[{"publication_status":"published","publication_identifier":{"eissn":["1664-462X"]},"pmid":1,"_id":"7182","article_processing_charge":"No","scopus_import":"1","file_date_updated":"2020-07-14T12:47:52Z","abstract":[{"text":"During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host’s immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome.","lang":"eng"}],"doi":"10.3389/fpls.2019.01437","department":[{"_id":"JiFr"}],"intvolume":"        10","issue":"11","date_created":"2019-12-15T23:00:43Z","author":[{"last_name":"Alcântara","first_name":"André","full_name":"Alcântara, André"},{"full_name":"Bosch, Jason","first_name":"Jason","last_name":"Bosch"},{"last_name":"Nazari","first_name":"Fahimeh","full_name":"Nazari, Fahimeh"},{"first_name":"Gesa","last_name":"Hoffmann","full_name":"Hoffmann, Gesa"},{"full_name":"Gallei, Michelle C","first_name":"Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Uhse, Simon","last_name":"Uhse","first_name":"Simon"},{"full_name":"Darino, Martin A.","last_name":"Darino","first_name":"Martin A."},{"full_name":"Olukayode, Toluwase","last_name":"Olukayode","first_name":"Toluwase"},{"full_name":"Reumann, Daniel","last_name":"Reumann","first_name":"Daniel"},{"full_name":"Baggaley, Laura","last_name":"Baggaley","first_name":"Laura"},{"first_name":"Armin","last_name":"Djamei","full_name":"Djamei, Armin"}],"has_accepted_license":"1","ddc":["580"],"publisher":"Frontiers","isi":1,"type":"journal_article","publication":"Frontiers in Plant Science","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":10,"year":"2019","month":"11","language":[{"iso":"eng"}],"date_published":"2019-11-14T00:00:00Z","date_updated":"2026-04-16T08:34:31Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"content_type":"application/pdf","checksum":"995aa838aec2064d93550de82b40bbd1","file_size":1532505,"date_created":"2019-12-16T07:58:43Z","creator":"dernst","relation":"main_file","file_name":"2019_FrontiersPlant_Alcantara.pdf","file_id":"7185","access_level":"open_access","date_updated":"2020-07-14T12:47:52Z"}],"citation":{"ama":"Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive effector-complex formation. <i>Frontiers in Plant Science</i>. 2019;10(11). doi:<a href=\"https://doi.org/10.3389/fpls.2019.01437\">10.3389/fpls.2019.01437</a>","apa":"Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S., … Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex formation. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2019.01437\">https://doi.org/10.3389/fpls.2019.01437</a>","ista":"Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA, Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437.","chicago":"Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” <i>Frontiers in Plant Science</i>. Frontiers, 2019. <a href=\"https://doi.org/10.3389/fpls.2019.01437\">https://doi.org/10.3389/fpls.2019.01437</a>.","short":"A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A. Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science 10 (2019).","mla":"Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” <i>Frontiers in Plant Science</i>, vol. 10, no. 11, 1437, Frontiers, 2019, doi:<a href=\"https://doi.org/10.3389/fpls.2019.01437\">10.3389/fpls.2019.01437</a>.","ieee":"A. Alcântara <i>et al.</i>, “Systematic Y2H screening reveals extensive effector-complex formation,” <i>Frontiers in Plant Science</i>, vol. 10, no. 11. Frontiers, 2019."},"article_type":"original","status":"public","article_number":"1437","title":"Systematic Y2H screening reveals extensive effector-complex formation","day":"14","external_id":{"isi":["000499821700001"],"pmid":["31803201"]},"oa":1,"quality_controlled":"1","oa_version":"Published Version"},{"isi":1,"publisher":"Wiley","publication":"Molecular ecology","type":"journal_article","volume":28,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"date_published":"2019-04-01T00:00:00Z","date_updated":"2026-04-16T08:33:17Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2019","month":"04","page":"1579-1581","file":[{"creator":"dernst","date_created":"2019-05-20T11:49:06Z","file_id":"6472","file_name":"2019_MolecularEcology_Field.pdf","date_updated":"2020-07-14T12:47:31Z","access_level":"open_access","relation":"main_file","file_size":367711,"checksum":"521e3aff3e9263ddf2ffbfe0b6157715","content_type":"application/pdf"}],"citation":{"ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” <i>Molecular ecology</i>, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” <i>Molecular Ecology</i>, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:<a href=\"https://doi.org/10.1111/mec.15048\">10.1111/mec.15048</a>.","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581.","chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.15048\">https://doi.org/10.1111/mec.15048</a>.","ama":"Field D, Fraisse C. Breaking down barriers in morning glories. <i>Molecular ecology</i>. 2019;28(7):1579-1581. doi:<a href=\"https://doi.org/10.1111/mec.15048\">10.1111/mec.15048</a>","apa":"Field, D., &#38; Fraisse, C. (2019). Breaking down barriers in morning glories. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15048\">https://doi.org/10.1111/mec.15048</a>"},"status":"public","title":"Breaking down barriers in morning glories","quality_controlled":"1","oa_version":"Published Version","external_id":{"isi":["000474808300001"]},"day":"01","oa":1,"publication_status":"published","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"article_processing_charge":"No","_id":"6466","abstract":[{"lang":"eng","text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates."}],"file_date_updated":"2020-07-14T12:47:31Z","scopus_import":"1","doi":"10.1111/mec.15048","department":[{"_id":"NiBa"}],"intvolume":"        28","author":[{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","last_name":"Field","first_name":"David"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle"}],"issue":"7","date_created":"2019-05-19T21:59:15Z","ddc":["580","576"],"has_accepted_license":"1"},{"scopus_import":"1","abstract":[{"lang":"eng","text":"Motivated by recent experimental observations of coherent many-body revivals in a constrained Rydbergatom chain, we construct a weak quasilocal deformation of the Rydberg-blockaded Hamiltonian, whichmakes the revivals virtually perfect. Our analysis suggests the existence of an underlying nonintegrableHamiltonian which supports an emergent SU(2)-spin dynamics within a small subspace of the many-bodyHilbert space. We show that such perfect dynamics necessitates the existence of atypical, nonergodicenergy eigenstates—quantum many-body scars. Furthermore, using these insights, we construct a toymodel that hosts exact quantum many-body scars, providing an intuitive explanation of their origin. Ourresults offer specific routes to enhancing coherent many-body revivals and provide a step towardestablishing the stability of quantum many-body scars in the thermodynamic limit."}],"department":[{"_id":"MaSe"}],"doi":"10.1103/PhysRevLett.122.220603","publication_status":"published","_id":"6575","article_processing_charge":"No","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"date_created":"2019-06-23T21:59:13Z","issue":"22","author":[{"full_name":"Choi, Soonwon","first_name":"Soonwon","last_name":"Choi"},{"last_name":"Turner","first_name":"Christopher J.","full_name":"Turner, Christopher J."},{"first_name":"Hannes","last_name":"Pichler","full_name":"Pichler, Hannes"},{"full_name":"Ho, Wen Wei","last_name":"Ho","first_name":"Wen Wei"},{"full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym"},{"first_name":"Mikhail D.","last_name":"Lukin","full_name":"Lukin, Mikhail D."},{"first_name":"Dmitry A.","last_name":"Abanin","full_name":"Abanin, Dmitry A."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1812.05561"}],"intvolume":"       122","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","arxiv":1,"volume":122,"month":"06","year":"2019","date_updated":"2026-04-16T08:33:54Z","language":[{"iso":"eng"}],"date_published":"2019-06-07T00:00:00Z","publisher":"American Physical Society","isi":1,"type":"journal_article","publication":"Physical Review Letters","title":"Emergent SU(2) dynamics and perfect quantum many-body scars","oa":1,"day":"07","external_id":{"arxiv":["1812.05561"],"isi":["000470885800005"]},"oa_version":"Preprint","quality_controlled":"1","citation":{"chicago":"Choi, Soonwon, Christopher J. Turner, Hannes Pichler, Wen Wei Ho, Alexios Michailidis, Zlatko Papić, Maksym Serbyn, Mikhail D. Lukin, and Dmitry A. Abanin. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” <i>Physical Review Letters</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevLett.122.220603\">https://doi.org/10.1103/PhysRevLett.122.220603</a>.","ista":"Choi S, Turner CJ, Pichler H, Ho WW, Michailidis A, Papić Z, Serbyn M, Lukin MD, Abanin DA. 2019. Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. 122(22), 220603.","ama":"Choi S, Turner CJ, Pichler H, et al. Emergent SU(2) dynamics and perfect quantum many-body scars. <i>Physical Review Letters</i>. 2019;122(22). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.122.220603\">10.1103/PhysRevLett.122.220603</a>","apa":"Choi, S., Turner, C. J., Pichler, H., Ho, W. W., Michailidis, A., Papić, Z., … Abanin, D. A. (2019). Emergent SU(2) dynamics and perfect quantum many-body scars. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.122.220603\">https://doi.org/10.1103/PhysRevLett.122.220603</a>","ieee":"S. Choi <i>et al.</i>, “Emergent SU(2) dynamics and perfect quantum many-body scars,” <i>Physical Review Letters</i>, vol. 122, no. 22. American Physical Society, 2019.","mla":"Choi, Soonwon, et al. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” <i>Physical Review Letters</i>, vol. 122, no. 22, 220603, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.122.220603\">10.1103/PhysRevLett.122.220603</a>.","short":"S. Choi, C.J. Turner, H. Pichler, W.W. Ho, A. Michailidis, Z. Papić, M. Serbyn, M.D. Lukin, D.A. Abanin, Physical Review Letters 122 (2019)."},"article_type":"original","status":"public","article_number":"220603"},{"abstract":[{"text":"Single cells are constantly interacting with their environment and each other, more importantly, the accurate perception of environmental cues is crucial for growth, survival, and reproduction. This communication between cells and their environment can be formalized in mathematical terms and be quantified as the information flow between them, as prescribed by information theory. \r\nThe recent availability of real–time dynamical patterns of signaling molecules in single cells has allowed us to identify encoding about the identity of the environment in the time–series. However, efficient estimation of the information transmitted by these signals has been a data–analysis challenge due to the high dimensionality of the trajectories and the limited number of samples. In the first part of this thesis, we develop and evaluate decoding–based estimation methods to lower bound the mutual information and derive model–based precise information estimates for biological reaction networks governed by the chemical master equation. This is followed by applying the decoding-based methods to study the intracellular representation of extracellular changes in budding yeast, by observing the transient dynamics of nuclear translocation of 10 transcription factors in response to 3 stress conditions. Additionally, we apply these estimators to previously published data on ERK and Ca2+ signaling and yeast stress response. We argue that this single cell decoding-based measure of information provides an unbiased, quantitative and interpretable measure for the fidelity of biological signaling processes. \r\nFinally, in the last section, we deal with gene regulation which is primarily controlled by transcription factors (TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate TFs activate transcription diminishes the accuracy of regulation with potentially disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored source of noise in biochemical networks and puts a strong constraint on their performance. To mitigate erroneous initiation we propose an out of equilibrium scheme that implements kinetic proofreading. We show that such architectures are favored  over their equilibrium counterparts for complex organisms despite introducing noise in gene expression. ","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:31Z","doi":"10.15479/AT:ISTA:6473","department":[{"_id":"GaTk"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"_id":"6473","article_processing_charge":"No","related_material":{"record":[{"id":"2016","relation":"dissertation_contains","status":"public"},{"id":"281","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"1576"},{"id":"6900","status":"public","relation":"dissertation_contains"}]},"alternative_title":["ISTA Thesis"],"keyword":["Information estimation","Time-series","data analysis"],"author":[{"id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez","first_name":"Sarah A","full_name":"Cepeda Humerez, Sarah A"}],"date_created":"2019-05-21T00:11:23Z","OA_place":"publisher","ddc":["004"],"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2019-05-23T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-04-16T08:37:38Z","year":"2019","month":"05","publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"type":"dissertation","title":"Estimating information flow in single cells","corr_author":"1","oa_version":"Published Version","day":"23","oa":1,"page":"135","file":[{"creator":"scepeda","date_created":"2019-05-23T11:18:16Z","date_updated":"2020-07-14T12:47:31Z","access_level":"closed","file_name":"Thesis_Cepeda.zip","file_id":"6480","relation":"source_file","file_size":23937464,"checksum":"75f9184c1346e10a5de5f9cc7338309a","content_type":"application/zip"},{"access_level":"open_access","file_id":"6481","file_name":"CepedaThesis.pdf","date_updated":"2020-07-14T12:47:31Z","relation":"main_file","creator":"scepeda","date_created":"2019-05-23T11:18:13Z","file_size":16646985,"content_type":"application/pdf","checksum":"afdc0633ddbd71d5b13550d7fb4f4454"}],"citation":{"ista":"Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute of Science and Technology Austria.","chicago":"Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6473\">https://doi.org/10.15479/AT:ISTA:6473</a>.","ama":"Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6473\">10.15479/AT:ISTA:6473</a>","apa":"Cepeda Humerez, S. A. (2019). <i>Estimating information flow in single cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6473\">https://doi.org/10.15479/AT:ISTA:6473</a>","ieee":"S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute of Science and Technology Austria, 2019.","mla":"Cepeda Humerez, Sarah A. <i>Estimating Information Flow in Single Cells</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6473\">10.15479/AT:ISTA:6473</a>.","short":"S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019."},"status":"public"},{"doi":"10.1371/journal.pcbi.1007290","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:44Z","abstract":[{"text":"Across diverse biological systems—ranging from neural networks to intracellular signaling and genetic regulatory networks—the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes. A pressing data-analysis challenge has thus been to efficiently estimate the amount of information that these dynamics convey from experimental data. Here we develop and evaluate decoding-based estimation methods to lower bound the mutual information about a finite set of inputs, encoded in single-cell high-dimensional time series data. For biological reaction networks governed by the chemical Master equation, we derive model-based information approximations and analytical upper bounds, against which we benchmark our proposed model-free decoding estimators. In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based estimators robustly extract a large fraction of the available information from high-dimensional trajectories with a realistic number of data samples. We apply these estimators to previously published data on Erk and Ca2+ signaling in mammalian cells and to yeast stress-response, and find that substantial amount of information about environmental state can be encoded by non-trivial response statistics even in stationary signals. We argue that these single-cell, decoding-based information estimates, rather than the commonly-used tests for significant differences between selected population response statistics, provide a proper and unbiased measure for the performance of biological signaling networks.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6473"}]},"_id":"6900","article_processing_charge":"No","pmid":1,"publication_status":"published","ddc":["570"],"has_accepted_license":"1","author":[{"first_name":"Sarah A","last_name":"Cepeda Humerez","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","full_name":"Cepeda Humerez, Sarah A"},{"last_name":"Ruess","orcid":"0000-0003-1615-3282","first_name":"Jakob","full_name":"Ruess, Jakob"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455"}],"issue":"9","date_created":"2019-09-22T22:00:37Z","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"intvolume":"        15","date_published":"2019-09-03T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2026-04-16T08:37:39Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2019","month":"09","volume":15,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication":"PLoS computational biology","type":"journal_article","isi":1,"publisher":"Public Library of Science","oa_version":"Published Version","quality_controlled":"1","external_id":{"isi":["000489741800021"],"pmid":["31479447"]},"day":"03","oa":1,"title":"Estimating information in time-varying signals","status":"public","page":"e1007290","file":[{"file_size":3081855,"checksum":"81bdce1361c9aa8395d6fa635fb6ab47","content_type":"application/pdf","file_name":"2019_PLoS_Cepeda-Humerez.pdf","date_updated":"2020-07-14T12:47:44Z","file_id":"6925","access_level":"open_access","relation":"main_file","creator":"kschuh","date_created":"2019-10-01T10:53:45Z"}],"citation":{"ista":"Cepeda Humerez SA, Ruess J, Tkačik G. 2019. Estimating information in time-varying signals. PLoS computational biology. 15(9), e1007290.","chicago":"Cepeda Humerez, Sarah A, Jakob Ruess, and Gašper Tkačik. “Estimating Information in Time-Varying Signals.” <i>PLoS Computational Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">https://doi.org/10.1371/journal.pcbi.1007290</a>.","apa":"Cepeda Humerez, S. A., Ruess, J., &#38; Tkačik, G. (2019). Estimating information in time-varying signals. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">https://doi.org/10.1371/journal.pcbi.1007290</a>","ama":"Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying signals. <i>PLoS computational biology</i>. 2019;15(9):e1007290. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">10.1371/journal.pcbi.1007290</a>","ieee":"S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in time-varying signals,” <i>PLoS computational biology</i>, vol. 15, no. 9. Public Library of Science, p. e1007290, 2019.","mla":"Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” <i>PLoS Computational Biology</i>, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">10.1371/journal.pcbi.1007290</a>.","short":"S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019) e1007290."}},{"status":"public","article_number":"641","file":[{"file_size":1917374,"content_type":"application/pdf","checksum":"7a30357efdcf8f66587ed495c0927724","file_id":"7221","date_updated":"2020-07-14T12:47:54Z","file_name":"2019_BMCBioinfo_Aganezov.pdf","access_level":"open_access","relation":"main_file","creator":"dernst","date_created":"2020-01-02T16:10:58Z"}],"citation":{"ieee":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” <i>BMC Bioinformatics</i>, vol. 20. BMC, 2019.","short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019).","mla":"Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” <i>BMC Bioinformatics</i>, vol. 20, 641, BMC, 2019, doi:<a href=\"https://doi.org/10.1186/s12859-019-3208-4\">10.1186/s12859-019-3208-4</a>.","chicago":"Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” <i>BMC Bioinformatics</i>. BMC, 2019. <a href=\"https://doi.org/10.1186/s12859-019-3208-4\">https://doi.org/10.1186/s12859-019-3208-4</a>.","ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.","apa":"Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., &#38; Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. <i>BMC Bioinformatics</i>. BMC. <a href=\"https://doi.org/10.1186/s12859-019-3208-4\">https://doi.org/10.1186/s12859-019-3208-4</a>","ama":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. <i>BMC Bioinformatics</i>. 2019;20. doi:<a href=\"https://doi.org/10.1186/s12859-019-3208-4\">10.1186/s12859-019-3208-4</a>"},"article_type":"original","day":"17","external_id":{"isi":["000511618800007"]},"oa":1,"oa_version":"Published Version","quality_controlled":"1","title":"Recovering rearranged cancer chromosomes from karyotype graphs","type":"journal_article","publication":"BMC Bioinformatics","publisher":"BMC","isi":1,"year":"2019","month":"12","date_published":"2019-12-17T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-04-16T08:35:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":20,"intvolume":"        20","has_accepted_license":"1","ddc":["570"],"date_created":"2019-12-29T23:00:46Z","author":[{"full_name":"Aganezov, Sergey","last_name":"Aganezov","first_name":"Sergey"},{"full_name":"Zban, Ilya","last_name":"Zban","first_name":"Ilya"},{"id":"2980135A-F248-11E8-B48F-1D18A9856A87","last_name":"Aksenov","first_name":"Vitalii","full_name":"Aksenov, Vitalii"},{"last_name":"Alexeev","first_name":"Nikita","full_name":"Alexeev, Nikita"},{"last_name":"Schatz","first_name":"Michael C.","full_name":"Schatz, Michael C."}],"publication_identifier":{"eissn":["1471-2105"]},"_id":"7214","article_processing_charge":"No","publication_status":"published","doi":"10.1186/s12859-019-3208-4","department":[{"_id":"DaAl"}],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:54Z","abstract":[{"text":"Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer.","lang":"eng"}]},{"department":[{"_id":"HeEd"}],"conference":{"start_date":"2019-08-08","end_date":"2019-08-10","name":"CCCG: Canadian Conference in Computational Geometry","location":"Edmonton, Canada"},"scopus_import":"1","abstract":[{"lang":"eng","text":"When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with hole(s) to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special simple holes guarantee foldability. "}],"_id":"6989","related_material":{"record":[{"id":"8317","relation":"extended_version","status":"public"}]},"article_processing_charge":"No","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://sites.ualberta.ca/~cccg2019/cccg2019_proceedings.pdf"}],"date_created":"2019-11-04T16:46:11Z","author":[{"first_name":"Oswin","last_name":"Aichholzer","full_name":"Aichholzer, Oswin"},{"full_name":"Akitaya, Hugo A","first_name":"Hugo A","last_name":"Akitaya"},{"full_name":"Cheung, Kenneth C","first_name":"Kenneth C","last_name":"Cheung"},{"last_name":"Demaine","first_name":"Erik D","full_name":"Demaine, Erik D"},{"first_name":"Martin L","last_name":"Demaine","full_name":"Demaine, Martin L"},{"full_name":"Fekete, Sandor P","first_name":"Sandor P","last_name":"Fekete"},{"last_name":"Kleist","first_name":"Linda","full_name":"Kleist, Linda"},{"last_name":"Kostitsyna","first_name":"Irina","full_name":"Kostitsyna, Irina"},{"full_name":"Löffler, Maarten","first_name":"Maarten","last_name":"Löffler"},{"full_name":"Masárová, Zuzana","first_name":"Zuzana","orcid":"0000-0002-6660-1322","last_name":"Masárová","id":"45CFE238-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mundilova, Klara","last_name":"Mundilova","first_name":"Klara"},{"full_name":"Schmidt, Christiane","last_name":"Schmidt","first_name":"Christiane"}],"acknowledgement":"This research was performed in part at the 33rd Bellairs Winter Workshop on Computational  Geometry. We thank all other participants for a fruitful atmosphere.","year":"2019","month":"08","date_published":"2019-08-01T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2026-04-16T09:14:30Z","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","publication":"Proceedings of the 31st Canadian Conference on Computational Geometry","publisher":"Canadian Conference on Computational Geometry","day":"01","external_id":{"arxiv":["1910.09917"]},"oa":1,"oa_version":"Published Version","quality_controlled":"1","title":"Folding polyominoes with holes into a cube","status":"public","citation":{"chicago":"Aichholzer, Oswin, Hugo A Akitaya, Kenneth C Cheung, Erik D Demaine, Martin L Demaine, Sandor P Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” In <i>Proceedings of the 31st Canadian Conference on Computational Geometry</i>, 164–70. Canadian Conference on Computational Geometry, 2019.","ista":"Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2019. Folding polyominoes with holes into a cube. Proceedings of the 31st Canadian Conference on Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 164–170.","ama":"Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. In: <i>Proceedings of the 31st Canadian Conference on Computational Geometry</i>. Canadian Conference on Computational Geometry; 2019:164-170.","apa":"Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2019). Folding polyominoes with holes into a cube. In <i>Proceedings of the 31st Canadian Conference on Computational Geometry</i> (pp. 164–170). Edmonton, Canada: Canadian Conference on Computational Geometry.","ieee":"O. Aichholzer <i>et al.</i>, “Folding polyominoes with holes into a cube,” in <i>Proceedings of the 31st Canadian Conference on Computational Geometry</i>, Edmonton, Canada, 2019, pp. 164–170.","mla":"Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” <i>Proceedings of the 31st Canadian Conference on Computational Geometry</i>, Canadian Conference on Computational Geometry, 2019, pp. 164–70.","short":"O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, in:, Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–170."},"page":"164-170"},{"day":"12","external_id":{"isi":["000470332600049"]},"oa":1,"oa_version":"Published Version","quality_controlled":"1","corr_author":"1","title":"Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure","status":"public","file":[{"file_size":1948014,"content_type":"application/pdf","checksum":"45bf040bbce1cea274f6013fa18ba21b","date_updated":"2020-07-14T12:47:28Z","file_id":"6362","file_name":"2019_MolecularBioReport_Temnov.pdf","access_level":"open_access","relation":"main_file","creator":"dernst","date_created":"2019-04-30T09:52:36Z"}],"citation":{"short":"A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019).","mla":"Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” <i>Molecular Biology Reports</i>, Springer, 2019, doi:<a href=\"https://doi.org/10.1007/s11033-019-04765-z\">10.1007/s11033-019-04765-z</a>.","ieee":"A. A. Temnov <i>et al.</i>, “Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure,” <i>Molecular Biology Reports</i>. Springer, 2019.","ama":"Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. <i>Molecular Biology Reports</i>. 2019. doi:<a href=\"https://doi.org/10.1007/s11033-019-04765-z\">10.1007/s11033-019-04765-z</a>","apa":"Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M., Djinovic-Carugo, K., &#38; Charnagalov, A. (2019). Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. <i>Molecular Biology Reports</i>. Springer. <a href=\"https://doi.org/10.1007/s11033-019-04765-z\">https://doi.org/10.1007/s11033-019-04765-z</a>","ista":"Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports.","chicago":"Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo, and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” <i>Molecular Biology Reports</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s11033-019-04765-z\">https://doi.org/10.1007/s11033-019-04765-z</a>."},"year":"2019","month":"04","date_published":"2019-04-12T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-04-16T09:49:11Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"journal_article","publication":"Molecular Biology Reports","publisher":"Springer","isi":1,"has_accepted_license":"1","ddc":["570"],"date_created":"2019-04-28T21:59:14Z","author":[{"full_name":"Temnov, Andrey Alexandrovich","last_name":"Temnov","first_name":"Andrey Alexandrovich"},{"last_name":"Rogov","first_name":"Konstantin Arkadevich","full_name":"Rogov, Konstantin Arkadevich"},{"first_name":"Alla Nikolaevna","last_name":"Sklifas","full_name":"Sklifas, Alla Nikolaevna"},{"full_name":"Klychnikova, Elena Valerievna","last_name":"Klychnikova","first_name":"Elena Valerievna"},{"full_name":"Hartl, Markus","first_name":"Markus","last_name":"Hartl"},{"full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo","first_name":"Kristina"},{"full_name":"Charnagalov, Alexej","last_name":"Charnagalov","id":"49F06DBA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexej"}],"acknowledgement":"The studies were supported by the Austrian Federal Ministry of Economy, Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding the Center of Optimized Structural Stud-ies, grant No. 253275","doi":"10.1007/s11033-019-04765-z","department":[{"_id":"LeSa"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10%  O2) and normal (21%  O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different  O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure."}],"file_date_updated":"2020-07-14T12:47:28Z","publication_identifier":{"eissn":["1573-4978"],"issn":["0301-4851"]},"_id":"6352","article_processing_charge":"Yes (via OA deal)","publication_status":"published"},{"publication_status":"published","_id":"7183","alternative_title":["LNCS"],"article_processing_charge":"No","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783030317836"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2)."}],"department":[{"_id":"KrCh"}],"doi":"10.1007/978-3-030-31784-3_27","conference":{"name":"ATVA: Automated TEchnology for Verification and Analysis","location":"Taipei, Taiwan","start_date":"2019-10-28","end_date":"2019-10-31"},"intvolume":"     11781","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"date_created":"2019-12-15T23:00:44Z","author":[{"full_name":"Brázdil, Tomás","first_name":"Tomás","last_name":"Brázdil"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Kucera","first_name":"Antonín","full_name":"Kucera, Antonín"},{"first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotný","full_name":"Novotný, Petr"},{"last_name":"Velan","first_name":"Dominik","full_name":"Velan, Dominik"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.11010"}],"publisher":"Springer Nature","isi":1,"type":"conference","publication":"International Symposium on Automated Technology for Verification and Analysis","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","arxiv":1,"volume":11781,"month":"10","year":"2019","date_updated":"2026-04-16T09:51:24Z","language":[{"iso":"eng"}],"date_published":"2019-10-21T00:00:00Z","citation":{"mla":"Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” <i>International Symposium on Automated Technology for Verification and Analysis</i>, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:<a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">10.1007/978-3-030-31784-3_27</a>.","short":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2019, pp. 462–478.","ieee":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding fast termination for probabilistic VASS with nondeterminism,” in <i>International Symposium on Automated Technology for Verification and Analysis</i>, Taipei, Taiwan, 2019, vol. 11781, pp. 462–478.","apa":"Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., &#38; Velan, D. (2019). Deciding fast termination for probabilistic VASS with nondeterminism. In <i>International Symposium on Automated Technology for Verification and Analysis</i> (Vol. 11781, pp. 462–478). Taipei, Taiwan: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">https://doi.org/10.1007/978-3-030-31784-3_27</a>","ama":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination for probabilistic VASS with nondeterminism. In: <i>International Symposium on Automated Technology for Verification and Analysis</i>. Vol 11781. Springer Nature; 2019:462-478. doi:<a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">10.1007/978-3-030-31784-3_27</a>","chicago":"Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” In <i>International Symposium on Automated Technology for Verification and Analysis</i>, 11781:462–78. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">https://doi.org/10.1007/978-3-030-31784-3_27</a>.","ista":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast termination for probabilistic VASS with nondeterminism. International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology for Verification and Analysis, LNCS, vol. 11781, 462–478."},"page":"462-478","status":"public","title":"Deciding fast termination for probabilistic VASS with nondeterminism","oa":1,"external_id":{"isi":["000723515700027"],"arxiv":["1907.11010"]},"day":"21","quality_controlled":"1","oa_version":"Preprint"},{"publication_status":"published","pmid":1,"_id":"5830","article_processing_charge":"No","publication_identifier":{"issn":["0140-7791"]},"OA_type":"free access","abstract":[{"text":"CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants.","lang":"eng"}],"scopus_import":"1","department":[{"_id":"JiFr"}],"doi":"10.1111/pce.13475","acknowledgement":"We thank Drs. Juan Xu, Yongfeng Guo, and Annie Marion-Poll for sharing materials. We are grateful to Profs. Xiaoping She for helpful discussion and Zhezhi Wang for his generosity in providing laboratory facilities. The study is supported by the National Natural Science Foundation of China (31771556, 31271575, and 31200902 to G. W.), by the 100-Talent Program of Shaanxi Province (to G. W.), by the Fundamental Research Funds for the Central Universities (GK201702016 to G. W.; GK201603110 to L. C.), partly by the open funds of the State Key Laboratory of Plant Physiology and Biochemistry (SKLPPBKF1805), and by the Initial Project for Post-Graduates of Hubei University of Medicine (2016QDJZR14 to Y. Z.).","intvolume":"        42","author":[{"full_name":"Zhang, Luosha","last_name":"Zhang","first_name":"Luosha"},{"last_name":"Shi","first_name":"Xiong","full_name":"Shi, Xiong"},{"last_name":"Zhang","first_name":"Yutao","full_name":"Zhang, Yutao"},{"full_name":"Wang, Jiajing","last_name":"Wang","first_name":"Jiajing"},{"last_name":"Yang","first_name":"Jingwei","full_name":"Yang, Jingwei"},{"full_name":"Ishida, Takashi","last_name":"Ishida","first_name":"Takashi"},{"last_name":"Jiang","first_name":"Wenqian","full_name":"Jiang, Wenqian"},{"full_name":"Han, Xiangyu","first_name":"Xiangyu","last_name":"Han"},{"last_name":"Kang","first_name":"Jingke","full_name":"Kang, Jingke"},{"last_name":"Wang","first_name":"Xuening","full_name":"Wang, Xuening"},{"last_name":"Pan","first_name":"Lixia","full_name":"Pan, Lixia"},{"full_name":"Lv, Shuo","last_name":"Lv","first_name":"Shuo"},{"last_name":"Cao","first_name":"Bing","full_name":"Cao, Bing"},{"full_name":"Zhang, Yonghong","last_name":"Zhang","first_name":"Yonghong"},{"first_name":"Jinbin","last_name":"Wu","full_name":"Wu, Jinbin"},{"full_name":"Han, Huibin","first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hu","first_name":"Zhubing","full_name":"Hu, Zhubing"},{"full_name":"Cui, Langjun","last_name":"Cui","first_name":"Langjun"},{"full_name":"Sawa, Shinichiro","last_name":"Sawa","first_name":"Shinichiro"},{"last_name":"He","first_name":"Junmin","full_name":"He, Junmin"},{"full_name":"Wang, Guodong","first_name":"Guodong","last_name":"Wang"}],"OA_place":"publisher","date_created":"2019-01-13T22:59:11Z","issue":"3","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30378140"}],"isi":1,"publisher":"Wiley","publication":"Plant Cell and Environment","type":"journal_article","volume":42,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-16T09:47:37Z","language":[{"iso":"eng"}],"date_published":"2019-03-01T00:00:00Z","month":"03","year":"2019","page":"1033-1044","citation":{"ieee":"L. Zhang <i>et al.</i>, “CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,” <i>Plant Cell and Environment</i>, vol. 42, no. 3. Wiley, pp. 1033–1044, 2019.","short":"L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han, J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui, S. Sawa, J. He, G. Wang, Plant Cell and Environment 42 (2019) 1033–1044.","mla":"Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” <i>Plant Cell and Environment</i>, vol. 42, no. 3, Wiley, 2019, pp. 1033–44, doi:<a href=\"https://doi.org/10.1111/pce.13475\">10.1111/pce.13475</a>.","ista":"Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J, Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang G. 2019. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. 42(3), 1033–1044.","chicago":"Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” <i>Plant Cell and Environment</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/pce.13475\">https://doi.org/10.1111/pce.13475</a>.","apa":"Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2019). CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. <i>Plant Cell and Environment</i>. Wiley. <a href=\"https://doi.org/10.1111/pce.13475\">https://doi.org/10.1111/pce.13475</a>","ama":"Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. <i>Plant Cell and Environment</i>. 2019;42(3):1033-1044. doi:<a href=\"https://doi.org/10.1111/pce.13475\">10.1111/pce.13475</a>"},"article_type":"original","status":"public","title":"CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana","oa_version":"Published Version","quality_controlled":"1","oa":1,"external_id":{"pmid":["30378140"],"isi":["000459014800021"]},"day":"01"},{"doi":"10.1016/j.tree.2018.12.005","department":[{"_id":"NiBa"}],"scopus_import":"1","abstract":[{"text":"Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved.","lang":"eng"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:47:13Z","publication_identifier":{"issn":["0169-5347"]},"_id":"5911","article_processing_charge":"No","publication_status":"published","has_accepted_license":"1","ddc":["570"],"issue":"3","date_created":"2019-02-03T22:59:15Z","author":[{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"intvolume":"        34","year":"2019","month":"03","language":[{"iso":"eng"}],"date_published":"2019-03-01T00:00:00Z","date_updated":"2026-04-16T09:48:52Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":34,"type":"journal_article","publication":"Trends in Ecology and Evolution","publisher":"Elsevier","isi":1,"external_id":{"isi":["000459899000013"]},"day":"01","oa":1,"quality_controlled":"1","oa_version":"Published Version","title":"Evolving inversions","status":"public","file":[{"file_size":1946795,"content_type":"application/pdf","checksum":"ef24572d6ebcc1452c067e05410cc4a2","file_id":"7245","file_name":"2019_Trends_Evolution_Faria.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:13Z","relation":"main_file","creator":"cziletti","date_created":"2020-01-09T10:55:58Z"}],"citation":{"ista":"Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248.","chicago":"Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” <i>Trends in Ecology and Evolution</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.tree.2018.12.005\">https://doi.org/10.1016/j.tree.2018.12.005</a>.","ama":"Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. <i>Trends in Ecology and Evolution</i>. 2019;34(3):239-248. doi:<a href=\"https://doi.org/10.1016/j.tree.2018.12.005\">10.1016/j.tree.2018.12.005</a>","apa":"Faria, R., Johannesson, K., Butlin, R. K., &#38; Westram, A. M. (2019). Evolving inversions. <i>Trends in Ecology and Evolution</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tree.2018.12.005\">https://doi.org/10.1016/j.tree.2018.12.005</a>","ieee":"R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” <i>Trends in Ecology and Evolution</i>, vol. 34, no. 3. Elsevier, pp. 239–248, 2019.","mla":"Faria, Rui, et al. “Evolving Inversions.” <i>Trends in Ecology and Evolution</i>, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:<a href=\"https://doi.org/10.1016/j.tree.2018.12.005\">10.1016/j.tree.2018.12.005</a>.","short":"R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248."},"article_type":"original","page":"239-248"},{"page":"75-111","article_type":"original","citation":{"apa":"Demay, G., Gazi, P., Maurer, U., &#38; Tackmann, B. (2019). Per-session security: Password-based cryptography revisited. <i>Journal of Computer Security</i>. IOS Press. <a href=\"https://doi.org/10.3233/JCS-181131\">https://doi.org/10.3233/JCS-181131</a>","ama":"Demay G, Gazi P, Maurer U, Tackmann B. Per-session security: Password-based cryptography revisited. <i>Journal of Computer Security</i>. 2019;27(1):75-111. doi:<a href=\"https://doi.org/10.3233/JCS-181131\">10.3233/JCS-181131</a>","chicago":"Demay, Gregory, Peter Gazi, Ueli Maurer, and Bjorn Tackmann. “Per-Session Security: Password-Based Cryptography Revisited.” <i>Journal of Computer Security</i>. IOS Press, 2019. <a href=\"https://doi.org/10.3233/JCS-181131\">https://doi.org/10.3233/JCS-181131</a>.","ista":"Demay G, Gazi P, Maurer U, Tackmann B. 2019. Per-session security: Password-based cryptography revisited. Journal of Computer Security. 27(1), 75–111.","short":"G. Demay, P. Gazi, U. Maurer, B. Tackmann, Journal of Computer Security 27 (2019) 75–111.","mla":"Demay, Gregory, et al. “Per-Session Security: Password-Based Cryptography Revisited.” <i>Journal of Computer Security</i>, vol. 27, no. 1, IOS Press, 2019, pp. 75–111, doi:<a href=\"https://doi.org/10.3233/JCS-181131\">10.3233/JCS-181131</a>.","ieee":"G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Per-session security: Password-based cryptography revisited,” <i>Journal of Computer Security</i>, vol. 27, no. 1. IOS Press, pp. 75–111, 2019."},"status":"public","title":"Per-session security: Password-based cryptography revisited","quality_controlled":"1","oa_version":"Preprint","oa":1,"day":"01","publisher":"IOS Press","publication":"Journal of Computer Security","type":"journal_article","volume":27,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-16T09:48:36Z","language":[{"iso":"eng"}],"date_published":"2019-01-01T00:00:00Z","month":"01","year":"2019","intvolume":"        27","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"author":[{"full_name":"Demay, Gregory","first_name":"Gregory","last_name":"Demay"},{"full_name":"Gazi, Peter","last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"full_name":"Maurer, Ueli","first_name":"Ueli","last_name":"Maurer"},{"full_name":"Tackmann, Bjorn","last_name":"Tackmann","first_name":"Bjorn"}],"date_created":"2019-01-27T22:59:10Z","issue":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/166"}],"publication_status":"published","_id":"5887","article_processing_charge":"No","publication_identifier":{"issn":["0926-227X"]},"abstract":[{"text":"Cryptographic security is usually defined as a guarantee that holds except when a bad event with negligible probability occurs, and nothing is guaranteed in that bad case. However, in settings where such failure can happen with substantial probability, one needs to provide guarantees even for the bad case. A typical example is where a (possibly weak) password is used instead of a secure cryptographic key to protect a session, the bad event being that the adversary correctly guesses the password. In a situation with multiple such sessions, a per-session guarantee is desired: any session for which the password has not been guessed remains secure, independently of whether other sessions have been compromised. A new formalism for stating such gracefully degrading security guarantees is introduced and applied to analyze the examples of password-based message authentication and password-based encryption. While a natural per-message guarantee is achieved for authentication, the situation of password-based encryption is more delicate: a per-session confidentiality guarantee only holds against attackers for which the distribution of password-guessing effort over the sessions is known in advance. In contrast, for more general attackers without such a restriction, a strong, composable notion of security cannot be achieved.","lang":"eng"}],"ec_funded":1,"scopus_import":"1","department":[{"_id":"KrPi"}],"doi":"10.3233/JCS-181131"},{"date_created":"2019-05-13T07:58:35Z","author":[{"last_name":"Song","first_name":"Baofang","full_name":"Song, Baofang"},{"first_name":"Carlos","last_name":"Plana","full_name":"Plana, Carlos"},{"first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Alonso","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M"},{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07351"}],"intvolume":"       117","scopus_import":"1","abstract":[{"lang":"eng","text":"Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase."}],"doi":"10.1016/j.ijmultiphaseflow.2019.04.027","department":[{"_id":"BjHo"}],"publication_status":"published","publication_identifier":{"issn":["0301-9322"]},"_id":"6413","article_processing_charge":"No","title":"Phase-field simulation of core-annular pipe flow","external_id":{"arxiv":["1902.07351"],"isi":["000474496000002"]},"day":"01","oa":1,"oa_version":"Preprint","quality_controlled":"1","article_type":"original","citation":{"ieee":"B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” <i>International Journal of Multiphase Flow</i>, vol. 117. Elsevier, pp. 14–24, 2019.","short":"B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24.","mla":"Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” <i>International Journal of Multiphase Flow</i>, vol. 117, Elsevier, 2019, pp. 14–24, doi:<a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">10.1016/j.ijmultiphaseflow.2019.04.027</a>.","chicago":"Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” <i>International Journal of Multiphase Flow</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027</a>.","ista":"Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.","ama":"Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. <i>International Journal of Multiphase Flow</i>. 2019;117:14-24. doi:<a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">10.1016/j.ijmultiphaseflow.2019.04.027</a>","apa":"Song, B., Plana, C., Lopez Alonso, J. M., &#38; Avila, M. (2019). Phase-field simulation of core-annular pipe flow. <i>International Journal of Multiphase Flow</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027</a>"},"page":"14-24","status":"public","arxiv":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":117,"year":"2019","month":"08","date_published":"2019-08-01T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2026-04-16T09:49:27Z","publisher":"Elsevier","isi":1,"type":"journal_article","publication":"International Journal of Multiphase Flow"},{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"intvolume":"        91","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.2399"}],"issue":"4","date_created":"2018-12-30T22:59:15Z","author":[{"full_name":"Chaplick, Steven","last_name":"Chaplick","first_name":"Steven"},{"full_name":"Fulek, Radoslav","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","orcid":"0000-0001-8485-1774"},{"last_name":"Klavík","first_name":"Pavel","full_name":"Klavík, Pavel"}],"publication_identifier":{"issn":["0364-9024"]},"article_processing_charge":"No","_id":"5790","publication_status":"published","doi":"10.1002/jgt.22436","department":[{"_id":"UlWa"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest."}],"ec_funded":1,"status":"public","article_type":"original","citation":{"ista":"Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of circle graphs. Journal of Graph Theory. 91(4), 365–394.","chicago":"Chaplick, Steven, Radoslav Fulek, and Pavel Klavík. “Extending Partial Representations of Circle Graphs.” <i>Journal of Graph Theory</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/jgt.22436\">https://doi.org/10.1002/jgt.22436</a>.","ama":"Chaplick S, Fulek R, Klavík P. Extending partial representations of circle graphs. <i>Journal of Graph Theory</i>. 2019;91(4):365-394. doi:<a href=\"https://doi.org/10.1002/jgt.22436\">10.1002/jgt.22436</a>","apa":"Chaplick, S., Fulek, R., &#38; Klavík, P. (2019). Extending partial representations of circle graphs. <i>Journal of Graph Theory</i>. Wiley. <a href=\"https://doi.org/10.1002/jgt.22436\">https://doi.org/10.1002/jgt.22436</a>","ieee":"S. Chaplick, R. Fulek, and P. Klavík, “Extending partial representations of circle graphs,” <i>Journal of Graph Theory</i>, vol. 91, no. 4. Wiley, pp. 365–394, 2019.","mla":"Chaplick, Steven, et al. “Extending Partial Representations of Circle Graphs.” <i>Journal of Graph Theory</i>, vol. 91, no. 4, Wiley, 2019, pp. 365–94, doi:<a href=\"https://doi.org/10.1002/jgt.22436\">10.1002/jgt.22436</a>.","short":"S. Chaplick, R. Fulek, P. Klavík, Journal of Graph Theory 91 (2019) 365–394."},"page":"365-394","external_id":{"arxiv":["1309.2399"],"isi":["000485392800004"]},"day":"01","oa":1,"oa_version":"Preprint","quality_controlled":"1","title":"Extending partial representations of circle graphs","type":"journal_article","publication":"Journal of Graph Theory","publisher":"Wiley","isi":1,"year":"2019","month":"08","language":[{"iso":"eng"}],"date_published":"2019-08-01T00:00:00Z","date_updated":"2026-04-16T09:47:19Z","arxiv":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":91},{"oa_version":"Preprint","quality_controlled":"1","day":"30","external_id":{"arxiv":["1708.08037"],"isi":["000466061100020"]},"oa":1,"title":"Thrackles: An improved upper bound","status":"public","page":"266-231","citation":{"chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” <i>Discrete Applied Mathematics</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.dam.2018.12.025\">https://doi.org/10.1016/j.dam.2018.12.025</a>.","ista":"Fulek R, Pach J. 2019. Thrackles: An improved upper bound. Discrete Applied Mathematics. 259(4), 266–231.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. <i>Discrete Applied Mathematics</i>. 2019;259(4):266-231. doi:<a href=\"https://doi.org/10.1016/j.dam.2018.12.025\">10.1016/j.dam.2018.12.025</a>","apa":"Fulek, R., &#38; Pach, J. (2019). Thrackles: An improved upper bound. <i>Discrete Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dam.2018.12.025\">https://doi.org/10.1016/j.dam.2018.12.025</a>","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” <i>Discrete Applied Mathematics</i>, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.","mla":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” <i>Discrete Applied Mathematics</i>, vol. 259, no. 4, Elsevier, 2019, pp. 266–231, doi:<a href=\"https://doi.org/10.1016/j.dam.2018.12.025\">10.1016/j.dam.2018.12.025</a>.","short":"R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231."},"article_type":"original","date_published":"2019-04-30T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2026-04-16T09:48:11Z","year":"2019","month":"04","volume":259,"arxiv":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication":"Discrete Applied Mathematics","type":"journal_article","isi":1,"publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"author":[{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"first_name":"János","last_name":"Pach","full_name":"Pach, János"}],"issue":"4","date_created":"2019-01-20T22:59:17Z","project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"intvolume":"       259","doi":"10.1016/j.dam.2018.12.025","department":[{"_id":"UlWa"}],"abstract":[{"lang":"eng","text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is [Formula presented](n−1), and that this bound is best possible for infinitely many values of n."}],"scopus_import":"1","publication_identifier":{"issn":["0166-218X"]},"_id":"5857","related_material":{"record":[{"id":"433","relation":"earlier_version","status":"public"}]},"article_processing_charge":"No","publication_status":"published"},{"publication_status":"published","alternative_title":["LNCS"],"_id":"6430","article_processing_charge":"No","related_material":{"record":[{"id":"10035","relation":"dissertation_contains","status":"public"}]},"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783030172589"]},"abstract":[{"lang":"eng","text":"A proxy re-encryption (PRE) scheme is a public-key encryption scheme that allows the holder of a key pk to derive a re-encryption key for any other key 𝑝𝑘′. This re-encryption key lets anyone transform ciphertexts under pk into ciphertexts under 𝑝𝑘′ without having to know the underlying message, while transformations from 𝑝𝑘′ to pk should not be possible (unidirectional). Security is defined in a multi-user setting against an adversary that gets the users’ public keys and can ask for re-encryption keys and can corrupt users by requesting their secret keys. Any ciphertext that the adversary cannot trivially decrypt given the obtained secret and re-encryption keys should be secure.\r\n\r\nAll existing security proofs for PRE only show selective security, where the adversary must first declare the users it wants to corrupt. This can be lifted to more meaningful adaptive security by guessing the set of corrupted users among the n users, which loses a factor exponential in  Open image in new window , rendering the result meaningless already for moderate Open image in new window .\r\n\r\nJafargholi et al. (CRYPTO’17) proposed a framework that in some cases allows to give adaptive security proofs for schemes which were previously only known to be selectively secure, while avoiding the exponential loss that results from guessing the adaptive choices made by an adversary. We apply their framework to PREs that satisfy some natural additional properties. Concretely, we give a more fine-grained reduction for several unidirectional PREs, proving adaptive security at a much smaller loss. The loss depends on the graph of users whose edges represent the re-encryption keys queried by the adversary. For trees and chains the loss is quasi-polynomial in the size and for general graphs it is exponential in their depth and indegree (instead of their size as for previous reductions). Fortunately, trees and low-depth graphs cover many, if not most, interesting applications.\r\n\r\nOur results apply e.g. to the bilinear-map based PRE schemes by Ateniese et al. (NDSS’05 and CT-RSA’09), Gentry’s FHE-based scheme (STOC’09) and the LWE-based scheme by Chandran et al. (PKC’14)."}],"ec_funded":1,"scopus_import":"1","conference":{"end_date":"2019-04-17","start_date":"2019-04-14","location":"Beijing, China","name":"PKC: Public-Key Cryptograhy"},"department":[{"_id":"KrPi"}],"doi":"10.1007/978-3-030-17259-6_11","intvolume":"     11443","project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"},{"first_name":"Chethan","last_name":"Kamath Hosdurg","orcid":"0009-0006-6812-7317","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","full_name":"Klein, Karen"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2019-05-13T08:13:46Z","main_file_link":[{"url":"https://eprint.iacr.org/2018/426","open_access":"1"}],"isi":1,"publisher":"Springer Nature","type":"conference","volume":11443,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-16T09:52:04Z","date_published":"2019-04-06T00:00:00Z","language":[{"iso":"eng"}],"month":"04","year":"2019","page":"317-346","citation":{"chicago":"Fuchsbauer, Georg, Chethan Kamath Hosdurg, Karen Klein, and Krzysztof Z Pietrzak. “Adaptively Secure Proxy Re-Encryption,” 11443:317–46. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">https://doi.org/10.1007/978-3-030-17259-6_11</a>.","ista":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. 2019. Adaptively secure proxy re-encryption. PKC: Public-Key Cryptograhy, LNCS, vol. 11443, 317–346.","apa":"Fuchsbauer, G., Kamath Hosdurg, C., Klein, K., &#38; Pietrzak, K. Z. (2019). Adaptively secure proxy re-encryption (Vol. 11443, pp. 317–346). Presented at the PKC: Public-Key Cryptograhy, Beijing, China: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">https://doi.org/10.1007/978-3-030-17259-6_11</a>","ama":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. Adaptively secure proxy re-encryption. In: Vol 11443. Springer Nature; 2019:317-346. doi:<a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">10.1007/978-3-030-17259-6_11</a>","ieee":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “Adaptively secure proxy re-encryption,” presented at the PKC: Public-Key Cryptograhy, Beijing, China, 2019, vol. 11443, pp. 317–346.","mla":"Fuchsbauer, Georg, et al. <i>Adaptively Secure Proxy Re-Encryption</i>. Vol. 11443, Springer Nature, 2019, pp. 317–46, doi:<a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">10.1007/978-3-030-17259-6_11</a>.","short":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, Springer Nature, 2019, pp. 317–346."},"status":"public","title":"Adaptively secure proxy re-encryption","quality_controlled":"1","oa_version":"Preprint","oa":1,"day":"06","external_id":{"isi":["001299215500011"]}},{"oa":1,"external_id":{"isi":["000452849400001"],"arxiv":["1805.06040"]},"day":"01","oa_version":"Published Version","quality_controlled":"1","title":"On the geometry of geodesics in discrete optimal transport","status":"public","article_number":"19","article_type":"original","citation":{"ama":"Erbar M, Maas J, Wirth M. On the geometry of geodesics in discrete optimal transport. <i>Calculus of Variations and Partial Differential Equations</i>. 2019;58(1). doi:<a href=\"https://doi.org/10.1007/s00526-018-1456-1\">10.1007/s00526-018-1456-1</a>","apa":"Erbar, M., Maas, J., &#38; Wirth, M. (2019). On the geometry of geodesics in discrete optimal transport. <i>Calculus of Variations and Partial Differential Equations</i>. Springer. <a href=\"https://doi.org/10.1007/s00526-018-1456-1\">https://doi.org/10.1007/s00526-018-1456-1</a>","chicago":"Erbar, Matthias, Jan Maas, and Melchior Wirth. “On the Geometry of Geodesics in Discrete Optimal Transport.” <i>Calculus of Variations and Partial Differential Equations</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s00526-018-1456-1\">https://doi.org/10.1007/s00526-018-1456-1</a>.","ista":"Erbar M, Maas J, Wirth M. 2019. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 58(1), 19.","short":"M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential Equations 58 (2019).","mla":"Erbar, Matthias, et al. “On the Geometry of Geodesics in Discrete Optimal Transport.” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 58, no. 1, 19, Springer, 2019, doi:<a href=\"https://doi.org/10.1007/s00526-018-1456-1\">10.1007/s00526-018-1456-1</a>.","ieee":"M. Erbar, J. Maas, and M. Wirth, “On the geometry of geodesics in discrete optimal transport,” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 58, no. 1. Springer, 2019."},"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:55Z","file_name":"2018_Calculus_Erbar.pdf","file_id":"5895","relation":"main_file","creator":"dernst","date_created":"2019-01-28T15:37:11Z","file_size":645565,"checksum":"ba05ac2d69de4c58d2cd338b63512798","content_type":"application/pdf"}],"month":"02","year":"2019","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-04-16T09:51:42Z","language":[{"iso":"eng"}],"date_published":"2019-02-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","arxiv":1,"volume":58,"type":"journal_article","publication":"Calculus of Variations and Partial Differential Equations","publisher":"Springer","isi":1,"has_accepted_license":"1","ddc":["510"],"date_created":"2018-12-11T11:44:29Z","issue":"1","author":[{"first_name":"Matthias","last_name":"Erbar","full_name":"Erbar, Matthias"},{"first_name":"Jan","last_name":"Maas","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan"},{"last_name":"Wirth","first_name":"Melchior","full_name":"Wirth, Melchior"}],"intvolume":"        58","project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"F06504","name":"Taming Complexity in Partial Differential Systems","call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"department":[{"_id":"JaMa"}],"doi":"10.1007/s00526-018-1456-1","scopus_import":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"We consider the space of probability measures on a discrete set X, endowed with a dynamical optimal transport metric. Given two probability measures supported in a subset Y⊆X, it is natural to ask whether they can be connected by a constant speed geodesic with support in Y at all times. Our main result answers this question affirmatively, under a suitable geometric condition on Y introduced in this paper. The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi equations, which is of independent interest."}],"file_date_updated":"2020-07-14T12:47:55Z","_id":"73","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["0944-2669"]},"publication_status":"published"},{"degree_awarded":"PhD","publication_identifier":{"eissn":["2663-337X"]},"_id":"6894","article_processing_charge":"No","related_material":{"record":[{"id":"647","relation":"part_of_dissertation","status":"public"},{"id":"631","relation":"part_of_dissertation","status":"public"},{"id":"140","relation":"part_of_dissertation","status":"public"}]},"alternative_title":["ISTA Thesis"],"publication_status":"published","doi":"10.15479/AT:ISTA:6894","department":[{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks."}],"file_date_updated":"2020-07-14T12:47:43Z","ddc":["000"],"has_accepted_license":"1","author":[{"full_name":"Giacobbe, Mirco","first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","last_name":"Giacobbe"}],"OA_place":"publisher","date_created":"2019-09-22T14:08:44Z","supervisor":[{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","date_published":"2019-09-30T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-04-16T09:55:03Z","year":"2019","month":"09","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","page":"132","file":[{"checksum":"773beaf4a85dc2acc2c12b578fbe1965","content_type":"application/pdf","file_size":4100685,"date_created":"2019-09-27T14:15:05Z","creator":"mgiacobbe","relation":"main_file","file_name":"giacobbe_thesis.pdf","access_level":"open_access","file_id":"6916","date_updated":"2020-07-14T12:47:43Z"},{"creator":"mgiacobbe","date_created":"2019-09-27T14:22:04Z","access_level":"closed","file_id":"6917","date_updated":"2020-07-14T12:47:43Z","file_name":"giacobbe_thesis_src.tar.gz","relation":"source_file","file_size":7959732,"checksum":"97f1c3da71feefd27e6e625d32b4c75b","content_type":"application/gzip"}],"citation":{"apa":"Giacobbe, M. (2019). <i>Automatic time-unbounded reachability analysis of hybrid systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>","ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>","chicago":"Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>.","ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria.","short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019.","mla":"Giacobbe, Mirco. <i>Automatic Time-Unbounded Reachability Analysis of Hybrid Systems</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>.","ieee":"M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019."},"oa_version":"Published Version","day":"30","oa":1,"title":"Automatic time-unbounded reachability analysis of hybrid systems","corr_author":"1"},{"publication_status":"published","_id":"7147","article_processing_charge":"No","alternative_title":["LNCS"],"publication_identifier":{"issn":["0302-9743"],"isbn":["9783030313036"],"eisbn":["9783030313043"],"eissn":["1611-3349"]},"abstract":[{"lang":"eng","text":"The expression of a gene is characterised by its transcription factors and the function processing them. If the transcription factors are not affected by gene products, the regulating function is often represented as a combinational logic circuit, where the outputs (product) are determined by current input values (transcription factors) only, and are hence independent on their relative arrival times. However, the simultaneous arrival of transcription factors (TFs) in genetic circuits is a strong assumption, given that the processes of transcription and translation of a gene into a protein introduce intrinsic time delays and that there is no global synchronisation among the arrival times of different molecular species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally implementable genetic circuit with two inputs and a single output, such that, in presence of small delays in input arrival, the circuit exhibits qualitatively distinct observable phenotypes. In particular, these phenotypes are long lived transients: they all converge to a single value, but so slowly, that they seem stable for an extended time period, longer than typical experiment duration. We used rule-based language to prototype our circuit, and we implemented a search for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe behaviour of our prototype circuit has wide implications. First, it suggests that GRNs can exploit event timing to create phenotypes. Second, it opens the possibility that GRNs are using event timing to react to stimuli and memorise events, without explicit feedback in regulation. From the modelling perspective, our prototype circuit demonstrates the critical importance of analysing the transient dynamics at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions."}],"scopus_import":"1","conference":{"start_date":"2019-09-18","end_date":"2019-09-20","name":"CMSB: Computational Methods in Systems Biology","location":"Trieste, Italy"},"department":[{"_id":"CaGu"},{"_id":"ToHe"}],"doi":"10.1007/978-3-030-31304-3_9","intvolume":"     11773","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture","grant_number":"24573"}],"author":[{"full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7777-546X","last_name":"Igler","full_name":"Igler, Claudia"},{"orcid":"0000-0002-9041-0905","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","full_name":"Petrov, Tatjana"},{"first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","full_name":"Sezgin, Ali"}],"date_created":"2019-12-04T16:07:50Z","isi":1,"publisher":"Springer Nature","publication":"17th International Conference on Computational Methods in Systems Biology","type":"conference","volume":11773,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-16T10:26:49Z","language":[{"iso":"eng"}],"date_published":"2019-09-17T00:00:00Z","month":"09","year":"2019","page":"155-187","citation":{"ista":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory in gene regulation. 17th International Conference on Computational Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773, 155–187.","chicago":"Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. “Transient Memory in Gene Regulation.” In <i>17th International Conference on Computational Methods in Systems Biology</i>, 11773:155–87. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">https://doi.org/10.1007/978-3-030-31304-3_9</a>.","apa":"Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., &#38; Sezgin, A. (2019). Transient memory in gene regulation. In <i>17th International Conference on Computational Methods in Systems Biology</i> (Vol. 11773, pp. 155–187). Trieste, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">https://doi.org/10.1007/978-3-030-31304-3_9</a>","ama":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene regulation. In: <i>17th International Conference on Computational Methods in Systems Biology</i>. Vol 11773. Springer Nature; 2019:155-187. doi:<a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">10.1007/978-3-030-31304-3_9</a>","ieee":"C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient memory in gene regulation,” in <i>17th International Conference on Computational Methods in Systems Biology</i>, Trieste, Italy, 2019, vol. 11773, pp. 155–187.","mla":"Guet, Calin C., et al. “Transient Memory in Gene Regulation.” <i>17th International Conference on Computational Methods in Systems Biology</i>, vol. 11773, Springer Nature, 2019, pp. 155–87, doi:<a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">10.1007/978-3-030-31304-3_9</a>.","short":"C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International Conference on Computational Methods in Systems Biology, Springer Nature, 2019, pp. 155–187."},"status":"public","title":"Transient memory in gene regulation","quality_controlled":"1","oa_version":"None","day":"17","external_id":{"isi":["000557875100009"]}},{"intvolume":"        68","has_accepted_license":"1","ddc":["570"],"date_created":"2019-11-04T16:20:19Z","author":[{"full_name":"McDougall, Alex","last_name":"McDougall","first_name":"Alex"},{"first_name":"Janet","last_name":"Chenevert","full_name":"Chenevert, Janet"},{"full_name":"Godard, Benoit G","first_name":"Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87","last_name":"Godard"},{"last_name":"Dumollard","first_name":"Remi","full_name":"Dumollard, Remi"}],"article_processing_charge":"No","_id":"6987","alternative_title":["RESULTS"],"pmid":1,"publication_identifier":{"eissn":["1861-0412"],"eisbn":["9783030234591"],"issn":["0080-1844"],"isbn":["9783030234584"]},"publication_status":"published","department":[{"_id":"CaHe"}],"doi":"10.1007/978-3-030-23459-1_6","scopus_import":"1","file_date_updated":"2020-07-14T12:47:46Z","abstract":[{"text":"Cells are arranged into species-specific patterns during early embryogenesis. Such cell division patterns are important since they often reflect the distribution of localized cortical factors from eggs/fertilized eggs to specific cells as well as the emergence of organismal form. However, it has proven difficult to reveal the mechanisms that underlie the emergence of cell positioning patterns that underlie embryonic shape, likely because a systems-level approach is required that integrates cell biological, genetic, developmental, and mechanical parameters. The choice of organism to address such questions is also important. Because ascidians display the most extreme form of invariant cleavage pattern among the metazoans, we have been analyzing the cell biological mechanisms that underpin three aspects of cell division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous cell cycles) which affect the overall shape of the blastula-stage ascidian embryo composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell stage that in turn undergo two further successive rounds of UCD. Starting at the 16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages. Perturbing either UCD or the alternate cell division rhythm perturbs cell position. We propose that dynamic cell shape changes propagate throughout the embryo via cell-cell contacts to create the ascidian-specific invariant cleavage pattern.","lang":"eng"}],"editor":[{"full_name":"Tworzydlo, Waclaw","first_name":"Waclaw","last_name":"Tworzydlo"},{"full_name":"Bilinski, Szczepan M.","first_name":"Szczepan M.","last_name":"Bilinski"}],"status":"public","citation":{"mla":"McDougall, Alex, et al. “Emergence of Embryo Shape during Cleavage Divisions.” <i>Evo-Devo: Non-Model Species in Cell and Developmental Biology</i>, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, vol. 68, Springer Nature, 2019, pp. 127–54, doi:<a href=\"https://doi.org/10.1007/978-3-030-23459-1_6\">10.1007/978-3-030-23459-1_6</a>.","short":"A. McDougall, J. Chenevert, B.G. Godard, R. Dumollard, in:, W. Tworzydlo, S.M. Bilinski (Eds.), Evo-Devo: Non-Model Species in Cell and Developmental Biology, Springer Nature, 2019, pp. 127–154.","ieee":"A. McDougall, J. Chenevert, B. G. Godard, and R. Dumollard, “Emergence of embryo shape during cleavage divisions,” in <i>Evo-Devo: Non-model species in cell and developmental biology</i>, vol. 68, W. Tworzydlo and S. M. Bilinski, Eds. Springer Nature, 2019, pp. 127–154.","apa":"McDougall, A., Chenevert, J., Godard, B. G., &#38; Dumollard, R. (2019). Emergence of embryo shape during cleavage divisions. In W. Tworzydlo &#38; S. M. Bilinski (Eds.), <i>Evo-Devo: Non-model species in cell and developmental biology</i> (Vol. 68, pp. 127–154). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-23459-1_6\">https://doi.org/10.1007/978-3-030-23459-1_6</a>","ama":"McDougall A, Chenevert J, Godard BG, Dumollard R. Emergence of embryo shape during cleavage divisions. In: Tworzydlo W, Bilinski SM, eds. <i>Evo-Devo: Non-Model Species in Cell and Developmental Biology</i>. Vol 68. Springer Nature; 2019:127-154. doi:<a href=\"https://doi.org/10.1007/978-3-030-23459-1_6\">10.1007/978-3-030-23459-1_6</a>","chicago":"McDougall, Alex, Janet Chenevert, Benoit G Godard, and Remi Dumollard. “Emergence of Embryo Shape during Cleavage Divisions.” In <i>Evo-Devo: Non-Model Species in Cell and Developmental Biology</i>, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, 68:127–54. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-23459-1_6\">https://doi.org/10.1007/978-3-030-23459-1_6</a>.","ista":"McDougall A, Chenevert J, Godard BG, Dumollard R. 2019.Emergence of embryo shape during cleavage divisions. In: Evo-Devo: Non-model species in cell and developmental biology. RESULTS, vol. 68, 127–154."},"file":[{"file_size":19317348,"content_type":"application/pdf","checksum":"7f43e1e3706d15061475c5c57efc2786","file_id":"7829","date_updated":"2020-07-14T12:47:46Z","file_name":"2019_RESULTS_McDougall.pdf","access_level":"open_access","relation":"main_file","creator":"dernst","date_created":"2020-05-14T10:09:30Z"}],"page":"127-154","oa":1,"external_id":{"pmid":["31598855"]},"day":"10","oa_version":"Submitted Version","quality_controlled":"1","title":"Emergence of embryo shape during cleavage divisions","type":"book_chapter","publication":"Evo-Devo: Non-model species in cell and developmental biology","publisher":"Springer Nature","month":"10","year":"2019","date_updated":"2026-04-16T10:26:18Z","language":[{"iso":"eng"}],"date_published":"2019-10-10T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":68}]