[{"file":[{"checksum":"8a5f2d77560e552af87eb1982437a43b","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T11:53:56Z","date_updated":"2020-07-14T12:46:55Z","creator":"system","file_name":"IST-2015-334-v1+1_report.pdf","access_level":"open_access","file_size":422573,"file_id":"5518"}],"date_created":"2018-12-12T11:39:20Z","date_updated":"2026-07-06T13:27:53Z","pubrep_id":"334","status":"public","has_accepted_license":"1","related_material":{"record":[{"relation":"later_version","id":"1610","status":"public"},{"status":"public","relation":"later_version","id":"465"}]},"language":[{"iso":"eng"}],"ddc":["004"],"type":"technical_report","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Otop, Jan","first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["IST Austria Technical Report"],"publication_status":"published","file_date_updated":"2020-07-14T12:46:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","oa_version":"Published Version","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. <i>Edit Distance for Pushdown Automata</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-334-v1-1\">https://doi.org/10.15479/AT:IST-2015-334-v1-1</a>.","ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. <i>Edit Distance for Pushdown Automata</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-334-v1-1\">10.15479/AT:IST-2015-334-v1-1</a>","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, <i>Edit distance for pushdown automata</i>. IST Austria, 2015.","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., &#38; Otop, J. (2015). <i>Edit distance for pushdown automata</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-334-v1-1\">https://doi.org/10.15479/AT:IST-2015-334-v1-1</a>","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for pushdown automata, IST Austria, 15p.","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Edit Distance for Pushdown Automata, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. <i>Edit Distance for Pushdown Automata</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-334-v1-1\">10.15479/AT:IST-2015-334-v1-1</a>."},"publisher":"IST Austria","page":"15","year":"2015","doi":"10.15479/AT:IST-2015-334-v1-1","day":"05","fulldoi":"https://doi.org/10.15479/AT:IST-2015-334-v1-1","abstract":[{"text":"The edit distance between two words w1, w2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w1 to w2. The edit distance generalizes to languages L1, L2, where the edit distance is the minimal number k such that for every word from L1 there exists a word in L2 with edit distance at most k. We study the edit distance computation problem between pushdown automata and their subclasses.\r\nThe problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for deciding whether, for a given threshold k, the edit distance from a pushdown automaton to a finite automaton is at most k. ","lang":"eng"}],"title":"Edit distance for pushdown automata","date_published":"2015-05-05T00:00:00Z","department":[{"_id":"KrCh"}],"oa":1,"publication_identifier":{"issn":["2664-1690"]},"_id":"5438"},{"_id":"1661","department":[{"_id":"KrCh"}],"oa":1,"date_published":"2015-07-01T00:00:00Z","scopus_import":"1","title":"Improved algorithms for one-pair and k-pair Streett objectives","article_number":"7174888","volume":"2015-July","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"abstract":[{"text":"The computation of the winning set for one-pair Streett objectives and for k-pair Streett objectives in (standard) graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formed ness of specifications, and the synthesis of reactive systems. We give faster algorithms for the computation of the winning set for (1) one-pair Streett objectives (aka parity-3 problem) in game graphs and (2) for k-pair Streett objectives in graphs. For both problems this represents the first improvement in asymptotic running time in 15 years.","lang":"eng"}],"fulldoi":"https://doi.org/10.1109/LICS.2015.34","acknowledgement":"K. C. is supported by the Austrian Science Fund (FWF): P23499-N23 and S11407-N23 (RiSE), an ERC Start Grant (279307: Graph Games), and a Microsoft Faculty Fellows Award. M. H. is supported by the Austrian Science Fund (FWF): P23499-N23 and the Vienna Science and Technology Fund (WWTF) grant ICT10-002. V. L. is supported by the Vienna Science and Technology Fund (WWTF) grant ICT10-002. The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement no. 340506.","day":"01","doi":"10.1109/LICS.2015.34","year":"2015","publication":"Proceedings - Symposium on Logic in Computer Science","external_id":{"isi":["000380427100026"]},"publisher":"IEEE","main_file_link":[{"url":"https://eprints.cs.univie.ac.at/4368/","open_access":"1"}],"oa_version":"Submitted Version","citation":{"short":"K. Chatterjee, M. Henzinger, V. Loitzenbauer, in:, Proceedings - Symposium on Logic in Computer Science, IEEE, 2015.","ista":"Chatterjee K, Henzinger M, Loitzenbauer V. 2015. Improved algorithms for one-pair and k-pair Streett objectives. Proceedings - Symposium on Logic in Computer Science. LICS: Logic in Computer Science vol. 2015–July, 7174888.","mla":"Chatterjee, Krishnendu, et al. “Improved Algorithms for One-Pair and k-Pair Streett Objectives.” <i>Proceedings - Symposium on Logic in Computer Science</i>, vol. 2015–July, 7174888, IEEE, 2015, doi:<a href=\"https://doi.org/10.1109/LICS.2015.34\">10.1109/LICS.2015.34</a>.","chicago":"Chatterjee, Krishnendu, Monika Henzinger, and Veronika Loitzenbauer. “Improved Algorithms for One-Pair and k-Pair Streett Objectives.” In <i>Proceedings - Symposium on Logic in Computer Science</i>, Vol. 2015–July. IEEE, 2015. <a href=\"https://doi.org/10.1109/LICS.2015.34\">https://doi.org/10.1109/LICS.2015.34</a>.","ama":"Chatterjee K, Henzinger M, Loitzenbauer V. Improved algorithms for one-pair and k-pair Streett objectives. In: <i>Proceedings - Symposium on Logic in Computer Science</i>. Vol 2015-July. IEEE; 2015. doi:<a href=\"https://doi.org/10.1109/LICS.2015.34\">10.1109/LICS.2015.34</a>","ieee":"K. Chatterjee, M. Henzinger, and V. Loitzenbauer, “Improved algorithms for one-pair and k-pair Streett objectives,” in <i>Proceedings - Symposium on Logic in Computer Science</i>, Kyoto, Japan, 2015, vol. 2015–July.","apa":"Chatterjee, K., Henzinger, M., &#38; Loitzenbauer, V. (2015). Improved algorithms for one-pair and k-pair Streett objectives. In <i>Proceedings - Symposium on Logic in Computer Science</i> (Vol. 2015–July). Kyoto, Japan: IEEE. <a href=\"https://doi.org/10.1109/LICS.2015.34\">https://doi.org/10.1109/LICS.2015.34</a>"},"month":"07","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","conference":{"location":"Kyoto, Japan","end_date":"2015-07-10","start_date":"2015-07-06","name":"LICS: Logic in Computer Science"},"quality_controlled":"1","publication_status":"published","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Monika H","first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika","first_name":"Veronika"}],"type":"conference","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"464"}]},"isi":1,"status":"public","publist_id":"5489","date_created":"2018-12-11T11:53:19Z","date_updated":"2026-07-06T13:28:05Z"},{"publisher":"Public Library of Science","publication":"PLoS Computational Biology","external_id":{"isi":["000364399700067"]},"year":"2015","doi":"10.1371/journal.pcbi.1004541","acknowledgement":"We acknowledge the support by the EU Joint Programme in Neurodegenerative Diseases (JPND AC14/00037) project. The project is supported through the following funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland, National Science Centre; and Spain, ISCIII. ","day":"23","fulldoi":"https://doi.org/10.1371/journal.pcbi.1004541","abstract":[{"text":"Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease.","lang":"eng"}],"volume":11,"article_number":"e1004541","intvolume":"        11","title":"An exploration of the universe of polyglutamine structures","scopus_import":"1","date_published":"2015-10-23T00:00:00Z","department":[{"_id":"CaHe"}],"oa":1,"_id":"1566","file":[{"file_name":"IST-2016-478-v1+1_journal.pcbi.1004541.pdf","creator":"system","relation":"main_file","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:16:21Z","content_type":"application/pdf","checksum":"8b67d729be663bfc9af04bfd94459655","file_id":"5207","file_size":1412511,"access_level":"open_access"}],"date_updated":"2026-07-06T13:54:28Z","date_created":"2018-12-11T11:52:45Z","pubrep_id":"478","publist_id":"5605","status":"public","has_accepted_license":"1","issue":"10","isi":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9714"}]},"ddc":["570"],"language":[{"iso":"eng"}],"type":"journal_article","author":[{"last_name":"Gómez Sicilia","first_name":"Àngel","full_name":"Gómez Sicilia, Àngel"},{"full_name":"Sikora, Mateusz K","first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cieplak","first_name":"Marek","full_name":"Cieplak, Marek"},{"first_name":"Mariano","full_name":"Carrión Vázquez, Mariano","last_name":"Carrión Vázquez"}],"publication_status":"published","quality_controlled":"1","file_date_updated":"2020-07-14T12:45:02Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","month":"10","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational Biology 11 (2015).","ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 11(10), e1004541.","mla":"Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine Structures.” <i>PLoS Computational Biology</i>, vol. 11, no. 10, e1004541, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004541\">10.1371/journal.pcbi.1004541</a>.","chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” <i>PLoS Computational Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004541\">https://doi.org/10.1371/journal.pcbi.1004541</a>.","ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures. <i>PLoS Computational Biology</i>. 2015;11(10). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004541\">10.1371/journal.pcbi.1004541</a>","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures,” <i>PLoS Computational Biology</i>, vol. 11, no. 10. Public Library of Science, 2015.","apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., &#38; Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004541\">https://doi.org/10.1371/journal.pcbi.1004541</a>"},"oa_version":"Published Version"},{"day":"23","fulldoi":"https://doi.org/10.1371/journal.pcbi.1004541.s001","status":"public","year":"2015","doi":"10.1371/journal.pcbi.1004541.s001","related_material":{"record":[{"relation":"used_in_publication","id":"1566","status":"public"}]},"publisher":"Public Library of Science","date_updated":"2026-07-06T13:54:29Z","date_created":"2021-07-23T12:05:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"CaHe"}],"citation":{"mla":"Gómez Sicilia, Àngel, et al. <i>An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">10.1371/journal.pcbi.1004541.s001</a>.","ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures - submission to PLOS journals, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">10.1371/journal.pcbi.1004541.s001</a>.","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015).","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures - submission to PLOS journals.” Public Library of Science, 2015.","apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., &#38; Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures - submission to PLOS journals. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">https://doi.org/10.1371/journal.pcbi.1004541.s001</a>","ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures - submission to PLOS journals. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">10.1371/journal.pcbi.1004541.s001</a>","chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">https://doi.org/10.1371/journal.pcbi.1004541.s001</a>."},"oa_version":"Published Version","month":"10","_id":"9714","type":"research_data_reference","author":[{"last_name":"Gómez Sicilia","first_name":"Àngel","full_name":"Gómez Sicilia, Àngel"},{"last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K","first_name":"Mateusz K"},{"last_name":"Cieplak","full_name":"Cieplak, Marek","first_name":"Marek"},{"full_name":"Carrión Vázquez, Mariano","first_name":"Mariano","last_name":"Carrión Vázquez"}],"title":"An exploration of the universe of polyglutamine structures - submission to PLOS journals","date_published":"2015-10-23T00:00:00Z"},{"intvolume":"        14","title":"Rich bifurcation structure in a two patch vaccination model","scopus_import":"1","article_type":"original","date_published":"2015-01-01T00:00:00Z","department":[{"_id":"HeEd"}],"oa":1,"publication_identifier":{"eissn":["1536-0040"]},"_id":"1555","main_file_link":[{"url":"http://discovery.ucl.ac.uk/1473750/1/99393.pdf","open_access":"1"}],"publisher":"Society for Industrial and Applied Mathematics","page":"980 - 1017","publication":"SIAM Journal on Applied Dynamical Systems","external_id":{"isi":["000357310400015"]},"das_tickbox":"1","year":"2015","doi":"10.1137/140993934","day":"01","acknowledgement":"Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria (pawel.pilarczyk@ist.ac.at). This author’s work was partially supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 622033, by Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC), by the Portuguese national funds through Funda ̧caoparaaCiˆencia e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008), and by European Research Council through StG 259559 in the framework of the EPIDELAY project.","fulldoi":"https://doi.org/10.1137/140993934","ec_funded":1,"abstract":[{"lang":"eng","text":"We show that incorporating spatial dispersal of individuals into a simple vaccination epidemic model may give rise to a model that exhibits rich dynamical behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as a basis, we describe the spread of an infectious disease in a population split into two regions. In each subpopulation, both forward and backward bifurcations can occur. This implies that for disconnected regions the two-patch system may admit several steady states. We consider traveling between the regions and investigate the impact of spatial dispersal of individuals on the model dynamics. We establish conditions for the existence of multiple nontrivial steady states in the system, and we study the structure of the equilibria. The mathematical analysis reveals an unusually rich dynamical behavior, not normally found in the simple epidemic models. In addition to the disease-free equilibrium, eight endemic equilibria emerge from backward transcritical and saddle-node bifurcation points, forming an interesting bifurcation diagram. Stability of steady states, their bifurcations, and the global dynamics are investigated with analytical tools, numerical simulations, and rigorous set-oriented numerical computations."}],"project":[{"grant_number":"622033","call_identifier":"FP7","_id":"255F06BE-B435-11E9-9278-68D0E5697425","name":"Persistent Homology - Images, Data and Maps"}],"volume":14,"type":"journal_article","author":[{"last_name":"Knipl","full_name":"Knipl, Diána","first_name":"Diána"},{"id":"3768D56A-F248-11E8-B48F-1D18A9856A87","last_name":"Pilarczyk","first_name":"Pawel","full_name":"Pilarczyk, Pawel"},{"full_name":"Röst, Gergely","first_name":"Gergely","last_name":"Röst"}],"publication_status":"published","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","month":"01","citation":{"short":"D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems 14 (2015) 980–1017.","ista":"Knipl D, Pilarczyk P, Röst G. 2015. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 14(2), 980–1017.","mla":"Knipl, Diána, et al. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” <i>SIAM Journal on Applied Dynamical Systems</i>, vol. 14, no. 2, Society for Industrial and Applied Mathematics, 2015, pp. 980–1017, doi:<a href=\"https://doi.org/10.1137/140993934\">10.1137/140993934</a>.","chicago":"Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” <i>SIAM Journal on Applied Dynamical Systems</i>. Society for Industrial and Applied Mathematics, 2015. <a href=\"https://doi.org/10.1137/140993934\">https://doi.org/10.1137/140993934</a>.","ieee":"D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two patch vaccination model,” <i>SIAM Journal on Applied Dynamical Systems</i>, vol. 14, no. 2. Society for Industrial and Applied Mathematics, pp. 980–1017, 2015.","apa":"Knipl, D., Pilarczyk, P., &#38; Röst, G. (2015). Rich bifurcation structure in a two patch vaccination model. <i>SIAM Journal on Applied Dynamical Systems</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/140993934\">https://doi.org/10.1137/140993934</a>","ama":"Knipl D, Pilarczyk P, Röst G. Rich bifurcation structure in a two patch vaccination model. <i>SIAM Journal on Applied Dynamical Systems</i>. 2015;14(2):980-1017. doi:<a href=\"https://doi.org/10.1137/140993934\">10.1137/140993934</a>"},"oa_version":"Published Version","date_created":"2018-12-11T11:52:42Z","date_updated":"2026-07-06T13:59:25Z","status":"public","publist_id":"5616","isi":1,"issue":"2","ddc":["510"],"language":[{"iso":"eng"}]},{"publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","publication":"VÖB Mitteilungen","page":"580 - 607","das_tickbox":"1","year":"2015","doi":"10.5281/zenodo.33178","OA_type":"gold","day":"12","fulldoi":"https://doi.org/10.5281/zenodo.33178","abstract":[{"text":"Based on 16 recommendations, efforts should be made to achieve the following goal: By 2025, all scholarly publication activity in Austria should be Open Access. In other words, the final versions of all scholarly publications resulting from the support of public resources must be freely accessible on the Internet without delay (Gold Open Access). The resources required to meet this obligation shall be provided to the authors, or the cost of the publication venues shall be borne directly by the research organisations.","lang":"eng"}],"volume":68,"intvolume":"        68","scopus_import":"1","title":"Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA","article_type":"original","date_published":"2015-11-12T00:00:00Z","oa":1,"department":[{"_id":"E-Lib"}],"_id":"1525","file":[{"file_id":"5317","access_level":"open_access","file_size":931707,"relation":"main_file","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:17:59Z","file_name":"IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf","creator":"system","checksum":"a495fe253bbc7615b1d60e9e85c94408","content_type":"application/pdf"}],"pubrep_id":"720","date_updated":"2026-07-07T06:11:42Z","date_created":"2018-12-11T11:52:31Z","publist_id":"5648","status":"public","has_accepted_license":"1","issue":"3","ddc":["020"],"language":[{"iso":"eng"}],"OA_place":"publisher","type":"journal_article","author":[{"last_name":"Bauer","first_name":"Bruno","full_name":"Bauer, Bruno"},{"full_name":"Blechl, Guido","first_name":"Guido","last_name":"Blechl"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","last_name":"Danowski","orcid":"0000-0002-6026-4409","first_name":"Patrick","full_name":"Danowski, Patrick"},{"full_name":"Ferus, Andreas","first_name":"Andreas","last_name":"Ferus"},{"last_name":"Graschopf","full_name":"Graschopf, Anton","first_name":"Anton"},{"full_name":"König, Thomas","first_name":"Thomas","last_name":"König"},{"last_name":"Mayer","first_name":"Katja","full_name":"Mayer, Katja"},{"first_name":"Falk","full_name":"Reckling, Falk","last_name":"Reckling"},{"last_name":"Rieck","first_name":"Katharina","full_name":"Rieck, Katharina"},{"first_name":"Peter","full_name":"Seitz, Peter","last_name":"Seitz"},{"last_name":"Stöger","full_name":"Stöger, Herwig","first_name":"Herwig"},{"last_name":"Welzig","full_name":"Welzig, Elvira","first_name":"Elvira"}],"publication_status":"published","quality_controlled":"1","file_date_updated":"2020-07-14T12:45:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","month":"11","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"chicago":"Bauer, Bruno, Guido Blechl, Christoph Bock, Patrick Danowski, Andreas Ferus, Anton Graschopf, Thomas König, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” <i>VÖB Mitteilungen</i>. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2015. <a href=\"https://doi.org/10.5281/zenodo.33178\">https://doi.org/10.5281/zenodo.33178</a>.","ama":"Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. <i>VÖB Mitteilungen</i>. 2015;68(3):580-607. doi:<a href=\"https://doi.org/10.5281/zenodo.33178\">10.5281/zenodo.33178</a>","apa":"Bauer, B., Blechl, G., Bock, C., Danowski, P., Ferus, A., Graschopf, A., … Welzig, E. (2015). Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. <i>VÖB Mitteilungen</i>. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. <a href=\"https://doi.org/10.5281/zenodo.33178\">https://doi.org/10.5281/zenodo.33178</a>","ieee":"B. Bauer <i>et al.</i>, “Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA,” <i>VÖB Mitteilungen</i>, vol. 68, no. 3. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 580–607, 2015.","ista":"Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer K, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E. 2015. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 68(3), 580–607.","short":"B. Bauer, G. Blechl, C. Bock, P. Danowski, A. Ferus, A. Graschopf, T. König, K. Mayer, F. Reckling, K. Rieck, P. Seitz, H. Stöger, E. Welzig, VÖB Mitteilungen 68 (2015) 580–607.","mla":"Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” <i>VÖB Mitteilungen</i>, vol. 68, no. 3, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2015, pp. 580–607, doi:<a href=\"https://doi.org/10.5281/zenodo.33178\">10.5281/zenodo.33178</a>."}},{"date_published":"2015-01-01T00:00:00Z","title":"Probabilistic opacity for Markov decision processes","scopus_import":"1","intvolume":"       115","_id":"2034","department":[{"_id":"KrCh"}],"oa":1,"external_id":{"arxiv":["1407.4225"],"isi":["000345478700010"]},"page":"52 - 59","publication":"Information Processing Letters","publisher":"Elsevier","arxiv":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.4225"}],"abstract":[{"lang":"eng","text":"Opacity is a generic security property, that has been defined on (non-probabilistic) transition systems and later on Markov chains with labels. For a secret predicate, given as a subset of runs, and a function describing the view of an external observer, the value of interest for opacity is a measure of the set of runs disclosing the secret. We extend this definition to the richer framework of Markov decision processes, where non-deterministicchoice is combined with probabilistic transitions, and we study related decidability problems with partial or complete observation hypotheses for the schedulers. We prove that all questions are decidable with complete observation and ω-regular secrets. With partial observation, we prove that all quantitative questions are undecidable but the question whether a system is almost surely non-opaquebecomes decidable for a restricted class of ω-regular secrets, as well as for all ω-regular secrets under finite-memory schedulers."}],"ec_funded":1,"volume":115,"project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"doi":"10.1016/j.ipl.2014.09.001","das_tickbox":"1","year":"2015","fulldoi":"https://doi.org/10.1016/j.ipl.2014.09.001","day":"01","quality_controlled":"1","author":[{"first_name":"Béatrice","full_name":"Bérard, Béatrice","last_name":"Bérard"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Nathalie","full_name":"Sznajder, Nathalie","last_name":"Sznajder"}],"type":"journal_article","publication_status":"published","month":"01","oa_version":"Preprint","citation":{"ista":"Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov decision processes. Information Processing Letters. 115(1), 52–59.","short":"B. Bérard, K. Chatterjee, N. Sznajder, Information Processing Letters 115 (2015) 52–59.","mla":"Bérard, Béatrice, et al. “Probabilistic Opacity for Markov Decision Processes.” <i>Information Processing Letters</i>, vol. 115, no. 1, Elsevier, 2015, pp. 52–59, doi:<a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">10.1016/j.ipl.2014.09.001</a>.","chicago":"Bérard, Béatrice, Krishnendu Chatterjee, and Nathalie Sznajder. “Probabilistic Opacity for Markov Decision Processes.” <i>Information Processing Letters</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">https://doi.org/10.1016/j.ipl.2014.09.001</a>.","ieee":"B. Bérard, K. Chatterjee, and N. Sznajder, “Probabilistic opacity for Markov decision processes,” <i>Information Processing Letters</i>, vol. 115, no. 1. Elsevier, pp. 52–59, 2015.","apa":"Bérard, B., Chatterjee, K., &#38; Sznajder, N. (2015). Probabilistic opacity for Markov decision processes. <i>Information Processing Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">https://doi.org/10.1016/j.ipl.2014.09.001</a>","ama":"Bérard B, Chatterjee K, Sznajder N. Probabilistic opacity for Markov decision processes. <i>Information Processing Letters</i>. 2015;115(1):52-59. doi:<a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">10.1016/j.ipl.2014.09.001</a>"},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-07T13:10:27Z","date_created":"2018-12-11T11:55:20Z","issue":"1","isi":1,"language":[{"iso":"eng"}],"publist_id":"5025","status":"public"},{"date_published":"2015-10-21T00:00:00Z","intvolume":"       383","title":"Toward a unifying framework for evolutionary processes","scopus_import":"1","_id":"1542","corr_author":"1","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"oa":1,"publisher":"Elsevier","external_id":{"isi":["000362056300005"]},"publication":"Journal of Theoretical Biology","page":"28 - 43","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618091"},{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"volume":383,"abstract":[{"text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. ","lang":"eng"}],"ec_funded":1,"day":"21","fulldoi":"https://doi.org/10.1016/j.jtbi.2015.07.011","doi":"10.1016/j.jtbi.2015.07.011","year":"2015","das_tickbox":"1","file_date_updated":"2020-07-14T12:45:01Z","quality_controlled":"1","publication_status":"published","type":"journal_article","author":[{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953","first_name":"Tiago","full_name":"Paixao, Tiago"},{"last_name":"Badkobeh","first_name":"Golnaz","full_name":"Badkobeh, Golnaz"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"last_name":"Çörüş","first_name":"Doğan","full_name":"Çörüş, Doğan"},{"first_name":"Duccuong","full_name":"Dang, Duccuong","last_name":"Dang"},{"last_name":"Friedrich","full_name":"Friedrich, Tobias","first_name":"Tobias"},{"last_name":"Lehre","first_name":"Per","full_name":"Lehre, Per"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"full_name":"Sutton, Andrew","first_name":"Andrew","last_name":"Sutton"},{"full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"}],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa_version":"Published Version","citation":{"ieee":"T. Paixao <i>et al.</i>, “Toward a unifying framework for evolutionary processes,” <i>Journal of Theoretical Biology</i>, vol. 383. Elsevier, pp. 28–43, 2015.","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. <i>Journal of Theoretical Biology</i>. 2015;383:28-43. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>","chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” <i>Journal of Theoretical Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>.","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” <i>Journal of Theoretical Biology</i>, vol. 383, Elsevier, 2015, pp. 28–43, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>.","ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43.","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43."},"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_created":"2018-12-11T11:52:37Z","date_updated":"2026-07-07T13:12:13Z","pubrep_id":"483","file":[{"file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","creator":"system","date_created":"2018-12-12T10:16:53Z","date_updated":"2020-07-14T12:45:01Z","relation":"main_file","content_type":"application/pdf","checksum":"33b60ecfea60764756a9ee9df5eb65ca","file_id":"5244","file_size":595307,"access_level":"open_access"}],"language":[{"iso":"eng"}],"ddc":["570"],"isi":1,"status":"public","publist_id":"5629","has_accepted_license":"1"},{"date_updated":"2026-07-07T14:01:10Z","date_created":"2018-12-11T11:53:17Z","isi":1,"language":[{"iso":"eng"}],"OA_place":"repository","related_material":{"record":[{"id":"5415","relation":"earlier_version","status":"public"},{"status":"public","id":"5436","relation":"earlier_version"},{"relation":"later_version","id":"467","status":"public"}]},"status":"public","publist_id":"5494","quality_controlled":"1","type":"conference","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","first_name":"Jan"}],"publication_status":"published","month":"07","oa_version":"Preprint","citation":{"mla":"Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” <i>Proceedings - Symposium on Logic in Computer Science</i>, vol. 2015–July, 7174926, IEEE, 2015, doi:<a href=\"https://doi.org/10.1109/LICS.2015.72\">10.1109/LICS.2015.72</a>.","ista":"Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata. Proceedings - Symposium on Logic in Computer Science. LICS: Logic in Computer Science vol. 2015–July, 7174926.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings - Symposium on Logic in Computer Science, IEEE, 2015.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2015). Nested weighted automata. In <i>Proceedings - Symposium on Logic in Computer Science</i> (Vol. 2015–July). Kyoto, Japan: IEEE. <a href=\"https://doi.org/10.1109/LICS.2015.72\">https://doi.org/10.1109/LICS.2015.72</a>","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” in <i>Proceedings - Symposium on Logic in Computer Science</i>, Kyoto, Japan, 2015, vol. 2015–July.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. In: <i>Proceedings - Symposium on Logic in Computer Science</i>. Vol 2015-July. IEEE; 2015. doi:<a href=\"https://doi.org/10.1109/LICS.2015.72\">10.1109/LICS.2015.72</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” In <i>Proceedings - Symposium on Logic in Computer Science</i>, Vol. 2015–July. IEEE, 2015. <a href=\"https://doi.org/10.1109/LICS.2015.72\">https://doi.org/10.1109/LICS.2015.72</a>."},"conference":{"start_date":"2015-07-06","name":"LICS: Logic in Computer Science","end_date":"2015-07-10","location":"Kyoto, Japan"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","publisher":"IEEE","arxiv":1,"publication":"Proceedings - Symposium on Logic in Computer Science","external_id":{"arxiv":["1606.03598"],"isi":["000380427100064"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1606.03598"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata, nor in any other know decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in run-time verification. We establish an almost complete decidability picture for the basic decision problems about nested weighted automata, and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties."}],"project":[{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"},{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"volume":"2015-July","year":"2015","doi":"10.1109/LICS.2015.72","day":"31","OA_type":"green","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE), Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.\r\nA Technical Report of the paper is available at: \r\nhttps://repository.ist.ac.at/331/\r\n","fulldoi":"https://doi.org/10.1109/LICS.2015.72","date_published":"2015-07-31T00:00:00Z","article_number":"7174926","title":"Nested weighted automata","scopus_import":"1","_id":"1656","oa":1,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"corr_author":"1"},{"day":"24","fulldoi":"https://doi.org/10.15479/AT:IST-2015-170-v2-2","doi":"10.15479/AT:IST-2015-170-v2-2","year":"2015","abstract":[{"lang":"eng","text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata, nor in any other know decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata which makes it possible to express important quantitative properties such as average response time.\r\nIn nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in run-time verification. We establish an almost complete decidability picture for the basic decision problems about nested weighted automata, and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties."}],"publisher":"IST Austria","page":"29","publication_identifier":{"issn":["2664-1690"]},"oa":1,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"_id":"5436","title":"Nested weighted automata","date_published":"2015-04-24T00:00:00Z","status":"public","has_accepted_license":"1","ddc":["000"],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5415"},{"id":"1656","relation":"later_version","status":"public"},{"relation":"later_version","id":"467","status":"public"}]},"file":[{"file_name":"IST-2015-170-v2+2_report.pdf","creator":"system","date_updated":"2020-07-14T12:46:54Z","relation":"main_file","date_created":"2018-12-12T11:54:19Z","content_type":"application/pdf","checksum":"3c402f47d3669c28d04d1af405a08e3f","file_id":"5541","access_level":"open_access","file_size":569991}],"pubrep_id":"331","date_created":"2018-12-12T11:39:19Z","date_updated":"2026-07-07T14:01:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Nested Weighted Automata</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-170-v2-2\">10.15479/AT:IST-2015-170-v2-2</a>.","ista":"Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata, IST Austria, 29p.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria, 2015.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, <i>Nested weighted automata</i>. IST Austria, 2015.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2015). <i>Nested weighted automata</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-170-v2-2\">https://doi.org/10.15479/AT:IST-2015-170-v2-2</a>","ama":"Chatterjee K, Henzinger TA, Otop J. <i>Nested Weighted Automata</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-170-v2-2\">10.15479/AT:IST-2015-170-v2-2</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. <i>Nested Weighted Automata</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-170-v2-2\">https://doi.org/10.15479/AT:IST-2015-170-v2-2</a>."},"month":"04","alternative_title":["IST Austria Technical Report"],"publication_status":"published","type":"technical_report","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","first_name":"Jan","full_name":"Otop, Jan"}],"file_date_updated":"2020-07-14T12:46:54Z"},{"conference":{"end_date":"2015-06-19","name":"ISIT: International Symposium on Information Theory","start_date":"2015-06-14","location":"Hong Kong, China"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","month":"07","citation":{"short":"E. Abbe, Y. Wigderson, in:, 2015 IEEE International Symposium on Information Theory, IEEE, 2015.","ista":"Abbe E, Wigderson Y. 2015. High-girth matrices and polarization. 2015 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory.","mla":"Abbe, Emmanuel, and Yuval Wigderson. “High-Girth Matrices and Polarization.” <i>2015 IEEE International Symposium on Information Theory</i>, IEEE, 2015, doi:<a href=\"https://doi.org/10.1109/isit.2015.7282898\">10.1109/isit.2015.7282898</a>.","chicago":"Abbe, Emmanuel, and Yuval Wigderson. “High-Girth Matrices and Polarization.” In <i>2015 IEEE International Symposium on Information Theory</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/isit.2015.7282898\">https://doi.org/10.1109/isit.2015.7282898</a>.","ieee":"E. Abbe and Y. Wigderson, “High-girth matrices and polarization,” in <i>2015 IEEE International Symposium on Information Theory</i>, Hong Kong, China, 2015.","apa":"Abbe, E., &#38; Wigderson, Y. (2015). High-girth matrices and polarization. In <i>2015 IEEE International Symposium on Information Theory</i>. Hong Kong, China: IEEE. <a href=\"https://doi.org/10.1109/isit.2015.7282898\">https://doi.org/10.1109/isit.2015.7282898</a>","ama":"Abbe E, Wigderson Y. High-girth matrices and polarization. In: <i>2015 IEEE International Symposium on Information Theory</i>. IEEE; 2015. doi:<a href=\"https://doi.org/10.1109/isit.2015.7282898\">10.1109/isit.2015.7282898</a>"},"oa_version":"Preprint","type":"conference","author":[{"first_name":"Emmanuel","full_name":"Abbe, Emmanuel","last_name":"Abbe"},{"last_name":"Wigderson","id":"2d0023a0-1567-11f0-833d-d5c1e476d4b5","full_name":"Wigderson, Yuval","first_name":"Yuval"}],"publication_status":"published","quality_controlled":"1","extern":"1","status":"public","language":[{"iso":"eng"}],"OA_place":"repository","date_updated":"2026-07-14T08:54:51Z","date_created":"2026-06-29T10:57:04Z","oa":1,"publication_identifier":{"isbn":["9781467377041"]},"_id":"22173","scopus_import":"1","title":"High-girth matrices and polarization","date_published":"2015-07-01T00:00:00Z","doi":"10.1109/isit.2015.7282898","year":"2015","OA_type":"green","day":"01","fulldoi":"https://doi.org/10.1109/isit.2015.7282898","abstract":[{"lang":"eng","text":"The girth of a matrix is the least number of linearly dependent columns, in contrast to the rank which is the largest number of linearly independent columns. This paper considers the construction of high-girth matrices, whose probabilistic girth is close to their rank. Random matrices can be used to show the existence of high-girth matrices. This paper uses a recursive construction based on conditional ranks (inspired by polar codes) to obtain a deterministic and efficient construction of high-girth matrices for arbitrary relative ranks. Interestingly, the construction is agnostic to the underlying field and applies to both finite and continuous fields with the same binary matrix. The construction gives in particular the following: (i) over the binary field, high-girth matrices are equivalent to capacity-achieving codes, and our construction turns out to match exactly the BEC polar codes (even at finite block length). It hence gives a different interpretation of BEC polar codes, using the parity-check matrix instead of the generator matrix, and basic linear algebra instead of the mutual information, and generalizes to larger fields; (ii) for the BSC, our construction gives an operational meaning to the Bhattacharyya upper-bound process used in polar codes; (iii) for the reals, it gives an explicit candidate matrix for sparse recovery."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1501.06528"}],"arxiv":1,"publisher":"IEEE","publication":"2015 IEEE International Symposium on Information Theory","external_id":{"arxiv":["1501.06528"]}},{"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"12","oa_version":"None","citation":{"chicago":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” <i>Journal of Complexity</i>. Academic Press, 2015. <a href=\"https://doi.org/10.1016/j.jco.2015.06.002\">https://doi.org/10.1016/j.jco.2015.06.002</a>.","apa":"Pausinger, F., &#38; Svane, A. (2015). A Koksma-Hlawka inequality for general discrepancy systems. <i>Journal of Complexity</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jco.2015.06.002\">https://doi.org/10.1016/j.jco.2015.06.002</a>","ieee":"F. Pausinger and A. Svane, “A Koksma-Hlawka inequality for general discrepancy systems,” <i>Journal of Complexity</i>, vol. 31, no. 6. Academic Press, pp. 773–797, 2015.","ama":"Pausinger F, Svane A. A Koksma-Hlawka inequality for general discrepancy systems. <i>Journal of Complexity</i>. 2015;31(6):773-797. doi:<a href=\"https://doi.org/10.1016/j.jco.2015.06.002\">10.1016/j.jco.2015.06.002</a>","short":"F. Pausinger, A. Svane, Journal of Complexity 31 (2015) 773–797.","ista":"Pausinger F, Svane A. 2015. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 31(6), 773–797.","mla":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” <i>Journal of Complexity</i>, vol. 31, no. 6, Academic Press, 2015, pp. 773–97, doi:<a href=\"https://doi.org/10.1016/j.jco.2015.06.002\">10.1016/j.jco.2015.06.002</a>."},"author":[{"orcid":"0000-0002-8379-3768","last_name":"Pausinger","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","full_name":"Pausinger, Florian","first_name":"Florian"},{"last_name":"Svane","first_name":"Anne","full_name":"Svane, Anne"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","status":"public","publist_id":"5320","isi":1,"issue":"6","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1399"}]},"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:54:02Z","date_updated":"2026-07-29T10:08:33Z","department":[{"_id":"HeEd"}],"corr_author":"1","_id":"1792","title":"A Koksma-Hlawka inequality for general discrepancy systems","scopus_import":"1","intvolume":"        31","date_published":"2015-12-01T00:00:00Z","doi":"10.1016/j.jco.2015.06.002","year":"2015","fulldoi":"https://doi.org/10.1016/j.jco.2015.06.002","day":"01","acknowledgement":"F.P. is supported by the Graduate School of IST Austria, A.M.S is supported by the Centre for Stochastic Geometry and Advanced Bioimaging funded by a grant from the Villum Foundation.","abstract":[{"lang":"eng","text":"Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop a new concept of variation of multivariate functions on a compact Hausdorff space with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka theorem that holds for this notion of variation and discrepancy with respect to D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions, such as extreme or isotropic discrepancy. For extreme discrepancy, our result coincides with the usual Koksma-Hlawka theorem. We show that the space of functions of bounded D-variation contains important discontinuous functions and is closed under natural algebraic operations. Finally, we illustrate the results on concrete integration problems from integral geometry and stereology."}],"volume":31,"external_id":{"isi":["000362926900001"]},"publication":"Journal of Complexity","page":"773 - 797","publisher":"Academic Press"},{"publisher":"Institute of Science and Technology Austria","page":"144","date_created":"2018-12-11T11:51:48Z","date_updated":"2026-07-29T10:08:34Z","doi_confirm":"1","day":"01","publist_id":"5808","status":"public","year":"2015","OA_place":"publisher","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1662","status":"public"},{"status":"public","id":"1792","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"2255","status":"public"}]},"degree_awarded":"PhD","abstract":[{"lang":"eng","text":"This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold."}],"supervisor":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","type":"dissertation","author":[{"id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger","orcid":"0000-0002-8379-3768","first_name":"Florian","full_name":"Pausinger, Florian"}],"title":"On the approximation of intrinsic volumes","date_published":"2015-06-01T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","corr_author":"1","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"oa_version":"None","citation":{"ama":"Pausinger F. On the approximation of intrinsic volumes. 2015.","apa":"Pausinger, F. (2015). <i>On the approximation of intrinsic volumes</i>. Institute of Science and Technology Austria.","ieee":"F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science and Technology Austria, 2015.","chicago":"Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute of Science and Technology Austria, 2015.","mla":"Pausinger, Florian. <i>On the Approximation of Intrinsic Volumes</i>. Institute of Science and Technology Austria, 2015.","ista":"Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of Science and Technology Austria.","short":"F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science and Technology Austria, 2015."},"month":"06","_id":"1399"},{"publist_id":"5425","status":"public","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"1400","status":"public"}]},"isi":1,"issue":"1812","date_updated":"2026-07-29T10:15:25Z","date_created":"2018-12-11T11:53:35Z","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Submitted Version","citation":{"ama":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. Biological auctions with multiple rewards. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2015;282(1812). doi:<a href=\"https://doi.org/10.1098/rspb.2015.1041\">10.1098/rspb.2015.1041</a>","apa":"Reiter, J., Kanodia, A., Gupta, R., Nowak, M., &#38; Chatterjee, K. (2015). Biological auctions with multiple rewards. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rspb.2015.1041\">https://doi.org/10.1098/rspb.2015.1041</a>","ieee":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, and K. Chatterjee, “Biological auctions with multiple rewards,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1812. Royal Society, 2015.","chicago":"Reiter, Johannes, Ayush Kanodia, Raghav Gupta, Martin Nowak, and Krishnendu Chatterjee. “Biological Auctions with Multiple Rewards.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, 2015. <a href=\"https://doi.org/10.1098/rspb.2015.1041\">https://doi.org/10.1098/rspb.2015.1041</a>.","mla":"Reiter, Johannes, et al. “Biological Auctions with Multiple Rewards.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1812, Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rspb.2015.1041\">10.1098/rspb.2015.1041</a>.","ista":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. 2015. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1812).","short":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, K. Chatterjee, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015)."},"month":"07","publication_status":"published","author":[{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","orcid":"0000-0002-0170-7353","first_name":"Johannes","full_name":"Reiter, Johannes"},{"last_name":"Kanodia","first_name":"Ayush","full_name":"Kanodia, Ayush"},{"first_name":"Raghav","full_name":"Gupta, Raghav","last_name":"Gupta"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"type":"journal_article","quality_controlled":"1","fulldoi":"https://doi.org/10.1098/rspb.2015.1041","day":"15","acknowledgement":"This work was supported by grants from the John Templeton Foundation, ERC Start Grant (279307: Graph Games), FWF NFN Grant (No S11407N23 RiSE/SHiNE), FWF Grant (No P23499N23) and a Microsoft faculty fellows award.","year":"2015","doi":"10.1098/rspb.2015.1041","volume":282,"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards."}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528522/"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","external_id":{"pmid":["26180069"],"isi":["000362305500021"]},"publisher":"Royal Society","pmid":1,"corr_author":"1","oa":1,"department":[{"_id":"KrCh"}],"_id":"1709","scopus_import":"1","title":"Biological auctions with multiple rewards","intvolume":"       282","date_published":"2015-07-15T00:00:00Z","article_type":"original"},{"date_published":"2015-04-01T00:00:00Z","supervisor":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"author":[{"orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","first_name":"Johannes","full_name":"Reiter, Johannes"}],"title":"The subclonal evolution of cancer","type":"dissertation","oa_version":"None","citation":{"ista":"Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and Technology Austria.","short":"J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology Austria, 2015.","mla":"Reiter, Johannes. <i>The Subclonal Evolution of Cancer</i>. Institute of Science and Technology Austria, 2015.","chicago":"Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science and Technology Austria, 2015.","ieee":"J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology Austria, 2015.","apa":"Reiter, J. (2015). <i>The subclonal evolution of cancer</i>. Institute of Science and Technology Austria.","ama":"Reiter J. The subclonal evolution of cancer. 2015."},"month":"04","_id":"1400","corr_author":"1","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:51:48Z","date_updated":"2026-07-29T10:15:25Z","page":"183","publisher":"Institute of Science and Technology Austria","doi_confirm":"1","language":[{"iso":"eng"}],"OA_place":"publisher","related_material":{"record":[{"id":"2000","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1709","relation":"part_of_dissertation"},{"id":"2858","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"2816","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"2247","status":"public"},{"relation":"part_of_dissertation","id":"3260","status":"public"},{"status":"public","id":"3157","relation":"part_of_dissertation"}]},"abstract":[{"text":"Cancer results from an uncontrolled growth of abnormal cells. Sequentially accumulated genetic and epigenetic alterations decrease cell death and increase cell replication. We used mathematical models to quantify the effect of driver gene mutations. The recently developed targeted therapies can lead to dramatic regressions. However, in solid cancers, clinical responses are often short-lived because resistant cancer cells evolve. We estimated that approximately 50 different mutations can confer resistance to a typical targeted therapeutic agent. We find that resistant cells are likely to be present in expanded subclones before the start of the treatment. The dominant strategy to prevent the evolution of resistance is combination therapy. Our analytical results suggest that in most patients, dual therapy, but not monotherapy, can result in long-term disease control. However, long-term control can only occur if there are no possible mutations in the genome that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous therapy with two drugs is much more likely to result in long-term disease control than sequential therapy with the same drugs. To improve our understanding of the underlying subclonal evolution we reconstruct the evolutionary history of a patient's cancer from next-generation sequencing data of spatially-distinct DNA samples. Using a quantitative measure of genetic relatedness, we found that pancreatic cancers and their metastases demonstrated a higher level of relatedness than that expected for any two cells randomly taken from a normal tissue. This minimal amount of genetic divergence among advanced lesions indicates that genetic heterogeneity, when quantitatively defined, is not a fundamental feature of the natural history of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics finds evidence for seeding patterns of metastases and can directly be used to discover rules governing the evolution of solid malignancies to transform cancer into a more predictable disease.","lang":"eng"}],"degree_awarded":"PhD","day":"01","year":"2015","publist_id":"5807","status":"public"},{"date_updated":"2026-07-29T11:31:13Z","date_created":"2018-12-11T11:53:21Z","pubrep_id":"463","file":[{"date_updated":"2020-07-14T12:45:10Z","relation":"main_file","date_created":"2018-12-12T10:07:58Z","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","creator":"system","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","content_type":"application/pdf","file_id":"4657","access_level":"open_access","file_size":2580778}],"isi":1,"issue":"11","related_material":{"record":[{"id":"9712","relation":"research_data","status":"public"},{"id":"1131","relation":"dissertation_contains","status":"public"}]},"ddc":["576"],"language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","publist_id":"5483","quality_controlled":"1","file_date_updated":"2020-07-14T12:45:10Z","author":[{"orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul","first_name":"Murat","full_name":"Tugrul, Murat"},{"orcid":"0000-0003-2361-3953","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","first_name":"Tiago"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"type":"journal_article","publication_status":"published","month":"11","citation":{"ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>, vol. 11, no. 11, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>.","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>.","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” <i>PLoS Genetics</i>, vol. 11, no. 11. Public Library of Science, 2015.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. 2015;11(11). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"PLoS Genetics","external_id":{"isi":["000366179000022"]},"publisher":"Public Library of Science","ec_funded":1,"abstract":[{"text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics.","lang":"eng"}],"volume":11,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"}],"year":"2015","doi":"10.1371/journal.pgen.1005639","fulldoi":"https://doi.org/10.1371/journal.pgen.1005639","day":"06","date_published":"2015-11-06T00:00:00Z","scopus_import":"1","title":"Dynamics of transcription factor binding site evolution","intvolume":"        11","_id":"1666","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"oa":1},{"volume":34,"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020"}],"ec_funded":1,"abstract":[{"text":"We present a method for simulating brittle fracture under the assumptions of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture surfaces. The computational cost of the BEM is alleviated by using a low-resolution mesh and interpolating the resulting stress intensity factors when propagating the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture surfaces with high spatial and temporal resolution, taking spatial variation of material toughness and/or strength into account. It also allows for crack initiation to be handled separately from crack propagation, which is not only more reasonable from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating the resolution of the crack-front from the resolution of the computational mesh increases the efficiency and therefore the amount of visual detail on the resulting fracture surfaces. The BEM also allows us to re-use previously computed blocks of the system matrix.","lang":"eng"}],"fulldoi":"https://doi.org/10.1145/2766896","day":"27","doi":"10.1145/2766896","year":"2015","external_id":{"isi":["000358786600117"]},"publisher":"ACM","_id":"1633","corr_author":"1","department":[{"_id":"ChWo"}],"oa":1,"date_published":"2015-07-27T00:00:00Z","scopus_import":"1","title":"High-resolution brittle fracture simulation with boundary elements","article_number":"151","intvolume":"        34","ddc":["000"],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"839","relation":"dissertation_contains"}]},"isi":1,"issue":"4","has_accepted_license":"1","status":"public","publist_id":"5522","pubrep_id":"609","date_updated":"2026-07-29T13:27:24Z","date_created":"2018-12-11T11:53:09Z","file":[{"access_level":"open_access","file_size":20154270,"file_id":"5131","content_type":"application/pdf","checksum":"955aee971983f6b6152bcc1c9b4a7c20","creator":"system","file_name":"IST-2016-609-v1+1_FractureBEM.pdf","relation":"main_file","date_created":"2018-12-12T10:15:13Z","date_updated":"2020-07-14T12:45:07Z"}],"citation":{"ieee":"D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","apa":"Hahn, D., &#38; Wojtan, C. (2015). High-resolution brittle fracture simulation with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2766896\">https://doi.org/10.1145/2766896</a>","ama":"Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary elements. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766896\">10.1145/2766896</a>","chicago":"Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation with Boundary Elements,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766896\">https://doi.org/10.1145/2766896</a>.","mla":"Hahn, David, and Chris Wojtan. <i>High-Resolution Brittle Fracture Simulation with Boundary Elements</i>. Vol. 34, no. 4, 151, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766896\">10.1145/2766896</a>.","ista":"Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 151.","short":"D. Hahn, C. Wojtan, in:, ACM, 2015."},"oa_version":"Submitted Version","month":"07","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","conference":{"end_date":"2015-08-13","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","start_date":"2015-08-09","location":"Los Angeles, CA, United States"},"file_date_updated":"2020-07-14T12:45:07Z","quality_controlled":"1","publication_status":"published","author":[{"first_name":"David","full_name":"Hahn, David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","last_name":"Hahn"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"type":"conference"},{"status":"public","issue":"5","OA_place":"publisher","language":[{"iso":"eng"}],"ddc":["550"],"date_updated":"2026-08-03T13:39:10Z","date_created":"2026-07-27T12:30:24Z","DOAJ_listed":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","citation":{"mla":"Fatichi, Simone, et al. “Abiotic and Biotic Controls of Soil Moisture Spatiotemporal Variability and the Occurrence of Hysteresis.” <i>Water Resources Research</i>, vol. 51, no. 5, American Geophysical Union, 2015, pp. 3505–24, doi:<a href=\"https://doi.org/10.1002/2014wr016102\">10.1002/2014wr016102</a>.","ista":"Fatichi S, Katul GG, Ivanov VY, Pappas C, Paschalis A, Consolo A, Kim J, Burlando P. 2015. Abiotic and biotic controls of soil moisture spatiotemporal variability and the occurrence of hysteresis. Water Resources Research. 51(5), 3505–3524.","short":"S. Fatichi, G.G. Katul, V.Y. Ivanov, C. Pappas, A. Paschalis, A. Consolo, J. Kim, P. Burlando, Water Resources Research 51 (2015) 3505–3524.","ieee":"S. Fatichi <i>et al.</i>, “Abiotic and biotic controls of soil moisture spatiotemporal variability and the occurrence of hysteresis,” <i>Water Resources Research</i>, vol. 51, no. 5. American Geophysical Union, pp. 3505–3524, 2015.","apa":"Fatichi, S., Katul, G. G., Ivanov, V. Y., Pappas, C., Paschalis, A., Consolo, A., … Burlando, P. (2015). Abiotic and biotic controls of soil moisture spatiotemporal variability and the occurrence of hysteresis. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/2014wr016102\">https://doi.org/10.1002/2014wr016102</a>","ama":"Fatichi S, Katul GG, Ivanov VY, et al. Abiotic and biotic controls of soil moisture spatiotemporal variability and the occurrence of hysteresis. <i>Water Resources Research</i>. 2015;51(5):3505-3524. doi:<a href=\"https://doi.org/10.1002/2014wr016102\">10.1002/2014wr016102</a>","chicago":"Fatichi, Simone, Gabriel G. Katul, Valeriy Y. Ivanov, Christoforos Pappas, Athanasios Paschalis, Ada Consolo, Jongho Kim, and Paolo Burlando. “Abiotic and Biotic Controls of Soil Moisture Spatiotemporal Variability and the Occurrence of Hysteresis.” <i>Water Resources Research</i>. American Geophysical Union, 2015. <a href=\"https://doi.org/10.1002/2014wr016102\">https://doi.org/10.1002/2014wr016102</a>."},"oa_version":"Published Version","author":[{"id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi","first_name":"Simone","full_name":"Fatichi, Simone"},{"full_name":"Katul, Gabriel G.","first_name":"Gabriel G.","last_name":"Katul"},{"full_name":"Ivanov, Valeriy Y.","first_name":"Valeriy Y.","last_name":"Ivanov"},{"full_name":"Pappas, Christoforos","first_name":"Christoforos","last_name":"Pappas"},{"first_name":"Athanasios","full_name":"Paschalis, Athanasios","last_name":"Paschalis"},{"first_name":"Ada","full_name":"Consolo, Ada","last_name":"Consolo"},{"first_name":"Jongho","full_name":"Kim, Jongho","last_name":"Kim"},{"full_name":"Burlando, Paolo","first_name":"Paolo","last_name":"Burlando"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","extern":"1","das_tickbox":"1","doi":"10.1002/2014wr016102","year":"2015","fulldoi":"https://doi.org/10.1002/2014wr016102","OA_type":"free access","day":"01","abstract":[{"lang":"eng","text":"An expression that separates biotic and abiotic controls on the temporal dynamics of the soilmoisture spatial coefficient of variation C v(h) was explored via numerical simulations using a mechanisticecohydrological model, Tethys-Chloris. Continuous soil moisture spatiotemporal dynamics at an exemplaryhillslope domain were computed for six case studies characterized by different climate and vegetationcover and for three configurations of soil properties. It was shown that abiotic controls largely exceed theirbiotic counterparts in wet climates. Biotic controls on C v(h) were found to be more pronounced in Mediter-ranean climates. The relation between Cv(h) and spatial mean soil moisture h was found to be unique in wetlocations, regardless of the soil properties. For the case of homogeneous soil texture, hysteretic cyclesbetween C v(h) and h were observed in all Mediterranean climate locations considered here and to a lesserextent in a deciduous temperate forest. Heterogeneity in soil properties increased C v(h) to values commen-surate with field observations and weakened signatures of hysteresis at all of the studied locations. Thisfinding highlights the role of site-specific heterogeneities in hiding or even eliminating the signature ofclimatic and biotic controls on C v(h), thereby offering a new perspective on causes of confounding resultsreported across field experiments."}],"volume":51,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/2014WR016102"}],"publication":"Water Resources Research","page":"3505-3524","publisher":"American Geophysical Union","oa":1,"publication_identifier":{"issn":["0043-1397"],"eissn":["1944-7973"]},"_id":"22495","title":"Abiotic and biotic controls of soil moisture spatiotemporal variability and the occurrence of hysteresis","scopus_import":"1","intvolume":"        51","date_published":"2015-05-01T00:00:00Z","article_type":"original"},{"date_updated":"2026-08-03T14:15:02Z","date_created":"2026-07-27T12:30:24Z","status":"public","language":[{"iso":"eng"}],"issue":"3","publication_status":"published","type":"journal_article","author":[{"last_name":"Francipane","first_name":"A.","full_name":"Francipane, A."},{"first_name":"Simone","full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi"},{"first_name":"V. Y.","full_name":"Ivanov, V. Y.","last_name":"Ivanov"},{"last_name":"Noto","full_name":"Noto, L. V.","first_name":"L. V."}],"extern":"1","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","citation":{"chicago":"Francipane, A., Simone Fatichi, V. Y. Ivanov, and L. V. Noto. “Stochastic Assessment of Climate Impacts on Hydrology and Geomorphology of Semiarid Headwater Basins Using a Physically Based Model.” <i>Journal of Geophysical Research: Earth Surface</i>. American Geophysical Union, 2015. <a href=\"https://doi.org/10.1002/2014jf003232\">https://doi.org/10.1002/2014jf003232</a>.","apa":"Francipane, A., Fatichi, S., Ivanov, V. Y., &#38; Noto, L. V. (2015). Stochastic assessment of climate impacts on hydrology and geomorphology of semiarid headwater basins using a physically based model. <i>Journal of Geophysical Research: Earth Surface</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/2014jf003232\">https://doi.org/10.1002/2014jf003232</a>","ieee":"A. Francipane, S. Fatichi, V. Y. Ivanov, and L. V. Noto, “Stochastic assessment of climate impacts on hydrology and geomorphology of semiarid headwater basins using a physically based model,” <i>Journal of Geophysical Research: Earth Surface</i>, vol. 120, no. 3. American Geophysical Union, pp. 507–533, 2015.","ama":"Francipane A, Fatichi S, Ivanov VY, Noto LV. Stochastic assessment of climate impacts on hydrology and geomorphology of semiarid headwater basins using a physically based model. <i>Journal of Geophysical Research: Earth Surface</i>. 2015;120(3):507-533. doi:<a href=\"https://doi.org/10.1002/2014jf003232\">10.1002/2014jf003232</a>","ista":"Francipane A, Fatichi S, Ivanov VY, Noto LV. 2015. Stochastic assessment of climate impacts on hydrology and geomorphology of semiarid headwater basins using a physically based model. Journal of Geophysical Research: Earth Surface. 120(3), 507–533.","short":"A. Francipane, S. Fatichi, V.Y. Ivanov, L.V. Noto, Journal of Geophysical Research: Earth Surface 120 (2015) 507–533.","mla":"Francipane, A., et al. “Stochastic Assessment of Climate Impacts on Hydrology and Geomorphology of Semiarid Headwater Basins Using a Physically Based Model.” <i>Journal of Geophysical Research: Earth Surface</i>, vol. 120, no. 3, American Geophysical Union, 2015, pp. 507–33, doi:<a href=\"https://doi.org/10.1002/2014jf003232\">10.1002/2014jf003232</a>."},"oa_version":"None","month":"03","publisher":"American Geophysical Union","publication":"Journal of Geophysical Research: Earth Surface","page":"507-533","day":"01","OA_type":"closed access","fulldoi":"https://doi.org/10.1002/2014jf003232","year":"2015","doi":"10.1002/2014jf003232","das_tickbox":"1","volume":120,"abstract":[{"lang":"eng","text":"Hydrologic and geomorphic responses of watersheds to changes in climate are difficult to assess due to projection uncertainties and nonlinearity of the processes that are involved. Yet such assessments are increasingly needed and call for mechanistic approaches within a probabilistic framework. This study employs an integrated hydrology‐geomorphology model, the Triangulated Irregular Network‐based Real‐time Integrated Basin Simulator (tRIBS)‐Erosion, to analyze runoff and erosion sensitivity of seven semiarid headwater basins to projected climate conditions. The Advanced Weather Generator is used to produce two climate ensembles representative of the historic and future climate conditions for the Walnut Gulch Experimental Watershed located in the southwest U.S. The former ensemble incorporates the stochastic variability of the observed climate, while the latter includes the stochastic variability and the uncertainty of multimodel climate change projections. The ensembles are used as forcing for tRIBS‐Erosion that simulates runoff and sediment basin responses leading to probabilistic inferences of future changes. The results show that annual precipitation for the area is generally expected to decrease in the future, with lower hourly intensities and similar daily rates. The smaller hourly rainfall generally results in lower mean annual runoff. However, a non‐negligible probability of runoff increase in the future is identified, resulting from stochastic combinations of years with low and high runoff. On average, the magnitudes of mean and extreme events of sediment yield are expected to decrease with a very high probability. Importantly, the projected variability of annual sediment transport for the future conditions is comparable to that for the historic conditions, despite the fact that the former account for a much wider range of possible climate “alternatives.” This result demonstrates that the historic natural climate variability of sediment yield is already so high, that it is comparable to the variability for a projected and highly uncertain future. Additionally, changes in the scaling relationship between specific sediment yield/runoff and drainage basin area are detected."}],"intvolume":"       120","scopus_import":"1","title":"Stochastic assessment of climate impacts on hydrology and geomorphology of semiarid headwater basins using a physically based model","article_type":"original","date_published":"2015-03-01T00:00:00Z","publication_identifier":{"eissn":["2169-9011"],"issn":["2169-9003"]},"_id":"22509"},{"date_created":"2026-07-27T12:30:24Z","date_updated":"2026-08-06T07:55:55Z","status":"public","issue":"9","language":[{"iso":"eng"}],"OA_place":"publisher","type":"journal_article","author":[{"first_name":"Grigorios G.","full_name":"Anagnostopoulos, Grigorios G.","last_name":"Anagnostopoulos"},{"first_name":"Simone","full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi"},{"first_name":"Paolo","full_name":"Burlando, Paolo","last_name":"Burlando"}],"publication_status":"published","quality_controlled":"1","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","month":"09","oa_version":"Published Version","citation":{"mla":"Anagnostopoulos, Grigorios G., et al. “An Advanced Process-Based Distributed Model for the Investigation of Rainfall-Induced Landslides: The Effect of Process Representation and Boundary Conditions.” <i>Water Resources Research</i>, vol. 51, no. 9, American Geophysical Union, 2015, pp. 7501–23, doi:<a href=\"https://doi.org/10.1002/2015wr016909\">10.1002/2015wr016909</a>.","short":"G.G. Anagnostopoulos, S. Fatichi, P. Burlando, Water Resources Research 51 (2015) 7501–7523.","ista":"Anagnostopoulos GG, Fatichi S, Burlando P. 2015. An advanced process-based distributed model for the investigation of rainfall-induced landslides: The effect of process representation and boundary conditions. Water Resources Research. 51(9), 7501–7523.","ama":"Anagnostopoulos GG, Fatichi S, Burlando P. An advanced process-based distributed model for the investigation of rainfall-induced landslides: The effect of process representation and boundary conditions. <i>Water Resources Research</i>. 2015;51(9):7501-7523. doi:<a href=\"https://doi.org/10.1002/2015wr016909\">10.1002/2015wr016909</a>","ieee":"G. G. Anagnostopoulos, S. Fatichi, and P. Burlando, “An advanced process-based distributed model for the investigation of rainfall-induced landslides: The effect of process representation and boundary conditions,” <i>Water Resources Research</i>, vol. 51, no. 9. American Geophysical Union, pp. 7501–7523, 2015.","apa":"Anagnostopoulos, G. G., Fatichi, S., &#38; Burlando, P. (2015). An advanced process-based distributed model for the investigation of rainfall-induced landslides: The effect of process representation and boundary conditions. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/2015wr016909\">https://doi.org/10.1002/2015wr016909</a>","chicago":"Anagnostopoulos, Grigorios G., Simone Fatichi, and Paolo Burlando. “An Advanced Process-Based Distributed Model for the Investigation of Rainfall-Induced Landslides: The Effect of Process Representation and Boundary Conditions.” <i>Water Resources Research</i>. American Geophysical Union, 2015. <a href=\"https://doi.org/10.1002/2015wr016909\">https://doi.org/10.1002/2015wr016909</a>."},"main_file_link":[{"url":" https://doi.org/10.1002/2015WR016909","open_access":"1"}],"publisher":"American Geophysical Union","publication":"Water Resources Research","page":"7501-7523","das_tickbox":"1","year":"2015","doi":"10.1002/2015wr016909","day":"01","OA_type":"free access","fulldoi":"https://doi.org/10.1002/2015wr016909","abstract":[{"lang":"eng","text":"Extreme rainfall events are the major driver of shallow landslide occurrences in mountainous and steep terrain regions around the world. Subsurface hydrology has a dominant role on the initiation of rainfall-induced shallow landslides, since changes in the soil water content affect significantly the soil shear strength. Rainfall infiltration produces an increase of soil water potential, which is followed by a rapid drop in apparent cohesion. Especially on steep slopes of shallow soils, this loss of shear strength can lead to failure even in unsaturated conditions before positive water pressures are developed. We present HYDROlisthisis, a process-based model, fully distributed in space with fine time resolution, in order to investigate the interactions between surface and subsurface hydrology and shallow landslides initiation. Fundamental elements of the approach are the dependence of shear strength on the three-dimensional (3-D) field of soil water potential, as well as the temporal evolution of soil water potential during the wetting and drying phases. Specifically, 3-D variably saturated flow conditions, including soil hydraulic hysteresis and preferential flow phenomena, are simulated for the subsurface flow, coupled with a surface runoff routine based on the kinematic wave approximation. The geotechnical component of the model is based on a multidimensional limit equilibrium analysis, which takes into account the basic principles of unsaturated soil mechanics. A series of numerical simulations were carried out with various boundary conditions and using different hydrological and geotechnical components. Boundary conditions in terms of distributed soil depth were generated using both empirical and process-based models. The effect of including preferential flow and soil hydraulic hysteresis was tested together with the replacement of the infinite slope assumption with the multidimensional limit equilibrium analysis. The results show that boundary conditions play a crucial role in the model performance and that the introduced hydrological (preferential flow and soil hydraulic hysteresis) and geotechnical components (multidimensional limit equilibrium analysis) significantly improve predictive capabilities in the presented case study."}],"volume":51,"intvolume":"        51","scopus_import":"1","title":"An advanced process-based distributed model for the investigation of rainfall-induced landslides: The effect of process representation and boundary conditions","article_type":"original","date_published":"2015-09-01T00:00:00Z","oa":1,"publication_identifier":{"issn":["0043-1397"],"eissn":["1944-7973"]},"_id":"22512"}]