[{"department":[{"_id":"ToBo"},{"_id":"GaTk"}],"date_updated":"2026-04-08T14:21:56Z","author":[{"last_name":"Mitosch","full_name":"Mitosch, Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin"},{"last_name":"Rieckh","full_name":"Rieckh, Georg","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","full_name":"Bollenbach, Tobias","first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (in subscription journal)","type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1016/j.cels.2017.03.001","status":"public","isi":1,"publication_identifier":{"issn":["2405-4712"]},"file":[{"file_id":"5041","date_created":"2018-12-12T10:13:54Z","access_level":"open_access","creator":"system","content_type":"application/pdf","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf","date_updated":"2020-07-14T12:47:35Z","checksum":"04ff20011c3d9a601c514aa999a5fe1a","relation":"main_file","file_size":2438660}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"818"}]},"page":"393 - 403","external_id":{"isi":["000402747300005"]},"month":"04","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","project":[{"grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics"},{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"}],"file_date_updated":"2020-07-14T12:47:35Z","scopus_import":"1","language":[{"iso":"eng"}],"pubrep_id":"901","citation":{"mla":"Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” <i>Cell Systems</i>, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:<a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">10.1016/j.cels.2017.03.001</a>.","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” <i>Cell Systems</i>, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403.","ama":"Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. <i>Cell Systems</i>. 2017;4(4):393-403. doi:<a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">10.1016/j.cels.2017.03.001</a>","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” <i>Cell Systems</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">https://doi.org/10.1016/j.cels.2017.03.001</a>.","apa":"Mitosch, K., Rieckh, G., &#38; Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. <i>Cell Systems</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">https://doi.org/10.1016/j.cels.2017.03.001</a>"},"has_accepted_license":"1","year":"2017","issue":"4","date_published":"2017-04-26T00:00:00Z","oa":1,"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","date_created":"2018-12-11T11:47:48Z","abstract":[{"lang":"eng","text":"Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors."}],"intvolume":"         4","publication":"Cell Systems","ec_funded":1,"title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","publist_id":"7061","volume":4,"publisher":"Cell Press","day":"26","_id":"666","ddc":["576","610"]},{"ec_funded":1,"title":"Algorithmic advances in program analysis and their applications","publist_id":"6828","OA_place":"publisher","ddc":["000"],"supervisor":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"publisher":"Institute of Science and Technology Austria","day":"09","_id":"821","oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"year":"2017","alternative_title":["ISTA Thesis"],"date_published":"2017-08-09T00:00:00Z","degree_awarded":"PhD","date_created":"2018-12-11T11:48:41Z","abstract":[{"text":"This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between  traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method  called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games.","lang":"eng"}],"month":"08","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"page":"418","file":[{"access_level":"open_access","date_created":"2018-12-12T10:11:44Z","file_id":"4900","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:48:10Z","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","file_size":4103115,"relation":"main_file","checksum":"3a3ec003f6ee73f41f82a544d63dfc77"},{"access_level":"closed","date_created":"2019-04-05T07:59:31Z","file_id":"6201","content_type":"application/zip","creator":"dernst","date_updated":"2020-07-14T12:48:10Z","file_name":"2017_thesis_Pavlogiannis.zip","file_size":14744374,"relation":"source_file","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1602"},{"id":"1604","relation":"part_of_dissertation","status":"public"},{"id":"1437","status":"public","relation":"part_of_dissertation"},{"id":"1071","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1607"},{"relation":"part_of_dissertation","status":"public","id":"1714"}]},"acknowledgement":"First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here.  I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta,  Arjun Radhakrishna,  Petr Novontý,  Christian Hilbe,  Jakob Ruess,  Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey.  Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process.","language":[{"iso":"eng"}],"pubrep_id":"854","citation":{"chicago":"Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">https://doi.org/10.15479/AT:ISTA:th_854</a>.","apa":"Pavlogiannis, A. (2017). <i>Algorithmic advances in program analysis and their applications</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">https://doi.org/10.15479/AT:ISTA:th_854</a>","ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">10.15479/AT:ISTA:th_854</a>","mla":"Pavlogiannis, Andreas. <i>Algorithmic Advances in Program Analysis and Their Applications</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">10.15479/AT:ISTA:th_854</a>.","ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017.","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017.","ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria."},"has_accepted_license":"1","corr_author":"1","file_date_updated":"2020-07-14T12:48:10Z","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"}],"author":[{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"}],"article_processing_charge":"No","department":[{"_id":"KrCh"}],"date_updated":"2026-04-08T14:22:17Z","status":"public","type":"dissertation","oa_version":"Published Version","publication_status":"published","doi":"10.15479/AT:ISTA:th_854"},{"oa":1,"date_published":"2017-01-02T00:00:00Z","alternative_title":["ISTA Thesis"],"year":"2017","degree_awarded":"PhD","abstract":[{"text":"This dissertation concerns the automatic verification of probabilistic systems and programs with arrays by statistical and logical methods. Although statistical and logical methods are different in nature, we show that they can be successfully combined for system analysis. In the first part of the dissertation we present a new statistical algorithm for the verification of probabilistic systems with respect to unbounded properties, including linear temporal logic. Our algorithm often performs faster than the previous approaches, and at the same time requires less information about the system. In addition, our method can be generalized to unbounded quantitative properties such as mean-payoff bounds. In the second part, we introduce two techniques for comparing probabilistic systems. Probabilistic systems are typically compared using the notion of equivalence, which requires the systems to have the equal probability of all behaviors. However, this notion is often too strict, since probabilities are typically only empirically estimated, and any imprecision may break the relation between processes. On the one hand, we propose to replace the Boolean notion of equivalence by a quantitative distance of similarity. For this purpose, we introduce a statistical framework for estimating distances between Markov chains based on their simulation runs, and we investigate which distances can be approximated in our framework. On the other hand, we propose to compare systems with respect to a new qualitative logic, which expresses that behaviors occur with probability one or a positive probability. This qualitative analysis is robust with respect to modeling errors and applicable to many domains. In the last part, we present a new quantifier-free logic for integer arrays, which allows us to express counting. Counting properties are prevalent in array-manipulating programs, however they cannot be expressed in the quantified fragments of the theory of arrays. We present a decision procedure for our logic, and provide several complexity results.","lang":"eng"}],"date_created":"2018-12-11T11:50:27Z","OA_place":"publisher","publist_id":"6203","title":"Statistical and logical methods for property checking","ec_funded":1,"ddc":["004","005"],"_id":"1155","day":"02","supervisor":[{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw","last_name":"Daca"}],"article_processing_charge":"No","date_updated":"2026-04-15T10:02:13Z","department":[{"_id":"ToHe"}],"status":"public","doi":"10.15479/AT:ISTA:TH_730","publication_status":"published","oa_version":"Published Version","type":"dissertation","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2063"},{"id":"1093","status":"public","relation":"part_of_dissertation"},{"id":"1391","relation":"part_of_dissertation","status":"public"},{"id":"1234","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1230"},{"id":"1501","status":"public","relation":"part_of_dissertation"},{"id":"1502","status":"public","relation":"part_of_dissertation"},{"id":"2167","status":"public","relation":"part_of_dissertation"}]},"file":[{"file_id":"4880","access_level":"open_access","date_created":"2018-12-12T10:11:26Z","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:44:34Z","file_name":"IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf","relation":"main_file","checksum":"1406a681cb737508234fde34766be2c2","file_size":1028586}],"acknowledgement":" First of all, I want to thank my advisor, prof. Thomas A. Henzinger, for his guidance during my PhD program. I am grateful for the freedom I was given to pursue my research interests, and his continuous support. Working with prof. Henzinger was a truly inspiring experience and taught me what it means to be a scientist. I want to express my gratitude to my collaborators: Nikola Beneš, Krishnendu Chatterjee, Martin Chmelík, Ashutosh Gupta, Willibald Krenn, Jan Kˇretínský, Dejan Nickovic, Andrey Kupriyanov, and Tatjana Petrov. I have learned a great deal from my collaborators, and without their help this thesis would not be possible. In addition, I want to thank the members of my thesis committee: Dirk Beyer, Dejan Nickovic, and Georg Weissenbacher for their advice and reviewing this dissertation. I would especially like to acknowledge the late Helmut Veith, who was a member of my committee. I will remember Helmut for his kindness, enthusiasm, and wit, as well as for being an inspiring scientist. Finally, I would like to thank my colleagues for making my stay at IST such a pleasant experience: Guy Avni, Sergiy Bogomolov, Ventsislav Chonev, Rasmus Ibsen-Jensen, Mirco Giacobbe, Bernhard Kragl, Hui Kong, Petr Novotný, Jan Otop, Andreas Pavlogiannis, Tantjana Petrov, Arjun Radhakrishna, Jakob Ruess, Thorsten Tarrach, as well as other members of groups Henzinger and Chatterjee. ","page":"163","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","citation":{"ama":"Daca P. Statistical and logical methods for property checking. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_730\">10.15479/AT:ISTA:TH_730</a>","chicago":"Daca, Przemyslaw. “Statistical and Logical Methods for Property Checking.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_730\">https://doi.org/10.15479/AT:ISTA:TH_730</a>.","apa":"Daca, P. (2017). <i>Statistical and logical methods for property checking</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_730\">https://doi.org/10.15479/AT:ISTA:TH_730</a>","mla":"Daca, Przemyslaw. <i>Statistical and Logical Methods for Property Checking</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_730\">10.15479/AT:ISTA:TH_730</a>.","ieee":"P. Daca, “Statistical and logical methods for property checking,” Institute of Science and Technology Austria, 2017.","ista":"Daca P. 2017. Statistical and logical methods for property checking. Institute of Science and Technology Austria.","short":"P. Daca, Statistical and Logical Methods for Property Checking, Institute of Science and Technology Austria, 2017."},"language":[{"iso":"eng"}],"pubrep_id":"730","file_date_updated":"2020-07-14T12:44:34Z","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"corr_author":"1"},{"date_updated":"2026-04-16T08:59:01Z","department":[{"_id":"JaMa"}],"author":[{"full_name":"Maas, Jan","last_name":"Maas","first_name":"Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","doi":"10.1007/978-3-319-58002-9_5","publication_status":"published","oa_version":"None","type":"book_chapter","status":"public","page":"159 - 174","publication_identifier":{"isbn":["9783319580012"],"eisbn":["9783319580029"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"10","scopus_import":"1","corr_author":"1","citation":{"ama":"Maas J. Entropic Ricci curvature for discrete spaces. In: Najman L, Romon P, eds. <i>Modern Approaches to Discrete Curvature</i>. Vol 2184. Lecture Notes in Mathematics. Springer; 2017:159-174. doi:<a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">10.1007/978-3-319-58002-9_5</a>","chicago":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” In <i>Modern Approaches to Discrete Curvature</i>, edited by Laurent Najman and Pascal Romon, 2184:159–74. Lecture Notes in Mathematics. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">https://doi.org/10.1007/978-3-319-58002-9_5</a>.","apa":"Maas, J. (2017). Entropic Ricci curvature for discrete spaces. In L. Najman &#38; P. Romon (Eds.), <i>Modern Approaches to Discrete Curvature</i> (Vol. 2184, pp. 159–174). Springer. <a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">https://doi.org/10.1007/978-3-319-58002-9_5</a>","mla":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” <i>Modern Approaches to Discrete Curvature</i>, edited by Laurent Najman and Pascal Romon, vol. 2184, Springer, 2017, pp. 159–74, doi:<a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">10.1007/978-3-319-58002-9_5</a>.","ieee":"J. Maas, “Entropic Ricci curvature for discrete spaces,” in <i>Modern Approaches to Discrete Curvature</i>, vol. 2184, L. Najman and P. Romon, Eds. Springer, 2017, pp. 159–174.","ista":"Maas J. 2017.Entropic Ricci curvature for discrete spaces. In: Modern Approaches to Discrete Curvature. vol. 2184, 159–174.","short":"J. Maas, in:, L. Najman, P. Romon (Eds.), Modern Approaches to Discrete Curvature, Springer, 2017, pp. 159–174."},"language":[{"iso":"eng"}],"date_published":"2017-10-05T00:00:00Z","year":"2017","intvolume":"      2184","abstract":[{"text":"We give a short overview on a recently developed notion of Ricci curvature for discrete spaces. This notion relies on geodesic convexity properties of the relative entropy along geodesics in the space of probability densities, for a metric which is similar to (but different from) the 2-Wasserstein metric. The theory can be considered as a discrete counterpart to the theory of Ricci curvature for geodesic measure spaces developed by Lott–Sturm–Villani.","lang":"eng"}],"date_created":"2018-12-11T11:47:42Z","series_title":"Lecture Notes in Mathematics","quality_controlled":"1","publication":"Modern Approaches to Discrete Curvature","volume":2184,"publist_id":"7123","title":"Entropic Ricci curvature for discrete spaces","_id":"649","day":"05","publisher":"Springer","editor":[{"first_name":"Laurent","last_name":"Najman","full_name":"Najman, Laurent"},{"first_name":"Pascal","last_name":"Romon","full_name":"Romon, Pascal"}]},{"date_published":"2017-06-01T00:00:00Z","year":"2017","issue":"2","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"intvolume":"        78","date_created":"2018-12-11T11:51:27Z","abstract":[{"text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.","lang":"eng"}],"quality_controlled":"1","publication":"Algorithmica","publist_id":"5931","volume":78,"ec_funded":1,"title":"Towards a runtime comparison of natural and artificial evolution","_id":"1336","publisher":"Springer","day":"01","ddc":["576"],"date_updated":"2026-04-16T09:55:33Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"article_processing_charge":"No","author":[{"full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"},{"first_name":"Jorge","last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"last_name":"Trubenova","full_name":"Trubenova, Barbora","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"}],"publication_status":"published","doi":"10.1007/s00453-016-0212-1","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","file":[{"file_id":"4805","access_level":"open_access","date_created":"2018-12-12T10:10:19Z","creator":"system","content_type":"application/pdf","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","date_updated":"2020-07-14T12:44:44Z","relation":"main_file","checksum":"7873f665a0c598ac747c908f34cb14b9","file_size":710206}],"page":"681 - 713","external_id":{"isi":["000400379500013"]},"publication_identifier":{"issn":["0178-4617"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"06","scopus_import":"1","file_date_updated":"2020-07-14T12:44:44Z","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618091"}],"citation":{"mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>.","ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” <i>Algorithmica</i>, vol. 78, no. 2. Springer, pp. 681–713, 2017.","ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. 2017;78(2):681-713. doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>","chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>.","apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>"},"has_accepted_license":"1","language":[{"iso":"eng"}],"pubrep_id":"658"},{"date_updated":"2026-04-16T09:55:44Z","department":[{"_id":"LaEr"}],"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","last_name":"Ajanki","full_name":"Ajanki, Oskari H"},{"last_name":"Erdös","full_name":"Erdös, László","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krüger, Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","first_name":"Torben H"}],"publication_status":"published","doi":"10.1007/s00440-016-0740-2","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","page":"667 - 727","file":[{"access_level":"open_access","date_created":"2018-12-12T10:08:25Z","file_id":"4686","creator":"system","content_type":"application/pdf","file_name":"IST-2017-657-v1+2_s00440-016-0740-2.pdf","date_updated":"2020-07-14T12:44:44Z","file_size":988843,"relation":"main_file","checksum":"29f5a72c3f91e408aeb9e78344973803"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).  ","external_id":{"isi":["000414358400002"]},"publication_identifier":{"issn":["0178-8051"]},"month":"12","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","corr_author":"1","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"file_date_updated":"2020-07-14T12:44:44Z","citation":{"apa":"Ajanki, O. H., Erdös, L., &#38; Krüger, T. H. (2017). Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>.","ama":"Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. 2017;169(3-4):667-727. doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>","ista":"Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 169(3–4), 667–727.","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type matrices,” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4. Springer, pp. 667–727, 2017.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 169 (2017) 667–727.","mla":"Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4, Springer, 2017, pp. 667–727, doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>."},"has_accepted_license":"1","pubrep_id":"657","language":[{"iso":"eng"}],"date_published":"2017-12-01T00:00:00Z","year":"2017","issue":"3-4","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_created":"2018-12-11T11:51:27Z","abstract":[{"lang":"eng","text":"We consider the local eigenvalue distribution of large self-adjoint N×N random matrices H=H∗ with centered independent entries. In contrast to previous works the matrix of variances sij=\\mathbbmE|hij|2 is not assumed to be stochastic. Hence the density of states is not the Wigner semicircle law. Its possible shapes are described in the companion paper (Ajanki et al. in Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z)) solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We prove a local law down to the smallest spectral resolution scale, and bulk universality for both real symmetric and complex hermitian symmetry classes."}],"intvolume":"       169","quality_controlled":"1","publication":"Probability Theory and Related Fields","publist_id":"5930","volume":169,"ec_funded":1,"title":"Universality for general Wigner-type matrices","_id":"1337","publisher":"Springer","day":"01","ddc":["510","530"]},{"date_created":"2018-12-11T11:50:29Z","abstract":[{"text":"We investigate the effect of the electron-hole (e-h) symmetry breaking on d-wave superconductivity induced by non-local effects of correlations in the generalized Hubbard model. The symmetry breaking is introduced in a two-fold manner: by the next-to-nearest neighbor hopping of electrons and by the charge-bond interaction - the off-diagonal term of the Coulomb potential. Both terms lead to a pronounced asymmetry of the superconducting order parameter. The next-to-nearest neighbor hopping enhances superconductivity for h-doping, while diminishes it for e-doping. The charge-bond interaction alone leads to the opposite effect and, additionally, to the kinetic-energy gain upon condensation in the underdoped regime. With both terms included, with similar amplitudes, the height of the superconducting dome and the critical doping remain in favor of h-doping. The influence of the charge-bond interaction on deviations from symmetry of the shape of the gap at the Fermi surface in the momentum space is briefly discussed.","lang":"eng"}],"intvolume":"        29","quality_controlled":"1","date_published":"2017-01-16T00:00:00Z","year":"2017","issue":"8","_id":"1163","publisher":"IOP Publishing","day":"16","publist_id":"6194","volume":29,"ec_funded":1,"title":"Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms","publication":"Journal of Physics: Condensed Matter","isi":1,"status":"public","publication_status":"published","doi":"10.1088/1361-648X/aa532f","type":"journal_article","oa_version":"None","article_processing_charge":"No","author":[{"first_name":"Marcin","last_name":"Wysokiński","full_name":"Wysokiński, Marcin"},{"first_name":"Jan","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1629-3675","last_name":"Kaczmarczyk","full_name":"Kaczmarczyk, Jan"}],"date_updated":"2026-04-16T09:55:16Z","department":[{"_id":"MiLe"}],"citation":{"short":"M. Wysokiński, J. Kaczmarczyk, Journal of Physics: Condensed Matter 29 (2017).","ista":"Wysokiński M, Kaczmarczyk J. 2017. Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics: Condensed Matter. 29(8), 085604.","ieee":"M. Wysokiński and J. Kaczmarczyk, “Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms,” <i>Journal of Physics: Condensed Matter</i>, vol. 29, no. 8. IOP Publishing, 2017.","mla":"Wysokiński, Marcin, and Jan Kaczmarczyk. “Unconventional Superconductivity in Generalized Hubbard Model Role of Electron–Hole Symmetry Breaking Terms.” <i>Journal of Physics: Condensed Matter</i>, vol. 29, no. 8, 085604, IOP Publishing, 2017, doi:<a href=\"https://doi.org/10.1088/1361-648X/aa532f\">10.1088/1361-648X/aa532f</a>.","ama":"Wysokiński M, Kaczmarczyk J. Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms. <i>Journal of Physics: Condensed Matter</i>. 2017;29(8). doi:<a href=\"https://doi.org/10.1088/1361-648X/aa532f\">10.1088/1361-648X/aa532f</a>","apa":"Wysokiński, M., &#38; Kaczmarczyk, J. (2017). Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/aa532f\">https://doi.org/10.1088/1361-648X/aa532f</a>","chicago":"Wysokiński, Marcin, and Jan Kaczmarczyk. “Unconventional Superconductivity in Generalized Hubbard Model Role of Electron–Hole Symmetry Breaking Terms.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2017. <a href=\"https://doi.org/10.1088/1361-648X/aa532f\">https://doi.org/10.1088/1361-648X/aa532f</a>."},"article_number":"085604","language":[{"iso":"eng"}],"scopus_import":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"month":"01","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","external_id":{"isi":["000393955500001"]},"publication_identifier":{"issn":["0953-8984"]}},{"quality_controlled":"1","intvolume":"     10206","abstract":[{"text":"Time-triggered switched networks are a deterministic communication infrastructure used by real-time distributed embedded systems. Due to the criticality of the applications running over them, developers need to ensure that end-to-end communication is dependable and predictable. Traditional approaches assume static networks that are not flexible to changes caused by reconfigurations or, more importantly, faults, which are dealt with in the application using redundancy. We adopt the concept of handling faults in the switches from non-real-time networks while maintaining the required predictability. \r\n\r\nWe study a class of forwarding schemes that can handle various types of failures. We consider probabilistic failures. We study a class of forwarding schemes that can handle various types of failures. We consider probabilistic failures. For a given network with a forwarding scheme and a constant ℓ, we compute the {\\em score} of the scheme, namely the probability (induced by faults) that at least ℓ messages arrive on time. We reduce the scoring problem to a reachability problem on a Markov chain with a &quot;product-like&quot; structure. Its special structure allows us to reason about it symbolically, and reduce the scoring problem to #SAT. Our solution is generic and can be adapted to different networks and other contexts. Also, we show the computational complexity of the scoring problem is #P-complete, and we study methods to estimate the score. We evaluate the effectiveness of our techniques with an implementation. ","lang":"eng"}],"date_created":"2018-12-11T11:50:14Z","year":"2017","alternative_title":["LNCS"],"date_published":"2017-03-31T00:00:00Z","oa":1,"publisher":"Springer","day":"31","_id":"1116","ddc":["000"],"title":"Computing scores of forwarding schemes in switched networks with probabilistic faults","publist_id":"6246","volume":10206,"type":"conference","oa_version":"Submitted Version","publication_status":"published","doi":"10.1007/978-3-662-54580-5_10","status":"public","isi":1,"department":[{"_id":"ToHe"}],"date_updated":"2026-04-16T09:56:24Z","author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni"},{"last_name":"Goel","full_name":"Goel, Shubham","first_name":"Shubham"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"first_name":"Guillermo","last_name":"Rodríguez Navas","full_name":"Rodríguez Navas, Guillermo"}],"article_processing_charge":"No","corr_author":"1","project":[{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211"}],"file_date_updated":"2018-12-12T10:08:37Z","scopus_import":"1","language":[{"iso":"eng"}],"pubrep_id":"758","citation":{"chicago":"Avni, Guy, Shubham Goel, Thomas A Henzinger, and Guillermo Rodríguez Navas. “Computing Scores of Forwarding Schemes in Switched Networks with Probabilistic Faults,” 10206:169–87. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-662-54580-5_10\">https://doi.org/10.1007/978-3-662-54580-5_10</a>.","apa":"Avni, G., Goel, S., Henzinger, T. A., &#38; Rodríguez Navas, G. (2017). Computing scores of forwarding schemes in switched networks with probabilistic faults (Vol. 10206, pp. 169–187). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-662-54580-5_10\">https://doi.org/10.1007/978-3-662-54580-5_10</a>","ama":"Avni G, Goel S, Henzinger TA, Rodríguez Navas G. Computing scores of forwarding schemes in switched networks with probabilistic faults. In: Vol 10206. Springer; 2017:169-187. doi:<a href=\"https://doi.org/10.1007/978-3-662-54580-5_10\">10.1007/978-3-662-54580-5_10</a>","mla":"Avni, Guy, et al. <i>Computing Scores of Forwarding Schemes in Switched Networks with Probabilistic Faults</i>. Vol. 10206, Springer, 2017, pp. 169–87, doi:<a href=\"https://doi.org/10.1007/978-3-662-54580-5_10\">10.1007/978-3-662-54580-5_10</a>.","short":"G. Avni, S. Goel, T.A. Henzinger, G. Rodríguez Navas, in:, Springer, 2017, pp. 169–187.","ista":"Avni G, Goel S, Henzinger TA, Rodríguez Navas G. 2017. Computing scores of forwarding schemes in switched networks with probabilistic faults. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10206, 169–187.","ieee":"G. Avni, S. Goel, T. A. Henzinger, and G. Rodríguez Navas, “Computing scores of forwarding schemes in switched networks with probabilistic faults,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10206, pp. 169–187."},"has_accepted_license":"1","publication_identifier":{"issn":["0302-9743"]},"file":[{"date_updated":"2018-12-12T10:08:37Z","file_name":"IST-2017-758-v1+1_tacas-cr.pdf","relation":"main_file","file_size":321800,"file_id":"4698","access_level":"open_access","date_created":"2018-12-12T10:08:37Z","creator":"system","content_type":"application/pdf"}],"page":"169 - 187","external_id":{"isi":["000440733400010"]},"month":"03","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","conference":{"end_date":"2017-04-29","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2017-04-22","location":"Uppsala, Sweden"}},{"publication_identifier":{"issn":["0178-8051"]},"acknowledgement":"Z. Bao was supported by ERC Advanced Grant RANMAT No. 338804; L. Erdős was partially supported by ERC Advanced Grant RANMAT No. 338804.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to the anonymous referees for careful reading and valuable comments, which helped to improve the organization.","page":"673 - 776","file":[{"file_id":"4665","date_created":"2018-12-12T10:08:05Z","access_level":"open_access","creator":"system","content_type":"application/pdf","file_name":"IST-2016-489-v1+1_s00440-015-0692-y.pdf","date_updated":"2020-07-14T12:45:00Z","checksum":"67afa85ff1e220cbc1f9f477a828513c","relation":"main_file","file_size":1615755}],"external_id":{"isi":["000398842700004"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"04","corr_author":"1","file_date_updated":"2020-07-14T12:45:00Z","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804"}],"scopus_import":"1","language":[{"iso":"eng"}],"pubrep_id":"489","citation":{"chicago":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-015-0692-y\">https://doi.org/10.1007/s00440-015-0692-y</a>.","apa":"Bao, Z., &#38; Erdös, L. (2017). Delocalization for a class of random block band matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-015-0692-y\">https://doi.org/10.1007/s00440-015-0692-y</a>","ama":"Bao Z, Erdös L. Delocalization for a class of random block band matrices. <i>Probability Theory and Related Fields</i>. 2017;167(3-4):673-776. doi:<a href=\"https://doi.org/10.1007/s00440-015-0692-y\">10.1007/s00440-015-0692-y</a>","mla":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” <i>Probability Theory and Related Fields</i>, vol. 167, no. 3–4, Springer, 2017, pp. 673–776, doi:<a href=\"https://doi.org/10.1007/s00440-015-0692-y\">10.1007/s00440-015-0692-y</a>.","ista":"Bao Z, Erdös L. 2017. Delocalization for a class of random block band matrices. Probability Theory and Related Fields. 167(3–4), 673–776.","short":"Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 673–776.","ieee":"Z. Bao and L. Erdös, “Delocalization for a class of random block band matrices,” <i>Probability Theory and Related Fields</i>, vol. 167, no. 3–4. Springer, pp. 673–776, 2017."},"has_accepted_license":"1","department":[{"_id":"LaEr"}],"date_updated":"2026-04-16T09:55:56Z","article_processing_charge":"Yes (via OA deal)","author":[{"orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","full_name":"Bao, Zhigang","last_name":"Bao"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"Erdös, László"}],"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1007/s00440-015-0692-y","status":"public","isi":1,"publication":"Probability Theory and Related Fields","ec_funded":1,"article_type":"original","title":"Delocalization for a class of random block band matrices","volume":167,"publist_id":"5644","publisher":"Springer","day":"01","_id":"1528","ddc":["530"],"year":"2017","issue":"3-4","date_published":"2017-04-01T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"quality_controlled":"1","date_created":"2018-12-11T11:52:32Z","intvolume":"       167","abstract":[{"text":"We consider N×N Hermitian random matrices H consisting of blocks of size M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian in the four moment matching sense, but their distribution varies from block to block to form a block-band structure, with an essential band width M. We show that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys 155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors in the middle of the spectrum are fully delocalized.","lang":"eng"}]},{"doi":"10.1016/j.gde.2017.03.010","publication_status":"published","oa_version":"Submitted Version","type":"journal_article","isi":1,"status":"public","date_updated":"2026-04-16T09:56:36Z","department":[{"_id":"EvBe"}],"author":[{"id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983","first_name":"Krisztina","full_name":"Ötvös, Krisztina","last_name":"Ötvös"},{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"article_processing_charge":"No","scopus_import":"1","file_date_updated":"2019-04-17T08:00:36Z","project":[{"grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","citation":{"ista":"Ötvös K, Benková E. 2017. Spatiotemporal mechanisms of root branching. Current Opinion in Genetics &#38; Development. 45, 82–89.","short":"K. Ötvös, E. Benková, Current Opinion in Genetics &#38; Development 45 (2017) 82–89.","ieee":"K. Ötvös and E. Benková, “Spatiotemporal mechanisms of root branching,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 45. Elsevier, pp. 82–89, 2017.","mla":"Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 45, Elsevier, 2017, pp. 82–89, doi:<a href=\"https://doi.org/10.1016/j.gde.2017.03.010\">10.1016/j.gde.2017.03.010</a>.","ama":"Ötvös K, Benková E. Spatiotemporal mechanisms of root branching. <i>Current Opinion in Genetics &#38; Development</i>. 2017;45:82-89. doi:<a href=\"https://doi.org/10.1016/j.gde.2017.03.010\">10.1016/j.gde.2017.03.010</a>","apa":"Ötvös, K., &#38; Benková, E. (2017). Spatiotemporal mechanisms of root branching. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2017.03.010\">https://doi.org/10.1016/j.gde.2017.03.010</a>","chicago":"Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.gde.2017.03.010\">https://doi.org/10.1016/j.gde.2017.03.010</a>."},"language":[{"iso":"eng"}],"pubrep_id":"1017","external_id":{"pmid":["28391060"],"isi":["000404880400013"]},"page":"82 - 89","file":[{"date_updated":"2019-04-17T08:00:36Z","file_name":"Otvos_Benkova_CurOpDevBiol_2017.pdf","relation":"main_file","file_size":364133,"file_id":"6336","date_created":"2019-04-17T08:00:36Z","access_level":"open_access","success":1,"creator":"dernst","content_type":"application/pdf"}],"publication_identifier":{"issn":["0959-437X"]},"month":"08","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2018-12-11T11:49:38Z","intvolume":"        45","abstract":[{"text":"The fundamental tasks of the root system are, besides anchoring, mediating interactions between plant and soil and providing the plant with water and nutrients. The architecture of the root system is controlled by endogenous mechanisms that constantly integrate environmental signals, such as availability of nutrients and water. Extremely important for efficient soil exploitation and survival under less favorable conditions is the developmental flexibility of the root system that is largely determined by its postembryonic branching capacity. Modulation of initiation and outgrowth of lateral roots provides roots with an exceptional plasticity, allows optimal adjustment to underground heterogeneity, and enables effective soil exploitation and use of resources. Here we discuss recent advances in understanding the molecular mechanisms that shape the plant root system and integrate external cues to adapt to the changing environment.","lang":"eng"}],"quality_controlled":"1","date_published":"2017-08-01T00:00:00Z","year":"2017","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"oa":1,"_id":"1004","day":"01","publisher":"Elsevier","ddc":["575"],"pmid":1,"publication":"Current Opinion in Genetics & Development","volume":45,"publist_id":"6394","title":"Spatiotemporal mechanisms of root branching"},{"month":"05","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"external_id":{"isi":["000400466700011"]},"page":"517 - 533.e3","publication_identifier":{"issn":["0896-6273"]},"citation":{"ieee":"R. J. Beattie <i>et al.</i>, “Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells,” <i>Neuron</i>, vol. 94, no. 3. Cell Press, p. 517–533.e3, 2017.","ista":"Beattie RJ, Postiglione MP, Burnett L, Laukoter S, Streicher C, Pauler F, Xiao G, Klezovitch O, Vasioukhin V, Ghashghaei T, Hippenmeyer S. 2017. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 94(3), 517–533.e3.","short":"R.J. Beattie, M.P. Postiglione, L. Burnett, S. Laukoter, C. Streicher, F. Pauler, G. Xiao, O. Klezovitch, V. Vasioukhin, T. Ghashghaei, S. Hippenmeyer, Neuron 94 (2017) 517–533.e3.","mla":"Beattie, Robert J., et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” <i>Neuron</i>, vol. 94, no. 3, Cell Press, 2017, p. 517–533.e3, doi:<a href=\"https://doi.org/10.1016/j.neuron.2017.04.012\">10.1016/j.neuron.2017.04.012</a>.","apa":"Beattie, R. J., Postiglione, M. P., Burnett, L., Laukoter, S., Streicher, C., Pauler, F., … Hippenmeyer, S. (2017). Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2017.04.012\">https://doi.org/10.1016/j.neuron.2017.04.012</a>","chicago":"Beattie, Robert J, Maria P Postiglione, Laura Burnett, Susanne Laukoter, Carmen Streicher, Florian Pauler, Guanxi Xiao, et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” <i>Neuron</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.neuron.2017.04.012\">https://doi.org/10.1016/j.neuron.2017.04.012</a>.","ama":"Beattie RJ, Postiglione MP, Burnett L, et al. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. <i>Neuron</i>. 2017;94(3):517-533.e3. doi:<a href=\"https://doi.org/10.1016/j.neuron.2017.04.012\">10.1016/j.neuron.2017.04.012</a>"},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7"},{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014"}],"corr_author":"1","article_processing_charge":"No","author":[{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","first_name":"Robert J","full_name":"Beattie, Robert J","last_name":"Beattie"},{"first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","full_name":"Postiglione, Maria P","last_name":"Postiglione"},{"first_name":"Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X","full_name":"Burnett, Laura","last_name":"Burnett"},{"full_name":"Laukoter, Susanne","last_name":"Laukoter","orcid":"0000-0002-7903-3010","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","first_name":"Susanne"},{"last_name":"Streicher","full_name":"Streicher, Carmen","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pauler, Florian","last_name":"Pauler","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"first_name":"Guanxi","full_name":"Xiao, Guanxi","last_name":"Xiao"},{"last_name":"Klezovitch","full_name":"Klezovitch, Olga","first_name":"Olga"},{"first_name":"Valeri","last_name":"Vasioukhin","full_name":"Vasioukhin, Valeri"},{"first_name":"Troy","full_name":"Ghashghaei, Troy","last_name":"Ghashghaei"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-16T09:57:27Z","department":[{"_id":"SiHi"},{"_id":"MaJö"}],"isi":1,"status":"public","doi":"10.1016/j.neuron.2017.04.012","publication_status":"published","oa_version":"None","type":"journal_article","volume":94,"publist_id":"6473","title":"Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells","ec_funded":1,"publication":"Neuron","_id":"944","day":"03","publisher":"Cell Press","date_published":"2017-05-03T00:00:00Z","issue":"3","year":"2017","intvolume":"        94","date_created":"2018-12-11T11:49:20Z","abstract":[{"lang":"eng","text":"The concerted production of neurons and glia by neural stem cells (NSCs) is essential for neural circuit assembly. In the developing cerebral cortex, radial glia progenitors (RGPs) generate nearly all neocortical neurons and certain glia lineages. RGP proliferation behavior shows a high degree of non-stochasticity, thus a deterministic characteristic of neuron and glia production. However, the cellular and molecular mechanisms controlling RGP behavior and proliferation dynamics in neurogenesis and glia generation remain unknown. By using mosaic analysis with double markers (MADM)-based genetic paradigms enabling the sparse and global knockout with unprecedented single-cell resolution, we identified Lgl1 as a critical regulatory component. We uncover Lgl1-dependent tissue-wide community effects required for embryonic cortical neurogenesis and novel cell-autonomous Lgl1 functions controlling RGP-mediated glia genesis and postnatal NSC behavior. These results suggest that NSC-mediated neuron and glia production is tightly regulated through the concerted interplay of sequential Lgl1-dependent global and cell intrinsic mechanisms."}],"quality_controlled":"1"},{"publisher":"Oxford University Press","day":"01","_id":"1016","publication":"Human Molecular Genetics","title":"Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability","publist_id":"6379","volume":26,"quality_controlled":"1","date_created":"2018-12-11T11:49:42Z","intvolume":"        26","abstract":[{"text":"The integrity and dynamic properties of the microtubule cytoskeleton are indispensable for the development of the mammalian brain. Consequently, mutations in the genes that encode the structural component (the α/β-tubulin heterodimer) can give rise to severe, sporadic neurodevelopmental disorders. These are commonly referred to as the tubulinopathies. Here we report the addition of recessive quadrupedalism, also known as Uner Tan syndrome (UTS), to the growing list of diseases caused by tubulin variants. Analysis of a consanguineous UTS family identified a biallelic TUBB2B mutation, resulting in a p.R390Q amino acid substitution. In addition to the identifying quadrupedal locomotion, all three patients showed severe cerebellar hypoplasia. None, however, displayed the basal ganglia malformations typically associated with TUBB2B mutations. Functional analysis of the R390Q substitution revealed that it did not affect the ability of β-tubulin to fold or become assembled into the α/β-heterodimer, nor did it influence the incorporation of mutant-containing heterodimers into microtubule polymers. The 390Q mutation in S. cerevisiae TUB2 did not affect growth under basal conditions, but did result in increased sensitivity to microtubule-depolymerizing drugs, indicative of a mild impact of this mutation on microtubule function. The TUBB2B mutation described here represents an unusual recessive mode of inheritance for missense-mediated tubulinopathies and reinforces the sensitivity of the developing cerebellum to microtubule defects.","lang":"eng"}],"year":"2017","issue":"2","date_published":"2017-01-01T00:00:00Z","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"ama":"Breuss M, Nguyen T, Srivatsan A, et al. Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. <i>Human Molecular Genetics</i>. 2017;26(2):258-269. doi:<a href=\"https://doi.org/10.1093/hmg/ddw383\">10.1093/hmg/ddw383</a>","apa":"Breuss, M., Nguyen, T., Srivatsan, A., Leca, I., Tian, G., Fritz, T., … Gleeson, J. (2017). Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. <i>Human Molecular Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/hmg/ddw383\">https://doi.org/10.1093/hmg/ddw383</a>","chicago":"Breuss, Martin, Thai Nguyen, Anjana Srivatsan, Ines Leca, Guoling Tian, Tanja Fritz, Andi H Hansen, et al. “Uner Tan Syndrome Caused by a Homozygous TUBB2B Mutation Affecting Microtubule Stability.” <i>Human Molecular Genetics</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/hmg/ddw383\">https://doi.org/10.1093/hmg/ddw383</a>.","ista":"Breuss M, Nguyen T, Srivatsan A, Leca I, Tian G, Fritz T, Hansen AH, Musaev D, Mcevoy Venneri J, Kiely J, Rosti R, Scott E, Tan U, Kolodner R, Cowan N, Keays D, Gleeson J. 2017. Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability. Human Molecular Genetics. 26(2), 258–269.","short":"M. Breuss, T. Nguyen, A. Srivatsan, I. Leca, G. Tian, T. Fritz, A.H. Hansen, D. Musaev, J. Mcevoy Venneri, J. Kiely, R. Rosti, E. Scott, U. Tan, R. Kolodner, N. Cowan, D. Keays, J. Gleeson, Human Molecular Genetics 26 (2017) 258–269.","ieee":"M. Breuss <i>et al.</i>, “Uner Tan syndrome caused by a homozygous TUBB2B mutation affecting microtubule stability,” <i>Human Molecular Genetics</i>, vol. 26, no. 2. Oxford University Press, pp. 258–269, 2017.","mla":"Breuss, Martin, et al. “Uner Tan Syndrome Caused by a Homozygous TUBB2B Mutation Affecting Microtubule Stability.” <i>Human Molecular Genetics</i>, vol. 26, no. 2, Oxford University Press, 2017, pp. 258–69, doi:<a href=\"https://doi.org/10.1093/hmg/ddw383\">10.1093/hmg/ddw383</a>."},"publication_identifier":{"issn":["0964-6906"]},"page":"258 - 269","external_id":{"isi":["000397066400002"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"01","type":"journal_article","oa_version":"None","publication_status":"published","doi":"10.1093/hmg/ddw383","status":"public","isi":1,"department":[{"_id":"SiHi"}],"date_updated":"2026-04-16T09:56:51Z","author":[{"last_name":"Breuss","full_name":"Breuss, Martin","first_name":"Martin"},{"last_name":"Nguyen","full_name":"Nguyen, Thai","first_name":"Thai"},{"first_name":"Anjana","full_name":"Srivatsan, Anjana","last_name":"Srivatsan"},{"first_name":"Ines","last_name":"Leca","full_name":"Leca, Ines"},{"first_name":"Guoling","full_name":"Tian, Guoling","last_name":"Tian"},{"last_name":"Fritz","full_name":"Fritz, Tanja","first_name":"Tanja"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","full_name":"Hansen, Andi H","last_name":"Hansen"},{"first_name":"Damir","full_name":"Musaev, Damir","last_name":"Musaev"},{"full_name":"Mcevoy Venneri, Jennifer","last_name":"Mcevoy Venneri","first_name":"Jennifer"},{"last_name":"Kiely","full_name":"Kiely, James","first_name":"James"},{"first_name":"Rasim","full_name":"Rosti, Rasim","last_name":"Rosti"},{"last_name":"Scott","full_name":"Scott, Eric","first_name":"Eric"},{"full_name":"Tan, Uner","last_name":"Tan","first_name":"Uner"},{"first_name":"Richard","full_name":"Kolodner, Richard","last_name":"Kolodner"},{"last_name":"Cowan","full_name":"Cowan, Nicholas","first_name":"Nicholas"},{"full_name":"Keays, David","last_name":"Keays","first_name":"David"},{"last_name":"Gleeson","full_name":"Gleeson, Joseph","first_name":"Joseph"}],"article_processing_charge":"No"},{"author":[{"first_name":"Viviana","full_name":"Agus, Viviana","last_name":"Agus"},{"last_name":"Janovjak","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L"}],"article_processing_charge":"No","department":[{"_id":"HaJa"}],"date_updated":"2026-04-16T09:57:03Z","status":"public","isi":1,"type":"journal_article","oa_version":"None","publication_status":"published","doi":"10.1016/j.copbio.2017.02.006","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"12","publication_identifier":{"issn":["0958-1669"]},"acknowledgement":"This work was supported by grants of the European Union Seventh Framework Programme (CIG-303564), the Human Frontier Science Program (RGY0084_2012), and the Austrian Science Fund FWF (W1232 MolecularDrugTargets).","page":"8 - 14","external_id":{"isi":["000418313200003"]},"language":[{"iso":"eng"}],"citation":{"mla":"Agus, Viviana, and Harald L. Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” <i>Current Opinion in Biotechnology</i>, vol. 48, Elsevier, 2017, pp. 8–14, doi:<a href=\"https://doi.org/10.1016/j.copbio.2017.02.006\">10.1016/j.copbio.2017.02.006</a>.","short":"V. Agus, H.L. Janovjak, Current Opinion in Biotechnology 48 (2017) 8–14.","ieee":"V. Agus and H. L. Janovjak, “Optogenetic methods in drug screening: Technologies and applications,” <i>Current Opinion in Biotechnology</i>, vol. 48. Elsevier, pp. 8–14, 2017.","ista":"Agus V, Janovjak HL. 2017. Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. 48, 8–14.","ama":"Agus V, Janovjak HL. Optogenetic methods in drug screening: Technologies and applications. <i>Current Opinion in Biotechnology</i>. 2017;48:8-14. doi:<a href=\"https://doi.org/10.1016/j.copbio.2017.02.006\">10.1016/j.copbio.2017.02.006</a>","chicago":"Agus, Viviana, and Harald L Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” <i>Current Opinion in Biotechnology</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.copbio.2017.02.006\">https://doi.org/10.1016/j.copbio.2017.02.006</a>.","apa":"Agus, V., &#38; Janovjak, H. L. (2017). Optogenetic methods in drug screening: Technologies and applications. <i>Current Opinion in Biotechnology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.copbio.2017.02.006\">https://doi.org/10.1016/j.copbio.2017.02.006</a>"},"corr_author":"1","project":[{"grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"},{"grant_number":"303564","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232-B24","call_identifier":"FWF","_id":"255A6082-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"scopus_import":"1","year":"2017","date_published":"2017-12-01T00:00:00Z","quality_controlled":"1","date_created":"2018-12-11T11:49:45Z","intvolume":"        48","abstract":[{"lang":"eng","text":"The optogenetic revolution enabled spatially-precise and temporally-precise control over protein function, signaling pathway activation, and animal behavior with tremendous success in the dissection of signaling networks and neural circuits. Very recently, optogenetic methods have been paired with optical reporters in novel drug screening platforms. In these all-optical platforms, light remotely activated ion channels and kinases thereby obviating the use of electrophysiology or reagents. Consequences were remarkable operational simplicity, throughput, and cost-effectiveness that culminated in the identification of new drug candidates. These blueprints for all-optical assays also revealed potential pitfalls and inspire all-optical variants of other screens, such as those that aim at better understanding dynamic drug action or orphan protein function."}],"ec_funded":1,"article_type":"original","title":"Optogenetic methods in drug screening: Technologies and applications","volume":48,"publist_id":"6365","publication":"Current Opinion in Biotechnology","publisher":"Elsevier","day":"01","_id":"1026"},{"page":"16 - 31","external_id":{"isi":["000398059200002"]},"publication_identifier":{"issn":[" 0950-382X"]},"month":"04","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","citation":{"ama":"Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. <i>Molecular Microbiology</i>. 2017;104(1):16-31. doi:<a href=\"https://doi.org/10.1111/mmi.13597\">10.1111/mmi.13597</a>","chicago":"Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” <i>Molecular Microbiology</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/mmi.13597\">https://doi.org/10.1111/mmi.13597</a>.","apa":"Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., &#38; Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. <i>Molecular Microbiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mmi.13597\">https://doi.org/10.1111/mmi.13597</a>","mla":"Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” <i>Molecular Microbiology</i>, vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:<a href=\"https://doi.org/10.1111/mmi.13597\">10.1111/mmi.13597</a>.","ieee":"C. Fang <i>et al.</i>, “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” <i>Molecular Microbiology</i>, vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017.","short":"C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31.","ista":"Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T. 2017. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31."},"language":[{"iso":"eng"}],"date_updated":"2026-04-16T09:56:09Z","department":[{"_id":"CaGu"}],"article_processing_charge":"No","author":[{"last_name":"Fang","full_name":"Fang, Chong","first_name":"Chong"},{"full_name":"Nagy-Staron, Anna A","last_name":"Nagy-Staron","first_name":"Anna A","orcid":"0000-0002-1391-8377","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grafe, Martin","last_name":"Grafe","first_name":"Martin"},{"full_name":"Heermann, Ralf","last_name":"Heermann","first_name":"Ralf"},{"first_name":"Kirsten","full_name":"Jung, Kirsten","last_name":"Jung"},{"last_name":"Gebhard","full_name":"Gebhard, Susanne","first_name":"Susanne"},{"last_name":"Mascher","full_name":"Mascher, Thorsten","first_name":"Thorsten"}],"publication_status":"published","doi":"10.1111/mmi.13597","type":"journal_article","oa_version":"None","isi":1,"status":"public","publication":"Molecular Microbiology","publist_id":"6294","volume":104,"title":"Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis","_id":"1084","publisher":"Wiley-Blackwell","day":"01","date_published":"2017-04-01T00:00:00Z","year":"2017","issue":"1","abstract":[{"text":"BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities.","lang":"eng"}],"intvolume":"       104","date_created":"2018-12-11T11:50:03Z","quality_controlled":"1"},{"isi":1,"status":"public","doi":"10.1016/j.comgeo.2017.07.002","publication_status":"published","oa_version":"Submitted Version","type":"journal_article","article_processing_charge":"No","author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"},{"first_name":"Hossein","full_name":"Mojarrad, Hossein","last_name":"Mojarrad"},{"first_name":"Márton","full_name":"Naszódi, Márton","last_name":"Naszódi"},{"last_name":"Solymosi","full_name":"Solymosi, József","first_name":"József"},{"first_name":"Sebastian","last_name":"Stich","full_name":"Stich, Sebastian"},{"full_name":"Szedlák, May","last_name":"Szedlák","first_name":"May"}],"date_updated":"2026-04-16T09:57:17Z","department":[{"_id":"UlWa"}],"citation":{"mla":"Fulek, Radoslav, et al. “On the Existence of Ordinary Triangles.” <i>Computational Geometry: Theory and Applications</i>, vol. 66, Elsevier, 2017, pp. 28–31, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">10.1016/j.comgeo.2017.07.002</a>.","ieee":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, and M. Szedlák, “On the existence of ordinary triangles,” <i>Computational Geometry: Theory and Applications</i>, vol. 66. Elsevier, pp. 28–31, 2017.","ista":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. 2017. On the existence of ordinary triangles. Computational Geometry: Theory and Applications. 66, 28–31.","short":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, M. Szedlák, Computational Geometry: Theory and Applications 66 (2017) 28–31.","chicago":"Fulek, Radoslav, Hossein Mojarrad, Márton Naszódi, József Solymosi, Sebastian Stich, and May Szedlák. “On the Existence of Ordinary Triangles.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">https://doi.org/10.1016/j.comgeo.2017.07.002</a>.","apa":"Fulek, R., Mojarrad, H., Naszódi, M., Solymosi, J., Stich, S., &#38; Szedlák, M. (2017). On the existence of ordinary triangles. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">https://doi.org/10.1016/j.comgeo.2017.07.002</a>","ama":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. On the existence of ordinary triangles. <i>Computational Geometry: Theory and Applications</i>. 2017;66:28-31. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">10.1016/j.comgeo.2017.07.002</a>"},"language":[{"iso":"eng"}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"month":"01","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","external_id":{"isi":["000412039700003"],"arxiv":["1701.08183"]},"page":"28 - 31","publication_identifier":{"issn":["0925-7721"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1701.08183"}],"intvolume":"        66","date_created":"2018-12-11T11:48:32Z","abstract":[{"text":"Let P be a finite point set in the plane. A cordinary triangle in P is a subset of P consisting of three non-collinear points such that each of the three lines determined by the three points contains at most c points of P . Motivated by a question of Erdös, and answering a question of de Zeeuw, we prove that there exists a constant c &gt; 0such that P contains a c-ordinary triangle, provided that P is not contained in the union of two lines. Furthermore, the number of c-ordinary triangles in P is Ω(| P |). ","lang":"eng"}],"quality_controlled":"1","oa":1,"date_published":"2017-01-01T00:00:00Z","year":"2017","_id":"793","day":"01","publisher":"Elsevier","arxiv":1,"volume":66,"publist_id":"6861","title":"On the existence of ordinary triangles","ec_funded":1,"publication":"Computational Geometry: Theory and Applications"},{"abstract":[{"text":"While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera.","lang":"eng"}],"intvolume":"        34","date_created":"2018-12-11T11:49:20Z","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2017-07-06T00:00:00Z","issue":"10","year":"2017","ddc":["570","576"],"_id":"945","day":"06","publisher":"Oxford University Press","publist_id":"6472","volume":34,"title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","publication":"Molecular Biology and Evolution","isi":1,"status":"public","doi":"10.1093/molbev/msx190","publication_status":"published","oa_version":"Published Version","type":"journal_article","author":[{"last_name":"Huylmans","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K"},{"last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (in subscription journal)","date_updated":"2026-04-16T09:58:19Z","department":[{"_id":"BeVi"}],"has_accepted_license":"1","citation":{"ama":"Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. 2017;34(10):2637-2649. doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>","chicago":"Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>.","apa":"Huylmans, A. K., Macon, A., &#38; Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>","mla":"Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>.","ista":"Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649.","short":"A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649.","ieee":"A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017."},"pubrep_id":"848","language":[{"iso":"eng"}],"scopus_import":"1","project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"file_date_updated":"2020-07-14T12:48:15Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"07","external_id":{"isi":["000411814800016"]},"file":[{"date_updated":"2020-07-14T12:48:15Z","file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","checksum":"009fd68043211d645ceb9d1de28274f2","relation":"main_file","file_size":462863,"file_id":"4810","date_created":"2018-12-12T10:10:23Z","access_level":"open_access","creator":"system","content_type":"application/pdf"}],"page":"2637 - 2649","publication_identifier":{"issn":["0737-4038"]}},{"publication_identifier":{"issn":["0146-0404"]},"external_id":{"isi":["000426781300012"]},"page":"6091 - 6104","file":[{"file_name":"IST-2018-920-v1+1_i1552-5783-58-14-6091.pdf","date_updated":"2020-07-14T12:47:04Z","file_size":2955559,"checksum":"d7a7b6f1fa9211a04e5e65634a0265d9","relation":"main_file","date_created":"2018-12-12T10:17:53Z","access_level":"open_access","file_id":"5311","content_type":"application/pdf","creator":"system"}],"month":"12","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2020-07-14T12:47:04Z","scopus_import":"1","pubrep_id":"920","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"apa":"Nickells, R., Schmitt, H., Maes, M. E., &#38; Schlamp, C. (2017). AAV2 mediated transduction of the mouse retina after optic nerve injury. <i>Investigative Ophthalmology and Visual Science</i>. Association for Research in Vision and Ophthalmology. <a href=\"https://doi.org/10.1167/iovs.17-22634\">https://doi.org/10.1167/iovs.17-22634</a>","chicago":"Nickells, Robert, Heather Schmitt, Margaret E Maes, and Cassandra Schlamp. “AAV2 Mediated Transduction of the Mouse Retina after Optic Nerve Injury.” <i>Investigative Ophthalmology and Visual Science</i>. Association for Research in Vision and Ophthalmology, 2017. <a href=\"https://doi.org/10.1167/iovs.17-22634\">https://doi.org/10.1167/iovs.17-22634</a>.","ama":"Nickells R, Schmitt H, Maes ME, Schlamp C. AAV2 mediated transduction of the mouse retina after optic nerve injury. <i>Investigative Ophthalmology and Visual Science</i>. 2017;58(14):6091-6104. doi:<a href=\"https://doi.org/10.1167/iovs.17-22634\">10.1167/iovs.17-22634</a>","short":"R. Nickells, H. Schmitt, M.E. Maes, C. Schlamp, Investigative Ophthalmology and Visual Science 58 (2017) 6091–6104.","ista":"Nickells R, Schmitt H, Maes ME, Schlamp C. 2017. AAV2 mediated transduction of the mouse retina after optic nerve injury. Investigative Ophthalmology and Visual Science. 58(14), 6091–6104.","ieee":"R. Nickells, H. Schmitt, M. E. Maes, and C. Schlamp, “AAV2 mediated transduction of the mouse retina after optic nerve injury,” <i>Investigative Ophthalmology and Visual Science</i>, vol. 58, no. 14. Association for Research in Vision and Ophthalmology, pp. 6091–6104, 2017.","mla":"Nickells, Robert, et al. “AAV2 Mediated Transduction of the Mouse Retina after Optic Nerve Injury.” <i>Investigative Ophthalmology and Visual Science</i>, vol. 58, no. 14, Association for Research in Vision and Ophthalmology, 2017, pp. 6091–104, doi:<a href=\"https://doi.org/10.1167/iovs.17-22634\">10.1167/iovs.17-22634</a>."},"department":[{"_id":"SaSi"}],"date_updated":"2026-04-16T09:58:51Z","author":[{"first_name":"Robert","last_name":"Nickells","full_name":"Nickells, Robert"},{"last_name":"Schmitt","full_name":"Schmitt, Heather","first_name":"Heather"},{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","first_name":"Margaret E","full_name":"Maes, Margaret E","last_name":"Maes"},{"full_name":"Schlamp, Cassandra","last_name":"Schlamp","first_name":"Cassandra"}],"article_processing_charge":"No","oa_version":"Published Version","type":"journal_article","doi":"10.1167/iovs.17-22634","publication_status":"published","status":"public","isi":1,"publication":"Investigative Ophthalmology and Visual Science","title":"AAV2 mediated transduction of the mouse retina after optic nerve injury","volume":58,"publist_id":"7254","day":"14","publisher":"Association for Research in Vision and Ophthalmology","_id":"557","ddc":["576"],"issue":"14","year":"2017","date_published":"2017-12-14T00:00:00Z","oa":1,"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","date_created":"2018-12-11T11:47:10Z","intvolume":"        58","abstract":[{"lang":"eng","text":"PURPOSE. Gene therapy of retinal ganglion cells (RGCs) has promise as a powerful therapeutic for the rescue and regeneration of these cells after optic nerve damage. However, early after damage, RGCs undergo atrophic changes, including gene silencing. It is not known if these changes will deleteriously affect transduction and transgene expression, or if the therapeutic protein can influence reactivation of the endogenous genome. METHODS. Double-transgenic mice carrying a Rosa26-(LoxP)-tdTomato reporter, and a mutant allele for the proapoptotic Bax gene were reared. The Bax mutant blocks apoptosis, but RGCs still exhibit nuclear atrophy and gene silencing. At times ranging from 1 hour to 4 weeks after optic nerve crush (ONC), eyes received an intravitreal injection of AAV2 virus carrying the Cre recombinase. Successful transduction was monitored by expression of the tdTomato reporter. Immunostaining was used to localize tdTomato expression in select cell types. RESULTS. Successful transduction of RGCs was achieved at all time points after ONC using AAV2 expressing Cre from the phosphoglycerate kinase (Pgk) promoter, but not the CMV promoter. ONC promoted an increase in the transduction of cell types in the inner nuclear layer, including Müller cells and rod bipolar neurons. There was minimal evidence of transduction of amacrine cells and astrocytes in the inner retina or optic nerve. CONCLUSIONS. Damaged RGCs can be transduced and at least some endogenous genes can be subsequently activated. Optic nerve damage may change retinal architecture to allow greater penetration of an AAV2 virus to transduce several additional cell types in the inner nuclear layer."}]},{"isi":1,"status":"public","publication_status":"published","doi":"10.1145/3072959.3073678","type":"journal_article","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Jeschke","full_name":"Jeschke, Stefan","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4330-8884"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan"}],"date_updated":"2026-04-16T09:58:39Z","department":[{"_id":"ChWo"}],"citation":{"chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” <i>ACM Transactions on Graphics</i>. ACM, 2017. <a href=\"https://doi.org/10.1145/3072959.3073678\">https://doi.org/10.1145/3072959.3073678</a>.","apa":"Jeschke, S., &#38; Wojtan, C. (2017). Water wave packets. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3072959.3073678\">https://doi.org/10.1145/3072959.3073678</a>","ama":"Jeschke S, Wojtan C. Water wave packets. <i>ACM Transactions on Graphics</i>. 2017;36(4). doi:<a href=\"https://doi.org/10.1145/3072959.3073678\">10.1145/3072959.3073678</a>","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” <i>ACM Transactions on Graphics</i>, vol. 36, no. 4, 103, ACM, 2017, doi:<a href=\"https://doi.org/10.1145/3072959.3073678\">10.1145/3072959.3073678</a>.","ista":"Jeschke S, Wojtan C. 2017. Water wave packets. ACM Transactions on Graphics. 36(4), 103.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 36 (2017).","ieee":"S. Jeschke and C. Wojtan, “Water wave packets,” <i>ACM Transactions on Graphics</i>, vol. 36, no. 4. ACM, 2017."},"has_accepted_license":"1","article_number":"103","language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2020-07-14T12:46:34Z","project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176"}],"month":"07","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_id":"7359","access_level":"open_access","date_created":"2020-01-24T09:32:35Z","creator":"wojtan","content_type":"application/pdf","file_name":"wavepackets_final.pdf","date_updated":"2020-07-14T12:46:34Z","relation":"main_file","checksum":"82a3b2bfeee4ddef16ecc21675d1a48a","file_size":13131683}],"external_id":{"isi":["000406432100071"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["0730-0301"]},"abstract":[{"text":"This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios.","lang":"eng"}],"date_created":"2018-12-11T11:46:39Z","intvolume":"        36","quality_controlled":"1","oa":1,"date_published":"2017-07-01T00:00:00Z","year":"2017","issue":"4","ddc":["006"],"_id":"470","publisher":"ACM","day":"01","volume":36,"publist_id":"7350","ec_funded":1,"article_type":"original","title":"Water wave packets","publication":"ACM Transactions on Graphics"},{"has_accepted_license":"1","citation":{"short":"A. Kicheva, N. Rivron, Development 144 (2017) 733–736.","ieee":"A. Kicheva and N. Rivron, “Creating to understand – developmental biology meets engineering in Paris,” <i>Development</i>, vol. 144, no. 5. Company of Biologists, pp. 733–736, 2017.","ista":"Kicheva A, Rivron N. 2017. Creating to understand – developmental biology meets engineering in Paris. Development. 144(5), 733–736.","mla":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” <i>Development</i>, vol. 144, no. 5, Company of Biologists, 2017, pp. 733–36, doi:<a href=\"https://doi.org/10.1242/dev.144915\">10.1242/dev.144915</a>.","apa":"Kicheva, A., &#38; Rivron, N. (2017). Creating to understand – developmental biology meets engineering in Paris. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.144915\">https://doi.org/10.1242/dev.144915</a>","chicago":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” <i>Development</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/dev.144915\">https://doi.org/10.1242/dev.144915</a>.","ama":"Kicheva A, Rivron N. Creating to understand – developmental biology meets engineering in Paris. <i>Development</i>. 2017;144(5):733-736. doi:<a href=\"https://doi.org/10.1242/dev.144915\">10.1242/dev.144915</a>"},"language":[{"iso":"eng"}],"pubrep_id":"987","scopus_import":"1","file_date_updated":"2020-07-14T12:47:33Z","project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","grant_number":"680037"}],"corr_author":"1","month":"03","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","external_id":{"isi":["000395650100001"]},"file":[{"checksum":"eef22a0f42a55b232cb2d1188a2322cb","relation":"main_file","file_size":228206,"file_name":"IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf","date_updated":"2020-07-14T12:47:33Z","content_type":"application/pdf","creator":"system","file_id":"5139","date_created":"2018-12-12T10:15:20Z","access_level":"open_access"}],"page":"733 - 736","publication_identifier":{"issn":["0950-1991"]},"isi":1,"status":"public","doi":"10.1242/dev.144915","publication_status":"published","oa_version":"Submitted Version","type":"journal_article","author":[{"full_name":"Kicheva, Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"},{"last_name":"Rivron","full_name":"Rivron, Nicolas","first_name":"Nicolas"}],"article_processing_charge":"No","date_updated":"2026-04-16T09:59:52Z","department":[{"_id":"AnKi"}],"ddc":["571"],"_id":"654","day":"01","publisher":"Company of Biologists","volume":144,"publist_id":"7089","title":"Creating to understand – developmental biology meets engineering in Paris","ec_funded":1,"publication":"Development","abstract":[{"text":"In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations.","lang":"eng"}],"date_created":"2018-12-11T11:47:44Z","intvolume":"       144","quality_controlled":"1","oa":1,"date_published":"2017-03-01T00:00:00Z","issue":"5","year":"2017"},{"department":[{"_id":"GaNo"}],"date_updated":"2026-04-16T09:59:22Z","author":[{"full_name":"Hill Yardin, Elisa","last_name":"Hill Yardin","first_name":"Elisa"},{"last_name":"Mckeown","full_name":"Mckeown, Sonja","first_name":"Sonja"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino"},{"last_name":"Grabrucker","full_name":"Grabrucker, Andreas","first_name":"Andreas"}],"article_processing_charge":"No","oa_version":"None","type":"book_chapter","doi":"10.1007/978-3-319-52498-6_9","publication_status":"published","status":"public","isi":1,"publication_identifier":{"isbn":["9783319524962"],"issn":["0301-5556"]},"external_id":{"isi":["000443802500010"]},"page":"159 - 187","month":"05","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"apa":"Hill Yardin, E., Mckeown, S., Novarino, G., &#38; Grabrucker, A. (2017). Extracerebral dysfunction in animal models of autism spectrum disorder. In M. Schmeisser &#38; T. Boekers (Eds.), <i>Translational Anatomy and Cell Biology of Autism Spectrum Disorder</i> (Vol. 224, pp. 159–187). Springer. <a href=\"https://doi.org/10.1007/978-3-319-52498-6_9\">https://doi.org/10.1007/978-3-319-52498-6_9</a>","chicago":"Hill Yardin, Elisa, Sonja Mckeown, Gaia Novarino, and Andreas Grabrucker. “Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” In <i>Translational Anatomy and Cell Biology of Autism Spectrum Disorder</i>, edited by Michael Schmeisser and Tobias Boekers, 224:159–87. Advances in Anatomy Embryology and Cell Biology. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-52498-6_9\">https://doi.org/10.1007/978-3-319-52498-6_9</a>.","ama":"Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. Extracerebral dysfunction in animal models of autism spectrum disorder. In: Schmeisser M, Boekers T, eds. <i>Translational Anatomy and Cell Biology of Autism Spectrum Disorder</i>. Vol 224. Advances in Anatomy Embryology and Cell Biology. Springer; 2017:159-187. doi:<a href=\"https://doi.org/10.1007/978-3-319-52498-6_9\">10.1007/978-3-319-52498-6_9</a>","ista":"Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. 2017.Extracerebral dysfunction in animal models of autism spectrum disorder. In: Translational Anatomy and Cell Biology of Autism Spectrum Disorder. ADVSANAT, vol. 224, 159–187.","short":"E. Hill Yardin, S. Mckeown, G. Novarino, A. Grabrucker, in:, M. Schmeisser, T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder, Springer, 2017, pp. 159–187.","ieee":"E. Hill Yardin, S. Mckeown, G. Novarino, and A. Grabrucker, “Extracerebral dysfunction in animal models of autism spectrum disorder,” in <i>Translational Anatomy and Cell Biology of Autism Spectrum Disorder</i>, vol. 224, M. Schmeisser and T. Boekers, Eds. Springer, 2017, pp. 159–187.","mla":"Hill Yardin, Elisa, et al. “Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” <i>Translational Anatomy and Cell Biology of Autism Spectrum Disorder</i>, edited by Michael Schmeisser and Tobias Boekers, vol. 224, Springer, 2017, pp. 159–87, doi:<a href=\"https://doi.org/10.1007/978-3-319-52498-6_9\">10.1007/978-3-319-52498-6_9</a>."},"alternative_title":["ADVSANAT"],"year":"2017","date_published":"2017-05-28T00:00:00Z","series_title":"Advances in Anatomy Embryology and Cell Biology","quality_controlled":"1","abstract":[{"text":"Genetic factors might be largely responsible for the development of autism spectrum disorder (ASD) that alone or in combination with specific environmental risk factors trigger the pathology. Multiple mutations identified in ASD patients that impair synaptic function in the central nervous system are well studied in animal models. How these mutations might interact with other risk factors is not fully understood though. Additionally, how systems outside of the brain are altered in the context of ASD is an emerging area of research. Extracerebral influences on the physiology could begin in utero and contribute to changes in the brain and in the development of other body systems and further lead to epigenetic changes. Therefore, multiple recent studies have aimed at elucidating the role of gene-environment interactions in ASD. Here we provide an overview on the extracerebral systems that might play an important associative role in ASD and review evidence regarding the potential roles of inflammation, trace metals, metabolism, genetic susceptibility, enteric nervous system function and the microbiota of the gastrointestinal (GI) tract on the development of endophenotypes in animal models of ASD. By influencing environmental conditions, it might be possible to reduce or limit the severity of ASD pathology.","lang":"eng"}],"intvolume":"       224","date_created":"2018-12-11T11:47:33Z","publication":"Translational Anatomy and Cell Biology of Autism Spectrum Disorder","title":"Extracerebral dysfunction in animal models of autism spectrum disorder","volume":224,"publist_id":"7177","day":"28","publisher":"Springer","_id":"623","editor":[{"last_name":"Schmeisser","full_name":"Schmeisser, Michael","first_name":"Michael"},{"first_name":"Tobias","full_name":"Boekers, Tobias","last_name":"Boekers"}]}]