[{"article_processing_charge":"No","month":"11","oa_version":"Published Version","_id":"9712","citation":{"ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison &#38; for interacting TFBSs.” Public Library of Science, 2015.","mla":"Tugrul, Murat, et al. <i>Other Fitness Models for Comparison &#38; for Interacting TFBSs</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison &#38; for interacting TFBSs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>.","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Other fitness models for comparison &#38; for interacting TFBSs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">https://doi.org/10.1371/journal.pgen.1005639.s001</a>","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison &#38; for Interacting TFBSs.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">https://doi.org/10.1371/journal.pgen.1005639.s001</a>.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison &#38; for interacting TFBSs. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>"},"year":"2015","type":"research_data_reference","title":"Other fitness models for comparison & for interacting TFBSs","related_material":{"record":[{"status":"public","id":"1666","relation":"used_in_publication"}]},"doi":"10.1371/journal.pgen.1005639.s001","publisher":"Public Library of Science","day":"06","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"author":[{"first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","last_name":"Tugrul"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455"}],"date_created":"2021-07-23T12:00:37Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","date_published":"2015-11-06T00:00:00Z","date_updated":"2025-09-23T08:31:14Z"},{"date_created":"2021-07-23T12:05:28Z","department":[{"_id":"CaHe"}],"author":[{"last_name":"Gómez Sicilia","first_name":"Àngel","full_name":"Gómez Sicilia, Àngel"},{"first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K","last_name":"Sikora"},{"full_name":"Cieplak, Marek","first_name":"Marek","last_name":"Cieplak"},{"first_name":"Mariano","full_name":"Carrión Vázquez, Mariano","last_name":"Carrión Vázquez"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2015-10-23T00:00:00Z","status":"public","date_updated":"2025-09-23T07:52:17Z","article_processing_charge":"No","month":"10","_id":"9714","citation":{"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>.","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.","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>.","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>","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>."},"year":"2015","oa_version":"Published Version","publisher":"Public Library of Science ","doi":"10.1371/journal.pcbi.1004541.s001","day":"23","type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","id":"1566","status":"public"}]},"title":"An exploration of the universe of polyglutamine structures - submission to PLOS journals"},{"doi":"10.1371/journal.pone.0126907.s001","day":"18","publisher":"Public Library of Science","title":"Mathematical inference of the results","related_material":{"record":[{"relation":"used_in_publication","id":"1809","status":"public"}]},"type":"research_data_reference","year":"2015","_id":"9715","citation":{"ama":"Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">https://doi.org/10.1371/journal.pone.0126907.s001</a>.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","ieee":"B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015.","mla":"Trubenova, Barbora, et al. <i>Mathematical Inference of the Results</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Mathematical inference of the results. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">https://doi.org/10.1371/journal.pone.0126907.s001</a>","ista":"Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>."},"oa_version":"Published Version","month":"05","article_processing_charge":"No","date_updated":"2025-09-23T09:21:54Z","date_published":"2015-05-18T00:00:00Z","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-07-23T12:11:30Z","author":[{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","first_name":"Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak"},{"first_name":"Reinmar","full_name":"Hager, Reinmar","last_name":"Hager"}],"department":[{"_id":"NiBa"}]},{"date_updated":"2025-09-23T08:43:16Z","status":"public","date_published":"2015-03-23T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"GaTk"}],"author":[{"first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar","last_name":"Friedlander"},{"last_name":"Mayo","full_name":"Mayo, Avraham E.","first_name":"Avraham E."},{"last_name":"Tlusty","full_name":"Tlusty, Tsvi","first_name":"Tsvi"},{"last_name":"Alon","first_name":"Uri","full_name":"Alon, Uri"}],"date_created":"2021-07-26T08:35:23Z","type":"research_data_reference","title":"Supporting information text","related_material":{"record":[{"status":"public","id":"1827","relation":"used_in_publication"}]},"day":"23","doi":"10.1371/journal.pcbi.1004055.s001","publisher":"Public Library of Science","oa_version":"Published Version","_id":"9718","citation":{"ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">10.1371/journal.pcbi.1004055.s001</a>.","mla":"Friedlander, Tamar, et al. <i>Supporting Information Text</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">10.1371/journal.pcbi.1004055.s001</a>.","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., &#38; Alon, U. (2015). Supporting information text. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">https://doi.org/10.1371/journal.pcbi.1004055.s001</a>","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting Information Text.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">https://doi.org/10.1371/journal.pcbi.1004055.s001</a>.","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">10.1371/journal.pcbi.1004055.s001</a>"},"year":"2015","month":"03","article_processing_charge":"No"},{"author":[{"full_name":"Theis, Fabian","first_name":"Fabian","last_name":"Theis"},{"orcid":"0000-0003-1832-8883","last_name":"Ugelvig","full_name":"Ugelvig, Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V"},{"full_name":"Marr, Carsten","first_name":"Carsten","last_name":"Marr"},{"orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"department":[{"_id":"SyCr"}],"date_created":"2021-07-26T09:38:36Z","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","abstract":[{"text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.","lang":"eng"}],"date_published":"2015-12-29T00:00:00Z","date_updated":"2025-09-23T09:44:52Z","article_processing_charge":"No","month":"12","main_file_link":[{"url":"https://doi.org/10.5061/dryad.dj2bf","open_access":"1"}],"oa_version":"Published Version","year":"2015","citation":{"ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming on disease transmission in ant societies. 2015. doi:<a href=\"https://doi.org/10.5061/dryad.dj2bf\">10.5061/dryad.dj2bf</a>","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Dryad, 2015. <a href=\"https://doi.org/10.5061/dryad.dj2bf\">https://doi.org/10.5061/dryad.dj2bf</a>.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects of allogrooming on disease transmission in ant societies, Dryad, <a href=\"https://doi.org/10.5061/dryad.dj2bf\">10.5061/dryad.dj2bf</a>.","apa":"Theis, F., Ugelvig, L. V., Marr, C., &#38; Cremer, S. (2015). Data from: Opposing effects of allogrooming on disease transmission in ant societies. Dryad. <a href=\"https://doi.org/10.5061/dryad.dj2bf\">https://doi.org/10.5061/dryad.dj2bf</a>","mla":"Theis, Fabian, et al. <i>Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies</i>. Dryad, 2015, doi:<a href=\"https://doi.org/10.5061/dryad.dj2bf\">10.5061/dryad.dj2bf</a>.","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects of allogrooming on disease transmission in ant societies.” Dryad, 2015."},"_id":"9721","title":"Data from: Opposing effects of allogrooming on disease transmission in ant societies","related_material":{"record":[{"id":"1830","relation":"used_in_publication","status":"public"}]},"type":"research_data_reference","publisher":"Dryad","doi":"10.5061/dryad.dj2bf","day":"29"},{"type":"research_data_reference","related_material":{"record":[{"id":"1793","relation":"used_in_publication","status":"public"}]},"title":"Root traits computed by DynamicRoots for the maize root shown in fig 2","day":"01","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0127657.s001","oa_version":"Published Version","citation":{"chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">https://doi.org/10.1371/journal.pone.0127657.s001</a>.","ama":"Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots for the maize root shown in fig 2.” Public Library of Science, 2015.","apa":"Symonova, O., Topp, C., &#38; Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">https://doi.org/10.1371/journal.pone.0127657.s001</a>","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots for the maize root shown in fig 2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>.","mla":"Symonova, Olga, et al. <i>Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>.","short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015)."},"_id":"9737","year":"2015","month":"06","article_processing_charge":"No","date_updated":"2025-09-23T08:30:43Z","status":"public","date_published":"2015-06-01T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"author":[{"first_name":"Olga","full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","orcid":"0000-0003-2012-9947"},{"first_name":"Christopher","full_name":"Topp, Christopher","last_name":"Topp"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"}],"date_created":"2021-07-28T06:20:13Z"},{"related_material":{"record":[{"status":"public","id":"2161","relation":"used_in_publication"}]},"title":"Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant","type":"research_data_reference","doi":"10.5061/dryad.7kc79","publisher":"Dryad","day":"09","oa_version":"Published Version","year":"2015","_id":"9742","citation":{"ama":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. 2015. doi:<a href=\"https://doi.org/10.5061/dryad.7kc79\">10.5061/dryad.7kc79</a>","chicago":"Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums, and Sylvia Cremer. “Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Dryad, 2015. <a href=\"https://doi.org/10.5061/dryad.7kc79\">https://doi.org/10.5061/dryad.7kc79</a>.","short":"C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015).","ieee":"C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer, “Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant.” Dryad, 2015.","ista":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2015. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant, Dryad, <a href=\"https://doi.org/10.5061/dryad.7kc79\">10.5061/dryad.7kc79</a>.","apa":"Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., &#38; Cremer, S. (2015). Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Dryad. <a href=\"https://doi.org/10.5061/dryad.7kc79\">https://doi.org/10.5061/dryad.7kc79</a>","mla":"Westhus, Claudia, et al. <i>Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant</i>. Dryad, 2015, doi:<a href=\"https://doi.org/10.5061/dryad.7kc79\">10.5061/dryad.7kc79</a>."},"month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.7kc79"}],"article_processing_charge":"No","date_updated":"2025-09-29T11:42:25Z","status":"public","date_published":"2015-07-09T00:00:00Z","abstract":[{"text":"Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects.","lang":"eng"}],"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Westhus, Claudia","first_name":"Claudia","last_name":"Westhus"},{"orcid":"0000-0003-1832-8883","last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V","first_name":"Line V"},{"first_name":"Edouard","full_name":"Tourdot, Edouard","last_name":"Tourdot"},{"full_name":"Heinze, Jürgen","first_name":"Jürgen","last_name":"Heinze"},{"full_name":"Doums, Claudie","first_name":"Claudie","last_name":"Doums"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"department":[{"_id":"SyCr"}],"date_created":"2021-07-28T08:52:53Z"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"ToBo"}],"author":[{"last_name":"Chevereau","full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","first_name":"Guillaume"},{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","first_name":"Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova"},{"last_name":"Batur","first_name":"Tugce","full_name":"Batur, Tugce"},{"first_name":"Aysegul","full_name":"Guvenek, Aysegul","last_name":"Guvenek"},{"first_name":"Dilay Hazal","full_name":"Ayhan, Dilay Hazal","last_name":"Ayhan"},{"first_name":"Erdal","full_name":"Toprak, Erdal","last_name":"Toprak"},{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"date_created":"2021-08-03T07:05:16Z","date_updated":"2025-09-23T09:58:54Z","status":"public","date_published":"2015-11-18T00:00:00Z","month":"11","article_processing_charge":"No","type":"research_data_reference","title":"Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs","related_material":{"record":[{"relation":"used_in_publication","id":"1619","status":"public"}]},"publisher":"Public Library of Science","day":"18","doi":"10.1371/journal.pbio.1002299.s008","oa_version":"Published Version","citation":{"ieee":"G. Chevereau <i>et al.</i>, “Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs.” Public Library of Science, 2015.","mla":"Chevereau, Guillaume, et al. <i>Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">10.1371/journal.pbio.1002299.s008</a>.","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">10.1371/journal.pbio.1002299.s008</a>.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., &#38; Bollenbach, M. T. (2015). Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">https://doi.org/10.1371/journal.pbio.1002299.s008</a>","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">https://doi.org/10.1371/journal.pbio.1002299.s008</a>.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">10.1371/journal.pbio.1002299.s008</a>"},"_id":"9765","year":"2015"},{"date_created":"2021-08-05T12:55:20Z","department":[{"_id":"NiBa"}],"author":[{"full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X"},{"first_name":"Reinmar","full_name":"Hager, Reinmar","last_name":"Hager"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2015-05-18T00:00:00Z","status":"public","date_updated":"2025-09-23T09:21:54Z","article_processing_charge":"No","month":"05","_id":"9772","citation":{"ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Description of the agent based simulations. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>","mla":"Trubenova, Barbora, et al. <i>Description of the Agent Based Simulations</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>.","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>.","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>"},"year":"2015","oa_version":"Published Version","day":"18","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0126907.s003","type":"research_data_reference","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1809"}]},"title":"Description of the agent based simulations"},{"year":"2015","_id":"9773","citation":{"ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">10.1371/journal.pcbi.1004055.s002</a>.","mla":"Friedlander, Tamar, et al. <i>Evolutionary Simulation Code</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">10.1371/journal.pcbi.1004055.s002</a>.","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., &#38; Alon, U. (2015). Evolutionary simulation code. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">https://doi.org/10.1371/journal.pcbi.1004055.s002</a>","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">https://doi.org/10.1371/journal.pcbi.1004055.s002</a>.","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">10.1371/journal.pcbi.1004055.s002</a>"},"oa_version":"Published Version","day":"23","doi":"10.1371/journal.pcbi.1004055.s002","publisher":"Public Library of Science","title":"Evolutionary simulation code","related_material":{"record":[{"status":"public","id":"1827","relation":"used_in_publication"}]},"type":"research_data_reference","article_processing_charge":"No","month":"03","date_published":"2015-03-23T00:00:00Z","status":"public","date_updated":"2025-09-23T08:43:16Z","date_created":"2021-08-05T12:58:07Z","author":[{"first_name":"Tamar","full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander"},{"full_name":"Mayo, Avraham E.","first_name":"Avraham E.","last_name":"Mayo"},{"first_name":"Tsvi","full_name":"Tlusty, Tsvi","last_name":"Tlusty"},{"full_name":"Alon, Uri","first_name":"Uri","last_name":"Alon"}],"department":[{"_id":"GaTk"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"publication":"Nature Materials","main_file_link":[{"url":"https://arxiv.org/abs/1403.4906","open_access":"1"}],"extern":1,"publist_id":"6419","month":"03","_id":"981","issue":"3","citation":{"chicago":"Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” <i>Nature Materials</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nmat4215\">https://doi.org/10.1038/nmat4215</a>.","ama":"Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. <i>Nature Materials</i>. 2015;14(3):318-324. doi:<a href=\"https://doi.org/10.1038/nmat4215\">10.1038/nmat4215</a>","ieee":"I. Zeljkovic <i>et al.</i>, “Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators,” <i>Nature Materials</i>, vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.","ista":"Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G, Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 14(3), 318–324.","apa":"Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. <i>Nature Materials</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nmat4215\">https://doi.org/10.1038/nmat4215</a>","mla":"Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” <i>Nature Materials</i>, vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:<a href=\"https://doi.org/10.1038/nmat4215\">10.1038/nmat4215</a>.","short":"I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu, G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature Materials 14 (2015) 318–324."},"year":"2015","volume":14,"day":"01","doi":"10.1038/nmat4215","publisher":"Nature Publishing Group","page":"318 - 324","type":"journal_article","title":"Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators","publication_status":"published","date_created":"2018-12-11T11:49:31Z","author":[{"first_name":"Ilija","full_name":"Zeljkovic, Ilija","last_name":"Zeljkovic"},{"first_name":"Yoshinori","full_name":"Okada, Yoshinori","last_name":"Okada"},{"orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Maksym Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"last_name":"Sankar","full_name":"Sankar, Raman","first_name":"Raman"},{"first_name":"Daniel","full_name":"Walkup, Daniel","last_name":"Walkup"},{"last_name":"Zhou","first_name":"Wenwen","full_name":"Zhou, Wenwen"},{"last_name":"Liu","first_name":"Junwei","full_name":"Liu, Junwei"},{"last_name":"Chang","full_name":"Chang, Guoqing","first_name":"Guoqing"},{"first_name":"Yungjui","full_name":"Wang, Yungjui","last_name":"Wang"},{"last_name":"Hasan","full_name":"Hasan, Md Z","first_name":"Md"},{"last_name":"Chou","first_name":"Fangcheng","full_name":"Chou, Fangcheng"},{"last_name":"Lin","full_name":"Lin, Hsin","first_name":"Hsin"},{"last_name":"Bansil","full_name":"Bansil, Arun","first_name":"Arun"},{"first_name":"Liang","full_name":"Fu, Liang","last_name":"Fu"},{"last_name":"Madhavan","first_name":"Vidya","full_name":"Madhavan, Vidya"}],"oa":1,"date_published":"2015-03-01T00:00:00Z","abstract":[{"text":"The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials.","lang":"eng"}],"quality_controlled":0,"intvolume":"        14","status":"public","date_updated":"2021-01-12T08:22:24Z","acknowledgement":"We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny, A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon for help with EDS measurements. V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts Institute of Technology is supported by US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526 (L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University is supported by the US Department of Energy grant number DE-FG02-07ER46352, and benefited from Northeastern University’s Advanced Scientific Computation Center (ASCC), theory support at the Advanced Light Source, Berkeley and the allocation of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work at Princeton University is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004."},{"ddc":["539"],"status":"public","abstract":[{"text":"We prove that nonlinear Gibbs measures can be obtained from the corresponding many-body, grand-canonical, quantum Gibbs states, in a mean-field limit where the temperature T diverges and the interaction strength behaves as 1/T. We proceed by characterizing the interacting Gibbs state as minimizing a functional counting the free-energy relatively to the non-interacting case. We then perform an infinite-dimensional analogue of phase-space semiclassical analysis, using fine properties of the quantum relative entropy, the link between quantum de Finetti measures and upper/lower symbols in a coherent state basis, as well as Berezin-Lieb type inequalities. Our results cover the measure built on the defocusing nonlinear Schrödinger functional on a finite interval, as well as smoother interactions in dimensions d 2.","lang":"eng"}],"scopus_import":1,"date_published":"2015-01-01T00:00:00Z","oa":1,"file":[{"file_id":"4974","file_size":1084254,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"system","date_created":"2018-12-12T10:12:53Z","date_updated":"2020-07-14T12:46:35Z","file_name":"IST-2018-951-v1+1_2015_Thanh-Nam_Derivation_of.pdf","checksum":"a40eb4016717ddc9927154798a4c164a"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Lewin","first_name":"Mathieu","full_name":"Lewin, Mathieu"},{"full_name":"Phan Thanh, Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Nam","last_name":"Phan Thanh"},{"last_name":"Rougerie","first_name":"Nicolas","full_name":"Rougerie, Nicolas"}],"license":"https://creativecommons.org/licenses/by-nd/4.0/","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","title":"Derivation of nonlinear gibbs measures from many-body quantum mechanics","oa_version":"Published Version","year":"2015","_id":"473","month":"01","date_updated":"2021-01-12T08:00:52Z","has_accepted_license":"1","intvolume":"         2","language":[{"iso":"eng"}],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"department":[{"_id":"RoSe"}],"date_created":"2018-12-11T11:46:40Z","file_date_updated":"2020-07-14T12:46:35Z","type":"journal_article","ec_funded":1,"page":"65 - 115","pubrep_id":"951","doi":"10.5802/jep.18","day":"01","publisher":"Ecole Polytechnique","volume":2,"citation":{"ieee":"M. Lewin, P. Nam, and N. Rougerie, “Derivation of nonlinear gibbs measures from many-body quantum mechanics,” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 2. Ecole Polytechnique, pp. 65–115, 2015.","ista":"Lewin M, Nam P, Rougerie N. 2015. Derivation of nonlinear gibbs measures from many-body quantum mechanics. Journal de l’Ecole Polytechnique - Mathematiques. 2, 65–115.","apa":"Lewin, M., Nam, P., &#38; Rougerie, N. (2015). Derivation of nonlinear gibbs measures from many-body quantum mechanics. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique. <a href=\"https://doi.org/10.5802/jep.18\">https://doi.org/10.5802/jep.18</a>","mla":"Lewin, Mathieu, et al. “Derivation of Nonlinear Gibbs Measures from Many-Body Quantum Mechanics.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 2, Ecole Polytechnique, 2015, pp. 65–115, doi:<a href=\"https://doi.org/10.5802/jep.18\">10.5802/jep.18</a>.","short":"M. Lewin, P. Nam, N. Rougerie, Journal de l’Ecole Polytechnique - Mathematiques 2 (2015) 65–115.","chicago":"Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “Derivation of Nonlinear Gibbs Measures from Many-Body Quantum Mechanics.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique, 2015. <a href=\"https://doi.org/10.5802/jep.18\">https://doi.org/10.5802/jep.18</a>.","ama":"Lewin M, Nam P, Rougerie N. Derivation of nonlinear gibbs measures from many-body quantum mechanics. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. 2015;2:65-115. doi:<a href=\"https://doi.org/10.5802/jep.18\">10.5802/jep.18</a>"},"publist_id":"7344","publication":"Journal de l'Ecole Polytechnique - Mathematiques"},{"year":"2015","issue":"15","_id":"477","oa_version":"None","title":"The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells","article_processing_charge":"No","month":"06","date_published":"2015-06-15T00:00:00Z","abstract":[{"text":"Dendritic cells are potent antigen-presenting cells endowed with the unique ability to initiate adaptive immune responses upon inflammation. Inflammatory processes are often associated with an increased production of serotonin, which operates by activating specific receptors. However, the functional role of serotonin receptors in regulation of dendritic cell functions is poorly understood. Here, we demonstrate that expression of serotonin receptor 5-HT7 (5-HT7TR) as well as its downstream effector Cdc42 is upregulated in dendritic cells upon maturation. Although dendritic cell maturation was independent of 5-HT7TR, receptor stimulation affected dendritic cell morphology through Cdc42-mediated signaling. In addition, basal activity of 5-HT7TR was required for the proper expression of the chemokine receptor CCR7, which is a key factor that controls dendritic cell migration. Consistent with this, we observed that 5-HT7TR enhances chemotactic motility of dendritic cells in vitro by modulating their directionality and migration velocity. Accordingly, migration of dendritic cells in murine colon explants was abolished after pharmacological receptor inhibition. Our results indicate that there is a crucial role for 5-HT7TR-Cdc42-mediated signaling in the regulation of dendritic cell morphology and motility, suggesting that 5-HT7TR could be a new target for treatment of a variety of inflammatory and immune disorders.","lang":"eng"}],"scopus_import":"1","status":"public","publication_status":"published","author":[{"first_name":"Katrin","full_name":"Holst, Katrin","last_name":"Holst"},{"last_name":"Guseva","first_name":"Daria","full_name":"Guseva, Daria"},{"last_name":"Schindler","full_name":"Schindler, Susann","first_name":"Susann"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"full_name":"Braun, Armin","first_name":"Armin","last_name":"Braun"},{"last_name":"Chopra","full_name":"Chopra, Himpriya","first_name":"Himpriya"},{"last_name":"Pabst","first_name":"Oliver","full_name":"Pabst, Oliver"},{"last_name":"Ponimaskin","full_name":"Ponimaskin, Evgeni","first_name":"Evgeni"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"citation":{"chicago":"Holst, Katrin, Daria Guseva, Susann Schindler, Michael K Sixt, Armin Braun, Himpriya Chopra, Oliver Pabst, and Evgeni Ponimaskin. “The Serotonin Receptor 5-HT7R Regulates the Morphology and Migratory Properties of Dendritic Cells.” <i>Journal of Cell Science</i>. Company of Biologists, 2015. <a href=\"https://doi.org/10.1242/jcs.167999\">https://doi.org/10.1242/jcs.167999</a>.","ama":"Holst K, Guseva D, Schindler S, et al. The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells. <i>Journal of Cell Science</i>. 2015;128(15):2866-2880. doi:<a href=\"https://doi.org/10.1242/jcs.167999\">10.1242/jcs.167999</a>","ieee":"K. Holst <i>et al.</i>, “The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells,” <i>Journal of Cell Science</i>, vol. 128, no. 15. Company of Biologists, pp. 2866–2880, 2015.","apa":"Holst, K., Guseva, D., Schindler, S., Sixt, M. K., Braun, A., Chopra, H., … Ponimaskin, E. (2015). The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.167999\">https://doi.org/10.1242/jcs.167999</a>","ista":"Holst K, Guseva D, Schindler S, Sixt MK, Braun A, Chopra H, Pabst O, Ponimaskin E. 2015. The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells. Journal of Cell Science. 128(15), 2866–2880.","mla":"Holst, Katrin, et al. “The Serotonin Receptor 5-HT7R Regulates the Morphology and Migratory Properties of Dendritic Cells.” <i>Journal of Cell Science</i>, vol. 128, no. 15, Company of Biologists, 2015, pp. 2866–80, doi:<a href=\"https://doi.org/10.1242/jcs.167999\">10.1242/jcs.167999</a>.","short":"K. Holst, D. Guseva, S. Schindler, M.K. Sixt, A. Braun, H. Chopra, O. Pabst, E. Ponimaskin, Journal of Cell Science 128 (2015) 2866–2880."},"volume":128,"page":"2866 - 2880","day":"15","publisher":"Company of Biologists","doi":"10.1242/jcs.167999","type":"journal_article","publication":"Journal of Cell Science","publist_id":"7343","intvolume":"       128","language":[{"iso":"eng"}],"quality_controlled":"1","date_updated":"2025-09-23T14:16:38Z","external_id":{"isi":["000359782100013"]},"date_created":"2018-12-11T11:46:41Z","department":[{"_id":"MiSi"}]},{"arxiv":1,"date_published":"2015-03-24T00:00:00Z","abstract":[{"text":"We consider two-player games played on weighted directed graphs with mean-payoff and total-payoff objectives, two classical quantitative objectives. While for single-dimensional games the complexity and memory bounds for both objectives coincide, we show that in contrast to multi-dimensional mean-payoff games that are known to be coNP-complete, multi-dimensional total-payoff games are undecidable. We introduce conservative approximations of these objectives, where the payoff is considered over a local finite window sliding along a play, instead of the whole play. For single dimension, we show that (i) if the window size is polynomial, deciding the winner takes polynomial time, and (ii) the existence of a bounded window can be decided in NP ∩ coNP, and is at least as hard as solving mean-payoff games. For multiple dimensions, we show that (i) the problem with fixed window size is EXPTIME-complete, and (ii) there is no primitive-recursive algorithm to decide the existence of a bounded window.","lang":"eng"}],"scopus_import":"1","status":"public","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"publication_status":"published","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"last_name":"Randour","full_name":"Randour, Mickael","first_name":"Mickael"},{"first_name":"Jean","full_name":"Raskin, Jean","last_name":"Raskin"}],"title":"Looking at mean-payoff and total-payoff through windows","issue":"6","_id":"523","year":"2015","oa_version":"Preprint","month":"03","article_processing_charge":"No","date_updated":"2025-09-23T09:29:55Z","external_id":{"arxiv":["1302.4248"],"isi":["000355664900003"]},"quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"       242","date_created":"2018-12-11T11:46:57Z","department":[{"_id":"KrCh"}],"day":"24","doi":"10.1016/j.ic.2015.03.010","publisher":"Elsevier","page":"25 - 52","type":"journal_article","ec_funded":1,"related_material":{"record":[{"status":"public","id":"2279","relation":"earlier_version"}]},"citation":{"short":"K. Chatterjee, L. Doyen, M. Randour, J. Raskin, Information and Computation 242 (2015) 25–52.","ista":"Chatterjee K, Doyen L, Randour M, Raskin J. 2015. Looking at mean-payoff and total-payoff through windows. Information and Computation. 242(6), 25–52.","mla":"Chatterjee, Krishnendu, et al. “Looking at Mean-Payoff and Total-Payoff through Windows.” <i>Information and Computation</i>, vol. 242, no. 6, Elsevier, 2015, pp. 25–52, doi:<a href=\"https://doi.org/10.1016/j.ic.2015.03.010\">10.1016/j.ic.2015.03.010</a>.","apa":"Chatterjee, K., Doyen, L., Randour, M., &#38; Raskin, J. (2015). Looking at mean-payoff and total-payoff through windows. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2015.03.010\">https://doi.org/10.1016/j.ic.2015.03.010</a>","ieee":"K. Chatterjee, L. Doyen, M. Randour, and J. Raskin, “Looking at mean-payoff and total-payoff through windows,” <i>Information and Computation</i>, vol. 242, no. 6. Elsevier, pp. 25–52, 2015.","ama":"Chatterjee K, Doyen L, Randour M, Raskin J. Looking at mean-payoff and total-payoff through windows. <i>Information and Computation</i>. 2015;242(6):25-52. doi:<a href=\"https://doi.org/10.1016/j.ic.2015.03.010\">10.1016/j.ic.2015.03.010</a>","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Mickael Randour, and Jean Raskin. “Looking at Mean-Payoff and Total-Payoff through Windows.” <i>Information and Computation</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ic.2015.03.010\">https://doi.org/10.1016/j.ic.2015.03.010</a>."},"volume":242,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1302.4248"}],"publist_id":"7296","publication":"Information and Computation"},{"arxiv":1,"scopus_import":"1","date_published":"2015-10-11T00:00:00Z","abstract":[{"text":"We consider concurrent games played by two players on a finite-state graph, where in every round the players simultaneously choose a move, and the current state along with the joint moves determine the successor state. We study the most fundamental objective for concurrent games, namely, mean-payoff or limit-average objective, where a reward is associated to each transition, and the goal of player 1 is to maximize the long-run average of the rewards, and the objective of player 2 is strictly the opposite (i.e., the games are zero-sum). The path constraint for player 1 could be qualitative, i.e., the mean-payoff is the maximal reward, or arbitrarily close to it; or quantitative, i.e., a given threshold between the minimal and maximal reward. We consider the computation of the almost-sure (resp. positive) winning sets, where player 1 can ensure that the path constraint is satisfied with probability 1 (resp. positive probability). Almost-sure winning with qualitative constraint exactly corresponds to the question of whether there exists a strategy to ensure that the payoff is the maximal reward of the game. Our main results for qualitative path constraints are as follows: (1) we establish qualitative determinacy results that show that for every state either player 1 has a strategy to ensure almost-sure (resp. positive) winning against all player-2 strategies, or player 2 has a spoiling strategy to falsify almost-sure (resp. positive) winning against all player-1 strategies; (2) we present optimal strategy complexity results that precisely characterize the classes of strategies required for almost-sure and positive winning for both players; and (3) we present quadratic time algorithms to compute the almost-sure and the positive winning sets, matching the best known bound of the algorithms for much simpler problems (such as reachability objectives). For quantitative constraints we show that a polynomial time solution for the almost-sure or the positive winning set would imply a solution to a long-standing open problem (of solving the value problem of turn-based deterministic mean-payoff games) that is not known to be solvable in polynomial time.","lang":"eng"}],"status":"public","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"publication_status":"published","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus"}],"title":"Qualitative analysis of concurrent mean payoff games","_id":"524","issue":"6","year":"2015","oa_version":"Preprint","month":"10","article_processing_charge":"No","date_updated":"2025-09-23T09:56:28Z","corr_author":"1","external_id":{"isi":["000355664900002"],"arxiv":["1409.5306"]},"quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"       242","date_created":"2018-12-11T11:46:57Z","department":[{"_id":"KrCh"}],"day":"11","doi":"10.1016/j.ic.2015.03.009","publisher":"Elsevier","page":"2 - 24","type":"journal_article","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5403"}]},"citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, Information and Computation 242 (2015) 2–24.","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2015). Qualitative analysis of concurrent mean payoff games. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2015.03.009\">https://doi.org/10.1016/j.ic.2015.03.009</a>","ista":"Chatterjee K, Ibsen-Jensen R. 2015. Qualitative analysis of concurrent mean payoff games. Information and Computation. 242(6), 2–24.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Qualitative Analysis of Concurrent Mean Payoff Games.” <i>Information and Computation</i>, vol. 242, no. 6, Elsevier, 2015, pp. 2–24, doi:<a href=\"https://doi.org/10.1016/j.ic.2015.03.009\">10.1016/j.ic.2015.03.009</a>.","ieee":"K. Chatterjee and R. Ibsen-Jensen, “Qualitative analysis of concurrent mean payoff games,” <i>Information and Computation</i>, vol. 242, no. 6. Elsevier, pp. 2–24, 2015.","ama":"Chatterjee K, Ibsen-Jensen R. Qualitative analysis of concurrent mean payoff games. <i>Information and Computation</i>. 2015;242(6):2-24. doi:<a href=\"https://doi.org/10.1016/j.ic.2015.03.009\">10.1016/j.ic.2015.03.009</a>","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Qualitative Analysis of Concurrent Mean Payoff Games.” <i>Information and Computation</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ic.2015.03.009\">https://doi.org/10.1016/j.ic.2015.03.009</a>."},"volume":242,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1409.5306"}],"publist_id":"7295","publication":"Information and Computation"},{"article_processing_charge":"No","month":"10","_id":"532","issue":"3","year":"2015","oa_version":"None","title":"EIN2-directed translational regulation of ethylene signaling in arabidopsis","publication_status":"published","author":[{"last_name":"Li","first_name":"Wenyang","full_name":"Li, Wenyang"},{"full_name":"Ma, Mengdi","first_name":"Mengdi","last_name":"Ma"},{"full_name":"Feng, Ying","first_name":"Ying","last_name":"Feng"},{"last_name":"Li","orcid":"0000-0001-5039-9660","first_name":"Hongjiang","full_name":"Li, Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wang","full_name":"Wang, Yichuan","first_name":"Yichuan"},{"full_name":"Ma, Yutong","first_name":"Yutong","last_name":"Ma"},{"first_name":"Mingzhe","full_name":"Li, Mingzhe","last_name":"Li"},{"full_name":"An, Fengying","first_name":"Fengying","last_name":"An"},{"first_name":"Hongwei","full_name":"Guo, Hongwei","last_name":"Guo"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","date_published":"2015-10-22T00:00:00Z","abstract":[{"lang":"eng","text":"Ethylene is a gaseous phytohormone that plays vital roles in plant growth and development. Previous studies uncovered EIN2 as an essential signal transducer linking ethylene perception on ER to transcriptional regulation in the nucleus through a “cleave and shuttle” model. In this study, we report another mechanism of EIN2-mediated ethylene signaling, whereby EIN2 imposes the translational repression of EBF1 and EBF2 mRNA. We find that the EBF1/2 3′ UTRs mediate EIN2-directed translational repression and identify multiple poly-uridylates (PolyU) motifs as functional cis elements of 3′ UTRs. Furthermore, we demonstrate that ethylene induces EIN2 to associate with 3′ UTRs and target EBF1/2 mRNA to cytoplasmic processing-body (P-body) through interacting with multiple P-body factors, including EIN5 and PABs. Our study illustrates translational regulation as a key step in ethylene signaling and presents mRNA 3′ UTR functioning as a “signal transducer” to sense and relay cellular signaling in plants."}],"status":"public","publication":"Cell","publist_id":"7285","citation":{"short":"W. Li, M. Ma, Y. Feng, H. Li, Y. Wang, Y. Ma, M. Li, F. An, H. Guo, Cell 163 (2015) 670–683.","ista":"Li W, Ma M, Feng Y, Li H, Wang Y, Ma Y, Li M, An F, Guo H. 2015. EIN2-directed translational regulation of ethylene signaling in arabidopsis. Cell. 163(3), 670–683.","apa":"Li, W., Ma, M., Feng, Y., Li, H., Wang, Y., Ma, Y., … Guo, H. (2015). EIN2-directed translational regulation of ethylene signaling in arabidopsis. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2015.09.037\">https://doi.org/10.1016/j.cell.2015.09.037</a>","mla":"Li, Wenyang, et al. “EIN2-Directed Translational Regulation of Ethylene Signaling in Arabidopsis.” <i>Cell</i>, vol. 163, no. 3, Cell Press, 2015, pp. 670–83, doi:<a href=\"https://doi.org/10.1016/j.cell.2015.09.037\">10.1016/j.cell.2015.09.037</a>.","ieee":"W. Li <i>et al.</i>, “EIN2-directed translational regulation of ethylene signaling in arabidopsis,” <i>Cell</i>, vol. 163, no. 3. Cell Press, pp. 670–683, 2015.","ama":"Li W, Ma M, Feng Y, et al. EIN2-directed translational regulation of ethylene signaling in arabidopsis. <i>Cell</i>. 2015;163(3):670-683. doi:<a href=\"https://doi.org/10.1016/j.cell.2015.09.037\">10.1016/j.cell.2015.09.037</a>","chicago":"Li, Wenyang, Mengdi Ma, Ying Feng, Hongjiang Li, Yichuan Wang, Yutong Ma, Mingzhe Li, Fengying An, and Hongwei Guo. “EIN2-Directed Translational Regulation of Ethylene Signaling in Arabidopsis.” <i>Cell</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cell.2015.09.037\">https://doi.org/10.1016/j.cell.2015.09.037</a>."},"volume":163,"doi":"10.1016/j.cell.2015.09.037","day":"22","publisher":"Cell Press","page":"670 - 683","type":"journal_article","date_created":"2018-12-11T11:47:00Z","department":[{"_id":"JiFr"}],"quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"       163","date_updated":"2025-09-23T08:40:43Z","external_id":{"isi":["000364828900020"]}},{"alternative_title":["IST Austria Technical Report"],"month":"01","_id":"5429","citation":{"chicago":"Chatterjee, Krishnendu, Zuzana Komarkova, and Jan Kretinsky. <i>Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-318-v1-1\">https://doi.org/10.15479/AT:IST-2015-318-v1-1</a>.","ama":"Chatterjee K, Komarkova Z, Kretinsky J. <i>Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-318-v1-1\">10.15479/AT:IST-2015-318-v1-1</a>","mla":"Chatterjee, Krishnendu, et al. <i>Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-318-v1-1\">10.15479/AT:IST-2015-318-v1-1</a>.","apa":"Chatterjee, K., Komarkova, Z., &#38; Kretinsky, J. (2015). <i>Unifying two views on multiple mean-payoff objectives in Markov decision processes</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-318-v1-1\">https://doi.org/10.15479/AT:IST-2015-318-v1-1</a>","ista":"Chatterjee K, Komarkova Z, Kretinsky J. 2015. Unifying two views on multiple mean-payoff objectives in Markov decision processes, IST Austria, 41p.","ieee":"K. Chatterjee, Z. Komarkova, and J. Kretinsky, <i>Unifying two views on multiple mean-payoff objectives in Markov decision processes</i>. IST Austria, 2015.","short":"K. Chatterjee, Z. Komarkova, J. Kretinsky, Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes, IST Austria, 2015."},"year":"2015","oa_version":"Published Version","day":"12","publisher":"IST Austria","doi":"10.15479/AT:IST-2015-318-v1-1","pubrep_id":"318","page":"41","type":"technical_report","related_material":{"record":[{"status":"public","id":"5435","relation":"later_version"},{"id":"466","relation":"later_version","status":"public"},{"relation":"later_version","id":"1657","status":"public"}]},"title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","date_created":"2018-12-12T11:39:17Z","file_date_updated":"2020-07-14T12:46:52Z","publication_status":"published","department":[{"_id":"KrCh"}],"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"full_name":"Komarkova, Zuzana","first_name":"Zuzana","last_name":"Komarkova"},{"last_name":"Kretinsky","orcid":"0000-0002-8122-2881","first_name":"Jan","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T11:54:11Z","creator":"system","file_id":"5533","relation":"main_file","file_size":689863,"checksum":"e4869a584567c506349abda9c8ec7db3","date_updated":"2020-07-14T12:46:52Z","file_name":"IST-2015-318-v1+1_main.pdf"}],"oa":1,"date_published":"2015-01-12T00:00:00Z","language":[{"iso":"eng"}],"abstract":[{"text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. \r\nThere have been two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector.  \r\nWe consider the problem where the goal is to optimize the expectation under the constraint that the satisfaction semantics is ensured, and thus consider a generalization that unifies the existing semantics.\r\nOur problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensures certain probabilistic guarantee).\r\nOur main results are algorithms for the decision problem which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions.\r\nFinally, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem.","lang":"eng"}],"status":"public","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","date_updated":"2025-09-29T11:00:42Z","ddc":["004"]},{"ddc":["000"],"has_accepted_license":"1","date_updated":"2025-09-23T08:47:23Z","publication_identifier":{"issn":["2664-1690"]},"status":"public","language":[{"iso":"eng"}],"abstract":[{"text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean- payoff property, the ratio property, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m = O ( n ) ) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a mul- tiplicative factor of ∊ in time O ( n · log( n/∊ )) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O ( n · log( | a · b · n | )) = O ( n · log( n · W )) , when the output is a b , as compared to the previously best known algorithm with running time O ( n 2 · log( n · W )) . Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O ( n 2 · m ) time and the associated decision problem can be solved in O ( n · m ) time, improving the previous known O ( n 3 · m · log( n · W )) and O ( n 2 · m ) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O ( n · log n ) time, improving the previous known O ( n 4 · log( n · W )) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks.","lang":"eng"}],"date_published":"2015-02-10T00:00:00Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2015-319-v1+1_long.pdf","date_updated":"2020-07-14T12:46:52Z","checksum":"62c6ea01e342553dcafb88a070fb1ad5","file_id":"5482","relation":"main_file","file_size":1089651,"content_type":"application/pdf","date_created":"2018-12-12T11:53:21Z","creator":"system","access_level":"open_access"}],"department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","file_date_updated":"2020-07-14T12:46:52Z","date_created":"2018-12-12T11:39:17Z","type":"technical_report","title":"Faster algorithms for quantitative verification in constant treewidth graphs","related_material":{"record":[{"status":"public","relation":"later_version","id":"5437"},{"id":"1607","relation":"later_version","status":"public"}]},"day":"10","doi":"10.15479/AT:IST-2015-319-v1-1","publisher":"IST Austria","page":"31","pubrep_id":"319","oa_version":"Published Version","citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. <i>Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-319-v1-1\">https://doi.org/10.15479/AT:IST-2015-319-v1-1</a>.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. <i>Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-319-v1-1\">10.15479/AT:IST-2015-319-v1-1</a>","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2015). <i>Faster algorithms for quantitative verification in constant treewidth graphs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-319-v1-1\">https://doi.org/10.15479/AT:IST-2015-319-v1-1</a>","mla":"Chatterjee, Krishnendu, et al. <i>Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-319-v1-1\">10.15479/AT:IST-2015-319-v1-1</a>.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs, IST Austria, 31p.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, <i>Faster algorithms for quantitative verification in constant treewidth graphs</i>. IST Austria, 2015.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs, IST Austria, 2015."},"_id":"5430","year":"2015","month":"02","alternative_title":["IST Austria Technical Report"]},{"has_accepted_license":"1","date_updated":"2021-01-12T08:02:13Z","ddc":["005","519"],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We consider finite-state concurrent stochastic games, played by k>=2 players for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. We consider reachability objectives that given a target set of states require that some state in the target set is visited, and the dual safety objectives that given a target set require that only states in the target set are visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed.\r\n\r\n Our main results are as follows: We show that in two-player zero-sum concurrent stochastic games (with reachability objective for one player and the complementary safety objective for the other player): (i) the optimal bound on the patience of optimal and epsilon-optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. In general we study the class of non-zero-sum games admitting epsilon-Nash equilibria. We show that if there is at least one player with reachability objective, then doubly-exponential patience is needed in general for epsilon-Nash equilibrium strategies, whereas in contrast if all players have safety objectives, then the optimal bound on patience for epsilon-Nash equilibrium strategies is only exponential."}],"date_published":"2015-02-19T00:00:00Z","publication_identifier":{"issn":["2664-1690"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":661015,"relation":"main_file","file_id":"5491","access_level":"open_access","creator":"system","date_created":"2018-12-12T11:53:31Z","content_type":"application/pdf","date_updated":"2020-07-14T12:46:53Z","file_name":"IST-2015-322-v1+1_safetygames.pdf","checksum":"bfb858262c30445b8e472c40069178a2"}],"oa":1,"file_date_updated":"2020-07-14T12:46:53Z","publication_status":"published","date_created":"2018-12-12T11:39:17Z","department":[{"_id":"KrCh"}],"author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus"},{"last_name":"Hansen","full_name":"Hansen, Kristoffer","first_name":"Kristoffer"}],"doi":"10.15479/AT:IST-2015-322-v1-1","day":"19","publisher":"IST Austria","page":"25","pubrep_id":"322","type":"technical_report","title":"The patience of concurrent stochastic games with safety and reachability objectives","citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Hansen K. <i>The Patience of Concurrent Stochastic Games with Safety and Reachability Objectives</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-322-v1-1\">10.15479/AT:IST-2015-322-v1-1</a>","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Kristoffer Hansen. <i>The Patience of Concurrent Stochastic Games with Safety and Reachability Objectives</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-322-v1-1\">https://doi.org/10.15479/AT:IST-2015-322-v1-1</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, K. Hansen, The Patience of Concurrent Stochastic Games with Safety and Reachability Objectives, IST Austria, 2015.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and K. Hansen, <i>The patience of concurrent stochastic games with safety and reachability objectives</i>. IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. <i>The Patience of Concurrent Stochastic Games with Safety and Reachability Objectives</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-322-v1-1\">10.15479/AT:IST-2015-322-v1-1</a>.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Hansen, K. (2015). <i>The patience of concurrent stochastic games with safety and reachability objectives</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-322-v1-1\">https://doi.org/10.15479/AT:IST-2015-322-v1-1</a>","ista":"Chatterjee K, Ibsen-Jensen R, Hansen K. 2015. The patience of concurrent stochastic games with safety and reachability objectives, IST Austria, 25p."},"_id":"5431","year":"2015","oa_version":"Published Version","month":"02","alternative_title":["IST Austria Technical Report"]},{"publication_status":"published","file_date_updated":"2020-07-14T12:46:53Z","date_created":"2018-12-12T11:39:18Z","department":[{"_id":"KrCh"}],"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"546c1b291d545e7b24aaaf4199dac671","file_name":"IST-2015-323-v1+1_main.pdf","date_updated":"2020-07-14T12:46:53Z","content_type":"application/pdf","date_created":"2018-12-12T11:53:57Z","creator":"system","access_level":"open_access","file_id":"5519","file_size":576347,"relation":"main_file"}],"oa":1,"language":[{"iso":"eng"}],"date_published":"2015-02-19T00:00:00Z","abstract":[{"lang":"eng","text":"Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom in the context of evolution.The replacement graph specifies who competes with whom for reproduction. \r\nThe vertices of the two graphs are the same, and each vertex corresponds to an individual of the population. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. \r\nOur main results are:\r\n(1) We show that the qualitative question is NP-complete and the quantitative approximation question is #P-hard in the special case when the interaction and the replacement graphs coincide and even with the restriction that the resident individuals do not reproduce (which corresponds to an invading population taking over an empty structure).\r\n(2) We show that in general the qualitative question is PSPACE-complete and the quantitative approximation question is PSPACE-hard and can be solved in exponential time.\r\n"}],"status":"public","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","date_updated":"2023-02-23T12:26:33Z","ddc":["005","576"],"alternative_title":["IST Austria Technical Report"],"month":"02","_id":"5432","citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary Games on Graphs, IST Austria, 2015.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, <i>The complexity of evolutionary games on graphs</i>. IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. <i>The Complexity of Evolutionary Games on Graphs</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-323-v1-1\">10.15479/AT:IST-2015-323-v1-1</a>.","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary games on graphs, IST Austria, 29p.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Nowak, M. (2015). <i>The complexity of evolutionary games on graphs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-323-v1-1\">https://doi.org/10.15479/AT:IST-2015-323-v1-1</a>","ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. <i>The Complexity of Evolutionary Games on Graphs</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-323-v1-1\">10.15479/AT:IST-2015-323-v1-1</a>","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. <i>The Complexity of Evolutionary Games on Graphs</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-323-v1-1\">https://doi.org/10.15479/AT:IST-2015-323-v1-1</a>."},"year":"2015","oa_version":"Published Version","doi":"10.15479/AT:IST-2015-323-v1-1","day":"19","publisher":"IST Austria","pubrep_id":"323","page":"29","type":"technical_report","related_material":{"record":[{"id":"5421","relation":"earlier_version","status":"public"},{"id":"5440","relation":"later_version","status":"public"}]},"title":"The complexity of evolutionary games on graphs"}]