--- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21746' 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. acknowledged_ssus: - _id: Bio - _id: LifeSc 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.).' article_number: '117227' article_processing_charge: Yes article_type: original author: - first_name: David full_name: Vijatovic, David id: cf391e77-ec3c-11ea-a124-d69323410b58 last_name: Vijatovic orcid: 0000-0002-5494-0941 - first_name: 'Florina Alexandra ' full_name: 'Toma, Florina Alexandra ' id: 2f73f876-f128-11eb-9611-b96b5a30cb0e last_name: Toma - first_name: Y full_name: Ignatyev, Y last_name: Ignatyev - first_name: Zoe P full_name: Harrington, Zoe P id: a8144562-32c9-11ee-b5ce-d9800628bda2 last_name: Harrington orcid: 0009-0008-0158-4032 - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Matthijs Geert full_name: Smits, Matthijs Geert id: 7a231d52-e216-11ee-a0bb-8acd55f8f1f0 last_name: Smits - first_name: Marco full_name: Dalla Vecchia, Marco id: 02a7a869-ff06-11ed-a87f-86649d6077e5 last_name: Dalla Vecchia - first_name: Alexandra J. full_name: Trevisan, Alexandra J. last_name: Trevisan - first_name: Phillip full_name: Chapman, Phillip last_name: Chapman - first_name: Mara full_name: Julseth, Mara id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1 last_name: Julseth - first_name: Susan full_name: Brenner-Morton, Susan last_name: Brenner-Morton - first_name: Mariano I. full_name: Gabitto, Mariano I. last_name: Gabitto - first_name: Jeremy S. full_name: Dasen, Jeremy S. last_name: Dasen - first_name: Jay B. full_name: Bikoff, Jay B. last_name: Bikoff - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 citation: ama: Vijatovic D, Toma FA, Ignatyev Y, et al. Multifold increase in spinal inhibitory cell types with emergence of limb movement. Cell Reports. 2026;45(4). doi:10.1016/j.celrep.2026.117227 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. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2026.117227 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.” Cell Reports. Cell Press, 2026. https://doi.org/10.1016/j.celrep.2026.117227. ieee: D. Vijatovic et al., “Multifold increase in spinal inhibitory cell types with emergence of limb movement,” Cell Reports, vol. 45, no. 4. Cell Press, 2026. 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. mla: Vijatovic, David, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” Cell Reports, vol. 45, no. 4, 117227, Cell Press, 2026, doi:10.1016/j.celrep.2026.117227. 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). corr_author: '1' date_created: 2026-04-19T22:07:43Z date_published: 2026-04-28T00:00:00Z date_updated: 2026-10-20T09:04:23Z day: '28' ddc: - '570' department: - _id: LoSw - _id: GradSch - _id: TiVo - _id: Bio - _id: NiBa doi: 10.1016/j.celrep.2026.117227 external_id: pmid: - '41964955 ' file: - access_level: open_access checksum: 0d26cdb5b8d8dec3a911d8261a65cdef content_type: application/pdf creator: dernst date_created: 2026-05-04T12:20:10Z date_updated: 2026-05-04T12:20:10Z file_id: '21795' file_name: 2026_CellReports_Vijatovic.pdf file_size: 14925958 relation: main_file success: 1 file_date_updated: 2026-05-04T12:20:10Z fulldoi: https://doi.org/10.1016/j.celrep.2026.117227 has_accepted_license: '1' intvolume: ' 45' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae grant_number: '101041551' name: Development and Evolution of Tetrapod Motor Circuits - _id: 8da85f50-16d5-11f0-9cad-eab8b0ff6c9e grant_number: F7814 name: 'Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity' - _id: c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473 grant_number: CZI01 name: Tools for automation and feedback microscopy - _id: bd73af52-d553-11ed-ba76-912049f0ac7a grant_number: FTI21-D-046 name: Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis - _id: cf428362-b037-11f1-b015-8277a8a2f63d grant_number: COE16 name: Neuronal circuits in health and disease (Sweeney) publication: Cell Reports publication_identifier: eissn: - 2211-1247 issn: - 2639-1856 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: record: - id: '22667' relation: dissertation_contains status: public scopus_import: '1' status: public title: Multifold increase in spinal inhibitory cell types with emergence of limb movement tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21987' 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.' acknowledged_ssus: - _id: ScienComp 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)." article_number: '101277' article_processing_charge: Yes article_type: original author: - first_name: Ilse full_name: Krätschmer, Ilse id: 30d4014e-7753-11eb-b44b-db6d61112e73 last_name: Krätschmer orcid: 0000-0002-5636-9259 - first_name: Laura full_name: Hegemann, Laura last_name: Hegemann - first_name: Robin J. full_name: Hofmeister, Robin J. last_name: Hofmeister - first_name: Elizabeth C. full_name: Corfield, Elizabeth C. last_name: Corfield - first_name: Mahdi full_name: Mahmoudi, Mahdi last_name: Mahmoudi - first_name: Olivier full_name: Delaneau, Olivier last_name: Delaneau - first_name: Ole A. full_name: Andreassen, Ole A. last_name: Andreassen - first_name: Archie full_name: Campbell, Archie last_name: Campbell - first_name: Caroline full_name: Hayward, Caroline last_name: Hayward - first_name: Riccardo E. full_name: Marioni, Riccardo E. last_name: Marioni - first_name: Eivind full_name: Ystrom, Eivind last_name: Ystrom - first_name: Alexandra full_name: Havdahl, Alexandra last_name: Havdahl - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Krätschmer I, Hegemann L, Hofmeister RJ, et al. Separating direct, indirect, and parent-of-origin genetic effects in the human population. Cell Genomics. 2026;6(7). doi:10.1016/j.xgen.2026.101277 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. Cell Genomics. Cell Press. https://doi.org/10.1016/j.xgen.2026.101277 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.” Cell Genomics. Cell Press, 2026. https://doi.org/10.1016/j.xgen.2026.101277. ieee: I. Krätschmer et al., “Separating direct, indirect, and parent-of-origin genetic effects in the human population,” Cell Genomics, vol. 6, no. 7. Cell Press, 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.” Cell Genomics, vol. 6, no. 7, 101277, Cell Press, 2026, doi:10.1016/j.xgen.2026.101277. 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). corr_author: '1' das_tickbox: '1' 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." date_created: 2026-06-10T07:39:08Z date_published: 2026-07-08T00:00:00Z date_updated: 2026-10-20T09:03:50Z day: '08' ddc: - '570' department: - _id: MaRo doi: 10.1016/j.xgen.2026.101277 external_id: pmid: - '40909755' file: - access_level: open_access checksum: f896b510480d2d4e4a7fd46c2e2761f4 content_type: application/pdf creator: dernst date_created: 2026-07-28T07:24:50Z date_updated: 2026-07-28T07:24:50Z file_id: '22597' file_name: 2026_CellGenomics_Kraetschmer.pdf file_size: 3679297 relation: main_file success: 1 file_date_updated: 2026-07-28T07:24:50Z fulldoi: https://doi.org/10.1016/j.xgen.2026.101277 has_accepted_license: '1' intvolume: ' 6' issue: '7' keyword: - direct genetic effects - DGE - indirect genetic effects - IGE - parent-of-origin effects - phenotypic variation - assortative mating - within-family GWAS - MoBa - EstBB language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A grant_number: PCEGP3_181181 name: Improving estimation and prediction of common complex disease risk publication: Cell Genomics publication_identifier: eissn: - 2666-979X publication_status: published publisher: Cell Press quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/human-traits-beyond-inherited-genes/ researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Separating direct, indirect, and parent-of-origin genetic effects in the human population tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2026' ... --- OA_place: publisher _id: '22258' 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." acknowledged_ssus: - _id: ScienComp 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Al full_name: Depope, Al id: 0b77531d-dbcd-11ea-9d1d-a8eee0bf3830 last_name: Depope citation: ama: 'Depope A. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. 2026. doi:10.15479/AT-ISTA-22258' apa: '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. https://doi.org/10.15479/AT-ISTA-22258' 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. https://doi.org/10.15479/AT-ISTA-22258.' 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.' mla: '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, doi:10.15479/AT-ISTA-22258.' 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.' corr_author: '1' das_tickbox: '1' date_created: 2026-07-10T13:27:20Z date_published: 2026-07-11T00:00:00Z date_updated: 2026-10-20T09:03:21Z day: '11' ddc: - '576' - '610' - '006' degree_awarded: PhD department: - _id: GradSch - _id: MaRo - _id: MaMo doi: 10.15479/AT-ISTA-22258 doi_confirm: '1' file: - access_level: open_access checksum: 9ab386790515628d957a194f30a7ccb4 content_type: application/pdf creator: adepope date_created: 2026-07-13T14:52:19Z date_updated: 2026-07-13T14:52:19Z file_id: '22316' file_name: 2026_Depope_Al_Thesis.pdf file_size: 25109878 relation: main_file - access_level: closed checksum: 8ed8fb63f76a695d5b6fec35343f4b90 content_type: application/zip creator: adepope date_created: 2026-07-13T14:56:41Z date_updated: 2026-07-13T14:56:41Z file_id: '22317' file_name: 2026_Depope_Al_Thesis.zip file_size: 1203199939 relation: source_file file_date_updated: 2026-07-13T14:56:41Z fulldoi: https://doi.org/10.15479/AT-ISTA-22258 has_accepted_license: '1' keyword: - Approximate Message Passing - GWAS - Genomics - Proteomics - Survival modeling language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '169' project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli - _id: 911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf grant_number: '101161364' name: 'Inference in High Dimensions: Light-speed Algorithms and Information Limits' - _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A grant_number: PCEGP3_181181 name: Improving estimation and prediction of common complex disease risk publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '21488' relation: part_of_dissertation status: public status: public supervisor: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 title: 'From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21488' abstract: - lang: eng 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. 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. article_number: '101162' article_processing_charge: Yes article_type: original author: - first_name: Al full_name: Depope, Al id: 0b77531d-dbcd-11ea-9d1d-a8eee0bf3830 last_name: Depope - first_name: Jakub full_name: Bajzik, Jakub id: b995e25b-8c4b-11ed-a6d8-f71b7bcd6122 last_name: Bajzik - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Depope A, Bajzik J, Mondelli M, Robinson MR. Joint modeling of whole-genome sequencing data for human height via approximate message passing. Cell Genomics. 2026;6(5). doi:10.1016/j.xgen.2026.101162 apa: Depope, A., Bajzik, J., Mondelli, M., & Robinson, M. R. (2026). Joint modeling of whole-genome sequencing data for human height via approximate message passing. Cell Genomics. Cell Press. https://doi.org/10.1016/j.xgen.2026.101162 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.” Cell Genomics. Cell Press, 2026. https://doi.org/10.1016/j.xgen.2026.101162. 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,” Cell Genomics, 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.” Cell Genomics, vol. 6, no. 5, 101162, Cell Press, 2026, doi:10.1016/j.xgen.2026.101162. short: A. Depope, J. Bajzik, M. Mondelli, M.R. Robinson, Cell Genomics 6 (2026). corr_author: '1' das_tickbox: '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." date_created: 2026-03-23T15:10:03Z date_published: 2026-05-13T00:00:00Z date_updated: 2026-10-20T09:03:22Z day: '13' ddc: - '000' - '570' department: - _id: MaMo - _id: MaRo doi: 10.1016/j.xgen.2026.101162 external_id: pmid: - '41713425' file: - access_level: open_access checksum: 6b59686f8d9733add4f23d23f3dd9df0 content_type: application/pdf creator: dernst date_created: 2026-07-28T07:06:26Z date_updated: 2026-07-28T07:06:26Z file_id: '22596' file_name: 2026_CellGenomics_Depope.pdf file_size: 3736705 relation: main_file success: 1 file_date_updated: 2026-07-28T07:06:26Z fulldoi: https://doi.org/10.1016/j.xgen.2026.101162 has_accepted_license: '1' intvolume: ' 6' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli - _id: 911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf grant_number: '101161364' name: 'Inference in High Dimensions: Light-speed Algorithms and Information Limits' - _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A grant_number: PCEGP3_181181 name: Improving estimation and prediction of common complex disease risk publication: Cell Genomics publication_identifier: eissn: - 2666-979X publication_status: published publisher: Cell Press quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/big-data-and-human-height/ record: - id: '22258' relation: dissertation_contains status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Joint modeling of whole-genome sequencing data for human height via approximate message passing tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '22267' abstract: - lang: eng 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. 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.). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Chee Kiang full_name: Ewe, Chee Kiang last_name: Ewe - first_name: Hanna full_name: Achache, Hanna last_name: Achache - first_name: Hanna full_name: Schön, Hanna id: C8E17EDC-D7AA-11E9-B7B7-45ECE5697425 last_name: Schön - first_name: Leonid full_name: Kontorovich, Leonid last_name: Kontorovich - first_name: Guy full_name: Teichman, Guy last_name: Teichman - first_name: Shir full_name: Weiss, Shir last_name: Weiss - first_name: Anna full_name: Mogilevskaya, Anna last_name: Mogilevskaya - first_name: Myriam full_name: Valenski, Myriam last_name: Valenski - first_name: Sarit full_name: Anava, Sarit last_name: Anava - first_name: Rutwik full_name: Bardapurkar, Rutwik last_name: Bardapurkar - first_name: Hila full_name: Gingold, Hila last_name: Gingold - first_name: Rachel full_name: Posner, Rachel last_name: Posner - first_name: Olga full_name: Antonova, Olga last_name: Antonova - first_name: Mario full_name: De Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: De Bono orcid: 0000-0001-8347-0443 - first_name: Yonatan B. full_name: Tzur, Yonatan B. last_name: Tzur - first_name: Oded full_name: Rechavi, Oded last_name: Rechavi citation: ama: Ewe CK, Achache H, Schön H, et al. Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. Current Biology. 2026;36(14):3566-3579.e5. doi:10.1016/j.cub.2026.06.016 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. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2026.06.016 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.” Current Biology. Cell Press, 2026. https://doi.org/10.1016/j.cub.2026.06.016. ieee: C. K. Ewe et al., “Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress,” Current Biology, vol. 36, no. 14. Cell Press, p. 3566–3579.e5, 2026. 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.” Current Biology, vol. 36, no. 14, Cell Press, 2026, p. 3566–3579.e5, doi:10.1016/j.cub.2026.06.016. 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. das_tickbox: '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." date_created: 2026-07-12T22:02:18Z date_published: 2026-07-20T00:00:00Z date_updated: 2026-10-20T09:03:35Z day: '20' ddc: - '570' department: - _id: MaDe doi: 10.1016/j.cub.2026.06.016 external_id: pmid: - '42409014' file: - access_level: open_access checksum: 5ec4472d81fd44de03ccb92b1eb690a6 content_type: application/pdf creator: dernst date_created: 2026-07-28T07:31:44Z date_updated: 2026-07-28T07:31:44Z file_id: '22598' file_name: 2026_CurrentBiology_KiangEwe.pdf file_size: 6795092 relation: main_file success: 1 file_date_updated: 2026-07-28T07:31:44Z fulldoi: https://doi.org/10.1016/j.cub.2026.06.016 has_accepted_license: '1' intvolume: ' 36' issue: '14' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 3566-3579.e5 pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '22148' abstract: - lang: eng 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.' acknowledged_ssus: - _id: EM-Fac - _id: ScienComp 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Ziyu full_name: Zhao, Ziyu id: a63fe682-9f3a-11ee-bf8c-cfdf919b9850 last_name: Zhao - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 biorxivid: 1 citation: ama: Zhao Z, Sazanov LA. Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. Molecular Cell. doi:10.1016/j.molcel.2026.05.026 apa: Zhao, Z., & Sazanov, L. A. (n.d.). Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2026.05.026 chicago: Zhao, Ziyu, and Leonid A Sazanov. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo.” Molecular Cell. Cell Press, n.d. https://doi.org/10.1016/j.molcel.2026.05.026. ieee: Z. Zhao and L. A. Sazanov, “Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo,” Molecular Cell. Cell Press. ista: Zhao Z, Sazanov LA. Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. Molecular Cell. mla: Zhao, Ziyu, and Leonid A. Sazanov. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo.” Molecular Cell, Cell Press, doi:10.1016/j.molcel.2026.05.026. short: Z. Zhao, L.A. Sazanov, Molecular Cell (n.d.). corr_author: '1' das_tickbox: '1' 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." date_created: 2026-06-28T22:01:35Z date_published: 2026-06-22T00:00:00Z date_updated: 2026-10-20T09:04:07Z day: '22' ddc: - '570' department: - _id: LeSa doi: 10.1016/j.molcel.2026.05.026 external_id: biorxivid: - 10.1101/2025.09.16.676506 fulldoi: https://doi.org/10.1016/j.molcel.2026.05.026 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.molcel.2026.05.026 month: '06' oa: 1 oa_version: Published Version publication: Molecular Cell publication_identifier: eissn: - 1097-4164 issn: - 1097-2765 publication_status: inpress publisher: Cell Press quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/the-gate-for-bulky-cargo/ record: - id: '22189' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher _id: '22667' acknowledged_ssus: - _id: Bio - _id: LifeSc 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. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: David full_name: Vijatovic, David id: cf391e77-ec3c-11ea-a124-d69323410b58 last_name: Vijatovic orcid: 0000-0002-5494-0941 citation: ama: Vijatovic D. Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. 2026. doi:10.15479/AT-ISTA-22667 apa: Vijatovic, D. (2026). Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22667 chicago: Vijatovic, David. “Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22667. ieee: 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. mla: Vijatovic, David. Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22667. short: D. Vijatovic, Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-08-10T13:44:30Z date_published: 2026-08-10T00:00:00Z date_updated: 2026-10-20T09:04:22Z day: '10' ddc: - '573' degree_awarded: PhD department: - _id: GradSch - _id: LoSw doi: 10.15479/AT-ISTA-22667 doi_confirm: '1' file: - access_level: closed checksum: e3acfea4b1a3abf99e74224656740a15 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dvijatov date_created: 2026-08-10T13:35:39Z date_updated: 2026-08-10T13:35:39Z file_id: '22669' file_name: 2026_Vijatovic_David_Thesis.docx file_size: 14322760 relation: source_file - access_level: closed checksum: dc8c78ae14f69e54faa41e65db5c6402 content_type: application/pdf creator: dvijatov date_created: 2026-08-12T13:44:36Z date_updated: 2026-08-12T13:44:36Z embargo: 2027-08-10 embargo_to: open_access file_id: '22695' file_name: 2026_Vijatovic_David_Thesis.pdf file_size: 116926375 relation: main_file file_date_updated: 2026-08-12T13:44:36Z fulldoi: https://doi.org/10.15479/AT-ISTA-22667 has_accepted_license: '1' language: - iso: eng month: '08' oa_version: Published Version page: '172' project: - _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae grant_number: '101041551' name: Development and Evolution of Tetrapod Motor Circuits - _id: bd73af52-d553-11ed-ba76-912049f0ac7a grant_number: FTI21-D-046 name: Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis - _id: 34a02c70-11ca-11ed-8bc3-fbfd2c86c88f grant_number: 3(GG016346-01) name: Development of Viral Vectors for Amphibian Gene Delivery and Manipulation publication_identifier: isbn: - 978-3-99078-082-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '15016' relation: part_of_dissertation status: public - id: '21746' relation: part_of_dissertation status: public status: public supervisor: - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 title: Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository OA_type: green _id: '20858' 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. 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. article_processing_charge: No article_type: original author: - first_name: Ramona full_name: Rica, Ramona last_name: Rica - first_name: Klara full_name: Klein, Klara last_name: Klein - first_name: Litty full_name: Johnson, Litty last_name: Johnson - first_name: Gabriele full_name: Carta, Gabriele last_name: Carta - first_name: Mirza full_name: Sarcevic, Mirza last_name: Sarcevic - first_name: Freyja full_name: Langer, Freyja id: 3C1BE782-F248-11E8-B48F-1D18A9856A87 last_name: Langer - first_name: Christoph full_name: Rademacher, Christoph last_name: Rademacher - first_name: Robert full_name: Wawrzinek, Robert last_name: Wawrzinek - first_name: Federica full_name: Quattrone, Federica last_name: Quattrone - first_name: Florian full_name: Sparber, Florian last_name: Sparber biorxivid: 1 citation: ama: Rica R, Klein K, Johnson L, et al. Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response. Molecular Therapy. 2026;34(1):397-406. doi:10.1016/j.ymthe.2025.10.008 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. Molecular Therapy. Cell Press. https://doi.org/10.1016/j.ymthe.2025.10.008 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.” Molecular Therapy. Cell Press, 2026. https://doi.org/10.1016/j.ymthe.2025.10.008. ieee: R. Rica et al., “Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response,” Molecular Therapy, vol. 34, no. 1. Cell Press, pp. 397–406, 2026. 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. mla: Rica, Ramona, et al. “Langerhans Cell-Targeted Protein Delivery Enhances Antigen-Specific Cellular Immune Response.” Molecular Therapy, vol. 34, no. 1, Cell Press, 2026, pp. 397–406, doi:10.1016/j.ymthe.2025.10.008. 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. dataavailabilitystatement: The data that support the findings of this study are available on request from the corresponding authors. date_created: 2025-12-28T23:01:26Z date_published: 2026-01-07T00:00:00Z date_updated: 2026-10-20T09:03:08Z day: '07' department: - _id: PreCl doi: 10.1016/j.ymthe.2025.10.008 external_id: biorxivid: - 10.1101/2025.05.05.652195 fulldoi: https://doi.org/10.1016/j.ymthe.2025.10.008 intvolume: ' 34' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.05.05.652195 month: '01' oa: 1 oa_version: Preprint page: 397-406 publication: Molecular Therapy publication_identifier: eissn: - 1525-0024 issn: - 1525-0016 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2026' ... --- OA_place: publisher OA_type: gold _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. article_processing_charge: No author: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Sazanov LA. Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al. 2026. doi:10.17632/V2G3P9N985.1 apa: Sazanov, L. A. (2026). Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al. Mendeley Data. https://doi.org/10.17632/V2G3P9N985.1 chicago: Sazanov, Leonid A. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo. Zhao et Al.” Mendeley Data, 2026. https://doi.org/10.17632/V2G3P9N985.1. ieee: L. A. Sazanov, “Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al.” Mendeley Data, 2026. ista: Sazanov LA. 2026. Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al., Mendeley Data, 10.17632/V2G3P9N985.1. mla: Sazanov, Leonid A. Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo. Zhao et Al. Mendeley Data, 2026, doi:10.17632/V2G3P9N985.1. short: L.A. Sazanov, (2026). corr_author: '1' date_created: 2026-06-29T12:54:45Z date_published: 2026-05-15T00:00:00Z date_updated: 2026-10-20T09:04:06Z day: '15' ddc: - '570' department: - _id: LeSa doi: 10.17632/V2G3P9N985.1 fulldoi: https://doi.org/10.17632/V2G3P9N985.1 has_accepted_license: '1' keyword: - Protein Purification main_file_link: - open_access: '1' url: https://doi.org/10.17632/v2g3p9n985.1 month: '05' oa: 1 oa_version: Published Version publisher: Mendeley Data related_material: record: - id: '22148' relation: used_in_publication status: public status: public title: Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al. tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22955' 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. 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." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Ricardo full_name: Barrientos, Ricardo last_name: Barrientos - first_name: Billie full_name: Meadowcroft, Billie id: a4725fd6-932b-11ed-81e2-c098c7f37ae1 last_name: Meadowcroft orcid: 0000-0003-3441-1337 - first_name: Besaiz J. full_name: Sánchez-Sánchez, Besaiz J. last_name: Sánchez-Sánchez - first_name: Brian M. full_name: Stramer, Brian M. last_name: Stramer - first_name: Ewa K. full_name: Paluch, Ewa K. last_name: Paluch - first_name: Guillaume full_name: Charras, Guillaume last_name: Charras - first_name: Shiladitya full_name: Banerjee, Shiladitya last_name: Banerjee - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Yanlan full_name: Mao, Yanlan last_name: Mao citation: ama: Barrientos R, Meadowcroft B, Sánchez-Sánchez BJ, et al. Basement membrane turnover controls cell shape. Cell. 2026;189(18):5611-5624.e4. doi:10.1016/j.cell.2026.07.010 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. Cell. Cell Press. https://doi.org/10.1016/j.cell.2026.07.010 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.” Cell. Cell Press, 2026. https://doi.org/10.1016/j.cell.2026.07.010. ieee: R. Barrientos et al., “Basement membrane turnover controls cell shape,” Cell, vol. 189, no. 18. Cell Press, p. 5611–5624.e4, 2026. 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. mla: Barrientos, Ricardo, et al. “Basement Membrane Turnover Controls Cell Shape.” Cell, vol. 189, no. 18, Cell Press, 2026, p. 5611–5624.e4, doi:10.1016/j.cell.2026.07.010. 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. das_tickbox: '1' 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." date_created: 2026-09-17T11:06:06Z date_published: 2026-09-03T00:00:00Z date_updated: 2026-10-20T09:04:52Z day: '03' ddc: - '570' department: - _id: AnSa doi: 10.1016/j.cell.2026.07.010 ec_funded: 1 external_id: pmid: - '42532043' file: - access_level: open_access checksum: 01e74f866223ca9ea8680b617d4aa4e3 content_type: application/pdf creator: dernst date_created: 2026-09-24T12:35:11Z date_updated: 2026-09-24T12:35:11Z file_id: '22990' file_name: 2026_Cell_Barrientos.pdf file_size: 5642382 relation: main_file success: 1 file_date_updated: 2026-09-24T12:35:11Z fulldoi: https://doi.org/10.1016/j.cell.2026.07.010 has_accepted_license: '1' intvolume: ' 189' issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 5611-5624.e4 pmid: 1 project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Cell Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Basement membrane turnover controls cell shape tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 189 year: '2026' ... --- OA_type: closed access _id: '21996' 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. acknowledgement: This work was supported by the Austrian Science Fund (FWF) (10.55776/PAT1617625). article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Williams-Jones, Daniel id: 128eaab9-b327-11f0-bdbe-e02d5abac73b last_name: Williams-Jones - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 citation: ama: 'Williams-Jones D, Bravo JPK. NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. Cell Host & Microbe. 2026;34(6):978-980. doi:10.1016/j.chom.2026.05.013' apa: 'Williams-Jones, D., & Bravo, J. P. K. (2026). NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. Cell Host & Microbe. Cell Press. https://doi.org/10.1016/j.chom.2026.05.013' 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.” Cell Host & Microbe. Cell Press, 2026. https://doi.org/10.1016/j.chom.2026.05.013.' 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,” Cell Host & Microbe, 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 & Microbe. 34(6), 978–980.' 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.” Cell Host & Microbe, vol. 34, no. 6, Cell Press, 2026, pp. 978–80, doi:10.1016/j.chom.2026.05.013.' short: D. Williams-Jones, J.P.K. Bravo, Cell Host & Microbe 34 (2026) 978–980. corr_author: '1' das_tickbox: '1' date_created: 2026-06-14T22:01:42Z date_published: 2026-06-10T00:00:00Z date_updated: 2026-10-20T09:04:35Z day: '10' department: - _id: JaBr doi: 10.1016/j.chom.2026.05.013 external_id: pmid: - '42269584' fulldoi: https://doi.org/10.1016/j.chom.2026.05.013 intvolume: ' 34' issue: '6' language: - iso: eng month: '06' oa_version: None page: 978-980 pmid: 1 project: - _id: 9f295cab-ad08-11f1-bc83-9e197d0f6d50 grant_number: PAT1617625 name: 'Search & Destroy: Mechanisms of anti-plasmid immunity' publication: Cell Host & Microbe publication_identifier: eissn: - 1934-6069 issn: - 1931-3128 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: 'NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2026' ... --- OA_place: repository OA_type: green _id: '22104' abstract: - lang: eng 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.' 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." article_processing_charge: No arxiv: 1 author: - first_name: Amartya full_name: Hatua, Amartya last_name: Hatua - first_name: Trung T. full_name: Nguyen, Trung T. last_name: Nguyen - first_name: Filip full_name: Cano Cordoba, Filip id: 708cad98-e86a-11ef-8098-bdae2d7c6af1 last_name: Cano Cordoba orcid: 0000-0002-0783-904X - first_name: Andrew H. full_name: Sung, Andrew H. last_name: Sung citation: ama: 'Hatua A, Nguyen TT, Cano Cordoba F, Sung AH. Machine unlearning using forgetting neural networks. In: Proceedings of the 18th International Conference on Agents and Artificial Intelligence. Vol 2. Science and Technology Publications; 2026:1536-1546. doi:10.5220/0014326500004052' apa: 'Hatua, A., Nguyen, T. T., Cano Cordoba, F., & Sung, A. H. (2026). Machine unlearning using forgetting neural networks. In Proceedings of the 18th International Conference on Agents and Artificial Intelligence (Vol. 2, pp. 1536–1546). Marbella, Spain: Science and Technology Publications. https://doi.org/10.5220/0014326500004052' chicago: Hatua, Amartya, Trung T. Nguyen, Filip Cano Cordoba, and Andrew H. Sung. “Machine Unlearning Using Forgetting Neural Networks.” In Proceedings of the 18th International Conference on Agents and Artificial Intelligence, 2:1536–46. Science and Technology Publications, 2026. https://doi.org/10.5220/0014326500004052. ieee: A. Hatua, T. T. Nguyen, F. Cano Cordoba, and A. H. Sung, “Machine unlearning using forgetting neural networks,” in Proceedings of the 18th International Conference on Agents and Artificial Intelligence, Marbella, Spain, 2026, vol. 2, pp. 1536–1546. 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.' mla: Hatua, Amartya, et al. “Machine Unlearning Using Forgetting Neural Networks.” Proceedings of the 18th International Conference on Agents and Artificial Intelligence, vol. 2, Science and Technology Publications, 2026, pp. 1536–46, doi:10.5220/0014326500004052. 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. conference: end_date: 2026-03-08 location: Marbella, Spain name: 'ICAART: International Conference on Agents and Artificial Intelligence' start_date: 2026-03-05 das_tickbox: '0' date_created: 2026-06-21T22:03:01Z date_published: 2026-04-01T00:00:00Z date_updated: 2026-10-20T14:05:02Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.5220/0014326500004052 ec_funded: 1 external_id: arxiv: - '2410.22374' file: - access_level: open_access checksum: d0f5212846c8f3129509b081648465cb content_type: application/pdf creator: dernst date_created: 2026-10-20T14:00:27Z date_updated: 2026-10-20T14:00:27Z file_id: '23178' file_name: 2026_CAART_Hatua.pdf file_size: 779692 relation: main_file success: 1 file_date_updated: 2026-10-20T14:00:27Z fulldoi: https://doi.org/10.5220/0014326500004052 has_accepted_license: '1' intvolume: ' 2' keyword: - Machine Unlearning - Neuroscience-Inspired Machine Learning - Membership Inference Attacks language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1536-1546 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: Proceedings of the 18th International Conference on Agents and Artificial Intelligence publication_identifier: eissn: - 2184-433X isbn: - '9789897587962' issn: - 2184-3589 publication_status: published publisher: Science and Technology Publications quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Machine unlearning using forgetting neural networks tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22970' 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]. 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). article_number: '260' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Francois L full_name: Visconti, Francois L id: 8d897387-8b69-11f1-b3df-9a1e4632e81d last_name: Visconti citation: ama: Visconti FL. Average-field approximation for dilute almost-bosonic anyons. Calculus of Variations and Partial Differential Equations. 2026;65(9). doi:10.1007/s00526-026-03428-9 apa: Visconti, F. L. (2026). Average-field approximation for dilute almost-bosonic anyons. Calculus of Variations and Partial Differential Equations. Springer. https://doi.org/10.1007/s00526-026-03428-9 chicago: Visconti, Francois L. “Average-Field Approximation for Dilute Almost-Bosonic Anyons.” Calculus of Variations and Partial Differential Equations. Springer, 2026. https://doi.org/10.1007/s00526-026-03428-9. ieee: F. L. Visconti, “Average-field approximation for dilute almost-bosonic anyons,” Calculus of Variations and Partial Differential Equations, vol. 65, no. 9. Springer, 2026. ista: Visconti FL. 2026. Average-field approximation for dilute almost-bosonic anyons. Calculus of Variations and Partial Differential Equations. 65(9), 260. mla: Visconti, Francois L. “Average-Field Approximation for Dilute Almost-Bosonic Anyons.” Calculus of Variations and Partial Differential Equations, vol. 65, no. 9, 260, Springer, 2026, doi:10.1007/s00526-026-03428-9. short: F.L. Visconti, Calculus of Variations and Partial Differential Equations 65 (2026). das_tickbox: '1' dataavailabilitystatement: Data sharing not applicable to this article as no datasets were generated or analysed during the current study. date_created: 2026-09-22T05:35:39Z date_published: 2026-09-12T00:00:00Z date_updated: 2026-10-20T14:10:55Z day: '12' ddc: - '500' doi: 10.1007/s00526-026-03428-9 extern: '1' external_id: pmid: - '42733399' file: - access_level: open_access checksum: 4599427a622cd93a96e3ca0465e0ccf5 content_type: application/pdf creator: dernst date_created: 2026-10-20T14:08:18Z date_updated: 2026-10-20T14:08:18Z file_id: '23179' file_name: 2026_CalculusVariations_Visconti.pdf file_size: 587149 relation: main_file success: 1 file_date_updated: 2026-10-20T14:08:18Z fulldoi: https://doi.org/10.1007/s00526-026-03428-9 has_accepted_license: '1' intvolume: ' 65' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Calculus of Variations and Partial Differential Equations publication_identifier: eissn: - 1432-0835 issn: - 0944-2669 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Average-field approximation for dilute almost-bosonic anyons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 65 year: '2026' ... --- OA_place: repository OA_type: green _id: '22359' 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. acknowledgement: Supported by ERC Advanced Grant “RMTBeyond” No. 101020331 article_number: '2607.05848' article_processing_charge: No arxiv: 1 author: - first_name: Jaehun full_name: Lee, Jaehun id: 96155047-f36a-11ef-b766-8b5ae7cecd49 last_name: Lee - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: ama: Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. arXiv. doi:10.48550/arXiv.2607.05848 apa: Lee, J., & Erdös, L. (n.d.). Mesoscopic eigenvalue statistics for correlated random matrices. arXiv. https://doi.org/10.48550/arXiv.2607.05848 chicago: Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2607.05848. ieee: J. Lee and L. Erdös, “Mesoscopic eigenvalue statistics for correlated random matrices,” arXiv. . ista: Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. arXiv, 2607.05848. mla: Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices.” ArXiv, 2607.05848, doi:10.48550/arXiv.2607.05848. short: J. Lee, L. Erdös, ArXiv (n.d.). corr_author: '1' das_tickbox: '1' date_created: 2026-07-18T08:59:02Z date_published: 2026-07-07T00:00:00Z date_updated: 2026-10-20T10:06:12Z day: '07' department: - _id: LaEr doi: 10.48550/arXiv.2607.05848 ec_funded: 1 external_id: arxiv: - '2607.05848' fulldoi: https://doi.org/10.48550/arXiv.2607.05848 keyword: - Central limit theorem - universality - matrix Dyson equation - multi-resolvent local law language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2607.05848 month: '07' oa: 1 oa_version: Preprint project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: arXiv publication_status: submitted status: public title: Mesoscopic eigenvalue statistics for correlated random matrices type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: diamond PlanS_conform: '1' _id: '22381' 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." 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)." article_number: A387 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: G. full_name: Marcel, G. last_name: Marcel - first_name: S. G. D. full_name: Turner, S. G. D. last_name: Turner - first_name: B. J. full_name: Ricketts, B. J. last_name: Ricketts - first_name: V. full_name: López-Barquero, V. last_name: López-Barquero - first_name: D. J. K. full_name: Buisson, D. J. K. last_name: Buisson - first_name: F. full_name: Vincentelli, F. last_name: Vincentelli - first_name: M. full_name: Middleton, M. last_name: Middleton - first_name: C.S. full_name: Reynolds, C.S. last_name: Reynolds - first_name: Mark full_name: Avara, Mark id: c9b42585-7787-11f0-9bdd-bf7d947cf79d last_name: Avara citation: 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. Astronomy & Astrophysics. 2026;710. doi:10.1051/0004-6361/202558103' 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. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202558103' 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.” Astronomy & Astrophysics. EDP Sciences, 2026. https://doi.org/10.1051/0004-6361/202558103.' ieee: 'G. Marcel et al., “Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations,” Astronomy & Astrophysics, vol. 710. EDP Sciences, 2026.' 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 & Astrophysics. 710, A387.' mla: 'Marcel, G., et al. “Disk Warping and Black Hole X-Ray Binaries: I. Tentative Unification of Low-Frequency Quasi-Periodic Oscillations.” Astronomy & Astrophysics, vol. 710, A387, EDP Sciences, 2026, doi:10.1051/0004-6361/202558103.' 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 & Astrophysics 710 (2026). das_tickbox: '0' date_created: 2026-07-21T10:29:36Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-10-21T06:33:09Z day: '01' ddc: - '520' department: - _id: ZoHa doi: 10.1051/0004-6361/202558103 external_id: arxiv: - '2511.10474' file: - access_level: open_access checksum: 95c1695f3c7183b2ad9d58167500b18d content_type: application/pdf creator: dernst date_created: 2026-07-21T12:20:49Z date_updated: 2026-07-21T12:20:49Z file_id: '22382' file_name: 2026_AstronomyAstrophysics_Marcel.pdf file_size: 3286905 relation: main_file success: 1 file_date_updated: 2026-07-21T12:20:49Z fulldoi: https://doi.org/10.1051/0004-6361/202558103 has_accepted_license: '1' intvolume: ' 710' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: 'Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 710 year: '2026' ... --- OA_place: publisher _id: '22399' alternative_title: - ISTA Master’s Thesis article_processing_charge: No author: - first_name: Aleksa full_name: Spasić, Aleksa id: ecee9d38-4040-11ef-8843-b941efb445d6 last_name: Spasić citation: ama: Spasić A. Studying the evolutionary systems biology of the lac operon. 2026. doi:10.15479/AT-ISTA-22399 apa: Spasić, A. (2026). Studying the evolutionary systems biology of the lac operon. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22399 chicago: Spasić, Aleksa. “Studying the Evolutionary Systems Biology of the Lac Operon.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22399. ieee: A. Spasić, “Studying the evolutionary systems biology of the lac operon,” Institute of Science and Technology Austria, 2026. ista: Spasić A. 2026. Studying the evolutionary systems biology of the lac operon. Institute of Science and Technology Austria. mla: Spasić, Aleksa. Studying the Evolutionary Systems Biology of the Lac Operon. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22399. short: A. Spasić, Studying the Evolutionary Systems Biology of the Lac Operon, Institute of Science and Technology Austria, 2026. corr_author: '1' das_tickbox: '0' date_created: 2026-07-25T13:08:32Z date_published: 2026-07-27T00:00:00Z date_updated: 2026-10-21T07:47:08Z day: '27' ddc: - '576' degree_awarded: MS department: - _id: GradSch - _id: GaTk - _id: CaGu doi: 10.15479/AT-ISTA-22399 doi_confirm: '1' file: - access_level: closed checksum: c29880dd71fcc37f23ac6e2843066ede content_type: application/pdf creator: aspasic date_created: 2026-07-27T13:00:07Z date_updated: 2026-10-20T08:47:40Z embargo: 2027-07-30 embargo_to: open_access file_id: '22588' file_name: Aleksa_Spasic_Thesis_final.pdf file_size: 1986078 relation: main_file - access_level: closed checksum: 4ebe3bd2d833d913c0756343cca5e5f0 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: aspasic date_created: 2026-07-27T13:00:22Z date_updated: 2026-07-27T13:07:23Z file_id: '22589' file_name: Thesis_final.docx file_size: 1868853 relation: source_file file_date_updated: 2026-10-20T08:47:40Z fulldoi: https://doi.org/10.15479/AT-ISTA-22399 has_accepted_license: '1' language: - iso: eng month: '07' oa_version: Published Version page: '32' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 title: Studying the evolutionary systems biology of the lac operon type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '22281' 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." 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Antoine full_name: El-Hayek, Antoine id: 888a098e-fcac-11ee-aff7-d347be57b725 last_name: El-Hayek orcid: 0000-0003-4268-7368 citation: ama: 'El-Hayek A. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. 2026. doi:10.15479/AT-ISTA-22281' apa: 'El-Hayek, A. (2026). Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22281' chicago: 'El-Hayek, Antoine. “Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22281.' ieee: 'A. El-Hayek, “Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks,” Institute of Science and Technology Austria, 2026.' ista: 'El-Hayek A. 2026. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. Institute of Science and Technology Austria.' mla: 'El-Hayek, Antoine. Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22281.' short: 'A. El-Hayek, Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks, Institute of Science and Technology Austria, 2026.' corr_author: '1' date_created: 2026-07-13T09:39:59Z date_published: 2026-07-13T00:00:00Z date_updated: 2026-10-21T08:05:35Z day: '13' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: MoHe doi: 10.15479/AT-ISTA-22281 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: 923e4ca769c9ef2f6b0b005444faf462 content_type: application/pdf creator: aelhayek date_created: 2026-07-17T11:39:47Z date_updated: 2026-07-17T11:39:47Z file_id: '22356' file_name: 2026_El-Hayek_Antoine_Thesis.pdf file_size: 5465973 relation: main_file success: 1 - access_level: closed checksum: 262689f9df27dd6c2c7c7861f1de7329 content_type: application/x-zip-compressed creator: aelhayek date_created: 2026-07-17T11:40:34Z date_updated: 2026-07-20T11:29:38Z file_id: '22357' file_name: 2026_El-Hayek_Antoine_Thesis.zip file_size: 9116107 relation: source_file file_date_updated: 2026-07-20T11:29:38Z fulldoi: https://doi.org/10.15479/AT-ISTA-22281 has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '244' project: - _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62 call_identifier: H2020 grant_number: '101019564' name: The design and evaluation of modern fully dynamic data structures - _id: bda196b2-d553-11ed-ba76-8e8ee6c21103 grant_number: I05982 name: Static and Dynamic Hierarchical Graph Decompositions - _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe grant_number: P33775 name: Fast Algorithms for a Reactive Network Layer publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publisher_comment: Sections 2.4 and 7.1 and chapter 6 are not CC-BY 4.0, they are All Rights Reserved. related_material: record: - id: '20051' relation: part_of_dissertation status: public - id: '19982' relation: part_of_dissertation status: public - id: '21720' relation: part_of_dissertation status: public - id: '22374' relation: part_of_dissertation status: public - id: '22373' relation: part_of_dissertation status: public - id: '18557' relation: part_of_dissertation status: public status: public supervisor: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 title: 'Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '20991' 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." 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)" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Diego Fernando full_name: Garcia Castillo, Diego Fernando id: ae681a14-dc74-11ea-a0a7-c6ef18161701 last_name: Garcia Castillo citation: ama: Garcia Castillo DF. The genomic architecture of local adaptation in introduced populations. 2026. doi:10.15479/AT-ISTA-20991 apa: Garcia Castillo, D. F. (2026). The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20991 chicago: Garcia Castillo, Diego Fernando. “The Genomic Architecture of Local Adaptation in Introduced Populations.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-20991. ieee: D. F. Garcia Castillo, “The genomic architecture of local adaptation in introduced populations,” Institute of Science and Technology Austria, 2026. ista: Garcia Castillo DF. 2026. The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria. mla: Garcia Castillo, Diego Fernando. The Genomic Architecture of Local Adaptation in Introduced Populations. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-20991. short: D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced Populations, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-01-16T09:47:59Z date_published: 2026-01-16T00:00:00Z date_updated: 2026-10-21T08:18:21Z day: '16' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/AT-ISTA-20991 file: - access_level: closed checksum: 841f1bc073d667125729b2a017f8c37a content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dgarciac date_created: 2026-01-16T12:25:13Z date_updated: 2026-01-16T12:25:13Z file_id: '20996' file_name: 2026_Garcia_Diego_Thesis.docx file_size: 22456421 relation: source_file - access_level: open_access checksum: a1f33d4f183ce7072eee42a6ccf5340b content_type: application/pdf creator: dgarciac date_created: 2026-01-16T12:25:13Z date_updated: 2026-01-16T12:25:13Z file_id: '20997' file_name: 2026_Garcia_Diego_Thesis.pdf file_size: 9556719 relation: main_file success: 1 - access_level: closed checksum: 98a80691067174c30fe53f38ce7344e6 content_type: application/x-compressed creator: dgarciac date_created: 2026-01-16T13:08:14Z date_updated: 2026-01-16T13:08:14Z 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. file_id: '20998' file_name: 2026_DiegoGarcia_LittorinaDB Source Code and Protocols.rar file_size: 54491433 relation: supplementary_material - access_level: open_access checksum: 99a3cab2fa36666b9a92eefc27d586da content_type: application/x-compressed creator: dgarciac date_created: 2026-01-16T13:08:14Z date_updated: 2026-01-16T13:08:14Z file_id: '20999' file_name: 2026_DiegoGarcia_Thesis-Supplementary_Material.rar file_size: 7982811 relation: supplementary_material - access_level: open_access checksum: 255fdf56b2932c46bf27c63aa6106a4f content_type: text/plain creator: dgarciac date_created: 2026-01-16T13:08:59Z date_updated: 2026-01-16T13:08:59Z file_id: '21000' file_name: README.txt file_size: 732 relation: supplementary_material file_date_updated: 2026-01-16T13:08:59Z fulldoi: https://doi.org/10.15479/AT-ISTA-20991 has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '199' publication_identifier: isbn: - 978-3-99078-077-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18498' relation: research_data status: public - id: '18491' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 title: The genomic architecture of local adaptation in introduced populations tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2026' ... --- OA_place: publisher _id: '22684' abstract: - lang: eng 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." acknowledged_ssus: - _id: NanoFab - _id: ScienComp - _id: LifeSc - _id: M-Shop - _id: EM-Fac 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Felix full_name: Pertl, Felix id: 6313aec0-15b2-11ec-abd3-ed67d16139af last_name: Pertl orcid: 0000-0003-0463-5794 citation: ama: Pertl F. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. 2026. doi:10.15479/AT-ISTA-22684 apa: Pertl, F. (2026). Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22684 chicago: Pertl, Felix. “Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22684. 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. mla: Pertl, Felix. Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22684. short: F. Pertl, Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-08-12T09:44:40Z date_published: 2026-08-12T00:00:00Z date_updated: 2026-10-21T08:39:24Z day: '12' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: ScWa doi: 10.15479/AT-ISTA-22684 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: 0a4f5a941c40b921447e72291d72bc6f content_type: application/x-zip-compressed creator: fpertl date_created: 2026-08-12T13:04:21Z date_updated: 2026-08-12T13:04:21Z file_id: '22690' file_name: 2026_Pertl_Felix_Thesis.zip file_size: 31192621 relation: source_file - access_level: open_access checksum: ae60dcdb363222138886b2857643d4e3 content_type: application/pdf creator: fpertl date_created: 2026-08-12T13:04:21Z date_updated: 2026-08-12T13:04:21Z file_id: '22691' file_name: 2026_Pertl_Felix_Thesis.pdf file_size: 27882509 relation: main_file file_date_updated: 2026-08-12T13:04:21Z fulldoi: https://doi.org/10.15479/AT-ISTA-22684 has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '107' project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication_identifier: isbn: - 978-3-99078-083-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20481' relation: part_of_dissertation status: public - id: '12109' relation: part_of_dissertation status: public - id: '19278' relation: part_of_dissertation status: public - id: '17373' relation: part_of_dissertation status: public status: public supervisor: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 title: Experimental probing of nanoscale charge features and surface morphology changes during tribocharging tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '17437' 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. 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." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Tanguy full_name: Vernet, Tanguy id: 19f1e3bf-c59a-11ee-a1af-ed269948817b last_name: Vernet citation: ama: Vernet T. Rational singularities for moment maps of totally negative quivers. Transformation Groups. 2026;31:1047-1083. doi:10.1007/s00031-024-09873-0 apa: Vernet, T. (2026). Rational singularities for moment maps of totally negative quivers. Transformation Groups. Springer Nature. https://doi.org/10.1007/s00031-024-09873-0 chicago: Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” Transformation Groups. Springer Nature, 2026. https://doi.org/10.1007/s00031-024-09873-0. ieee: T. Vernet, “Rational singularities for moment maps of totally negative quivers,” Transformation Groups, vol. 31. Springer Nature, pp. 1047–1083, 2026. ista: Vernet T. 2026. Rational singularities for moment maps of totally negative quivers. Transformation Groups. 31, 1047–1083. mla: Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” Transformation Groups, vol. 31, Springer Nature, 2026, pp. 1047–83, doi:10.1007/s00031-024-09873-0. short: T. Vernet, Transformation Groups 31 (2026) 1047–1083. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: Not applicable. date_created: 2024-08-18T22:01:04Z date_published: 2026-03-01T00:00:00Z date_updated: 2026-10-21T10:55:21Z day: '01' ddc: - '510' department: - _id: TaHa doi: 10.1007/s00031-024-09873-0 ec_funded: 1 external_id: isi: - '001287455300001' file: - access_level: open_access checksum: 8985b4154b730284d3412ddc9e55d965 content_type: application/pdf creator: dernst date_created: 2026-07-23T05:50:09Z date_updated: 2026-07-23T05:50:09Z file_id: '22385' file_name: 2026_TransformationGroups_Vernet.pdf file_size: 912029 relation: main_file success: 1 file_date_updated: 2026-07-23T05:50:09Z fulldoi: https://doi.org/10.1007/s00031-024-09873-0 has_accepted_license: '1' intvolume: ' 31' isi: 1 language: - iso: eng mathsc: - 14B05 - 14D23 - 14G20 - 16G20 month: '03' oa: 1 oa_version: Published Version page: 1047-1083 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Transformation Groups publication_identifier: eissn: - 1531-586X issn: - 1083-4362 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: not applicable scopus_import: '1' status: public supplementarymaterial: no title: Rational singularities for moment maps of totally negative quivers tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 31 year: '2026' ...