[{"day":"08","article_processing_charge":"No","type":"other_academic_publication","supplementarymaterial":"no","page":"R3-R5","corr_author":"1","author":[{"full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"publication_identifier":{"eissn":["1879-0445"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2023.11.039"}],"external_id":{"pmid":["38194926"]},"date_published":"2024-01-08T00:00:00Z","pmid":1,"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1016/j.cub.2023.11.039","ddc":["580"],"publisher":"Elsevier","status":"public","issue":"1","quality_controlled":"1","abstract":[{"lang":"eng","text":"Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability."}],"title":"Eva Benkova","volume":34,"year":"2024","researchdata_availability":"not applicable","publication_status":"published","citation":{"ama":"Benková E. <i>Eva Benkova</i>. Vol 34. Elsevier; 2024:R3-R5. doi:<a href=\"https://doi.org/10.1016/j.cub.2023.11.039\">10.1016/j.cub.2023.11.039</a>","mla":"Benková, Eva. “Eva Benkova.” <i>Current Biology</i>, vol. 34, no. 1, Elsevier, 2024, pp. R3–5, doi:<a href=\"https://doi.org/10.1016/j.cub.2023.11.039\">10.1016/j.cub.2023.11.039</a>.","ista":"Benková E. 2024. Eva Benkova, Elsevier,p.","short":"E. Benková, Eva Benkova, Elsevier, 2024.","ieee":"E. Benková, <i>Eva Benkova</i>, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.","chicago":"Benková, Eva. <i>Eva Benkova</i>. <i>Current Biology</i>. Vol. 34. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cub.2023.11.039\">https://doi.org/10.1016/j.cub.2023.11.039</a>.","apa":"Benková, E. (2024). <i>Eva Benkova</i>. <i>Current Biology</i> (Vol. 34, pp. R3–R5). Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2023.11.039\">https://doi.org/10.1016/j.cub.2023.11.039</a>"},"doi":"10.1016/j.cub.2023.11.039","intvolume":"        34","publication":"Current Biology","oa_version":"Published Version","oa":1,"date_updated":"2026-10-01T11:17:58Z","das_tickbox":"0","department":[{"_id":"EvBe"}],"date_created":"2024-01-21T23:00:56Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"01","_id":"14842"},{"fulldoi":"https://doi.org/10.5061/dryad.p5hqbzkw0","month":"02","ddc":["570"],"_id":"23025","department":[{"_id":"EM-Fac"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2026-10-01T11:13:02Z","oa":1,"date_updated":"2026-10-01T11:15:29Z","related_material":{"record":[{"id":"18920","status":"public","relation":"used_in_publication"}]},"date_published":"2024-02-07T00:00:00Z","oa_version":"None","OA_type":"green","author":[{"last_name":"Homola","full_name":"Homola, Miroslav","first_name":"Miroslav"},{"last_name":"Büttner","full_name":"Büttner, Carina","first_name":"Carina"},{"last_name":"Füzik","full_name":"Füzik, Tibor","first_name":"Tibor"},{"last_name":"Krepelka","full_name":"Krepelka, Pavel","first_name":"Pavel"},{"full_name":"Holbová, Radka","first_name":"Radka","last_name":"Holbová"},{"first_name":"Marten","full_name":"Chaillet, Marten","last_name":"Chaillet"},{"last_name":"Nováček","first_name":"Jiří","full_name":"Nováček, Jiří"},{"last_name":"Förster","first_name":"Friedrich","full_name":"Förster, Friedrich"},{"last_name":"Wilson","first_name":"William","full_name":"Wilson, William"},{"last_name":"Schroeder","full_name":"Schroeder, Declan","first_name":"Declan"},{"last_name":"Plevka","first_name":"Pavel","full_name":"Plevka, Pavel"}],"doi":"10.5061/dryad.p5hqbzkw0","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.p5hqbzkw0"}],"year":"2024","citation":{"apa":"Homola, M., Büttner, C., Füzik, T., Krepelka, P., Holbová, R., Chaillet, M., … Plevka, P. (2024). Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Dryad. <a href=\"https://doi.org/10.5061/dryad.p5hqbzkw0\">https://doi.org/10.5061/dryad.p5hqbzkw0</a>","chicago":"Homola, Miroslav, Carina Büttner, Tibor Füzik, Pavel Krepelka, Radka Holbová, Marten Chaillet, Jiří Nováček, et al. “Data: Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Dryad, 2024. <a href=\"https://doi.org/10.5061/dryad.p5hqbzkw0\">https://doi.org/10.5061/dryad.p5hqbzkw0</a>.","ieee":"M. Homola <i>et al.</i>, “Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi.” Dryad, 2024.","short":"M. Homola, C. Büttner, T. Füzik, P. Krepelka, R. Holbová, M. Chaillet, J. Nováček, F. Förster, W. Wilson, D. Schroeder, P. Plevka, (2024).","ista":"Homola M, Büttner C, Füzik T, Krepelka P, Holbová R, Chaillet M, Nováček J, Förster F, Wilson W, Schroeder D, Plevka P. 2024. Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi, Dryad, <a href=\"https://doi.org/10.5061/dryad.p5hqbzkw0\">10.5061/dryad.p5hqbzkw0</a>.","mla":"Homola, Miroslav, et al. <i>Data: Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi</i>. Dryad, 2024, doi:<a href=\"https://doi.org/10.5061/dryad.p5hqbzkw0\">10.5061/dryad.p5hqbzkw0</a>.","ama":"Homola M, Büttner C, Füzik T, et al. Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. 2024. doi:<a href=\"https://doi.org/10.5061/dryad.p5hqbzkw0\">10.5061/dryad.p5hqbzkw0</a>"},"OA_place":"repository","title":"Data: Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi","abstract":[{"text":"The globally distributed marine alga Emiliania huxleyi produces reflective calcite disks (coccoliths) that increase the albedo of ocean water and thus reduce the heat absorption in the ocean, which cools the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane decorated with numerous transmembrane proteins. The virions are prone to deformation, and parts of their capsids deviate from the icosahedral arrangement. EhV-201 virions infect E. huxleyi by using their fivefold vertex to bind to a host cell and fuse the virus’s inner membrane with the plasma membrane. Whereas the replication of EhV-201 probably occurs in the nucleus, virions assemble in the cytoplasm at the surface of endoplasmic reticulum-derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. Upon the completion of genome packaging, the capsids change conformation, which enables them to acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which allows the continuous release of virions by exocytosis. Our results provide insight into how EhVs bypass the surface protective layers of E. huxleyi and exploit the organelles of an infected cell for progeny assembly.","lang":"eng"}],"article_processing_charge":"No","type":"research_data_reference","day":"07","publisher":"Dryad","status":"public"},{"ec_funded":1,"_id":"15146","dataavailabilitystatement":"Representative tomograms containing the data shown in Fig. 3, and Figs. S5 and S9 have been deposited in the Electron Microscopy Data Bank under accession codes: EMD-18490, EMD-18491, EMD-18492, EMD-18493, and EMD-18494. All tilt series, including frames, raw tilt series, and reconstructed IsoNet-filtered tomograms, were deposited in the Electron Microscopy Public Image Archive database under the accession code EMPIAR-11897.","month":"03","date_created":"2024-03-21T06:45:51Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"article_type":"original","das_tickbox":"1","file":[{"creator":"dernst","file_name":"2024_JCB_Zens.pdf","date_updated":"2024-03-25T12:52:04Z","file_id":"15188","success":1,"content_type":"application/pdf","date_created":"2024-03-25T12:52:04Z","access_level":"open_access","relation":"main_file","checksum":"90d1984a93660735e506c2a304bc3f73","file_size":11907016}],"date_updated":"2026-10-01T11:24:27Z","isi":1,"oa":1,"oa_version":"Published Version","publication":"Journal of Cell Biology","file_date_updated":"2024-03-25T12:52:04Z","intvolume":"       223","doi":"10.1083/jcb.202309125","publication_status":"published","citation":{"mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>.","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. 2024;223(6). doi:<a href=\"https://doi.org/10.1083/jcb.202309125\">10.1083/jcb.202309125</a>","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125.","ieee":"B. Zens <i>et al.</i>, “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” <i>Journal of Cell Biology</i>, vol. 223, no. 6. Rockefeller University Press, 2024.","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>","chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2024. <a href=\"https://doi.org/10.1083/jcb.202309125\">https://doi.org/10.1083/jcb.202309125</a>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2024","volume":223,"researchdata_availability":"yes","acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly."}],"quality_controlled":"1","license":"https://creativecommons.org/licenses/by/4.0/","status":"public","issue":"6","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","_id":"7bd318a1-9f16-11ee-852c-cc9217763180","grant_number":"E435"},{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"21317","_id":"2615199A-B435-11E9-9278-68D0E5697425","name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis"},{"name":"CryoMinflux-guided in-situ visual proteomics and structure determination","grant_number":"CZI01","_id":"62909c6f-2b32-11ec-9570-e1476aab5308"}],"publisher":"Rockefeller University Press","has_accepted_license":"1","ddc":["570"],"fulldoi":"https://doi.org/10.1083/jcb.202309125","language":[{"iso":"eng"}],"date_published":"2024-03-20T00:00:00Z","external_id":{"isi":["001264190100001"],"pmid":["38506714"]},"pmid":1,"scopus_import":"1","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","full_name":"Zens, Bettina","last_name":"Zens","orcid":"0000-0002-9561-1239"},{"last_name":"Fäßler","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Fäßler, Florian"},{"last_name":"Hansen","orcid":"0000-0001-7967-2085","full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","first_name":"Jesse"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"last_name":"Datler","orcid":"0000-0002-3616-8580","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Datler, Julia"},{"full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3904-947X","last_name":"Hodirnau"},{"orcid":"0000-0002-9438-4783","last_name":"Zheden","full_name":"Zheden, Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"full_name":"Alanko, Jonna H","first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","last_name":"Alanko"},{"full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"}],"corr_author":"1","article_number":"e202309125","supplementarymaterial":"yes","type":"journal_article","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"article_processing_charge":"Yes (via OA deal)","day":"20"},{"external_id":{"pmid":["39143214"],"isi":["001300534300019"]},"pmid":1,"date_published":"2024-08-22T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","ddc":["570"],"fulldoi":"https://doi.org/10.1038/s41586-024-07813-2","day":"22","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","corr_author":"1","page":"911–920 ","supplementarymaterial":"yes","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"scopus_import":"1","author":[{"full_name":"Pillai, Arvind","first_name":"Arvind","last_name":"Pillai"},{"first_name":"Abbas","full_name":"Idris, Abbas","last_name":"Idris"},{"full_name":"Philomin, Annika","first_name":"Annika","last_name":"Philomin"},{"full_name":"Weidle, Connor","first_name":"Connor","last_name":"Weidle"},{"first_name":"Rebecca","full_name":"Skotheim, Rebecca","last_name":"Skotheim"},{"full_name":"Leung, Philip J.Y.","first_name":"Philip J.Y.","last_name":"Leung"},{"full_name":"Broerman, Adam","first_name":"Adam","last_name":"Broerman"},{"last_name":"Demakis","full_name":"Demakis, Cullen","first_name":"Cullen"},{"last_name":"Borst","full_name":"Borst, Andrew J.","first_name":"Andrew J."},{"full_name":"Praetorius, Florian M","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","orcid":"0000-0002-0806-8101"},{"last_name":"Baker","first_name":"David","full_name":"Baker, David"}],"publication":"Nature","oa_version":"Published Version","file_date_updated":"2024-09-09T12:01:14Z","intvolume":"       632","das_tickbox":"1","date_updated":"2026-10-01T11:19:54Z","file":[{"file_name":"2024_Nature_Pillai.pdf","creator":"dernst","success":1,"date_updated":"2024-09-09T12:01:14Z","file_id":"18005","access_level":"open_access","date_created":"2024-09-09T12:01:14Z","content_type":"application/pdf","checksum":"39127601621a360ec0edc538627eb211","file_size":16572040,"relation":"main_file"}],"isi":1,"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-08-25T22:01:08Z","department":[{"_id":"FlPr"}],"article_type":"original","_id":"17463","dataavailabilitystatement":"All data are available either in the main text or as Supplementary Information. PDB models and sequences for designs shown in main text figures are available in the attached Supplementary Information, along with source data for plots in main text figures. Structures determined by cryo-EM were deposited in the PDB as 8UP1, 8URE and 8UTM, and maps were deposited in the EMDB under accession numbers EMD-42442, EMD-42491 and EMD-42542.","month":"08","quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","status":"public","publisher":"Springer Nature","acknowledgement":"We thank D. D. Sahtoe, R. D. Kiber, Y. Hsia, N. Bethel and A. Favor for helpful discussions and K. VanWormer and L. Goldschmidt for technical support. We also thank X. Li and M. Lamb for mass spectrometry support. This work was supported by the Washington Research Foundation Postdoctoral Fellowship (grant no. GR027504, A. Pillai), a National Science Foundation Graduate Research Fellowship (grant no. DGE-2140004, A.I.), a Human Frontier Science Program Long Term Fellowship (grant no. LT000880/2019, F.P.), the Audacious Project at the Institute for Protein Design (A.B., A. Pillai, A. Philomin, A.I. and D.B.), a National Energy Research Scientific Computing Centre award (grant no. BER-ERCAP0022018), the Howard Hughes Medical Institute (D.B.), the Open Philanthropy Project Improving Protein Design Fund (P.J.Y.L., C.D. and D.B.) a gift from Microsoft (D.B.) and a grant from DARPA supporting the Harnessing Enzymatic Activity for Lifesaving Remedies programme (grant no. HR001120S0052, contract no. HR0011-21-2-0012, D.B.).","abstract":[{"lang":"eng","text":"Allosteric modulation of protein function, wherein the binding of an effector to a protein triggers conformational changes at distant functional sites, plays a central part in the control of metabolism and cell signalling1,2,3. There has been considerable interest in designing allosteric systems, both to gain insight into the mechanisms underlying such ‘action at a distance’ modulation and to create synthetic proteins whose functions can be regulated by effectors4,5,6,7. However, emulating the subtle conformational changes distributed across many residues, characteristic of natural allosteric proteins, is a significant challenge8,9. Here, inspired by the classic Monod–Wyman–Changeux model of cooperativity10, we investigate the de novo design of allostery through rigid-body coupling of peptide-switchable hinge modules11 to protein interfaces12 that direct the formation of alternative oligomeric states. We find that this approach can be used to generate a wide variety of allosterically switchable systems, including cyclic rings that incorporate or eject subunits in response to peptide binding and dihedral cages that undergo effector-induced disassembly. Size-exclusion chromatography, mass photometry13 and electron microscopy reveal that these designed allosteric protein assemblies closely resemble the design models in both the presence and absence of peptide effectors and can have ligand-binding cooperativity comparable to classic natural systems such as haemoglobin14. Our results indicate that allostery can arise from global coupling of the energetics of protein substructures without optimized side-chain–side-chain allosteric communication pathways and provide a roadmap for generating allosterically triggerable delivery systems, protein nanomachines and cellular feedback control circuitry."}],"title":"De novo design of allosterically switchable protein assemblies","publication_status":"published","citation":{"apa":"Pillai, A., Idris, A., Philomin, A., Weidle, C., Skotheim, R., Leung, P. J. Y., … Baker, D. (2024). De novo design of allosterically switchable protein assemblies. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-07813-2\">https://doi.org/10.1038/s41586-024-07813-2</a>","chicago":"Pillai, Arvind, Abbas Idris, Annika Philomin, Connor Weidle, Rebecca Skotheim, Philip J.Y. Leung, Adam Broerman, et al. “De Novo Design of Allosterically Switchable Protein Assemblies.” <i>Nature</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41586-024-07813-2\">https://doi.org/10.1038/s41586-024-07813-2</a>.","ieee":"A. Pillai <i>et al.</i>, “De novo design of allosterically switchable protein assemblies,” <i>Nature</i>, vol. 632. Springer Nature, pp. 911–920, 2024.","short":"A. Pillai, A. Idris, A. Philomin, C. Weidle, R. Skotheim, P.J.Y. Leung, A. Broerman, C. Demakis, A.J. Borst, F.M. Praetorius, D. Baker, Nature 632 (2024) 911–920.","ista":"Pillai A, Idris A, Philomin A, Weidle C, Skotheim R, Leung PJY, Broerman A, Demakis C, Borst AJ, Praetorius FM, Baker D. 2024. De novo design of allosterically switchable protein assemblies. Nature. 632, 911–920.","mla":"Pillai, Arvind, et al. “De Novo Design of Allosterically Switchable Protein Assemblies.” <i>Nature</i>, vol. 632, Springer Nature, 2024, pp. 911–920, doi:<a href=\"https://doi.org/10.1038/s41586-024-07813-2\">10.1038/s41586-024-07813-2</a>.","ama":"Pillai A, Idris A, Philomin A, et al. De novo design of allosterically switchable protein assemblies. <i>Nature</i>. 2024;632:911–920. doi:<a href=\"https://doi.org/10.1038/s41586-024-07813-2\">10.1038/s41586-024-07813-2</a>"},"year":"2024","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)"},"researchdata_availability":"yes (supplementary data)","volume":632,"doi":"10.1038/s41586-024-07813-2"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-01-29T07:58:40Z","article_type":"original","department":[{"_id":"FlSc"}],"_id":"18934","month":"03","oa_version":"Published Version","publication":"Molecular Biology of the Cell","intvolume":"        35","file_date_updated":"2025-01-29T08:12:11Z","das_tickbox":"0","oa":1,"file":[{"checksum":"d7deb6390f294da69321cfbe352ed611","file_size":1699180,"relation":"main_file","access_level":"open_access","date_created":"2025-01-29T08:12:11Z","content_type":"application/pdf","success":1,"date_updated":"2025-01-29T08:12:11Z","file_id":"18935","file_name":"2024_MolecularBioCell_Sarkany.pdf","creator":"dernst"}],"date_updated":"2026-10-01T11:22:53Z","OA_place":"publisher","publication_status":"published","citation":{"short":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, P.M. Martins, Molecular Biology of the Cell 35 (2024).","ieee":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, and P. M. Martins, “NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation,” <i>Molecular Biology of the Cell</i>, vol. 35, no. 3. American Society for Cell Biology, 2024.","chicago":"Sárkány, Zsuzsa, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro M. Martins. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2024. <a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">https://doi.org/10.1091/mbc.e23-07-0289</a>.","apa":"Sárkány, Z., Figueiredo, F., Macedo-Ribeiro, S., &#38; Martins, P. M. (2024). NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">https://doi.org/10.1091/mbc.e23-07-0289</a>","ama":"Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. <i>Molecular Biology of the Cell</i>. 2024;35(3). doi:<a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">10.1091/mbc.e23-07-0289</a>","mla":"Sárkány, Zsuzsa, et al. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” <i>Molecular Biology of the Cell</i>, vol. 35, no. 3, mr1, American Society for Cell Biology, 2024, doi:<a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">10.1091/mbc.e23-07-0289</a>.","ista":"Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. 2024. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Molecular Biology of the Cell. 35(3), mr1."},"year":"2024","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"researchdata_availability":"yes","volume":35,"doi":"10.1091/mbc.e23-07-0289","OA_type":"hybrid","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","quality_controlled":"1","publisher":"American Society for Cell Biology","issue":"3","status":"public","acknowledgement":"We thank Professor José Paulo Leal, Department of Computer Science − Faculdade de Ciências da Universidade do Porto, for his invaluable help during the Implementation of NAGPKin. This work is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 952334 (PhasAGE). This research was funded by the Portuguese Foundation for Science and Technology (FCT) in the framework of project PTDC/QUI-COL/2444/2021.","abstract":[{"lang":"eng","text":"The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt ."}],"title":"NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation","has_accepted_license":"1","fulldoi":"https://doi.org/10.1091/mbc.e23-07-0289","ddc":["570"],"external_id":{"pmid":["38117593"]},"date_published":"2024-03-01T00:00:00Z","pmid":1,"language":[{"iso":"eng"}],"article_number":"mr1","supplementarymaterial":"no","publication_identifier":{"eissn":["1939-4586"],"issn":["1059-1524"]},"scopus_import":"1","author":[{"full_name":"Sárkány, Zsuzsa","first_name":"Zsuzsa","last_name":"Sárkány"},{"full_name":"Figueiredo, Francisco","first_name":"Francisco","id":"8125cbe2-9661-11ed-a754-afe96018f37d","last_name":"Figueiredo"},{"last_name":"Macedo-Ribeiro","first_name":"Sandra","full_name":"Macedo-Ribeiro, Sandra"},{"first_name":"Pedro M.","full_name":"Martins, Pedro M.","last_name":"Martins"}],"day":"01","type":"journal_article","article_processing_charge":"Yes (in subscription journal)"},{"month":"12","dataavailabilitystatement":"Source code is available via GitHub, (copy archived at Last, 2024), software available on the python package index as 'Ais-cryoET'. Trained neural networks have been uploaded to aiscryoet.org.","DOAJ_listed":"1","_id":"18757","article_type":"original","department":[{"_id":"FlPr"}],"date_created":"2025-01-05T23:01:57Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"date_updated":"2026-10-01T11:22:32Z","file":[{"relation":"main_file","checksum":"a4f0f906e4d5c1078208b317e78699d1","file_size":7445664,"content_type":"application/pdf","date_created":"2025-01-08T08:51:45Z","access_level":"open_access","date_updated":"2025-01-08T08:51:45Z","file_id":"18774","success":1,"file_name":"2024_eLife_Last.pdf","creator":"dernst"}],"das_tickbox":"1","intvolume":"        13","file_date_updated":"2025-01-08T08:51:45Z","oa_version":"Published Version","publication":"eLife","OA_type":"gold","doi":"10.7554/eLife.98552","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2024","researchdata_availability":"yes","volume":13,"OA_place":"publisher","publication_status":"published","citation":{"ieee":"M. G. F. Last, L. Abendstein, L. M. Voortman, and T. H. Sharp, “Streamlining segmentation of cryo-electron tomography datasets with Ais,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","short":"M.G.F. Last, L. Abendstein, L.M. Voortman, T.H. Sharp, ELife 13 (2024).","apa":"Last, M. G. F., Abendstein, L., Voortman, L. M., &#38; Sharp, T. H. (2024). Streamlining segmentation of cryo-electron tomography datasets with Ais. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.98552\">https://doi.org/10.7554/eLife.98552</a>","chicago":"Last, Mart G.F., Leoni Abendstein, Lenard M. Voortman, and Thomas H. Sharp. “Streamlining Segmentation of Cryo-Electron Tomography Datasets with Ais.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/eLife.98552\">https://doi.org/10.7554/eLife.98552</a>.","mla":"Last, Mart G. F., et al. “Streamlining Segmentation of Cryo-Electron Tomography Datasets with Ais.” <i>ELife</i>, vol. 13, 98552, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/eLife.98552\">10.7554/eLife.98552</a>.","ama":"Last MGF, Abendstein L, Voortman LM, Sharp TH. Streamlining segmentation of cryo-electron tomography datasets with Ais. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/eLife.98552\">10.7554/eLife.98552</a>","ista":"Last MGF, Abendstein L, Voortman LM, Sharp TH. 2024. Streamlining segmentation of cryo-electron tomography datasets with Ais. eLife. 13, 98552."},"title":"Streamlining segmentation of cryo-electron tomography datasets with Ais","abstract":[{"text":"Segmentation is a critical data processing step in many applications of cryo-electron tomography. Downstream analyses, such as subtomogram averaging, are often based on segmentation results, and are thus critically dependent on the availability of open-source software for accurate as well as high-throughput tomogram segmentation. There is a need for more user-friendly, flexible, and comprehensive segmentation software that offers an insightful overview of all steps involved in preparing automated segmentations. Here, we present Ais: a dedicated tomogram segmentation package that is geared towards both high performance and accessibility, available on GitHub. In this report, we demonstrate two common processing steps that can be greatly accelerated with Ais: particle picking for subtomogram averaging, and generating many-feature segmentations of cellular architecture based on in situ tomography data. Featuring comprehensive annotation, segmentation, and rendering functionality, as well as an open repository for trained models at aiscryoet.org, we hope that Ais will help accelerate research and dissemination of data involving cryoET.","lang":"eng"}],"acknowledgement":"We thank A Koster and M Barcena for helpful discussions and kindly sharing the coronaviral replication organelle datasets. We are also grateful to van den Hoek et al., 2022 and Wu et al., 2023, for uploading the data that we used for Figure 5 onto EMPIAR and EMDB, as well as to the authors of various other datasets uploaded to these databases that are not discussed in this manuscript but that were useful for testing the software. We also thank the reviewers, whose comments were very helpful in improving the manuscript and the software. Finally, we are grateful the early Ais users who provided us with feedback on the software and reported issues. This research was supported by the following grants to THS: European Research Council H202 Grant 759517; European Union’s Horizon Europe Program IMAGINE grant 101094250, and the Netherlands Organization for Scientific Research Grant VI.Vidi.193.014.","publisher":"eLife Sciences Publications","status":"public","quality_controlled":"1","fulldoi":"https://doi.org/10.7554/eLife.98552","ddc":["570"],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2024-12-20T00:00:00Z","external_id":{"pmid":["39704648"]},"pmid":1,"author":[{"full_name":"Last, Mart G.F.","first_name":"Mart G.F.","last_name":"Last"},{"orcid":"0000-0001-7634-5353","last_name":"Abendstein","first_name":"Leoni","id":"14f1f051-cd9d-11ef-9c94-8b942a882560","full_name":"Abendstein, Leoni"},{"last_name":"Voortman","full_name":"Voortman, Lenard M.","first_name":"Lenard M."},{"first_name":"Thomas H.","full_name":"Sharp, Thomas H.","last_name":"Sharp"}],"scopus_import":"1","publication_identifier":{"eissn":["2050-084X"]},"supplementarymaterial":"yes","article_number":"98552","article_processing_charge":"Yes","type":"journal_article","day":"20"},{"date_published":"2024-10-05T00:00:00Z","pmid":1,"external_id":{"pmid":["39366958"],"isi":["001409493300014"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","fulldoi":"https://doi.org/10.1038/s41467-024-52762-z","ddc":["570"],"day":"05","type":"journal_article","article_processing_charge":"Yes (via OA deal)","PlanS_conform":"1","article_number":"8631","supplementarymaterial":"yes","publication_identifier":{"eissn":["2041-1723"]},"scopus_import":"1","author":[{"full_name":"Zupančič, Maja","first_name":"Maja","last_name":"Zupančič"},{"last_name":"Keimpema","first_name":"Erik","full_name":"Keimpema, Erik"},{"full_name":"Tretiakov, Evgenii O.","first_name":"Evgenii O.","last_name":"Tretiakov"},{"last_name":"Eder","first_name":"Stephanie J.","full_name":"Eder, Stephanie J."},{"full_name":"Lev, Itamar","first_name":"Itamar","last_name":"Lev"},{"full_name":"Englmaier, Lukas","first_name":"Lukas","last_name":"Englmaier"},{"orcid":"0000-0003-0863-4481","last_name":"Bhandari","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep"},{"last_name":"Fietz","full_name":"Fietz, Simone A.","first_name":"Simone A."},{"last_name":"Härtig","first_name":"Wolfgang","full_name":"Härtig, Wolfgang"},{"full_name":"Renaux, Estelle","first_name":"Estelle","last_name":"Renaux"},{"last_name":"Villunger","full_name":"Villunger, Andreas","first_name":"Andreas"},{"last_name":"Hökfelt","first_name":"Tomas","full_name":"Hökfelt, Tomas"},{"full_name":"Zimmer, Manuel","first_name":"Manuel","last_name":"Zimmer"},{"last_name":"Clotman","full_name":"Clotman, Frédéric","first_name":"Frédéric"},{"full_name":"Harkany, Tibor","first_name":"Tibor","last_name":"Harkany"}],"oa_version":"Published Version","publication":"Nature Communications","intvolume":"        15","file_date_updated":"2024-10-21T12:15:38Z","das_tickbox":"1","related_material":{"record":[{"relation":"research_data","id":"22961","status":"public"}]},"oa":1,"date_updated":"2026-10-01T12:17:25Z","isi":1,"file":[{"creator":"dernst","file_name":"2024_NatureComm_Zupancic.pdf","success":1,"date_updated":"2024-10-21T12:15:38Z","file_id":"18460","access_level":"open_access","date_created":"2024-10-21T12:15:38Z","content_type":"application/pdf","file_size":7215329,"checksum":"03d6dd1b84efa24e9e9ede748d08764d","relation":"main_file"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-10-20T22:02:05Z","article_type":"original","department":[{"_id":"RySh"}],"DOAJ_listed":"1","_id":"18445","month":"10","dataavailabilitystatement":"The snRNA-seq data generated in this study have been deposited in the NCBI Gene Expression Omnibus database under accession code GSE132730 and as ‘Supplementary Data 1 - Neuro2a-onecut3-overexpression’. All other primary data were made publically available at https://github.com/Harkany-Lab/Zupancic_2023 and deposited to Figshare.com with https://doi.org/10.6084/m9.figshare.22680433. Source data are provided with this paper.","quality_controlled":"1","publisher":"Springer Nature","status":"public","acknowledgement":"The authors thank Z. Máté, G. Szabó, and F. Erdélyi for the custom generation of transgenic mouse lines, C. Fekete for Trh transgenic tissues (all from the Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary), A. Goudmaeker for IVF recovery of a frozen mouse line (SSS animal facility, Université catholique de Louvain), and Y. Yanagawa (Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Japan) for providing GAD67gfp/+ mice. We also thank S. Cloer, D. Preininger, and A. Weissenbacher (Tiergarten Schönbrunn, Vienna, Austria) for providing naked mole rats, Seba’s fruit bats, and Indian flying foxes, as well as F. Aujard (CNRS, UMR 7179 ‘Adaptive mechanisms and evolution’, France) for Microcebus tissues. I. Milenkovic and G.G. Kovács (Clinical Institute of Neurology, Medical University of Vienna, Vienna, Austria) are acknowledged for providing post-mortem human brain samples. We are indebted to S. Rehman (Medical University of Vienna), M. Kalusa (University of Leipzig, Leipzig, Germany), and W. Reimann (Paul Flechsig Institute for Brain Research, Leipzig, Germany) for their technical assistance. C. elegans strains were provided by the National Bioresource Project for the nematode, Japan, and the CGC, with the latter being funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). This work was supported by the Austrian Science Fund (FWF, P 34121-B; to E.K.), the Swedish Research Council (2023-03058, T.Ha; 2020-01688, T.Hö.), the Swedish Brain Foundation (Hjärnfonden, FO2022-0300, to T.Ha.), the Novo Nordisk Foundation (NNF23OC0084476, to T.Ha.), the European Research Council (FOODFORLIFE, ERC-2020-AdG-101021016; to T.Ha.), the Université Catholique de Louvain (‘Fonds spéciaux de recherche’-FSR, to F.C.), and Fonds de la Recherche Scientifique F.R.S.-FNRS (‘Project de recherche (PDR)’ #T.0039.21, to F.C.). S.J.E. is supported by the Simons Foundation #543069. I.L. is supported by a post-doctoral fellowship from the Human Frontiers Science Program (LT000335/2020-L). E.R. holds a PhD grant from the FRIA (F.R.S.-FNRS, Belgium). F.C. is a Research Director of the F.R.S.-FNRS (Belgium).\r\nOpen access funding provided by Karolinska Institute.","title":"Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3","abstract":[{"text":"Acquisition of specialized cellular features is controlled by the ordered expression of transcription factors (TFs) along differentiation trajectories. Here, we find a member of the Onecut TF family, ONECUT3, expressed in postmitotic neurons that leave their Ascl1+/Onecut1/2+ proliferative domain in the vertebrate hypothalamus to instruct neuronal differentiation. We combined single-cell RNA-seq and gain-of-function experiments for gene network reconstruction to show that ONECUT3 affects the polarization and morphogenesis of both hypothalamic GABA-derived dopamine and thyrotropin-releasing hormone (TRH)+ glutamate neurons through neuron navigator-2 (NAV2). In vivo, siRNA-mediated knockdown of ONECUT3 in neonatal mice reduced NAV2 mRNA, as well as neurite complexity in Onecut3-containing neurons, while genetic deletion of Onecut3/ceh-48 in C. elegans impaired neurocircuit wiring, and sensory discrimination-based behaviors. Thus, ONECUT3, conserved across neuronal subtypes and many species, underpins the polarization and morphological plasticity of phenotypically distinct neurons that descend from a common pool of Ascl1+ progenitors in the hypothalamus.","lang":"eng"}],"OA_place":"publisher","citation":{"ista":"Zupančič M, Keimpema E, Tretiakov EO, Eder SJ, Lev I, Englmaier L, Bhandari P, Fietz SA, Härtig W, Renaux E, Villunger A, Hökfelt T, Zimmer M, Clotman F, Harkany T. 2024. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. Nature Communications. 15, 8631.","mla":"Zupančič, Maja, et al. “Concerted Transcriptional Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” <i>Nature Communications</i>, vol. 15, 8631, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-52762-z\">10.1038/s41467-024-52762-z</a>.","ama":"Zupančič M, Keimpema E, Tretiakov EO, et al. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-52762-z\">10.1038/s41467-024-52762-z</a>","apa":"Zupančič, M., Keimpema, E., Tretiakov, E. O., Eder, S. J., Lev, I., Englmaier, L., … Harkany, T. (2024). Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-52762-z\">https://doi.org/10.1038/s41467-024-52762-z</a>","chicago":"Zupančič, Maja, Erik Keimpema, Evgenii O. Tretiakov, Stephanie J. Eder, Itamar Lev, Lukas Englmaier, Pradeep Bhandari, et al. “Concerted Transcriptional Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-52762-z\">https://doi.org/10.1038/s41467-024-52762-z</a>.","ieee":"M. Zupančič <i>et al.</i>, “Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","short":"M. Zupančič, E. Keimpema, E.O. Tretiakov, S.J. Eder, I. Lev, L. Englmaier, P. Bhandari, S.A. Fietz, W. Härtig, E. Renaux, A. Villunger, T. Hökfelt, M. Zimmer, F. Clotman, T. Harkany, Nature Communications 15 (2024)."},"publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"researchdata_availability":"yes","volume":15,"year":"2024","doi":"10.1038/s41467-024-52762-z","OA_type":"gold"},{"month":"01","conference":{"name":"CPAL: Conference on Parsimony and Learning","end_date":"2024-01-03","location":"Hong Kong, China","start_date":"2024-01-03"},"_id":"14213","department":[{"_id":"FrLo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2023-08-22T14:19:59Z","oa":1,"date_updated":"2026-10-01T11:25:45Z","file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2024-02-12T08:40:36Z","file_size":8038511,"checksum":"8fad894c34f1b3d5a14fb8ffb12f7277","relation":"main_file","file_name":"2024_CPAL_Lao.pdf","creator":"dernst","date_updated":"2024-02-12T08:40:36Z","file_id":"14978","success":1}],"das_tickbox":"0","file_date_updated":"2024-02-12T08:40:36Z","publication":"1st Conference on Parsimony and Learning","oa_version":"Published Version","year":"2024","researchdata_availability":"no","publication_status":"published","citation":{"ista":"Lao D, Hu Z, Locatello F, Yang Y, Soatto S. 2024. Divided attention: Unsupervised multi-object discovery with contextually separated slots. 1st Conference on Parsimony and Learning. CPAL: Conference on Parsimony and Learning.","mla":"Lao, Dong, et al. “Divided Attention: Unsupervised Multi-Object Discovery with Contextually Separated Slots.” <i>1st Conference on Parsimony and Learning</i>, 2024.","ama":"Lao D, Hu Z, Locatello F, Yang Y, Soatto S. Divided attention: Unsupervised multi-object discovery with contextually separated slots. In: <i>1st Conference on Parsimony and Learning</i>. ; 2024.","apa":"Lao, D., Hu, Z., Locatello, F., Yang, Y., &#38; Soatto, S. (2024). Divided attention: Unsupervised multi-object discovery with contextually separated slots. In <i>1st Conference on Parsimony and Learning</i>. Hong Kong, China.","chicago":"Lao, Dong, Zhengyang Hu, Francesco Locatello, Yanchao Yang, and Stefano Soatto. “Divided Attention: Unsupervised Multi-Object Discovery with Contextually Separated Slots.” In <i>1st Conference on Parsimony and Learning</i>, 2024.","ieee":"D. Lao, Z. Hu, F. Locatello, Y. Yang, and S. Soatto, “Divided attention: Unsupervised multi-object discovery with contextually separated slots,” in <i>1st Conference on Parsimony and Learning</i>, Hong Kong, China, 2024.","short":"D. Lao, Z. Hu, F. Locatello, Y. Yang, S. Soatto, in:, 1st Conference on Parsimony and Learning, 2024."},"title":"Divided attention: Unsupervised multi-object discovery with contextually separated slots","abstract":[{"lang":"eng","text":"We introduce a method to segment the visual field into independently moving regions, trained with no ground truth or supervision. It consists of an adversarial conditional encoder-decoder architecture based on Slot Attention, modified to use the image as context to decode optical flow without attempting to reconstruct the image itself. In the resulting multi-modal representation, one modality (flow) feeds the encoder to produce separate latent codes (slots), whereas the other modality (image) conditions the decoder to generate the first (flow) from the slots. This design frees the representation from having to encode complex nuisance variability in the image due to, for instance, illumination and reflectance properties of the scene. Since customary autoencoding based on minimizing the reconstruction error does not preclude the entire flow from being encoded into a single slot, we modify the loss to an adversarial criterion based on Contextual Information Separation. The resulting min-max optimization fosters the separation of objects and their assignment to different attention slots, leading to Divided Attention, or DivA. DivA outperforms recent unsupervised multi-object motion segmentation methods while tripling run-time speed up to 104FPS and reducing the performance gap from supervised methods to 12% or less. DivA can handle different numbers of objects and different image sizes at training and test time, is invariant to permutation of object labels, and does not require explicit regularization."}],"status":"public","quality_controlled":"1","ddc":["000"],"has_accepted_license":"1","language":[{"iso":"eng"}],"arxiv":1,"date_published":"2024-01-03T00:00:00Z","external_id":{"arxiv":["2304.01430"]},"author":[{"last_name":"Lao","full_name":"Lao, Dong","first_name":"Dong"},{"last_name":"Hu","full_name":"Hu, Zhengyang","first_name":"Zhengyang"},{"last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Yang","full_name":"Yang, Yanchao","first_name":"Yanchao"},{"first_name":"Stefano","full_name":"Soatto, Stefano","last_name":"Soatto"}],"supplementarymaterial":"no","article_processing_charge":"No","type":"conference","day":"03"},{"supplementarymaterial":"no","page":"40484-40501","author":[{"full_name":"Pervez, Adeel A","id":"fca6d90c-d47f-11ee-bc87-93ff51604981","first_name":"Adeel A","last_name":"Pervez"},{"last_name":"Locatello","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco"},{"first_name":"Efstratios","full_name":"Gavves, Efstratios","last_name":"Gavves"}],"publication_identifier":{"eissn":["2640-3498"]},"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2402.13077","open_access":"1"}],"day":"01","article_processing_charge":"No","type":"conference","ddc":["000"],"arxiv":1,"external_id":{"arxiv":["2402.13077"]},"alternative_title":["PMLR"],"date_published":"2024-09-01T00:00:00Z","language":[{"iso":"eng"}],"volume":235,"researchdata_availability":"no","year":"2024","publication_status":"published","citation":{"mla":"Pervez, Adeel A., et al. “Mechanistic Neural Networks for Scientific Machine Learning.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 40484–501.","ama":"Pervez AA, Locatello F, Gavves E. Mechanistic neural networks for scientific machine learning. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:40484-40501.","ista":"Pervez AA, Locatello F, Gavves E. 2024. Mechanistic neural networks for scientific machine learning. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 40484–40501.","ieee":"A. A. Pervez, F. Locatello, and E. Gavves, “Mechanistic neural networks for scientific machine learning,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 40484–40501.","short":"A.A. Pervez, F. Locatello, E. Gavves, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 40484–40501.","apa":"Pervez, A. A., Locatello, F., &#38; Gavves, E. (2024). Mechanistic neural networks for scientific machine learning. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 40484–40501). Vienna, Austria: ML Research Press.","chicago":"Pervez, Adeel A, Francesco Locatello, and Efstratios Gavves. “Mechanistic Neural Networks for Scientific Machine Learning.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:40484–501. ML Research Press, 2024."},"OA_place":"publisher","OA_type":"diamond","publisher":"ML Research Press","status":"public","quality_controlled":"1","title":"Mechanistic neural networks for scientific machine learning","abstract":[{"lang":"eng","text":"This paper presents Mechanistic Neural Networks, a neural network design for machine learning applications in the sciences. It incorporates a new Mechanistic Block in standard architectures to explicitly learn governing differential equations as representations, revealing the underlying dynamics of data and enhancing interpretability and efficiency in data modeling. Central to our approach is a novel Relaxed Linear Programming Solver (NeuRLP) inspired by a technique that reduces solving linear ODEs to solving linear programs. This integrates well with neural networks and surpasses the limitations of traditional ODE solvers enabling scalable GPU parallel processing. Overall, Mechanistic Neural Networks demonstrate their versatility for scientific machine learning applications, adeptly managing tasks from equation discovery to dynamic systems modeling. We prove their comprehensive capabilities in analyzing and interpreting complex scientific data across various applications, showing significant performance against specialized state-of-the-art methods. Source code is available at https://github.com/alpz/mech-nn."}],"department":[{"_id":"FrLo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-09-22T22:01:43Z","month":"09","conference":{"start_date":"2024-07-21","location":"Vienna, Austria","end_date":"2024-07-27","name":"ICML: International Conference on Machine Learning"},"_id":"18114","intvolume":"       235","oa_version":"Published Version","publication":"Proceedings of the 41st International Conference on Machine Learning","oa":1,"date_updated":"2026-10-01T11:26:09Z","related_material":{"link":[{"url":"https://github.com/alpz/mech-nn","relation":"software"}]},"das_tickbox":"0"},{"fulldoi":"https://doi.org/10.1109/cvpr52733.2024.02176","language":[{"iso":"eng"}],"external_id":{"isi":["001342515506043"],"arxiv":["2406.09196"]},"date_published":"2024-06-15T00:00:00Z","arxiv":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2406.09196","open_access":"1"}],"publication_identifier":{"eisbn":["9798350353006"]},"author":[{"first_name":"Ke","full_name":"Fan, Ke","last_name":"Fan"},{"first_name":"Zechen","full_name":"Bai, Zechen","last_name":"Bai"},{"last_name":"Xiao","first_name":"Tianjun","full_name":"Xiao, Tianjun"},{"full_name":"He, Tong","first_name":"Tong","last_name":"He"},{"full_name":"Horn, Max","first_name":"Max","last_name":"Horn"},{"last_name":"Fu","full_name":"Fu, Yanwei","first_name":"Yanwei"},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"first_name":"Zheng","full_name":"Zhang, Zheng","last_name":"Zhang"}],"supplementarymaterial":"no","type":"conference","article_processing_charge":"No","day":"15","_id":"18964","conference":{"start_date":"2024-06-16","location":"Seattle, WA, United States","end_date":"2024-06-22","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"month":"06","date_created":"2025-01-29T14:27:39Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"FrLo"}],"related_material":{"link":[{"relation":"software","url":"https://kfan21.github.io/AdaSlot/"}]},"das_tickbox":"0","date_updated":"2026-10-02T08:47:53Z","isi":1,"oa":1,"publication":"2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition","oa_version":"Preprint","doi":"10.1109/cvpr52733.2024.02176","OA_type":"green","citation":{"mla":"Fan, Ke, et al. “Adaptive Slot Attention: Object Discovery with Dynamic Slot Number.” <i>2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2024, doi:<a href=\"https://doi.org/10.1109/cvpr52733.2024.02176\">10.1109/cvpr52733.2024.02176</a>.","ama":"Fan K, Bai Z, Xiao T, et al. Adaptive slot attention: Object discovery with dynamic slot number. In: <i>2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2024. doi:<a href=\"https://doi.org/10.1109/cvpr52733.2024.02176\">10.1109/cvpr52733.2024.02176</a>","ista":"Fan K, Bai Z, Xiao T, He T, Horn M, Fu Y, Locatello F, Zhang Z. 2024. Adaptive slot attention: Object discovery with dynamic slot number. 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition.","ieee":"K. Fan <i>et al.</i>, “Adaptive slot attention: Object discovery with dynamic slot number,” in <i>2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Seattle, WA, United States, 2024.","short":"K. Fan, Z. Bai, T. Xiao, T. He, M. Horn, Y. Fu, F. Locatello, Z. Zhang, in:, 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2024.","apa":"Fan, K., Bai, Z., Xiao, T., He, T., Horn, M., Fu, Y., … Zhang, Z. (2024). Adaptive slot attention: Object discovery with dynamic slot number. In <i>2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. Seattle, WA, United States: IEEE. <a href=\"https://doi.org/10.1109/cvpr52733.2024.02176\">https://doi.org/10.1109/cvpr52733.2024.02176</a>","chicago":"Fan, Ke, Zechen Bai, Tianjun Xiao, Tong He, Max Horn, Yanwei Fu, Francesco Locatello, and Zheng Zhang. “Adaptive Slot Attention: Object Discovery with Dynamic Slot Number.” In <i>2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE, 2024. <a href=\"https://doi.org/10.1109/cvpr52733.2024.02176\">https://doi.org/10.1109/cvpr52733.2024.02176</a>."},"publication_status":"published","OA_place":"repository","researchdata_availability":"yes","year":"2024","acknowledgement":"Yanwei Fu is the corresponding authour. Yanwei Fu is with School of Data Science, Fudan University, Shanghai Key Lab of Intelligent Information Processing, Fudan University, and Fudan ISTBI-ZJNU Algorithm Centre for Brain-inspired Intelligence, Zhejiang Normal University, Jinhua, China.","abstract":[{"lang":"eng","text":"Object-centric learning (OCL) extracts the representation of objects with slots, offering an exceptional blend of flexibility and interpretability for abstracting low-level perceptual features. A widely adopted method within OCL is slot attention, which utilizes attention mechanisms to iteratively refine slot representations. However, a major draw-back of most object-centric models, including slot attention, is their reliance on predefining the number of slots. This not only necessitates prior knowledge of the dataset but also overlooks the inherent variability in the number of objects present in each instance. To overcome this fundamental limitation, we present a novel complexity-aware object auto-encoder framework. Within this framework, we introduce an adaptive slot attention (AdaSlot) mecha-nism that dynamically determines the optimal number of slots based on the content of the data. This is achieved by proposing a discrete slot sampling module that is responsible for selecting an appropriate number of slots from a candidate list. Furthermore, we introduce a masked slot decoder that suppresses unselected slots during the decoding process. Our framework, tested extensively on object discovery tasks with various datasets, shows performance matching or exceeding top fixed-slot models. Moreover, our analysis substantiates that our method exhibits the capability to dynamically adapt the slot number according to each instance's complexity, offering the potential for further exploration in slot attention research. Project will be available at https://kfan21.github.io/AdaSlot/"}],"title":"Adaptive slot attention: Object discovery with dynamic slot number","quality_controlled":"1","status":"public","publisher":"IEEE"},{"doi":"10.1109/icip51287.2024.10647499","OA_type":"green","OA_place":"repository","publication_status":"published","citation":{"ista":"Demirel B, Ozkan H. 2024. Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image. 2024 IEEE International Conference on Image Processing. ICIP: International Conference on Image Processing, 977–983.","mla":"Demirel, Berker, and Huseyin Ozkan. “Decompl: Decompositional Learning with Attention Pooling for Group Activity Recognition from a Single Volleyball Image.” <i>2024 IEEE International Conference on Image Processing</i>, IEEE, 2024, pp. 977–83, doi:<a href=\"https://doi.org/10.1109/icip51287.2024.10647499\">10.1109/icip51287.2024.10647499</a>.","ama":"Demirel B, Ozkan H. Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image. In: <i>2024 IEEE International Conference on Image Processing</i>. IEEE; 2024:977-983. doi:<a href=\"https://doi.org/10.1109/icip51287.2024.10647499\">10.1109/icip51287.2024.10647499</a>","apa":"Demirel, B., &#38; Ozkan, H. (2024). Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image. In <i>2024 IEEE International Conference on Image Processing</i> (pp. 977–983). Abu Dhabi, United Arab Emirates: IEEE. <a href=\"https://doi.org/10.1109/icip51287.2024.10647499\">https://doi.org/10.1109/icip51287.2024.10647499</a>","chicago":"Demirel, Berker, and Huseyin Ozkan. “Decompl: Decompositional Learning with Attention Pooling for Group Activity Recognition from a Single Volleyball Image.” In <i>2024 IEEE International Conference on Image Processing</i>, 977–83. IEEE, 2024. <a href=\"https://doi.org/10.1109/icip51287.2024.10647499\">https://doi.org/10.1109/icip51287.2024.10647499</a>.","ieee":"B. Demirel and H. Ozkan, “Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image,” in <i>2024 IEEE International Conference on Image Processing</i>, Abu Dhabi, United Arab Emirates, 2024, pp. 977–983.","short":"B. Demirel, H. Ozkan, in:, 2024 IEEE International Conference on Image Processing, IEEE, 2024, pp. 977–983."},"researchdata_availability":"yes","year":"2024","title":"Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image","abstract":[{"lang":"eng","text":"Group Activity Recognition (GAR) aims to detect the activity performed by multiple actors in a scene. Prior works model the spatio-temporal features based on the RGB, optical flow or keypoint data types. On the contrary, our hypothesis is that by only using the RGB data without temporality, the performance can be maintained with a negligible loss in accuracy. To that end, we propose a novel GAR technique for volleyball videos, DECOMPL, which consists of two complementary branches. In the visual branch, it extracts the features using attention pooling. In the coordinate branch, it considers the configuration of the players and extracts the spatial information from the box coordinates. Moreover, we analyzed the Volleyball dataset that the recent literature is mostly based on, and systematically reannotated it to emphasize the group concept. Experimental results demonstrated the effectiveness of the proposed model DECOMPL, which delivered the best/second best GAR performance with the reannotations/original annotations among the comparable state-of-the-art methods. Code and new annotations are available at GitHub: https://github.com/berkerdemirel/decompl"}],"quality_controlled":"1","publisher":"IEEE","status":"public","conference":{"name":"ICIP: International Conference on Image Processing","end_date":"2024-10-30","location":"Abu Dhabi, United Arab Emirates","start_date":"2024-10-27"},"_id":"18956","month":"11","date_created":"2025-01-29T12:22:24Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"FrLo"}],"das_tickbox":"0","related_material":{"link":[{"url":"https://github.com/berkerdemirel/decompl","relation":"software"}]},"oa":1,"isi":1,"date_updated":"2026-10-02T08:47:17Z","oa_version":"Preprint","publication":"2024 IEEE International Conference on Image Processing","publication_identifier":{"eisbn":["9798350349399"],"eissn":["2381-8549"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.06439"}],"author":[{"last_name":"Demirel","first_name":"Berker","id":"8b4bc47f-3200-11ee-973b-8f0e7be21a9f","full_name":"Demirel, Berker"},{"last_name":"Ozkan","first_name":"Huseyin","full_name":"Ozkan, Huseyin"}],"corr_author":"1","page":"977-983","supplementarymaterial":"no","type":"conference","article_processing_charge":"No","day":"01","fulldoi":"https://doi.org/10.1109/icip51287.2024.10647499","language":[{"iso":"eng"}],"external_id":{"arxiv":["2303.06439"],"isi":["001442947000143"]},"date_published":"2024-11-01T00:00:00Z","arxiv":1},{"oa_version":"Published Version","publication":"12th International Conference on Learning Representations","file_date_updated":"2025-02-04T12:34:23Z","das_tickbox":"0","date_updated":"2026-10-02T08:48:50Z","file":[{"relation":"main_file","file_size":1713606,"checksum":"8ed3c34706eeec622c7e8968dc0f747a","content_type":"application/pdf","date_created":"2025-02-04T12:34:23Z","access_level":"open_access","file_id":"18995","date_updated":"2025-02-04T12:34:23Z","success":1,"creator":"dernst","file_name":"2024_ICLR_Yao.pdf"}],"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-02-07T14:28:34Z","department":[{"_id":"FrLo"}],"_id":"14946","conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2024-05-07","location":"Vienna, Austria","start_date":"2024-05-07"},"month":"11","quality_controlled":"1","status":"public","publisher":"Curran Associates","acknowledgement":"This work was initiated at the Second Bellairs Workshop on Causality held at the Bellairs Research Institute, January 6–13, 2022; we thank all workshop participants for providing a stimulating research environment. Further, we thank Cian Eastwood, Luigi Gresele, Stefano Soatto, Marco Bagatella and A. René Geist for helpful discussion. GM is a member of the Machine Learning Cluster of Excellence, EXC number 2064/1 – Project number 390727645. JvK and GM acknowledge support from the German Federal Ministry of Education and Research (BMBF) through the Tübingen AI Center (FKZ: 01IS18039B). The research of DX and SM was supported by the Air Force Office of Scientific Research under award number FA8655-22-1-7155. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the United States Air Force. We also thank SURF for the support in using the Dutch National Supercomputer Snellius. SL was supported by an IVADO excellence PhD scholarship and by Samsung Electronics Co., Ldt. DY was supported by an Amazon fellowship, the International Max Planck Research School for Intelligent Systems (IMPRS-IS) and the ISTA graduate school. Work done outside of Amazon.","title":"Multi-view causal representation learning with partial observability","abstract":[{"text":"We present a unified framework for studying the identifiability of representations learned from simultaneously observed views, such as different data modalities. We allow a partially observed setting in which each view constitutes a nonlinear mixture of a subset of underlying latent variables, which can be causally related. We prove that the information shared across all subsets of any number of views can be learned up to a smooth bijection using contrastive learning and a single encoder per view. We also provide graphical criteria indicating which latent variables can be identified through a simple set of rules, which we refer to as identifiability algebra. Our general framework and theoretical results unify and extend several previous work on multi-view nonlinear ICA, disentanglement, and causal representation learning. We experimentally validate our claims on numerical, image, and multi-modal data sets. Further, we demonstrate that the performance of prior methods is recovered in different special cases of our setup. Overall, we find that access to multiple partial views offers unique opportunities for identifiable representation learning, enabling the discovery of latent structures from purely observational data.","lang":"eng"}],"citation":{"mla":"Yao, Dingling, et al. “Multi-View Causal Representation Learning with Partial Observability.” <i>12th International Conference on Learning Representations</i>, Curran Associates, 2024.","ama":"Yao D, Xu D, Lachapelle S, et al. Multi-view causal representation learning with partial observability. In: <i>12th International Conference on Learning Representations</i>. Curran Associates; 2024.","ista":"Yao D, Xu D, Lachapelle S, Magliacane S, Taslakian P, Martius G, Kügelgen J von, Locatello F. 2024. Multi-view causal representation learning with partial observability. 12th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ieee":"D. Yao <i>et al.</i>, “Multi-view causal representation learning with partial observability,” in <i>12th International Conference on Learning Representations</i>, Vienna, Austria, 2024.","short":"D. Yao, D. Xu, S. Lachapelle, S. Magliacane, P. Taslakian, G. Martius, J. von Kügelgen, F. Locatello, in:, 12th International Conference on Learning Representations, Curran Associates, 2024.","apa":"Yao, D., Xu, D., Lachapelle, S., Magliacane, S., Taslakian, P., Martius, G., … Locatello, F. (2024). Multi-view causal representation learning with partial observability. In <i>12th International Conference on Learning Representations</i>. Vienna, Austria: Curran Associates.","chicago":"Yao, Dingling, Danru Xu, Sébastien Lachapelle, Sara Magliacane, Perouz Taslakian, Georg Martius, Julius von Kügelgen, and Francesco Locatello. “Multi-View Causal Representation Learning with Partial Observability.” In <i>12th International Conference on Learning Representations</i>. Curran Associates, 2024."},"OA_place":"repository","publication_status":"published","researchdata_availability":"no","year":"2024","OA_type":"green","external_id":{"arxiv":["2311.04056"]},"date_published":"2024-11-07T00:00:00Z","arxiv":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","ddc":["000"],"day":"07","type":"conference","article_processing_charge":"No","corr_author":"1","supplementarymaterial":"no","author":[{"last_name":"Yao","first_name":"Dingling","id":"d3e02e50-48a8-11ee-8f62-c108061797fa","full_name":"Yao, Dingling"},{"first_name":"Danru","full_name":"Xu, Danru","last_name":"Xu"},{"full_name":"Lachapelle, Sébastien","first_name":"Sébastien","last_name":"Lachapelle"},{"last_name":"Magliacane","full_name":"Magliacane, Sara","first_name":"Sara"},{"full_name":"Taslakian, Perouz","first_name":"Perouz","last_name":"Taslakian"},{"last_name":"Martius","first_name":"Georg","full_name":"Martius, Georg"},{"first_name":"Julius von","full_name":"Kügelgen, Julius von","last_name":"Kügelgen"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683"}]},{"department":[{"_id":"FrPe"}],"article_type":"original","date_created":"2024-07-22T09:46:52Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"07","_id":"17302","intvolume":"         2","oa_version":"Submitted Version","publication":"Nature Water","isi":1,"date_updated":"2026-10-02T08:51:26Z","oa":1,"das_tickbox":"0","researchdata_availability":"no","volume":2,"year":"2024","OA_place":"repository","publication_status":"published","citation":{"chicago":"Tiel, Marit van, Caroline Aubry-Wake, Lauren Somers, Christoff Andermann, Francesco Avanzi, Michel Baraer, Gabriele Chiogna, et al. “Cryosphere–Groundwater Connectivity Is a Missing Link in the Mountain Water Cycle.” <i>Nature Water</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s44221-024-00277-8\">https://doi.org/10.1038/s44221-024-00277-8</a>.","apa":"van Tiel, M., Aubry-Wake, C., Somers, L., Andermann, C., Avanzi, F., Baraer, M., … Yapiyev, V. (2024). Cryosphere–groundwater connectivity is a missing link in the mountain water cycle. <i>Nature Water</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s44221-024-00277-8\">https://doi.org/10.1038/s44221-024-00277-8</a>","short":"M. van Tiel, C. Aubry-Wake, L. Somers, C. Andermann, F. Avanzi, M. Baraer, G. Chiogna, C. Daigre, S. Das, F. Drenkhan, D. Farinotti, C.L. Fyffe, I. de Graaf, S. Hanus, W. Immerzeel, F. Koch, J.M. McKenzie, T. Müller, A.L. Popp, Z. Saidaliyeva, B. Schaefli, O.S. Schilling, K. Teagai, J.M. Thornton, V. Yapiyev, Nature Water 2 (2024) 624–637.","ieee":"M. van Tiel <i>et al.</i>, “Cryosphere–groundwater connectivity is a missing link in the mountain water cycle,” <i>Nature Water</i>, vol. 2. Springer Nature, pp. 624–637, 2024.","ista":"van Tiel M, Aubry-Wake C, Somers L, Andermann C, Avanzi F, Baraer M, Chiogna G, Daigre C, Das S, Drenkhan F, Farinotti D, Fyffe CL, de Graaf I, Hanus S, Immerzeel W, Koch F, McKenzie JM, Müller T, Popp AL, Saidaliyeva Z, Schaefli B, Schilling OS, Teagai K, Thornton JM, Yapiyev V. 2024. Cryosphere–groundwater connectivity is a missing link in the mountain water cycle. Nature Water. 2, 624–637.","ama":"van Tiel M, Aubry-Wake C, Somers L, et al. Cryosphere–groundwater connectivity is a missing link in the mountain water cycle. <i>Nature Water</i>. 2024;2:624-637. doi:<a href=\"https://doi.org/10.1038/s44221-024-00277-8\">10.1038/s44221-024-00277-8</a>","mla":"van Tiel, Marit, et al. “Cryosphere–Groundwater Connectivity Is a Missing Link in the Mountain Water Cycle.” <i>Nature Water</i>, vol. 2, Springer Nature, 2024, pp. 624–37, doi:<a href=\"https://doi.org/10.1038/s44221-024-00277-8\">10.1038/s44221-024-00277-8</a>."},"OA_type":"green","doi":"10.1038/s44221-024-00277-8","status":"public","publisher":"Springer Nature","quality_controlled":"1","abstract":[{"lang":"eng","text":"The mountain cryosphere and groundwater play pivotal roles in shaping the hydrological cycle, yet their connectivity remains incompletely understood. Current knowledge on meltwater recharge and consequent groundwater discharge processes is better developed for snow–groundwater connectivity than for glacier–groundwater connectivity. Estimates of meltwater recharge vary considerably, which is probably a function of not only inherent catchment characteristics but also of the different spatio-temporal scales involved and the uncertainties in the methods used. This hinders a comprehensive understanding of the mountain water cycle. As glaciers retreat, permafrost thaws and snowpack diminishes, the relative importance of mountain groundwater is expected to increase. However, shifting and declining recharge from the cryosphere may decrease absolute groundwater amounts and fluxes with as-yet unknown effects on catchment-scale hydrological processes. We therefore stress the need to better quantify mountain cryosphere–groundwater connectivity to predict climate change impacts on mountain water supply and to support sustainable water resource management of downstream socio-ecological systems."}],"title":"Cryosphere–groundwater connectivity is a missing link in the mountain water cycle","acknowledgement":"We acknowledge the Mountain Research Initiative (MRI) for sponsoring the workshop ‘Cryosphere-groundwater Interactions: A Missing Link in Mountain Water Research’ via their funding from the Swiss Academy of Sciences (SCNAT) under project no. FNW0004 004-2019-00. M.v.T. was supported by a Walter Benjamin fellowship from the German Research Foundation (DFG) under project no. 510684314. C.A.-W. was supported by the Banting Postdoctoral Fellowships programme, administered by the government of Canada. G.C. acknowledges the support of the DFG research unit (FOR2793/2) investigating the ‘Sensitivity of High Alpine Geosystems to Climate Change since 1850’ (SEHAG) under grant CH981/3-2. F.D. acknowledges funding from the Dirección de Fomento de la Investigación at PUCP. I.d.G. acknowledges funding from the European Research Council (ERC) under grant agreement GROW-101041110. V.Y. was supported by Nazarbayev University under CRP research grant no. 021220CRP2122. We thank D. Masovic of VAW, ETH Zurich, for drawing Fig. 1.","fulldoi":"https://doi.org/10.1038/s44221-024-00277-8","external_id":{"isi":["001390137500016"]},"date_published":"2024-07-19T00:00:00Z","language":[{"iso":"eng"}],"supplementarymaterial":"no","page":"624-637","author":[{"first_name":"Marit","full_name":"van Tiel, Marit","last_name":"van Tiel"},{"full_name":"Aubry-Wake, Caroline","first_name":"Caroline","last_name":"Aubry-Wake"},{"last_name":"Somers","first_name":"Lauren","full_name":"Somers, Lauren"},{"first_name":"Christoff","full_name":"Andermann, Christoff","last_name":"Andermann"},{"last_name":"Avanzi","first_name":"Francesco","full_name":"Avanzi, Francesco"},{"last_name":"Baraer","first_name":"Michel","full_name":"Baraer, Michel"},{"last_name":"Chiogna","first_name":"Gabriele","full_name":"Chiogna, Gabriele"},{"last_name":"Daigre","full_name":"Daigre, Clémence","first_name":"Clémence"},{"last_name":"Das","full_name":"Das, Soumik","first_name":"Soumik"},{"full_name":"Drenkhan, Fabian","first_name":"Fabian","last_name":"Drenkhan"},{"full_name":"Farinotti, Daniel","first_name":"Daniel","last_name":"Farinotti"},{"full_name":"Fyffe, Catriona Louise","first_name":"Catriona Louise","id":"001b0422-8d15-11ed-bc51-cab6c037a228","last_name":"Fyffe"},{"first_name":"Inge","full_name":"de Graaf, Inge","last_name":"de Graaf"},{"full_name":"Hanus, Sarah","first_name":"Sarah","last_name":"Hanus"},{"full_name":"Immerzeel, Walter","first_name":"Walter","last_name":"Immerzeel"},{"last_name":"Koch","first_name":"Franziska","full_name":"Koch, Franziska"},{"last_name":"McKenzie","full_name":"McKenzie, Jeffrey M.","first_name":"Jeffrey M."},{"first_name":"Tom","full_name":"Müller, Tom","last_name":"Müller"},{"last_name":"Popp","first_name":"Andrea L.","full_name":"Popp, Andrea L."},{"first_name":"Zarina","full_name":"Saidaliyeva, Zarina","last_name":"Saidaliyeva"},{"full_name":"Schaefli, Bettina","first_name":"Bettina","last_name":"Schaefli"},{"first_name":"Oliver S.","full_name":"Schilling, Oliver S.","last_name":"Schilling"},{"last_name":"Teagai","full_name":"Teagai, Kapiolani","first_name":"Kapiolani"},{"first_name":"James M.","full_name":"Thornton, James M.","last_name":"Thornton"},{"last_name":"Yapiyev","full_name":"Yapiyev, Vadim","first_name":"Vadim"}],"main_file_link":[{"url":"https://insu.hal.science/insu-04674297","open_access":"1"}],"publication_identifier":{"issn":["2731-6084"]},"scopus_import":"1","day":"19","article_processing_charge":"No","type":"journal_article"},{"acknowledgement":"We acknowledge the support of the Canada CIFAR AI Chair Program and IVADO. We thank Mila and Compute Canada for providing computational resources.\r\n","title":"Unsupervised concept discovery mitigates spurious correlations","abstract":[{"text":"Models prone to spurious correlations in training data often produce brittle predictions and introduce unintended biases. Addressing this challenge typically involves methods relying on prior knowledge and group annotation to remove spurious correlations, which may not be readily available in many applications. In this paper, we establish a novel connection between unsupervised object-centric learning and mitigation of spurious correlations. Instead of directly inferring subgroups with varying correlations with labels, our approach focuses on discovering concepts: discrete ideas that are shared across input samples. Leveraging existing object-centric representation learning, we introduce CoBalT: a concept balancing technique that effectively mitigates spurious correlations without requiring human labeling of subgroups. Evaluation across the benchmark datasets for sub-population shifts demonstrate superior or competitive performance compared state-of-the-art baselines, without the need for group annotation. Code is available at https://github.com/rarefin/CoBalT","lang":"eng"}],"quality_controlled":"1","publisher":"ML Research Press","status":"public","OA_type":"green","citation":{"apa":"Arefin, R., Zhang, Y., Baratin, A., Locatello, F., Rish, I., Liu, D., &#38; Kawaguchi, K. (2024). Unsupervised concept discovery mitigates spurious correlations. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 1672–1688). Vienna, Austria: ML Research Press.","chicago":"Arefin, Rifat, Yan Zhang, Aristide Baratin, Francesco Locatello, Irina Rish, Dianbo Liu, and Kenji Kawaguchi. “Unsupervised Concept Discovery Mitigates Spurious Correlations.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:1672–88. ML Research Press, 2024.","ieee":"R. Arefin <i>et al.</i>, “Unsupervised concept discovery mitigates spurious correlations,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 1672–1688.","short":"R. Arefin, Y. Zhang, A. Baratin, F. Locatello, I. Rish, D. Liu, K. Kawaguchi, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 1672–1688.","ista":"Arefin R, Zhang Y, Baratin A, Locatello F, Rish I, Liu D, Kawaguchi K. 2024. Unsupervised concept discovery mitigates spurious correlations. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 1672–1688.","mla":"Arefin, Rifat, et al. “Unsupervised Concept Discovery Mitigates Spurious Correlations.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 1672–88.","ama":"Arefin R, Zhang Y, Baratin A, et al. Unsupervised concept discovery mitigates spurious correlations. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:1672-1688."},"OA_place":"repository","publication_status":"published","volume":235,"researchdata_availability":"no","year":"2024","related_material":{"link":[{"relation":"software","url":"https://github.com/rarefin/CoBalT"}]},"das_tickbox":"0","oa":1,"date_updated":"2026-10-02T08:48:23Z","oa_version":"Preprint","publication":"Proceedings of the 41st International Conference on Machine Learning","intvolume":"       235","conference":{"end_date":"2024-07-27","name":"ICML: International Conference on Machine Learning","location":"Vienna, Austria","start_date":"2024-07-21"},"_id":"18971","month":"07","date_created":"2025-01-30T07:21:57Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"FrLo"}],"type":"conference","article_processing_charge":"No","day":"30","scopus_import":"1","publication_identifier":{"eissn":["2640-3498"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2402.13368"}],"author":[{"last_name":"Arefin","full_name":"Arefin, Rifat","first_name":"Rifat"},{"first_name":"Yan","full_name":"Zhang, Yan","last_name":"Zhang"},{"first_name":"Aristide","full_name":"Baratin, Aristide","last_name":"Baratin"},{"full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683"},{"last_name":"Rish","first_name":"Irina","full_name":"Rish, Irina"},{"last_name":"Liu","full_name":"Liu, Dianbo","first_name":"Dianbo"},{"first_name":"Kenji","full_name":"Kawaguchi, Kenji","last_name":"Kawaguchi"}],"page":"1672-1688","supplementarymaterial":"no","language":[{"iso":"eng"}],"alternative_title":["PMLR"],"date_published":"2024-07-30T00:00:00Z","external_id":{"arxiv":["2402.13368"]},"arxiv":1},{"date_published":"2024-04-09T00:00:00Z","external_id":{"isi":["001198892300001"]},"language":[{"iso":"eng"}],"keyword":["Public Health","Environmental and Occupational Health","General Environmental Science","Renewable Energy","Sustainability and the Environment"],"fulldoi":"https://doi.org/10.1088/1748-9326/ad25a0","ddc":["550"],"has_accepted_license":"1","day":"09","article_processing_charge":"Yes","type":"journal_article","supplementarymaterial":"no","article_number":"044057","corr_author":"1","author":[{"full_name":"Fugger, Stefan","id":"86698d64-c4c6-11ee-af02-cdf1e6a7d31f","first_name":"Stefan","last_name":"Fugger"},{"last_name":"Shaw","orcid":"0000-0001-7640-6152","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","first_name":"Thomas","full_name":"Shaw, Thomas"},{"last_name":"Jouberton","first_name":"Achille","full_name":"Jouberton, Achille"},{"last_name":"Miles","full_name":"Miles, Evan","first_name":"Evan"},{"last_name":"Buri","full_name":"Buri, Pascal","first_name":"Pascal","id":"317987aa-9421-11ee-ac5a-b941b041abba"},{"first_name":"Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","full_name":"McCarthy, Michael","last_name":"McCarthy"},{"last_name":"Fyffe","first_name":"Catriona Louise","id":"001b0422-8d15-11ed-bc51-cab6c037a228","full_name":"Fyffe, Catriona Louise"},{"last_name":"Fatichi","first_name":"Simone","full_name":"Fatichi, Simone"},{"last_name":"Kneib","first_name":"Marin","full_name":"Kneib, Marin"},{"last_name":"Molnar","first_name":"Peter","full_name":"Molnar, Peter"},{"first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca","orcid":"0000-0002-5554-8087","last_name":"Pellicciotti"}],"scopus_import":"1","publication_identifier":{"issn":["1748-9326"]},"intvolume":"        19","file_date_updated":"2024-07-22T09:14:44Z","publication":"Environmental Research Letters","oa_version":"Published Version","oa":1,"isi":1,"file":[{"file_name":"2024_EnvironmResearch_Fugger.pdf","creator":"dernst","date_updated":"2024-07-22T09:14:44Z","file_id":"17295","success":1,"content_type":"application/pdf","date_created":"2024-07-22T09:14:44Z","access_level":"open_access","relation":"main_file","checksum":"27999359b51c30fec6d81e48cdf0ee0d","file_size":4433401}],"date_updated":"2026-10-02T09:04:55Z","das_tickbox":"1","article_type":"original","department":[{"_id":"FrPe"}],"date_created":"2024-02-05T09:01:11Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"04","dataavailabilitystatement":"The data that support the findings of this study are openly available at the following URL/DOI: 10.5281/zenodo.10407300.","_id":"14938","publisher":"IOP Publishing","status":"public","quality_controlled":"1","title":"Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia","abstract":[{"lang":"eng","text":"High elevation headwater catchments are complex hydrological systems that seasonally buffer water and release it in the form of snow and ice melt, modulating downstream runoff regimes and water availability. In High Mountain Asia (HMA), where a wide range of climates from semi-arid to monsoonal exist, the importance of the cryospheric contributions to the water budget varies with the amount and seasonal distribution of precipitation. Losses due to evapotranspiration and sublimation are to date largely unquantified components of the water budget in such catchments, although they can be comparable in magnitude to glacier melt contributions to streamflow. &amp;#xD;Here, we simulate the hydrology of three high elevation headwater catchments in distinct climates in HMA over 10 years using an ecohydrological model geared towards high-mountain areas including snow and glaciers, forced with reanalysis data. &amp;#xD;Our results show that evapotranspiration and sublimation together are most important at the semi-arid site, Kyzylsu, on the northernmost slopes of the Pamir mountain range. Here, the evaporative loss amounts to 28% of the water throughput, which we define as the total water added to, or removed from the water balance within a year. In comparison, evaporative losses are 19% at the Central Himalayan site Langtang and 13% at the wettest site, 24K, on the Southeastern Tibetan Plateau. At the three sites, respectively, sublimation removes 15%, 13% and 6% of snowfall, while evapotranspiration removes the equivalent of 76%, 28% and 19% of rainfall. In absolute terms, and across a comparable elevation range, the highest ET flux is 413 mm yr-1 at 24K, while the highest sublimation flux is 91 mm yr-1 at Kyzylsu. During warm and dry years, glacier melt was found to only partially compensate for the annual supply deficit."}],"acknowledgement":"We would like to thank the team at the Center for the Research of Glaciers, Tajik National Academy of Sciences, Abduhamid Kayumov, Khusrav Kabutov, Ardamehr Halimov, among others, for their invaluable support over multiple field seasons in Kyzylsu. We thank Wei Yang, Zhao Xhuanxi and Zhen Cheng from the Institute of Tibetan Plateau Research, Chinese Academy of Sciences, for facilitating and supporting fieldwork and for sharing crucial data from the Parlung 24K catchment. We thank Reeju Shrestha and Himalayan Research Expeditions for their great support in Langtang. We extend our thanks to Jakob Steiner and the team at ICIMOD for their relentless efforts in data acquisition and curation in Langtang. Additionally, we are indebted to Masashi Niwano from the Meteorological Research Institute, Japan Meteorological Agency, for providing NHM atmospheric simulation outputs, which proved very valuable in the downscaling process.\r\nThis project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program Grant Agreements No. 772751 (RAVEN, Rapid mass losses of debris-covered glaciers in High Mountain Asia). Further funding was provided by JSPS-SNSF (Japan Society for the Promotion of Science and Swiss National Science Foundation) Bilateral Programmes project (HOPE, High-elevation precipitation in High Mountain Asia; Grant 183633). Fieldwork support for Tajikistan was received from the Swiss Polar Institute Flagship Programme PAMIR, SPI-FLAG-2021-001. The project also received funding from the ESA and NRSCC Dragon 5 cooperation project 'Cryosphere-hydrosphere interactions of the Asian water towers: using remote sensing to drive hyper-resolution ecohydrological modeling' (grant no. 59199). The National Natural Science Foundation of China (41961134035) financially supported the data collection at 24K.","year":"2024","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"researchdata_availability":"yes","volume":19,"citation":{"chicago":"Fugger, Stefan, Thomas Shaw, Achille Jouberton, Evan Miles, Pascal Buri, Michael McCarthy, Catriona Louise Fyffe, et al. “Hydrological Regimes and Evaporative Flux Partitioning at the Climatic Ends of High Mountain Asia.” <i>Environmental Research Letters</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.1088/1748-9326/ad25a0\">https://doi.org/10.1088/1748-9326/ad25a0</a>.","apa":"Fugger, S., Shaw, T., Jouberton, A., Miles, E., Buri, P., McCarthy, M., … Pellicciotti, F. (2024). Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. <i>Environmental Research Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1748-9326/ad25a0\">https://doi.org/10.1088/1748-9326/ad25a0</a>","short":"S. Fugger, T. Shaw, A. Jouberton, E. Miles, P. Buri, M. McCarthy, C.L. Fyffe, S. Fatichi, M. Kneib, P. Molnar, F. Pellicciotti, Environmental Research Letters 19 (2024).","ieee":"S. Fugger <i>et al.</i>, “Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia,” <i>Environmental Research Letters</i>, vol. 19. IOP Publishing, 2024.","ista":"Fugger S, Shaw T, Jouberton A, Miles E, Buri P, McCarthy M, Fyffe CL, Fatichi S, Kneib M, Molnar P, Pellicciotti F. 2024. Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters. 19, 044057.","ama":"Fugger S, Shaw T, Jouberton A, et al. Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. <i>Environmental Research Letters</i>. 2024;19. doi:<a href=\"https://doi.org/10.1088/1748-9326/ad25a0\">10.1088/1748-9326/ad25a0</a>","mla":"Fugger, Stefan, et al. “Hydrological Regimes and Evaporative Flux Partitioning at the Climatic Ends of High Mountain Asia.” <i>Environmental Research Letters</i>, vol. 19, 044057, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.1088/1748-9326/ad25a0\">10.1088/1748-9326/ad25a0</a>."},"publication_status":"published","doi":"10.1088/1748-9326/ad25a0"},{"status":"public","issue":"3","publisher":"Taylor & Francis","quality_controlled":"1","title":"Land surface modeling informed by earth observation data: Toward understanding blue–green–white water fluxes in High Mountain Asia","abstract":[{"text":"Mountains are important suppliers of freshwater to downstream areas, affecting large populations in particular in High Mountain Asia (HMA). Yet, the propagation of water from HMA headwaters to downstream areas is not fully understood, as interactions in the mountain water cycle between the cryo-, hydro- and biosphere remain elusive. We review the definition of blue and green water fluxes as liquid water that contributes to runoff at the outlet of the selected domain (blue) and water lost to the atmosphere through vapor fluxes, that is evaporation from water, ground, and interception plus transpiration (green) and propose to add the term white water to account for the (often neglected) evaporation and sublimation from snow and ice. We provide an assessment of models that can simulate the cryo-hydro-biosphere continuum and the interactions between spheres in high mountain catchments, going beyond disciplinary separations. Land surface models are uniquely able to account for such complexity, since they solve the coupled fluxes of water, energy, and carbon between the land surface and atmosphere. Due to the mechanistic nature of such models, specific variables can be compared systematically to independent remote sensing observations – providing vital insights into model accuracy and enabling the understanding of the complex watersheds of HMA. We discuss recent developments in spaceborne earth observation products that have the potential to support catchment modeling in high mountain regions. We then present a pilot study application of the mechanistic land surface model Tethys & Chloris to a glacierized watershed in the Nepalese Himalayas and discuss the use of high-resolution earth observation data to constrain the meteorological forcing uncertainty and validate model results. We use these insights to highlight the remaining challenges and future opportunities that remote sensing data presents for land surface modeling in HMA.","lang":"eng"}],"acknowledgement":"This work was supported by the ESA and NRSCC Dragon 5 cooperation project “Cryosphere-hydrosphere interactions of the Asian water towers: using remote sensing to drive hyper-resolution ecohydrological modelling” [Grant no. 59199]. PB and FP acknowledge funding from the SNSF (High-elevation precipitation in High Mountain Asia, HOPE)) [Grant no. 183633]. ESM, MK, SFu and FP acknowledge funding from the ERC under the European Union’s Horizon 2020 research and innovation program (Rapid mass losses of debris-covered glaciers in High Mountain Asia, RAVEN) [Grant no. 772751]. LJ, CZ and MMe acknowledge the Second Tibetan Plateau Scientific Expedition and Research Program (STEP) [grant no. 2019QZKK010308, no. 2019QZKK0206], the National Natural Science Foundation of China projects (Grant no. 42171039, no. 91737205), the Chinese Academy of Sciences President’s International Fellowship Initiative [Grant no. 2020VTA0001], and the MOST High-Level Foreign Expert Program [Grant no. G2022055010L].","year":"2024","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":27,"researchdata_availability":"no","publication_status":"published","citation":{"ista":"Buri P, Fatichi S, Shaw T, Fyffe CL, Miles ES, McCarthy M, Kneib M, Ren S, Jouberton A, Fugger S, Jia L, Zhang J, Shen C, Zheng C, Menenti M, Pellicciotti F. 2024. Land surface modeling informed by earth observation data: Toward understanding blue–green–white water fluxes in High Mountain Asia. Geo-Spatial Information Science. 27(3), 703–727.","mla":"Buri, Pascal, et al. “Land Surface Modeling Informed by Earth Observation Data: Toward Understanding Blue–Green–White Water Fluxes in High Mountain Asia.” <i>Geo-Spatial Information Science</i>, vol. 27, no. 3, Taylor &#38; Francis, 2024, pp. 703–27, doi:<a href=\"https://doi.org/10.1080/10095020.2024.2330546\">10.1080/10095020.2024.2330546</a>.","ama":"Buri P, Fatichi S, Shaw T, et al. Land surface modeling informed by earth observation data: Toward understanding blue–green–white water fluxes in High Mountain Asia. <i>Geo-Spatial Information Science</i>. 2024;27(3):703-727. doi:<a href=\"https://doi.org/10.1080/10095020.2024.2330546\">10.1080/10095020.2024.2330546</a>","apa":"Buri, P., Fatichi, S., Shaw, T., Fyffe, C. L., Miles, E. S., McCarthy, M., … Pellicciotti, F. (2024). Land surface modeling informed by earth observation data: Toward understanding blue–green–white water fluxes in High Mountain Asia. <i>Geo-Spatial Information Science</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10095020.2024.2330546\">https://doi.org/10.1080/10095020.2024.2330546</a>","chicago":"Buri, Pascal, Simone Fatichi, Thomas Shaw, Catriona Louise Fyffe, Evan S. Miles, Michael McCarthy, Marin Kneib, et al. “Land Surface Modeling Informed by Earth Observation Data: Toward Understanding Blue–Green–White Water Fluxes in High Mountain Asia.” <i>Geo-Spatial Information Science</i>. Taylor &#38; Francis, 2024. <a href=\"https://doi.org/10.1080/10095020.2024.2330546\">https://doi.org/10.1080/10095020.2024.2330546</a>.","ieee":"P. Buri <i>et al.</i>, “Land surface modeling informed by earth observation data: Toward understanding blue–green–white water fluxes in High Mountain Asia,” <i>Geo-Spatial Information Science</i>, vol. 27, no. 3. Taylor &#38; Francis, pp. 703–727, 2024.","short":"P. Buri, S. Fatichi, T. Shaw, C.L. Fyffe, E.S. Miles, M. McCarthy, M. Kneib, S. Ren, A. Jouberton, S. Fugger, L. Jia, J. Zhang, C. Shen, C. Zheng, M. Menenti, F. Pellicciotti, Geo-Spatial Information Science 27 (2024) 703–727."},"doi":"10.1080/10095020.2024.2330546","file_date_updated":"2024-07-29T11:34:54Z","intvolume":"        27","oa_version":"Published Version","publication":"Geo-Spatial Information Science","isi":1,"date_updated":"2026-10-02T09:12:24Z","file":[{"file_size":15678450,"checksum":"afbfc4e9f1bf2a00711efc30ad667c40","relation":"main_file","access_level":"open_access","date_created":"2024-07-29T11:34:54Z","content_type":"application/pdf","success":1,"date_updated":"2024-07-29T11:34:54Z","file_id":"17342","file_name":"2024_GeoSpatialInfo_Buri.pdf","creator":"dernst"}],"oa":1,"das_tickbox":"0","department":[{"_id":"FrPe"}],"article_type":"original","date_created":"2024-04-07T22:00:56Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"03","_id":"15298","day":"22","article_processing_charge":"Yes","type":"journal_article","supplementarymaterial":"yes","page":"703-727","author":[{"full_name":"Buri, Pascal","first_name":"Pascal","last_name":"Buri"},{"first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","full_name":"Fatichi, Simone","last_name":"Fatichi"},{"orcid":"0000-0001-7640-6152","last_name":"Shaw","first_name":"Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","full_name":"Shaw, Thomas"},{"first_name":"Catriona Louise","id":"001b0422-8d15-11ed-bc51-cab6c037a228","full_name":"Fyffe, Catriona Louise","last_name":"Fyffe"},{"last_name":"Miles","first_name":"Evan S.","full_name":"Miles, Evan S."},{"last_name":"Mccarthy","full_name":"Mccarthy, Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","first_name":"Michael"},{"last_name":"Kneib","full_name":"Kneib, Marin","first_name":"Marin"},{"first_name":"Shaoting","full_name":"Ren, Shaoting","last_name":"Ren"},{"full_name":"Jouberton, Achille","first_name":"Achille","last_name":"Jouberton"},{"first_name":"Stefan","full_name":"Fugger, Stefan","last_name":"Fugger"},{"first_name":"Li","full_name":"Jia, Li","last_name":"Jia"},{"last_name":"Zhang","first_name":"Jing","full_name":"Zhang, Jing"},{"full_name":"Shen, Cong","first_name":"Cong","last_name":"Shen"},{"last_name":"Zheng","full_name":"Zheng, Chaolei","first_name":"Chaolei"},{"first_name":"Massimo","full_name":"Menenti, Massimo","last_name":"Menenti"},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","orcid":"0000-0002-5554-8087"}],"publication_identifier":{"issn":["1009-5020"]},"scopus_import":"1","external_id":{"isi":["001189470100001"]},"date_published":"2024-03-22T00:00:00Z","language":[{"iso":"eng"}],"ddc":["550"],"fulldoi":"https://doi.org/10.1080/10095020.2024.2330546","has_accepted_license":"1"},{"language":[{"iso":"eng"}],"external_id":{"isi":["001146838000001"]},"date_published":"2024-01-28T00:00:00Z","ddc":["550"],"fulldoi":"https://doi.org/10.1029/2023JD040214","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","type":"journal_article","day":"28","author":[{"id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","first_name":"Thomas","full_name":"Shaw, Thomas","last_name":"Shaw","orcid":"0000-0001-7640-6152"},{"last_name":"Buri","full_name":"Buri, Pascal","first_name":"Pascal","id":"317987aa-9421-11ee-ac5a-b941b041abba"},{"last_name":"Mccarthy","first_name":"Michael","id":"22a2674a-61ce-11ee-94b5-d18813baf16f","full_name":"Mccarthy, Michael"},{"last_name":"Miles","full_name":"Miles, Evan S.","first_name":"Evan S."},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","orcid":"0000-0002-5554-8087"}],"scopus_import":"1","publication_identifier":{"eissn":["2169-8996"],"issn":["2169-897X"]},"supplementarymaterial":"yes","corr_author":"1","article_number":"e2023JD040214","isi":1,"date_updated":"2026-10-02T08:59:02Z","file":[{"creator":"dernst","file_name":"2024_JGRAtmospheres_Shaw.pdf","file_id":"14943","date_updated":"2024-02-06T08:38:27Z","success":1,"content_type":"application/pdf","date_created":"2024-02-06T08:38:27Z","access_level":"open_access","relation":"main_file","checksum":"cad5b93caadb40c14e5faedc34f7bba7","file_size":7481087}],"oa":1,"related_material":{"record":[{"id":"14919","status":"public","relation":"research_data"},{"id":"23030","status":"public","relation":"research_data"}]},"das_tickbox":"1","file_date_updated":"2024-02-06T08:38:27Z","intvolume":"       129","publication":"Journal of Geophysical Research: Atmospheres","oa_version":"Published Version","dataavailabilitystatement":"The meteorological data used in this analysis (Shaw, Buri, McCarthy, Miles, & Pelliciotti, 2023) are made publicly available at the following repository: https://zenodo.org/record/8277285. The source code of the T&C model is available at https://doi.org/10.24433/CO.0905087.v2. Reanalysis data are openly available from the ECMWF (https://cds.climate.copernicus.eu/). MeteoSwiss data can be acquired through direct request to the company.","month":"01","_id":"14885","department":[{"_id":"FrPe"}],"article_type":"original","date_created":"2024-01-28T23:01:42Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"The near-surface boundary layer can mediate the response of mountain glaciers to external climate, cooling the overlying air and promoting a density-driven glacier wind. The fundamental processes are conceptually well understood, though the magnitudes of cooling and presence of glacier winds are poorly quantified in space and time, increasing the forcing uncertainty for melt models. We utilize a new data set of on-glacier meteorological measurements on three neighboring glaciers in the Swiss Alps to explore their distinct response to regional climate under the extreme 2022 summer. We find that synoptic wind origins and local terrain modifications, not only glacier size, play an important role in the ability of a glacier to cool the near-surface air. Warm air intrusions from valley or synoptically-driven winds onto the glacier can occur between ∼19% and 64% of the time and contribute between 3% and 81% of the total sensible heat flux to the surface during warm afternoon hours, depending on the fetch of the glacier flowline and its susceptibility to boundary layer erosion. In the context of extreme summer warmth, indicative of future conditions, the boundary layer cooling (up to 6.5°C cooler than its surroundings) and resultant katabatic wind flow are highly heterogeneous between the study glaciers, highlighting the complex and likely non-linear response of glaciers to an uncertain future."}],"title":"Local controls on near-surface glacier cooling under warm atmospheric conditions","acknowledgement":"This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 101026058. The authors acknowledge the invaluable field assistance of Marta Corrà, Achille Jouberton, Marin Kneib, Stefan Fugger, Celine Ducret and Alexander Groos. The authors would also like to thank Luca Carturan for advice regarding AWS setup and maintenance and Simone Fatichi for provision and support in the use of the Tethys-Chloris model. Open access funding provided by ETH-Bereich Forschungsanstalten.","issue":"2","status":"public","publisher":"Wiley","quality_controlled":"1","doi":"10.1029/2023JD040214","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2024","volume":129,"researchdata_availability":"yes","publication_status":"published","citation":{"mla":"Shaw, Thomas, et al. “Local Controls on Near-Surface Glacier Cooling under Warm Atmospheric Conditions.” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 129, no. 2, e2023JD040214, Wiley, 2024, doi:<a href=\"https://doi.org/10.1029/2023JD040214\">10.1029/2023JD040214</a>.","ama":"Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. Local controls on near-surface glacier cooling under warm atmospheric conditions. <i>Journal of Geophysical Research: Atmospheres</i>. 2024;129(2). doi:<a href=\"https://doi.org/10.1029/2023JD040214\">10.1029/2023JD040214</a>","ista":"Shaw T, Buri P, McCarthy M, Miles ES, Pellicciotti F. 2024. Local controls on near-surface glacier cooling under warm atmospheric conditions. Journal of Geophysical Research: Atmospheres. 129(2), e2023JD040214.","ieee":"T. Shaw, P. Buri, M. McCarthy, E. S. Miles, and F. Pellicciotti, “Local controls on near-surface glacier cooling under warm atmospheric conditions,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 129, no. 2. Wiley, 2024.","short":"T. Shaw, P. Buri, M. McCarthy, E.S. Miles, F. Pellicciotti, Journal of Geophysical Research: Atmospheres 129 (2024).","apa":"Shaw, T., Buri, P., McCarthy, M., Miles, E. S., &#38; Pellicciotti, F. (2024). Local controls on near-surface glacier cooling under warm atmospheric conditions. <i>Journal of Geophysical Research: Atmospheres</i>. Wiley. <a href=\"https://doi.org/10.1029/2023JD040214\">https://doi.org/10.1029/2023JD040214</a>","chicago":"Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan S. Miles, and Francesca Pellicciotti. “Local Controls on Near-Surface Glacier Cooling under Warm Atmospheric Conditions.” <i>Journal of Geophysical Research: Atmospheres</i>. Wiley, 2024. <a href=\"https://doi.org/10.1029/2023JD040214\">https://doi.org/10.1029/2023JD040214</a>."}},{"language":[{"iso":"eng"}],"date_published":"2024-11-12T00:00:00Z","ddc":["550"],"fulldoi":"https://doi.org/10.3390/hydrology11110193","has_accepted_license":"1","article_processing_charge":"Yes","type":"journal_article","day":"12","author":[{"last_name":"De Andrés","full_name":"De Andrés, Eva","first_name":"Eva"},{"id":"e1037a6d-646e-11ef-b402-e0ed9ab0901e","first_name":"José M","full_name":"Muñoz Hermosilla, José M","last_name":"Muñoz Hermosilla","orcid":"0000-0002-1990-8508"},{"full_name":"Shahateet, Kaian","first_name":"Kaian","last_name":"Shahateet"},{"last_name":"Otero","full_name":"Otero, Jaime","first_name":"Jaime"}],"scopus_import":"1","publication_identifier":{"eissn":["2306-5338"]},"supplementarymaterial":"no","corr_author":"1","article_number":"193","date_updated":"2026-10-02T09:16:55Z","file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2024-12-09T09:43:33Z","checksum":"0665c5bfca97782bf0b041f23dd7e8d7","file_size":5709093,"relation":"main_file","creator":"dernst","file_name":"2024_Hydrology_deAndres.pdf","date_updated":"2024-12-09T09:43:33Z","file_id":"18635","success":1}],"oa":1,"das_tickbox":"1","related_material":{"record":[{"relation":"used_in_publication","id":"18634","status":"public"},{"relation":"research_data","status":"public","id":"23031"}]},"file_date_updated":"2024-12-09T09:43:33Z","intvolume":"        11","oa_version":"Published Version","publication":"Hydrology","dataavailabilitystatement":"The data that support the results of this study and form the basis for all the figures presented in this paper are openly available from Zenodo at https://doi.org/10.5281/zenodo.8005258 (accessed on 6 November 2024).","month":"11","_id":"18628","DOAJ_listed":"1","department":[{"_id":"FrPe"}],"article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-12-08T23:01:55Z","title":"The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard","abstract":[{"text":"Arctic tidewater glaciers are retreating, serving as key indicators of global warming. This study aims to assess how subglacial hydrology affects glacier front retreat by comparing two glacier–fjord models of the Hansbreen glacier: one incorporating a detailed subglacial hydrology model and another simplifying the subglacial discharge to a single channel centered in the flow line. We first validate the subglacial hydrology model by comparing its discharge channels with observations of plume activity. Simulations conducted from April to December 2010 revealed that the glacier front position aligns more closely with the observations in the coupled model than in the simplified version. Furthermore, the mass loss due to calving and submarine melting is greater in the coupled model, with the calving mass loss reaching 6 Mt by the end of the simulation compared to 4 Mt in the simplified model. These findings highlight the critical role of subglacial hydrology in predicting glacier dynamics and emphasize the importance of detailed modeling in understanding the responses of Arctic tidewater glaciers to climate change.","lang":"eng"}],"acknowledgement":"E. De Andrés is supported by Margarita-Salas Grant No. UP2021-035 under the Next Generation-EU program. This research was also funded by grant PID2020-113051RB-C31 from MCIN/AEI/10.13039/501100011033/FEDER, UE.\r\nWe gratefully acknowledge Michal Cieply and Dariusz Ignatiuk from the Faculty of Natural Sciences, University of Silesia in Katowice, Poland, for their essential contributions to the Hansbreen data collection. We also extend our sincere thanks to Waldemar Walczowski from the Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland, for providing Hansbuka data. Additionally, we would like to thank two anonymous reviewers for their constructive feedback, which helped to enhance the quality and clarity of this work.","status":"public","issue":"11","publisher":"MDPI","quality_controlled":"1","OA_type":"gold","doi":"10.3390/hydrology11110193","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2024","researchdata_availability":"yes","volume":11,"citation":{"chicago":"De Andrés, Eva, José M Muñoz Hermosilla, Kaian Shahateet, and Jaime Otero. “The Importance of Solving Subglaciar Hydrology in Modeling Glacier Retreat: A Case Study of Hansbreen, Svalbard.” <i>Hydrology</i>. MDPI, 2024. <a href=\"https://doi.org/10.3390/hydrology11110193\">https://doi.org/10.3390/hydrology11110193</a>.","apa":"De Andrés, E., Muñoz Hermosilla, J. M., Shahateet, K., &#38; Otero, J. (2024). The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard. <i>Hydrology</i>. MDPI. <a href=\"https://doi.org/10.3390/hydrology11110193\">https://doi.org/10.3390/hydrology11110193</a>","short":"E. De Andrés, J.M. Muñoz Hermosilla, K. Shahateet, J. Otero, Hydrology 11 (2024).","ieee":"E. De Andrés, J. M. Muñoz Hermosilla, K. Shahateet, and J. Otero, “The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard,” <i>Hydrology</i>, vol. 11, no. 11. MDPI, 2024.","ista":"De Andrés E, Muñoz Hermosilla JM, Shahateet K, Otero J. 2024. The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard. Hydrology. 11(11), 193.","ama":"De Andrés E, Muñoz Hermosilla JM, Shahateet K, Otero J. The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard. <i>Hydrology</i>. 2024;11(11). doi:<a href=\"https://doi.org/10.3390/hydrology11110193\">10.3390/hydrology11110193</a>","mla":"De Andrés, Eva, et al. “The Importance of Solving Subglaciar Hydrology in Modeling Glacier Retreat: A Case Study of Hansbreen, Svalbard.” <i>Hydrology</i>, vol. 11, no. 11, 193, MDPI, 2024, doi:<a href=\"https://doi.org/10.3390/hydrology11110193\">10.3390/hydrology11110193</a>."},"OA_place":"publisher","publication_status":"published"},{"fulldoi":"https://doi.org/10.1038/s41431-024-01598-8","ddc":["570"],"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2024-07-01T00:00:00Z","external_id":{"isi":["001207703200001"],"pmid":["38658779"]},"pmid":1,"author":[{"last_name":"Andrianova","first_name":"Maria A.","full_name":"Andrianova, Maria A."},{"full_name":"Seplyarskiy, Vladimir B.","first_name":"Vladimir B.","last_name":"Seplyarskiy"},{"full_name":"Terradas, Mariona","first_name":"Mariona","last_name":"Terradas"},{"last_name":"Sánchez-Heras","full_name":"Sánchez-Heras, Ana Beatriz","first_name":"Ana Beatriz"},{"full_name":"Mur, Pilar","first_name":"Pilar","last_name":"Mur"},{"full_name":"Soto, José Luis","first_name":"José Luis","last_name":"Soto"},{"last_name":"Aiza","first_name":"Gemma","full_name":"Aiza, Gemma"},{"first_name":"Emma","full_name":"Borràs, Emma","last_name":"Borràs"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"},{"last_name":"Kondrashov","first_name":"Alexey S.","full_name":"Kondrashov, Alexey S."},{"full_name":"Bazykin, Georgii A.","first_name":"Georgii A.","last_name":"Bazykin"},{"full_name":"Valle, Laura","first_name":"Laura","last_name":"Valle"}],"scopus_import":"1","publication_identifier":{"issn":["1018-4813"],"eissn":["1476-5438"]},"supplementarymaterial":"yes","page":"837-845","article_processing_charge":"No","type":"journal_article","day":"01","month":"07","dataavailabilitystatement":"DNA sequencing data are deposited in the European Genome-Phenome Archive (EGA) with accession code EGAS00001006434. Called de novo and somatic mutations are available online (https://figshare.com/account/home#/projects/156404).","ec_funded":1,"_id":"15362","article_type":"original","department":[{"_id":"FyKo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-05-05T22:01:04Z","oa":1,"date_updated":"2026-10-02T09:48:07Z","isi":1,"file":[{"relation":"main_file","file_size":3060724,"checksum":"e45fc987f4e9ebafdd0ec4f0e9027de4","content_type":"application/pdf","date_created":"2025-01-09T09:21:25Z","access_level":"open_access","date_updated":"2025-01-09T09:21:25Z","file_id":"18799","success":1,"creator":"dernst","file_name":"2024_EJHG_Andrianova.pdf"}],"das_tickbox":"1","intvolume":"        32","file_date_updated":"2025-01-09T09:21:25Z","oa_version":"Published Version","publication":"European Journal of Human Genetics","OA_type":"hybrid","doi":"10.1038/s41431-024-01598-8","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"researchdata_availability":"yes","volume":32,"year":"2024","OA_place":"publisher","citation":{"chicago":"Andrianova, Maria A., Vladimir B. Seplyarskiy, Mariona Terradas, Ana Beatriz Sánchez-Heras, Pilar Mur, José Luis Soto, Gemma Aiza, et al. “Discovery of Recessive Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal and Cancer Cells.” <i>European Journal of Human Genetics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41431-024-01598-8\">https://doi.org/10.1038/s41431-024-01598-8</a>.","apa":"Andrianova, M. A., Seplyarskiy, V. B., Terradas, M., Sánchez-Heras, A. B., Mur, P., Soto, J. L., … Valle, L. (2024). Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-024-01598-8\">https://doi.org/10.1038/s41431-024-01598-8</a>","short":"M.A. Andrianova, V.B. Seplyarskiy, M. Terradas, A.B. Sánchez-Heras, P. Mur, J.L. Soto, G. Aiza, E. Borràs, F. Kondrashov, A.S. Kondrashov, G.A. Bazykin, L. Valle, European Journal of Human Genetics 32 (2024) 837–845.","ieee":"M. A. Andrianova <i>et al.</i>, “Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells,” <i>European Journal of Human Genetics</i>, vol. 32. Springer Nature, pp. 837–845, 2024.","ista":"Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL, Aiza G, Borràs E, Kondrashov F, Kondrashov AS, Bazykin GA, Valle L. 2024. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics. 32, 837–845.","ama":"Andrianova MA, Seplyarskiy VB, Terradas M, et al. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. <i>European Journal of Human Genetics</i>. 2024;32:837-845. doi:<a href=\"https://doi.org/10.1038/s41431-024-01598-8\">10.1038/s41431-024-01598-8</a>","mla":"Andrianova, Maria A., et al. “Discovery of Recessive Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal and Cancer Cells.” <i>European Journal of Human Genetics</i>, vol. 32, Springer Nature, 2024, pp. 837–45, doi:<a href=\"https://doi.org/10.1038/s41431-024-01598-8\">10.1038/s41431-024-01598-8</a>."},"publication_status":"published","abstract":[{"lang":"eng","text":"Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate."}],"title":"Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells","acknowledgement":"This study was funded by the Spanish Ministry of Science and Innovation (Agencia Estatal de Investigación), co-funded by FEDER funds a way to build Europe [PID2020-112595RB-I00 (LV)], Instituto de Salud Carlos III [CIBERONC CB16/12/00234 (LV); ISCIII-AES-2017 PI17/01082 (JLS), PMP22/00064], Government of Catalonia [AGAUR 2021SGR01112, CERCA Program for institutional support (LV)], Scientific Foundation Asociación Española Contra el Cáncer [AECC Investigador (MT)], Austrian Science Fund FWF [Grant Agreement # I5127-B (FK)], German Research Foundation DFG [Grant Agreement # 429960716 (FK)], and ERC Consolidator [Grant Agreement # 771209 ChrFL (FK)].","project":[{"_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","grant_number":"429960716","name":"Evolution of Sensorimotor Transformation Across Diptera"},{"name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","grant_number":"I05127","name":"Evolutionary analysis of gene regulation"}],"publisher":"Springer Nature","status":"public","quality_controlled":"1"},{"article_number":"adk1992","supplementarymaterial":"yes","publication_identifier":{"eissn":["2375-2548"]},"scopus_import":"1","author":[{"last_name":"Palkina","full_name":"Palkina, Kseniia A.","first_name":"Kseniia A."},{"first_name":"Tatiana A.","full_name":"Karataeva, Tatiana A.","last_name":"Karataeva"},{"last_name":"Perfilov","first_name":"Maxim M.","full_name":"Perfilov, Maxim M."},{"full_name":"Fakhranurova, Liliia I.","first_name":"Liliia I.","last_name":"Fakhranurova"},{"last_name":"Markina","first_name":"Nadezhda M.","full_name":"Markina, Nadezhda M."},{"full_name":"Gonzalez Somermeyer, Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa","last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383"},{"first_name":"Elena","full_name":"Garcia-Perez, Elena","last_name":"Garcia-Perez"},{"first_name":"Marta","full_name":"Vazquez-Vilar, Marta","last_name":"Vazquez-Vilar"},{"last_name":"Rodriguez-Rodriguez","full_name":"Rodriguez-Rodriguez, Marta","first_name":"Marta"},{"first_name":"Victor","full_name":"Vazquez-Vilriales, Victor","last_name":"Vazquez-Vilriales"},{"first_name":"Ekaterina S.","full_name":"Shakhova, Ekaterina S.","last_name":"Shakhova"},{"last_name":"Mitiouchkina","full_name":"Mitiouchkina, Tatiana","first_name":"Tatiana"},{"first_name":"Olga A.","full_name":"Belozerova, Olga A.","last_name":"Belozerova"},{"last_name":"Kovalchuk","full_name":"Kovalchuk, Sergey I.","first_name":"Sergey I."},{"last_name":"Alekberova","full_name":"Alekberova, Anna","first_name":"Anna"},{"last_name":"Malyshevskaia","full_name":"Malyshevskaia, Alena K.","first_name":"Alena K."},{"last_name":"Bugaeva","first_name":"Evgenia N.","full_name":"Bugaeva, Evgenia N."},{"full_name":"Guglya, Elena B.","first_name":"Elena B.","last_name":"Guglya"},{"full_name":"Balakireva, Anastasia","first_name":"Anastasia","last_name":"Balakireva"},{"first_name":"Nikita","full_name":"Sytov, Nikita","last_name":"Sytov"},{"full_name":"Bezlikhotnova, Anastasia","first_name":"Anastasia","last_name":"Bezlikhotnova"},{"full_name":"Boldyreva, Daria I.","first_name":"Daria I.","last_name":"Boldyreva"},{"first_name":"Vladislav V.","full_name":"Babenko, Vladislav V.","last_name":"Babenko"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"},{"full_name":"Choob, Vladimir V.","first_name":"Vladimir V.","last_name":"Choob"},{"last_name":"Orzaez","full_name":"Orzaez, Diego","first_name":"Diego"},{"last_name":"Yampolsky","first_name":"Ilia V.","full_name":"Yampolsky, Ilia V."},{"last_name":"Mishin","first_name":"Alexander S.","full_name":"Mishin, Alexander S."},{"last_name":"Sarkisyan","first_name":"Karen S.","full_name":"Sarkisyan, Karen S."}],"day":"01","type":"journal_article","article_processing_charge":"Yes","has_accepted_license":"1","fulldoi":"https://doi.org/10.1126/sciadv.adk1992","ddc":["580"],"date_published":"2024-03-01T00:00:00Z","pmid":1,"external_id":{"pmid":["38457503"],"isi":["001187580500013"]},"language":[{"iso":"eng"}],"citation":{"short":"K.A. Palkina, T.A. Karataeva, M.M. Perfilov, L.I. Fakhranurova, N.M. Markina, L. Gonzalez Somermeyer, E. Garcia-Perez, M. Vazquez-Vilar, M. Rodriguez-Rodriguez, V. Vazquez-Vilriales, E.S. Shakhova, T. Mitiouchkina, O.A. Belozerova, S.I. Kovalchuk, A. Alekberova, A.K. Malyshevskaia, E.N. Bugaeva, E.B. Guglya, A. Balakireva, N. Sytov, A. Bezlikhotnova, D.I. Boldyreva, V.V. Babenko, F. Kondrashov, V.V. Choob, D. Orzaez, I.V. Yampolsky, A.S. Mishin, K.S. Sarkisyan, Science Advances 10 (2024).","ieee":"K. A. Palkina <i>et al.</i>, “A hybrid pathway for self-sustained luminescence,” <i>Science Advances</i>, vol. 10, no. 10. American Association for the Advancement of Science, 2024.","chicago":"Palkina, Kseniia A., Tatiana A. Karataeva, Maxim M. Perfilov, Liliia I. Fakhranurova, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, Elena Garcia-Perez, et al. “A Hybrid Pathway for Self-Sustained Luminescence.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adk1992\">https://doi.org/10.1126/sciadv.adk1992</a>.","apa":"Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina, N. M., Gonzalez Somermeyer, L., … Sarkisyan, K. S. (2024). A hybrid pathway for self-sustained luminescence. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adk1992\">https://doi.org/10.1126/sciadv.adk1992</a>","ama":"Palkina KA, Karataeva TA, Perfilov MM, et al. A hybrid pathway for self-sustained luminescence. <i>Science Advances</i>. 2024;10(10). doi:<a href=\"https://doi.org/10.1126/sciadv.adk1992\">10.1126/sciadv.adk1992</a>","mla":"Palkina, Kseniia A., et al. “A Hybrid Pathway for Self-Sustained Luminescence.” <i>Science Advances</i>, vol. 10, no. 10, adk1992, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adk1992\">10.1126/sciadv.adk1992</a>.","ista":"Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances. 10(10), adk1992."},"publication_status":"published","OA_place":"publisher","researchdata_availability":"yes (supplementary data)","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2024","volume":10,"doi":"10.1126/sciadv.adk1992","OA_type":"gold","quality_controlled":"1","publisher":"American Association for the Advancement of Science","issue":"10","status":"public","acknowledgement":"We thank Milaboratory (milaboratory.com) for the access to computing and storage infrastructure. We thank J. Petrasek for providing the BY-2 cell culture line. We thank Konstantin Lukyanov laboratory and Sergey Deyev laboratory for assistance with experiments.\r\nThis study was partially funded by Light Bio and Planta. The Synthetic biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0). Cloning and luminescent assays performed in BY-2 were partially supported by RSF, project number 22-14-00400, https://rscf.ru/project/22-14-00400/. Plant transformations were funded by RFBR and MOST, project number 21-54-52004. Plant imaging experiments were funded by RSF, project number 22-74-00124, https://rscf.ru/project/22-74-00124/. Viral delivery experiments were funded by the grant PID2019-108203RB-I00 Plan Nacional I + D from the Ministerio de Ciencia e Innovación (Spain) through the Agencia Estatal de Investigación (cofinanced by the European Regional Development Fund).","abstract":[{"lang":"eng","text":"The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors."}],"title":"A hybrid pathway for self-sustained luminescence","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-03-25T08:54:33Z","article_type":"original","department":[{"_id":"FyKo"}],"DOAJ_listed":"1","_id":"15179","month":"03","dataavailabilitystatement":"All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. The plasmids used in this study will be made available for noncommercial use through Addgene under the terms of UBMTA (www.addgene.org/agreement/1). The data are available at https://doi.org/10.6084/m9.figshare.24772872.","oa_version":"Published Version","publication":"Science Advances","intvolume":"        10","file_date_updated":"2024-03-25T09:42:10Z","related_material":{"record":[{"id":"23032","status":"public","relation":"research_data"}]},"das_tickbox":"1","oa":1,"file":[{"creator":"dernst","file_name":"2024_ScienceAdv_Palkina.pdf","date_updated":"2024-03-25T09:42:10Z","file_id":"15185","success":1,"content_type":"application/pdf","date_created":"2024-03-25T09:42:10Z","access_level":"open_access","relation":"main_file","file_size":1499302,"checksum":"a19c43b260ea0bbaf895a29712e3153c"}],"isi":1,"date_updated":"2026-10-02T09:22:29Z"}]