[{"_id":"9706","date_created":"2021-07-23T08:59:15Z","citation":{"mla":"Hillary, Robert F., et al. <i>Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults</i>. Springer Nature, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">10.6084/m9.figshare.12629697.v1</a>.","chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Springer Nature, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">https://doi.org/10.6084/m9.figshare.12629697.v1</a>.","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">https://doi.org/10.6084/m9.figshare.12629697.v1</a>","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, (2020).","ista":"Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">10.6084/m9.figshare.12629697.v1</a>.","ieee":"R. F. Hillary <i>et al.</i>, “Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Springer Nature, 2020.","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">10.6084/m9.figshare.12629697.v1</a>"},"type":"research_data_reference","oa_version":"Published Version","other_data_license":"CC0 + CC BY (4.0)","oa":1,"publisher":"Springer Nature","title":"Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","department":[{"_id":"MaRo"}],"month":"07","year":"2020","date_published":"2020-07-09T00:00:00Z","abstract":[{"lang":"eng","text":"Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19)."}],"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.12629697.v1","open_access":"1"}],"has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8133"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-22T07:55:36Z","day":"09","author":[{"first_name":"Robert F.","full_name":"Hillary, Robert F.","last_name":"Hillary"},{"first_name":"Daniel","full_name":"Trejo-Banos, Daniel","last_name":"Trejo-Banos"},{"first_name":"Athanasios","last_name":"Kousathanas","full_name":"Kousathanas, Athanasios"},{"last_name":"McCartney","full_name":"McCartney, Daniel L.","first_name":"Daniel L."},{"last_name":"Harris","full_name":"Harris, Sarah E.","first_name":"Sarah E."},{"first_name":"Anna J.","full_name":"Stevenson, Anna J.","last_name":"Stevenson"},{"first_name":"Marion","full_name":"Patxot, Marion","last_name":"Patxot"},{"full_name":"Ojavee, Sven Erik","last_name":"Ojavee","first_name":"Sven Erik"},{"first_name":"Qian","last_name":"Zhang","full_name":"Zhang, Qian"},{"last_name":"Liewald","full_name":"Liewald, David C.","first_name":"David C."},{"full_name":"Ritchie, Craig W.","last_name":"Ritchie","first_name":"Craig W."},{"first_name":"Kathryn L.","full_name":"Evans, Kathryn L.","last_name":"Evans"},{"full_name":"Tucker-Drob, Elliot M.","last_name":"Tucker-Drob","first_name":"Elliot M."},{"full_name":"Wray, Naomi R.","last_name":"Wray","first_name":"Naomi R."},{"first_name":"Allan F. ","full_name":"McRae, Allan F. ","last_name":"McRae"},{"full_name":"Visscher, Peter M.","last_name":"Visscher","first_name":"Peter M."},{"full_name":"Deary, Ian J.","last_name":"Deary","first_name":"Ian J."},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"},{"first_name":"Riccardo E. ","last_name":"Marioni","full_name":"Marioni, Riccardo E. "}],"article_processing_charge":"No","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.6084/m9.figshare.12629697.v1","license":"https://creativecommons.org/licenses/by/4.0/"},{"abstract":[{"text":"This research data supports 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file for plotting each figure is provided.","lang":"eng"}],"has_accepted_license":"1","main_file_link":[{"url":"https://doi.org/10.17863/CAM.50169","open_access":"1"}],"related_material":{"record":[{"id":"7942","status":"public","relation":"used_in_publication"}]},"date_published":"2020-05-29T00:00:00Z","date_updated":"2023-08-21T07:06:48Z","day":"29","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Mate","last_name":"Hartstein","full_name":"Hartstein, Mate"},{"first_name":"Yu-Te","last_name":"Hsu","full_name":"Hsu, Yu-Te"},{"last_name":"Modic","full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147","first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"},{"first_name":"Juan","full_name":"Porras, Juan","last_name":"Porras"},{"first_name":"Toshinao","last_name":"Loew","full_name":"Loew, Toshinao"},{"first_name":"Matthieu","last_name":"Le Tacon","full_name":"Le Tacon, Matthieu"},{"first_name":"Huakun","full_name":"Zuo, Huakun","last_name":"Zuo"},{"first_name":"Jinhua","last_name":"Wang","full_name":"Wang, Jinhua"},{"full_name":"Zhu, Zengwei","last_name":"Zhu","first_name":"Zengwei"},{"first_name":"Mun","last_name":"Chan","full_name":"Chan, Mun"},{"first_name":"Ross","last_name":"McDonald","full_name":"McDonald, Ross"},{"first_name":"Gilbert","full_name":"Lonzarich, Gilbert","last_name":"Lonzarich"},{"first_name":"Bernhard","full_name":"Keimer, Bernhard","last_name":"Keimer"},{"first_name":"Suchitra","last_name":"Sebastian","full_name":"Sebastian, Suchitra"},{"first_name":"Neil","full_name":"Harrison, Neil","last_name":"Harrison"}],"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","doi":"10.17863/cam.50169","citation":{"mla":"Hartstein, Mate, et al. <i>Accompanying Dataset for “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.”</i> Apollo - University of Cambridge, 2020, doi:<a href=\"https://doi.org/10.17863/cam.50169\">10.17863/cam.50169</a>.","chicago":"Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.’” Apollo - University of Cambridge, 2020. <a href=\"https://doi.org/10.17863/cam.50169\">https://doi.org/10.17863/cam.50169</a>.","apa":"Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M., … Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” Apollo - University of Cambridge. <a href=\"https://doi.org/10.17863/cam.50169\">https://doi.org/10.17863/cam.50169</a>","short":"M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H. Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian, N. Harrison, (2020).","ista":"Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N. 2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University of Cambridge, <a href=\"https://doi.org/10.17863/cam.50169\">10.17863/cam.50169</a>.","ieee":"M. Hartstein <i>et al.</i>, “Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.’” Apollo - University of Cambridge, 2020.","ama":"Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” 2020. doi:<a href=\"https://doi.org/10.17863/cam.50169\">10.17863/cam.50169</a>"},"date_created":"2021-07-23T10:00:35Z","oa_version":"Published Version","type":"research_data_reference","_id":"9708","publisher":"Apollo - University of Cambridge","oa":1,"title":"Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'","department":[{"_id":"KiMo"}],"month":"05","year":"2020"},{"publisher":"American Chemical Society ","oa_version":"Published Version","type":"research_data_reference","citation":{"apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Supporting information. American Chemical Society . <a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">https://doi.org/10.1021/jacs.9b13450.s001</a>","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Supporting Information.” American Chemical Society , 2020. <a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">https://doi.org/10.1021/jacs.9b13450.s001</a>.","mla":"Gupta, Chitrak, et al. <i>Supporting Information</i>. American Chemical Society , 2020, doi:<a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">10.1021/jacs.9b13450.s001</a>.","ama":"Gupta C, Khaniya U, Chan CK, et al. Supporting information. 2020. doi:<a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">10.1021/jacs.9b13450.s001</a>","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ieee":"C. Gupta <i>et al.</i>, “Supporting information.” American Chemical Society , 2020.","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Supporting information, American Chemical Society , <a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">10.1021/jacs.9b13450.s001</a>."},"date_created":"2021-07-23T12:02:39Z","_id":"9713","year":"2020","month":"05","department":[{"_id":"LeSa"}],"title":"Supporting information","day":"20","date_updated":"2023-08-22T07:49:38Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8040"}]},"abstract":[{"lang":"eng","text":"Additional analyses of the trajectories"}],"date_published":"2020-05-20T00:00:00Z","doi":"10.1021/jacs.9b13450.s001","status":"public","article_processing_charge":"No","author":[{"last_name":"Gupta","full_name":"Gupta, Chitrak","first_name":"Chitrak"},{"last_name":"Khaniya","full_name":"Khaniya, Umesh","first_name":"Umesh"},{"first_name":"Chun Kit","last_name":"Chan","full_name":"Chan, Chun Kit"},{"first_name":"Francois","full_name":"Dehez, Francois","last_name":"Dehez"},{"full_name":"Shekhar, Mrinal","last_name":"Shekhar","first_name":"Mrinal"},{"full_name":"Gunner, M.R.","last_name":"Gunner","first_name":"M.R."},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989"},{"full_name":"Chipot, Christophe","last_name":"Chipot","first_name":"Christophe"},{"first_name":"Abhishek","last_name":"Singharoy","full_name":"Singharoy, Abhishek"}]},{"oa":1,"publisher":"Cold Spring Harbor Laboratory","publication_status":"published","_id":"9750","oa_version":"Preprint","type":"preprint","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"SSU"}],"citation":{"apa":"Slovakova, J., Sikora, M. K., Caballero Mancebo, S., Krens, G., Kaufmann, W., Huljev, K., &#38; Heisenberg, C.-P. J. (2020). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.11.20.391284\">https://doi.org/10.1101/2020.11.20.391284</a>","chicago":"Slovakova, Jana, Mateusz K Sikora, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Karla Huljev, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2020. <a href=\"https://doi.org/10.1101/2020.11.20.391284\">https://doi.org/10.1101/2020.11.20.391284</a>.","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2020, doi:<a href=\"https://doi.org/10.1101/2020.11.20.391284\">10.1101/2020.11.20.391284</a>.","ama":"Slovakova J, Sikora MK, Caballero Mancebo S, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. <i>bioRxiv</i>. 2020. doi:<a href=\"https://doi.org/10.1101/2020.11.20.391284\">10.1101/2020.11.20.391284</a>","ieee":"J. Slovakova <i>et al.</i>, “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2020.","short":"J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K. Huljev, C.-P.J. Heisenberg, BioRxiv (2020).","ista":"Slovakova J, Sikora MK, Caballero Mancebo S, Krens G, Kaufmann W, Huljev K, Heisenberg C-PJ. 2020. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv, <a href=\"https://doi.org/10.1101/2020.11.20.391284\">10.1101/2020.11.20.391284</a>."},"date_created":"2021-07-29T11:29:50Z","page":"41","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","_id":"2521E28E-B435-11E9-9278-68D0E5697425","grant_number":"187-2013"}],"month":"11","year":"2020","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"acknowledgement":"We would like to thank Edouard Hannezo for discussions, Shayan Shami Pour and Daniel Capek for help with data analysis, Vanessa Barone and other members of the Heisenberg laboratory for thoughtful discussions and comments on the manuscript. We also thank Jack Merrin for preparing the microwells, and the Scientific Service Units at IST Austria, specifically Bioimaging and Electron Microscopy, and the Zebrafish Facility for continuous support. We acknowledge Hitoshi Morita for the kind gift of VinculinB-GFP plasmid. This research was supported by an ERC Advanced Grant (MECSPEC) to C.-P.H, EMBO Long Term grant (ALTF 187-2013) to M.S and IST Fellow Marie-Curie COFUND No. P_IST_EU01 to J.S.","day":"20","publication":"bioRxiv","date_updated":"2024-03-25T23:30:10Z","date_published":"2020-11-20T00:00:00Z","related_material":{"record":[{"id":"10766","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"9623"}]},"main_file_link":[{"url":"https://doi.org/10.1101/2020.11.20.391284","open_access":"1"}],"abstract":[{"text":"Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase, and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension stabilizing E-cadherin-actin complexes at the contact.","lang":"eng"}],"doi":"10.1101/2020.11.20.391284","status":"public","ec_funded":1,"author":[{"last_name":"Slovakova","full_name":"Slovakova, Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","first_name":"Jana"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","last_name":"Sikora","full_name":"Sikora, Mateusz K"},{"first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","last_name":"Krens","full_name":"Krens, Gabriel"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla","last_name":"Huljev"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"article_processing_charge":"No"},{"date_updated":"2023-08-18T06:47:47Z","day":"25","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7569"}]},"date_published":"2020-02-25T00:00:00Z","doi":"10.1371/journal.pcbi.1007642.s001","article_processing_charge":"No","author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah"},{"full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar"}],"status":"public","publisher":"Public Library of Science","citation":{"mla":"Grah, Rok, and Tamar Friedlander. <i>Supporting Information</i>. Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s001\">10.1371/journal.pcbi.1007642.s001</a>.","apa":"Grah, R., &#38; Friedlander, T. (2020). Supporting information. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s001\">https://doi.org/10.1371/journal.pcbi.1007642.s001</a>","chicago":"Grah, Rok, and Tamar Friedlander. “Supporting Information.” Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s001\">https://doi.org/10.1371/journal.pcbi.1007642.s001</a>.","ama":"Grah R, Friedlander T. Supporting information. 2020. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s001\">10.1371/journal.pcbi.1007642.s001</a>","ieee":"R. Grah and T. Friedlander, “Supporting information.” Public Library of Science, 2020.","short":"R. Grah, T. Friedlander, (2020).","ista":"Grah R, Friedlander T. 2020. Supporting information, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s001\">10.1371/journal.pcbi.1007642.s001</a>."},"date_created":"2021-08-06T07:15:04Z","oa_version":"Published Version","type":"research_data_reference","_id":"9776","year":"2020","month":"02","title":"Supporting information","department":[{"_id":"GaTk"}]},{"department":[{"_id":"GaTk"}],"title":"Maximizing crosstalk","year":"2020","month":"02","oa_version":"None","type":"research_data_reference","citation":{"ista":"Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s002\">10.1371/journal.pcbi.1007642.s002</a>.","short":"R. Grah, T. Friedlander, (2020).","ieee":"R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.","ama":"Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s002\">10.1371/journal.pcbi.1007642.s002</a>","chicago":"Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s002\">https://doi.org/10.1371/journal.pcbi.1007642.s002</a>.","apa":"Grah, R., &#38; Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s002\">https://doi.org/10.1371/journal.pcbi.1007642.s002</a>","mla":"Grah, Rok, and Tamar Friedlander. <i>Maximizing Crosstalk</i>. Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s002\">10.1371/journal.pcbi.1007642.s002</a>."},"date_created":"2021-08-06T07:21:51Z","_id":"9777","publisher":"Public Library of Science","oa":1,"status":"public","author":[{"orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok"},{"last_name":"Friedlander","full_name":"Friedlander, Tamar","first_name":"Tamar"}],"article_processing_charge":"No","doi":"10.1371/journal.pcbi.1007642.s002","related_material":{"record":[{"id":"7569","relation":"used_in_publication","status":"public"}]},"main_file_link":[{"url":"https://doi.org/10.1371/journal.pcbi.1007642.s002","open_access":"1"}],"date_published":"2020-02-25T00:00:00Z","day":"25","date_updated":"2023-09-12T11:02:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Public Library of Science","type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-06T07:24:37Z","citation":{"ama":"Grah R, Friedlander T. Distribution of crosstalk values. 2020. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s003\">10.1371/journal.pcbi.1007642.s003</a>","ieee":"R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library of Science, 2020.","ista":"Grah R, Friedlander T. 2020. Distribution of crosstalk values, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s003\">10.1371/journal.pcbi.1007642.s003</a>.","short":"R. Grah, T. Friedlander, (2020).","mla":"Grah, Rok, and Tamar Friedlander. <i>Distribution of Crosstalk Values</i>. Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s003\">10.1371/journal.pcbi.1007642.s003</a>.","apa":"Grah, R., &#38; Friedlander, T. (2020). Distribution of crosstalk values. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s003\">https://doi.org/10.1371/journal.pcbi.1007642.s003</a>","chicago":"Grah, Rok, and Tamar Friedlander. “Distribution of Crosstalk Values.” Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642.s003\">https://doi.org/10.1371/journal.pcbi.1007642.s003</a>."},"_id":"9779","year":"2020","month":"02","department":[{"_id":"GaTk"}],"title":"Distribution of crosstalk values","day":"25","date_updated":"2023-08-18T06:47:47Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"status":"public","relation":"research_data","id":"7569"}]},"date_published":"2020-02-25T00:00:00Z","doi":"10.1371/journal.pcbi.1007642.s003","status":"public","author":[{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah"},{"last_name":"Friedlander","full_name":"Friedlander, Tamar","first_name":"Tamar"}],"article_processing_charge":"No"},{"date_published":"2020-03-22T00:00:00Z","abstract":[{"lang":"eng","text":"PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol\r\nSpace Group: C 2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8329"}]},"main_file_link":[{"url":"https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-05T16:03:47Z","day":"22","article_processing_charge":"No","author":[{"full_name":"Schlemmer, Werner","last_name":"Schlemmer","first_name":"Werner"},{"full_name":"Nothdurft, Philipp","last_name":"Nothdurft","first_name":"Philipp"},{"first_name":"Alina","last_name":"Petzold","full_name":"Petzold, Alina"},{"first_name":"Gisbert","last_name":"Riess","full_name":"Riess, Gisbert"},{"last_name":"Frühwirt","full_name":"Frühwirt, Philipp","first_name":"Philipp"},{"first_name":"Max","last_name":"Schmallegger","full_name":"Schmallegger, Max"},{"last_name":"Gescheidt-Demner","full_name":"Gescheidt-Demner, Georg","first_name":"Georg"},{"full_name":"Fischer, Roland","last_name":"Fischer","first_name":"Roland"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319"},{"full_name":"Kern, Wolfgang","last_name":"Kern","first_name":"Wolfgang"},{"first_name":"Stefan","last_name":"Spirk","full_name":"Spirk, Stefan"}],"status":"public","doi":"10.5517/ccdc.csd.cc24vsrk","_id":"9780","citation":{"ama":"Schlemmer W, Nothdurft P, Petzold A, et al. CCDC 1991959: Experimental Crystal Structure Determination. 2020. doi:<a href=\"https://doi.org/10.5517/ccdc.csd.cc24vsrk\">10.5517/ccdc.csd.cc24vsrk</a>","short":"W. Schlemmer, P. Nothdurft, A. Petzold, G. Riess, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, (2020).","ieee":"W. Schlemmer <i>et al.</i>, “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020.","ista":"Schlemmer W, Nothdurft P, Petzold A, Riess G, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. CCDC 1991959: Experimental Crystal Structure Determination, CCDC, <a href=\"https://doi.org/10.5517/ccdc.csd.cc24vsrk\">10.5517/ccdc.csd.cc24vsrk</a>.","apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Riess, G., Frühwirt, P., Schmallegger, M., … Spirk, S. (2020). CCDC 1991959: Experimental Crystal Structure Determination. CCDC. <a href=\"https://doi.org/10.5517/ccdc.csd.cc24vsrk\">https://doi.org/10.5517/ccdc.csd.cc24vsrk</a>","chicago":"Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Gisbert Riess, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, et al. “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020. <a href=\"https://doi.org/10.5517/ccdc.csd.cc24vsrk\">https://doi.org/10.5517/ccdc.csd.cc24vsrk</a>.","mla":"Schlemmer, Werner, et al. <i>CCDC 1991959: Experimental Crystal Structure Determination</i>. CCDC, 2020, doi:<a href=\"https://doi.org/10.5517/ccdc.csd.cc24vsrk\">10.5517/ccdc.csd.cc24vsrk</a>."},"date_created":"2021-08-06T07:41:07Z","oa_version":"Published Version","type":"research_data_reference","oa":1,"publisher":"CCDC","title":"CCDC 1991959: Experimental Crystal Structure Determination","department":[{"_id":"StFr"}],"year":"2020","month":"03"},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"id":"41A639AA-F248-11E8-B48F-1D18A9856A87","first_name":"Dario","orcid":"0000-0003-0754-8530","last_name":"Feliciangeli","full_name":"Feliciangeli, Dario"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"status":"public","date_updated":"2023-09-07T13:30:11Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"We consider the Pekar functional on a ball in ℝ3. We prove uniqueness of minimizers, and a quadratic lower bound in terms of the distance to the minimizer. The latter follows from nondegeneracy of the Hessian at the minimum.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.08647"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9733"}]},"keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"scopus_import":"1","isi":1,"publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"year":"2020","month":"02","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"department":[{"_id":"RoSe"}],"article_type":"original","publisher":"Society for Industrial & Applied Mathematics ","ddc":["510"],"oa_version":"Preprint","type":"journal_article","_id":"9781","issue":"1","publication_status":"published","external_id":{"arxiv":["1904.08647 "],"isi":["000546967700022"]},"doi":"10.1137/19m126284x","ec_funded":1,"article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"volume":52,"publication":"SIAM Journal on Mathematical Analysis","acknowledgement":"We are grateful for the hospitality at the Mittag-Leffler Institute, where part of this work has been done. The work of the authors was supported by the European Research Council (ERC)under the European Union's Horizon 2020 research and innovation programme grant 694227.","day":"12","has_accepted_license":"1","intvolume":"        52","date_published":"2020-02-12T00:00:00Z","page":"605-622","title":"Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball","oa":1,"citation":{"mla":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 1, Society for Industrial &#38; Applied Mathematics , 2020, pp. 605–22, doi:<a href=\"https://doi.org/10.1137/19m126284x\">10.1137/19m126284x</a>.","apa":"Feliciangeli, D., &#38; Seiringer, R. (2020). Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial &#38; Applied Mathematics . <a href=\"https://doi.org/10.1137/19m126284x\">https://doi.org/10.1137/19m126284x</a>","chicago":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial &#38; Applied Mathematics , 2020. <a href=\"https://doi.org/10.1137/19m126284x\">https://doi.org/10.1137/19m126284x</a>.","ama":"Feliciangeli D, Seiringer R. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. <i>SIAM Journal on Mathematical Analysis</i>. 2020;52(1):605-622. doi:<a href=\"https://doi.org/10.1137/19m126284x\">10.1137/19m126284x</a>","ieee":"D. Feliciangeli and R. Seiringer, “Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 1. Society for Industrial &#38; Applied Mathematics , pp. 605–622, 2020.","short":"D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 605–622.","ista":"Feliciangeli D, Seiringer R. 2020. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 52(1), 605–622."},"date_created":"2021-08-06T07:34:16Z","quality_controlled":"1","arxiv":1},{"oa":1,"publisher":"Royal Society of London","_id":"9798","citation":{"apa":"Fraisse, C., &#38; Welch, J. J. (2020). Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. <a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">https://doi.org/10.6084/m9.figshare.7957472.v1</a>","chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">https://doi.org/10.6084/m9.figshare.7957472.v1</a>.","mla":"Fraisse, Christelle, and John J. Welch. <i>Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes</i>. Royal Society of London, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">10.6084/m9.figshare.7957472.v1</a>.","ama":"Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">10.6084/m9.figshare.7957472.v1</a>","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, <a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">10.6084/m9.figshare.7957472.v1</a>.","short":"C. Fraisse, J.J. Welch, (2020).","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020."},"date_created":"2021-08-06T11:18:15Z","type":"research_data_reference","oa_version":"Published Version","year":"2020","month":"10","title":"Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-25T10:34:41Z","day":"15","date_published":"2020-10-15T00:00:00Z","abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7957472.v1"}],"related_material":{"record":[{"id":"6467","status":"public","relation":"used_in_publication"}]},"doi":"10.6084/m9.figshare.7957472.v1","article_processing_charge":"No","author":[{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"last_name":"Welch","full_name":"Welch, John J.","first_name":"John J."}],"status":"public"},{"doi":"10.6084/m9.figshare.7957469.v1","article_processing_charge":"No","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075"},{"first_name":"John J.","full_name":"Welch, John J.","last_name":"Welch"}],"status":"public","date_updated":"2023-08-25T10:34:41Z","day":"15","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6467"}]},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7957469.v1","open_access":"1"}],"date_published":"2020-10-15T00:00:00Z","year":"2020","month":"10","title":"Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Royal Society of London","oa":1,"date_created":"2021-08-06T11:26:57Z","citation":{"ama":"Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>","short":"C. Fraisse, J.J. Welch, (2020).","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>.","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","apa":"Fraisse, C., &#38; Welch, J. J. (2020). Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">https://doi.org/10.6084/m9.figshare.7957469.v1</a>","chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">https://doi.org/10.6084/m9.figshare.7957469.v1</a>.","mla":"Fraisse, Christelle, and John J. Welch. <i>Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes</i>. Royal Society of London, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>."},"type":"research_data_reference","oa_version":"Published Version","_id":"9799"},{"doi":"10.6084/m9.figshare.5973013.v1","author":[{"orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"article_processing_charge":"No","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-10-18T06:36:00Z","day":"15","date_published":"2020-10-15T00:00:00Z","abstract":[{"text":"Data and mathematica notebooks for plotting figures from Language learning with communication between learners","lang":"eng"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"198"}]},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.5973013.v1","open_access":"1"}],"year":"2020","month":"10","title":"Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners","department":[{"_id":"KrCh"}],"oa":1,"publisher":"Royal Society","_id":"9814","citation":{"ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">10.6084/m9.figshare.5973013.v1</a>","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners.” Royal Society, 2020.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, (2020).","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2020. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners, Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">10.6084/m9.figshare.5973013.v1</a>.","mla":"Ibsen-Jensen, Rasmus, et al. <i>Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners</i>. Royal Society, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">10.6084/m9.figshare.5973013.v1</a>.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2020). Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">https://doi.org/10.6084/m9.figshare.5973013.v1</a>","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners.” Royal Society, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.5973013.v1\">https://doi.org/10.6084/m9.figshare.5973013.v1</a>."},"date_created":"2021-08-06T13:09:57Z","oa_version":"Published Version","type":"research_data_reference"},{"department":[{"_id":"LeSa"}],"title":"Movies","year":"2020","month":"05","_id":"9878","type":"research_data_reference","oa_version":"Published Version","citation":{"ama":"Gupta C, Khaniya U, Chan CK, et al. Movies. 2020. doi:<a href=\"https://doi.org/10.1021/jacs.9b13450.s002\">10.1021/jacs.9b13450.s002</a>","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Movies, American Chemical Society, <a href=\"https://doi.org/10.1021/jacs.9b13450.s002\">10.1021/jacs.9b13450.s002</a>.","ieee":"C. Gupta <i>et al.</i>, “Movies.” American Chemical Society, 2020.","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Movies. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.9b13450.s002\">https://doi.org/10.1021/jacs.9b13450.s002</a>","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Movies.” American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/jacs.9b13450.s002\">https://doi.org/10.1021/jacs.9b13450.s002</a>.","mla":"Gupta, Chitrak, et al. <i>Movies</i>. American Chemical Society, 2020, doi:<a href=\"https://doi.org/10.1021/jacs.9b13450.s002\">10.1021/jacs.9b13450.s002</a>."},"date_created":"2021-08-11T09:18:54Z","publisher":"American Chemical Society","status":"public","article_processing_charge":"No","author":[{"full_name":"Gupta, Chitrak","last_name":"Gupta","first_name":"Chitrak"},{"last_name":"Khaniya","full_name":"Khaniya, Umesh","first_name":"Umesh"},{"first_name":"Chun Kit","last_name":"Chan","full_name":"Chan, Chun Kit"},{"full_name":"Dehez, Francois","last_name":"Dehez","first_name":"Francois"},{"first_name":"Mrinal","last_name":"Shekhar","full_name":"Shekhar, Mrinal"},{"last_name":"Gunner","full_name":"Gunner, M.R.","first_name":"M.R."},{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"},{"last_name":"Chipot","full_name":"Chipot, Christophe","first_name":"Christophe"},{"last_name":"Singharoy","full_name":"Singharoy, Abhishek","first_name":"Abhishek"}],"doi":"10.1021/jacs.9b13450.s002","date_published":"2020-05-20T00:00:00Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8040"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"20","date_updated":"2023-08-22T07:49:38Z"},{"date_published":"2020-01-08T00:00:00Z","abstract":[{"text":"Data obtained from the fine-grained simulations used in Figures 2-5, data obtained from the coarse-grained numerical calculations used in Figure 6, and a sample script for the fine-grained simulation as a Jupyter notebook (ZIP)","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7166"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-17T14:07:52Z","day":"08","author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","last_name":"Ucar","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217"},{"first_name":"Reinhard","full_name":"Lipowsky, Reinhard","last_name":"Lipowsky"}],"article_processing_charge":"No","status":"public","doi":"10.1021/acs.nanolett.9b04445.s002","_id":"9885","date_created":"2021-08-11T13:16:03Z","citation":{"short":"M.C. Ucar, R. Lipowsky, (2020).","ista":"Ucar MC, Lipowsky R. 2020. MURL_Dataz, American Chemical Society , <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s002\">10.1021/acs.nanolett.9b04445.s002</a>.","ieee":"M. C. Ucar and R. Lipowsky, “MURL_Dataz.” American Chemical Society , 2020.","ama":"Ucar MC, Lipowsky R. MURL_Dataz. 2020. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s002\">10.1021/acs.nanolett.9b04445.s002</a>","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “MURL_Dataz.” American Chemical Society , 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s002\">https://doi.org/10.1021/acs.nanolett.9b04445.s002</a>.","apa":"Ucar, M. C., &#38; Lipowsky, R. (2020). MURL_Dataz. American Chemical Society . <a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s002\">https://doi.org/10.1021/acs.nanolett.9b04445.s002</a>","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. <i>MURL_Dataz</i>. American Chemical Society , 2020, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b04445.s002\">10.1021/acs.nanolett.9b04445.s002</a>."},"oa_version":"Published Version","type":"research_data_reference","publisher":"American Chemical Society ","title":"MURL_Dataz","department":[{"_id":"EdHa"}],"year":"2020","month":"01"},{"status":"public","author":[{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg","full_name":"Amberg, Nicole"},{"first_name":"Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","last_name":"Laukoter"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"scopus_import":"1","abstract":[{"text":"The cerebral cortex is composed of a large variety of distinct cell-types including projection neurons, interneurons and glial cells which emerge from distinct neural stem cell (NSC) lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells (RGPs) in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that NSC and RGP lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell-type diversity during cortical development. This article is protected by copyright. All rights reserved.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-11T13:40:26Z","article_type":"review","department":[{"_id":"SiHi"}],"project":[{"_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","grant_number":"LS13-002"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014"},{"grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"year":"2019","month":"04","isi":1,"publication_status":"published","external_id":{"isi":["000462680200002"]},"_id":"27","issue":"1","oa_version":"Published Version","ddc":["570"],"type":"journal_article","file":[{"creator":"kschuh","file_id":"7239","relation":"main_file","file_name":"2019_Wiley_Amberg.pdf","checksum":"db027721a95d36f5de36aadcd0bdf7e6","file_size":889709,"date_created":"2020-01-07T13:35:52Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:45Z"}],"publisher":"Wiley","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"file_date_updated":"2020-07-14T12:45:45Z","doi":"10.1111/jnc.14601","date_published":"2019-04-01T00:00:00Z","intvolume":"       149","has_accepted_license":"1","acknowledgement":" This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung \r\nn[f+b]   (C13-002)   to   SH;   a   program   grant   from   the   Human   Frontiers   Science   Program (RGP0053/2014)  to SH;  the  People  Programme  (Marie  Curie  Actions)  of  the  European  Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No 618444 to SH, and the  European  Research  Council  (ERC)  under  the  European  Union’s  Horizon  2020  research  and innovation programme (grant agreement No 725780 LinPro)to SH.\r\n","day":"01","publication":"Journal of Neurochemistry","volume":149,"title":"Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex","page":"12-26","quality_controlled":"1","citation":{"mla":"Amberg, Nicole, et al. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” <i>Journal of Neurochemistry</i>, vol. 149, no. 1, Wiley, 2019, pp. 12–26, doi:<a href=\"https://doi.org/10.1111/jnc.14601\">10.1111/jnc.14601</a>.","apa":"Amberg, N., Laukoter, S., &#38; Hippenmeyer, S. (2019). Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. <i>Journal of Neurochemistry</i>. Wiley. <a href=\"https://doi.org/10.1111/jnc.14601\">https://doi.org/10.1111/jnc.14601</a>","chicago":"Amberg, Nicole, Susanne Laukoter, and Simon Hippenmeyer. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” <i>Journal of Neurochemistry</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/jnc.14601\">https://doi.org/10.1111/jnc.14601</a>.","ama":"Amberg N, Laukoter S, Hippenmeyer S. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. <i>Journal of Neurochemistry</i>. 2019;149(1):12-26. doi:<a href=\"https://doi.org/10.1111/jnc.14601\">10.1111/jnc.14601</a>","ieee":"N. Amberg, S. Laukoter, and S. Hippenmeyer, “Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex,” <i>Journal of Neurochemistry</i>, vol. 149, no. 1. Wiley, pp. 12–26, 2019.","short":"N. Amberg, S. Laukoter, S. Hippenmeyer, Journal of Neurochemistry 149 (2019) 12–26.","ista":"Amberg N, Laukoter S, Hippenmeyer S. 2019. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. 149(1), 12–26."},"date_created":"2018-12-11T11:44:14Z","oa":1},{"oa_version":"Preprint","type":"journal_article","external_id":{"arxiv":["1611.04177"],"isi":["000458945300012"]},"publication_status":"published","_id":"301","issue":"3","publisher":"Elsevier","department":[{"_id":"JaMa"}],"article_type":"original","isi":1,"year":"2019","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.04177"}],"abstract":[{"text":"A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-08-24T14:20:49Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","author":[{"last_name":"Gerencser","full_name":"Gerencser, Mate","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"István","last_name":"Gyöngy","full_name":"Gyöngy, István"}],"date_created":"2018-12-11T11:45:42Z","citation":{"ista":"Gerencser M, Gyöngy I. 2019. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 129(3), 995–1012.","short":"M. Gerencser, I. Gyöngy, Stochastic Processes and Their Applications 129 (2019) 995–1012.","ieee":"M. Gerencser and I. Gyöngy, “A Feynman–Kac formula for stochastic Dirichlet problems,” <i>Stochastic Processes and their Applications</i>, vol. 129, no. 3. Elsevier, pp. 995–1012, 2019.","ama":"Gerencser M, Gyöngy I. A Feynman–Kac formula for stochastic Dirichlet problems. <i>Stochastic Processes and their Applications</i>. 2019;129(3):995-1012. doi:<a href=\"https://doi.org/10.1016/j.spa.2018.04.003\">10.1016/j.spa.2018.04.003</a>","mla":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” <i>Stochastic Processes and Their Applications</i>, vol. 129, no. 3, Elsevier, 2019, pp. 995–1012, doi:<a href=\"https://doi.org/10.1016/j.spa.2018.04.003\">10.1016/j.spa.2018.04.003</a>.","chicago":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” <i>Stochastic Processes and Their Applications</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.spa.2018.04.003\">https://doi.org/10.1016/j.spa.2018.04.003</a>.","apa":"Gerencser, M., &#38; Gyöngy, I. (2019). A Feynman–Kac formula for stochastic Dirichlet problems. <i>Stochastic Processes and Their Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.spa.2018.04.003\">https://doi.org/10.1016/j.spa.2018.04.003</a>"},"arxiv":1,"quality_controlled":"1","oa":1,"title":"A Feynman–Kac formula for stochastic Dirichlet problems","page":"995-1012","intvolume":"       129","date_published":"2019-03-01T00:00:00Z","day":"01","publication":"Stochastic Processes and their Applications","volume":129,"article_processing_charge":"No","doi":"10.1016/j.spa.2018.04.003"},{"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"year":"2019","month":"04","publication_identifier":{"issn":["01788051"],"eissn":["14322064"]},"isi":1,"article_type":"original","department":[{"_id":"JaMa"}],"publisher":"Springer","external_id":{"isi":["000463613800001"]},"publication_status":"published","issue":"3-4","_id":"319","file":[{"file_name":"2018_ProbTheory_Gerencser.pdf","creator":"dernst","file_id":"5722","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:03Z","file_size":893182,"checksum":"288d16ef7291242f485a9660979486e3","date_created":"2018-12-17T16:25:24Z"}],"type":"journal_article","oa_version":"Published Version","ddc":["510"],"status":"public","author":[{"full_name":"Gerencser, Mate","last_name":"Gerencser","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hairer","full_name":"Hairer, Martin","first_name":"Martin"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-24T14:38:32Z","scopus_import":"1","abstract":[{"lang":"eng","text":"We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition."}],"publist_id":"7546","page":"697–758","title":"Singular SPDEs in domains with boundaries","oa":1,"quality_controlled":"1","date_created":"2018-12-11T11:45:48Z","citation":{"ama":"Gerencser M, Hairer M. Singular SPDEs in domains with boundaries. <i>Probability Theory and Related Fields</i>. 2019;173(3-4):697–758. doi:<a href=\"https://doi.org/10.1007/s00440-018-0841-1\">10.1007/s00440-018-0841-1</a>","short":"M. Gerencser, M. Hairer, Probability Theory and Related Fields 173 (2019) 697–758.","ieee":"M. Gerencser and M. Hairer, “Singular SPDEs in domains with boundaries,” <i>Probability Theory and Related Fields</i>, vol. 173, no. 3–4. Springer, pp. 697–758, 2019.","ista":"Gerencser M, Hairer M. 2019. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 173(3–4), 697–758.","mla":"Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” <i>Probability Theory and Related Fields</i>, vol. 173, no. 3–4, Springer, 2019, pp. 697–758, doi:<a href=\"https://doi.org/10.1007/s00440-018-0841-1\">10.1007/s00440-018-0841-1</a>.","apa":"Gerencser, M., &#38; Hairer, M. (2019). Singular SPDEs in domains with boundaries. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-018-0841-1\">https://doi.org/10.1007/s00440-018-0841-1</a>","chicago":"Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” <i>Probability Theory and Related Fields</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s00440-018-0841-1\">https://doi.org/10.1007/s00440-018-0841-1</a>."},"file_date_updated":"2020-07-14T12:46:03Z","doi":"10.1007/s00440-018-0841-1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","publication":"Probability Theory and Related Fields","acknowledgement":"MG thanks the support of the LMS Postdoctoral Mobility Grant.\r\n\r\n","day":"01","volume":173,"date_published":"2019-04-01T00:00:00Z","intvolume":"       173","has_accepted_license":"1"},{"title":"Modular invariants for genus 3 hyperelliptic curves","date_created":"2022-03-18T12:09:48Z","citation":{"ama":"Ionica S, Kılıçer P, Lauter K, et al. Modular invariants for genus 3 hyperelliptic curves. <i>Research in Number Theory</i>. 2019;5. doi:<a href=\"https://doi.org/10.1007/s40993-018-0146-6\">10.1007/s40993-018-0146-6</a>","ieee":"S. Ionica <i>et al.</i>, “Modular invariants for genus 3 hyperelliptic curves,” <i>Research in Number Theory</i>, vol. 5. Springer Nature, 2019.","ista":"Ionica S, Kılıçer P, Lauter K, Lorenzo García E, Manzateanu M-A, Massierer M, Vincent C. 2019. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 5, 9.","short":"S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M. Massierer, C. Vincent, Research in Number Theory 5 (2019).","apa":"Ionica, S., Kılıçer, P., Lauter, K., Lorenzo García, E., Manzateanu, M.-A., Massierer, M., &#38; Vincent, C. (2019). Modular invariants for genus 3 hyperelliptic curves. <i>Research in Number Theory</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40993-018-0146-6\">https://doi.org/10.1007/s40993-018-0146-6</a>","chicago":"Ionica, Sorina, Pınar Kılıçer, Kristin Lauter, Elisa Lorenzo García, Maria-Adelina Manzateanu, Maike Massierer, and Christelle Vincent. “Modular Invariants for Genus 3 Hyperelliptic Curves.” <i>Research in Number Theory</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s40993-018-0146-6\">https://doi.org/10.1007/s40993-018-0146-6</a>.","mla":"Ionica, Sorina, et al. “Modular Invariants for Genus 3 Hyperelliptic Curves.” <i>Research in Number Theory</i>, vol. 5, 9, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1007/s40993-018-0146-6\">10.1007/s40993-018-0146-6</a>."},"quality_controlled":"1","arxiv":1,"oa":1,"article_number":"9","article_processing_charge":"No","doi":"10.1007/s40993-018-0146-6","intvolume":"         5","date_published":"2019-01-02T00:00:00Z","acknowledgement":"The authors would like to thank the Lorentz Center in Leiden for hosting the Women in Numbers Europe 2 workshop and providing a productive and enjoyable environment for our initial work on this project. We are grateful to the organizers of WIN-E2, Irene Bouw, Rachel Newton and Ekin Ozman, for making this conference and this collaboration possible. We\r\nthank Irene Bouw and Christophe Ritzenhaler for helpful discussions. Ionica acknowledges support from the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. Most of Kılıçer’s work was carried out during her stay in Universiteit Leiden and Carl von Ossietzky Universität Oldenburg. Massierer was supported by the Australian Research Council (DP150101689). Vincent is supported by the National Science Foundation under Grant No. DMS-1802323 and by the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. ","publication":"Research in Number Theory","day":"02","volume":5,"department":[{"_id":"TiBr"}],"article_type":"original","publication_identifier":{"eissn":["2363-9555"],"issn":["2522-0160"]},"month":"01","year":"2019","type":"journal_article","oa_version":"Preprint","publication_status":"published","external_id":{"arxiv":["1807.08986"]},"_id":"10874","publisher":"Springer Nature","status":"public","author":[{"first_name":"Sorina","last_name":"Ionica","full_name":"Ionica, Sorina"},{"full_name":"Kılıçer, Pınar","last_name":"Kılıçer","first_name":"Pınar"},{"full_name":"Lauter, Kristin","last_name":"Lauter","first_name":"Kristin"},{"first_name":"Elisa","full_name":"Lorenzo García, Elisa","last_name":"Lorenzo García"},{"first_name":"Maria-Adelina","id":"be8d652e-a908-11ec-82a4-e2867729459c","last_name":"Manzateanu","full_name":"Manzateanu, Maria-Adelina"},{"last_name":"Massierer","full_name":"Massierer, Maike","first_name":"Maike"},{"first_name":"Christelle","full_name":"Vincent, Christelle","last_name":"Vincent"}],"main_file_link":[{"url":"https://arxiv.org/abs/1807.08986","open_access":"1"}],"keyword":["Algebra and Number Theory"],"abstract":[{"lang":"eng","text":"In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler, and Zykin, which allows us to connect invariants of binary octics to Siegel modular forms of genus 3. We use this connection to show that certain modular functions, when restricted to the hyperelliptic locus, assume values whose denominators are products of powers of primes of bad reduction for the associated hyperelliptic curves. We illustrate our theorem with explicit computations. This work is motivated by the study of the values of these modular functions at CM points of the Siegel upper half-space, which, if their denominators are known, can be used to effectively compute models of (hyperelliptic, in our case) curves with CM."}],"scopus_import":"1","date_updated":"2023-09-05T15:39:31Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"year":"2019","month":"05","publication_identifier":{"issn":["2398-7340"]},"department":[{"_id":"ToHe"}],"publisher":"EasyChair","publication_status":"published","alternative_title":["EPiC Series in Computing"],"_id":"10877","ddc":["000"],"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2022-05-17T06:55:49Z","file_size":346415,"checksum":"4b92e333db7b4e2349501a804dfede69","success":1,"date_created":"2022-05-17T06:55:49Z","file_name":"2019_EPiCs_Frehse.pdf","file_id":"11391","creator":"dernst","relation":"main_file"}],"oa_version":"Published Version","type":"conference","status":"public","author":[{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"full_name":"Abate, Alessandro","last_name":"Abate","first_name":"Alessandro"},{"first_name":"Dieky","last_name":"Adzkiya","full_name":"Adzkiya, Dieky"},{"first_name":"Anna","last_name":"Becchi","full_name":"Becchi, Anna"},{"first_name":"Lei","last_name":"Bu","full_name":"Bu, Lei"},{"full_name":"Cimatti, Alessandro","last_name":"Cimatti","first_name":"Alessandro"},{"first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco","last_name":"Giacobbe","orcid":"0000-0001-8180-0904"},{"full_name":"Griggio, Alberto","last_name":"Griggio","first_name":"Alberto"},{"first_name":"Sergio","last_name":"Mover","full_name":"Mover, Sergio"},{"first_name":"Muhammad Syifa'ul","full_name":"Mufid, Muhammad Syifa'ul","last_name":"Mufid"},{"first_name":"Idriss","last_name":"Riouak","full_name":"Riouak, Idriss"},{"last_name":"Tonetta","full_name":"Tonetta, Stefano","first_name":"Stefano"},{"last_name":"Zaffanella","full_name":"Zaffanella, Enea","first_name":"Enea"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2022-05-17T07:09:47Z","scopus_import":"1","abstract":[{"lang":"eng","text":"This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with piecewise constant dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this third edition, six tools have been applied to solve five different benchmark problems in the category for piecewise constant dynamics: BACH, Lyse, Hy- COMP, PHAVer/SX, PHAVerLite, and VeriSiMPL. Compared to last year, a new tool has participated (HyCOMP) and PHAVerLite has replaced PHAVer-lite. The result is a snap- shot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results probably provide the most complete assessment of tools for the safety verification of continuous and hybrid systems with piecewise constant dynamics up to this date."}],"page":"1-13","title":"ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics","oa":1,"quality_controlled":"1","conference":{"location":"Montreal, Canada","end_date":"2019-04-15","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems","start_date":"2019-04-15"},"date_created":"2022-03-18T12:29:23Z","citation":{"short":"G. Frehse, A. Abate, D. Adzkiya, A. Becchi, L. Bu, A. Cimatti, M. Giacobbe, A. Griggio, S. Mover, M.S. Mufid, I. Riouak, S. Tonetta, E. Zaffanella, in:, G. Frehse, M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, EasyChair, 2019, pp. 1–13.","ista":"Frehse G, Abate A, Adzkiya D, Becchi A, Bu L, Cimatti A, Giacobbe M, Griggio A, Mover S, Mufid MS, Riouak I, Tonetta S, Zaffanella E. 2019. ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems, EPiC Series in Computing, vol. 61, 1–13.","ieee":"G. Frehse <i>et al.</i>, “ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics,” in <i>ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems</i>, Montreal, Canada, 2019, vol. 61, pp. 1–13.","ama":"Frehse G, Abate A, Adzkiya D, et al. ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. In: Frehse G, Althoff M, eds. <i>ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems</i>. Vol 61. EasyChair; 2019:1-13. doi:<a href=\"https://doi.org/10.29007/rjwn\">10.29007/rjwn</a>","chicago":"Frehse, Goran, Alessandro Abate, Dieky Adzkiya, Anna Becchi, Lei Bu, Alessandro Cimatti, Mirco Giacobbe, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise Constant Dynamics.” In <i>ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems</i>, edited by Goran Frehse and Matthias Althoff, 61:1–13. EasyChair, 2019. <a href=\"https://doi.org/10.29007/rjwn\">https://doi.org/10.29007/rjwn</a>.","apa":"Frehse, G., Abate, A., Adzkiya, D., Becchi, A., Bu, L., Cimatti, A., … Zaffanella, E. (2019). ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. In G. Frehse &#38; M. Althoff (Eds.), <i>ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems</i> (Vol. 61, pp. 1–13). Montreal, Canada: EasyChair. <a href=\"https://doi.org/10.29007/rjwn\">https://doi.org/10.29007/rjwn</a>","mla":"Frehse, Goran, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise Constant Dynamics.” <i>ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems</i>, edited by Goran Frehse and Matthias Althoff, vol. 61, EasyChair, 2019, pp. 1–13, doi:<a href=\"https://doi.org/10.29007/rjwn\">10.29007/rjwn</a>."},"file_date_updated":"2022-05-17T06:55:49Z","doi":"10.29007/rjwn","article_processing_charge":"No","day":"25","acknowledgement":"The authors gratefully acknowledge \fnancial support by the European Commission project\r\nUnCoVerCPS under grant number 643921. Lei Bu is supported by the National Natural Science\r\nFoundation of China (No.61572249).","publication":"ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems","volume":61,"date_published":"2019-05-25T00:00:00Z","editor":[{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"first_name":"Matthias","full_name":"Althoff, Matthias","last_name":"Althoff"}],"intvolume":"        61","has_accepted_license":"1"},{"status":"public","author":[{"last_name":"Flandoli","full_name":"Flandoli, Franco","first_name":"Franco"},{"first_name":"Enrico","last_name":"Priola","full_name":"Priola, Enrico"},{"id":"47491882-F248-11E8-B48F-1D18A9856A87","first_name":"Giovanni A","last_name":"Zanco","full_name":"Zanco, Giovanni A"}],"date_updated":"2023-09-08T11:34:45Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.04156"}],"keyword":["Applied Mathematics","Discrete Mathematics and Combinatorics","Analysis"],"abstract":[{"lang":"eng","text":"Starting from a microscopic model for a system of neurons evolving in time which individually follow a stochastic integrate-and-fire type model, we study a mean-field limit of the system. Our model is described by a system of SDEs with discontinuous coefficients for the action potential of each neuron and takes into account the (random) spatial configuration of neurons allowing the interaction to depend on it. In the limit as the number of particles tends to infinity, we obtain a nonlinear Fokker-Planck type PDE in two variables, with derivatives only with respect to one variable and discontinuous coefficients. We also study strong well-posedness of the system of SDEs and prove the existence and uniqueness of a weak measure-valued solution to the PDE, obtained as the limit of the laws of the empirical measures for the system of particles."}],"scopus_import":"1","publication_identifier":{"issn":["1553-5231"]},"isi":1,"project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"month":"06","year":"2019","department":[{"_id":"JaMa"}],"article_type":"original","publisher":"American Institute of Mathematical Sciences","oa_version":"Preprint","type":"journal_article","publication_status":"published","external_id":{"isi":["000459954800003"],"arxiv":["1708.04156"]},"issue":"6","_id":"10878","doi":"10.3934/dcds.2019126","article_processing_charge":"No","day":"01","acknowledgement":"The second author has been partially supported by INdAM through the GNAMPA Research\r\nProject (2017) “Sistemi stocastici singolari: buona posizione e problemi di controllo”. The third\r\nauthor was partly funded by the Austrian Science Fund (FWF) project F 65.","publication":"Discrete and Continuous Dynamical Systems","volume":39,"intvolume":"        39","date_published":"2019-06-01T00:00:00Z","page":"3037-3067","title":"A mean-field model with discontinuous coefficients for neurons with spatial interaction","oa":1,"citation":{"ama":"Flandoli F, Priola E, Zanco GA. A mean-field model with discontinuous coefficients for neurons with spatial interaction. <i>Discrete and Continuous Dynamical Systems</i>. 2019;39(6):3037-3067. doi:<a href=\"https://doi.org/10.3934/dcds.2019126\">10.3934/dcds.2019126</a>","ieee":"F. Flandoli, E. Priola, and G. A. Zanco, “A mean-field model with discontinuous coefficients for neurons with spatial interaction,” <i>Discrete and Continuous Dynamical Systems</i>, vol. 39, no. 6. American Institute of Mathematical Sciences, pp. 3037–3067, 2019.","short":"F. Flandoli, E. Priola, G.A. Zanco, Discrete and Continuous Dynamical Systems 39 (2019) 3037–3067.","ista":"Flandoli F, Priola E, Zanco GA. 2019. A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. 39(6), 3037–3067.","apa":"Flandoli, F., Priola, E., &#38; Zanco, G. A. (2019). A mean-field model with discontinuous coefficients for neurons with spatial interaction. <i>Discrete and Continuous Dynamical Systems</i>. American Institute of Mathematical Sciences. <a href=\"https://doi.org/10.3934/dcds.2019126\">https://doi.org/10.3934/dcds.2019126</a>","chicago":"Flandoli, Franco, Enrico Priola, and Giovanni A Zanco. “A Mean-Field Model with Discontinuous Coefficients for Neurons with Spatial Interaction.” <i>Discrete and Continuous Dynamical Systems</i>. American Institute of Mathematical Sciences, 2019. <a href=\"https://doi.org/10.3934/dcds.2019126\">https://doi.org/10.3934/dcds.2019126</a>.","mla":"Flandoli, Franco, et al. “A Mean-Field Model with Discontinuous Coefficients for Neurons with Spatial Interaction.” <i>Discrete and Continuous Dynamical Systems</i>, vol. 39, no. 6, American Institute of Mathematical Sciences, 2019, pp. 3037–67, doi:<a href=\"https://doi.org/10.3934/dcds.2019126\">10.3934/dcds.2019126</a>."},"date_created":"2022-03-18T12:33:34Z","quality_controlled":"1","arxiv":1}]