[{"publication":"Proceedings of the ACM on Programming Languages","scopus_import":"1","publisher":"Association for Computing Machinery","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"abstract":[{"text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.","lang":"eng"}],"publication_status":"published","article_type":"original","citation":{"apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., &#38; Vaidya, K. (2017). Data-centric dynamic partial order reduction. <i>Proceedings of the ACM on Programming Languages</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3158119\">https://doi.org/10.1145/3158119</a>","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2017. <a href=\"https://doi.org/10.1145/3158119\">https://doi.org/10.1145/3158119</a>.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. <i>Proceedings of the ACM on Programming Languages</i>. 2017;2(POPL). doi:<a href=\"https://doi.org/10.1145/3158119\">10.1145/3158119</a>","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2017).","mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL, 31, Association for Computing Machinery, 2017, doi:<a href=\"https://doi.org/10.1145/3158119\">10.1145/3158119</a>.","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL. Association for Computing Machinery, 2017.","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31."},"quality_controlled":"1","issue":"POPL","ec_funded":1,"month":"12","article_number":"31","intvolume":"         2","type":"journal_article","arxiv":1,"main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3158119","open_access":"1"}],"date_published":"2017-12-27T00:00:00Z","day":"27","external_id":{"arxiv":["1610.01188"]},"volume":2,"date_created":"2021-12-05T23:01:49Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1145/3158119","status":"public","author":[{"first_name":"Marek","full_name":"Chalupa, Marek","last_name":"Chalupa"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas"},{"last_name":"Sinha","first_name":"Nishant","full_name":"Sinha, Nishant"},{"first_name":"Kapil","full_name":"Vaidya, Kapil","last_name":"Vaidya"}],"oa_version":"Published Version","publication_identifier":{"eissn":["2475-1421"]},"oa":1,"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","year":"2017","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5448"},{"status":"public","id":"5456","relation":"earlier_version"}]},"conference":{"name":"POPL: Programming Languages","location":"Los Angeles, CA, United States","end_date":"2018-01-13","start_date":"2018-01-07"},"_id":"10417","date_updated":"2023-02-23T12:27:16Z","article_processing_charge":"No","title":"Data-centric dynamic partial order reduction"},{"quality_controlled":"1","citation":{"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.","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.","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>.","short":"A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM on Programming Languages 2 (2017).","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>","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>","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>."},"publication_status":"published","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"abstract":[{"lang":"eng","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."}],"scopus_import":"1","publication":"Proceedings of the ACM on Programming Languages","publisher":"Association for Computing Machinery","main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3158121","open_access":"1"}],"arxiv":1,"type":"journal_article","month":"12","intvolume":"         2","article_number":"33","issue":"POPL","author":[{"last_name":"Mciver","first_name":"Annabelle","full_name":"Mciver, Annabelle"},{"last_name":"Morgan","full_name":"Morgan, Carroll","first_name":"Carroll"},{"full_name":"Kaminski, Benjamin Lucien","first_name":"Benjamin Lucien","last_name":"Kaminski"},{"first_name":"Joost P","full_name":"Katoen, Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","last_name":"Katoen"}],"status":"public","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2021-12-05T23:01:49Z","volume":2,"doi":"10.1145/3158121","external_id":{"arxiv":["1711.03588"]},"date_published":"2017-12-07T00:00:00Z","day":"07","title":"A new proof rule for almost-sure termination","article_processing_charge":"No","conference":{"name":"POPL: Programming Languages","location":"Los Angeles, CA, United States","start_date":"2018-01-07","end_date":"2018-01-13"},"date_updated":"2021-12-07T08:04:14Z","_id":"10418","year":"2017","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.","publication_identifier":{"eissn":["2475-1421"]},"oa":1},{"day":"01","date_published":"2017-04-01T00:00:00Z","external_id":{"isi":["000398545200003"]},"doi":"10.1111/evo.13191","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:49:57Z","volume":71,"oa_version":"Submitted Version","author":[{"last_name":"Uecker","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","first_name":"Hildegard"}],"status":"public","oa":1,"publication_identifier":{"issn":["00143820"]},"year":"2017","project":[{"call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"date_updated":"2025-05-28T11:42:51Z","_id":"1063","title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","article_processing_charge":"No","publisher":"Wiley-Blackwell","publication":"Evolution","scopus_import":"1","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"}],"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"publist_id":"6327","publication_status":"published","quality_controlled":"1","citation":{"ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” <i>Evolution</i>, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858.","short":"H. Uecker, Evolution 71 (2017) 845–858.","mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” <i>Evolution</i>, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58, doi:<a href=\"https://doi.org/10.1111/evo.13191\">10.1111/evo.13191</a>.","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-Blackwell. <a href=\"https://doi.org/10.1111/evo.13191\">https://doi.org/10.1111/evo.13191</a>","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” <i>Evolution</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/evo.13191\">https://doi.org/10.1111/evo.13191</a>."},"page":"845 - 858","ec_funded":1,"issue":"4","intvolume":"        71","isi":1,"month":"04","type":"journal_article","main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2016/10/14/081042"}]},{"ddc":["000"],"type":"journal_article","month":"06","isi":1,"intvolume":"       122","pubrep_id":"991","page":"25 - 29","ec_funded":1,"quality_controlled":"1","citation":{"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.","short":"K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.","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>.","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>","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>.","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>"},"publication_status":"published","department":[{"_id":"KrCh"},{"_id":"HeEd"}],"language":[{"iso":"eng"}],"publist_id":"6323","abstract":[{"lang":"eng","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."}],"file_date_updated":"2019-10-15T07:44:51Z","scopus_import":"1","file":[{"file_id":"4998","creator":"system","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf","date_updated":"2019-10-15T07:44:51Z","file_size":247657,"date_created":"2018-12-12T10:13:17Z","relation":"main_file"}],"publication":"Information Processing Letters","publisher":"Elsevier","article_processing_charge":"No","title":"Pushdown reachability with constant treewidth","date_updated":"2023-09-20T12:08:18Z","_id":"1065","has_accepted_license":"1","year":"2017","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"}],"publication_identifier":{"issn":["00200190"]},"oa":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","first_name":"Georg F"}],"status":"public","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:49:57Z","volume":122,"doi":"10.1016/j.ipl.2017.02.003","external_id":{"isi":["000399506600005"]},"date_published":"2017-06-01T00:00:00Z","day":"01"},{"related_material":{"record":[{"status":"public","id":"5428","relation":"earlier_version"}]},"_id":"1066","date_updated":"2023-09-20T12:07:48Z","title":"Quantitative fair simulation games","article_processing_charge":"No","year":"2017","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"volume":254,"date_created":"2018-12-11T11:49:58Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1016/j.ic.2016.10.006","status":"public","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Otop, Jan"},{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"}],"oa_version":"None","date_published":"2017-06-01T00:00:00Z","day":"01","external_id":{"isi":["000402025600002"]},"type":"journal_article","issue":"2","ec_funded":1,"page":"143 - 166","isi":1,"month":"06","intvolume":"       254","publication_status":"published","citation":{"ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","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.","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>.","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>","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>."},"quality_controlled":"1","scopus_import":"1","publication":"Information and Computation","publisher":"Elsevier","language":[{"iso":"eng"}],"publist_id":"6322","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"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"}]},{"publication_identifier":{"issn":["15345807"]},"oa":1,"has_accepted_license":"1","year":"2017","project":[{"grant_number":"201439","call_identifier":"FP7","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","_id":"2524F500-B435-11E9-9278-68D0E5697425"}],"_id":"1067","date_updated":"2023-09-20T12:06:27Z","title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","article_processing_charge":"No","date_published":"2017-02-27T00:00:00Z","day":"27","external_id":{"isi":["000395368300007"]},"volume":40,"date_created":"2018-12-11T11:49:58Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1016/j.devcel.2017.01.010","author":[{"last_name":"Morita","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","first_name":"Hitoshi","full_name":"Morita, Hitoshi"},{"full_name":"Grigolon, Silvia","first_name":"Silvia","last_name":"Grigolon"},{"last_name":"Bock","first_name":"Martin","full_name":"Bock, Martin"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","full_name":"Krens, Gabriel","first_name":"Gabriel","orcid":"0000-0003-4761-5996"},{"last_name":"Salbreux","full_name":"Salbreux, Guillaume","first_name":"Guillaume"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa_version":"Published Version","issue":"4","ec_funded":1,"acknowledged_ssus":[{"_id":"PreCl"}],"page":"354 - 366","isi":1,"month":"02","pubrep_id":"869","intvolume":"        40","type":"journal_article","ddc":["572","597"],"file":[{"relation":"main_file","date_created":"2018-12-12T10:10:57Z","file_size":6866187,"date_updated":"2018-12-12T10:10:57Z","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","content_type":"application/pdf","access_level":"open_access","creator":"system","file_id":"4849"}],"scopus_import":"1","file_date_updated":"2018-12-12T10:10:57Z","publication":"Developmental Cell","publisher":"Cell Press","department":[{"_id":"CaHe"}],"publist_id":"6320","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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."}],"publication_status":"published","citation":{"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>","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>","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.","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.","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>.","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366."},"quality_controlled":"1"},{"day":"01","date_published":"2017-05-01T00:00:00Z","external_id":{"arxiv":["1312.1231"],"isi":["000398030400024"]},"doi":"10.1090/tran/6991","volume":369,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:49:59Z","oa_version":"Preprint","author":[{"id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","last_name":"Bauer","first_name":"Ulrich","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724"},{"orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"status":"public","oa":1,"year":"2017","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”.","project":[{"grant_number":"318493","call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"_id":"1072","date_updated":"2023-09-20T12:05:56Z","title":"The Morse theory of Čech and delaunay complexes","article_processing_charge":"No","publisher":"American Mathematical Society","scopus_import":"1","publication":"Transactions of the American Mathematical Society","abstract":[{"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.","lang":"eng"}],"publist_id":"6311","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"article_type":"original","publication_status":"published","citation":{"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>.","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762.","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.","ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762.","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>.","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>","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>"},"quality_controlled":"1","ec_funded":1,"page":"3741 - 3762","issue":"5","intvolume":"       369","month":"05","isi":1,"type":"journal_article","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1312.1231"}]},{"date_updated":"2023-09-20T12:01:28Z","_id":"1073","article_processing_charge":"No","title":"Algorithmic solvability of the lifting extension problem","oa":1,"publication_identifier":{"issn":["01795376"]},"year":"2017","doi":"10.1007/s00454-016-9855-6","date_created":"2018-12-11T11:50:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":54,"oa_version":"Submitted Version","author":[{"full_name":"Čadek, Martin","first_name":"Martin","last_name":"Čadek"},{"full_name":"Krcál, Marek","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","last_name":"Krcál"},{"full_name":"Vokřínek, Lukáš","first_name":"Lukáš","last_name":"Vokřínek"}],"status":"public","day":"01","date_published":"2017-06-01T00:00:00Z","external_id":{"isi":["000400072700008"]},"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1307.6444","open_access":"1"}],"page":"915 - 965","issue":"4","intvolume":"        54","isi":1,"month":"06","publication_status":"published","quality_controlled":"1","citation":{"short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete &#38; Computational Geometry 54 (2017) 915–965.","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.","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.","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>.","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>","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>"},"publisher":"Springer","scopus_import":"1","publication":"Discrete & Computational Geometry","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."}],"department":[{"_id":"UlWa"}],"publist_id":"6309","language":[{"iso":"eng"}]},{"main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/early/2016/09/23/076810"}],"type":"journal_article","intvolume":"       205","month":"03","isi":1,"page":"1335 - 1351","ec_funded":1,"issue":"3","quality_controlled":"1","citation":{"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.","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.","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.","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>.","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>","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>.","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>"},"publication_status":"published","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"6307","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publication":"Genetics","scopus_import":"1","title":"Inferring recent demography from isolation by distance of long shared sequence blocks","article_processing_charge":"No","date_updated":"2025-05-28T11:42:51Z","_id":"1074","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"200"}]},"year":"2017","project":[{"call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"oa":1,"publication_identifier":{"issn":["00166731"]},"oa_version":"Preprint","status":"public","author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","first_name":"Harald","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682"},{"first_name":"Graham","full_name":"Coop, Graham","last_name":"Coop"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"doi":"10.1534/genetics.116.196220","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:50:00Z","volume":205,"external_id":{"isi":["000395807200023"]},"day":"01","date_published":"2017-03-01T00:00:00Z"},{"isi":1,"month":"02","article_number":"023403","intvolume":"        95","issue":"2","ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/1609.07018","open_access":"1"}],"type":"journal_article","publist_id":"6305","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"abstract":[{"text":"Signatures of the Coulomb corrections in the photoelectron momentum distribution during laser-induced ionization of atoms or ions in tunneling and multiphoton regimes are investigated analytically in the case of a one-dimensional problem. A high-order Coulomb-corrected strong-field approximation is applied, where the exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov state including the second-order corrections to the eikonal. Although without high-order corrections our theory coincides with the known analytical R-matrix (ARM) theory, we propose a simplified procedure for the matrix element derivation. Rather than matching the eikonal Coulomb-Volkov wave function with the bound state as in the ARM theory to remove the Coulomb singularity, we calculate the matrix element via the saddle-point integration method by time as well as by coordinate, and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron momentum distribution with respect to the ARM theory due to high-order corrections is analyzed for tunneling and multiphoton regimes. The relation of the quantum corrections to the tunneling delay time is discussed.","lang":"eng"}],"scopus_import":"1","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","publisher":"American Physical Society","citation":{"short":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel,  Physical Review A - Atomic, Molecular, and Optical Physics 95 (2017).","mla":"Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">10.1103/PhysRevA.95.023403</a>.","ieee":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field ionization via a high-order Coulomb-corrected strong-field approximation,” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 95, no. 2. American Physical Society, 2017.","ista":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation.  Physical Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403.","chicago":"Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan, and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">https://doi.org/10.1103/PhysRevA.95.023403</a>.","apa":"Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., &#38; Keitel, C. (2017). Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">https://doi.org/10.1103/PhysRevA.95.023403</a>","ama":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2017;95(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">10.1103/PhysRevA.95.023403</a>"},"quality_controlled":"1","publication_status":"published","year":"2017","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"publication_identifier":{"issn":["24699926"]},"oa":1,"title":"Strong-field ionization via a high-order Coulomb-corrected strong-field approximation","article_processing_charge":"No","_id":"1076","date_updated":"2023-09-20T11:57:23Z","external_id":{"isi":["000400571700011"]},"date_published":"2017-02-01T00:00:00Z","day":"01","author":[{"last_name":"Klaiber","first_name":"Michael","full_name":"Klaiber, Michael"},{"full_name":"Daněk, Jiří","first_name":"Jiří","last_name":"Daněk"},{"full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu"},{"last_name":"Hatsagortsyan","first_name":"Karen","full_name":"Hatsagortsyan, Karen"},{"full_name":"Keitel, Christoph","first_name":"Christoph","last_name":"Keitel"}],"status":"public","oa_version":"Submitted Version","volume":95,"date_created":"2018-12-11T11:50:01Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1103/PhysRevA.95.023403"},{"publication_identifier":{"issn":["17425689"]},"oa":1,"has_accepted_license":"1","year":"2017","project":[{"call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","grant_number":"648440"}],"related_material":{"record":[{"status":"public","id":"9864","relation":"research_data"}]},"_id":"1077","date_updated":"2025-05-28T11:42:51Z","article_processing_charge":"Yes (in subscription journal)","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","date_published":"2017-01-04T00:00:00Z","day":"04","external_id":{"isi":["000393380400001"]},"volume":14,"date_created":"2018-12-11T11:50:01Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1098/rsif.2016.0139","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"Vladar","first_name":"Harold","full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653"},{"last_name":"Włodarski","full_name":"Włodarski, Tomasz","first_name":"Tomasz"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","issue":"126","ec_funded":1,"isi":1,"month":"01","article_number":"20160139","intvolume":"        14","type":"journal_article","ddc":["570"],"scopus_import":"1","file":[{"file_id":"5843","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_updated":"2019-01-18T09:14:02Z","file_name":"2017_JRSI_Redondo.pdf","date_created":"2019-01-18T09:14:02Z","file_size":1092015,"success":1,"relation":"main_file"}],"publication":"Journal of the Royal Society Interface","file_date_updated":"2019-01-18T09:14:02Z","publisher":"Royal Society of London","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publist_id":"6303","language":[{"iso":"eng"}],"abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"publication_status":"published","citation":{"ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. 2017;14(126). doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>. Royal Society of London, 2017. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126. Royal Society of London, 2017.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139.","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017)."},"quality_controlled":"1"},{"oa":1,"project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"year":"2017","has_accepted_license":"1","date_updated":"2025-05-07T11:12:33Z","_id":"1078","related_material":{"record":[{"id":"5565","relation":"popular_science","status":"public"}]},"title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","article_processing_charge":"No","day":"18","date_published":"2017-01-18T00:00:00Z","external_id":{"isi":["000397847200041"]},"doi":"10.3791/55044","date_created":"2018-12-11T11:50:01Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":2017,"oa_version":"Published Version","author":[{"last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","full_name":"Von Wangenheim, Daniel","first_name":"Daniel"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"status":"public","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"ec_funded":1,"issue":"119","intvolume":"      2017","pubrep_id":"808","article_number":"e55044","isi":1,"month":"01","ddc":["580"],"type":"journal_article","publisher":"Journal of Visualized Experiments","publication":"Journal of visualized experiments JoVE","file_date_updated":"2018-12-12T10:16:32Z","file":[{"relation":"main_file","file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf","date_updated":"2018-12-12T10:16:31Z","date_created":"2018-12-12T10:16:31Z","file_size":57678,"creator":"system","access_level":"open_access","content_type":"application/pdf","file_id":"5219"},{"relation":"main_file","date_created":"2018-12-12T10:16:32Z","file_size":1317820,"file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","date_updated":"2018-12-12T10:16:32Z","content_type":"application/pdf","creator":"system","access_level":"open_access","file_id":"5220"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. "}],"publist_id":"6302","department":[{"_id":"JiFr"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"publication_status":"published","citation":{"short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017).","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>.","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017(119), e55044.","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” <i>Journal of visualized experiments JoVE</i>, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments, 2017. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>.","apa":"von Wangenheim, D., Hauschild, R., &#38; Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of visualized experiments JoVE</i>. 2017;2017(119). doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>"}},{"volume":20,"date_created":"2018-12-11T11:50:02Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1007/s11040-017-9238-0","author":[{"full_name":"Nam, Phan","first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam"},{"full_name":"Van Den Bosch, Hanne","first_name":"Hanne","last_name":"Van Den Bosch"}],"status":"public","oa_version":"Submitted Version","date_published":"2017-06-01T00:00:00Z","day":"01","external_id":{"isi":["000401270000004"]},"_id":"1079","date_updated":"2023-09-20T11:53:35Z","article_processing_charge":"No","title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","publication_identifier":{"issn":["13850172"]},"oa":1,"project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF"}],"year":"2017","publication_status":"published","citation":{"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>","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>.","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>","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.","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.","short":"P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017).","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>."},"quality_controlled":"1","publication":"Mathematical Physics, Analysis and Geometry","scopus_import":"1","publisher":"Springer","language":[{"iso":"eng"}],"publist_id":"6300","department":[{"_id":"RoSe"}],"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"}],"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1603.07368","open_access":"1"}],"issue":"2","isi":1,"month":"06","article_number":"6","intvolume":"        20"},{"pubrep_id":"786","intvolume":"         8","article_number":"14114","isi":1,"month":"01","ec_funded":1,"ddc":["004","006"],"type":"journal_article","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."}],"language":[{"iso":"eng"}],"publist_id":"6301","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","file_date_updated":"2018-12-12T10:15:15Z","file":[{"access_level":"open_access","creator":"system","content_type":"application/pdf","file_id":"5133","relation":"main_file","date_updated":"2018-12-12T10:15:15Z","file_name":"IST-2017-786-v1+1_ncomms14114.pdf","date_created":"2018-12-12T10:15:15Z","file_size":897050}],"publication":"Nature Communications","scopus_import":"1","quality_controlled":"1","citation":{"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>.","short":"J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017).","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>","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>","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>."},"publication_status":"published","year":"2017","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"}],"has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["20411723"]},"title":"Reconstructing metastatic seeding patterns of human cancers","article_processing_charge":"No","date_updated":"2023-09-20T11:55:31Z","_id":"1080","external_id":{"isi":["000393096600001"]},"day":"31","date_published":"2017-01-31T00:00:00Z","oa_version":"Published Version","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","first_name":"Johannes"},{"first_name":"Alvin","full_name":"Makohon Moore, Alvin","last_name":"Makohon Moore"},{"first_name":"Jeffrey","full_name":"Gerold, Jeffrey","last_name":"Gerold"},{"full_name":"Božić, Ivana","first_name":"Ivana","last_name":"Božić"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Iacobuzio Donahue, Christine","first_name":"Christine","last_name":"Iacobuzio Donahue"},{"first_name":"Bert","full_name":"Vogelstein, Bert","last_name":"Vogelstein"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"doi":"10.1038/ncomms14114","date_created":"2018-12-11T11:50:02Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":8},{"abstract":[{"lang":"eng","text":"Recently there has been a proliferation of automated program repair (APR) techniques, targeting various programming languages. Such techniques can be generally classified into two families: syntactic- and semantics-based. Semantics-based APR, on which we focus, typically uses symbolic execution to infer semantic constraints and then program synthesis to construct repairs conforming to them. While syntactic-based APR techniques have been shown successful on bugs in real-world programs written in both C and Java, semantics-based APR techniques mostly target C programs. This leaves empirical comparisons of the APR families not fully explored, and developers without a Java-based semantics APR technique. We present JFix, a semantics-based APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs. It extends one particular APR technique (Angelix), and is designed to be sufficiently generic to support a variety of such techniques. We demonstrate that semantics-based APR can indeed efficiently and effectively repair a variety of classes of bugs in large real-world Java programs. This supports our claim that the framework can both support developers seeking semantics-based repair of bugs in Java programs, as well as enable larger scale empirical studies comparing syntactic- and semantics-based APR targeting Java. The demonstration of our tool is available via the project website at: https://xuanbachle.github.io/semanticsrepair/ "}],"publist_id":"6478","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"publisher":"ACM","day":"10","publication":"Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis","scopus_import":1,"date_published":"2017-07-10T00:00:00Z","oa_version":"None","citation":{"ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair of Java programs via symbolic  PathFinder. Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ISSTA: International Symposium on Software Testing and Analysis, 376–379.","ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based repair of Java programs via symbolic  PathFinder,” in <i>Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis</i>, Santa Barbara, CA, United States, 2017, pp. 376–379.","mla":"Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic  PathFinder.” <i>Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis</i>, ACM, 2017, pp. 376–79, doi:<a href=\"https://doi.org/10.1145/3092703.3098225\">10.1145/3092703.3098225</a>.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–379.","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of Java programs via symbolic  PathFinder. In: <i>Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis</i>. ACM; 2017:376-379. doi:<a href=\"https://doi.org/10.1145/3092703.3098225\">10.1145/3092703.3098225</a>","apa":"Le, X., Chu, D. H., Lo, D., Le Goues, C., &#38; Visser, W. (2017). JFIX: Semantics-based repair of Java programs via symbolic  PathFinder. In <i>Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis</i> (pp. 376–379). Santa Barbara, CA, United States: ACM. <a href=\"https://doi.org/10.1145/3092703.3098225\">https://doi.org/10.1145/3092703.3098225</a>","chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “JFIX: Semantics-Based Repair of Java Programs via Symbolic  PathFinder.” In <i>Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis</i>, 376–79. ACM, 2017. <a href=\"https://doi.org/10.1145/3092703.3098225\">https://doi.org/10.1145/3092703.3098225</a>."},"status":"public","quality_controlled":"1","author":[{"first_name":"Xuan","full_name":"Le, Xuan","last_name":"Le"},{"first_name":"Duc Hiep","full_name":"Chu, Duc Hiep","id":"3598E630-F248-11E8-B48F-1D18A9856A87","last_name":"Chu"},{"full_name":"Lo, David","first_name":"David","last_name":"Lo"},{"full_name":"Le Goues, Claire","first_name":"Claire","last_name":"Le Goues"},{"last_name":"Visser","full_name":"Visser, Willem","first_name":"Willem"}],"doi":"10.1145/3092703.3098225","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:49:19Z","publication_status":"published","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"year":"2017","month":"07","page":"376 - 379 ","title":"JFIX: Semantics-based repair of Java programs via symbolic  PathFinder","type":"conference","_id":"941","date_updated":"2021-01-12T08:22:05Z","conference":{"location":"Santa Barbara, CA, United States","name":"ISSTA: International Symposium on Software Testing and Analysis","start_date":"2017-07-10","end_date":"2017-07-14"}},{"year":"2017","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"}],"publication_identifier":{"isbn":["978-145035105-8"]},"title":"S3: Syntax- and semantic-guided repair synthesis via programming by examples","article_processing_charge":"No","_id":"942","date_updated":"2023-09-26T15:38:36Z","conference":{"name":"FSE: Foundations of Software Engineering","location":"Paderborn, Germany","end_date":"2017-09-08","start_date":"2017-09-04"},"external_id":{"isi":["000414279300055"]},"day":"01","date_published":"2017-09-01T00:00:00Z","oa_version":"None","status":"public","author":[{"last_name":"Le","first_name":"Xuan","full_name":"Le, Xuan"},{"last_name":"Chu","id":"3598E630-F248-11E8-B48F-1D18A9856A87","first_name":"Duc Hiep","full_name":"Chu, Duc Hiep"},{"first_name":"David","full_name":"Lo, David","last_name":"Lo"},{"full_name":"Le Goues, Claire","first_name":"Claire","last_name":"Le Goues"},{"last_name":"Visser","first_name":"Willem","full_name":"Visser, Willem"}],"doi":"10.1145/3106237.3106309","volume":"F130154","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:49:19Z","isi":1,"month":"09","page":"593 - 604","type":"conference","abstract":[{"text":"A notable class of techniques for automatic program repair is known as semantics-based. Such techniques, e.g., Angelix, infer semantic specifications via symbolic execution, and then use program synthesis to construct new code that satisfies those inferred specifications. However, the obtained specifications are naturally incomplete, leaving the synthesis engine with a difficult task of synthesizing a general solution from a sparse space of many possible solutions that are consistent with the provided specifications but that do not necessarily generalize. We present S3, a new repair synthesis engine that leverages programming-by-examples methodology to synthesize high-quality bug repairs. The novelty in S3 that allows it to tackle the sparse search space to create more general repairs is three-fold: (1) A systematic way to customize and constrain the syntactic search space via a domain-specific language, (2) An efficient enumeration-based search strategy over the constrained search space, and (3) A number of ranking features based on measures of the syntactic and semantic distances between candidate solutions and the original buggy program. We compare S3’s repair effectiveness with state-of-the-art synthesis engines Angelix, Enumerative, and CVC4. S3 can successfully and correctly fix at least three times more bugs than the best baseline on datasets of 52 bugs in small programs, and 100 bugs in real-world large programs. ","lang":"eng"}],"publist_id":"6477","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"publisher":"ACM","scopus_import":"1","citation":{"apa":"Le, X., Chu, D. H., Lo, D., Le Goues, C., &#38; Visser, W. (2017). S3: Syntax- and semantic-guided repair synthesis via programming by examples (Vol. F130154, pp. 593–604). Presented at the FSE: Foundations of Software Engineering, Paderborn, Germany: ACM. <a href=\"https://doi.org/10.1145/3106237.3106309\">https://doi.org/10.1145/3106237.3106309</a>","chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples,” F130154:593–604. ACM, 2017. <a href=\"https://doi.org/10.1145/3106237.3106309\">https://doi.org/10.1145/3106237.3106309</a>.","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. S3: Syntax- and semantic-guided repair synthesis via programming by examples. In: Vol F130154. ACM; 2017:593-604. doi:<a href=\"https://doi.org/10.1145/3106237.3106309\">10.1145/3106237.3106309</a>","mla":"Le, Xuan, et al. <i>S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples</i>. Vol. F130154, ACM, 2017, pp. 593–604, doi:<a href=\"https://doi.org/10.1145/3106237.3106309\">10.1145/3106237.3106309</a>.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, ACM, 2017, pp. 593–604.","ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “S3: Syntax- and semantic-guided repair synthesis via programming by examples,” presented at the FSE: Foundations of Software Engineering, Paderborn, Germany, 2017, vol. F130154, pp. 593–604.","ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. S3: Syntax- and semantic-guided repair synthesis via programming by examples. FSE: Foundations of Software Engineering vol. F130154, 593–604."},"quality_controlled":"1","publication_status":"published"},{"author":[{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","full_name":"Zagórski, Marcin P","first_name":"Marcin P","orcid":"0000-0001-7896-7762"},{"full_name":"Tabata, Yoji","first_name":"Yoji","last_name":"Tabata"},{"first_name":"Nathalie","full_name":"Brandenberg, Nathalie","last_name":"Brandenberg"},{"last_name":"Lutolf","first_name":"Matthias","full_name":"Lutolf, Matthias"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","full_name":"Bollenbach, Tobias","first_name":"Tobias"},{"last_name":"Briscoe","full_name":"Briscoe, James","first_name":"James"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","first_name":"Anna","orcid":"0000-0003-4509-4998"}],"status":"public","oa_version":"Submitted Version","date_created":"2018-12-11T11:49:20Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":356,"pmid":1,"doi":"10.1126/science.aam5887","external_id":{"pmid":["28663499"],"isi":["000404351500036"]},"date_published":"2017-06-30T00:00:00Z","day":"30","article_processing_charge":"No","title":"Decoding of position in the developing neural tube from antiparallel morphogen gradients","date_updated":"2023-09-26T15:38:05Z","_id":"943","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","grant_number":"P28844-B27"},{"call_identifier":"H2020","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"},{"call_identifier":"FP7","grant_number":"201439","_id":"2524F500-B435-11E9-9278-68D0E5697425","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish"}],"year":"2017","publication_identifier":{"issn":["00368075"]},"oa":1,"quality_controlled":"1","citation":{"ieee":"M. P. Zagórski <i>et al.</i>, “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” <i>Science</i>, vol. 356, no. 6345. American Association for the Advancement of Science, pp. 1379–1383, 2017.","ista":"Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383.","short":"M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.","mla":"Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” <i>Science</i>, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:<a href=\"https://doi.org/10.1126/science.aam5887\">10.1126/science.aam5887</a>.","ama":"Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. <i>Science</i>. 2017;356(6345):1379-1383. doi:<a href=\"https://doi.org/10.1126/science.aam5887\">10.1126/science.aam5887</a>","chicago":"Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aam5887\">https://doi.org/10.1126/science.aam5887</a>.","apa":"Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aam5887\">https://doi.org/10.1126/science.aam5887</a>"},"publication_status":"published","language":[{"iso":"eng"}],"publist_id":"6474","department":[{"_id":"AnKi"},{"_id":"GaTk"}],"abstract":[{"text":"Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation.","lang":"eng"}],"scopus_import":"1","publication":"Science","publisher":"American Association for the Advancement of Science","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/","open_access":"1"}],"type":"journal_article","isi":1,"month":"06","intvolume":"       356","issue":"6345","page":"1379 - 1383","ec_funded":1},{"year":"2017","project":[{"grant_number":"618444","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"}],"publication_identifier":{"issn":["08966273"]},"title":"Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells","article_processing_charge":"No","_id":"944","date_updated":"2023-09-26T15:37:02Z","external_id":{"isi":["000400466700011"]},"day":"03","date_published":"2017-05-03T00:00:00Z","oa_version":"None","status":"public","author":[{"last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","first_name":"Robert J"},{"first_name":"Maria P","full_name":"Postiglione, Maria P","last_name":"Postiglione","id":"2C67902A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X","first_name":"Laura","full_name":"Burnett, Laura"},{"last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","first_name":"Susanne"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","full_name":"Streicher, Carmen","first_name":"Carmen"},{"orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xiao","first_name":"Guanxi","full_name":"Xiao, Guanxi"},{"first_name":"Olga","full_name":"Klezovitch, Olga","last_name":"Klezovitch"},{"last_name":"Vasioukhin","full_name":"Vasioukhin, Valeri","first_name":"Valeri"},{"last_name":"Ghashghaei","full_name":"Ghashghaei, Troy","first_name":"Troy"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"doi":"10.1016/j.neuron.2017.04.012","volume":94,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:49:20Z","intvolume":"        94","month":"05","isi":1,"ec_funded":1,"page":"517 - 533.e3","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"issue":"3","type":"journal_article","abstract":[{"lang":"eng","text":"The concerted production of neurons and glia by neural stem cells (NSCs) is essential for neural circuit assembly. In the developing cerebral cortex, radial glia progenitors (RGPs) generate nearly all neocortical neurons and certain glia lineages. RGP proliferation behavior shows a high degree of non-stochasticity, thus a deterministic characteristic of neuron and glia production. However, the cellular and molecular mechanisms controlling RGP behavior and proliferation dynamics in neurogenesis and glia generation remain unknown. By using mosaic analysis with double markers (MADM)-based genetic paradigms enabling the sparse and global knockout with unprecedented single-cell resolution, we identified Lgl1 as a critical regulatory component. We uncover Lgl1-dependent tissue-wide community effects required for embryonic cortical neurogenesis and novel cell-autonomous Lgl1 functions controlling RGP-mediated glia genesis and postnatal NSC behavior. These results suggest that NSC-mediated neuron and glia production is tightly regulated through the concerted interplay of sequential Lgl1-dependent global and cell intrinsic mechanisms."}],"publist_id":"6473","language":[{"iso":"eng"}],"department":[{"_id":"SiHi"},{"_id":"MaJö"}],"publisher":"Cell Press","scopus_import":"1","publication":"Neuron","citation":{"ieee":"R. J. Beattie <i>et al.</i>, “Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells,” <i>Neuron</i>, vol. 94, no. 3. Cell Press, p. 517–533.e3, 2017.","ista":"Beattie RJ, Postiglione MP, Burnett L, Laukoter S, Streicher C, Pauler F, Xiao G, Klezovitch O, Vasioukhin V, Ghashghaei T, Hippenmeyer S. 2017. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 94(3), 517–533.e3.","short":"R.J. Beattie, M.P. Postiglione, L. Burnett, S. Laukoter, C. Streicher, F. Pauler, G. Xiao, O. Klezovitch, V. Vasioukhin, T. Ghashghaei, S. Hippenmeyer, Neuron 94 (2017) 517–533.e3.","mla":"Beattie, Robert J., et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” <i>Neuron</i>, vol. 94, no. 3, Cell Press, 2017, p. 517–533.e3, doi:<a href=\"https://doi.org/10.1016/j.neuron.2017.04.012\">10.1016/j.neuron.2017.04.012</a>.","ama":"Beattie RJ, Postiglione MP, Burnett L, et al. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. <i>Neuron</i>. 2017;94(3):517-533.e3. doi:<a href=\"https://doi.org/10.1016/j.neuron.2017.04.012\">10.1016/j.neuron.2017.04.012</a>","chicago":"Beattie, Robert J, Maria P Postiglione, Laura Burnett, Susanne Laukoter, Carmen Streicher, Florian Pauler, Guanxi Xiao, et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” <i>Neuron</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.neuron.2017.04.012\">https://doi.org/10.1016/j.neuron.2017.04.012</a>.","apa":"Beattie, R. J., Postiglione, M. P., Burnett, L., Laukoter, S., Streicher, C., Pauler, F., … Hippenmeyer, S. (2017). Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2017.04.012\">https://doi.org/10.1016/j.neuron.2017.04.012</a>"},"quality_controlled":"1","publication_status":"published"},{"_id":"9445","date_updated":"2021-12-14T07:54:36Z","article_processing_charge":"No","title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","oa":1,"publication_identifier":{"eissn":["2050-084X"]},"year":"2017","has_accepted_license":"1","doi":"10.7554/elife.30674","pmid":1,"volume":6,"date_created":"2021-06-02T14:28:58Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","extern":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"first_name":"David B","full_name":"Lyons, David B","last_name":"Lyons"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"}],"day":"15","date_published":"2017-11-15T00:00:00Z","external_id":{"pmid":["29140247"]},"type":"journal_article","ddc":["570"],"article_number":"e30674","intvolume":"         6","month":"11","article_type":"original","publication_status":"published","citation":{"chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/elife.30674\">https://doi.org/10.7554/elife.30674</a>.","apa":"Lyons, D. B., &#38; Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.30674\">https://doi.org/10.7554/elife.30674</a>","ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/elife.30674\">10.7554/elife.30674</a>","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” <i>ELife</i>, vol. 6, e30674, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/elife.30674\">10.7554/elife.30674</a>.","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674."},"quality_controlled":"1","publisher":"eLife Sciences Publications","publication":"eLife","file":[{"date_created":"2021-06-02T14:33:36Z","success":1,"file_size":1603102,"file_name":"2017_eLife_Lyons.pdf","date_updated":"2021-06-02T14:33:36Z","relation":"main_file","file_id":"9446","content_type":"application/pdf","checksum":"4cfcdd67511ae4aed3d993550e46e146","creator":"cziletti","access_level":"open_access"}],"file_date_updated":"2021-06-02T14:33:36Z","scopus_import":"1","abstract":[{"text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}]},{"title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","article_processing_charge":"Yes (in subscription journal)","date_updated":"2023-09-26T15:36:34Z","_id":"945","has_accepted_license":"1","year":"2017","project":[{"call_identifier":"FWF","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety"}],"publication_identifier":{"issn":["07374038"]},"oa":1,"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"full_name":"Huylmans, Ann K","first_name":"Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:49:20Z","volume":34,"doi":"10.1093/molbev/msx190","external_id":{"isi":["000411814800016"]},"date_published":"2017-07-06T00:00:00Z","day":"06","ddc":["570","576"],"type":"journal_article","month":"07","isi":1,"pubrep_id":"848","intvolume":"        34","issue":"10","page":"2637 - 2649","quality_controlled":"1","citation":{"short":"A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649.","mla":"Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>.","ista":"Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649.","ieee":"A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017.","chicago":"Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>.","apa":"Huylmans, A. K., Macon, A., &#38; Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>","ama":"Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. 2017;34(10):2637-2649. doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>"},"publication_status":"published","department":[{"_id":"BeVi"}],"language":[{"iso":"eng"}],"publist_id":"6472","abstract":[{"lang":"eng","text":"While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera."}],"file":[{"date_updated":"2020-07-14T12:48:15Z","file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","date_created":"2018-12-12T10:10:23Z","file_size":462863,"relation":"main_file","file_id":"4810","access_level":"open_access","creator":"system","checksum":"009fd68043211d645ceb9d1de28274f2","content_type":"application/pdf"}],"publication":"Molecular Biology and Evolution","file_date_updated":"2020-07-14T12:48:15Z","scopus_import":"1","publisher":"Oxford University Press"}]