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Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. 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Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6072","checksum":"e60a72de35d270b31f1a23d50f224ec0","file_size":20995465,"date_updated":"2020-07-14T12:47:18Z","creator":"rprizak","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","date_created":"2019-03-06T16:05:07Z"},{"content_type":"application/zip","access_level":"closed","relation":"source_file","file_id":"6073","checksum":"67c2630333d05ebafef5f018863a8465","date_updated":"2020-07-14T12:47:18Z","file_size":85705272,"creator":"rprizak","title":"Latex files","date_created":"2019-03-06T16:09:39Z","file_name":"thesis_v2_merge.zip"}],"related_material":{"record":[{"id":"1358","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"955"}]},"_id":"6071","type":"dissertation","status":"public","date_updated":"2023-09-22T10:00:48Z","supervisor":[{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"ddc":["576"],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:18Z"},{"intvolume":" 24","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"For an ordinary K3 surface over an algebraically closed field of positive characteristic we show that every automorphism lifts to characteristic zero. Moreover, we show that the Fourier-Mukai partners of an ordinary K3 surface are in one-to-one correspondence with the Fourier-Mukai partners of the geometric generic fiber of its canonical lift. We also prove that the explicit counting formula for Fourier-Mukai partners of the K3 surfaces with Picard rank two and with discriminant equal to minus of a prime number, in terms of the class number of the prime, holds over a field of positive characteristic as well. We show that the image of the derived autoequivalence group of a K3 surface of finite height in the group of isometries of its crystalline cohomology has index at least two. Moreover, we provide a conditional upper bound on the kernel of this natural cohomological descent map. Further, we give an extended remark in the appendix on the possibility of an F-crystal structure on the crystalline cohomology of a K3 surface over an algebraically closed field of positive characteristic and show that the naive F-crystal structure fails in being compatible with inner product. 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K. Srivastava, “On derived equivalences of k3 surfaces in positive characteristic,” Documenta Mathematica, vol. 24. EMS Press, pp. 1135–1177, 2019.","short":"T.K. Srivastava, Documenta Mathematica 24 (2019) 1135–1177.","apa":"Srivastava, T. K. (2019). On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. EMS Press. https://doi.org/10.25537/dm.2019v24.1135-1177","ama":"Srivastava TK. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 2019;24:1135-1177. doi:10.25537/dm.2019v24.1135-1177","mla":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” Documenta Mathematica, vol. 24, EMS Press, 2019, pp. 1135–77, doi:10.25537/dm.2019v24.1135-1177.","ista":"Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 24, 1135–1177.","chicago":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” Documenta Mathematica. EMS Press, 2019. https://doi.org/10.25537/dm.2019v24.1135-1177."}},{"status":"public","article_type":"original","type":"journal_article","_id":"72","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"date_updated":"2023-10-17T08:53:45Z","month":"09","intvolume":" 55","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02323"}],"oa_version":"Preprint","abstract":[{"text":"We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ<λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t.","lang":"eng"}],"issue":"3","volume":55,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0246-0203"]},"publication_status":"published","project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"}],"title":"Limit law of a second class particle in TASEP with non-random initial condition","author":[{"full_name":"Ferrari, Patrick","last_name":"Ferrari","first_name":"Patrick"},{"first_name":"Promit","last_name":"Ghosal","full_name":"Ghosal, Promit"},{"first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","full_name":"Nejjar, Peter","last_name":"Nejjar"}],"external_id":{"isi":["000487763200001"],"arxiv":["1710.02323"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3, Institute of Mathematical Statistics, 2019, pp. 1203–25, doi:10.1214/18-AIHP916.","short":"P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B) Probability and Statistics 55 (2019) 1203–1225.","ieee":"P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle in TASEP with non-random initial condition,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3. Institute of Mathematical Statistics, pp. 1203–1225, 2019.","ama":"Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2019;55(3):1203-1225. doi:10.1214/18-AIHP916","apa":"Ferrari, P., Ghosal, P., & Nejjar, P. (2019). Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AIHP916","chicago":"Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AIHP916.","ista":"Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 55(3), 1203–1225."},"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1,"doi":"10.1214/18-AIHP916","date_published":"2019-09-25T00:00:00Z","date_created":"2018-12-11T11:44:29Z","page":"1203-1225","day":"25","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","isi":1,"year":"2019"},{"publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","quality_controlled":"1","oa":1,"page":"59-65","doi":"10.31263/voebm.v72i1.2276","date_published":"2019-05-17T00:00:00Z","date_created":"2019-07-21T21:59:15Z","has_accepted_license":"1","year":"2019","day":"17","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","author":[{"full_name":"Danowski, Patrick","orcid":"0000-0002-6026-4409","last_name":"Danowski","first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors","citation":{"mla":"Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 72, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019, pp. 59–65, doi:10.31263/voebm.v72i1.2276.","ama":"Danowski P. An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2019;72(1):59-65. doi:10.31263/voebm.v72i1.2276","apa":"Danowski, P. (2019). An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v72i1.2276","ieee":"P. Danowski, “An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 72, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 59–65, 2019.","short":"P. Danowski, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 72 (2019) 59–65.","chicago":"Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019. https://doi.org/10.31263/voebm.v72i1.2276.","ista":"Danowski P. 2019. An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 72(1), 59–65."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","month":"05","intvolume":" 72","abstract":[{"lang":"eng","text":"In this article a model is described how Open Access definitions can be formed on the basis of objective criteria. The common Open Access definitions such as \"gold\" and \"green\" are not exactly defined. This becomes a problem as soon as one begins to measure Open Access, for example if the development of the Open Access share should be monitored. This was discussed in the working group on Open Access Monitoring of the AT2OA project and the present model was developed, which is based on 5 critics with 4 characteristics: location, licence, version, embargo and conditions of the Open Access publication are taken into account. In the meantime, the model has also been tested in practice using R scripts, and the initial results are quite promising."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5686"}]},"volume":72,"issue":"1","publication_identifier":{"eissn":["1022-2588"]},"publication_status":"published","file":[{"checksum":"c0d2695d6d0d34e62ba06fb3f0ebaaed","file_id":"6661","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-07-22T08:45:03Z","file_name":"2019_MitteilungenDerVOEB_Danowski.pdf","date_updated":"2020-07-14T12:47:35Z","file_size":468558,"creator":"apreinsp"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","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)"},"status":"public","_id":"6657","file_date_updated":"2020-07-14T12:47:35Z","department":[{"_id":"E-Lib"}],"date_updated":"2023-10-17T11:33:58Z","ddc":["020"]},{"doi":"10.1364/cleo_at.2019.jtu2a.52","date_published":"2019-05-01T00:00:00Z","date_created":"2019-07-17T09:40:44Z","publication_identifier":{"isbn":["9781943580576"]},"publication_status":"published","year":"2019","day":"01","publication":"CLEO: Applications and Technology","language":[{"iso":"eng"}],"quality_controlled":"1","scopus_import":"1","publisher":"Optica Publishing Group","month":"05","abstract":[{"text":"We demonstrate robust retention of valley coherence and its control via polariton pseudospin precession through the optical TE-TM splitting in bilayer WS2 microcavity exciton polaritons at room temperature.","lang":"eng"}],"oa_version":"None","author":[{"full_name":"Khatoniar, Mandeep","last_name":"Khatoniar","first_name":"Mandeep"},{"full_name":"Yama, Nicholas","last_name":"Yama","first_name":"Nicholas"},{"last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sriram","full_name":"Guddala, Sriram","last_name":"Guddala"},{"full_name":"Ghaemi, Pouyan","last_name":"Ghaemi","first_name":"Pouyan"},{"full_name":"Menon, Vinod","last_name":"Menon","first_name":"Vinod"}],"article_processing_charge":"No","department":[{"_id":"MiLe"}],"title":"Room temperature control of valley coherence in bilayer WS2 exciton polaritons","date_updated":"2023-10-17T12:14:29Z","citation":{"mla":"Khatoniar, Mandeep, et al. “Room Temperature Control of Valley Coherence in Bilayer WS2 Exciton Polaritons.” CLEO: Applications and Technology, paper JTu2A.52, Optica Publishing Group, 2019, doi:10.1364/cleo_at.2019.jtu2a.52.","apa":"Khatoniar, M., Yama, N., Ghazaryan, A., Guddala, S., Ghaemi, P., & Menon, V. (2019). Room temperature control of valley coherence in bilayer WS2 exciton polaritons. In CLEO: Applications and Technology. San Jose, CA, United States: Optica Publishing Group. https://doi.org/10.1364/cleo_at.2019.jtu2a.52","ama":"Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. Room temperature control of valley coherence in bilayer WS2 exciton polaritons. In: CLEO: Applications and Technology. Optica Publishing Group; 2019. doi:10.1364/cleo_at.2019.jtu2a.52","short":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, V. Menon, in:, CLEO: Applications and Technology, Optica Publishing Group, 2019.","ieee":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, and V. Menon, “Room temperature control of valley coherence in bilayer WS2 exciton polaritons,” in CLEO: Applications and Technology, San Jose, CA, United States, 2019.","chicago":"Khatoniar, Mandeep, Nicholas Yama, Areg Ghazaryan, Sriram Guddala, Pouyan Ghaemi, and Vinod Menon. “Room Temperature Control of Valley Coherence in Bilayer WS2 Exciton Polaritons.” In CLEO: Applications and Technology. Optica Publishing Group, 2019. https://doi.org/10.1364/cleo_at.2019.jtu2a.52.","ista":"Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. 2019. Room temperature control of valley coherence in bilayer WS2 exciton polaritons. CLEO: Applications and Technology. CLEO: Conference on Lasers and Electro-Optics, paper JTu2A.52."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","conference":{"start_date":"2019-05-05","location":"San Jose, CA, United States","end_date":"2019-05-10","name":"CLEO: Conference on Lasers and Electro-Optics"},"status":"public","_id":"6646","article_number":"paper JTu2A.52"},{"month":"07","scopus_import":"1","publisher":"Optica Publishing Group","quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"We demonstrate electro-optic frequency comb generation using a doubly resonant system comprising a whispering gallery mode disk resonator made of lithium niobate mounted inside a three dimensional copper cavity. We observe 180 sidebands centred at 1550 nm."}],"date_created":"2020-01-05T23:00:48Z","doi":"10.1364/NLO.2019.NM2A.5","date_published":"2019-07-15T00:00:00Z","language":[{"iso":"eng"}],"publication":"Nonlinear Optics, OSA Technical Digest","day":"15","publication_status":"published","year":"2019","publication_identifier":{"isbn":["9781557528209"]},"status":"public","conference":{"start_date":"2019-07-15","location":"Waikoloa Beach, Hawaii (HI), United States","end_date":"2019-07-19","name":"NLO: Nonlinear Optics"},"type":"conference","article_number":"NM2A.5","_id":"7233","department":[{"_id":"JoFi"}],"title":"Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity","article_processing_charge":"No","author":[{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez"},{"first_name":"Florian","full_name":"Sedlmeir, Florian","last_name":"Sedlmeir"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"first_name":"Madhuri","full_name":"Kumari, Madhuri","last_name":"Kumari"},{"first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L.","last_name":"Schwefel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kumari, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” In Nonlinear Optics, OSA Technical Digest. Optica Publishing Group, 2019. https://doi.org/10.1364/NLO.2019.NM2A.5.","ista":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. 2019. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. Nonlinear Optics, OSA Technical Digest. NLO: Nonlinear Optics, NM2A.5.","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” Nonlinear Optics, OSA Technical Digest, NM2A.5, Optica Publishing Group, 2019, doi:10.1364/NLO.2019.NM2A.5.","ama":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In: Nonlinear Optics, OSA Technical Digest. Optica Publishing Group; 2019. doi:10.1364/NLO.2019.NM2A.5","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kumari, M., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In Nonlinear Optics, OSA Technical Digest. Waikoloa Beach, Hawaii (HI), United States: Optica Publishing Group. https://doi.org/10.1364/NLO.2019.NM2A.5","short":"A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, H.G.L. Schwefel, in:, Nonlinear Optics, OSA Technical Digest, Optica Publishing Group, 2019.","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, and H. G. L. Schwefel, “Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity,” in Nonlinear Optics, OSA Technical Digest, Waikoloa Beach, Hawaii (HI), United States, 2019."},"date_updated":"2023-10-17T12:14:46Z"},{"department":[{"_id":"LaEr"}],"date_updated":"2023-10-17T12:20:20Z","status":"public","type":"journal_article","_id":"6240","ec_funded":1,"issue":"2","volume":55,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0246-0203"]},"intvolume":" 55","month":"05","main_file_link":[{"url":"https://arxiv.org/abs/1706.08343","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"For a general class of large non-Hermitian random block matrices X we prove that there are no eigenvalues away from a deterministic set with very high probability. This set is obtained from the Dyson equation of the Hermitization of X as the self-consistent approximation of the pseudospectrum. We demonstrate that the analysis of the matrix Dyson equation from (Probab. Theory Related Fields (2018)) offers a unified treatment of many structured matrix ensembles.","lang":"eng"}],"title":"Location of the spectrum of Kronecker random matrices","article_processing_charge":"No","external_id":{"arxiv":["1706.08343"],"isi":["000467793600003"]},"author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt","full_name":"Alt, Johannes"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger"},{"last_name":"Nemish","full_name":"Nemish, Yuriy","orcid":"0000-0002-7327-856X","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","first_name":"Yuriy"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Alt J, Erdös L, Krüger TH, Nemish Y. 2019. Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. 55(2), 661–696.","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Yuriy Nemish. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare. Institut Henri Poincaré, 2019. https://doi.org/10.1214/18-AIHP894.","apa":"Alt, J., Erdös, L., Krüger, T. H., & Nemish, Y. (2019). Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. Institut Henri Poincaré. https://doi.org/10.1214/18-AIHP894","ama":"Alt J, Erdös L, Krüger TH, Nemish Y. Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. 2019;55(2):661-696. doi:10.1214/18-AIHP894","ieee":"J. Alt, L. Erdös, T. H. Krüger, and Y. Nemish, “Location of the spectrum of Kronecker random matrices,” Annales de l’institut Henri Poincare, vol. 55, no. 2. Institut Henri Poincaré, pp. 661–696, 2019.","short":"J. Alt, L. Erdös, T.H. Krüger, Y. Nemish, Annales de l’institut Henri Poincare 55 (2019) 661–696.","mla":"Alt, Johannes, et al. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare, vol. 55, no. 2, Institut Henri Poincaré, 2019, pp. 661–96, doi:10.1214/18-AIHP894."},"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2019-04-08T14:05:04Z","date_published":"2019-05-01T00:00:00Z","doi":"10.1214/18-AIHP894","page":"661-696","publication":"Annales de l'institut Henri Poincare","day":"01","year":"2019","isi":1,"oa":1,"publisher":"Institut Henri Poincaré","quality_controlled":"1"},{"volume":15,"issue":"7","publication_status":"published","publication_identifier":{"issn":["1553-7404"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"2f51fc91e4a4199827adc51d432ad864","file_id":"7446","date_updated":"2020-07-14T12:47:57Z","file_size":2302307,"creator":"dernst","date_created":"2020-02-04T10:11:55Z","file_name":"2019_PlosGenetics_Andergassen.pdf"}],"scopus_import":"1","intvolume":" 15","month":"07","abstract":[{"text":"Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"SiHi"}],"date_updated":"2023-10-17T12:30:27Z","ddc":["570"],"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)"},"type":"journal_article","article_type":"original","status":"public","_id":"7399","date_created":"2020-01-29T16:14:07Z","doi":"10.1371/journal.pgen.1008268","date_published":"2019-07-22T00:00:00Z","year":"2019","isi":1,"has_accepted_license":"1","publication":"PLoS Genetics","day":"22","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","external_id":{"isi":["000478689100025"],"pmid":["31329595"]},"article_processing_charge":"No","author":[{"first_name":"Daniel","full_name":"Andergassen, Daniel","last_name":"Andergassen"},{"first_name":"Markus","full_name":"Muckenhuber, Markus","last_name":"Muckenhuber"},{"first_name":"Philipp C.","full_name":"Bammer, Philipp C.","last_name":"Bammer"},{"first_name":"Tomasz M.","last_name":"Kulinski","full_name":"Kulinski, Tomasz M."},{"full_name":"Theussl, Hans-Christian","last_name":"Theussl","first_name":"Hans-Christian"},{"first_name":"Takahiko","last_name":"Shimizu","full_name":"Shimizu, Takahiko"},{"first_name":"Josef M.","last_name":"Penninger","full_name":"Penninger, Josef M."},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","last_name":"Pauler"},{"full_name":"Hudson, Quanah J.","last_name":"Hudson","first_name":"Quanah J."}],"title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","citation":{"ieee":"D. Andergassen et al., “The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes,” PLoS Genetics, vol. 15, no. 7. Public Library of Science, 2019.","short":"D. Andergassen, M. Muckenhuber, P.C. Bammer, T.M. Kulinski, H.-C. Theussl, T. Shimizu, J.M. Penninger, F. Pauler, Q.J. Hudson, PLoS Genetics 15 (2019).","apa":"Andergassen, D., Muckenhuber, M., Bammer, P. C., Kulinski, T. M., Theussl, H.-C., Shimizu, T., … Hudson, Q. J. (2019). The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008268","ama":"Andergassen D, Muckenhuber M, Bammer PC, et al. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. 2019;15(7). doi:10.1371/journal.pgen.1008268","mla":"Andergassen, Daniel, et al. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics, vol. 15, no. 7, e1008268, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008268.","ista":"Andergassen D, Muckenhuber M, Bammer PC, Kulinski TM, Theussl H-C, Shimizu T, Penninger JM, Pauler F, Hudson QJ. 2019. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. 15(7), e1008268.","chicago":"Andergassen, Daniel, Markus Muckenhuber, Philipp C. Bammer, Tomasz M. Kulinski, Hans-Christian Theussl, Takahiko Shimizu, Josef M. Penninger, Florian Pauler, and Quanah J. Hudson. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008268."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e1008268"},{"article_number":"e1007268","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268.","chicago":"Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet, and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007268.","apa":"Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., & Ivanov, P. C. (2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007268","ama":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 2019;15(11). doi:10.1371/journal.pcbi.1007268","ieee":"J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture,” PLoS Computational Biology, vol. 15, no. 11. Public Library of Science, 2019.","short":"J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019).","mla":"Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS Computational Biology, vol. 15, no. 11, e1007268, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007268."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jilin W. J. L.","full_name":"Wang, Jilin W. J. L.","last_name":"Wang"},{"orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio","last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio"},{"last_name":"Zhang","full_name":"Zhang, Xiyun","first_name":"Xiyun"},{"last_name":"Anaclet","full_name":"Anaclet, Christelle","first_name":"Christelle"},{"full_name":"Ivanov, Plamen Ch.","last_name":"Ivanov","first_name":"Plamen Ch."}],"article_processing_charge":"No","external_id":{"isi":["000500976100014"],"pmid":["31725712"]},"title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"01","publication":"PLoS Computational Biology","doi":"10.1371/journal.pcbi.1007268","date_published":"2019-11-01T00:00:00Z","date_created":"2019-11-25T08:20:47Z","_id":"7103","article_type":"original","type":"journal_article","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)"},"status":"public","date_updated":"2023-10-17T12:30:07Z","ddc":["570","000"],"file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"GaTk"}],"abstract":[{"text":"Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"11","intvolume":" 15","publication_identifier":{"issn":["1553-7358"]},"publication_status":"published","file":[{"date_updated":"2020-07-14T12:47:49Z","file_size":3982516,"creator":"dernst","date_created":"2019-11-25T08:24:01Z","file_name":"2019_PLOSComBio_Wang.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","file_id":"7104"}],"language":[{"iso":"eng"}],"volume":15,"issue":"11","ec_funded":1},{"day":"13","publication":"Proceedings of the 36th International Conference on Machine Learning","has_accepted_license":"1","year":"2019","date_published":"2019-06-13T00:00:00Z","date_created":"2019-06-20T18:23:03Z","page":"5142-5151","publisher":"ML Research Press","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Phuong and C. Lampert, “Towards understanding knowledge distillation,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, United States, 2019, vol. 97, pp. 5142–5151.","short":"M. Phuong, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 5142–5151.","apa":"Phuong, M., & Lampert, C. (2019). Towards understanding knowledge distillation. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 5142–5151). Long Beach, CA, United States: ML Research Press.","ama":"Phuong M, Lampert C. Towards understanding knowledge distillation. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:5142-5151.","mla":"Phuong, Mary, and Christoph Lampert. “Towards Understanding Knowledge Distillation.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 5142–51.","ista":"Phuong M, Lampert C. 2019. Towards understanding knowledge distillation. Proceedings of the 36th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 97, 5142–5151.","chicago":"Phuong, Mary, and Christoph Lampert. “Towards Understanding Knowledge Distillation.” In Proceedings of the 36th International Conference on Machine Learning, 97:5142–51. ML Research Press, 2019."},"title":"Towards understanding knowledge distillation","author":[{"last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong","first_name":"Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"}],"article_processing_charge":"No","file":[{"checksum":"a66d00e2694d749250f8507f301320ca","file_id":"6570","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-06-20T18:22:56Z","file_name":"paper.pdf","creator":"bphuong","date_updated":"2020-07-14T12:47:33Z","file_size":686432}],"language":[{"iso":"eng"}],"publication_status":"published","volume":97,"oa_version":"Published Version","abstract":[{"text":"Knowledge distillation, i.e. one classifier being trained on the outputs of another classifier, is an empirically very successful technique for knowledge transfer between classifiers. It has even been observed that classifiers learn much faster and more reliably if trained with the outputs of another classifier as soft labels, instead of from ground truth data. So far, however, there is no satisfactory theoretical explanation of this phenomenon. In this work, we provide the first insights into the working mechanisms of distillation by studying the special case of linear and deep linear classifiers. Specifically, we prove a generalization bound that establishes fast convergence of the expected risk of a distillation-trained linear classifier. From the bound and its proof we extract three keyfactors that determine the success of distillation: data geometry – geometric properties of the datadistribution, in particular class separation, has an immediate influence on the convergence speed of the risk; optimization bias– gradient descentoptimization finds a very favorable minimum of the distillation objective; and strong monotonicity– the expected risk of the student classifier always decreases when the size of the training set grows.","lang":"eng"}],"month":"06","intvolume":" 97","scopus_import":"1","ddc":["000"],"date_updated":"2023-10-17T12:31:38Z","department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:47:33Z","_id":"6569","status":"public","type":"conference","conference":{"start_date":"2019-06-10","location":"Long Beach, CA, United States","end_date":"2019-06-15","name":"ICML: International Conference on Machine Learning"}}]