[{"type":"conference","doi":"10.1007/978-3-642-28756-5_46","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-642-28756-5_46"}],"oa":1,"title":"HSF(C): A software verifier based on Horn clauses","publication_identifier":{"issn":["0302-9743"],"isbn":["9783642287558"],"eisbn":["9783642287565"],"eissn":["1611-3349"]},"author":[{"last_name":"Grebenshchikov","full_name":"Grebenshchikov, Sergey","first_name":"Sergey"},{"first_name":"Ashutosh","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta"},{"full_name":"Lopes, Nuno P.","last_name":"Lopes","first_name":"Nuno P."},{"first_name":"Corneliu","last_name":"Popeea","full_name":"Popeea, Corneliu"},{"full_name":"Rybalchenko, Andrey","last_name":"Rybalchenko","first_name":"Andrey"}],"publication":"Tools and Algorithms for the Construction and Analysis of Systems","scopus_import":"1","conference":{"end_date":"2012-04-01","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Tallinn, Estonia","start_date":"2012-03-24"},"corr_author":"1","quality_controlled":"1","place":"Berlin, Heidelberg","article_processing_charge":"No","date_created":"2022-03-21T08:03:30Z","month":"04","publication_status":"published","volume":7214,"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"series_title":"LNCS","page":"549-551","fulldoi":"https://doi.org/10.1007/978-3-642-28756-5_46","date_published":"2012-04-01T00:00:00Z","OA_type":"free access","ddc":["000"],"abstract":[{"lang":"eng","text":"HSF(C) is a tool that automates verification of safety and liveness properties for C programs. This paper describes the verification approach taken by HSF(C) and provides instructions on how to install and use the tool."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-28T09:23:52Z","alternative_title":["LNCS"],"intvolume":"      7214","publisher":"Springer","year":"2012","citation":{"ieee":"S. Grebenshchikov, A. Gupta, N. P. Lopes, C. Popeea, and A. Rybalchenko, “HSF(C): A software verifier based on Horn clauses,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Tallinn, Estonia, 2012, vol. 7214, pp. 549–551.","apa":"Grebenshchikov, S., Gupta, A., Lopes, N. P., Popeea, C., &#38; Rybalchenko, A. (2012). HSF(C): A software verifier based on Horn clauses. In C. Flanagan &#38; B. König (Eds.), <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 7214, pp. 549–551). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">https://doi.org/10.1007/978-3-642-28756-5_46</a>","ama":"Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. HSF(C): A software verifier based on Horn clauses. In: Flanagan C, König B, eds. <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 7214. LNCS. Berlin, Heidelberg: Springer; 2012:549-551. doi:<a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">10.1007/978-3-642-28756-5_46</a>","ista":"Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. 2012. HSF(C): A software verifier based on Horn clauses. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of SystemsLNCS, LNCS, vol. 7214, 549–551.","mla":"Grebenshchikov, Sergey, et al. “HSF(C): A Software Verifier Based on Horn Clauses.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, edited by Cormac Flanagan and Barbara König, vol. 7214, Springer, 2012, pp. 549–51, doi:<a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">10.1007/978-3-642-28756-5_46</a>.","short":"S. Grebenshchikov, A. Gupta, N.P. Lopes, C. Popeea, A. Rybalchenko, in:, C. Flanagan, B. König (Eds.), Tools and Algorithms for the Construction and Analysis of Systems, Springer, Berlin, Heidelberg, 2012, pp. 549–551.","chicago":"Grebenshchikov, Sergey, Ashutosh Gupta, Nuno P. Lopes, Corneliu Popeea, and Andrey Rybalchenko. “HSF(C): A Software Verifier Based on Horn Clauses.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, edited by Cormac Flanagan and Barbara König, 7214:549–51. LNCS. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">https://doi.org/10.1007/978-3-642-28756-5_46</a>."},"das_tickbox":"1","day":"01","oa_version":"Published Version","editor":[{"first_name":"Cormac","last_name":"Flanagan","full_name":"Flanagan, Cormac"},{"first_name":"Barbara","last_name":"König","full_name":"König, Barbara"}],"_id":"10906","status":"public"},{"author":[{"full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"publication":"Journal of Cell Biology","scopus_import":"1","corr_author":"1","type":"journal_article","doi":"10.1083/jcb.201204039","oa":1,"title":"Cell migration: Fibroblasts find a new way to get ahead","license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","month":"04","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"MiSi"}],"volume":197,"page":"347 - 349","quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T11:46:51Z","file_date_updated":"2020-07-14T12:46:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-28T09:22:21Z","publist_id":"7314","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode","short":"CC BY-NC-SA (3.0)"},"fulldoi":"https://doi.org/10.1083/jcb.201204039","article_type":"original","date_published":"2012-04-30T00:00:00Z","has_accepted_license":"1","ddc":["570"],"publisher":"Rockefeller University Press","year":"2012","citation":{"ieee":"M. K. Sixt, “Cell migration: Fibroblasts find a new way to get ahead,” <i>Journal of Cell Biology</i>, vol. 197, no. 3. Rockefeller University Press, pp. 347–349, 2012.","apa":"Sixt, M. K. (2012). Cell migration: Fibroblasts find a new way to get ahead. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201204039\">https://doi.org/10.1083/jcb.201204039</a>","ista":"Sixt MK. 2012. Cell migration: Fibroblasts find a new way to get ahead. Journal of Cell Biology. 197(3), 347–349.","ama":"Sixt MK. Cell migration: Fibroblasts find a new way to get ahead. <i>Journal of Cell Biology</i>. 2012;197(3):347-349. doi:<a href=\"https://doi.org/10.1083/jcb.201204039\">10.1083/jcb.201204039</a>","short":"M.K. Sixt, Journal of Cell Biology 197 (2012) 347–349.","mla":"Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.” <i>Journal of Cell Biology</i>, vol. 197, no. 3, Rockefeller University Press, 2012, pp. 347–49, doi:<a href=\"https://doi.org/10.1083/jcb.201204039\">10.1083/jcb.201204039</a>.","chicago":"Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2012. <a href=\"https://doi.org/10.1083/jcb.201204039\">https://doi.org/10.1083/jcb.201204039</a>."},"isi":1,"day":"30","das_tickbox":"1","oa_version":"Published Version","status":"public","_id":"506","intvolume":"       197","file":[{"date_created":"2019-02-12T09:03:09Z","file_size":986566,"file_name":"2012_CellBiology_Sixt.pdf","file_id":"5957","creator":"kschuh","date_updated":"2020-07-14T12:46:36Z","content_type":"application/pdf","checksum":"45c02be33ebd99fc3077d60b9c90bdfa","access_level":"open_access","relation":"main_file"}],"issue":"3","external_id":{"isi":["000303467800004"]}},{"scopus_import":"1","corr_author":"1","conference":{"start_date":"2012-09-04","location":"Newcastle upon Tyne, United Kingdom","end_date":"2012-09-07","name":"CONCUR: Conference on Concurrency Theory"},"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mickael","last_name":"Randour","full_name":"Randour, Mickael"},{"last_name":"Raskin","full_name":"Raskin, Jean-François","first_name":"Jean-François"}],"publication":"CONCUR 2012 - Concurrency Theory","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1201.5073","open_access":"1"}],"doi":"10.1007/978-3-642-32940-1_10","type":"conference","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783642329401"],"eissn":["1611-3349"],"isbn":["9783642329395"]},"title":"Strategy synthesis for multi-dimensional quantitative objectives","oa":1,"department":[{"_id":"KrCh"}],"volume":7454,"language":[{"iso":"eng"}],"publication_status":"published","page":"115-131","month":"09","date_created":"2022-03-21T08:00:21Z","article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"later_version","id":"2716"}]},"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"place":"Berlin, Heidelberg","alternative_title":["LNCS"],"date_updated":"2026-07-28T11:24:51Z","ec_funded":1,"abstract":[{"lang":"eng","text":"Multi-dimensional mean-payoff and energy games provide the mathematical foundation for the quantitative study of reactive systems, and play a central role in the emerging quantitative theory of verification and synthesis. In this work, we study the strategy synthesis problem for games with such multi-dimensional objectives along with a parity condition, a canonical way to express ω-regular conditions. While in general, the winning strategies in such games may require infinite memory, for synthesis the most relevant problem is the construction of a finite-memory winning strategy (if one exists). Our main contributions are as follows. First, we show a tight exponential bound (matching upper and lower bounds) on the memory required for finite-memory winning strategies in both multi-dimensional mean-payoff and energy games along with parity objectives. This significantly improves the triple exponential upper bound for multi energy games (without parity) that could be derived from results in literature for games on VASS (vector addition systems with states). Second, we present an optimal symbolic and incremental algorithm to compute a finite-memory winning strategy (if one exists) in such games. Finally, we give a complete characterization of when finite memory of strategies can be traded off for randomness. In particular, we show that for one-dimension mean-payoff parity games, randomized memoryless strategies are as powerful as their pure finite-memory counterparts."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1007/978-3-642-32940-1_10","date_published":"2012-09-15T00:00:00Z","OA_type":"green","OA_place":"repository","oa_version":"Preprint","editor":[{"full_name":"Koutny, Maciej","last_name":"Koutny","first_name":"Maciej"},{"last_name":"Ulidowski","full_name":"Ulidowski, Irek","first_name":"Irek"}],"status":"public","_id":"10904","acknowledgement":"Author supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407 (RiSE), ERC Start Grant (279307: Graph Games), Microsoft faculty fellowship.","citation":{"apa":"Chatterjee, K., Randour, M., &#38; Raskin, J.-F. (2012). Strategy synthesis for multi-dimensional quantitative objectives. In M. Koutny &#38; I. Ulidowski (Eds.), <i>CONCUR 2012 - Concurrency Theory</i> (Vol. 7454, pp. 115–131). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">https://doi.org/10.1007/978-3-642-32940-1_10</a>","ieee":"K. Chatterjee, M. Randour, and J.-F. Raskin, “Strategy synthesis for multi-dimensional quantitative objectives,” in <i>CONCUR 2012 - Concurrency Theory</i>, Newcastle upon Tyne, United Kingdom, 2012, vol. 7454, pp. 115–131.","ama":"Chatterjee K, Randour M, Raskin J-F. Strategy synthesis for multi-dimensional quantitative objectives. In: Koutny M, Ulidowski I, eds. <i>CONCUR 2012 - Concurrency Theory</i>. Vol 7454. Berlin, Heidelberg: Springer; 2012:115-131. doi:<a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">10.1007/978-3-642-32940-1_10</a>","ista":"Chatterjee K, Randour M, Raskin J-F. 2012. Strategy synthesis for multi-dimensional quantitative objectives. CONCUR 2012 - Concurrency Theory. CONCUR: Conference on Concurrency Theory, LNCS, vol. 7454, 115–131.","short":"K. Chatterjee, M. Randour, J.-F. Raskin, in:, M. Koutny, I. Ulidowski (Eds.), CONCUR 2012 - Concurrency Theory, Springer, Berlin, Heidelberg, 2012, pp. 115–131.","mla":"Chatterjee, Krishnendu, et al. “Strategy Synthesis for Multi-Dimensional Quantitative Objectives.” <i>CONCUR 2012 - Concurrency Theory</i>, edited by Maciej Koutny and Irek Ulidowski, vol. 7454, Springer, 2012, pp. 115–31, doi:<a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">10.1007/978-3-642-32940-1_10</a>.","chicago":"Chatterjee, Krishnendu, Mickael Randour, and Jean-François Raskin. “Strategy Synthesis for Multi-Dimensional Quantitative Objectives.” In <i>CONCUR 2012 - Concurrency Theory</i>, edited by Maciej Koutny and Irek Ulidowski, 7454:115–31. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">https://doi.org/10.1007/978-3-642-32940-1_10</a>."},"year":"2012","publisher":"Springer","arxiv":1,"day":"15","intvolume":"      7454","external_id":{"arxiv":["1201.5073"]}},{"ddc":["020"],"OA_type":"free access","date_published":"2012-03-01T00:00:00Z","article_type":"comment","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Wie wandelt sich das Berufsbild in Wissenschaftlichen Bibliotheken? Patrick Danowski gibt seine Einschätzung ab. ","lang":"eng"}],"date_updated":"2026-07-28T09:15:13Z","publist_id":"3433","issue":"1","intvolume":"      2012","das_tickbox":"1","day":"01","year":"2012","citation":{"ieee":"P. Danowski, “Zwischen Technologie und Kommunikation,” <i>Büchereiperspektiven</i>, vol. 2012, no. 1. Büchereiverband Österreichs, p. 11, 2012.","apa":"Danowski, P. (2012). Zwischen Technologie und Kommunikation. <i>Büchereiperspektiven</i>. Büchereiverband Österreichs.","ista":"Danowski P. 2012. Zwischen Technologie und Kommunikation. Büchereiperspektiven. 2012(1), 11.","ama":"Danowski P. Zwischen Technologie und Kommunikation. <i>Büchereiperspektiven</i>. 2012;2012(1):11.","mla":"Danowski, Patrick. “Zwischen Technologie und Kommunikation.” <i>Büchereiperspektiven</i>, vol. 2012, no. 1, Büchereiverband Österreichs, 2012, p. 11.","short":"P. Danowski, Büchereiperspektiven 2012 (2012) 11.","chicago":"Danowski, Patrick. “Zwischen Technologie und Kommunikation.” <i>Büchereiperspektiven</i>. Büchereiverband Österreichs, 2012."},"publisher":"Büchereiverband Österreichs","status":"public","_id":"3243","oa_version":"Published Version","publication_identifier":{"issn":["1607-7172"]},"title":"Zwischen Technologie und Kommunikation","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.bvoe.at/sites/default/files/2022-07/BP_1_12.pdf"}],"type":"journal_article","publication":"Büchereiperspektiven","author":[{"id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","last_name":"Danowski","full_name":"Danowski, Patrick","orcid":"0000-0002-6026-4409","first_name":"Patrick"}],"corr_author":"1","date_created":"2018-12-11T12:02:13Z","article_processing_charge":"No","month":"03","popular_science":"1","page":"11","volume":2012,"language":[{"iso":"ger"}],"department":[{"_id":"E-Lib"}],"publication_status":"published"},{"abstract":[{"text":"Contractile actomyosin rings drive various fundamental morphogenetic processes ranging from cytokinesis to wound healing. Actomyosin rings are generally thought to function by circumferential contraction. Here, we show that the spreading of the enveloping cell layer (EVL) over the yolk cell during zebrafish gastrulation is driven by a contractile actomyosin ring. In contrast to previous suggestions, we find that this ring functions not only by circumferential contraction but also by a flow-friction mechanism. This generates a pulling force through resistance against retrograde actomyosin flow. EVL spreading proceeds normally in situations where circumferential contraction is unproductive, indicating that the flow-friction mechanism is sufficient. Thus, actomyosin rings can function in epithelial morphogenesis through a combination of cable-constriction and flow-friction mechanisms.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-07-29T10:07:18Z","publist_id":"3778","fulldoi":"https://doi.org/10.1126/science.1224143","article_type":"original","date_published":"2012-10-12T00:00:00Z","OA_type":"closed access","acknowledgement":"We are grateful to M. Sixt, T. Bollenbach, and E. Martin-Blanco for advice and the service facilities of the IST Austria and MPI-CBG for continuous help. M.B., G.S., S.W.G., and C.-P.H. synergistically and equally developed the presented ideas and the experimental and theoretical approaches. M.B. and P.C. performed the experiments; G.S. developed the theory; and R.H., F.O., and J.R. contributed to the experimental work. This work was supported by a grant from the Fonds zur Förderung der wissenschaftlichen Forschung (FWF) and the Deutsche Forschungsgemeinschaft (DFG) (I930-B20) to C.-P.H., S.W.G., and G.S.","citation":{"short":"M. Behrndt, G. Salbreux, P. Campinho, R. Hauschild, F. Oswald, J. Roensch, S. Grill, C.-P.J. Heisenberg, Science 338 (2012) 257–260.","mla":"Behrndt, Martin, et al. “Forces Driving Epithelial Spreading in Zebrafish Gastrulation.” <i>Science</i>, vol. 338, no. 6104, American Association for the Advancement of Science, 2012, pp. 257–60, doi:<a href=\"https://doi.org/10.1126/science.1224143\">10.1126/science.1224143</a>.","chicago":"Behrndt, Martin, Guillaume Salbreux, Pedro Campinho, Robert Hauschild, Felix Oswald, Julia Roensch, Stephan Grill, and Carl-Philipp J Heisenberg. “Forces Driving Epithelial Spreading in Zebrafish Gastrulation.” <i>Science</i>. American Association for the Advancement of Science, 2012. <a href=\"https://doi.org/10.1126/science.1224143\">https://doi.org/10.1126/science.1224143</a>.","ieee":"M. Behrndt <i>et al.</i>, “Forces driving epithelial spreading in zebrafish gastrulation,” <i>Science</i>, vol. 338, no. 6104. American Association for the Advancement of Science, pp. 257–260, 2012.","apa":"Behrndt, M., Salbreux, G., Campinho, P., Hauschild, R., Oswald, F., Roensch, J., … Heisenberg, C.-P. J. (2012). Forces driving epithelial spreading in zebrafish gastrulation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1224143\">https://doi.org/10.1126/science.1224143</a>","ista":"Behrndt M, Salbreux G, Campinho P, Hauschild R, Oswald F, Roensch J, Grill S, Heisenberg C-PJ. 2012. Forces driving epithelial spreading in zebrafish gastrulation. Science. 338(6104), 257–260.","ama":"Behrndt M, Salbreux G, Campinho P, et al. Forces driving epithelial spreading in zebrafish gastrulation. <i>Science</i>. 2012;338(6104):257-260. doi:<a href=\"https://doi.org/10.1126/science.1224143\">10.1126/science.1224143</a>"},"year":"2012","publisher":"American Association for the Advancement of Science","day":"12","isi":1,"oa_version":"None","status":"public","_id":"2950","intvolume":"       338","external_id":{"pmid":["23066079"],"isi":["000309712300046"]},"issue":"6104","acknowledged_ssus":[{"_id":"SSU"}],"author":[{"full_name":"Behrndt, Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"last_name":"Salbreux","full_name":"Salbreux, Guillaume","first_name":"Guillaume"},{"full_name":"Campinho, Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","last_name":"Campinho","orcid":"0000-0002-8526-5416","first_name":"Pedro"},{"first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"first_name":"Felix","last_name":"Oswald","full_name":"Oswald, Felix"},{"first_name":"Julia","full_name":"Roensch, Julia","id":"4220E59C-F248-11E8-B48F-1D18A9856A87","last_name":"Roensch"},{"first_name":"Stephan","full_name":"Grill, Stephan","last_name":"Grill"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"publication":"Science","scopus_import":"1","corr_author":"1","doi":"10.1126/science.1224143","type":"journal_article","pmid":1,"title":"Forces driving epithelial spreading in zebrafish gastrulation","month":"10","department":[{"_id":"CaHe"},{"_id":"Bio"}],"volume":338,"language":[{"iso":"eng"}],"publication_status":"published","page":"257 - 260","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1403"}]},"quality_controlled":"1","project":[{"grant_number":"I930-B20","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","call_identifier":"FWF"}],"date_created":"2018-12-11T12:00:30Z","article_processing_charge":"No"},{"publist_id":"3537","date_updated":"2026-07-29T10:15:25Z","ec_funded":1,"abstract":[{"text":"Colorectal tumours that are wild type for KRAS are often sensitive to EGFR blockade, but almost always develop resistance within several months of initiating therapy. The mechanisms underlying this acquired resistance to anti-EGFR antibodies are largely unknown. This situation is in marked contrast to that of small-molecule targeted agents, such as inhibitors of ABL, EGFR, BRAF and MEK, in which mutations in the genes encoding the protein targets render the tumours resistant to the effects of the drugs. The simplest hypothesis to account for the development of resistance to EGFR blockade is that rare cells with KRAS mutations pre-exist at low levels in tumours with ostensibly wild-type KRAS genes. Although this hypothesis would seem readily testable, there is no evidence in pre-clinical models to support it, nor is there data from patients. To test this hypothesis, we determined whether mutant KRAS DNA could be detected in the circulation of 28 patients receiving monotherapy with panitumumab, a therapeutic anti-EGFR antibody. We found that 9 out of 24 (38%) patients whose tumours were initially KRAS wild type developed detectable mutations in KRAS in their sera, three of which developed multiple different KRAS mutations. The appearance of these mutations was very consistent, generally occurring between 5 and 6months following treatment. Mathematical modelling indicated that the mutations were present in expanded subclones before the initiation of panitumumab treatment. These results suggest that the emergence of KRAS mutations is a mediator of acquired resistance to EGFR blockade and that these mutations can be detected in a non-invasive manner. They explain why solid tumours develop resistance to targeted therapies in a highly reproducible fashion.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1038/nature11219","date_published":"2012-06-28T00:00:00Z","oa_version":"Submitted Version","status":"public","_id":"3157","publisher":"Nature Publishing Group","year":"2012","citation":{"ieee":"L. Diaz Jr <i>et al.</i>, “The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers,” <i>Nature</i>, vol. 486, no. 7404. Nature Publishing Group, pp. 537–540, 2012.","apa":"Diaz Jr, L., Williams, R., Wu, J., Kinde, I., Hecht, J., Berlin, J., … Vogelstein, B. (2012). The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature11219\">https://doi.org/10.1038/nature11219</a>","ama":"Diaz Jr L, Williams R, Wu J, et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. <i>Nature</i>. 2012;486(7404):537-540. doi:<a href=\"https://doi.org/10.1038/nature11219\">10.1038/nature11219</a>","ista":"Diaz Jr L, Williams R, Wu J, Kinde I, Hecht J, Berlin J, Allen B, Božić I, Reiter J, Nowak M, Kinzler K, Oliner K, Vogelstein B. 2012. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 486(7404), 537–540.","short":"L. Diaz Jr, R. Williams, J. Wu, I. Kinde, J. Hecht, J. Berlin, B. Allen, I. Božić, J. Reiter, M. Nowak, K. Kinzler, K. Oliner, B. Vogelstein, Nature 486 (2012) 537–540.","mla":"Diaz Jr, Luis, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” <i>Nature</i>, vol. 486, no. 7404, Nature Publishing Group, 2012, pp. 537–40, doi:<a href=\"https://doi.org/10.1038/nature11219\">10.1038/nature11219</a>.","chicago":"Diaz Jr, Luis, Richard Williams, Jian Wu, Isaac Kinde, Joel Hecht, Jordan Berlin, Benjamin Allen, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” <i>Nature</i>. Nature Publishing Group, 2012. <a href=\"https://doi.org/10.1038/nature11219\">https://doi.org/10.1038/nature11219</a>."},"isi":1,"day":"28","intvolume":"       486","issue":"7404","external_id":{"pmid":["22722843"],"isi":["000305760600044"]},"scopus_import":"1","author":[{"full_name":"Diaz Jr, Luis","last_name":"Diaz Jr","first_name":"Luis"},{"full_name":"Williams, Richard","last_name":"Williams","first_name":"Richard"},{"last_name":"Wu","full_name":"Wu, Jian","first_name":"Jian"},{"last_name":"Kinde","full_name":"Kinde, Isaac","first_name":"Isaac"},{"full_name":"Hecht, Joel","last_name":"Hecht","first_name":"Joel"},{"first_name":"Jordan","last_name":"Berlin","full_name":"Berlin, Jordan"},{"last_name":"Allen","full_name":"Allen, Benjamin","first_name":"Benjamin"},{"full_name":"Božić, Ivana","last_name":"Božić","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":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"},{"first_name":"Kenneth","full_name":"Kinzler, Kenneth","last_name":"Kinzler"},{"full_name":"Oliner, Kelly","last_name":"Oliner","first_name":"Kelly"},{"last_name":"Vogelstein","full_name":"Vogelstein, Bert","first_name":"Bert"}],"publication":"Nature","type":"journal_article","doi":"10.1038/nature11219","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436069/"}],"title":"The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers","oa":1,"pmid":1,"publication_status":"published","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"volume":486,"page":"537 - 540","month":"06","article_processing_charge":"No","date_created":"2018-12-11T12:01:43Z","related_material":{"record":[{"status":"public","id":"1400","relation":"dissertation_contains"}]},"quality_controlled":"1","project":[{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}]},{"corr_author":"1","scopus_import":"1","publication":"Theoretical Population Biology","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes","first_name":"Johannes","orcid":"0000-0002-0170-7353"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"pmid":1,"title":"Evolutionary dynamics of biological auctions","oa":1,"doi":"10.1016/j.tpb.2011.11.003","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279759/ ","open_access":"1"}],"type":"journal_article","page":"69 - 80","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"volume":81,"publication_status":"published","month":"02","date_created":"2018-12-11T12:02:19Z","article_processing_charge":"No","project":[{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"related_material":{"record":[{"id":"1400","relation":"dissertation_contains","status":"public"}]},"quality_controlled":"1","date_updated":"2026-07-29T10:15:25Z","publist_id":"3388","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Many scenarios in the living world, where individual organisms compete for winning positions (or resources), have properties of auctions. Here we study the evolution of bids in biological auctions. For each auction, n individuals are drawn at random from a population of size N. Each individual makes a bid which entails a cost. The winner obtains a benefit of a certain value. Costs and benefits are translated into reproductive success (fitness). Therefore, successful bidding strategies spread in the population. We compare two types of auctions. In “biological all-pay auctions”, the costs are the bid for every participating individual. In “biological second price all-pay auctions”, the cost for everyone other than the winner is the bid, but the cost for the winner is the second highest bid. Second price all-pay auctions are generalizations of the “war of attrition” introduced by Maynard Smith. We study evolutionary dynamics in both types of auctions. We calculate pairwise invasion plots and evolutionarily stable distributions over the continuous strategy space. We find that the average bid in second price all-pay auctions is higher than in all-pay auctions, but the average cost for the winner is similar in both auctions. In both cases, the average bid is a declining function of the number of participants, n. The more individuals participate in an auction the smaller is the chance of winning, and thus expensive bids must be avoided.\r\n","lang":"eng"}],"ec_funded":1,"date_published":"2012-02-01T00:00:00Z","fulldoi":"https://doi.org/10.1016/j.tpb.2011.11.003","status":"public","_id":"3260","oa_version":"Submitted Version","day":"01","isi":1,"year":"2012","citation":{"chicago":"Chatterjee, Krishnendu, Johannes Reiter, and Martin Nowak. “Evolutionary Dynamics of Biological Auctions.” <i>Theoretical Population Biology</i>. Academic Press, 2012. <a href=\"https://doi.org/10.1016/j.tpb.2011.11.003\">https://doi.org/10.1016/j.tpb.2011.11.003</a>.","short":"K. Chatterjee, J. Reiter, M. Nowak, Theoretical Population Biology 81 (2012) 69–80.","mla":"Chatterjee, Krishnendu, et al. “Evolutionary Dynamics of Biological Auctions.” <i>Theoretical Population Biology</i>, vol. 81, no. 1, Academic Press, 2012, pp. 69–80, doi:<a href=\"https://doi.org/10.1016/j.tpb.2011.11.003\">10.1016/j.tpb.2011.11.003</a>.","ista":"Chatterjee K, Reiter J, Nowak M. 2012. Evolutionary dynamics of biological auctions. Theoretical Population Biology. 81(1), 69–80.","ama":"Chatterjee K, Reiter J, Nowak M. Evolutionary dynamics of biological auctions. <i>Theoretical Population Biology</i>. 2012;81(1):69-80. doi:<a href=\"https://doi.org/10.1016/j.tpb.2011.11.003\">10.1016/j.tpb.2011.11.003</a>","apa":"Chatterjee, K., Reiter, J., &#38; Nowak, M. (2012). Evolutionary dynamics of biological auctions. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2011.11.003\">https://doi.org/10.1016/j.tpb.2011.11.003</a>","ieee":"K. Chatterjee, J. Reiter, and M. Nowak, “Evolutionary dynamics of biological auctions,” <i>Theoretical Population Biology</i>, vol. 81, no. 1. Academic Press, pp. 69–80, 2012."},"publisher":"Academic Press","external_id":{"pmid":["22120126"],"isi":["000298938200006"]},"issue":"1","intvolume":"        81"},{"author":[{"last_name":"Fatichi","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","full_name":"Fatichi, Simone","first_name":"Simone"},{"first_name":"V. Y.","last_name":"Ivanov","full_name":"Ivanov, V. Y."},{"first_name":"E.","full_name":"Caporali, E.","last_name":"Caporali"}],"publication":"Journal of Advances in Modeling Earth Systems","scopus_import":"1","extern":"1","article_number":"2011MS000087","type":"journal_article","doi":"10.1029/2011ms000087","title":"A mechanistic ecohydrological model to investigate complex interactions in cold and warm water‐controlled environments: 2. Spatiotemporal analyses","publication_identifier":{"eissn":["1942-2466"]},"month":"05","publication_status":"published","volume":4,"language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","date_created":"2026-07-27T12:30:23Z","abstract":[{"lang":"eng","text":"An ecohydrological model Tethys‐Chloris (T&amp;C) described in the companion paper is applied to two semiarid systems characterized by different climate and vegetation cover conditions. The Lucky Hills watershed in Arizona represents a typical small, “unit‐source” catchment of a desert shrub system of the U.S. southwest. Two nested basins of the Reynolds Creek Experimental watershed (Idaho, U.S.A.), the Reynolds Creek Mountain East and Tollgate catchments, are representative of a semiarid cold climate with seasonal snow cover. Both exhibit a highly non‐uniform vegetation cover. A range of ecohydrological metrics of the long‐term model performance is presented to highlight the model capabilities in reproducing hydrological and vegetation dynamics both at the plot and the watershed scales. A diverse set of observations is used to confirm the simulated dynamics. Highly satisfactory results are obtained without significant (or any) calibration efforts despite the large phase‐space dimensionality of the model, the uncertainty of imposed boundary conditions, and limited data availability. It is argued that a significant investment into the model design based on the description of physical, biophysical, and ecological processes leads to such a consistent simulation skill. The simulated patterns mimic the outcome of hydrological and vegetation dynamics with high realism, as confirmed from spatially distributed remote sensing data. Further community efforts are warranted to address the issue of thorough quantitative assessment. The current lack of appropriate data hampers the development and testing of process‐based ecohydrological models. It is further argued that the mechanistic nature of the T&amp;C model can be valuable for designing virtual experiments and developing questions of scientific inquiry at a range of spatiotemporal scales."}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-08-03T14:04:42Z","DOAJ_listed":"1","article_type":"original","fulldoi":"https://doi.org/10.1029/2011ms000087","date_published":"2012-05-30T00:00:00Z","OA_type":"closed access","publisher":"American Geophysical Union","year":"2012","citation":{"short":"S. Fatichi, V.Y. Ivanov, E. Caporali, Journal of Advances in Modeling Earth Systems 4 (2012).","mla":"Fatichi, Simone, et al. “A Mechanistic Ecohydrological Model to Investigate Complex Interactions in Cold and Warm Water‐controlled Environments: 2. Spatiotemporal Analyses.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 4, no. 2, 2011MS000087, American Geophysical Union, 2012, doi:<a href=\"https://doi.org/10.1029/2011ms000087\">10.1029/2011ms000087</a>.","chicago":"Fatichi, Simone, V. Y. Ivanov, and E. Caporali. “A Mechanistic Ecohydrological Model to Investigate Complex Interactions in Cold and Warm Water‐controlled Environments: 2. Spatiotemporal Analyses.” <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union, 2012. <a href=\"https://doi.org/10.1029/2011ms000087\">https://doi.org/10.1029/2011ms000087</a>.","apa":"Fatichi, S., Ivanov, V. Y., &#38; Caporali, E. (2012). A mechanistic ecohydrological model to investigate complex interactions in cold and warm water‐controlled environments: 2. Spatiotemporal analyses. <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2011ms000087\">https://doi.org/10.1029/2011ms000087</a>","ieee":"S. Fatichi, V. Y. Ivanov, and E. Caporali, “A mechanistic ecohydrological model to investigate complex interactions in cold and warm water‐controlled environments: 2. Spatiotemporal analyses,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 4, no. 2. American Geophysical Union, 2012.","ista":"Fatichi S, Ivanov VY, Caporali E. 2012. A mechanistic ecohydrological model to investigate complex interactions in cold and warm water‐controlled environments: 2. Spatiotemporal analyses. Journal of Advances in Modeling Earth Systems. 4(2), 2011MS000087.","ama":"Fatichi S, Ivanov VY, Caporali E. A mechanistic ecohydrological model to investigate complex interactions in cold and warm water‐controlled environments: 2. Spatiotemporal analyses. <i>Journal of Advances in Modeling Earth Systems</i>. 2012;4(2). doi:<a href=\"https://doi.org/10.1029/2011ms000087\">10.1029/2011ms000087</a>"},"das_tickbox":"1","day":"30","oa_version":"None","_id":"22482","status":"public","intvolume":"         4","issue":"2"},{"month":"08","page":"5512-5523","language":[{"iso":"eng"}],"volume":25,"publication_status":"published","quality_controlled":"1","date_created":"2026-07-27T12:30:24Z","article_processing_charge":"No","publication":"Journal of Climate","author":[{"first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi","full_name":"Fatichi, Simone"},{"last_name":"Ivanov","full_name":"Ivanov, V. Yu.","first_name":"V. Yu."},{"last_name":"Caporali","full_name":"Caporali, E.","first_name":"E."}],"scopus_import":"1","extern":"1","publication_identifier":{"eissn":["1520-0442"],"issn":["0894-8755"]},"title":"Investigating interannual variability of precipitation at the global scale: Is there a connection with seasonality?","doi":"10.1175/jcli-d-11-00356.1","type":"journal_article","day":"15","das_tickbox":"1","year":"2012","citation":{"ista":"Fatichi S, Ivanov VY, Caporali E. 2012. Investigating interannual variability of precipitation at the global scale: Is there a connection with seasonality? Journal of Climate. 25(16), 5512–5523.","ama":"Fatichi S, Ivanov VY, Caporali E. Investigating interannual variability of precipitation at the global scale: Is there a connection with seasonality? <i>Journal of Climate</i>. 2012;25(16):5512-5523. doi:<a href=\"https://doi.org/10.1175/jcli-d-11-00356.1\">10.1175/jcli-d-11-00356.1</a>","ieee":"S. Fatichi, V. Y. Ivanov, and E. Caporali, “Investigating interannual variability of precipitation at the global scale: Is there a connection with seasonality?,” <i>Journal of Climate</i>, vol. 25, no. 16. American Meteorological Society, pp. 5512–5523, 2012.","apa":"Fatichi, S., Ivanov, V. Y., &#38; Caporali, E. (2012). Investigating interannual variability of precipitation at the global scale: Is there a connection with seasonality? <i>Journal of Climate</i>. American Meteorological Society. <a href=\"https://doi.org/10.1175/jcli-d-11-00356.1\">https://doi.org/10.1175/jcli-d-11-00356.1</a>","chicago":"Fatichi, Simone, V. Yu. Ivanov, and E. Caporali. “Investigating Interannual Variability of Precipitation at the Global Scale: Is There a Connection with Seasonality?” <i>Journal of Climate</i>. American Meteorological Society, 2012. <a href=\"https://doi.org/10.1175/jcli-d-11-00356.1\">https://doi.org/10.1175/jcli-d-11-00356.1</a>.","short":"S. Fatichi, V.Y. Ivanov, E. Caporali, Journal of Climate 25 (2012) 5512–5523.","mla":"Fatichi, Simone, et al. “Investigating Interannual Variability of Precipitation at the Global Scale: Is There a Connection with Seasonality?” <i>Journal of Climate</i>, vol. 25, no. 16, American Meteorological Society, 2012, pp. 5512–23, doi:<a href=\"https://doi.org/10.1175/jcli-d-11-00356.1\">10.1175/jcli-d-11-00356.1</a>."},"publisher":"American Meteorological Society","_id":"22518","status":"public","oa_version":"None","issue":"16","intvolume":"        25","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"lang":"eng","text":"Interannual variability of precipitation can directly or indirectly affect many hydrological, ecological, and biogeochemical processes that, in turn, influence climate. Despite the significant importance of the phenomenon, few studies have attempted to elucidate spatial patterns of this variability at the global scale. This study uses land gauge precipitation records of the Global Historical Climatology Network, version 2, as well as reanalysis data to provide an assessment of the spatial organization of characteristics of precipitation interannual variability. The coefficient of variation, skewness, and short- and long-range dependence of the precipitation variability are analyzed. Among the major inferences is that the coefficient of variation of annual precipitation shows a significant correlation with intra-annual seasonality. Specifically, subyearly precipitation anomalies occurring in locations with pronounced seasonality affect the total yearly amount, imposing a higher variability in the annual precipitation fluctuations. Furthermore, the study illustrates that a positive skewness of the distribution of annual precipitation is a robust property worldwide and its magnitude is related to the coefficient of variation. Additionally, annual precipitation exhibits very weak small-lag autocorrelation. Conversely, the intensity of long-memory–long-range dependence is significantly larger than zero, hinting that organized long-term variations are an important feature of the interannual variability of precipitation.\r\n\r\n"}],"date_updated":"2026-08-06T09:54:05Z","date_published":"2012-08-15T00:00:00Z","OA_type":"closed access","article_type":"original","fulldoi":"https://doi.org/10.1175/jcli-d-11-00356.1"},{"quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T11:56:38Z","month":"12","publication_status":"published","pubrep_id":"387","volume":1,"department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"page":"1200 - 1203","type":"journal_article","doi":"10.1242/bio.20122287","title":"A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors","oa":1,"author":[{"last_name":"Liang","full_name":"Liang, Huixuan","first_name":"Huixuan"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"full_name":"Ghashghaei, H.","last_name":"Ghashghaei","first_name":"H."}],"publication":"Biology Open","scopus_import":"1","intvolume":"         1","file":[{"access_level":"open_access","checksum":"605a1800b81227848c361fd6ba7d22ba","relation":"main_file","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:45:35Z","file_id":"4990","date_created":"2018-12-12T10:13:09Z","file_size":726695,"file_name":"IST-2015-387-v1+1_1200.full.pdf"}],"issue":"12","external_id":{"isi":["000209205700005"]},"publisher":"Company of Biologists","citation":{"short":"H. Liang, S. Hippenmeyer, H. Ghashghaei, Biology Open 1 (2012) 1200–1203.","mla":"Liang, Huixuan, et al. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.” <i>Biology Open</i>, vol. 1, no. 12, Company of Biologists, 2012, pp. 1200–03, doi:<a href=\"https://doi.org/10.1242/bio.20122287\">10.1242/bio.20122287</a>.","chicago":"Liang, Huixuan, Simon Hippenmeyer, and H. Ghashghaei. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.” <i>Biology Open</i>. Company of Biologists, 2012. <a href=\"https://doi.org/10.1242/bio.20122287\">https://doi.org/10.1242/bio.20122287</a>.","apa":"Liang, H., Hippenmeyer, S., &#38; Ghashghaei, H. (2012). A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. <i>Biology Open</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/bio.20122287\">https://doi.org/10.1242/bio.20122287</a>","ieee":"H. Liang, S. Hippenmeyer, and H. Ghashghaei, “A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors,” <i>Biology Open</i>, vol. 1, no. 12. Company of Biologists, pp. 1200–1203, 2012.","ista":"Liang H, Hippenmeyer S, Ghashghaei H. 2012. A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. Biology Open. 1(12), 1200–1203.","ama":"Liang H, Hippenmeyer S, Ghashghaei H. A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. <i>Biology Open</i>. 2012;1(12):1200-1203. doi:<a href=\"https://doi.org/10.1242/bio.20122287\">10.1242/bio.20122287</a>"},"year":"2012","isi":1,"day":"15","oa_version":"Published Version","_id":"2263","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"fulldoi":"https://doi.org/10.1242/bio.20122287","date_published":"2012-12-15T00:00:00Z","has_accepted_license":"1","ddc":["576"],"file_date_updated":"2020-07-14T12:45:35Z","abstract":[{"lang":"eng","text":"Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4682","date_updated":"2026-08-12T09:32:12Z"},{"publication_status":"published","volume":4,"language":[{"iso":"eng"}],"month":"05","article_processing_charge":"No","date_created":"2026-07-27T12:30:24Z","quality_controlled":"1","scopus_import":"1","author":[{"full_name":"Fatichi, Simone","last_name":"Fatichi","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","first_name":"Simone"},{"first_name":"V. Y.","full_name":"Ivanov, V. Y.","last_name":"Ivanov"},{"first_name":"E.","last_name":"Caporali","full_name":"Caporali, E."}],"publication":"Journal of Advances in Modeling Earth Systems","type":"journal_article","doi":"10.1029/2011ms000086","main_file_link":[{"url":"https://doi.org/10.1029/2011MS000086","open_access":"1"}],"title":"A mechanistic ecohydrological model to investigate complex interactions in cold and warm water‐controlled environments: 1. Theoretical framework and plot‐scale analysis","oa":1,"publication_identifier":{"eissn":["1942-2466"]},"extern":"1","article_number":"2011MS000086","oa_version":"Published Version","status":"public","_id":"22538","publisher":"American Geophysical Union","year":"2012","citation":{"chicago":"Fatichi, Simone, V. Y. Ivanov, and E. Caporali. “A Mechanistic Ecohydrological Model to Investigate Complex Interactions in Cold and Warm Water‐controlled Environments: 1. Theoretical Framework and Plot‐scale Analysis.” <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union, 2012. <a href=\"https://doi.org/10.1029/2011ms000086\">https://doi.org/10.1029/2011ms000086</a>.","mla":"Fatichi, Simone, et al. “A Mechanistic Ecohydrological Model to Investigate Complex Interactions in Cold and Warm Water‐controlled Environments: 1. Theoretical Framework and Plot‐scale Analysis.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 4, no. 2, 2011MS000086, American Geophysical Union, 2012, doi:<a href=\"https://doi.org/10.1029/2011ms000086\">10.1029/2011ms000086</a>.","short":"S. Fatichi, V.Y. Ivanov, E. Caporali, Journal of Advances in Modeling Earth Systems 4 (2012).","ista":"Fatichi S, Ivanov VY, Caporali E. 2012. A mechanistic ecohydrological model to investigate complex interactions in cold and warm water‐controlled environments: 1. Theoretical framework and plot‐scale analysis. Journal of Advances in Modeling Earth Systems. 4(2), 2011MS000086.","ama":"Fatichi S, Ivanov VY, Caporali E. A mechanistic ecohydrological model to investigate complex interactions in cold and warm water‐controlled environments: 1. Theoretical framework and plot‐scale analysis. <i>Journal of Advances in Modeling Earth Systems</i>. 2012;4(2). doi:<a href=\"https://doi.org/10.1029/2011ms000086\">10.1029/2011ms000086</a>","apa":"Fatichi, S., Ivanov, V. Y., &#38; Caporali, E. (2012). A mechanistic ecohydrological model to investigate complex interactions in cold and warm water‐controlled environments: 1. Theoretical framework and plot‐scale analysis. <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2011ms000086\">https://doi.org/10.1029/2011ms000086</a>","ieee":"S. Fatichi, V. Y. Ivanov, and E. Caporali, “A mechanistic ecohydrological model to investigate complex interactions in cold and warm water‐controlled environments: 1. Theoretical framework and plot‐scale analysis,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 4, no. 2. American Geophysical Union, 2012."},"das_tickbox":"1","day":"30","intvolume":"         4","issue":"2","date_updated":"2026-08-12T12:02:45Z","abstract":[{"lang":"eng","text":"Numerous studies have explored the role of vegetation in controlling and mediating hydrological states and fluxes at the level of individual processes, which has led to improvements in our understanding of plot-scale dynamics. Relatively less effort has been directed toward spatially-explicit studies of vegetation-hydrology interactions at larger scales of a landscape. Only few continuous, process-oriented ecohydrological models had been proposed with structures of varying complexity. This study contributes to their further evolution and presents a novel ecohydrological model, Tethys-Chloris. The model synthesizes the state-of-the-art knowledge on individual processes and coupling mechanisms drawn from the disciplines of hydrology, plant physiology, and ecology. Specifically, the model reproduces all essential components of the hydrological cycle: it resolves the mass and energy budgets in the atmospheric surface layer at the hourly scale, while representing up to two layers of vegetation; it includes a module of snowpack evolution; it describes the saturated and unsaturated soil water dynamics, processes of runoff generation and flow routing. The component of vegetation dynamics parameterizes life cycle processes of different plant functional types, including photosynthesis, phenology, carbon allocation, and tissue turnover. This study presents a confirmation of the long-term, plot-scale model performance by simulating two types of ecosystems corresponding to different climate conditions. A consistent and highly satisfactory model skill in reproducing the energy and water budgets as well as physiological cycles of plants with minimum calibration overhead is demonstrated. Furthermore, these applications demonstrate that the model permits the identification of data types and observation frequencies crucial for appropriate evaluation of modeled dynamics. More importantly, through a synthesis of a wide array of process representations, the model ensures that climate, soil, vegetation, and topography collectively identify essential modes controlling ecohydrological systems, i.e., that satisfactory performance is a result of appropriate mimicking of internal processes."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","fulldoi":"https://doi.org/10.1029/2011ms000086","OA_type":"gold","date_published":"2012-05-30T00:00:00Z","DOAJ_listed":"1","OA_place":"publisher"},{"date_created":"2018-12-11T12:00:35Z","article_processing_charge":"No","language":[{"iso":"ger"}],"department":[{"_id":"E-Lib"}],"volume":65,"publication_status":"published","pubrep_id":"95","page":"200 - 212","month":"09","popular_science":"1","main_file_link":[{"url":" http://hdl.handle.net/10760/17625","open_access":"1"}],"type":"journal_article","oa":1,"title":"Kontext Open Access: Creative Commons","scopus_import":"1","corr_author":"1","author":[{"id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","last_name":"Danowski","full_name":"Danowski, Patrick","first_name":"Patrick","orcid":"0000-0002-6026-4409"}],"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","file":[{"file_name":"IST-2012-95-v1+1_sp-beitrag_danowski_kontext_open_access_creative_commons.pdf","file_size":503345,"date_created":"2018-12-12T10:08:42Z","file_id":"4703","date_updated":"2020-07-14T12:45:57Z","content_type":"application/pdf","creator":"system","relation":"main_file","access_level":"open_access","checksum":"162eea47d9d840c26b496ba6ae4d1c09"}],"intvolume":"        65","issue":"2","oa_version":"Published Version","_id":"2965","status":"public","year":"2012","citation":{"ieee":"P. Danowski, “Kontext Open Access: Creative Commons,” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 65, no. 2. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 200–212, 2012.","apa":"Danowski, P. (2012). Kontext Open Access: Creative Commons. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare.","ista":"Danowski P. 2012. Kontext Open Access: Creative Commons. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 65(2), 200–212.","ama":"Danowski P. Kontext Open Access: Creative Commons. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. 2012;65(2):200-212.","short":"P. Danowski, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 65 (2012) 200–212.","mla":"Danowski, Patrick. “Kontext Open Access: Creative Commons.” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 65, no. 2, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2012, pp. 200–12.","chicago":"Danowski, Patrick. “Kontext Open Access: Creative Commons.” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2012."},"publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","day":"01","das_tickbox":"1","tmp":{"image":"/images/cc_by.png","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)"},"ddc":["020"],"date_published":"2012-09-01T00:00:00Z","has_accepted_license":"1","publist_id":"3754","date_updated":"2026-08-12T14:15:14Z","file_date_updated":"2020-07-14T12:45:57Z","abstract":[{"text":"Dieser Artikel soll die sechs verschiedenen Creative Commons Lizenzen erläutern und ihre Bedeutung im Rahmen des wissenschaftlichen Publizierens und des Open Access erklären (CC-BY, CC-BY-SA, CC-BY-NC, CC-BY-ND, CC-BYNC-SA, CC-BY-NC-ND).","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_number":"041903","doi":"10.1103/PhysRevE.85.041903","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1112.5026"}],"type":"journal_article","title":"Optimizing information flow in small genetic networks. III. A self-interacting gene","oa":1,"author":[{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455"},{"first_name":"Aleksandra","full_name":"Walczak, Aleksandra","last_name":"Walczak"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"}],"publication":"Physical Review E","scopus_import":"1","corr_author":"1","quality_controlled":"1","date_created":"2018-12-11T12:02:20Z","article_processing_charge":"No","month":"04","department":[{"_id":"GaTk"}],"volume":85,"language":[{"iso":"eng"}],"publication_status":"published","fulldoi":"https://doi.org/10.1103/PhysRevE.85.041903","date_published":"2012-04-01T00:00:00Z","abstract":[{"text":"Living cells must control the reading out or &quot;expression&quot; of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of nearby genes. But the expression of transcription factor proteins is itself regulated, and many transcription factors regulate their own expression in addition to responding to other input signals. Here we analyze the simplest of such self-regulatory circuits, asking how parameters can be chosen to optimize information transmission from inputs to outputs in the steady state. Some nonzero level of self-regulation is almost always optimal, with self-activation dominant when transcription factor concentrations are low and self-repression dominant when concentrations are high. In steady state the optimal self-activation is never strong enough to induce bistability, although there is a limit in which the optimal parameters are very close to the critical point.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3386","date_updated":"2026-08-12T14:29:02Z","intvolume":"        85","external_id":{"isi":["000302410200006"],"arxiv":["1112.5026"]},"issue":"4","acknowledgement":"We thank T. Gregor, E. F. Wieschaus, and, especially, C. G. Callan for helpful discussions.\r\nWork at Princeton was supported in part by NSF Grants No. PHY–0957573 and No. CCF–0939370, by NIH Grant No. R01 GM077599, and by the W. M. Keck Foundation. For part of this work, G.T. was supported in part by NSF Grant No. EF–0928048 and by the Vice Provost for Research at the University of Pennsylvania.","citation":{"chicago":"Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” <i>Physical Review E</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/PhysRevE.85.041903\">https://doi.org/10.1103/PhysRevE.85.041903</a>.","short":"G. Tkačik, A. Walczak, W. Bialek, Physical Review E 85 (2012).","mla":"Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” <i>Physical Review E</i>, vol. 85, no. 4, 041903, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/PhysRevE.85.041903\">10.1103/PhysRevE.85.041903</a>.","ama":"Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic networks. III. A self-interacting gene. <i>Physical Review E</i>. 2012;85(4). doi:<a href=\"https://doi.org/10.1103/PhysRevE.85.041903\">10.1103/PhysRevE.85.041903</a>","ista":"Tkačik G, Walczak A, Bialek W. 2012. Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E. 85(4), 041903.","ieee":"G. Tkačik, A. Walczak, and W. Bialek, “Optimizing information flow in small genetic networks. III. A self-interacting gene,” <i>Physical Review E</i>, vol. 85, no. 4. American Physical Society, 2012.","apa":"Tkačik, G., Walczak, A., &#38; Bialek, W. (2012). Optimizing information flow in small genetic networks. III. A self-interacting gene. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.85.041903\">https://doi.org/10.1103/PhysRevE.85.041903</a>"},"year":"2012","publisher":"American Physical Society","day":"01","arxiv":1,"das_tickbox":"1","isi":1,"oa_version":"Preprint","_id":"3262","status":"public"},{"title":"Finite automata with time delay blocks","oa":1,"type":"conference","doi":"10.1145/2380356.2380370","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.7019"}],"publication":"Proceedings of the 10th ACM international conference on Embedded software","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Prabhu, Vinayak","last_name":"Prabhu","first_name":"Vinayak"}],"conference":{"start_date":"2012-10-07","name":"EMSOFT: Embedded Software ","end_date":"2012-10-12","location":"Tampere, Finland"},"scopus_import":"1","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T12:00:26Z","month":"10","page":"43 - 52","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_published":"2012-10-01T00:00:00Z","fulldoi":"https://doi.org/10.1145/2380356.2380370","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The notion of delays arises naturally in many computational models, such as, in the design of circuits, control systems, and dataflow languages. In this work, we introduce automata with delay blocks (ADBs), extending finite state automata with variable time delay blocks, for deferring individual transition output symbols, in a discrete-time setting. We show that the ADB languages strictly subsume the regular languages, and are incomparable in expressive power to the context-free languages. We show that ADBs are closed under union, concatenation and Kleene star, and under intersection with regular languages, but not closed under complementation and intersection with other ADB languages. We show that the emptiness and the membership problems are decidable in polynomial time for ADBs, whereas the universality problem is undecidable. Finally we consider the linear-time model checking problem, i.e., whether the language of an ADB is contained in a regular language, and show that the model checking problem is PSPACE-complete. Copyright 2012 ACM."}],"ec_funded":1,"date_updated":"2026-08-12T14:34:15Z","publist_id":"3799","external_id":{"arxiv":["1207.7019"]},"day":"01","arxiv":1,"publisher":"ACM","citation":{"ieee":"K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Finite automata with time delay blocks,” in <i>Proceedings of the 10th ACM international conference on Embedded software</i>, Tampere, Finland, 2012, pp. 43–52.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Prabhu, V. (2012). Finite automata with time delay blocks. In <i>Proceedings of the 10th ACM international conference on Embedded software</i> (pp. 43–52). Tampere, Finland: ACM. <a href=\"https://doi.org/10.1145/2380356.2380370\">https://doi.org/10.1145/2380356.2380370</a>","ama":"Chatterjee K, Henzinger TA, Prabhu V. Finite automata with time delay blocks. In: <i>Proceedings of the 10th ACM International Conference on Embedded Software</i>. ACM; 2012:43-52. doi:<a href=\"https://doi.org/10.1145/2380356.2380370\">10.1145/2380356.2380370</a>","ista":"Chatterjee K, Henzinger TA, Prabhu V. 2012. Finite automata with time delay blocks. Proceedings of the 10th ACM international conference on Embedded software. EMSOFT: Embedded Software , 43–52.","mla":"Chatterjee, Krishnendu, et al. “Finite Automata with Time Delay Blocks.” <i>Proceedings of the 10th ACM International Conference on Embedded Software</i>, ACM, 2012, pp. 43–52, doi:<a href=\"https://doi.org/10.1145/2380356.2380370\">10.1145/2380356.2380370</a>.","short":"K. Chatterjee, T.A. Henzinger, V. Prabhu, in:, Proceedings of the 10th ACM International Conference on Embedded Software, ACM, 2012, pp. 43–52.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Finite Automata with Time Delay Blocks.” In <i>Proceedings of the 10th ACM International Conference on Embedded Software</i>, 43–52. ACM, 2012. <a href=\"https://doi.org/10.1145/2380356.2380370\">https://doi.org/10.1145/2380356.2380370</a>."},"year":"2012","acknowledgement":"This work has been financially supported in part by the European Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract # 270180 (NOPTILUS); by Fundacao para Ciencia e Tecnologia under project PTDC/EEA-CRO/104901/2008 (Modeling and control of Networked vehicle systems in persistent autonomous operations); by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification; FWF NFN Grant No S11407-N23 (RiSE); ERC Start grant (279307: Graph Games); Microsoft faculty fellows award; ERC Advanced grant QUAREM; and FWF Grant No S11403-N23 (RiSE).","status":"public","_id":"2936","oa_version":"Preprint"}]