[{"date_published":"2015-08-01T00:00:00Z","abstract":[{"text":"Motivated by biological questions, we study configurations of equal-sized disks in the Euclidean plane that neither pack nor cover. Measuring the quality by the probability that a random point lies in exactly one disk, we show that the regular hexagonal grid gives the maximum among lattice configurations. ","lang":"eng"}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-11T06:38:01Z","publist_id":"5684","external_id":{"arxiv":["1505.03402"]},"year":"2015","citation":{"chicago":"Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed Disk Packing.” In <i>Proceedings of the 27th Canadian Conference on Computational Geometry</i>, 2015–August:128–35. Queen’s University, 2015.","mla":"Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” <i>Proceedings of the 27th Canadian Conference on Computational Geometry</i>, vol. 2015–August, Queen’s University, 2015, pp. 128–35.","short":"H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135.","ista":"Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry vol. 2015–August, 128–135.","ama":"Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: <i>Proceedings of the 27th Canadian Conference on Computational Geometry</i>. Vol 2015-August. Queen’s University; 2015:128-135.","ieee":"H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in <i>Proceedings of the 27th Canadian Conference on Computational Geometry</i>, Ontario, Canada, 2015, vol. 2015–August, pp. 128–135.","apa":"Edelsbrunner, H., Iglesias Ham, M., &#38; Kurlin, V. (2015). Relaxed disk packing. In <i>Proceedings of the 27th Canadian Conference on Computational Geometry</i> (Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University."},"publisher":"Queen's University","day":"01","arxiv":1,"oa_version":"Submitted Version","status":"public","_id":"1495","main_file_link":[{"url":"https://arxiv.org/abs/1505.03402","open_access":"1"}],"type":"conference","oa":1,"title":"Relaxed disk packing","author":[{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel","first_name":"Mabel"},{"first_name":"Vitaliy","full_name":"Kurlin, Vitaliy","last_name":"Kurlin"}],"publication":"Proceedings of the 27th Canadian Conference on Computational Geometry","scopus_import":"1","conference":{"location":"Ontario, Canada","name":"CCCG: Canadian Conference on Computational Geometry","end_date":"2015-08-12","start_date":"2015-08-10"},"quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","grant_number":"318493"}],"date_created":"2018-12-11T11:52:21Z","article_processing_charge":"No","month":"08","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"volume":"2015-August","publication_status":"published","page":"128-135"},{"external_id":{"isi":["000366410900009"]},"issue":"21","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:44:58Z","creator":"dernst","access_level":"open_access","checksum":"385b83854fd0eb2e4f386867da2823e2","relation":"main_file","file_name":"2015_NucleicAcidsRes_Andergassen.pdf","file_size":6863297,"date_created":"2018-12-20T14:18:57Z","file_id":"5768"}],"intvolume":"        43","day":"21","isi":1,"citation":{"ieee":"D. Andergassen <i>et al.</i>, “Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data,” <i>Nucleic Acids Research</i>, vol. 43, no. 21. Oxford University Press, 2015.","apa":"Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow, D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkv727\">https://doi.org/10.1093/nar/gkv727</a>","ista":"Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 43(21), e146.","ama":"Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. <i>Nucleic Acids Research</i>. 2015;43(21). doi:<a href=\"https://doi.org/10.1093/nar/gkv727\">10.1093/nar/gkv727</a>","short":"D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow, F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015).","mla":"Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” <i>Nucleic Acids Research</i>, vol. 43, no. 21, e146, Oxford University Press, 2015, doi:<a href=\"https://doi.org/10.1093/nar/gkv727\">10.1093/nar/gkv727</a>.","chicago":"Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl, Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” <i>Nucleic Acids Research</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/nar/gkv727\">https://doi.org/10.1093/nar/gkv727</a>."},"year":"2015","acknowledgement":"Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09]. Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser for advice during the early stages of this project. High-throughput sequencing was conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna.","publisher":"Oxford University Press","status":"public","_id":"1497","oa_version":"Published Version","ddc":["570"],"date_published":"2015-07-21T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.1093/nar/gkv727","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:58Z","date_updated":"2025-09-23T07:45:31Z","publist_id":"5682","quality_controlled":"1","date_created":"2018-12-11T11:52:22Z","article_processing_charge":"No","month":"07","license":"https://creativecommons.org/licenses/by/4.0/","volume":43,"language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"publication_status":"published","article_number":"e146","oa":1,"title":"Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data","doi":"10.1093/nar/gkv727","type":"journal_article","publication":"Nucleic Acids Research","author":[{"last_name":"Andergassen","full_name":"Andergassen, Daniel","first_name":"Daniel"},{"full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","first_name":"Christoph","orcid":"0000-0002-9033-9096"},{"first_name":"Tomasz","full_name":"Kulinski, Tomasz","last_name":"Kulinski"},{"last_name":"Guenzl","full_name":"Guenzl, Philipp","first_name":"Philipp"},{"first_name":"Philipp","full_name":"Bammer, Philipp","last_name":"Bammer"},{"first_name":"Denise","last_name":"Barlow","full_name":"Barlow, Denise"},{"last_name":"Pauler","full_name":"Pauler, Florian","first_name":"Florian"},{"full_name":"Hudson, Quanah","last_name":"Hudson","first_name":"Quanah"}],"scopus_import":"1"},{"file":[{"creator":"system","date_updated":"2020-07-14T12:44:58Z","content_type":"application/pdf","checksum":"cf5e94baa89a2dc4c5de01abc676eda8","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:14:02Z","file_size":489362,"file_name":"IST-2016-499-v1+1_9.pdf","file_id":"5050"}],"intvolume":"        32","oa_version":"Published Version","status":"public","_id":"1498","year":"2015","citation":{"ista":"Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for fault-tolerant distributed systems. 32, 90–102.","ama":"Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant distributed systems. 2015;32:90-102. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SNAPL.2015.90\">10.4230/LIPIcs.SNAPL.2015.90</a>","ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 90–102, 2015.","apa":"Dragoi, C., Henzinger, T. A., &#38; Zufferey, D. (2015). The need for language support for fault-tolerant distributed systems. Presented at the SNAPL: Summit oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SNAPL.2015.90\">https://doi.org/10.4230/LIPIcs.SNAPL.2015.90</a>","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for Language Support for Fault-Tolerant Distributed Systems.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.SNAPL.2015.90\">https://doi.org/10.4230/LIPIcs.SNAPL.2015.90</a>.","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102.","mla":"Dragoi, Cezara, et al. <i>The Need for Language Support for Fault-Tolerant Distributed Systems</i>. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SNAPL.2015.90\">10.4230/LIPIcs.SNAPL.2015.90</a>."},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"01","fulldoi":"https://doi.org/10.4230/LIPIcs.SNAPL.2015.90","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["005"],"date_published":"2015-01-01T00:00:00Z","has_accepted_license":"1","date_updated":"2025-04-15T06:26:02Z","publist_id":"5681","alternative_title":["LIPIcs"],"ec_funded":1,"abstract":[{"lang":"eng","text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. Nonetheless there is surprisingly little language and verification support to build distributed systems based on fault-tolerant algorithms. In this paper, we present some of the challenges that a designer has to overcome to implement a fault-tolerant distributed system. Then we review different models that have been proposed to reason about distributed algorithms and sketch how such a model can form the basis for a domain-specific programming language. Adopting a high-level programming model can simplify the programmer's life and make the code amenable to automated verification, while still compiling to efficiently executable code. We conclude by summarizing the current status of an ongoing language design and implementation project that is based on this idea."}],"file_date_updated":"2020-07-14T12:44:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:22Z","quality_controlled":"1","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"volume":32,"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"pubrep_id":"499","publication_status":"published","page":"90 - 102","series_title":"Leibniz International Proceedings in Informatics","month":"01","doi":"10.4230/LIPIcs.SNAPL.2015.90","type":"conference","publication_identifier":{"isbn":["978-3-939897-80-4 "]},"oa":1,"title":"The need for language support for fault-tolerant distributed systems","scopus_import":1,"corr_author":"1","conference":{"end_date":"2015-05-06","name":"SNAPL: Summit oN Advances in Programming Languages","location":"Asilomar, CA, United States","start_date":"2015-05-03"},"author":[{"id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","last_name":"Dragoi","full_name":"Dragoi, Cezara","first_name":"Cezara"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Zufferey, Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien","orcid":"0000-0002-3197-8736"}]},{"file":[{"relation":"main_file","checksum":"49eb5021caafaabe5356c65b9c5f8c9c","access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:44:58Z","content_type":"application/pdf","file_id":"4672","date_created":"2018-12-12T10:08:12Z","file_size":623563,"file_name":"IST-2016-498-v1+1_32.pdf"}],"intvolume":"        42","oa_version":"Published Version","status":"public","_id":"1499","citation":{"ieee":"J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability of weighted synchronization under partial observability,” presented at the CONCUR: Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.","apa":"Kretinsky, J., Larsen, K., Laursen, S., &#38; Srba, J. (2015). Polynomial time decidability of weighted synchronization under partial observability (Vol. 42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2015.142\">https://doi.org/10.4230/LIPIcs.CONCUR.2015.142</a>","ista":"Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability of weighted synchronization under partial observability. CONCUR: Concurrency Theory, LIPIcs, vol. 42, 142–154.","ama":"Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:142-154. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2015.142\">10.4230/LIPIcs.CONCUR.2015.142</a>","short":"J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–154.","mla":"Kretinsky, Jan, et al. <i>Polynomial Time Decidability of Weighted Synchronization under Partial Observability</i>. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–54, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2015.142\">10.4230/LIPIcs.CONCUR.2015.142</a>.","chicago":"Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time Decidability of Weighted Synchronization under Partial Observability,” 42:142–54. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2015.142\">https://doi.org/10.4230/LIPIcs.CONCUR.2015.142</a>."},"year":"2015","acknowledgement":"The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement 601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM), the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Czech Science Foundation under grant agreement P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"01","fulldoi":"https://doi.org/10.4230/LIPIcs.CONCUR.2015.142","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["000","003"],"has_accepted_license":"1","date_published":"2015-01-01T00:00:00Z","alternative_title":["LIPIcs"],"publist_id":"5680","date_updated":"2025-04-15T06:26:02Z","file_date_updated":"2020-07-14T12:44:58Z","ec_funded":1,"abstract":[{"text":"We consider weighted automata with both positive and negative integer weights on edges and\r\nstudy the problem of synchronization using adaptive strategies that may only observe whether\r\nthe current weight-level is negative or nonnegative. We show that the synchronization problem is decidable in polynomial time for deterministic weighted automata.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:22Z","quality_controlled":"1","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"},{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"volume":42,"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"language":[{"iso":"eng"}],"pubrep_id":"498","publication_status":"published","page":"142 - 154","month":"01","doi":"10.4230/LIPIcs.CONCUR.2015.142","type":"conference","title":"Polynomial time decidability of weighted synchronization under partial observability","oa":1,"scopus_import":1,"conference":{"end_date":"2015-09-04","name":"CONCUR: Concurrency Theory","location":"Madrid, Spain","start_date":"2015-09-01"},"author":[{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","full_name":"Kretinsky, Jan","first_name":"Jan","orcid":"0000-0002-8122-2881"},{"full_name":"Larsen, Kim","last_name":"Larsen","first_name":"Kim"},{"last_name":"Laursen","full_name":"Laursen, Simon","first_name":"Simon"},{"last_name":"Srba","full_name":"Srba, Jiří","first_name":"Jiří"}]},{"oa_version":"Preprint","_id":"1501","status":"public","citation":{"ista":"Chatterjee K, Chmelik M, Daca P. 2015. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 47(2), 230–264.","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for compositional analysis of qualitative properties in Markov decision processes. <i>Formal Methods in System Design</i>. 2015;47(2):230-264. doi:<a href=\"https://doi.org/10.1007/s10703-015-0235-2\">10.1007/s10703-015-0235-2</a>","apa":"Chatterjee, K., Chmelik, M., &#38; Daca, P. (2015). CEGAR for compositional analysis of qualitative properties in Markov decision processes. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-015-0235-2\">https://doi.org/10.1007/s10703-015-0235-2</a>","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for compositional analysis of qualitative properties in Markov decision processes,” <i>Formal Methods in System Design</i>, vol. 47, no. 2. Springer, pp. 230–264, 2015.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” <i>Formal Methods in System Design</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s10703-015-0235-2\">https://doi.org/10.1007/s10703-015-0235-2</a>.","short":"K. Chatterjee, M. Chmelik, P. Daca, Formal Methods in System Design 47 (2015) 230–264.","mla":"Chatterjee, Krishnendu, et al. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” <i>Formal Methods in System Design</i>, vol. 47, no. 2, Springer, 2015, pp. 230–64, doi:<a href=\"https://doi.org/10.1007/s10703-015-0235-2\">10.1007/s10703-015-0235-2</a>."},"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No. P23499- N23, FWF NFN Grant No. S11407-N23, FWF Grant S11403-N23 (RiSE), and FWF Grant Z211-N23 (Wittgenstein Award), ERC Start Grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).","year":"2015","publisher":"Springer","arxiv":1,"day":"01","isi":1,"intvolume":"        47","external_id":{"arxiv":["1405.0835"],"isi":["000361752300003"]},"issue":"2","date_updated":"2026-04-15T10:02:12Z","publist_id":"5677","ec_funded":1,"abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. "}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1007/s10703-015-0235-2","date_published":"2015-10-01T00:00:00Z","language":[{"iso":"eng"}],"volume":47,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","page":"230 - 264","month":"10","date_created":"2018-12-11T11:52:23Z","article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1155"}]},"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"}],"scopus_import":"1","corr_author":"1","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","first_name":"Martin"},{"first_name":"Przemyslaw","last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw"}],"publication":"Formal Methods in System Design","doi":"10.1007/s10703-015-0235-2","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1405.0835"}],"type":"journal_article","oa":1,"title":"CEGAR for compositional analysis of qualitative properties in Markov decision processes"},{"date_published":"2015-05-01T00:00:00Z","has_accepted_license":"1","ddc":["000"],"fulldoi":"https://doi.org/10.1145/2737166.2737175","alternative_title":["Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering "],"date_updated":"2026-04-15T10:02:12Z","publist_id":"5676","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system.","lang":"eng"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:44:59Z","external_id":{"isi":["000380554800013"]},"file":[{"file_name":"IST-2016-625-v1+1_conf-cbse-BenesDHKN15.pdf","date_created":"2018-12-12T10:17:46Z","file_size":467561,"file_id":"5303","date_updated":"2020-07-14T12:44:59Z","content_type":"application/pdf","creator":"system","access_level":"open_access","checksum":"c6ce681035c163a158751f240cb7d389","relation":"main_file"}],"_id":"1502","status":"public","oa_version":"Submitted Version","isi":1,"day":"01","publisher":"ACM","citation":{"mla":"Beneš, Nikola, et al. <i>Complete Composition Operators for IOCO-Testing Theory</i>. ACM, 2015, pp. 101–10, doi:<a href=\"https://doi.org/10.1145/2737166.2737175\">10.1145/2737166.2737175</a>.","short":"N. Beneš, P. Daca, T.A. Henzinger, J. Kretinsky, D. Nickovic, in:, ACM, 2015, pp. 101–110.","chicago":"Beneš, Nikola, Przemyslaw Daca, Thomas A Henzinger, Jan Kretinsky, and Dejan Nickovic. “Complete Composition Operators for IOCO-Testing Theory,” 101–10. ACM, 2015. <a href=\"https://doi.org/10.1145/2737166.2737175\">https://doi.org/10.1145/2737166.2737175</a>.","apa":"Beneš, N., Daca, P., Henzinger, T. A., Kretinsky, J., &#38; Nickovic, D. (2015). Complete composition operators for IOCO-testing theory (pp. 101–110). Presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada: ACM. <a href=\"https://doi.org/10.1145/2737166.2737175\">https://doi.org/10.1145/2737166.2737175</a>","ieee":"N. Beneš, P. Daca, T. A. Henzinger, J. Kretinsky, and D. Nickovic, “Complete composition operators for IOCO-testing theory,” presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada, 2015, pp. 101–110.","ista":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. 2015. Complete composition operators for IOCO-testing theory. CBSE: Component-Based Software Engineering , Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering , , 101–110.","ama":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. Complete composition operators for IOCO-testing theory. In: ACM; 2015:101-110. doi:<a href=\"https://doi.org/10.1145/2737166.2737175\">10.1145/2737166.2737175</a>"},"year":"2015","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23(RiSE) and Z211-N23 (Wittgestein Award), by People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 291734, and by the ARTEMIS JU under grant agreement 295373 (nSafeCer).  Jan Křetínský has been partially supported by the Czech Science Foundation, grant No.  P202/12/G061.  Nikola Beneš has been supported by the\r\nMEYS project No. CZ.1.07/2.3.00/30.0009 Employment of Newly Graduated Doctors of Science for Scientific Excellence.","oa":1,"title":"Complete composition operators for IOCO-testing theory","publication_identifier":{"isbn":["978-1-4503-3471-6"]},"type":"conference","doi":"10.1145/2737166.2737175","conference":{"location":"Montreal, QC, Canada","end_date":"2015-05-08","name":"CBSE: Component-Based Software Engineering ","start_date":"2015-05-04"},"scopus_import":"1","author":[{"first_name":"Nikola","last_name":"Beneš","full_name":"Beneš, Nikola"},{"last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw","first_name":"Przemyslaw"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"orcid":"0000-0002-8122-2881","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","full_name":"Kretinsky, Jan"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"}],"article_processing_charge":"No","date_created":"2018-12-11T11:52:24Z","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1155"}]},"page":"101 - 110","pubrep_id":"625","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"month":"05"},{"publist_id":"5672","date_updated":"2025-09-29T11:02:34Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"This paper is aimed at deriving the universality of the largest eigenvalue of a class of high-dimensional real or complex sample covariance matrices of the form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality, we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic positive-definite M × M matrices Σ , under some additional assumptions on the distribution of xij 's, we show that the limiting behavior of the largest eigenvalue of W N is universal, via pursuing a Green function comparison strategy raised in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515] by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann. Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case (&amp;Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing this universality property and the results known for Gaussian matrices obtained by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after an appropriate normalization the largest eigenvalue of W N converges weakly to the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom limit TW1 holds for the normalized largest eigenvalue of W N , which extends a result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario of nondiagonal Σ and more generally distributed X . In summary, we establish the Tracy-Widom type universality for the largest eigenvalue of generally distributed sample covariance matrices under quite light assumptions on &amp;Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed.","lang":"eng"}],"date_published":"2015-02-01T00:00:00Z","fulldoi":"https://doi.org/10.1214/14-AOS1281","status":"public","_id":"1505","oa_version":"Preprint","arxiv":1,"day":"01","isi":1,"acknowledgement":"B.Z. was supported  in  part  by  NSFC  Grant  11071213,  ZJNSF  Grant  R6090034  and  SRFDP  Grant 20100101110001. P.G. was supported in part by the Ministry of Education, Singapore, under Grant ARC 14/11. Z.W. was supported  in  part  by  the  Ministry  of  Education,  Singapore,  under  Grant  ARC  14/11,  and  by a Grant R-155-000-131-112 at the National University of Singapore\r\n","year":"2015","citation":{"ieee":"Z. Bao, G. Pan, and W. Zhou, “Universality for the largest eigenvalue of sample covariance matrices with general population,” <i>Annals of Statistics</i>, vol. 43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015.","apa":"Bao, Z., Pan, G., &#38; Zhou, W. (2015). Universality for the largest eigenvalue of sample covariance matrices with general population. <i>Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/14-AOS1281\">https://doi.org/10.1214/14-AOS1281</a>","ama":"Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance matrices with general population. <i>Annals of Statistics</i>. 2015;43(1):382-421. doi:<a href=\"https://doi.org/10.1214/14-AOS1281\">10.1214/14-AOS1281</a>","ista":"Bao Z, Pan G, Zhou W. 2015. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 43(1), 382–421.","short":"Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421.","mla":"Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” <i>Annals of Statistics</i>, vol. 43, no. 1, Institute of Mathematical Statistics, 2015, pp. 382–421, doi:<a href=\"https://doi.org/10.1214/14-AOS1281\">10.1214/14-AOS1281</a>.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” <i>Annals of Statistics</i>. Institute of Mathematical Statistics, 2015. <a href=\"https://doi.org/10.1214/14-AOS1281\">https://doi.org/10.1214/14-AOS1281</a>."},"publisher":"Institute of Mathematical Statistics","external_id":{"isi":["000349738500014"],"arxiv":["1304.5690"]},"issue":"1","intvolume":"        43","publication":"Annals of Statistics","author":[{"last_name":"Bao","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475","first_name":"Zhigang"},{"full_name":"Pan, Guangming","last_name":"Pan","first_name":"Guangming"},{"first_name":"Wang","full_name":"Zhou, Wang","last_name":"Zhou"}],"title":"Universality for the largest eigenvalue of sample covariance matrices with general population","oa":1,"doi":"10.1214/14-AOS1281","main_file_link":[{"url":"https://arxiv.org/abs/1304.5690","open_access":"1"}],"type":"journal_article","page":"382 - 421","language":[{"iso":"eng"}],"volume":43,"department":[{"_id":"LaEr"}],"publication_status":"published","month":"02","date_created":"2018-12-11T11:52:25Z","article_processing_charge":"No","quality_controlled":"1"},{"month":"08","page":"1600 - 1628","publication_status":"published","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"volume":21,"quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T11:52:25Z","publication":"Bernoulli","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","full_name":"Bao, Zhigang","first_name":"Zhigang","orcid":"0000-0003-3036-1475"},{"first_name":"Guangming","last_name":"Pan","full_name":"Pan, Guangming"},{"first_name":"Wang","full_name":"Zhou, Wang","last_name":"Zhou"}],"oa":1,"title":"The logarithmic law of random determinant","type":"journal_article","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1208.5823"}],"doi":"10.3150/14-BEJ615","isi":1,"day":"01","arxiv":1,"publisher":"Bernoulli Society for Mathematical Statistics and Probability","citation":{"ama":"Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. <i>Bernoulli</i>. 2015;21(3):1600-1628. doi:<a href=\"https://doi.org/10.3150/14-BEJ615\">10.3150/14-BEJ615</a>","ista":"Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli. 21(3), 1600–1628.","apa":"Bao, Z., Pan, G., &#38; Zhou, W. (2015). The logarithmic law of random determinant. <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability. <a href=\"https://doi.org/10.3150/14-BEJ615\">https://doi.org/10.3150/14-BEJ615</a>","ieee":"Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,” <i>Bernoulli</i>, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics and Probability, pp. 1600–1628, 2015.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random Determinant.” <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability, 2015. <a href=\"https://doi.org/10.3150/14-BEJ615\">https://doi.org/10.3150/14-BEJ615</a>.","short":"Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628.","mla":"Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” <i>Bernoulli</i>, vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability, 2015, pp. 1600–28, doi:<a href=\"https://doi.org/10.3150/14-BEJ615\">10.3150/14-BEJ615</a>."},"year":"2015","_id":"1506","status":"public","oa_version":"Preprint","issue":"3","external_id":{"arxiv":["1208.5823"],"isi":["000356993100012"]},"intvolume":"        21","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij &lt;∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1).","lang":"eng"}],"date_updated":"2025-09-23T13:59:56Z","publist_id":"5671","date_published":"2015-08-01T00:00:00Z","fulldoi":"https://doi.org/10.3150/14-BEJ615"},{"date_updated":"2025-04-15T07:48:03Z","publist_id":"5668","abstract":[{"lang":"eng","text":"The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1."}],"ec_funded":1,"file_date_updated":"2020-07-14T12:44:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.12688/f1000research.7143.1","has_accepted_license":"1","date_published":"2015-10-01T00:00:00Z","ddc":["570"],"oa_version":"Published Version","status":"public","_id":"1509","publisher":"F1000 Research","year":"2015","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”.\r\nData associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication). \r\n\r\nData availability: \r\nF1000Research: Dataset 1. Dataset 1, 10.5256/f1000research.7143.d104552\r\n\r\nF1000Research: Dataset 2. Dataset 2, 10.5256/f1000research.7143.d104553\r\n\r\nF1000Research: Dataset 3. Dataset 3, 10.5256/f1000research.7143.d104554","citation":{"ista":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. 2015. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 4.","ama":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. <i>F1000 Research </i>. 2015;4. doi:<a href=\"https://doi.org/10.12688/f1000research.7143.1\">10.12688/f1000research.7143.1</a>","ieee":"J. Michalko, M. Lukacisinova, M. T. Bollenbach, and J. Friml, “Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene,” <i>F1000 Research </i>, vol. 4. F1000 Research, 2015.","apa":"Michalko, J., Lukacisinova, M., Bollenbach, M. T., &#38; Friml, J. (2015). Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. <i>F1000 Research </i>. F1000 Research. <a href=\"https://doi.org/10.12688/f1000research.7143.1\">https://doi.org/10.12688/f1000research.7143.1</a>","chicago":"Michalko, Jaroslav, Marta Lukacisinova, Mark Tobias Bollenbach, and Jiří Friml. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” <i>F1000 Research </i>. F1000 Research, 2015. <a href=\"https://doi.org/10.12688/f1000research.7143.1\">https://doi.org/10.12688/f1000research.7143.1</a>.","short":"J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research  4 (2015).","mla":"Michalko, Jaroslav, et al. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” <i>F1000 Research </i>, vol. 4, F1000 Research, 2015, doi:<a href=\"https://doi.org/10.12688/f1000research.7143.1\">10.12688/f1000research.7143.1</a>."},"day":"01","intvolume":"         4","file":[{"file_id":"5198","file_size":4414248,"date_created":"2018-12-12T10:16:12Z","file_name":"IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf","relation":"main_file","checksum":"8beae5cbe988e1060265ae7de2ee8306","access_level":"open_access","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:44:59Z"}],"scopus_import":"1","corr_author":"1","author":[{"first_name":"Jaroslav","full_name":"Michalko, Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","last_name":"Michalko"},{"last_name":"Dravecka","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Dravecka, Marta","orcid":"0000-0002-2519-8004","first_name":"Marta"},{"full_name":"Bollenbach, Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Tobias","orcid":"0000-0003-4398-476X"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"publication":"F1000 Research ","type":"journal_article","doi":"10.12688/f1000research.7143.1","oa":1,"title":"Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene","publication_status":"published","pubrep_id":"497","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"},{"_id":"ToBo"}],"volume":4,"month":"10","article_processing_charge":"No","date_created":"2018-12-11T11:52:26Z","quality_controlled":"1","project":[{"grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}]},{"title":"On computability and triviality of well groups","oa":1,"type":"conference","doi":"10.4230/LIPIcs.SOCG.2015.842","conference":{"end_date":"2015-06-25","name":"SoCG: Symposium on Computational Geometry","location":"Eindhoven, Netherlands","start_date":"2015-06-22"},"scopus_import":1,"author":[{"orcid":"0000-0001-8878-8397","first_name":"Peter","full_name":"Franek, Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","last_name":"Franek"},{"full_name":"Krcál, Marek","last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"}],"date_created":"2018-12-11T11:52:26Z","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"1408"}]},"quality_controlled":"1","page":"842 - 856","publication_status":"published","pubrep_id":"503","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"},{"_id":"HeEd"}],"volume":34,"month":"06","date_published":"2015-06-11T00:00:00Z","has_accepted_license":"1","ddc":["510"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.4230/LIPIcs.SOCG.2015.842","date_updated":"2025-09-18T14:30:52Z","alternative_title":["LIPIcs"],"publist_id":"5667","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:44:59Z","abstract":[{"text":"The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r &gt; 0. The main drawback of the approach is that the computability of well groups was shown only when dim K = n or n = 1. Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of R^n by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and dim K &lt; 2n-2, our approximation of the (dim K-n)th well group is exact. For the second part, we find examples of maps f, f' from K to R^n with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status. ","lang":"eng"}],"ec_funded":1,"intvolume":"        34","file":[{"creator":"system","date_updated":"2020-07-14T12:44:59Z","content_type":"application/pdf","relation":"main_file","checksum":"49eb5021caafaabe5356c65b9c5f8c9c","access_level":"open_access","date_created":"2018-12-12T10:13:19Z","file_size":623563,"file_name":"IST-2016-503-v1+1_32.pdf","file_id":"5001"}],"_id":"1510","status":"public","oa_version":"Published Version","day":"11","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2015","citation":{"chicago":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups,” 34:842–56. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.842\">https://doi.org/10.4230/LIPIcs.SOCG.2015.842</a>.","short":"P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–856.","mla":"Franek, Peter, and Marek Krcál. <i>On Computability and Triviality of Well Groups</i>. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–56, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.842\">10.4230/LIPIcs.SOCG.2015.842</a>.","ista":"Franek P, Krcál M. 2015. On computability and triviality of well groups. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 842–856.","ama":"Franek P, Krcál M. On computability and triviality of well groups. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:842-856. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.842\">10.4230/LIPIcs.SOCG.2015.842</a>","apa":"Franek, P., &#38; Krcál, M. (2015). On computability and triviality of well groups (Vol. 34, pp. 842–856). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.842\">https://doi.org/10.4230/LIPIcs.SOCG.2015.842</a>","ieee":"P. Franek and M. Krcál, “On computability and triviality of well groups,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 842–856."}},{"title":"On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result","oa":1,"type":"conference","doi":"10.4230/LIPIcs.SOCG.2015.476","author":[{"last_name":"Goaoc","full_name":"Goaoc, Xavier","first_name":"Xavier"},{"first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","last_name":"Mabillard","full_name":"Mabillard, Isaac"},{"full_name":"Paták, Pavel","last_name":"Paták","first_name":"Pavel"},{"first_name":"Zuzana","orcid":"0000-0002-3975-1683","full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova"},{"last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","first_name":"Martin"},{"first_name":"Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"}],"conference":{"end_date":"2015-06-25","name":"SoCG: Symposium on Computational Geometry","location":"Eindhoven, Netherlands","start_date":"2015-06-22"},"scopus_import":1,"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"related_material":{"record":[{"relation":"later_version","id":"610","status":"public"}]},"quality_controlled":"1","date_created":"2018-12-11T11:52:27Z","month":"06","page":"476 - 490","pubrep_id":"502","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"volume":"34 ","date_published":"2015-06-11T00:00:00Z","has_accepted_license":"1","ddc":["510"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.4230/LIPIcs.SOCG.2015.476","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The fact that the complete graph K_5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph K_n embeds in a closed surface M if and only if (n-3)(n-4) is at most 6b_1(M), where b_1(M) is the first Z_2-Betti number of M. On the other hand, Van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of K_{n+1}) embeds in R^{2k} if and only if n is less or equal to 2k+2. Two decades ago, Kuhnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k-1)-connected 2k-manifold with kth Z_2-Betti number b_k only if the following generalized Heawood inequality holds: binom{n-k-1}{k+1} is at most binom{2k+1}{k+1} b_k. This is a common generalization of the case of graphs on surfaces as well as the Van Kampen--Flores theorem. In the spirit of Kuhnel's conjecture, we prove that if the k-skeleton of the n-simplex embeds in a 2k-manifold with kth Z_2-Betti number b_k, then n is at most 2b_k binom{2k+2}{k} + 2k + 5. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k-1)-connected. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition."}],"file_date_updated":"2020-07-14T12:44:59Z","ec_funded":1,"date_updated":"2025-09-11T07:35:35Z","alternative_title":["LIPIcs"],"publist_id":"5666","file":[{"creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:44:59Z","relation":"main_file","access_level":"open_access","checksum":"0945811875351796324189312ca29e9e","date_created":"2018-12-12T10:11:18Z","file_size":636735,"file_name":"IST-2016-502-v1+1_42.pdf","file_id":"4871"}],"day":"11","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","citation":{"apa":"Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2015). On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result (Vol. 34, pp. 476–490). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.476\">https://doi.org/10.4230/LIPIcs.SOCG.2015.476</a>","ieee":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 476–490.","ama":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:476-490. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.476\">10.4230/LIPIcs.SOCG.2015.476</a>","ista":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2015. On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 476–490.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–490.","mla":"Goaoc, Xavier, et al. <i>On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type Nonembeddability Result</i>. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 476–90, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.476\">10.4230/LIPIcs.SOCG.2015.476</a>.","chicago":"Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A Van Kampen–Flores-Type Nonembeddability Result,” 34:476–90. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.476\">https://doi.org/10.4230/LIPIcs.SOCG.2015.476</a>."},"year":"2015","acknowledgement":"The work by Z. P. was partially supported by the Charles University Grant SVV-2014-260103. The\r\nwork by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of\r\nthe Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research\r\nwork of M. T. was conducted at IST Austria, supported by an IST Fellowship. The work by U.W.\r\nwas partially supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and\r\nSNSF-PP00P2-138948).","status":"public","_id":"1511","oa_version":"Published Version"},{"abstract":[{"text":"We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b,d) such that the following holds. If F is a finite family of subsets of R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent interest.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5665","alternative_title":["LIPIcs"],"date_updated":"2026-06-18T18:48:48Z","fulldoi":"https://doi.org/10.4230/LIPIcs.SOCG.2015.507","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["510"],"has_accepted_license":"1","date_published":"2015-01-01T00:00:00Z","acknowledgement":"PP, ZP and MT were partially supported by the Charles University Grant GAUK 421511. ZP was\r\npartially supported by the Charles University Grant SVV-2014-260103. ZP and MT were partially\r\nsupported by the ERC Advanced Grant No. 267165 and by the project CE-ITI (GACR P202/12/G061)\r\nof the Czech Science Foundation. UW was partially supported by the Swiss National Science Foundation\r\n(grants SNSF-200020-138230 and SNSF-PP00P2-138948). Part of this work was done when XG was affiliated with INRIA Nancy Grand-Est and when MT was affiliated with Institutionen för matematik, Kungliga Tekniska Högskolan, then IST Austria.","citation":{"ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2015. Bounding Helly numbers via Betti numbers. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 507–521.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Bounding Helly numbers via Betti numbers. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:507-521. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.507\">10.4230/LIPIcs.SOCG.2015.507</a>","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2015). Bounding Helly numbers via Betti numbers (Vol. 34, pp. 507–521). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.507\">https://doi.org/10.4230/LIPIcs.SOCG.2015.507</a>","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Bounding Helly numbers via Betti numbers,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 507–521.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Bounding Helly Numbers via Betti Numbers,” 34:507–21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.507\">https://doi.org/10.4230/LIPIcs.SOCG.2015.507</a>.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–521.","mla":"Goaoc, Xavier, et al. <i>Bounding Helly Numbers via Betti Numbers</i>. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 507–21, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SOCG.2015.507\">10.4230/LIPIcs.SOCG.2015.507</a>."},"year":"2015","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"01","oa_version":"Submitted Version","status":"public","_id":"1512","file":[{"file_name":"IST-2016-501-v1+1_46.pdf","date_created":"2018-12-12T10:10:09Z","file_size":633712,"file_id":"4794","content_type":"application/pdf","date_updated":"2020-07-14T12:45:00Z","creator":"system","relation":"main_file","access_level":"open_access","checksum":"e6881df44d87fe0c2529c9f7b2724614"}],"intvolume":"        34","author":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"first_name":"Pavel","full_name":"Paták, Pavel","last_name":"Paták"},{"full_name":"Patakova, Zuzana","last_name":"Patakova","first_name":"Zuzana","orcid":"0000-0002-3975-1683"},{"full_name":"Tancer, Martin","last_name":"Tancer","orcid":"0000-0002-1191-6714","first_name":"Martin"},{"first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","conference":{"location":"Eindhoven, Netherlands","name":"SoCG: Symposium on Computational Geometry","end_date":"2015-06-25","start_date":"2015-06-22"},"doi":"10.4230/LIPIcs.SOCG.2015.507","type":"conference","oa":1,"title":"Bounding Helly numbers via Betti numbers","month":"01","volume":34,"department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"pubrep_id":"501","publication_status":"published","page":"507 - 521","quality_controlled":"1","related_material":{"record":[{"id":"424","relation":"later_version","status":"public"}]},"date_created":"2018-12-11T11:52:27Z","article_processing_charge":"No"},{"doi":"10.1093/gbe/evv215","type":"journal_article","oa":1,"title":"The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression","scopus_import":"1","corr_author":"1","author":[{"full_name":"Pal, Arka","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","first_name":"Arka"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"publication":"Genome Biology and Evolution","date_created":"2018-12-11T11:52:27Z","article_processing_charge":"No","quality_controlled":"1","project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"language":[{"iso":"eng"}],"volume":7,"department":[{"_id":"BeVi"}],"publication_status":"published","pubrep_id":"496","page":"3259 - 3268","month":"12","fulldoi":"https://doi.org/10.1093/gbe/evv215","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"date_published":"2015-12-01T00:00:00Z","has_accepted_license":"1","date_updated":"2025-09-23T14:18:15Z","publist_id":"5664","ec_funded":1,"file_date_updated":"2020-07-14T12:45:00Z","abstract":[{"text":"Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. ","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:45:00Z","checksum":"2b56b8c2e2a1d4cc3c9cb8daba26dd9b","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:29Z","file_size":858027,"file_name":"IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf","file_id":"5284"}],"intvolume":"         7","external_id":{"isi":["000366498700008"]},"issue":"12","oa_version":"Published Version","status":"public","_id":"1513","year":"2015","citation":{"apa":"Pal, A., &#38; Vicoso, B. (2015). The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evv215\">https://doi.org/10.1093/gbe/evv215</a>","ieee":"A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression,” <i>Genome Biology and Evolution</i>, vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.","ista":"Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12), 3259–3268.","ama":"Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. <i>Genome Biology and Evolution</i>. 2015;7(12):3259-3268. doi:<a href=\"https://doi.org/10.1093/gbe/evv215\">10.1093/gbe/evv215</a>","short":"A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268.","mla":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” <i>Genome Biology and Evolution</i>, vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:<a href=\"https://doi.org/10.1093/gbe/evv215\">10.1093/gbe/evv215</a>.","chicago":"Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/gbe/evv215\">https://doi.org/10.1093/gbe/evv215</a>."},"publisher":"Oxford University Press","day":"01","isi":1},{"type":"journal_article","doi":"10.1214/ECP.v20-4315","title":"From large deviations to Wasserstein gradient flows in multiple dimensions","oa":1,"article_number":"89","scopus_import":"1","author":[{"full_name":"Erbar, Matthias","last_name":"Erbar","first_name":"Matthias"},{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","orcid":"0000-0002-0845-1338","first_name":"Jan"},{"full_name":"Renger, Michiel","last_name":"Renger","first_name":"Michiel"}],"publication":"Electronic Communications in Probability","article_processing_charge":"No","date_created":"2018-12-11T11:52:29Z","quality_controlled":"1","pubrep_id":"494","publication_status":"published","department":[{"_id":"JaMa"}],"language":[{"iso":"eng"}],"volume":20,"month":"11","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1214/ECP.v20-4315","has_accepted_license":"1","date_published":"2015-11-29T00:00:00Z","ddc":["519"],"date_updated":"2025-09-23T08:53:14Z","publist_id":"5660","file_date_updated":"2020-07-14T12:45:00Z","abstract":[{"text":"We study the large deviation rate functional for the empirical distribution of independent Brownian particles with drift. In one dimension, it has been shown by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent (in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher dimensions, part of this statement (the lower bound) has been recently proved by Duong, Laschos and Renger, but the upper bound remained open, since the proof of Duong et al relies on regularity properties of optimal transport maps that are restricted to one dimension. In this note we present a new proof of the upper bound, thereby generalising the result of Adams et al to arbitrary dimensions.\r\n","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        20","file":[{"file_id":"4828","date_created":"2018-12-12T10:10:39Z","file_size":230525,"file_name":"IST-2016-494-v1+1_4315-23820-1-PB.pdf","checksum":"135741c17d3e1547ca696b6fbdcd559c","access_level":"open_access","relation":"main_file","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:45:00Z"}],"external_id":{"isi":["000365470700001"]},"oa_version":"Published Version","_id":"1517","status":"public","publisher":"Institute of Mathematical Statistics","year":"2015","citation":{"chicago":"Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics, 2015. <a href=\"https://doi.org/10.1214/ECP.v20-4315\">https://doi.org/10.1214/ECP.v20-4315</a>.","short":"M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20 (2015).","mla":"Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” <i>Electronic Communications in Probability</i>, vol. 20, 89, Institute of Mathematical Statistics, 2015, doi:<a href=\"https://doi.org/10.1214/ECP.v20-4315\">10.1214/ECP.v20-4315</a>.","ista":"Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 20, 89.","ama":"Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows in multiple dimensions. <i>Electronic Communications in Probability</i>. 2015;20. doi:<a href=\"https://doi.org/10.1214/ECP.v20-4315\">10.1214/ECP.v20-4315</a>","ieee":"M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient flows in multiple dimensions,” <i>Electronic Communications in Probability</i>, vol. 20. Institute of Mathematical Statistics, 2015.","apa":"Erbar, M., Maas, J., &#38; Renger, M. (2015). From large deviations to Wasserstein gradient flows in multiple dimensions. <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/ECP.v20-4315\">https://doi.org/10.1214/ECP.v20-4315</a>"},"isi":1,"day":"29"},{"publisher":"Wiley","citation":{"chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” <i>Evolution</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/evo.12641\">https://doi.org/10.1111/evo.12641</a>.","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.","mla":"Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” <i>Evolution</i>, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:<a href=\"https://doi.org/10.1111/evo.12641\">10.1111/evo.12641</a>.","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112.","ama":"Barton NH, Servedio M. The interpretation of selection coefficients. <i>Evolution</i>. 2015;69(5):1101-1112. doi:<a href=\"https://doi.org/10.1111/evo.12641\">10.1111/evo.12641</a>","ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” <i>Evolution</i>, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","apa":"Barton, N. H., &#38; Servedio, M. (2015). The interpretation of selection coefficients. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12641\">https://doi.org/10.1111/evo.12641</a>"},"year":"2015","isi":1,"day":"19","oa_version":"Submitted Version","_id":"1519","status":"public","intvolume":"        69","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:00Z","creator":"system","access_level":"open_access","checksum":"fd8d23f476bc194419929b72ca265c02","relation":"main_file","file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf","date_created":"2018-12-12T10:10:34Z","file_size":188872,"file_id":"4822"},{"relation":"main_file","checksum":"b774911e70044641d556e258efcb52ef","access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf","file_id":"4823","date_created":"2018-12-12T10:10:35Z","file_size":577415,"file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf"}],"issue":"5","external_id":{"isi":["000354561600001"]},"file_date_updated":"2020-07-14T12:45:00Z","abstract":[{"lang":"eng","text":"Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under &quot;direct&quot; versus &quot;indirect&quot; selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so."}],"ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T13:53:01Z","publist_id":"5656","fulldoi":"https://doi.org/10.1111/evo.12641","date_published":"2015-03-19T00:00:00Z","has_accepted_license":"1","ddc":["570"],"month":"03","publication_status":"published","pubrep_id":"560","volume":69,"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"page":"1101 - 1112","quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"article_processing_charge":"No","date_created":"2018-12-11T11:52:29Z","author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Servedio","full_name":"Servedio, Maria","first_name":"Maria"}],"publication":"Evolution","scopus_import":"1","corr_author":"1","type":"journal_article","doi":"10.1111/evo.12641","oa":1,"title":"The interpretation of selection coefficients"},{"department":[{"_id":"BeBi"}],"language":[{"iso":"eng"}],"publication_status":"published","oa_version":"None","_id":"1520","page":"93 - 100","status":"public","year":"2015","citation":{"ieee":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, and H. Pfister, “Computational design of walking automata,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States, 2015, pp. 93–100.","apa":"Bharaj, G., Coros, S., Thomaszewski, B., Tompkin, J., Bickel, B., &#38; Pfister, H. (2015). Computational design of walking automata (pp. 93–100). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2786784.2786803\">https://doi.org/10.1145/2786784.2786803</a>","ama":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. Computational design of walking automata. In: ACM; 2015:93-100. doi:<a href=\"https://doi.org/10.1145/2786784.2786803\">10.1145/2786784.2786803</a>","ista":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. 2015. Computational design of walking automata. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 93–100.","mla":"Bharaj, Gaurav, et al. <i>Computational Design of Walking Automata</i>. ACM, 2015, pp. 93–100, doi:<a href=\"https://doi.org/10.1145/2786784.2786803\">10.1145/2786784.2786803</a>.","short":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, H. Pfister, in:, ACM, 2015, pp. 93–100.","chicago":"Bharaj, Gaurav, Stelian Coros, Bernhard Thomaszewski, James Tompkin, Bernd Bickel, and Hanspeter Pfister. “Computational Design of Walking Automata,” 93–100. ACM, 2015. <a href=\"https://doi.org/10.1145/2786784.2786803\">https://doi.org/10.1145/2786784.2786803</a>."},"publisher":"ACM","day":"01","month":"08","date_created":"2018-12-11T11:52:30Z","quality_controlled":"1","scopus_import":1,"conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","end_date":"2015-08-09","location":"Los Angeles, CA, United States","start_date":"2015-08-07"},"date_updated":"2021-01-12T06:51:21Z","publist_id":"5655","author":[{"last_name":"Bharaj","full_name":"Bharaj, Gaurav","first_name":"Gaurav"},{"first_name":"Stelian","last_name":"Coros","full_name":"Coros, Stelian"},{"full_name":"Thomaszewski, Bernhard","last_name":"Thomaszewski","first_name":"Bernhard"},{"first_name":"James","full_name":"Tompkin, James","last_name":"Tompkin"},{"orcid":"0000-0001-6511-9385","first_name":"Bernd","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"}],"abstract":[{"text":"Creating mechanical automata that can walk in stable and pleasing manners is a challenging task that requires both skill and expertise. We propose to use computational design to offset the technical difficulties of this process. A simple drag-and-drop interface allows casual users to create personalized walking toys from a library of pre-defined template mechanisms. Provided with this input, our method leverages physical simulation and evolutionary optimization to refine the mechanical designs such that the resulting toys are able to walk. The optimization process is guided by an intuitive set of objectives that measure the quality of the walking motions. We demonstrate our approach on a set of simulated mechanical toys with different numbers of legs and various distinct gaits. Two fabricated prototypes showcase the feasibility of our designs.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1145/2786784.2786803","doi":"10.1145/2786784.2786803","type":"conference","publication_identifier":{"isbn":["978-1-4503-3496-9"]},"date_published":"2015-08-01T00:00:00Z","title":"Computational design of walking automata"},{"publist_id":"5641","date_updated":"2025-09-23T09:19:53Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"In growing cells, protein synthesis and cell growth are typically not synchronous, and, thus, protein concentrations vary over the cell division cycle. We have developed a theoretical description of genetic regulatory systems in bacteria that explicitly considers the cell division cycle to investigate its impact on gene expression. We calculate the cell-to-cell variations arising from cells being at different stages in the division cycle for unregulated genes and for basic regulatory mechanisms. These variations contribute to the extrinsic noise observed in single-cell experiments, and are most significant for proteins with short lifetimes. Negative autoregulation buffers against variation of protein concentration over the division cycle, but the effect is found to be relatively weak. Stronger buffering is achieved by an increased protein lifetime. Positive autoregulation can strongly amplify such variation if the parameters are set to values that lead to resonance-like behaviour. For cooperative positive autoregulation, the concentration variation over the division cycle diminishes the parameter region of bistability and modulates the switching times between the two stable states. The same effects are seen for a two-gene mutual-repression toggle switch. By contrast, an oscillatory circuit, the repressilator, is only weakly affected by the division cycle.","lang":"eng"}],"date_published":"2015-09-25T00:00:00Z","fulldoi":"https://doi.org/10.1088/1478-3975/12/6/066003","_id":"1530","status":"public","oa_version":"None","day":"25","isi":1,"year":"2015","citation":{"ista":"Bierbaum V, Klumpp S. 2015. Impact of the cell division cycle on gene circuits. Physical Biology. 12(6), 066003.","ama":"Bierbaum V, Klumpp S. Impact of the cell division cycle on gene circuits. <i>Physical Biology</i>. 2015;12(6). doi:<a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">10.1088/1478-3975/12/6/066003</a>","apa":"Bierbaum, V., &#38; Klumpp, S. (2015). Impact of the cell division cycle on gene circuits. <i>Physical Biology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">https://doi.org/10.1088/1478-3975/12/6/066003</a>","ieee":"V. Bierbaum and S. Klumpp, “Impact of the cell division cycle on gene circuits,” <i>Physical Biology</i>, vol. 12, no. 6. IOP Publishing, 2015.","chicago":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” <i>Physical Biology</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">https://doi.org/10.1088/1478-3975/12/6/066003</a>.","mla":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” <i>Physical Biology</i>, vol. 12, no. 6, 066003, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">10.1088/1478-3975/12/6/066003</a>.","short":"V. Bierbaum, S. Klumpp, Physical Biology 12 (2015)."},"publisher":"IOP Publishing","external_id":{"isi":["000368186300009"]},"issue":"6","intvolume":"        12","corr_author":"1","scopus_import":"1","publication":"Physical Biology","author":[{"first_name":"Veronika","full_name":"Bierbaum, Veronika","last_name":"Bierbaum","id":"3FD04378-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Klumpp, Stefan","last_name":"Klumpp","first_name":"Stefan"}],"title":"Impact of the cell division cycle on gene circuits","doi":"10.1088/1478-3975/12/6/066003","type":"journal_article","article_number":"066003","department":[{"_id":"MiSi"}],"language":[{"iso":"eng"}],"volume":12,"publication_status":"published","month":"09","date_created":"2018-12-11T11:52:33Z","article_processing_charge":"No","quality_controlled":"1"},{"date_published":"2015-01-01T00:00:00Z","fulldoi":"https://doi.org/10.1007/978-3-319-15090-1_13","publist_id":"5640","date_updated":"2022-06-10T09:50:14Z","alternative_title":["Mathematics and Visualization"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The Heat Kernel Signature (HKS) is a scalar quantity which is derived from the heat kernel of a given shape. Due to its robustness, isometry invariance, and multiscale nature, it has been successfully applied in many geometric applications. From a more general point of view, the HKS can be considered as a descriptor of the metric of a Riemannian manifold. Given a symmetric positive definite tensor field we may interpret it as the metric of some Riemannian manifold and thereby apply the HKS to visualize and analyze the given tensor data. In this paper, we propose a generalization of this approach that enables the treatment of indefinite tensor fields, like the stress tensor, by interpreting them as a generator of a positive definite tensor field. To investigate the usefulness of this approach we consider the stress tensor from the two-point-load model example and from a mechanical work piece.","lang":"eng"}],"intvolume":"        40","status":"public","_id":"1531","oa_version":"None","editor":[{"last_name":"Hotz","full_name":"Hotz, Ingrid","first_name":"Ingrid"},{"full_name":"Schultz, Thomas","last_name":"Schultz","first_name":"Thomas"}],"day":"01","publisher":"Springer","year":"2015","citation":{"apa":"Zobel, V., Reininghaus, J., &#38; Hotz, I. (2015). Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In I. Hotz &#38; T. Schultz (Eds.), <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i> (1st ed., Vol. 40, pp. 257–267). Springer. <a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">https://doi.org/10.1007/978-3-319-15090-1_13</a>","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature,” in <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, 1st ed., vol. 40, I. Hotz and T. Schultz, Eds. Springer, 2015, pp. 257–267.","ista":"Zobel V, Reininghaus J, Hotz I. 2015.Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Mathematics and Visualization, vol. 40, 257–267.","ama":"Zobel V, Reininghaus J, Hotz I. Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Hotz I, Schultz T, eds. <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>. Vol 40. 1st ed. Springer; 2015:257-267. doi:<a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">10.1007/978-3-319-15090-1_13</a>","mla":"Zobel, Valentin, et al. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, edited by Ingrid Hotz and Thomas Schultz, 1st ed., vol. 40, Springer, 2015, pp. 257–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">10.1007/978-3-319-15090-1_13</a>.","short":"V. Zobel, J. Reininghaus, I. Hotz, in:, I. Hotz, T. Schultz (Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., Springer, 2015, pp. 257–267.","chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” In <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, edited by Ingrid Hotz and Thomas Schultz, 1st ed., 40:257–67. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">https://doi.org/10.1007/978-3-319-15090-1_13</a>."},"title":"Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature","publication_identifier":{"isbn":["978-3-319-15089-5"]},"type":"book_chapter","doi":"10.1007/978-3-319-15090-1_13","edition":"1","scopus_import":"1","publication":"Visualization and Processing of Higher Order Descriptors for Multi-Valued Data","author":[{"first_name":"Valentin","last_name":"Zobel","full_name":"Zobel, Valentin"},{"first_name":"Jan","full_name":"Reininghaus, Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus"},{"first_name":"Ingrid","full_name":"Hotz, Ingrid","last_name":"Hotz"}],"article_processing_charge":"No","date_created":"2018-12-11T11:52:33Z","quality_controlled":"1","page":"257 - 267","publication_status":"published","volume":40,"language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"month":"01"},{"doi":"10.1071/FP14171","type":"journal_article","pmid":1,"publication_identifier":{"issn":["1445-4408"]},"title":"Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source","author":[{"last_name":"Yang","full_name":"Yang, Huaiyu","first_name":"Huaiyu"},{"first_name":"Jenny","last_name":"Von Der Fecht Bartenbach","full_name":"Von Der Fecht Bartenbach, Jenny"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"last_name":"Lohmann","full_name":"Lohmann, Jan","first_name":"Jan"},{"last_name":"Neuhäuser","full_name":"Neuhäuser, Benjamin","first_name":"Benjamin"},{"first_name":"Uwe","full_name":"Ludewig, Uwe","last_name":"Ludewig"}],"publication":"Functional Plant Biology","scopus_import":"1","quality_controlled":"1","date_created":"2018-12-11T11:52:34Z","article_processing_charge":"No","month":"03","volume":42,"language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publication_status":"published","page":"239 - 251","article_type":"original","fulldoi":"https://doi.org/10.1071/FP14171","date_published":"2015-03-01T00:00:00Z","abstract":[{"lang":"eng","text":"Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T07:59:44Z","publist_id":"5639","intvolume":"        42","external_id":{"pmid":["32480670"],"isi":["000349635900003"]},"issue":"3","citation":{"mla":"Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” <i>Functional Plant Biology</i>, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:<a href=\"https://doi.org/10.1071/FP14171\">10.1071/FP14171</a>.","short":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251.","chicago":"Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann, Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” <i>Functional Plant Biology</i>. CSIRO, 2015. <a href=\"https://doi.org/10.1071/FP14171\">https://doi.org/10.1071/FP14171</a>.","ieee":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source,” <i>Functional Plant Biology</i>, vol. 42, no. 3. CSIRO, pp. 239–251, 2015.","apa":"Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser, B., &#38; Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. <i>Functional Plant Biology</i>. CSIRO. <a href=\"https://doi.org/10.1071/FP14171\">https://doi.org/10.1071/FP14171</a>","ama":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. <i>Functional Plant Biology</i>. 2015;42(3):239-251. doi:<a href=\"https://doi.org/10.1071/FP14171\">10.1071/FP14171</a>","ista":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251."},"year":"2015","publisher":"CSIRO","day":"01","isi":1,"oa_version":"None","status":"public","_id":"1532"},{"fulldoi":"https://doi.org/10.1109/TCSVT.2014.2379972","date_published":"2015-08-01T00:00:00Z","publist_id":"5638","date_updated":"2025-09-23T10:44:22Z","abstract":[{"lang":"eng","text":"This paper addresses the problem of semantic segmentation, where the possible class labels are from a predefined set. We exploit top-down guidance, i.e., the coarse localization of the objects and their class labels provided by object detectors. For each detected bounding box, figure-ground segmentation is performed and the final result is achieved by merging the figure-ground segmentations. The main idea of the proposed approach, which is presented in our preliminary work, is to reformulate the figure-ground segmentation problem as sparse reconstruction pursuing the object mask in a nonparametric manner. The latent segmentation mask should be coherent subject to sparse error caused by intra-category diversity; thus, the object mask is inferred by making use of sparse representations over the training set. To handle local spatial deformations, local patch-level masks are also considered and inferred by sparse representations over the spatially nearby patches. The sparse reconstruction coefficients and the latent mask are alternately optimized by applying the Lasso algorithm and the accelerated proximal gradient method. The proposed formulation results in a convex optimization problem; thus, the global optimal solution is achieved. In this paper, we provide theoretical analysis of the convergence and optimality. We also give an extended numerical analysis of the proposed algorithm and a comprehensive comparison with the related semantic segmentation methods on the challenging PASCAL visual object class object segmentation datasets and the Weizmann horse dataset. The experimental results demonstrate that the proposed algorithm achieves a competitive performance when compared with the state of the arts."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        25","issue":"8","external_id":{"isi":["000359213400004"]},"oa_version":"None","status":"public","_id":"1533","publisher":"IEEE","year":"2015","citation":{"mla":"Xia, Wei, et al. “Segmentation over Detection via Optimal Sparse Reconstructions.” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>, vol. 25, no. 8, IEEE, 2015, pp. 1295–308, doi:<a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">10.1109/TCSVT.2014.2379972</a>.","short":"W. Xia, C. Domokos, J. Xiong, L. Cheong, S. Yan, IEEE Transactions on Circuits and Systems for Video Technology 25 (2015) 1295–1308.","chicago":"Xia, Wei, Csaba Domokos, Junjun Xiong, Loongfah Cheong, and Shuicheng Yan. “Segmentation over Detection via Optimal Sparse Reconstructions.” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">https://doi.org/10.1109/TCSVT.2014.2379972</a>.","apa":"Xia, W., Domokos, C., Xiong, J., Cheong, L., &#38; Yan, S. (2015). Segmentation over detection via optimal sparse reconstructions. <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. IEEE. <a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">https://doi.org/10.1109/TCSVT.2014.2379972</a>","ieee":"W. Xia, C. Domokos, J. Xiong, L. Cheong, and S. Yan, “Segmentation over detection via optimal sparse reconstructions,” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>, vol. 25, no. 8. IEEE, pp. 1295–1308, 2015.","ista":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. 2015. Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. 25(8), 1295–1308.","ama":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. Segmentation over detection via optimal sparse reconstructions. <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. 2015;25(8):1295-1308. doi:<a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">10.1109/TCSVT.2014.2379972</a>"},"isi":1,"day":"01","type":"journal_article","doi":"10.1109/TCSVT.2014.2379972","title":"Segmentation over detection via optimal sparse reconstructions","scopus_import":"1","author":[{"first_name":"Wei","last_name":"Xia","full_name":"Xia, Wei"},{"first_name":"Csaba","id":"492DACF8-F248-11E8-B48F-1D18A9856A87","last_name":"Domokos","full_name":"Domokos, Csaba"},{"full_name":"Xiong, Junjun","last_name":"Xiong","first_name":"Junjun"},{"first_name":"Loongfah","full_name":"Cheong, Loongfah","last_name":"Cheong"},{"first_name":"Shuicheng","last_name":"Yan","full_name":"Yan, Shuicheng"}],"publication":"IEEE Transactions on Circuits and Systems for Video Technology","article_processing_charge":"No","date_created":"2018-12-11T11:52:34Z","quality_controlled":"1","publication_status":"published","volume":25,"department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"page":"1295 - 1308","month":"08"}]