator":"system","checksum":"e60b484bd6f55c08eb66a189cb72c923","date_updated":"2020-07-14T12:47:08Z","access_level":"open_access","relation":"main_file","file_size":11918144,"file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","date_created":"2018-12-12T13:02:35Z","content_type":"application/zip","file_id":"5601"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)."}],"datarep_id":"109","date_published":"2018-07-24T00:00:00Z","month":"07","date_updated":"2024-02-21T13:45:12Z","year":"2018","related_material":{"record":[{"id":"131","relation":"research_paper","status":"public"}]},"day":"24","ddc":["570"],"oa":1,"doi":"10.15479/AT:ISTA:109","file_date_updated":"2020-07-14T12:47:08Z","author":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"date_created":"2018-12-12T12:31:40Z","keyword":["schistosoma","Z-chromosome","gene expression"],"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"contributor":[{"orcid":"0000-0002-8101-2518","first_name":"Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard"}],"citation":{"chicago":"Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:109.","mla":"Vicoso, Beatriz. Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018). Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:109.","ista":"Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, 10.15479/AT:ISTA:109.","ama":"Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:10.15479/AT:ISTA:109","short":"B. Vicoso, (2018).","apa":"Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:109","ieee":"B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018."},"oa_version":"Published Version","type":"research_data","title":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public"}]