[{"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"22667"}]},"citation":{"chicago":"Vijatovic, David, Florina Alexandra  Toma, Y Ignatyev, Zoe P Harrington, Christoph M Sommer, Robert Hauschild, Matthijs Geert Smits, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” <i>Cell Reports</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">https://doi.org/10.1016/j.celrep.2026.117227</a>.","apa":"Vijatovic, D., Toma, F. A., Ignatyev, Y., Harrington, Z. P., Sommer, C. M., Hauschild, R., … Sweeney, L. B. (2026). Multifold increase in spinal inhibitory cell types with emergence of limb movement. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">https://doi.org/10.1016/j.celrep.2026.117227</a>","ama":"Vijatovic D, Toma FA, Ignatyev Y, et al. Multifold increase in spinal inhibitory cell types with emergence of limb movement. <i>Cell Reports</i>. 2026;45(4). doi:<a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">10.1016/j.celrep.2026.117227</a>","mla":"Vijatovic, David, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” <i>Cell Reports</i>, vol. 45, no. 4, 117227, Cell Press, 2026, doi:<a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">10.1016/j.celrep.2026.117227</a>.","ista":"Vijatovic D, Toma FA, Ignatyev Y, Harrington ZP, Sommer CM, Hauschild R, Smits MG, Dalla Vecchia M, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney LB. 2026. Multifold increase in spinal inhibitory cell types with emergence of limb movement. Cell Reports. 45(4), 117227.","short":"D. Vijatovic, F.A. Toma, Y. Ignatyev, Z.P. Harrington, C.M. Sommer, R. Hauschild, M.G. Smits, M. Dalla Vecchia, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton, M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, Cell Reports 45 (2026).","ieee":"D. Vijatovic <i>et al.</i>, “Multifold increase in spinal inhibitory cell types with emergence of limb movement,” <i>Cell Reports</i>, vol. 45, no. 4. Cell Press, 2026."},"DOAJ_listed":"1","project":[{"_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","name":"Development and Evolution of Tetrapod Motor Circuits","grant_number":"101041551"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity","_id":"8da85f50-16d5-11f0-9cad-eab8b0ff6c9e","grant_number":"F7814"},{"_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","name":"Tools for automation and feedback microscopy","grant_number":"CZI01"},{"grant_number":"FTI21-D-046","name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis","_id":"bd73af52-d553-11ed-ba76-912049f0ac7a"},{"grant_number":"COE16","_id":"cf428362-b037-11f1-b015-8277a8a2f63d","name":"Neuronal circuits in health and disease (Sweeney)"}],"date_updated":"2026-10-20T09:04:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","PlanS_conform":"1","title":"Multifold increase in spinal inhibitory cell types with emergence of limb movement","_id":"21746","author":[{"full_name":"Vijatovic, David","orcid":"0000-0002-5494-0941","id":"cf391e77-ec3c-11ea-a124-d69323410b58","last_name":"Vijatovic","first_name":"David"},{"first_name":"Florina Alexandra ","last_name":"Toma","id":"2f73f876-f128-11eb-9611-b96b5a30cb0e","full_name":"Toma, Florina Alexandra "},{"full_name":"Ignatyev, Y","first_name":"Y","last_name":"Ignatyev"},{"orcid":"0009-0008-0158-4032","full_name":"Harrington, Zoe P","first_name":"Zoe P","last_name":"Harrington","id":"a8144562-32c9-11ee-b5ce-d9800628bda2"},{"orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","last_name":"Sommer"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Smits","first_name":"Matthijs Geert","id":"7a231d52-e216-11ee-a0bb-8acd55f8f1f0","full_name":"Smits, Matthijs Geert"},{"id":"02a7a869-ff06-11ed-a87f-86649d6077e5","last_name":"Dalla Vecchia","first_name":"Marco","full_name":"Dalla Vecchia, Marco"},{"first_name":"Alexandra J.","last_name":"Trevisan","full_name":"Trevisan, Alexandra J."},{"first_name":"Phillip","last_name":"Chapman","full_name":"Chapman, Phillip"},{"full_name":"Julseth, Mara","last_name":"Julseth","first_name":"Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1"},{"full_name":"Brenner-Morton, Susan","last_name":"Brenner-Morton","first_name":"Susan"},{"first_name":"Mariano I.","last_name":"Gabitto","full_name":"Gabitto, Mariano I."},{"full_name":"Dasen, Jeremy S.","first_name":"Jeremy S.","last_name":"Dasen"},{"last_name":"Bikoff","first_name":"Jay B.","full_name":"Bikoff, Jay B."},{"id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger","full_name":"Sweeney, Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601"}],"status":"public","date_created":"2026-04-19T22:07:43Z","type":"journal_article","oa_version":"Published Version","article_type":"original","abstract":[{"lang":"eng","text":"As vertebrates transitioned from water to land, locomotion shifted from undulatory swimming to limb-based movement. How spinal circuits and their cell types evolved to support this transition remains unclear. We leverage frog metamorphosis, which recapitulates this transition within a single organism, to define how spinal circuits generate aquatic versus terrestrial motor patterns. At swim stages, spinal architecture is uniform, with a transcriptionally and anatomically homogeneous motor and interneurons. As limbs develop and their movement complexifies, spinal circuits expand in neuron number and subtype diversity. This expansion is most pronounced for V1 inhibitory neurons, which increase ∼70-fold and diversify into transcriptionally distinct subtypes. Disrupting transcription factors defining emerging motor and V1 populations reveals molecular segregation between swim and limb circuits, highlighting the role of subtype diversity in motor coordination. A multifold increase in inhibitory neuron diversity thus underlies the tail-to-limb locomotor transition, providing a framework for spinal circuit adaptation during vertebrate evolution."}],"OA_place":"publisher","OA_type":"gold","language":[{"iso":"eng"}],"publication":"Cell Reports","scopus_import":"1","issue":"4","publication_identifier":{"issn":["2639-1856"],"eissn":["2211-1247"]},"acknowledgement":"We would like to thank the members of the Sweeney Lab, Mario de Bono, Michael Forsthofer, Katharina Lust, and Meital Oren, for comments on the manuscript. We are also grateful to Tom Jessell and Chris Kintner for their scientific insight and mentorship during the conception of this project. It would also have not been possible without the technical support of the Aquatics and Imaging and Optics Facility support teams (ISTA). We thank Martin Estermann for preparing the initial draft of the graphical abstract and Niki Barolini for the final version. In addition, we thank our funding sources for providing the resources to do these experiments: GFF NÖ FTI Strategy Lower Austria dissertation grant FT121-D-046 (to D.V.), Horizon Europe ERC starting grant 101041551 (to Y.I., L.B.S., F.A.T., and D.V.), Special Research Program (SFB) of the Austrian Science Fund (FWF) project F7814-B (to L.B.S.), Austrian Science Fund (FWF) 10.55776/COE16 (to Y.I. and L.B.S.), NINDS 5R35NS116858 (to J.S.D.), CZI grant DAF2020-225401 (DOI) 10.37921/120055ratwvi (to R.H.), NIH grant R01NS123116 (to J.B.B.), American Lebanese Syrian Associated Charities (ALSAC) (to J.B.B.), German Academic Exchange Service (DAAD) IFI grant 57515251-91853472 (to Z.H.), and Project A.L.S. (to S.B.-M.).","has_accepted_license":"1","file_date_updated":"2026-05-04T12:20:10Z","date_published":"2026-04-28T00:00:00Z","article_processing_charge":"Yes","fulldoi":"https://doi.org/10.1016/j.celrep.2026.117227","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"publication_status":"published","year":"2026","pmid":1,"quality_controlled":"1","intvolume":"        45","article_number":"117227","volume":45,"doi":"10.1016/j.celrep.2026.117227","file":[{"creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"0d26cdb5b8d8dec3a911d8261a65cdef","date_created":"2026-05-04T12:20:10Z","success":1,"file_size":14925958,"file_name":"2026_CellReports_Vijatovic.pdf","content_type":"application/pdf","date_updated":"2026-05-04T12:20:10Z","file_id":"21795"}],"day":"28","oa":1,"corr_author":"1","external_id":{"pmid":["41964955 "]},"publisher":"Cell Press","department":[{"_id":"LoSw"},{"_id":"GradSch"},{"_id":"TiVo"},{"_id":"Bio"},{"_id":"NiBa"}],"month":"04"},{"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"ddc":["570"],"intvolume":"         6","quality_controlled":"1","year":"2026","pmid":1,"publication_status":"published","keyword":["direct genetic effects","DGE","indirect genetic effects","IGE","parent-of-origin effects","phenotypic variation","assortative mating","within-family GWAS","MoBa","EstBB"],"article_processing_charge":"Yes","date_published":"2026-07-08T00:00:00Z","file_date_updated":"2026-07-28T07:24:50Z","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"fulldoi":"https://doi.org/10.1016/j.xgen.2026.101277","das_tickbox":"1","oa":1,"corr_author":"1","day":"08","dataavailabilitystatement":"Information on how to access the MoBaPsychGen post-imputation QC data are available here: https://www.fhi.no/en/me/the-psychgen-centre-for-genetic-epidemiology-and-mental-health/access-to-genetic-data-after-quality-control-by-the-mobapsychgen-pipeline-v/.\r\nEstonian Biobank data (https://genomics.ut.ee/en/content/estonian-biobank) were used in this project. For access to be granted to the Estonian Biobank genotypic and corresponding phenotypic data, a preliminary application must be presented to the oversight committee, who must first approve the project. Ethics permission must then be obtained from the Estonian Committee on Bioethics and Human Research. Finally, a full project must be submitted and approved by the Estonian Biobank.\r\nAccess to the Generation Scotland data is available with appropriate permission from the Generation Scotland Access Committee. Applications should be made to access@generationscotland.org (https://genscot.ed.ac.uk/).\r\nThe code for JODIE developed in this work is open source and is publicly available on zenodo (https://doi.org/10.5281/zenodo.19593928) and GitHub (https://github.com/medical-genomics-group/JODIE).\r\nHaplotype Reference Consortium Release 1.1 data (https://ega-archive.org/datasets/EGAD00001002729) are available by application to a Data Access Committee (DAC) of the Wellcome Trust Sanger Institute.\r\nThe Common Metabolic Diseases Atlas can be accessed here: https://cmdga.org.","month":"07","department":[{"_id":"MaRo"}],"publisher":"Cell Press","external_id":{"pmid":["40909755"]},"article_number":"101277","file":[{"file_id":"22597","content_type":"application/pdf","date_updated":"2026-07-28T07:24:50Z","file_name":"2026_CellGenomics_Kraetschmer.pdf","file_size":3679297,"success":1,"checksum":"f896b510480d2d4e4a7fd46c2e2761f4","date_created":"2026-07-28T07:24:50Z","access_level":"open_access","creator":"dernst","relation":"main_file"}],"researchdata_availability":"yes","doi":"10.1016/j.xgen.2026.101277","volume":6,"author":[{"full_name":"Krätschmer, Ilse","orcid":"0000-0002-5636-9259","last_name":"Krätschmer","first_name":"Ilse","id":"30d4014e-7753-11eb-b44b-db6d61112e73"},{"last_name":"Hegemann","first_name":"Laura","full_name":"Hegemann, Laura"},{"full_name":"Hofmeister, Robin J.","first_name":"Robin J.","last_name":"Hofmeister"},{"last_name":"Corfield","first_name":"Elizabeth C.","full_name":"Corfield, Elizabeth C."},{"full_name":"Mahmoudi, Mahdi","last_name":"Mahmoudi","first_name":"Mahdi"},{"full_name":"Delaneau, Olivier","first_name":"Olivier","last_name":"Delaneau"},{"first_name":"Ole A.","last_name":"Andreassen","full_name":"Andreassen, Ole A."},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"last_name":"Hayward","first_name":"Caroline","full_name":"Hayward, Caroline"},{"first_name":"Riccardo E.","last_name":"Marioni","full_name":"Marioni, Riccardo E."},{"full_name":"Ystrom, Eivind","first_name":"Eivind","last_name":"Ystrom"},{"full_name":"Havdahl, Alexandra","last_name":"Havdahl","first_name":"Alexandra"},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"date_created":"2026-06-10T07:39:08Z","status":"public","_id":"21987","title":"Separating direct, indirect, and parent-of-origin genetic effects in the human population","abstract":[{"lang":"eng","text":"We introduce JODIE, a genetic joint modeling approach that estimates how DNA loci influence human traits by partitioning genetic effects into four components: direct effects (from a child’s alleles), indirect maternal and paternal effects (from parents’ alleles), and parent-of-origin (PofO) effects (dependent on parental transmission of alleles), while uniquely accounting for assortative mating. We analyze 30,000 child-mother-father trios from the Estonian Biobank and the Norwegian Mother, Father, and Child Cohort, focusing on height, body mass index, and childhood educational test scores. We find direct effects to be the largest contributor to trait variation, but combined, indirect parental and PofO effects are similarly substantial. We support our results by within-family genome-wide association testing and identify 276 independently associated DNA regions with a complex interplay between direct, indirect, and PofO effects. By joint modeling, we show that direct, indirect, and PofO effects collectively shape human phenotypic variation across loci genome-wide."}],"article_type":"original","oa_version":"Published Version","type":"journal_article","project":[{"name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181"}],"DOAJ_listed":"1","citation":{"ieee":"I. Krätschmer <i>et al.</i>, “Separating direct, indirect, and parent-of-origin genetic effects in the human population,” <i>Cell Genomics</i>, vol. 6, no. 7. Cell Press, 2026.","short":"I. Krätschmer, L. Hegemann, R.J. Hofmeister, E.C. Corfield, M. Mahmoudi, O. Delaneau, O.A. Andreassen, A. Campbell, C. Hayward, R.E. Marioni, E. Ystrom, A. Havdahl, M.R. Robinson, Cell Genomics 6 (2026).","ista":"Krätschmer I, Hegemann L, Hofmeister RJ, Corfield EC, Mahmoudi M, Delaneau O, Andreassen OA, Campbell A, Hayward C, Marioni RE, Ystrom E, Havdahl A, Robinson MR. 2026. Separating direct, indirect, and parent-of-origin genetic effects in the human population. Cell Genomics. 6(7), 101277.","mla":"Krätschmer, Ilse, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell Genomics</i>, vol. 6, no. 7, 101277, Cell Press, 2026, doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">10.1016/j.xgen.2026.101277</a>.","ama":"Krätschmer I, Hegemann L, Hofmeister RJ, et al. Separating direct, indirect, and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>. 2026;6(7). doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">10.1016/j.xgen.2026.101277</a>","apa":"Krätschmer, I., Hegemann, L., Hofmeister, R. J., Corfield, E. C., Mahmoudi, M., Delaneau, O., … Robinson, M. R. (2026). Separating direct, indirect, and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">https://doi.org/10.1016/j.xgen.2026.101277</a>","chicago":"Krätschmer, Ilse, Laura Hegemann, Robin J. Hofmeister, Elizabeth C. Corfield, Mahdi Mahmoudi, Olivier Delaneau, Ole A. Andreassen, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell Genomics</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">https://doi.org/10.1016/j.xgen.2026.101277</a>."},"related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/human-traits-beyond-inherited-genes/"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","supplementarymaterial":"yes","date_updated":"2026-10-20T09:03:50Z","issue":"7","scopus_import":"1","publication":"Cell Genomics","acknowledgement":"We thank Zoltan Kutalik, Peter Visscher, and members of the Robinson group at ISTA for their comments, which improved this manuscript. This work was funded by an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria.\r\nThe Norwegian Mother, Father, and Child Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research. We are grateful to all the participating families in Norway who take part in this on-going cohort study. We thank the Norwegian Institute of Public Health (NIPH) for generating high-quality genomic data. The research is part of the HARVEST collaboration, supported by the Research Council of Norway (#229624). We also thank the NORMENT Center for providing genotype data, funded by the Research Council of Norway (#223273), South East Norway Health Authorities, and Stiftelsen Kristian Gerhard Jebsen, and in collaboration with deCODE Genetics. We further thank the Center for Diabetes Research, the University of Bergen for providing genotype data funded by the ERC AdG project SELECTionPREDISPOSED, Stiftelsen Kristian Gerhard Jebsen, Trond Mohn Foundation, the Research Council of Norway, the Novo Nordisk Foundation, the University of Bergen, and the Western Norway Health Authorities. The MoBa work was performed on the TSD (Tjeneste for Sensitive Data) facilities, owned by the University of Oslo, operated and developed by the TSD service group at the University of Oslo, IT Department (USIT, tsd-drift@usit.uio.no). E.Y. is supported by the European Union (grant numbers 101045526 and 101073237) and the Research Council of Norway (grant numbers 336078, 288083, and 331640).\r\nWe would like to acknowledge the participants and investigators of the Generation Scotland Cohort study. Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). Genotyping and methylation typing of the GS:SFHS samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” [STRADL] ref. 104036/Z/14/Z).\r\nWe would like to thank and acknowledge the participants and investigators of the Estonian Biobank (EstBB) study. The research was conducted using the Estonian Center of Genomics/Roadmap II funded by the Estonian Research Council (project number TT17).\r\nNorwegian analyses were performed on resources provided by Sigma2 - the National Infrastructure for High-Performance Computing and Data Storage in Norway. Estonian Data analysis was carried out in the High-Performance Computing Center cloud provided by University of Tartu. Analysis of the Generation Scotland data and the summary statistics obtained from the other analyses was conducted at IST Austria and is supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","publication_identifier":{"eissn":["2666-979X"]},"OA_place":"publisher","OA_type":"gold","language":[{"iso":"eng"}]},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"21488"}]},"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits","_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","grant_number":"101161364"},{"grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"citation":{"apa":"Depope, A. (2026). <i>From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22258\">https://doi.org/10.15479/AT-ISTA-22258</a>","chicago":"Depope, Al. “From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22258\">https://doi.org/10.15479/AT-ISTA-22258</a>.","short":"A. Depope, From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics, Institute of Science and Technology Austria, 2026.","ieee":"A. Depope, “From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics,” Institute of Science and Technology Austria, 2026.","ista":"Depope A. 2026. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. Institute of Science and Technology Austria.","ama":"Depope A. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22258\">10.15479/AT-ISTA-22258</a>","mla":"Depope, Al. <i>From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22258\">10.15479/AT-ISTA-22258</a>."},"page":"169","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-10-20T09:03:21Z","_id":"22258","title":"From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics","date_created":"2026-07-10T13:27:20Z","author":[{"full_name":"Depope, Al","first_name":"Al","last_name":"Depope","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830"}],"status":"public","oa_version":"Published Version","supervisor":[{"first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","last_name":"Mondelli"}],"type":"dissertation","abstract":[{"lang":"eng","text":"Uncovering the genetic architecture of complex traits and pinpointing causal molecular drivers require the ability to distinguish true signals from noise within massive, high-dimensional omics datasets. To extract meaningful biological insights from these datasets, such as identifying causal genetic variants and proteins, scalable and accurate inference methods are essential. To this end, this thesis develops novel Bayesian inference frameworks based on Vector Approximate Message Passing and demonstrates their effectiveness in the modeling of disease onset times and quantitative physical and clinical measures.\r\n\r\nFirst, we introduce gVAMP, a Bayesian framework tailored for Genome-Wide Association Studies that enables the joint modeling of quantitative complex traits across millions of genetic variants. gVAMP demonstrates superior accuracy in variable selection and out-of-sample polygenic risk prediction compared to state-of-the-art approaches. We model human height using 17 million whole-genome sequence variants from the UK Biobank, incorporating a vast number of rare variants and revealing novel associations. gVAMP achieves a prediction accuracy of approximately 46% for human height, representing the highest reported performance for this trait to date. \r\n\r\nSecond, we present vampW, a Bayesian framework for survival analysis applied to proteomic data. By effectively handling right-censoring and complex protein dependencies within the UK Biobank Pharma Proteomics Project dataset, vampW identifies 219 protein associations across 24 disease outcomes, the majority of which are not among the top marginal discoveries. We further adjust protein levels for exponential age effects, yielding 1,308 associations and highlighting the sensitivity of the analysis to the chosen age-correction methodology. Finally, vampW improves upon the variable selection capabilities of the commonly used (penalized) variants of the Cox proportional hazards model and delivers state-of-the-art out-of-sample prediction of disease onset times.\r\n\r\nCollectively, these methods provide powerful tools for dissecting the genetic architecture of complex traits and the proteomic drivers of disease onset. Furthermore, by delivering accurate polygenic risk scores and precise predictions of onset times, this work advances the capabilities of personalized medicine and clinical risk stratification."}],"OA_place":"publisher","language":[{"iso":"eng"}],"acknowledgement":"This work was supported in part by the Swiss National Science Foundation through the\r\nEccellenza Grant \"Improving estimation and prediction of common complex disease risk\"\r\n(grant number PCEGP3_181181); the European Research Council through the grant\r\n\"Inference in High Dimensions: Light-speed Algorithms and Information Limits\" (grant\r\nnumber 101161364); and the Fondation Jean-Jacques et Felicia Lopez-Loreta through the\r\nPrix Lopez-Loretta 2019.\r\n","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"date_published":"2026-07-11T00:00:00Z","file_date_updated":"2026-07-13T14:56:41Z","has_accepted_license":"1","keyword":["Approximate Message Passing","GWAS","Genomics","Proteomics","Survival modeling"],"article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-22258","degree_awarded":"PhD","das_tickbox":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["576","610","006"],"year":"2026","publication_status":"published","file":[{"file_id":"22316","file_size":25109878,"content_type":"application/pdf","date_updated":"2026-07-13T14:52:19Z","file_name":"2026_Depope_Al_Thesis.pdf","date_created":"2026-07-13T14:52:19Z","checksum":"9ab386790515628d957a194f30a7ccb4","creator":"adepope","relation":"main_file","access_level":"open_access"},{"access_level":"closed","relation":"source_file","creator":"adepope","date_created":"2026-07-13T14:56:41Z","checksum":"8ed8fb63f76a695d5b6fec35343f4b90","content_type":"application/zip","date_updated":"2026-07-13T14:56:41Z","file_name":"2026_Depope_Al_Thesis.zip","file_size":1203199939,"file_id":"22317"}],"doi":"10.15479/AT-ISTA-22258","day":"11","oa":1,"corr_author":"1","doi_confirm":"1","department":[{"_id":"GradSch"},{"_id":"MaRo"},{"_id":"MaMo"}],"month":"07","publisher":"Institute of Science and Technology Austria"},{"doi":"10.1016/j.xgen.2026.101162","researchdata_availability":"yes","file":[{"date_created":"2026-07-28T07:06:26Z","checksum":"6b59686f8d9733add4f23d23f3dd9df0","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"22596","file_size":3736705,"file_name":"2026_CellGenomics_Depope.pdf","content_type":"application/pdf","date_updated":"2026-07-28T07:06:26Z"}],"volume":6,"article_number":"101162","publisher":"Cell Press","month":"05","department":[{"_id":"MaMo"},{"_id":"MaRo"}],"external_id":{"pmid":["41713425"]},"corr_author":"1","oa":1,"dataavailabilitystatement":"This project uses the UK Biobank data under project number 35520. UK Biobank genotypic and phenotypic data are available through a formal request at http://www.ukbiobank.ac.uk. It also uses genotypic and phenotypic data from the All of Us study, which are also available through a formal request at https://www.researchallofus.org/data-tools/data-access/. All summary statistic estimates are released publicly on Dryad: https://doi.org/10.5061/dryad.cz8w9gjjc.\r\n•\r\nThe gVAMP code developed in this work is open source and has been deposited on GitHub, where it is publicly available at https://github.com/medical-genomics-group/gVAMP, and the code used to generate the data in the manuscript are available from Zenodo https://doi.org/10.5281/zenodo.17935521. The URLs of other software used are listed in the key resources table.","day":"13","das_tickbox":"1","fulldoi":"https://doi.org/10.1016/j.xgen.2026.101162","article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2026-07-28T07:06:26Z","date_published":"2026-05-13T00:00:00Z","intvolume":"         6","publication_status":"published","year":"2026","pmid":1,"quality_controlled":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"ddc":["000","570"],"language":[{"iso":"eng"}],"OA_place":"publisher","OA_type":"gold","publication_identifier":{"eissn":["2666-979X"]},"acknowledgement":"We thank Malgorzata Borczyk for creating the gene burden scores. We thank Robin Beaumont, Amedeo Roberto Esposito, Gareth Hawkes, Philip Schniter, Matthew Stephens, Pragya Sur, Peter Visscher, Michael Weedon, and Harry Wright for providing valuable suggestions and comments on earlier versions of the work. This project was funded by a Lopez-Loreta Prize to M.M., an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181), an ERC Starting Grant to M.M. (INF2, project number 101161364), and core funding from ISTA. High-performance computing was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We would like to acknowledge the participants and investigators of the UK Biobank study. We gratefully acknowledge the All of Us participants for their contributions, without whom this research would not have been possible. We also thank the National Institutes of Health All of Us Research Program for making available the participant data (and/or samples and/or cohort) examined in this study.","scopus_import":"1","issue":"5","publication":"Cell Genomics","supplementarymaterial":"yes","date_updated":"2026-10-20T09:03:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A. Depope, J. Bajzik, M. Mondelli, M.R. Robinson, Cell Genomics 6 (2026).","ieee":"A. Depope, J. Bajzik, M. Mondelli, and M. R. Robinson, “Joint modeling of whole-genome sequencing data for human height via approximate message passing,” <i>Cell Genomics</i>, vol. 6, no. 5. Cell Press, 2026.","ista":"Depope A, Bajzik J, Mondelli M, Robinson MR. 2026. Joint modeling of whole-genome sequencing data for human height via approximate message passing. Cell Genomics. 6(5), 101162.","mla":"Depope, Al, et al. “Joint Modeling of Whole-Genome Sequencing Data for Human Height via Approximate Message Passing.” <i>Cell Genomics</i>, vol. 6, no. 5, 101162, Cell Press, 2026, doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101162\">10.1016/j.xgen.2026.101162</a>.","ama":"Depope A, Bajzik J, Mondelli M, Robinson MR. Joint modeling of whole-genome sequencing data for human height via approximate message passing. <i>Cell Genomics</i>. 2026;6(5). doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101162\">10.1016/j.xgen.2026.101162</a>","apa":"Depope, A., Bajzik, J., Mondelli, M., &#38; Robinson, M. R. (2026). Joint modeling of whole-genome sequencing data for human height via approximate message passing. <i>Cell Genomics</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.xgen.2026.101162\">https://doi.org/10.1016/j.xgen.2026.101162</a>","chicago":"Depope, Al, Jakub Bajzik, Marco Mondelli, and Matthew Richard Robinson. “Joint Modeling of Whole-Genome Sequencing Data for Human Height via Approximate Message Passing.” <i>Cell Genomics</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.xgen.2026.101162\">https://doi.org/10.1016/j.xgen.2026.101162</a>."},"DOAJ_listed":"1","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits","_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","grant_number":"101161364"},{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk","grant_number":"PCEGP3_181181"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"22258","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/big-data-and-human-height/","description":"News on ISTA website","relation":"press_release"}]},"abstract":[{"text":"Human height is a model for the genetic analysis of complex traits, and recent studies suggest the presence of thousands of common genetic variant associations and hundreds of low-frequency/rare variants. Here, we develop a new algorithmic paradigm based on approximate message passing (genomic vector approximate message passing [gVAMP]) for identifying DNA sequence variants associated with complex traits and common diseases in large-scale whole-genome sequencing (WGS) data. We show that gVAMP accurately localizes associations to variants with the correct frequency and position in the DNA, outperforming existing fine-mapping methods in selecting the appropriate genetic variants within WGS data. We then apply gVAMP to jointly model the relationship of tens of millions of WGS variants with human height in hundreds of thousands of UK Biobank individuals. We identify 59 rare variants and gene burden scores alongside many hundreds of DNA regions containing common variant associations and show that understanding the genetic basis of complex traits will require the joint analysis of hundreds of millions of variables measured on millions of people. The polygenic risk scores obtained from gVAMP have high accuracy (including a prediction accuracy of ∼46% for human height) and outperform current methods for downstream tasks such as mixed linear model association testing across 13 UK Biobank traits. In conclusion, gVAMP offers a scalable foundation for a wider range of analyses in WGS data.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","article_type":"original","status":"public","date_created":"2026-03-23T15:10:03Z","author":[{"id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830","last_name":"Depope","first_name":"Al","full_name":"Depope, Al"},{"last_name":"Bajzik","first_name":"Jakub","id":"b995e25b-8c4b-11ed-a6d8-f71b7bcd6122","full_name":"Bajzik, Jakub"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"}],"title":"Joint modeling of whole-genome sequencing data for human height via approximate message passing","_id":"21488"},{"oa":1,"dataavailabilitystatement":"* All NGS data are available through GEO under accession number GSE331410.\r\n* This paper does not report original code.\r\n* Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","day":"20","publisher":"Cell Press","month":"07","department":[{"_id":"MaDe"}],"external_id":{"pmid":["42409014"]},"researchdata_availability":"upon request","doi":"10.1016/j.cub.2026.06.016","file":[{"success":1,"date_created":"2026-07-28T07:31:44Z","checksum":"5ec4472d81fd44de03ccb92b1eb690a6","access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"22598","file_name":"2026_CurrentBiology_KiangEwe.pdf","date_updated":"2026-07-28T07:31:44Z","content_type":"application/pdf","file_size":6795092}],"volume":36,"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"        36","publication_status":"published","year":"2026","pmid":1,"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","file_date_updated":"2026-07-28T07:31:44Z","date_published":"2026-07-20T00:00:00Z","das_tickbox":"1","fulldoi":"https://doi.org/10.1016/j.cub.2026.06.016","scopus_import":"1","issue":"14","publication":"Current Biology","acknowledgement":"We thank Itai Reiger for their assistance with experiments. We thank Cori Bargmann (Rockefeller University) for providing introgressed strains carrying HW alleles of npr-1 and glb-5. Some graphics were created with Biorender.com. We are grateful to WormBase for providing valuable data and resources. Some strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). O.R. is grateful for the support of the Morris Kahn Foundation. C.K.E. was supported by an EMBO fellowship ALTF 6-2022. This work is funded by Eric and Wendy Schmidt Fund for Strategic Innovation Polymath Award 0140001000 (O.R.); European Research Council grant 335624 (O.R.); Israel Science Foundation 979/21 (Y.B.T.); and the US-Israel Binational Science Foundation 2023036 (Y.B.T.).","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"OA_place":"publisher","OA_type":"hybrid","language":[{"iso":"eng"}],"author":[{"first_name":"Chee Kiang","last_name":"Ewe","full_name":"Ewe, Chee Kiang"},{"last_name":"Achache","first_name":"Hanna","full_name":"Achache, Hanna"},{"id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","last_name":"Schön","first_name":"Hanna","full_name":"Schön, Hanna"},{"full_name":"Kontorovich, Leonid","first_name":"Leonid","last_name":"Kontorovich"},{"first_name":"Guy","last_name":"Teichman","full_name":"Teichman, Guy"},{"full_name":"Weiss, Shir","first_name":"Shir","last_name":"Weiss"},{"first_name":"Anna","last_name":"Mogilevskaya","full_name":"Mogilevskaya, Anna"},{"full_name":"Valenski, Myriam","first_name":"Myriam","last_name":"Valenski"},{"last_name":"Anava","first_name":"Sarit","full_name":"Anava, Sarit"},{"first_name":"Rutwik","last_name":"Bardapurkar","full_name":"Bardapurkar, Rutwik"},{"first_name":"Hila","last_name":"Gingold","full_name":"Gingold, Hila"},{"first_name":"Rachel","last_name":"Posner","full_name":"Posner, Rachel"},{"last_name":"Antonova","first_name":"Olga","full_name":"Antonova, Olga"},{"last_name":"De Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443"},{"full_name":"Tzur, Yonatan B.","last_name":"Tzur","first_name":"Yonatan B."},{"last_name":"Rechavi","first_name":"Oded","full_name":"Rechavi, Oded"}],"status":"public","date_created":"2026-07-12T22:02:18Z","title":"Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress","_id":"22267","abstract":[{"text":"Thermal pollution, whether local or driven by global warming, threatens biodiversity in part through its detrimental effects on reproduction. Non-coding small RNAs (sRNAs) are crucial for maintaining germline developmental robustness under heat stress. Remarkably, we uncovered that neuronal sRNAs regulate germ cells’ thermotolerance, affecting both spermatogenic and oogenic germlines in a cell-non-autonomous manner. Furthermore, we demonstrate that, in RNAi mutants, an oxygen-sensing neural circuit, modulated by neuropeptide signaling, antagonizes germline maintenance, likely reflecting the nematode’s innate association of reduced oxygen levels with food availability and reproductive permissive environments. Finally, we provide evidence that laboratory-domesticated alleles of oxygen-response genes encoding neuropeptide receptor NPR-1 and hexacoordinated globin GLB-5 compromise germline thermotolerance. Hence, our findings raise the possibility that sensory perception, independent of direct environmental change, modulates germline integrity, highlighting a novel mechanism by which neural circuits integrate environmental information to safeguard reproductive fitness in fluctuating environments.","lang":"eng"}],"oa_version":"Published Version","type":"journal_article","article_type":"original","citation":{"ieee":"C. K. Ewe <i>et al.</i>, “Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress,” <i>Current Biology</i>, vol. 36, no. 14. Cell Press, p. 3566–3579.e5, 2026.","short":"C.K. Ewe, H. Achache, H. Schön, L. Kontorovich, G. Teichman, S. Weiss, A. Mogilevskaya, M. Valenski, S. Anava, R. Bardapurkar, H. Gingold, R. Posner, O. Antonova, M. de Bono, Y.B. Tzur, O. Rechavi, Current Biology 36 (2026) 3566–3579.e5.","ista":"Ewe CK, Achache H, Schön H, Kontorovich L, Teichman G, Weiss S, Mogilevskaya A, Valenski M, Anava S, Bardapurkar R, Gingold H, Posner R, Antonova O, de Bono M, Tzur YB, Rechavi O. 2026. Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. Current Biology. 36(14), 3566–3579.e5.","mla":"Ewe, Chee Kiang, et al. “Neuronal RNAi and Oxygen-Sensing Circuit Shape Germline Resilience to Heat Stress.” <i>Current Biology</i>, vol. 36, no. 14, Cell Press, 2026, p. 3566–3579.e5, doi:<a href=\"https://doi.org/10.1016/j.cub.2026.06.016\">10.1016/j.cub.2026.06.016</a>.","ama":"Ewe CK, Achache H, Schön H, et al. Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. <i>Current Biology</i>. 2026;36(14):3566-3579.e5. doi:<a href=\"https://doi.org/10.1016/j.cub.2026.06.016\">10.1016/j.cub.2026.06.016</a>","apa":"Ewe, C. K., Achache, H., Schön, H., Kontorovich, L., Teichman, G., Weiss, S., … Rechavi, O. (2026). Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2026.06.016\">https://doi.org/10.1016/j.cub.2026.06.016</a>","chicago":"Ewe, Chee Kiang, Hanna Achache, Hanna Schön, Leonid Kontorovich, Guy Teichman, Shir Weiss, Anna Mogilevskaya, et al. “Neuronal RNAi and Oxygen-Sensing Circuit Shape Germline Resilience to Heat Stress.” <i>Current Biology</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.cub.2026.06.016\">https://doi.org/10.1016/j.cub.2026.06.016</a>."},"page":"3566-3579.e5","supplementarymaterial":"yes","date_updated":"2026-10-20T09:03:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"OA_type":"hybrid","OA_place":"publisher","acknowledgement":"We thank IST Austria for providing the funding. We thank IST Austria EM facility for the use of Titan Krios TEM. Data processing was performed using IST high-performance computer cluster. We thank Dr. R. Roemhild and Professor C. Guet (ISTA) for help in constructing Tat deletion strains and Dr. A. Charnagalov (ISTA) for technical help.","publication_identifier":{"issn":["1097-2765"],"eissn":["1097-4164"]},"publication":"Molecular Cell","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","supplementarymaterial":"yes","date_updated":"2026-10-20T09:04:07Z","related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-gate-for-bulky-cargo/","description":"News on ISTA website","relation":"press_release"}],"record":[{"status":"public","id":"22189","relation":"research_data"}]},"citation":{"apa":"Zhao, Z., &#38; Sazanov, L. A. (n.d.). Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. <i>Molecular Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molcel.2026.05.026\">https://doi.org/10.1016/j.molcel.2026.05.026</a>","chicago":"Zhao, Ziyu, and Leonid A Sazanov. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo.” <i>Molecular Cell</i>. Cell Press, n.d. <a href=\"https://doi.org/10.1016/j.molcel.2026.05.026\">https://doi.org/10.1016/j.molcel.2026.05.026</a>.","ista":"Zhao Z, Sazanov LA. Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. Molecular Cell.","ieee":"Z. Zhao and L. A. Sazanov, “Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo,” <i>Molecular Cell</i>. Cell Press.","short":"Z. Zhao, L.A. Sazanov, Molecular Cell (n.d.).","ama":"Zhao Z, Sazanov LA. Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. <i>Molecular Cell</i>. doi:<a href=\"https://doi.org/10.1016/j.molcel.2026.05.026\">10.1016/j.molcel.2026.05.026</a>","mla":"Zhao, Ziyu, and Leonid A. Sazanov. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo.” <i>Molecular Cell</i>, Cell Press, doi:<a href=\"https://doi.org/10.1016/j.molcel.2026.05.026\">10.1016/j.molcel.2026.05.026</a>."},"article_type":"original","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"How the twin-arginine translocase (Tat) system transports fully folded substrate proteins across cellular membranes without disrupting membrane integrity has been a fundamental question in cell biology for decades. The Tat system, found in prokaryotes and plant organelles, recognizes a cargo signal peptide via a conserved twin-arginine motif. The multi-subunit Tat complex facilitates the proton-motive-force-dependent translocation process, yet its overall architecture has remained unknown. Here, we present the cryo-electron microscopy (cryo-EM) structure of the Escherichia coli (E. coli) trimeric TatB₃C₃ complex with bound substrate SufI, assembled in vivo. The complex adopts an unusual, wide-open, bowl-shaped architecture with a polar inner cavity. Unexpectedly, the cargo is engaged in a dual-contact mode: while the signal peptide binds inside one TatBC unit, the folded domain docks tightly onto an adjacent unit, possibly performing a proofreading function. This structure provides a mechanistic framework for substrate engagement and suggests the direct involvement of the entire Tat complex in substrate translocation.","lang":"eng"}],"_id":"22148","title":"Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo","date_created":"2026-06-28T22:01:35Z","status":"public","author":[{"full_name":"Zhao, Ziyu","first_name":"Ziyu","last_name":"Zhao","id":"a63fe682-9f3a-11ee-bf8c-cfdf919b9850"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov"}],"researchdata_availability":"yes","doi":"10.1016/j.molcel.2026.05.026","external_id":{"biorxivid":["10.1101/2025.09.16.676506"]},"month":"06","biorxivid":1,"department":[{"_id":"LeSa"}],"publisher":"Cell Press","day":"22","dataavailabilitystatement":"This study did not generate new unique reagents. Strains and plasmids generated in this study are available from the lead contact without restrictions.\r\n• Source data are provided within this paper. The cryo-EM map is deposited in the Electron Microscopy Data Bank under accession number EMD-53848. The model is deposited in the Protein Data Bank under accession number 9R91. The structural data are publicly available as of the date of publication. Raw images of spot assays, SDS-PAGE and BN-PAGE gels with Coomassie staining and immunoblot images are available at Mendeley Data (https://doi.org/10.17632/v2g3p9n985.1).\r\n• This paper does not report original code.\r\n• Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","corr_author":"1","oa":1,"fulldoi":"https://doi.org/10.1016/j.molcel.2026.05.026","das_tickbox":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"ScienComp"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2026.05.026","open_access":"1"}],"date_published":"2026-06-22T00:00:00Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","year":"2026","quality_controlled":"1","publication_status":"inpress","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"ddc":["570"]},{"title":"Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis","_id":"22667","author":[{"id":"cf391e77-ec3c-11ea-a124-d69323410b58","last_name":"Vijatovic","first_name":"David","full_name":"Vijatovic, David","orcid":"0000-0002-5494-0941"}],"date_created":"2026-08-10T13:44:30Z","status":"public","type":"dissertation","oa_version":"Published Version","supervisor":[{"id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger","full_name":"Sweeney, Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601"}],"related_material":{"record":[{"status":"public","id":"15016","relation":"part_of_dissertation"},{"id":"21746","relation":"part_of_dissertation","status":"public"}]},"page":"172","citation":{"ama":"Vijatovic D. Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22667\">10.15479/AT-ISTA-22667</a>","mla":"Vijatovic, David. <i>Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22667\">10.15479/AT-ISTA-22667</a>.","ieee":"D. Vijatovic, “Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis,” Institute of Science and Technology Austria, 2026.","short":"D. Vijatovic, Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis, Institute of Science and Technology Austria, 2026.","ista":"Vijatovic D. 2026. Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. Institute of Science and Technology Austria.","chicago":"Vijatovic, David. “Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22667\">https://doi.org/10.15479/AT-ISTA-22667</a>.","apa":"Vijatovic, D. (2026). <i>Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22667\">https://doi.org/10.15479/AT-ISTA-22667</a>"},"project":[{"_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","name":"Development and Evolution of Tetrapod Motor Circuits","grant_number":"101041551"},{"_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis","grant_number":"FTI21-D-046"},{"_id":"34a02c70-11ca-11ed-8bc3-fbfd2c86c88f","name":"Development of Viral Vectors for Amphibian Gene Delivery and Manipulation","grant_number":"3(GG016346-01)"}],"date_updated":"2026-10-20T09:04:22Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-082-4"]},"acknowledgement":"I am also grateful for the financial support that made this work possible, including the\r\nEuropean Research Council (ERC Starting Grant 101041551), the Austrian Science\r\nFund (FWF, Cluster of Excellence 10.55776/COE16), the GFF Lower Austria FTI\r\nStrategy Dissertation Fellowship (FTI21-D-046), and the FENS/IBRO-PERC\r\nExchange Fellowship. ","OA_place":"publisher","language":[{"iso":"eng"}],"ddc":["573"],"publication_status":"published","year":"2026","has_accepted_license":"1","date_published":"2026-08-10T00:00:00Z","alternative_title":["ISTA Thesis"],"file_date_updated":"2026-08-12T13:44:36Z","article_processing_charge":"No","degree_awarded":"PhD","fulldoi":"https://doi.org/10.15479/AT-ISTA-22667","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"day":"10","corr_author":"1","doi_confirm":"1","publisher":"Institute of Science and Technology Austria","month":"08","department":[{"_id":"GradSch"},{"_id":"LoSw"}],"doi":"10.15479/AT-ISTA-22667","file":[{"file_size":14322760,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-08-10T13:35:39Z","file_name":"2026_Vijatovic_David_Thesis.docx","file_id":"22669","creator":"dvijatov","relation":"source_file","access_level":"closed","date_created":"2026-08-10T13:35:39Z","checksum":"e3acfea4b1a3abf99e74224656740a15"},{"access_level":"closed","relation":"main_file","creator":"dvijatov","checksum":"dc8c78ae14f69e54faa41e65db5c6402","date_created":"2026-08-12T13:44:36Z","embargo":"2027-08-10","content_type":"application/pdf","date_updated":"2026-08-12T13:44:36Z","file_name":"2026_Vijatovic_David_Thesis.pdf","file_size":116926375,"embargo_to":"open_access","file_id":"22695"}]},{"article_type":"original","type":"journal_article","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Targeted antigen delivery to immune cells, particularly dendritic cells, has emerged as a promising strategy to enhance therapeutic efficacy of vaccines, while minimizing adverse effects associated with conventional immunization. In this study, we use our previously described small glycomimetic molecule that is selectively recognized by the Langerhans cell (LC)-specific surface receptor Langerin and demonstrate specific delivery of protein antigens to these specialized dendritic cells. Our results show that Langerin-mediated antigen delivery significantly enhances the immune response in vivo, resulting in increased expansion and activation of antigen-specific T cells, compared to immunization with unmodified antigen. We demonstrate the feasibility of our LC-targeted platform for immune cell-specific immunization with protein antigen and underscore the potential of LCs as an access point for next-generation vaccines and immunotherapies."}],"_id":"20858","title":"Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response","author":[{"full_name":"Rica, Ramona","first_name":"Ramona","last_name":"Rica"},{"last_name":"Klein","first_name":"Klara","full_name":"Klein, Klara"},{"full_name":"Johnson, Litty","last_name":"Johnson","first_name":"Litty"},{"first_name":"Gabriele","last_name":"Carta","full_name":"Carta, Gabriele"},{"last_name":"Sarcevic","first_name":"Mirza","full_name":"Sarcevic, Mirza"},{"first_name":"Freyja","last_name":"Langer","id":"3C1BE782-F248-11E8-B48F-1D18A9856A87","full_name":"Langer, Freyja"},{"first_name":"Christoph","last_name":"Rademacher","full_name":"Rademacher, Christoph"},{"first_name":"Robert","last_name":"Wawrzinek","full_name":"Wawrzinek, Robert"},{"last_name":"Quattrone","first_name":"Federica","full_name":"Quattrone, Federica"},{"first_name":"Florian","last_name":"Sparber","full_name":"Sparber, Florian"}],"date_created":"2025-12-28T23:01:26Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-20T09:03:08Z","supplementarymaterial":"yes","citation":{"chicago":"Rica, Ramona, Klara Klein, Litty Johnson, Gabriele Carta, Mirza Sarcevic, Freyja Langer, Christoph Rademacher, Robert Wawrzinek, Federica Quattrone, and Florian Sparber. “Langerhans Cell-Targeted Protein Delivery Enhances Antigen-Specific Cellular Immune Response.” <i>Molecular Therapy</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.ymthe.2025.10.008\">https://doi.org/10.1016/j.ymthe.2025.10.008</a>.","apa":"Rica, R., Klein, K., Johnson, L., Carta, G., Sarcevic, M., Langer, F., … Sparber, F. (2026). Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response. <i>Molecular Therapy</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.ymthe.2025.10.008\">https://doi.org/10.1016/j.ymthe.2025.10.008</a>","ama":"Rica R, Klein K, Johnson L, et al. Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response. <i>Molecular Therapy</i>. 2026;34(1):397-406. doi:<a href=\"https://doi.org/10.1016/j.ymthe.2025.10.008\">10.1016/j.ymthe.2025.10.008</a>","mla":"Rica, Ramona, et al. “Langerhans Cell-Targeted Protein Delivery Enhances Antigen-Specific Cellular Immune Response.” <i>Molecular Therapy</i>, vol. 34, no. 1, Cell Press, 2026, pp. 397–406, doi:<a href=\"https://doi.org/10.1016/j.ymthe.2025.10.008\">10.1016/j.ymthe.2025.10.008</a>.","ista":"Rica R, Klein K, Johnson L, Carta G, Sarcevic M, Langer F, Rademacher C, Wawrzinek R, Quattrone F, Sparber F. 2026. Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response. Molecular Therapy. 34(1), 397–406.","ieee":"R. Rica <i>et al.</i>, “Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response,” <i>Molecular Therapy</i>, vol. 34, no. 1. Cell Press, pp. 397–406, 2026.","short":"R. Rica, K. Klein, L. Johnson, G. Carta, M. Sarcevic, F. Langer, C. Rademacher, R. Wawrzinek, F. Quattrone, F. Sparber, Molecular Therapy 34 (2026) 397–406."},"page":"397-406","publication_identifier":{"issn":["1525-0016"],"eissn":["1525-0024"]},"acknowledgement":"This project was generously supported by Seedfinancing (grant no. P2282679) of the Austrian Bundesministerium für Digitalisierung und Wirtschaftsstandort and the Bundesministerium für Klimaschutz, Umwelt, Energie, Mobilität, Innovation, und Technologie, handled by the Austrian Wirtschaftsservice (aws), as well as by Life Science Call 2022 (grant no. FO999896442) of the Austrian Research Promotion Agency (FFG). We thank Mag. Michael Schunn from the PCF of the Institute of Science and Technology Austria for his continuous technical support.","publication":"Molecular Therapy","issue":"1","scopus_import":"1","language":[{"iso":"eng"}],"OA_place":"repository","OA_type":"green","quality_controlled":"1","year":"2026","publication_status":"published","intvolume":"        34","fulldoi":"https://doi.org/10.1016/j.ymthe.2025.10.008","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.05.05.652195"}],"date_published":"2026-01-07T00:00:00Z","article_processing_charge":"No","external_id":{"biorxivid":["10.1101/2025.05.05.652195"]},"biorxivid":1,"department":[{"_id":"PreCl"}],"month":"01","publisher":"Cell Press","dataavailabilitystatement":"The data that support the findings of this study are available on request from the corresponding authors.","day":"07","oa":1,"volume":34,"doi":"10.1016/j.ymthe.2025.10.008","researchdata_availability":"upon request"},{"OA_place":"publisher","OA_type":"gold","doi":"10.17632/V2G3P9N985.1","corr_author":"1","oa":1,"day":"15","publisher":"Mendeley Data","month":"05","department":[{"_id":"LeSa"}],"article_processing_charge":"No","citation":{"apa":"Sazanov, L. A. (2026). Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al. Mendeley Data. <a href=\"https://doi.org/10.17632/V2G3P9N985.1\">https://doi.org/10.17632/V2G3P9N985.1</a>","chicago":"Sazanov, Leonid A. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo. Zhao et Al.” Mendeley Data, 2026. <a href=\"https://doi.org/10.17632/V2G3P9N985.1\">https://doi.org/10.17632/V2G3P9N985.1</a>.","ista":"Sazanov LA. 2026. Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al., Mendeley Data, <a href=\"https://doi.org/10.17632/V2G3P9N985.1\">10.17632/V2G3P9N985.1</a>.","ieee":"L. A. Sazanov, “Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al.” Mendeley Data, 2026.","short":"L.A. Sazanov, (2026).","ama":"Sazanov LA. Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al. 2026. doi:<a href=\"https://doi.org/10.17632/V2G3P9N985.1\">10.17632/V2G3P9N985.1</a>","mla":"Sazanov, Leonid A. <i>Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo. Zhao et Al.</i> Mendeley Data, 2026, doi:<a href=\"https://doi.org/10.17632/V2G3P9N985.1\">10.17632/V2G3P9N985.1</a>."},"keyword":["Protein Purification"],"has_accepted_license":"1","date_published":"2026-05-15T00:00:00Z","related_material":{"record":[{"status":"public","id":"22148","relation":"used_in_publication"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.17632/v2g3p9n985.1"}],"date_updated":"2026-10-20T09:04:06Z","fulldoi":"https://doi.org/10.17632/V2G3P9N985.1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A"}],"date_created":"2026-06-29T12:54:45Z","title":"Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al.","_id":"22189","abstract":[{"lang":"eng","text":"Raw images for SDS and Blue Native gels, western blots and spot growth assays, related to figures S1 and S2."}],"oa_version":"Published Version","type":"research_data_reference","year":"2026"},{"month":"09","department":[{"_id":"AnSa"}],"publisher":"Cell Press","external_id":{"pmid":["42532043"]},"oa":1,"day":"03","dataavailabilitystatement":"The fly line generated in this study is available from the lead contact without restriction.\r\nData and code availability\r\n•\r\nCollagen IV fluorescent timer image data and associated data analysis code have been deposited in the UCL Research Data Repository at https://doi.org/10.5522/04/32647191 and are publicly available as of the date of publication.\r\n•\r\nAll original code associated with the tissue mechanics model has also been deposited in the UCL Research Data Repository at https://doi.org/10.5522/04/32647191 and is publicly available as of the date of publication.\r\n•\r\nAll original code associated with the collagen IV network model has been deposited on Zenodo at https://doi.org/10.5281/zenodo.20719515 and is publicly available as of the date of publication.\r\n•\r\nAny additional information reported in this paper is available from the lead contact upon request.","file":[{"file_size":5642382,"file_name":"2026_Cell_Barrientos.pdf","date_updated":"2026-09-24T12:35:11Z","content_type":"application/pdf","file_id":"22990","creator":"dernst","relation":"main_file","access_level":"open_access","date_created":"2026-09-24T12:35:11Z","checksum":"01e74f866223ca9ea8680b617d4aa4e3","success":1}],"researchdata_availability":"no","doi":"10.1016/j.cell.2026.07.010","volume":189,"intvolume":"       189","quality_controlled":"1","pmid":1,"year":"2026","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"fulldoi":"https://doi.org/10.1016/j.cell.2026.07.010","das_tickbox":"1","article_processing_charge":"Yes (in subscription journal)","date_published":"2026-09-03T00:00:00Z","file_date_updated":"2026-09-24T12:35:11Z","has_accepted_license":"1","ec_funded":1,"acknowledgement":"We thank all members of the Mao lab for insightful discussions throughout the project, and we thank Giulia Paci and Nargess Khalilgharibi for critical reading of the manuscript. We thank Jonathan Chubb for molecular biology guidance and WellGenetics for generating the timer protein fly lines.\r\nR.B. was funded by a UCL COMPLEX PhD studentship and a Leverhulme Trust project grant RPG-2020-068 awarded to Y.M. B.M. and A.S. were funded by the European Union Horizon 2020 research and innovation programme (ERC starting grant no. 802960). S.B. was funded by NIH R35 GM143042. G.C. was funded by EPSRC Physics of Life, grants EP/W023806 and EP/W023865. B.J.S.S. and B.M.S. are funded by the Wellcome Trust (grant no. 301803/Z/23/Z to B.M.S.). E.K.P. was funded by the Medical Research Council UK (MRC programme award MC_UU_12018/5). Y.M. was funded by MRC award MR/W027437/1, a Lister Institute Research Prize, and the EMBO Young Investigator Programme.","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"issue":"18","scopus_import":"1","publication":"Cell","language":[{"iso":"eng"}],"OA_place":"publisher","OA_type":"hybrid","abstract":[{"lang":"eng","text":"The regulation of 3D cell shape is a fundamental problem of life. In multicellular tissues, cell shape emerges through the balance of forces inside and outside the cell. In epithelia, the basement membrane (BM) is the first extracellular barrier that cells sense biochemically and mechanically. Despite this, little is known about how BM mechanical properties are regulated and how they impact cell shape. Through mathematical modeling, we show that the stress relaxation time of the BM can regulate cell shape. Using molecular dynamics simulations, we show that the stress relaxation time of a collagen IV network can be inferred from the lifetime of collagen IV molecules. To measure collagen IV lifetime in vivo, we develop a fluorescent timer reporter for collagen IV and show that perlecan modifies collagen IV lifetime. This cross-disciplinary approach establishes a multiscale framework to probe matrix turnover, and its regulation and function in cell shape control."}],"article_type":"original","type":"journal_article","oa_version":"Published Version","author":[{"full_name":"Barrientos, Ricardo","last_name":"Barrientos","first_name":"Ricardo"},{"full_name":"Meadowcroft, Billie","orcid":"0000-0003-3441-1337","last_name":"Meadowcroft","first_name":"Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1"},{"last_name":"Sánchez-Sánchez","first_name":"Besaiz J.","full_name":"Sánchez-Sánchez, Besaiz J."},{"full_name":"Stramer, Brian M.","last_name":"Stramer","first_name":"Brian M."},{"last_name":"Paluch","first_name":"Ewa K.","full_name":"Paluch, Ewa K."},{"full_name":"Charras, Guillaume","last_name":"Charras","first_name":"Guillaume"},{"full_name":"Banerjee, Shiladitya","last_name":"Banerjee","first_name":"Shiladitya"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"last_name":"Mao","first_name":"Yanlan","full_name":"Mao, Yanlan"}],"date_created":"2026-09-17T11:06:06Z","status":"public","_id":"22955","title":"Basement membrane turnover controls cell shape","PlanS_conform":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-20T09:04:52Z","supplementarymaterial":"yes","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","grant_number":"802960"}],"page":"5611-5624.e4","citation":{"chicago":"Barrientos, Ricardo, Billie Meadowcroft, Besaiz J. Sánchez-Sánchez, Brian M. Stramer, Ewa K. Paluch, Guillaume Charras, Shiladitya Banerjee, Anđela Šarić, and Yanlan Mao. “Basement Membrane Turnover Controls Cell Shape.” <i>Cell</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.cell.2026.07.010\">https://doi.org/10.1016/j.cell.2026.07.010</a>.","apa":"Barrientos, R., Meadowcroft, B., Sánchez-Sánchez, B. J., Stramer, B. M., Paluch, E. K., Charras, G., … Mao, Y. (2026). Basement membrane turnover controls cell shape. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2026.07.010\">https://doi.org/10.1016/j.cell.2026.07.010</a>","mla":"Barrientos, Ricardo, et al. “Basement Membrane Turnover Controls Cell Shape.” <i>Cell</i>, vol. 189, no. 18, Cell Press, 2026, p. 5611–5624.e4, doi:<a href=\"https://doi.org/10.1016/j.cell.2026.07.010\">10.1016/j.cell.2026.07.010</a>.","ama":"Barrientos R, Meadowcroft B, Sánchez-Sánchez BJ, et al. Basement membrane turnover controls cell shape. <i>Cell</i>. 2026;189(18):5611-5624.e4. doi:<a href=\"https://doi.org/10.1016/j.cell.2026.07.010\">10.1016/j.cell.2026.07.010</a>","ieee":"R. Barrientos <i>et al.</i>, “Basement membrane turnover controls cell shape,” <i>Cell</i>, vol. 189, no. 18. Cell Press, p. 5611–5624.e4, 2026.","short":"R. Barrientos, B. Meadowcroft, B.J. Sánchez-Sánchez, B.M. Stramer, E.K. Paluch, G. Charras, S. Banerjee, A. Šarić, Y. Mao, Cell 189 (2026) 5611–5624.e4.","ista":"Barrientos R, Meadowcroft B, Sánchez-Sánchez BJ, Stramer BM, Paluch EK, Charras G, Banerjee S, Šarić A, Mao Y. 2026. Basement membrane turnover controls cell shape. Cell. 189(18), 5611–5624.e4."}},{"department":[{"_id":"JaBr"}],"month":"06","publisher":"Cell Press","external_id":{"pmid":["42269584"]},"corr_author":"1","day":"10","doi":"10.1016/j.chom.2026.05.013","volume":34,"intvolume":"        34","year":"2026","pmid":1,"quality_controlled":"1","publication_status":"published","fulldoi":"https://doi.org/10.1016/j.chom.2026.05.013","das_tickbox":"1","article_processing_charge":"No","date_published":"2026-06-10T00:00:00Z","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) (10.55776/PAT1617625).","publication_identifier":{"eissn":["1934-6069"],"issn":["1931-3128"]},"issue":"6","scopus_import":"1","publication":"Cell Host & Microbe","language":[{"iso":"eng"}],"OA_type":"closed access","abstract":[{"lang":"eng","text":"In this issue of Cell Host & Microbe, Osterman et al. discover aRES,1 a new family of bacterial immune proteins that deplete cellular NAD+, generating cleavage products that cannot be utilized by canonical phage NAD+ regeneration pathways. They identify the invader-specific trigger for aRES and characterize two distinct evolutionary countermeasures employed by phages to resist aRES."}],"article_type":"original","type":"journal_article","oa_version":"None","status":"public","date_created":"2026-06-14T22:01:42Z","author":[{"id":"128eaab9-b327-11f0-bdbe-e02d5abac73b","last_name":"Williams-Jones","first_name":"Daniel","full_name":"Williams-Jones, Daniel"},{"id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo","first_name":"Jack Peter Kelly","orcid":"0000-0003-0456-0753","full_name":"Bravo, Jack Peter Kelly"}],"_id":"21996","title":"NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-20T09:04:35Z","project":[{"grant_number":"PAT1617625","name":"Search & Destroy: Mechanisms of anti-plasmid immunity","_id":"9f295cab-ad08-11f1-bc83-9e197d0f6d50"}],"citation":{"apa":"Williams-Jones, D., &#38; Bravo, J. P. K. (2026). NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. <i>Cell Host &#38; Microbe</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.chom.2026.05.013\">https://doi.org/10.1016/j.chom.2026.05.013</a>","chicago":"Williams-Jones, Daniel, and Jack Peter Kelly Bravo. “NAD to the Bone: How Bacteria Put Phages under ARES-t … and How Phages Fight Back.” <i>Cell Host &#38; Microbe</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.chom.2026.05.013\">https://doi.org/10.1016/j.chom.2026.05.013</a>.","ieee":"D. Williams-Jones and J. P. K. Bravo, “NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back,” <i>Cell Host &#38; Microbe</i>, vol. 34, no. 6. Cell Press, pp. 978–980, 2026.","ista":"Williams-Jones D, Bravo JPK. 2026. NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. Cell Host &#38; Microbe. 34(6), 978–980.","short":"D. Williams-Jones, J.P.K. Bravo, Cell Host &#38; Microbe 34 (2026) 978–980.","ama":"Williams-Jones D, Bravo JPK. NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. <i>Cell Host &#38; Microbe</i>. 2026;34(6):978-980. doi:<a href=\"https://doi.org/10.1016/j.chom.2026.05.013\">10.1016/j.chom.2026.05.013</a>","mla":"Williams-Jones, Daniel, and Jack Peter Kelly Bravo. “NAD to the Bone: How Bacteria Put Phages under ARES-t … and How Phages Fight Back.” <i>Cell Host &#38; Microbe</i>, vol. 34, no. 6, Cell Press, 2026, pp. 978–80, doi:<a href=\"https://doi.org/10.1016/j.chom.2026.05.013\">10.1016/j.chom.2026.05.013</a>."},"page":"978-980"},{"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"ddc":["000"],"publication_status":"published","year":"2026","quality_controlled":"1","intvolume":"         2","has_accepted_license":"1","conference":{"name":"ICAART: International Conference on Agents and Artificial Intelligence","start_date":"2026-03-05","end_date":"2026-03-08","location":"Marbella, Spain"},"file_date_updated":"2026-10-20T14:00:27Z","date_published":"2026-04-01T00:00:00Z","article_processing_charge":"No","keyword":["Machine Unlearning","Neuroscience-Inspired Machine Learning","Membership Inference Attacks"],"das_tickbox":"0","fulldoi":"https://doi.org/10.5220/0014326500004052","arxiv":1,"day":"01","oa":1,"external_id":{"arxiv":["2410.22374"]},"publisher":"Science and Technology Publications","department":[{"_id":"ToHe"}],"month":"04","volume":2,"researchdata_availability":"no","doi":"10.5220/0014326500004052","file":[{"access_level":"open_access","creator":"dernst","relation":"main_file","success":1,"checksum":"d0f5212846c8f3129509b081648465cb","date_created":"2026-10-20T14:00:27Z","date_updated":"2026-10-20T14:00:27Z","content_type":"application/pdf","file_name":"2026_CAART_Hatua.pdf","file_size":779692,"file_id":"23178"}],"title":"Machine unlearning using forgetting neural networks","_id":"22104","author":[{"full_name":"Hatua, Amartya","last_name":"Hatua","first_name":"Amartya"},{"last_name":"Nguyen","first_name":"Trung T.","full_name":"Nguyen, Trung T."},{"full_name":"Cano Cordoba, Filip","orcid":"0000-0002-0783-904X","id":"708cad98-e86a-11ef-8098-bdae2d7c6af1","last_name":"Cano Cordoba","first_name":"Filip"},{"full_name":"Sung, Andrew H.","first_name":"Andrew H.","last_name":"Sung"}],"status":"public","date_created":"2026-06-21T22:03:01Z","oa_version":"Published Version","type":"conference","abstract":[{"text":" Modern computer systems store vast amounts of personal data, enabling advances in AI and ML but risking user privacy and trust. For privacy reasons, it is sometimes desired for an ML model to forget part of the data it was trained on. In this paper, we introduce a novel unlearning approach based on Forgetting Neural Networks (FNNs), a neuroscience-inspired architecture that explicitly encodes forgetting through multiplicative decay factors. While FNNs had previously been studied as a theoretical construct, we provide the first concrete implementation and demonstrate their effectiveness for targeted unlearning. We propose several variants with per-neuron forgetting factors, including rank-based assignments guided by activation levels, and evaluate them on MNIST and Fashion-MNIST benchmarks. Our method systematically removes information associated with forget sets while preserving performance on retained data. Membership inference attacks confirm the effectiveness of FNN-based unlearning in erasing information about the training data from the neural network. These results establish FNNs as a promising foundation for efficient and interpretable unlearning.","lang":"eng"}],"citation":{"chicago":"Hatua, Amartya, Trung T. Nguyen, Filip Cano Cordoba, and Andrew H. Sung. “Machine Unlearning Using Forgetting Neural Networks.” In <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, 2:1536–46. Science and Technology Publications, 2026. <a href=\"https://doi.org/10.5220/0014326500004052\">https://doi.org/10.5220/0014326500004052</a>.","apa":"Hatua, A., Nguyen, T. T., Cano Cordoba, F., &#38; Sung, A. H. (2026). Machine unlearning using forgetting neural networks. In <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i> (Vol. 2, pp. 1536–1546). Marbella, Spain: Science and Technology Publications. <a href=\"https://doi.org/10.5220/0014326500004052\">https://doi.org/10.5220/0014326500004052</a>","ama":"Hatua A, Nguyen TT, Cano Cordoba F, Sung AH. Machine unlearning using forgetting neural networks. In: <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>. Vol 2. Science and Technology Publications; 2026:1536-1546. doi:<a href=\"https://doi.org/10.5220/0014326500004052\">10.5220/0014326500004052</a>","mla":"Hatua, Amartya, et al. “Machine Unlearning Using Forgetting Neural Networks.” <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, vol. 2, Science and Technology Publications, 2026, pp. 1536–46, doi:<a href=\"https://doi.org/10.5220/0014326500004052\">10.5220/0014326500004052</a>.","ista":"Hatua A, Nguyen TT, Cano Cordoba F, Sung AH. 2026. Machine unlearning using forgetting neural networks. Proceedings of the 18th International Conference on Agents and Artificial Intelligence. ICAART: International Conference on Agents and Artificial Intelligence vol. 2, 1536–1546.","ieee":"A. Hatua, T. T. Nguyen, F. Cano Cordoba, and A. H. Sung, “Machine unlearning using forgetting neural networks,” in <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, Marbella, Spain, 2026, vol. 2, pp. 1536–1546.","short":"A. Hatua, T.T. Nguyen, F. Cano Cordoba, A.H. Sung, in:, Proceedings of the 18th International Conference on Agents and Artificial Intelligence, Science and Technology Publications, 2026, pp. 1536–1546."},"page":"1536-1546","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093"}],"supplementarymaterial":"no","date_updated":"2026-10-20T14:05:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the 18th International Conference on Agents and Artificial Intelligence","scopus_import":"1","acknowledgement":"This work has been supported by the European Research\r\nCouncil under Grant No.: ERC-2020-AdG\r\n101020093. We thank Brian Subirana for the original\r\nideation of the concept of forgetting neural networks\r\nand his belief in their potential.","publication_identifier":{"eissn":["2184-433X"],"isbn":["9789897587962"],"issn":["2184-3589"]},"ec_funded":1,"OA_type":"green","OA_place":"repository","language":[{"iso":"eng"}]},{"author":[{"full_name":"Visconti, Francois L","id":"8d897387-8b69-11f1-b3df-9a1e4632e81d","first_name":"Francois L","last_name":"Visconti"}],"date_created":"2026-09-22T05:35:39Z","status":"public","title":"Average-field approximation for dilute almost-bosonic anyons","_id":"22970","extern":"1","abstract":[{"lang":"eng","text":"We study the ground state of a system of N two-dimensional trapped almost-bosonic anyons. This setup can equivalently be viewed as bosons interacting through long-range magnetic potentials generated by magnetic charges carried by each particle. These magnetic charges are assumed to be smeared over discs of radius R—a model known as extended anyons. To recover the point-like anyons perspective, we consider the joint limit R -> 0 as N →∞. We rigorously justify the average-field approximation for any radius R that decays polynomially, and even for certain exponentially decaying R. The average-field approximation asserts that the particles behave like independent, identical bosons interacting through a self-consistent magnetic field. Our result significantly improves upon the best-known estimates from [1, 2], and it in particular covers radii that are much smaller than the mean interparticle distance. The proof strategy builds on a recent work on two-dimensional attractive Bose gases by Junge and the author [3]."}],"oa_version":"Published Version","type":"journal_article","article_type":"original","citation":{"short":"F.L. Visconti, Calculus of Variations and Partial Differential Equations 65 (2026).","ista":"Visconti FL. 2026. Average-field approximation for dilute almost-bosonic anyons. Calculus of Variations and Partial Differential Equations. 65(9), 260.","ieee":"F. L. Visconti, “Average-field approximation for dilute almost-bosonic anyons,” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 65, no. 9. Springer, 2026.","mla":"Visconti, Francois L. “Average-Field Approximation for Dilute Almost-Bosonic Anyons.” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 65, no. 9, 260, Springer, 2026, doi:<a href=\"https://doi.org/10.1007/s00526-026-03428-9\">10.1007/s00526-026-03428-9</a>.","ama":"Visconti FL. Average-field approximation for dilute almost-bosonic anyons. <i>Calculus of Variations and Partial Differential Equations</i>. 2026;65(9). doi:<a href=\"https://doi.org/10.1007/s00526-026-03428-9\">10.1007/s00526-026-03428-9</a>","apa":"Visconti, F. L. (2026). Average-field approximation for dilute almost-bosonic anyons. <i>Calculus of Variations and Partial Differential Equations</i>. Springer. <a href=\"https://doi.org/10.1007/s00526-026-03428-9\">https://doi.org/10.1007/s00526-026-03428-9</a>","chicago":"Visconti, Francois L. “Average-Field Approximation for Dilute Almost-Bosonic Anyons.” <i>Calculus of Variations and Partial Differential Equations</i>. Springer, 2026. <a href=\"https://doi.org/10.1007/s00526-026-03428-9\">https://doi.org/10.1007/s00526-026-03428-9</a>."},"DOAJ_listed":"1","PlanS_conform":"1","date_updated":"2026-10-20T14:10:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","issue":"9","publication":"Calculus of Variations and Partial Differential Equations","acknowledgement":"The author would like to express his sincere gratitude to Nicolas Rougerie for introducing him to the problem, for his hospitality, and for the precious discussions. The author would also like to thank Douglas Lundholm and the anonymous referee for their precious feedback. Partial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the TRR 352 Project ID 470903074 and by the European Research Council through the ERC CoG RAMBAS Project Nr. 101044249 is acknowledged. Open access funding provided by Institute of Science and Technology (IST Austria).","publication_identifier":{"issn":["0944-2669"],"eissn":["1432-0835"]},"OA_place":"publisher","OA_type":"hybrid","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["500"],"intvolume":"        65","publication_status":"published","pmid":1,"year":"2026","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","date_published":"2026-09-12T00:00:00Z","file_date_updated":"2026-10-20T14:08:18Z","das_tickbox":"1","fulldoi":"https://doi.org/10.1007/s00526-026-03428-9","oa":1,"dataavailabilitystatement":"Data sharing not applicable to this article as no datasets were generated or analysed during the current study.","day":"12","publisher":"Springer","month":"09","external_id":{"pmid":["42733399"]},"article_number":"260","doi":"10.1007/s00526-026-03428-9","file":[{"creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"4599427a622cd93a96e3ca0465e0ccf5","date_created":"2026-10-20T14:08:18Z","success":1,"file_size":587149,"file_name":"2026_CalculusVariations_Visconti.pdf","date_updated":"2026-10-20T14:08:18Z","content_type":"application/pdf","file_id":"23179"}],"volume":65},{"year":"2026","publication_status":"submitted","fulldoi":"https://doi.org/10.48550/arXiv.2607.05848","das_tickbox":"1","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2607.05848"}],"date_published":"2026-07-07T00:00:00Z","keyword":["Central limit theorem","universality","matrix Dyson equation","multi-resolvent local law"],"article_processing_charge":"No","external_id":{"arxiv":["2607.05848"]},"department":[{"_id":"LaEr"}],"month":"07","day":"07","corr_author":"1","oa":1,"doi":"10.48550/arXiv.2607.05848","article_number":"2607.05848","type":"preprint","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We prove a mesoscopic central limit theorem for linear eigenvalue statistics of correlated Hermitian random matrices. The class considered here includes Wigner and Wigner-type matrices, as well as models whose entry correlations decay polynomially in the distance between index pairs. The proof combines a multivariate cumulant expansion with multi-resolvent local laws and a detailed analysis of the resulting variance kernel on the operator-level."}],"_id":"22359","title":"Mesoscopic eigenvalue statistics for correlated random matrices","author":[{"full_name":"Lee, Jaehun","first_name":"Jaehun","last_name":"Lee","id":"96155047-f36a-11ef-b766-8b5ae7cecd49"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"}],"date_created":"2026-07-18T08:59:02Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-20T10:06:12Z","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331"}],"citation":{"ista":"Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. arXiv, 2607.05848.","ieee":"J. Lee and L. Erdös, “Mesoscopic eigenvalue statistics for correlated random matrices,” <i>arXiv</i>. .","short":"J. Lee, L. Erdös, ArXiv (n.d.).","mla":"Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices.” <i>ArXiv</i>, 2607.05848, doi:<a href=\"https://doi.org/10.48550/arXiv.2607.05848\">10.48550/arXiv.2607.05848</a>.","ama":"Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2607.05848\">10.48550/arXiv.2607.05848</a>","apa":"Lee, J., &#38; Erdös, L. (n.d.). Mesoscopic eigenvalue statistics for correlated random matrices. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2607.05848\">https://doi.org/10.48550/arXiv.2607.05848</a>","chicago":"Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2607.05848\">https://doi.org/10.48550/arXiv.2607.05848</a>."},"acknowledgement":"Supported by ERC Advanced Grant “RMTBeyond” No. 101020331","ec_funded":1,"publication":"arXiv","language":[{"iso":"eng"}],"OA_place":"repository","OA_type":"green"},{"abstract":[{"lang":"eng","text":"Context. X-ray binaries exhibit complex variability patterns studied in the power spectrum. These include the broadband noise (BBN)\r\ncomponents and various types of narrow components called quasi-periodic oscillations (QPOs). There is currently no consensus about\r\nwhat determines the presence or absence of the BBN or what generates the QPOs. Many believe that QPO generation is due to framedragging effects caused by Lense–Thirring torques.\r\nAims. We investigated the potential impact of frame-dragging effects on the accretion disk itself. In particular, we focused on its\r\nimpact on the observed variability and on the presence (and types) of associated QPOs.\r\nMethods. We made analytical estimates to assess the potential presence of a geometric warp in the inner accretion disk during state\r\ntransitions.\r\nResults. We show that the presence of a warp can modify the spectral-timing properties in a way that matches the observed transition\r\nbetween QPO types during outbursts. We also discuss the peculiar case of Cyg X-1, as well as how the hard-to-soft transition could\r\nbe driven by the warp itself.\r\nConclusions. The (expected) emergence of a warp provides a consistent explanation for the evolution of both the BBN and the QPO\r\nproperties during state transitions. This offers a first path toward unifying the variability of black hole X-ray binaries."}],"article_type":"original","type":"journal_article","oa_version":"Published Version","date_created":"2026-07-21T10:29:36Z","author":[{"full_name":"Marcel, G.","last_name":"Marcel","first_name":"G."},{"first_name":"S. G. D.","last_name":"Turner","full_name":"Turner, S. G. D."},{"first_name":"B. J.","last_name":"Ricketts","full_name":"Ricketts, B. J."},{"full_name":"López-Barquero, V.","first_name":"V.","last_name":"López-Barquero"},{"full_name":"Buisson, D. J. K.","first_name":"D. J. K.","last_name":"Buisson"},{"full_name":"Vincentelli, F.","last_name":"Vincentelli","first_name":"F."},{"full_name":"Middleton, M.","first_name":"M.","last_name":"Middleton"},{"first_name":"C.S.","last_name":"Reynolds","full_name":"Reynolds, C.S."},{"first_name":"Mark","last_name":"Avara","id":"c9b42585-7787-11f0-9bdd-bf7d947cf79d","full_name":"Avara, Mark"}],"status":"public","_id":"22381","title":"Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations","PlanS_conform":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-21T06:33:09Z","supplementarymaterial":"yes","citation":{"apa":"Marcel, G., Turner, S. G. D., Ricketts, B. J., López-Barquero, V., Buisson, D. J. K., Vincentelli, F., … Avara, M. (2026). Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202558103\">https://doi.org/10.1051/0004-6361/202558103</a>","chicago":"Marcel, G., S. G. D. Turner, B. J. Ricketts, V. López-Barquero, D. J. K. Buisson, F. Vincentelli, M. Middleton, C.S. Reynolds, and Mark Avara. “Disk Warping and Black Hole X-Ray Binaries: I. Tentative Unification of Low-Frequency Quasi-Periodic Oscillations.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2026. <a href=\"https://doi.org/10.1051/0004-6361/202558103\">https://doi.org/10.1051/0004-6361/202558103</a>.","ista":"Marcel G, Turner SGD, Ricketts BJ, López-Barquero V, Buisson DJK, Vincentelli F, Middleton M, Reynolds CS, Avara M. 2026. Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations. Astronomy &#38; Astrophysics. 710, A387.","short":"G. Marcel, S.G.D. Turner, B.J. Ricketts, V. López-Barquero, D.J.K. Buisson, F. Vincentelli, M. Middleton, C.S. Reynolds, M. Avara, Astronomy &#38; Astrophysics 710 (2026).","ieee":"G. Marcel <i>et al.</i>, “Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations,” <i>Astronomy &#38; Astrophysics</i>, vol. 710. EDP Sciences, 2026.","ama":"Marcel G, Turner SGD, Ricketts BJ, et al. Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations. <i>Astronomy &#38; Astrophysics</i>. 2026;710. doi:<a href=\"https://doi.org/10.1051/0004-6361/202558103\">10.1051/0004-6361/202558103</a>","mla":"Marcel, G., et al. “Disk Warping and Black Hole X-Ray Binaries: I. Tentative Unification of Low-Frequency Quasi-Periodic Oscillations.” <i>Astronomy &#38; Astrophysics</i>, vol. 710, A387, EDP Sciences, 2026, doi:<a href=\"https://doi.org/10.1051/0004-6361/202558103\">10.1051/0004-6361/202558103</a>."},"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"acknowledgement":"GM acknowledges support from the Polish National Science Center grant 2023/48/Q/ST9/00138 and the Academy of Finland grant 355672. The authors thank the Editor for their insightful comments and effective stewardship of the review process. SGDT acknowledges support under\r\nSTFC Grant ST/X001113/1. This work made use of the python packages\r\nMatplotlib (Hunter 2007), NumPy (Harris et al. 2020), and Stingray v2.2\r\n(Huppenkothen et al. 2019; Bachetti et al. 2024b,a).","scopus_import":"1","publication":"Astronomy & Astrophysics","language":[{"iso":"eng"}],"OA_place":"publisher","OA_type":"diamond","intvolume":"       710","year":"2026","quality_controlled":"1","publication_status":"published","ddc":["520"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"arxiv":1,"fulldoi":"https://doi.org/10.1051/0004-6361/202558103","das_tickbox":"0","article_processing_charge":"No","file_date_updated":"2026-07-21T12:20:49Z","date_published":"2026-06-01T00:00:00Z","has_accepted_license":"1","month":"06","department":[{"_id":"ZoHa"}],"publisher":"EDP Sciences","external_id":{"arxiv":["2511.10474"]},"oa":1,"day":"01","file":[{"checksum":"95c1695f3c7183b2ad9d58167500b18d","date_created":"2026-07-21T12:20:49Z","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"22382","file_size":3286905,"file_name":"2026_AstronomyAstrophysics_Marcel.pdf","date_updated":"2026-07-21T12:20:49Z","content_type":"application/pdf"}],"researchdata_availability":"no","doi":"10.1051/0004-6361/202558103","volume":710,"article_number":"A387"},{"language":[{"iso":"eng"}],"OA_place":"publisher","publication_identifier":{"issn":["2791-4585"]},"date_updated":"2026-10-21T07:47:08Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"32","citation":{"ama":"Spasić A. Studying the evolutionary systems biology of the lac operon. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22399\">10.15479/AT-ISTA-22399</a>","mla":"Spasić, Aleksa. <i>Studying the Evolutionary Systems Biology of the Lac Operon</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22399\">10.15479/AT-ISTA-22399</a>.","ista":"Spasić A. 2026. Studying the evolutionary systems biology of the lac operon. Institute of Science and Technology Austria.","ieee":"A. Spasić, “Studying the evolutionary systems biology of the lac operon,” Institute of Science and Technology Austria, 2026.","short":"A. Spasić, Studying the Evolutionary Systems Biology of the Lac Operon, Institute of Science and Technology Austria, 2026.","chicago":"Spasić, Aleksa. “Studying the Evolutionary Systems Biology of the Lac Operon.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22399\">https://doi.org/10.15479/AT-ISTA-22399</a>.","apa":"Spasić, A. (2026). <i>Studying the evolutionary systems biology of the lac operon</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22399\">https://doi.org/10.15479/AT-ISTA-22399</a>"},"supervisor":[{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","oa_version":"Published Version","author":[{"id":"ecee9d38-4040-11ef-8843-b941efb445d6","last_name":"Spasić","first_name":"Aleksa","full_name":"Spasić, Aleksa"}],"status":"public","date_created":"2026-07-25T13:08:32Z","title":"Studying the evolutionary systems biology of the lac operon","_id":"22399","doi":"10.15479/AT-ISTA-22399","file":[{"checksum":"c29880dd71fcc37f23ac6e2843066ede","date_created":"2026-07-27T13:00:07Z","creator":"aspasic","relation":"main_file","access_level":"closed","file_id":"22588","embargo_to":"open_access","file_size":1986078,"file_name":"Aleksa_Spasic_Thesis_final.pdf","embargo":"2027-07-30","date_updated":"2026-10-20T08:47:40Z","content_type":"application/pdf"},{"access_level":"closed","creator":"aspasic","relation":"source_file","date_created":"2026-07-27T13:00:22Z","checksum":"4ebe3bd2d833d913c0756343cca5e5f0","file_name":"Thesis_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-07-27T13:07:23Z","file_size":1868853,"file_id":"22589"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"GaTk"},{"_id":"CaGu"}],"month":"07","doi_confirm":"1","corr_author":"1","day":"27","degree_awarded":"MS","das_tickbox":"0","fulldoi":"https://doi.org/10.15479/AT-ISTA-22399","article_processing_charge":"No","has_accepted_license":"1","alternative_title":["ISTA Master’s Thesis"],"date_published":"2026-07-27T00:00:00Z","file_date_updated":"2026-10-20T08:47:40Z","publication_status":"published","year":"2026","ddc":["576"]},{"doi":"10.15479/AT-ISTA-22281","file":[{"creator":"aelhayek","relation":"main_file","access_level":"open_access","date_created":"2026-07-17T11:39:47Z","checksum":"923e4ca769c9ef2f6b0b005444faf462","success":1,"file_size":5465973,"content_type":"application/pdf","date_updated":"2026-07-17T11:39:47Z","file_name":"2026_El-Hayek_Antoine_Thesis.pdf","file_id":"22356"},{"file_size":9116107,"file_name":"2026_El-Hayek_Antoine_Thesis.zip","content_type":"application/x-zip-compressed","date_updated":"2026-07-20T11:29:38Z","file_id":"22357","creator":"aelhayek","relation":"source_file","access_level":"closed","checksum":"262689f9df27dd6c2c7c7861f1de7329","date_created":"2026-07-17T11:40:34Z"}],"doi_confirm":"1","publisher":"Institute of Science and Technology Austria","month":"07","department":[{"_id":"GradSch"},{"_id":"MoHe"}],"day":"13","corr_author":"1","oa":1,"degree_awarded":"PhD","fulldoi":"https://doi.org/10.15479/AT-ISTA-22281","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"date_published":"2026-07-13T00:00:00Z","file_date_updated":"2026-07-20T11:29:38Z","article_processing_charge":"No","publication_status":"published","year":"2026","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["000"],"language":[{"iso":"eng"}],"OA_place":"publisher","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct, No. 101019564)\r\n\"The Design and Evaluation of Modern Fully Dynamic Data Structures\" , from the\r\nAustrian Science Fund (FWF) grant DOI 10.55776/I5982 \"Static and Dynamic Hierarchical\r\nGraph Decompositions\", and from the Austrian Science Fund (FWF) and netIDEE SCIENCE\r\nproject P 33775-N, \"Fast Algorithms for a Reactive Network Layer\".\r\n","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"publisher_comment":"Sections 2.4 and 7.1 and chapter 6 are not CC-BY 4.0, they are All Rights Reserved.","date_updated":"2026-10-21T08:05:35Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"20051"},{"status":"public","id":"19982","relation":"part_of_dissertation"},{"id":"21720","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"22374"},{"relation":"part_of_dissertation","id":"22373","status":"public"},{"id":"18557","relation":"part_of_dissertation","status":"public"}]},"citation":{"chicago":"El-Hayek, Antoine. “Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22281\">https://doi.org/10.15479/AT-ISTA-22281</a>.","apa":"El-Hayek, A. (2026). <i>Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22281\">https://doi.org/10.15479/AT-ISTA-22281</a>","mla":"El-Hayek, Antoine. <i>Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22281\">10.15479/AT-ISTA-22281</a>.","ama":"El-Hayek A. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22281\">10.15479/AT-ISTA-22281</a>","ista":"El-Hayek A. 2026. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. Institute of Science and Technology Austria.","short":"A. El-Hayek, Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks, Institute of Science and Technology Austria, 2026.","ieee":"A. El-Hayek, “Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks,” Institute of Science and Technology Austria, 2026."},"page":"244","project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775"}],"oa_version":"Published Version","type":"dissertation","supervisor":[{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"abstract":[{"lang":"eng","text":"In this thesis, we took a look at networks, and more specifically, at networks that change over time, whether those are networks in the distributed algorithms sense of the word, or the graph algorithm sense. \r\n\r\nIn distributed algorithms, we looked at two main problems. First, the broadcast problem: given n agents, each agent is tasked to forward a (unique) message to every other agent. Agents collaborate and can copy and forward all messages they have received up until that point. Broadcast is achieved when one agent has successfully broadcast its message to everyone else. We studied the case where the communication network is controlled by an adversary, under the condition that the graph is rooted in every round of communication. We show that the adversary can delay broadcast for at most  l\r\n(1 + √\r\n2)n\r\nm\r\n rounds, improving on the $O(n\\log\\log n)$ previous upper bound~\\cite{fugger2020radius}, and asymptotically matching the $\\sim 1.5n$ lower bound~\\cite{schwarz2017linear}.\r\n\r\nWe then looked at the stochastic version of the problem: here, the adversary -- parametrized by $k$ where $k=0$ signifies that the adversary has no control,  and $k=n$ that the adversary has full control -- can choose parts of the graph, and the graph is then completed stochastically. Here, we are able to look at a stronger version of broadcast: instead of having $n$ messages trying to be broadcast in parallel, we can assume that only one message needs to be broadcasted. We show the bound $\\Theta(k+\\log n)$.\r\n\r\nThen, we looked at undecided states dynamics in population protocols: given a population of $n$ agents, where each initially holds an opinion among $k$ different ones. In each round, two agents are chosen uniformly at random, and can interact. If they have different opinions, they forget their opinions and become undecided. If one of them is undecided while the other has an opinion, they undecided agent copies they opinion of the decided one. The question is then, how many interactions does it take for the whole population to share the same opinion? We show a $\\Omega(kn\\log \\frac {\\sqrt n} {k \\log n})$ lower bound  for any $k = o\\left(\\frac {\\sqrt n}{\\log n}\\right)$.\r\nThis is tight for any $ k \\le n^{\\frac 1 2 - \\epsilon}$, where $\\epsilon >0$ can be any small constant, matching the known $O(kn\\log n)$ upper bound for $k = O\\left(\\frac {\\sqrt n} {\\log ^2 n}\\right)$~\\cite{DBLP:conf/podc/AmirABBHKL23}.\r\n\r\nFinally, in dynamic algorithms, we study the minimum cut problem: we are given a graph, whose vertex set we want to partition into two subsets such that the number of edges crossing from one subset to the other is minimized. Then, the graph can be updated via edge insertions or deletions, and we must update the solution without recomputing everything from scratch. We present an exact fully-dynamic minimum cut algorithm that runs in $n^{o(1)}$ deterministic update time when the minimum cut size is at most $2^{\\Theta(\\log^{3/4-c}n)}$ for any $c>0$, improving on the previous algorithm~\\cite{DBLP:conf/soda/JinST24} whose minimum cut size limit is $(\\log n)^{o(1)}$. Using sparsification and randomization techniques, we are able to extend this to all values of the minimum cut in weighted graphs, at the cost of a $(1+o(1))$-approximation ratio."}],"title":"Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks","_id":"22281","date_created":"2026-07-13T09:39:59Z","status":"public","author":[{"full_name":"El-Hayek, Antoine","orcid":"0000-0003-4268-7368","last_name":"El-Hayek","first_name":"Antoine","id":"888a098e-fcac-11ee-aff7-d347be57b725"}]},{"publication_status":"published","year":"2026","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"ddc":["576"],"degree_awarded":"PhD","fulldoi":"https://doi.org/10.15479/AT-ISTA-20991","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2026-01-16T13:08:59Z","alternative_title":["ISTA Thesis"],"date_published":"2026-01-16T00:00:00Z","publisher":"Institute of Science and Technology Austria","month":"01","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"oa":1,"corr_author":"1","day":"16","doi":"10.15479/AT-ISTA-20991","file":[{"file_name":"2026_Garcia_Diego_Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-01-16T12:25:13Z","file_size":22456421,"file_id":"20996","access_level":"closed","relation":"source_file","creator":"dgarciac","date_created":"2026-01-16T12:25:13Z","checksum":"841f1bc073d667125729b2a017f8c37a"},{"success":1,"checksum":"a1f33d4f183ce7072eee42a6ccf5340b","date_created":"2026-01-16T12:25:13Z","access_level":"open_access","relation":"main_file","creator":"dgarciac","file_id":"20997","date_updated":"2026-01-16T12:25:13Z","content_type":"application/pdf","file_name":"2026_Garcia_Diego_Thesis.pdf","file_size":9556719},{"file_size":54491433,"date_updated":"2026-01-16T13:08:14Z","content_type":"application/x-compressed","file_name":"2026_DiegoGarcia_LittorinaDB Source Code and Protocols.rar","file_id":"20998","description":"Source code of the PostgreSQL database, front-end and back-end of the LittorinaDB web application developed as a product of the 4th chapter of the thesis.","creator":"dgarciac","relation":"supplementary_material","access_level":"closed","date_created":"2026-01-16T13:08:14Z","checksum":"98a80691067174c30fe53f38ce7344e6"},{"date_updated":"2026-01-16T13:08:14Z","content_type":"application/x-compressed","file_name":"2026_DiegoGarcia_Thesis-Supplementary_Material.rar","file_size":7982811,"file_id":"20999","access_level":"open_access","creator":"dgarciac","relation":"supplementary_material","date_created":"2026-01-16T13:08:14Z","checksum":"99a3cab2fa36666b9a92eefc27d586da"},{"file_id":"21000","file_size":732,"date_updated":"2026-01-16T13:08:59Z","content_type":"text/plain","file_name":"README.txt","checksum":"255fdf56b2932c46bf27c63aa6106a4f","date_created":"2026-01-16T13:08:59Z","creator":"dgarciac","relation":"supplementary_material","access_level":"open_access"}],"abstract":[{"lang":"eng","text":"Rapid local adaptation to new environments is critical for species persistence, especially in introduced populations. The evolutionary success of these populations is fundamentally dictated by the organization of genetic variation—the genomic architecture—in the face of severe demographic constraints, such as the founder effects and genetic bottlenecks that frequently accompany colonization. A central question in evolutionary biology is whether rapid adaptation relies on major-effect loci, such as chromosomal inversions, or on many small-effect loci dispersed across the genome. Furthermore, the genomic architecture strongly influences the extent to which evolutionary outcomes are predictable. Using introduced populations of the marine snail, Littorina saxatilis, as a model, this thesis investigates how genetic variation and genomic structure drive adaptation following introduction. We employed a population genomics approach on experimentally and accidentally introduced populations to dissect the specific genomic features that underpin divergence in newly colonized environments.\r\n\r\nIn Chapter 2, we tested the predictability of local adaptation through an uncommon 30-year transplant experiment in nature. By distinguishing allele and chromosomal inversion frequency changes from neutral expectations, we found that evolutionary change was highly predictable at the macro-scale (phenotypes and chromosomal inversions), but less robust at the level of individual collinear loci. This result demonstrates that evolution can be predictable when a population possesses sufficient standing genetic variation (SGV), with chromosomal inversions acting as key integrated units that facilitate a rapid response to selection. Building on this, Chapter 3 applied whole-genome sequencing to three accidentally introduced populations (Venice, San Francisco, and Redwood City) to investigate their likely source and genomic patterns of divergence. We identified genomic regions of remarkable divergence potentially associated with local adaptation, and likely fuelled by SGV, while explicitly acknowledging the difficulty in disentangling selection signals from the genome-wide effects of demographic processes. Furthermore, we found that the divergence patterns relied extensively on the collinear genome in these introduced populations, and less clearly on the chromosomal inversions. This observation contrasts with local adaptation observed in the experimental system that relied on both collinear loci and highly selected chromosomal inversions, highlighting how demographic history and genomic architecture influence the detectable signature of local adaptation.\r\n\r\nA major limitation to conducting large-scale comparative evolutionary studies is the lack of data standardization, which prevents the integration of community knowledge and high-resolution environmental and genetic data. Chapter 4 addresses this by developing a community database for the Littorina system. This platform implements standardized protocols for the integration of diverse phenotypic and environmental data from multiple Littorina species. Likewise, the platform also centralizes the availability of associated genomic data through links to external repositories. This database represents a crucial tool to test complex, large-scale evolutionary hypotheses.\r\n\r\nCollectively, this thesis strongly reinforces the fundamental importance of SGV as the raw material for successful local adaptation, a conclusion supported by evidence in both experimental and accidental introductions. Furthermore, this work highlights the critical role of the genomic architecture—specifically chromosomal inversions—in driving the predictability and effectiveness of adaptive responses. Our findings underscore how the interplay between SGV and genomic architecture dictates the trajectory and detectability of evolution in colonizing populations, while simultaneously providing a necessary tool to advance comparative evolutionary genomics in emerging model organisms."}],"supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","type":"dissertation","status":"public","author":[{"full_name":"Garcia Castillo, Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","last_name":"Garcia Castillo","first_name":"Diego Fernando"}],"date_created":"2026-01-16T09:47:59Z","title":"The genomic architecture of local adaptation in introduced populations","_id":"20991","date_updated":"2026-10-21T08:18:21Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"199","citation":{"ama":"Garcia Castillo DF. The genomic architecture of local adaptation in introduced populations. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20991\">10.15479/AT-ISTA-20991</a>","mla":"Garcia Castillo, Diego Fernando. <i>The Genomic Architecture of Local Adaptation in Introduced Populations</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20991\">10.15479/AT-ISTA-20991</a>.","ista":"Garcia Castillo DF. 2026. The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria.","short":"D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced Populations, Institute of Science and Technology Austria, 2026.","ieee":"D. F. Garcia Castillo, “The genomic architecture of local adaptation in introduced populations,” Institute of Science and Technology Austria, 2026.","chicago":"Garcia Castillo, Diego Fernando. “The Genomic Architecture of Local Adaptation in Introduced Populations.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-20991\">https://doi.org/10.15479/AT-ISTA-20991</a>.","apa":"Garcia Castillo, D. F. (2026). <i>The genomic architecture of local adaptation in introduced populations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20991\">https://doi.org/10.15479/AT-ISTA-20991</a>"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","related_material":{"record":[{"status":"public","id":"18498","relation":"research_data"},{"status":"public","id":"18491","relation":"part_of_dissertation"}]},"publication_identifier":{"isbn":["978-3-99078-077-0"],"issn":["2663-337X"]},"acknowledgement":"I acknowledge the funding agencies 1Norwegian Research Council RCN project 315287.\r\n2The FIASCO project \"Illuminating range shifts through evolutionary FIASCO: contrasting\r\nFaIling And Successful ColOnizations in replicated wild populations\", funded by the\r\nEuropean Union - Next Generation EU (Piano Nazionale di Ripresa e Resilienza - MUR\r\ncode: P202229JBC, CUP: C53D23007100001). 3Ecotypic formation in Littorina saxatilis\r\nin the Western Atlantic and comparisons across the North Atlantic. University of\r\nGothenburg Research Travel Grant, Tjarno Marine Laboratory, Sweden. $3023 (2018).\r\n4JIN project (Young Researchers, Spanish Ministry of Science, RTI2018-101274-J-I00)","language":[{"iso":"eng"}],"OA_place":"publisher"},{"day":"12","corr_author":"1","oa":1,"doi_confirm":"1","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"ScWa"}],"month":"08","doi":"10.15479/AT-ISTA-22684","file":[{"file_size":31192621,"date_updated":"2026-08-12T13:04:21Z","content_type":"application/x-zip-compressed","file_name":"2026_Pertl_Felix_Thesis.zip","file_id":"22690","creator":"fpertl","relation":"source_file","access_level":"closed","date_created":"2026-08-12T13:04:21Z","checksum":"0a4f5a941c40b921447e72291d72bc6f"},{"date_created":"2026-08-12T13:04:21Z","checksum":"ae60dcdb363222138886b2857643d4e3","access_level":"open_access","relation":"main_file","creator":"fpertl","file_id":"22691","date_updated":"2026-08-12T13:04:21Z","content_type":"application/pdf","file_name":"2026_Pertl_Felix_Thesis.pdf","file_size":27882509}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["530"],"publication_status":"published","year":"2026","has_accepted_license":"1","file_date_updated":"2026-08-12T13:04:21Z","alternative_title":["ISTA Thesis"],"date_published":"2026-08-12T00:00:00Z","article_processing_charge":"No","degree_awarded":"PhD","fulldoi":"https://doi.org/10.15479/AT-ISTA-22684","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-083-1"]},"acknowledgement":"This project has received financing from the European Research Council grant agreement\r\nno. 949120 under the European Union’s Horizon 2020 research and innovation programme.\r\nThis research was supported by the Scientific Service Units of The Institute of Science\r\nand Technology Austria (ISTA) through resources provided by the Miba Machine Shop, the\r\nNanofabrication Facility, the Lab Support Facility, the Scientific Computing Facility and the\r\nElectron Microscopy Facility. We thank Florian Stumpf from Park Systems for useful discussions\r\nand support with scanning probe microscopy. We thank Joaquin Garcia-Suarez and Guillaume\r\nAnciaux for the suggestion to look into the roughness power spectral density. We thank\r\nIrina-Malina Strugaru for help with testing the device for Young’s modulus measurements.\r\n","ec_funded":1,"OA_place":"publisher","language":[{"iso":"eng"}],"title":"Experimental probing of nanoscale charge features and surface morphology changes during tribocharging","_id":"22684","author":[{"id":"6313aec0-15b2-11ec-abd3-ed67d16139af","last_name":"Pertl","first_name":"Felix","full_name":"Pertl, Felix","orcid":"0000-0003-0463-5794"}],"status":"public","date_created":"2026-08-12T09:44:40Z","oa_version":"Published Version","supervisor":[{"last_name":"Waitukaitis","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R"}],"type":"dissertation","abstract":[{"text":"Contact electrification (CE) is a simple yet elusive phenomenon that occurs when two materials come into contact and separate, leaving behind net electrical charge. Despite its ubiquity, the microscopic origin of CE remains unclear. In this thesis, we investigate CE from three complementary perspectives: developing a quantitative method to measure charge at the nanoscale, exploring the dynamic behavior of charge on insulating surfaces, and uncovering the role of mechanical history in forming a triboelectric series.\r\n\r\nIn the first part, we establish a rigorous framework for converting qualitative Kelvin probe force microscopy (KPFM) voltage maps into quantitative charge density distributions. Using finite element method (FEM) simulations, we determine the point-spread function of the KPFM tip–sample geometry and demonstrate that the true surface charge can be reconstructed by numerical deconvolution. This procedure enables the recovery of both the magnitude and sign of charge density with high fidelity, resolving nanoscale features that are otherwise obscured. Applying the method to contact-charged SiO$_2$ surfaces, we show that existing analytical approximations, such as parallel plate or spherical models, can miscalculate charge magnitude by orders of magnitude. Our hybrid FEM/KPFM approach therefore provides a fast and general method to convert qualitative KPFM signals into quantitative charge data, enabling nanoscale charge mapping under realistic experimental conditions.\r\n\r\nIn the second part, we study the temporal stability of CE-induced charges and identify the key material factors that determine whether KPFM can capture meaningful charge patterns. Through time-resolved experiments combining a custom-built transfer system with both microscopic and macroscopic measurements, we demonstrate that only the best insulators, such as SiO$_2$, preserve CE charge long enough for stationary imaging. For less conductive polymers, such as PDMS, charge decays within the duration of a single KPFM scan due to bulk conduction. Using a simple capacitor-based model, we reproduce the observed decay dynamics and confirm that the transferred charge decays characteristic to the sample's bulk conductivity. Further, we always observe homogeneous charge transfer.\r\n\r\nIn the third part, we address the question: can we form a triboelectric series with identical materials? Using controlled repetitive contact experiments, we show that nominally identical materials can progressively order themselves into a triboelectric series, where surfaces with more contact history charge negatively relative to fresher ones. By constructing a minimal model based on this ``contact bias'', we replicate the evolution from random to ordered charging observed in experiments. Supporting surface analyses, including atomic force microscopy, reveal that repeated contact induces nanoscale morphological changes, suggesting a mechanism tightly coupled to mechanical strain. These results highlight the crucial role of surface history and nanoscale mechanics in dictating charge transfer, motivating further exploration of mechanisms such as mechanochemical bond cleavage and flexoelectric polarization.","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"20481"},{"id":"12109","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"19278"},{"status":"public","relation":"part_of_dissertation","id":"17373"}]},"citation":{"mla":"Pertl, Felix. <i>Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22684\">10.15479/AT-ISTA-22684</a>.","ama":"Pertl F. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22684\">10.15479/AT-ISTA-22684</a>","ieee":"F. Pertl, “Experimental probing of nanoscale charge features and surface morphology changes during tribocharging,” Institute of Science and Technology Austria, 2026.","ista":"Pertl F. 2026. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. Institute of Science and Technology Austria.","short":"F. Pertl, Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging, Institute of Science and Technology Austria, 2026.","chicago":"Pertl, Felix. “Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22684\">https://doi.org/10.15479/AT-ISTA-22684</a>.","apa":"Pertl, F. (2026). <i>Experimental probing of nanoscale charge features and surface morphology changes during tribocharging</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22684\">https://doi.org/10.15479/AT-ISTA-22684</a>"},"page":"107","project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020","grant_number":"949120"}],"date_updated":"2026-10-21T08:39:24Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"type":"journal_article","oa_version":"Published Version","article_type":"original","abstract":[{"lang":"eng","text":"We prove that the zero-fiber of the moment map of a totally negative quiver has rational singularities. Our proof consists in generalizing dimension bounds on jet spaces of this fiber, which were introduced by Budur. We also transfer the rational singularities property to other moduli spaces of objects in 2-Calabi-Yau categories, based on recent work of Davison. This has interesting arithmetic applications on quiver moment maps and moduli spaces of objects in 2-Calabi-Yau categories. First, we generalize results of Wyss on the asymptotic behaviour of counts of jets of quiver moment maps over finite fields. Moreover, we interpret the limit of counts of jets on a given moduli space as its p-adic volume under a canonical measure analogous to the measure built by Carocci, Orecchia and Wyss on certain moduli spaces of coherent sheaves."}],"title":"Rational singularities for moment maps of totally negative quivers","_id":"17437","author":[{"first_name":"Tanguy","last_name":"Vernet","id":"19f1e3bf-c59a-11ee-a1af-ed269948817b","full_name":"Vernet, Tanguy"}],"status":"public","date_created":"2024-08-18T22:01:04Z","date_updated":"2026-10-21T10:55:21Z","supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","PlanS_conform":"1","citation":{"chicago":"Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” <i>Transformation Groups</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00031-024-09873-0\">https://doi.org/10.1007/s00031-024-09873-0</a>.","apa":"Vernet, T. (2026). Rational singularities for moment maps of totally negative quivers. <i>Transformation Groups</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00031-024-09873-0\">https://doi.org/10.1007/s00031-024-09873-0</a>","ama":"Vernet T. Rational singularities for moment maps of totally negative quivers. <i>Transformation Groups</i>. 2026;31:1047-1083. doi:<a href=\"https://doi.org/10.1007/s00031-024-09873-0\">10.1007/s00031-024-09873-0</a>","mla":"Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” <i>Transformation Groups</i>, vol. 31, Springer Nature, 2026, pp. 1047–83, doi:<a href=\"https://doi.org/10.1007/s00031-024-09873-0\">10.1007/s00031-024-09873-0</a>.","ista":"Vernet T. 2026. Rational singularities for moment maps of totally negative quivers. Transformation Groups. 31, 1047–1083.","ieee":"T. Vernet, “Rational singularities for moment maps of totally negative quivers,” <i>Transformation Groups</i>, vol. 31. Springer Nature, pp. 1047–1083, 2026.","short":"T. Vernet, Transformation Groups 31 (2026) 1047–1083."},"page":"1047-1083","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"publication_identifier":{"issn":["1083-4362"],"eissn":["1531-586X"]},"ec_funded":1,"acknowledgement":"I would like to warmly thank Dimitri Wyss for his guidance and supervision and Nero Budur for helpful discussions and answering all my questions on his previous works. I would also like to thank Francesca Carocci, Ben Davison, Lucien Hennecart and Olivier Schiffmann for helpful remarks and discussions during the writing of this paper. Finally, I would like to thank the anonymous referees for their careful reading and suggesting improvements in the exposition.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). This work was supported by the Swiss National Science Foundation [No. 196960]. This project has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","publication":"Transformation Groups","scopus_import":"1","language":[{"iso":"eng"}],"OA_place":"publisher","OA_type":"hybrid","publication_status":"published","year":"2026","quality_controlled":"1","intvolume":"        31","ddc":["510"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"das_tickbox":"1","fulldoi":"https://doi.org/10.1007/s00031-024-09873-0","has_accepted_license":"1","date_published":"2026-03-01T00:00:00Z","file_date_updated":"2026-07-23T05:50:09Z","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001287455300001"]},"publisher":"Springer Nature","mathsc":["14B05","14D23","14G20","16G20"],"month":"03","department":[{"_id":"TaHa"}],"day":"01","dataavailabilitystatement":"Not applicable.","oa":1,"corr_author":"1","volume":31,"researchdata_availability":"not applicable","doi":"10.1007/s00031-024-09873-0","file":[{"file_name":"2026_TransformationGroups_Vernet.pdf","date_updated":"2026-07-23T05:50:09Z","content_type":"application/pdf","file_size":912029,"file_id":"22385","access_level":"open_access","creator":"dernst","relation":"main_file","success":1,"date_created":"2026-07-23T05:50:09Z","checksum":"8985b4154b730284d3412ddc9e55d965"}],"isi":1}]