[{"date_created":"2022-04-10T22:01:40Z","publication_identifier":{"issn":["0272-5428"],"isbn":["9781665420556"]},"isi":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2012.10584","open_access":"1"}],"date_published":"2022-02-01T00:00:00Z","author":[{"last_name":"Ferber","first_name":"Asaf","full_name":"Ferber, Asaf"},{"orcid":"0000-0002-4003-7567","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan"},{"first_name":"Lisa","full_name":"Sauermann, Lisa","last_name":"Sauermann"}],"conference":{"name":"FOCS: Foundations of Computer Science","location":"Denver, CO, United States","start_date":"2022-02-07","end_date":"2022-02-10"},"page":"720-726","publisher":"IEEE","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"11145","scopus_import":"1","arxiv":1,"oa_version":"Preprint","day":"01","quality_controlled":"1","related_material":{"record":[{"id":"10775","relation":"later_version","status":"public"}]},"abstract":[{"lang":"eng","text":"List-decodability of Reed-Solomon codes has re-ceived a lot of attention, but the best-possible dependence between the parameters is still not well-understood. In this work, we focus on the case where the list-decoding radius is of the form r=1−ε for ε tending to zero. Our main result states that there exist Reed-Solomon codes with rate Ω(ε) which are (1−ε,O(1/ε) -list-decodable, meaning that any Hamming ball of radius 1−ε contains at most O(1/ε) codewords. This trade-off between rate and list-decoding radius is best-possible for any code with list size less than exponential in the block length. By achieving this trade-off between rate and list-decoding radius we improve a recent result of Guo, Li, Shangguan, Tamo, and Wootters, and resolve the main motivating question of their work. Moreover, while their result requires the field to be exponentially large in the block length, we only need the field size to be polynomially large (and in fact, almost-linear suffices). We deduce our main result from a more general theorem, in which we prove good list-decodability properties of random puncturings of any given code with very large distance."}],"type":"conference","publication_status":"published","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","intvolume":"      2022","volume":2022,"oa":1,"date_updated":"2025-07-10T11:50:08Z","publication":"62nd Annual IEEE Symposium on Foundations of Computer Science","citation":{"short":"A. Ferber, M.A. Kwan, L. Sauermann, in:, 62nd Annual IEEE Symposium on Foundations of Computer Science, IEEE, 2022, pp. 720–726.","ieee":"A. Ferber, M. A. Kwan, and L. Sauermann, “List-decodability with large radius for Reed-Solomon codes,” in <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i>, Denver, CO, United States, 2022, vol. 2022, pp. 720–726.","ama":"Ferber A, Kwan MA, Sauermann L. List-decodability with large radius for Reed-Solomon codes. In: <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i>. Vol 2022. IEEE; 2022:720-726. doi:<a href=\"https://doi.org/10.1109/FOCS52979.2021.00075\">10.1109/FOCS52979.2021.00075</a>","ista":"Ferber A, Kwan MA, Sauermann L. 2022. List-decodability with large radius for Reed-Solomon codes. 62nd Annual IEEE Symposium on Foundations of Computer Science. FOCS: Foundations of Computer Science vol. 2022, 720–726.","apa":"Ferber, A., Kwan, M. A., &#38; Sauermann, L. (2022). List-decodability with large radius for Reed-Solomon codes. In <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i> (Vol. 2022, pp. 720–726). Denver, CO, United States: IEEE. <a href=\"https://doi.org/10.1109/FOCS52979.2021.00075\">https://doi.org/10.1109/FOCS52979.2021.00075</a>","mla":"Ferber, Asaf, et al. “List-Decodability with Large Radius for Reed-Solomon Codes.” <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i>, vol. 2022, IEEE, 2022, pp. 720–26, doi:<a href=\"https://doi.org/10.1109/FOCS52979.2021.00075\">10.1109/FOCS52979.2021.00075</a>.","chicago":"Ferber, Asaf, Matthew Alan Kwan, and Lisa Sauermann. “List-Decodability with Large Radius for Reed-Solomon Codes.” In <i>62nd Annual IEEE Symposium on Foundations of Computer Science</i>, 2022:720–26. IEEE, 2022. <a href=\"https://doi.org/10.1109/FOCS52979.2021.00075\">https://doi.org/10.1109/FOCS52979.2021.00075</a>."},"doi":"10.1109/FOCS52979.2021.00075","department":[{"_id":"MaKw"}],"external_id":{"isi":["000802209600065"],"arxiv":["2012.10584"]},"title":"List-decodability with large radius for Reed-Solomon codes","status":"public"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D. This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We thank Dustin Morado for providing the software SubTOM for data processing. We also thank William Wan for critical reading of the manuscript and valuable feedback.","isi":1,"publication_identifier":{"issn":["1047-8477"]},"file_date_updated":"2022-08-02T11:07:58Z","date_created":"2022-04-15T07:10:26Z","ddc":["570"],"issue":"2","_id":"11155","article_number":"107852","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","grant_number":"P31445"}],"scopus_import":"1","author":[{"first_name":"Martin","full_name":"Obr, Martin","orcid":"0000-0003-1756-6564","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wim J.H.","full_name":"Hagen, Wim J.H.","last_name":"Hagen"},{"last_name":"Dick","full_name":"Dick, Robert A.","first_name":"Robert A."},{"last_name":"Yu","first_name":"Lingbo","full_name":"Yu, Lingbo"},{"first_name":"Abhay","full_name":"Kotecha, Abhay","last_name":"Kotecha"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"date_published":"2022-06-01T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","publisher":"Elsevier","has_accepted_license":"1","type":"journal_article","abstract":[{"text":"The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"quality_controlled":"1","corr_author":"1","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"06","year":"2022","publication_status":"published","keyword":["Structural Biology"],"pmid":1,"oa_version":"Published Version","doi":"10.1016/j.jsb.2022.107852","citation":{"short":"M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022).","ieee":"M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs,” <i>Journal of Structural Biology</i>, vol. 214, no. 2. Elsevier, 2022.","ama":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. 2022;214(2). doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>","ista":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 214(2), 107852.","apa":"Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., &#38; Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>","mla":"Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>, vol. 214, no. 2, 107852, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">10.1016/j.jsb.2022.107852</a>.","chicago":"Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” <i>Journal of Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jsb.2022.107852\">https://doi.org/10.1016/j.jsb.2022.107852</a>."},"publication":"Journal of Structural Biology","status":"public","title":"Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs","external_id":{"isi":["000790733600001"],"pmid":["35351542"]},"department":[{"_id":"FlSc"}],"intvolume":"       214","file":[{"file_id":"11722","checksum":"0b1eb53447aae8e95ae4c12d193b0b00","success":1,"relation":"main_file","creator":"dernst","file_size":7080863,"date_created":"2022-08-02T11:07:58Z","content_type":"application/pdf","access_level":"open_access","file_name":"2022_JourStructuralBiology_Obr.pdf","date_updated":"2022-08-02T11:07:58Z"}],"license":"https://creativecommons.org/licenses/by/4.0/","article_type":"original","date_updated":"2025-04-15T08:24:50Z","volume":214,"oa":1},{"author":[{"id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut","full_name":"Kampjut, Domen","first_name":"Domen"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov"}],"date_published":"2022-06-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"publisher":"Elsevier","has_accepted_license":"1","_id":"11167","article_number":"102350","scopus_import":"1","file_date_updated":"2022-08-05T05:56:03Z","date_created":"2022-04-15T09:32:35Z","ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"publication_identifier":{"issn":["0959-440X"]},"intvolume":"        74","file":[{"relation":"main_file","success":1,"file_id":"11725","checksum":"72bdde48853643a32d42b75f54965c44","date_updated":"2022-08-05T05:56:03Z","file_name":"2022_CurrentOpStructBiology_Kampjut.pdf","file_size":815607,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2022-08-05T05:56:03Z"}],"article_type":"original","date_updated":"2024-10-09T21:02:00Z","oa":1,"volume":74,"citation":{"short":"D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022).","ieee":"D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging blueprint for the mechanism,” <i>Current Opinion in Structural Biology</i>, vol. 74. Elsevier, 2022.","ama":"Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. 2022;74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>","ista":"Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350.","apa":"Kampjut, D., &#38; Sazanov, L. A. (2022). Structure of respiratory complex I – An emerging blueprint for the mechanism. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>, vol. 74, 102350, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">10.1016/j.sbi.2022.102350</a>.","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.sbi.2022.102350\">https://doi.org/10.1016/j.sbi.2022.102350</a>."},"doi":"10.1016/j.sbi.2022.102350","publication":"Current Opinion in Structural Biology","status":"public","external_id":{"isi":["000829029500020"],"pmid":["35316665"]},"title":"Structure of respiratory complex I – An emerging blueprint for the mechanism","department":[{"_id":"LeSa"}],"pmid":1,"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I."}],"quality_controlled":"1","corr_author":"1","day":"01","month":"06","year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["Molecular Biology","Structural Biology"],"publication_status":"published"},{"publication_identifier":{"eissn":["2041-1723"]},"isi":1,"acknowledgement":"We are grateful to Bernhard Brutscher, Alicia Vallet, and Adrien Favier for excellent NMR\r\nplatform operation and management. The plasmid coding for TET2 was kindly provided\r\nby Bruno Franzetti and Jerome Boisbouvier (IBS Grenoble). We thank Anne-Marie Villard\r\nand the RoBioMol platform for preparing the loop deletion construct. The RoBioMol\r\nplatform is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEAUGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL (ANR-10-LABX-49-01), financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBHEUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P. S.) and the French Agence Nationale de la Recherche (ANR), under grant ANR-14-ACHN-0016 (M.P. and A.B.).","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"date_created":"2022-04-17T22:01:45Z","file_date_updated":"2022-05-02T08:48:00Z","scopus_import":"1","article_number":"1927","_id":"11179","has_accepted_license":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2022-04-08T00:00:00Z","author":[{"last_name":"Gauto","first_name":"Diego F.","full_name":"Gauto, Diego F."},{"last_name":"Macek","first_name":"Pavel","full_name":"Macek, Pavel"},{"full_name":"Malinverni, Duccio","first_name":"Duccio","last_name":"Malinverni"},{"first_name":"Hugo","full_name":"Fraga, Hugo","last_name":"Fraga"},{"last_name":"Paloni","first_name":"Matteo","full_name":"Paloni, Matteo"},{"last_name":"Sučec","full_name":"Sučec, Iva","first_name":"Iva"},{"last_name":"Hessel","full_name":"Hessel, Audrey","first_name":"Audrey"},{"last_name":"Bustamante","first_name":"Juan Pablo","full_name":"Bustamante, Juan Pablo"},{"full_name":"Barducci, Alessandro","first_name":"Alessandro","last_name":"Barducci"},{"full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","year":"2022","day":"08","corr_author":"1","quality_controlled":"1","abstract":[{"lang":"eng","text":"Large oligomeric enzymes control a myriad of cellular processes, from protein synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase, a prototypical protease important for cellular homeostasis, degrades peptides within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms of substrate trafficking and processing remain debated. Here, we integrate magic-angle spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics simulations and reveal that a loop in the catalytic chamber is a key element for enzymatic function. The loop is able to stabilize ligands in the active site and may additionally have a direct role in activating the catalytic water molecule whereby a conserved histidine plays a key role. Our data provide a strong case for the functional importance of highly dynamic - and often overlooked - parts of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic resolution."}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-31243-1"}]},"type":"journal_article","oa_version":"Published Version","pmid":1,"department":[{"_id":"PaSc"}],"external_id":{"pmid":["35395851"],"isi":["000781498700009"]},"title":"Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR","status":"public","publication":"Nature Communications","doi":"10.1038/s41467-022-29423-0","citation":{"ista":"Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante JP, Barducci A, Schanda P. 2022. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nature Communications. 13, 1927.","ama":"Gauto DF, Macek P, Malinverni D, et al. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-29423-0\">10.1038/s41467-022-29423-0</a>","ieee":"D. F. Gauto <i>et al.</i>, “Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","short":"D.F. Gauto, P. Macek, D. Malinverni, H. Fraga, M. Paloni, I. Sučec, A. Hessel, J.P. Bustamante, A. Barducci, P. Schanda, Nature Communications 13 (2022).","chicago":"Gauto, Diego F., Pavel Macek, Duccio Malinverni, Hugo Fraga, Matteo Paloni, Iva Sučec, Audrey Hessel, Juan Pablo Bustamante, Alessandro Barducci, and Paul Schanda. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop Revealed by MAS NMR.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-29423-0\">https://doi.org/10.1038/s41467-022-29423-0</a>.","mla":"Gauto, Diego F., et al. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop Revealed by MAS NMR.” <i>Nature Communications</i>, vol. 13, 1927, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-29423-0\">10.1038/s41467-022-29423-0</a>.","apa":"Gauto, D. F., Macek, P., Malinverni, D., Fraga, H., Paloni, M., Sučec, I., … Schanda, P. (2022). Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-29423-0\">https://doi.org/10.1038/s41467-022-29423-0</a>"},"volume":13,"oa":1,"date_updated":"2025-06-11T13:31:55Z","article_type":"original","intvolume":"        13","file":[{"file_id":"11348","checksum":"db61d5534e988743d6266d3675d77b08","success":1,"relation":"main_file","content_type":"application/pdf","date_created":"2022-05-02T08:48:00Z","access_level":"open_access","creator":"dernst","file_size":2637590,"date_updated":"2022-05-02T08:48:00Z","file_name":"2022_NatureCommunications_Gauto.pdf"}]},{"publisher":"Association for Computing Machinery","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2022-04-02T00:00:00Z","conference":{"start_date":"2022-04-02","end_date":"2022-04-06","location":"Seoul, Republic of Korea","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"page":"353-367","author":[{"first_name":"Anastasiia","full_name":"Postnikova, Anastasiia","last_name":"Postnikova"},{"first_name":"Nikita","full_name":"Koval, Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Giorgi","full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","orcid":"0000-0001-5634-0731","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"scopus_import":"1","_id":"11180","date_created":"2022-04-17T22:01:46Z","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.00657"}],"acknowledgement":"We would like to thank the anonymous reviewers for their useful comments. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML).","publication_identifier":{"isbn":["9781450392044"]},"isi":1,"oa":1,"date_updated":"2025-04-14T07:49:13Z","title":"Multi-queues can be state-of-the-art priority schedulers","external_id":{"isi":["000883318200025"],"arxiv":["2109.00657"]},"status":"public","department":[{"_id":"DaAl"}],"publication":"Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","ec_funded":1,"doi":"10.1145/3503221.3508432","citation":{"ieee":"A. Postnikova, N. Koval, G. Nadiradze, and D.-A. Alistarh, “Multi-queues can be state-of-the-art priority schedulers,” in <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Seoul, Republic of Korea, 2022, pp. 353–367.","short":"A. Postnikova, N. Koval, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2022, pp. 353–367.","ista":"Postnikova A, Koval N, Nadiradze G, Alistarh D-A. 2022. Multi-queues can be state-of-the-art priority schedulers. Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 353–367.","ama":"Postnikova A, Koval N, Nadiradze G, Alistarh D-A. Multi-queues can be state-of-the-art priority schedulers. In: <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2022:353-367. doi:<a href=\"https://doi.org/10.1145/3503221.3508432\">10.1145/3503221.3508432</a>","chicago":"Postnikova, Anastasiia, Nikita Koval, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” In <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 353–67. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3503221.3508432\">https://doi.org/10.1145/3503221.3508432</a>.","mla":"Postnikova, Anastasiia, et al. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2022, pp. 353–67, doi:<a href=\"https://doi.org/10.1145/3503221.3508432\">10.1145/3503221.3508432</a>.","apa":"Postnikova, A., Koval, N., Nadiradze, G., &#38; Alistarh, D.-A. (2022). Multi-queues can be state-of-the-art priority schedulers. In <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 353–367). Seoul, Republic of Korea: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3503221.3508432\">https://doi.org/10.1145/3503221.3508432</a>"},"oa_version":"Preprint","arxiv":1,"publication_status":"published","month":"04","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","abstract":[{"text":"Designing and implementing efficient parallel priority schedulers is an active research area. An intriguing proposed design is the Multi-Queue: given n threads and m ≥ n distinct priority queues, task insertions are performed uniformly at random, while, to delete, a thread picks two queues uniformly at random, and removes the observed task of higher priority. This approach scales well, and has probabilistic rank guarantees: roughly, the rank of each task removed, relative to remaining tasks in all other queues, is O (m) in expectation. Yet, the performance of this pattern is below that of well-engineered schedulers, which eschew theoretical guarantees for practical efficiency.\r\n\r\nWe investigate whether it is possible to design and implement a Multi-Queue-based task scheduler that is both highly-efficient and has analytical guarantees. We propose a new variant called the Stealing Multi-Queue (SMQ), a cache-efficient variant of the Multi-Queue, which leverages both queue affinity---each thread has a local queue, from which tasks are usually removed; but, with some probability, threads also attempt to steal higher-priority tasks from the other queues---and task batching, that is, the processing of several tasks in a single insert / remove step. These ideas are well-known for task scheduling without priorities; our theoretical contribution is showing that, despite relaxations, this design can still provide rank guarantees, which in turn implies bounds on total work performed. We provide a general SMQ implementation which can surpass state-of-the-art schedulers such as OBIM and PMOD in terms of performance on popular graph-processing benchmarks. Notably, the performance improvement comes mainly from the superior rank guarantees provided by our scheduler, confirming that analytically-reasoned approaches can still provide performance improvements for priority task scheduling.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"13076","relation":"research_data"}]},"type":"conference","day":"02","quality_controlled":"1","corr_author":"1"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Collaborative Research and Development grant: CRDPJ 539431-19, the\r\nCanada Foundation for Innovation John R. Evans Leaders Fund with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512, Waterloo Huawei Joint Innovation Lab project “Scalable Infrastructure for Next Generation Data Management Systems”, NSERC Discovery Launch Supplement: DGECR-2019-00048, NSERC Discovery\r\nProgram under the grants: RGPIN-2019-04227 and RGPIN04512-2018, and the University of Waterloo. We would also like to thank the reviewers for their insightful comments.","isi":1,"publication_identifier":{"isbn":["9781450392044"]},"file_date_updated":"2022-08-05T09:19:29Z","date_created":"2022-04-17T22:01:46Z","ddc":["000"],"_id":"11181","scopus_import":"1","page":"385-399","author":[{"full_name":"Brown, Trevor A","first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown"},{"first_name":"William","full_name":"Sigouin, William","last_name":"Sigouin"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"}],"conference":{"name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","location":"Seoul, Republic of Korea","end_date":"2022-04-06","start_date":"2022-04-02"},"date_published":"2022-04-02T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Association for Computing Machinery","has_accepted_license":"1","type":"conference","abstract":[{"text":"To maximize the performance of concurrent data structures, researchers have often turned to highly complex fine-grained techniques, resulting in efficient and elegant algorithms, which can however be often difficult to understand and prove correct. While simpler techniques exist, such as transactional memory, they can have limited performance or portability relative to their fine-grained counterparts. Approaches at both ends of this complexity-performance spectrum have been extensively explored, but relatively less is known about the middle ground: approaches that are willing to sacrifice some performance for simplicity, while remaining competitive with state-of-the-art handcrafted designs. In this paper, we explore this middle ground, and present PathCAS, a primitive that combines ideas from multi-word CAS (KCAS) and transactional memory approaches, while carefully avoiding overhead. We show how PathCAS can be used to implement efficient search data structures relatively simply, using an internal binary search tree as an example, then extending this to an AVL tree. Our best implementations outperform many handcrafted search trees: in search-heavy workloads, it rivals the BCCO tree [5], the fastest known concurrent binary tree in terms of search performance [3]. Our results suggest that PathCAS can yield concurrent data structures that are relatively easy to build and prove correct, while offering surprisingly high performance.","lang":"eng"}],"quality_controlled":"1","corr_author":"1","day":"02","year":"2022","month":"04","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","oa_version":"Published Version","doi":"10.1145/3503221.3508410","citation":{"ieee":"T. A. Brown, W. Sigouin, and D.-A. Alistarh, “PathCAS: An efficient middle ground for concurrent search data structures,” in <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Seoul, Republic of Korea, 2022, pp. 385–399.","short":"T.A. Brown, W. Sigouin, D.-A. Alistarh, in:, Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2022, pp. 385–399.","ista":"Brown TA, Sigouin W, Alistarh D-A. 2022. PathCAS: An efficient middle ground for concurrent search data structures. Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 385–399.","ama":"Brown TA, Sigouin W, Alistarh D-A. PathCAS: An efficient middle ground for concurrent search data structures. In: <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2022:385-399. doi:<a href=\"https://doi.org/10.1145/3503221.3508410\">10.1145/3503221.3508410</a>","chicago":"Brown, Trevor A, William Sigouin, and Dan-Adrian Alistarh. “PathCAS: An Efficient Middle Ground for Concurrent Search Data Structures.” In <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 385–99. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3503221.3508410\">https://doi.org/10.1145/3503221.3508410</a>.","mla":"Brown, Trevor A., et al. “PathCAS: An Efficient Middle Ground for Concurrent Search Data Structures.” <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2022, pp. 385–99, doi:<a href=\"https://doi.org/10.1145/3503221.3508410\">10.1145/3503221.3508410</a>.","apa":"Brown, T. A., Sigouin, W., &#38; Alistarh, D.-A. (2022). PathCAS: An efficient middle ground for concurrent search data structures. In <i>Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 385–399). Seoul, Republic of Korea: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3503221.3508410\">https://doi.org/10.1145/3503221.3508410</a>"},"publication":"Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","status":"public","external_id":{"isi":["000883318200027"]},"title":"PathCAS: An efficient middle ground for concurrent search data structures","department":[{"_id":"DaAl"}],"file":[{"file_id":"11731","checksum":"8ceea411fa133795cd4903529498eb6b","success":1,"relation":"main_file","file_size":1128343,"creator":"dernst","content_type":"application/pdf","date_created":"2022-08-05T09:19:29Z","access_level":"open_access","file_name":"2022_PPoPP_Brown.pdf","date_updated":"2022-08-05T09:19:29Z"}],"date_updated":"2024-10-09T21:02:23Z","oa":1},{"scopus_import":"1","article_number":"e407","OA_place":"publisher","_id":"11182","has_accepted_license":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Wiley","author":[{"first_name":"Janina","full_name":"Kroll, Janina","last_name":"Kroll"},{"last_name":"Ruiz-Fernandez","full_name":"Ruiz-Fernandez, Mauricio J.A.","first_name":"Mauricio J.A."},{"first_name":"Malte B.","full_name":"Braun, Malte B.","last_name":"Braun"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack"},{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","full_name":"Renkawitz, Jörg","first_name":"Jörg"}],"date_published":"2022-04-05T00:00:00Z","publication_identifier":{"eissn":["2691-1299"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank Kasia Stefanowski for excellent technical assistance, and the Core Facility Bioimaging of the Biomedical Center (BMC) of the Ludwig-Maximilian University for excellent support. We gratefully acknowledge financial support from the Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin (to J.R), from the DFG (Collaborative Research Center SFB914, project A12; and Priority Programme SPP2332, project 492014049; both to J.R) and from the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to J.R).\r\nOpen access funding enabled and organized by Projekt DEAL.","issue":"4","date_created":"2022-04-17T22:01:46Z","ddc":["570"],"file_date_updated":"2022-05-02T08:16:10Z","department":[{"_id":"NanoFab"}],"status":"public","external_id":{"pmid":["35384410"]},"title":"Quantifying the probing and selection of microenvironmental pores by motile immune cells","OA_type":"hybrid","doi":"10.1002/cpz1.407","citation":{"short":"J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current Protocols 2 (2022).","ieee":"J. Kroll, M. J. A. Ruiz-Fernandez, M. B. Braun, J. Merrin, and J. Renkawitz, “Quantifying the probing and selection of microenvironmental pores by motile immune cells,” <i>Current Protocols</i>, vol. 2, no. 4. Wiley, 2022.","ama":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. Quantifying the probing and selection of microenvironmental pores by motile immune cells. <i>Current Protocols</i>. 2022;2(4). doi:<a href=\"https://doi.org/10.1002/cpz1.407\">10.1002/cpz1.407</a>","ista":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. 2022. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2(4), e407.","apa":"Kroll, J., Ruiz-Fernandez, M. J. A., Braun, M. B., Merrin, J., &#38; Renkawitz, J. (2022). Quantifying the probing and selection of microenvironmental pores by motile immune cells. <i>Current Protocols</i>. Wiley. <a href=\"https://doi.org/10.1002/cpz1.407\">https://doi.org/10.1002/cpz1.407</a>","chicago":"Kroll, Janina, Mauricio J.A. Ruiz-Fernandez, Malte B. Braun, Jack Merrin, and Jörg Renkawitz. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” <i>Current Protocols</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/cpz1.407\">https://doi.org/10.1002/cpz1.407</a>.","mla":"Kroll, Janina, et al. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” <i>Current Protocols</i>, vol. 2, no. 4, e407, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/cpz1.407\">10.1002/cpz1.407</a>."},"publication":"Current Protocols","date_updated":"2024-10-14T13:16:54Z","volume":2,"oa":1,"article_type":"original","intvolume":"         2","file":[{"relation":"main_file","success":1,"file_id":"11347","checksum":"72152d005c367777f6cf2f6a477f0d52","date_updated":"2022-05-02T08:16:10Z","file_name":"2022_CurrentProtocols_Kroll.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2022-05-02T08:16:10Z","file_size":2142703,"creator":"dernst"}],"year":"2022","month":"04","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","publication_status":"published","quality_controlled":"1","day":"05","type":"journal_article","abstract":[{"lang":"eng","text":"Immune cells are constantly on the move through multicellular organisms to explore and respond to pathogens and other harmful insults. While moving, immune cells efficiently traverse microenvironments composed of tissue cells and extracellular fibers, which together form complex environments of various porosity, stiffness, topography, and chemical composition. In this protocol we describe experimental procedures to investigate immune cell migration through microenvironments of heterogeneous porosity. In particular, we describe micro-channels, micro-pillars, and collagen networks as cell migration paths with alternative pore size choices. Employing micro-channels or micro-pillars that divide at junctions into alternative paths with initially differentially sized pores allows us to precisely (1) measure the cellular translocation time through these porous path junctions, (2) quantify the cellular preference for individual pore sizes, and (3) image cellular components like the nucleus and the cytoskeleton. This reductionistic experimental setup thus can elucidate how immune cells perform decisions in complex microenvironments of various porosity like the interstitium. The setup further allows investigation of the underlying forces of cellular squeezing and the consequences of cellular deformation on the integrity of the cell and its organelles. As a complementary approach that does not require any micro-engineering expertise, we describe the usage of three-dimensional collagen networks with different pore sizes. Whereas we here focus on dendritic cells as a model for motile immune cells, the described protocols are versatile as they are also applicable for other immune cell types like neutrophils and non-immune cell types such as mesenchymal and cancer cells. In summary, we here describe protocols to identify the mechanisms and principles of cellular probing, decision making, and squeezing during cellular movement through microenvironments of heterogeneous porosity."}],"oa_version":"Published Version","pmid":1},{"publication_identifier":{"isbn":["9783959772198"],"issn":["1868-8969"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"Amir Nikabadi: Supported by the LABEX MILYON (ANR-10-LABX-0070) of Université de Lyon, within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR). Janne H. Korhonen: Supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML).\r\nWe thank François Le Gall and Masayuki Miyamoto for sharing their work on lower bounds for induced subgraph detection [36].","date_created":"2022-04-17T22:01:47Z","ddc":["510"],"file_date_updated":"2022-05-02T07:53:00Z","scopus_import":"1","alternative_title":["LIPIcs"],"project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"article_number":"15","editor":[{"full_name":"Bramas, Quentin","first_name":"Quentin","last_name":"Bramas"},{"full_name":"Gramoli, Vincent","first_name":"Vincent","last_name":"Gramoli"},{"last_name":"Milani","first_name":"Alessia","full_name":"Milani, Alessia"}],"_id":"11183","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"start_date":"2021-12-13","end_date":"2021-12-15","location":"Strasbourg, France","name":"OPODIS"},"author":[{"last_name":"Nikabadi","full_name":"Nikabadi, Amir","first_name":"Amir"},{"full_name":"Korhonen, Janne","first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","last_name":"Korhonen"}],"date_published":"2022-02-01T00:00:00Z","year":"2022","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","corr_author":"1","quality_controlled":"1","day":"01","type":"conference","abstract":[{"lang":"eng","text":"Subgraph detection has recently been one of the most studied problems in the CONGEST model of distributed computing. In this work, we study the distributed complexity of problems closely related to subgraph detection, mainly focusing on induced subgraph detection. The main line of this work presents lower bounds and parameterized algorithms w.r.t structural parameters of the input graph:\r\n- On general graphs, we give unconditional lower bounds for induced detection of cycles and patterns of treewidth 2 in CONGEST. Moreover, by adapting reductions from centralized parameterized complexity, we prove lower bounds in CONGEST for detecting patterns with a 4-clique, and for induced path detection conditional on the hardness of triangle detection in the congested clique.\r\n- On graphs of bounded degeneracy, we show that induced paths can be detected fast in CONGEST using techniques from parameterized algorithms, while detecting cycles and patterns of treewidth 2 is hard.\r\n- On graphs of bounded vertex cover number, we show that induced subgraph detection is easy in CONGEST for any pattern graph. More specifically, we adapt a centralized parameterized algorithm for a more general maximum common induced subgraph detection problem to the distributed setting. In addition to these induced subgraph detection results, we study various related problems in the CONGEST and congested clique models, including for multicolored versions of subgraph-detection-like problems."}],"oa_version":"Published Version","department":[{"_id":"DaAl"}],"status":"public","title":"Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters","doi":"10.4230/LIPIcs.OPODIS.2021.15","citation":{"apa":"Nikabadi, A., &#38; Korhonen, J. (2022). Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters. In Q. Bramas, V. Gramoli, &#38; A. Milani (Eds.), <i>25th International Conference on Principles of Distributed Systems</i> (Vol. 217). Strasbourg, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.15\">https://doi.org/10.4230/LIPIcs.OPODIS.2021.15</a>","mla":"Nikabadi, Amir, and Janne Korhonen. “Beyond Distributed Subgraph Detection: Induced Subgraphs, Multicolored Problems and Graph Parameters.” <i>25th International Conference on Principles of Distributed Systems</i>, edited by Quentin Bramas et al., vol. 217, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.15\">10.4230/LIPIcs.OPODIS.2021.15</a>.","chicago":"Nikabadi, Amir, and Janne Korhonen. “Beyond Distributed Subgraph Detection: Induced Subgraphs, Multicolored Problems and Graph Parameters.” In <i>25th International Conference on Principles of Distributed Systems</i>, edited by Quentin Bramas, Vincent Gramoli, and Alessia Milani, Vol. 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.15\">https://doi.org/10.4230/LIPIcs.OPODIS.2021.15</a>.","short":"A. Nikabadi, J. Korhonen, in:, Q. Bramas, V. Gramoli, A. Milani (Eds.), 25th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","ieee":"A. Nikabadi and J. Korhonen, “Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters,” in <i>25th International Conference on Principles of Distributed Systems</i>, Strasbourg, France, 2022, vol. 217.","ama":"Nikabadi A, Korhonen J. Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters. In: Bramas Q, Gramoli V, Milani A, eds. <i>25th International Conference on Principles of Distributed Systems</i>. Vol 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.15\">10.4230/LIPIcs.OPODIS.2021.15</a>","ista":"Nikabadi A, Korhonen J. 2022. Beyond distributed subgraph detection: Induced subgraphs, multicolored problems and graph parameters. 25th International Conference on Principles of Distributed Systems. OPODIS, LIPIcs, vol. 217, 15."},"publication":"25th International Conference on Principles of Distributed Systems","ec_funded":1,"date_updated":"2025-04-14T07:49:13Z","oa":1,"volume":217,"intvolume":"       217","file":[{"date_updated":"2022-05-02T07:53:00Z","file_name":"2022_LIPICs_Nikabadi.pdf","date_created":"2022-05-02T07:53:00Z","content_type":"application/pdf","access_level":"open_access","file_size":790396,"creator":"dernst","relation":"main_file","success":1,"checksum":"626551c14de5d4091573200ed0535752","file_id":"11345"}]},{"publication":"25th International Conference on Principles of Distributed Systems","ec_funded":1,"doi":"10.4230/LIPIcs.OPODIS.2021.14","citation":{"apa":"Alistarh, D.-A., Gelashvili, R., &#38; Rybicki, J. (2022). Fast graphical population protocols. In Q. Bramas, V. Gramoli, &#38; A. Milani (Eds.), <i>25th International Conference on Principles of Distributed Systems</i> (Vol. 217). Strasbourg, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.14\">https://doi.org/10.4230/LIPIcs.OPODIS.2021.14</a>","mla":"Alistarh, Dan-Adrian, et al. “Fast Graphical Population Protocols.” <i>25th International Conference on Principles of Distributed Systems</i>, edited by Quentin Bramas et al., vol. 217, 14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.14\">10.4230/LIPIcs.OPODIS.2021.14</a>.","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Joel Rybicki. “Fast Graphical Population Protocols.” In <i>25th International Conference on Principles of Distributed Systems</i>, edited by Quentin Bramas, Vincent Gramoli, and Alessia Milani, Vol. 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.14\">https://doi.org/10.4230/LIPIcs.OPODIS.2021.14</a>.","ama":"Alistarh D-A, Gelashvili R, Rybicki J. Fast graphical population protocols. In: Bramas Q, Gramoli V, Milani A, eds. <i>25th International Conference on Principles of Distributed Systems</i>. Vol 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2021.14\">10.4230/LIPIcs.OPODIS.2021.14</a>","ista":"Alistarh D-A, Gelashvili R, Rybicki J. 2022. Fast graphical population protocols. 25th International Conference on Principles of Distributed Systems. OPODIS, LIPIcs, vol. 217, 14.","short":"D.-A. Alistarh, R. Gelashvili, J. Rybicki, in:, Q. Bramas, V. Gramoli, A. Milani (Eds.), 25th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","ieee":"D.-A. Alistarh, R. Gelashvili, and J. Rybicki, “Fast graphical population protocols,” in <i>25th International Conference on Principles of Distributed Systems</i>, Strasbourg, France, 2022, vol. 217."},"external_id":{"arxiv":["2102.08808"]},"title":"Fast graphical population protocols","status":"public","department":[{"_id":"DaAl"}],"file":[{"checksum":"2c7c982174c6f98c4ca6e92539d15086","file_id":"11346","success":1,"relation":"main_file","file_size":959406,"creator":"dernst","access_level":"open_access","date_created":"2022-05-02T08:06:33Z","content_type":"application/pdf","date_updated":"2022-05-02T08:06:33Z","file_name":"2022_LIPICs_Alistarh.pdf"}],"intvolume":"       217","volume":217,"oa":1,"date_updated":"2025-04-14T07:49:13Z","abstract":[{"lang":"eng","text":"Let G be a graph on n nodes. In the stochastic population protocol model, a collection of n indistinguishable, resource-limited nodes collectively solve tasks via pairwise interactions. In each interaction, two randomly chosen neighbors first read each other’s states, and then update their local states. A rich line of research has established tight upper and lower bounds on the complexity of fundamental tasks, such as majority and leader election, in this model, when G is a clique. Specifically, in the clique, these tasks can be solved fast, i.e., in n polylog n pairwise interactions, with high probability, using at most polylog n states per node.\r\nIn this work, we consider the more general setting where G is an arbitrary regular graph, and present a technique for simulating protocols designed for fully-connected networks in any connected regular graph. Our main result is a simulation that is efficient on many interesting graph families: roughly, the simulation overhead is polylogarithmic in the number of nodes, and quadratic in the conductance of the graph. As a sample application, we show that, in any regular graph with conductance φ, both leader election and exact majority can be solved in φ^{-2} ⋅ n polylog n pairwise interactions, with high probability, using at most φ^{-2} ⋅ polylog n states per node. This shows that there are fast and space-efficient population protocols for leader election and exact majority on graphs with good expansion properties. We believe our results will prove generally useful, as they allow efficient technology transfer between the well-mixed (clique) case, and the under-explored spatial setting."}],"type":"conference","day":"01","corr_author":"1","quality_controlled":"1","publication_status":"published","year":"2022","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"oa_version":"Published Version","_id":"11184","editor":[{"last_name":"Bramas","full_name":"Bramas, Quentin","first_name":"Quentin"},{"full_name":"Gramoli, Vincent","first_name":"Vincent","last_name":"Gramoli"},{"first_name":"Alessia","full_name":"Milani, Alessia","last_name":"Milani"}],"article_number":"14","alternative_title":["LIPIcs"],"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223"},{"grant_number":"840605","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020"}],"scopus_import":"1","date_published":"2022-02-01T00:00:00Z","conference":{"name":"OPODIS","end_date":"2021-12-15","start_date":"2021-12-13","location":"Strasbourg, France"},"author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"last_name":"Gelashvili","full_name":"Gelashvili, Rati","first_name":"Rati"},{"orcid":"0000-0002-6432-6646","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel","full_name":"Rybicki, Joel"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_processing_charge":"No","language":[{"iso":"eng"}],"has_accepted_license":"1","acknowledgement":"Dan Alistarh: This project has received funding from the European Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation programme (grant agreement No.805223 ScaleML).\r\nJoel Rybicki: This project has received from the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie grant agreement No. 840605.\r\nAcknowledgements We grateful to Giorgi Nadiradze for pointing out a generalisation of the phase clock construction to non-regular graphs. We also thank anonymous reviewers for their useful comments on earlier versions of this manuscript.","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772198"]},"file_date_updated":"2022-05-02T08:06:33Z","ddc":["510"],"date_created":"2022-04-17T22:01:47Z"},{"intvolume":"     13174","volume":13174,"oa":1,"date_updated":"2025-09-10T09:35:56Z","publication":"WALCOM 2022: Algorithms and Computation","ec_funded":1,"doi":"10.1007/978-3-030-96731-4_31","citation":{"apa":"Arroyo Guevara, A. M., &#38; Felsner, S. (2022). Approximating the bundled crossing number. In <i>WALCOM 2022: Algorithms and Computation</i> (Vol. 13174, pp. 383–395). Jember, Indonesia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">https://doi.org/10.1007/978-3-030-96731-4_31</a>","mla":"Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing Number.” <i>WALCOM 2022: Algorithms and Computation</i>, vol. 13174, Springer Nature, 2022, pp. 383–95, doi:<a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">10.1007/978-3-030-96731-4_31</a>.","chicago":"Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled Crossing Number.” In <i>WALCOM 2022: Algorithms and Computation</i>, 13174:383–95. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">https://doi.org/10.1007/978-3-030-96731-4_31</a>.","ama":"Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. In: <i>WALCOM 2022: Algorithms and Computation</i>. Vol 13174. LNCS. Springer Nature; 2022:383-395. doi:<a href=\"https://doi.org/10.1007/978-3-030-96731-4_31\">10.1007/978-3-030-96731-4_31</a>","ista":"Arroyo Guevara AM, Felsner S. 2022. Approximating the bundled crossing number. WALCOM 2022: Algorithms and Computation. WALCOM: Algorithms and ComputationLNCS vol. 13174, 383–395.","short":"A.M. Arroyo Guevara, S. Felsner, in:, WALCOM 2022: Algorithms and Computation, Springer Nature, 2022, pp. 383–395.","ieee":"A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing number,” in <i>WALCOM 2022: Algorithms and Computation</i>, Jember, Indonesia, 2022, vol. 13174, pp. 383–395."},"department":[{"_id":"UlWa"}],"title":"Approximating the bundled crossing number","external_id":{"isi":["001435074700031"],"arxiv":["2109.14892"]},"status":"public","arxiv":1,"oa_version":"Preprint","day":"16","quality_controlled":"1","related_material":{"record":[{"relation":"later_version","id":"13969","status":"public"}]},"abstract":[{"text":"Bundling crossings is a strategy which can enhance the readability of graph drawings. In this paper we consider bundlings for families of pseudosegments, i.e., simple curves such that any two have share at most one point at which they cross. Our main result is that there is a polynomial-time algorithm to compute an 8-approximation of the bundled crossing number of such instances (up to adding a term depending on the facial structure). This 8-approximation also holds for bundlings of good drawings of graphs. In the special case of circular drawings the approximation factor is 8 (no extra term), this improves upon the 10-approximation of Fink et al. [6]. We also show how to compute a 92-approximation when the intersection graph of the pseudosegments is bipartite.","lang":"eng"}],"type":"conference","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"03","year":"2022","date_published":"2022-03-16T00:00:00Z","author":[{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670","last_name":"Arroyo Guevara","full_name":"Arroyo Guevara, Alan M","first_name":"Alan M"},{"last_name":"Felsner","full_name":"Felsner, Stefan","first_name":"Stefan"}],"conference":{"name":"WALCOM: Algorithms and Computation","end_date":"2022-03-26","start_date":"2022-03-24","location":"Jember, Indonesia"},"page":"383-395","series_title":"LNCS","publisher":"Springer Nature","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"11185","scopus_import":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"date_created":"2022-04-17T22:01:47Z","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030967307"]},"isi":1,"acknowledgement":"This work was initiated during the Workshop on Geometric Graphs in November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during the workshop. The first author has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie grant agreement No 754411. The second author has been supported by the German Research Foundation DFG Project FE 340/12-1.","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2109.14892","open_access":"1"}]},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","article_type":"original","date_updated":"2024-10-09T21:02:21Z","volume":54,"oa":1,"intvolume":"        54","file":[{"success":1,"relation":"main_file","file_id":"12499","checksum":"02d74e7ae955ba3c808e2a8aebe6ef98","date_updated":"2023-02-03T09:43:38Z","file_name":"2022_BulletinMathSociety_Kwan.pdf","content_type":"application/pdf","date_created":"2023-02-03T09:43:38Z","access_level":"open_access","file_size":233758,"creator":"dernst"}],"status":"public","external_id":{"isi":["000779920900001"],"arxiv":["2106.11932"]},"title":"Large deviations in random latin squares","department":[{"_id":"MaKw"}],"citation":{"ama":"Kwan MA, Sah A, Sawhney M. Large deviations in random latin squares. <i>Bulletin of the London Mathematical Society</i>. 2022;54(4):1420-1438. doi:<a href=\"https://doi.org/10.1112/blms.12638\">10.1112/blms.12638</a>","ista":"Kwan MA, Sah A, Sawhney M. 2022. Large deviations in random latin squares. Bulletin of the London Mathematical Society. 54(4), 1420–1438.","short":"M.A. Kwan, A. Sah, M. Sawhney, Bulletin of the London Mathematical Society 54 (2022) 1420–1438.","ieee":"M. A. Kwan, A. Sah, and M. Sawhney, “Large deviations in random latin squares,” <i>Bulletin of the London Mathematical Society</i>, vol. 54, no. 4. Wiley, pp. 1420–1438, 2022.","apa":"Kwan, M. A., Sah, A., &#38; Sawhney, M. (2022). Large deviations in random latin squares. <i>Bulletin of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/blms.12638\">https://doi.org/10.1112/blms.12638</a>","mla":"Kwan, Matthew Alan, et al. “Large Deviations in Random Latin Squares.” <i>Bulletin of the London Mathematical Society</i>, vol. 54, no. 4, Wiley, 2022, pp. 1420–38, doi:<a href=\"https://doi.org/10.1112/blms.12638\">10.1112/blms.12638</a>.","chicago":"Kwan, Matthew Alan, Ashwin Sah, and Mehtaab Sawhney. “Large Deviations in Random Latin Squares.” <i>Bulletin of the London Mathematical Society</i>. Wiley, 2022. <a href=\"https://doi.org/10.1112/blms.12638\">https://doi.org/10.1112/blms.12638</a>."},"doi":"10.1112/blms.12638","publication":"Bulletin of the London Mathematical Society","oa_version":"Published Version","arxiv":1,"month":"08","year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","type":"journal_article","abstract":[{"text":"In this note, we study large deviations of the number  𝐍  of intercalates ( 2×2  combinatorial subsquares which are themselves Latin squares) in a random  𝑛×𝑛  Latin square. In particular, for constant  𝛿>0  we prove that  exp(−𝑂(𝑛2log𝑛))⩽Pr(𝐍⩽(1−𝛿)𝑛2/4)⩽exp(−Ω(𝑛2))  and  exp(−𝑂(𝑛4/3(log𝑛)))⩽Pr(𝐍⩾(1+𝛿)𝑛2/4)⩽exp(−Ω(𝑛4/3(log𝑛)2/3)) . As a consequence, we deduce that a typical order- 𝑛  Latin square has  (1+𝑜(1))𝑛2/4  intercalates, matching a lower bound due to Kwan and Sudakov and resolving an old conjecture of McKay and Wanless.","lang":"eng"}],"quality_controlled":"1","corr_author":"1","day":"01","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Wiley","has_accepted_license":"1","page":"1420-1438","author":[{"first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","last_name":"Kwan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sah","first_name":"Ashwin","full_name":"Sah, Ashwin"},{"last_name":"Sawhney","first_name":"Mehtaab","full_name":"Sawhney, Mehtaab"}],"date_published":"2022-08-01T00:00:00Z","scopus_import":"1","_id":"11186","issue":"4","file_date_updated":"2023-02-03T09:43:38Z","date_created":"2022-04-17T22:01:48Z","ddc":["510"],"tmp":{"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","image":"/images/cc_by_nc.png"},"acknowledgement":"We thank Zach Hunter for pointing out some important typographical errors. We also thank the referee for several remarks which helped improve the paper substantially.\r\nKwan was supported by NSF grant DMS-1953990. Sah and Sawhney were supported by NSF Graduate Research Fellowship Program DGE-1745302.","isi":1,"publication_identifier":{"eissn":["1469-2120"],"issn":["0024-6093"]}},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-022-01444-z"}],"acknowledgement":"Our paper is dedicated to all freedom-loving people around the world, and to the people of Ukraine who fight for our freedom. We thank William M. Switzer and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions. We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially supported by National Science Foundation grants 2041984. T.L. is supported by the NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund (R7021-20), Innovation and Technology Commission’s InnoHK funding (D24H) and Health and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828. M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human Genome Project for technical and financial support (https://shgp.kacst.edu.sa) N.W. was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S. acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly supported by Molecular Basis of Disease at Georgia State University and NIH awards R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported by NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond to COVID-19, CDC project 30055281 with Scripps led by Kristian Andersen, Genomic sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread. J.O.W. was supported by NIH–National Institute of Allergy and Infectious Diseases (NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V. is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry of Science and Higher Education of the Russian Federation within the framework of state support for the creation and development of World-Class Research Centers “Digital biodesign and personalized healthcare” N◦075-15-2020-926. E.B. was supported by a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395) and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the California Department of Public Health, the Innovative Genomics Institute (IGI) at the University of California, Berkeley, and University of California, San Francisco, NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project 206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C. acknowledges support from the US NSF award EEID-IOS-2109688. F.K.’s work was supported by an ERC Consolidator grant to F.K. (771209–CharFL).","isi":1,"publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"issue":"4","date_created":"2022-04-17T22:01:48Z","project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales"}],"scopus_import":"1","_id":"11187","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Springer Nature","author":[{"last_name":"Knyazev","first_name":"Sergey","full_name":"Knyazev, Sergey"},{"full_name":"Chhugani, Karishma","first_name":"Karishma","last_name":"Chhugani"},{"first_name":"Varuni","full_name":"Sarwal, Varuni","last_name":"Sarwal"},{"last_name":"Ayyala","first_name":"Ram","full_name":"Ayyala, Ram"},{"full_name":"Singh, Harman","first_name":"Harman","last_name":"Singh"},{"last_name":"Karthikeyan","full_name":"Karthikeyan, Smruthi","first_name":"Smruthi"},{"last_name":"Deshpande","first_name":"Dhrithi","full_name":"Deshpande, Dhrithi"},{"first_name":"Pelin Icer","full_name":"Baykal, Pelin Icer","last_name":"Baykal"},{"full_name":"Comarova, Zoia","first_name":"Zoia","last_name":"Comarova"},{"last_name":"Lu","first_name":"Angela","full_name":"Lu, Angela"},{"full_name":"Porozov, Yuri","first_name":"Yuri","last_name":"Porozov"},{"last_name":"Vasylyeva","first_name":"Tetyana I.","full_name":"Vasylyeva, Tetyana I."},{"first_name":"Joel O.","full_name":"Wertheim, Joel O.","last_name":"Wertheim"},{"last_name":"Tierney","full_name":"Tierney, Braden T.","first_name":"Braden T."},{"full_name":"Chiu, Charles Y.","first_name":"Charles Y.","last_name":"Chiu"},{"full_name":"Sun, Ren","first_name":"Ren","last_name":"Sun"},{"last_name":"Wu","full_name":"Wu, Aiping","first_name":"Aiping"},{"last_name":"Abedalthagafi","full_name":"Abedalthagafi, Malak S.","first_name":"Malak S."},{"last_name":"Pak","first_name":"Victoria M.","full_name":"Pak, Victoria M."},{"last_name":"Nagaraj","first_name":"Shivashankar H.","full_name":"Nagaraj, Shivashankar H."},{"first_name":"Adam L.","full_name":"Smith, Adam L.","last_name":"Smith"},{"first_name":"Pavel","full_name":"Skums, Pavel","last_name":"Skums"},{"first_name":"Bogdan","full_name":"Pasaniuc, Bogdan","last_name":"Pasaniuc"},{"first_name":"Andrey","full_name":"Komissarov, Andrey","last_name":"Komissarov"},{"full_name":"Mason, Christopher E.","first_name":"Christopher E.","last_name":"Mason"},{"first_name":"Eric","full_name":"Bortz, Eric","last_name":"Bortz"},{"full_name":"Lemey, Philippe","first_name":"Philippe","last_name":"Lemey"},{"first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Beerenwinkel, Niko","first_name":"Niko","last_name":"Beerenwinkel"},{"last_name":"Lam","first_name":"Tommy Tsan Yuk","full_name":"Lam, Tommy Tsan Yuk"},{"last_name":"Wu","full_name":"Wu, Nicholas C.","first_name":"Nicholas C."},{"last_name":"Zelikovsky","full_name":"Zelikovsky, Alex","first_name":"Alex"},{"full_name":"Knight, Rob","first_name":"Rob","last_name":"Knight"},{"first_name":"Keith A.","full_name":"Crandall, Keith A.","last_name":"Crandall"},{"last_name":"Mangul","full_name":"Mangul, Serghei","first_name":"Serghei"}],"page":"374-380","date_published":"2022-04-08T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","month":"04","publication_status":"published","type":"journal_article","abstract":[{"lang":"eng","text":"During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing."}],"quality_controlled":"1","day":"08","pmid":1,"oa_version":"Published Version","status":"public","title":"Unlocking capacities of genomics for the COVID-19 response and future pandemics","external_id":{"pmid":["35396471"],"isi":["000781199600011"]},"department":[{"_id":"FyKo"}],"citation":{"chicago":"Knyazev, Sergey, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” <i>Nature Methods</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41592-022-01444-z\">https://doi.org/10.1038/s41592-022-01444-z</a>.","mla":"Knyazev, Sergey, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” <i>Nature Methods</i>, vol. 19, no. 4, Springer Nature, 2022, pp. 374–80, doi:<a href=\"https://doi.org/10.1038/s41592-022-01444-z\">10.1038/s41592-022-01444-z</a>.","apa":"Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response and future pandemics. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-022-01444-z\">https://doi.org/10.1038/s41592-022-01444-z</a>","ista":"Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 19(4), 374–380.","ama":"Knyazev S, Chhugani K, Sarwal V, et al. Unlocking capacities of genomics for the COVID-19 response and future pandemics. <i>Nature Methods</i>. 2022;19(4):374-380. doi:<a href=\"https://doi.org/10.1038/s41592-022-01444-z\">10.1038/s41592-022-01444-z</a>","ieee":"S. Knyazev <i>et al.</i>, “Unlocking capacities of genomics for the COVID-19 response and future pandemics,” <i>Nature Methods</i>, vol. 19, no. 4. Springer Nature, pp. 374–380, 2022.","short":"S. Knyazev, K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan, D. Deshpande, P.I. Baykal, Z. Comarova, A. Lu, Y. Porozov, T.I. Vasylyeva, J.O. Wertheim, B.T. Tierney, C.Y. Chiu, R. Sun, A. Wu, M.S. Abedalthagafi, V.M. Pak, S.H. Nagaraj, A.L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C.E. Mason, E. Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T.T.Y. Lam, N.C. Wu, A. Zelikovsky, R. Knight, K.A. Crandall, S. Mangul, Nature Methods 19 (2022) 374–380."},"doi":"10.1038/s41592-022-01444-z","publication":"Nature Methods","ec_funded":1,"article_type":"letter_note","date_updated":"2025-04-14T07:49:45Z","volume":19,"oa":1,"intvolume":"        19"},{"date_published":"2022-04-28T00:00:00Z","author":[{"orcid":"0000-0001-6395-386X","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","full_name":"Surendranadh, Parvathy"},{"full_name":"Arathoon, Louise S","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","orcid":"0000-0003-1771-714X"},{"first_name":"Carina","full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574","last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Melinda","full_name":"Pickup, Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_updated":"2022-04-22T09:39:03Z","file_name":"Data_Code.zip","date_created":"2022-04-22T09:39:03Z","content_type":"application/x-zip-compressed","access_level":"open_access","file_size":13260571,"creator":"larathoo","success":1,"relation":"main_file","file_id":"11326","checksum":"96c1b86cdf25481f2a52972fcc45ca7f"}],"oa":1,"date_updated":"2025-04-15T08:20:40Z","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","contributor":[{"last_name":"Arathoon","contributor_type":"project_member","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","contributor_type":"project_member","orcid":"0000-0002-7354-8574","first_name":"Carina"},{"contributor_type":"project_member","orcid":"0000-0002-4014-8478","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"last_name":"Pickup","orcid":"0000-0001-6118-0541","contributor_type":"project_member","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","contributor_type":"project_member","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"_id":"11321","citation":{"ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11321\">10.15479/at:ista:11321</a>","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:11321\">10.15479/at:ista:11321</a>.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022).","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2022.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11321\">https://doi.org/10.15479/at:ista:11321</a>","mla":"Surendranadh, Parvathy, et al. <i>Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11321\">10.15479/at:ista:11321</a>.","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11321\">https://doi.org/10.15479/at:ista:11321</a>."},"doi":"10.15479/at:ista:11321","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","status":"public","ddc":["570"],"date_created":"2022-04-22T09:42:24Z","file_date_updated":"2022-04-22T09:39:03Z","oa_version":"Published Version","day":"28","corr_author":"1","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus\" Further information are summed up in the README document. "}],"related_material":{"record":[{"status":"public","id":"9192","relation":"earlier_version"},{"relation":"earlier_version","id":"8254","status":"public"},{"relation":"used_in_publication","id":"11411","status":"public"}]},"type":"research_data","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","month":"04"},{"date_published":"2022-04-08T00:00:00Z","author":[{"id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","last_name":"Wirth","full_name":"Wirth, Melchior","first_name":"Melchior"}],"has_accepted_license":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","article_number":"19","_id":"11330","scopus_import":"1","project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"}],"ddc":["510","530"],"date_created":"2022-04-24T22:01:43Z","file_date_updated":"2022-04-29T11:24:23Z","issue":"2","publication_identifier":{"eissn":["1572-9613"],"issn":["0022-4715"]},"isi":1,"acknowledgement":"The author wants to thank Jan Maas for helpful comments. He also acknowledges financial support from the Austrian Science Fund (FWF) through Grant Number F65 and from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 716117).\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2022-04-29T11:24:23Z","file_name":"2022_JourStatisticalPhysics_Wirth.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2022-04-29T11:24:23Z","creator":"dernst","file_size":362119,"relation":"main_file","success":1,"checksum":"f3e0b00884b7dde31347a3756788b473","file_id":"11338"}],"intvolume":"       187","oa":1,"volume":187,"date_updated":"2025-06-12T06:17:37Z","article_type":"original","publication":"Journal of Statistical Physics","ec_funded":1,"citation":{"ama":"Wirth M. A dual formula for the noncommutative transport distance. <i>Journal of Statistical Physics</i>. 2022;187(2). doi:<a href=\"https://doi.org/10.1007/s10955-022-02911-9\">10.1007/s10955-022-02911-9</a>","ista":"Wirth M. 2022. A dual formula for the noncommutative transport distance. Journal of Statistical Physics. 187(2), 19.","short":"M. Wirth, Journal of Statistical Physics 187 (2022).","ieee":"M. Wirth, “A dual formula for the noncommutative transport distance,” <i>Journal of Statistical Physics</i>, vol. 187, no. 2. Springer Nature, 2022.","apa":"Wirth, M. (2022). A dual formula for the noncommutative transport distance. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-022-02911-9\">https://doi.org/10.1007/s10955-022-02911-9</a>","mla":"Wirth, Melchior. “A Dual Formula for the Noncommutative Transport Distance.” <i>Journal of Statistical Physics</i>, vol. 187, no. 2, 19, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s10955-022-02911-9\">10.1007/s10955-022-02911-9</a>.","chicago":"Wirth, Melchior. “A Dual Formula for the Noncommutative Transport Distance.” <i>Journal of Statistical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10955-022-02911-9\">https://doi.org/10.1007/s10955-022-02911-9</a>."},"doi":"10.1007/s10955-022-02911-9","department":[{"_id":"JaMa"}],"external_id":{"isi":["000780305000001"],"pmid":["35509951"]},"title":"A dual formula for the noncommutative transport distance","status":"public","oa_version":"Published Version","pmid":1,"day":"08","quality_controlled":"1","corr_author":"1","abstract":[{"lang":"eng","text":"In this article we study the noncommutative transport distance introduced by Carlen and Maas and its entropic regularization defined by Becker and Li. We prove a duality formula that can be understood as a quantum version of the dual Benamou–Brenier formulation of the Wasserstein distance in terms of subsolutions of a Hamilton–Jacobi–Bellmann equation."}],"type":"journal_article","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","month":"04"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","month":"03","publication_status":"published","type":"conference","abstract":[{"text":"We propose separating the task of reliable transaction dissemination from transaction ordering, to enable high-performance Byzantine fault-tolerant quorum-based consensus. We design and evaluate a mempool protocol, Narwhal, specializing in high-throughput reliable dissemination and storage of causal histories of transactions. Narwhal tolerates an asynchronous network and maintains high performance despite failures. Narwhal is designed to easily scale-out using multiple workers at each validator, and we demonstrate that there is no foreseeable limit to the throughput we can achieve.\r\nComposing Narwhal with a partially synchronous consensus protocol (Narwhal-HotStuff) yields significantly better throughput even in the presence of faults or intermittent loss of liveness due to asynchrony. However, loss of liveness can result in higher latency. To achieve overall good performance when faults occur we design Tusk, a zero-message overhead asynchronous consensus protocol, to work with Narwhal. We demonstrate its high performance under a variety of configurations and faults.\r\nAs a summary of results, on a WAN, Narwhal-Hotstuff achieves over 130,000 tx/sec at less than 2-sec latency compared with 1,800 tx/sec at 1-sec latency for Hotstuff. Additional workers increase throughput linearly to 600,000 tx/sec without any latency increase. Tusk achieves 160,000 tx/sec with about 3 seconds latency. Under faults, both protocols maintain high throughput, but Narwhal-HotStuff suffers from increased latency.","lang":"eng"}],"quality_controlled":"1","day":"28","oa_version":"Preprint","arxiv":1,"status":"public","external_id":{"isi":["000926506800003"],"arxiv":["2105.11827"]},"title":"Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus","department":[{"_id":"ElKo"}],"citation":{"apa":"Danezis, G., Kokoris Kogias, E., Sonnino, A., &#38; Spiegelman, A. (2022). Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus. In <i>Proceedings of the 17th European Conference on Computer Systems</i> (pp. 34–50). Rennes, France: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3492321.3519594\">https://doi.org/10.1145/3492321.3519594</a>","mla":"Danezis, George, et al. “Narwhal and Tusk: A DAG-Based Mempool and Efficient BFT Consensus.” <i>Proceedings of the 17th European Conference on Computer Systems</i>, Association for Computing Machinery, 2022, pp. 34–50, doi:<a href=\"https://doi.org/10.1145/3492321.3519594\">10.1145/3492321.3519594</a>.","chicago":"Danezis, George, Eleftherios Kokoris Kogias, Alberto Sonnino, and Alexander Spiegelman. “Narwhal and Tusk: A DAG-Based Mempool and Efficient BFT Consensus.” In <i>Proceedings of the 17th European Conference on Computer Systems</i>, 34–50. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3492321.3519594\">https://doi.org/10.1145/3492321.3519594</a>.","short":"G. Danezis, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, in:, Proceedings of the 17th European Conference on Computer Systems, Association for Computing Machinery, 2022, pp. 34–50.","ieee":"G. Danezis, E. Kokoris Kogias, A. Sonnino, and A. Spiegelman, “Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus,” in <i>Proceedings of the 17th European Conference on Computer Systems</i>, Rennes, France, 2022, pp. 34–50.","ama":"Danezis G, Kokoris Kogias E, Sonnino A, Spiegelman A. Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus. In: <i>Proceedings of the 17th European Conference on Computer Systems</i>. Association for Computing Machinery; 2022:34-50. doi:<a href=\"https://doi.org/10.1145/3492321.3519594\">10.1145/3492321.3519594</a>","ista":"Danezis G, Kokoris Kogias E, Sonnino A, Spiegelman A. 2022. Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus. Proceedings of the 17th European Conference on Computer Systems. EuroSys: European Conference on Computer Systems, 34–50."},"doi":"10.1145/3492321.3519594","publication":"Proceedings of the 17th European Conference on Computer Systems","date_updated":"2023-08-03T06:38:40Z","oa":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2105.11827","open_access":"1"}],"isi":1,"publication_identifier":{"isbn":["9781450391627"]},"date_created":"2022-04-24T22:01:43Z","scopus_import":"1","_id":"11331","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Association for Computing Machinery","conference":{"end_date":"2022-04-08","start_date":"2022-04-05","location":"Rennes, France","name":"EuroSys: European Conference on Computer Systems"},"page":"34-50","author":[{"first_name":"George","full_name":"Danezis, George","last_name":"Danezis"},{"first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Sonnino, Alberto","first_name":"Alberto","last_name":"Sonnino"},{"last_name":"Spiegelman","full_name":"Spiegelman, Alexander","first_name":"Alexander"}],"date_published":"2022-03-28T00:00:00Z"},{"status":"public","title":"Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices","external_id":{"pmid":["35765414"],"arxiv":["2102.04330"],"isi":["000782737200001"]},"department":[{"_id":"LaEr"}],"doi":"10.1007/s00220-022-04377-y","citation":{"ama":"Schnelli K, Xu Y. Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices. <i>Communications in Mathematical Physics</i>. 2022;393:839-907. doi:<a href=\"https://doi.org/10.1007/s00220-022-04377-y\">10.1007/s00220-022-04377-y</a>","ista":"Schnelli K, Xu Y. 2022. Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices. Communications in Mathematical Physics. 393, 839–907.","short":"K. Schnelli, Y. Xu, Communications in Mathematical Physics 393 (2022) 839–907.","ieee":"K. Schnelli and Y. Xu, “Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices,” <i>Communications in Mathematical Physics</i>, vol. 393. Springer Nature, pp. 839–907, 2022.","apa":"Schnelli, K., &#38; Xu, Y. (2022). Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-022-04377-y\">https://doi.org/10.1007/s00220-022-04377-y</a>","chicago":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Wigner Matrices.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00220-022-04377-y\">https://doi.org/10.1007/s00220-022-04377-y</a>.","mla":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Wigner Matrices.” <i>Communications in Mathematical Physics</i>, vol. 393, Springer Nature, 2022, pp. 839–907, doi:<a href=\"https://doi.org/10.1007/s00220-022-04377-y\">10.1007/s00220-022-04377-y</a>."},"publication":"Communications in Mathematical Physics","ec_funded":1,"article_type":"original","date_updated":"2025-06-11T14:01:05Z","oa":1,"volume":393,"file":[{"access_level":"open_access","date_created":"2022-08-05T06:01:13Z","content_type":"application/pdf","creator":"dernst","file_size":1141462,"file_name":"2022_CommunMathPhys_Schnelli.pdf","date_updated":"2022-08-05T06:01:13Z","checksum":"bee0278c5efa9a33d9a2dc8d354a6c51","file_id":"11726","relation":"main_file","success":1}],"intvolume":"       393","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","month":"07","publication_status":"published","type":"journal_article","abstract":[{"text":"We show that the fluctuations of the largest eigenvalue of a real symmetric or complex Hermitian Wigner matrix of size N converge to the Tracy–Widom laws at a rate O(N^{-1/3+\\omega }), as N tends to infinity. For Wigner matrices this improves the previous rate O(N^{-2/9+\\omega }) obtained by Bourgade (J Eur Math Soc, 2021) for generalized Wigner matrices. Our result follows from a Green function comparison theorem, originally introduced by Erdős et al. (Adv Math 229(3):1435–1515, 2012) to prove edge universality, on a finer spectral parameter scale with improved error estimates. The proof relies on the continuous Green function flow induced by a matrix-valued Ornstein–Uhlenbeck process. Precise estimates on leading contributions from the third and fourth order moments of the matrix entries are obtained using iterative cumulant expansions and recursive comparisons for correlation functions, along with uniform convergence estimates for correlation kernels of the Gaussian invariant ensembles.","lang":"eng"}],"quality_controlled":"1","day":"01","pmid":1,"oa_version":"Published Version","arxiv":1,"project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"scopus_import":"1","_id":"11332","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","page":"839-907","author":[{"orcid":"0000-0003-0954-3231","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin","full_name":"Schnelli, Kevin"},{"full_name":"Xu, Yuanyuan","first_name":"Yuanyuan","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3","orcid":"0000-0003-1559-1205","last_name":"Xu"}],"date_published":"2022-07-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"Kevin Schnelli is supported in parts by the Swedish Research Council Grant VR-2017-05195, and the Knut and Alice Wallenberg Foundation. Yuanyuan Xu is supported by the Swedish Research Council Grant VR-2017-05195 and the ERC Advanced Grant “RMTBeyond” No. 101020331.","isi":1,"publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"file_date_updated":"2022-08-05T06:01:13Z","date_created":"2022-04-24T22:01:44Z","ddc":["510"]},{"isi":1,"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"tmp":{"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","image":"/images/cc_by_nc.png"},"acknowledgement":"The authors thank A. van der Meijden and F. Ahmadzadeh for providing specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski for support during field work. The authors also thank S. Qiu for assistance with python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for his comments on\r\na previous version of the manuscript. SF was funded by FCT grant SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation (grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian program for training in modern conservation biology” of Gulbenkian Foundation (Portugal) and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal).","issue":"5","date_created":"2022-04-24T22:01:44Z","ddc":["570"],"file_date_updated":"2022-08-05T06:19:28Z","scopus_import":"1","project":[{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747"}],"_id":"11334","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Wiley","page":"899-914","author":[{"last_name":"Freitas","full_name":"Freitas, Susana","first_name":"Susana"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M"},{"last_name":"Schwander","full_name":"Schwander, Tanja","first_name":"Tanja"},{"full_name":"Arakelyan, Marine","first_name":"Marine","last_name":"Arakelyan"},{"full_name":"Ilgaz, Çetin","first_name":"Çetin","last_name":"Ilgaz"},{"last_name":"Kumlutas","first_name":"Yusuf","full_name":"Kumlutas, Yusuf"},{"full_name":"Harris, David James","first_name":"David James","last_name":"Harris"},{"last_name":"Carretero","full_name":"Carretero, Miguel A.","first_name":"Miguel A."},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"date_published":"2022-05-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"05","year":"2022","publication_status":"published","quality_controlled":"1","day":"01","type":"journal_article","abstract":[{"lang":"eng","text":"Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction."}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"NiBa"},{"_id":"BeVi"}],"status":"public","title":"Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization","external_id":{"isi":["000781632500001"],"pmid":["35323995"]},"citation":{"ama":"Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. <i>Evolution</i>. 2022;76(5):899-914. doi:<a href=\"https://doi.org/10.1111/evo.14462\">10.1111/evo.14462</a>","ista":"Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 76(5), 899–914.","short":"S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas, D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.","ieee":"S. Freitas <i>et al.</i>, “Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization,” <i>Evolution</i>, vol. 76, no. 5. Wiley, pp. 899–914, 2022.","apa":"Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas, Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14462\">https://doi.org/10.1111/evo.14462</a>","chicago":"Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14462\">https://doi.org/10.1111/evo.14462</a>.","mla":"Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” <i>Evolution</i>, vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:<a href=\"https://doi.org/10.1111/evo.14462\">10.1111/evo.14462</a>."},"doi":"10.1111/evo.14462","ec_funded":1,"publication":"Evolution","date_updated":"2025-04-14T07:48:21Z","volume":76,"oa":1,"article_type":"original","file":[{"checksum":"c27c025ae9afcf6c804d46a909775ee5","file_id":"11729","success":1,"relation":"main_file","file_size":2855214,"creator":"dernst","date_created":"2022-08-05T06:19:28Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2022-08-05T06:19:28Z","file_name":"2022_Evolution_Freitas.pdf"}],"intvolume":"        76"},{"file":[{"relation":"main_file","success":1,"file_id":"12742","checksum":"0117023e188542082ca6693cf39e7f03","file_name":"sciadv.abq1263.pdf","date_updated":"2023-03-21T14:18:10Z","creator":"patrickd","file_size":2973998,"access_level":"open_access","date_created":"2023-03-21T14:18:10Z","content_type":"application/pdf"}],"intvolume":"         8","article_type":"original","volume":8,"oa":1,"date_updated":"2025-09-09T14:30:38Z","publication":"Science Advances","ec_funded":1,"doi":"10.1126/sciadv.abq1263","citation":{"ieee":"N. Amberg, F. Pauler, C. Streicher, and S. Hippenmeyer, “Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression,” <i>Science Advances</i>, vol. 8, no. 44. American Association for the Advancement of Science, 2022.","short":"N. Amberg, F. Pauler, C. Streicher, S. Hippenmeyer, Science Advances 8 (2022).","ista":"Amberg N, Pauler F, Streicher C, Hippenmeyer S. 2022. Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression. Science Advances. 8(44), abq1263.","ama":"Amberg N, Pauler F, Streicher C, Hippenmeyer S. Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression. <i>Science Advances</i>. 2022;8(44). doi:<a href=\"https://doi.org/10.1126/sciadv.abq1263\">10.1126/sciadv.abq1263</a>","mla":"Amberg, Nicole, et al. “Tissue-Wide Genetic and Cellular Landscape Shapes the Execution of Sequential PRC2 Functions in Neural Stem Cell Lineage Progression.” <i>Science Advances</i>, vol. 8, no. 44, abq1263, American Association for the Advancement of Science, 2022, doi:<a href=\"https://doi.org/10.1126/sciadv.abq1263\">10.1126/sciadv.abq1263</a>.","chicago":"Amberg, Nicole, Florian Pauler, Carmen Streicher, and Simon Hippenmeyer. “Tissue-Wide Genetic and Cellular Landscape Shapes the Execution of Sequential PRC2 Functions in Neural Stem Cell Lineage Progression.” <i>Science Advances</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/sciadv.abq1263\">https://doi.org/10.1126/sciadv.abq1263</a>.","apa":"Amberg, N., Pauler, F., Streicher, C., &#38; Hippenmeyer, S. (2022). Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abq1263\">https://doi.org/10.1126/sciadv.abq1263</a>"},"title":"Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression","external_id":{"isi":["000918406800019"],"pmid":["36322669"]},"status":"public","department":[{"_id":"SiHi"}],"pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"The generation of a correctly-sized cerebral cortex with all-embracing neuronal and glial cell-type diversity critically depends on faithful radial glial progenitor (RGP) cell proliferation/differentiation programs. Temporal RGP lineage progression is regulated by Polycomb Repressive Complex 2 (PRC2) and loss of PRC2 activity results in severe neurogenesis defects and microcephaly. How PRC2-dependent gene expression instructs RGP lineage progression is unknown. Here we utilize Mosaic Analysis with Double Markers (MADM)-based single cell technology and demonstrate that PRC2 is not cell-autonomously required in neurogenic RGPs but rather acts at the global tissue-wide level. Conversely, cortical astrocyte production and maturation is cell-autonomously controlled by PRC2-dependent transcriptional regulation. We thus reveal highly distinct and sequential PRC2 functions in RGP lineage progression that are dependent on complex interplays between intrinsic and tissue-wide properties. In a broader context our results imply a critical role for the genetic and cellular niche environment in neural stem cell behavior."}],"related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/whole-tissue-shapes-brain-development/"}]},"type":"journal_article","day":"01","quality_controlled":"1","corr_author":"1","publication_status":"published","year":"2022","month":"11","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2022-11-01T00:00:00Z","author":[{"orcid":"0000-0002-3183-8207","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","full_name":"Amberg, Nicole"},{"first_name":"Florian","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Streicher, Carmen","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon"}],"publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","_id":"11336","article_number":"abq1263","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","grant_number":"T01031"}],"scopus_import":"1","file_date_updated":"2023-03-21T14:18:10Z","ddc":["570"],"date_created":"2022-04-26T15:04:50Z","issue":"44","acknowledgement":"We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and C. Czepe (VBCF GmbH, NGS  Unit)  and  S.  Gharagozlou  for  technical  support.  This  research  was  supported  by  the  Scientific  Service  Units  (SSU)  of  IST  Austria  through  resources  provided  by  the  Imaging  &  Optics Facility (IOF), Lab Support Facility (LSF), and Preclinical Facility (PCF). N.A. received funding   from   the   FWF   Firnberg-Programm   (T   1031).   The   work   was   supported   by   IST   institutional  funds  and  by  the  European  Research  Council  (ERC)  under  the  European  Union’s  Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H.","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["2375-2548"]},"isi":1},{"date_published":"2022-04-15T00:00:00Z","author":[{"full_name":"De Nicola, Stefano","first_name":"Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4842-6671","last_name":"De Nicola"},{"last_name":"Michailidis","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","full_name":"Michailidis, Alexios"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym"}],"publisher":"American Physical Society","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"11337","article_number":"165149","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","date_created":"2022-04-28T08:06:10Z","acknowledgement":"We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 850899).\r\nS.D.N. also acknowledges funding from the Institute of Science and Technology (IST) Austria, and from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","publication_identifier":{"eisbn":["2469-9969"],"issn":["2469-9950"]},"isi":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2112.11273","open_access":"1"}],"intvolume":"       105","article_type":"original","volume":105,"oa":1,"date_updated":"2025-04-14T07:43:57Z","publication":"Physical Review B","ec_funded":1,"doi":"10.1103/PhysRevB.105.165149","citation":{"mla":"De Nicola, Stefano, et al. “Entanglement and Precession in Two-Dimensional Dynamical Quantum Phase Transitions.” <i>Physical Review B</i>, vol. 105, 165149, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevB.105.165149\">10.1103/PhysRevB.105.165149</a>.","chicago":"De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement and Precession in Two-Dimensional Dynamical Quantum Phase Transitions.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevB.105.165149\">https://doi.org/10.1103/PhysRevB.105.165149</a>.","apa":"De Nicola, S., Michailidis, A., &#38; Serbyn, M. (2022). Entanglement and precession in two-dimensional dynamical quantum phase transitions. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.105.165149\">https://doi.org/10.1103/PhysRevB.105.165149</a>","ieee":"S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement and precession in two-dimensional dynamical quantum phase transitions,” <i>Physical Review B</i>, vol. 105. American Physical Society, 2022.","short":"S. De Nicola, A. Michailidis, M. Serbyn, Physical Review B 105 (2022).","ista":"De Nicola S, Michailidis A, Serbyn M. 2022. Entanglement and precession in two-dimensional dynamical quantum phase transitions. Physical Review B. 105, 165149.","ama":"De Nicola S, Michailidis A, Serbyn M. Entanglement and precession in two-dimensional dynamical quantum phase transitions. <i>Physical Review B</i>. 2022;105. doi:<a href=\"https://doi.org/10.1103/PhysRevB.105.165149\">10.1103/PhysRevB.105.165149</a>"},"title":"Entanglement and precession in two-dimensional dynamical quantum phase transitions","external_id":{"isi":["000806812400004"],"arxiv":["2112.11273"]},"status":"public","department":[{"_id":"MaSe"}],"arxiv":1,"oa_version":"Preprint","abstract":[{"text":"Nonanalytic points in the return probability of a quantum state as a function of time, known as dynamical quantum phase transitions (DQPTs), have received great attention in recent years, but the understanding of their mechanism is still incomplete. In our recent work [Phys. Rev. Lett. 126, 040602 (2021)], we demonstrated that one-dimensional DQPTs can be produced by two distinct mechanisms, namely semiclassical precession and entanglement generation, leading to the definition of precession (pDQPTs) and entanglement (eDQPTs) dynamical quantum phase transitions. In this manuscript, we extend and investigate the notion of p- and eDQPTs in two-dimensional systems by considering semi-infinite ladders of varying width. For square lattices, we find that pDQPTs and eDQPTs persist and are characterized by similar phenomenology as in 1D: pDQPTs are associated with a magnetization sign change and a wide entanglement gap, while eDQPTs correspond to suppressed local observables and avoided crossings in the entanglement spectrum. However, DQPTs show higher sensitivity to the ladder width and other details, challenging the extrapolation to the thermodynamic limit especially for eDQPTs. Moving to honeycomb lattices, we also demonstrate that lattices with an odd number of nearest neighbors give rise to phenomenologies beyond the one-dimensional classification.","lang":"eng"}],"type":"journal_article","day":"15","corr_author":"1","quality_controlled":"1","publication_status":"published","month":"04","year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"citation":{"mla":"Glover, Georgina, et al. “Nutrient and Salt Depletion Synergistically Boosts Glucose Metabolism in Individual Escherichia Coli Cells.” <i>Communications Biology</i>, vol. 5, 385, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03336-6\">10.1038/s42003-022-03336-6</a>.","chicago":"Glover, Georgina, Margaritis Voliotis, Urszula Łapińska, Brandon M. Invergo, Darren Soanes, Paul O’Neill, Karen Moore, et al. “Nutrient and Salt Depletion Synergistically Boosts Glucose Metabolism in Individual Escherichia Coli Cells.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03336-6\">https://doi.org/10.1038/s42003-022-03336-6</a>.","apa":"Glover, G., Voliotis, M., Łapińska, U., Invergo, B. M., Soanes, D., O’Neill, P., … Pagliara, S. (2022). Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03336-6\">https://doi.org/10.1038/s42003-022-03336-6</a>","ista":"Glover G, Voliotis M, Łapińska U, Invergo BM, Soanes D, O’Neill P, Moore K, Nikolic N, Petrov P, Milner DS, Roy S, Heesom K, Richards TA, Tsaneva-Atanasova K, Pagliara S. 2022. Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. Communications Biology. 5, 385.","ama":"Glover G, Voliotis M, Łapińska U, et al. Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. <i>Communications Biology</i>. 2022;5. doi:<a href=\"https://doi.org/10.1038/s42003-022-03336-6\">10.1038/s42003-022-03336-6</a>","ieee":"G. Glover <i>et al.</i>, “Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells,” <i>Communications Biology</i>, vol. 5. Springer Nature, 2022.","short":"G. Glover, M. Voliotis, U. Łapińska, B.M. Invergo, D. Soanes, P. O’Neill, K. Moore, N. Nikolic, P. Petrov, D.S. Milner, S. Roy, K. Heesom, T.A. Richards, K. Tsaneva-Atanasova, S. Pagliara, Communications Biology 5 (2022)."},"doi":"10.1038/s42003-022-03336-6","publication":"Communications Biology","department":[{"_id":"CaGu"}],"status":"public","external_id":{"isi":["000784143400001"],"pmid":["35444215"]},"title":"Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells","intvolume":"         5","file":[{"file_name":"2022_CommBiology_Glover.pdf","date_updated":"2022-05-02T06:26:26Z","access_level":"open_access","date_created":"2022-05-02T06:26:26Z","content_type":"application/pdf","file_size":2827723,"creator":"dernst","success":1,"relation":"main_file","checksum":"7c6f76ab17393d650825cc240edc84b3","file_id":"11342"}],"date_updated":"2023-08-03T06:45:26Z","volume":5,"oa":1,"article_type":"original","quality_controlled":"1","day":"20","type":"journal_article","abstract":[{"text":"The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.","lang":"eng"}],"year":"2022","month":"04","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","oa_version":"Published Version","pmid":1,"article_number":"385","_id":"11339","scopus_import":"1","author":[{"last_name":"Glover","first_name":"Georgina","full_name":"Glover, Georgina"},{"full_name":"Voliotis, Margaritis","first_name":"Margaritis","last_name":"Voliotis"},{"last_name":"Łapińska","full_name":"Łapińska, Urszula","first_name":"Urszula"},{"first_name":"Brandon M.","full_name":"Invergo, Brandon M.","last_name":"Invergo"},{"last_name":"Soanes","first_name":"Darren","full_name":"Soanes, Darren"},{"first_name":"Paul","full_name":"O’Neill, Paul","last_name":"O’Neill"},{"first_name":"Karen","full_name":"Moore, Karen","last_name":"Moore"},{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","last_name":"Nikolic","full_name":"Nikolic, Nela","first_name":"Nela"},{"full_name":"Petrov, Peter","first_name":"Peter","last_name":"Petrov"},{"last_name":"Milner","full_name":"Milner, David S.","first_name":"David S."},{"last_name":"Roy","first_name":"Sumita","full_name":"Roy, Sumita"},{"last_name":"Heesom","full_name":"Heesom, Kate","first_name":"Kate"},{"last_name":"Richards","full_name":"Richards, Thomas A.","first_name":"Thomas A."},{"last_name":"Tsaneva-Atanasova","full_name":"Tsaneva-Atanasova, Krasimira","first_name":"Krasimira"},{"last_name":"Pagliara","full_name":"Pagliara, Stefano","first_name":"Stefano"}],"date_published":"2022-04-20T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Springer Nature","isi":1,"publication_identifier":{"eissn":["2399-3642"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"G.G. was supported by an EPSRC DTP PhD studentship (EP/M506527/1). M.V. and K.T.A. gratefully acknowledge financial support from the EPSRC (EP/N014391/1). U.L. was supported through a BBSRC grant (BB/V008021/1) and an MRC Proximity to Discovery EXCITEME2 grant (MCPC17189). This work was further supported by a Royal Society Research Grant (RG180007) awarded to S.P. and a QUEX Initiator grant awarded to S.P. and K.T.A.. D.S.M., T.A.R. and S.P.’s work in this area is also supported by a Marie Skłodowska-Curie project SINGEK (H2020-MSCA-ITN-2015-675752) and the Gordon and Betty Moore Foundation Marine Microbiology Initiative (GBMF5514). B.M.I. acknowledges support from a Wellcome Trust Institutional Strategic Support Award to the University of Exeter (204909/Z/16/Z). This project utilised equipment funded by the Wellcome Trust Institutional Strategic Support Fund (WT097835MF), Wellcome Trust Multi User Equipment Award (WT101650MA) and BBSRC LOLA award (BB/K003240/1).","date_created":"2022-05-01T22:01:41Z","ddc":["570"],"file_date_updated":"2022-05-02T06:26:26Z"}]