[{"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)"},"external_id":{"pmid":["41249070"]},"article_processing_charge":"Yes (via OA deal)","OA_place":"publisher","scopus_import":"1","PlanS_conform":"1","_id":"20725","status":"public","author":[{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"quality_controlled":"1","doi":"10.1016/j.tplants.2025.10.018","intvolume":"        31","oa_version":"Published Version","corr_author":"1","ddc":["580"],"fulldoi":"https://doi.org/10.1016/j.tplants.2025.10.018","year":"2026","abstract":[{"lang":"eng","text":"The canonical mechanism by which the phytohormone auxin regulates transcription has been one of the cornerstones of plant signaling. The recent unexpected discovery of cyclic AMP (cAMP) as a second messenger in this pathway has revised its foundations while leaving many open questions and gaps in our understanding; these will be discussed in this forum article."}],"researchdata_availability":"no","date_published":"2026-02-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Role of cAMP in TIR1/AFB auxin signaling: Open issues","month":"02","citation":{"ista":"Friml J. 2026. Role of cAMP in TIR1/AFB auxin signaling: Open issues. Trends in Plant Science. 31(2), 136–138.","mla":"Friml, Jiří. “Role of CAMP in TIR1/AFB Auxin Signaling: Open Issues.” <i>Trends in Plant Science</i>, vol. 31, no. 2, Cell Press, 2026, pp. 136–38, doi:<a href=\"https://doi.org/10.1016/j.tplants.2025.10.018\">10.1016/j.tplants.2025.10.018</a>.","ama":"Friml J. Role of cAMP in TIR1/AFB auxin signaling: Open issues. <i>Trends in Plant Science</i>. 2026;31(2):136-138. doi:<a href=\"https://doi.org/10.1016/j.tplants.2025.10.018\">10.1016/j.tplants.2025.10.018</a>","chicago":"Friml, Jiří. “Role of CAMP in TIR1/AFB Auxin Signaling: Open Issues.” <i>Trends in Plant Science</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.tplants.2025.10.018\">https://doi.org/10.1016/j.tplants.2025.10.018</a>.","ieee":"J. Friml, “Role of cAMP in TIR1/AFB auxin signaling: Open issues,” <i>Trends in Plant Science</i>, vol. 31, no. 2. Cell Press, pp. 136–138, 2026.","apa":"Friml, J. (2026). Role of cAMP in TIR1/AFB auxin signaling: Open issues. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2025.10.018\">https://doi.org/10.1016/j.tplants.2025.10.018</a>","short":"J. Friml, Trends in Plant Science 31 (2026) 136–138."},"project":[{"_id":"8f347782-16d5-11f0-9cad-8c19706ee739","name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051"}],"day":"01","language":[{"iso":"eng"}],"OA_type":"hybrid","publication_status":"published","department":[{"_id":"JiFr"}],"file_date_updated":"2026-07-27T08:26:40Z","file":[{"date_updated":"2026-07-27T08:26:40Z","file_name":"2026_TrendsPlantScience_Friml.pdf","file_id":"22413","date_created":"2026-07-27T08:26:40Z","content_type":"application/pdf","file_size":432792,"success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","checksum":"e60e903fb4b3e917dba763976ec652cd"}],"article_type":"review","supplementarymaterial":"no","license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2026-10-20T09:01:46Z","page":"136-138","publisher":"Cell Press","type":"journal_article","pmid":1,"publication_identifier":{"issn":["1360-1385"],"eissn":["1878-4372"]},"issue":"2","date_created":"2025-12-02T16:29:22Z","volume":31,"has_accepted_license":"1","acknowledgement":"I apologize to colleagues whose relevant work I was unable to cite due to space limitations. This work was funded by the European Union (ERC, CYNIPS, 101142681) and Austrian Science Fund (FWF; 37051-B). I thank Drs Huihuang Chen, Yuanrong Pei, Jason Reed, Linlin Qi, and Dolf Weijers for inspiration and critical input.","das_tickbox":"0","publication":"Trends in Plant Science","oa":1},{"scopus_import":"1","article_processing_charge":"No","external_id":{"pmid":["41043435"]},"fulldoi":"https://doi.org/10.1016/j.devcel.2025.09.009","oa_version":"None","intvolume":"        61","doi":"10.1016/j.devcel.2025.09.009","quality_controlled":"1","_id":"20636","status":"public","author":[{"last_name":"Huang","full_name":"Huang, R","first_name":"R"},{"first_name":"J","full_name":"Wang, J","last_name":"Wang"},{"last_name":"Chang","full_name":"Chang, M","first_name":"M"},{"last_name":"Tang","full_name":"Tang, W","first_name":"W"},{"last_name":"Yu","first_name":"Y","full_name":"Yu, Y"},{"full_name":"Zhang, Y","first_name":"Y","last_name":"Zhang"},{"first_name":"Y","full_name":"Peng, Y","last_name":"Peng"},{"last_name":"Wang","first_name":"Y","full_name":"Wang, Y"},{"first_name":"Y","full_name":"Guo, Y","last_name":"Guo"},{"last_name":"Lu","first_name":"T","full_name":"Lu, T"},{"first_name":"Y","full_name":"Cao, Y","last_name":"Cao"},{"full_name":"Zhou, Y","first_name":"Y","last_name":"Zhou"},{"last_name":"Zhang","full_name":"Zhang, Q","first_name":"Q"},{"last_name":"Huang","first_name":"Y","full_name":"Huang, Y"},{"last_name":"Wu","full_name":"Wu, A","first_name":"A"},{"first_name":"L","full_name":"Ren, L","last_name":"Ren"},{"full_name":"Gallei, Michelle C","first_name":"Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"first_name":"J","full_name":"Dong, J","last_name":"Dong"},{"last_name":"Chen","first_name":"H","full_name":"Chen, H"},{"last_name":"He","first_name":"J","full_name":"He, J"},{"last_name":"Wen","first_name":"M","full_name":"Wen, M"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"},{"full_name":"Sun, L","first_name":"L","last_name":"Sun"},{"last_name":"Xiong","full_name":"Xiong, Y","first_name":"Y"},{"full_name":"Yang, Z","first_name":"Z","last_name":"Yang"},{"first_name":"T","full_name":"Xu, T","last_name":"Xu"}],"title":"TMK-PIN1 drives a short self-organizing circuit for auxin export and signaling in Arabidopsis","month":"01","citation":{"ama":"Huang R, Wang J, Chang M, et al. TMK-PIN1 drives a short self-organizing circuit for auxin export and signaling in Arabidopsis. <i>Developmental Cell</i>. 2026;61(1):73-84. doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.09.009\">10.1016/j.devcel.2025.09.009</a>","chicago":"Huang, R, J Wang, M Chang, W Tang, Y Yu, Y Zhang, Y Peng, et al. “TMK-PIN1 Drives a Short Self-Organizing Circuit for Auxin Export and Signaling in Arabidopsis.” <i>Developmental Cell</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.devcel.2025.09.009\">https://doi.org/10.1016/j.devcel.2025.09.009</a>.","short":"R. Huang, J. Wang, M. Chang, W. Tang, Y. Yu, Y. Zhang, Y. Peng, Y. Wang, Y. Guo, T. Lu, Y. Cao, Y. Zhou, Q. Zhang, Y. Huang, A. Wu, L. Ren, M.C. Gallei, J. Dong, H. Chen, J. He, M. Wen, J. Friml, L. Sun, Y. Xiong, Z. Yang, T. Xu, Developmental Cell 61 (2026) 73–84.","apa":"Huang, R., Wang, J., Chang, M., Tang, W., Yu, Y., Zhang, Y., … Xu, T. (2026). TMK-PIN1 drives a short self-organizing circuit for auxin export and signaling in Arabidopsis. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2025.09.009\">https://doi.org/10.1016/j.devcel.2025.09.009</a>","ieee":"R. Huang <i>et al.</i>, “TMK-PIN1 drives a short self-organizing circuit for auxin export and signaling in Arabidopsis,” <i>Developmental Cell</i>, vol. 61, no. 1. Cell Press, pp. 73–84, 2026.","mla":"Huang, R., et al. “TMK-PIN1 Drives a Short Self-Organizing Circuit for Auxin Export and Signaling in Arabidopsis.” <i>Developmental Cell</i>, vol. 61, no. 1, Cell Press, 2026, pp. 73–84, doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.09.009\">10.1016/j.devcel.2025.09.009</a>.","ista":"Huang R, Wang J, Chang M, Tang W, Yu Y, Zhang Y, Peng Y, Wang Y, Guo Y, Lu T, Cao Y, Zhou Y, Zhang Q, Huang Y, Wu A, Ren L, Gallei MC, Dong J, Chen H, He J, Wen M, Friml J, Sun L, Xiong Y, Yang Z, Xu T. 2026. TMK-PIN1 drives a short self-organizing circuit for auxin export and signaling in Arabidopsis. Developmental Cell. 61(1), 73–84."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The versatile and pivotal roles of the phytohormone auxin in regulating plant growth and development are typically linked to its directional transport, relying on the polarized PIN-FORMED (PIN) auxin exporters at the plasma membrane (PM). For decades, auxin has been proposed to promote PIN polarization, generating self-regulatory feedback mediating much of plant development, but mechanistic insight into this regulation is lacking. Here, we uncover an auxin-induced protein complex at the PM, containing auxin co-receptors transmembrane kinases (TMKs) and PIN1 auxin exporter, as the core machinery that underlies this feedback regulation. Auxin promotes PIN1 phosphorylation by TMKs, modulating PIN1 polarization and transport activity. We also provide evidence that PIN1-exported extracellular auxin is crucial for TMK activation and cell elongation, thus forming the simplest two-element self-regulatory feedback circuit. Thus, these findings offer direct mechanistic insights into a potential self-organizing circuit for auxin signaling and transport to ensure proper plant development in Arabidopsis.","lang":"eng"}],"date_published":"2026-01-14T00:00:00Z","researchdata_availability":"upon request","year":"2026","department":[{"_id":"JiFr"}],"publication_status":"published","OA_type":"closed access","day":"14","language":[{"iso":"eng"}],"date_updated":"2026-10-20T09:02:01Z","supplementarymaterial":"yes","article_type":"original","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"pmid":1,"type":"journal_article","publisher":"Cell Press","page":"73-84","das_tickbox":"1","publication":"Developmental Cell","acknowledgement":"We thank Lukáš Fiedler‬ for helping with the writing. This work was supported by the National Key Research and Development Program of China (2023YFA0913500) to T.X., R.H., Y.Y., Y.X., and M.W. and by the National Natural Science Foundation of China grants to T.X. (32130010), Z.Y. (3241101698), and R.H. (32070309 and 32470276) and startup funds from the Fujian Agriculture and Forestry University and the Shanghai Plant Stress Biology Center, Chinese Academy of Sciences to T.X.","volume":61,"date_created":"2025-11-12T10:03:39Z","issue":"1","dataavailabilitystatement":"Plasmids and genetic materials generated in this study will be made available upon request from the lead contact.The mass spectrometry data reported in this work have been deposited at the iProX database. Original western blot gel images have been deposited to Mendeley Data. The accession code and the DOI are listed in the key resources table.\r\nThis paper does not report original code. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request."},{"date_created":"2026-07-13T09:39:40Z","issue":"13","das_tickbox":"0","publication":"Current Biology","volume":36,"article_type":"original","date_updated":"2026-10-20T09:00:35Z","supplementarymaterial":"no","type":"journal_article","publisher":"Cell Press","page":"R739-R744","publication_identifier":{"issn":["0960-9822"]},"pmid":1,"year":"2026","citation":{"chicago":"Leitner, Valentin, and Eva Benková. “Auxin and the Control of Plant Growth and Development.” <i>Current Biology</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.cub.2026.04.047\">https://doi.org/10.1016/j.cub.2026.04.047</a>.","ama":"Leitner V, Benková E. Auxin and the control of plant growth and development. <i>Current Biology</i>. 2026;36(13):R739-R744. doi:<a href=\"https://doi.org/10.1016/j.cub.2026.04.047\">10.1016/j.cub.2026.04.047</a>","apa":"Leitner, V., &#38; Benková, E. (2026). Auxin and the control of plant growth and development. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2026.04.047\">https://doi.org/10.1016/j.cub.2026.04.047</a>","ieee":"V. Leitner and E. Benková, “Auxin and the control of plant growth and development,” <i>Current Biology</i>, vol. 36, no. 13. Cell Press, pp. R739–R744, 2026.","short":"V. Leitner, E. Benková, Current Biology 36 (2026) R739–R744.","ista":"Leitner V, Benková E. 2026. Auxin and the control of plant growth and development. Current Biology. 36(13), R739–R744.","mla":"Leitner, Valentin, and Eva Benková. “Auxin and the Control of Plant Growth and Development.” <i>Current Biology</i>, vol. 36, no. 13, Cell Press, 2026, pp. R739–44, doi:<a href=\"https://doi.org/10.1016/j.cub.2026.04.047\">10.1016/j.cub.2026.04.047</a>."},"month":"07","title":"Auxin and the control of plant growth and development","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","researchdata_availability":"no","date_published":"2026-07-06T00:00:00Z","abstract":[{"text":"Plants are remarkable organisms. Unlike animals, they cannot flee and, rooted in one place, they must cope with whatever challenges arise — nutrient scarcity, drought, shade, wind or obstacles in the soil. Their extraordinary ability to survive in such unstable environmental conditions lies in their capacity to adapt. In response to environmental signals, plants can rapidly adjust the rate of organ growth, change the direction of growth, bend toward resources, or remodel their body architecture by promoting or suppressing the formation of new organs such as lateral roots, branches, leaves, or flowers. This unique developmental plasticity depends on chemical signals, plant hormones that serve as regulators and coordinators of endogenous molecular and cellular processes. Chief among these signals is auxin, a plant hormone central to nearly every aspect of plant life.","lang":"eng"}],"OA_type":"closed access","language":[{"iso":"eng"}],"day":"06","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"publication_status":"published","external_id":{"pmid":["42407441"]},"scopus_import":"1","article_processing_charge":"No","corr_author":"1","oa_version":"None","doi":"10.1016/j.cub.2026.04.047","intvolume":"        36","_id":"22286","quality_controlled":"1","status":"public","author":[{"id":"4c665ce3-0016-11ec-bea0-e44de7a4fa3d","last_name":"Leitner","first_name":"Valentin","full_name":"Leitner, Valentin"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"}],"fulldoi":"https://doi.org/10.1016/j.cub.2026.04.047"},{"issue":"10","date_created":"2026-07-13T10:51:27Z","volume":114,"publication":"Neuron","das_tickbox":"0","article_type":"letter_note","supplementarymaterial":"no","date_updated":"2026-10-20T09:00:56Z","page":"1706-1708","publisher":"Cell Press","type":"journal_article","pmid":1,"publication_identifier":{"issn":["0896-6273"]},"year":"2026","researchdata_availability":"no","abstract":[{"lang":"eng","text":"Active dendrites enrich the repertoire of single-neuron computations. Whereas a lot is known about the function of dendrites in vitro, information about their in vivo properties is limited. A new study1 uses advanced imaging to study hippocampal CA1 pyramidal neuron dendrites in head-fixed, awake animals."}],"date_published":"2026-05-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mission impossible? Quantitative analysis of dendritic computations in vivo","month":"05","citation":{"mla":"Bhattacharya, Subhodeep, and Peter M. Jonas. “Mission Impossible? Quantitative Analysis of Dendritic Computations in Vivo.” <i>Neuron</i>, vol. 114, no. 10, Cell Press, 2026, pp. 1706–08, doi:<a href=\"https://doi.org/10.1016/j.neuron.2026.04.002\">10.1016/j.neuron.2026.04.002</a>.","ista":"Bhattacharya S, Jonas PM. 2026. Mission impossible? Quantitative analysis of dendritic computations in vivo. Neuron. 114(10), 1706–1708.","apa":"Bhattacharya, S., &#38; Jonas, P. M. (2026). Mission impossible? Quantitative analysis of dendritic computations in vivo. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2026.04.002\">https://doi.org/10.1016/j.neuron.2026.04.002</a>","short":"S. Bhattacharya, P.M. Jonas, Neuron 114 (2026) 1706–1708.","ieee":"S. Bhattacharya and P. M. Jonas, “Mission impossible? Quantitative analysis of dendritic computations in vivo,” <i>Neuron</i>, vol. 114, no. 10. Cell Press, pp. 1706–1708, 2026.","chicago":"Bhattacharya, Subhodeep, and Peter M Jonas. “Mission Impossible? Quantitative Analysis of Dendritic Computations in Vivo.” <i>Neuron</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.neuron.2026.04.002\">https://doi.org/10.1016/j.neuron.2026.04.002</a>.","ama":"Bhattacharya S, Jonas PM. Mission impossible? Quantitative analysis of dendritic computations in vivo. <i>Neuron</i>. 2026;114(10):1706-1708. doi:<a href=\"https://doi.org/10.1016/j.neuron.2026.04.002\">10.1016/j.neuron.2026.04.002</a>"},"language":[{"iso":"eng"}],"day":"20","OA_type":"closed access","publication_status":"published","department":[{"_id":"PeJo"}],"external_id":{"pmid":["42161246"]},"article_processing_charge":"No","scopus_import":"1","_id":"22305","quality_controlled":"1","status":"public","author":[{"last_name":"Bhattacharya","orcid":"0009-0009-0334-9068","id":"45f74010-66f6-11f0-a7d4-c441fa3685ff","full_name":"Bhattacharya, Subhodeep","first_name":"Subhodeep"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"doi":"10.1016/j.neuron.2026.04.002","intvolume":"       114","oa_version":"None","corr_author":"1","fulldoi":"https://doi.org/10.1016/j.neuron.2026.04.002"},{"date_updated":"2026-10-20T09:04:23Z","file":[{"date_created":"2026-05-04T12:20:10Z","file_id":"21795","file_name":"2026_CellReports_Vijatovic.pdf","date_updated":"2026-05-04T12:20:10Z","checksum":"0d26cdb5b8d8dec3a911d8261a65cdef","relation":"main_file","creator":"dernst","success":1,"access_level":"open_access","file_size":14925958,"content_type":"application/pdf"}],"article_type":"original","pmid":1,"publication_identifier":{"eissn":["2211-1247"],"issn":["2639-1856"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"22667"}]},"type":"journal_article","publisher":"Cell Press","volume":45,"publication":"Cell Reports","has_accepted_license":"1","acknowledgement":"We would like to thank the members of the Sweeney Lab, Mario de Bono, Michael Forsthofer, Katharina Lust, and Meital Oren, for comments on the manuscript. We are also grateful to Tom Jessell and Chris Kintner for their scientific insight and mentorship during the conception of this project. It would also have not been possible without the technical support of the Aquatics and Imaging and Optics Facility support teams (ISTA). We thank Martin Estermann for preparing the initial draft of the graphical abstract and Niki Barolini for the final version. In addition, we thank our funding sources for providing the resources to do these experiments: GFF NÖ FTI Strategy Lower Austria dissertation grant FT121-D-046 (to D.V.), Horizon Europe ERC starting grant 101041551 (to Y.I., L.B.S., F.A.T., and D.V.), Special Research Program (SFB) of the Austrian Science Fund (FWF) project F7814-B (to L.B.S.), Austrian Science Fund (FWF) 10.55776/COE16 (to Y.I. and L.B.S.), NINDS 5R35NS116858 (to J.S.D.), CZI grant DAF2020-225401 (DOI) 10.37921/120055ratwvi (to R.H.), NIH grant R01NS123116 (to J.B.B.), American Lebanese Syrian Associated Charities (ALSAC) (to J.B.B.), German Academic Exchange Service (DAAD) IFI grant 57515251-91853472 (to Z.H.), and Project A.L.S. (to S.B.-M.).","date_created":"2026-04-19T22:07:43Z","issue":"4","oa":1,"OA_place":"publisher","article_processing_charge":"Yes","scopus_import":"1","PlanS_conform":"1","external_id":{"pmid":["41964955 "]},"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)"},"article_number":"117227","ddc":["570"],"fulldoi":"https://doi.org/10.1016/j.celrep.2026.117227","intvolume":"        45","doi":"10.1016/j.celrep.2026.117227","_id":"21746","quality_controlled":"1","status":"public","author":[{"full_name":"Vijatovic, David","first_name":"David","last_name":"Vijatovic","id":"cf391e77-ec3c-11ea-a124-d69323410b58","orcid":"0000-0002-5494-0941"},{"full_name":"Toma, Florina Alexandra ","first_name":"Florina Alexandra ","last_name":"Toma","id":"2f73f876-f128-11eb-9611-b96b5a30cb0e"},{"last_name":"Ignatyev","full_name":"Ignatyev, Y","first_name":"Y"},{"id":"a8144562-32c9-11ee-b5ce-d9800628bda2","orcid":"0009-0008-0158-4032","last_name":"Harrington","first_name":"Zoe P","full_name":"Harrington, Zoe P"},{"first_name":"Christoph M","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthijs Geert","full_name":"Smits, Matthijs Geert","id":"7a231d52-e216-11ee-a0bb-8acd55f8f1f0","last_name":"Smits"},{"last_name":"Dalla Vecchia","id":"02a7a869-ff06-11ed-a87f-86649d6077e5","full_name":"Dalla Vecchia, Marco","first_name":"Marco"},{"full_name":"Trevisan, Alexandra J.","first_name":"Alexandra J.","last_name":"Trevisan"},{"last_name":"Chapman","first_name":"Phillip","full_name":"Chapman, Phillip"},{"last_name":"Julseth","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","full_name":"Julseth, Mara","first_name":"Mara"},{"last_name":"Brenner-Morton","full_name":"Brenner-Morton, Susan","first_name":"Susan"},{"first_name":"Mariano I.","full_name":"Gabitto, Mariano I.","last_name":"Gabitto"},{"full_name":"Dasen, Jeremy S.","first_name":"Jeremy S.","last_name":"Dasen"},{"last_name":"Bikoff","first_name":"Jay B.","full_name":"Bikoff, Jay B."},{"last_name":"Sweeney","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","orcid":"0000-0001-9242-5601","full_name":"Sweeney, Lora Beatrice Jaeger","first_name":"Lora Beatrice Jaeger"}],"corr_author":"1","oa_version":"Published Version","DOAJ_listed":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"As vertebrates transitioned from water to land, locomotion shifted from undulatory swimming to limb-based movement. How spinal circuits and their cell types evolved to support this transition remains unclear. We leverage frog metamorphosis, which recapitulates this transition within a single organism, to define how spinal circuits generate aquatic versus terrestrial motor patterns. At swim stages, spinal architecture is uniform, with a transcriptionally and anatomically homogeneous motor and interneurons. As limbs develop and their movement complexifies, spinal circuits expand in neuron number and subtype diversity. This expansion is most pronounced for V1 inhibitory neurons, which increase ∼70-fold and diversify into transcriptionally distinct subtypes. Disrupting transcription factors defining emerging motor and V1 populations reveals molecular segregation between swim and limb circuits, highlighting the role of subtype diversity in motor coordination. A multifold increase in inhibitory neuron diversity thus underlies the tail-to-limb locomotor transition, providing a framework for spinal circuit adaptation during vertebrate evolution."}],"date_published":"2026-04-28T00:00:00Z","month":"04","title":"Multifold increase in spinal inhibitory cell types with emergence of limb movement","citation":{"ista":"Vijatovic D, Toma FA, Ignatyev Y, Harrington ZP, Sommer CM, Hauschild R, Smits MG, Dalla Vecchia M, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney LB. 2026. Multifold increase in spinal inhibitory cell types with emergence of limb movement. Cell Reports. 45(4), 117227.","mla":"Vijatovic, David, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” <i>Cell Reports</i>, vol. 45, no. 4, 117227, Cell Press, 2026, doi:<a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">10.1016/j.celrep.2026.117227</a>.","apa":"Vijatovic, D., Toma, F. A., Ignatyev, Y., Harrington, Z. P., Sommer, C. M., Hauschild, R., … Sweeney, L. B. (2026). Multifold increase in spinal inhibitory cell types with emergence of limb movement. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">https://doi.org/10.1016/j.celrep.2026.117227</a>","short":"D. Vijatovic, F.A. Toma, Y. Ignatyev, Z.P. Harrington, C.M. Sommer, R. Hauschild, M.G. Smits, M. Dalla Vecchia, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton, M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, Cell Reports 45 (2026).","ieee":"D. Vijatovic <i>et al.</i>, “Multifold increase in spinal inhibitory cell types with emergence of limb movement,” <i>Cell Reports</i>, vol. 45, no. 4. Cell Press, 2026.","ama":"Vijatovic D, Toma FA, Ignatyev Y, et al. Multifold increase in spinal inhibitory cell types with emergence of limb movement. <i>Cell Reports</i>. 2026;45(4). doi:<a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">10.1016/j.celrep.2026.117227</a>","chicago":"Vijatovic, David, Florina Alexandra  Toma, Y Ignatyev, Zoe P Harrington, Christoph M Sommer, Robert Hauschild, Matthijs Geert Smits, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” <i>Cell Reports</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.celrep.2026.117227\">https://doi.org/10.1016/j.celrep.2026.117227</a>."},"year":"2026","publication_status":"published","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"department":[{"_id":"LoSw"},{"_id":"GradSch"},{"_id":"TiVo"},{"_id":"Bio"},{"_id":"NiBa"}],"file_date_updated":"2026-05-04T12:20:10Z","day":"28","language":[{"iso":"eng"}],"project":[{"name":"Development and Evolution of Tetrapod Motor Circuits","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","grant_number":"101041551"},{"grant_number":"F7814","_id":"8da85f50-16d5-11f0-9cad-eab8b0ff6c9e","name":"Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity"},{"_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","name":"Tools for automation and feedback microscopy","grant_number":"CZI01"},{"grant_number":"FTI21-D-046","name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis","_id":"bd73af52-d553-11ed-ba76-912049f0ac7a"},{"grant_number":"COE16","name":"Neuronal circuits in health and disease (Sweeney)","_id":"cf428362-b037-11f1-b015-8277a8a2f63d"}],"OA_type":"gold"},{"intvolume":"         6","doi":"10.1016/j.xgen.2026.101277","quality_controlled":"1","_id":"21987","status":"public","author":[{"orcid":"0000-0002-5636-9259","id":"30d4014e-7753-11eb-b44b-db6d61112e73","last_name":"Krätschmer","first_name":"Ilse","full_name":"Krätschmer, Ilse"},{"first_name":"Laura","full_name":"Hegemann, Laura","last_name":"Hegemann"},{"full_name":"Hofmeister, Robin J.","first_name":"Robin J.","last_name":"Hofmeister"},{"last_name":"Corfield","first_name":"Elizabeth C.","full_name":"Corfield, Elizabeth C."},{"last_name":"Mahmoudi","first_name":"Mahdi","full_name":"Mahmoudi, Mahdi"},{"last_name":"Delaneau","first_name":"Olivier","full_name":"Delaneau, Olivier"},{"last_name":"Andreassen","first_name":"Ole A.","full_name":"Andreassen, Ole A."},{"last_name":"Campbell","first_name":"Archie","full_name":"Campbell, Archie"},{"first_name":"Caroline","full_name":"Hayward, Caroline","last_name":"Hayward"},{"last_name":"Marioni","first_name":"Riccardo E.","full_name":"Marioni, Riccardo E."},{"full_name":"Ystrom, Eivind","first_name":"Eivind","last_name":"Ystrom"},{"full_name":"Havdahl, Alexandra","first_name":"Alexandra","last_name":"Havdahl"},{"first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","last_name":"Robinson"}],"corr_author":"1","DOAJ_listed":"1","oa_version":"Published Version","ddc":["570"],"fulldoi":"https://doi.org/10.1016/j.xgen.2026.101277","external_id":{"pmid":["40909755"]},"article_number":"101277","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","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"},"OA_place":"publisher","article_processing_charge":"Yes","scopus_import":"1","day":"08","language":[{"iso":"eng"}],"project":[{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk","grant_number":"PCEGP3_181181"}],"OA_type":"gold","publication_status":"published","acknowledged_ssus":[{"_id":"ScienComp"}],"file_date_updated":"2026-07-28T07:24:50Z","department":[{"_id":"MaRo"}],"year":"2026","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","researchdata_availability":"yes","abstract":[{"text":"We introduce JODIE, a genetic joint modeling approach that estimates how DNA loci influence human traits by partitioning genetic effects into four components: direct effects (from a child’s alleles), indirect maternal and paternal effects (from parents’ alleles), and parent-of-origin (PofO) effects (dependent on parental transmission of alleles), while uniquely accounting for assortative mating. We analyze 30,000 child-mother-father trios from the Estonian Biobank and the Norwegian Mother, Father, and Child Cohort, focusing on height, body mass index, and childhood educational test scores. We find direct effects to be the largest contributor to trait variation, but combined, indirect parental and PofO effects are similarly substantial. We support our results by within-family genome-wide association testing and identify 276 independently associated DNA regions with a complex interplay between direct, indirect, and PofO effects. By joint modeling, we show that direct, indirect, and PofO effects collectively shape human phenotypic variation across loci genome-wide.","lang":"eng"}],"date_published":"2026-07-08T00:00:00Z","title":"Separating direct, indirect, and parent-of-origin genetic effects in the human population","month":"07","citation":{"ista":"Krätschmer I, Hegemann L, Hofmeister RJ, Corfield EC, Mahmoudi M, Delaneau O, Andreassen OA, Campbell A, Hayward C, Marioni RE, Ystrom E, Havdahl A, Robinson MR. 2026. Separating direct, indirect, and parent-of-origin genetic effects in the human population. Cell Genomics. 6(7), 101277.","mla":"Krätschmer, Ilse, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell Genomics</i>, vol. 6, no. 7, 101277, Cell Press, 2026, doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">10.1016/j.xgen.2026.101277</a>.","short":"I. Krätschmer, L. Hegemann, R.J. Hofmeister, E.C. Corfield, M. Mahmoudi, O. Delaneau, O.A. Andreassen, A. Campbell, C. Hayward, R.E. Marioni, E. Ystrom, A. Havdahl, M.R. Robinson, Cell Genomics 6 (2026).","ieee":"I. Krätschmer <i>et al.</i>, “Separating direct, indirect, and parent-of-origin genetic effects in the human population,” <i>Cell Genomics</i>, vol. 6, no. 7. Cell Press, 2026.","apa":"Krätschmer, I., Hegemann, L., Hofmeister, R. J., Corfield, E. C., Mahmoudi, M., Delaneau, O., … Robinson, M. R. (2026). Separating direct, indirect, and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">https://doi.org/10.1016/j.xgen.2026.101277</a>","chicago":"Krätschmer, Ilse, Laura Hegemann, Robin J. Hofmeister, Elizabeth C. Corfield, Mahdi Mahmoudi, Olivier Delaneau, Ole A. Andreassen, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell Genomics</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">https://doi.org/10.1016/j.xgen.2026.101277</a>.","ama":"Krätschmer I, Hegemann L, Hofmeister RJ, et al. Separating direct, indirect, and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>. 2026;6(7). doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">10.1016/j.xgen.2026.101277</a>"},"related_material":{"link":[{"url":"https://ista.ac.at/en/news/human-traits-beyond-inherited-genes/","relation":"press_release","description":"News on ISTA website"}]},"keyword":["direct genetic effects","DGE","indirect genetic effects","IGE","parent-of-origin effects","phenotypic variation","assortative mating","within-family GWAS","MoBa","EstBB"],"type":"journal_article","publisher":"Cell Press","pmid":1,"publication_identifier":{"eissn":["2666-979X"]},"file":[{"file_id":"22597","file_name":"2026_CellGenomics_Kraetschmer.pdf","date_updated":"2026-07-28T07:24:50Z","date_created":"2026-07-28T07:24:50Z","success":1,"access_level":"open_access","content_type":"application/pdf","file_size":3679297,"checksum":"f896b510480d2d4e4a7fd46c2e2761f4","relation":"main_file","creator":"dernst"}],"article_type":"original","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","supplementarymaterial":"yes","date_updated":"2026-10-20T09:03:50Z","oa":1,"dataavailabilitystatement":"Information on how to access the MoBaPsychGen post-imputation QC data are available here: https://www.fhi.no/en/me/the-psychgen-centre-for-genetic-epidemiology-and-mental-health/access-to-genetic-data-after-quality-control-by-the-mobapsychgen-pipeline-v/.\r\nEstonian Biobank data (https://genomics.ut.ee/en/content/estonian-biobank) were used in this project. For access to be granted to the Estonian Biobank genotypic and corresponding phenotypic data, a preliminary application must be presented to the oversight committee, who must first approve the project. Ethics permission must then be obtained from the Estonian Committee on Bioethics and Human Research. Finally, a full project must be submitted and approved by the Estonian Biobank.\r\nAccess to the Generation Scotland data is available with appropriate permission from the Generation Scotland Access Committee. Applications should be made to access@generationscotland.org (https://genscot.ed.ac.uk/).\r\nThe code for JODIE developed in this work is open source and is publicly available on zenodo (https://doi.org/10.5281/zenodo.19593928) and GitHub (https://github.com/medical-genomics-group/JODIE).\r\nHaplotype Reference Consortium Release 1.1 data (https://ega-archive.org/datasets/EGAD00001002729) are available by application to a Data Access Committee (DAC) of the Wellcome Trust Sanger Institute.\r\nThe Common Metabolic Diseases Atlas can be accessed here: https://cmdga.org.","date_created":"2026-06-10T07:39:08Z","issue":"7","volume":6,"publication":"Cell Genomics","das_tickbox":"1","has_accepted_license":"1","acknowledgement":"We thank Zoltan Kutalik, Peter Visscher, and members of the Robinson group at ISTA for their comments, which improved this manuscript. This work was funded by an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria.\r\nThe Norwegian Mother, Father, and Child Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research. We are grateful to all the participating families in Norway who take part in this on-going cohort study. We thank the Norwegian Institute of Public Health (NIPH) for generating high-quality genomic data. The research is part of the HARVEST collaboration, supported by the Research Council of Norway (#229624). We also thank the NORMENT Center for providing genotype data, funded by the Research Council of Norway (#223273), South East Norway Health Authorities, and Stiftelsen Kristian Gerhard Jebsen, and in collaboration with deCODE Genetics. We further thank the Center for Diabetes Research, the University of Bergen for providing genotype data funded by the ERC AdG project SELECTionPREDISPOSED, Stiftelsen Kristian Gerhard Jebsen, Trond Mohn Foundation, the Research Council of Norway, the Novo Nordisk Foundation, the University of Bergen, and the Western Norway Health Authorities. The MoBa work was performed on the TSD (Tjeneste for Sensitive Data) facilities, owned by the University of Oslo, operated and developed by the TSD service group at the University of Oslo, IT Department (USIT, tsd-drift@usit.uio.no). E.Y. is supported by the European Union (grant numbers 101045526 and 101073237) and the Research Council of Norway (grant numbers 336078, 288083, and 331640).\r\nWe would like to acknowledge the participants and investigators of the Generation Scotland Cohort study. Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). Genotyping and methylation typing of the GS:SFHS samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” [STRADL] ref. 104036/Z/14/Z).\r\nWe would like to thank and acknowledge the participants and investigators of the Estonian Biobank (EstBB) study. The research was conducted using the Estonian Center of Genomics/Roadmap II funded by the Estonian Research Council (project number TT17).\r\nNorwegian analyses were performed on resources provided by Sigma2 - the National Infrastructure for High-Performance Computing and Data Storage in Norway. Estonian Data analysis was carried out in the High-Performance Computing Center cloud provided by University of Tartu. Analysis of the Generation Scotland data and the summary statistics obtained from the other analyses was conducted at IST Austria and is supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp)."},{"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"grant_number":"101161364","_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits"},{"grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"day":"11","language":[{"iso":"eng"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaRo"},{"_id":"MaMo"}],"file_date_updated":"2026-07-13T14:56:41Z","acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2026","abstract":[{"text":"Uncovering the genetic architecture of complex traits and pinpointing causal molecular drivers require the ability to distinguish true signals from noise within massive, high-dimensional omics datasets. To extract meaningful biological insights from these datasets, such as identifying causal genetic variants and proteins, scalable and accurate inference methods are essential. To this end, this thesis develops novel Bayesian inference frameworks based on Vector Approximate Message Passing and demonstrates their effectiveness in the modeling of disease onset times and quantitative physical and clinical measures.\r\n\r\nFirst, we introduce gVAMP, a Bayesian framework tailored for Genome-Wide Association Studies that enables the joint modeling of quantitative complex traits across millions of genetic variants. gVAMP demonstrates superior accuracy in variable selection and out-of-sample polygenic risk prediction compared to state-of-the-art approaches. We model human height using 17 million whole-genome sequence variants from the UK Biobank, incorporating a vast number of rare variants and revealing novel associations. gVAMP achieves a prediction accuracy of approximately 46% for human height, representing the highest reported performance for this trait to date. \r\n\r\nSecond, we present vampW, a Bayesian framework for survival analysis applied to proteomic data. By effectively handling right-censoring and complex protein dependencies within the UK Biobank Pharma Proteomics Project dataset, vampW identifies 219 protein associations across 24 disease outcomes, the majority of which are not among the top marginal discoveries. We further adjust protein levels for exponential age effects, yielding 1,308 associations and highlighting the sensitivity of the analysis to the chosen age-correction methodology. Finally, vampW improves upon the variable selection capabilities of the commonly used (penalized) variants of the Cox proportional hazards model and delivers state-of-the-art out-of-sample prediction of disease onset times.\r\n\r\nCollectively, these methods provide powerful tools for dissecting the genetic architecture of complex traits and the proteomic drivers of disease onset. Furthermore, by delivering accurate polygenic risk scores and precise predictions of onset times, this work advances the capabilities of personalized medicine and clinical risk stratification.","lang":"eng"}],"date_published":"2026-07-11T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Depope, A. (2026). <i>From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22258\">https://doi.org/10.15479/AT-ISTA-22258</a>","short":"A. Depope, From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics, Institute of Science and Technology Austria, 2026.","ieee":"A. Depope, “From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics,” Institute of Science and Technology Austria, 2026.","chicago":"Depope, Al. “From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22258\">https://doi.org/10.15479/AT-ISTA-22258</a>.","ama":"Depope A. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22258\">10.15479/AT-ISTA-22258</a>","mla":"Depope, Al. <i>From Sparse Selection to Risk Prediction: Approximate Message Passing for Proteomic Survival Models and Large-Scale Genomics</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22258\">10.15479/AT-ISTA-22258</a>.","ista":"Depope A. 2026. From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics. Institute of Science and Technology Austria."},"title":"From sparse selection to risk prediction: Approximate message passing for proteomic survival models and large-scale genomics","month":"07","status":"public","_id":"22258","author":[{"full_name":"Depope, Al","first_name":"Al","last_name":"Depope","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830"}],"doi":"10.15479/AT-ISTA-22258","oa_version":"Published Version","corr_author":"1","ddc":["576","610","006"],"supervisor":[{"last_name":"Robinson","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard"},{"orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-22258","article_processing_charge":"No","OA_place":"publisher","oa":1,"date_created":"2026-07-10T13:27:20Z","alternative_title":["ISTA Thesis"],"acknowledgement":"This work was supported in part by the Swiss National Science Foundation through the\r\nEccellenza Grant \"Improving estimation and prediction of common complex disease risk\"\r\n(grant number PCEGP3_181181); the European Research Council through the grant\r\n\"Inference in High Dimensions: Light-speed Algorithms and Information Limits\" (grant\r\nnumber 101161364); and the Fondation Jean-Jacques et Felicia Lopez-Loreta through the\r\nPrix Lopez-Loretta 2019.\r\n","has_accepted_license":"1","das_tickbox":"1","page":"169","keyword":["Approximate Message Passing","GWAS","Genomics","Proteomics","Survival modeling"],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"21488"}]},"publisher":"Institute of Science and Technology Austria","type":"dissertation","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"doi_confirm":"1","file":[{"date_created":"2026-07-13T14:52:19Z","date_updated":"2026-07-13T14:52:19Z","file_id":"22316","file_name":"2026_Depope_Al_Thesis.pdf","creator":"adepope","relation":"main_file","checksum":"9ab386790515628d957a194f30a7ccb4","file_size":25109878,"content_type":"application/pdf","access_level":"open_access"},{"file_size":1203199939,"content_type":"application/zip","access_level":"closed","relation":"source_file","creator":"adepope","checksum":"8ed8fb63f76a695d5b6fec35343f4b90","date_updated":"2026-07-13T14:56:41Z","file_name":"2026_Depope_Al_Thesis.zip","file_id":"22317","date_created":"2026-07-13T14:56:41Z"}],"date_updated":"2026-10-20T09:03:21Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-05-13T00:00:00Z","abstract":[{"lang":"eng","text":"Human height is a model for the genetic analysis of complex traits, and recent studies suggest the presence of thousands of common genetic variant associations and hundreds of low-frequency/rare variants. Here, we develop a new algorithmic paradigm based on approximate message passing (genomic vector approximate message passing [gVAMP]) for identifying DNA sequence variants associated with complex traits and common diseases in large-scale whole-genome sequencing (WGS) data. We show that gVAMP accurately localizes associations to variants with the correct frequency and position in the DNA, outperforming existing fine-mapping methods in selecting the appropriate genetic variants within WGS data. We then apply gVAMP to jointly model the relationship of tens of millions of WGS variants with human height in hundreds of thousands of UK Biobank individuals. We identify 59 rare variants and gene burden scores alongside many hundreds of DNA regions containing common variant associations and show that understanding the genetic basis of complex traits will require the joint analysis of hundreds of millions of variables measured on millions of people. The polygenic risk scores obtained from gVAMP have high accuracy (including a prediction accuracy of ∼46% for human height) and outperform current methods for downstream tasks such as mixed linear model association testing across 13 UK Biobank traits. In conclusion, gVAMP offers a scalable foundation for a wider range of analyses in WGS data."}],"researchdata_availability":"yes","title":"Joint modeling of whole-genome sequencing data for human height via approximate message passing","month":"05","citation":{"mla":"Depope, Al, et al. “Joint Modeling of Whole-Genome Sequencing Data for Human Height via Approximate Message Passing.” <i>Cell Genomics</i>, vol. 6, no. 5, 101162, Cell Press, 2026, doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101162\">10.1016/j.xgen.2026.101162</a>.","ista":"Depope A, Bajzik J, Mondelli M, Robinson MR. 2026. Joint modeling of whole-genome sequencing data for human height via approximate message passing. Cell Genomics. 6(5), 101162.","chicago":"Depope, Al, Jakub Bajzik, Marco Mondelli, and Matthew Richard Robinson. “Joint Modeling of Whole-Genome Sequencing Data for Human Height via Approximate Message Passing.” <i>Cell Genomics</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.xgen.2026.101162\">https://doi.org/10.1016/j.xgen.2026.101162</a>.","ama":"Depope A, Bajzik J, Mondelli M, Robinson MR. Joint modeling of whole-genome sequencing data for human height via approximate message passing. <i>Cell Genomics</i>. 2026;6(5). doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101162\">10.1016/j.xgen.2026.101162</a>","short":"A. Depope, J. Bajzik, M. Mondelli, M.R. Robinson, Cell Genomics 6 (2026).","apa":"Depope, A., Bajzik, J., Mondelli, M., &#38; Robinson, M. R. (2026). Joint modeling of whole-genome sequencing data for human height via approximate message passing. <i>Cell Genomics</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.xgen.2026.101162\">https://doi.org/10.1016/j.xgen.2026.101162</a>","ieee":"A. Depope, J. Bajzik, M. Mondelli, and M. R. Robinson, “Joint modeling of whole-genome sequencing data for human height via approximate message passing,” <i>Cell Genomics</i>, vol. 6, no. 5. Cell Press, 2026."},"year":"2026","publication_status":"published","file_date_updated":"2026-07-28T07:06:26Z","department":[{"_id":"MaMo"},{"_id":"MaRo"}],"day":"13","language":[{"iso":"eng"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"101161364","name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits","_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf"},{"name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181"}],"OA_type":"gold","OA_place":"publisher","article_processing_charge":"Yes","scopus_import":"1","external_id":{"pmid":["41713425"]},"article_number":"101162","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","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"},"ddc":["000","570"],"fulldoi":"https://doi.org/10.1016/j.xgen.2026.101162","doi":"10.1016/j.xgen.2026.101162","intvolume":"         6","status":"public","_id":"21488","author":[{"full_name":"Depope, Al","first_name":"Al","last_name":"Depope","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830"},{"id":"b995e25b-8c4b-11ed-a6d8-f71b7bcd6122","last_name":"Bajzik","first_name":"Jakub","full_name":"Bajzik, Jakub"},{"first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli"},{"last_name":"Robinson","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard"}],"quality_controlled":"1","corr_author":"1","oa_version":"Published Version","DOAJ_listed":"1","volume":6,"das_tickbox":"1","publication":"Cell Genomics","acknowledgement":"We thank Malgorzata Borczyk for creating the gene burden scores. We thank Robin Beaumont, Amedeo Roberto Esposito, Gareth Hawkes, Philip Schniter, Matthew Stephens, Pragya Sur, Peter Visscher, Michael Weedon, and Harry Wright for providing valuable suggestions and comments on earlier versions of the work. This project was funded by a Lopez-Loreta Prize to M.M., an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181), an ERC Starting Grant to M.M. (INF2, project number 101161364), and core funding from ISTA. High-performance computing was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We would like to acknowledge the participants and investigators of the UK Biobank study. We gratefully acknowledge the All of Us participants for their contributions, without whom this research would not have been possible. We also thank the National Institutes of Health All of Us Research Program for making available the participant data (and/or samples and/or cohort) examined in this study.","has_accepted_license":"1","date_created":"2026-03-23T15:10:03Z","issue":"5","oa":1,"dataavailabilitystatement":"This project uses the UK Biobank data under project number 35520. UK Biobank genotypic and phenotypic data are available through a formal request at http://www.ukbiobank.ac.uk. It also uses genotypic and phenotypic data from the All of Us study, which are also available through a formal request at https://www.researchallofus.org/data-tools/data-access/. All summary statistic estimates are released publicly on Dryad: https://doi.org/10.5061/dryad.cz8w9gjjc.\r\n•\r\nThe gVAMP code developed in this work is open source and has been deposited on GitHub, where it is publicly available at https://github.com/medical-genomics-group/gVAMP, and the code used to generate the data in the manuscript are available from Zenodo https://doi.org/10.5281/zenodo.17935521. The URLs of other software used are listed in the key resources table.","supplementarymaterial":"yes","date_updated":"2026-10-20T09:03:22Z","file":[{"checksum":"6b59686f8d9733add4f23d23f3dd9df0","creator":"dernst","relation":"main_file","access_level":"open_access","success":1,"content_type":"application/pdf","file_size":3736705,"date_created":"2026-07-28T07:06:26Z","file_name":"2026_CellGenomics_Depope.pdf","file_id":"22596","date_updated":"2026-07-28T07:06:26Z"}],"article_type":"original","pmid":1,"publication_identifier":{"eissn":["2666-979X"]},"related_material":{"record":[{"relation":"dissertation_contains","id":"22258","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/big-data-and-human-height/","description":"News on ISTA website","relation":"press_release"}]},"type":"journal_article","publisher":"Cell Press"},{"pmid":1,"publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"page":"3566-3579.e5","publisher":"Cell Press","type":"journal_article","supplementarymaterial":"yes","date_updated":"2026-10-20T09:03:35Z","file":[{"access_level":"open_access","success":1,"file_size":6795092,"content_type":"application/pdf","checksum":"5ec4472d81fd44de03ccb92b1eb690a6","creator":"dernst","relation":"main_file","file_id":"22598","file_name":"2026_CurrentBiology_KiangEwe.pdf","date_updated":"2026-07-28T07:31:44Z","date_created":"2026-07-28T07:31:44Z"}],"article_type":"original","oa":1,"dataavailabilitystatement":"* All NGS data are available through GEO under accession number GSE331410.\r\n* This paper does not report original code.\r\n* Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","volume":36,"acknowledgement":"We thank Itai Reiger for their assistance with experiments. We thank Cori Bargmann (Rockefeller University) for providing introgressed strains carrying HW alleles of npr-1 and glb-5. Some graphics were created with Biorender.com. We are grateful to WormBase for providing valuable data and resources. Some strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). O.R. is grateful for the support of the Morris Kahn Foundation. C.K.E. was supported by an EMBO fellowship ALTF 6-2022. This work is funded by Eric and Wendy Schmidt Fund for Strategic Innovation Polymath Award 0140001000 (O.R.); European Research Council grant 335624 (O.R.); Israel Science Foundation 979/21 (Y.B.T.); and the US-Israel Binational Science Foundation 2023036 (Y.B.T.).","has_accepted_license":"1","publication":"Current Biology","das_tickbox":"1","issue":"14","date_created":"2026-07-12T22:02:18Z","ddc":["570"],"fulldoi":"https://doi.org/10.1016/j.cub.2026.06.016","_id":"22267","status":"public","author":[{"first_name":"Chee Kiang","full_name":"Ewe, Chee Kiang","last_name":"Ewe"},{"last_name":"Achache","first_name":"Hanna","full_name":"Achache, Hanna"},{"first_name":"Hanna","full_name":"Schön, Hanna","id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","last_name":"Schön"},{"first_name":"Leonid","full_name":"Kontorovich, Leonid","last_name":"Kontorovich"},{"full_name":"Teichman, Guy","first_name":"Guy","last_name":"Teichman"},{"last_name":"Weiss","first_name":"Shir","full_name":"Weiss, Shir"},{"last_name":"Mogilevskaya","full_name":"Mogilevskaya, Anna","first_name":"Anna"},{"last_name":"Valenski","full_name":"Valenski, Myriam","first_name":"Myriam"},{"last_name":"Anava","full_name":"Anava, Sarit","first_name":"Sarit"},{"full_name":"Bardapurkar, Rutwik","first_name":"Rutwik","last_name":"Bardapurkar"},{"full_name":"Gingold, Hila","first_name":"Hila","last_name":"Gingold"},{"last_name":"Posner","full_name":"Posner, Rachel","first_name":"Rachel"},{"last_name":"Antonova","first_name":"Olga","full_name":"Antonova, Olga"},{"full_name":"De Bono, Mario","first_name":"Mario","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443"},{"first_name":"Yonatan B.","full_name":"Tzur, Yonatan B.","last_name":"Tzur"},{"first_name":"Oded","full_name":"Rechavi, Oded","last_name":"Rechavi"}],"quality_controlled":"1","intvolume":"        36","doi":"10.1016/j.cub.2026.06.016","oa_version":"Published Version","OA_place":"publisher","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","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)"},"external_id":{"pmid":["42409014"]},"publication_status":"published","file_date_updated":"2026-07-28T07:31:44Z","department":[{"_id":"MaDe"}],"day":"20","language":[{"iso":"eng"}],"OA_type":"hybrid","abstract":[{"text":"Thermal pollution, whether local or driven by global warming, threatens biodiversity in part through its detrimental effects on reproduction. Non-coding small RNAs (sRNAs) are crucial for maintaining germline developmental robustness under heat stress. Remarkably, we uncovered that neuronal sRNAs regulate germ cells’ thermotolerance, affecting both spermatogenic and oogenic germlines in a cell-non-autonomous manner. Furthermore, we demonstrate that, in RNAi mutants, an oxygen-sensing neural circuit, modulated by neuropeptide signaling, antagonizes germline maintenance, likely reflecting the nematode’s innate association of reduced oxygen levels with food availability and reproductive permissive environments. Finally, we provide evidence that laboratory-domesticated alleles of oxygen-response genes encoding neuropeptide receptor NPR-1 and hexacoordinated globin GLB-5 compromise germline thermotolerance. Hence, our findings raise the possibility that sensory perception, independent of direct environmental change, modulates germline integrity, highlighting a novel mechanism by which neural circuits integrate environmental information to safeguard reproductive fitness in fluctuating environments.","lang":"eng"}],"date_published":"2026-07-20T00:00:00Z","researchdata_availability":"upon request","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress","citation":{"mla":"Ewe, Chee Kiang, et al. “Neuronal RNAi and Oxygen-Sensing Circuit Shape Germline Resilience to Heat Stress.” <i>Current Biology</i>, vol. 36, no. 14, Cell Press, 2026, p. 3566–3579.e5, doi:<a href=\"https://doi.org/10.1016/j.cub.2026.06.016\">10.1016/j.cub.2026.06.016</a>.","ista":"Ewe CK, Achache H, Schön H, Kontorovich L, Teichman G, Weiss S, Mogilevskaya A, Valenski M, Anava S, Bardapurkar R, Gingold H, Posner R, Antonova O, de Bono M, Tzur YB, Rechavi O. 2026. Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. Current Biology. 36(14), 3566–3579.e5.","ama":"Ewe CK, Achache H, Schön H, et al. Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. <i>Current Biology</i>. 2026;36(14):3566-3579.e5. doi:<a href=\"https://doi.org/10.1016/j.cub.2026.06.016\">10.1016/j.cub.2026.06.016</a>","chicago":"Ewe, Chee Kiang, Hanna Achache, Hanna Schön, Leonid Kontorovich, Guy Teichman, Shir Weiss, Anna Mogilevskaya, et al. “Neuronal RNAi and Oxygen-Sensing Circuit Shape Germline Resilience to Heat Stress.” <i>Current Biology</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.cub.2026.06.016\">https://doi.org/10.1016/j.cub.2026.06.016</a>.","ieee":"C. K. Ewe <i>et al.</i>, “Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress,” <i>Current Biology</i>, vol. 36, no. 14. Cell Press, p. 3566–3579.e5, 2026.","short":"C.K. Ewe, H. Achache, H. Schön, L. Kontorovich, G. Teichman, S. Weiss, A. Mogilevskaya, M. Valenski, S. Anava, R. Bardapurkar, H. Gingold, R. Posner, O. Antonova, M. de Bono, Y.B. Tzur, O. Rechavi, Current Biology 36 (2026) 3566–3579.e5.","apa":"Ewe, C. K., Achache, H., Schön, H., Kontorovich, L., Teichman, G., Weiss, S., … Rechavi, O. (2026). Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2026.06.016\">https://doi.org/10.1016/j.cub.2026.06.016</a>"},"month":"07","year":"2026"},{"has_accepted_license":"1","acknowledgement":"We thank IST Austria for providing the funding. We thank IST Austria EM facility for the use of Titan Krios TEM. Data processing was performed using IST high-performance computer cluster. We thank Dr. R. Roemhild and Professor C. Guet (ISTA) for help in constructing Tat deletion strains and Dr. A. Charnagalov (ISTA) for technical help.","publication":"Molecular Cell","das_tickbox":"1","date_created":"2026-06-28T22:01:35Z","main_file_link":[{"url":"https://doi.org/10.1016/j.molcel.2026.05.026","open_access":"1"}],"oa":1,"dataavailabilitystatement":"This study did not generate new unique reagents. Strains and plasmids generated in this study are available from the lead contact without restrictions.\r\n• Source data are provided within this paper. The cryo-EM map is deposited in the Electron Microscopy Data Bank under accession number EMD-53848. The model is deposited in the Protein Data Bank under accession number 9R91. The structural data are publicly available as of the date of publication. Raw images of spot assays, SDS-PAGE and BN-PAGE gels with Coomassie staining and immunoblot images are available at Mendeley Data (https://doi.org/10.17632/v2g3p9n985.1).\r\n• This paper does not report original code.\r\n• Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","supplementarymaterial":"yes","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_updated":"2026-10-20T09:04:07Z","article_type":"original","publication_identifier":{"issn":["1097-2765"],"eissn":["1097-4164"]},"related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/the-gate-for-bulky-cargo/"}],"record":[{"relation":"research_data","id":"22189","status":"public"}]},"publisher":"Cell Press","type":"journal_article","date_published":"2026-06-22T00:00:00Z","abstract":[{"text":"How the twin-arginine translocase (Tat) system transports fully folded substrate proteins across cellular membranes without disrupting membrane integrity has been a fundamental question in cell biology for decades. The Tat system, found in prokaryotes and plant organelles, recognizes a cargo signal peptide via a conserved twin-arginine motif. The multi-subunit Tat complex facilitates the proton-motive-force-dependent translocation process, yet its overall architecture has remained unknown. Here, we present the cryo-electron microscopy (cryo-EM) structure of the Escherichia coli (E. coli) trimeric TatB₃C₃ complex with bound substrate SufI, assembled in vivo. The complex adopts an unusual, wide-open, bowl-shaped architecture with a polar inner cavity. Unexpectedly, the cargo is engaged in a dual-contact mode: while the signal peptide binds inside one TatBC unit, the folded domain docks tightly onto an adjacent unit, possibly performing a proofreading function. This structure provides a mechanistic framework for substrate engagement and suggests the direct involvement of the entire Tat complex in substrate translocation.","lang":"eng"}],"researchdata_availability":"yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Zhao, Ziyu, and Leonid A Sazanov. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo.” <i>Molecular Cell</i>. Cell Press, n.d. <a href=\"https://doi.org/10.1016/j.molcel.2026.05.026\">https://doi.org/10.1016/j.molcel.2026.05.026</a>.","ama":"Zhao Z, Sazanov LA. Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. <i>Molecular Cell</i>. doi:<a href=\"https://doi.org/10.1016/j.molcel.2026.05.026\">10.1016/j.molcel.2026.05.026</a>","apa":"Zhao, Z., &#38; Sazanov, L. A. (n.d.). Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. <i>Molecular Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molcel.2026.05.026\">https://doi.org/10.1016/j.molcel.2026.05.026</a>","ieee":"Z. Zhao and L. A. Sazanov, “Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo,” <i>Molecular Cell</i>. Cell Press.","short":"Z. Zhao, L.A. Sazanov, Molecular Cell (n.d.).","ista":"Zhao Z, Sazanov LA. Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo. Molecular Cell.","mla":"Zhao, Ziyu, and Leonid A. Sazanov. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo.” <i>Molecular Cell</i>, Cell Press, doi:<a href=\"https://doi.org/10.1016/j.molcel.2026.05.026\">10.1016/j.molcel.2026.05.026</a>."},"month":"06","title":"Structure of E. Coli twin-arginine translocase (Tat) complex with bound cargo","year":"2026","publication_status":"inpress","biorxivid":1,"department":[{"_id":"LeSa"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"day":"22","OA_type":"hybrid","OA_place":"publisher","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"external_id":{"biorxivid":["10.1101/2025.09.16.676506"]},"ddc":["570"],"fulldoi":"https://doi.org/10.1016/j.molcel.2026.05.026","_id":"22148","status":"public","quality_controlled":"1","author":[{"last_name":"Zhao","id":"a63fe682-9f3a-11ee-bf8c-cfdf919b9850","full_name":"Zhao, Ziyu","first_name":"Ziyu"},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","first_name":"Leonid A"}],"doi":"10.1016/j.molcel.2026.05.026","oa_version":"Published Version","corr_author":"1"},{"date_created":"2026-08-10T13:44:30Z","has_accepted_license":"1","acknowledgement":"I am also grateful for the financial support that made this work possible, including the\r\nEuropean Research Council (ERC Starting Grant 101041551), the Austrian Science\r\nFund (FWF, Cluster of Excellence 10.55776/COE16), the GFF Lower Austria FTI\r\nStrategy Dissertation Fellowship (FTI21-D-046), and the FENS/IBRO-PERC\r\nExchange Fellowship. ","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","type":"dissertation","related_material":{"record":[{"relation":"part_of_dissertation","id":"15016","status":"public"},{"status":"public","id":"21746","relation":"part_of_dissertation"}]},"page":"172","doi_confirm":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-082-4"]},"degree_awarded":"PhD","file":[{"date_updated":"2026-08-10T13:35:39Z","file_name":"2026_Vijatovic_David_Thesis.docx","file_id":"22669","date_created":"2026-08-10T13:35:39Z","file_size":14322760,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","creator":"dvijatov","relation":"source_file","checksum":"e3acfea4b1a3abf99e74224656740a15"},{"embargo_to":"open_access","date_created":"2026-08-12T13:44:36Z","embargo":"2027-08-10","file_name":"2026_Vijatovic_David_Thesis.pdf","file_id":"22695","date_updated":"2026-08-12T13:44:36Z","checksum":"dc8c78ae14f69e54faa41e65db5c6402","relation":"main_file","creator":"dvijatov","access_level":"closed","content_type":"application/pdf","file_size":116926375}],"date_updated":"2026-10-20T09:04:22Z","project":[{"grant_number":"101041551","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","name":"Development and Evolution of Tetrapod Motor Circuits"},{"_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis","grant_number":"FTI21-D-046"},{"grant_number":"3(GG016346-01)","name":"Development of Viral Vectors for Amphibian Gene Delivery and Manipulation","_id":"34a02c70-11ca-11ed-8bc3-fbfd2c86c88f"}],"day":"10","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"LoSw"}],"file_date_updated":"2026-08-12T13:44:36Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication_status":"published","year":"2026","title":"Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis","citation":{"ista":"Vijatovic D. 2026. Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. Institute of Science and Technology Austria.","mla":"Vijatovic, David. <i>Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22667\">10.15479/AT-ISTA-22667</a>.","short":"D. Vijatovic, Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis, Institute of Science and Technology Austria, 2026.","ieee":"D. Vijatovic, “Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis,” Institute of Science and Technology Austria, 2026.","apa":"Vijatovic, D. (2026). <i>Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22667\">https://doi.org/10.15479/AT-ISTA-22667</a>","ama":"Vijatovic D. Dissecting the molecular and functional basis of motor control in the frog Xenopus laevis. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22667\">10.15479/AT-ISTA-22667</a>","chicago":"Vijatovic, David. “Dissecting the Molecular and Functional Basis of Motor Control in the Frog Xenopus Laevis.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22667\">https://doi.org/10.15479/AT-ISTA-22667</a>."},"month":"08","date_published":"2026-08-10T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","corr_author":"1","author":[{"first_name":"David","full_name":"Vijatovic, David","id":"cf391e77-ec3c-11ea-a124-d69323410b58","orcid":"0000-0002-5494-0941","last_name":"Vijatovic"}],"_id":"22667","status":"public","doi":"10.15479/AT-ISTA-22667","fulldoi":"https://doi.org/10.15479/AT-ISTA-22667","ddc":["573"],"supervisor":[{"orcid":"0000-0001-9242-5601","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger","full_name":"Sweeney, Lora Beatrice Jaeger"}],"OA_place":"publisher","article_processing_charge":"No"},{"volume":34,"publication":"Molecular Therapy","acknowledgement":"This project was generously supported by Seedfinancing (grant no. P2282679) of the Austrian Bundesministerium für Digitalisierung und Wirtschaftsstandort and the Bundesministerium für Klimaschutz, Umwelt, Energie, Mobilität, Innovation, und Technologie, handled by the Austrian Wirtschaftsservice (aws), as well as by Life Science Call 2022 (grant no. FO999896442) of the Austrian Research Promotion Agency (FFG). We thank Mag. Michael Schunn from the PCF of the Institute of Science and Technology Austria for his continuous technical support.","date_created":"2025-12-28T23:01:26Z","issue":"1","main_file_link":[{"url":"https://doi.org/10.1101/2025.05.05.652195","open_access":"1"}],"oa":1,"dataavailabilitystatement":"The data that support the findings of this study are available on request from the corresponding authors.","supplementarymaterial":"yes","date_updated":"2026-10-20T09:03:08Z","article_type":"original","publication_identifier":{"eissn":["1525-0024"],"issn":["1525-0016"]},"page":"397-406","type":"journal_article","publisher":"Cell Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Targeted antigen delivery to immune cells, particularly dendritic cells, has emerged as a promising strategy to enhance therapeutic efficacy of vaccines, while minimizing adverse effects associated with conventional immunization. In this study, we use our previously described small glycomimetic molecule that is selectively recognized by the Langerhans cell (LC)-specific surface receptor Langerin and demonstrate specific delivery of protein antigens to these specialized dendritic cells. Our results show that Langerin-mediated antigen delivery significantly enhances the immune response in vivo, resulting in increased expansion and activation of antigen-specific T cells, compared to immunization with unmodified antigen. We demonstrate the feasibility of our LC-targeted platform for immune cell-specific immunization with protein antigen and underscore the potential of LCs as an access point for next-generation vaccines and immunotherapies."}],"date_published":"2026-01-07T00:00:00Z","researchdata_availability":"upon request","citation":{"mla":"Rica, Ramona, et al. “Langerhans Cell-Targeted Protein Delivery Enhances Antigen-Specific Cellular Immune Response.” <i>Molecular Therapy</i>, vol. 34, no. 1, Cell Press, 2026, pp. 397–406, doi:<a href=\"https://doi.org/10.1016/j.ymthe.2025.10.008\">10.1016/j.ymthe.2025.10.008</a>.","ista":"Rica R, Klein K, Johnson L, Carta G, Sarcevic M, Langer F, Rademacher C, Wawrzinek R, Quattrone F, Sparber F. 2026. Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response. Molecular Therapy. 34(1), 397–406.","chicago":"Rica, Ramona, Klara Klein, Litty Johnson, Gabriele Carta, Mirza Sarcevic, Freyja Langer, Christoph Rademacher, Robert Wawrzinek, Federica Quattrone, and Florian Sparber. “Langerhans Cell-Targeted Protein Delivery Enhances Antigen-Specific Cellular Immune Response.” <i>Molecular Therapy</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.ymthe.2025.10.008\">https://doi.org/10.1016/j.ymthe.2025.10.008</a>.","ama":"Rica R, Klein K, Johnson L, et al. Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response. <i>Molecular Therapy</i>. 2026;34(1):397-406. doi:<a href=\"https://doi.org/10.1016/j.ymthe.2025.10.008\">10.1016/j.ymthe.2025.10.008</a>","apa":"Rica, R., Klein, K., Johnson, L., Carta, G., Sarcevic, M., Langer, F., … Sparber, F. (2026). Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response. <i>Molecular Therapy</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.ymthe.2025.10.008\">https://doi.org/10.1016/j.ymthe.2025.10.008</a>","ieee":"R. Rica <i>et al.</i>, “Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response,” <i>Molecular Therapy</i>, vol. 34, no. 1. Cell Press, pp. 397–406, 2026.","short":"R. Rica, K. Klein, L. Johnson, G. Carta, M. Sarcevic, F. Langer, C. Rademacher, R. Wawrzinek, F. Quattrone, F. Sparber, Molecular Therapy 34 (2026) 397–406."},"title":"Langerhans cell-targeted protein delivery enhances antigen-specific cellular immune response","month":"01","year":"2026","publication_status":"published","department":[{"_id":"PreCl"}],"biorxivid":1,"language":[{"iso":"eng"}],"day":"07","OA_type":"green","article_processing_charge":"No","OA_place":"repository","scopus_import":"1","external_id":{"biorxivid":["10.1101/2025.05.05.652195"]},"fulldoi":"https://doi.org/10.1016/j.ymthe.2025.10.008","intvolume":"        34","doi":"10.1016/j.ymthe.2025.10.008","status":"public","_id":"20858","author":[{"last_name":"Rica","full_name":"Rica, Ramona","first_name":"Ramona"},{"last_name":"Klein","full_name":"Klein, Klara","first_name":"Klara"},{"last_name":"Johnson","full_name":"Johnson, Litty","first_name":"Litty"},{"full_name":"Carta, Gabriele","first_name":"Gabriele","last_name":"Carta"},{"last_name":"Sarcevic","full_name":"Sarcevic, Mirza","first_name":"Mirza"},{"last_name":"Langer","id":"3C1BE782-F248-11E8-B48F-1D18A9856A87","full_name":"Langer, Freyja","first_name":"Freyja"},{"first_name":"Christoph","full_name":"Rademacher, Christoph","last_name":"Rademacher"},{"first_name":"Robert","full_name":"Wawrzinek, Robert","last_name":"Wawrzinek"},{"last_name":"Quattrone","full_name":"Quattrone, Federica","first_name":"Federica"},{"first_name":"Florian","full_name":"Sparber, Florian","last_name":"Sparber"}],"quality_controlled":"1","oa_version":"Preprint"},{"OA_type":"gold","day":"15","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.17632/v2g3p9n985.1"}],"department":[{"_id":"LeSa"}],"date_created":"2026-06-29T12:54:45Z","year":"2026","month":"05","title":"Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al.","citation":{"mla":"Sazanov, Leonid A. <i>Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo. Zhao et Al.</i> Mendeley Data, 2026, doi:<a href=\"https://doi.org/10.17632/V2G3P9N985.1\">10.17632/V2G3P9N985.1</a>.","ista":"Sazanov LA. 2026. Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al., Mendeley Data, <a href=\"https://doi.org/10.17632/V2G3P9N985.1\">10.17632/V2G3P9N985.1</a>.","chicago":"Sazanov, Leonid A. “Structure of E. Coli Twin-Arginine Translocase (Tat) Complex with Bound Cargo. Zhao et Al.” Mendeley Data, 2026. <a href=\"https://doi.org/10.17632/V2G3P9N985.1\">https://doi.org/10.17632/V2G3P9N985.1</a>.","ama":"Sazanov LA. Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al. 2026. doi:<a href=\"https://doi.org/10.17632/V2G3P9N985.1\">10.17632/V2G3P9N985.1</a>","apa":"Sazanov, L. A. (2026). Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al. Mendeley Data. <a href=\"https://doi.org/10.17632/V2G3P9N985.1\">https://doi.org/10.17632/V2G3P9N985.1</a>","ieee":"L. A. Sazanov, “Structure of E. coli twin-arginine translocase (Tat) complex with bound cargo. Zhao et al.” Mendeley Data, 2026.","short":"L.A. Sazanov, (2026)."},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Raw images for SDS and Blue Native gels, western blots and spot growth assays, related to figures S1 and S2.","lang":"eng"}],"date_published":"2026-05-15T00:00:00Z","corr_author":"1","type":"research_data_reference","oa_version":"Published Version","publisher":"Mendeley Data","doi":"10.17632/V2G3P9N985.1","related_material":{"record":[{"relation":"used_in_publication","id":"22148","status":"public"}]},"_id":"22189","author":[{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A"}],"status":"public","keyword":["Protein Purification"],"fulldoi":"https://doi.org/10.17632/V2G3P9N985.1","ddc":["570"],"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)"},"date_updated":"2026-10-20T09:04:06Z","OA_place":"publisher","article_processing_charge":"No"},{"pmid":1,"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"page":"5611-5624.e4","type":"journal_article","publisher":"Cell Press","supplementarymaterial":"yes","date_updated":"2026-10-20T09:04:52Z","file":[{"relation":"main_file","creator":"dernst","checksum":"01e74f866223ca9ea8680b617d4aa4e3","file_size":5642382,"content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2026-09-24T12:35:11Z","date_updated":"2026-09-24T12:35:11Z","file_name":"2026_Cell_Barrientos.pdf","file_id":"22990"}],"article_type":"original","oa":1,"dataavailabilitystatement":"The fly line generated in this study is available from the lead contact without restriction.\r\nData and code availability\r\n•\r\nCollagen IV fluorescent timer image data and associated data analysis code have been deposited in the UCL Research Data Repository at https://doi.org/10.5522/04/32647191 and are publicly available as of the date of publication.\r\n•\r\nAll original code associated with the tissue mechanics model has also been deposited in the UCL Research Data Repository at https://doi.org/10.5522/04/32647191 and is publicly available as of the date of publication.\r\n•\r\nAll original code associated with the collagen IV network model has been deposited on Zenodo at https://doi.org/10.5281/zenodo.20719515 and is publicly available as of the date of publication.\r\n•\r\nAny additional information reported in this paper is available from the lead contact upon request.","ec_funded":1,"volume":189,"das_tickbox":"1","publication":"Cell","acknowledgement":"We thank all members of the Mao lab for insightful discussions throughout the project, and we thank Giulia Paci and Nargess Khalilgharibi for critical reading of the manuscript. We thank Jonathan Chubb for molecular biology guidance and WellGenetics for generating the timer protein fly lines.\r\nR.B. was funded by a UCL COMPLEX PhD studentship and a Leverhulme Trust project grant RPG-2020-068 awarded to Y.M. B.M. and A.S. were funded by the European Union Horizon 2020 research and innovation programme (ERC starting grant no. 802960). S.B. was funded by NIH R35 GM143042. G.C. was funded by EPSRC Physics of Life, grants EP/W023806 and EP/W023865. B.J.S.S. and B.M.S. are funded by the Wellcome Trust (grant no. 301803/Z/23/Z to B.M.S.). E.K.P. was funded by the Medical Research Council UK (MRC programme award MC_UU_12018/5). Y.M. was funded by MRC award MR/W027437/1, a Lister Institute Research Prize, and the EMBO Young Investigator Programme.","has_accepted_license":"1","date_created":"2026-09-17T11:06:06Z","issue":"18","ddc":["570"],"fulldoi":"https://doi.org/10.1016/j.cell.2026.07.010","doi":"10.1016/j.cell.2026.07.010","intvolume":"       189","_id":"22955","status":"public","author":[{"last_name":"Barrientos","first_name":"Ricardo","full_name":"Barrientos, Ricardo"},{"full_name":"Meadowcroft, Billie","first_name":"Billie","last_name":"Meadowcroft","orcid":"0000-0003-3441-1337","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1"},{"full_name":"Sánchez-Sánchez, Besaiz J.","first_name":"Besaiz J.","last_name":"Sánchez-Sánchez"},{"last_name":"Stramer","first_name":"Brian M.","full_name":"Stramer, Brian M."},{"first_name":"Ewa K.","full_name":"Paluch, Ewa K.","last_name":"Paluch"},{"first_name":"Guillaume","full_name":"Charras, Guillaume","last_name":"Charras"},{"last_name":"Banerjee","full_name":"Banerjee, Shiladitya","first_name":"Shiladitya"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"},{"last_name":"Mao","first_name":"Yanlan","full_name":"Mao, Yanlan"}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","OA_place":"publisher","PlanS_conform":"1","scopus_import":"1","external_id":{"pmid":["42532043"]},"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)"},"publication_status":"published","file_date_updated":"2026-09-24T12:35:11Z","department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"day":"03","project":[{"call_identifier":"H2020","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","researchdata_availability":"no","abstract":[{"lang":"eng","text":"The regulation of 3D cell shape is a fundamental problem of life. In multicellular tissues, cell shape emerges through the balance of forces inside and outside the cell. In epithelia, the basement membrane (BM) is the first extracellular barrier that cells sense biochemically and mechanically. Despite this, little is known about how BM mechanical properties are regulated and how they impact cell shape. Through mathematical modeling, we show that the stress relaxation time of the BM can regulate cell shape. Using molecular dynamics simulations, we show that the stress relaxation time of a collagen IV network can be inferred from the lifetime of collagen IV molecules. To measure collagen IV lifetime in vivo, we develop a fluorescent timer reporter for collagen IV and show that perlecan modifies collagen IV lifetime. This cross-disciplinary approach establishes a multiscale framework to probe matrix turnover, and its regulation and function in cell shape control."}],"date_published":"2026-09-03T00:00:00Z","citation":{"mla":"Barrientos, Ricardo, et al. “Basement Membrane Turnover Controls Cell Shape.” <i>Cell</i>, vol. 189, no. 18, Cell Press, 2026, p. 5611–5624.e4, doi:<a href=\"https://doi.org/10.1016/j.cell.2026.07.010\">10.1016/j.cell.2026.07.010</a>.","ista":"Barrientos R, Meadowcroft B, Sánchez-Sánchez BJ, Stramer BM, Paluch EK, Charras G, Banerjee S, Šarić A, Mao Y. 2026. Basement membrane turnover controls cell shape. Cell. 189(18), 5611–5624.e4.","ieee":"R. Barrientos <i>et al.</i>, “Basement membrane turnover controls cell shape,” <i>Cell</i>, vol. 189, no. 18. Cell Press, p. 5611–5624.e4, 2026.","short":"R. Barrientos, B. Meadowcroft, B.J. Sánchez-Sánchez, B.M. Stramer, E.K. Paluch, G. Charras, S. Banerjee, A. Šarić, Y. Mao, Cell 189 (2026) 5611–5624.e4.","apa":"Barrientos, R., Meadowcroft, B., Sánchez-Sánchez, B. J., Stramer, B. M., Paluch, E. K., Charras, G., … Mao, Y. (2026). Basement membrane turnover controls cell shape. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2026.07.010\">https://doi.org/10.1016/j.cell.2026.07.010</a>","ama":"Barrientos R, Meadowcroft B, Sánchez-Sánchez BJ, et al. Basement membrane turnover controls cell shape. <i>Cell</i>. 2026;189(18):5611-5624.e4. doi:<a href=\"https://doi.org/10.1016/j.cell.2026.07.010\">10.1016/j.cell.2026.07.010</a>","chicago":"Barrientos, Ricardo, Billie Meadowcroft, Besaiz J. Sánchez-Sánchez, Brian M. Stramer, Ewa K. Paluch, Guillaume Charras, Shiladitya Banerjee, Anđela Šarić, and Yanlan Mao. “Basement Membrane Turnover Controls Cell Shape.” <i>Cell</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.cell.2026.07.010\">https://doi.org/10.1016/j.cell.2026.07.010</a>."},"title":"Basement membrane turnover controls cell shape","month":"09","year":"2026"},{"publication_identifier":{"eissn":["1934-6069"],"issn":["1931-3128"]},"pmid":1,"publisher":"Cell Press","type":"journal_article","page":"978-980","date_updated":"2026-10-20T09:04:35Z","article_type":"original","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) (10.55776/PAT1617625).","das_tickbox":"1","publication":"Cell Host & Microbe","volume":34,"issue":"6","date_created":"2026-06-14T22:01:42Z","fulldoi":"https://doi.org/10.1016/j.chom.2026.05.013","oa_version":"None","corr_author":"1","author":[{"last_name":"Williams-Jones","id":"128eaab9-b327-11f0-bdbe-e02d5abac73b","full_name":"Williams-Jones, Daniel","first_name":"Daniel"},{"orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly"}],"_id":"21996","quality_controlled":"1","status":"public","intvolume":"        34","doi":"10.1016/j.chom.2026.05.013","scopus_import":"1","article_processing_charge":"No","external_id":{"pmid":["42269584"]},"department":[{"_id":"JaBr"}],"publication_status":"published","OA_type":"closed access","project":[{"name":"Search & Destroy: Mechanisms of anti-plasmid immunity","_id":"9f295cab-ad08-11f1-bc83-9e197d0f6d50","grant_number":"PAT1617625"}],"day":"10","language":[{"iso":"eng"}],"title":"NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back","month":"06","citation":{"ama":"Williams-Jones D, Bravo JPK. NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. <i>Cell Host &#38; Microbe</i>. 2026;34(6):978-980. doi:<a href=\"https://doi.org/10.1016/j.chom.2026.05.013\">10.1016/j.chom.2026.05.013</a>","chicago":"Williams-Jones, Daniel, and Jack Peter Kelly Bravo. “NAD to the Bone: How Bacteria Put Phages under ARES-t … and How Phages Fight Back.” <i>Cell Host &#38; Microbe</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.chom.2026.05.013\">https://doi.org/10.1016/j.chom.2026.05.013</a>.","apa":"Williams-Jones, D., &#38; Bravo, J. P. K. (2026). NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. <i>Cell Host &#38; Microbe</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.chom.2026.05.013\">https://doi.org/10.1016/j.chom.2026.05.013</a>","short":"D. Williams-Jones, J.P.K. Bravo, Cell Host &#38; Microbe 34 (2026) 978–980.","ieee":"D. Williams-Jones and J. P. K. Bravo, “NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back,” <i>Cell Host &#38; Microbe</i>, vol. 34, no. 6. Cell Press, pp. 978–980, 2026.","mla":"Williams-Jones, Daniel, and Jack Peter Kelly Bravo. “NAD to the Bone: How Bacteria Put Phages under ARES-t … and How Phages Fight Back.” <i>Cell Host &#38; Microbe</i>, vol. 34, no. 6, Cell Press, 2026, pp. 978–80, doi:<a href=\"https://doi.org/10.1016/j.chom.2026.05.013\">10.1016/j.chom.2026.05.013</a>.","ista":"Williams-Jones D, Bravo JPK. 2026. NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back. Cell Host &#38; Microbe. 34(6), 978–980."},"date_published":"2026-06-10T00:00:00Z","abstract":[{"text":"In this issue of Cell Host & Microbe, Osterman et al. discover aRES,1 a new family of bacterial immune proteins that deplete cellular NAD+, generating cleavage products that cannot be utilized by canonical phage NAD+ regeneration pathways. They identify the invader-specific trigger for aRES and characterize two distinct evolutionary countermeasures employed by phages to resist aRES.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2026"},{"oa":1,"date_created":"2026-06-21T22:03:01Z","ec_funded":1,"volume":2,"das_tickbox":"0","publication":"Proceedings of the 18th International Conference on Agents and Artificial Intelligence","acknowledgement":"This work has been supported by the European Research\r\nCouncil under Grant No.: ERC-2020-AdG\r\n101020093. We thank Brian Subirana for the original\r\nideation of the concept of forgetting neural networks\r\nand his belief in their potential.","has_accepted_license":"1","page":"1536-1546","keyword":["Machine Unlearning","Neuroscience-Inspired Machine Learning","Membership Inference Attacks"],"type":"conference","publisher":"Science and Technology Publications","publication_identifier":{"issn":["2184-3589"],"eissn":["2184-433X"],"isbn":["9789897587962"]},"file":[{"relation":"main_file","creator":"dernst","checksum":"d0f5212846c8f3129509b081648465cb","file_size":779692,"content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2026-10-20T14:00:27Z","date_updated":"2026-10-20T14:00:27Z","file_id":"23178","file_name":"2026_CAART_Hatua.pdf"}],"supplementarymaterial":"no","date_updated":"2026-10-20T14:05:02Z","day":"01","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"OA_type":"green","publication_status":"published","file_date_updated":"2026-10-20T14:00:27Z","department":[{"_id":"ToHe"}],"year":"2026","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","researchdata_availability":"no","abstract":[{"lang":"eng","text":" Modern computer systems store vast amounts of personal data, enabling advances in AI and ML but risking user privacy and trust. For privacy reasons, it is sometimes desired for an ML model to forget part of the data it was trained on. In this paper, we introduce a novel unlearning approach based on Forgetting Neural Networks (FNNs), a neuroscience-inspired architecture that explicitly encodes forgetting through multiplicative decay factors. While FNNs had previously been studied as a theoretical construct, we provide the first concrete implementation and demonstrate their effectiveness for targeted unlearning. We propose several variants with per-neuron forgetting factors, including rank-based assignments guided by activation levels, and evaluate them on MNIST and Fashion-MNIST benchmarks. Our method systematically removes information associated with forget sets while preserving performance on retained data. Membership inference attacks confirm the effectiveness of FNN-based unlearning in erasing information about the training data from the neural network. These results establish FNNs as a promising foundation for efficient and interpretable unlearning."}],"date_published":"2026-04-01T00:00:00Z","month":"04","citation":{"ama":"Hatua A, Nguyen TT, Cano Cordoba F, Sung AH. Machine unlearning using forgetting neural networks. In: <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>. Vol 2. Science and Technology Publications; 2026:1536-1546. doi:<a href=\"https://doi.org/10.5220/0014326500004052\">10.5220/0014326500004052</a>","chicago":"Hatua, Amartya, Trung T. Nguyen, Filip Cano Cordoba, and Andrew H. Sung. “Machine Unlearning Using Forgetting Neural Networks.” In <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, 2:1536–46. Science and Technology Publications, 2026. <a href=\"https://doi.org/10.5220/0014326500004052\">https://doi.org/10.5220/0014326500004052</a>.","ieee":"A. Hatua, T. T. Nguyen, F. Cano Cordoba, and A. H. Sung, “Machine unlearning using forgetting neural networks,” in <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, Marbella, Spain, 2026, vol. 2, pp. 1536–1546.","apa":"Hatua, A., Nguyen, T. T., Cano Cordoba, F., &#38; Sung, A. H. (2026). Machine unlearning using forgetting neural networks. In <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i> (Vol. 2, pp. 1536–1546). Marbella, Spain: Science and Technology Publications. <a href=\"https://doi.org/10.5220/0014326500004052\">https://doi.org/10.5220/0014326500004052</a>","short":"A. Hatua, T.T. Nguyen, F. Cano Cordoba, A.H. Sung, in:, Proceedings of the 18th International Conference on Agents and Artificial Intelligence, Science and Technology Publications, 2026, pp. 1536–1546.","ista":"Hatua A, Nguyen TT, Cano Cordoba F, Sung AH. 2026. Machine unlearning using forgetting neural networks. Proceedings of the 18th International Conference on Agents and Artificial Intelligence. ICAART: International Conference on Agents and Artificial Intelligence vol. 2, 1536–1546.","mla":"Hatua, Amartya, et al. “Machine Unlearning Using Forgetting Neural Networks.” <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, vol. 2, Science and Technology Publications, 2026, pp. 1536–46, doi:<a href=\"https://doi.org/10.5220/0014326500004052\">10.5220/0014326500004052</a>."},"title":"Machine unlearning using forgetting neural networks","doi":"10.5220/0014326500004052","intvolume":"         2","_id":"22104","quality_controlled":"1","author":[{"first_name":"Amartya","full_name":"Hatua, Amartya","last_name":"Hatua"},{"full_name":"Nguyen, Trung T.","first_name":"Trung T.","last_name":"Nguyen"},{"first_name":"Filip","full_name":"Cano Cordoba, Filip","orcid":"0000-0002-0783-904X","id":"708cad98-e86a-11ef-8098-bdae2d7c6af1","last_name":"Cano Cordoba"},{"full_name":"Sung, Andrew H.","first_name":"Andrew H.","last_name":"Sung"}],"status":"public","oa_version":"Published Version","ddc":["000"],"fulldoi":"https://doi.org/10.5220/0014326500004052","conference":{"end_date":"2026-03-08","location":"Marbella, Spain","start_date":"2026-03-05","name":"ICAART: International Conference on Agents and Artificial Intelligence"},"external_id":{"arxiv":["2410.22374"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","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"},"OA_place":"repository","article_processing_charge":"No","arxiv":1,"scopus_import":"1"},{"corr_author":"1","oa_version":"Preprint","doi":"10.48550/arXiv.2607.05848","_id":"22359","status":"public","author":[{"full_name":"Lee, Jaehun","first_name":"Jaehun","last_name":"Lee","id":"96155047-f36a-11ef-b766-8b5ae7cecd49"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"}],"fulldoi":"https://doi.org/10.48550/arXiv.2607.05848","external_id":{"arxiv":["2607.05848"]},"article_number":"2607.05848","article_processing_charge":"No","OA_place":"repository","arxiv":1,"OA_type":"green","day":"07","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"department":[{"_id":"LaEr"}],"publication_status":"submitted","year":"2026","month":"07","title":"Mesoscopic eigenvalue statistics for correlated random matrices","citation":{"ieee":"J. Lee and L. Erdös, “Mesoscopic eigenvalue statistics for correlated random matrices,” <i>arXiv</i>. .","apa":"Lee, J., &#38; Erdös, L. (n.d.). Mesoscopic eigenvalue statistics for correlated random matrices. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2607.05848\">https://doi.org/10.48550/arXiv.2607.05848</a>","short":"J. Lee, L. Erdös, ArXiv (n.d.).","ama":"Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2607.05848\">10.48550/arXiv.2607.05848</a>","chicago":"Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2607.05848\">https://doi.org/10.48550/arXiv.2607.05848</a>.","mla":"Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices.” <i>ArXiv</i>, 2607.05848, doi:<a href=\"https://doi.org/10.48550/arXiv.2607.05848\">10.48550/arXiv.2607.05848</a>.","ista":"Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. arXiv, 2607.05848."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-07-07T00:00:00Z","abstract":[{"lang":"eng","text":"We prove a mesoscopic central limit theorem for linear eigenvalue statistics of correlated Hermitian random matrices. The class considered here includes Wigner and Wigner-type matrices, as well as models whose entry correlations decay polynomially in the distance between index pairs. The proof combines a multivariate cumulant expansion with multi-resolvent local laws and a detailed analysis of the resulting variance kernel on the operator-level."}],"type":"preprint","keyword":["Central limit theorem","universality","matrix Dyson equation","multi-resolvent local law"],"date_updated":"2026-10-20T10:06:12Z","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2607.05848","open_access":"1"}],"date_created":"2026-07-18T08:59:02Z","publication":"arXiv","das_tickbox":"1","acknowledgement":"Supported by ERC Advanced Grant “RMTBeyond” No. 101020331","ec_funded":1},{"fulldoi":"https://doi.org/10.1051/0004-6361/202558103","ddc":["520"],"oa_version":"Published Version","intvolume":"       710","doi":"10.1051/0004-6361/202558103","author":[{"last_name":"Marcel","first_name":"G.","full_name":"Marcel, G."},{"last_name":"Turner","full_name":"Turner, S. G. D.","first_name":"S. G. D."},{"last_name":"Ricketts","first_name":"B. J.","full_name":"Ricketts, B. J."},{"last_name":"López-Barquero","first_name":"V.","full_name":"López-Barquero, V."},{"first_name":"D. J. K.","full_name":"Buisson, D. J. K.","last_name":"Buisson"},{"last_name":"Vincentelli","first_name":"F.","full_name":"Vincentelli, F."},{"full_name":"Middleton, M.","first_name":"M.","last_name":"Middleton"},{"last_name":"Reynolds","first_name":"C.S.","full_name":"Reynolds, C.S."},{"first_name":"Mark","full_name":"Avara, Mark","id":"c9b42585-7787-11f0-9bdd-bf7d947cf79d","last_name":"Avara"}],"_id":"22381","quality_controlled":"1","status":"public","scopus_import":"1","PlanS_conform":"1","OA_place":"publisher","article_processing_charge":"No","arxiv":1,"external_id":{"arxiv":["2511.10474"]},"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)"},"article_number":"A387","department":[{"_id":"ZoHa"}],"file_date_updated":"2026-07-21T12:20:49Z","publication_status":"published","OA_type":"diamond","day":"01","language":[{"iso":"eng"}],"month":"06","citation":{"ista":"Marcel G, Turner SGD, Ricketts BJ, López-Barquero V, Buisson DJK, Vincentelli F, Middleton M, Reynolds CS, Avara M. 2026. Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations. Astronomy &#38; Astrophysics. 710, A387.","mla":"Marcel, G., et al. “Disk Warping and Black Hole X-Ray Binaries: I. Tentative Unification of Low-Frequency Quasi-Periodic Oscillations.” <i>Astronomy &#38; Astrophysics</i>, vol. 710, A387, EDP Sciences, 2026, doi:<a href=\"https://doi.org/10.1051/0004-6361/202558103\">10.1051/0004-6361/202558103</a>.","ieee":"G. Marcel <i>et al.</i>, “Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations,” <i>Astronomy &#38; Astrophysics</i>, vol. 710. EDP Sciences, 2026.","apa":"Marcel, G., Turner, S. G. D., Ricketts, B. J., López-Barquero, V., Buisson, D. J. K., Vincentelli, F., … Avara, M. (2026). Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202558103\">https://doi.org/10.1051/0004-6361/202558103</a>","short":"G. Marcel, S.G.D. Turner, B.J. Ricketts, V. López-Barquero, D.J.K. Buisson, F. Vincentelli, M. Middleton, C.S. Reynolds, M. Avara, Astronomy &#38; Astrophysics 710 (2026).","chicago":"Marcel, G., S. G. D. Turner, B. J. Ricketts, V. López-Barquero, D. J. K. Buisson, F. Vincentelli, M. Middleton, C.S. Reynolds, and Mark Avara. “Disk Warping and Black Hole X-Ray Binaries: I. Tentative Unification of Low-Frequency Quasi-Periodic Oscillations.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2026. <a href=\"https://doi.org/10.1051/0004-6361/202558103\">https://doi.org/10.1051/0004-6361/202558103</a>.","ama":"Marcel G, Turner SGD, Ricketts BJ, et al. Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations. <i>Astronomy &#38; Astrophysics</i>. 2026;710. doi:<a href=\"https://doi.org/10.1051/0004-6361/202558103\">10.1051/0004-6361/202558103</a>"},"title":"Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","researchdata_availability":"no","date_published":"2026-06-01T00:00:00Z","abstract":[{"text":"Context. X-ray binaries exhibit complex variability patterns studied in the power spectrum. These include the broadband noise (BBN)\r\ncomponents and various types of narrow components called quasi-periodic oscillations (QPOs). There is currently no consensus about\r\nwhat determines the presence or absence of the BBN or what generates the QPOs. Many believe that QPO generation is due to framedragging effects caused by Lense–Thirring torques.\r\nAims. We investigated the potential impact of frame-dragging effects on the accretion disk itself. In particular, we focused on its\r\nimpact on the observed variability and on the presence (and types) of associated QPOs.\r\nMethods. We made analytical estimates to assess the potential presence of a geometric warp in the inner accretion disk during state\r\ntransitions.\r\nResults. We show that the presence of a warp can modify the spectral-timing properties in a way that matches the observed transition\r\nbetween QPO types during outbursts. We also discuss the peculiar case of Cyg X-1, as well as how the hard-to-soft transition could\r\nbe driven by the warp itself.\r\nConclusions. The (expected) emergence of a warp provides a consistent explanation for the evolution of both the BBN and the QPO\r\nproperties during state transitions. This offers a first path toward unifying the variability of black hole X-ray binaries.","lang":"eng"}],"year":"2026","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"type":"journal_article","publisher":"EDP Sciences","date_updated":"2026-10-21T06:33:09Z","supplementarymaterial":"yes","article_type":"original","file":[{"file_id":"22382","file_name":"2026_AstronomyAstrophysics_Marcel.pdf","date_updated":"2026-07-21T12:20:49Z","date_created":"2026-07-21T12:20:49Z","success":1,"access_level":"open_access","content_type":"application/pdf","file_size":3286905,"checksum":"95c1695f3c7183b2ad9d58167500b18d","relation":"main_file","creator":"dernst"}],"oa":1,"das_tickbox":"0","publication":"Astronomy & Astrophysics","acknowledgement":"GM acknowledges support from the Polish National Science Center grant 2023/48/Q/ST9/00138 and the Academy of Finland grant 355672. The authors thank the Editor for their insightful comments and effective stewardship of the review process. SGDT acknowledges support under\r\nSTFC Grant ST/X001113/1. This work made use of the python packages\r\nMatplotlib (Hunter 2007), NumPy (Harris et al. 2020), and Stingray v2.2\r\n(Huppenkothen et al. 2019; Bachetti et al. 2024b,a).","has_accepted_license":"1","volume":710,"date_created":"2026-07-21T10:29:36Z"},{"date_created":"2026-07-25T13:08:32Z","has_accepted_license":"1","das_tickbox":"0","alternative_title":["ISTA Master’s Thesis"],"file":[{"embargo_to":"open_access","date_created":"2026-07-27T13:00:07Z","date_updated":"2026-10-20T08:47:40Z","file_name":"Aleksa_Spasic_Thesis_final.pdf","file_id":"22588","embargo":"2027-07-30","creator":"aspasic","relation":"main_file","checksum":"c29880dd71fcc37f23ac6e2843066ede","content_type":"application/pdf","file_size":1986078,"access_level":"closed"},{"creator":"aspasic","relation":"source_file","checksum":"4ebe3bd2d833d913c0756343cca5e5f0","file_size":1868853,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_created":"2026-07-27T13:00:22Z","date_updated":"2026-07-27T13:07:23Z","file_id":"22589","file_name":"Thesis_final.docx"}],"date_updated":"2026-10-21T07:47:08Z","publisher":"Institute of Science and Technology Austria","type":"dissertation","page":"32","publication_identifier":{"issn":["2791-4585"]},"doi_confirm":"1","degree_awarded":"MS","year":"2026","title":"Studying the evolutionary systems biology of the lac operon","month":"07","citation":{"ama":"Spasić A. Studying the evolutionary systems biology of the lac operon. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22399\">10.15479/AT-ISTA-22399</a>","chicago":"Spasić, Aleksa. “Studying the Evolutionary Systems Biology of the Lac Operon.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22399\">https://doi.org/10.15479/AT-ISTA-22399</a>.","apa":"Spasić, A. (2026). <i>Studying the evolutionary systems biology of the lac operon</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22399\">https://doi.org/10.15479/AT-ISTA-22399</a>","ieee":"A. Spasić, “Studying the evolutionary systems biology of the lac operon,” Institute of Science and Technology Austria, 2026.","short":"A. Spasić, Studying the Evolutionary Systems Biology of the Lac Operon, Institute of Science and Technology Austria, 2026.","mla":"Spasić, Aleksa. <i>Studying the Evolutionary Systems Biology of the Lac Operon</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22399\">10.15479/AT-ISTA-22399</a>.","ista":"Spasić A. 2026. Studying the evolutionary systems biology of the lac operon. Institute of Science and Technology Austria."},"date_published":"2026-07-27T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"27","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"GaTk"},{"_id":"CaGu"}],"file_date_updated":"2026-10-20T08:47:40Z","publication_status":"published","article_processing_charge":"No","OA_place":"publisher","oa_version":"Published Version","corr_author":"1","_id":"22399","author":[{"first_name":"Aleksa","full_name":"Spasić, Aleksa","id":"ecee9d38-4040-11ef-8843-b941efb445d6","last_name":"Spasić"}],"status":"public","doi":"10.15479/AT-ISTA-22399","fulldoi":"https://doi.org/10.15479/AT-ISTA-22399","ddc":["576"],"supervisor":[{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"}]},{"fulldoi":"https://doi.org/10.15479/AT-ISTA-22281","ddc":["000"],"supervisor":[{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H"}],"oa_version":"Published Version","corr_author":"1","status":"public","_id":"22281","author":[{"orcid":"0000-0003-4268-7368","id":"888a098e-fcac-11ee-aff7-d347be57b725","last_name":"El-Hayek","first_name":"Antoine","full_name":"El-Hayek, Antoine"}],"doi":"10.15479/AT-ISTA-22281","article_processing_charge":"No","OA_place":"publisher","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)"},"file_date_updated":"2026-07-20T11:29:38Z","department":[{"_id":"GradSch"},{"_id":"MoHe"}],"publication_status":"published","project":[{"name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","grant_number":"101019564"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775"}],"day":"13","language":[{"iso":"eng"}],"month":"07","title":"Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks","citation":{"mla":"El-Hayek, Antoine. <i>Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22281\">10.15479/AT-ISTA-22281</a>.","ista":"El-Hayek A. 2026. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. Institute of Science and Technology Austria.","chicago":"El-Hayek, Antoine. “Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22281\">https://doi.org/10.15479/AT-ISTA-22281</a>.","ama":"El-Hayek A. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22281\">10.15479/AT-ISTA-22281</a>","apa":"El-Hayek, A. (2026). <i>Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22281\">https://doi.org/10.15479/AT-ISTA-22281</a>","short":"A. El-Hayek, Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks, Institute of Science and Technology Austria, 2026.","ieee":"A. El-Hayek, “Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks,” Institute of Science and Technology Austria, 2026."},"date_published":"2026-07-13T00:00:00Z","abstract":[{"lang":"eng","text":"In this thesis, we took a look at networks, and more specifically, at networks that change over time, whether those are networks in the distributed algorithms sense of the word, or the graph algorithm sense. \r\n\r\nIn distributed algorithms, we looked at two main problems. First, the broadcast problem: given n agents, each agent is tasked to forward a (unique) message to every other agent. Agents collaborate and can copy and forward all messages they have received up until that point. Broadcast is achieved when one agent has successfully broadcast its message to everyone else. We studied the case where the communication network is controlled by an adversary, under the condition that the graph is rooted in every round of communication. We show that the adversary can delay broadcast for at most  l\r\n(1 + √\r\n2)n\r\nm\r\n rounds, improving on the $O(n\\log\\log n)$ previous upper bound~\\cite{fugger2020radius}, and asymptotically matching the $\\sim 1.5n$ lower bound~\\cite{schwarz2017linear}.\r\n\r\nWe then looked at the stochastic version of the problem: here, the adversary -- parametrized by $k$ where $k=0$ signifies that the adversary has no control,  and $k=n$ that the adversary has full control -- can choose parts of the graph, and the graph is then completed stochastically. Here, we are able to look at a stronger version of broadcast: instead of having $n$ messages trying to be broadcast in parallel, we can assume that only one message needs to be broadcasted. We show the bound $\\Theta(k+\\log n)$.\r\n\r\nThen, we looked at undecided states dynamics in population protocols: given a population of $n$ agents, where each initially holds an opinion among $k$ different ones. In each round, two agents are chosen uniformly at random, and can interact. If they have different opinions, they forget their opinions and become undecided. If one of them is undecided while the other has an opinion, they undecided agent copies they opinion of the decided one. The question is then, how many interactions does it take for the whole population to share the same opinion? We show a $\\Omega(kn\\log \\frac {\\sqrt n} {k \\log n})$ lower bound  for any $k = o\\left(\\frac {\\sqrt n}{\\log n}\\right)$.\r\nThis is tight for any $ k \\le n^{\\frac 1 2 - \\epsilon}$, where $\\epsilon >0$ can be any small constant, matching the known $O(kn\\log n)$ upper bound for $k = O\\left(\\frac {\\sqrt n} {\\log ^2 n}\\right)$~\\cite{DBLP:conf/podc/AmirABBHKL23}.\r\n\r\nFinally, in dynamic algorithms, we study the minimum cut problem: we are given a graph, whose vertex set we want to partition into two subsets such that the number of edges crossing from one subset to the other is minimized. Then, the graph can be updated via edge insertions or deletions, and we must update the solution without recomputing everything from scratch. We present an exact fully-dynamic minimum cut algorithm that runs in $n^{o(1)}$ deterministic update time when the minimum cut size is at most $2^{\\Theta(\\log^{3/4-c}n)}$ for any $c>0$, improving on the previous algorithm~\\cite{DBLP:conf/soda/JinST24} whose minimum cut size limit is $(\\log n)^{o(1)}$. Using sparsification and randomization techniques, we are able to extend this to all values of the minimum cut in weighted graphs, at the cost of a $(1+o(1))$-approximation ratio."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2026","doi_confirm":"1","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","type":"dissertation","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"20051"},{"id":"19982","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"21720","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"22374"},{"status":"public","id":"22373","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"18557"}]},"page":"244","date_updated":"2026-10-21T08:05:35Z","publisher_comment":"Sections 2.4 and 7.1 and chapter 6 are not CC-BY 4.0, they are All Rights Reserved.","file":[{"date_updated":"2026-07-17T11:39:47Z","file_name":"2026_El-Hayek_Antoine_Thesis.pdf","file_id":"22356","date_created":"2026-07-17T11:39:47Z","file_size":5465973,"content_type":"application/pdf","success":1,"access_level":"open_access","relation":"main_file","creator":"aelhayek","checksum":"923e4ca769c9ef2f6b0b005444faf462"},{"checksum":"262689f9df27dd6c2c7c7861f1de7329","creator":"aelhayek","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_size":9116107,"date_created":"2026-07-17T11:40:34Z","file_name":"2026_El-Hayek_Antoine_Thesis.zip","file_id":"22357","date_updated":"2026-07-20T11:29:38Z"}],"oa":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct, No. 101019564)\r\n\"The Design and Evaluation of Modern Fully Dynamic Data Structures\" , from the\r\nAustrian Science Fund (FWF) grant DOI 10.55776/I5982 \"Static and Dynamic Hierarchical\r\nGraph Decompositions\", and from the Austrian Science Fund (FWF) and netIDEE SCIENCE\r\nproject P 33775-N, \"Fast Algorithms for a Reactive Network Layer\".\r\n","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"ec_funded":1,"date_created":"2026-07-13T09:39:59Z"}]