[{"department":[{"_id":"MaHe"}],"citation":{"mla":"Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” <i>Cell</i>, vol. 154, no. 5, Elsevier, 2013, pp. 971–82, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">10.1016/j.cell.2013.07.037</a>.","short":"B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates, M. Hetzer, Cell 154 (2013) 971–982.","apa":"Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates, J. R., &#38; Hetzer, M. (2013). Identification of long-lived proteins reveals exceptional stability of essential cellular structures. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">https://doi.org/10.1016/j.cell.2013.07.037</a>","ieee":"B. H. Toyama <i>et al.</i>, “Identification of long-lived proteins reveals exceptional stability of essential cellular structures,” <i>Cell</i>, vol. 154, no. 5. Elsevier, pp. 971–982, 2013.","chicago":"Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris, Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">https://doi.org/10.1016/j.cell.2013.07.037</a>.","ama":"Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. <i>Cell</i>. 2013;154(5):971-982. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">10.1016/j.cell.2013.07.037</a>","ista":"Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. 154(5), 971–982."},"year":"2013","publisher":"Elsevier","volume":154,"OA_place":"publisher","doi":"10.1016/j.cell.2013.07.037","date_updated":"2026-07-28T10:15:26Z","pmid":1,"external_id":{"pmid":["23993091"]},"scopus_import":"1","publication_identifier":{"issn":["0092-8674"]},"das_tickbox":"1","issue":"5","fulldoi":"https://doi.org/10.1016/j.cell.2013.07.037","publication":"Cell","author":[{"last_name":"Toyama","full_name":"Toyama, Brandon H.","first_name":"Brandon H."},{"last_name":"Savas","full_name":"Savas, Jeffrey N.","first_name":"Jeffrey N."},{"last_name":"Park","full_name":"Park, Sung Kyu","first_name":"Sung Kyu"},{"first_name":"Michael S.","full_name":"Harris, Michael S.","last_name":"Harris"},{"last_name":"Ingolia","first_name":"Nicholas T.","full_name":"Ingolia, Nicholas T."},{"last_name":"Yates","first_name":"John R.","full_name":"Yates, John R."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X","first_name":"Martin W","full_name":"HETZER, Martin W"}],"title":"Identification of long-lived proteins reveals exceptional stability of essential cellular structures","page":"971-982","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","status":"public","abstract":[{"text":"Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process.","lang":"eng"}],"publication_status":"published","date_published":"2013-08-29T00:00:00Z","extern":"1","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.07.037","open_access":"1"}],"month":"08","intvolume":"       154","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-04-07T07:51:08Z","keyword":["General Biochemistry","Genetics and Molecular Biology"],"OA_type":"free access","oa":1,"day":"29","_id":"11087","type":"journal_article","quality_controlled":"1"},{"oa_version":"Submitted Version","date_published":"2013-01-14T00:00:00Z","status":"public","has_accepted_license":"1","publication_status":"published","abstract":[{"text":"We describe new extensions of the Vampire theorem prover for computing tree interpolants. These extensions generalize Craig interpolation in Vampire, and can also be used to derive sequence interpolants. We evaluated our implementation on a large number of examples over the theory of linear integer arithmetic and integer-indexed arrays, with and without quantifiers. When compared to other methods, our experiments show that some examples could only be solved by our implementation.","lang":"eng"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publist_id":"4724","alternative_title":["LNCS"],"quality_controlled":"1","_id":"2237","type":"conference","day":"14","oa":1,"series_title":"Lecture Notes in Computer Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:56:29Z","intvolume":"      8312","month":"01","scopus_import":"1","date_updated":"2026-07-28T10:10:38Z","doi":"10.1007/978-3-642-45221-5_13","publisher":"Springer","volume":8312,"year":"2013","citation":{"mla":"Blanc, Régis, et al. <i>Tree Interpolation in Vampire</i>. Vol. 8312, Springer, 2013, pp. 173–81, doi:<a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">10.1007/978-3-642-45221-5_13</a>.","apa":"Blanc, R., Gupta, A., Kovács, L., &#38; Kragl, B. (2013). Tree interpolation in Vampire. Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Stellenbosch, South Africa: Springer. <a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">https://doi.org/10.1007/978-3-642-45221-5_13</a>","short":"R. Blanc, A. Gupta, L. Kovács, B. Kragl, 8312 (2013) 173–181.","chicago":"Blanc, Régis, Ashutosh Gupta, Laura Kovács, and Bernhard Kragl. “Tree Interpolation in Vampire.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">https://doi.org/10.1007/978-3-642-45221-5_13</a>.","ama":"Blanc R, Gupta A, Kovács L, Kragl B. Tree interpolation in Vampire. 2013;8312:173-181. doi:<a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">10.1007/978-3-642-45221-5_13</a>","ista":"Blanc R, Gupta A, Kovács L, Kragl B. 2013. Tree interpolation in Vampire. 8312, 173–181.","ieee":"R. Blanc, A. Gupta, L. Kovács, and B. Kragl, “Tree interpolation in Vampire,” vol. 8312. Springer, pp. 173–181, 2013."},"department":[{"_id":"ToHe"}],"page":"173 - 181","title":"Tree interpolation in Vampire","author":[{"last_name":"Blanc","full_name":"Blanc, Régis","first_name":"Régis"},{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kovács","first_name":"Laura","full_name":"Kovács, Laura"},{"first_name":"Bernhard","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"fulldoi":"https://doi.org/10.1007/978-3-642-45221-5_13","conference":{"location":"Stellenbosch, South Africa","start_date":"2013-12-14","name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning","end_date":"2013-12-19"},"file":[{"file_size":279206,"date_created":"2020-05-15T11:10:40Z","file_name":"2013_LPAR_Blanc.pdf","file_id":"7858","relation":"main_file","creator":"dernst","date_updated":"2020-07-14T12:45:34Z","content_type":"application/pdf","checksum":"9cebaafca032e6769d273f393305c705","access_level":"open_access"}],"acknowledgement":"This research was partly supported by the Austrian National Research Network RiSE (FWF grants S11402-N23 and S11410-N23) and the WWTF PROSEED grant (ICT C-050).","ddc":["000"],"file_date_updated":"2020-07-14T12:45:34Z","das_tickbox":"1"},{"doi_confirm":"1","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"citation":{"ieee":"P. Campinho, “Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading,” Institute of Science and Technology Austria, 2013.","chicago":"Campinho, Pedro. “Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading.” Institute of Science and Technology Austria, 2013.","ama":"Campinho P. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. 2013.","ista":"Campinho P. 2013. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. Institute of Science and Technology Austria.","mla":"Campinho, Pedro. <i>Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading</i>. Institute of Science and Technology Austria, 2013.","apa":"Campinho, P. (2013). <i>Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading</i>. Institute of Science and Technology Austria.","short":"P. Campinho, Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading, Institute of Science and Technology Austria, 2013."},"year":"2013","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"OA_place":"publisher","language":[{"iso":"eng"}],"publist_id":"5801","date_published":"2013-10-01T00:00:00Z","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Epithelial spreading is a critical part of various developmental and wound repair processes. Here we use zebrafish epiboly as a model system to study the cellular and molecular mechanisms underlying the spreading of epithelial sheets. During zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the embryo to eventually cover the entire yolk cell by the end of gastrulation. The EVL leading edge is anchored through tight junctions to the yolk syncytial layer (YSL), where directly adjacent to the EVL margin a contractile actomyosin ring is formed that is thought to drive EVL epiboly. The prevalent view in the field was that the contractile ring exerts a pulling force on the EVL margin, which pulls the EVL towards the vegetal pole. However, how this force is generated and how it affects EVL morphology still remains elusive. Moreover, the cellular mechanisms mediating the increase in EVL surface area, while maintaining tissue integrity and function are still unclear. Here we show that the YSL actomyosin ring pulls on the EVL margin by two distinct force-generating mechanisms. One mechanism is based on contraction of the ring around its circumference, as previously proposed. The second mechanism is based on actomyosin retrogade flows, generating force through resistance against the substrate. The latter can function at any epiboly stage even in situations where the contraction-based mechanism is unproductive. Additionally, we demonstrate that during epiboly the EVL is subjected to anisotropic tension, which guides the orientation of EVL cell division along the main axis (animal-vegetal) of tension. The influence of tension in cell division orientation involves cell elongation and requires myosin-2 activity for proper spindle alignment. Strikingly, we reveal that tension-oriented cell divisions release anisotropic tension within the EVL and that in the absence of such divisions, EVL cells undergo ectopic fusions. We conclude that forces applied to the EVL by the action of the YSL actomyosin ring generate a tension anisotropy in the EVL that orients cell divisions, which in turn limit tissue tension increase thereby facilitating tissue spreading."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"article_processing_charge":"No","oa_version":"None","date_updated":"2026-07-29T10:00:09Z","date_created":"2018-12-11T11:51:50Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"]},"month":"10","author":[{"last_name":"Campinho","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","full_name":"Campinho, Pedro","first_name":"Pedro","orcid":"0000-0002-8526-5416"}],"page":"123","corr_author":"1","title":"Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading","supervisor":[{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"type":"dissertation","_id":"1406","day":"01"},{"external_id":{"isi":["000327944200005"]},"date_updated":"2026-07-29T10:07:18Z","doi":"10.1038/ncb2869","scopus_import":"1","year":"2013","citation":{"mla":"Campinho, Pedro, et al. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” <i>Nature Cell Biology</i>, vol. 15, Nature Publishing Group, 2013, pp. 1405–14, doi:<a href=\"https://doi.org/10.1038/ncb2869\">10.1038/ncb2869</a>.","short":"P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, C.-P.J. Heisenberg, Nature Cell Biology 15 (2013) 1405–1414.","apa":"Campinho, P., Behrndt, M., Ranft, J., Risler, T., Minc, N., &#38; Heisenberg, C.-P. J. (2013). Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb2869\">https://doi.org/10.1038/ncb2869</a>","ieee":"P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, and C.-P. J. Heisenberg, “Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly,” <i>Nature Cell Biology</i>, vol. 15. Nature Publishing Group, pp. 1405–1414, 2013.","chicago":"Campinho, Pedro, Martin Behrndt, Jonas Ranft, Thomas Risler, Nicolas Minc, and Carl-Philipp J Heisenberg. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/ncb2869\">https://doi.org/10.1038/ncb2869</a>.","ama":"Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. <i>Nature Cell Biology</i>. 2013;15:1405-1414. doi:<a href=\"https://doi.org/10.1038/ncb2869\">10.1038/ncb2869</a>","ista":"Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. 2013. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. 15, 1405–1414."},"department":[{"_id":"CaHe"}],"publisher":"Nature Publishing Group","volume":15,"fulldoi":"https://doi.org/10.1038/ncb2869","project":[{"_id":"252ABD0A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I930-B20","name":"Control of Epithelial Cell Layer Spreading in Zebrafish"}],"author":[{"last_name":"Campinho","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416","first_name":"Pedro","full_name":"Campinho, Pedro"},{"full_name":"Behrndt, Martin","first_name":"Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ranft, Jonas","first_name":"Jonas","last_name":"Ranft"},{"last_name":"Risler","first_name":"Thomas","full_name":"Risler, Thomas"},{"first_name":"Nicolas","full_name":"Minc, Nicolas","last_name":"Minc"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"publication":"Nature Cell Biology","page":"1405 - 1414","title":"Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1403"}]},"acknowledgement":"This work was supported by the IST Austria and MPI-CBG ","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"isi":1,"article_processing_charge":"No","date_published":"2013-11-10T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. Here we show that orienting cell divisions by tension constitutes an efficient mechanism by which the enveloping cell layer (EVL) releases anisotropic tension while undergoing spreading during zebrafish epiboly. The control of EVL cell-division orientation by tension involves cell elongation and requires myosin II activity to align the mitotic spindle with the main tension axis. We also found that in the absence of tension-oriented cell divisions and in the presence of increased tissue tension, EVL cells undergo ectopic fusions, suggesting that the reduction of tension anisotropy by oriented cell divisions is required to prevent EVL cells from fusing. We conclude that cell-division orientation by tension constitutes a key mechanism for limiting tension anisotropy and thus promoting tissue spreading during EVL epiboly."}],"publication_status":"published","oa_version":"Submitted Version","language":[{"iso":"eng"}],"publist_id":"4652","oa":1,"_id":"2282","day":"10","type":"journal_article","corr_author":"1","quality_controlled":"1","intvolume":"        15","month":"11","main_file_link":[{"url":"http://hal.upmc.fr/hal-00983313/","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:56:45Z"},{"department":[{"_id":"KrCh"}],"year":"2013","citation":{"chicago":"Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0080814\">https://doi.org/10.1371/journal.pone.0080814</a>.","ama":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . <i>PLoS One</i>. 2013;8(12). doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814\">10.1371/journal.pone.0080814</a>","ista":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma . PLoS One. 8(12), e80814.","ieee":"B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma ,” <i>PLoS One</i>, vol. 8, no. 12. Public Library of Science, 2013.","mla":"Zagorsky, Benjamin, et al. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” <i>PLoS One</i>, vol. 8, no. 12, e80814, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814\">10.1371/journal.pone.0080814</a>.","apa":"Zagorsky, B., Reiter, J., Chatterjee, K., &#38; Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0080814\">https://doi.org/10.1371/journal.pone.0080814</a>","short":"B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, PLoS One 8 (2013)."},"volume":8,"publisher":"Public Library of Science","ec_funded":1,"date_updated":"2026-07-29T10:15:25Z","doi":"10.1371/journal.pone.0080814","external_id":{"isi":["000328731800009"]},"scopus_import":"1","related_material":{"record":[{"status":"public","id":"9749","relation":"research_data"},{"status":"public","id":"1400","relation":"dissertation_contains"}]},"license":"https://creativecommons.org/licenses/by/4.0/","issue":"12","file_date_updated":"2020-07-14T12:45:34Z","pubrep_id":"409","ddc":["000"],"file":[{"file_id":"4868","relation":"main_file","date_updated":"2020-07-14T12:45:34Z","creator":"system","content_type":"application/pdf","checksum":"808e8b9e6e89658bee4ffbbfac1bd19d","access_level":"open_access","file_size":1050042,"file_name":"IST-2016-409-v1+1_journal.pone.0080814.pdf","date_created":"2018-12-12T10:11:15Z"}],"fulldoi":"https://doi.org/10.1371/journal.pone.0080814","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publication":"PLoS One","author":[{"last_name":"Zagorsky","first_name":"Benjamin","full_name":"Zagorsky, Benjamin"},{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","first_name":"Johannes"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"title":"Forgiver triumphs in alternating prisoner's dilemma ","publist_id":"4702","language":[{"iso":"eng"}],"article_number":"e80814","article_processing_charge":"No","isi":1,"abstract":[{"text":"Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise.","lang":"eng"}],"status":"public","has_accepted_license":"1","publication_status":"published","date_published":"2013-12-12T00:00:00Z","oa_version":"Published Version","month":"12","intvolume":"         8","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:56:33Z","tmp":{"short":"CC BY (4.0)","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"},"oa":1,"day":"12","_id":"2247","type":"journal_article","quality_controlled":"1"},{"issue":"1","file_date_updated":"2020-07-14T12:45:51Z","ddc":["570"],"pubrep_id":"415","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1400"}]},"title":"The effect of one additional driver mutation on tumor progression","page":"34 - 45","file":[{"file_size":1172037,"file_name":"IST-2016-415-v1+1_Reiter_et_al-2013-Evolutionary_Applications.pdf","date_created":"2018-12-12T10:15:50Z","checksum":"e2955b3889f8a823c3d5a72cb16f8957","content_type":"application/pdf","creator":"system","date_updated":"2020-07-14T12:45:51Z","relation":"main_file","file_id":"5173","access_level":"open_access"}],"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"}],"fulldoi":"https://doi.org/10.1111/eva.12020","author":[{"orcid":"0000-0002-0170-7353","first_name":"Johannes","full_name":"Reiter, Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Božić","first_name":"Ivana","full_name":"Božić, Ivana"},{"first_name":"Benjamin","full_name":"Allen, Benjamin","id":"135B5B70-E9D2-11E9-BD74-BB415DA2B523","last_name":"Allen"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"publication":"Evolutionary Applications","department":[{"_id":"KrCh"}],"citation":{"apa":"Reiter, J., Božić, I., Allen, B., Chatterjee, K., &#38; Nowak, M. (2013). The effect of one additional driver mutation on tumor progression. <i>Evolutionary Applications</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/eva.12020\">https://doi.org/10.1111/eva.12020</a>","short":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, M. Nowak, Evolutionary Applications 6 (2013) 34–45.","mla":"Reiter, Johannes, et al. “The Effect of One Additional Driver Mutation on Tumor Progression.” <i>Evolutionary Applications</i>, vol. 6, no. 1, Wiley-Blackwell, 2013, pp. 34–45, doi:<a href=\"https://doi.org/10.1111/eva.12020\">10.1111/eva.12020</a>.","ama":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. The effect of one additional driver mutation on tumor progression. <i>Evolutionary Applications</i>. 2013;6(1):34-45. doi:<a href=\"https://doi.org/10.1111/eva.12020\">10.1111/eva.12020</a>","ista":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. 2013. The effect of one additional driver mutation on tumor progression. Evolutionary Applications. 6(1), 34–45.","chicago":"Reiter, Johannes, Ivana Božić, Benjamin Allen, Krishnendu Chatterjee, and Martin Nowak. “The Effect of One Additional Driver Mutation on Tumor Progression.” <i>Evolutionary Applications</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/eva.12020\">https://doi.org/10.1111/eva.12020</a>.","ieee":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, and M. Nowak, “The effect of one additional driver mutation on tumor progression,” <i>Evolutionary Applications</i>, vol. 6, no. 1. Wiley-Blackwell, pp. 34–45, 2013."},"year":"2013","volume":6,"publisher":"Wiley-Blackwell","date_updated":"2026-07-29T10:15:25Z","doi":"10.1111/eva.12020","external_id":{"isi":["000313878800004"]},"scopus_import":"1","ec_funded":1,"tmp":{"short":"CC BY (4.0)","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"},"month":"01","intvolume":"         6","date_created":"2018-12-11T11:59:58Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2858","type":"journal_article","day":"01","corr_author":"1","quality_controlled":"1","oa":1,"publist_id":"3931","language":[{"iso":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","isi":1,"abstract":[{"text":"Tumor growth is caused by the acquisition of driver mutations, which enhance the net reproductive rate of cells. Driver mutations may increase cell division, reduce cell death, or allow cells to overcome density-limiting effects. We study the dynamics of tumor growth as one additional driver mutation is acquired. Our models are based on two-type branching processes that terminate in either tumor disappearance or tumor detection. In our first model, both cell types grow exponentially, with a faster rate for cells carrying the additional driver. We find that the additional driver mutation does not affect the survival probability of the lesion, but can substantially reduce the time to reach the detectable size if the lesion is slow growing. In our second model, cells lacking the additional driver cannot exceed a fixed carrying capacity, due to density limitations. In this case, the time to detection depends strongly on this carrying capacity. Our model provides a quantitative framework for studying tumor dynamics during different stages of progression. We observe that early, small lesions need additional drivers, while late stage metastases are only marginally affected by them. These results help to explain why additional driver mutations are typically not detected in fast-growing metastases.","lang":"eng"}],"publication_status":"published","has_accepted_license":"1","status":"public","date_published":"2013-01-01T00:00:00Z"},{"doi":"10.7554/eLife.00747","date_updated":"2026-07-29T10:15:25Z","external_id":{"isi":["000328619300005"]},"scopus_import":"1","department":[{"_id":"KrCh"}],"year":"2013","citation":{"chicago":"Božić, Ivana, Johannes Reiter, Benjamin Allen, Tibor Antal, Krishnendu Chatterjee, Preya Shah, Yo Moon, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” <i>ELife</i>. eLife Sciences Publications, 2013. <a href=\"https://doi.org/10.7554/eLife.00747\">https://doi.org/10.7554/eLife.00747</a>.","ama":"Božić I, Reiter J, Allen B, et al. Evolutionary dynamics of cancer in response to targeted combination therapy. <i>eLife</i>. 2013;2. doi:<a href=\"https://doi.org/10.7554/eLife.00747\">10.7554/eLife.00747</a>","ista":"Božić I, Reiter J, Allen B, Antal T, Chatterjee K, Shah P, Moon Y, Yaqubie A, Kelly N, Le D, Lipson E, Chapman P, Diaz L, Vogelstein B, Nowak M. 2013. Evolutionary dynamics of cancer in response to targeted combination therapy. eLife. 2, e00747.","ieee":"I. Božić <i>et al.</i>, “Evolutionary dynamics of cancer in response to targeted combination therapy,” <i>eLife</i>, vol. 2. eLife Sciences Publications, 2013.","mla":"Božić, Ivana, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” <i>ELife</i>, vol. 2, e00747, eLife Sciences Publications, 2013, doi:<a href=\"https://doi.org/10.7554/eLife.00747\">10.7554/eLife.00747</a>.","short":"I. Božić, J. Reiter, B. Allen, T. Antal, K. Chatterjee, P. Shah, Y. Moon, A. Yaqubie, N. Kelly, D. Le, E. Lipson, P. Chapman, L. Diaz, B. Vogelstein, M. Nowak, ELife 2 (2013).","apa":"Božić, I., Reiter, J., Allen, B., Antal, T., Chatterjee, K., Shah, P., … Nowak, M. (2013). Evolutionary dynamics of cancer in response to targeted combination therapy. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.00747\">https://doi.org/10.7554/eLife.00747</a>"},"volume":2,"publisher":"eLife Sciences Publications","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:45:49Z","file_id":"4967","relation":"main_file","creator":"system","content_type":"application/pdf","checksum":"2c38c47815eacd8fa66cb8b404cf7c61","file_name":"IST-2013-134-v1+1_e00747.full.pdf","date_created":"2018-12-12T10:12:48Z","file_size":3358321}],"fulldoi":"https://doi.org/10.7554/eLife.00747","publication":"eLife","author":[{"last_name":"Božić","full_name":"Božić, Ivana","first_name":"Ivana"},{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","first_name":"Johannes"},{"first_name":"Benjamin","full_name":"Allen, Benjamin","last_name":"Allen"},{"full_name":"Antal, Tibor","first_name":"Tibor","last_name":"Antal"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Preya","full_name":"Shah, Preya","last_name":"Shah"},{"last_name":"Moon","first_name":"Yo","full_name":"Moon, Yo"},{"full_name":"Yaqubie, Amin","first_name":"Amin","last_name":"Yaqubie"},{"first_name":"Nicole","full_name":"Kelly, Nicole","last_name":"Kelly"},{"first_name":"Dung","full_name":"Le, Dung","last_name":"Le"},{"last_name":"Lipson","first_name":"Evan","full_name":"Lipson, Evan"},{"full_name":"Chapman, Paul","first_name":"Paul","last_name":"Chapman"},{"full_name":"Diaz, Luis","first_name":"Luis","last_name":"Diaz"},{"last_name":"Vogelstein","full_name":"Vogelstein, Bert","first_name":"Bert"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"title":"Evolutionary dynamics of cancer in response to targeted combination therapy","related_material":{"record":[{"status":"public","id":"1400","relation":"dissertation_contains"}]},"file_date_updated":"2020-07-14T12:45:49Z","pubrep_id":"134","ddc":["570","610"],"article_processing_charge":"No","isi":1,"has_accepted_license":"1","publication_status":"published","abstract":[{"lang":"eng","text":"In solid tumors, targeted treatments can lead to dramatic regressions, but responses are often short-lived because resistant cancer cells arise. The major strategy proposed for overcoming resistance is combination therapy. We present a mathematical model describing the evolutionary dynamics of lesions in response to treatment. We first studied 20 melanoma patients receiving vemurafenib. We then applied our model to an independent set of pancreatic, colorectal, and melanoma cancer patients with metastatic disease. We find that dual therapy results in long-term disease control for most patients, if there are no single mutations that cause cross-resistance to both drugs; in patients with large disease burden, triple therapy is needed. We also find that simultaneous therapy with two drugs is much more effective than sequential therapy. Our results provide realistic expectations for the efficacy of new drug combinations and inform the design of trials for new cancer therapeutics."}],"status":"public","date_published":"2013-06-25T00:00:00Z","oa_version":"Published Version","publist_id":"3985","language":[{"iso":"eng"}],"article_number":"e00747","oa":1,"_id":"2816","type":"journal_article","day":"25","quality_controlled":"1","month":"06","intvolume":"         2","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:59:45Z","tmp":{"short":"CC BY (4.0)","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"}},{"publist_id":"5077","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"oa_version":"Preprint","publication_status":"published","abstract":[{"text":"In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics.","lang":"eng"}],"status":"public","date_published":"2013-01-01T00:00:00Z","arxiv":1,"series_title":"Lecture Notes in Computer Science","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1303.5251"}],"month":"01","intvolume":"      8044","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:55:08Z","_id":"2000","day":"01","type":"conference","quality_controlled":"1","oa":1,"department":[{"_id":"KrCh"}],"year":"2013","citation":{"mla":"Reiter, Johannes, et al. “TTP: Tool for Tumor Progression.” <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, vol. 8044, Springer, 2013, pp. 101–06, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>.","apa":"Reiter, J., Božić, I., Chatterjee, K., &#38; Nowak, M. (2013). TTP: Tool for tumor progression. In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i> (Vol. 8044, pp. 101–106). St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>","short":"J. Reiter, I. Božić, K. Chatterjee, M. Nowak, in:, Proceedings of 25th Int. Conf. on Computer Aided Verification, Springer, 2013, pp. 101–106.","ieee":"J. Reiter, I. Božić, K. Chatterjee, and M. Nowak, “TTP: Tool for tumor progression,” in <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, St. Petersburg, Russia, 2013, vol. 8044, pp. 101–106.","chicago":"Reiter, Johannes, Ivana Božić, Krishnendu Chatterjee, and Martin Nowak. “TTP: Tool for Tumor Progression.” In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, 8044:101–6. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>.","ista":"Reiter J, Božić I, Chatterjee K, Nowak M. 2013. TTP: Tool for tumor progression. Proceedings of 25th Int. Conf. on Computer Aided Verification. CAV: Computer Aided VerificationLecture Notes in Computer Science, LNCS, vol. 8044, 101–106.","ama":"Reiter J, Božić I, Chatterjee K, Nowak M. TTP: Tool for tumor progression. In: <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>. Vol 8044. Lecture Notes in Computer Science. Springer; 2013:101-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>"},"volume":8044,"publisher":"Springer","date_updated":"2026-07-29T10:15:25Z","doi":"10.1007/978-3-642-39799-8_6","external_id":{"arxiv":["1303.5251"]},"scopus_import":1,"ec_funded":1,"related_material":{"record":[{"status":"public","id":"5399","relation":"earlier_version"},{"id":"1400","status":"public","relation":"dissertation_contains"}]},"title":"TTP: Tool for tumor progression","page":"101 - 106","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.1007/978-3-642-39799-8_6","conference":{"end_date":"2013-07-19","name":"CAV: Computer Aided Verification","start_date":"2013-07-13","location":"St. Petersburg, Russia"},"publication":"Proceedings of 25th Int. Conf. on Computer Aided Verification","author":[{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","full_name":"Reiter, Johannes","first_name":"Johannes","orcid":"0000-0002-0170-7353"},{"last_name":"Božić","first_name":"Ivana","full_name":"Božić, Ivana"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}]},{"oa":1,"type":"journal_article","_id":"450","day":"07","quality_controlled":"1","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/"}],"month":"01","intvolume":"       280","date_created":"2018-12-11T11:46:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","isi":1,"publication_status":"published","abstract":[{"text":"Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations.","lang":"eng"}],"status":"public","date_published":"2013-01-07T00:00:00Z","oa_version":"Submitted Version","publist_id":"7372","language":[{"iso":"eng"}],"article_number":"2058","fulldoi":"https://doi.org/10.1098/rspb.2012.2058","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","author":[{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","orcid":"0000-0002-4014-8478","first_name":"David","full_name":"Field, David"},{"last_name":"Rowell","full_name":"Rowell, David","first_name":"David"},{"last_name":"Young","first_name":"Andrew","full_name":"Young, Andrew"}],"title":"Source population characteristics affect heterosis following genetic rescue of fragmented plant populations","issue":"1750","date_updated":"2026-08-12T06:25:53Z","doi":"10.1098/rspb.2012.2058","external_id":{"pmid":["23173202"],"isi":["000311943100012"]},"pmid":1,"department":[{"_id":"NiBa"}],"citation":{"short":"M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).","apa":"Pickup, M., Field, D., Rowell, D., &#38; Young, A. (2013). Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rspb.2012.2058\">https://doi.org/10.1098/rspb.2012.2058</a>","mla":"Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1750, 2058, Royal Society, 2013, doi:<a href=\"https://doi.org/10.1098/rspb.2012.2058\">10.1098/rspb.2012.2058</a>.","ama":"Pickup M, Field D, Rowell D, Young A. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2013;280(1750). doi:<a href=\"https://doi.org/10.1098/rspb.2012.2058\">10.1098/rspb.2012.2058</a>","ista":"Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1750), 2058.","chicago":"Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, 2013. <a href=\"https://doi.org/10.1098/rspb.2012.2058\">https://doi.org/10.1098/rspb.2012.2058</a>.","ieee":"M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1750. Royal Society, 2013."},"year":"2013","publisher":"Royal Society","volume":280},{"oa":1,"_id":"2811","type":"journal_article","day":"18","quality_controlled":"1","intvolume":"        87","month":"06","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1306.5890"}],"date_created":"2018-12-11T11:59:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"isi":1,"article_processing_charge":"No","date_published":"2013-06-18T00:00:00Z","abstract":[{"lang":"eng","text":"In pipe, channel, and boundary layer flows turbulence first occurs intermittently in space and time: at moderate Reynolds numbers domains of disordered turbulent motion are separated by quiescent laminar regions. Based on direct numerical simulations of pipe flow we argue here that the spatial intermittency has its origin in a nearest neighbor interaction between turbulent regions. We further show that in this regime turbulent flows are intrinsically intermittent with a well-defined equilibrium turbulent fraction but without ever assuming a steady pattern. This transition scenario is analogous to that found in simple models such as coupled map lattices. The scaling observed implies that laminar intermissions of the turbulent flow will persist to arbitrarily large Reynolds numbers."}],"status":"public","publication_status":"published","oa_version":"Preprint","language":[{"iso":"eng"}],"publist_id":"4074","article_number":"063012","fulldoi":"https://doi.org/10.1103/PhysRevE.87.063012","project":[{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"publication":"Physical Review E","author":[{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn"}],"title":"Nature of laminar-turbulence intermittency in shear flows","issue":"6","ec_funded":1,"external_id":{"isi":["000320645700009"],"arxiv":["1306.5890"]},"date_updated":"2026-08-12T14:29:19Z","doi":"10.1103/PhysRevE.87.063012","scopus_import":"1","citation":{"short":"M. Avila, B. Hof, Physical Review E 87 (2013).","apa":"Avila, M., &#38; Hof, B. (2013). Nature of laminar-turbulence intermittency in shear flows. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">https://doi.org/10.1103/PhysRevE.87.063012</a>","mla":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” <i>Physical Review E</i>, vol. 87, no. 6, 063012, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">10.1103/PhysRevE.87.063012</a>.","ista":"Avila M, Hof B. 2013. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 87(6), 063012.","ama":"Avila M, Hof B. Nature of laminar-turbulence intermittency in shear flows. <i>Physical Review E</i>. 2013;87(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">10.1103/PhysRevE.87.063012</a>","chicago":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” <i>Physical Review E</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">https://doi.org/10.1103/PhysRevE.87.063012</a>.","ieee":"M. Avila and B. Hof, “Nature of laminar-turbulence intermittency in shear flows,” <i>Physical Review E</i>, vol. 87, no. 6. American Physical Society, 2013."},"year":"2013","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","volume":87},{"edition":"1","fulldoi":"https://doi.org/10.1007/978-1-4614-3903-5_6","author":[{"last_name":"zur Nedden","id":"3C77F464-F248-11E8-B48F-1D18A9856A87","full_name":"zur Nedden, Stephanie","first_name":"Stephanie"},{"full_name":"Doney, Alexander S.","first_name":"Alexander S.","last_name":"Doney"},{"full_name":"Frenguelli, Bruno G.","first_name":"Bruno G.","last_name":"Frenguelli"}],"publication":"Adenosine","title":"The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books","page":"109-129","publication_identifier":{"isbn":["9781461439028"],"eisbn":["9781461439035"]},"place":"New York","acknowledgement":"We are grateful to Research into Ageing/Ageing UK and The Dunhill Trust for funding SzN’s graduate studies, and to Prof Nicholas Dale for his valuable input.","doi":"10.1007/978-1-4614-3903-5_6","date_updated":"2022-06-21T11:51:58Z","scopus_import":"1","department":[{"_id":"HaJa"}],"citation":{"ieee":"S. zur Nedden, A. S. Doney, and B. G. Frenguelli, “The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books,” in <i>Adenosine</i>, 1st ed., S. Masino and D. Boison, Eds. New York: Springer, 2012, pp. 109–129.","ista":"zur Nedden S, Doney AS, Frenguelli BG. 2012.The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In: Adenosine. , 109–129.","ama":"zur Nedden S, Doney AS, Frenguelli BG. The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In: Masino S, Boison D, eds. <i>Adenosine</i>. 1st ed. New York: Springer; 2012:109-129. doi:<a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">10.1007/978-1-4614-3903-5_6</a>","chicago":"Nedden, Stephanie zur, Alexander S. Doney, and Bruno G. Frenguelli. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” In <i>Adenosine</i>, edited by Susan Masino and Detlev Boison, 1st ed., 109–29. New York: Springer, 2012. <a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">https://doi.org/10.1007/978-1-4614-3903-5_6</a>.","apa":"zur Nedden, S., Doney, A. S., &#38; Frenguelli, B. G. (2012). The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In S. Masino &#38; D. Boison (Eds.), <i>Adenosine</i> (1st ed., pp. 109–129). New York: Springer. <a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">https://doi.org/10.1007/978-1-4614-3903-5_6</a>","short":"S. zur Nedden, A.S. Doney, B.G. Frenguelli, in:, S. Masino, D. Boison (Eds.), Adenosine, 1st ed., Springer, New York, 2012, pp. 109–129.","mla":"zur Nedden, Stephanie, et al. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” <i>Adenosine</i>, edited by Susan Masino and Detlev Boison, 1st ed., Springer, 2012, pp. 109–29, doi:<a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">10.1007/978-1-4614-3903-5_6</a>."},"year":"2012","editor":[{"first_name":"Susan","full_name":"Masino, Susan","last_name":"Masino"},{"last_name":"Boison","first_name":"Detlev","full_name":"Boison, Detlev"}],"publisher":"Springer","type":"book_chapter","_id":"10896","day":"23","quality_controlled":"1","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-03-21T07:16:12Z","article_processing_charge":"No","status":"public","publication_status":"published","abstract":[{"text":"Under physiological conditions the brain, via the purine salvage pathway, reuses the preformed purine bases hypoxanthine, derived from ATP degradation, and adenine (Ade), derived from polyamine synthesis, to restore its ATP pool. However, the massive degradation of ATP during ischemia, although providing valuable neuroprotective adenosine, results in the accumulation and loss of diffusible purine metabolites and thereby leads to a protracted reduction in the post-ischemic ATP pool size. In vivo, this may both limit the ability to deploy ATP-dependent reparative mechanisms and reduce the subsequent availability of adenosine, whilst in brain slices results in tissue with substantially lower levels of ATP than in vivo. In the present review, we describe the mechanisms by which brain tissue replenishes its ATP, how this can be improved with the clinically tolerated chemicals D-ribose and adenine, and the functional, and potential therapeutic, implications of doing so.","lang":"eng"}],"date_published":"2012-07-23T00:00:00Z","oa_version":"None","language":[{"iso":"eng"}]},{"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2012-10-15T00:00:00Z","status":"public","publication_status":"published","abstract":[{"text":"We propose a logic-based framework for automated reasoning about sequential programs manipulating singly-linked lists and arrays with unbounded data. We introduce the logic SLAD, which allows combining shape constraints, written in a fragment of Separation Logic, with data and size constraints. We address the problem of checking the entailment between SLAD formulas, which is crucial in performing pre-post condition reasoning. Although this problem is undecidable in general for SLAD, we propose a sound and powerful procedure that is able to solve this problem for a large class of formulas, beyond the capabilities of existing techniques and tools. We prove that this procedure is complete, i.e., it is actually a decision procedure for this problem, for an important fragment of SLAD including known decidable logics. We implemented this procedure and shown its preciseness and its efficiency on a significant benchmark of formulas.","lang":"eng"}],"oa_version":"None","intvolume":"      7561","month":"10","date_created":"2022-03-21T07:58:39Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","series_title":"LNCS","_id":"10903","day":"15","type":"conference","corr_author":"1","quality_controlled":"1","year":"2012","citation":{"short":"A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Automated Technology for Verification and Analysis, Springer, Berlin, Heidelberg, 2012, pp. 167–182.","apa":"Bouajjani, A., Dragoi, C., Enea, C., &#38; Sighireanu, M. (2012). Accurate invariant checking for programs manipulating lists and arrays with infinite data. In <i>Automated Technology for Verification and Analysis</i> (Vol. 7561, pp. 167–182). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">https://doi.org/10.1007/978-3-642-33386-6_14</a>","mla":"Bouajjani, Ahmed, et al. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Springer, 2012, pp. 167–82, doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">10.1007/978-3-642-33386-6_14</a>.","ama":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. Accurate invariant checking for programs manipulating lists and arrays with infinite data. In: <i>Automated Technology for Verification and Analysis</i>. Vol 7561. LNCS. Berlin, Heidelberg: Springer; 2012:167-182. doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">10.1007/978-3-642-33386-6_14</a>","ista":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Accurate invariant checking for programs manipulating lists and arrays with infinite data. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and AnalysisLNCS, LNCS, vol. 7561, 167–182.","chicago":"Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” In <i>Automated Technology for Verification and Analysis</i>, 7561:167–82. LNCS. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">https://doi.org/10.1007/978-3-642-33386-6_14</a>.","ieee":"A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Accurate invariant checking for programs manipulating lists and arrays with infinite data,” in <i>Automated Technology for Verification and Analysis</i>, Thiruvananthapuram, India, 2012, vol. 7561, pp. 167–182."},"department":[{"_id":"ToHe"}],"volume":7561,"publisher":"Springer","date_updated":"2024-10-09T21:02:34Z","doi":"10.1007/978-3-642-33386-6_14","scopus_import":"1","publication_identifier":{"isbn":["9783642333859"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783642333866"]},"acknowledgement":"This work has been partially supported by the French ANR project Veridyc","place":"Berlin, Heidelberg","fulldoi":"https://doi.org/10.1007/978-3-642-33386-6_14","conference":{"location":"Thiruvananthapuram, India","name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2012-10-06","start_date":"2012-10-03"},"author":[{"last_name":"Bouajjani","full_name":"Bouajjani, Ahmed","first_name":"Ahmed"},{"full_name":"Dragoi, Cezara","first_name":"Cezara","last_name":"Dragoi","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Constantin","full_name":"Enea, Constantin","last_name":"Enea"},{"last_name":"Sighireanu","full_name":"Sighireanu, Mihaela","first_name":"Mihaela"}],"publication":"Automated Technology for Verification and Analysis","page":"167-182","title":"Accurate invariant checking for programs manipulating lists and arrays with infinite data"},{"month":"02","intvolume":"       335","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-04-07T07:52:01Z","_id":"11092","type":"journal_article","day":"02","quality_controlled":"1","language":[{"iso":"eng"}],"article_type":"letter_note","article_processing_charge":"No","publication_status":"published","abstract":[{"lang":"eng","text":"To combat the functional decline of the proteome, cells use the process of protein turnover to replace potentially impaired polypeptides with new functional copies. We found that extremely long-lived proteins (ELLPs) did not turn over in postmitotic cells of the rat central nervous system. These ELLPs were associated with chromatin and the nuclear pore complex, the central transport channels that mediate all molecular trafficking in and out of the nucleus. The longevity of these proteins would be expected to expose them to potentially harmful metabolites, putting them at risk of accumulating damage over extended periods of time. Thus, it is possible that failure to maintain proper levels and functional integrity of ELLPs in nonproliferative cells might contribute to age-related deterioration in cell and tissue function."}],"status":"public","date_published":"2012-02-02T00:00:00Z","extern":"1","oa_version":"None","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"issue":"6071","fulldoi":"https://doi.org/10.1126/science.1217421","author":[{"full_name":"Savas, Jeffrey N.","first_name":"Jeffrey N.","last_name":"Savas"},{"first_name":"Brandon H.","full_name":"Toyama, Brandon H.","last_name":"Toyama"},{"last_name":"Xu","first_name":"Tao","full_name":"Xu, Tao"},{"first_name":"John R.","full_name":"Yates, John R.","last_name":"Yates"},{"full_name":"HETZER, Martin W","first_name":"Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER"}],"publication":"Science","title":"Extremely long-lived nuclear pore proteins in the rat brain","page":"942-942","department":[{"_id":"MaHe"}],"citation":{"ama":"Savas JN, Toyama BH, Xu T, Yates JR, Hetzer M. Extremely long-lived nuclear pore proteins in the rat brain. <i>Science</i>. 2012;335(6071):942-942. doi:<a href=\"https://doi.org/10.1126/science.1217421\">10.1126/science.1217421</a>","ista":"Savas JN, Toyama BH, Xu T, Yates JR, Hetzer M. 2012. Extremely long-lived nuclear pore proteins in the rat brain. Science. 335(6071), 942–942.","chicago":"Savas, Jeffrey N., Brandon H. Toyama, Tao Xu, John R. Yates, and Martin Hetzer. “Extremely Long-Lived Nuclear Pore Proteins in the Rat Brain.” <i>Science</i>. American Association for the Advancement of Science, 2012. <a href=\"https://doi.org/10.1126/science.1217421\">https://doi.org/10.1126/science.1217421</a>.","ieee":"J. N. Savas, B. H. Toyama, T. Xu, J. R. Yates, and M. Hetzer, “Extremely long-lived nuclear pore proteins in the rat brain,” <i>Science</i>, vol. 335, no. 6071. American Association for the Advancement of Science, pp. 942–942, 2012.","short":"J.N. Savas, B.H. Toyama, T. Xu, J.R. Yates, M. Hetzer, Science 335 (2012) 942–942.","apa":"Savas, J. N., Toyama, B. H., Xu, T., Yates, J. R., &#38; Hetzer, M. (2012). Extremely long-lived nuclear pore proteins in the rat brain. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1217421\">https://doi.org/10.1126/science.1217421</a>","mla":"Savas, Jeffrey N., et al. “Extremely Long-Lived Nuclear Pore Proteins in the Rat Brain.” <i>Science</i>, vol. 335, no. 6071, American Association for the Advancement of Science, 2012, pp. 942–942, doi:<a href=\"https://doi.org/10.1126/science.1217421\">10.1126/science.1217421</a>."},"year":"2012","volume":335,"publisher":"American Association for the Advancement of Science","doi":"10.1126/science.1217421","date_updated":"2025-12-15T10:03:06Z","external_id":{"pmid":["22300851"]},"pmid":1,"scopus_import":"1"},{"quality_controlled":"1","corr_author":"1","_id":"2302","day":"03","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:56:52Z","month":"07","intvolume":"        10","publication_status":"published","status":"public","abstract":[{"text":"We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only &quot;significant&quot; mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables.","lang":"eng"}],"date_published":"2012-07-03T00:00:00Z","article_processing_charge":"No","isi":1,"oa_version":"None","publist_id":"4625","language":[{"iso":"eng"}],"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Mateescu, Maria","first_name":"Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","last_name":"Mateescu"}],"publication":"IEEE ACM Transactions on Computational Biology and Bioinformatics","fulldoi":"https://doi.org/10.1109/TCBB.2012.91","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"The propagation approach for computing biochemical reaction networks","page":"310 - 322","issue":"2","ec_funded":1,"scopus_import":"1","date_updated":"2025-09-29T14:17:43Z","doi":"10.1109/TCBB.2012.91","pmid":1,"external_id":{"pmid":["22778152"],"isi":["000323504100006"]},"publisher":"IEEE","volume":10,"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"year":"2012","citation":{"ieee":"T. A. Henzinger and M. Mateescu, “The propagation approach for computing biochemical reaction networks,” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>, vol. 10, no. 2. IEEE, pp. 310–322, 2012.","ama":"Henzinger TA, Mateescu M. The propagation approach for computing biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. 2012;10(2):310-322. doi:<a href=\"https://doi.org/10.1109/TCBB.2012.91\">10.1109/TCBB.2012.91</a>","ista":"Henzinger TA, Mateescu M. 2012. The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. 10(2), 310–322.","chicago":"Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. IEEE, 2012. <a href=\"https://doi.org/10.1109/TCBB.2012.91\">https://doi.org/10.1109/TCBB.2012.91</a>.","short":"T.A. Henzinger, M. Mateescu, IEEE ACM Transactions on Computational Biology and Bioinformatics 10 (2012) 310–322.","apa":"Henzinger, T. A., &#38; Mateescu, M. (2012). The propagation approach for computing biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. IEEE. <a href=\"https://doi.org/10.1109/TCBB.2012.91\">https://doi.org/10.1109/TCBB.2012.91</a>","mla":"Henzinger, Thomas A., and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>, vol. 10, no. 2, IEEE, 2012, pp. 310–22, doi:<a href=\"https://doi.org/10.1109/TCBB.2012.91\">10.1109/TCBB.2012.91</a>."}},{"file":[{"file_size":754922,"date_created":"2018-12-12T10:13:30Z","file_name":"IST-2015-384-v1+1_Mol_Biol_Evol-2012-Ebersberger-1319-34.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:40Z","creator":"system","file_id":"5013","relation":"main_file","checksum":"d565dcac27d1736c0c378ea6fcf22d69","access_level":"open_access"}],"fulldoi":"https://doi.org/10.1093/molbev/msr285","author":[{"first_name":"Ingo","full_name":"Ebersberger, Ingo","last_name":"Ebersberger"},{"full_name":"De Matos Simoes, Ricardo","first_name":"Ricardo","last_name":"De Matos Simoes"},{"id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok","full_name":"Kupczok, Anne","first_name":"Anne"},{"last_name":"Gube","full_name":"Gube, Matthias","first_name":"Matthias"},{"full_name":"Kothe, Erika","first_name":"Erika","last_name":"Kothe"},{"full_name":"Voigt, Kerstin","first_name":"Kerstin","last_name":"Voigt"},{"last_name":"Von Haeseler","first_name":"Arndt","full_name":"Von Haeseler, Arndt"}],"publication":"Molecular Biology and Evolution","title":"A consistent phylogenetic backbone for the fungi","page":"1319 - 1334","issue":"5","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2020-07-14T12:45:40Z","ddc":["570","576"],"pubrep_id":"384","doi":"10.1093/molbev/msr285","date_updated":"2025-09-30T08:21:34Z","external_id":{"isi":["000303603300004"]},"scopus_import":"1","department":[{"_id":"JoBo"}],"citation":{"mla":"Ebersberger, Ingo, et al. “A Consistent Phylogenetic Backbone for the Fungi.” <i>Molecular Biology and Evolution</i>, vol. 29, no. 5, Oxford University Press, 2012, pp. 1319–34, doi:<a href=\"https://doi.org/10.1093/molbev/msr285\">10.1093/molbev/msr285</a>.","short":"I. Ebersberger, R. De Matos Simoes, A. Kupczok, M. Gube, E. Kothe, K. Voigt, A. Von Haeseler, Molecular Biology and Evolution 29 (2012) 1319–1334.","apa":"Ebersberger, I., De Matos Simoes, R., Kupczok, A., Gube, M., Kothe, E., Voigt, K., &#38; Von Haeseler, A. (2012). A consistent phylogenetic backbone for the fungi. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msr285\">https://doi.org/10.1093/molbev/msr285</a>","chicago":"Ebersberger, Ingo, Ricardo De Matos Simoes, Anne Kupczok, Matthias Gube, Erika Kothe, Kerstin Voigt, and Arndt Von Haeseler. “A Consistent Phylogenetic Backbone for the Fungi.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2012. <a href=\"https://doi.org/10.1093/molbev/msr285\">https://doi.org/10.1093/molbev/msr285</a>.","ista":"Ebersberger I, De Matos Simoes R, Kupczok A, Gube M, Kothe E, Voigt K, Von Haeseler A. 2012. A consistent phylogenetic backbone for the fungi. Molecular Biology and Evolution. 29(5), 1319–1334.","ama":"Ebersberger I, De Matos Simoes R, Kupczok A, et al. A consistent phylogenetic backbone for the fungi. <i>Molecular Biology and Evolution</i>. 2012;29(5):1319-1334. doi:<a href=\"https://doi.org/10.1093/molbev/msr285\">10.1093/molbev/msr285</a>","ieee":"I. Ebersberger <i>et al.</i>, “A consistent phylogenetic backbone for the fungi,” <i>Molecular Biology and Evolution</i>, vol. 29, no. 5. Oxford University Press, pp. 1319–1334, 2012."},"year":"2012","publisher":"Oxford University Press","volume":29,"oa":1,"_id":"2411","day":"01","type":"journal_article","quality_controlled":"1","month":"05","intvolume":"        29","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:57:30Z","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"article_processing_charge":"No","isi":1,"publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses."}],"has_accepted_license":"1","date_published":"2012-05-01T00:00:00Z","oa_version":"Published Version","publist_id":"4515","language":[{"iso":"eng"}]},{"ec_funded":1,"doi":"10.4230/LIPIcs.FSTTCS.2012.461","date_updated":"2025-09-23T08:00:31Z","scopus_import":1,"department":[{"_id":"KrCh"}],"year":"2012","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Average Case Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives</i>. Vol. 18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 461–73, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461\">10.4230/LIPIcs.FSTTCS.2012.461</a>.","short":"K. Chatterjee, M. Joglekar, N. Shah, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 461–473.","apa":"Chatterjee, K., Joglekar, M., &#38; Shah, N. (2012). Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives (Vol. 18, pp. 461–473). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Hyderabad, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461\">https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461</a>","chicago":"Chatterjee, Krishnendu, Manas Joglekar, and Nisarg Shah. “Average Case Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives,” 18:461–73. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461\">https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461</a>.","ista":"Chatterjee K, Joglekar M, Shah N. 2012. Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 18, 461–473.","ama":"Chatterjee K, Joglekar M, Shah N. Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. In: Vol 18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2012:461-473. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461\">10.4230/LIPIcs.FSTTCS.2012.461</a>","ieee":"K. Chatterjee, M. Joglekar, and N. Shah, “Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Hyderabad, India, 2012, vol. 18, pp. 461–473."},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","volume":18,"file":[{"file_size":519040,"file_name":"IST-2016-525-v1+1_42_1_.pdf","date_created":"2018-12-12T10:13:53Z","checksum":"d4d644ed1a885dbfc4fa1ef4c5724dab","file_id":"5040","date_updated":"2020-07-14T12:45:45Z","creator":"system","relation":"main_file","content_type":"application/pdf","access_level":"open_access"}],"fulldoi":"https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"conference":{"start_date":"2012-12-15","end_date":"2012-12-17","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","location":"Hyderabad, India"},"author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Joglekar, Manas","first_name":"Manas","last_name":"Joglekar"},{"full_name":"Shah, Nisarg","first_name":"Nisarg","last_name":"Shah"}],"title":"Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives","page":"461 - 473","related_material":{"record":[{"relation":"later_version","id":"1598","status":"public"}]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:45:45Z","ddc":["000"],"pubrep_id":"525","has_accepted_license":"1","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) with specifications given as Büchi (liveness) objectives. We consider the problem of computing the set of almost-sure winning vertices from where the objective can be ensured with probability 1. We study for the first time the average case complexity of the classical algorithm for computing the set of almost-sure winning vertices for MDPs with Büchi objectives. Our contributions are as follows: First, we show that for MDPs with constant out-degree the expected number of iterations is at most logarithmic and the average case running time is linear (as compared to the worst case linear number of iterations and quadratic time complexity). Second, for the average case analysis over all MDPs we show that the expected number of iterations is constant and the average case running time is linear (again as compared to the worst case linear number of iterations and quadratic time complexity). Finally we also show that given that all MDPs are equally likely, the probability that the classical algorithm requires more than constant number of iterations is exponentially small."}],"status":"public","publication_status":"published","date_published":"2012-12-10T00:00:00Z","oa_version":"Published Version","alternative_title":["LIPIcs"],"publist_id":"4180","language":[{"iso":"eng"}],"oa":1,"type":"conference","_id":"2715","day":"10","quality_controlled":"1","month":"12","intvolume":"        18","date_created":"2018-12-11T11:59:13Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"}},{"oa_version":"None","scopus_import":"1","date_updated":"2025-06-03T11:46:36Z","date_published":"2012-12-01T00:00:00Z","publication_status":"published","status":"public","abstract":[{"text":"We study the problem of maximum marginal prediction (MMP) in probabilistic graphical models, a task that occurs, for example, as the Bayes optimal decision rule under a Hamming loss. MMP is typically performed as a two-stage procedure: one estimates each variable's marginal probability and then forms a prediction from the states of maximal probability. In this work we propose a simple yet effective technique for accelerating MMP when inference is sampling-based: instead of the above two-stage procedure we directly estimate the posterior probability of each decision variable. This allows us to identify the point of time when we are sufficiently certain about any individual decision. Whenever this is the case, we dynamically prune the variables we are confident about from the underlying factor graph. Consequently, at any time only samples of variables whose decision is still uncertain need to be created. Experiments in two prototypical scenarios, multi-label classification and image inpainting, show that adaptive sampling can drastically accelerate MMP without sacrificing prediction accuracy.","lang":"eng"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publist_id":"3975","volume":1,"publisher":"Neural Information Processing Systems Foundation","citation":{"ieee":"C. Lampert, “Dynamic pruning of factor graphs for maximum marginal prediction,” presented at the NIPS: Neural Information Processing Systems, Lake Tahoe, NV, United States, 2012, vol. 1, pp. 82–90.","chicago":"Lampert, Christoph. “Dynamic Pruning of Factor Graphs for Maximum Marginal Prediction,” 1:82–90. Neural Information Processing Systems Foundation, 2012.","ista":"Lampert C. 2012. Dynamic pruning of factor graphs for maximum marginal prediction. NIPS: Neural Information Processing Systems vol. 1, 82–90.","ama":"Lampert C. Dynamic pruning of factor graphs for maximum marginal prediction. In: Vol 1. Neural Information Processing Systems Foundation; 2012:82-90.","mla":"Lampert, Christoph. <i>Dynamic Pruning of Factor Graphs for Maximum Marginal Prediction</i>. Vol. 1, Neural Information Processing Systems Foundation, 2012, pp. 82–90.","apa":"Lampert, C. (2012). Dynamic pruning of factor graphs for maximum marginal prediction (Vol. 1, pp. 82–90). Presented at the NIPS: Neural Information Processing Systems, Lake Tahoe, NV, United States: Neural Information Processing Systems Foundation.","short":"C. Lampert, in:, Neural Information Processing Systems Foundation, 2012, pp. 82–90."},"year":"2012","department":[{"_id":"ChLa"}],"page":"82 - 90","corr_author":"1","quality_controlled":"1","title":"Dynamic pruning of factor graphs for maximum marginal prediction","_id":"2825","day":"01","type":"conference","author":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"conference":{"start_date":"2012-12-03","end_date":"2012-12-06","name":"NIPS: Neural Information Processing Systems","location":"Lake Tahoe, NV, United States"},"date_created":"2018-12-11T11:59:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         1","month":"12"},{"language":[{"iso":"eng"}],"publist_id":"3946","oa_version":"Submitted Version","date_published":"2012-05-21T00:00:00Z","status":"public","publication_status":"published","abstract":[{"text":"We study evolutionary game theory in a setting where individuals learn from each other. We extend the traditional approach by assuming that a population contains individuals with different learning abilities. In particular, we explore the situation where individuals have different search spaces, when attempting to learn the strategies of others. The search space of an individual specifies the set of strategies learnable by that individual. The search space is genetically given and does not change under social evolutionary dynamics. We introduce a general framework and study a specific example in the context of direct reciprocity. For this example, we obtain the counter intuitive result that cooperation can only evolve for intermediate benefit-to-cost ratios, while small and large benefit-to-cost ratios favor defection. Our paper is a step toward making a connection between computational learning theory and evolutionary game dynamics.","lang":"eng"}],"isi":1,"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:59:55Z","intvolume":"       301","month":"05","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322297/"}],"quality_controlled":"1","corr_author":"1","type":"journal_article","_id":"2848","day":"21","oa":1,"publisher":"Elsevier","volume":301,"citation":{"apa":"Chatterjee, K., Zufferey, D., &#38; Nowak, M. (2012). Evolutionary game dynamics in populations with different learners. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2012.02.021\">https://doi.org/10.1016/j.jtbi.2012.02.021</a>","short":"K. Chatterjee, D. Zufferey, M. Nowak, Journal of Theoretical Biology 301 (2012) 161–173.","mla":"Chatterjee, Krishnendu, et al. “Evolutionary Game Dynamics in Populations with Different Learners.” <i>Journal of Theoretical Biology</i>, vol. 301, Elsevier, 2012, pp. 161–73, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2012.02.021\">10.1016/j.jtbi.2012.02.021</a>.","ieee":"K. Chatterjee, D. Zufferey, and M. Nowak, “Evolutionary game dynamics in populations with different learners,” <i>Journal of Theoretical Biology</i>, vol. 301. Elsevier, pp. 161–173, 2012.","ista":"Chatterjee K, Zufferey D, Nowak M. 2012. Evolutionary game dynamics in populations with different learners. Journal of Theoretical Biology. 301, 161–173.","ama":"Chatterjee K, Zufferey D, Nowak M. Evolutionary game dynamics in populations with different learners. <i>Journal of Theoretical Biology</i>. 2012;301:161-173. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2012.02.021\">10.1016/j.jtbi.2012.02.021</a>","chicago":"Chatterjee, Krishnendu, Damien Zufferey, and Martin Nowak. “Evolutionary Game Dynamics in Populations with Different Learners.” <i>Journal of Theoretical Biology</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.jtbi.2012.02.021\">https://doi.org/10.1016/j.jtbi.2012.02.021</a>."},"year":"2012","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"scopus_import":"1","pmid":1,"external_id":{"pmid":["22394652"],"isi":["000303079500016"]},"date_updated":"2025-09-30T08:20:22Z","doi":"10.1016/j.jtbi.2012.02.021","ec_funded":1,"page":"161 - 173","title":"Evolutionary game dynamics in populations with different learners","publication":"Journal of Theoretical Biology","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Damien","orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"fulldoi":"https://doi.org/10.1016/j.jtbi.2012.02.021","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_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"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}]},{"scopus_import":"1","doi":"10.1070/RM2012v067n06ABEH004820","date_updated":"2025-09-30T08:19:37Z","external_id":{"isi":["000315950100005"]},"volume":67,"publisher":"IOP Publishing","department":[{"_id":"HeEd"}],"year":"2012","citation":{"mla":"Edelsbrunner, Herbert, and Nataliya Strelkova. “On the Configuration Space of Steiner Minimal Trees.” <i>Russian Mathematical Surveys</i>, vol. 67, no. 6, IOP Publishing, 2012, pp. 1167–68, doi:<a href=\"https://doi.org/10.1070/RM2012v067n06ABEH004820\">10.1070/RM2012v067n06ABEH004820</a>.","apa":"Edelsbrunner, H., &#38; Strelkova, N. (2012). On the configuration space of Steiner minimal trees. <i>Russian Mathematical Surveys</i>. IOP Publishing. <a href=\"https://doi.org/10.1070/RM2012v067n06ABEH004820\">https://doi.org/10.1070/RM2012v067n06ABEH004820</a>","short":"H. Edelsbrunner, N. Strelkova, Russian Mathematical Surveys 67 (2012) 1167–1168.","ieee":"H. Edelsbrunner and N. Strelkova, “On the configuration space of Steiner minimal trees,” <i>Russian Mathematical Surveys</i>, vol. 67, no. 6. IOP Publishing, pp. 1167–1168, 2012.","chicago":"Edelsbrunner, Herbert, and Nataliya Strelkova. “On the Configuration Space of Steiner Minimal Trees.” <i>Russian Mathematical Surveys</i>. IOP Publishing, 2012. <a href=\"https://doi.org/10.1070/RM2012v067n06ABEH004820\">https://doi.org/10.1070/RM2012v067n06ABEH004820</a>.","ista":"Edelsbrunner H, Strelkova N. 2012. On the configuration space of Steiner minimal trees. Russian Mathematical Surveys. 67(6), 1167–1168.","ama":"Edelsbrunner H, Strelkova N. On the configuration space of Steiner minimal trees. <i>Russian Mathematical Surveys</i>. 2012;67(6):1167-1168. doi:<a href=\"https://doi.org/10.1070/RM2012v067n06ABEH004820\">10.1070/RM2012v067n06ABEH004820</a>"},"title":"On the configuration space of Steiner minimal trees","page":"1167 - 1168","publication":"Russian Mathematical Surveys","author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"full_name":"Strelkova, Nataliya","first_name":"Nataliya","last_name":"Strelkova"}],"file":[{"access_level":"open_access","content_type":"application/pdf","file_id":"5078","creator":"system","date_updated":"2020-07-14T12:45:51Z","relation":"main_file","checksum":"44ee8d173487e8ed41a51136816bbeb4","file_name":"IST-2016-546-v1+1_2014-J-05-SteinerMinTrees.pdf","date_created":"2018-12-12T10:14:26Z","file_size":392021}],"fulldoi":"https://doi.org/10.1070/RM2012v067n06ABEH004820","pubrep_id":"546","ddc":["000"],"issue":"6","file_date_updated":"2020-07-14T12:45:51Z","oa_version":"Submitted Version","status":"public","publication_status":"published","has_accepted_license":"1","date_published":"2012-01-01T00:00:00Z","article_processing_charge":"No","isi":1,"publist_id":"3943","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","_id":"2849","day":"01","oa":1,"date_created":"2018-12-11T11:59:55Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"01","intvolume":"        67"},{"scopus_import":"1","date_updated":"2025-05-20T07:30:56Z","doi":"10.1007/978-3-642-33666-9_1","ec_funded":1,"volume":7590,"publisher":"Springer","year":"2012","citation":{"ista":"Henzinger TA. 2012. Quantitative reactive models. 15th International Conference on Model Driven Engineering Languages and Systems. MODELS: Model-driven Engineering Languages and Systems, LNCS, vol. 7590, 1–2.","ama":"Henzinger TA. Quantitative reactive models. In: <i>15th International Conference on Model Driven Engineering Languages and Systems</i>. Vol 7590. Springer; 2012:1-2. doi:<a href=\"https://doi.org/10.1007/978-3-642-33666-9_1\">10.1007/978-3-642-33666-9_1</a>","chicago":"Henzinger, Thomas A. “Quantitative Reactive Models.” In <i>15th International Conference on Model Driven Engineering Languages and Systems</i>, 7590:1–2. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33666-9_1\">https://doi.org/10.1007/978-3-642-33666-9_1</a>.","ieee":"T. A. Henzinger, “Quantitative reactive models,” in <i>15th International Conference on Model Driven Engineering Languages and Systems</i>, Innsbruck, Austria, 2012, vol. 7590, pp. 1–2.","apa":"Henzinger, T. A. (2012). Quantitative reactive models. In <i>15th International Conference on Model Driven Engineering Languages and Systems</i> (Vol. 7590, pp. 1–2). Innsbruck, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33666-9_1\">https://doi.org/10.1007/978-3-642-33666-9_1</a>","short":"T.A. Henzinger, in:, 15th International Conference on Model Driven Engineering Languages and Systems, Springer, 2012, pp. 1–2.","mla":"Henzinger, Thomas A. “Quantitative Reactive Models.” <i>15th International Conference on Model Driven Engineering Languages and Systems</i>, vol. 7590, Springer, 2012, pp. 1–2, doi:<a href=\"https://doi.org/10.1007/978-3-642-33666-9_1\">10.1007/978-3-642-33666-9_1</a>."},"department":[{"_id":"ToHe"}],"page":"1 - 2","title":"Quantitative reactive models","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"publication":"15th International Conference on Model Driven Engineering Languages and Systems","fulldoi":"https://doi.org/10.1007/978-3-642-33666-9_1","conference":{"location":"Innsbruck, Austria","start_date":"2012-09-30","end_date":"2012-10-05","name":"MODELS: Model-driven Engineering Languages and Systems"},"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publication_identifier":{"eisbn":["9783642336669"],"eissn":["1611-3349"]},"oa_version":"None","date_published":"2012-09-01T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Formal verification aims to improve the quality of hardware and software by detecting errors before they do harm. At the basis of formal verification lies the logical notion of correctness, which purports to capture whether or not a circuit or program behaves as desired. We suggest that the boolean partition into correct and incorrect systems falls short of the practical need to assess the behavior of hardware and software in a more nuanced fashion against multiple criteria."}],"publication_status":"published","article_processing_charge":"No","language":[{"iso":"eng"}],"publist_id":"3870","alternative_title":["LNCS"],"corr_author":"1","quality_controlled":"1","day":"01","_id":"2888","type":"conference","OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:00:09Z","intvolume":"      7590","month":"09"}]