[{"day":"11","article_processing_charge":"No","has_accepted_license":"1","date_published":"2019-03-11T00:00:00Z","citation":{"short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. 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","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","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria."},"page":"189","abstract":[{"lang":"eng","text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. 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. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","access_level":"open_access","file_size":20995465,"content_type":"application/pdf","creator":"rprizak","relation":"main_file","file_id":"6072","date_created":"2019-03-06T16:05:07Z","date_updated":"2020-07-14T12:47:18Z","checksum":"e60a72de35d270b31f1a23d50f224ec0"},{"date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:09:39Z","checksum":"67c2630333d05ebafef5f018863a8465","title":"Latex files","file_id":"6073","relation":"source_file","creator":"rprizak","file_size":85705272,"content_type":"application/zip","file_name":"thesis_v2_merge.zip","access_level":"closed"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6071","status":"public","title":"Coevolution of transcription factors and their binding sites in sequence space","ddc":["576"],"month":"03","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:th6071","degree_awarded":"PhD","supervisor":[{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"file_date_updated":"2020-07-14T12:47:18Z","author":[{"first_name":"Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1358"},{"status":"public","relation":"part_of_dissertation","id":"955"}]},"date_created":"2019-03-06T16:16:10Z","date_updated":"2023-09-22T10:00:48Z","year":"2019","publication_status":"published","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria"},{"file":[{"relation":"main_file","file_id":"7104","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T08:24:01Z","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","file_name":"2019_PLOSComBio_Wang.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3982516,"creator":"dernst"}],"oa_version":"Published Version","_id":"7103","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 15","ddc":["570","000"],"status":"public","title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","issue":"11","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2019-11-01T00:00:00Z","citation":{"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","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.","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.","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","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.","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."},"publication":"PLoS Computational Biology","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","author":[{"full_name":"Wang, Jilin W. J. L.","last_name":"Wang","first_name":"Jilin W. J. L."},{"full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","first_name":"Fabrizio"},{"full_name":"Zhang, Xiyun","last_name":"Zhang","first_name":"Xiyun"},{"last_name":"Anaclet","first_name":"Christelle","full_name":"Anaclet, Christelle"},{"full_name":"Ivanov, Plamen Ch.","last_name":"Ivanov","first_name":"Plamen Ch."}],"volume":15,"date_updated":"2023-10-17T12:30:07Z","date_created":"2019-11-25T08:20:47Z","pmid":1,"year":"2019","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:49Z","article_number":"e1007268","doi":"10.1371/journal.pcbi.1007268","language":[{"iso":"eng"}],"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":["000500976100014"],"pmid":["31725712"]},"oa":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["1553-7358"]},"month":"11"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6090","intvolume":" 99","status":"public","title":"Receptor crosstalk improves concentration sensing of multiple ligands","oa_version":"Preprint","type":"journal_article","issue":"2","abstract":[{"text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing.","lang":"eng"}],"citation":{"apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423","ieee":"M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.","ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423.","ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423","chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423."},"publication":"Physical Review E","date_published":"2019-02-26T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"26","year":"2019","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"American Physical Society","publication_status":"published","author":[{"first_name":"Martín","last_name":"Carballo-Pacheco","full_name":"Carballo-Pacheco, Martín"},{"last_name":"Desponds","first_name":"Jonathan","full_name":"Desponds, Jonathan"},{"full_name":"Gavrilchenko, Tatyana","last_name":"Gavrilchenko","first_name":"Tatyana"},{"full_name":"Mayer, Andreas","first_name":"Andreas","last_name":"Mayer"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan","full_name":"Prizak, Roshan"},{"first_name":"Gautam","last_name":"Reddy","full_name":"Reddy, Gautam"},{"first_name":"Ilya","last_name":"Nemenman","full_name":"Nemenman, Ilya"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"}],"volume":99,"date_updated":"2024-02-28T13:12:06Z","date_created":"2019-03-10T22:59:20Z","article_number":"022423","oa":1,"external_id":{"isi":["000459916500007"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract"}],"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevE.99.022423","language":[{"iso":"eng"}],"month":"02"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1812.01475"}],"external_id":{"arxiv":["1812.01475"],"isi":["000540384500015"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"conference":{"name":"Information Theory Workshop","start_date":"2019-08-25","location":"Visby, Sweden","end_date":"2019-08-28"},"doi":"10.1109/ITW44776.2019.8989292","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"isbn":["9781538669006"]},"year":"2019","publication_status":"published","publisher":"IEEE","department":[{"_id":"GaTk"}],"author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal","full_name":"Hledik, Michal"},{"first_name":"Thomas R","last_name":"Sokolowski","id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15020"}]},"date_updated":"2024-03-06T14:22:51Z","date_created":"2020-03-22T23:00:47Z","article_number":"8989292","ec_funded":1,"publication":"IEEE Information Theory Workshop, ITW 2019","citation":{"ama":"Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information. In: IEEE Information Theory Workshop, ITW 2019. IEEE; 2019. doi:10.1109/ITW44776.2019.8989292","apa":"Hledik, M., Sokolowski, T. R., & Tkačik, G. (2019). A tight upper bound on mutual information. In IEEE Information Theory Workshop, ITW 2019. Visby, Sweden: IEEE. https://doi.org/10.1109/ITW44776.2019.8989292","ieee":"M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual information,” in IEEE Information Theory Workshop, ITW 2019, Visby, Sweden, 2019.","ista":"Hledik M, Sokolowski TR, Tkačik G. 2019. A tight upper bound on mutual information. IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292.","short":"M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop, ITW 2019, IEEE, 2019.","mla":"Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” IEEE Information Theory Workshop, ITW 2019, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292.","chicago":"Hledik, Michal, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper Bound on Mutual Information.” In IEEE Information Theory Workshop, ITW 2019. IEEE, 2019. https://doi.org/10.1109/ITW44776.2019.8989292."},"date_published":"2019-08-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7606","status":"public","title":"A tight upper bound on mutual information","oa_version":"Preprint","type":"conference","abstract":[{"text":"We derive a tight lower bound on equivocation (conditional entropy), or equivalently a tight upper bound on mutual information between a signal variable and channel outputs. The bound is in terms of the joint distribution of the signals and maximum a posteriori decodes (most probable signals given channel output). As part of our derivation, we describe the key properties of the distribution of signals, channel outputs and decodes, that minimizes equivocation and maximizes mutual information. This work addresses a problem in data analysis, where mutual information between signals and decodes is sometimes used to lower bound the mutual information between signals and channel outputs. Our result provides a corresponding upper bound.","lang":"eng"}]},{"file":[{"file_id":"5929","relation":"main_file","date_created":"2019-02-06T07:36:24Z","date_updated":"2020-07-14T12:45:59Z","checksum":"67010cf5e3b3e0637c659371714a715a","file_name":"2018_Heliyon_DeMartino.pdf","access_level":"open_access","creator":"dernst","file_size":994490,"content_type":"application/pdf"}],"oa_version":"Published Version","title":"An introduction to the maximum entropy approach and its application to inference problems in biology","ddc":["530"],"status":"public","intvolume":" 4","_id":"306","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data."}],"issue":"4","type":"journal_article","date_published":"2018-04-01T00:00:00Z","publication":"Heliyon","citation":{"ama":"De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 2018;4(4). doi:10.1016/j.heliyon.2018.e00596","ista":"De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 4(4), e00596.","apa":"De Martino, A., & De Martino, D. (2018). An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596","ieee":"A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4. Elsevier, 2018.","mla":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon, vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596.","short":"A. De Martino, D. De Martino, Heliyon 4 (2018).","chicago":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon. Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596."},"day":"01","has_accepted_license":"1","scopus_import":1,"date_created":"2018-12-11T11:45:44Z","date_updated":"2021-01-12T07:40:46Z","volume":4,"author":[{"full_name":"De Martino, Andrea","first_name":"Andrea","last_name":"De Martino"},{"full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","first_name":"Daniele"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"GaTk"}],"year":"2018","file_date_updated":"2020-07-14T12:45:59Z","ec_funded":1,"article_number":"e00596","language":[{"iso":"eng"}],"doi":"10.1016/j.heliyon.2018.e00596","quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"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"},"month":"04"}]