[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Markov decision processes (MDPs) and simple stochastic games (SSGs) provide a rich mathematical framework to study many important problems related to probabilistic systems. MDPs and SSGs with finite-horizon objectives, where the goal is to maximize the probability to reach a target state in a given finite time, is a classical and well-studied problem. In this work we consider the strategy complexity of finite-horizon MDPs and SSGs. We show that for all ε > 0, the natural class of counter-based strategies require at most log log/(1/ε) + n + 1 memory states, and memory of size Omega(log log(1/ε) + n) is required, for ε-optimality, where n is the number of states of the MDP (resp. SSG). Thus our bounds are asymptotically optimal. We then study the periodic property of optimal strategies, and show a sub-exponential lower bound on the period for optimal strategies."}],"article_processing_charge":"No","scopus_import":"1","OA_type":"green","language":[{"iso":"eng"}],"volume":7721,"external_id":{"arxiv":["1209.3617"]},"doi":"10.1007/978-3-642-36046-6_11","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"publication":"Mathematical and Engineering Methods in Computer Science","publisher":"Springer Nature","ec_funded":1,"page":"106-117","acknowledgement":"Work of the second author supported by the Sino-Danish Center for the Theory of Interactive Computation, funded by the Danish National Research Foundation and the National Science Foundation of China (under the grant 61061130540). The second author acknowledge support from the Center for research in the Foundations of Electronic Markets (CFEM), supported by the Danish Strategic Research Council. The first author was supported by FWF Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","status":"public","date_created":"2025-07-10T14:08:49Z","day":"17","type":"conference","arxiv":1,"date_updated":"2025-09-23T09:24:13Z","publication_status":"published","oa_version":"Preprint","year":"2013","OA_place":"repository","date_published":"2013-01-17T00:00:00Z","corr_author":"1","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389"}],"citation":{"chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of Finite-Horizon Markov Decision Processes and Simple Stochastic Games.” In <i>Mathematical and Engineering Methods in Computer Science</i>, 7721:106–17. Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">https://doi.org/10.1007/978-3-642-36046-6_11</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Mathematical and Engineering Methods in Computer Science, Springer Nature, 2013, pp. 106–117.","ista":"Chatterjee K, Ibsen-Jensen R. 2013. Strategy complexity of finite-horizon Markov decision processes and simple stochastic games. Mathematical and Engineering Methods in Computer Science. MEMICS: Mathematical and Engineering Methods in Computer Science, LNCS, vol. 7721, 106–117.","ama":"Chatterjee K, Ibsen-Jensen R. Strategy complexity of finite-horizon Markov decision processes and simple stochastic games. In: <i>Mathematical and Engineering Methods in Computer Science</i>. Vol 7721. Springer Nature; 2013:106-117. doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">10.1007/978-3-642-36046-6_11</a>","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2013). Strategy complexity of finite-horizon Markov decision processes and simple stochastic games. In <i>Mathematical and Engineering Methods in Computer Science</i> (Vol. 7721, pp. 106–117). Znojmo, Czech Republic: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">https://doi.org/10.1007/978-3-642-36046-6_11</a>","ieee":"K. Chatterjee and R. Ibsen-Jensen, “Strategy complexity of finite-horizon Markov decision processes and simple stochastic games,” in <i>Mathematical and Engineering Methods in Computer Science</i>, Znojmo, Czech Republic, 2013, vol. 7721, pp. 106–117.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of Finite-Horizon Markov Decision Processes and Simple Stochastic Games.” <i>Mathematical and Engineering Methods in Computer Science</i>, vol. 7721, Springer Nature, 2013, pp. 106–17, doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_11\">10.1007/978-3-642-36046-6_11</a>."},"month":"01","oa":1,"department":[{"_id":"KrCh"}],"conference":{"location":"Znojmo, Czech Republic","start_date":"2012-10-25","end_date":"2012-10-28","name":"MEMICS: Mathematical and Engineering Methods in Computer Science"},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1209.3617","open_access":"1"}],"quality_controlled":"1","alternative_title":["LNCS"],"intvolume":"      7721","publication_identifier":{"isbn":["9783642360442"],"eisbn":["9783642360466"],"issn":["0302-9743"],"eissn":["1611-3349"]},"_id":"19995","title":"Strategy complexity of finite-horizon Markov decision processes and simple stochastic games"},{"date_created":"2018-12-11T11:55:08Z","status":"public","date_updated":"2024-12-11T11:35:05Z","arxiv":1,"series_title":"Lecture Notes in Computer Science","day":"01","type":"conference","publication":"Proceedings of 25th Int. Conf. on Computer Aided Verification","ec_funded":1,"publisher":"Springer","page":"101 - 106","volume":8044,"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"external_id":{"arxiv":["1303.5251"]},"doi":"10.1007/978-3-642-39799-8_6","abstract":[{"text":"In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"scopus_import":1,"intvolume":"      8044","quality_controlled":"1","alternative_title":["LNCS"],"_id":"2000","title":"TTP: Tool for tumor progression","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1303.5251"}],"department":[{"_id":"KrCh"}],"conference":{"location":"St. Petersburg, Russia","name":"CAV: Computer Aided Verification","start_date":"2013-07-13","end_date":"2013-07-19"},"publist_id":"5077","author":[{"orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes","first_name":"Johannes","last_name":"Reiter"},{"full_name":"Božić, Ivana","first_name":"Ivana","last_name":"Božić"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"citation":{"short":"J. Reiter, I. Božić, K. Chatterjee, M. Nowak, in:, Proceedings of 25th Int. Conf. on Computer Aided Verification, Springer, 2013, pp. 101–106.","chicago":"Reiter, Johannes, Ivana Božić, Krishnendu Chatterjee, and Martin Nowak. “TTP: Tool for Tumor Progression.” In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, 8044:101–6. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>.","ista":"Reiter J, Božić I, Chatterjee K, Nowak M. 2013. TTP: Tool for tumor progression. Proceedings of 25th Int. Conf. on Computer Aided Verification. CAV: Computer Aided VerificationLecture Notes in Computer Science, LNCS, vol. 8044, 101–106.","ama":"Reiter J, Božić I, Chatterjee K, Nowak M. TTP: Tool for tumor progression. In: <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>. Vol 8044. Lecture Notes in Computer Science. Springer; 2013:101-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>","ieee":"J. Reiter, I. Božić, K. Chatterjee, and M. Nowak, “TTP: Tool for tumor progression,” in <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, St. Petersburg, Russia, 2013, vol. 8044, pp. 101–106.","apa":"Reiter, J., Božić, I., Chatterjee, K., &#38; Nowak, M. (2013). TTP: Tool for tumor progression. In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i> (Vol. 8044, pp. 101–106). St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>","mla":"Reiter, Johannes, et al. “TTP: Tool for Tumor Progression.” <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, vol. 8044, Springer, 2013, pp. 101–06, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>."},"month":"01","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5399"},{"relation":"dissertation_contains","status":"public","id":"1400"}]},"date_published":"2013-01-01T00:00:00Z","oa_version":"Preprint","publication_status":"published","year":"2013"},{"day":"01","type":"journal_article","_id":"2009","title":"Privacy-preserving data sharing for genome-wide association studies","date_updated":"2021-01-12T06:54:41Z","quality_controlled":"1","intvolume":"         5","status":"public","date_created":"2018-12-11T11:55:11Z","department":[{"_id":"CaUh"}],"page":"137 - 166","publist_id":"5067","main_file_link":[{"open_access":"1","url":"http://repository.cmu.edu/jpc/vol5/iss1/6"}],"oa":1,"publication":"Journal of Privacy and Confidentiality ","publisher":"Carnegie Mellon University","doi":"10.29012/jpc.v5i1.629","citation":{"mla":"Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1, Carnegie Mellon University, 2013, pp. 137–66, doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>.","apa":"Uhler, C., Slavkovic, A., &#38; Fienberg, S. (2013). Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>","ieee":"C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing for genome-wide association studies,” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013.","ama":"Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. 2013;5(1):137-166. doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>","ista":"Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 5(1), 137–166.","chicago":"Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University, 2013. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>.","short":"C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality  5 (2013) 137–166."},"issue":"1","month":"08","volume":5,"author":[{"orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","first_name":"Caroline","last_name":"Uhler"},{"first_name":"Aleksandra","last_name":"Slavkovic","full_name":"Slavkovic, Aleksandra"},{"last_name":"Fienberg","first_name":"Stephen","full_name":"Fienberg, Stephen"}],"language":[{"iso":"eng"}],"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","year":"2013","abstract":[{"text":"Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression.","lang":"eng"}],"date_published":"2013-08-01T00:00:00Z","article_processing_charge":"No"},{"main_file_link":[{"url":"www.doi.org/10.1214/12-AOS1080","open_access":"1"}],"publist_id":"5066","department":[{"_id":"CaUh"}],"oa":1,"title":"Geometry of the faithfulness assumption in causal inference","_id":"2010","intvolume":"        41","quality_controlled":"1","date_published":"2013-04-01T00:00:00Z","year":"2013","oa_version":"Published Version","publication_status":"published","month":"04","citation":{"apa":"Uhler, C., Raskutti, G., Bühlmann, P., &#38; Yu, B. (2013). Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>","ieee":"C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness assumption in causal inference,” <i>The Annals of Statistics</i>, vol. 41, no. 2. Institute of Mathematical Statistics, pp. 436–463, 2013.","mla":"Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>, vol. 41, no. 2, Institute of Mathematical Statistics, 2013, pp. 436–63, doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>.","ama":"Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. 2013;41(2):436-463. doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>","chicago":"Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>. Institute of Mathematical Statistics, 2013. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>.","short":"C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013) 436–463.","ista":"Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. 41(2), 436–463."},"issue":"2","author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","last_name":"Uhler","first_name":"Caroline","full_name":"Uhler, Caroline"},{"full_name":"Raskutti, Garvesh","last_name":"Raskutti","first_name":"Garvesh"},{"last_name":"Bühlmann","first_name":"Peter","full_name":"Bühlmann, Peter"},{"full_name":"Yu, Bin","last_name":"Yu","first_name":"Bin"}],"page":"436 - 463","publisher":"Institute of Mathematical Statistics","publication":"The Annals of Statistics","isi":1,"arxiv":1,"date_updated":"2025-09-29T14:31:39Z","type":"journal_article","day":"01","date_created":"2018-12-11T11:55:11Z","status":"public","language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","abstract":[{"text":"Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1214/12-AOS1080","external_id":{"arxiv":["1207.0547"],"isi":["000320488200002"]},"volume":41},{"status":"public","intvolume":"       110","date_created":"2018-12-11T11:55:33Z","quality_controlled":0,"title":"Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution","date_updated":"2021-01-12T06:55:08Z","_id":"2074","type":"journal_article","day":"16","publisher":"National Academy of Sciences","publication":"PNAS","extern":1,"publist_id":"4964","page":"6453 - 6458","author":[{"full_name":"Beatriz Vicoso","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaiser","first_name":"Vera","full_name":"Kaiser, Vera B"},{"last_name":"Bachtrog","first_name":"Doris","full_name":"Bachtrog, Doris"}],"volume":110,"month":"04","issue":"16","citation":{"ama":"Vicoso B, Kaiser V, Bachtrog D. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. 2013;110(16):6453-6458. doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>","ieee":"B. Vicoso, V. Kaiser, and D. Bachtrog, “Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution,” <i>PNAS</i>, vol. 110, no. 16. National Academy of Sciences, pp. 6453–6458, 2013.","apa":"Vicoso, B., Kaiser, V., &#38; Bachtrog, D. (2013). Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>","mla":"Vicoso, Beatriz, et al. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>, vol. 110, no. 16, National Academy of Sciences, 2013, pp. 6453–58, doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>.","chicago":"Vicoso, Beatriz, Vera Kaiser, and Doris Bachtrog. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>.","short":"B. Vicoso, V. Kaiser, D. Bachtrog, PNAS 110 (2013) 6453–6458.","ista":"Vicoso B, Kaiser V, Bachtrog D. 2013. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. 110(16), 6453–6458."},"doi":"10.1073/pnas.1217027110","abstract":[{"text":"Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic mutations on protosex chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic sex chromosomes. Recombination suppression and differentiation are generally viewed as the default path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally sex-biased for all sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu sex chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by sexually antagonistic mutations: some lineages eliminate recombination along the protosex chromosomes to physically restrict sexually antagonistic alleles to one sex, whereas ratites evolved sex-biased expression to confine the product of a sexually antagonistic allele to the sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic sex chromosomes in other lineages and illustrates the importance of sexually antagonistic mutations driving the evolution of sex chromosomes. ","lang":"eng"}],"date_published":"2013-04-16T00:00:00Z","year":"2013","publication_status":"published"},{"publist_id":"4962","acknowledgement":"Funded by NIH grants (R01GM076007 and R01GM093182) and a Packard Fellowship to DB.","extern":1,"publisher":"Public Library of Science","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"PLoS Biology","type":"journal_article","day":"27","title":"Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation","date_updated":"2021-01-12T06:55:09Z","_id":"2076","quality_controlled":0,"date_created":"2018-12-11T11:55:34Z","intvolume":"        11","status":"public","year":"2013","publication_status":"published","date_published":"2013-08-27T00:00:00Z","abstract":[{"lang":"eng","text":"Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution.\n"}],"doi":"10.1371/journal.pbio.1001643","month":"08","citation":{"chicago":"Vicoso, Beatriz, Jr Emerson, Yulia Zektser, Shivani Mahajan, and Doris Bachtrog. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>.","short":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, D. Bachtrog, PLoS Biology 11 (2013).","ista":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. 2013. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. 11(8).","apa":"Vicoso, B., Emerson, J., Zektser, Y., Mahajan, S., &#38; Bachtrog, D. (2013). Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>","ieee":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, and D. Bachtrog, “Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation,” <i>PLoS Biology</i>, vol. 11, no. 8. Public Library of Science, 2013.","mla":"Vicoso, Beatriz, et al. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>, vol. 11, no. 8, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>.","ama":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. 2013;11(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>"},"issue":"8","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Beatriz Vicoso","first_name":"Beatriz","last_name":"Vicoso"},{"full_name":"Emerson, Jr J.","first_name":"Jr","last_name":"Emerson"},{"full_name":"Zektser, Yulia","first_name":"Yulia","last_name":"Zektser"},{"last_name":"Mahajan","first_name":"Shivani","full_name":"Mahajan, Shivani"},{"full_name":"Bachtrog, Doris","first_name":"Doris","last_name":"Bachtrog"}],"volume":11},{"author":[{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov","full_name":"Leonid Sazanov"},{"first_name":"Rozbeh","last_name":"Baradaran","full_name":"Baradaran, Rozbeh "},{"first_name":"Rouslan","last_name":"Efremov","full_name":"Efremov, Rouslan G"},{"full_name":"Berrisford, John M","first_name":"John","last_name":"Berrisford"},{"full_name":"Minhas, Gurdeep S","last_name":"Minhas","first_name":"Gurdeep"}],"volume":41,"month":"10","citation":{"mla":"Sazanov, Leonid A., et al. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” <i>Biochemical Society Transactions</i>, vol. 41, no. 5, Portland Press, 2013, pp. 1265–71, doi:<a href=\"https://doi.org/10.1042/BST20130193\">10.1042/BST20130193</a>.","apa":"Sazanov, L. A., Baradaran, R., Efremov, R., Berrisford, J., &#38; Minhas, G. (2013). A long road towards the structure of respiratory complex I, a giant molecular proton pump. <i>Biochemical Society Transactions</i>. Portland Press. <a href=\"https://doi.org/10.1042/BST20130193\">https://doi.org/10.1042/BST20130193</a>","ieee":"L. A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, and G. Minhas, “A long road towards the structure of respiratory complex I, a giant molecular proton pump,” <i>Biochemical Society Transactions</i>, vol. 41, no. 5. Portland Press, pp. 1265–1271, 2013.","ama":"Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. A long road towards the structure of respiratory complex I, a giant molecular proton pump. <i>Biochemical Society Transactions</i>. 2013;41(5):1265-1271. doi:<a href=\"https://doi.org/10.1042/BST20130193\">10.1042/BST20130193</a>","ista":"Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. 2013. A long road towards the structure of respiratory complex I, a giant molecular proton pump. Biochemical Society Transactions. 41(5), 1265–1271.","chicago":"Sazanov, Leonid A, Rozbeh Baradaran, Rouslan Efremov, John Berrisford, and Gurdeep Minhas. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” <i>Biochemical Society Transactions</i>. Portland Press, 2013. <a href=\"https://doi.org/10.1042/BST20130193\">https://doi.org/10.1042/BST20130193</a>.","short":"L.A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, G. Minhas, Biochemical Society Transactions 41 (2013) 1265–1271."},"issue":"5","doi":"10.1042/BST20130193","date_published":"2013-10-01T00:00:00Z","abstract":[{"text":"Complex I (NADH:ubiquinone oxidoreductase) is central to cellular energy production, being the first and largest enzyme of the respiratory chain in mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the inner mitochondrial membrane and is involved in a wide range of human neurodegenerative disorders. Mammalian complex I is composed of 44 different subunits, whereas the 'minimal' bacterial version contains 14 highly conserved 'core' subunits. The L-shaped assembly consists of hydrophilic and membrane domains. We have determined all known atomic structures of complex I, starting from the hydrophilic domain of Thermus thermophilus enzyme (eight subunits, nine Fe-S clusters), followed by the membrane domains of the Escherichia coli (six subunits, 55 transmembrane helices) and T. thermophilus (seven subunits, 64 transmembrane helices) enzymes, and finally culminating in a recent crystal structure of the entire intact complex I from T. thermophilus (536 kDa, 16 subunits, nine Fe-S clusters, 64 transmembrane helices). The structure suggests an unusual and unique coupling mechanism via longrange conformational changes. Determination of the structure of the entire complex was possible only through this step-by-step approach, building on from smaller subcomplexes towards the entire assembly. Large membrane proteins are notoriously difficult to crystallize, and so various non-standard and sometimes counterintuitive approaches were employed in order to achieve crystal diffraction to high resolution and solve the structures. These steps, as well as the implications from the final structure, are discussed in the present review.","lang":"eng"}],"year":"2013","publication_status":"published","date_created":"2018-12-11T11:55:00Z","status":"public","intvolume":"        41","quality_controlled":0,"date_updated":"2021-01-12T06:54:28Z","title":"A long road towards the structure of respiratory complex I, a giant molecular proton pump","_id":"1977","type":"journal_article","day":"01","publisher":"Portland Press","publication":"Biochemical Society Transactions","acknowledgement":"This work was funded by the Medical Research Council.","extern":1,"publist_id":"5106","page":"1265 - 1271"},{"publication_identifier":{"eissn":["1742-2051"],"issn":["1742-206X"]},"title":"Large-scale cytological profiling for functional analysis of bioactive compounds","_id":"15162","quality_controlled":"1","intvolume":"         9","extern":"1","month":"08","issue":"11","citation":{"ista":"Woehrmann MH, Bray WM, Durbin JK, Nisam SC, Michael AK, Glassey E, Stuart JM, Lokey RS. 2013. Large-scale cytological profiling for functional analysis of bioactive compounds. Molecular BioSystems. 9(11), 2604.","short":"M.H. Woehrmann, W.M. Bray, J.K. Durbin, S.C. Nisam, A.K. Michael, E. Glassey, J.M. Stuart, R.S. Lokey, Molecular BioSystems 9 (2013).","chicago":"Woehrmann, Marcos H., Walter M. Bray, James K. Durbin, Sean C. Nisam, Alicia K. Michael, Emerson Glassey, Joshua M. Stuart, and R. Scott Lokey. “Large-Scale Cytological Profiling for Functional Analysis of Bioactive Compounds.” <i>Molecular BioSystems</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3mb70245f\">https://doi.org/10.1039/c3mb70245f</a>.","ama":"Woehrmann MH, Bray WM, Durbin JK, et al. Large-scale cytological profiling for functional analysis of bioactive compounds. <i>Molecular BioSystems</i>. 2013;9(11). doi:<a href=\"https://doi.org/10.1039/c3mb70245f\">10.1039/c3mb70245f</a>","mla":"Woehrmann, Marcos H., et al. “Large-Scale Cytological Profiling for Functional Analysis of Bioactive Compounds.” <i>Molecular BioSystems</i>, vol. 9, no. 11, 2604, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3mb70245f\">10.1039/c3mb70245f</a>.","ieee":"M. H. Woehrmann <i>et al.</i>, “Large-scale cytological profiling for functional analysis of bioactive compounds,” <i>Molecular BioSystems</i>, vol. 9, no. 11. Royal Society of Chemistry, 2013.","apa":"Woehrmann, M. H., Bray, W. M., Durbin, J. K., Nisam, S. C., Michael, A. K., Glassey, E., … Lokey, R. S. (2013). Large-scale cytological profiling for functional analysis of bioactive compounds. <i>Molecular BioSystems</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3mb70245f\">https://doi.org/10.1039/c3mb70245f</a>"},"author":[{"full_name":"Woehrmann, Marcos H.","first_name":"Marcos H.","last_name":"Woehrmann"},{"full_name":"Bray, Walter M.","last_name":"Bray","first_name":"Walter M."},{"full_name":"Durbin, James K.","last_name":"Durbin","first_name":"James K."},{"first_name":"Sean C.","last_name":"Nisam","full_name":"Nisam, Sean C."},{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia Kathleen","last_name":"Michael","first_name":"Alicia Kathleen"},{"last_name":"Glassey","first_name":"Emerson","full_name":"Glassey, Emerson"},{"last_name":"Stuart","first_name":"Joshua M.","full_name":"Stuart, Joshua M."},{"last_name":"Lokey","first_name":"R. Scott","full_name":"Lokey, R. Scott"}],"keyword":["Molecular Biology","Biotechnology"],"article_type":"original","year":"2013","oa_version":"None","publication_status":"published","date_published":"2013-08-20T00:00:00Z","type":"journal_article","day":"20","date_updated":"2024-03-25T11:45:46Z","date_created":"2024-03-21T07:58:57Z","status":"public","publisher":"Royal Society of Chemistry","publication":"Molecular BioSystems","doi":"10.1039/c3mb70245f","volume":9,"scopus_import":"1","language":[{"iso":"eng"}],"article_number":"2604","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"text":"Cytological profiling (CP) is an unbiased image-based screening technique that uses automated microscopy and image analysis to profile compounds based on numerous quantifiable phenotypic features. We used CP to evaluate a library of nearly 500 compounds with documented mechanisms of action (MOAs) spanning a wide range of biological pathways. We developed informatics techniques for generating dosage-independent phenotypic “fingerprints” for each compound, and for quantifying the likelihood that a compound's CP fingerprint corresponds to its annotated MOA. We identified groups of features that distinguish classes with closely related phenotypes, such as microtubule poisons vs. HSP90 inhibitors, and DNA synthesis vs. proteasome inhibitors. We tested several cases in which cytological profiles indicated novel mechanisms, including a tyrphostin kinase inhibitor involved in mitochondrial uncoupling, novel microtubule poisons, and a nominal PPAR-gamma ligand that acts as a proteasome inhibitor, using independent biochemical assays to confirm the MOAs predicted by the CP signatures. We also applied maximal-information statistics to identify correlations between cytological features and kinase inhibitory activities by combining the CP fingerprints of 24 kinase inhibitors with published data on their specificities against a diverse panel of kinases. The resulting analysis suggests a strategy for probing the biological functions of specific kinases by compiling cytological data from inhibitors of varying specificities.","lang":"eng"}]},{"date_created":"2022-02-08T10:34:29Z","status":"public","day":"01","type":"conference","date_updated":"2022-02-08T10:48:06Z","publication":"APS March Meeting 2013","publisher":"American Physical Society","acknowledgement":"This work was supported by the Center for Emergent Superconductivity, an Energy Frontier Research Center funded by the US DOE, Office of Science.","volume":58,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Fluxoid quantization provides a direct means to study phase coherence. In cuprate superconductors, there have been observations which suggest that phase coherent superconducting fluctuations may persist at temperatures significantly above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate superconducting samples to directly probe phase coherence over a wide range of temperatures. We present cantilever torque susceptometry measurements of micron and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique allowed observation of transitions between different fluxoid states of a single ring, and the discrete vortex states of micron size disks. The dependence of magnetic susceptibility on diameter and wall thickness of the ring was investigated. Measurements were made at different values of the in-plane magnetic field, and over a wide range of temperatures."}],"article_processing_charge":"No","article_number":"N36.00001","language":[{"iso":"eng"}],"quality_controlled":"1","alternative_title":["Bulletin of the American Physical Society"],"intvolume":"        58","publication_identifier":{"issn":["0003-0503"]},"_id":"10749","title":"Cantilever micro-susceptometry of mesoscopic Bi2212 samples","oa":1,"conference":{"start_date":"2013-03-18","end_date":"2013-03-22","name":"APS: American Physical Society","location":"Baltimore, MD, United States"},"extern":"1","main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR13/Event/186873","open_access":"1"}],"author":[{"full_name":"Polshyn, Hryhoriy","last_name":"Polshyn","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"},{"full_name":"Gu, Genda","last_name":"Gu","first_name":"Genda"}],"issue":"1","citation":{"ista":"Polshyn H, Budakian R, Gu G. 2013. Cantilever micro-susceptometry of mesoscopic Bi2212 samples. APS March Meeting 2013. APS: American Physical Society, Bulletin of the American Physical Society, vol. 58, N36.00001.","chicago":"Polshyn, Hryhoriy, Raffi Budakian, and Genda Gu. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212 Samples.” In <i>APS March Meeting 2013</i>, Vol. 58. American Physical Society, 2013.","short":"H. Polshyn, R. Budakian, G. Gu, in:, APS March Meeting 2013, American Physical Society, 2013.","mla":"Polshyn, Hryhoriy, et al. “Cantilever Micro-Susceptometry of Mesoscopic Bi2212 Samples.” <i>APS March Meeting 2013</i>, vol. 58, no. 1, N36.00001, American Physical Society, 2013.","ieee":"H. Polshyn, R. Budakian, and G. Gu, “Cantilever micro-susceptometry of mesoscopic Bi2212 samples,” in <i>APS March Meeting 2013</i>, Baltimore, MD, United States, 2013, vol. 58, no. 1.","apa":"Polshyn, H., Budakian, R., &#38; Gu, G. (2013). Cantilever micro-susceptometry of mesoscopic Bi2212 samples. In <i>APS March Meeting 2013</i> (Vol. 58). Baltimore, MD, United States: American Physical Society.","ama":"Polshyn H, Budakian R, Gu G. Cantilever micro-susceptometry of mesoscopic Bi2212 samples. In: <i>APS March Meeting 2013</i>. Vol 58. American Physical Society; 2013."},"month":"03","publication_status":"published","oa_version":"Published Version","year":"2013","date_published":"2013-03-01T00:00:00Z"},{"article_type":"original","corr_author":"1","year":"2013","oa_version":"Published Version","publication_status":"published","date_published":"2013-10-21T00:00:00Z","month":"10","citation":{"ama":"Vanneste S, Friml J. Calcium: The missing link in auxin action. <i>Plants</i>. 2013;2(4):650-675. doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>","apa":"Vanneste, S., &#38; Friml, J. (2013). Calcium: The missing link in auxin action. <i>Plants</i>. MDPI. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>","ieee":"S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” <i>Plants</i>, vol. 2, no. 4. MDPI, pp. 650–675, 2013.","mla":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>.","chicago":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>. MDPI, 2013. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>.","short":"S. Vanneste, J. Friml, Plants 2 (2013) 650–675.","ista":"Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants. 2(4), 650–675."},"issue":"4","author":[{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"keyword":["Plant Science","Ecology","Ecology","Evolution","Behavior and Systematics"],"department":[{"_id":"JiFr"}],"has_accepted_license":"1","ddc":["580"],"oa":1,"publication_identifier":{"issn":["2223-7747"]},"file":[{"success":1,"file_id":"10916","date_created":"2022-03-21T12:12:56Z","file_size":670188,"creator":"dernst","date_updated":"2022-03-21T12:12:56Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2013_Plants_Vanneste.pdf","checksum":"fb4ff2e820e344e253c9197544610be6"}],"title":"Calcium: The missing link in auxin action","_id":"10895","quality_controlled":"1","intvolume":"         2","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. "}],"doi":"10.3390/plants2040650","external_id":{"pmid":["27137397"]},"volume":2,"page":"650-675","pmid":1,"file_date_updated":"2022-03-21T12:12:56Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"publisher":"MDPI","publication":"Plants","type":"journal_article","day":"21","date_updated":"2024-10-09T21:01:52Z","date_created":"2022-03-21T07:13:49Z","status":"public"},{"place":"Berlin, Heidelberg","intvolume":"      7877","quality_controlled":"1","title":"Persistent homology in image processing","_id":"10897","publication_identifier":{"isbn":["9783642382208"],"issn":["0302-9743"],"eisbn":["9783642382215"],"eissn":["1611-3349"]},"conference":{"location":"Vienna, Austria","name":"GbRPR: Graph-based Representations in Pattern Recognition","end_date":"2013-05-17","start_date":"2013-05-15"},"department":[{"_id":"HeEd"}],"author":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"month":"06","citation":{"mla":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” <i>Graph-Based Representations in Pattern Recognition</i>, vol. 7877, Springer Nature, 2013, pp. 182–83, doi:<a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">10.1007/978-3-642-38221-5_19</a>.","apa":"Edelsbrunner, H. (2013). Persistent homology in image processing. In <i>Graph-Based Representations in Pattern Recognition</i> (Vol. 7877, pp. 182–183). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">https://doi.org/10.1007/978-3-642-38221-5_19</a>","ieee":"H. Edelsbrunner, “Persistent homology in image processing,” in <i>Graph-Based Representations in Pattern Recognition</i>, Vienna, Austria, 2013, vol. 7877, pp. 182–183.","ama":"Edelsbrunner H. Persistent homology in image processing. In: <i>Graph-Based Representations in Pattern Recognition</i>. Vol 7877. LNCS. Berlin, Heidelberg: Springer Nature; 2013:182-183. doi:<a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">10.1007/978-3-642-38221-5_19</a>","ista":"Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNCS vol. 7877, 182–183.","short":"H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition, Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183.","chicago":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In <i>Graph-Based Representations in Pattern Recognition</i>, 7877:182–83. LNCS. Berlin, Heidelberg: Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">https://doi.org/10.1007/978-3-642-38221-5_19</a>."},"date_published":"2013-06-01T00:00:00Z","year":"2013","oa_version":"None","publication_status":"published","corr_author":"1","status":"public","date_created":"2022-03-21T07:30:33Z","date_updated":"2025-04-15T08:37:54Z","type":"conference","series_title":"LNCS","day":"01","ec_funded":1,"publisher":"Springer Nature","publication":"Graph-Based Representations in Pattern Recognition","acknowledgement":"This research is partially supported by the European Science Foundation (ESF) under the Research Network Programme, the European Union under the Toposys Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053.","page":"182-183","volume":7877,"project":[{"name":"Topological Complex Systems","grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/978-3-642-38221-5_19","article_processing_charge":"No","abstract":[{"text":"Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"scopus_import":"1"},{"publication_status":"published","oa_version":"None","year":"2013","date_published":"2013-05-14T00:00:00Z","author":[{"first_name":"Andreas","last_name":"Haas","full_name":"Haas, Andreas"},{"full_name":"Lippautz, Michael","first_name":"Michael","last_name":"Lippautz"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Payer, Hannes","first_name":"Hannes","last_name":"Payer"},{"last_name":"Sokolova","first_name":"Ana","full_name":"Sokolova, Ana"},{"full_name":"Kirsch, Christoph M.","first_name":"Christoph M.","last_name":"Kirsch"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","last_name":"Sezgin","full_name":"Sezgin, Ali"}],"citation":{"ista":"Haas A, Lippautz M, Henzinger TA, Payer H, Sokolova A, Kirsch CM, Sezgin A. 2013. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. CF: Conference on Computing Frontiers, 17.","chicago":"Haas, Andreas, Michael Lippautz, Thomas A Henzinger, Hannes Payer, Ana Sokolova, Christoph M. Kirsch, and Ali Sezgin. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” In <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/10.1145/2482767.2482789</a>.","short":"A. Haas, M. Lippautz, T.A. Henzinger, H. Payer, A. Sokolova, C.M. Kirsch, A. Sezgin, in:, Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, ACM, 2013.","ama":"Haas A, Lippautz M, Henzinger TA, et al. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In: <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. ACM; 2013. doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>","mla":"Haas, Andreas, et al. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>, no. 5, 17, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>.","apa":"Haas, A., Lippautz, M., Henzinger, T. A., Payer, H., Sokolova, A., Kirsch, C. M., &#38; Sezgin, A. (2013). Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. Ischia, Italy: ACM. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/10.1145/2482767.2482789</a>","ieee":"A. Haas <i>et al.</i>, “Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation,” in <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>, Ischia, Italy, 2013, no. 5."},"issue":"5","month":"05","department":[{"_id":"ToHe"}],"conference":{"location":"Ischia, Italy","name":"CF: Conference on Computing Frontiers","start_date":"2013-05-14","end_date":"2013-05-16"},"quality_controlled":"1","publication_identifier":{"isbn":["978-145032053-5"]},"_id":"10898","title":"Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered.","lang":"eng"}],"article_processing_charge":"No","scopus_import":"1","article_number":"17","language":[{"iso":"eng"}],"doi":"10.1145/2482767.2482789","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication":"Proceedings of the ACM International Conference on Computing Frontiers - CF '13","publisher":"ACM","ec_funded":1,"acknowledgement":"This work has been supported by the European Research Council advanced grant on Quantitative Reactive Modeling (QUAREM) and the National Research Network RiSE on Rigorous Systems Engineering (Austrian Science Fund S11402-N23 and S11404-N23).","date_created":"2022-03-21T07:33:22Z","status":"public","day":"14","type":"conference","date_updated":"2025-05-14T11:23:58Z"},{"publication":"Encyclopedia of Biodiversity","publisher":"Elsevier","page":"508-515","department":[{"_id":"NiBa"}],"date_created":"2022-03-21T07:46:22Z","status":"public","quality_controlled":"1","_id":"10899","date_updated":"2024-10-09T21:02:37Z","title":"Differentiation","day":"01","type":"book_chapter","publication_identifier":{"isbn":["978-0-12-384720-1"]},"date_published":"2013-01-01T00:00:00Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publication_status":"published","year":"2013","language":[{"iso":"eng"}],"corr_author":"1","scopus_import":"1","keyword":["Adaptive landscape","Cline","Coalescent process","Gene flow","Hybrid zone","Local adaptation","Natural selection","Neutral theory","Population structure","Speciation"],"author":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"edition":"2","citation":{"ista":"Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.","chicago":"Barton, Nicholas H. “Differentiation.” In <i>Encyclopedia of Biodiversity</i>, 2nd ed., 508–15. Elsevier, 2013. <a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">https://doi.org/10.1016/b978-0-12-384719-5.00031-9</a>.","short":"N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","ama":"Barton NH. Differentiation. In: <i>Encyclopedia of Biodiversity</i>. 2nd ed. Elsevier; 2013:508-515. doi:<a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">10.1016/b978-0-12-384719-5.00031-9</a>","mla":"Barton, Nicholas H. “Differentiation.” <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–15, doi:<a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">10.1016/b978-0-12-384719-5.00031-9</a>.","apa":"Barton, N. H. (2013). Differentiation. In <i>Encyclopedia of Biodiversity</i> (2nd ed., pp. 508–515). Elsevier. <a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">https://doi.org/10.1016/b978-0-12-384719-5.00031-9</a>","ieee":"N. H. Barton, “Differentiation,” in <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–515."},"month":"01","doi":"10.1016/b978-0-12-384719-5.00031-9"},{"intvolume":"      1013","place":"Totowa, NJ","quality_controlled":"1","alternative_title":["Methods in Molecular Biology"],"_id":"10900","title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations","publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781627034265"],"isbn":["9781627034258"]},"department":[{"_id":"MiSi"}],"author":[{"id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","full_name":"Weber, Michele","first_name":"Michele","last_name":"Weber"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}],"citation":{"chicago":"Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ: Humana Press, 2013. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>.","short":"M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 2013, pp. 215–226.","ista":"Weber M, Sixt MK. 2013.Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Chemokines. Methods in Molecular Biology, vol. 1013, 215–226.","ama":"Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. <i>Chemokines</i>. Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>","ieee":"M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations,” in <i>Chemokines</i>, vol. 1013, A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.","apa":"Weber, M., &#38; Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona &#38; E. Ubogu (Eds.), <i>Chemokines</i> (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press. <a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">https://doi.org/10.1007/978-1-62703-426-5_14</a>","mla":"Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” <i>Chemokines</i>, edited by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26, doi:<a href=\"https://doi.org/10.1007/978-1-62703-426-5_14\">10.1007/978-1-62703-426-5_14</a>."},"month":"04","date_published":"2013-04-03T00:00:00Z","publication_status":"published","oa_version":"None","year":"2013","corr_author":"1","status":"public","date_created":"2022-03-21T07:47:41Z","date_updated":"2024-10-09T21:02:37Z","day":"03","series_title":"MIMB","type":"book_chapter","publication":"Chemokines","publisher":"Humana Press","pmid":1,"acknowledgement":"We would like to thank Alexander Eichner and Ingrid de Vries for discussion and critical reading of the manuscript, and Mary Frank for assistance with the recording of videos and images in Fig. 1. M.S. is supported through funding from the German Research Foundation (DFG). M.W. acknowledges the Alexander von Humboldt Foundation for funding.","page":"215-226","volume":1013,"editor":[{"last_name":"Cardona","first_name":"Astrid","full_name":"Cardona, Astrid"},{"full_name":"Ubogu, Eroboghene","first_name":"Eroboghene","last_name":"Ubogu"}],"external_id":{"pmid":["23625502"]},"doi":"10.1007/978-1-62703-426-5_14","abstract":[{"lang":"eng","text":"Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays."}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"scopus_import":"1"},{"quality_controlled":"1","alternative_title":["LNCS"],"intvolume":"      7810","place":"Berlin, Heidelberg","publication_identifier":{"isbn":["9783642370632"],"eisbn":["9783642370649"],"issn":["0302-9743"],"eissn":["1611-3349"]},"_id":"10902","title":"How to travel between languages","department":[{"_id":"KrCh"}],"conference":{"location":"Bilbao, Spain","name":"LATA: Language and Automata Theory and Applications","start_date":"2013-04-02","end_date":"2013-04-05"},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Siddhesh","last_name":"Chaubal","full_name":"Chaubal, Siddhesh"},{"id":"2EC51194-F248-11E8-B48F-1D18A9856A87","last_name":"Rubin","first_name":"Sasha","full_name":"Rubin, Sasha"}],"citation":{"ama":"Chatterjee K, Chaubal S, Rubin S. How to travel between languages. In: <i>7th International Conference on Language and Automata Theory and Applications</i>. Vol 7810. LNCS. Berlin, Heidelberg: Springer Nature; 2013:214-225. doi:<a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">10.1007/978-3-642-37064-9_20</a>","apa":"Chatterjee, K., Chaubal, S., &#38; Rubin, S. (2013). How to travel between languages. In <i>7th International Conference on Language and Automata Theory and Applications</i> (Vol. 7810, pp. 214–225). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">https://doi.org/10.1007/978-3-642-37064-9_20</a>","ieee":"K. Chatterjee, S. Chaubal, and S. Rubin, “How to travel between languages,” in <i>7th International Conference on Language and Automata Theory and Applications</i>, Bilbao, Spain, 2013, vol. 7810, pp. 214–225.","mla":"Chatterjee, Krishnendu, et al. “How to Travel between Languages.” <i>7th International Conference on Language and Automata Theory and Applications</i>, vol. 7810, Springer Nature, 2013, pp. 214–25, doi:<a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">10.1007/978-3-642-37064-9_20</a>.","short":"K. Chatterjee, S. Chaubal, S. Rubin, in:, 7th International Conference on Language and Automata Theory and Applications, Springer Nature, Berlin, Heidelberg, 2013, pp. 214–225.","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Sasha Rubin. “How to Travel between Languages.” In <i>7th International Conference on Language and Automata Theory and Applications</i>, 7810:214–25. LNCS. Berlin, Heidelberg: Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-37064-9_20\">https://doi.org/10.1007/978-3-642-37064-9_20</a>.","ista":"Chatterjee K, Chaubal S, Rubin S. 2013. How to travel between languages. 7th International Conference on Language and Automata Theory and Applications. LATA: Language and Automata Theory and ApplicationsLNCS, LNCS, vol. 7810, 214–225."},"month":"04","publication_status":"published","oa_version":"None","year":"2013","date_published":"2013-04-15T00:00:00Z","corr_author":"1","status":"public","date_created":"2022-03-21T07:56:21Z","series_title":"LNCS","day":"15","type":"conference","date_updated":"2025-07-10T11:50:03Z","publication":"7th International Conference on Language and Automata Theory and Applications","publisher":"Springer Nature","ec_funded":1,"page":"214-225","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award. Thanks to Gabriele Puppis for suggesting the problem of identifying a deterministic transducer to compute the optimal cost, and to Martin Chmelik for his comments on the introduction.","volume":7810,"doi":"10.1007/978-3-642-37064-9_20","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider how to edit strings from a source language so that the edited strings belong to a target language, where the languages are given as deterministic finite automata. Non-streaming (or offline) transducers perform edits given the whole source string. We show that the class of deterministic one-pass transducers with registers along with increment and min operation suffices for computing optimal edit distance, whereas the same class of transducers without the min operation is not sufficient. Streaming (or online) transducers perform edits as the letters of the source string are received. We present a polynomial time algorithm for the partial-repair problem that given a bound α asks for the construction of a deterministic streaming transducer (if one exists) that ensures that the ‘maximum fraction’ η of the strings of the source language are edited, within cost α, to the target language."}],"article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}]},{"article_processing_charge":"No","abstract":[{"text":"Nuclear pore complex (NPC) proteins are known for their critical roles in regulating nucleocytoplasmic traffic of macromolecules across the nuclear envelope. However, recent findings suggest that some nucleoporins (Nups), including Nup98, have additional functions in developmental gene regulation. Nup98, which exhibits transcription-dependent mobility at the NPC but can also bind chromatin away from the nuclear envelope, is frequently involved in chromosomal translocations in a subset of patients suffering from acute myeloid leukemia (AML). A common paradigm suggests that Nup98 translocations cause aberrant transcription when they are recuited to aberrant genomic loci. Importantly, this model fails to account for the potential loss of wild type (WT) Nup98 function in the presence of Nup98 translocation mutants. Here we examine how the cell might regulate Nup98 nucleoplasmic protein levels to control transcription in healthy cells. In addition, we discuss the possibility that dominant negative Nup98 fusion proteins disrupt the transcriptional activity of WT Nup98 in the nucleoplasm to drive AML.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"scopus_import":"1","volume":23,"doi":"10.1016/j.tcb.2012.10.013","external_id":{"pmid":["23246429"]},"publisher":"Elsevier","publication":"Trends in Cell Biology","pmid":1,"page":"112-117","status":"public","date_created":"2022-04-07T07:50:33Z","date_updated":"2024-10-14T11:23:44Z","type":"journal_article","day":"01","date_published":"2013-03-01T00:00:00Z","year":"2013","oa_version":"None","publication_status":"published","article_type":"letter_note","author":[{"first_name":"Tobias M.","last_name":"Franks","full_name":"Franks, Tobias M."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","first_name":"Martin W","last_name":"HETZER"}],"keyword":["Cell Biology"],"month":"03","issue":"3","citation":{"ista":"Franks TM, Hetzer M. 2013. The role of Nup98 in transcription regulation in healthy and diseased cells. Trends in Cell Biology. 23(3), 112–117.","short":"T.M. Franks, M. Hetzer, Trends in Cell Biology 23 (2013) 112–117.","chicago":"Franks, Tobias M., and Martin Hetzer. “The Role of Nup98 in Transcription Regulation in Healthy and Diseased Cells.” <i>Trends in Cell Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.tcb.2012.10.013\">https://doi.org/10.1016/j.tcb.2012.10.013</a>.","ama":"Franks TM, Hetzer M. The role of Nup98 in transcription regulation in healthy and diseased cells. <i>Trends in Cell Biology</i>. 2013;23(3):112-117. doi:<a href=\"https://doi.org/10.1016/j.tcb.2012.10.013\">10.1016/j.tcb.2012.10.013</a>","mla":"Franks, Tobias M., and Martin Hetzer. “The Role of Nup98 in Transcription Regulation in Healthy and Diseased Cells.” <i>Trends in Cell Biology</i>, vol. 23, no. 3, Elsevier, 2013, pp. 112–17, doi:<a href=\"https://doi.org/10.1016/j.tcb.2012.10.013\">10.1016/j.tcb.2012.10.013</a>.","apa":"Franks, T. M., &#38; Hetzer, M. (2013). The role of Nup98 in transcription regulation in healthy and diseased cells. <i>Trends in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcb.2012.10.013\">https://doi.org/10.1016/j.tcb.2012.10.013</a>","ieee":"T. M. Franks and M. Hetzer, “The role of Nup98 in transcription regulation in healthy and diseased cells,” <i>Trends in Cell Biology</i>, vol. 23, no. 3. Elsevier, pp. 112–117, 2013."},"extern":"1","intvolume":"        23","quality_controlled":"1","title":"The role of Nup98 in transcription regulation in healthy and diseased cells","_id":"11083","publication_identifier":{"issn":["0962-8924"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Protein turnover is an effective way of maintaining a functional proteome, as old and potentially damaged polypeptides are destroyed and replaced by newly synthesized copies. An increasing number of intracellular proteins, however, have been identified that evade this turnover process and instead are maintained over a cell's lifetime. This diverse group of long-lived proteins might be particularly prone to accumulation of damage and thus have a crucial role in the functional deterioration of key regulatory processes during ageing."}],"article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"volume":14,"external_id":{"pmid":["23258296"]},"doi":"10.1038/nrm3496","publication":"Nature Reviews Molecular Cell Biology","publisher":"Springer Nature","page":"55-61","pmid":1,"status":"public","date_created":"2022-04-07T07:50:43Z","day":"01","type":"journal_article","date_updated":"2024-10-14T11:24:09Z","publication_status":"published","oa_version":"None","year":"2013","date_published":"2013-01-01T00:00:00Z","article_type":"original","keyword":["Cell Biology","Molecular Biology"],"author":[{"full_name":"Toyama, Brandon H.","last_name":"Toyama","first_name":"Brandon H."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W"}],"citation":{"mla":"Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long, Won’t Prosper.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 14, Springer Nature, 2013, pp. 55–61, doi:<a href=\"https://doi.org/10.1038/nrm3496\">10.1038/nrm3496</a>.","ieee":"B. H. Toyama and M. Hetzer, “Protein homeostasis: Live long, won’t prosper,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 14. Springer Nature, pp. 55–61, 2013.","apa":"Toyama, B. H., &#38; Hetzer, M. (2013). Protein homeostasis: Live long, won’t prosper. <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nrm3496\">https://doi.org/10.1038/nrm3496</a>","ama":"Toyama BH, Hetzer M. Protein homeostasis: Live long, won’t prosper. <i>Nature Reviews Molecular Cell Biology</i>. 2013;14:55-61. doi:<a href=\"https://doi.org/10.1038/nrm3496\">10.1038/nrm3496</a>","ista":"Toyama BH, Hetzer M. 2013. Protein homeostasis: Live long, won’t prosper. Nature Reviews Molecular Cell Biology. 14, 55–61.","chicago":"Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long, Won’t Prosper.” <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1038/nrm3496\">https://doi.org/10.1038/nrm3496</a>.","short":"B.H. Toyama, M. Hetzer, Nature Reviews Molecular Cell Biology 14 (2013) 55–61."},"month":"01","extern":"1","quality_controlled":"1","intvolume":"        14","publication_identifier":{"issn":["1471-0072","1471-0080"]},"_id":"11084","title":"Protein homeostasis: Live long, won't prosper"},{"abstract":[{"lang":"eng","text":"During mitotic exit, missegregated chromosomes can recruit their own nuclear envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to primary nuclei in the same cell, although the two compartments appear to be structurally comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization during interphase due to NE collapse. This disruption of the MN, which is induced by defects in nuclear lamina assembly, drastically reduces nuclear functions and can trigger massive DNA damage. MN disruption is associated with chromatin compaction and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting that disrupted MN could be a useful objective biomarker for genomic instability in solid tumors. Our study shows that NE collapse is a key event underlying MN dysfunction and establishes a link between aberrant NE organization and aneuploidy."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"scopus_import":"1","volume":154,"external_id":{"pmid":["23827674"]},"doi":"10.1016/j.cell.2013.06.007","publication":"Cell","publisher":"Elsevier","pmid":1,"page":"47-60","date_created":"2022-04-07T07:50:51Z","status":"public","date_updated":"2024-10-14T11:24:29Z","day":"03","type":"journal_article","date_published":"2013-07-03T00:00:00Z","publication_status":"published","oa_version":"Published Version","year":"2013","article_type":"original","keyword":["General Biochemistry","Genetics and Molecular Biology"],"author":[{"last_name":"Hatch","first_name":"Emily M.","full_name":"Hatch, Emily M."},{"full_name":"Fischer, Andrew H.","last_name":"Fischer","first_name":"Andrew H."},{"full_name":"Deerinck, Thomas J.","last_name":"Deerinck","first_name":"Thomas J."},{"orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W"}],"issue":"1","citation":{"ama":"Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. Catastrophic nuclear envelope collapse in cancer cell micronuclei. <i>Cell</i>. 2013;154(1):47-60. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.06.007\">10.1016/j.cell.2013.06.007</a>","apa":"Hatch, E. M., Fischer, A. H., Deerinck, T. J., &#38; Hetzer, M. (2013). Catastrophic nuclear envelope collapse in cancer cell micronuclei. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.06.007\">https://doi.org/10.1016/j.cell.2013.06.007</a>","ieee":"E. M. Hatch, A. H. Fischer, T. J. Deerinck, and M. Hetzer, “Catastrophic nuclear envelope collapse in cancer cell micronuclei,” <i>Cell</i>, vol. 154, no. 1. Elsevier, pp. 47–60, 2013.","mla":"Hatch, Emily M., et al. “Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” <i>Cell</i>, vol. 154, no. 1, Elsevier, 2013, pp. 47–60, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.06.007\">10.1016/j.cell.2013.06.007</a>.","short":"E.M. Hatch, A.H. Fischer, T.J. Deerinck, M. Hetzer, Cell 154 (2013) 47–60.","chicago":"Hatch, Emily M., Andrew H. Fischer, Thomas J. Deerinck, and Martin Hetzer. “Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.06.007\">https://doi.org/10.1016/j.cell.2013.06.007</a>.","ista":"Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. 2013. Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell. 154(1), 47–60."},"month":"07","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.06.007","open_access":"1"}],"extern":"1","intvolume":"       154","quality_controlled":"1","_id":"11085","title":"Catastrophic nuclear envelope collapse in cancer cell micronuclei","publication_identifier":{"issn":["0092-8674"]}},{"date_updated":"2024-10-14T11:24:40Z","type":"journal_article","day":"28","status":"public","date_created":"2022-04-07T07:50:59Z","pmid":1,"publisher":"Public Library of Science","publication":"PLoS Genetics","doi":"10.1371/journal.pgen.1003308","external_id":{"pmid":["23468646"]},"volume":9,"language":[{"iso":"eng"}],"article_number":"e1003308","scopus_import":"1","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Dynamic association of NUP98 with the human genome","_id":"11086","publication_identifier":{"issn":["1553-7404"]},"intvolume":"         9","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1003308"}],"extern":"1","oa":1,"month":"02","citation":{"ista":"Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. 2013. Dynamic association of NUP98 with the human genome. PLoS Genetics. 9(2), e1003308.","short":"Y. Liang, T.M. Franks, M.C. Marchetto, F.H. Gage, M. Hetzer, PLoS Genetics 9 (2013).","chicago":"Liang, Yun, Tobias M. Franks, Maria C. Marchetto, Fred H. Gage, and Martin Hetzer. “Dynamic Association of NUP98 with the Human Genome.” <i>PLoS Genetics</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pgen.1003308\">https://doi.org/10.1371/journal.pgen.1003308</a>.","ama":"Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. Dynamic association of NUP98 with the human genome. <i>PLoS Genetics</i>. 2013;9(2). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1003308\">10.1371/journal.pgen.1003308</a>","mla":"Liang, Yun, et al. “Dynamic Association of NUP98 with the Human Genome.” <i>PLoS Genetics</i>, vol. 9, no. 2, e1003308, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1003308\">10.1371/journal.pgen.1003308</a>.","apa":"Liang, Y., Franks, T. M., Marchetto, M. C., Gage, F. H., &#38; Hetzer, M. (2013). Dynamic association of NUP98 with the human genome. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1003308\">https://doi.org/10.1371/journal.pgen.1003308</a>","ieee":"Y. Liang, T. M. Franks, M. C. Marchetto, F. H. Gage, and M. Hetzer, “Dynamic association of NUP98 with the human genome,” <i>PLoS Genetics</i>, vol. 9, no. 2. Public Library of Science, 2013."},"issue":"2","author":[{"full_name":"Liang, Yun","first_name":"Yun","last_name":"Liang"},{"last_name":"Franks","first_name":"Tobias M.","full_name":"Franks, Tobias M."},{"first_name":"Maria C.","last_name":"Marchetto","full_name":"Marchetto, Maria C."},{"last_name":"Gage","first_name":"Fred H.","full_name":"Gage, Fred H."},{"first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"article_type":"original","date_published":"2013-02-28T00:00:00Z","year":"2013","publication_status":"published","oa_version":"Published Version"},{"date_created":"2022-04-07T07:51:08Z","status":"public","date_updated":"2025-12-15T10:02:46Z","day":"29","type":"journal_article","publication":"Cell","publisher":"Elsevier","pmid":1,"page":"971-982","volume":154,"external_id":{"pmid":["23993091"]},"doi":"10.1016/j.cell.2013.07.037","abstract":[{"text":"Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process.","lang":"eng"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":"       154","quality_controlled":"1","_id":"11087","title":"Identification of long-lived proteins reveals exceptional stability of essential cellular structures","publication_identifier":{"issn":["0092-8674"]},"oa":1,"extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2013.07.037"}],"department":[{"_id":"MaHe"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"author":[{"full_name":"Toyama, Brandon H.","first_name":"Brandon H.","last_name":"Toyama"},{"full_name":"Savas, Jeffrey N.","first_name":"Jeffrey N.","last_name":"Savas"},{"last_name":"Park","first_name":"Sung Kyu","full_name":"Park, Sung Kyu"},{"full_name":"Harris, Michael S.","last_name":"Harris","first_name":"Michael S."},{"full_name":"Ingolia, Nicholas T.","first_name":"Nicholas T.","last_name":"Ingolia"},{"first_name":"John R.","last_name":"Yates","full_name":"Yates, John R."},{"last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X"}],"issue":"5","citation":{"ista":"Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. 154(5), 971–982.","short":"B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates, M. Hetzer, Cell 154 (2013) 971–982.","chicago":"Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris, Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">https://doi.org/10.1016/j.cell.2013.07.037</a>.","mla":"Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” <i>Cell</i>, vol. 154, no. 5, Elsevier, 2013, pp. 971–82, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">10.1016/j.cell.2013.07.037</a>.","ieee":"B. H. Toyama <i>et al.</i>, “Identification of long-lived proteins reveals exceptional stability of essential cellular structures,” <i>Cell</i>, vol. 154, no. 5. Elsevier, pp. 971–982, 2013.","apa":"Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates, J. R., &#38; Hetzer, M. (2013). Identification of long-lived proteins reveals exceptional stability of essential cellular structures. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">https://doi.org/10.1016/j.cell.2013.07.037</a>","ama":"Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. <i>Cell</i>. 2013;154(5):971-982. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">10.1016/j.cell.2013.07.037</a>"},"month":"08","date_published":"2013-08-29T00:00:00Z","publication_status":"published","oa_version":"Published Version","year":"2013","article_type":"original"}]