[{"oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2(POPL), 30.","mla":"Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL, 30, Association for Computing Machinery, 2017, doi:<a href=\"https://doi.org/10.1145/3158118\">10.1145/3158118</a>.","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability for data-dependence and Alias analysis,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL. Association for Computing Machinery, 2017.","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2017. <a href=\"https://doi.org/10.1145/3158118\">https://doi.org/10.1145/3158118</a>.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 2 (2017).","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence and Alias analysis. <i>Proceedings of the ACM on Programming Languages</i>. 2017;2(POPL). doi:<a href=\"https://doi.org/10.1145/3158118\">10.1145/3158118</a>","apa":"Chatterjee, K., Choudhary, B., &#38; Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and Alias analysis. <i>Proceedings of the ACM on Programming Languages</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3158118\">https://doi.org/10.1145/3158118</a>"},"corr_author":"1","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Bhavya","last_name":"Choudhary","full_name":"Choudhary, Bhavya"},{"last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"arxiv":["1910.00241"]},"ddc":["000"],"abstract":[{"lang":"eng","text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks."}],"department":[{"_id":"KrCh"}],"date_updated":"2025-04-15T07:26:20Z","arxiv":1,"date_published":"2017-12-27T00:00:00Z","publisher":"Association for Computing Machinery","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5455"}]},"issue":"POPL","conference":{"start_date":"2018-01-07","location":"Los Angeles, CA, United States","name":"POPL: Programming Languages","end_date":"2018-01-13"},"title":"Optimal Dyck reachability for data-dependence and Alias analysis","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"intvolume":"         2","file":[{"file_name":"2017_ACMProgLang_Chatterjee.pdf","file_size":460188,"date_updated":"2021-12-07T08:06:28Z","content_type":"application/pdf","creator":"cchlebak","file_id":"10421","relation":"main_file","date_created":"2021-12-07T08:06:28Z","checksum":"faa3f7b3fe8aab84b50ed805c26a0ee5","access_level":"open_access","success":1}],"volume":2,"month":"12","article_processing_charge":"No","day":"27","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n","date_created":"2021-12-05T23:01:48Z","ec_funded":1,"scopus_import":"1","publication":"Proceedings of the ACM on Programming Languages","article_number":"30","doi":"10.1145/3158118","publication_identifier":{"eissn":["2475-1421"]},"_id":"10416","oa":1,"article_type":"original","has_accepted_license":"1","type":"journal_article","status":"public","file_date_updated":"2021-12-07T08:06:28Z","publication_status":"published","year":"2017","quality_controlled":"1"},{"date_published":"2017-12-07T00:00:00Z","arxiv":1,"issue":"POPL","conference":{"end_date":"2018-01-13","name":"POPL: Programming Languages","location":"Los Angeles, CA, United States","start_date":"2018-01-07"},"publisher":"Association for Computing Machinery","external_id":{"arxiv":["1711.03588"]},"ddc":["000"],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2026-06-18T08:40:04Z","abstract":[{"text":"We present a new proof rule for proving almost-sure termination of probabilistic programs, including those that contain demonic non-determinism. An important question for a probabilistic program is whether the probability mass of all its diverging runs is zero, that is that it terminates \"almost surely\". Proving that can be hard, and this paper presents a new method for doing so. It applies directly to the program's source code, even if the program contains demonic choice. Like others, we use variant functions (a.k.a. \"super-martingales\") that are real-valued and decrease randomly on each loop iteration; but our key innovation is that the amount as well as the probability of the decrease are parametric. We prove the soundness of the new rule, indicate where its applicability goes beyond existing rules, and explain its connection to classical results on denumerable (non-demonic) Markov chains.","lang":"eng"}],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Mciver","first_name":"Annabelle","full_name":"Mciver, Annabelle"},{"last_name":"Morgan","first_name":"Carroll","full_name":"Morgan, Carroll"},{"full_name":"Kaminski, Benjamin Lucien","first_name":"Benjamin Lucien","last_name":"Kaminski"},{"first_name":"Joost P","last_name":"Katoen","id":"4524F760-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6143-1926","full_name":"Katoen, Joost P"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"mla":"Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL, 33, Association for Computing Machinery, 2017, doi:<a href=\"https://doi.org/10.1145/3158121\">10.1145/3158121</a>.","ista":"Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33.","ieee":"A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule for almost-sure termination,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL. Association for Computing Machinery, 2017.","chicago":"Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost P Katoen. “A New Proof Rule for Almost-Sure Termination.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2017. <a href=\"https://doi.org/10.1145/3158121\">https://doi.org/10.1145/3158121</a>.","ama":"Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure termination. <i>Proceedings of the ACM on Programming Languages</i>. 2017;2(POPL). doi:<a href=\"https://doi.org/10.1145/3158121\">10.1145/3158121</a>","short":"A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM on Programming Languages 2 (2017).","apa":"Mciver, A., Morgan, C., Kaminski, B. L., &#38; Katoen, J. P. (2017). A new proof rule for almost-sure termination. <i>Proceedings of the ACM on Programming Languages</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3158121\">https://doi.org/10.1145/3158121</a>"},"quality_controlled":"1","status":"public","type":"journal_article","year":"2017","publication_status":"published","publication_identifier":{"eissn":["2475-1421"]},"doi":"10.1145/3158121","_id":"10418","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3158121"}],"article_number":"33","oa":1,"article_type":"original","date_created":"2021-12-05T23:01:49Z","acknowledgement":"McIver and Morgan are grateful to David Basin and the Information Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during part of which this work began. And thanks particularly to Andreas Lochbihler, who shared with us the probabilistic termination problem that led to it. They acknowledge the support of ARC grant DP140101119. Part of this work was carried out during the Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden. Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4.","scopus_import":"1","day":"07","publication":"Proceedings of the ACM on Programming Languages","intvolume":"         2","title":"A new proof rule for almost-sure termination","article_processing_charge":"No","month":"12","volume":2},{"das_tickbox":"1","year":"2017","publication_status":"published","type":"journal_article","status":"public","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/081042","open_access":"1"}],"_id":"1063","publication_identifier":{"issn":["0014-3820"]},"doi":"10.1111/evo.13191","publication":"Evolution","day":"01","scopus_import":"1","ec_funded":1,"date_created":"2018-12-11T11:49:57Z","volume":71,"article_processing_charge":"No","month":"04","page":"845 - 858","title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","intvolume":"        71","project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"publisher":"Wiley","issue":"4","date_published":"2017-04-01T00:00:00Z","abstract":[{"text":"Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations.","lang":"eng"}],"biorxivid":1,"date_updated":"2026-06-22T14:05:53Z","department":[{"_id":"NiBa"}],"external_id":{"biorxivid":["10.1101/081042"],"isi":["000398545200003"]},"isi":1,"author":[{"full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","last_name":"Uecker","first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"H. Uecker, Evolution 71 (2017) 845–858.","ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. <i>Evolution</i>. 2017;71(4):845-858. doi:<a href=\"https://doi.org/10.1111/evo.13191\">10.1111/evo.13191</a>","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.13191\">https://doi.org/10.1111/evo.13191</a>","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858.","mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” <i>Evolution</i>, vol. 71, no. 4, Wiley, 2017, pp. 845–58, doi:<a href=\"https://doi.org/10.1111/evo.13191\">10.1111/evo.13191</a>.","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” <i>Evolution</i>, vol. 71, no. 4. Wiley, pp. 845–858, 2017.","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” <i>Evolution</i>. Wiley, 2017. <a href=\"https://doi.org/10.1111/evo.13191\">https://doi.org/10.1111/evo.13191</a>."},"publist_id":"6327","language":[{"iso":"eng"}],"oa_version":"Submitted Version"},{"status":"public","type":"journal_article","publication_status":"published","file_date_updated":"2019-10-15T07:44:51Z","year":"2017","quality_controlled":"1","oa":1,"has_accepted_license":"1","doi":"10.1016/j.ipl.2017.02.003","publication_identifier":{"issn":["0020-0190"]},"_id":"1065","publication":"Information Processing Letters","pubrep_id":"991","day":"01","date_created":"2018-12-11T11:49:57Z","ec_funded":1,"scopus_import":"1","file":[{"file_name":"IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf","file_size":247657,"date_updated":"2019-10-15T07:44:51Z","content_type":"application/pdf","file_id":"4998","creator":"system","relation":"main_file","date_created":"2018-12-12T10:13:17Z","access_level":"open_access"}],"volume":122,"month":"06","article_processing_charge":"No","page":"25 - 29","title":"Pushdown reachability with constant treewidth","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"intvolume":"       122","publisher":"Elsevier","date_published":"2017-06-01T00:00:00Z","abstract":[{"text":"We consider the problem of reachability in pushdown graphs. We study the problem for pushdown graphs with constant treewidth. Even for pushdown graphs with treewidth 1, for the reachability problem we establish the following: (i) the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem would contradict the k-clique conjecture and imply faster combinatorial algorithms for cliques in graphs.","lang":"eng"}],"department":[{"_id":"KrCh"},{"_id":"HeEd"}],"date_updated":"2025-07-10T11:49:53Z","isi":1,"external_id":{"isi":["000399506600005"]},"ddc":["000"],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Osang","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant Treewidth.” <i>Information Processing Letters</i>, vol. 122, Elsevier, 2017, pp. 25–29, doi:<a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">10.1016/j.ipl.2017.02.003</a>.","ista":"Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth. Information Processing Letters. 122, 25–29.","ieee":"K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,” <i>Information Processing Letters</i>, vol. 122. Elsevier, pp. 25–29, 2017.","chicago":"Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with Constant Treewidth.” <i>Information Processing Letters</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">https://doi.org/10.1016/j.ipl.2017.02.003</a>.","ama":"Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. <i>Information Processing Letters</i>. 2017;122:25-29. doi:<a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">10.1016/j.ipl.2017.02.003</a>","short":"K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.","apa":"Chatterjee, K., &#38; Osang, G. F. (2017). Pushdown reachability with constant treewidth. <i>Information Processing Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">https://doi.org/10.1016/j.ipl.2017.02.003</a>"},"publist_id":"6323","oa_version":"Submitted Version","language":[{"iso":"eng"}]},{"publist_id":"6322","citation":{"short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation games. <i>Information and Computation</i>. 2017;254(2):143-166. doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">10.1016/j.ic.2016.10.006</a>","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Velner, Y. (2017). Quantitative fair simulation games. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">https://doi.org/10.1016/j.ic.2016.10.006</a>","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair simulation games,” <i>Information and Computation</i>, vol. 254, no. 2. Elsevier, pp. 143–166, 2017.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. “Quantitative Fair Simulation Games.” <i>Information and Computation</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">https://doi.org/10.1016/j.ic.2016.10.006</a>.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” <i>Information and Computation</i>, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">10.1016/j.ic.2016.10.006</a>."},"oa_version":"Published Version","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","first_name":"Jan","full_name":"Otop, Jan"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"corr_author":"1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2026-06-18T08:47:01Z","abstract":[{"text":"Simulation is an attractive alternative to language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. While fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable in general, whereas the (quantitative) simulation reduces to quantitative games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games, yet they still admit pseudo-polynomial time algorithms.","lang":"eng"}],"external_id":{"isi":["000402025600002"]},"isi":1,"ddc":["000"],"issue":"2","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5428"}]},"publisher":"Elsevier","date_published":"2017-06-01T00:00:00Z","article_processing_charge":"No","month":"06","volume":254,"project":[{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"intvolume":"       254","page":"143 - 166","title":"Quantitative fair simulation games","publication":"Information and Computation","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreements 267989 (QUAREM), 279307 (Graph Games), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE), S11407-N23 (RiSE), P23499-N23, and Microsoft faculty fellows award.","date_created":"2018-12-11T11:49:58Z","OA_place":"publisher","ec_funded":1,"scopus_import":"1","OA_type":"free access","day":"01","oa":1,"article_type":"original","doi":"10.1016/j.ic.2016.10.006","_id":"1066","main_file_link":[{"url":"https://doi.org/10.1016/j.ic.2016.10.006","open_access":"1"}],"quality_controlled":"1","status":"public","type":"journal_article","year":"2017","publication_status":"published"},{"article_processing_charge":"No","month":"02","volume":40,"file":[{"file_size":6866187,"content_type":"application/pdf","date_updated":"2018-12-12T10:10:57Z","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","access_level":"open_access","creator":"system","file_id":"4849","relation":"main_file","date_created":"2018-12-12T10:10:57Z"}],"intvolume":"        40","project":[{"call_identifier":"FP7","grant_number":"201439","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","_id":"2524F500-B435-11E9-9278-68D0E5697425"}],"title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","page":"354 - 366","publication":"Developmental Cell","scopus_import":"1","date_created":"2018-12-11T11:49:58Z","ec_funded":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"27","pubrep_id":"869","has_accepted_license":"1","oa":1,"_id":"1067","doi":"10.1016/j.devcel.2017.01.010","publication_identifier":{"issn":["1534-5807"]},"quality_controlled":"1","file_date_updated":"2018-12-12T10:10:57Z","publication_status":"published","year":"2017","type":"journal_article","status":"public","publist_id":"6320","citation":{"mla":"Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>, vol. 40, no. 4, Cell Press, 2017, pp. 354–66, doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">10.1016/j.devcel.2017.01.010</a>.","ista":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 40(4), 354–366.","chicago":"Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>.","ieee":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg, “The physical basis of coordinated tissue spreading in zebrafish gastrulation,” <i>Developmental Cell</i>, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.","apa":"Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., &#38; Heisenberg, C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish gastrulation. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366.","ama":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical basis of coordinated tissue spreading in zebrafish gastrulation. <i>Developmental Cell</i>. 2017;40(4):354-366. doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">10.1016/j.devcel.2017.01.010</a>"},"language":[{"iso":"eng"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","last_name":"Morita","first_name":"Hitoshi","full_name":"Morita, Hitoshi"},{"full_name":"Grigolon, Silvia","last_name":"Grigolon","first_name":"Silvia"},{"full_name":"Bock, Martin","first_name":"Martin","last_name":"Bock"},{"first_name":"Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"corr_author":"1","acknowledged_ssus":[{"_id":"PreCl"}],"date_updated":"2025-07-10T11:49:55Z","department":[{"_id":"CaHe"}],"abstract":[{"text":"Embryo morphogenesis relies on highly coordinated movements of different tissues. However, remarkably little is known about how tissues coordinate their movements to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements first become apparent during “doming,” when the blastoderm begins to spread over the yolk sac, a process involving coordinated epithelial surface cell layer expansion and mesenchymal deep cell intercalations. Here, we find that active surface cell expansion represents the key process coordinating tissue movements during doming. By using a combination of theory and experiments, we show that epithelial surface cells not only trigger blastoderm expansion by reducing tissue surface tension, but also drive blastoderm thinning by inducing tissue contraction through radial deep cell intercalations. Thus, coordinated tissue expansion and thinning during doming relies on surface cells simultaneously controlling tissue surface tension and radial tissue contraction.","lang":"eng"}],"ddc":["572","597"],"external_id":{"isi":["000395368300007"]},"isi":1,"issue":"4","publisher":"Cell Press","date_published":"2017-02-27T00:00:00Z"},{"publisher":"American Mathematical Society","issue":"5","arxiv":1,"date_published":"2017-05-01T00:00:00Z","abstract":[{"lang":"eng","text":"Given a finite set of points in Rn and a radius parameter, we study the Čech, Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel sets of generalized discrete Morse functions, we prove that the four complexes are simple-homotopy equivalent by a sequence of simplicial collapses, which are explicitly described by a single discrete gradient field."}],"department":[{"_id":"HeEd"}],"date_updated":"2025-04-15T08:37:54Z","external_id":{"isi":["000398030400024"],"arxiv":["1312.1231"]},"isi":1,"author":[{"orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","last_name":"Bauer"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762.","ama":"Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. 2017;369(5):3741-3762. doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>","apa":"Bauer, U., &#38; Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/6991\">https://doi.org/10.1090/tran/6991</a>","ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762.","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” <i>Transactions of the American Mathematical Society</i>, vol. 369, no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>.","ieee":"U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,” <i>Transactions of the American Mathematical Society</i>, vol. 369, no. 5. American Mathematical Society, pp. 3741–3762, 2017.","chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2017. <a href=\"https://doi.org/10.1090/tran/6991\">https://doi.org/10.1090/tran/6991</a>."},"publist_id":"6311","oa_version":"Preprint","language":[{"iso":"eng"}],"type":"journal_article","status":"public","year":"2017","publication_status":"published","quality_controlled":"1","oa":1,"article_type":"original","doi":"10.1090/tran/6991","_id":"1072","main_file_link":[{"url":"https://arxiv.org/abs/1312.1231","open_access":"1"}],"publication":"Transactions of the American Mathematical Society","day":"01","date_created":"2018-12-11T11:49:59Z","acknowledgement":"This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP), by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”.","ec_funded":1,"scopus_import":"1","volume":369,"month":"05","article_processing_charge":"No","page":"3741 - 3762","title":"The Morse theory of Čech and delaunay complexes","project":[{"call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"intvolume":"       369"},{"language":[{"iso":"eng"}],"oa_version":"Submitted Version","publist_id":"6309","citation":{"chicago":"Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>.","ieee":"M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting extension problem,” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4. Springer, pp. 915–965, 2017.","mla":"Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4, Springer, 2017, pp. 915–65, doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>.","ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete &#38; Computational Geometry. 54(4), 915–965.","apa":"Čadek, M., Krcál, M., &#38; Vokřínek, L. (2017). Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>","short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete &#38; Computational Geometry 54 (2017) 915–965.","ama":"Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. 2017;54(4):915-965. doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Martin","last_name":"Čadek","full_name":"Čadek, Martin"},{"last_name":"Krcál","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek"},{"first_name":"Lukáš","last_name":"Vokřínek","full_name":"Vokřínek, Lukáš"}],"isi":1,"external_id":{"isi":["000400072700008"],"arxiv":["1307.6444"]},"date_updated":"2025-06-04T08:11:10Z","department":[{"_id":"UlWa"}],"abstract":[{"lang":"eng","text":"Let X and Y be finite simplicial sets (e.g. finite simplicial complexes), both equipped with a free simplicial action of a finite group G. Assuming that Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|; the existence of such a map can be decided even for dimX≤2d+1. This yields the first algorithm for deciding topological embeddability of a k-dimensional finite simplicial complex into Rn under the condition k≤23n−1. More generally, we present an algorithm that, given a lifting-extension problem satisfying an appropriate stability assumption, computes the set of all homotopy classes of solutions. This result is new even in the non-equivariant situation."}],"date_published":"2017-06-01T00:00:00Z","arxiv":1,"issue":"4","publisher":"Springer","intvolume":"        54","page":"915 - 965","title":"Algorithmic solvability of the lifting extension problem","article_processing_charge":"No","month":"06","volume":54,"scopus_import":"1","date_created":"2018-12-11T11:50:00Z","day":"01","publication":"Discrete & Computational Geometry","_id":"1073","main_file_link":[{"url":"https://arxiv.org/abs/1307.6444","open_access":"1"}],"doi":"10.1007/s00454-016-9855-6","publication_identifier":{"issn":["01795376"]},"oa":1,"quality_controlled":"1","publication_status":"published","year":"2017","type":"journal_article","status":"public"},{"publication_identifier":{"issn":["0016-6731"]},"doi":"10.1534/genetics.116.196220","main_file_link":[{"url":"http://www.biorxiv.org/content/early/2016/09/23/076810","open_access":"1"}],"_id":"1074","oa":1,"type":"journal_article","status":"public","year":"2017","publication_status":"published","quality_controlled":"1","page":"1335 - 1351","title":"Inferring recent demography from isolation by distance of long shared sequence blocks","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"intvolume":"       205","volume":205,"month":"03","article_processing_charge":"No","day":"01","ec_funded":1,"date_created":"2018-12-11T11:50:00Z","scopus_import":"1","publication":"Genetics","external_id":{"isi":["000395807200023"]},"isi":1,"abstract":[{"lang":"eng","text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance."}],"department":[{"_id":"NiBa"}],"date_updated":"2026-04-08T14:06:35Z","date_published":"2017-03-01T00:00:00Z","related_material":{"record":[{"id":"200","status":"public","relation":"dissertation_contains"}]},"publisher":"Genetics Society of America","issue":"3","oa_version":"Preprint","language":[{"iso":"eng"}],"citation":{"ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” <i>Genetics</i>, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>.","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>.","ista":"Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.","ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. 2017;205(3):1335-1351. doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.","apa":"Ringbauer, H., Coop, G., &#38; Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>"},"publist_id":"6307","author":[{"full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","last_name":"Ringbauer","first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Graham","last_name":"Coop","full_name":"Coop, Graham"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"text":"We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory for atoms and molecules. We prove the nonexistence of minimizers for the energy functional when the number of electrons is large and the total nuclear charge is small. This nonexistence result also applies to external potentials decaying faster than the Coulomb potential. In the case of arbitrary nuclear charges, we obtain the nonexistence of stable minimizers and radial minimizers.","lang":"eng"}],"date_updated":"2025-06-04T08:11:50Z","department":[{"_id":"RoSe"}],"isi":1,"external_id":{"arxiv":["1603.07368"],"isi":["000401270000004"]},"publisher":"Springer","issue":"2","arxiv":1,"date_published":"2017-06-01T00:00:00Z","citation":{"apa":"Nam, P., &#38; Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>","short":"P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017).","ama":"Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. 2017;20(2). doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>","ista":"Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 20(2), 6.","mla":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2, 6, Springer, 2017, doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>.","chicago":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>.","ieee":"P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2. Springer, 2017."},"publist_id":"6300","language":[{"iso":"eng"}],"oa_version":"Submitted Version","author":[{"full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam"},{"full_name":"Van Den Bosch, Hanne","last_name":"Van Den Bosch","first_name":"Hanne"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"article_number":"6","main_file_link":[{"url":"https://arxiv.org/abs/1603.07368","open_access":"1"}],"_id":"1079","publication_identifier":{"issn":["1385-0172"]},"doi":"10.1007/s11040-017-9238-0","publication_status":"published","year":"2017","type":"journal_article","status":"public","quality_controlled":"1","volume":20,"month":"06","article_processing_charge":"No","title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","intvolume":"        20","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}],"publication":"Mathematical Physics, Analysis and Geometry","day":"01","scopus_import":"1","date_created":"2018-12-11T11:50:02Z"},{"abstract":[{"lang":"eng","text":"Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods."}],"department":[{"_id":"KrCh"}],"date_updated":"2025-07-10T11:50:00Z","external_id":{"isi":["000393096600001"]},"isi":1,"ddc":["004","006"],"publisher":"Nature Publishing Group","date_published":"2017-01-31T00:00:00Z","citation":{"apa":"Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>","ama":"Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>","short":"J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017).","chicago":"Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>.","ieee":"J. Reiter <i>et al.</i>, “Reconstructing metastatic seeding patterns of human cancers,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","ista":"Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 8, 14114.","mla":"Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>, vol. 8, 14114, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>."},"publist_id":"6301","oa_version":"Published Version","language":[{"iso":"eng"}],"author":[{"last_name":"Reiter","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes"},{"full_name":"Makohon Moore, Alvin","last_name":"Makohon Moore","first_name":"Alvin"},{"first_name":"Jeffrey","last_name":"Gerold","full_name":"Gerold, Jeffrey"},{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Christine","last_name":"Iacobuzio Donahue","full_name":"Iacobuzio Donahue, Christine"},{"full_name":"Vogelstein, Bert","last_name":"Vogelstein","first_name":"Bert"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"has_accepted_license":"1","article_number":"14114","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/ncomms14114","_id":"1080","status":"public","type":"journal_article","publication_status":"published","file_date_updated":"2018-12-12T10:15:15Z","year":"2017","quality_controlled":"1","file":[{"file_name":"IST-2017-786-v1+1_ncomms14114.pdf","date_updated":"2018-12-12T10:15:15Z","content_type":"application/pdf","file_size":897050,"date_created":"2018-12-12T10:15:15Z","relation":"main_file","creator":"system","file_id":"5133","access_level":"open_access"}],"volume":8,"month":"01","article_processing_charge":"No","title":"Reconstructing metastatic seeding patterns of human cancers","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"}],"intvolume":"         8","publication":"Nature Communications","pubrep_id":"786","day":"31","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2018-12-11T11:50:02Z","ec_funded":1,"scopus_import":"1"},{"publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","day":"26","scopus_import":"1","date_created":"2018-12-11T11:48:31Z","volume":"Part F129314","article_processing_charge":"No","month":"07","page":"283 - 292","title":"The power of choice in priority scheduling","year":"2017","publication_status":"published","type":"conference","status":"public","quality_controlled":"1","oa":1,"_id":"791","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.04178"}],"doi":"10.1145/3087801.3087810","publication_identifier":{"isbn":["978-145034992-5"]},"author":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"first_name":"Justin","last_name":"Kopinsky","full_name":"Kopinsky, Justin"},{"full_name":"Li, Jerry","first_name":"Jerry","last_name":"Li"},{"orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Alistarh, D.-A., Kopinsky, J., Li, J., &#38; Nadiradze, G. (2017). The power of choice in priority scheduling. In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i> (Vol. Part F129314, pp. 283–292). Washington, WA, USA: ACM. <a href=\"https://doi.org/10.1145/3087801.3087810\">https://doi.org/10.1145/3087801.3087810</a>","short":"D.-A. Alistarh, J. Kopinsky, J. Li, G. Nadiradze, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, ACM, 2017, pp. 283–292.","ama":"Alistarh D-A, Kopinsky J, Li J, Nadiradze G. The power of choice in priority scheduling. In: <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>. Vol Part F129314. ACM; 2017:283-292. doi:<a href=\"https://doi.org/10.1145/3087801.3087810\">10.1145/3087801.3087810</a>","mla":"Alistarh, Dan-Adrian, et al. “The Power of Choice in Priority Scheduling.” <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, vol. Part F129314, ACM, 2017, pp. 283–92, doi:<a href=\"https://doi.org/10.1145/3087801.3087810\">10.1145/3087801.3087810</a>.","ista":"Alistarh D-A, Kopinsky J, Li J, Nadiradze G. 2017. The power of choice in priority scheduling. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing vol. Part F129314, 283–292.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Giorgi Nadiradze. “The Power of Choice in Priority Scheduling.” In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Part F129314:283–92. ACM, 2017. <a href=\"https://doi.org/10.1145/3087801.3087810\">https://doi.org/10.1145/3087801.3087810</a>.","ieee":"D.-A. Alistarh, J. Kopinsky, J. Li, and G. Nadiradze, “The power of choice in priority scheduling,” in <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Washington, WA, USA, 2017, vol. Part F129314, pp. 283–292."},"publist_id":"6864","language":[{"iso":"eng"}],"oa_version":"Submitted Version","publisher":"ACM","conference":{"location":"Washington, WA, USA","start_date":"2017-07-25","end_date":"2017-07-27","name":"PODC: Principles of Distributed Computing"},"arxiv":1,"date_published":"2017-07-26T00:00:00Z","abstract":[{"text":"Consider the following random process: we are given n queues, into which elements of increasing labels are inserted uniformly at random. To remove an element, we pick two queues at random, and remove the element of lower label (higher priority) among the two. The cost of a removal is the rank of the label removed, among labels still present in any of the queues, that is, the distance from the optimal choice at each step. Variants of this strategy are prevalent in state-of-the-art concurrent priority queue implementations. Nonetheless, it is not known whether such implementations provide any rank guarantees, even in a sequential model. We answer this question, showing that this strategy provides surprisingly strong guarantees: Although the single-choice process, where we always insert and remove from a single randomly chosen queue, has degrading cost, going to infinity as we increase the number of steps, in the two choice process, the expected rank of a removed element is O(n) while the expected worst-case cost is O(n log n). These bounds are tight, and hold irrespective of the number of steps for which we run the process. The argument is based on a new technical connection between &quot;heavily loaded&quot; balls-into-bins processes and priority scheduling. Our analytic results inspire a new concurrent priority queue implementation, which improves upon the state of the art in terms of practical performance.","lang":"eng"}],"date_updated":"2025-06-04T09:44:47Z","department":[{"_id":"DaAl"}],"external_id":{"arxiv":["1706.04178"],"isi":["000462995000035"]},"isi":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","first_name":"Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Short, Kimberly","last_name":"Short","first_name":"Kimberly"},{"first_name":"Mohammad","last_name":"Farazmand","full_name":"Farazmand, Mohammad"},{"first_name":"Ashley","last_name":"Willis","full_name":"Willis, Ashley"},{"full_name":"Cvitanović, Predrag","last_name":"Cvitanović","first_name":"Predrag"}],"publist_id":"6862","citation":{"mla":"Budanur, Nazmi B., et al. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 833, Cambridge University Press, 2017, pp. 274–301, doi:<a href=\"https://doi.org/10.1017/jfm.2017.699\">10.1017/jfm.2017.699</a>.","ista":"Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. 2017. Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. 833, 274–301.","chicago":"Budanur, Nazmi B, Kimberly Short, Mohammad Farazmand, Ashley Willis, and Predrag Cvitanović. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jfm.2017.699\">https://doi.org/10.1017/jfm.2017.699</a>.","ieee":"N. B. Budanur, K. Short, M. Farazmand, A. Willis, and P. Cvitanović, “Relative periodic orbits form the backbone of turbulent pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 833. Cambridge University Press, pp. 274–301, 2017.","apa":"Budanur, N. B., Short, K., Farazmand, M., Willis, A., &#38; Cvitanović, P. (2017). Relative periodic orbits form the backbone of turbulent pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2017.699\">https://doi.org/10.1017/jfm.2017.699</a>","ama":"Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. Relative periodic orbits form the backbone of turbulent pipe flow. <i>Journal of Fluid Mechanics</i>. 2017;833:274-301. doi:<a href=\"https://doi.org/10.1017/jfm.2017.699\">10.1017/jfm.2017.699</a>","short":"N.B. Budanur, K. Short, M. Farazmand, A. Willis, P. Cvitanović, Journal of Fluid Mechanics 833 (2017) 274–301."},"language":[{"iso":"eng"}],"oa_version":"Submitted Version","publisher":"Cambridge University Press","date_published":"2017-12-25T00:00:00Z","arxiv":1,"date_updated":"2025-06-04T09:45:57Z","department":[{"_id":"BjHo"}],"abstract":[{"lang":"eng","text":"The chaotic dynamics of low-dimensional systems, such as Lorenz or Rössler flows, is guided by the infinity of periodic orbits embedded in their strange attractors. Whether this is also the case for the infinite-dimensional dynamics of Navier–Stokes equations has long been speculated, and is a topic of ongoing study. Periodic and relative periodic solutions have been shown to be involved in transitions to turbulence. Their relevance to turbulent dynamics – specifically, whether periodic orbits play the same role in high-dimensional nonlinear systems like the Navier–Stokes equations as they do in lower-dimensional systems – is the focus of the present investigation. We perform here a detailed study of pipe flow relative periodic orbits with energies and mean dissipations close to turbulent values. We outline several approaches to reduction of the translational symmetry of the system. We study pipe flow in a minimal computational cell at   Re=2500, and report a library of invariant solutions found with the aid of the method of slices. Detailed study of the unstable manifolds of a sample of these solutions is consistent with the picture that relative periodic orbits are embedded in the chaotic saddle and that they guide the turbulent dynamics."}],"external_id":{"isi":["000414641700001"],"arxiv":["1705.03720"]},"isi":1,"publication":"Journal of Fluid Mechanics","scopus_import":"1","date_created":"2018-12-11T11:48:32Z","day":"25","article_processing_charge":"No","month":"12","volume":833,"intvolume":"       833","project":[{"_id":"25636330-B435-11E9-9278-68D0E5697425","grant_number":"11-NSF-1070","name":"Genome-wide Analysis of Root Traits"}],"title":"Relative periodic orbits form the backbone of turbulent pipe flow","page":"274 - 301","quality_controlled":"1","year":"2017","publication_status":"published","type":"journal_article","status":"public","oa":1,"_id":"792","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.03720"}],"publication_identifier":{"issn":["0022-1120"]},"doi":"10.1017/jfm.2017.699"},{"abstract":[{"text":"Let P be a finite point set in the plane. A cordinary triangle in P is a subset of P consisting of three non-collinear points such that each of the three lines determined by the three points contains at most c points of P . Motivated by a question of Erdös, and answering a question of de Zeeuw, we prove that there exists a constant c &gt; 0such that P contains a c-ordinary triangle, provided that P is not contained in the union of two lines. Furthermore, the number of c-ordinary triangles in P is Ω(| P |). ","lang":"eng"}],"date_updated":"2026-04-16T09:57:17Z","department":[{"_id":"UlWa"}],"isi":1,"external_id":{"arxiv":["1701.08183"],"isi":["000412039700003"]},"publisher":"Elsevier","arxiv":1,"date_published":"2017-01-01T00:00:00Z","citation":{"ama":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. On the existence of ordinary triangles. <i>Computational Geometry: Theory and Applications</i>. 2017;66:28-31. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">10.1016/j.comgeo.2017.07.002</a>","short":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, M. Szedlák, Computational Geometry: Theory and Applications 66 (2017) 28–31.","apa":"Fulek, R., Mojarrad, H., Naszódi, M., Solymosi, J., Stich, S., &#38; Szedlák, M. (2017). On the existence of ordinary triangles. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">https://doi.org/10.1016/j.comgeo.2017.07.002</a>","mla":"Fulek, Radoslav, et al. “On the Existence of Ordinary Triangles.” <i>Computational Geometry: Theory and Applications</i>, vol. 66, Elsevier, 2017, pp. 28–31, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">10.1016/j.comgeo.2017.07.002</a>.","ista":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. 2017. On the existence of ordinary triangles. Computational Geometry: Theory and Applications. 66, 28–31.","ieee":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, and M. Szedlák, “On the existence of ordinary triangles,” <i>Computational Geometry: Theory and Applications</i>, vol. 66. Elsevier, pp. 28–31, 2017.","chicago":"Fulek, Radoslav, Hossein Mojarrad, Márton Naszódi, József Solymosi, Sebastian Stich, and May Szedlák. “On the Existence of Ordinary Triangles.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">https://doi.org/10.1016/j.comgeo.2017.07.002</a>."},"publist_id":"6861","language":[{"iso":"eng"}],"oa_version":"Submitted Version","author":[{"first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"last_name":"Mojarrad","first_name":"Hossein","full_name":"Mojarrad, Hossein"},{"first_name":"Márton","last_name":"Naszódi","full_name":"Naszódi, Márton"},{"full_name":"Solymosi, József","first_name":"József","last_name":"Solymosi"},{"full_name":"Stich, Sebastian","first_name":"Sebastian","last_name":"Stich"},{"last_name":"Szedlák","first_name":"May","full_name":"Szedlák, May"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1701.08183"}],"_id":"793","doi":"10.1016/j.comgeo.2017.07.002","publication_identifier":{"issn":["0925-7721"]},"year":"2017","publication_status":"published","status":"public","type":"journal_article","quality_controlled":"1","volume":66,"month":"01","article_processing_charge":"No","title":"On the existence of ordinary triangles","page":"28 - 31","intvolume":"        66","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication":"Computational Geometry: Theory and Applications","day":"01","ec_funded":1,"date_created":"2018-12-11T11:48:32Z"},{"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1165"}]},"publisher":"Elsevier","date_published":"2017-12-01T00:00:00Z","arxiv":1,"date_updated":"2025-09-22T09:54:02Z","department":[{"_id":"UlWa"}],"abstract":[{"text":"We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle.","lang":"eng"}],"isi":1,"external_id":{"arxiv":["1602.01346"],"isi":["000412039700001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav"}],"publist_id":"6860","citation":{"short":"R. Fulek, Computational Geometry: Theory and Applications 66 (2017) 1–13.","ama":"Fulek R. C-planarity of embedded cyclic c-graphs. <i>Computational Geometry: Theory and Applications</i>. 2017;66:1-13. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">10.1016/j.comgeo.2017.06.016</a>","apa":"Fulek, R. (2017). C-planarity of embedded cyclic c-graphs. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">https://doi.org/10.1016/j.comgeo.2017.06.016</a>","ista":"Fulek R. 2017. C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. 66, 1–13.","mla":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” <i>Computational Geometry: Theory and Applications</i>, vol. 66, Elsevier, 2017, pp. 1–13, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">10.1016/j.comgeo.2017.06.016</a>.","ieee":"R. Fulek, “C-planarity of embedded cyclic c-graphs,” <i>Computational Geometry: Theory and Applications</i>, vol. 66. Elsevier, pp. 1–13, 2017.","chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">https://doi.org/10.1016/j.comgeo.2017.06.016</a>."},"language":[{"iso":"eng"}],"oa_version":"Preprint","quality_controlled":"1","year":"2017","publication_status":"published","status":"public","type":"journal_article","oa":1,"_id":"794","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.01346"}],"doi":"10.1016/j.comgeo.2017.06.016","publication":"Computational Geometry: Theory and Applications","scopus_import":"1","date_created":"2018-12-11T11:48:32Z","acknowledgement":"I would like to thank Jan Kynčl, Dömötör Pálvölgyi and anonymous referees for many comments and suggestions that helped to improve the presentation of the result.","day":"01","article_processing_charge":"No","month":"12","volume":66,"intvolume":"        66","page":"1 - 13","title":"C-planarity of embedded cyclic c-graphs"},{"arxiv":1,"date_published":"2017-07-01T00:00:00Z","publisher":"American Institute of Physics","issue":"4","isi":1,"external_id":{"isi":["000406779700031"],"arxiv":["1703.10195"]},"abstract":[{"text":"We present the fabrication and characterization of an aluminum transmon qubit on a silicon-on-insulator substrate. Key to the qubit fabrication is the use of an anhydrous hydrofluoric vapor process which selectively removes the lossy silicon oxide buried underneath the silicon device layer. For a 5.6 GHz qubit measured dispersively by a 7.1 GHz resonator, we find T1 = 3.5 μs and T∗2 = 2.2 μs. This process in principle permits the co-fabrication of silicon photonic and mechanical elements, providing a route towards chip-scale integration of electro-opto-mechanical transducers for quantum networking of superconducting microwave quantum circuits. The additional processing steps are compatible with established fabrication techniques for aluminum transmon qubits on silicon.","lang":"eng"}],"date_updated":"2025-06-04T09:48:41Z","department":[{"_id":"JoFi"}],"author":[{"last_name":"Keller","first_name":"Andrew J","full_name":"Keller, Andrew J"},{"last_name":"Dieterle","first_name":"Paul","full_name":"Dieterle, Paul"},{"full_name":"Fang, Michael","last_name":"Fang","first_name":"Michael"},{"last_name":"Berger","first_name":"Brett","full_name":"Berger, Brett"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Painter","first_name":"Oskar","full_name":"Painter, Oskar"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"oa_version":"Submitted Version","citation":{"ista":"Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. 2017. Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. 111(4), 042603.","mla":"Keller, Andrew J., et al. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” <i>Applied Physics Letters</i>, vol. 111, no. 4, 042603, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1063/1.4994661\">10.1063/1.4994661</a>.","chicago":"Keller, Andrew J, Paul Dieterle, Michael Fang, Brett Berger, Johannes M Fink, and Oskar Painter. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” <i>Applied Physics Letters</i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1063/1.4994661\">https://doi.org/10.1063/1.4994661</a>.","ieee":"A. J. Keller, P. Dieterle, M. Fang, B. Berger, J. M. Fink, and O. Painter, “Al transmon qubits on silicon on insulator for quantum device integration,” <i>Applied Physics Letters</i>, vol. 111, no. 4. American Institute of Physics, 2017.","apa":"Keller, A. J., Dieterle, P., Fang, M., Berger, B., Fink, J. M., &#38; Painter, O. (2017). Al transmon qubits on silicon on insulator for quantum device integration. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4994661\">https://doi.org/10.1063/1.4994661</a>","short":"A.J. Keller, P. Dieterle, M. Fang, B. Berger, J.M. Fink, O. Painter, Applied Physics Letters 111 (2017).","ama":"Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. Al transmon qubits on silicon on insulator for quantum device integration. <i>Applied Physics Letters</i>. 2017;111(4). doi:<a href=\"https://doi.org/10.1063/1.4994661\">10.1063/1.4994661</a>"},"publist_id":"6857","publication_status":"published","year":"2017","status":"public","type":"journal_article","quality_controlled":"1","article_number":"042603","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.10195"}],"_id":"796","publication_identifier":{"issn":["0003-6951"]},"doi":"10.1063/1.4994661","oa":1,"day":"01","scopus_import":"1","date_created":"2018-12-11T11:48:33Z","acknowledgement":"This work was supported by the AFOSR MURI Quantum Photonic Matter (Grant No. 16RT0696), the AFOSR MURI Wiring Quantum Networks with Mechanical Transducers (Grant No. FA9550-15-1-0015), the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center (Grant No. PHY-1125565) with the support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. A.J.K. acknowledges the IQIM Postdoctoral Fellowship.","publication":"Applied Physics Letters","title":"Al transmon qubits on silicon on insulator for quantum device integration","intvolume":"       111","volume":111,"article_processing_charge":"No","month":"07"},{"month":"05","article_processing_charge":"No","publist_id":"6856","volume":48,"citation":{"ieee":"J. M. Fink, “Photonenblockade aufgelöst,” <i>Physik in unserer Zeit</i>, vol. 48, no. 3. Wiley, pp. 111–113, 2017.","chicago":"Fink, Johannes M. “Photonenblockade Aufgelöst.” <i>Physik in Unserer Zeit</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/piuz.201770305\">https://doi.org/10.1002/piuz.201770305</a>.","ista":"Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3), 111–113.","mla":"Fink, Johannes M. “Photonenblockade Aufgelöst.” <i>Physik in Unserer Zeit</i>, vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:<a href=\"https://doi.org/10.1002/piuz.201770305\">10.1002/piuz.201770305</a>.","ama":"Fink JM. Photonenblockade aufgelöst. <i>Physik in unserer Zeit</i>. 2017;48(3):111-113. doi:<a href=\"https://doi.org/10.1002/piuz.201770305\">10.1002/piuz.201770305</a>","short":"J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.","apa":"Fink, J. M. (2017). Photonenblockade aufgelöst. <i>Physik in Unserer Zeit</i>. Wiley. <a href=\"https://doi.org/10.1002/piuz.201770305\">https://doi.org/10.1002/piuz.201770305</a>"},"intvolume":"        48","page":"111 - 113","language":[{"iso":"eng"}],"title":"Photonenblockade aufgelöst","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Physik in unserer Zeit","author":[{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M"}],"corr_author":"1","date_created":"2018-12-11T11:48:33Z","day":"01","date_updated":"2024-10-09T20:57:34Z","department":[{"_id":"JoFi"}],"article_type":"original","abstract":[{"lang":"ger","text":"Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten [1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung von undurchsichtig zu transparent nachgewiesen werden."}],"_id":"797","doi":"10.1002/piuz.201770305","issue":"3","publisher":"Wiley","quality_controlled":"1","date_published":"2017-05-01T00:00:00Z","publication_status":"published","year":"2017","type":"journal_article","status":"public"},{"title":"Mechanical on chip microwave circulator","project":[{"call_identifier":"H2020","grant_number":"732894","name":"Hybrid Optomechanical Technologies","_id":"257EB838-B435-11E9-9278-68D0E5697425"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","grant_number":"707438"}],"intvolume":"         8","file":[{"access_level":"open_access","creator":"system","file_id":"5145","relation":"main_file","date_created":"2018-12-12T10:15:25Z","checksum":"b68dafa71d1834c23b742cd9987a3d5f","file_size":1467696,"date_updated":"2020-07-14T12:48:06Z","content_type":"application/pdf","file_name":"IST-2017-867-v1+1_s41467-017-01304-x.pdf"}],"volume":8,"article_processing_charge":"Yes (in subscription journal)","month":"10","day":"16","pubrep_id":"867","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2018-12-11T11:48:33Z","ec_funded":1,"scopus_import":"1","publication":"Nature Communications","article_number":"1304","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-017-01304-x","_id":"798","oa":1,"has_accepted_license":"1","status":"public","type":"journal_article","year":"2017","publication_status":"published","file_date_updated":"2020-07-14T12:48:06Z","quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ama":"Barzanjeh S, Wulf M, Peruzzo M, et al. Mechanical on chip microwave circulator. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01304-x\">10.1038/s41467-017-01304-x</a>","short":"S. Barzanjeh, M. Wulf, M. Peruzzo, M. Kalaee, P. Dieterle, O. Painter, J.M. Fink, Nature Communications 8 (2017).","apa":"Barzanjeh, S., Wulf, M., Peruzzo, M., Kalaee, M., Dieterle, P., Painter, O., &#38; Fink, J. M. (2017). Mechanical on chip microwave circulator. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01304-x\">https://doi.org/10.1038/s41467-017-01304-x</a>","ieee":"S. Barzanjeh <i>et al.</i>, “Mechanical on chip microwave circulator,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","chicago":"Barzanjeh, Shabir, Matthias Wulf, Matilda Peruzzo, Mahmoud Kalaee, Paul Dieterle, Oskar Painter, and Johannes M Fink. “Mechanical on Chip Microwave Circulator.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01304-x\">https://doi.org/10.1038/s41467-017-01304-x</a>.","mla":"Barzanjeh, Shabir, et al. “Mechanical on Chip Microwave Circulator.” <i>Nature Communications</i>, vol. 8, no. 1, 1304, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01304-x\">10.1038/s41467-017-01304-x</a>.","ista":"Barzanjeh S, Wulf M, Peruzzo M, Kalaee M, Dieterle P, Painter O, Fink JM. 2017. Mechanical on chip microwave circulator. Nature Communications. 8(1), 1304."},"publist_id":"6855","corr_author":"1","author":[{"last_name":"Barzanjeh","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"},{"orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","last_name":"Wulf","first_name":"Matthias"},{"full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","first_name":"Matilda"},{"last_name":"Kalaee","first_name":"Mahmoud","full_name":"Kalaee, Mahmoud"},{"last_name":"Dieterle","first_name":"Paul","full_name":"Dieterle, Paul"},{"last_name":"Painter","first_name":"Oskar","full_name":"Painter, Oskar"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"external_id":{"isi":["000412999700021"]},"ddc":["539"],"abstract":[{"lang":"eng","text":"Nonreciprocal circuit elements form an integral part of modern measurement and communication systems. Mathematically they require breaking of time-reversal symmetry, typically achieved using magnetic materials and more recently using the quantum Hall effect, parametric permittivity modulation or Josephson nonlinearities. Here we demonstrate an on-chip magnetic-free circulator based on reservoir-engineered electromechanic interactions. Directional circulation is achieved with controlled phase-sensitive interference of six distinct electro-mechanical signal conversion paths. The presented circulator is compact, its silicon-on-insulator platform is compatible with both superconducting qubits and silicon photonics, and its noise performance is close to the quantum limit. With a high dynamic range, a tunable bandwidth of up to 30 MHz and an in situ reconfigurability as beam splitter or wavelength converter, it could pave the way for superconducting qubit processors with multiplexed on-chip signal processing and readout."}],"department":[{"_id":"JoFi"}],"date_updated":"2025-07-10T11:54:54Z","date_published":"2017-10-16T00:00:00Z","publisher":"Nature Publishing Group","issue":"1"},{"publist_id":"6854","citation":{"chicago":"Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/pcp/pcx118\">https://doi.org/10.1093/pcp/pcx118</a>.","ieee":"S. Kitakura <i>et al.</i>, “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,” <i>Plant and Cell Physiology</i>, vol. 58, no. 10. Oxford University Press, 2017.","mla":"Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” <i>Plant and Cell Physiology</i>, vol. 58, no. 10, 1801–1811, Oxford University Press, 2017, doi:<a href=\"https://doi.org/10.1093/pcp/pcx118\">10.1093/pcp/pcx118</a>.","ista":"Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 58(10), 1801–1811.","apa":"Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima, K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcx118\">https://doi.org/10.1093/pcp/pcx118</a>","short":"S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima, C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017).","ama":"Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. <i>Plant and Cell Physiology</i>. 2017;58(10). doi:<a href=\"https://doi.org/10.1093/pcp/pcx118\">10.1093/pcp/pcx118</a>"},"oa_version":"Submitted Version","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Saeko","last_name":"Kitakura","full_name":"Kitakura, Saeko"},{"full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","first_name":"Maciek"},{"last_name":"Matsuura","first_name":"Yuki","full_name":"Matsuura, Yuki"},{"full_name":"Santuari, Luca","last_name":"Santuari","first_name":"Luca"},{"first_name":"Hirotaka","last_name":"Kouno","full_name":"Kouno, Hirotaka"},{"last_name":"Arima","first_name":"Kohei","full_name":"Arima, Kohei"},{"full_name":"Hardtke, Christian","first_name":"Christian","last_name":"Hardtke"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tatsuo","last_name":"Kakimoto","full_name":"Kakimoto, Tatsuo"},{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"}],"department":[{"_id":"JiFr"}],"date_updated":"2025-07-10T11:54:55Z","abstract":[{"lang":"eng","text":"Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA), which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been revealed fully. In a previous study, we have identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2 as a crucial component of this BFA action at the level of TGN/EE. Furthermore, ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis."}],"external_id":{"pmid":["29016942"],"isi":["000413220400019"]},"isi":1,"ddc":["581"],"issue":"10","publisher":"Oxford University Press","date_published":"2017-08-21T00:00:00Z","month":"08","article_processing_charge":"No","file":[{"file_size":1352913,"content_type":"application/pdf","date_updated":"2020-07-14T12:48:06Z","file_name":"2017_PlantCellPhysio_Kitakura.pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"6333","date_created":"2019-04-17T07:52:34Z","checksum":"bd3e3a94d55416739cbb19624bb977f8"}],"volume":58,"intvolume":"        58","title":"BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana","publication":"Plant and Cell Physiology","date_created":"2018-12-11T11:48:34Z","scopus_import":"1","pubrep_id":"1009","day":"21","pmid":1,"has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["0032-0781"]},"doi":"10.1093/pcp/pcx118","_id":"799","article_number":"1801-1811","quality_controlled":"1","type":"journal_article","status":"public","publication_status":"published","file_date_updated":"2020-07-14T12:48:06Z","year":"2017"},{"oa_version":"Published Version","language":[{"iso":"eng"}],"publist_id":"6853","citation":{"ista":"Strüber M, Sauer J, Jonas PM, Bartos M. 2017. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 8(1), 758.","mla":"Strüber, Michael, et al. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” <i>Nature Communications</i>, vol. 8, no. 1, 758, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-00936-3\">10.1038/s41467-017-00936-3</a>.","ieee":"M. Strüber, J. Sauer, P. M. Jonas, and M. Bartos, “Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","chicago":"Strüber, Michael, Jonas Sauer, Peter M Jonas, and Marlene Bartos. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-00936-3\">https://doi.org/10.1038/s41467-017-00936-3</a>.","short":"M. Strüber, J. Sauer, P.M. Jonas, M. Bartos, Nature Communications 8 (2017).","ama":"Strüber M, Sauer J, Jonas PM, Bartos M. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-00936-3\">10.1038/s41467-017-00936-3</a>","apa":"Strüber, M., Sauer, J., Jonas, P. M., &#38; Bartos, M. (2017). Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-00936-3\">https://doi.org/10.1038/s41467-017-00936-3</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Strüber","first_name":"Michael","full_name":"Strüber, Michael"},{"full_name":"Sauer, Jonas","first_name":"Jonas","last_name":"Sauer"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas"},{"last_name":"Bartos","first_name":"Marlene","full_name":"Bartos, Marlene"}],"isi":1,"external_id":{"isi":["000412053100004"]},"ddc":["571"],"department":[{"_id":"PeJo"}],"date_updated":"2025-07-10T11:54:59Z","abstract":[{"lang":"eng","text":"Gamma oscillations (30–150 Hz) in neuronal networks are associated with the processing and recall of information. We measured local field potentials in the dentate gyrus of freely moving mice and found that gamma activity occurs in bursts, which are highly heterogeneous in their spatial extensions, ranging from focal to global coherent events. Synaptic communication among perisomatic-inhibitory interneurons (PIIs) is thought to play an important role in the generation of hippocampal gamma patterns. However, how neuronal circuits can generate synchronous oscillations at different spatial scales is unknown. We analyzed paired recordings in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron synapses is distance dependent. Synaptic strength declines whereas the duration of inhibitory signals increases with axonal distance among interconnected PIIs. Using neuronal network modeling, we show that distance-dependent inhibition generates multiple highly synchronous focal gamma bursts allowing the network to process complex inputs in parallel in flexibly organized neuronal centers."}],"date_published":"2017-10-02T00:00:00Z","issue":"1","publisher":"Nature Publishing Group","project":[{"grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"intvolume":"         8","title":"Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus","month":"10","article_processing_charge":"No","file":[{"creator":"system","file_id":"5135","relation":"main_file","date_created":"2018-12-12T10:15:17Z","checksum":"7e2c7621afd5f802338e92e8619f024d","access_level":"open_access","file_name":"IST-2017-914-v1+1_s41467-017-00936-3.pdf","file_size":4261832,"content_type":"application/pdf","date_updated":"2020-07-14T12:48:07Z"}],"volume":8,"ec_funded":1,"date_created":"2018-12-11T11:48:34Z","scopus_import":"1","pubrep_id":"914","day":"02","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication":"Nature Communications","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-017-00936-3","_id":"800","article_number":"758","has_accepted_license":"1","oa":1,"quality_controlled":"1","status":"public","type":"journal_article","year":"2017","file_date_updated":"2020-07-14T12:48:07Z","publication_status":"published"}]