[{"page":"686-696","isi":1,"type":"journal_article","ec_funded":1,"oa":1,"publication_status":"published","year":"2019","article_processing_charge":"No","file":[{"file_id":"6845","date_updated":"2020-07-14T12:47:42Z","file_name":"2019_JournalAnatomy_Picco.pdf","checksum":"160f960844b204057f20896e0e1f8ee7","creator":"dernst","relation":"main_file","date_created":"2019-09-02T12:05:18Z","content_type":"application/pdf","access_level":"open_access","file_size":1192994}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-09-01T00:00:00Z","abstract":[{"text":"Studying the progression of the proliferative and differentiative patterns of neural stem cells at the individual cell level is crucial to the understanding of cortex development and how the disruption of such patterns can lead to malformations and neurodevelopmental diseases. However, our understanding of the precise lineage progression programme at single-cell resolution is still incomplete due to the technical variations in lineage- tracing approaches. One of the key challenges involves developing a robust theoretical framework in which we can integrate experimental observations and introduce correction factors to obtain a reliable and representative description of the temporal modulation of proliferation and differentiation. In order to obtain more conclusive insights, we carry out virtual clonal analysis using mathematical modelling and compare our results against experimental data. Using a dataset obtained with Mosaic Analysis with Double Markers, we illustrate how the theoretical description can be exploited to interpret and reconcile the disparity between virtual and experimental results.","lang":"eng"}],"date_created":"2019-09-02T11:57:28Z","has_accepted_license":"1","publisher":"Wiley","language":[{"iso":"eng"}],"intvolume":"       235","issue":"3","publication":"Journal of Anatomy","ddc":["570"],"month":"09","status":"public","day":"01","publication_identifier":{"eissn":["1469-7580"],"issn":["0021-8782"]},"article_type":"original","file_date_updated":"2020-07-14T12:47:42Z","external_id":{"isi":["000482426800017"]},"author":[{"first_name":"Noemi","last_name":"Picco","full_name":"Picco, Noemi"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"id":"3C70A038-F248-11E8-B48F-1D18A9856A87","full_name":"Rodarte, Julio","last_name":"Rodarte","first_name":"Julio"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","first_name":"Carmen","last_name":"Streicher"},{"first_name":"Zoltán","last_name":"Molnár","full_name":"Molnár, Zoltán"},{"first_name":"Philip K.","last_name":"Maini","full_name":"Maini, Philip K."},{"first_name":"Thomas E.","last_name":"Woolley","full_name":"Woolley, Thomas E."}],"title":"A mathematical insight into cell labelling experiments for clonal analysis","date_updated":"2025-04-14T07:43:05Z","department":[{"_id":"SiHi"}],"scopus_import":"1","volume":235,"project":[{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"ama":"Picco N, Hippenmeyer S, Rodarte J, et al. A mathematical insight into cell labelling experiments for clonal analysis. <i>Journal of Anatomy</i>. 2019;235(3):686-696. doi:<a href=\"https://doi.org/10.1111/joa.13001\">10.1111/joa.13001</a>","ista":"Picco N, Hippenmeyer S, Rodarte J, Streicher C, Molnár Z, Maini PK, Woolley TE. 2019. A mathematical insight into cell labelling experiments for clonal analysis. Journal of Anatomy. 235(3), 686–696.","apa":"Picco, N., Hippenmeyer, S., Rodarte, J., Streicher, C., Molnár, Z., Maini, P. K., &#38; Woolley, T. E. (2019). A mathematical insight into cell labelling experiments for clonal analysis. <i>Journal of Anatomy</i>. Wiley. <a href=\"https://doi.org/10.1111/joa.13001\">https://doi.org/10.1111/joa.13001</a>","ieee":"N. Picco <i>et al.</i>, “A mathematical insight into cell labelling experiments for clonal analysis,” <i>Journal of Anatomy</i>, vol. 235, no. 3. Wiley, pp. 686–696, 2019.","mla":"Picco, Noemi, et al. “A Mathematical Insight into Cell Labelling Experiments for Clonal Analysis.” <i>Journal of Anatomy</i>, vol. 235, no. 3, Wiley, 2019, pp. 686–96, doi:<a href=\"https://doi.org/10.1111/joa.13001\">10.1111/joa.13001</a>.","short":"N. Picco, S. Hippenmeyer, J. Rodarte, C. Streicher, Z. Molnár, P.K. Maini, T.E. Woolley, Journal of Anatomy 235 (2019) 686–696.","chicago":"Picco, Noemi, Simon Hippenmeyer, Julio Rodarte, Carmen Streicher, Zoltán Molnár, Philip K. Maini, and Thomas E. Woolley. “A Mathematical Insight into Cell Labelling Experiments for Clonal Analysis.” <i>Journal of Anatomy</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/joa.13001\">https://doi.org/10.1111/joa.13001</a>."},"tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"doi":"10.1111/joa.13001","_id":"6844","quality_controlled":"1","oa_version":"Published Version"},{"scopus_import":"1","department":[{"_id":"NiBa"}],"volume":20,"citation":{"short":"G. Sella, N.H. Barton, Annual Review of Genomics and Human Genetics 20 (2019) 461–493.","chicago":"Sella, Guy, and Nicholas H Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” <i>Annual Review of Genomics and Human Genetics</i>. Annual Reviews, 2019. <a href=\"https://doi.org/10.1146/annurev-genom-083115-022316\">https://doi.org/10.1146/annurev-genom-083115-022316</a>.","ama":"Sella G, Barton NH. Thinking about the evolution of complex traits in the era of genome-wide association studies. <i>Annual Review of Genomics and Human Genetics</i>. 2019;20:461-493. doi:<a href=\"https://doi.org/10.1146/annurev-genom-083115-022316\">10.1146/annurev-genom-083115-022316</a>","ista":"Sella G, Barton NH. 2019. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 20, 461–493.","apa":"Sella, G., &#38; Barton, N. H. (2019). Thinking about the evolution of complex traits in the era of genome-wide association studies. <i>Annual Review of Genomics and Human Genetics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-genom-083115-022316\">https://doi.org/10.1146/annurev-genom-083115-022316</a>","mla":"Sella, Guy, and Nicholas H. Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” <i>Annual Review of Genomics and Human Genetics</i>, vol. 20, Annual Reviews, 2019, pp. 461–93, doi:<a href=\"https://doi.org/10.1146/annurev-genom-083115-022316\">10.1146/annurev-genom-083115-022316</a>.","ieee":"G. Sella and N. H. Barton, “Thinking about the evolution of complex traits in the era of genome-wide association studies,” <i>Annual Review of Genomics and Human Genetics</i>, vol. 20. Annual Reviews, pp. 461–493, 2019."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1146/annurev-genom-083115-022316","_id":"6855","oa_version":"Published Version","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:42Z","publication_identifier":{"eissn":["1545-293X"],"issn":["1527-8204"]},"day":"05","external_id":{"pmid":["31283361"],"isi":["000485148400020"]},"author":[{"full_name":"Sella, Guy","first_name":"Guy","last_name":"Sella"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"date_updated":"2024-10-09T20:58:59Z","title":"Thinking about the evolution of complex traits in the era of genome-wide association studies","pmid":1,"has_accepted_license":"1","date_created":"2019-09-07T14:28:29Z","abstract":[{"lang":"eng","text":"Many traits of interest are highly heritable and genetically complex, meaning that much of the variation they exhibit arises from differences at numerous loci in the genome. Complex traits and their evolution have been studied for more than a century, but only in the last decade have genome-wide association studies (GWASs) in humans begun to reveal their genetic basis. Here, we bring these threads of research together to ask how findings from GWASs can further our understanding of the processes that give rise to heritable variation in complex traits and of the genetic basis of complex trait evolution in response to changing selection pressures (i.e., of polygenic adaptation). Conversely, we ask how evolutionary thinking helps us to interpret findings from GWASs and informs related efforts of practical importance."}],"publisher":"Annual Reviews","language":[{"iso":"eng"}],"intvolume":"        20","month":"07","corr_author":"1","ddc":["576"],"status":"public","publication":"Annual Review of Genomics and Human Genetics","page":"461-493","isi":1,"type":"journal_article","oa":1,"article_processing_charge":"No","year":"2019","publication_status":"published","file":[{"date_created":"2019-09-09T07:22:12Z","relation":"main_file","checksum":"23d3978cf4739a89ce2c3e779f9305ca","file_name":"2019_AnnualReview_Sella.pdf","creator":"dernst","file_size":411491,"access_level":"open_access","content_type":"application/pdf","file_id":"6862","date_updated":"2020-07-14T12:47:42Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-07-05T00:00:00Z"},{"file":[{"file_size":193248,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-10-11T06:59:26Z","checksum":"8cc7551bff70b2658f8d5630f228ee12","creator":"dernst","file_name":"2019_BioEssays_Giese.pdf","date_updated":"2020-07-14T12:47:42Z","file_id":"6939"}],"publication_status":"published","article_processing_charge":"No","year":"2019","article_number":"1900151","date_published":"2019-11-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"type":"journal_article","isi":1,"issue":"11","publication":"BioEssays","ddc":["570"],"status":"public","month":"11","publisher":"Wiley","abstract":[{"text":"Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop.","lang":"eng"}],"date_created":"2019-09-07T14:40:03Z","has_accepted_license":"1","intvolume":"        41","language":[{"iso":"eng"}],"author":[{"last_name":"Giese","first_name":"B","full_name":"Giese, B"},{"last_name":"Friess","first_name":"J L","full_name":"Friess, J L"},{"full_name":"Schetelig, M F ","last_name":"Schetelig","first_name":"M F "},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Messer, Philip","last_name":"Messer","first_name":"Philip"},{"last_name":"Debarre","first_name":"Florence","full_name":"Debarre, Florence"},{"last_name":"Meimberg","first_name":"H","full_name":"Meimberg, H"},{"last_name":"Windbichler","first_name":"N","full_name":"Windbichler, N"},{"first_name":"C","last_name":"Boete","full_name":"Boete, C"}],"title":"Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna","date_updated":"2023-08-30T06:56:26Z","day":"01","file_date_updated":"2020-07-14T12:47:42Z","publication_identifier":{"eissn":["1521-1878"]},"article_type":"original","external_id":{"isi":["000489502000001"]},"oa_version":"Published Version","quality_controlled":"1","_id":"6857","volume":41,"department":[{"_id":"NiBa"}],"scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).","chicago":"Giese, B, J L Friess, M F  Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” <i>BioEssays</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/bies.201900151\">https://doi.org/10.1002/bies.201900151</a>.","apa":"Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. <i>BioEssays</i>. Wiley. <a href=\"https://doi.org/10.1002/bies.201900151\">https://doi.org/10.1002/bies.201900151</a>","ista":"Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.","ama":"Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. <i>BioEssays</i>. 2019;41(11). doi:<a href=\"https://doi.org/10.1002/bies.201900151\">10.1002/bies.201900151</a>","ieee":"B. Giese <i>et al.</i>, “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” <i>BioEssays</i>, vol. 41, no. 11. Wiley, 2019.","mla":"Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” <i>BioEssays</i>, vol. 41, no. 11, 1900151, Wiley, 2019, doi:<a href=\"https://doi.org/10.1002/bies.201900151\">10.1002/bies.201900151</a>."},"doi":"10.1002/bies.201900151"},{"publication":"National Science Review","ddc":["570"],"status":"public","month":"03","issue":"2","intvolume":"         6","language":[{"iso":"eng"}],"publisher":"Oxford University Press","date_created":"2019-09-07T14:43:02Z","has_accepted_license":"1","date_published":"2019-03-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","date_created":"2020-10-02T09:16:44Z","checksum":"571d60fa21a568607d1fd04e119da88c","file_name":"2019_NSR_Barton.pdf","creator":"dernst","file_size":106463,"content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"8595","date_updated":"2020-10-02T09:16:44Z"}],"publication_status":"published","article_processing_charge":"No","year":"2019","oa":1,"isi":1,"type":"journal_article","page":"291-292","quality_controlled":"1","oa_version":"Published Version","_id":"6858","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National Science Review. 6(2), 291–292.","ama":"Barton NH. Is speciation driven by cycles of mixing and isolation? <i>National Science Review</i>. 2019;6(2):291-292. doi:<a href=\"https://doi.org/10.1093/nsr/nwy113\">10.1093/nsr/nwy113</a>","apa":"Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation? <i>National Science Review</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nsr/nwy113\">https://doi.org/10.1093/nsr/nwy113</a>","mla":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” <i>National Science Review</i>, vol. 6, no. 2, Oxford University Press, 2019, pp. 291–92, doi:<a href=\"https://doi.org/10.1093/nsr/nwy113\">10.1093/nsr/nwy113</a>.","ieee":"N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” <i>National Science Review</i>, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.","short":"N.H. Barton, National Science Review 6 (2019) 291–292.","chicago":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” <i>National Science Review</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/nsr/nwy113\">https://doi.org/10.1093/nsr/nwy113</a>."},"doi":"10.1093/nsr/nwy113","volume":6,"scopus_import":"1","department":[{"_id":"NiBa"}],"title":"Is speciation driven by cycles of mixing and isolation?","date_updated":"2023-08-29T07:51:09Z","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"external_id":{"isi":["000467957400025"]},"day":"01","file_date_updated":"2020-10-02T09:16:44Z","publication_identifier":{"issn":["2095-5138"],"eissn":["2053-714X"]},"article_type":"review"},{"publisher":"Springer Nature","has_accepted_license":"1","abstract":[{"text":"A novel magnetic scratch method achieves repeatability, reproducibility and geometric control greater than pipette scratch assays and closely approximating the precision of cell exclusion assays while inducing the cell injury inherently necessary for wound healing assays. The magnetic scratch is affordable, easily implemented and standardisable and thus may contribute toward better comparability of data generated in different studies and laboratories.","lang":"eng"}],"date_created":"2019-09-15T22:00:42Z","pmid":1,"intvolume":"         9","language":[{"iso":"eng"}],"issue":"1","ddc":["570"],"status":"public","month":"09","publication":"Scientific Reports","oa":1,"type":"journal_article","isi":1,"file":[{"date_updated":"2020-07-14T12:47:42Z","file_id":"6879","access_level":"open_access","content_type":"application/pdf","file_size":3523795,"file_name":"2019_ScientificReports_Fenu.pdf","checksum":"9cfd986d4108e288cc72276ef047ab0c","creator":"dernst","date_created":"2019-09-16T12:42:40Z","relation":"main_file"}],"publication_status":"published","article_processing_charge":"No","year":"2019","article_number":"12625","date_published":"2019-09-02T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":9,"scopus_import":"1","department":[{"_id":"Bio"}],"citation":{"short":"M. Fenu, T. Bettermann, C. Vogl, N. Darwish-Miranda, J. Schramel, F. Jenner, I. Ribitsch, Scientific Reports 9 (2019).","chicago":"Fenu, M., T. Bettermann, C. Vogl, Nasser Darwish-Miranda, J. Schramel, F. Jenner, and I. Ribitsch. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” <i>Scientific Reports</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41598-019-48930-7\">https://doi.org/10.1038/s41598-019-48930-7</a>.","apa":"Fenu, M., Bettermann, T., Vogl, C., Darwish-Miranda, N., Schramel, J., Jenner, F., &#38; Ribitsch, I. (2019). A novel magnet-based scratch method for standardisation of wound-healing assays. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-019-48930-7\">https://doi.org/10.1038/s41598-019-48930-7</a>","ama":"Fenu M, Bettermann T, Vogl C, et al. A novel magnet-based scratch method for standardisation of wound-healing assays. <i>Scientific Reports</i>. 2019;9(1). doi:<a href=\"https://doi.org/10.1038/s41598-019-48930-7\">10.1038/s41598-019-48930-7</a>","ista":"Fenu M, Bettermann T, Vogl C, Darwish-Miranda N, Schramel J, Jenner F, Ribitsch I. 2019. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 9(1), 12625.","mla":"Fenu, M., et al. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” <i>Scientific Reports</i>, vol. 9, no. 1, 12625, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41598-019-48930-7\">10.1038/s41598-019-48930-7</a>.","ieee":"M. Fenu <i>et al.</i>, “A novel magnet-based scratch method for standardisation of wound-healing assays,” <i>Scientific Reports</i>, vol. 9, no. 1. Springer Nature, 2019."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41598-019-48930-7","oa_version":"Published Version","quality_controlled":"1","_id":"6867","day":"02","publication_identifier":{"eissn":["2045-2322"]},"file_date_updated":"2020-07-14T12:47:42Z","external_id":{"pmid":["31477739"],"isi":["000483697800007"]},"author":[{"full_name":"Fenu, M.","last_name":"Fenu","first_name":"M."},{"full_name":"Bettermann, T.","last_name":"Bettermann","first_name":"T."},{"last_name":"Vogl","first_name":"C.","full_name":"Vogl, C."},{"orcid":"0000-0002-8821-8236","last_name":"Darwish-Miranda","first_name":"Nasser","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","full_name":"Darwish-Miranda, Nasser"},{"first_name":"J.","last_name":"Schramel","full_name":"Schramel, J."},{"last_name":"Jenner","first_name":"F.","full_name":"Jenner, F."},{"full_name":"Ribitsch, I.","first_name":"I.","last_name":"Ribitsch"}],"title":"A novel magnet-based scratch method for standardisation of wound-healing assays","date_updated":"2026-04-03T09:39:11Z"},{"oa_version":"Published Version","quality_controlled":"1","_id":"6868","citation":{"mla":"Byczkowicz, Niklas, et al. “HCN Channel-Mediated Neuromodulation Can Control Action Potential Velocity and Fidelity in Central Axons.” <i>ELife</i>, vol. 8, e42766, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.42766\">10.7554/eLife.42766</a>.","ieee":"N. Byczkowicz <i>et al.</i>, “HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","apa":"Byczkowicz, N., Eshra, A., Montanaro-Punzengruber, J.-C., Trevisiol, A., Hirrlinger, J., Kole, M. H., … Hallermann, S. (2019). HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.42766\">https://doi.org/10.7554/eLife.42766</a>","ista":"Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, Trevisiol A, Hirrlinger J, Kole MH, Shigemoto R, Hallermann S. 2019. HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. eLife. 8, e42766.","ama":"Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, et al. HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.42766\">10.7554/eLife.42766</a>","chicago":"Byczkowicz, Niklas, Abdelmoneim Eshra, Jacqueline-Claire Montanaro-Punzengruber, Andrea Trevisiol, Johannes Hirrlinger, Maarten Hp Kole, Ryuichi Shigemoto, and Stefan Hallermann. “HCN Channel-Mediated Neuromodulation Can Control Action Potential Velocity and Fidelity in Central Axons.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.42766\">https://doi.org/10.7554/eLife.42766</a>.","short":"N. Byczkowicz, A. Eshra, J.-C. Montanaro-Punzengruber, A. Trevisiol, J. Hirrlinger, M.H. Kole, R. Shigemoto, S. Hallermann, ELife 8 (2019)."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.7554/eLife.42766","volume":8,"department":[{"_id":"RySh"}],"scopus_import":"1","title":"HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons","date_updated":"2026-04-03T09:40:28Z","author":[{"full_name":"Byczkowicz, Niklas","first_name":"Niklas","last_name":"Byczkowicz"},{"last_name":"Eshra","first_name":"Abdelmoneim","full_name":"Eshra, Abdelmoneim"},{"last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Trevisiol, Andrea","last_name":"Trevisiol","first_name":"Andrea"},{"first_name":"Johannes","last_name":"Hirrlinger","full_name":"Hirrlinger, Johannes"},{"full_name":"Kole, Maarten Hp","first_name":"Maarten Hp","last_name":"Kole"},{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"first_name":"Stefan","last_name":"Hallermann","full_name":"Hallermann, Stefan"}],"external_id":{"isi":["000485663900001"]},"day":"09","file_date_updated":"2020-07-14T12:47:42Z","publication_identifier":{"eissn":["2050-084X"]},"article_type":"original","status":"public","ddc":["570"],"month":"09","publication":"eLife","intvolume":"         8","language":[{"iso":"eng"}],"publisher":"eLife Sciences Publications","has_accepted_license":"1","abstract":[{"text":"Hyperpolarization-activated cyclic-nucleotide-gated (HCN) channels control electrical rhythmicity and excitability in the heart and brain, but the function of HCN channels at the subcellular level in axons remains poorly understood. Here, we show that the action potential conduction velocity in both myelinated and unmyelinated central axons can be bidirectionally modulated by a HCN channel blocker, cyclic adenosine monophosphate (cAMP), and neuromodulators. Recordings from mouse cerebellar mossy fiber boutons show that HCN channels ensure reliable high-frequency firing and are strongly modulated by cAMP (EC50 40 mM; estimated endogenous cAMP concentration 13 mM). In addition, immunogold-electron microscopy revealed HCN2 as the dominating subunit in cerebellar mossy fibers. Computational modeling indicated that HCN2 channels control conduction velocity primarily by altering the resting membrane potential\r\nand are associated with significant metabolic costs. These results suggest that the cAMP-HCN pathway provides neuromodulators with an opportunity to finely tune energy consumption and temporal delays across axons in the brain.","lang":"eng"}],"date_created":"2019-09-15T22:00:43Z","date_published":"2019-09-09T00:00:00Z","article_number":"e42766","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":4008137,"file_name":"2019_eLife_Byczkowicz.pdf","checksum":"c350b7861ef0fb537cae8a3232aec016","creator":"dernst","date_created":"2019-09-16T13:14:33Z","relation":"main_file","date_updated":"2020-07-14T12:47:42Z","file_id":"6880"}],"publication_status":"published","year":"2019","article_processing_charge":"No","oa":1,"type":"journal_article","isi":1},{"ec_funded":1,"type":"conference","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-08-01T00:00:00Z","article_number":"11","publication_status":"published","article_processing_charge":"No","year":"2019","file":[{"relation":"main_file","date_created":"2019-09-27T11:45:15Z","file_name":"2019_LIPIcs_Avni.pdf","checksum":"6346e116a4f4ed1414174d96d2c4fbd7","creator":"kschuh","file_size":554457,"content_type":"application/pdf","access_level":"open_access","file_id":"6913","date_updated":"2020-07-14T12:47:42Z"}],"language":[{"iso":"eng"}],"intvolume":"       138","abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the \"bank\" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding. ","lang":"eng"}],"date_created":"2019-09-18T08:04:26Z","has_accepted_license":"1","alternative_title":["LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public","corr_author":"1","month":"08","ddc":["004"],"conference":{"start_date":"2019-08-26","name":"MFCS: Mathematical Foundations of Computer Science","location":"Aachen, Germany","end_date":"2019-08-30"},"external_id":{"arxiv":["1905.03835"]},"day":"01","file_date_updated":"2020-07-14T12:47:42Z","related_material":{"record":[{"id":"9239","relation":"later_version","status":"public"}]},"arxiv":1,"title":"Bidding mechanisms in graph games","date_updated":"2025-07-10T11:53:57Z","author":[{"first_name":"Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zikelic","orcid":"0000-0002-4681-1699","first_name":"Dorde","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S11402-N23"}],"doi":"10.4230/LIPICS.MFCS.2019.11","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"G. Avni, T.A. Henzinger, D. Zikelic, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Avni, Guy, Thomas A Henzinger, and Dorde Zikelic. “Bidding Mechanisms in Graph Games,” Vol. 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.MFCS.2019.11\">https://doi.org/10.4230/LIPICS.MFCS.2019.11</a>.","apa":"Avni, G., Henzinger, T. A., &#38; Zikelic, D. (2019). Bidding mechanisms in graph games (Vol. 138). Presented at the MFCS: Mathematical Foundations of Computer Science, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.MFCS.2019.11\">https://doi.org/10.4230/LIPICS.MFCS.2019.11</a>","ista":"Avni G, Henzinger TA, Zikelic D. 2019. Bidding mechanisms in graph games. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 138, 11.","ama":"Avni G, Henzinger TA, Zikelic D. Bidding mechanisms in graph games. In: Vol 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.MFCS.2019.11\">10.4230/LIPICS.MFCS.2019.11</a>","mla":"Avni, Guy, et al. <i>Bidding Mechanisms in Graph Games</i>. Vol. 138, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.MFCS.2019.11\">10.4230/LIPICS.MFCS.2019.11</a>.","ieee":"G. Avni, T. A. Henzinger, and D. Zikelic, “Bidding mechanisms in graph games,” presented at the MFCS: Mathematical Foundations of Computer Science, Aachen, Germany, 2019, vol. 138."},"scopus_import":"1","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"volume":138,"_id":"6884","quality_controlled":"1","oa_version":"Published Version"},{"article_number":"27","date_published":"2019-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"4985e26e1572d1575d64d38acabd71d6","file_name":"2019_LIPIcs_Chatterjee.pdf","creator":"kschuh","relation":"main_file","date_created":"2019-09-27T12:09:35Z","content_type":"application/pdf","access_level":"open_access","file_size":538120,"file_id":"6914","date_updated":"2020-07-14T12:47:43Z"}],"year":"2019","article_processing_charge":"No","publication_status":"published","oa":1,"type":"conference","ddc":["000"],"status":"public","month":"08","corr_author":"1","intvolume":"       140","language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"date_created":"2019-09-18T08:06:14Z","abstract":[{"text":"A vector addition system with states (VASS) consists of a finite set of states and counters. A configuration is a state and a value for each counter; a transition changes the state and each counter is incremented, decremented, or left unchanged. While qualitative properties such as state and configuration reachability have been studied for VASS, we consider the long-run average cost of infinite computations of VASS. The cost of a configuration is for each state, a linear combination of the counter values. In the special case of uniform cost functions, the linear combination is the same for all states. The (regular) long-run emptiness problem is, given a VASS, a cost function, and a threshold value, if there is a (lasso-shaped) computation such that the long-run average value of the cost function does not exceed the threshold. For uniform cost functions, we show that the regular long-run emptiness problem is (a) decidable in polynomial time for integer-valued VASS, and (b) decidable but nonelementarily hard for natural-valued VASS (i.e., nonnegative counters). For general cost functions, we show that the problem is (c) NP-complete for integer-valued VASS, and (d) undecidable for natural-valued VASS. Our most interesting result is for (c) integer-valued VASS with general cost functions, where we establish a connection between the regular long-run emptiness problem and quadratic Diophantine inequalities. The general (nonregular) long-run emptiness problem is equally hard as the regular problem in all cases except (c), where it remains open. ","lang":"eng"}],"has_accepted_license":"1","date_updated":"2025-07-10T11:53:58Z","title":"Long-run average behavior of vector addition systems with states","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"last_name":"Otop","first_name":"Jan","full_name":"Otop, Jan"}],"conference":{"start_date":"2019-08-27","name":"CONCUR: Conference on Concurrency Theory","location":"Amsterdam, Netherlands","end_date":"2019-08-30"},"file_date_updated":"2020-07-14T12:47:43Z","day":"01","oa_version":"Published Version","quality_controlled":"1","_id":"6885","doi":"10.4230/LIPICS.CONCUR.2019.27","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Long-Run Average Behavior of Vector Addition Systems with States,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.27\">https://doi.org/10.4230/LIPICS.CONCUR.2019.27</a>.","ista":"Chatterjee K, Henzinger TA, Otop J. 2019. Long-run average behavior of vector addition systems with states. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 140, 27.","ama":"Chatterjee K, Henzinger TA, Otop J. Long-run average behavior of vector addition systems with states. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.27\">10.4230/LIPICS.CONCUR.2019.27</a>","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2019). Long-run average behavior of vector addition systems with states (Vol. 140). Presented at the CONCUR: Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.27\">https://doi.org/10.4230/LIPICS.CONCUR.2019.27</a>","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Long-run average behavior of vector addition systems with states,” presented at the CONCUR: Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","mla":"Chatterjee, Krishnendu, et al. <i>Long-Run Average Behavior of Vector Addition Systems with States</i>. Vol. 140, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.27\">10.4230/LIPICS.CONCUR.2019.27</a>."},"project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"name":"Rigorous Systems Engineering","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"}],"volume":140,"scopus_import":"1","department":[{"_id":"ToHe"},{"_id":"KrCh"}]},{"external_id":{"arxiv":["1905.03588"]},"conference":{"location":"Amsterdam, Netherlands","name":"CONCUR: Conference on Concurrency Theory","start_date":"2019-08-27","end_date":"2019-08-30"},"arxiv":1,"day":"01","file_date_updated":"2020-07-14T12:47:43Z","title":"Determinacy in discrete-bidding infinite-duration games","date_updated":"2025-07-10T11:53:58Z","author":[{"full_name":"Aghajohari, Milad","first_name":"Milad","last_name":"Aghajohari"},{"first_name":"Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"citation":{"short":"M. Aghajohari, G. Avni, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding Infinite-Duration Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.20\">https://doi.org/10.4230/LIPICS.CONCUR.2019.20</a>.","ama":"Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.20\">10.4230/LIPICS.CONCUR.2019.20</a>","apa":"Aghajohari, M., Avni, G., &#38; Henzinger, T. A. (2019). Determinacy in discrete-bidding infinite-duration games (Vol. 140). Presented at the CONCUR: Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.20\">https://doi.org/10.4230/LIPICS.CONCUR.2019.20</a>","ista":"Aghajohari M, Avni G, Henzinger TA. 2019. Determinacy in discrete-bidding infinite-duration games. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 140, 20.","mla":"Aghajohari, Milad, et al. <i>Determinacy in Discrete-Bidding Infinite-Duration Games</i>. Vol. 140, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.20\">10.4230/LIPICS.CONCUR.2019.20</a>.","ieee":"M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding infinite-duration games,” presented at the CONCUR: Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140."},"tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","image":"/images/cc_by.png"},"doi":"10.4230/LIPICS.CONCUR.2019.20","project":[{"name":"Rigorous Systems Engineering","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"}],"volume":140,"scopus_import":"1","department":[{"_id":"ToHe"}],"oa_version":"Published Version","quality_controlled":"1","_id":"6886","oa":1,"type":"conference","date_published":"2019-08-01T00:00:00Z","article_number":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","date_created":"2019-09-27T12:21:38Z","checksum":"4df6d3575c506edb17215adada03cc8e","creator":"kschuh","file_name":"2019_LIPIcs_Aghajohari.pdf","file_size":741425,"content_type":"application/pdf","access_level":"open_access","file_id":"6915","date_updated":"2020-07-14T12:47:43Z"}],"publication_status":"published","year":"2019","article_processing_charge":"No","intvolume":"       140","language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2019-09-18T08:06:58Z","abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner of the game. Such games are central in formal methods since they model the interaction between a non-terminating system and its environment. In bidding games the players bid for the right to move the token: in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Bidding games are known to have a clean and elegant mathematical structure that relies on the ability of the players to submit arbitrarily small bids. Many applications, however, require a fixed granularity for the bids, which can represent, for example, the monetary value expressed in cents. We study, for the first time, the combination of discrete-bidding and infinite-duration games. Our most important result proves that these games form a large determined subclass of concurrent games, where determinacy is the strong property that there always exists exactly one player who can guarantee winning the game. In particular, we show that, in contrast to non-discrete bidding games, the mechanism with which tied bids are resolved plays an important role in discrete-bidding games. We study several natural tie-breaking mechanisms and show that, while some do not admit determinacy, most natural mechanisms imply determinacy for every pair of initial budgets. ","lang":"eng"}],"has_accepted_license":"1","alternative_title":["LIPIcs"],"ddc":["000"],"status":"public","month":"08","corr_author":"1"},{"department":[{"_id":"KrCh"}],"scopus_import":"1","volume":140,"project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.4230/LIPICS.CONCUR.2019.7","citation":{"ieee":"K. Chatterjee, W. Dvorák, M. Henzinger, and A. Svozil, “Near-linear time algorithms for Streett objectives in graphs and MDPs,” in <i>Leibniz International Proceedings in Informatics</i>, Amsterdam, Netherlands, 2019, vol. 140.","mla":"Chatterjee, Krishnendu, et al. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.” <i>Leibniz International Proceedings in Informatics</i>, vol. 140, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.7\">10.4230/LIPICS.CONCUR.2019.7</a>.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M., &#38; Svozil, A. (2019). Near-linear time algorithms for Streett objectives in graphs and MDPs. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 140). Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.7\">https://doi.org/10.4230/LIPICS.CONCUR.2019.7</a>","ama":"Chatterjee K, Dvorák W, Henzinger M, Svozil A. Near-linear time algorithms for Streett objectives in graphs and MDPs. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.7\">10.4230/LIPICS.CONCUR.2019.7</a>","ista":"Chatterjee K, Dvorák W, Henzinger M, Svozil A. 2019. Near-linear time algorithms for Streett objectives in graphs and MDPs. Leibniz International Proceedings in Informatics. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 140, 7.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika Henzinger, and Alexander Svozil. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.7\">https://doi.org/10.4230/LIPICS.CONCUR.2019.7</a>.","short":"K. Chatterjee, W. Dvorák, M. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019."},"_id":"6887","quality_controlled":"1","oa_version":"Published Version","day":"01","file_date_updated":"2020-07-14T12:47:43Z","conference":{"start_date":"2019-08-27","location":"Amsterdam, Netherlands","name":"CONCUR: Conference on Concurrency Theory","end_date":"2019-08-30"},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Dvorák, Wolfgang","last_name":"Dvorák","first_name":"Wolfgang"},{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Svozil, Alexander","last_name":"Svozil","first_name":"Alexander"}],"title":"Near-linear time algorithms for Streett objectives in graphs and MDPs","date_updated":"2025-07-10T11:53:59Z","has_accepted_license":"1","date_created":"2019-09-18T08:07:58Z","abstract":[{"lang":"eng","text":"The fundamental model-checking problem, given as input a model and a specification, asks for the algorithmic verification of whether the model satisfies the specification. Two classical models for reactive systems are graphs and Markov decision processes (MDPs). A basic specification formalism in the verification of reactive systems is the strong fairness (aka Streett) objective, where given different types of requests and corresponding grants, the requirement is that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All omega-regular objectives can be expressed as Streett objectives and hence they are canonical in verification. Consider graphs/MDPs with n vertices, m edges, and a Streett objectives with k pairs, and let b denote the size of the description of the Streett objective for the sets of requests and grants. The current best-known algorithm for the problem requires time O(min(n^2, m sqrt{m log n}) + b log n). In this work we present randomized near-linear time algorithms, with expected running time O~(m + b), where the O~ notation hides poly-log factors. Our randomized algorithms are near-linear in the size of the input, and hence optimal up to poly-log factors. "}],"alternative_title":["LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","language":[{"iso":"eng"}],"intvolume":"       140","corr_author":"1","month":"08","ddc":["000"],"status":"public","publication":"Leibniz International Proceedings in Informatics","ec_funded":1,"type":"conference","oa":1,"publication_status":"published","article_processing_charge":"No","year":"2019","file":[{"file_id":"6922","date_updated":"2020-07-14T12:47:43Z","relation":"main_file","date_created":"2019-10-01T08:20:30Z","file_name":"2019_LIPIcs_Chatterjee.pdf","checksum":"e1f0e4061212454574f34a1368d018ec","creator":"kschuh","file_size":730112,"content_type":"application/pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-08-01T00:00:00Z","article_number":"7"},{"_id":"6888","quality_controlled":"1","oa_version":"Submitted Version","scopus_import":"1","department":[{"_id":"ToHe"}],"volume":"2019-May","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems"}],"doi":"10.1109/icra.2019.8793840","citation":{"chicago":"Lechner, Mathias, Ramin Hasani, Manuel Zimmer, Thomas A Henzinger, and Radu Grosu. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” In <i>Proceedings - IEEE International Conference on Robotics and Automation</i>, Vol. 2019–May. IEEE, 2019. <a href=\"https://doi.org/10.1109/icra.2019.8793840\">https://doi.org/10.1109/icra.2019.8793840</a>.","short":"M. Lechner, R. Hasani, M. Zimmer, T.A. Henzinger, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2019.","ieee":"M. Lechner, R. Hasani, M. Zimmer, T. A. Henzinger, and R. Grosu, “Designing worm-inspired neural networks for interpretable robotic control,” in <i>Proceedings - IEEE International Conference on Robotics and Automation</i>, Montreal, QC, Canada, 2019, vol. 2019–May.","mla":"Lechner, Mathias, et al. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” <i>Proceedings - IEEE International Conference on Robotics and Automation</i>, vol. 2019–May, 8793840, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/icra.2019.8793840\">10.1109/icra.2019.8793840</a>.","ista":"Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. 2019. Designing worm-inspired neural networks for interpretable robotic control. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, vol. 2019–May, 8793840.","ama":"Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. Designing worm-inspired neural networks for interpretable robotic control. In: <i>Proceedings - IEEE International Conference on Robotics and Automation</i>. Vol 2019-May. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/icra.2019.8793840\">10.1109/icra.2019.8793840</a>","apa":"Lechner, M., Hasani, R., Zimmer, M., Henzinger, T. A., &#38; Grosu, R. (2019). Designing worm-inspired neural networks for interpretable robotic control. In <i>Proceedings - IEEE International Conference on Robotics and Automation</i> (Vol. 2019–May). Montreal, QC, Canada: IEEE. <a href=\"https://doi.org/10.1109/icra.2019.8793840\">https://doi.org/10.1109/icra.2019.8793840</a>"},"author":[{"last_name":"Lechner","first_name":"Mathias","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ramin","last_name":"Hasani","full_name":"Hasani, Ramin"},{"full_name":"Zimmer, Manuel","last_name":"Zimmer","first_name":"Manuel"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"}],"date_updated":"2025-09-10T10:42:55Z","title":"Designing worm-inspired neural networks for interpretable robotic control","file_date_updated":"2020-10-08T17:30:38Z","publication_identifier":{"isbn":["9781538660270"]},"day":"01","conference":{"end_date":"2019-05-24","location":"Montreal, QC, Canada","name":"ICRA: International Conference on Robotics and Automation","start_date":"2019-05-20"},"external_id":{"isi":["000494942300011"]},"publication":"Proceedings - IEEE International Conference on Robotics and Automation","month":"05","status":"public","ddc":["000"],"alternative_title":["ICRA"],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"In this paper, we design novel liquid time-constant recurrent neural networks for robotic control, inspired by the brain of the nematode, C. elegans. In the worm's nervous system, neurons communicate through nonlinear time-varying synaptic links established amongst them by their particular wiring structure. This property enables neurons to express liquid time-constants dynamics and therefore allows the network to originate complex behaviors with a small number of neurons. We identify neuron-pair communication motifs as design operators and use them to configure compact neuronal network structures to govern sequential robotic tasks. The networks are systematically designed to map the environmental observations to motor actions, by their hierarchical topology from sensory neurons, through recurrently-wired interneurons, to motor neurons. The networks are then parametrized in a supervised-learning scheme by a search-based algorithm. We demonstrate that obtained networks realize interpretable dynamics. We evaluate their performance in controlling mobile and arm robots, and compare their attributes to other artificial neural network-based control agents. Finally, we experimentally show their superior resilience to environmental noise, compared to the existing machine learning-based methods."}],"date_created":"2019-09-18T08:09:51Z","publisher":"IEEE","language":[{"iso":"eng"}],"year":"2019","article_processing_charge":"No","publication_status":"published","file":[{"file_size":3265107,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-10-08T17:30:38Z","file_name":"2019_ICRA_Lechner.pdf","creator":"dernst","checksum":"f5545a6b60c3ffd01feb3613f81d03b6","date_updated":"2020-10-08T17:30:38Z","file_id":"8636","success":1}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"8793840","date_published":"2019-05-01T00:00:00Z","isi":1,"type":"conference","oa":1},{"type":"conference","oa":1,"year":"2019","article_processing_charge":"No","publication_status":"published","file":[{"file_id":"6923","date_updated":"2020-07-14T12:47:43Z","relation":"main_file","date_created":"2019-10-01T08:49:45Z","creator":"kschuh","file_name":"2019_LIPIcs_Chatterjee.pdf","checksum":"7b2ecfd4d9d02360308c0ca986fc10a7","file_size":509163,"content_type":"application/pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"6","date_published":"2019-08-01T00:00:00Z","alternative_title":["LIPIcs"],"date_created":"2019-09-18T08:11:43Z","abstract":[{"text":"We study Markov decision processes and turn-based stochastic games with parity conditions. There are three qualitative winning criteria, namely, sure winning, which requires all paths to satisfy the condition, almost-sure winning, which requires the condition to be satisfied with probability 1, and limit-sure winning, which requires the condition to be satisfied with probability arbitrarily close to 1. We study the combination of two of these criteria for parity conditions, e.g., there are two parity conditions one of which must be won surely, and the other almost-surely. The problem has been studied recently by Berthon et al. for MDPs with combination of sure and almost-sure winning, under infinite-memory strategies, and the problem has been established to be in NP cap co-NP. Even in MDPs there is a difference between finite-memory and infinite-memory strategies. Our main results for combination of sure and almost-sure winning are as follows: (a) we show that for MDPs with finite-memory strategies the problem is in NP cap co-NP; (b) we show that for turn-based stochastic games the problem is co-NP-complete, both for finite-memory and infinite-memory strategies; and (c) we present algorithmic results for the finite-memory case, both for MDPs and turn-based stochastic games, by reduction to non-stochastic parity games. In addition we show that all the above complexity results also carry over to combination of sure and limit-sure winning, and results for all other combinations can be derived from existing results in the literature. Thus we present a complete picture for the study of combinations of two qualitative winning criteria for parity conditions in MDPs and turn-based stochastic games. ","lang":"eng"}],"has_accepted_license":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","language":[{"iso":"eng"}],"intvolume":"       140","ddc":["000"],"month":"08","status":"public","file_date_updated":"2020-07-14T12:47:43Z","day":"01","conference":{"start_date":"2019-08-27","location":"Amsterdam, Netherlands","name":"CONCUR: Conference on Concurrency Theory","end_date":"2019-08-30"},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nir","last_name":"Piterman","full_name":"Piterman, Nir"}],"date_updated":"2025-07-10T11:53:59Z","title":"Combinations of Qualitative Winning for Stochastic Parity Games","scopus_import":"1","department":[{"_id":"KrCh"}],"volume":140,"project":[{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.4230/LIPICS.CONCUR.2019.6","citation":{"apa":"Chatterjee, K., &#38; Piterman, N. (2019). Combinations of Qualitative Winning for Stochastic Parity Games (Vol. 140). Presented at the CONCUR: Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.6\">https://doi.org/10.4230/LIPICS.CONCUR.2019.6</a>","ama":"Chatterjee K, Piterman N. Combinations of Qualitative Winning for Stochastic Parity Games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.6\">10.4230/LIPICS.CONCUR.2019.6</a>","ista":"Chatterjee K, Piterman N. 2019. Combinations of Qualitative Winning for Stochastic Parity Games. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 140, 6.","mla":"Chatterjee, Krishnendu, and Nir Piterman. <i>Combinations of Qualitative Winning for Stochastic Parity Games</i>. Vol. 140, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.6\">10.4230/LIPICS.CONCUR.2019.6</a>.","ieee":"K. Chatterjee and N. Piterman, “Combinations of Qualitative Winning for Stochastic Parity Games,” presented at the CONCUR: Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","short":"K. Chatterjee, N. Piterman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Combinations of Qualitative Winning for Stochastic Parity Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.6\">https://doi.org/10.4230/LIPICS.CONCUR.2019.6</a>."},"_id":"6889","quality_controlled":"1","oa_version":"Published Version"},{"citation":{"mla":"Giacobbe, Mirco. <i>Automatic Time-Unbounded Reachability Analysis of Hybrid Systems</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>.","ieee":"M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019.","apa":"Giacobbe, M. (2019). <i>Automatic time-unbounded reachability analysis of hybrid systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>","ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria.","ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>","chicago":"Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>.","short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.15479/AT:ISTA:6894","department":[{"_id":"ToHe"}],"_id":"6894","oa_version":"Published Version","OA_place":"publisher","day":"30","file_date_updated":"2020-07-14T12:47:43Z","publication_identifier":{"eissn":["2663-337X"]},"related_material":{"record":[{"id":"647","relation":"part_of_dissertation","status":"public"},{"id":"631","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"140","status":"public"}]},"title":"Automatic time-unbounded reachability analysis of hybrid systems","date_updated":"2026-04-16T09:55:03Z","author":[{"first_name":"Mirco","last_name":"Giacobbe","orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"}],"supervisor":[{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks."}],"date_created":"2019-09-22T14:08:44Z","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","status":"public","month":"09","ddc":["000"],"corr_author":"1","degree_awarded":"PhD","type":"dissertation","oa":1,"page":"132","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2019-09-30T00:00:00Z","publication_status":"published","article_processing_charge":"No","year":"2019","file":[{"file_id":"6916","date_updated":"2020-07-14T12:47:43Z","creator":"mgiacobbe","checksum":"773beaf4a85dc2acc2c12b578fbe1965","file_name":"giacobbe_thesis.pdf","date_created":"2019-09-27T14:15:05Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":4100685},{"date_updated":"2020-07-14T12:47:43Z","file_id":"6917","file_size":7959732,"content_type":"application/gzip","access_level":"closed","relation":"source_file","date_created":"2019-09-27T14:22:04Z","file_name":"giacobbe_thesis_src.tar.gz","checksum":"97f1c3da71feefd27e6e625d32b4c75b","creator":"mgiacobbe"}]},{"date_updated":"2026-04-03T09:39:42Z","title":"Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"orcid":"0000-0003-1006-6639","last_name":"Bochkareva","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga"},{"last_name":"Shelyakin","first_name":"Pavel V.","full_name":"Shelyakin, Pavel V."},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E.","last_name":"Akkuratov"},{"full_name":"Burskaia, Valentina","first_name":"Valentina","last_name":"Burskaia"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"external_id":{"isi":["000485256100001"]},"related_material":{"record":[{"status":"public","id":"9731","relation":"research_data"},{"relation":"research_data","id":"9783","status":"public"},{"status":"public","id":"9890","relation":"research_data"},{"status":"public","relation":"research_data","id":"9892"},{"status":"public","id":"9893","relation":"research_data"},{"relation":"research_data","id":"9894","status":"public"},{"id":"9895","relation":"research_data","status":"public"},{"id":"9896","relation":"research_data","status":"public"},{"status":"public","id":"9897","relation":"research_data"},{"id":"9898","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9899"},{"id":"9900","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9901"}]},"publication_identifier":{"eissn":["1471-2164"]},"file_date_updated":"2020-07-14T12:47:44Z","day":"12","quality_controlled":"1","oa_version":"Published Version","_id":"6898","citation":{"short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, BMC Genomics 20 (2019).","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” <i>BMC Genomics</i>. BioMed Central, 2019. <a href=\"https://doi.org/10.1186/s12864-019-6059-5\">https://doi.org/10.1186/s12864-019-6059-5</a>.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. <i>BMC Genomics</i>. 2019;20(1). doi:<a href=\"https://doi.org/10.1186/s12864-019-6059-5\">10.1186/s12864-019-6059-5</a>","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 20(1), 710.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12864-019-6059-5\">https://doi.org/10.1186/s12864-019-6059-5</a>","ieee":"O. M. Sigalova <i>et al.</i>, “Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction,” <i>BMC Genomics</i>, vol. 20, no. 1. BioMed Central, 2019.","mla":"Sigalova, Olga M., et al. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” <i>BMC Genomics</i>, vol. 20, no. 1, 710, BioMed Central, 2019, doi:<a href=\"https://doi.org/10.1186/s12864-019-6059-5\">10.1186/s12864-019-6059-5</a>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1186/s12864-019-6059-5","volume":20,"department":[{"_id":"FyKo"}],"scopus_import":"1","article_number":"710","date_published":"2019-09-12T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_id":"6924","date_updated":"2020-07-14T12:47:44Z","relation":"main_file","date_created":"2019-10-01T10:33:17Z","creator":"kschuh","checksum":"b798773c5823012d31c812c9f7975da2","file_name":"2019_BioMed_Sigalova.pdf","file_size":4157175,"content_type":"application/pdf","access_level":"open_access"}],"year":"2019","article_processing_charge":"No","publication_status":"published","oa":1,"type":"journal_article","isi":1,"status":"public","publication":"BMC Genomics","month":"09","ddc":["570"],"issue":"1","intvolume":"        20","language":[{"iso":"eng"}],"publisher":"BioMed Central","date_created":"2019-09-22T22:00:36Z","abstract":[{"text":"Background\r\n\r\nChlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria.\r\nResults\r\n\r\nWe report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system.\r\nConclusions\r\n\r\nThis combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity.","lang":"eng"}],"has_accepted_license":"1"},{"file":[{"file_size":3905793,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-10-01T11:18:50Z","creator":"kschuh","checksum":"62c2512712e16d27c1797d318d14ba9f","file_name":"2019_Nature_Bornhorst.pdf","date_updated":"2020-07-14T12:47:44Z","file_id":"6926"}],"year":"2019","article_processing_charge":"No","publication_status":"published","date_published":"2019-09-11T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"4113","oa":1,"isi":1,"type":"journal_article","issue":"1","status":"public","month":"09","publication":"Nature communications","ddc":["570"],"publisher":"Nature Publishing Group","has_accepted_license":"1","pmid":1,"abstract":[{"lang":"eng","text":"Intra-organ communication guides morphogenetic processes that are essential for an organ to carry out complex physiological functions. In the heart, the growth of the myocardium is tightly coupled to that of the endocardium, a specialized endothelial tissue that lines its interior. Several molecular pathways have been implicated in the communication between these tissues including secreted factors, components of the extracellular matrix, or proteins involved in cell-cell communication. Yet, it is unknown how the growth of the endocardium is coordinated with that of the myocardium. Here, we show that an increased expansion of the myocardial atrial chamber volume generates higher junctional forces within endocardial cells. This leads to biomechanical signaling involving VE-cadherin, triggering nuclear localization of the Hippo pathway transcriptional regulator Yap1 and endocardial proliferation. Our work suggests that the growth of the endocardium results from myocardial chamber volume expansion and ends when the tension on the tissue is relaxed."}],"date_created":"2019-09-22T22:00:37Z","intvolume":"        10","language":[{"iso":"eng"}],"author":[{"first_name":"Dorothee","last_name":"Bornhorst","full_name":"Bornhorst, Dorothee"},{"first_name":"Peng","last_name":"Xia","orcid":"0000-0002-5419-7756","full_name":"Xia, Peng","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nakajima, Hiroyuki","last_name":"Nakajima","first_name":"Hiroyuki"},{"last_name":"Dingare","first_name":"Chaitanya","full_name":"Dingare, Chaitanya"},{"last_name":"Herzog","first_name":"Wiebke","full_name":"Herzog, Wiebke"},{"full_name":"Lecaudey, Virginie","last_name":"Lecaudey","first_name":"Virginie"},{"full_name":"Mochizuki, Naoki","last_name":"Mochizuki","first_name":"Naoki"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"},{"first_name":"Deborah","last_name":"Yelon","full_name":"Yelon, Deborah"},{"last_name":"Abdelilah-Seyfried","first_name":"Salim","full_name":"Abdelilah-Seyfried, Salim"}],"date_updated":"2026-04-03T09:40:44Z","title":"Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions","publication_identifier":{"eissn":["2041-1723"]},"file_date_updated":"2020-07-14T12:47:44Z","day":"11","external_id":{"pmid":["31511517"],"isi":["000485216800009"]},"quality_controlled":"1","oa_version":"Published Version","_id":"6899","volume":10,"scopus_import":"1","department":[{"_id":"CaHe"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-019-12068-x","citation":{"chicago":"Bornhorst, Dorothee, Peng Xia, Hiroyuki Nakajima, Chaitanya Dingare, Wiebke Herzog, Virginie Lecaudey, Naoki Mochizuki, Carl-Philipp J Heisenberg, Deborah Yelon, and Salim Abdelilah-Seyfried. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” <i>Nature Communications</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41467-019-12068-x\">https://doi.org/10.1038/s41467-019-12068-x</a>.","short":"D. Bornhorst, P. Xia, H. Nakajima, C. Dingare, W. Herzog, V. Lecaudey, N. Mochizuki, C.-P.J. Heisenberg, D. Yelon, S. Abdelilah-Seyfried, Nature Communications 10 (2019) 4113.","ieee":"D. Bornhorst <i>et al.</i>, “Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions,” <i>Nature communications</i>, vol. 10, no. 1. Nature Publishing Group, p. 4113, 2019.","mla":"Bornhorst, Dorothee, et al. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” <i>Nature Communications</i>, vol. 10, no. 1, Nature Publishing Group, 2019, p. 4113, doi:<a href=\"https://doi.org/10.1038/s41467-019-12068-x\">10.1038/s41467-019-12068-x</a>.","ama":"Bornhorst D, Xia P, Nakajima H, et al. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. <i>Nature communications</i>. 2019;10(1):4113. doi:<a href=\"https://doi.org/10.1038/s41467-019-12068-x\">10.1038/s41467-019-12068-x</a>","apa":"Bornhorst, D., Xia, P., Nakajima, H., Dingare, C., Herzog, W., Lecaudey, V., … Abdelilah-Seyfried, S. (2019). Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-019-12068-x\">https://doi.org/10.1038/s41467-019-12068-x</a>","ista":"Bornhorst D, Xia P, Nakajima H, Dingare C, Herzog W, Lecaudey V, Mochizuki N, Heisenberg C-PJ, Yelon D, Abdelilah-Seyfried S. 2019. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 10(1), 4113."}},{"ddc":["570"],"publication":"PLoS computational biology","status":"public","month":"09","issue":"9","intvolume":"        15","language":[{"iso":"eng"}],"publisher":"Public Library of Science","date_created":"2019-09-22T22:00:37Z","abstract":[{"text":"Across diverse biological systems—ranging from neural networks to intracellular signaling and genetic regulatory networks—the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes. A pressing data-analysis challenge has thus been to efficiently estimate the amount of information that these dynamics convey from experimental data. Here we develop and evaluate decoding-based estimation methods to lower bound the mutual information about a finite set of inputs, encoded in single-cell high-dimensional time series data. For biological reaction networks governed by the chemical Master equation, we derive model-based information approximations and analytical upper bounds, against which we benchmark our proposed model-free decoding estimators. In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based estimators robustly extract a large fraction of the available information from high-dimensional trajectories with a realistic number of data samples. We apply these estimators to previously published data on Erk and Ca2+ signaling in mammalian cells and to yeast stress-response, and find that substantial amount of information about environmental state can be encoded by non-trivial response statistics even in stationary signals. We argue that these single-cell, decoding-based information estimates, rather than the commonly-used tests for significant differences between selected population response statistics, provide a proper and unbiased measure for the performance of biological signaling networks.","lang":"eng"}],"pmid":1,"has_accepted_license":"1","date_published":"2019-09-03T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"file_id":"6925","date_updated":"2020-07-14T12:47:44Z","creator":"kschuh","file_name":"2019_PLoS_Cepeda-Humerez.pdf","checksum":"81bdce1361c9aa8395d6fa635fb6ab47","date_created":"2019-10-01T10:53:45Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":3081855}],"publication_status":"published","article_processing_charge":"No","year":"2019","oa":1,"type":"journal_article","isi":1,"page":"e1007290","oa_version":"Published Version","quality_controlled":"1","_id":"6900","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ama":"Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying signals. <i>PLoS computational biology</i>. 2019;15(9):e1007290. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">10.1371/journal.pcbi.1007290</a>","apa":"Cepeda Humerez, S. A., Ruess, J., &#38; Tkačik, G. (2019). Estimating information in time-varying signals. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">https://doi.org/10.1371/journal.pcbi.1007290</a>","ista":"Cepeda Humerez SA, Ruess J, Tkačik G. 2019. Estimating information in time-varying signals. PLoS computational biology. 15(9), e1007290.","ieee":"S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in time-varying signals,” <i>PLoS computational biology</i>, vol. 15, no. 9. Public Library of Science, p. e1007290, 2019.","mla":"Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” <i>PLoS Computational Biology</i>, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">10.1371/journal.pcbi.1007290</a>.","short":"S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019) e1007290.","chicago":"Cepeda Humerez, Sarah A, Jakob Ruess, and Gašper Tkačik. “Estimating Information in Time-Varying Signals.” <i>PLoS Computational Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">https://doi.org/10.1371/journal.pcbi.1007290</a>."},"doi":"10.1371/journal.pcbi.1007290","project":[{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"volume":15,"scopus_import":"1","department":[{"_id":"GaTk"}],"title":"Estimating information in time-varying signals","date_updated":"2026-04-16T08:37:39Z","author":[{"full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A","last_name":"Cepeda Humerez"},{"full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","last_name":"Ruess","first_name":"Jakob"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"}],"external_id":{"isi":["000489741800021"],"pmid":["31479447"]},"day":"03","file_date_updated":"2020-07-14T12:47:44Z","related_material":{"record":[{"id":"6473","relation":"part_of_dissertation","status":"public"}]},"publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]}},{"_id":"6919","oa_version":"Published Version","quality_controlled":"1","doi":"10.1126/sciadv.aaw6490","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"citation":{"chicago":"Qi, Chao, Giulio Di Minin, Irene Vercellino, Anton Wutz, and Volodymyr M. Korkhov. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” <i>Science Advances</i>. American Association for the Advancement of Science, 2019. <a href=\"https://doi.org/10.1126/sciadv.aaw6490\">https://doi.org/10.1126/sciadv.aaw6490</a>.","short":"C. Qi, G.D. Minin, I. Vercellino, A. Wutz, V.M. Korkhov, Science Advances 5 (2019).","ieee":"C. Qi, G. D. Minin, I. Vercellino, A. Wutz, and V. M. Korkhov, “Structural basis of sterol recognition by human hedgehog receptor PTCH1,” <i>Science Advances</i>, vol. 5, no. 9. American Association for the Advancement of Science, 2019.","mla":"Qi, Chao, et al. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” <i>Science Advances</i>, vol. 5, no. 9, eaaw6490, American Association for the Advancement of Science, 2019, doi:<a href=\"https://doi.org/10.1126/sciadv.aaw6490\">10.1126/sciadv.aaw6490</a>.","ama":"Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. Structural basis of sterol recognition by human hedgehog receptor PTCH1. <i>Science Advances</i>. 2019;5(9). doi:<a href=\"https://doi.org/10.1126/sciadv.aaw6490\">10.1126/sciadv.aaw6490</a>","ista":"Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. 2019. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 5(9), eaaw6490.","apa":"Qi, C., Minin, G. D., Vercellino, I., Wutz, A., &#38; Korkhov, V. M. (2019). Structural basis of sterol recognition by human hedgehog receptor PTCH1. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.aaw6490\">https://doi.org/10.1126/sciadv.aaw6490</a>"},"department":[{"_id":"LeSa"}],"scopus_import":"1","volume":5,"date_updated":"2026-04-03T09:43:31Z","title":"Structural basis of sterol recognition by human hedgehog receptor PTCH1","author":[{"last_name":"Qi","first_name":"Chao","full_name":"Qi, Chao"},{"first_name":"Giulio Di","last_name":"Minin","full_name":"Minin, Giulio Di"},{"id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","full_name":"Vercellino, Irene","orcid":"0000-0001-5618-3449","last_name":"Vercellino","first_name":"Irene"},{"last_name":"Wutz","first_name":"Anton","full_name":"Wutz, Anton"},{"full_name":"Korkhov, Volodymyr M.","last_name":"Korkhov","first_name":"Volodymyr M."}],"external_id":{"isi":["000491128800062"]},"publication_identifier":{"eissn":["2375-2548"]},"file_date_updated":"2020-07-14T12:47:44Z","day":"18","ddc":["570"],"publication":"Science Advances","month":"09","status":"public","issue":"9","language":[{"iso":"eng"}],"intvolume":"         5","has_accepted_license":"1","date_created":"2019-09-29T22:00:45Z","publisher":"American Association for the Advancement of Science","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_number":"eaaw6490","date_published":"2019-09-18T00:00:00Z","article_processing_charge":"No","year":"2019","publication_status":"published","file":[{"date_updated":"2020-07-14T12:47:44Z","file_id":"6928","content_type":"application/pdf","access_level":"open_access","file_size":1236101,"creator":"kschuh","checksum":"b2256c9117655bc15f621ba0babf219f","file_name":"2019_AAAS_Qi.pdf","relation":"main_file","date_created":"2019-10-02T11:13:54Z"}],"isi":1,"type":"journal_article","oa":1},{"date_created":"2019-10-08T12:41:38Z","has_accepted_license":"1","abstract":[{"text":"Consider a distributed system with n processors out of which f can be Byzantine faulty. In the\r\napproximate agreement task, each processor i receives an input value xi and has to decide on an\r\noutput value yi such that\r\n1. the output values are in the convex hull of the non-faulty processors’ input values,\r\n2. the output values are within distance d of each other.\r\n\r\n\r\nClassically, the values are assumed to be from an m-dimensional Euclidean space, where m ≥ 1.\r\nIn this work, we study the task in a discrete setting, where input values with some structure\r\nexpressible as a graph. Namely, the input values are vertices of a finite graph G and the goal is to\r\noutput vertices that are within distance d of each other in G, but still remain in the graph-induced\r\nconvex hull of the input values. For d = 0, the task reduces to consensus and cannot be solved with\r\na deterministic algorithm in an asynchronous system even with a single crash fault. For any d ≥ 1,\r\nwe show that the task is solvable in asynchronous systems when G is chordal and n > (ω + 1)f,\r\nwhere ω is the clique number of G. In addition, we give the first Byzantine-tolerant algorithm for a\r\nvariant of lattice agreement. For synchronous systems, we show tight resilience bounds for the exact\r\nvariants of these and related tasks over a large class of combinatorial structures.","lang":"eng"}],"alternative_title":["LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","language":[{"iso":"eng"}],"intvolume":"       146","ddc":["004"],"publication":"33rd International Symposium on Distributed Computing","month":"11","status":"public","page":"29:1--29:17","ec_funded":1,"type":"conference","oa":1,"publication_status":"published","article_processing_charge":"No","keyword":["consensus","approximate agreement","Byzantine faults","chordal graphs","lattice agreement"],"year":"2019","file":[{"date_updated":"2020-07-14T12:47:44Z","file_id":"6934","content_type":"application/pdf","access_level":"open_access","file_size":639378,"file_name":"LIPIcs-DISC-2019-29.pdf","checksum":"2d2202f90c6ac991e50876451627c4b5","creator":"jrybicki","relation":"main_file","date_created":"2019-10-08T12:47:19Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2019-11-01T00:00:00Z","scopus_import":"1","department":[{"_id":"DaAl"}],"volume":146,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"doi":"10.4230/LIPICS.DISC.2019.29","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"T. Nowak, J. Rybicki, in:, 33rd International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17.","chicago":"Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” In <i>33rd International Symposium on Distributed Computing</i>, 146:29:1--29:17. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.DISC.2019.29\">https://doi.org/10.4230/LIPICS.DISC.2019.29</a>.","apa":"Nowak, T., &#38; Rybicki, J. (2019). Byzantine approximate agreement on graphs. In <i>33rd International Symposium on Distributed Computing</i> (Vol. 146, p. 29:1--29:17). Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.DISC.2019.29\">https://doi.org/10.4230/LIPICS.DISC.2019.29</a>","ama":"Nowak T, Rybicki J. Byzantine approximate agreement on graphs. In: <i>33rd International Symposium on Distributed Computing</i>. Vol 146. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:29:1--29:17. doi:<a href=\"https://doi.org/10.4230/LIPICS.DISC.2019.29\">10.4230/LIPICS.DISC.2019.29</a>","ista":"Nowak T, Rybicki J. 2019. Byzantine approximate agreement on graphs. 33rd International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 146, 29:1--29:17.","ieee":"T. Nowak and J. Rybicki, “Byzantine approximate agreement on graphs,” in <i>33rd International Symposium on Distributed Computing</i>, Budapest, Hungary, 2019, vol. 146, p. 29:1--29:17.","mla":"Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” <i>33rd International Symposium on Distributed Computing</i>, vol. 146, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17, doi:<a href=\"https://doi.org/10.4230/LIPICS.DISC.2019.29\">10.4230/LIPICS.DISC.2019.29</a>."},"_id":"6931","oa_version":"Published Version","quality_controlled":"1","day":"01","file_date_updated":"2020-07-14T12:47:44Z","publication_identifier":{"eisbn":["978-3-95977-126-9"]},"arxiv":1,"conference":{"end_date":"2019-10-18","start_date":"2019-10-14","name":"DISC: Symposium on Distributed Computing","location":"Budapest, Hungary"},"external_id":{"arxiv":["1908.02743"]},"author":[{"first_name":"Thomas","last_name":"Nowak","full_name":"Nowak, Thomas"},{"first_name":"Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel"}],"title":"Byzantine approximate agreement on graphs","date_updated":"2025-07-10T11:54:03Z"},{"date_created":"2019-10-08T12:48:42Z","abstract":[{"text":"We design fast deterministic algorithms for distance computation in the CONGESTED CLIQUE model. Our key contributions include:\r\n\r\n - A (2+ε)-approximation for all-pairs shortest paths problem in O(log²n / ε) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n - A (1+ε)-approximation for multi-source shortest paths problem from O(√n) sources in O(log² n / ε) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in Õ(n^{1/6}) rounds.","lang":"eng"}],"publisher":"ACM","language":[{"iso":"eng"}],"status":"public","publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin","month":"08","page":"74-83","isi":1,"type":"conference","oa":1,"publication_status":"published","year":"2019","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-08-01T00:00:00Z","scopus_import":"1","department":[{"_id":"DaAl"}],"doi":"10.1145/3293611.3331633","citation":{"chicago":"Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” In <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin</i>, 74–83. ACM, 2019. <a href=\"https://doi.org/10.1145/3293611.3331633\">https://doi.org/10.1145/3293611.3331633</a>.","short":"K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, in:, Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, ACM, 2019, pp. 74–83.","ieee":"K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” in <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin</i>, Toronto, ON, Canada, 2019, pp. 74–83.","mla":"Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin</i>, ACM, 2019, pp. 74–83, doi:<a href=\"https://doi.org/10.1145/3293611.3331633\">10.1145/3293611.3331633</a>.","ista":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2019. Fast approximate shortest paths in the congested clique. Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin. PODC: Symposium on Principles of Distributed Computing, 74–83.","ama":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. In: <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin</i>. ACM; 2019:74-83. doi:<a href=\"https://doi.org/10.1145/3293611.3331633\">10.1145/3293611.3331633</a>","apa":"Censor-Hillel, K., Dory, M., Korhonen, J., &#38; Leitersdorf, D. (2019). Fast approximate shortest paths in the congested clique. In <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin</i> (pp. 74–83). Toronto, ON, Canada: ACM. <a href=\"https://doi.org/10.1145/3293611.3331633\">https://doi.org/10.1145/3293611.3331633</a>"},"_id":"6933","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.05956"}],"day":"01","publication_identifier":{"isbn":["9781450362177"]},"related_material":{"record":[{"status":"public","id":"7939","relation":"later_version"}]},"arxiv":1,"conference":{"end_date":"2019-08-02","start_date":"2019-07-29","name":"PODC: Symposium on Principles of Distributed Computing","location":"Toronto, ON, Canada"},"external_id":{"isi":["000570442000011"],"arxiv":["1903.05956"]},"author":[{"full_name":"Censor-Hillel, Keren","first_name":"Keren","last_name":"Censor-Hillel"},{"first_name":"Michal","last_name":"Dory","full_name":"Dory, Michal"},{"last_name":"Korhonen","first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","full_name":"Korhonen, Janne"},{"last_name":"Leitersdorf","first_name":"Dean","full_name":"Leitersdorf, Dean"}],"title":"Fast approximate shortest paths in the congested clique","date_updated":"2026-06-18T19:28:41Z"},{"author":[{"full_name":"Foerster, Klaus-Tycho","first_name":"Klaus-Tycho","last_name":"Foerster"},{"first_name":"Janne","last_name":"Korhonen","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","full_name":"Korhonen, Janne"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki","first_name":"Joel"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"}],"title":"Does preprocessing help under congestion?","date_updated":"2025-04-14T07:44:06Z","arxiv":1,"day":"01","publication_identifier":{"isbn":["9781450362177"]},"external_id":{"arxiv":["1905.03012"],"isi":["000570442000037"]},"conference":{"start_date":"2019-07-29","name":"PODC: Symposium on Principles of Distributed Computing","location":"Toronto, ON, Canada","end_date":"2019-08-02"},"quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1905.03012","open_access":"1"}],"_id":"6935","scopus_import":"1","department":[{"_id":"DaAl"}],"citation":{"short":"K.-T. Foerster, J. Korhonen, J. Rybicki, S. Schmid, in:, Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, ACM, 2019, pp. 259–261.","chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Joel Rybicki, and Stefan Schmid. “Does Preprocessing Help under Congestion?” In <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing</i>, 259–61. ACM, 2019. <a href=\"https://doi.org/10.1145/3293611.3331581\">https://doi.org/10.1145/3293611.3331581</a>.","ista":"Foerster K-T, Korhonen J, Rybicki J, Schmid S. 2019. Does preprocessing help under congestion? Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 259–261.","ama":"Foerster K-T, Korhonen J, Rybicki J, Schmid S. Does preprocessing help under congestion? In: <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing</i>. ACM; 2019:259-261. doi:<a href=\"https://doi.org/10.1145/3293611.3331581\">10.1145/3293611.3331581</a>","apa":"Foerster, K.-T., Korhonen, J., Rybicki, J., &#38; Schmid, S. (2019). Does preprocessing help under congestion? In <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing</i> (pp. 259–261). Toronto, ON, Canada: ACM. <a href=\"https://doi.org/10.1145/3293611.3331581\">https://doi.org/10.1145/3293611.3331581</a>","ieee":"K.-T. Foerster, J. Korhonen, J. Rybicki, and S. Schmid, “Does preprocessing help under congestion?,” in <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing</i>, Toronto, ON, Canada, 2019, pp. 259–261.","mla":"Foerster, Klaus-Tycho, et al. “Does Preprocessing Help under Congestion?” <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing</i>, ACM, 2019, pp. 259–61, doi:<a href=\"https://doi.org/10.1145/3293611.3331581\">10.1145/3293611.3331581</a>."},"doi":"10.1145/3293611.3331581","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"publication_status":"published","article_processing_charge":"No","year":"2019","date_published":"2019-08-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"259-261","oa":1,"isi":1,"type":"conference","ec_funded":1,"status":"public","publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing","month":"08","publisher":"ACM","abstract":[{"lang":"eng","text":"This paper investigates the power of preprocessing in the CONGEST model. Schmid and Suomela (ACM HotSDN 2013) introduced the SUPPORTED CONGEST model to study the application of distributed algorithms in Software-Defined Networks (SDNs). In this paper, we show that a large class of lower bounds in the CONGEST model still hold in the SUPPORTED model, highlighting the robustness of these bounds. This also raises the question how much does\r\npreprocessing help in the CONGEST model."}],"date_created":"2019-10-08T12:57:14Z","language":[{"iso":"eng"}]}]