[{"date_updated":"2026-07-28T06:49:58Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2026-03-01T00:00:00Z","article_number":"e2024RG000869","doi":"10.1029/2024RG000869","OA_place":"publisher","article_type":"original","oa":1,"ddc":["550"],"month":"03","PlanS_conform":"1","license":"https://creativecommons.org/licenses/by/4.0/","author":[{"last_name":"Sauter","full_name":"Sauter, T.","first_name":"T."},{"first_name":"B. W.","full_name":"Brock, B. W.","last_name":"Brock"},{"full_name":"Collier, E.","last_name":"Collier","first_name":"E."},{"first_name":"B.","full_name":"Goger, B.","last_name":"Goger"},{"full_name":"Groos, A. R.","last_name":"Groos","first_name":"A. R."},{"last_name":"Haualand","full_name":"Haualand, K. F.","first_name":"K. F."},{"full_name":"Mott, R.","last_name":"Mott","first_name":"R."},{"full_name":"Nicholson, L.","last_name":"Nicholson","first_name":"L."},{"last_name":"Prinz","full_name":"Prinz, R.","first_name":"R."},{"orcid":"0000-0001-7640-6152","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","first_name":"Thomas","last_name":"Shaw","full_name":"Shaw, Thomas"},{"first_name":"I.","full_name":"Stiperski, I.","last_name":"Stiperski"},{"first_name":"A.","full_name":"Georgi, A.","last_name":"Georgi"},{"last_name":"Haugeneder","full_name":"Haugeneder, M.","first_name":"M."},{"full_name":"Mandal, A.","last_name":"Mandal","first_name":"A."},{"first_name":"D.","full_name":"Reynolds, D.","last_name":"Reynolds"},{"first_name":"M.","full_name":"Saigger, M.","last_name":"Saigger"},{"last_name":"Sicart","full_name":"Sicart, J. E.","first_name":"J. E."},{"full_name":"Voordendag, A.","last_name":"Voordendag","first_name":"A."}],"date_created":"2026-01-11T23:01:33Z","das_tickbox":"1","publication":"Reviews of Geophysics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work is the result of collaboration and discussions within HEFEX II, and we are grateful to all colleagues who have contributed to and enriched these discussions in various ways. T. Sauter acknowledges funding from the German Research Foundation (DFG) (Grant 543257843). This research was funded in part by the Austrian Science Fund (FWF) (Grant https://doi.org/10.55776/P36624 and https://doi.org/10.55776/P36306) for which E. Collier and R. Prinz are grateful. A. R. Groos, T. E. Shaw, R. Mott and M. Haugeneder acknowledge Transnational Access from the European Union's H2020 project INTERACT III (Grant 871120) for participation in the HEFEX II campaign and working group. I. Stiperski (Grant Agreement No. 101001691) and A. R. Groos (Grant Agreement No. 948290) acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program. R. Mott acknowledges funding from the Swiss National Science Foundation (SNSF) (Grant 200021_219918). B. Goger is supported by EXCLAIM, a project funded by ETH Zurich. J.E. Sicart acknowledges LabEx OSUG@2020 (Investissements d'avenir - ANR10 LABX56) for participation in the HEFEX II campaign and working group. T. E. Shaw acknowledges funding from the EU Horizon 2020 Marie Skłodowska-Curie Grant 101026058 and 101034413. K. F. Haualand and T. Sauter are supported by the JOSTICE project funded by the Research Council of Norway (RCN Grant 302458).","dataavailabilitystatement":"Data were not used, nor created for this research. Software (other than for typesetting) was not used for this research.","citation":{"mla":"Sauter, T., et al. “Glacier-Atmosphere Interactions and Feedbacks in High-Mountain Regions - A Review.” <i>Reviews of Geophysics</i>, vol. 64, no. 1, e2024RG000869, Wiley, 2026, doi:<a href=\"https://doi.org/10.1029/2024RG000869\">10.1029/2024RG000869</a>.","chicago":"Sauter, T., B. W. Brock, E. Collier, B. Goger, A. R. Groos, K. F. Haualand, R. Mott, et al. “Glacier-Atmosphere Interactions and Feedbacks in High-Mountain Regions - A Review.” <i>Reviews of Geophysics</i>. Wiley, 2026. <a href=\"https://doi.org/10.1029/2024RG000869\">https://doi.org/10.1029/2024RG000869</a>.","ama":"Sauter T, Brock BW, Collier E, et al. Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review. <i>Reviews of Geophysics</i>. 2026;64(1). doi:<a href=\"https://doi.org/10.1029/2024RG000869\">10.1029/2024RG000869</a>","ista":"Sauter T, Brock BW, Collier E, Goger B, Groos AR, Haualand KF, Mott R, Nicholson L, Prinz R, Shaw T, Stiperski I, Georgi A, Haugeneder M, Mandal A, Reynolds D, Saigger M, Sicart JE, Voordendag A. 2026. Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review. Reviews of Geophysics. 64(1), e2024RG000869.","short":"T. Sauter, B.W. Brock, E. Collier, B. Goger, A.R. Groos, K.F. Haualand, R. Mott, L. Nicholson, R. Prinz, T. Shaw, I. Stiperski, A. Georgi, M. Haugeneder, A. Mandal, D. Reynolds, M. Saigger, J.E. Sicart, A. Voordendag, Reviews of Geophysics 64 (2026).","ieee":"T. Sauter <i>et al.</i>, “Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review,” <i>Reviews of Geophysics</i>, vol. 64, no. 1. Wiley, 2026.","apa":"Sauter, T., Brock, B. W., Collier, E., Goger, B., Groos, A. R., Haualand, K. F., … Voordendag, A. (2026). Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review. <i>Reviews of Geophysics</i>. Wiley. <a href=\"https://doi.org/10.1029/2024RG000869\">https://doi.org/10.1029/2024RG000869</a>"},"publication_identifier":{"eissn":["1944-9208"],"issn":["8755-1209"]},"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"day":"01","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publisher":"Wiley","issue":"1","volume":64,"has_accepted_license":"1","researchdata_availability":"no","file_date_updated":"2026-07-28T06:48:08Z","year":"2026","supplementarymaterial":"no","ec_funded":1,"file":[{"file_id":"22594","file_size":3012737,"success":1,"checksum":"9d46167619be91210c45ee9e1f187395","access_level":"open_access","date_updated":"2026-07-28T06:48:08Z","date_created":"2026-07-28T06:48:08Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_name":"2026_ReviewsGeophysics_Sauter.pdf"}],"status":"public","intvolume":"        64","type":"journal_article","title":"Glacier-atmosphere interactions and feedbacks in high-mountain regions - A review","abstract":[{"lang":"eng","text":"Mountain glaciers are among the natural systems most vulnerable to climate change. However, their interactions with the atmosphere are complex and not fully understood. These interactions can trigger rapid adjustments and climate feedbacks that either amplify or attenuate atmospheric signals, influencing both glacier response and large-scale atmospheric circulation. Observing this functional coupling in nature is challenging because the key processes occur over a wide range of spatial and temporal scales. However, recent advances in observational techniques and modeling have provided new insights into these interactions. In this review, we summarize the current state of knowledge on glacier-atmosphere interactions in high-mountain regions at different scales, and highlight recent advances in observational and numerical modeling. We also highlight important knowledge gaps and outline future research directions to improve the prediction of glacier change in a warming world."}],"department":[{"_id":"FrPe"}],"OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","_id":"20971"},{"acknowledgement":"We thank Nikolai R. Skrynnikov and Olga O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to Tobias Schubeis (Lyon) for advice with GB1 crystallization, and Rebecca Schmid for initial crystallization trials.\r\nWe thank Sebastian Falkner for assistance with constructing the structural model of the IgG:GB1 complex.\r\nThis research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank Petra Rovó and Margarita Valhondo Falcón for excellent support of the NMR facility.\r\nLea M. Becker is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01). Christophe Chipot acknowledges the European Research Council (grant project 101097272 ``MilliInMicro'') and the Métropole du Grand Nancy (grant project ``ARC''). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-02-05T13:54:39Z","citation":{"mla":"Becker, Lea Marie, et al. <i>Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.”</i> Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21145\">10.15479/AT-ISTA-21145</a>.","ieee":"L. M. Becker, P. Schanda, and C. Chipot, “Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2026.","short":"L.M. Becker, P. Schanda, C. Chipot, (2026).","ama":"Becker LM, Schanda P, Chipot C. Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21145\">10.15479/AT-ISTA-21145</a>","ista":"Becker LM, Schanda P, Chipot C. 2026. Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21145\">10.15479/AT-ISTA-21145</a>.","chicago":"Becker, Lea Marie, Paul Schanda, and Christophe Chipot. “Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21145\">https://doi.org/10.15479/AT-ISTA-21145</a>.","apa":"Becker, L. M., Schanda, P., &#38; Chipot, C. (2026). Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21145\">https://doi.org/10.15479/AT-ISTA-21145</a>"},"contributor":[{"last_name":"Fu","first_name":"Haohao","contributor_type":"researcher"},{"id":"71cda2f3-e604-11ee-a1df-da10587eda3f","contributor_type":"researcher","last_name":"Tatman","first_name":"Benjamin"},{"contributor_type":"researcher","last_name":"Dreydoppel","first_name":"Matthias"},{"last_name":"Kapitonova","first_name":"Anna","id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","contributor_type":"researcher"},{"id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","contributor_type":"researcher","orcid":"0000-0001-7597-043X","last_name":"Balazs","first_name":"Daniel"},{"contributor_type":"researcher","first_name":"Ulrich","last_name":"Weininger"},{"last_name":"Engilberge","first_name":"Sylvain","contributor_type":"researcher"}],"project":[{"grant_number":"26777","name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches","_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0"}],"day":"09","publisher":"Institute of Science and Technology Austria","date_published":"2026-02-09T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"oa_version":"Published Version","date_updated":"2026-07-28T06:59:15Z","month":"02","corr_author":"1","oa":1,"ddc":["572"],"doi":"10.15479/AT-ISTA-21145","author":[{"id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151","last_name":"Becker","full_name":"Becker, Lea Marie","first_name":"Lea Marie"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul"},{"last_name":"Chipot","full_name":"Chipot, Christophe","first_name":"Christophe"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","abstract":[{"lang":"eng","text":"Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions. "}],"title":"Additional Data for \"Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes\"","type":"research_data","related_material":{"record":[{"id":"20641","status":"public","relation":"earlier_version"},{"status":"public","id":"22105","relation":"used_in_publication"}]},"department":[{"_id":"GradSch"},{"_id":"PaSc"}],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"_id":"21145","has_accepted_license":"1","file_date_updated":"2026-02-05T13:52:41Z","year":"2026","status":"public","file":[{"checksum":"02a419cce8cea450bc952f35488d2df5","access_level":"open_access","file_id":"21146","file_size":4263,"content_type":"text/plain","date_updated":"2026-02-05T13:52:37Z","creator":"lbecker","date_created":"2026-02-05T13:52:37Z","file_name":"README.txt","relation":"table_of_contents"},{"content_type":"application/zip","date_updated":"2026-02-05T13:52:41Z","date_created":"2026-02-05T13:52:41Z","creator":"lbecker","file_name":"Research_Data.zip","relation":"main_file","file_id":"21147","file_size":50647107,"success":1,"checksum":"b0b82b1aa73985b0b308a3fa52d21aea","access_level":"open_access"}]},{"OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","_id":"20935","quality_controlled":"1","page":"213-230.e7","type":"journal_article","abstract":[{"text":"In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate the structures of biomolecules in their native context. However, challenges remain for the efficient production and sharing of large-scale cryo-ET datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB) milling with recent advances in cryo-ET acquisition and processing to generate a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii, which we provide as a community resource to drive method development and inspire biological discovery. To assay data quality, we performed subtomogram averaging of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset as well as the promise of modern cryo-ET workflows and open data sharing to empower visual proteomics.","lang":"eng"}],"title":"Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii","department":[{"_id":"AlMi"}],"year":"2026","supplementarymaterial":"yes","intvolume":"        86","status":"public","file":[{"content_type":"application/pdf","date_updated":"2026-07-28T07:38:45Z","creator":"dernst","date_created":"2026-07-28T07:38:45Z","file_name":"2026_MolecularCell_Kelley.pdf","relation":"main_file","file_id":"22599","file_size":26749637,"success":1,"checksum":"96a2f8519124d1a0d9de8d2594bf7147","access_level":"open_access"}],"issue":"1","has_accepted_license":"1","volume":86,"file_date_updated":"2026-07-28T07:38:45Z","researchdata_availability":"yes","publication_identifier":{"eissn":["1097-4164"],"issn":["1097-2765"]},"scopus_import":"1","language":[{"iso":"eng"}],"day":"08","publisher":"Elsevier","publication_status":"published","publication":"Molecular Cell","date_created":"2026-01-04T23:01:36Z","das_tickbox":"1","acknowledgement":"Calculations were performed at the Max Planck Institute of Biochemistry and the Raven Supercomputer of the Max Planck Computing and Data Facility (MPCDF) in Garching, Germany; at the sciCORE (http://scicore.unibas.ch/) scientific computing center at the University of Basel, Switzerland; and at Thermo Fisher Scientific, in Eindhoven, the Netherlands. This work was supported by Thermo Fisher Scientific. All lamella preparations and tilt-series collections used in this work were conducted at Thermo Fisher R&D facilities in Brno and Eindhoven, utilizing Arctis and Krios microscopes. This work was also supported by the ERC consolidator grant “cryOcean” (fulfilled by the Swiss State Secretariat for Education, Research and Innovation, M822.00045) as well as a Swiss Nanoscience Institute PhD school grant to B.D.E. and P.V.d.S., an EMBO long-term postdoctoral fellowship (ALTF-383-2022) to G.T., an SNSF Postdoctoral Fellowship (project 210561) to F.W., a Boehringer Ingelheim Fonds fellowship to L.L., and by the Max Planck Society to J.A.G.B. and J.M.P.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","dataavailabilitystatement":"Raw EM data are available at the EMPIAR under accession code EMPIAR: EMPIAR-11830. Annotation and processing information for all 1,829 tomograms are provided in spreadsheet format.153 The following subtomogram averages have been deposited at the Electron Microscopy Data Bank (EMDB): 80S ribosome (EMDB: EMD-51847), nucleosome (EMDB: EMD-19906), PSII (EMDB: EMD-51731), Rubisco (EMDB: EMD-51848), microtubule (EMDB: EMD-51804), clathrin (EMDB: EMD-51789), and ATP synthase (EMDB: EMD-51802). Segmentations shown in Figures 2 and 3 are deposited on Zenodo (https://doi.org/10.5281/zenodo.15875785). Particle positions and orientations used for STA, along with all resources derived from this work, are available on GitHub (https://github.com/Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations). Reconstructed tomograms and annotations are also available to explore interactively at the CZII Cryo-ET Data Portal (DS-10302, https://cryoetdataportal.czscience.com/datasets/10302/). Raw data for cryo-PFIB/SEM slice-and-view of a whole C. reinhardtii cell has also been deposited (EMPIAR: EMPIAR-11275).\r\n\r\nThis paper does not report original code.\r\n\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","citation":{"ista":"Kelley R, Khavnekar S, Righetto RD, Heebner J, Obr M, Zhang X, Chakraborty S, Tagiltsev G, Michael AK, Van Dorst S, Waltz F, Mccafferty CL, Lamm L, Zufferey S, Van Der Stappen P, Van Den Hoek H, Wietrzynski W, Harar P, Wan W, Briggs JAG, Plitzko JM, Engel BD, Kotecha A. 2026. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell. 86(1), 213–230.e7.","short":"R. Kelley, S. Khavnekar, R.D. Righetto, J. Heebner, M. Obr, X. Zhang, S. Chakraborty, G. Tagiltsev, A.K. Michael, S. Van Dorst, F. Waltz, C.L. Mccafferty, L. Lamm, S. Zufferey, P. Van Der Stappen, H. Van Den Hoek, W. Wietrzynski, P. Harar, W. Wan, J.A.G. Briggs, J.M. Plitzko, B.D. Engel, A. Kotecha, Molecular Cell 86 (2026) 213–230.e7.","chicago":"Kelley, Ron, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin Obr, Xianjun Zhang, Saikat Chakraborty, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” <i>Molecular Cell</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">https://doi.org/10.1016/j.molcel.2025.11.029</a>.","ama":"Kelley R, Khavnekar S, Righetto RD, et al. Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. <i>Molecular Cell</i>. 2026;86(1):213-230.e7. doi:<a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">10.1016/j.molcel.2025.11.029</a>","ieee":"R. Kelley <i>et al.</i>, “Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii,” <i>Molecular Cell</i>, vol. 86, no. 1. Elsevier, p. 213–230.e7, 2026.","apa":"Kelley, R., Khavnekar, S., Righetto, R. D., Heebner, J., Obr, M., Zhang, X., … Kotecha, A. (2026). Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">https://doi.org/10.1016/j.molcel.2025.11.029</a>","mla":"Kelley, Ron, et al. “Toward Community-Driven Visual Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” <i>Molecular Cell</i>, vol. 86, no. 1, Elsevier, 2026, p. 213–230.e7, doi:<a href=\"https://doi.org/10.1016/j.molcel.2025.11.029\">10.1016/j.molcel.2025.11.029</a>."},"article_type":"original","OA_place":"publisher","doi":"10.1016/j.molcel.2025.11.029","PlanS_conform":"1","month":"01","oa":1,"ddc":["570"],"author":[{"first_name":"Ron","full_name":"Kelley, Ron","last_name":"Kelley"},{"first_name":"Sagar","full_name":"Khavnekar, Sagar","last_name":"Khavnekar"},{"first_name":"Ricardo D.","last_name":"Righetto","full_name":"Righetto, Ricardo D."},{"first_name":"Jessica","last_name":"Heebner","full_name":"Heebner, Jessica"},{"last_name":"Obr","full_name":"Obr, Martin","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564"},{"first_name":"Xianjun","full_name":"Zhang, Xianjun","last_name":"Zhang"},{"full_name":"Chakraborty, Saikat","last_name":"Chakraborty","first_name":"Saikat"},{"first_name":"Grigory","full_name":"Tagiltsev, Grigory","last_name":"Tagiltsev"},{"last_name":"Michael","full_name":"Michael, Alicia","first_name":"Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","orcid":"0000-0002-6080-839X"},{"last_name":"Van Dorst","full_name":"Van Dorst, Sofie","first_name":"Sofie"},{"first_name":"Florent","last_name":"Waltz","full_name":"Waltz, Florent"},{"last_name":"Mccafferty","full_name":"Mccafferty, Caitlyn L.","first_name":"Caitlyn L."},{"full_name":"Lamm, Lorenz","last_name":"Lamm","first_name":"Lorenz"},{"full_name":"Zufferey, Simon","last_name":"Zufferey","first_name":"Simon"},{"first_name":"Philippe","full_name":"Van Der Stappen, Philippe","last_name":"Van Der Stappen"},{"full_name":"Van Den Hoek, Hugo","last_name":"Van Den Hoek","first_name":"Hugo"},{"full_name":"Wietrzynski, Wojciech","last_name":"Wietrzynski","first_name":"Wojciech"},{"first_name":"Pavol","last_name":"Harar","full_name":"Harar, Pavol","orcid":"0000-0001-5206-1794","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5"},{"last_name":"Wan","full_name":"Wan, William","first_name":"William"},{"full_name":"Briggs, John A.G.","last_name":"Briggs","first_name":"John A.G."},{"first_name":"Jürgen M.","last_name":"Plitzko","full_name":"Plitzko, Jürgen M."},{"first_name":"Benjamin D.","last_name":"Engel","full_name":"Engel, Benjamin D."},{"last_name":"Kotecha","full_name":"Kotecha, Abhay","first_name":"Abhay"}],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-07-28T07:39:23Z","date_published":"2026-01-08T00:00:00Z"},{"department":[{"_id":"PreCl"}],"type":"journal_article","title":"Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response","abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","_id":"20858","page":"397-406","OA_type":"green","article_processing_charge":"No","researchdata_availability":"upon request","issue":"1","biorxivid":1,"volume":34,"intvolume":"        34","status":"public","year":"2026","supplementarymaterial":"yes","dataavailabilitystatement":"The data that support the findings of this study are available on request from the corresponding authors.","citation":{"mla":"Rica, Ramona, et al. “Langerhans Cell-Targeted Protein Delivery Enhances Antigen-Specific Cellular Immune Response.” <i>Molecular Therapy</i>, vol. 34, no. 1, Elsevier, 2026, pp. 397–406, doi:<a href=\"https://doi.org/10.1016/j.ymthe.2025.10.008\">10.1016/j.ymthe.2025.10.008</a>.","apa":"Rica, R., Klein, K., Johnson, L., Carta, G., Sarcevic, M., Langer, F., … Sparber, F. (2026). Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response. <i>Molecular Therapy</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ymthe.2025.10.008\">https://doi.org/10.1016/j.ymthe.2025.10.008</a>","ieee":"R. Rica <i>et al.</i>, “Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response,” <i>Molecular Therapy</i>, vol. 34, no. 1. Elsevier, pp. 397–406, 2026.","short":"R. Rica, K. Klein, L. Johnson, G. Carta, M. Sarcevic, F. Langer, C. Rademacher, R. Wawrzinek, F. Quattrone, F. Sparber, Molecular Therapy 34 (2026) 397–406.","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.","chicago":"Rica, Ramona, Klara Klein, Litty Johnson, Gabriele Carta, Mirza Sarcevic, Freyja Langer, Christoph Rademacher, Robert Wawrzinek, Federica Quattrone, and Florian Sparber. “Langerhans Cell-Targeted Protein Delivery Enhances Antigen-Specific Cellular Immune Response.” <i>Molecular Therapy</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.ymthe.2025.10.008\">https://doi.org/10.1016/j.ymthe.2025.10.008</a>.","ama":"Rica R, Klein K, Johnson L, et al. Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response. <i>Molecular Therapy</i>. 2026;34(1):397-406. doi:<a href=\"https://doi.org/10.1016/j.ymthe.2025.10.008\">10.1016/j.ymthe.2025.10.008</a>"},"date_created":"2025-12-28T23:01:26Z","publication":"Molecular Therapy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","publisher":"Elsevier","publication_status":"published","publication_identifier":{"issn":["1525-0016"],"eissn":["1525-0024"]},"day":"07","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"biorxivid":["10.1101/2025.05.05.652195"]},"date_updated":"2026-07-28T07:37:08Z","oa_version":"Preprint","date_published":"2026-01-07T00:00:00Z","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","last_name":"Carta","full_name":"Carta, Gabriele"},{"first_name":"Mirza","full_name":"Sarcevic, Mirza","last_name":"Sarcevic"},{"first_name":"Freyja","full_name":"Langer, Freyja","last_name":"Langer","id":"3C1BE782-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rademacher, Christoph","last_name":"Rademacher","first_name":"Christoph"},{"first_name":"Robert","last_name":"Wawrzinek","full_name":"Wawrzinek, Robert"},{"full_name":"Quattrone, Federica","last_name":"Quattrone","first_name":"Federica"},{"first_name":"Florian","full_name":"Sparber, Florian","last_name":"Sparber"}],"doi":"10.1016/j.ymthe.2025.10.008","OA_place":"repository","article_type":"original","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.05.05.652195"}],"month":"01"},{"publication":"Synlett","das_tickbox":"1","date_created":"2025-10-26T23:01:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Pieber, Bartholomäus. “Photochemical Cross-Couplings Using Semiconducting Materials.” <i>Synlett</i>, vol. 37, no. 1, Georg Thieme Verlag, 2026, pp. 43–54, doi:<a href=\"https://doi.org/10.1055/a-2690-9269\">10.1055/a-2690-9269</a>.","apa":"Pieber, B. (2026). Photochemical cross-couplings using semiconducting materials. <i>Synlett</i>. Georg Thieme Verlag. <a href=\"https://doi.org/10.1055/a-2690-9269\">https://doi.org/10.1055/a-2690-9269</a>","chicago":"Pieber, Bartholomäus. “Photochemical Cross-Couplings Using Semiconducting Materials.” <i>Synlett</i>. Georg Thieme Verlag, 2026. <a href=\"https://doi.org/10.1055/a-2690-9269\">https://doi.org/10.1055/a-2690-9269</a>.","ama":"Pieber B. Photochemical cross-couplings using semiconducting materials. <i>Synlett</i>. 2026;37(1):43-54. doi:<a href=\"https://doi.org/10.1055/a-2690-9269\">10.1055/a-2690-9269</a>","ista":"Pieber B. 2026. Photochemical cross-couplings using semiconducting materials. Synlett. 37(1), 43–54.","short":"B. Pieber, Synlett 37 (2026) 43–54.","ieee":"B. Pieber, “Photochemical cross-couplings using semiconducting materials,” <i>Synlett</i>, vol. 37, no. 1. Georg Thieme Verlag, pp. 43–54, 2026."},"publication_identifier":{"eissn":["1437-2096"],"issn":["0936-5214"]},"language":[{"iso":"eng"}],"scopus_import":"1","day":"01","publisher":"Georg Thieme Verlag","publication_status":"published","oa_version":"None","date_updated":"2026-07-28T07:42:47Z","date_published":"2026-01-01T00:00:00Z","external_id":{"isi":["001582268500001"]},"article_type":"original","doi":"10.1055/a-2690-9269","corr_author":"1","month":"01","author":[{"orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus","full_name":"Pieber, Bartholomäus","last_name":"Pieber"}],"type":"journal_article","abstract":[{"text":"In this personal account, I describe the work performed in my research group on the development of methods that harness heterogeneous photocatalysts for light-mediated nickel-catalyzed cross-couplings. This includes catalytic systems using carbon nitride materials, dye-sensitized TiO₂, covalent organic frameworks (COFs), and conjugated polymers. The rationale behind the selection of materials and how their use led to the identification of catalyst deactivation, structure–activity relationships, and future opportunities is discussed.","lang":"eng"}],"title":"Photochemical cross-couplings using semiconducting materials","isi":1,"department":[{"_id":"BaPi"}],"OA_type":"closed access","article_processing_charge":"No","_id":"20537","quality_controlled":"1","page":"43-54","issue":"1","volume":37,"year":"2026","status":"public","intvolume":"        37"},{"publisher":"Elsevier","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","project":[{"grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk"}],"day":"08","publication_identifier":{"eissn":["2666-979X"]},"citation":{"apa":"Krätschmer, I., Hegemann, L., Hofmeister, R. J., Corfield, E. C., Mahmoudi, M., Delaneau, O., … Robinson, M. R. (2026). Separating direct, indirect, and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">https://doi.org/10.1016/j.xgen.2026.101277</a>","ama":"Krätschmer I, Hegemann L, Hofmeister RJ, et al. Separating direct, indirect, and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>. 2026;6(7). doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">10.1016/j.xgen.2026.101277</a>","chicago":"Krätschmer, Ilse, Laura Hegemann, Robin J. Hofmeister, Elizabeth C. Corfield, Mahdi Mahmoudi, Olivier Delaneau, Ole A. Andreassen, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell Genomics</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">https://doi.org/10.1016/j.xgen.2026.101277</a>.","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.","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).","ieee":"I. Krätschmer <i>et al.</i>, “Separating direct, indirect, and parent-of-origin genetic effects in the human population,” <i>Cell Genomics</i>, vol. 6, no. 7. Elsevier, 2026.","mla":"Krätschmer, Ilse, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell Genomics</i>, vol. 6, no. 7, 101277, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">10.1016/j.xgen.2026.101277</a>."},"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.","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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Cell Genomics","das_tickbox":"1","date_created":"2026-06-10T07:39:08Z","DOAJ_listed":"1","author":[{"last_name":"Krätschmer","full_name":"Krätschmer, Ilse","first_name":"Ilse","id":"30d4014e-7753-11eb-b44b-db6d61112e73","orcid":"0000-0002-5636-9259"},{"first_name":"Laura","last_name":"Hegemann","full_name":"Hegemann, Laura"},{"first_name":"Robin J.","last_name":"Hofmeister","full_name":"Hofmeister, Robin J."},{"first_name":"Elizabeth C.","full_name":"Corfield, Elizabeth C.","last_name":"Corfield"},{"last_name":"Mahmoudi","full_name":"Mahmoudi, Mahdi","first_name":"Mahdi"},{"first_name":"Olivier","full_name":"Delaneau, Olivier","last_name":"Delaneau"},{"first_name":"Ole A.","last_name":"Andreassen","full_name":"Andreassen, Ole A."},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"first_name":"Caroline","full_name":"Hayward, Caroline","last_name":"Hayward"},{"first_name":"Riccardo E.","full_name":"Marioni, Riccardo E.","last_name":"Marioni"},{"full_name":"Ystrom, Eivind","last_name":"Ystrom","first_name":"Eivind"},{"last_name":"Havdahl","full_name":"Havdahl, Alexandra","first_name":"Alexandra"},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","last_name":"Robinson"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"07","corr_author":"1","oa":1,"ddc":["570"],"OA_place":"publisher","article_type":"original","doi":"10.1016/j.xgen.2026.101277","article_number":"101277","external_id":{"pmid":["40909755"]},"date_published":"2026-07-08T00:00:00Z","oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","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)"},"date_updated":"2026-07-28T07:27:01Z","_id":"21987","quality_controlled":"1","article_processing_charge":"Yes","acknowledged_ssus":[{"_id":"ScienComp"}],"OA_type":"gold","keyword":["direct genetic effects","DGE","indirect genetic effects","IGE","parent-of-origin effects","phenotypic variation","assortative mating","within-family GWAS","MoBa","EstBB"],"department":[{"_id":"MaRo"}],"abstract":[{"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.","lang":"eng"}],"title":"Separating direct, indirect, and parent-of-origin genetic effects in the human population","type":"journal_article","intvolume":"         6","status":"public","file":[{"success":1,"access_level":"open_access","checksum":"f896b510480d2d4e4a7fd46c2e2761f4","file_id":"22597","file_size":3679297,"date_created":"2026-07-28T07:24:50Z","date_updated":"2026-07-28T07:24:50Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_name":"2026_CellGenomics_Kraetschmer.pdf"}],"supplementarymaterial":"yes","year":"2026","pmid":1,"file_date_updated":"2026-07-28T07:24:50Z","researchdata_availability":"yes","has_accepted_license":"1","volume":6,"issue":"7"},{"article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"page":"169","_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."}],"title":"From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics","type":"dissertation","alternative_title":["ISTA Thesis"],"keyword":["Approximate Message Passing","GWAS","Genomics","Proteomics","Survival modeling"],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"21488"}]},"department":[{"_id":"GradSch"},{"_id":"MaRo"},{"_id":"MaMo"}],"year":"2026","doi_confirm":"1","status":"public","file":[{"file_id":"22316","file_size":25109878,"checksum":"9ab386790515628d957a194f30a7ccb4","access_level":"open_access","content_type":"application/pdf","date_created":"2026-07-13T14:52:19Z","date_updated":"2026-07-13T14:52:19Z","creator":"adepope","file_name":"2026_Depope_Al_Thesis.pdf","relation":"main_file"},{"relation":"source_file","file_name":"2026_Depope_Al_Thesis.zip","content_type":"application/zip","creator":"adepope","date_updated":"2026-07-13T14:56:41Z","date_created":"2026-07-13T14:56:41Z","file_size":1203199939,"file_id":"22317","checksum":"8ed8fb63f76a695d5b6fec35343f4b90","access_level":"closed"}],"has_accepted_license":"1","file_date_updated":"2026-07-13T14:56:41Z","language":[{"iso":"eng"}],"day":"11","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits","_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","grant_number":"101161364"},{"name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","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","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2026-07-10T13:27:20Z","das_tickbox":"1","citation":{"mla":"Depope, Al. <i>From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22258\">10.15479/AT-ISTA-22258</a>.","chicago":"Depope, Al. “From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22258\">https://doi.org/10.15479/AT-ISTA-22258</a>.","ama":"Depope A. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22258\">10.15479/AT-ISTA-22258</a>","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.","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.","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.","apa":"Depope, A. (2026). <i>From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22258\">https://doi.org/10.15479/AT-ISTA-22258</a>"},"corr_author":"1","month":"07","oa":1,"ddc":["576","610","006"],"OA_place":"publisher","doi":"10.15479/AT-ISTA-22258","degree_awarded":"PhD","author":[{"id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830","first_name":"Al","full_name":"Depope, Al","last_name":"Depope"}],"date_published":"2026-07-11T00:00:00Z","oa_version":"Published Version","date_updated":"2026-07-28T07:08:15Z","supervisor":[{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","last_name":"Robinson","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco"}]},{"date_created":"2026-03-23T15:10:03Z","das_tickbox":"1","publication":"Cell Genomics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","citation":{"apa":"Depope, A., Bajzik, J., Mondelli, M., &#38; Robinson, M. R. (2026). Joint modeling of whole-genome sequencing data for human height via approximate message passing. <i>Cell Genomics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xgen.2026.101162\">https://doi.org/10.1016/j.xgen.2026.101162</a>","ieee":"A. Depope, J. Bajzik, M. Mondelli, and M. R. Robinson, “Joint modeling of whole-genome sequencing data for human height via approximate message passing,” <i>Cell Genomics</i>, vol. 6, no. 5. Elsevier, 2026.","ama":"Depope A, Bajzik J, Mondelli M, Robinson MR. Joint modeling of whole-genome sequencing data for human height via approximate message passing. <i>Cell Genomics</i>. 2026;6(5). doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101162\">10.1016/j.xgen.2026.101162</a>","short":"A. Depope, J. Bajzik, M. Mondelli, M.R. Robinson, Cell Genomics 6 (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.","chicago":"Depope, Al, Jakub Bajzik, Marco Mondelli, and Matthew Richard Robinson. “Joint Modeling of Whole-Genome Sequencing Data for Human Height via Approximate Message Passing.” <i>Cell Genomics</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.xgen.2026.101162\">https://doi.org/10.1016/j.xgen.2026.101162</a>.","mla":"Depope, Al, et al. “Joint Modeling of Whole-Genome Sequencing Data for Human Height via Approximate Message Passing.” <i>Cell Genomics</i>, vol. 6, no. 5, 101162, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101162\">10.1016/j.xgen.2026.101162</a>."},"publication_identifier":{"eissn":["2666-979X"]},"day":"13","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"101161364","_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits"},{"grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publisher":"Elsevier","date_updated":"2026-07-28T07:08:15Z","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","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)"},"oa_version":"Published Version","date_published":"2026-05-13T00:00:00Z","external_id":{"pmid":["41713425"]},"article_number":"101162","doi":"10.1016/j.xgen.2026.101162","OA_place":"publisher","article_type":"original","oa":1,"ddc":["000","570"],"corr_author":"1","month":"05","author":[{"last_name":"Depope","full_name":"Depope, Al","first_name":"Al","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830"},{"full_name":"Bajzik, Jakub","last_name":"Bajzik","first_name":"Jakub","id":"b995e25b-8c4b-11ed-a6d8-f71b7bcd6122"},{"first_name":"Marco","full_name":"Mondelli, Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","last_name":"Robinson","full_name":"Robinson, Matthew Richard"}],"DOAJ_listed":"1","type":"journal_article","title":"Joint modeling of whole-genome sequencing data for human height via approximate message passing","abstract":[{"text":"Human height is a model for the genetic analysis of complex traits, and recent studies suggest the presence of thousands of common genetic variant associations and hundreds of low-frequency/rare variants. Here, we develop a new algorithmic paradigm based on approximate message passing (genomic vector approximate message passing [gVAMP]) for identifying DNA sequence variants associated with complex traits and common diseases in large-scale whole-genome sequencing (WGS) data. We show that gVAMP accurately localizes associations to variants with the correct frequency and position in the DNA, outperforming existing fine-mapping methods in selecting the appropriate genetic variants within WGS data. We then apply gVAMP to jointly model the relationship of tens of millions of WGS variants with human height in hundreds of thousands of UK Biobank individuals. We identify 59 rare variants and gene burden scores alongside many hundreds of DNA regions containing common variant associations and show that understanding the genetic basis of complex traits will require the joint analysis of hundreds of millions of variables measured on millions of people. The polygenic risk scores obtained from gVAMP have high accuracy (including a prediction accuracy of ∼46% for human height) and outperform current methods for downstream tasks such as mixed linear model association testing across 13 UK Biobank traits. In conclusion, gVAMP offers a scalable foundation for a wider range of analyses in WGS data.","lang":"eng"}],"department":[{"_id":"MaMo"},{"_id":"MaRo"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"22258"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/big-data-and-human-height/","description":"News on ISTA website"}]},"OA_type":"gold","article_processing_charge":"Yes","quality_controlled":"1","_id":"21488","issue":"5","has_accepted_license":"1","volume":6,"researchdata_availability":"yes","file_date_updated":"2026-07-28T07:06:26Z","pmid":1,"year":"2026","supplementarymaterial":"yes","file":[{"success":1,"checksum":"6b59686f8d9733add4f23d23f3dd9df0","access_level":"open_access","file_id":"22596","file_size":3736705,"content_type":"application/pdf","creator":"dernst","date_updated":"2026-07-28T07:06:26Z","date_created":"2026-07-28T07:06:26Z","file_name":"2026_CellGenomics_Depope.pdf","relation":"main_file"}],"intvolume":"         6","status":"public"},{"year":"2026","supplementarymaterial":"yes","intvolume":"        36","status":"public","file":[{"content_type":"application/pdf","date_created":"2026-07-28T07:31:44Z","creator":"dernst","date_updated":"2026-07-28T07:31:44Z","file_name":"2026_CurrentBiology_KiangEwe.pdf","relation":"main_file","success":1,"access_level":"open_access","checksum":"5ec4472d81fd44de03ccb92b1eb690a6","file_id":"22598","file_size":6795092}],"issue":"14","volume":36,"has_accepted_license":"1","researchdata_availability":"upon request","file_date_updated":"2026-07-28T07:31:44Z","pmid":1,"OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","_id":"22267","quality_controlled":"1","page":"3566-3579.e5","type":"journal_article","abstract":[{"text":"Thermal pollution, whether local or driven by global warming, threatens biodiversity in part through its detrimental effects on reproduction. Non-coding small RNAs (sRNAs) are crucial for maintaining germline developmental robustness under heat stress. Remarkably, we uncovered that neuronal sRNAs regulate germ cells’ thermotolerance, affecting both spermatogenic and oogenic germlines in a cell-non-autonomous manner. Furthermore, we demonstrate that, in RNAi mutants, an oxygen-sensing neural circuit, modulated by neuropeptide signaling, antagonizes germline maintenance, likely reflecting the nematode’s innate association of reduced oxygen levels with food availability and reproductive permissive environments. Finally, we provide evidence that laboratory-domesticated alleles of oxygen-response genes encoding neuropeptide receptor NPR-1 and hexacoordinated globin GLB-5 compromise germline thermotolerance. Hence, our findings raise the possibility that sensory perception, independent of direct environmental change, modulates germline integrity, highlighting a novel mechanism by which neural circuits integrate environmental information to safeguard reproductive fitness in fluctuating environments.","lang":"eng"}],"title":"Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress","department":[{"_id":"MaDe"}],"article_type":"original","OA_place":"publisher","doi":"10.1016/j.cub.2026.06.016","month":"07","ddc":["570"],"oa":1,"author":[{"first_name":"Chee Kiang","last_name":"Ewe","full_name":"Ewe, Chee Kiang"},{"last_name":"Achache","full_name":"Achache, Hanna","first_name":"Hanna"},{"full_name":"Schön, Hanna","last_name":"Schön","first_name":"Hanna","id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425"},{"first_name":"Leonid","last_name":"Kontorovich","full_name":"Kontorovich, Leonid"},{"last_name":"Teichman","full_name":"Teichman, Guy","first_name":"Guy"},{"first_name":"Shir","last_name":"Weiss","full_name":"Weiss, Shir"},{"full_name":"Mogilevskaya, Anna","last_name":"Mogilevskaya","first_name":"Anna"},{"first_name":"Myriam","full_name":"Valenski, Myriam","last_name":"Valenski"},{"first_name":"Sarit","last_name":"Anava","full_name":"Anava, Sarit"},{"first_name":"Rutwik","full_name":"Bardapurkar, Rutwik","last_name":"Bardapurkar"},{"last_name":"Gingold","full_name":"Gingold, Hila","first_name":"Hila"},{"first_name":"Rachel","full_name":"Posner, Rachel","last_name":"Posner"},{"full_name":"Antonova, Olga","last_name":"Antonova","first_name":"Olga"},{"first_name":"Mario","full_name":"De Bono, Mario","last_name":"De Bono","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tzur, Yonatan B.","last_name":"Tzur","first_name":"Yonatan B."},{"first_name":"Oded","last_name":"Rechavi","full_name":"Rechavi, Oded"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","date_updated":"2026-07-28T07:32:06Z","date_published":"2026-07-20T00:00:00Z","external_id":{"pmid":["42409014"]},"publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"language":[{"iso":"eng"}],"scopus_import":"1","day":"20","publication_status":"published","publisher":"Elsevier","publication":"Current Biology","date_created":"2026-07-12T22:02:18Z","das_tickbox":"1","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.).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","citation":{"mla":"Ewe, Chee Kiang, et al. “Neuronal RNAi and Oxygen-Sensing Circuit Shape Germline Resilience to Heat Stress.” <i>Current Biology</i>, vol. 36, no. 14, Elsevier, 2026, p. 3566–3579.e5, doi:<a href=\"https://doi.org/10.1016/j.cub.2026.06.016\">10.1016/j.cub.2026.06.016</a>.","apa":"Ewe, C. K., Achache, H., Schön, H., Kontorovich, L., Teichman, G., Weiss, S., … Rechavi, O. (2026). Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2026.06.016\">https://doi.org/10.1016/j.cub.2026.06.016</a>","ama":"Ewe CK, Achache H, Schön H, et al. Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. <i>Current Biology</i>. 2026;36(14):3566-3579.e5. doi:<a href=\"https://doi.org/10.1016/j.cub.2026.06.016\">10.1016/j.cub.2026.06.016</a>","short":"C.K. Ewe, H. Achache, H. Schön, L. Kontorovich, G. Teichman, S. Weiss, A. Mogilevskaya, M. Valenski, S. Anava, R. Bardapurkar, H. Gingold, R. Posner, O. Antonova, M. de Bono, Y.B. Tzur, O. Rechavi, Current Biology 36 (2026) 3566–3579.e5.","ista":"Ewe CK, Achache H, Schön H, Kontorovich L, Teichman G, Weiss S, Mogilevskaya A, Valenski M, Anava S, Bardapurkar R, Gingold H, Posner R, Antonova O, de Bono M, Tzur YB, Rechavi O. 2026. Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. Current Biology. 36(14), 3566–3579.e5.","chicago":"Ewe, Chee Kiang, Hanna Achache, Hanna Schön, Leonid Kontorovich, Guy Teichman, Shir Weiss, Anna Mogilevskaya, et al. “Neuronal RNAi and Oxygen-Sensing Circuit Shape Germline Resilience to Heat Stress.” <i>Current Biology</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.cub.2026.06.016\">https://doi.org/10.1016/j.cub.2026.06.016</a>.","ieee":"C. K. Ewe <i>et al.</i>, “Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress,” <i>Current Biology</i>, vol. 36, no. 14. Elsevier, p. 3566–3579.e5, 2026."}},{"publication_status":"published","publisher":"American Chemical Society","day":"01","language":[{"iso":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"citation":{"mla":"Gulyaev, Artem, et al. “A Computationally Efficient and Accurate Method for Predicting Conductance of Single-Molecule Junctions.” <i>Nano Letters</i>, vol. 26, no. 22, American Chemical Society, 2026, pp. 7429–7434, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6c01462\">10.1021/acs.nanolett.6c01462</a>.","short":"A. Gulyaev, J. Hazarika, Z.-F. Liu, L. Venkataraman, Nano Letters 26 (2026) 7429–7434.","chicago":"Gulyaev, Artem, Jyotisman Hazarika, Zhen-Fei Liu, and Latha Venkataraman. “A Computationally Efficient and Accurate Method for Predicting Conductance of Single-Molecule Junctions.” <i>Nano Letters</i>. American Chemical Society, 2026. <a href=\"https://doi.org/10.1021/acs.nanolett.6c01462\">https://doi.org/10.1021/acs.nanolett.6c01462</a>.","ista":"Gulyaev A, Hazarika J, Liu Z-F, Venkataraman L. 2026. A computationally efficient and accurate method for predicting conductance of single-molecule junctions. Nano Letters. 26(22), 7429–7434.","ama":"Gulyaev A, Hazarika J, Liu Z-F, Venkataraman L. A computationally efficient and accurate method for predicting conductance of single-molecule junctions. <i>Nano Letters</i>. 2026;26(22):7429–7434. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6c01462\">10.1021/acs.nanolett.6c01462</a>","ieee":"A. Gulyaev, J. Hazarika, Z.-F. Liu, and L. Venkataraman, “A computationally efficient and accurate method for predicting conductance of single-molecule junctions,” <i>Nano Letters</i>, vol. 26, no. 22. American Chemical Society, pp. 7429–7434, 2026.","apa":"Gulyaev, A., Hazarika, J., Liu, Z.-F., &#38; Venkataraman, L. (2026). A computationally efficient and accurate method for predicting conductance of single-molecule junctions. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.6c01462\">https://doi.org/10.1021/acs.nanolett.6c01462</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported primarily by the Institute of Science and Technology Austria. L.V. was supported in part by the National Science Foundation (No. NSF-DMR 2241180). Z.-F.L. was supported by an NSF CAREER Award, No. DMR-2044552 and an Alfred P. Sloan Research Fellowship, No. FG-2024-21750.","das_tickbox":"1","date_created":"2026-06-10T07:27:19Z","publication":"Nano Letters","author":[{"id":"83ed7901-7380-11f0-bf20-a0788d5e654d","first_name":"Artem","full_name":"Gulyaev, Artem","last_name":"Gulyaev"},{"full_name":"Hazarika, Jyotisman","last_name":"Hazarika","first_name":"Jyotisman","id":"d87714c4-663d-11f0-bd06-caece19833e5","orcid":"0009-0007-2542-7878"},{"full_name":"Liu, Zhen-Fei","last_name":"Liu","first_name":"Zhen-Fei"},{"full_name":"Venkataraman, Latha","last_name":"Venkataraman","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","orcid":"0000-0002-6957-6089"}],"ddc":["540"],"oa":1,"corr_author":"1","month":"06","PlanS_conform":"1","doi":"10.1021/acs.nanolett.6c01462","OA_place":"publisher","article_type":"letter_note","external_id":{"chemrxivid":["10.26434/chemrxiv.15001696"],"pmid":["42223342"]},"date_published":"2026-06-01T00:00:00Z","date_updated":"2026-07-28T09:57:28Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"page":"7429–7434","quality_controlled":"1","_id":"21980","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","department":[{"_id":"LaVe"},{"_id":"GradSch"}],"title":"A computationally efficient and accurate method for predicting conductance of single-molecule junctions","abstract":[{"lang":"eng","text":"Despite significant progress in the field of molecular electronics over the last two decades, the quantitative prediction of metal-molecule-metal junction conductance remains a challenge. The standard computational framework combines density functional theory (DFT) with nonequilibrium Green’s functions (NEGF) using low-rung exchange-correlation functionals such as PBE, which overestimate the conductances. More advanced correction methods exist but require complex workflows and high computational cost, limiting their accessibility. Here, we introduce a physically motivated approach that approximates results obtained with high-rung functionals. Our method fits the PBE-calculated transmission to a Breit-Wigner form and subsequently refines the fit parameters using molecular orbital energies and metal densities of states computed for the isolated subsystems with high-rung functionals. This approach is applicable to a broad range of molecular junctions yielding conductance values in quantitative agreement with experiments. Our approach is simple, low-cost, and accurate, making it well-suited for routine and large-scale prediction of single-molecule junction conductance."}],"type":"journal_article","file":[{"relation":"main_file","file_name":"2026_NanoLetters_Gulyaev.pdf","content_type":"application/pdf","date_created":"2026-06-16T09:11:35Z","creator":"dernst","date_updated":"2026-06-16T09:11:35Z","checksum":"897551374cac28e0db26dcb0b676b8e7","access_level":"open_access","success":1,"file_size":3362800,"file_id":"22013"}],"status":"public","intvolume":"        26","year":"2026","pmid":1,"file_date_updated":"2026-06-16T09:11:35Z","has_accepted_license":"1","volume":26,"issue":"22","chemrxivid":1},{"page":"59","_id":"22017","article_processing_charge":"No","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"15182"},{"relation":"part_of_dissertation","status":"public","id":"12237"},{"status":"public","id":"20326","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"MaIb"}],"title":"Unraveling the origin and evolution of defects to enable advanced thermoelectric performance","type":"dissertation","status":"public","doi_confirm":"1","file":[{"checksum":"3df7e865a7d1da8972ccd8acb8b4c16c","access_level":"closed","file_size":15658266,"file_id":"22226","file_name":"2026_Kleinhanns_Tobias_Thesis_Source_File.docx","relation":"source_file","creator":"tkleinha","date_updated":"2026-06-30T09:17:15Z","date_created":"2026-06-30T09:17:15Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"date_created":"2026-07-01T07:35:17Z","date_updated":"2026-07-01T07:35:17Z","creator":"tkleinha","content_type":"application/pdf","relation":"main_file","file_name":"2026_Kleinhanns_Tobias_Thesis_Main_File_A4.pdf","file_id":"22232","file_size":9909375,"embargo":"2026-12-18","checksum":"40ec279272a963636ff29c964032dcba","embargo_to":"open_access","access_level":"closed"}],"year":"2026","file_date_updated":"2026-07-01T07:35:17Z","has_accepted_license":"1","publication_status":"published","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"day":"18","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"publication_identifier":{"isbn":["978-3-99078-081-7"],"issn":["2663-337X"]},"citation":{"ista":"Kleinhanns T. 2026. Unraveling the origin and evolution of defects to enable advanced thermoelectric performance. Institute of Science and Technology Austria.","chicago":"Kleinhanns, Tobias. “Unraveling the Origin and Evolution of Defects to Enable Advanced Thermoelectric Performance.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22017\">https://doi.org/10.15479/AT-ISTA-22017</a>.","ama":"Kleinhanns T. Unraveling the origin and evolution of defects to enable advanced thermoelectric performance. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22017\">10.15479/AT-ISTA-22017</a>","short":"T. Kleinhanns, Unraveling the Origin and Evolution of Defects to Enable Advanced Thermoelectric Performance, Institute of Science and Technology Austria, 2026.","ieee":"T. Kleinhanns, “Unraveling the origin and evolution of defects to enable advanced thermoelectric performance,” Institute of Science and Technology Austria, 2026.","apa":"Kleinhanns, T. (2026). <i>Unraveling the origin and evolution of defects to enable advanced thermoelectric performance</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22017\">https://doi.org/10.15479/AT-ISTA-22017</a>","mla":"Kleinhanns, Tobias. <i>Unraveling the Origin and Evolution of Defects to Enable Advanced Thermoelectric Performance</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22017\">10.15479/AT-ISTA-22017</a>."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2026-06-18T08:00:03Z","das_tickbox":"1","author":[{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","orcid":"0000-0003-1537-7436","last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias","first_name":"Tobias"}],"month":"06","corr_author":"1","ddc":["546","530"],"OA_place":"publisher","degree_awarded":"PhD","doi":"10.15479/AT-ISTA-22017","supervisor":[{"first_name":"Maria","full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2026-06-18T00:00:00Z","oa_version":"Published Version","date_updated":"2026-07-28T09:55:13Z"},{"related_material":{"record":[{"id":"19425","status":"public","relation":"earlier_version"}]},"department":[{"_id":"MiLe"}],"abstract":[{"text":"We demonstrate that periodically driven quantum rotors provide a promising and broadly applicable platform to implement multigap topological phases, where groups of bands can acquire topological invariants due to non-Abelian braiding of band degeneracies. By adiabatically varying the periodic kicks to the rotor we find nodal-line braiding, which causes sign flips of topological charges of band nodes and can prevent them from annihilating, indicated by nonzero values of the patch Euler class. In particular, we report on the emergence of an anomalous Dirac string phase arising in the strongly driven regime, a truly out-of-equilibrium phase of the quantum rotor. This phase emanates from braiding processes involving all (quasienergy) gaps and manifests itself with edge states at zero angular momentum. Our results reveal direct applications in state-of-the-art experiments of quantum rotors, such as linear molecules driven by periodic far-off-resonant laser pulses or artificial quantum rotors in optical lattices, whose extensive versatility offers precise modification and observation of novel non-Abelian topological properties.","lang":"eng"}],"title":"Anomalous multigap topological phases in periodically driven quantum rotors","type":"journal_article","_id":"21009","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","file_date_updated":"2026-01-21T09:04:48Z","volume":113,"has_accepted_license":"1","issue":"1","status":"public","intvolume":"       113","file":[{"checksum":"ca62a5050a234c0554e2583b1c126057","access_level":"open_access","success":1,"file_size":2650256,"file_id":"21029","file_name":"2026_PhysicalReviewA_Karle.pdf","relation":"main_file","content_type":"application/pdf","date_updated":"2026-01-21T09:04:48Z","date_created":"2026-01-21T09:04:48Z","creator":"dernst"}],"ec_funded":1,"year":"2026","citation":{"apa":"Karle, V., Lemeshko, M., Bouhon, A., Slager, R.-J., &#38; Ünal, F. N. (2026). Anomalous multigap topological phases in periodically driven quantum rotors. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/db9d-9bns\">https://doi.org/10.1103/db9d-9bns</a>","ama":"Karle V, Lemeshko M, Bouhon A, Slager R-J, Ünal FN. Anomalous multigap topological phases in periodically driven quantum rotors. <i>Physical Review A</i>. 2026;113(1). doi:<a href=\"https://doi.org/10.1103/db9d-9bns\">10.1103/db9d-9bns</a>","chicago":"Karle, Volker, Mikhail Lemeshko, Adrien Bouhon, Robert-Jan Slager, and F. Nur Ünal. “Anomalous Multigap Topological Phases in Periodically Driven Quantum Rotors.” <i>Physical Review A</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/db9d-9bns\">https://doi.org/10.1103/db9d-9bns</a>.","ista":"Karle V, Lemeshko M, Bouhon A, Slager R-J, Ünal FN. 2026. Anomalous multigap topological phases in periodically driven quantum rotors. Physical Review A. 113(1), 012216.","short":"V. Karle, M. Lemeshko, A. Bouhon, R.-J. Slager, F.N. Ünal, Physical Review A 113 (2026).","ieee":"V. Karle, M. Lemeshko, A. Bouhon, R.-J. Slager, and F. N. Ünal, “Anomalous multigap topological phases in periodically driven quantum rotors,” <i>Physical Review A</i>, vol. 113, no. 1. American Physical Society, 2026.","mla":"Karle, Volker, et al. “Anomalous Multigap Topological Phases in Periodically Driven Quantum Rotors.” <i>Physical Review A</i>, vol. 113, no. 1, 012216, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/db9d-9bns\">10.1103/db9d-9bns</a>."},"acknowledgement":"We thank G. M. Koutentakis, S. Wimberger, J. G. E. Harris, T. Enss, and A. Ghazaryan for fruitful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). R.-J.S. acknowledges funding from a EPSRC ERC underwrite (Grant No. EP/X025829/1), a EPSRC New Investigator Award (Grant No. EP/W00187X/1), and Trinity College, Cambridge. F.N.Ü. acknowledges support from the Marie Skłodowska-Curie Programme of the European Commission (Grant No. 893915), a Simons Investigator Award (Grant No. 511029), Trinity College Cambridge, and the Royal Society (Grant No. URF/R1/241667).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Physical Review A","date_created":"2026-01-20T10:06:07Z","publisher":"American Physical Society","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","project":[{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020"}],"day":"12","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"arxiv":1,"article_number":"012216","external_id":{"arxiv":["2408.16848"]},"date_published":"2026-01-12T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","date_updated":"2026-07-29T08:59:30Z","author":[{"first_name":"Volker","full_name":"Karle, Volker","last_name":"Karle","orcid":"0000-0002-6963-0129","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"first_name":"Adrien","full_name":"Bouhon, Adrien","last_name":"Bouhon"},{"first_name":"Robert-Jan","full_name":"Slager, Robert-Jan","last_name":"Slager"},{"full_name":"Ünal, F. Nur","last_name":"Ünal","first_name":"F. Nur"}],"PlanS_conform":"1","month":"01","corr_author":"1","oa":1,"ddc":["530"],"article_type":"original","OA_place":"publisher","doi":"10.1103/db9d-9bns"},{"date_updated":"2026-07-29T10:09:31Z","oa_version":"None","date_published":"2026-06-01T00:00:00Z","external_id":{"pmid":["41774948"]},"article_number":"119493","doi":"10.1016/j.marpolbul.2026.119493","article_type":"original","month":"06","author":[{"full_name":"Jöst, Anna B.","last_name":"Jöst","first_name":"Anna B."},{"full_name":"Rodriguez Moreno, Maximiliano J","last_name":"Rodriguez Moreno","first_name":"Maximiliano J","id":"59bea3b2-8c82-11ef-a41a-af7b0efd9065"},{"first_name":"Taihun","last_name":"Kim","full_name":"Kim, Taihun"},{"first_name":"David M.","last_name":"Baker","full_name":"Baker, David M."},{"first_name":"Moriaki","full_name":"Yasuhara, Moriaki","last_name":"Yasuhara"},{"first_name":"Christelle A.","last_name":"Not","full_name":"Not, Christelle A."},{"first_name":"Ivana","full_name":"Karanovic, Ivana","last_name":"Karanovic"}],"das_tickbox":"1","date_created":"2026-03-08T23:01:44Z","publication":"Marine Pollution Bulletin","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank the KIOST staff of the Jeju Marine Research Center for assisting sample collection, the research assistants and students of the Yoon Idea Lab led by Prof. Dr. Tae-Hyun Yoon at Hanyang University for facilitating and assisting in ICP-MS test runs involved in a pilot study preceding this study, Ms. Garance Perrois and Mr. Léonard Pons for assistance with statistics-related questions, and the two anonymous reviewers for their valuable comments and suggestions. The study described in this article was partially supported by grants from the Brain Pool Program through NRF funded by the Ministry of Science and ICT (reference code: 2019H1D3A1A01070922 to ABJ), by the Ministry of Oceans and Fisheries (grant number RS-2024-00406249 to TK), by the Korea Institute of Marine Science and Technology (KIMST), funded by the Ministry of Oceans and Fisheries (grant number RS-2025-02304432 to TK), and by the Korea Institute of Ocean Science and Technology (PEA0404 to TK).","dataavailabilitystatement":"The datasets analysed during the current study are available within the manuscript and the associated supplementary materials.","citation":{"apa":"Jöst, A. B., Rodriguez Moreno, M. J., Kim, T., Baker, D. M., Yasuhara, M., Not, C. A., &#38; Karanovic, I. (2026). Ostracod shell chemistry as proxy for coastal marine conditions of a highly urbanized megacity (Hong Kong SAR) and an agro-centric oceanic province (Jeju Island, Republic of Korea) – a preliminary comparative analysis. <i>Marine Pollution Bulletin</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.marpolbul.2026.119493\">https://doi.org/10.1016/j.marpolbul.2026.119493</a>","ieee":"A. B. Jöst <i>et al.</i>, “Ostracod shell chemistry as proxy for coastal marine conditions of a highly urbanized megacity (Hong Kong SAR) and an agro-centric oceanic province (Jeju Island, Republic of Korea) – a preliminary comparative analysis,” <i>Marine Pollution Bulletin</i>, vol. 227, no. 6. Elsevier, 2026.","short":"A.B. Jöst, M.J. Rodriguez Moreno, T. Kim, D.M. Baker, M. Yasuhara, C.A. Not, I. Karanovic, Marine Pollution Bulletin 227 (2026).","chicago":"Jöst, Anna B., Maximiliano J Rodriguez Moreno, Taihun Kim, David M. Baker, Moriaki Yasuhara, Christelle A. Not, and Ivana Karanovic. “Ostracod Shell Chemistry as Proxy for Coastal Marine Conditions of a Highly Urbanized Megacity (Hong Kong SAR) and an Agro-Centric Oceanic Province (Jeju Island, Republic of Korea) – a Preliminary Comparative Analysis.” <i>Marine Pollution Bulletin</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.marpolbul.2026.119493\">https://doi.org/10.1016/j.marpolbul.2026.119493</a>.","ista":"Jöst AB, Rodriguez Moreno MJ, Kim T, Baker DM, Yasuhara M, Not CA, Karanovic I. 2026. Ostracod shell chemistry as proxy for coastal marine conditions of a highly urbanized megacity (Hong Kong SAR) and an agro-centric oceanic province (Jeju Island, Republic of Korea) – a preliminary comparative analysis. Marine Pollution Bulletin. 227(6), 119493.","ama":"Jöst AB, Rodriguez Moreno MJ, Kim T, et al. Ostracod shell chemistry as proxy for coastal marine conditions of a highly urbanized megacity (Hong Kong SAR) and an agro-centric oceanic province (Jeju Island, Republic of Korea) – a preliminary comparative analysis. <i>Marine Pollution Bulletin</i>. 2026;227(6). doi:<a href=\"https://doi.org/10.1016/j.marpolbul.2026.119493\">10.1016/j.marpolbul.2026.119493</a>","mla":"Jöst, Anna B., et al. “Ostracod Shell Chemistry as Proxy for Coastal Marine Conditions of a Highly Urbanized Megacity (Hong Kong SAR) and an Agro-Centric Oceanic Province (Jeju Island, Republic of Korea) – a Preliminary Comparative Analysis.” <i>Marine Pollution Bulletin</i>, vol. 227, no. 6, 119493, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.marpolbul.2026.119493\">10.1016/j.marpolbul.2026.119493</a>."},"publication_identifier":{"issn":["002-5326X"],"eissn":["1879-3363"]},"day":"01","language":[{"iso":"eng"}],"scopus_import":"1","publication_status":"published","publisher":"Elsevier","issue":"6","volume":227,"researchdata_availability":"yes","pmid":1,"year":"2026","supplementarymaterial":"yes","intvolume":"       227","status":"public","type":"journal_article","title":"Ostracod shell chemistry as proxy for coastal marine conditions of a highly urbanized megacity (Hong Kong SAR) and an agro-centric oceanic province (Jeju Island, Republic of Korea) – a preliminary comparative analysis","abstract":[{"lang":"eng","text":"This preliminary study investigates the trace-element composition of ostracod shells (Ostracoda: Crustacea) as biogenic calcium carbonates in their role as environmental sentinels of pollution. Using high-resolution in-situ analysis, we compared two contrasting coastal systems: the highly urbanized seascape of metropolitan megacity Hong Kong (HKSAR) and the agriculturally dominated waters of rural retreat Jeju Island, Republic of Korea (ROK). The goal was to assess whether anthropogenic stress gradients affect trace element-to‑calcium ratios (E/Ca) in the carapaces of shallow-marine Neonesidea Maddocks, 1969 species. Hereby, the focus is laid on potential differences in the effects of extreme urbanization and extreme agriculturalization. We analyzed 12 trace elements commonly incorporated into ostracod shells using Inductively Coupled Plasma–Mass Spectrometry (ICP-MS). Only Mn/Ca, Mg/Ca, and Ni/Ca ratios showed strong correlations with specific seawater physicochemical parameters. Notably, Mn/Ca differed significantly between the two sites, seemingly driven mainly by variations in nitrite nitrogen levels. This suggests that Mn incorporation is sensitive to pollution source, urban versus agricultural, though species-specific uptake effects cannot be excluded. No significant differences in elemental uptake were found between adult and A-1 juvenile stages of Neonesidea mutsuensis Ishizaki, 1961 or Neonesidea elegans (Brady, 1969), supporting the use of both age groups in environmental reconstructions and increasing potential sample yields. While remaining empirical and exploratory, our tentative findings suggest that ostracod geochemistry holds promise for marine pollution monitoring and cautiously supports the application of ostracod Mn/Ca ratios to reconstruct anthropogenic, particularly nitrogen-related, impacts in nearshore environments using sediment core records."}],"department":[{"_id":"FrPe"}],"OA_type":"closed access","article_processing_charge":"No","quality_controlled":"1","_id":"21406"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank all members of the Heisenberg, Henkes, and Hannezo groups for their support. We are also grateful to the Imaging and Optics, Scientific Computing, Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their technical assistance and support. Numerical simulations were performed using the computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020 research and innovation programme (grant agreement No. 665385). This work was supported by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to C.-P.H.","das_tickbox":"1","date_created":"2026-07-29T09:10:35Z","publication":"Nature Communications","citation":{"apa":"Naik, S., Keta, Y.-E., Pranjic-Ferscha, K., Hannezo, E. B., Henkes, S., &#38; Heisenberg, C.-P. J. (2026). Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-026-72366-z\">https://doi.org/10.1038/s41467-026-72366-z</a>","ama":"Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ. Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. <i>Nature Communications</i>. 2026;17. doi:<a href=\"https://doi.org/10.1038/s41467-026-72366-z\">10.1038/s41467-026-72366-z</a>","short":"S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E.B. Hannezo, S. Henkes, C.-P.J. Heisenberg, Nature Communications 17 (2026).","chicago":"Naik, Suyash, Yann-Edwin Keta, Kornelija Pranjic-Ferscha, Edouard B Hannezo, Silke Henkes, and Carl-Philipp J Heisenberg. “Keratins Coordinate Tissue Spreading by Balancing Spreading Forces with Tissue Material Properties.” <i>Nature Communications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41467-026-72366-z\">https://doi.org/10.1038/s41467-026-72366-z</a>.","ista":"Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ. 2026. Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. Nature Communications. 17, 6499.","ieee":"S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E. B. Hannezo, S. Henkes, and C.-P. J. Heisenberg, “Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties,” <i>Nature Communications</i>, vol. 17. Springer Nature, 2026.","mla":"Naik, Suyash, et al. “Keratins Coordinate Tissue Spreading by Balancing Spreading Forces with Tissue Material Properties.” <i>Nature Communications</i>, vol. 17, 6499, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41467-026-72366-z\">10.1038/s41467-026-72366-z</a>."},"dataavailabilitystatement":"The authors declare that the minimum dataset that is necessary to\r\ninterpret, verify, and extend the research in this article is included in\r\nthe supplementary information, the source data, and the archived data\r\nrepository (https://doi.org/10.15479/AT-ISTA-21137). This is also available\r\non GitHub at https://github.com/Suyash-Naik/2026-\r\nKeratinepithlialspreadingcoordinate-Data. Source data are provided\r\nwith this paper. The framework to develop the vertex models used in this paper are\r\navailable online on GitHub and archived in the source data provided.\r\nCustom scripts used for analysis of imaging and simulation data are\r\nprovided along with data files for all panels in the source data for this\r\nmanuscript on GitHub and in data repo (https://doi.org/10.15479/ATISTA-\r\n21137). Framework for the vertex model is available at https://\r\ngithub.com/yketta/cells. Code for analysis is available on GitHub\r\nhttps://github.com/Suyash-Naik/2026-\r\nKeratinepithlialspreadingcoordinate-Data.","day":"17","project":[{"name":"Keratins in epithelial tissue spreading","_id":"8f060199-16d5-11f0-9cad-f3253b266c46","grant_number":"PAT 5044023"},{"name":"Nano-Analytics of Cellular Systems","_id":"252C3B08-B435-11E9-9278-68D0E5697425","grant_number":"W1250-B20","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","publisher":"Springer Nature","date_published":"2026-07-17T00:00:00Z","date_updated":"2026-07-29T10:33:31Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["42143048"]},"article_number":"6499","oa":1,"ddc":["570"],"corr_author":"1","month":"07","PlanS_conform":"1","doi":"10.1038/s41467-026-72366-z","article_type":"original","OA_place":"publisher","author":[{"orcid":"0000-0001-8421-5508","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","first_name":"Suyash","full_name":"Naik, Suyash","last_name":"Naik"},{"first_name":"Yann-Edwin","last_name":"Keta","full_name":"Keta, Yann-Edwin"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija","last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"first_name":"Silke","last_name":"Henkes","full_name":"Henkes, Silke"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"title":"Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties","abstract":[{"text":"For tissues to spread, they must deform while staying intact. How spreading tissues balance flexibility with integrity is not yet well understood. Here, we show that keratin intermediate filaments adapt tissue mechanical resilience to the stresses arising in epithelial tissues during spreading. By analyzing the expansion of the enveloping cell layer (EVL) over the yolk cell in zebrafish embryos in vivo, we find that keratin network maturation in EVL cells is promoted by stresses building up within the spreading tissue. Through genetic interference and tissue rheology experiments, complemented by a vertex model with mechanochemical feedback, we demonstrate that stress-induced keratin network maturation in the EVL increases tissue viscosity, to prevent tissue rupture. Further, keratins are required in the yolk cell for mechanosensitive actomyosin network contraction and flow, the forces pulling the EVL. These dual mechanosensitive functions of keratins enable a balance between pulling force production and EVL mechanical resilience, ensuring uniform and robust tissue spreading.","lang":"eng"}],"type":"journal_article","related_material":{"record":[{"relation":"earlier_version","id":"20465","status":"public"}]},"department":[{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EdHa"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"article_processing_charge":"Yes","OA_type":"gold","quality_controlled":"1","_id":"22608","volume":17,"has_accepted_license":"1","pmid":1,"researchdata_availability":"yes","file_date_updated":"2026-07-29T10:27:25Z","supplementarymaterial":"yes","year":"2026","file":[{"date_updated":"2026-07-29T10:27:25Z","date_created":"2026-07-29T10:27:25Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_name":"2026_NatureComm_Naik.pdf","success":1,"access_level":"open_access","checksum":"f26d96e180c1d034d9c9c8f57c3c258b","file_id":"22609","file_size":15363936}],"intvolume":"        17","status":"public"},{"article_number":"e5487708","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","date_updated":"2026-07-29T11:00:05Z","date_published":"2026-07-26T00:00:00Z","author":[{"first_name":"John R","last_name":"Hoffman Jr","full_name":"Hoffman Jr, John R","id":"0cf4072c-94e2-11ee-bdf9-90a13138901e"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander"},{"last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"}],"article_type":"original","OA_place":"publisher","doi":"10.1002/ange.5487708","month":"07","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/ange.5487708"}],"ddc":["540"],"oa":1,"dataavailabilitystatement":"The data that support the findings of this study are available from the corresponding author upon reasonable request.","citation":{"ieee":"J. R. Hoffman Jr, S. A. Freunberger, and S. R. Waitukaitis, “Ionentransfer während der Ionomer Kontaktelektrifizierung: Bindungsaffinität steuert Aufladung,” <i>Angewandte Chemie</i>. Wiley, 2026.","ista":"Hoffman Jr JR, Freunberger SA, Waitukaitis SR. 2026. Ionentransfer während der Ionomer Kontaktelektrifizierung: Bindungsaffinität steuert Aufladung. Angewandte Chemie., e5487708.","chicago":"Hoffman Jr, John R, Stefan Alexander Freunberger, and Scott R Waitukaitis. “Ionentransfer während der Ionomer Kontaktelektrifizierung: Bindungsaffinität steuert Aufladung.” <i>Angewandte Chemie</i>. Wiley, 2026. <a href=\"https://doi.org/10.1002/ange.5487708\">https://doi.org/10.1002/ange.5487708</a>.","ama":"Hoffman Jr JR, Freunberger SA, Waitukaitis SR. Ionentransfer während der Ionomer Kontaktelektrifizierung: Bindungsaffinität steuert Aufladung. <i>Angewandte Chemie</i>. 2026. doi:<a href=\"https://doi.org/10.1002/ange.5487708\">10.1002/ange.5487708</a>","short":"J.R. Hoffman Jr, S.A. Freunberger, S.R. Waitukaitis, Angewandte Chemie (2026).","apa":"Hoffman Jr, J. R., Freunberger, S. A., &#38; Waitukaitis, S. R. (2026). Ionentransfer während der Ionomer Kontaktelektrifizierung: Bindungsaffinität steuert Aufladung. <i>Angewandte Chemie</i>. Wiley. <a href=\"https://doi.org/10.1002/ange.5487708\">https://doi.org/10.1002/ange.5487708</a>","mla":"Hoffman Jr, John R., et al. “Ionentransfer während der Ionomer Kontaktelektrifizierung: Bindungsaffinität steuert Aufladung.” <i>Angewandte Chemie</i>, e5487708, Wiley, 2026, doi:<a href=\"https://doi.org/10.1002/ange.5487708\">10.1002/ange.5487708</a>."},"publication":"Angewandte Chemie","das_tickbox":"1","date_created":"2026-07-28T18:03:20Z","acknowledgement":"Diese Forschung wurde durch die Scientific Service Units (SSU) des IST Austria unterstützt, durch Nutzung von Ressourcen der Lab Support Facility (LSF).\r\nOpen Access funding provided by Institute of Science and Technology Austria.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","publication_status":"epub_ahead","publication_identifier":{"eissn":["1521-3757"],"issn":["0044-8249"]},"scopus_import":"1","language":[{"iso":"ger"}],"day":"26","researchdata_availability":"upon request","has_accepted_license":"1","status":"public","year":"2026","supplementarymaterial":"yes","department":[{"_id":"StFr"},{"_id":"ScWa"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Kontaktelektrifizierung tritt allgegenwärtig in der Natur auf, doch die Identität der Ladungsträger bleibt in den meisten Fällen unklar, mit Elektronen, Ionen oder nanoskopischen Materialfragmenten als mögliche Kandidaten. Ein Material, bei dem die übertragene Spezies mehr gewiss erscheint, sind Ionomere, d. h. Polymere mit mobilen Ionen, deren Ladung durch fest gebundene Gegenladungen ausgeglichen wird. Wenn Ionomere mit einer neutralen Oberfläche in Kontakt kommen, lädt sich diese mit dem Vorzeichen der mobilen Ionen auf, was stark auf Ionentransfer hindeutet. Der zugrundeliegende Mechanismus sowie die bestimmenden Einflussfaktoren dieses Transfers sind jedoch bislang nur unzureichend verstanden. In der vorliegenden Arbeit zeigen wir, dass die Bindungsaffinität zwischen den mobilen Ionen und dem Ionomer den Ladungstransfer maßgeblich bestimmt. Wir untersuchen Ionomere mit gebundenen Anionen und Kationen und erzeugen mittels Ionenaustausch Proben mit einer Reihe unterschiedlicher übertragbarer Ionen. Für das anionische Ionomer beobachten wir eine starke Abhängigkeit von der Bindungsaffinität, wobei mobile Kationen mit der höchsten Affinität am wenigsten Ladung übertragen. Eine schwächere, aber trotzdem klare Abhängigkeit wurde für das kationische Ionomer gemessen, welches der freien Hydratationsenergie der mobilen Anionen folgt. Mithilfe von optischer Emissionsspektroskopie mit induktiv gekoppeltem Plasma (ICP‐OES) bestätigen wir den Transfer von mobilen Ionen auf die Oberfläche der Gegenprobe. Unsere Ergebnisse bestätigen die Ladungsträgeridentität und den Mechanismus des Ladungstransfers bei ionomerischen Materialien, was auch für das allgemeine Verständnis von Kontaktelektrifizierung von Bedeutung sein könnte."}],"title":"Ionentransfer während der Ionomer Kontaktelektrifizierung: Bindungsaffinität steuert Aufladung","_id":"22601","quality_controlled":"1","OA_type":"hybrid","article_processing_charge":"No","acknowledged_ssus":[{"_id":"LifeSc"}]},{"OA_type":"green","article_processing_charge":"No","quality_controlled":"1","_id":"22404","type":"journal_article","title":"Longitudinal conductivity at integer quantum Hall transitions","abstract":[{"lang":"eng","text":"We consider a class of two-dimensional tight binding models displaying conical intersections of the Bloch bands at the Fermi level. The setting includes the case of generic transitions between quantum Hall phases. We consider the longitudinal conductivity, as given by Kubo formula, describing the variation of the current after introducing a space-homogeneous electric field, in an adiabatic way. We obtain an explicit expression for the longitudinal conductivity, completely determined by the number of conical intersections and by the shape of the cones. In particular, the formula reproduces the known quantized values found for graphene and for the critical Haldane model. Furthermore, we discuss the validity of Kubo formula in presence of conical intersections in the spectrum, starting from the time-dependent Schrödinger equation. For electric fields which are weak and slowly varying in space and in time, we prove the validity of linear response from quantum dynamics."}],"department":[{"_id":"RoSe"},{"_id":"GradSch"}],"year":"2026","supplementarymaterial":"no","status":"public","intvolume":"       116","issue":"4","volume":116,"researchdata_availability":"not applicable","mathsc":["81V70"],"arxiv":1,"publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"day":"01","language":[{"iso":"eng"}],"scopus_import":"1","publication_status":"published","publisher":"Springer Nature","date_created":"2026-07-26T22:01:40Z","das_tickbox":"1","publication":"Letters in Mathematical Physics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"G. M. and M. P. acknowledge support by the European Research Council through the ERC-StG MaMBoQ, n. 802901. G. M. acknowledges financial support from the Independent Research Fund Denmark–Natural Sciences, grant DFF–10.46540/2032-00005B and from the European Research Council through the ERC CoG UniCoSM, grant agreement n.724939. M. P. acknowledges support from the MUR, PRIN 2022 project MaIQuFi cod. 20223J85K3. This work has been carried out under the auspices of the GNFM of INdAM. We thank the anonymous referees for comments on a previous version of this manuscript.","dataavailabilitystatement":"Data sharing is not applicable to this article as no datasets were generated or analyzed during the current study.","citation":{"mla":"Marcelli, Giovanna, et al. “Longitudinal Conductivity at Integer Quantum Hall Transitions.” <i>Letters in Mathematical Physics</i>, vol. 116, no. 4, 82, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1007/s11005-026-02087-3\">10.1007/s11005-026-02087-3</a>.","chicago":"Marcelli, Giovanna, Lorenzo Pigozzi, and Marcello Porta. “Longitudinal Conductivity at Integer Quantum Hall Transitions.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s11005-026-02087-3\">https://doi.org/10.1007/s11005-026-02087-3</a>.","short":"G. Marcelli, L. Pigozzi, M. Porta, Letters in Mathematical Physics 116 (2026).","ista":"Marcelli G, Pigozzi L, Porta M. 2026. Longitudinal conductivity at integer quantum Hall transitions. Letters in Mathematical Physics. 116(4), 82.","ama":"Marcelli G, Pigozzi L, Porta M. Longitudinal conductivity at integer quantum Hall transitions. <i>Letters in Mathematical Physics</i>. 2026;116(4). doi:<a href=\"https://doi.org/10.1007/s11005-026-02087-3\">10.1007/s11005-026-02087-3</a>","ieee":"G. Marcelli, L. Pigozzi, and M. Porta, “Longitudinal conductivity at integer quantum Hall transitions,” <i>Letters in Mathematical Physics</i>, vol. 116, no. 4. Springer Nature, 2026.","apa":"Marcelli, G., Pigozzi, L., &#38; Porta, M. (2026). Longitudinal conductivity at integer quantum Hall transitions. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-026-02087-3\">https://doi.org/10.1007/s11005-026-02087-3</a>"},"doi":"10.1007/s11005-026-02087-3","OA_place":"repository","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2503.01381"}],"oa":1,"month":"08","author":[{"full_name":"Marcelli, Giovanna","last_name":"Marcelli","first_name":"Giovanna"},{"id":"efb8f850-3208-11ee-ac71-8c4f5803b9c6","last_name":"Pigozzi","full_name":"Pigozzi, Lorenzo","first_name":"Lorenzo"},{"first_name":"Marcello","full_name":"Porta, Marcello","last_name":"Porta"}],"date_updated":"2026-07-29T10:51:55Z","oa_version":"Preprint","date_published":"2026-08-01T00:00:00Z","external_id":{"arxiv":["2503.01381"]},"article_number":"82"},{"author":[{"id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","orcid":"0000-0001-5293-214X","last_name":"Dvorak","full_name":"Dvorak, Martin","first_name":"Martin"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir"}],"doi":"10.46298/afm.14253","OA_place":"publisher","article_type":"original","ddc":["500"],"PlanS_conform":"1","corr_author":"1","month":"03","external_id":{"arxiv":["2409.08119"]},"article_number":"14253","date_updated":"2026-07-29T10:50:17Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","date_published":"2026-03-13T00:00:00Z","publisher":"EPI Sciences","publication_status":"published","publication_identifier":{"eissn":["3117-4604"]},"arxiv":1,"day":"13","language":[{"iso":"eng"}],"citation":{"apa":"Dvorak, M., &#38; Kolmogorov, V. (2026). Duality theory in linear optimization and its extensions -- formally verified. <i>Annals of Formalized Mathematics</i>. EPI Sciences. <a href=\"https://doi.org/10.46298/afm.14253\">https://doi.org/10.46298/afm.14253</a>","ista":"Dvorak M, Kolmogorov V. 2026. Duality theory in linear optimization and its extensions -- formally verified. Annals of Formalized Mathematics. 2, 14253.","ama":"Dvorak M, Kolmogorov V. Duality theory in linear optimization and its extensions -- formally verified. <i>Annals of Formalized Mathematics</i>. 2026;2. doi:<a href=\"https://doi.org/10.46298/afm.14253\">10.46298/afm.14253</a>","short":"M. Dvorak, V. Kolmogorov, Annals of Formalized Mathematics 2 (2026).","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” <i>Annals of Formalized Mathematics</i>. EPI Sciences, 2026. <a href=\"https://doi.org/10.46298/afm.14253\">https://doi.org/10.46298/afm.14253</a>.","ieee":"M. Dvorak and V. Kolmogorov, “Duality theory in linear optimization and its extensions -- formally verified,” <i>Annals of Formalized Mathematics</i>, vol. 2. EPI Sciences, 2026.","mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” <i>Annals of Formalized Mathematics</i>, vol. 2, 14253, EPI Sciences, 2026, doi:<a href=\"https://doi.org/10.46298/afm.14253\">10.46298/afm.14253</a>."},"das_tickbox":"0","date_created":"2026-07-29T09:06:55Z","publication":"Annals of Formalized Mathematics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We would like to thank David Bartl and Jasmin Blanchette for frequent consultations.\r\nWe would also like to express gratitude to Henrik Böving for a help with generalization\r\nfrom extended rationals to extended linearly ordered fields and to Andrew Yang for the\r\nproof of Finset.univ_sum_of_zero_when_not. We would also like to acknowledge Antoine\r\nChambert-Loir, Apurva Nakade, Yaël Dillies, Richard Copley, Edward van de Meent, Markus\r\nHimmel, Mario Carneiro, and Kevin Buzzard.","status":"public","intvolume":"         2","year":"2026","supplementarymaterial":"no","researchdata_availability":"no","mathsc":["68V20","15A39","90C05"],"has_accepted_license":"1","volume":2,"quality_controlled":"1","_id":"22607","OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"VlKo"},{"_id":"GradSch"}],"related_material":{"record":[{"status":"public","id":"20071","relation":"earlier_version"}]},"keyword":["Farkas lemma","linear programming","extended reals","calculus of inductive constructions"],"type":"journal_article","title":"Duality theory in linear optimization and its extensions -- formally verified","abstract":[{"text":"Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take \"infinite values\".\r\nCode: https://github.com/madvorak/duality/tree/v3.2.0","lang":"eng"}]},{"year":"2026","supplementarymaterial":"yes","status":"public","has_accepted_license":"1","researchdata_availability":"upon request","pmid":1,"OA_type":"hybrid","acknowledged_ssus":[{"_id":"LifeSc"}],"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","_id":"22602","type":"journal_article","title":"Ion transfer during ionomer contact electrification: Binding affinity controls charging","abstract":[{"text":"Contact electrification occurs ubiquitously in nature, but the identity of charge carriers in most situations remains uncertain, with electrons, ions, or nanoscopic material fragments as viable candidates. One material where the species transferred seems more certain is ionomers, i.e., polymers that contain mobile ions balanced by fixed counter‐charges. When ionomers touch a neutral surface, the latter becomes charged in the sign of the mobile ion, strongly suggesting ion transfer. However, the mechanism and governing factors of transfer remain poorly understood. Here, we demonstrate that binding affinity between mobile ion and ionomer controls charge transfer with ionomers. We use ionomers with fixed anions and cations and perform ion exchange to create samples with a series of transferrable ions. We observe a strong binding‐affinity dependence for the anionic ionomer, such that mobile cations with the highest affinity transfers the least charge. Weaker, yet clear dependence was measured for the cationic ionomer, which follows the hydration free energy of the mobile anion. Using inductively coupled plasma optical emission spectroscopy (ICP‐OES), we confirm transfer of the mobile ions to the counter sample's surface. Our results confirm the identify and mechanism of charge transfer with ionomeric materials, with potential implications for contact electrification more broadly.","lang":"eng"}],"department":[{"_id":"StFr"},{"_id":"ScWa"}],"doi":"10.1002/anie.5487708","article_type":"original","OA_place":"publisher","ddc":["540"],"main_file_link":[{"url":"https://doi.org/10.1002/anie.5487708","open_access":"1"}],"oa":1,"month":"07","corr_author":"1","author":[{"last_name":"Hoffman Jr","full_name":"Hoffman Jr, John R","first_name":"John R","id":"0cf4072c-94e2-11ee-bdf9-90a13138901e"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","first_name":"Scott R"}],"date_updated":"2026-07-29T11:25:58Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","date_published":"2026-07-21T00:00:00Z","external_id":{"pmid":["42478784"]},"article_number":"e5487708","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"day":"21","language":[{"iso":"eng"}],"scopus_import":"1","publication_status":"epub_ahead","publisher":"Wiley","das_tickbox":"1","date_created":"2026-07-28T18:04:19Z","publication":"Angewandte Chemie International Edition","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Lab Support Facility (LSF).\r\nOpen Access funding provided by Institute of Science and Technology Austria.","dataavailabilitystatement":"The data that support the findings of this study are available from the corresponding author upon reasonable request.","citation":{"apa":"Hoffman Jr, J. R., Freunberger, S. A., &#38; Waitukaitis, S. R. (2026). Ion transfer during ionomer contact electrification: Binding affinity controls charging. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.5487708\">https://doi.org/10.1002/anie.5487708</a>","ieee":"J. R. Hoffman Jr, S. A. Freunberger, and S. R. Waitukaitis, “Ion transfer during ionomer contact electrification: Binding affinity controls charging,” <i>Angewandte Chemie International Edition</i>. Wiley, 2026.","short":"J.R. Hoffman Jr, S.A. Freunberger, S.R. Waitukaitis, Angewandte Chemie International Edition (2026).","ama":"Hoffman Jr JR, Freunberger SA, Waitukaitis SR. Ion transfer during ionomer contact electrification: Binding affinity controls charging. <i>Angewandte Chemie International Edition</i>. 2026. doi:<a href=\"https://doi.org/10.1002/anie.5487708\">10.1002/anie.5487708</a>","ista":"Hoffman Jr JR, Freunberger SA, Waitukaitis SR. 2026. Ion transfer during ionomer contact electrification: Binding affinity controls charging. Angewandte Chemie International Edition., e5487708.","chicago":"Hoffman Jr, John R, Stefan Alexander Freunberger, and Scott R Waitukaitis. “Ion Transfer during Ionomer Contact Electrification: Binding Affinity Controls Charging.” <i>Angewandte Chemie International Edition</i>. Wiley, 2026. <a href=\"https://doi.org/10.1002/anie.5487708\">https://doi.org/10.1002/anie.5487708</a>.","mla":"Hoffman Jr, John R., et al. “Ion Transfer during Ionomer Contact Electrification: Binding Affinity Controls Charging.” <i>Angewandte Chemie International Edition</i>, e5487708, Wiley, 2026, doi:<a href=\"https://doi.org/10.1002/anie.5487708\">10.1002/anie.5487708</a>."}},{"author":[{"orcid":"0000-0001-5293-214X","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","first_name":"Martin","full_name":"Dvorak, Martin","last_name":"Dvorak"}],"month":"03","corr_author":"1","oa":1,"ddc":["511","000"],"OA_place":"repository","degree_awarded":"PhD","doi":"10.15479/AT-ISTA-21393","supervisor":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"},{"last_name":"Blanchette","full_name":"Blanchette, Jasmin","first_name":"Jasmin"}],"date_published":"2026-03-04T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","date_updated":"2026-07-29T12:56:52Z","publication_status":"published","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"day":"04","publication_identifier":{"isbn":["978-3-99078-074-9"],"issn":["2663-337X"]},"citation":{"mla":"Dvorak, Martin. <i>Pursuit of Truth and Beauty in Lean 4: Formally Verified Theory of Grammars, Optimization, Matroids</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21393\">10.15479/AT-ISTA-21393</a>.","apa":"Dvorak, M. (2026). <i>Pursuit of truth and beauty in Lean 4: Formally verified theory of grammars, optimization, matroids</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21393\">https://doi.org/10.15479/AT-ISTA-21393</a>","ieee":"M. Dvorak, “Pursuit of truth and beauty in Lean 4: Formally verified theory of grammars, optimization, matroids,” Institute of Science and Technology Austria, 2026.","short":"M. Dvorak, Pursuit of Truth and Beauty in Lean 4: Formally Verified Theory of Grammars, Optimization, Matroids, Institute of Science and Technology Austria, 2026.","ama":"Dvorak M. Pursuit of truth and beauty in Lean 4: Formally verified theory of grammars, optimization, matroids. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21393\">10.15479/AT-ISTA-21393</a>","chicago":"Dvorak, Martin. “Pursuit of Truth and Beauty in Lean 4: Formally Verified Theory of Grammars, Optimization, Matroids.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21393\">https://doi.org/10.15479/AT-ISTA-21393</a>.","ista":"Dvorak M. 2026. Pursuit of truth and beauty in Lean 4: Formally verified theory of grammars, optimization, matroids. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2026-03-04T09:26:46Z","status":"public","doi_confirm":"1","file":[{"relation":"main_file","file_name":"2026_Dvorak_Martin_Thesis.pdf","date_updated":"2026-03-04T08:56:15Z","creator":"mdvorak","date_created":"2026-03-04T08:56:15Z","content_type":"application/pdf","checksum":"cface6dc18152680962b5361575f6e4f","access_level":"open_access","success":1,"file_size":1771231,"file_id":"21394"},{"file_name":"2026_Dvorak_Martin_Thesis.docx","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2026-03-04T09:03:37Z","date_updated":"2026-03-04T09:03:37Z","creator":"mdvorak","access_level":"closed","checksum":"290ddfacfb7e07fb07e6f0b334e67c90","file_size":864585,"file_id":"21395"}],"year":"2026","file_date_updated":"2026-03-04T09:03:37Z","has_accepted_license":"1","page":"160","_id":"21393","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"related_material":{"link":[{"relation":"software","url":"https://github.com/madvorak/duality/tree/v3.5.0","description":"Full version of all definitions, statements, and proofs for Chapter 3.1 (Linear duality)"},{"description":"Full version of all definitions, statements, and proofs for Chapter 3.2 (Valued Constraint Satisfaction Problems)","url":"https://github.com/madvorak/vcsp/tree/v8.2.0","relation":"software"},{"url":"https://github.com/Ivan-Sergeyev/seymour/tree/v1.2.0","relation":"software","description":"Full version of all definitions, statements, and proofs for Chapter 4 (Seymour project)"},{"url":"https://github.com/madvorak/chomsky/tree/v1.2.0","relation":"software","description":"Full version of all definitions, statements, and proofs for Chapter 5 (Theory of grammars)"},{"relation":"software","url":"https://github.com/madvorak/grammars","description":"Old version (Lean 3) of the project about grammars"},{"relation":"software","url":"https://github.com/madvorak/preliminaries/blob/main/Preliminaries.lean","description":"Demonstration of (minimal) requirements for selected algebraic classes used in my Ph.D. thesis"}],"record":[{"status":"public","id":"13120","relation":"part_of_dissertation"},{"id":"20071","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"21398"}]},"department":[{"_id":"GradSch"},{"_id":"VlKo"}],"abstract":[{"lang":"eng","text":"This thesis documents a voyage towards truth and beauty via formal verification of theorems. To this end, we develop libraries in Lean 4 that present definitions and results from diverse areas of MathematiCS (i.e., Mathematics and Computer Science). The aim is to create code that is understandable, believable, useful, and elegant. The code should stand for itself as much as possible without a need for documentation; however, this text redundantly documents our code artifacts and provides additional context that isn’t present in the code. This thesis is written for readers who know Lean 4 but are not familiar with any of the topics presented. We manifest truth and beauty in three formalized areas of MathematiCS.\r\n\r\nWe formalize general grammars in Lean 4 and use grammars to show closure of the class of type-0 languages under four operations; union, reversal, concatenation, and the Kleene star.\r\n\r\nOur second stop is the theory of optimization. Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take “infinite values”. Additionally, we develop the basics of the theory of optimization in terms of the framework called General-Valued Constraint Satisfaction Problems, and we prove that, if a Rational-Valued Constraint Satisfaction Problem template has symmetric fractional polymorphisms of all arities, then its basic LP relaxation is tight.\r\n\r\nOur third stop is matroid theory. Seymour’s decomposition theorem is a hallmark result in matroid theory, presenting a structural characterization of the class of regular matroids. We aim to formally verify Seymour’s theorem in Lean 4. First, we build a library for working with totally unimodular matrices. We define binary matroids and their standard representations, and we prove that they form a matroid in the sense how Mathlib defines matroids. We define regular matroids to be matroids for which there exists a full representation rational matrix that is totally unimodular, and we prove that all regular matroids are binary. We define 1-sum, 2-sum, and 3 sum of binary matroids as specific ways to compose their standard representation matrices. We prove that the 1-sum, the 2-sum, and the 3-sum of regular matroids are a regular matroid, which concludes the composition direction of the Seymour’s theorem. The (more difficult) decomposition direction remains unproved.\r\n\r\nIn the pursuit of truth, we focus on identifying the trusted code in each project and presenting it faithfully. We emphasize the readability and believability of definitions rather than choosing definitions that are easier to work with. In search for beauty, we focus on the philosophical framework of Roger Scruton, who emphasizes that beauty is not a mere decoration but, most importantly, beauty is the means for shaping our place in the world and a source of redemption, where it can be viewed as a substitute for religion."}],"title":"Pursuit of truth and beauty in Lean 4: Formally verified theory of grammars, optimization, matroids","type":"dissertation"},{"file_date_updated":"2026-07-23T11:14:05Z","researchdata_availability":"no","volume":75,"has_accepted_license":"1","intvolume":"        75","status":"public","file":[{"date_updated":"2026-07-23T11:14:05Z","date_created":"2026-07-23T11:14:05Z","creator":"dernst","content_type":"application/pdf","file_name":"2026_DiscreteCompGeom_Aronov.pdf","relation":"main_file","success":1,"access_level":"open_access","checksum":"a32774a0d14f46cafbd77bfb9d9ac4b6","file_id":"22395","file_size":525281}],"supplementarymaterial":"yes","year":"2026","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s00454-025-00759-w"}],"record":[{"status":"public","id":"18917","relation":"earlier_version"},{"status":"public","id":"20339","relation":"dissertation_contains"}]},"isi":1,"department":[{"_id":"UlWa"}],"abstract":[{"lang":"eng","text":"An eight-partition of a finite set of points (respectively, of a continuous mass distribution) in R^3\r\n consists of three planes that divide the space into 8 octants, such that each open octant contains at most 1/8 of the points (respectively, of the mass). In 1966, Hadwiger showed that any mass distribution in R^3 admits an eight-partition; moreover, one can prescribe the normal direction of one of the three planes. The analogous result for finite point sets follows by a standard limit argument. We prove the following variant of this result: any mass distribution (or point set) in R^3 admits an eight-partition for which the intersection of two of the planes is a line with a prescribed direction. Moreover, we present an efficient algorithm for calculating an eight-partition of a set of n points in R^3 (with prescribed normal direction of one of the planes) in time O(n^7/3). A preliminary version of this work appeared in SoCG’24 (Aronov et al., 40th International Symposium on Computational Geometry, 2024)."}],"title":"Eight-partitioning points in 3D, and efficiently too","type":"journal_article","page":"1331-1355","_id":"19860","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","external_id":{"arxiv":["2403.02627"],"isi":["001506904300001"]},"date_published":"2026-06-01T00:00:00Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-07-29T13:13:17Z","author":[{"last_name":"Aronov","full_name":"Aronov, Boris","first_name":"Boris"},{"first_name":"Abdul","last_name":"Basit","full_name":"Basit, Abdul"},{"first_name":"Indu","full_name":"Ramesh, Indu","last_name":"Ramesh"},{"id":"0433290C-AF8F-11E9-A4C7-F729E6697425","full_name":"Tasinato, Gianluca","last_name":"Tasinato","first_name":"Gianluca"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli"}],"month":"06","PlanS_conform":"1","oa":1,"ddc":["500"],"article_type":"original","OA_place":"publisher","doi":"10.1007/s00454-025-00739-0","citation":{"chicago":"Aronov, Boris, Abdul Basit, Indu Ramesh, Gianluca Tasinato, and Uli Wagner. “Eight-Partitioning Points in 3D, and Efficiently Too.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00454-025-00739-0\">https://doi.org/10.1007/s00454-025-00739-0</a>.","ama":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. Eight-partitioning points in 3D, and efficiently too. <i>Discrete &#38; Computational Geometry</i>. 2026;75:1331-1355. doi:<a href=\"https://doi.org/10.1007/s00454-025-00739-0\">10.1007/s00454-025-00739-0</a>","ista":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. 2026. Eight-partitioning points in 3D, and efficiently too. Discrete &#38; Computational Geometry. 75, 1331–1355.","short":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, U. Wagner, Discrete &#38; Computational Geometry 75 (2026) 1331–1355.","ieee":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, and U. Wagner, “Eight-partitioning points in 3D, and efficiently too,” <i>Discrete &#38; Computational Geometry</i>, vol. 75. Springer Nature, pp. 1331–1355, 2026.","apa":"Aronov, B., Basit, A., Ramesh, I., Tasinato, G., &#38; Wagner, U. (2026). Eight-partitioning points in 3D, and efficiently too. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-025-00739-0\">https://doi.org/10.1007/s00454-025-00739-0</a>","mla":"Aronov, Boris, et al. “Eight-Partitioning Points in 3D, and Efficiently Too.” <i>Discrete &#38; Computational Geometry</i>, vol. 75, Springer Nature, 2026, pp. 1331–55, doi:<a href=\"https://doi.org/10.1007/s00454-025-00739-0\">10.1007/s00454-025-00739-0</a>."},"acknowledgement":"Work by BA was supported by NSF grants CCF 15-40656 and CCF 20-08551, and by grant 2014/170 from the US-Israel Binational Science Foundation. Part of this research was conducted while BA was visiting ISTA in the summers of 2022 and 2023. The visit of BA to ISTA in the summer of 2022 was supported by an ISTA Visiting Professorship. Research of BA also partially supported by ERC grant no. 882971, “GeoScape,” and by the Erdős Center. Work by AB was supported by Australian Research Council grant DP220102212. Work by IR was supported by a Tandon School of Engineering Fellowship and by NSF Grant CCF-20-08551. BA and AB would like to thank William Steiger for insightful initial discussions of the problems addressed in this work. Open Access funding enabled and organized by CAUL and its Member Institutions.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Discrete & Computational Geometry","das_tickbox":"0","date_created":"2025-06-22T22:02:07Z","publisher":"Springer Nature","publication_status":"published","scopus_import":"1","language":[{"iso":"eng"}],"day":"01","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"arxiv":1}]