[{"status":"public","has_accepted_license":"1","type":"journal_article","license":"https://creativecommons.org/licenses/by/4.0/","project":[{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"issue":"POPL","ec_funded":1,"day":"27","date_updated":"2025-04-15T07:26:20Z","fulldoi":"https://doi.org/10.1145/3158118","ddc":["000"],"scopus_import":"1","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n","quality_controlled":"1","conference":{"end_date":"2018-01-13","location":"Los Angeles, CA, United States","start_date":"2018-01-07","name":"POPL: Programming Languages"},"arxiv":1,"department":[{"_id":"KrCh"}],"year":"2017","file":[{"file_size":460188,"checksum":"faa3f7b3fe8aab84b50ed805c26a0ee5","file_id":"10421","access_level":"open_access","date_created":"2021-12-07T08:06:28Z","success":1,"relation":"main_file","file_name":"2017_ACMProgLang_Chatterjee.pdf","content_type":"application/pdf","creator":"cchlebak","date_updated":"2021-12-07T08:06:28Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"date_published":"2017-12-27T00:00:00Z","month":"12","volume":2,"publisher":"Association for Computing Machinery","_id":"10416","title":"Optimal Dyck reachability for data-dependence and Alias analysis","article_type":"original","file_date_updated":"2021-12-07T08:06:28Z","article_number":"30","external_id":{"arxiv":["1910.00241"]},"abstract":[{"lang":"eng","text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks."}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Choudhary, Bhavya","first_name":"Bhavya","last_name":"Choudhary"},{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"}],"doi":"10.1145/3158118","publication_status":"published","date_created":"2021-12-05T23:01:48Z","article_processing_charge":"No","publication_identifier":{"eissn":["2475-1421"]},"oa_version":"Published Version","publication":"Proceedings of the ACM on Programming Languages","intvolume":"         2","citation":{"ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2(POPL), 30.","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability for data-dependence and Alias analysis,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL. Association for Computing Machinery, 2017.","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2017. <a href=\"https://doi.org/10.1145/3158118\">https://doi.org/10.1145/3158118</a>.","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence and Alias analysis. <i>Proceedings of the ACM on Programming Languages</i>. 2017;2(POPL). doi:<a href=\"https://doi.org/10.1145/3158118\">10.1145/3158118</a>","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 2 (2017).","mla":"Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL, 30, Association for Computing Machinery, 2017, doi:<a href=\"https://doi.org/10.1145/3158118\">10.1145/3158118</a>.","apa":"Chatterjee, K., Choudhary, B., &#38; Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and Alias analysis. <i>Proceedings of the ACM on Programming Languages</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3158118\">https://doi.org/10.1145/3158118</a>"},"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"5455","status":"public","relation":"earlier_version"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","corr_author":"1"},{"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.","quality_controlled":"1","conference":{"end_date":"2018-01-13","location":"Los Angeles, CA, United States","name":"POPL: Programming Languages","start_date":"2018-01-07"},"arxiv":1,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"year":"2017","status":"public","type":"journal_article","issue":"POPL","date_updated":"2026-06-18T08:40:04Z","day":"07","fulldoi":"https://doi.org/10.1145/3158121","ddc":["000"],"scopus_import":"1","article_number":"33","external_id":{"arxiv":["1711.03588"]},"author":[{"last_name":"Mciver","first_name":"Annabelle","full_name":"Mciver, Annabelle"},{"last_name":"Morgan","full_name":"Morgan, Carroll","first_name":"Carroll"},{"last_name":"Kaminski","first_name":"Benjamin Lucien","full_name":"Kaminski, Benjamin Lucien"},{"last_name":"Katoen","full_name":"Katoen, Joost P","first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6143-1926"}],"abstract":[{"text":"We present a new proof rule for proving almost-sure termination of probabilistic programs, including those that contain demonic non-determinism. An important question for a probabilistic program is whether the probability mass of all its diverging runs is zero, that is that it terminates \"almost surely\". Proving that can be hard, and this paper presents a new method for doing so. It applies directly to the program's source code, even if the program contains demonic choice. Like others, we use variant functions (a.k.a. \"super-martingales\") that are real-valued and decrease randomly on each loop iteration; but our key innovation is that the amount as well as the probability of the decrease are parametric. We prove the soundness of the new rule, indicate where its applicability goes beyond existing rules, and explain its connection to classical results on denumerable (non-demonic) Markov chains.","lang":"eng"}],"date_created":"2021-12-05T23:01:49Z","doi":"10.1145/3158121","publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","publication_identifier":{"eissn":["2475-1421"]},"publication":"Proceedings of the ACM on Programming Languages","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.","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>.","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.","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>","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>.","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>"},"intvolume":"         2","language":[{"iso":"eng"}],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_published":"2017-12-07T00:00:00Z","month":"12","volume":2,"publisher":"Association for Computing Machinery","_id":"10418","title":"A new proof rule for almost-sure termination","article_type":"original","main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3158121","open_access":"1"}]},{"month":"02","volume":16,"oa":1,"date_published":"2017-02-23T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Ethylene production with engineered Synechocystis sp PCC 6803 strains","_id":"1061","publisher":"BioMed Central","publication_identifier":{"issn":["14752859"]},"oa_version":"Published Version","doi":"10.1186/s12934-017-0645-5","date_created":"2018-12-11T11:49:56Z","publication_status":"published","article_processing_charge":"No","external_id":{"isi":["000397733000001"],"pmid":["28231787"]},"abstract":[{"text":"Background: Metabolic engineering and synthetic biology of cyanobacteria offer a promising sustainable alternative approach for fossil-based ethylene production, by using sunlight via oxygenic photosynthesis, to convert carbon dioxide directly into ethylene. Towards this, both well-studied cyanobacteria, i.e., Synechocystis sp PCC 6803 and Synechococcus elongatus PCC 7942, have been engineered to produce ethylene by introducing the ethylene-forming enzyme (Efe) from Pseudomonas syringae pv. phaseolicola PK2 (the Kudzu strain), which catalyzes the conversion of the ubiquitous tricarboxylic acid cycle intermediate 2-oxoglutarate into ethylene. Results: This study focuses on Synechocystis sp PCC 6803 and shows stable ethylene production through the integration of a codon-optimized version of the efe gene under control of the Ptrc promoter and the core Shine-Dalgarno sequence (5\\'-AGGAGG-3\\') as the ribosome-binding site (RBS), at the slr0168 neutral site. We have increased ethylene production twofold by RBS screening and further investigated improving ethylene production from a single gene copy of efe, using multiple tandem promoters and by putting our best construct on an RSF1010-based broad-host-self-replicating plasmid, which has a higher copy number than the genome. Moreover, to raise the intracellular amounts of the key Efe substrate, 2-oxoglutarate, from which ethylene is formed, we constructed a glycogen-synthesis knockout mutant (glgC) and introduced the ethylene biosynthetic pathway in it. Under nitrogen limiting conditions, the glycogen knockout strain has increased intracellular 2-oxoglutarate levels; however, surprisingly, ethylene production was lower in this strain than in the wild-type background. Conclusion: Making use of different RBS sequences, production of ethylene ranging over a 20-fold difference has been achieved. However, a further increase of production through multiple tandem promoters and a broad-host plasmid was not achieved speculating that the transcription strength and the gene copy number are not the limiting factors in our system.","lang":"eng"}],"author":[{"last_name":"Veetil","full_name":"Veetil, Vinod","first_name":"Vinod"},{"last_name":"Angermayr","orcid":"0000-0001-8619-2223","id":"4677C796-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Angermayr, Andreas"},{"last_name":"Hellingwerf","first_name":"Klaas","full_name":"Hellingwerf, Klaas"}],"file_date_updated":"2018-12-12T10:16:50Z","article_number":"34","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","extern":"1","language":[{"iso":"eng"}],"publication":"Microbial Cell Factories","intvolume":"        16","citation":{"apa":"Veetil, V., Angermayr, A., &#38; Hellingwerf, K. (2017). Ethylene production with engineered Synechocystis sp PCC 6803 strains. <i>Microbial Cell Factories</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12934-017-0645-5\">https://doi.org/10.1186/s12934-017-0645-5</a>","mla":"Veetil, Vinod, et al. “Ethylene Production with Engineered Synechocystis Sp PCC 6803 Strains.” <i>Microbial Cell Factories</i>, vol. 16, no. 1, 34, BioMed Central, 2017, doi:<a href=\"https://doi.org/10.1186/s12934-017-0645-5\">10.1186/s12934-017-0645-5</a>.","ama":"Veetil V, Angermayr A, Hellingwerf K. Ethylene production with engineered Synechocystis sp PCC 6803 strains. <i>Microbial Cell Factories</i>. 2017;16(1). doi:<a href=\"https://doi.org/10.1186/s12934-017-0645-5\">10.1186/s12934-017-0645-5</a>","short":"V. Veetil, A. Angermayr, K. Hellingwerf, Microbial Cell Factories 16 (2017).","ista":"Veetil V, Angermayr A, Hellingwerf K. 2017. Ethylene production with engineered Synechocystis sp PCC 6803 strains. Microbial Cell Factories. 16(1), 34.","chicago":"Veetil, Vinod, Andreas Angermayr, and Klaas Hellingwerf. “Ethylene Production with Engineered Synechocystis Sp PCC 6803 Strains.” <i>Microbial Cell Factories</i>. BioMed Central, 2017. <a href=\"https://doi.org/10.1186/s12934-017-0645-5\">https://doi.org/10.1186/s12934-017-0645-5</a>.","ieee":"V. Veetil, A. Angermayr, and K. Hellingwerf, “Ethylene production with engineered Synechocystis sp PCC 6803 strains,” <i>Microbial Cell Factories</i>, vol. 16, no. 1. BioMed Central, 2017."},"issue":"1","type":"journal_article","status":"public","has_accepted_license":"1","scopus_import":"1","ddc":["579"],"date_updated":"2023-09-20T12:09:21Z","day":"23","pmid":1,"fulldoi":"https://doi.org/10.1186/s12934-017-0645-5","quality_controlled":"1","year":"2017","file":[{"file_id":"5240","date_created":"2018-12-12T10:16:50Z","access_level":"open_access","file_size":1361313,"date_updated":"2018-12-12T10:16:50Z","creator":"system","content_type":"application/pdf","file_name":"IST-2017-792-v1+1_s12934-017-0645-5.pdf","relation":"main_file"}],"pubrep_id":"792","publist_id":"6325"},{"year":"2017","publist_id":"6326","quality_controlled":"1","fulldoi":"https://doi.org/10.1113/JP273735","day":"15","date_updated":"2023-09-20T12:09:47Z","issue":"8","page":"2587 - 2609 ","type":"journal_article","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","extern":"1","isi":1,"language":[{"iso":"eng"}],"citation":{"short":"L. Guarina, D.H. Vandael, V. Carabelli, E. Carbone, Journal of Physiology 595 (2017) 2587–2609.","ama":"Guarina L, Vandael DH, Carabelli V, Carbone E. Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells. <i>Journal of Physiology</i>. 2017;595(8):2587-2609. doi:<a href=\"https://doi.org/10.1113/JP273735\">10.1113/JP273735</a>","ieee":"L. Guarina, D. H. Vandael, V. Carabelli, and E. Carbone, “Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells,” <i>Journal of Physiology</i>, vol. 595, no. 8. Wiley-Blackwell, pp. 2587–2609, 2017.","ista":"Guarina L, Vandael DH, Carabelli V, Carbone E. 2017. Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells. Journal of Physiology. 595(8), 2587–2609.","chicago":"Guarina, Laura, David H Vandael, Valentina Carabelli, and Emilio Carbone. “Low PH Inf o Boosts Burst Firing and Catecholamine Release by Blocking TASK-1 and BK Channels While Preserving Cav1 Channels in Mouse Chromaffin Cells.” <i>Journal of Physiology</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1113/JP273735\">https://doi.org/10.1113/JP273735</a>.","mla":"Guarina, Laura, et al. “Low PH Inf o Boosts Burst Firing and Catecholamine Release by Blocking TASK-1 and BK Channels While Preserving Cav1 Channels in Mouse Chromaffin Cells.” <i>Journal of Physiology</i>, vol. 595, no. 8, Wiley-Blackwell, 2017, pp. 2587–609, doi:<a href=\"https://doi.org/10.1113/JP273735\">10.1113/JP273735</a>.","apa":"Guarina, L., Vandael, D. H., Carabelli, V., &#38; Carbone, E. (2017). Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells. <i>Journal of Physiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1113/JP273735\">https://doi.org/10.1113/JP273735</a>"},"intvolume":"       595","publication":"Journal of Physiology","oa_version":"None","publication_status":"published","doi":"10.1113/JP273735","date_created":"2018-12-11T11:49:56Z","article_processing_charge":"No","author":[{"first_name":"Laura","full_name":"Guarina, Laura","last_name":"Guarina"},{"first_name":"David H","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael"},{"first_name":"Valentina","full_name":"Carabelli, Valentina","last_name":"Carabelli"},{"last_name":"Carbone","first_name":"Emilio","full_name":"Carbone, Emilio"}],"abstract":[{"lang":"eng","text":"Mouse chromaffin cells (MCCs) generate action potential (AP) firing that regulates the Ca2+‐dependent release of catecholamines (CAs). Recent findings indicate that MCCs possess a variety of spontaneous firing modes that span from the common ‘tonic‐irregular’ to the less frequent ‘burst’ firing. This latter is evident in a small fraction of MCCs but occurs regularly when Nav1.3/1.7 channels are made less available or when the Slo1β2‐subunit responsible for BK channel inactivation is deleted. Burst firing causes large increases of Ca2+‐entry and potentiates CA release by ∼3.5‐fold and thus may be a key mechanism for regulating MCC function. With the aim to uncover a physiological role for burst‐firing we investigated the effects of acidosis on MCC activity. Lowering the extracellular pH (pHo) from 7.4 to 7.0 and 6.6 induces cell depolarizations of 10–15 mV that generate repeated bursts. Bursts at pHo 6.6 lasted ∼330 ms, occurred at 1–2 Hz and caused an ∼7‐fold increase of CA cumulative release. Burst firing originates from the inhibition of the pH‐sensitive TASK‐1/TASK‐3 channels and from a 40% BK channel conductance reduction at pHo 7.0. The same pHo had little or no effect on Nav, Cav, Kv and SK channels that support AP firing in MCCs. Burst firing of pHo 6.6 could be mimicked by mixtures of the TASK‐1 blocker A1899 (300 nm) and BK blocker paxilline (300 nm) and could be prevented by blocking L‐type channels by adding 3 μm nifedipine. Mixtures of the two blockers raised cumulative CA‐secretion even more than low pHo (∼12‐fold), showing that the action of protons on vesicle release is mainly a result of the ionic conductance changes that increase Ca2+‐entry during bursts. Our data provide direct evidence suggesting that MCCs respond to low pHo with sustained depolarization, burst firing and enhanced CA‐secretion, thus mimicking the physiological response of CCs to acute acidosis and hyperkalaemia generated during heavy exercise and muscle fatigue."}],"external_id":{"isi":["000399430300022"]},"title":"Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells","_id":"1062","publisher":"Wiley-Blackwell","month":"04","volume":595,"date_published":"2017-04-15T00:00:00Z"},{"type":"journal_article","status":"public","issue":"4","page":"845 - 858","ec_funded":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"fulldoi":"https://doi.org/10.1111/evo.13191","date_updated":"2026-06-22T14:05:53Z","day":"01","scopus_import":"1","quality_controlled":"1","year":"2017","department":[{"_id":"NiBa"}],"publist_id":"6327","month":"04","volume":71,"date_published":"2017-04-01T00:00:00Z","das_tickbox":"1","oa":1,"_id":"1063","publisher":"Wiley","main_file_link":[{"url":"https://doi.org/10.1101/081042","open_access":"1"}],"biorxivid":1,"title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","author":[{"full_name":"Uecker, Hildegard","first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","last_name":"Uecker"}],"abstract":[{"lang":"eng","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."}],"external_id":{"biorxivid":["10.1101/081042"],"isi":["000398545200003"]},"publication_identifier":{"issn":["0014-3820"]},"oa_version":"Submitted Version","doi":"10.1111/evo.13191","date_created":"2018-12-11T11:49:57Z","publication_status":"published","article_processing_charge":"No","citation":{"ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” <i>Evolution</i>, vol. 71, no. 4. Wiley, pp. 845–858, 2017.","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” <i>Evolution</i>. Wiley, 2017. <a href=\"https://doi.org/10.1111/evo.13191\">https://doi.org/10.1111/evo.13191</a>.","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.","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>","mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” <i>Evolution</i>, vol. 71, no. 4, Wiley, 2017, pp. 845–58, doi:<a href=\"https://doi.org/10.1111/evo.13191\">10.1111/evo.13191</a>.","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.13191\">https://doi.org/10.1111/evo.13191</a>"},"intvolume":"        71","publication":"Evolution","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"language":[{"iso":"eng"}]},{"file":[{"date_updated":"2019-10-15T07:44:51Z","creator":"system","relation":"main_file","file_name":"IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf","content_type":"application/pdf","file_id":"4998","date_created":"2018-12-12T10:13:17Z","access_level":"open_access","file_size":247657}],"year":"2017","publist_id":"6323","department":[{"_id":"KrCh"},{"_id":"HeEd"}],"pubrep_id":"991","quality_controlled":"1","fulldoi":"https://doi.org/10.1016/j.ipl.2017.02.003","date_updated":"2025-07-10T11:49:53Z","day":"01","scopus_import":"1","ddc":["000"],"type":"journal_article","has_accepted_license":"1","status":"public","page":"25 - 29","ec_funded":1,"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant Treewidth.” <i>Information Processing Letters</i>, vol. 122, Elsevier, 2017, pp. 25–29, doi:<a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">10.1016/j.ipl.2017.02.003</a>.","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>","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>.","ieee":"K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,” <i>Information Processing Letters</i>, vol. 122. Elsevier, pp. 25–29, 2017.","ista":"Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth. Information Processing Letters. 122, 25–29.","short":"K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.","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>"},"intvolume":"       122","publication":"Information Processing Letters","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"language":[{"iso":"eng"}],"abstract":[{"text":"We consider the problem of reachability in pushdown graphs. We study the problem for pushdown graphs with constant treewidth. Even for pushdown graphs with treewidth 1, for the reachability problem we establish the following: (i) the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem would contradict the k-clique conjecture and imply faster combinatorial algorithms for cliques in graphs.","lang":"eng"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","full_name":"Osang, Georg F","last_name":"Osang"}],"external_id":{"isi":["000399506600005"]},"file_date_updated":"2019-10-15T07:44:51Z","publication_identifier":{"issn":["0020-0190"]},"oa_version":"Submitted Version","doi":"10.1016/j.ipl.2017.02.003","publication_status":"published","date_created":"2018-12-11T11:49:57Z","article_processing_charge":"No","_id":"1065","publisher":"Elsevier","title":"Pushdown reachability with constant treewidth","month":"06","volume":122,"date_published":"2017-06-01T00:00:00Z","oa":1},{"month":"06","volume":254,"date_published":"2017-06-01T00:00:00Z","OA_place":"publisher","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ic.2016.10.006"}],"article_type":"original","title":"Quantitative fair simulation games","_id":"1066","publisher":"Elsevier","oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","doi":"10.1016/j.ic.2016.10.006","date_created":"2018-12-11T11:49:58Z","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"}],"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Otop, Jan","last_name":"Otop"},{"full_name":"Velner, Yaron","first_name":"Yaron","last_name":"Velner"}],"external_id":{"isi":["000402025600002"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","isi":1,"related_material":{"record":[{"relation":"earlier_version","id":"5428","status":"public"}]},"language":[{"iso":"eng"}],"citation":{"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>","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>.","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>.","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.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","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>"},"intvolume":"       254","publication":"Information and Computation","page":"143 - 166","issue":"2","ec_funded":1,"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"type":"journal_article","status":"public","scopus_import":"1","ddc":["000"],"fulldoi":"https://doi.org/10.1016/j.ic.2016.10.006","date_updated":"2026-06-18T08:47:01Z","day":"01","OA_type":"free access","quality_controlled":"1","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreements 267989 (QUAREM), 279307 (Graph Games), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE), S11407-N23 (RiSE), P23499-N23, and Microsoft faculty fellows award.","year":"2017","publist_id":"6322","department":[{"_id":"KrCh"},{"_id":"ToHe"}]},{"citation":{"mla":"Polshyn, Hryhoriy. <i>Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures</i>. University of Illinois at Urbana-Champaign, 2017.","apa":"Polshyn, H. (2017). <i>Magnetic force microscopy studies of mesoscopic superconducting structures</i>. University of Illinois at Urbana-Champaign.","ista":"Polshyn H. 2017. Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign.","chicago":"Polshyn, Hryhoriy. “Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures.” University of Illinois at Urbana-Champaign, 2017.","ieee":"H. Polshyn, “Magnetic force microscopy studies of mesoscopic superconducting structures,” University of Illinois at Urbana-Champaign, 2017.","short":"H. Polshyn, Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures, University of Illinois at Urbana-Champaign, 2017.","ama":"Polshyn H. Magnetic force microscopy studies of mesoscopic superconducting structures. 2017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","supervisor":[{"first_name":"Raffi","full_name":"Budakian, Raffi","last_name":"Budakian"}],"year":"2017","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The superconducting state of matter enables one to observe quantum effects on the macroscopic scale and hosts many fascinating phenomena. Topological defects of the superconducting order parameter, such as vortices and fluxoid states in multiply connected structures, are often the key ingredients of these phenomena. This dissertation describes a new mode of magnetic force microscopy (Φ0-MFM) for investigating vortex and fluxoid sates in mesoscopic superconducting (SC) structures. The technique relies on the magneto-mechanical coupling of a MFM cantilever to the motion of fluxons. The novelty of the technique is that a magnetic particle attached to the cantilever is used not only to sense the state of a SC structure, but also as a primary source of the inhomogeneous magnetic field which induces that state. Φ0-MFM enables us to map the transitions between tip-induced states during a scan: at the positions of the tip, where the two lowest energy states become degenerate, small oscillations of the tip drive the transitions between these states, which causes a significant shift in the resonant frequency and dissipation of the cantilever. For narrow-wall aluminum rings, the mapped fluxoid transitions form concentric contours on a scan. We show that the changes in the cantilever resonant frequency and dissipation are well-described by a stochastic resonance (SR) of cantilever-driven thermally activated phase slips (TAPS). The SR model allows us to experimentally determine the rate of TAPS and compare it to the Langer-Ambegaokar-McCumber-Halperin (LAMH) theory for TAPS in 1D superconducting structures. Further, we use the SR model to qualitatively study the effects of a locally applied magnetic field on the phase slip rate in rings containing constrictions. The states with multiple vortices or winding numbers could be useful for the development of novel superconducting devices, or the study of vortex interactions and interference effects. Using Φ0-MFM allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. We show that Φ0-MFM images of the fluxoid transitions allow us to identify the underlying states and to investigate their energetics and dynamics even in complicated structures."}],"author":[{"last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy"}],"oa_version":"Published Version","keyword":["physics","superconductivity","magnetic force microscopy","phase slips"],"publication_status":"published","date_created":"2022-01-25T14:54:14Z","article_processing_charge":"No","_id":"10663","day":"18","date_updated":"2024-10-14T11:13:43Z","publisher":"University of Illinois at Urbana-Champaign","main_file_link":[{"open_access":"1","url":"http://hdl.handle.net/2142/99178"}],"title":"Magnetic force microscopy studies of mesoscopic superconducting structures","type":"dissertation","status":"public","degree_awarded":"PhD","month":"09","alternative_title":["Graduate Dissertations and Theses at Illinois"],"date_published":"2017-09-18T00:00:00Z","page":"103","oa":1},{"title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","_id":"1067","publisher":"Cell Press","volume":40,"month":"02","oa":1,"date_published":"2017-02-27T00:00:00Z","acknowledged_ssus":[{"_id":"PreCl"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","language":[{"iso":"eng"}],"publication":"Developmental Cell","intvolume":"        40","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>","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366.","chicago":"Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>.","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.","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.","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>.","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>"},"publication_identifier":{"issn":["1534-5807"]},"oa_version":"Published Version","doi":"10.1016/j.devcel.2017.01.010","publication_status":"published","date_created":"2018-12-11T11:49:58Z","article_processing_charge":"No","external_id":{"isi":["000395368300007"]},"abstract":[{"text":"Embryo morphogenesis relies on highly coordinated movements of different tissues. However, remarkably little is known about how tissues coordinate their movements to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements first become apparent during “doming,” when the blastoderm begins to spread over the yolk sac, a process involving coordinated epithelial surface cell layer expansion and mesenchymal deep cell intercalations. Here, we find that active surface cell expansion represents the key process coordinating tissue movements during doming. By using a combination of theory and experiments, we show that epithelial surface cells not only trigger blastoderm expansion by reducing tissue surface tension, but also drive blastoderm thinning by inducing tissue contraction through radial deep cell intercalations. Thus, coordinated tissue expansion and thinning during doming relies on surface cells simultaneously controlling tissue surface tension and radial tissue contraction.","lang":"eng"}],"author":[{"last_name":"Morita","full_name":"Morita, Hitoshi","first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Silvia","full_name":"Grigolon, Silvia","last_name":"Grigolon"},{"last_name":"Bock","first_name":"Martin","full_name":"Bock, Martin"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","first_name":"Gabriel","last_name":"Krens"},{"last_name":"Salbreux","first_name":"Guillaume","full_name":"Salbreux, Guillaume"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"file_date_updated":"2018-12-12T10:10:57Z","scopus_import":"1","ddc":["572","597"],"day":"27","date_updated":"2025-07-10T11:49:55Z","fulldoi":"https://doi.org/10.1016/j.devcel.2017.01.010","project":[{"_id":"2524F500-B435-11E9-9278-68D0E5697425","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","grant_number":"201439","call_identifier":"FP7"}],"issue":"4","ec_funded":1,"page":"354 - 366","type":"journal_article","status":"public","has_accepted_license":"1","year":"2017","file":[{"content_type":"application/pdf","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","relation":"main_file","creator":"system","date_updated":"2018-12-12T10:10:57Z","file_size":6866187,"date_created":"2018-12-12T10:10:57Z","access_level":"open_access","file_id":"4849"}],"pubrep_id":"869","publist_id":"6320","department":[{"_id":"CaHe"}],"quality_controlled":"1"},{"project":[{"call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"issue":"5","page":"3741 - 3762","ec_funded":1,"type":"journal_article","status":"public","scopus_import":"1","date_updated":"2025-04-15T08:37:54Z","day":"01","fulldoi":"https://doi.org/10.1090/tran/6991","quality_controlled":"1","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”.","year":"2017","publist_id":"6311","department":[{"_id":"HeEd"}],"arxiv":1,"volume":369,"month":"05","oa":1,"date_published":"2017-05-01T00:00:00Z","article_type":"original","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1312.1231"}],"title":"The Morse theory of Čech and delaunay complexes","_id":"1072","publisher":"American Mathematical Society","oa_version":"Preprint","publication_status":"published","date_created":"2018-12-11T11:49:59Z","doi":"10.1090/tran/6991","article_processing_charge":"No","external_id":{"isi":["000398030400024"],"arxiv":["1312.1231"]},"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"}],"author":[{"last_name":"Bauer","first_name":"Ulrich","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"publication":"Transactions of the American Mathematical Society","citation":{"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>","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>.","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>.","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.","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762.","ama":"Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. 2017;369(5):3741-3762. doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>"},"intvolume":"       369"},{"date_published":"2017-06-01T00:00:00Z","oa":1,"month":"06","volume":54,"title":"Algorithmic solvability of the lifting extension problem","main_file_link":[{"url":"https://arxiv.org/abs/1307.6444","open_access":"1"}],"publisher":"Springer","_id":"1073","date_created":"2018-12-11T11:50:00Z","publication_status":"published","doi":"10.1007/s00454-016-9855-6","article_processing_charge":"No","oa_version":"Submitted Version","publication_identifier":{"issn":["01795376"]},"author":[{"first_name":"Martin","full_name":"Čadek, Martin","last_name":"Čadek"},{"id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek","first_name":"Marek","last_name":"Krcál"},{"last_name":"Vokřínek","first_name":"Lukáš","full_name":"Vokřínek, Lukáš"}],"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."}],"external_id":{"arxiv":["1307.6444"],"isi":["000400072700008"]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"intvolume":"        54","citation":{"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>.","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>","chicago":"Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>.","ieee":"M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting extension problem,” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4. Springer, pp. 915–965, 2017.","ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete &#38; Computational Geometry. 54(4), 915–965.","short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete &#38; Computational Geometry 54 (2017) 915–965.","ama":"Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. 2017;54(4):915-965. doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>"},"publication":"Discrete & Computational Geometry","page":"915 - 965","issue":"4","status":"public","type":"journal_article","scopus_import":"1","fulldoi":"https://doi.org/10.1007/s00454-016-9855-6","date_updated":"2025-06-04T08:11:10Z","day":"01","quality_controlled":"1","publist_id":"6309","department":[{"_id":"UlWa"}],"year":"2017","arxiv":1},{"main_file_link":[{"url":"http://www.biorxiv.org/content/early/2016/09/23/076810","open_access":"1"}],"title":"Inferring recent demography from isolation by distance of long shared sequence blocks","_id":"1074","publisher":"Genetics Society of America","volume":205,"month":"03","oa":1,"date_published":"2017-03-01T00:00:00Z","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"200","status":"public"}]},"publication":"Genetics","citation":{"ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. 2017;205(3):1335-1351. doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.","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.","chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>.","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>.","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>"},"intvolume":"       205","publication_identifier":{"issn":["0016-6731"]},"oa_version":"Preprint","date_created":"2018-12-11T11:50:00Z","article_processing_charge":"No","publication_status":"published","doi":"10.1534/genetics.116.196220","external_id":{"isi":["000395807200023"]},"author":[{"last_name":"Ringbauer","full_name":"Ringbauer, Harald","first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682"},{"first_name":"Graham","full_name":"Coop, Graham","last_name":"Coop"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"abstract":[{"lang":"eng","text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance."}],"scopus_import":"1","date_updated":"2026-04-08T14:06:35Z","day":"01","fulldoi":"https://doi.org/10.1534/genetics.116.196220","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"page":"1335 - 1351","ec_funded":1,"issue":"3","type":"journal_article","status":"public","year":"2017","department":[{"_id":"NiBa"}],"publist_id":"6307","quality_controlled":"1"},{"day":"01","date_updated":"2022-02-08T10:44:35Z","alternative_title":["Bulletin of the American Physical Society"],"issue":"4","type":"conference","status":"public","year":"2017","conference":{"name":"APS: American Physical Society","start_date":"2017-03-13","location":"New Orleans, LA, United States","end_date":"2017-03-17"},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR17/Session/P39.11"}],"title":" Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures","_id":"10745","publisher":"American Physical Society","month":"03","volume":62,"date_published":"2017-03-01T00:00:00Z","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","language":[{"iso":"eng"}],"intvolume":"        62","citation":{"ista":"Polshyn H, Naibert T, Budakian R. 2017.  Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. APS March Meeting 2017. APS: American Physical Society, Bulletin of the American Physical Society, vol. 62, P39.00011.","ieee":"H. Polshyn, T. Naibert, and R. Budakian, “ Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures,” in <i>APS March Meeting 2017</i>, New Orleans, LA, United States, 2017, vol. 62, no. 4.","chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” In <i>APS March Meeting 2017</i>, Vol. 62. American Physical Society, 2017.","short":"H. Polshyn, T. Naibert, R. Budakian, in:, APS March Meeting 2017, American Physical Society, 2017.","ama":"Polshyn H, Naibert T, Budakian R.  Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In: <i>APS March Meeting 2017</i>. Vol 62. American Physical Society; 2017.","apa":"Polshyn, H., Naibert, T., &#38; Budakian, R. (2017).  Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In <i>APS March Meeting 2017</i> (Vol. 62). New Orleans, LA, United States: American Physical Society.","mla":"Polshyn, Hryhoriy, et al. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” <i>APS March Meeting 2017</i>, vol. 62, no. 4, P39.00011, American Physical Society, 2017."},"publication":"APS March Meeting 2017","publication_identifier":{"issn":["0003-0503"]},"oa_version":"Published Version","article_processing_charge":"No","date_created":"2022-02-08T09:49:17Z","publication_status":"published","author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","last_name":"Polshyn"},{"last_name":"Naibert","first_name":"Tyler","full_name":"Naibert, Tyler"},{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"}],"abstract":[{"text":"New ways to investigate and manipulate fluxoid and vortex states of mesoscopic superconducting structures are of great interest. The states with multiple vortices or winding numbers could be useful for the study of vortex interactions and interference effects, the braiding of Majorana bound states by winding vortices, and the development of novel superconducting devices. We demonstrate a methodology based on magnetic force microscopy that allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. By using micro-magnet as a source of inhomogeneous magnetic field, we can efficiently explore the configuration space of fluxoid states. Scanning over the structure reveals the energy crossing points of the lowest laying fluxoid states. This is due the strong interaction of cantilever with thermally activated fluxoid transitions at points of degeneracy. We show that measured patterns of fluxoid transitions allow to identify the states, investigate their energetics, and manipulate them. Further, we show that the dynamics of driven fluxoid transitions can be described by stochastic resonance model, which provides a unique way of measuring fluxoid transition rate and related energy barrier for chosen transitions even in complicated structures","lang":"eng"}],"article_number":"P39.00011"},{"oa":1,"date_published":"2017-02-01T00:00:00Z","volume":15,"month":"02","title":"An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot;","publisher":"LIT Verlag Berlin-Münster-Wien-Zürich-London","_id":"1075","date_created":"2018-12-11T11:50:00Z","publication_status":"published","oa_version":"None","publication_identifier":{"isbn":["978-3643908124"]},"file_date_updated":"2018-12-12T10:08:06Z","author":[{"full_name":"Wenzl, Bernhard","first_name":"Bernhard","id":"479E9046-F248-11E8-B48F-1D18A9856A87","last_name":"Wenzl"}],"language":[{"iso":"eng"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","extern":"1","publication":"Austria and America: 20th-Century Cross-Cultural Encounters","citation":{"mla":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot;” <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>, edited by Joshua Parker and Ralph Poole, vol. 15, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","apa":"Wenzl, B. (2017). An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot; In J. Parker &#38; R. Poole (Eds.), <i>Austria and America: 20th-Century Cross-Cultural Encounters</i> (Vol. 15, pp. 73–80). LIT Verlag Berlin-Münster-Wien-Zürich-London.","short":"B. Wenzl, in:, J. Parker, R. Poole (Eds.), Austria and America: 20th-Century Cross-Cultural Encounters, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","ama":"Wenzl B. An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot; In: Parker J, Poole R, eds. <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>. Vol 15. LIT Verlag Berlin-Münster-Wien-Zürich-London; 2017:73-80.","ieee":"B. Wenzl, “An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot;,” in <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>, vol. 15, J. Parker and R. Poole, Eds. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","ista":"Wenzl B. 2017.An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot; In: Austria and America: 20th-Century Cross-Cultural Encounters. American Studies in Austria, vol. 15, 73–80.","chicago":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot;” In <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>, edited by Joshua Parker and Ralph Poole, 15:73–80. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017."},"intvolume":"        15","page":"73 - 80","alternative_title":["American Studies in Austria"],"status":"public","has_accepted_license":"1","type":"book_chapter","ddc":["001"],"date_updated":"2021-01-12T06:48:06Z","day":"01","editor":[{"last_name":"Parker","first_name":"Joshua","full_name":"Parker, Joshua"},{"last_name":"Poole","first_name":"Ralph","full_name":"Poole, Ralph"}],"publist_id":"6306","year":"2017","file":[{"file_name":"IST-2017-732-v1+1_Austria_and_America_Cross-Cultural_Encounters.pdf","relation":"main_file","content_type":"application/pdf","creator":"system","date_updated":"2018-12-12T10:08:06Z","file_size":380624,"access_level":"open_access","file_id":"4666","date_created":"2018-12-12T10:08:06Z"}]},{"quality_controlled":"1","publist_id":"6300","department":[{"_id":"RoSe"}],"year":"2017","arxiv":1,"issue":"2","project":[{"call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"status":"public","type":"journal_article","scopus_import":"1","fulldoi":"https://doi.org/10.1007/s11040-017-9238-0","date_updated":"2025-06-04T08:11:50Z","day":"01","publication_status":"published","date_created":"2018-12-11T11:50:02Z","article_processing_charge":"No","doi":"10.1007/s11040-017-9238-0","oa_version":"Submitted Version","publication_identifier":{"issn":["1385-0172"]},"article_number":"6","abstract":[{"lang":"eng","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."}],"author":[{"last_name":"Nam","first_name":"Phan","full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hanne","full_name":"Van Den Bosch, Hanne","last_name":"Van Den Bosch"}],"external_id":{"arxiv":["1603.07368"],"isi":["000401270000004"]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"citation":{"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.","chicago":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>.","ieee":"P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2. Springer, 2017.","short":"P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017).","ama":"Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. 2017;20(2). doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>","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>","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>."},"intvolume":"        20","publication":"Mathematical Physics, Analysis and Geometry","date_published":"2017-06-01T00:00:00Z","oa":1,"month":"06","volume":20,"title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","main_file_link":[{"url":"https://arxiv.org/abs/1603.07368","open_access":"1"}],"publisher":"Springer","_id":"1079"},{"ec_funded":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"}],"has_accepted_license":"1","status":"public","type":"journal_article","ddc":["004","006"],"scopus_import":"1","fulldoi":"https://doi.org/10.1038/ncomms14114","day":"31","date_updated":"2025-07-10T11:50:00Z","quality_controlled":"1","publist_id":"6301","department":[{"_id":"KrCh"}],"pubrep_id":"786","file":[{"date_updated":"2018-12-12T10:15:15Z","creator":"system","content_type":"application/pdf","relation":"main_file","file_name":"IST-2017-786-v1+1_ncomms14114.pdf","date_created":"2018-12-12T10:15:15Z","file_id":"5133","access_level":"open_access","file_size":897050}],"year":"2017","date_published":"2017-01-31T00:00:00Z","oa":1,"volume":8,"month":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Reconstructing metastatic seeding patterns of human cancers","publisher":"Nature Publishing Group","_id":"1080","date_created":"2018-12-11T11:50:02Z","publication_status":"published","article_processing_charge":"No","doi":"10.1038/ncomms14114","publication_identifier":{"issn":["2041-1723"]},"oa_version":"Published Version","article_number":"14114","file_date_updated":"2018-12-12T10:15:15Z","abstract":[{"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.","lang":"eng"}],"author":[{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","first_name":"Johannes","last_name":"Reiter"},{"last_name":"Makohon Moore","full_name":"Makohon Moore, Alvin","first_name":"Alvin"},{"last_name":"Gerold","full_name":"Gerold, Jeffrey","first_name":"Jeffrey"},{"first_name":"Ivana","full_name":"Božić, Ivana","last_name":"Božić"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Christine","full_name":"Iacobuzio Donahue, Christine","last_name":"Iacobuzio Donahue"},{"full_name":"Vogelstein, Bert","first_name":"Bert","last_name":"Vogelstein"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"external_id":{"isi":["000393096600001"]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"citation":{"apa":"Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>","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>.","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.","ieee":"J. Reiter <i>et al.</i>, “Reconstructing metastatic seeding patterns of human cancers,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","chicago":"Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>.","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>"},"intvolume":"         8","publication":"Nature Communications"},{"publication":"Nature Ecology & Evolution","citation":{"ama":"Reger J, Lind MI, Robinson MR, Beckerman AP. Predation drives local adaptation of phenotypic plasticity. <i>Nature Ecology &#38; Evolution</i>. 2017;2:100-107. doi:<a href=\"https://doi.org/10.1038/s41559-017-0373-6\">10.1038/s41559-017-0373-6</a>","short":"J. Reger, M.I. Lind, M.R. Robinson, A.P. Beckerman, Nature Ecology &#38; Evolution 2 (2017) 100–107.","chicago":"Reger, Julia, Martin I. Lind, Matthew Richard Robinson, and Andrew P. Beckerman. “Predation Drives Local Adaptation of Phenotypic Plasticity.” <i>Nature Ecology &#38; Evolution</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/s41559-017-0373-6\">https://doi.org/10.1038/s41559-017-0373-6</a>.","ista":"Reger J, Lind MI, Robinson MR, Beckerman AP. 2017. Predation drives local adaptation of phenotypic plasticity. Nature Ecology &#38; Evolution. 2, 100–107.","ieee":"J. Reger, M. I. Lind, M. R. Robinson, and A. P. Beckerman, “Predation drives local adaptation of phenotypic plasticity,” <i>Nature Ecology &#38; Evolution</i>, vol. 2. Springer Nature, pp. 100–107, 2017.","mla":"Reger, Julia, et al. “Predation Drives Local Adaptation of Phenotypic Plasticity.” <i>Nature Ecology &#38; Evolution</i>, vol. 2, Springer Nature, 2017, pp. 100–07, doi:<a href=\"https://doi.org/10.1038/s41559-017-0373-6\">10.1038/s41559-017-0373-6</a>.","apa":"Reger, J., Lind, M. I., Robinson, M. R., &#38; Beckerman, A. P. (2017). Predation drives local adaptation of phenotypic plasticity. <i>Nature Ecology &#38; Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-017-0373-6\">https://doi.org/10.1038/s41559-017-0373-6</a>"},"intvolume":"         2","language":[{"iso":"eng"}],"year":"2017","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Phenotypic plasticity is the ability of an individual genotype to alter aspects of its phenotype depending on the current environment. It is central to the persistence, resistance and resilience of populations facing variation in physical or biological factors. Genetic variation in plasticity is pervasive, which suggests its local adaptation is plausible. Existing studies on the adaptation of plasticity typically focus on single traits and a few populations, while theory about interactions among genes (for example, pleiotropy) suggests that a multi-trait, landscape scale (for example, multiple populations) perspective is required. We present data from a landscape scale, replicated, multi-trait experiment using a classic predator–prey system centred on the water flea Daphnia pulex. We find predator regime-driven differences in genetic variation of multivariate plasticity. These differences are associated with strong divergent selection linked to a predation regime. Our findings are evidence for local adaptation of plasticity, suggesting that responses of populations to environmental variation depend on the conditions in which they evolved in the past.","lang":"eng"}],"author":[{"last_name":"Reger","first_name":"Julia","full_name":"Reger, Julia"},{"full_name":"Lind, Martin I.","first_name":"Martin I.","last_name":"Lind"},{"last_name":"Robinson","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard"},{"full_name":"Beckerman, Andrew P.","first_name":"Andrew P.","last_name":"Beckerman"}],"publication_status":"published","article_processing_charge":"No","date_created":"2020-04-30T10:46:02Z","doi":"10.1038/s41559-017-0373-6","quality_controlled":"1","oa_version":"None","publication_identifier":{"issn":["2397-334X"]},"publisher":"Springer Nature","date_updated":"2021-01-12T08:15:07Z","_id":"7725","day":"27","fulldoi":"https://doi.org/10.1038/s41559-017-0373-6","title":"Predation drives local adaptation of phenotypic plasticity","article_type":"original","status":"public","type":"journal_article","date_published":"2017-11-27T00:00:00Z","page":"100-107","volume":2,"month":"11"},{"quality_controlled":"1","year":"2017","issue":"1868","type":"journal_article","status":"public","pmid":1,"fulldoi":"https://doi.org/10.1098/rspb.2017.1824","day":"06","date_updated":"2021-01-12T08:15:08Z","publication_identifier":{"issn":["0962-8452","1471-2954"]},"oa_version":"None","article_processing_charge":"No","doi":"10.1098/rspb.2017.1824","date_created":"2020-04-30T10:46:43Z","publication_status":"published","abstract":[{"lang":"eng","text":"Genes of the major histocompatibility complex (MHC) have been shown to influence social signalling and mate preferences in many species, including humans. First observations suggest that MHC signalling may also affect female fertility. To test this hypothesis, we exposed 191 female horses (Equus caballus) to either an MHC-similar or an MHC-dissimilar stimulus male around the time of ovulation and conception. A within-subject experimental design controlled for non-MHC-linked male characteristics, and instrumental insemination with semen of other males (n = 106) controlled for potential confounding effects of semen or embryo characteristics. We found that females were more likely to become pregnant if exposed to an MHC-dissimilar than to an MHC-similar male, while overall genetic distance to the stimulus males (based on microsatellite markers on 20 chromosomes) had no effect. Our results demonstrate that early pregnancy failures can be due to maternal life-history decisions (cryptic female choice) influenced by MHC-linked social signalling."}],"author":[{"last_name":"Burger","first_name":"D.","full_name":"Burger, D."},{"full_name":"Thomas, S.","first_name":"S.","last_name":"Thomas"},{"full_name":"Aepli, H.","first_name":"H.","last_name":"Aepli"},{"last_name":"Dreyer","first_name":"M.","full_name":"Dreyer, M."},{"full_name":"Fabre, G.","first_name":"G.","last_name":"Fabre"},{"last_name":"Marti","full_name":"Marti, E.","first_name":"E."},{"last_name":"Sieme","first_name":"H.","full_name":"Sieme, H."},{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","last_name":"Robinson"},{"last_name":"Wedekind","first_name":"C.","full_name":"Wedekind, C."}],"external_id":{"pmid":["29212724"]},"article_number":"20171824","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","language":[{"iso":"eng"}],"intvolume":"       284","citation":{"short":"D. Burger, S. Thomas, H. Aepli, M. Dreyer, G. Fabre, E. Marti, H. Sieme, M.R. Robinson, C. Wedekind, Proceedings of the Royal Society B: Biological Sciences 284 (2017).","ama":"Burger D, Thomas S, Aepli H, et al. Major histocompatibility complex-linked social signalling affects female fertility. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2017;284(1868). doi:<a href=\"https://doi.org/10.1098/rspb.2017.1824\">10.1098/rspb.2017.1824</a>","ieee":"D. Burger <i>et al.</i>, “Major histocompatibility complex-linked social signalling affects female fertility,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 284, no. 1868. The Royal Society, 2017.","ista":"Burger D, Thomas S, Aepli H, Dreyer M, Fabre G, Marti E, Sieme H, Robinson MR, Wedekind C. 2017. Major histocompatibility complex-linked social signalling affects female fertility. Proceedings of the Royal Society B: Biological Sciences. 284(1868), 20171824.","chicago":"Burger, D., S. Thomas, H. Aepli, M. Dreyer, G. Fabre, E. Marti, H. Sieme, Matthew Richard Robinson, and C. Wedekind. “Major Histocompatibility Complex-Linked Social Signalling Affects Female Fertility.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2017. <a href=\"https://doi.org/10.1098/rspb.2017.1824\">https://doi.org/10.1098/rspb.2017.1824</a>.","mla":"Burger, D., et al. “Major Histocompatibility Complex-Linked Social Signalling Affects Female Fertility.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 284, no. 1868, 20171824, The Royal Society, 2017, doi:<a href=\"https://doi.org/10.1098/rspb.2017.1824\">10.1098/rspb.2017.1824</a>.","apa":"Burger, D., Thomas, S., Aepli, H., Dreyer, M., Fabre, G., Marti, E., … Wedekind, C. (2017). Major histocompatibility complex-linked social signalling affects female fertility. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2017.1824\">https://doi.org/10.1098/rspb.2017.1824</a>"},"publication":"Proceedings of the Royal Society B: Biological Sciences","month":"12","volume":284,"date_published":"2017-12-06T00:00:00Z","article_type":"original","title":"Major histocompatibility complex-linked social signalling affects female fertility","_id":"7727","publisher":"The Royal Society"},{"type":"journal_article","status":"public","volume":1,"month":"09","date_published":"2017-09-11T00:00:00Z","page":"757-765","issue":"10","date_updated":"2021-01-12T08:15:08Z","_id":"7728","day":"11","fulldoi":"https://doi.org/10.1038/s41562-017-0195-1","publisher":"Springer Nature","article_type":"original","title":"Hidden heritability due to heterogeneity across seven populations","abstract":[{"lang":"eng","text":"Meta-analyses of genome-wide association studies, which dominate genetic discovery, are based on data from diverse historical time periods and populations. Genetic scores derived from genome-wide association studies explain only a fraction of the heritability estimates obtained from whole-genome studies on single populations, known as the ‘hidden heritability’ puzzle. Using seven sampling populations (n = 35,062), we test whether hidden heritability is attributed to heterogeneity across sampling populations and time, showing that estimates are substantially smaller across populations compared with within populations. We show that the hidden heritability varies substantially: from zero for height to 20% for body mass index, 37% for education, 40% for age at first birth and up to 75% for number of children. Simulations demonstrate that our results are more likely to reflect heterogeneity in phenotypic measurement or gene–environment interactions than genetic heterogeneity. These findings have substantial implications for genetic discovery, suggesting that large homogenous datasets are required for behavioural phenotypes and that gene–environment interaction may be a central challenge for genetic discovery."}],"author":[{"last_name":"Tropf","first_name":"Felix C.","full_name":"Tropf, Felix C."},{"last_name":"Lee","first_name":"S. Hong","full_name":"Lee, S. Hong"},{"last_name":"Verweij","full_name":"Verweij, Renske M.","first_name":"Renske M."},{"first_name":"Gert","full_name":"Stulp, Gert","last_name":"Stulp"},{"last_name":"van der Most","first_name":"Peter J.","full_name":"van der Most, Peter J."},{"last_name":"de Vlaming","full_name":"de Vlaming, Ronald","first_name":"Ronald"},{"last_name":"Bakshi","full_name":"Bakshi, Andrew","first_name":"Andrew"},{"full_name":"Briley, Daniel A.","first_name":"Daniel A.","last_name":"Briley"},{"last_name":"Rahal","first_name":"Charles","full_name":"Rahal, Charles"},{"last_name":"Hellpap","first_name":"Robert","full_name":"Hellpap, Robert"},{"last_name":"Iliadou","first_name":"Anastasia N.","full_name":"Iliadou, Anastasia N."},{"full_name":"Esko, Tõnu","first_name":"Tõnu","last_name":"Esko"},{"last_name":"Metspalu","full_name":"Metspalu, Andres","first_name":"Andres"},{"first_name":"Sarah E.","full_name":"Medland, Sarah E.","last_name":"Medland"},{"last_name":"Martin","first_name":"Nicholas G.","full_name":"Martin, Nicholas G."},{"first_name":"Nicola","full_name":"Barban, Nicola","last_name":"Barban"},{"full_name":"Snieder, Harold","first_name":"Harold","last_name":"Snieder"},{"last_name":"Robinson","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"},{"first_name":"Melinda C.","full_name":"Mills, Melinda C.","last_name":"Mills"}],"quality_controlled":"1","publication_identifier":{"issn":["2397-3374"]},"oa_version":"None","publication_status":"published","date_created":"2020-04-30T10:47:02Z","article_processing_charge":"No","doi":"10.1038/s41562-017-0195-1","publication":"Nature Human Behaviour","citation":{"mla":"Tropf, Felix C., et al. “Hidden Heritability Due to Heterogeneity across Seven Populations.” <i>Nature Human Behaviour</i>, vol. 1, no. 10, Springer Nature, 2017, pp. 757–65, doi:<a href=\"https://doi.org/10.1038/s41562-017-0195-1\">10.1038/s41562-017-0195-1</a>.","apa":"Tropf, F. C., Lee, S. H., Verweij, R. M., Stulp, G., van der Most, P. J., de Vlaming, R., … Mills, M. C. (2017). Hidden heritability due to heterogeneity across seven populations. <i>Nature Human Behaviour</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41562-017-0195-1\">https://doi.org/10.1038/s41562-017-0195-1</a>","ista":"Tropf FC, Lee SH, Verweij RM, Stulp G, van der Most PJ, de Vlaming R, Bakshi A, Briley DA, Rahal C, Hellpap R, Iliadou AN, Esko T, Metspalu A, Medland SE, Martin NG, Barban N, Snieder H, Robinson MR, Mills MC. 2017. Hidden heritability due to heterogeneity across seven populations. Nature Human Behaviour. 1(10), 757–765.","ieee":"F. C. Tropf <i>et al.</i>, “Hidden heritability due to heterogeneity across seven populations,” <i>Nature Human Behaviour</i>, vol. 1, no. 10. Springer Nature, pp. 757–765, 2017.","chicago":"Tropf, Felix C., S. Hong Lee, Renske M. Verweij, Gert Stulp, Peter J. van der Most, Ronald de Vlaming, Andrew Bakshi, et al. “Hidden Heritability Due to Heterogeneity across Seven Populations.” <i>Nature Human Behaviour</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/s41562-017-0195-1\">https://doi.org/10.1038/s41562-017-0195-1</a>.","ama":"Tropf FC, Lee SH, Verweij RM, et al. Hidden heritability due to heterogeneity across seven populations. <i>Nature Human Behaviour</i>. 2017;1(10):757-765. doi:<a href=\"https://doi.org/10.1038/s41562-017-0195-1\">10.1038/s41562-017-0195-1</a>","short":"F.C. Tropf, S.H. Lee, R.M. Verweij, G. Stulp, P.J. van der Most, R. de Vlaming, A. Bakshi, D.A. Briley, C. Rahal, R. Hellpap, A.N. Iliadou, T. Esko, A. Metspalu, S.E. Medland, N.G. Martin, N. Barban, H. Snieder, M.R. Robinson, M.C. Mills, Nature Human Behaviour 1 (2017) 757–765."},"intvolume":"         1","year":"2017","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}]},{"fulldoi":"https://doi.org/10.1073/pnas.1621096114","date_updated":"2021-01-12T08:15:09Z","day":"08","page":"8602-8607","issue":"32","status":"public","type":"journal_article","year":"2017","quality_controlled":"1","title":"Detection and quantification of inbreeding depression for complex traits from SNP data","article_type":"original","publisher":"Proceedings of the National Academy of Sciences","_id":"7729","date_published":"2017-08-08T00:00:00Z","volume":114,"month":"08","related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.1718598115","relation":"other"}]},"language":[{"iso":"eng"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       114","citation":{"short":"L. Yengo, Z. Zhu, N.R. Wray, B.S. Weir, J. Yang, M.R. Robinson, P.M. Visscher, Proceedings of the National Academy of Sciences 114 (2017) 8602–8607.","ama":"Yengo L, Zhu Z, Wray NR, et al. Detection and quantification of inbreeding depression for complex traits from SNP data. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(32):8602-8607. doi:<a href=\"https://doi.org/10.1073/pnas.1621096114\">10.1073/pnas.1621096114</a>","ista":"Yengo L, Zhu Z, Wray NR, Weir BS, Yang J, Robinson MR, Visscher PM. 2017. Detection and quantification of inbreeding depression for complex traits from SNP data. Proceedings of the National Academy of Sciences. 114(32), 8602–8607.","ieee":"L. Yengo <i>et al.</i>, “Detection and quantification of inbreeding depression for complex traits from SNP data,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 32. Proceedings of the National Academy of Sciences, pp. 8602–8607, 2017.","chicago":"Yengo, Loic, Zhihong Zhu, Naomi R. Wray, Bruce S. Weir, Jian Yang, Matthew Richard Robinson, and Peter M. Visscher. “Detection and Quantification of Inbreeding Depression for Complex Traits from SNP Data.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1621096114\">https://doi.org/10.1073/pnas.1621096114</a>.","apa":"Yengo, L., Zhu, Z., Wray, N. R., Weir, B. S., Yang, J., Robinson, M. R., &#38; Visscher, P. M. (2017). Detection and quantification of inbreeding depression for complex traits from SNP data. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1621096114\">https://doi.org/10.1073/pnas.1621096114</a>","mla":"Yengo, Loic, et al. “Detection and Quantification of Inbreeding Depression for Complex Traits from SNP Data.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 32, Proceedings of the National Academy of Sciences, 2017, pp. 8602–07, doi:<a href=\"https://doi.org/10.1073/pnas.1621096114\">10.1073/pnas.1621096114</a>."},"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","publication_status":"published","date_created":"2020-04-30T10:47:19Z","doi":"10.1073/pnas.1621096114","oa_version":"None","publication_identifier":{"issn":["0027-8424","1091-6490"]},"abstract":[{"lang":"eng","text":"Quantifying the effects of inbreeding is critical to characterizing the genetic architecture of complex traits. This study highlights through theory and simulations the strengths and shortcomings of three SNP-based inbreeding measures commonly used to estimate inbreeding depression (ID). We demonstrate that heterogeneity in linkage disequilibrium (LD) between causal variants and SNPs biases ID estimates, and we develop an approach to correct this bias using LD and minor allele frequency stratified inference (LDMS). We quantified ID in 25 traits measured in ∼140,000 participants of the UK Biobank, using LDMS, and confirmed previously published ID for 4 traits. We find unique evidence of ID for handgrip strength, waist/hip ratio, and visual and auditory acuity (ID between −2.3 and −5.2 phenotypic SDs for complete inbreeding; P<0.001). Our results illustrate that a careful choice of the measure of inbreeding combined with LDMS stratification improves both detection and quantification of ID using SNP data."}],"author":[{"first_name":"Loic","full_name":"Yengo, Loic","last_name":"Yengo"},{"first_name":"Zhihong","full_name":"Zhu, Zhihong","last_name":"Zhu"},{"last_name":"Wray","first_name":"Naomi R.","full_name":"Wray, Naomi R."},{"first_name":"Bruce S.","full_name":"Weir, Bruce S.","last_name":"Weir"},{"full_name":"Yang, Jian","first_name":"Jian","last_name":"Yang"},{"last_name":"Robinson","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard"},{"full_name":"Visscher, Peter M.","first_name":"Peter M.","last_name":"Visscher"}]}]