[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization","day":"01","department":[{"_id":"DaAl"}],"article_processing_charge":"No","publication_identifier":{"issn":["1532-4435"],"eissn":["1533-7928"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"file_size":11237154,"date_updated":"2021-06-23T07:09:41Z","file_name":"2021_JournalOfMachineLearningResearch_Ramezani-Kebrya.pdf","file_id":"9595","checksum":"6428aa8bcb67768b6949c99b55d5281d","success":1,"access_level":"open_access","relation":"main_file","creator":"asandaue","content_type":"application/pdf","date_created":"2021-06-23T07:09:41Z"}],"publisher":"Journal of Machine Learning Research","date_published":"2021-04-01T00:00:00Z","_id":"9571","quality_controlled":"1","year":"2021","file_date_updated":"2021-06-23T07:09:41Z","publication_status":"published","issue":"114","volume":22,"month":"04","author":[{"full_name":"Ramezani-Kebrya, Ali","last_name":"Ramezani-Kebrya","first_name":"Ali"},{"first_name":"Fartash","last_name":"Faghri","full_name":"Faghri, Fartash"},{"full_name":"Markov, Ilya","first_name":"Ilya","last_name":"Markov"},{"first_name":"Vitalii","last_name":"Aksenov","full_name":"Aksenov, Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"},{"full_name":"Roy, Daniel M.","last_name":"Roy","first_name":"Daniel M."}],"page":"1−43","intvolume":"        22","date_updated":"2025-07-10T12:01:54Z","ddc":["000"],"arxiv":1,"date_created":"2021-06-20T22:01:33Z","scopus_import":"1","publication":"Journal of Machine Learning Research","oa_version":"Published Version","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://www.jmlr.org/papers/v22/20-255.html"}],"corr_author":"1","abstract":[{"lang":"eng","text":"As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes gradients to reduce communication costs. The baseline variant of QSGD provides strong theoretical guarantees, however, for practical purposes, the authors proposed a heuristic variant which we call QSGDinf, which demonstrated impressive empirical gains for distributed training of large neural networks. In this paper, we build on this work to propose a new gradient quantization scheme, and show that it has both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical performance of the QSGDinf heuristic and of other compression methods."}],"status":"public","external_id":{"arxiv":["1908.06077"]},"has_accepted_license":"1","citation":{"chicago":"Ramezani-Kebrya, Ali, Fartash Faghri, Ilya Markov, Vitalii Aksenov, Dan-Adrian Alistarh, and Daniel M. Roy. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2021.","apa":"Ramezani-Kebrya, A., Faghri, F., Markov, I., Aksenov, V., Alistarh, D.-A., &#38; Roy, D. M. (2021). NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","ista":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. 2021. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 22(114), 1−43.","ama":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. <i>Journal of Machine Learning Research</i>. 2021;22(114):1−43.","ieee":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, and D. M. Roy, “NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization,” <i>Journal of Machine Learning Research</i>, vol. 22, no. 114. Journal of Machine Learning Research, p. 1−43, 2021.","mla":"Ramezani-Kebrya, Ali, et al. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” <i>Journal of Machine Learning Research</i>, vol. 22, no. 114, Journal of Machine Learning Research, 2021, p. 1−43.","short":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, D.M. Roy, Journal of Machine Learning Research 22 (2021) 1−43."},"article_type":"original","language":[{"iso":"eng"}]},{"ddc":["516"],"arxiv":1,"date_updated":"2025-05-14T11:23:45Z","language":[{"iso":"eng"}],"citation":{"chicago":"Dvorak, Martin, and Sara Nicholson. “Massively Winning Configurations in the Convex Grabbing Game on the Plane.” In <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>. Canadian Conference on Computational Geometry, 2021.","mla":"Dvorak, Martin, and Sara Nicholson. “Massively Winning Configurations in the Convex Grabbing Game on the Plane.” <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>, Canadian Conference on Computational Geometry, 2021.","short":"M. Dvorak, S. Nicholson, in:, Proceedings of the 33rd Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2021.","apa":"Dvorak, M., &#38; Nicholson, S. (2021). Massively winning configurations in the convex grabbing game on the plane. In <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>. Halifax, NS, Canada; Virtual: Canadian Conference on Computational Geometry.","ista":"Dvorak M, Nicholson S. 2021. Massively winning configurations in the convex grabbing game on the plane. Proceedings of the 33rd Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry.","ama":"Dvorak M, Nicholson S. Massively winning configurations in the convex grabbing game on the plane. In: <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>. Canadian Conference on Computational Geometry; 2021.","ieee":"M. Dvorak and S. Nicholson, “Massively winning configurations in the convex grabbing game on the plane,” in <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>, Halifax, NS, Canada; Virtual, 2021."},"type":"conference","oa_version":"Published Version","publication":"Proceedings of the 33rd Canadian Conference on Computational Geometry","date_created":"2021-06-22T15:57:11Z","external_id":{"arxiv":["2106.11247"]},"status":"public","has_accepted_license":"1","abstract":[{"text":"The convex grabbing game is a game where two players, Alice and Bob, alternate taking extremal points from the convex hull of a point set on the plane. Rational weights are given to the points. The goal of each player is to maximize the total weight over all points that they obtain. We restrict the setting to the case of binary weights. We show a construction of an arbitrarily large odd-sized point set that allows Bob to obtain almost 3/4 of the total weight. This construction answers a question asked by Matsumoto, Nakamigawa, and Sakuma in [Graphs and Combinatorics, 36/1 (2020)]. We also present an arbitrarily large even-sized point set where Bob can obtain the entirety of the total weight. Finally, we discuss conjectures about optimum moves in the convex grabbing game for both players in general.","lang":"eng"}],"month":"06","year":"2021","publication_status":"published","file_date_updated":"2021-08-12T10:57:21Z","author":[{"first_name":"Martin","orcid":"0000-0001-5293-214X","last_name":"Dvorak","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","full_name":"Dvorak, Martin"},{"first_name":"Sara","last_name":"Nicholson","full_name":"Nicholson, Sara"}],"file":[{"file_size":381306,"file_name":"Convex-Grabbing-Game_CCCG_proc_version.pdf","file_id":"9616","date_updated":"2021-06-28T20:23:13Z","checksum":"45accb1de9b7e0e4bb2fbfe5fd3e6239","success":1,"access_level":"open_access","creator":"mdvorak","relation":"main_file","date_created":"2021-06-28T20:23:13Z","content_type":"application/pdf"},{"access_level":"open_access","relation":"main_file","creator":"kschuh","date_created":"2021-08-12T10:57:21Z","content_type":"application/pdf","file_size":403645,"date_updated":"2021-08-12T10:57:21Z","file_id":"9902","file_name":"Convex-Grabbing-Game_FULL-VERSION.pdf","success":1,"checksum":"9199cf18c65658553487458cc24d0ab2"}],"publisher":"Canadian Conference on Computational Geometry","conference":{"start_date":"2021-08-10","location":"Halifax, NS, Canada; Virtual","end_date":"2021-08-12","name":"CCCG: Canadian Conference on Computational Geometry"},"date_published":"2021-06-29T00:00:00Z","_id":"9592","quality_controlled":"1","keyword":["convex grabbing game","graph grabbing game","combinatorial game","convex geometry"],"day":"29","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-nd/4.0/","title":"Massively winning configurations in the convex grabbing game on the plane","oa":1,"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png"}},{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2041-1723"]},"article_processing_charge":"No","title":"Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"SiHi"}],"day":"12","article_number":"3804","_id":"9601","date_published":"2021-07-12T00:00:00Z","quality_controlled":"1","publisher":"Springer Nature","doi":"10.1038/s41467-021-23510-4","acknowledgement":"The authors thank Robert Feil and Anton Wutz for helpful discussions and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates, and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF) for support with next-generation sequencing. We are grateful to animal care teams at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship. M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006) by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund FWF (I3786 and P31334).","isi":1,"file":[{"checksum":"75dd89d09945185b2d14b2434a0bcb50","success":1,"file_id":"9608","file_name":"2021_NatureCommunications_Santini.pdf","date_updated":"2021-06-28T08:04:22Z","file_size":2156554,"content_type":"application/pdf","date_created":"2021-06-28T08:04:22Z","creator":"asandaue","relation":"main_file","access_level":"open_access"}],"author":[{"full_name":"Santini, Laura","first_name":"Laura","last_name":"Santini"},{"full_name":"Halbritter, Florian","last_name":"Halbritter","first_name":"Florian"},{"first_name":"Fabian","last_name":"Titz-Teixeira","full_name":"Titz-Teixeira, Fabian"},{"full_name":"Suzuki, Toru","last_name":"Suzuki","first_name":"Toru"},{"full_name":"Asami, Maki","last_name":"Asami","first_name":"Maki"},{"first_name":"Xiaoyan","last_name":"Ma","full_name":"Ma, Xiaoyan"},{"first_name":"Julia","last_name":"Ramesmayer","full_name":"Ramesmayer, Julia"},{"full_name":"Lackner, Andreas","first_name":"Andreas","last_name":"Lackner"},{"first_name":"Nick","last_name":"Warr","full_name":"Warr, Nick"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"last_name":"Laue","first_name":"Ernest","full_name":"Laue, Ernest"},{"last_name":"Farlik","first_name":"Matthias","full_name":"Farlik, Matthias"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"full_name":"Beyer, Andreas","last_name":"Beyer","first_name":"Andreas"},{"full_name":"Perry, Anthony C.F.","first_name":"Anthony C.F.","last_name":"Perry"},{"full_name":"Leeb, Martin","first_name":"Martin","last_name":"Leeb"}],"publication_status":"published","file_date_updated":"2021-06-28T08:04:22Z","year":"2021","month":"07","volume":12,"issue":"1","external_id":{"isi":["000667248600005"]},"has_accepted_license":"1","status":"public","abstract":[{"text":"In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"type":"journal_article","scopus_import":"1","publication":"Nature Communications","date_created":"2021-06-27T22:01:46Z","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma, X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23510-4\">https://doi.org/10.1038/s41467-021-23510-4</a>","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23510-4\">10.1038/s41467-021-23510-4</a>","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 12(1), 3804.","ieee":"L. Santini <i>et al.</i>, “Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","mla":"Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” <i>Nature Communications</i>, vol. 12, no. 1, 3804, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23510-4\">10.1038/s41467-021-23510-4</a>.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma, J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021).","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23510-4\">https://doi.org/10.1038/s41467-021-23510-4</a>."},"article_type":"original","ddc":["570"],"date_updated":"2026-04-02T13:55:23Z","intvolume":"        12"},{"publication_identifier":{"issn":["0095-8956"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","department":[{"_id":"HeEd"}],"day":"09","oa":1,"title":"Erdős-Hajnal-type results for monotone paths","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-06-09T00:00:00Z","_id":"9602","quality_controlled":"1","publisher":"Elsevier","isi":1,"file":[{"file_size":418168,"checksum":"15fbc9064cd9d1c777ac0043b78c8f12","success":1,"file_name":"2021_JournalOfCombinatorialTheory_Pach.pdf","file_id":"9612","date_updated":"2021-06-28T13:33:23Z","creator":"asandaue","relation":"main_file","access_level":"open_access","date_created":"2021-06-28T13:33:23Z","content_type":"application/pdf"}],"acknowledgement":"We would like to thank the anonymous referees for their useful comments and suggestions. János Pach is partially supported by Austrian Science Fund (FWF) grant Z 342-N31 and by ERC Advanced grant “GeoScape.” István Tomon is partially supported by Swiss National Science Foundation grant no. 200021_196965, and thanks the support of MIPT Moscow. Both authors are partially supported by The Russian Government in the framework of MegaGrant no. 075-15-2019-1926.","doi":"10.1016/j.jctb.2021.05.004","page":"21-37","author":[{"first_name":"János","last_name":"Pach","full_name":"Pach, János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4"},{"full_name":"Tomon, István","last_name":"Tomon","first_name":"István"}],"month":"06","volume":151,"file_date_updated":"2021-06-28T13:33:23Z","publication_status":"published","year":"2021","article_type":"original","citation":{"apa":"Pach, J., &#38; Tomon, I. (2021). Erdős-Hajnal-type results for monotone paths. <i>Journal of Combinatorial Theory. Series B</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jctb.2021.05.004\">https://doi.org/10.1016/j.jctb.2021.05.004</a>","ieee":"J. Pach and I. Tomon, “Erdős-Hajnal-type results for monotone paths,” <i>Journal of Combinatorial Theory. Series B</i>, vol. 151. Elsevier, pp. 21–37, 2021.","ama":"Pach J, Tomon I. Erdős-Hajnal-type results for monotone paths. <i>Journal of Combinatorial Theory Series B</i>. 2021;151:21-37. doi:<a href=\"https://doi.org/10.1016/j.jctb.2021.05.004\">10.1016/j.jctb.2021.05.004</a>","ista":"Pach J, Tomon I. 2021. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. 151, 21–37.","mla":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” <i>Journal of Combinatorial Theory. Series B</i>, vol. 151, Elsevier, 2021, pp. 21–37, doi:<a href=\"https://doi.org/10.1016/j.jctb.2021.05.004\">10.1016/j.jctb.2021.05.004</a>.","short":"J. Pach, I. Tomon, Journal of Combinatorial Theory. Series B 151 (2021) 21–37.","chicago":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” <i>Journal of Combinatorial Theory. Series B</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jctb.2021.05.004\">https://doi.org/10.1016/j.jctb.2021.05.004</a>."},"language":[{"iso":"eng"}],"abstract":[{"text":"An ordered graph is a graph with a linear ordering on its vertex set. We prove that for every positive integer k, there exists a constant ck > 0 such that any ordered graph G on n vertices with the property that neither G nor its complement contains an induced monotone path of size k, has either a clique or an independent set of size at least n^ck . This strengthens a result of Bousquet, Lagoutte, and Thomassé, who proved the analogous result for unordered graphs.\r\nA key idea of the above paper was to show that any unordered graph on n vertices that does not contain an induced path of size k, and whose maximum degree is at most c(k)n for some small c(k) > 0, contains two disjoint linear size subsets with no edge between them. This approach fails for ordered graphs, because the analogous statement is false for k ≥ 3, by a construction of Fox. We provide some further examples showing that this statement also fails for ordered graphs avoiding other ordered trees.","lang":"eng"}],"status":"public","external_id":{"isi":["000702280800002"]},"has_accepted_license":"1","publication":"Journal of Combinatorial Theory. Series B","date_created":"2021-06-27T22:01:47Z","scopus_import":"1","oa_version":"Published Version","type":"journal_article","corr_author":"1","project":[{"call_identifier":"FWF","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"}],"date_updated":"2025-04-15T07:16:52Z","ddc":["510"],"intvolume":"       151"},{"date_updated":"2026-04-02T14:04:28Z","ddc":["570"],"intvolume":"        35","project":[{"grant_number":"24812","name":"Molecular mechanisms of radial neuronal migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"grant_number":"618444","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"abstract":[{"text":"Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division.","lang":"eng"}],"status":"public","has_accepted_license":"1","external_id":{"pmid":["34161767"],"isi":["000664463600016"]},"date_created":"2021-06-27T22:01:48Z","publication":"Cell Reports","oa_version":"Published Version","scopus_import":"1","type":"journal_article","citation":{"ista":"Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274.","ieee":"X. Contreras <i>et al.</i>, “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” <i>Cell Reports</i>, vol. 35, no. 12. Cell Press, 2021.","ama":"Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. <i>Cell Reports</i>. 2021;35(12). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">10.1016/j.celrep.2021.109274</a>","apa":"Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">https://doi.org/10.1016/j.celrep.2021.109274</a>","short":"X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).","mla":"Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” <i>Cell Reports</i>, vol. 35, no. 12, 109274, Cell Press, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">10.1016/j.celrep.2021.109274</a>.","chicago":"Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” <i>Cell Reports</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109274\">https://doi.org/10.1016/j.celrep.2021.109274</a>."},"ec_funded":1,"article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2021-06-28T14:06:24Z","publication_status":"published","year":"2021","month":"06","related_material":{"link":[{"url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"12","volume":35,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena","first_name":"Ximena","last_name":"Contreras"},{"first_name":"Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole"},{"first_name":"Amarbayasgalan","last_name":"Davaatseren","id":"70ADC922-B424-11E9-99E3-BA18E6697425","full_name":"Davaatseren, Amarbayasgalan"},{"last_name":"Hansen","first_name":"Andi H","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johanna","last_name":"Sonntag","id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87","full_name":"Sonntag, Johanna"},{"first_name":"Lill","last_name":"Andersen","full_name":"Andersen, Lill"},{"last_name":"Bernthaler","first_name":"Tina","full_name":"Bernthaler, Tina"},{"first_name":"Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"first_name":"Anna-Magdalena","last_name":"Heger","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","full_name":"Heger, Anna-Magdalena"},{"first_name":"Randy L.","last_name":"Johnson","full_name":"Johnson, Randy L."},{"last_name":"Schwarz","first_name":"Lindsay A.","full_name":"Schwarz, Lindsay A."},{"last_name":"Luo","first_name":"Liqun","full_name":"Luo, Liqun"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"publisher":"Cell Press","acknowledgement":"We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H.","file":[{"access_level":"open_access","creator":"asandaue","relation":"main_file","date_created":"2021-06-28T14:06:24Z","content_type":"application/pdf","file_size":7653149,"file_id":"9613","file_name":"2021_CellReports_Contreras.pdf","date_updated":"2021-06-28T14:06:24Z","success":1,"checksum":"d49520fdcbbb5c2f883bddb67cee5d77"}],"isi":1,"doi":"10.1016/j.celrep.2021.109274","article_number":"109274","_id":"9603","date_published":"2021-06-22T00:00:00Z","quality_controlled":"1","oa":1,"title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"day":"22","publication_identifier":{"eissn":["2211-1247"]},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_processing_charge":"No"},{"intvolume":"       189","ddc":["516"],"date_updated":"2025-07-10T12:01:56Z","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","name":"Persistent Homology, Algorithms and Stochastic Geometry","grant_number":"I4887"}],"type":"conference","publication":"Leibniz International Proceedings in Informatics","scopus_import":"1","date_created":"2021-06-27T22:01:48Z","oa_version":"Published Version","status":"public","has_accepted_license":"1","abstract":[{"text":"Generalizing Lee’s inductive argument for counting the cells of higher order Voronoi tessellations in ℝ² to ℝ³, we get precise relations in terms of Morse theoretic quantities for piecewise constant functions on planar arrangements. Specifically, we prove that for a generic set of n ≥ 5 points in ℝ³, the number of regions in the order-k Voronoi tessellation is N_{k-1} - binom(k,2)n + n, for 1 ≤ k ≤ n-1, in which N_{k-1} is the sum of Euler characteristics of these function’s first k-1 sublevel sets. We get similar expressions for the vertices, edges, and polygons of the order-k Voronoi tessellation.","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (2021). Counting cells of order-k voronoi tessellations in ℝ<sup>3</sup> with morse theory. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 189). Online: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.16\">https://doi.org/10.4230/LIPIcs.SoCG.2021.16</a>","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Counting cells of order-k voronoi tessellations in ℝ<sup>3</sup> with morse theory. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.16\">10.4230/LIPIcs.SoCG.2021.16</a>","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2021. Counting cells of order-k voronoi tessellations in ℝ<sup>3</sup> with morse theory. Leibniz International Proceedings in Informatics. SoCG: International Symposium on Computational Geometry, LIPIcs, vol. 189, 16.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Counting cells of order-k voronoi tessellations in ℝ<sup>3</sup> with morse theory,” in <i>Leibniz International Proceedings in Informatics</i>, Online, 2021, vol. 189.","mla":"Biswas, Ranita, et al. “Counting Cells of Order-k Voronoi Tessellations in ℝ<sup>3</sup> with Morse Theory.” <i>Leibniz International Proceedings in Informatics</i>, vol. 189, 16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.16\">10.4230/LIPIcs.SoCG.2021.16</a>.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Counting Cells of Order-k Voronoi Tessellations in ℝ<sup>3</sup> with Morse Theory.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.16\">https://doi.org/10.4230/LIPIcs.SoCG.2021.16</a>."},"ec_funded":1,"year":"2021","file_date_updated":"2021-06-28T13:11:39Z","publication_status":"published","volume":189,"month":"06","alternative_title":["LIPIcs"],"author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita","first_name":"Ranita","orcid":"0000-0002-5372-7890","last_name":"Biswas"},{"id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","first_name":"Sebastiano","orcid":"0000-0001-6249-0832"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Saghafian","first_name":"Morteza","full_name":"Saghafian, Morteza"}],"conference":{"start_date":"2021-06-07","location":"Online","end_date":"2021-06-11","name":"SoCG: International Symposium on Computational Geometry"},"file":[{"access_level":"open_access","creator":"asandaue","relation":"main_file","content_type":"application/pdf","date_created":"2021-06-28T13:11:39Z","file_size":727817,"file_name":"2021_LIPIcs_Biswas.pdf","file_id":"9611","date_updated":"2021-06-28T13:11:39Z","success":1,"checksum":"22b11a719018b22ecba2471b51f2eb40"}],"doi":"10.4230/LIPIcs.SoCG.2021.16","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","_id":"9604","quality_controlled":"1","date_published":"2021-06-02T00:00:00Z","article_number":"16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Counting cells of order-k voronoi tessellations in ℝ<sup>3</sup> with morse theory","oa":1,"day":"02","department":[{"_id":"HeEd"}],"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"isbn":["9783959771849"],"issn":["1868-8969"]}},{"conference":{"name":"SoCG: International Symposium on Computational Geometry","location":"Online","start_date":"2021-06-07","end_date":"2021-06-11"},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"The authors want to thank the reviewers for many helpful comments and suggestions.","file":[{"creator":"cziletti","relation":"main_file","access_level":"open_access","date_created":"2021-06-28T12:40:47Z","content_type":"application/pdf","file_size":"1367983","checksum":"0de217501e7ba8b267d58deed0d51761","success":1,"file_id":"9610","file_name":"2021_LIPIcs_Corbet.pdf","date_updated":"2021-06-28T12:40:47Z"}],"doi":"10.4230/LIPIcs.SoCG.2021.27","article_number":"27","_id":"9605","quality_controlled":"1","date_published":"2021-06-02T00:00:00Z","title":"Computing the multicover bifiltration","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"day":"02","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771849"]},"article_processing_charge":"No","arxiv":1,"ddc":["516"],"date_updated":"2025-07-10T12:01:57Z","intvolume":"       189","status":"public","has_accepted_license":"1","external_id":{"arxiv":["2103.07823"]},"abstract":[{"text":"Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness. ","lang":"eng"}],"type":"conference","publication":"Leibniz International Proceedings in Informatics","date_created":"2021-06-27T22:01:49Z","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"chicago":"Corbet, René, Michael Kerber, Michael Lesnick, and Georg F Osang. “Computing the Multicover Bifiltration.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.27\">https://doi.org/10.4230/LIPIcs.SoCG.2021.27</a>.","mla":"Corbet, René, et al. “Computing the Multicover Bifiltration.” <i>Leibniz International Proceedings in Informatics</i>, vol. 189, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.27\">10.4230/LIPIcs.SoCG.2021.27</a>.","short":"R. Corbet, M. Kerber, M. Lesnick, G.F. Osang, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","apa":"Corbet, R., Kerber, M., Lesnick, M., &#38; Osang, G. F. (2021). Computing the multicover bifiltration. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 189). Online: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.27\">https://doi.org/10.4230/LIPIcs.SoCG.2021.27</a>","ama":"Corbet R, Kerber M, Lesnick M, Osang GF. Computing the multicover bifiltration. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.27\">10.4230/LIPIcs.SoCG.2021.27</a>","ista":"Corbet R, Kerber M, Lesnick M, Osang GF. 2021. Computing the multicover bifiltration. Leibniz International Proceedings in Informatics. SoCG: International Symposium on Computational Geometry, LIPIcs, vol. 189, 27.","ieee":"R. Corbet, M. Kerber, M. Lesnick, and G. F. Osang, “Computing the multicover bifiltration,” in <i>Leibniz International Proceedings in Informatics</i>, Online, 2021, vol. 189."},"file_date_updated":"2021-06-28T12:40:47Z","publication_status":"published","year":"2021","month":"06","volume":189,"related_material":{"link":[{"url":"https://arxiv.org/abs/2103.07823","relation":"extended_version"}],"record":[{"relation":"later_version","status":"public","id":"12709"}]},"author":[{"full_name":"Corbet, René","last_name":"Corbet","first_name":"René"},{"full_name":"Kerber, Michael","first_name":"Michael","last_name":"Kerber"},{"first_name":"Michael","last_name":"Lesnick","full_name":"Lesnick, Michael"},{"full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","orcid":"0000-0002-8882-5116","first_name":"Georg F"}],"alternative_title":["LIPIcs"]},{"date_updated":"2025-07-10T12:01:58Z","arxiv":1,"intvolume":"       103","abstract":[{"lang":"eng","text":"Sound propagation is a macroscopic manifestation of the interplay between the equilibrium thermodynamics and the dynamical transport properties of fluids. Here, for a two-dimensional system of ultracold fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover, and we analyze the system response to an external perturbation. In the low-temperature regime we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of the first sound velocity, which, due to the decoupling of density and entropy fluctuations, is the sole mode excited by a density probe. Conversely, a heat perturbation excites only the second sound, which, being sensitive to the superfluid depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the modes occurs only in the finite-temperature BEC regime, where our theory converges to the purely bosonic results."}],"status":"public","external_id":{"isi":["000662296700014"],"arxiv":["2009.06491"]},"publication":"Physical Review A","date_created":"2021-06-27T22:01:49Z","oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.06491"}],"type":"journal_article","article_type":"letter_note","citation":{"chicago":"Tononi, A., Alberto Cappellaro, Giacomo Bighin, and L. Salasnich. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” <i>Physical Review A</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevA.103.L061303\">https://doi.org/10.1103/PhysRevA.103.L061303</a>.","ista":"Tononi A, Cappellaro A, Bighin G, Salasnich L. 2021. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 103(6), L061303.","ama":"Tononi A, Cappellaro A, Bighin G, Salasnich L. Propagation of first and second sound in a two-dimensional Fermi superfluid. <i>Physical Review A</i>. 2021;103(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.103.L061303\">10.1103/PhysRevA.103.L061303</a>","ieee":"A. Tononi, A. Cappellaro, G. Bighin, and L. Salasnich, “Propagation of first and second sound in a two-dimensional Fermi superfluid,” <i>Physical Review A</i>, vol. 103, no. 6. American Physical Society, 2021.","apa":"Tononi, A., Cappellaro, A., Bighin, G., &#38; Salasnich, L. (2021). Propagation of first and second sound in a two-dimensional Fermi superfluid. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.103.L061303\">https://doi.org/10.1103/PhysRevA.103.L061303</a>","short":"A. Tononi, A. Cappellaro, G. Bighin, L. Salasnich, Physical Review A 103 (2021).","mla":"Tononi, A., et al. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” <i>Physical Review A</i>, vol. 103, no. 6, L061303, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevA.103.L061303\">10.1103/PhysRevA.103.L061303</a>."},"language":[{"iso":"eng"}],"publication_status":"published","year":"2021","month":"06","issue":"6","volume":103,"author":[{"last_name":"Tononi","first_name":"A.","full_name":"Tononi, A."},{"full_name":"Cappellaro, Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","orcid":"0000-0001-6110-2359","first_name":"Alberto"},{"full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","first_name":"Giacomo","last_name":"Bighin"},{"full_name":"Salasnich, L.","first_name":"L.","last_name":"Salasnich"}],"publisher":"American Physical Society","isi":1,"doi":"10.1103/PhysRevA.103.L061303","acknowledgement":"G.B. acknowledges support from the Austrian Science Fund (FWF), under Project No. M2641-N27. This work was\r\npartially supported by the University of Padua, BIRD project “Superfluid properties of Fermi gases in optical potentials.”\r\nThe authors thank Miki Ota, Tomoki Ozawa, Sandro Stringari, Tilman Enss, Hauke Biss, Henning Moritz, and Nicolò Defenu for fruitful discussions. The authors thank Henning Moritz and Markus Bohlen for providing their experimental\r\ndata.","article_number":"L061303","_id":"9606","date_published":"2021-06-01T00:00:00Z","quality_controlled":"1","oa":1,"title":"Propagation of first and second sound in a two-dimensional Fermi superfluid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiLe"}],"day":"01","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"article_processing_charge":"No"},{"intvolume":"        10","date_updated":"2026-04-02T13:55:57Z","ddc":["570"],"oa_version":"Published Version","date_created":"2021-06-27T22:01:49Z","publication":"eLife","scopus_import":"1","type":"journal_article","abstract":[{"lang":"eng","text":"While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use."}],"external_id":{"pmid":["34028353"],"isi":["000661272000001"]},"has_accepted_license":"1","status":"public","article_type":"original","citation":{"mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” <i>ELife</i>, vol. 10, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.63294\">10.7554/eLife.63294</a>.","short":"A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021).","apa":"Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V., … Steckler, T. (2021). Introduction to the EQIPD quality system. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.63294\">https://doi.org/10.7554/eLife.63294</a>","ama":"Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.63294\">10.7554/eLife.63294</a>","ista":"Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L, De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction to the EQIPD quality system. eLife. 10.","ieee":"A. Bespalov <i>et al.</i>, “Introduction to the EQIPD quality system,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","chicago":"Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén, Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality System.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.63294\">https://doi.org/10.7554/eLife.63294</a>."},"language":[{"iso":"eng"}],"year":"2021","publication_status":"published","file_date_updated":"2021-06-28T11:35:30Z","volume":10,"month":"05","author":[{"first_name":"Anton","last_name":"Bespalov","full_name":"Bespalov, Anton"},{"full_name":"Bernard, René","first_name":"René","last_name":"Bernard"},{"full_name":"Gilis, Anja","first_name":"Anja","last_name":"Gilis"},{"full_name":"Gerlach, Björn","first_name":"Björn","last_name":"Gerlach"},{"first_name":"Javier","last_name":"Guillén","full_name":"Guillén, Javier"},{"full_name":"Castagné, Vincent","first_name":"Vincent","last_name":"Castagné"},{"first_name":"Isabel A.","last_name":"Lefevre","full_name":"Lefevre, Isabel A."},{"last_name":"Ducrey","first_name":"Fiona","full_name":"Ducrey, Fiona"},{"full_name":"Monk, Lee","last_name":"Monk","first_name":"Lee"},{"full_name":"Bongiovanni, Sandrine","last_name":"Bongiovanni","first_name":"Sandrine"},{"first_name":"Bruce","last_name":"Altevogt","full_name":"Altevogt, Bruce"},{"last_name":"Arroyo-Araujo","first_name":"María","full_name":"Arroyo-Araujo, María"},{"last_name":"Bikovski","first_name":"Lior","full_name":"Bikovski, Lior"},{"last_name":"De Bruin","first_name":"Natasja","full_name":"De Bruin, Natasja"},{"first_name":"Esmeralda","last_name":"Castaños-Vélez","full_name":"Castaños-Vélez, Esmeralda"},{"full_name":"Dityatev, Alexander","last_name":"Dityatev","first_name":"Alexander"},{"first_name":"Christoph H.","last_name":"Emmerich","full_name":"Emmerich, Christoph H."},{"full_name":"Fares, Raafat","first_name":"Raafat","last_name":"Fares"},{"full_name":"Ferland-Beckham, Chantelle","last_name":"Ferland-Beckham","first_name":"Chantelle"},{"first_name":"Christelle","last_name":"Froger-Colléaux","full_name":"Froger-Colléaux, Christelle"},{"first_name":"Valerie","last_name":"Gailus-Durner","full_name":"Gailus-Durner, Valerie"},{"last_name":"Hölter","first_name":"Sabine M.","full_name":"Hölter, Sabine M."},{"full_name":"Hofmann, Martine Cj","last_name":"Hofmann","first_name":"Martine Cj"},{"first_name":"Patricia","last_name":"Kabitzke","full_name":"Kabitzke, Patricia"},{"full_name":"Kas, Martien Jh","last_name":"Kas","first_name":"Martien Jh"},{"first_name":"Claudia","last_name":"Kurreck","full_name":"Kurreck, Claudia"},{"last_name":"Moser","first_name":"Paul","full_name":"Moser, Paul"},{"first_name":"Malgorzata","last_name":"Pietraszek","full_name":"Pietraszek, Malgorzata"},{"full_name":"Popik, Piotr","last_name":"Popik","first_name":"Piotr"},{"full_name":"Potschka, Heidrun","first_name":"Heidrun","last_name":"Potschka"},{"full_name":"Prado Montes De Oca, Ernesto","last_name":"Prado Montes De Oca","first_name":"Ernesto"},{"full_name":"Restivo, Leonardo","first_name":"Leonardo","last_name":"Restivo"},{"last_name":"Riedel","first_name":"Gernot","full_name":"Riedel, Gernot"},{"first_name":"Merel","last_name":"Ritskes-Hoitinga","full_name":"Ritskes-Hoitinga, Merel"},{"full_name":"Samardzic, Janko","last_name":"Samardzic","first_name":"Janko"},{"last_name":"Schunn","orcid":"0000-0003-4326-5300","first_name":"Michael","full_name":"Schunn, Michael","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stöger, Claudia","last_name":"Stöger","first_name":"Claudia"},{"last_name":"Voikar","first_name":"Vootele","full_name":"Voikar, Vootele"},{"last_name":"Vollert","first_name":"Jan","full_name":"Vollert, Jan"},{"full_name":"Wever, Kimberley E.","first_name":"Kimberley E.","last_name":"Wever"},{"full_name":"Wuyts, Kathleen","first_name":"Kathleen","last_name":"Wuyts"},{"full_name":"Macleod, Malcolm R.","first_name":"Malcolm R.","last_name":"Macleod"},{"first_name":"Ulrich","last_name":"Dirnagl","full_name":"Dirnagl, Ulrich"},{"last_name":"Steckler","first_name":"Thomas","full_name":"Steckler, Thomas"}],"pmid":1,"doi":"10.7554/eLife.63294","isi":1,"file":[{"content_type":"application/pdf","date_created":"2021-06-28T11:35:30Z","relation":"main_file","creator":"asandaue","access_level":"open_access","checksum":"885b746051a7a6b6e24e3d2781a48fde","success":1,"date_updated":"2021-06-28T11:35:30Z","file_id":"9609","file_name":"2021_ELife_Bespalov.pdf","file_size":2500720}],"acknowledgement":"This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen, Germany) for the exceptional IT support and programming the EQIPD Planning Tool and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati (PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating contributions to the discussions and comments on earlier versions of this manuscript. We also wish to express our thanks to Dr. Sara Stöber (concentris research management GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project. Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology bv (Wageningen, the Netherlands).","publisher":"eLife Sciences Publications","date_published":"2021-05-24T00:00:00Z","_id":"9607","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"title":"Introduction to the EQIPD quality system","day":"24","department":[{"_id":"PreCl"}],"article_processing_charge":"No","publication_identifier":{"eissn":["2050-084X"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"month":"03","volume":371,"issue":"6536","file_date_updated":"2021-09-23T14:00:05Z","publication_status":"published","year":"2021","page":"1355-1359","pmid":1,"author":[{"last_name":"Bluvstein","first_name":"D.","full_name":"Bluvstein, D."},{"full_name":"Omran, A.","first_name":"A.","last_name":"Omran"},{"last_name":"Levine","first_name":"H.","full_name":"Levine, H."},{"full_name":"Keesling, A.","last_name":"Keesling","first_name":"A."},{"full_name":"Semeghini, G.","first_name":"G.","last_name":"Semeghini"},{"full_name":"Ebadi, S.","first_name":"S.","last_name":"Ebadi"},{"full_name":"Wang, T. T.","first_name":"T. T.","last_name":"Wang"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios","last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064"},{"last_name":"Maskara","first_name":"N.","full_name":"Maskara, N."},{"full_name":"Ho, W. W.","first_name":"W. W.","last_name":"Ho"},{"full_name":"Choi, S.","last_name":"Choi","first_name":"S."},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Greiner","first_name":"M.","full_name":"Greiner, M."},{"first_name":"V.","last_name":"Vuletić","full_name":"Vuletić, V."},{"full_name":"Lukin, M. D.","first_name":"M. D.","last_name":"Lukin"}],"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}],"ddc":["539"],"arxiv":1,"date_updated":"2025-04-14T07:52:05Z","intvolume":"       371","language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Bluvstein, D., A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T. T. Wang, et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” <i>Science</i>. AAAS, 2021. <a href=\"https://doi.org/10.1126/science.abg2530\">https://doi.org/10.1126/science.abg2530</a>.","mla":"Bluvstein, D., et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” <i>Science</i>, vol. 371, no. 6536, AAAS, 2021, pp. 1355–59, doi:<a href=\"https://doi.org/10.1126/science.abg2530\">10.1126/science.abg2530</a>.","short":"D. Bluvstein, A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T.T. Wang, A. Michailidis, N. Maskara, W.W. Ho, S. Choi, M. Serbyn, M. Greiner, V. Vuletić, M.D. Lukin, Science 371 (2021) 1355–1359.","apa":"Bluvstein, D., Omran, A., Levine, H., Keesling, A., Semeghini, G., Ebadi, S., … Lukin, M. D. (2021). Controlling quantum many-body dynamics in driven Rydberg atom arrays. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.abg2530\">https://doi.org/10.1126/science.abg2530</a>","ieee":"D. Bluvstein <i>et al.</i>, “Controlling quantum many-body dynamics in driven Rydberg atom arrays,” <i>Science</i>, vol. 371, no. 6536. AAAS, pp. 1355–1359, 2021.","ista":"Bluvstein D, Omran A, Levine H, Keesling A, Semeghini G, Ebadi S, Wang TT, Michailidis A, Maskara N, Ho WW, Choi S, Serbyn M, Greiner M, Vuletić V, Lukin MD. 2021. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 371(6536), 1355–1359.","ama":"Bluvstein D, Omran A, Levine H, et al. Controlling quantum many-body dynamics in driven Rydberg atom arrays. <i>Science</i>. 2021;371(6536):1355-1359. doi:<a href=\"https://doi.org/10.1126/science.abg2530\">10.1126/science.abg2530</a>"},"ec_funded":1,"status":"public","external_id":{"pmid":["33632894"],"isi":["000636043400048"],"arxiv":["2012.12276"]},"has_accepted_license":"1","abstract":[{"lang":"eng","text":"The control of nonequilibrium quantum dynamics in many-body systems is challenging because interactions typically lead to thermalization and a chaotic spreading throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches in a many-body system composed of 3 to 200 strongly interacting qubits in one and two spatial dimensions. Using a programmable quantum simulator based on Rydberg atom arrays, we show that coherent revivals associated with so-called quantum many-body scars can be stabilized by periodic driving, which generates a robust subharmonic response akin to discrete time-crystalline order. We map Hilbert space dynamics, geometry dependence, phase diagrams, and system-size dependence of this emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body systems and enabling potential applications in quantum information science."}],"type":"journal_article","oa_version":"Preprint","publication":"Science","scopus_import":"1","date_created":"2021-06-29T12:04:05Z","department":[{"_id":"MaSe"}],"day":"26","keyword":["Multidisciplinary"],"title":"Controlling quantum many-body dynamics in driven Rydberg atom arrays","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"article_processing_charge":"No","publisher":"AAAS","file":[{"content_type":"application/pdf","date_created":"2021-09-23T14:00:05Z","relation":"main_file","creator":"patrickd","access_level":"open_access","checksum":"0b356fd10ab9bb95177d4c047d4e9c1a","success":1,"date_updated":"2021-09-23T14:00:05Z","file_name":"scars_subharmonic_combined_manuscript_2_11_2021 (2)-1.pdf","file_id":"10040","file_size":3671159}],"acknowledgement":"We thank many members of the Harvard AMO community, particularly E. Urbach, S. Dakoulas, and J. Doyle for their efforts enabling safe and productive operation of our laboratories during 2020. We thank D. Abanin, I. Cong, F. Machado, H. Pichler, N. Yao, B. Ye, and H. Zhou for stimulating discussions. Funding: We acknowledge financial support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy (LBNL QSA Center and grant no. DE-SC0021013), the Office of Naval Research, the Army Research Office MURI, the DARPA DRINQS program (grant no. D18AC00033), and the DARPA ONISQ program (grant no. W911NF2010021). The authors acknowledge support from the NSF Graduate Research Fellowship Program (grant DGE1745303) and The Fannie and John Hertz Foundation (D.B.); a National Defense Science and Engineering Graduate (NDSEG) fellowship (H.L.); a fellowship from the Max Planck/Harvard Research Center for Quantum Optics (G.S.); Gordon College (T.T.W.); the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 850899) (A.A.M. and M.S.); a Department of Energy Computational Science Graduate Fellowship under award number DE-SC0021110 (N.M.); the Moore Foundation’s EPiQS Initiative grant no. GBMF4306, the NUS Development grant AY2019/2020, and the Stanford Institute of Theoretical Physics (W.W.H.); and the Miller Institute for Basic Research in Science (S.C.). Author contributions: D.B., A.O., H.L., A.K., G.S., S.E., and T.T.W. contributed to the building of the experimental setup, performed the measurements, and analyzed the data. A.A.M., N.M., W.W.H., S.C., and M.S. performed theoretical analysis. All work was supervised by M.G., V.V., and M.D.L. All authors discussed the results and contributed to the manuscript. Competing interests: M.G., V.V., and M.D.L. are co-founders and shareholders of QuEra Computing. A.O. is a shareholder of QuEra Computing. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and the supplementary materials.","isi":1,"doi":"10.1126/science.abg2530","_id":"9618","quality_controlled":"1","date_published":"2021-03-26T00:00:00Z"},{"oa":1,"title":"Collecting coupons is faster with friends","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"DaAl"}],"day":"20","publication_identifier":{"eisbn":["9783030795276"],"issn":["0302-9743"],"isbn":["9783030795269"],"eissn":["1611-3349"]},"article_processing_charge":"No","conference":{"name":"SIROCCO: International Colloquium on Structural Information and Communication Complexity","start_date":"2021-06-28","location":"Wrocław, Poland","end_date":"2021-07-01"},"publisher":"Springer Nature","isi":1,"acknowledgement":"Peter Davies is supported by the European Union’s Horizon2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","doi":"10.1007/978-3-030-79527-6_1","file":[{"content_type":"application/pdf","date_created":"2021-07-01T11:21:40Z","access_level":"open_access","relation":"main_file","creator":"pdavies","date_updated":"2021-07-01T11:21:40Z","file_name":"Population_Coupon_Collector.pdf","file_id":"9621","checksum":"fe37fb9af3f5016c1084af9d6e7109bd","file_size":319728}],"_id":"9620","date_published":"2021-06-20T00:00:00Z","quality_controlled":"1","file_date_updated":"2021-07-01T11:21:40Z","publication_status":"published","year":"2021","month":"06","volume":12810,"author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"},{"last_name":"Davies","first_name":"Peter","orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425","full_name":"Davies, Peter"}],"alternative_title":["LNCS"],"page":"3-12","date_updated":"2025-09-10T10:04:46Z","ddc":["000"],"intvolume":"     12810","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"abstract":[{"text":"In this note, we introduce a distributed twist on the classic coupon collector problem: a set of m collectors wish to each obtain a set of n coupons; for this, they can each sample coupons uniformly at random, but can also meet in pairwise interactions, during which they can exchange coupons. By doing so, they hope to reduce the number of coupons that must be sampled by each collector in order to obtain a full set. This extension is natural when considering real-world manifestations of the coupon collector phenomenon, and has been remarked upon and studied empirically (Hayes and Hannigan 2006, Ahmad et al. 2014, Delmarcelle 2019).\r\n\r\nWe provide the first theoretical analysis for such a scenario. We find that “coupon collecting with friends” can indeed significantly reduce the number of coupons each collector must sample, and raises interesting connections to the more traditional variants of the problem. While our analysis is in most cases asymptotically tight, there are several open questions raised, regarding finer-grained analysis of both “coupon collecting with friends,” and of a long-studied variant of the original problem in which a collector requires multiple full sets of coupons.","lang":"eng"}],"has_accepted_license":"1","status":"public","external_id":{"isi":["001292788400001"]},"oa_version":"Preprint","scopus_import":"1","publication":"Structural Information and Communication Complexity","date_created":"2021-07-01T11:04:43Z","type":"conference","ec_funded":1,"citation":{"ista":"Alistarh D-A, Davies P. 2021. Collecting coupons is faster with friends. Structural Information and Communication Complexity. SIROCCO: International Colloquium on Structural Information and Communication Complexity, LNCS, vol. 12810, 3–12.","ieee":"D.-A. Alistarh and P. Davies, “Collecting coupons is faster with friends,” in <i>Structural Information and Communication Complexity</i>, Wrocław, Poland, 2021, vol. 12810, pp. 3–12.","ama":"Alistarh D-A, Davies P. Collecting coupons is faster with friends. In: <i>Structural Information and Communication Complexity</i>. Vol 12810. Springer Nature; 2021:3-12. doi:<a href=\"https://doi.org/10.1007/978-3-030-79527-6_1\">10.1007/978-3-030-79527-6_1</a>","apa":"Alistarh, D.-A., &#38; Davies, P. (2021). Collecting coupons is faster with friends. In <i>Structural Information and Communication Complexity</i> (Vol. 12810, pp. 3–12). Wrocław, Poland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-79527-6_1\">https://doi.org/10.1007/978-3-030-79527-6_1</a>","short":"D.-A. Alistarh, P. Davies, in:, Structural Information and Communication Complexity, Springer Nature, 2021, pp. 3–12.","mla":"Alistarh, Dan-Adrian, and Peter Davies. “Collecting Coupons Is Faster with Friends.” <i>Structural Information and Communication Complexity</i>, vol. 12810, Springer Nature, 2021, pp. 3–12, doi:<a href=\"https://doi.org/10.1007/978-3-030-79527-6_1\">10.1007/978-3-030-79527-6_1</a>.","chicago":"Alistarh, Dan-Adrian, and Peter Davies. “Collecting Coupons Is Faster with Friends.” In <i>Structural Information and Communication Complexity</i>, 12810:3–12. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-79527-6_1\">https://doi.org/10.1007/978-3-030-79527-6_1</a>."},"language":[{"iso":"eng"}]},{"article_processing_charge":"No","publication_identifier":{"eissn":["2542-5293"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation","day":"03","department":[{"_id":"MaIb"}],"_id":"9626","date_published":"2021-06-03T00:00:00Z","quality_controlled":"1","article_number":"100452","acknowledgement":"This work was supported by National Natural Science Foundation of China (51772012), National Key Research and Development Program of China (2018YFA0702100 and 2018YFB0703600), the Beijing Natural Science Foundation (JQ18004). This work was also supported by Lise Meitner Project (M2889-N) and the National Postdoctoral Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the High Performance Computing (HPC) resources at Beihang University, the National Science Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science and Technology Advanced Research (HPSTAR) for SEM measurements.","isi":1,"doi":"10.1016/j.mtphys.2021.100452","publisher":"Elsevier","author":[{"full_name":"Su, Lizhong","first_name":"Lizhong","last_name":"Su"},{"full_name":"Hong, Tao","first_name":"Tao","last_name":"Hong"},{"full_name":"Wang, Dongyang","first_name":"Dongyang","last_name":"Wang"},{"full_name":"Wang, Sining","first_name":"Sining","last_name":"Wang"},{"last_name":"Qin","first_name":"Bingchao","full_name":"Qin, Bingchao"},{"first_name":"Mengmeng","last_name":"Zhang","full_name":"Zhang, Mengmeng"},{"last_name":"Gao","first_name":"Xiang","full_name":"Gao, Xiang"},{"full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","first_name":"Cheng","last_name":"Chang"},{"last_name":"Zhao","first_name":"Li Dong","full_name":"Zhao, Li Dong"}],"year":"2021","publication_status":"published","volume":20,"month":"06","oa_version":"None","publication":"Materials Today Physics","scopus_import":"1","date_created":"2021-07-04T22:01:24Z","corr_author":"1","type":"journal_article","abstract":[{"text":"SnSe, a wide-bandgap semiconductor, has attracted significant attention from the thermoelectric (TE) community due to its outstanding TE performance deriving from the ultralow thermal conductivity and advantageous electronic structures. Here, we promoted the TE performance of n-type SnSe polycrystals through bandgap engineering and vacancy compensation. We found that PbTe can significantly reduce the wide bandgap of SnSe to reduce the impurity transition energy, largely enhancing the carrier concentration. Also, PbTe-induced crystal symmetry promotion increases the carrier mobility, preserving large Seebeck coefficient. Consequently, a maximum ZT of ∼1.4 at 793 K is obtained in Br doped SnSe–13%PbTe. Furthermore, we found that extra Sn in n-type SnSe can compensate for the intrinsic Sn vacancies and form electron donor-like metallic Sn nanophases. The Sn nanophases near the grain boundary could also reduce the intergrain energy barrier which largely enhances the carrier mobility. As a result, a maximum ZT value of ∼1.7 at 793 K and an average ZT (ZTave) of ∼0.58 in 300–793 K are achieved in Br doped Sn1.08Se–13%PbTe. Our findings provide a novel strategy to promote the TE performance in wide-bandgap semiconductors.","lang":"eng"}],"status":"public","external_id":{"isi":["000703159600010"]},"article_type":"original","citation":{"apa":"Su, L., Hong, T., Wang, D., Wang, S., Qin, B., Zhang, M., … Zhao, L. D. (2021). Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. <i>Materials Today Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mtphys.2021.100452\">https://doi.org/10.1016/j.mtphys.2021.100452</a>","ista":"Su L, Hong T, Wang D, Wang S, Qin B, Zhang M, Gao X, Chang C, Zhao LD. 2021. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 20, 100452.","ama":"Su L, Hong T, Wang D, et al. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. <i>Materials Today Physics</i>. 2021;20. doi:<a href=\"https://doi.org/10.1016/j.mtphys.2021.100452\">10.1016/j.mtphys.2021.100452</a>","ieee":"L. Su <i>et al.</i>, “Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation,” <i>Materials Today Physics</i>, vol. 20. Elsevier, 2021.","mla":"Su, Lizhong, et al. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” <i>Materials Today Physics</i>, vol. 20, 100452, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.mtphys.2021.100452\">10.1016/j.mtphys.2021.100452</a>.","short":"L. Su, T. Hong, D. Wang, S. Wang, B. Qin, M. Zhang, X. Gao, C. Chang, L.D. Zhao, Materials Today Physics 20 (2021).","chicago":"Su, Lizhong, Tao Hong, Dongyang Wang, Sining Wang, Bingchao Qin, Mengmeng Zhang, Xiang Gao, Cheng Chang, and Li Dong Zhao. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” <i>Materials Today Physics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.mtphys.2021.100452\">https://doi.org/10.1016/j.mtphys.2021.100452</a>."},"language":[{"iso":"eng"}],"intvolume":"        20","date_updated":"2024-10-09T21:00:40Z"},{"intvolume":"        64","arxiv":1,"ddc":["500"],"date_updated":"2026-06-18T19:54:27Z","main_file_link":[{"url":"https://doi.org/10.1017/S0013091521000080","open_access":"1"}],"type":"journal_article","corr_author":"1","date_created":"2021-07-04T22:01:24Z","oa_version":"Published Version","scopus_import":"1","publication":"Proceedings of the Edinburgh Mathematical Society","external_id":{"isi":["000721363700003"],"arxiv":["1912.03670"]},"status":"public","abstract":[{"lang":"eng","text":"We compute the deficiency spaces of operators of the form 𝐻𝐴⊗̂ 𝐼+𝐼⊗̂ 𝐻𝐵, for symmetric 𝐻𝐴 and self-adjoint 𝐻𝐵. This enables us to construct self-adjoint extensions (if they exist) by means of von Neumann's theory. The structure of the deficiency spaces for this case was asserted already in Ibort et al. [Boundary dynamics driven entanglement, J. Phys. A: Math. Theor. 47(38) (2014) 385301], but only proven under the restriction of 𝐻𝐵 having discrete, non-degenerate spectrum."}],"language":[{"iso":"eng"}],"citation":{"chicago":"Lenz, Daniel, Timon Weinmann, and Melchior Wirth. “Self-Adjoint Extensions of Bipartite Hamiltonians.” <i>Proceedings of the Edinburgh Mathematical Society</i>. Cambridge University Press, 2021. <a href=\"https://doi.org/10.1017/S0013091521000080\">https://doi.org/10.1017/S0013091521000080</a>.","ama":"Lenz D, Weinmann T, Wirth M. Self-adjoint extensions of bipartite Hamiltonians. <i>Proceedings of the Edinburgh Mathematical Society</i>. 2021;64(3):443-447. doi:<a href=\"https://doi.org/10.1017/S0013091521000080\">10.1017/S0013091521000080</a>","ieee":"D. Lenz, T. Weinmann, and M. Wirth, “Self-adjoint extensions of bipartite Hamiltonians,” <i>Proceedings of the Edinburgh Mathematical Society</i>, vol. 64, no. 3. Cambridge University Press, pp. 443–447, 2021.","ista":"Lenz D, Weinmann T, Wirth M. 2021. Self-adjoint extensions of bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society. 64(3), 443–447.","apa":"Lenz, D., Weinmann, T., &#38; Wirth, M. (2021). Self-adjoint extensions of bipartite Hamiltonians. <i>Proceedings of the Edinburgh Mathematical Society</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0013091521000080\">https://doi.org/10.1017/S0013091521000080</a>","short":"D. Lenz, T. Weinmann, M. Wirth, Proceedings of the Edinburgh Mathematical Society 64 (2021) 443–447.","mla":"Lenz, Daniel, et al. “Self-Adjoint Extensions of Bipartite Hamiltonians.” <i>Proceedings of the Edinburgh Mathematical Society</i>, vol. 64, no. 3, Cambridge University Press, 2021, pp. 443–47, doi:<a href=\"https://doi.org/10.1017/S0013091521000080\">10.1017/S0013091521000080</a>."},"article_type":"original","year":"2021","publication_status":"published","volume":64,"issue":"3","month":"08","author":[{"last_name":"Lenz","first_name":"Daniel","full_name":"Lenz, Daniel"},{"full_name":"Weinmann, Timon","last_name":"Weinmann","first_name":"Timon"},{"last_name":"Wirth","first_name":"Melchior","orcid":"0000-0002-0519-4241","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","full_name":"Wirth, Melchior"}],"page":"443-447","isi":1,"doi":"10.1017/S0013091521000080","acknowledgement":"M. W. gratefully acknowledges financial support by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes). T.W. thanks PAO Gazprom Neft, the Euler International Mathematical Institute in Saint Petersburg and ORISA GmbH for their financial support in the form of scholarships during his Master's and Bachelor's studies respectively. The authors want to thank Mark Malamud for pointing out the reference [1] to them. This work was supported by the Ministry of Science and Higher Education of the Russian Federation, agreement No 075-15-2019-1619.","publisher":"Cambridge University Press","quality_controlled":"1","_id":"9627","date_published":"2021-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Self-adjoint extensions of bipartite Hamiltonians","oa":1,"day":"01","department":[{"_id":"JaMa"}],"article_processing_charge":"No","publication_identifier":{"eissn":["1464-3839"],"issn":["0013-0915"]}},{"publication_status":"published","year":"2021","month":"06","volume":23,"author":[{"first_name":"Qiutan","last_name":"Yang","full_name":"Yang, Qiutan"},{"first_name":"Shi-lei","last_name":"Xue","full_name":"Xue, Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chan","first_name":"Chii Jou","full_name":"Chan, Chii Jou"},{"full_name":"Rempfler, Markus","last_name":"Rempfler","first_name":"Markus"},{"full_name":"Vischi, Dario","first_name":"Dario","last_name":"Vischi"},{"first_name":"Francisca","last_name":"Maurer-Gutierrez","full_name":"Maurer-Gutierrez, Francisca"},{"first_name":"Takashi","last_name":"Hiiragi","full_name":"Hiiragi, Takashi"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Liberali, Prisca","last_name":"Liberali","first_name":"Prisca"}],"page":"733–744","pmid":1,"date_updated":"2025-04-14T07:52:26Z","intvolume":"        23","project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639"}],"status":"public","external_id":{"isi":["000664016300003"],"pmid":["34155381"]},"abstract":[{"lang":"eng","text":"Intestinal organoids derived from single cells undergo complex crypt–villus patterning and morphogenesis. However, the nature and coordination of the underlying forces remains poorly characterized. Here, using light-sheet microscopy and large-scale imaging quantification, we demonstrate that crypt formation coincides with a stark reduction in lumen volume. We develop a 3D biophysical model to computationally screen different mechanical scenarios of crypt morphogenesis. Combining this with live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven crypt apical contraction and villus basal tension work synergistically with lumen volume reduction to drive crypt morphogenesis, and demonstrate the existence of a critical point in differential tensions above which crypt morphology becomes robust to volume changes. Finally, we identified a sodium/glucose cotransporter that is specific to differentiated enterocytes that modulates lumen volume reduction through cell swelling in the villus region. Together, our study uncovers the cellular basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust morphogenesis."}],"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.13.094359"}],"corr_author":"1","oa_version":"Preprint","date_created":"2021-07-04T22:01:25Z","publication":"Nature Cell Biology","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"mla":"Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” <i>Nature Cell Biology</i>, vol. 23, Springer Nature, 2021, pp. 733–744, doi:<a href=\"https://doi.org/10.1038/s41556-021-00700-2\">10.1038/s41556-021-00700-2</a>.","short":"Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez, T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.","apa":"Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez, F., … Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. <i>Nature Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41556-021-00700-2\">https://doi.org/10.1038/s41556-021-00700-2</a>","ieee":"Q. Yang <i>et al.</i>, “Cell fate coordinates mechano-osmotic forces in intestinal crypt formation,” <i>Nature Cell Biology</i>, vol. 23. Springer Nature, pp. 733–744, 2021.","ista":"Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 23, 733–744.","ama":"Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. <i>Nature Cell Biology</i>. 2021;23:733–744. doi:<a href=\"https://doi.org/10.1038/s41556-021-00700-2\">10.1038/s41556-021-00700-2</a>","chicago":"Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi, Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” <i>Nature Cell Biology</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41556-021-00700-2\">https://doi.org/10.1038/s41556-021-00700-2</a>."},"ec_funded":1,"article_type":"original","title":"Cell fate coordinates mechano-osmotic forces in intestinal crypt formation","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"EdHa"}],"day":"21","publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]},"article_processing_charge":"No","publisher":"Springer Nature","isi":1,"doi":"10.1038/s41556-021-00700-2","acknowledgement":"We acknowledge the members of the Lennon-Duménil laboratory for sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali laboratory and the FMI facilities for their support. We thank E. Tagliavini for IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531, to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to E.H.).","date_published":"2021-06-21T00:00:00Z","_id":"9629","quality_controlled":"1"},{"department":[{"_id":"AnHi"}],"related_material":{"record":[{"relation":"used_in_publication","id":"10029","status":"public"}]},"file_date_updated":"2021-07-07T20:37:28Z","oa":1,"title":"Data for \"Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid\"","year":"2021","license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_processing_charge":"No","author":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham"}],"publisher":"Institute of Science and Technology Austria","file":[{"date_created":"2021-07-07T20:37:28Z","content_type":"application/zip","access_level":"open_access","relation":"main_file","creator":"ahigginb","date_updated":"2021-07-07T20:37:28Z","file_name":"figures_data.zip","file_id":"9637","checksum":"18e90687ec7bbd75f8bfea4d8293fb30","success":1,"file_size":3345244}],"date_updated":"2025-04-15T06:54:43Z","citation":{"mla":"Higginbotham, Andrew P. <i>Data for “Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.”</i> Institute of Science and Technology Austria, 2021.","short":"A.P. Higginbotham, (2021).","apa":"Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.","ieee":"A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.’” Institute of Science and Technology Austria, 2021.","ista":"Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria.","ama":"Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 2021.","chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021."},"date_published":"2021-01-01T00:00:00Z","_id":"9636","status":"public","has_accepted_license":"1","date_created":"2021-07-07T20:43:10Z","oa_version":"Submitted Version","type":"research_data"},{"file_date_updated":"2021-07-19T13:02:20Z","publication_status":"published","year":"2021","month":"06","volume":12,"issue":"1","author":[{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"first_name":"Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"pmid":1,"ddc":["510"],"date_updated":"2026-04-02T14:04:10Z","intvolume":"        12","project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000671752100003"],"pmid":["34188036"]},"has_accepted_license":"1","status":"public","abstract":[{"text":"Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed.","lang":"eng"}],"type":"journal_article","date_created":"2021-07-11T22:01:15Z","oa_version":"Published Version","publication":"Nature Communications","scopus_import":"1","language":[{"iso":"eng"}],"ec_funded":1,"article_type":"original","citation":{"mla":"Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” <i>Nature Communications</i>, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-24271-w\">10.1038/s41467-021-24271-w</a>.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications 12 (2021).","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., &#38; Nowak, M. A. (2021). Fast and strong amplifiers of natural selection. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-24271-w\">https://doi.org/10.1038/s41467-021-24271-w</a>","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers of natural selection. Nature Communications. 12(1), 4009.","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong amplifiers of natural selection,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-24271-w\">10.1038/s41467-021-24271-w</a>","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-24271-w\">https://doi.org/10.1038/s41467-021-24271-w</a>."},"title":"Fast and strong amplifiers of natural selection","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"KrCh"}],"day":"29","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2041-1723"]},"article_processing_charge":"No","publisher":"Springer Nature","file":[{"date_created":"2021-07-19T13:02:20Z","content_type":"application/pdf","creator":"cziletti","relation":"main_file","access_level":"open_access","checksum":"5767418926a7f7fb76151de29473dae0","success":1,"file_name":"2021_NatCoom_Tkadlec.pdf","file_id":"9692","date_updated":"2021-07-19T13:02:20Z","file_size":628992}],"isi":1,"acknowledgement":"K.C. acknowledges support from ERC Start grant no. (279307: Graph Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF) grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","doi":"10.1038/s41467-021-24271-w","article_number":"4009","_id":"9640","date_published":"2021-06-29T00:00:00Z","quality_controlled":"1"},{"article_number":"107486","quality_controlled":"1","_id":"9641","date_published":"2021-06-30T00:00:00Z","publisher":"Elsevier","file":[{"file_size":1994793,"checksum":"8e8298a9e8c7df146ad23f32c2a63929","success":1,"date_updated":"2021-07-19T13:46:06Z","file_id":"9694","file_name":"2021_NeurobLearnMemory_Fredes.pdf","relation":"main_file","creator":"cziletti","access_level":"open_access","date_created":"2021-07-19T13:46:06Z","content_type":"application/pdf"}],"acknowledgement":"This work was supported by a European Research Council Advanced Grant 694539 to Ryuichi Shigemoto.","doi":"10.1016/j.nlm.2021.107486","isi":1,"publication_identifier":{"eissn":["1095-9564"],"issn":["1074-7427"]},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_processing_charge":"No","oa":1,"title":"The role of hippocampal mossy cells in novelty detection","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RySh"}],"day":"30","abstract":[{"lang":"eng","text":"At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation."}],"status":"public","has_accepted_license":"1","external_id":{"pmid":["34214666"],"isi":["000677694900004"]},"publication":"Neurobiology of Learning and Memory","oa_version":"Published Version","scopus_import":"1","date_created":"2021-07-11T22:01:16Z","type":"journal_article","article_type":"original","citation":{"short":"F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).","mla":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” <i>Neurobiology of Learning and Memory</i>, vol. 183, 107486, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">10.1016/j.nlm.2021.107486</a>.","ama":"Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection. <i>Neurobiology of Learning and Memory</i>. 2021;183. doi:<a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">10.1016/j.nlm.2021.107486</a>","ista":"Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 183, 107486.","ieee":"F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty detection,” <i>Neurobiology of Learning and Memory</i>, vol. 183. Elsevier, 2021.","apa":"Fredes, F., &#38; Shigemoto, R. (2021). The role of hippocampal mossy cells in novelty detection. <i>Neurobiology of Learning and Memory</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">https://doi.org/10.1016/j.nlm.2021.107486</a>","chicago":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” <i>Neurobiology of Learning and Memory</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">https://doi.org/10.1016/j.nlm.2021.107486</a>."},"ec_funded":1,"language":[{"iso":"eng"}],"date_updated":"2025-07-10T12:02:00Z","ddc":["610"],"intvolume":"       183","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"}],"author":[{"first_name":"Felipe","last_name":"Fredes","full_name":"Fredes, Felipe"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"}],"pmid":1,"publication_status":"published","file_date_updated":"2021-07-19T13:46:06Z","year":"2021","month":"06","volume":183},{"_id":"9642","quality_controlled":"1","date_published":"2021-07-06T00:00:00Z","article_number":"109313","isi":1,"acknowledgement":"We thank the scientific service units at IST Austria, especially the IST bioimaging facility, the preclinical facility, and, specifically, Michael Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King, and all Siegert group members for constant feedback on the project and manuscript; Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination for OD plasticity experiments; and Ana Morello from MIT for technical assistance with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian Academy of Sciences at the Institute of Science and Technology Austria to R.S., from the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the European Research Council (grant 715571 to S.S.), and the National Eye Institute of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.) and R01EY023037 (diversity supplement to H.D.J-C.).","doi":"10.1016/j.celrep.2021.109313","file":[{"file_size":56388540,"checksum":"f056255f6d01fd9a86b5387635928173","success":1,"file_name":"2021_CellReports_Venturino.pdf","file_id":"9693","date_updated":"2021-07-19T13:32:17Z","creator":"cziletti","relation":"main_file","access_level":"open_access","date_created":"2021-07-19T13:32:17Z","content_type":"application/pdf"}],"publisher":"Elsevier","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2211-1247"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain","oa":1,"day":"06","department":[{"_id":"SaSi"}],"type":"journal_article","publication":"Cell Reports","date_created":"2021-07-11T22:01:16Z","oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","external_id":{"pmid":["34233180"],"isi":["000670188500004"]},"status":"public","abstract":[{"text":"Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain.","lang":"eng"}],"language":[{"iso":"eng"}],"ec_funded":1,"article_type":"original","citation":{"ama":"Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. <i>Cell Reports</i>. 2021;36(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">10.1016/j.celrep.2021.109313</a>","ieee":"A. Venturino <i>et al.</i>, “Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,” <i>Cell Reports</i>, vol. 36, no. 1. Elsevier, 2021.","ista":"Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar F, Colombo G, Cubero RJ, Miteva FE, Bear MF, Siegert S. 2021. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.","apa":"Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar, F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">https://doi.org/10.1016/j.celrep.2021.109313</a>","short":"A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar, G. Colombo, R.J. Cubero, F.E. Miteva, M.F. Bear, S. Siegert, Cell Reports 36 (2021).","mla":"Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” <i>Cell Reports</i>, vol. 36, no. 1, 109313, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">10.1016/j.celrep.2021.109313</a>.","chicago":"Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” <i>Cell Reports</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">https://doi.org/10.1016/j.celrep.2021.109313</a>."},"intvolume":"        36","ddc":["570"],"date_updated":"2026-04-03T09:46:05Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"715571","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease","_id":"25D4A630-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","first_name":"Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino"},{"orcid":"0000-0001-5297-733X","first_name":"Rouven","last_name":"Schulz","full_name":"Schulz, Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Héctor","last_name":"De Jesús-Cortés","full_name":"De Jesús-Cortés, Héctor"},{"full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","orcid":"0000-0001-9642-1085","first_name":"Margaret E"},{"last_name":"Nagy","first_name":"Balint","id":"93C65ECC-A6F2-11E9-8DF9-9712E6697425","full_name":"Nagy, Balint"},{"full_name":"Reilly-Andújar, Francis","last_name":"Reilly-Andújar","first_name":"Francis"},{"last_name":"Colombo","first_name":"Gloria","orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","full_name":"Colombo, Gloria"},{"first_name":"Ryan J","orcid":"0000-0003-0002-1867","last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425","full_name":"Cubero, Ryan J"},{"id":"3526230C-F248-11E8-B48F-1D18A9856A87","full_name":"Schoot Uiterkamp, Florianne E","first_name":"Florianne E","last_name":"Schoot Uiterkamp"},{"first_name":"Mark F.","last_name":"Bear","full_name":"Bear, Mark F."},{"first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"pmid":1,"year":"2021","publication_status":"published","file_date_updated":"2021-07-19T13:32:17Z","volume":36,"issue":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-twinkle-and-the-brain/","description":"News on IST Homepage","relation":"press_release"}]},"month":"07"},{"publisher":"Association for Computing Machinery","isi":1,"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was partially supported by the ERCCoG 863818 (ForM-SMArt) and the Czech Science Foundation grant No. GJ19-15134Y.","doi":"10.1145/3453483.3454093","conference":{"location":"Online","start_date":"2021-06-20","end_date":"2021-06-26","name":"PLDI: Programming Language Design and Implementation"},"date_published":"2021-06-01T00:00:00Z","_id":"9644","quality_controlled":"1","department":[{"_id":"KrCh"}],"day":"01","oa":1,"title":"Proving non-termination by program reversal","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"isbn":["9781450383912"]},"article_processing_charge":"No","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"}],"date_updated":"2026-04-07T13:27:55Z","arxiv":1,"ec_funded":1,"citation":{"short":"K. Chatterjee, E.K. Goharshady, P. Novotný, D. Zikelic, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1033–1048.","mla":"Chatterjee, Krishnendu, et al. “Proving Non-Termination by Program Reversal.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 1033–48, doi:<a href=\"https://doi.org/10.1145/3453483.3454093\">10.1145/3453483.3454093</a>.","ista":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. 2021. Proving non-termination by program reversal. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1033–1048.","ieee":"K. Chatterjee, E. K. Goharshady, P. Novotný, and D. Zikelic, “Proving non-termination by program reversal,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 1033–1048.","ama":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. Proving non-termination by program reversal. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:1033-1048. doi:<a href=\"https://doi.org/10.1145/3453483.3454093\">10.1145/3453483.3454093</a>","apa":"Chatterjee, K., Goharshady, E. K., Novotný, P., &#38; Zikelic, D. (2021). Proving non-termination by program reversal. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 1033–1048). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454093\">https://doi.org/10.1145/3453483.3454093</a>","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, and Dorde Zikelic. “Proving Non-Termination by Program Reversal.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 1033–48. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454093\">https://doi.org/10.1145/3453483.3454093</a>."},"language":[{"iso":"eng"}],"abstract":[{"text":"We present a new approach to proving non-termination of non-deterministic integer programs. Our technique is rather simple but efficient. It relies on a purely syntactic reversal of the program's transition system followed by a constraint-based invariant synthesis with constraints coming from both the original and the reversed transition system. The latter task is performed by a simple call to an off-the-shelf SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover, our method offers a combination of features not present (as a whole) in previous approaches: it handles programs with non-determinism, provides relative completeness guarantees and supports programs with polynomial arithmetic. The experiments performed with our prototype tool RevTerm show that our approach, despite its simplicity and stronger theoretical guarantees, is at least on par with the state-of-the-art tools, often achieving a non-trivial improvement under a proper configuration of its parameters.","lang":"eng"}],"status":"public","external_id":{"isi":["000723661700067"],"arxiv":["2104.01189"]},"scopus_import":"1","oa_version":"Preprint","date_created":"2021-07-11T22:01:17Z","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.01189"}],"month":"06","related_material":{"record":[{"relation":"research_data","status":"public","id":"15284"},{"id":"14539","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","year":"2021","page":"1033-1048","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Goharshady","first_name":"Ehsan Kafshdar","full_name":"Goharshady, Ehsan Kafshdar"},{"last_name":"Novotný","first_name":"Petr","full_name":"Novotný, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","first_name":"Dorde","last_name":"Zikelic"}]},{"conference":{"location":"Online","start_date":"2021-06-20","end_date":"2021-06-26","name":"PLDI: Programming Language Design and Implementation"},"publisher":"Association for Computing Machinery","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).","isi":1,"doi":"10.1145/3453483.3454076","date_published":"2021-06-01T00:00:00Z","_id":"9645","quality_controlled":"1","oa":1,"title":"Polynomial reachability witnesses via Stellensätze","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"day":"01","publication_identifier":{"isbn":["9781450383912"]},"article_processing_charge":"No","date_updated":"2025-07-10T12:02:00Z","project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.\r\n\r\nWe first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods.","lang":"eng"}],"external_id":{"isi":["000723661700050"]},"status":"public","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","date_created":"2021-07-11T22:01:17Z","oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-03183862/"}],"type":"conference","citation":{"ista":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 772–787.","ieee":"A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial reachability witnesses via Stellensätze,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 772–787.","ama":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability witnesses via Stellensätze. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:772-787. doi:<a href=\"https://doi.org/10.1145/3453483.3454076\">10.1145/3453483.3454076</a>","apa":"Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., &#38; Mahdavi, M. (2021). Polynomial reachability witnesses via Stellensätze. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 772–787). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454076\">https://doi.org/10.1145/3453483.3454076</a>","short":"A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–787.","mla":"Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 772–87, doi:<a href=\"https://doi.org/10.1145/3453483.3454076\">10.1145/3453483.3454076</a>.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady, and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 772–87. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454076\">https://doi.org/10.1145/3453483.3454076</a>."},"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","year":"2021","month":"06","author":[{"first_name":"Ali","last_name":"Asadi","full_name":"Asadi, Ali"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","last_name":"Fu"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mohammad","last_name":"Mahdavi","full_name":"Mahdavi, Mohammad"}],"page":"772-787"}]