[{"_id":"14786","publication_status":"published","publication":"Science of The Total Environment","doi":"10.1016/j.scitotenv.2023.164010","abstract":[{"text":"Acanthocephalans, intestinal parasites of vertebrates, are characterised by orders of magnitude higher metal accumulation than free-living organisms, but the mechanism of such effective metal accumulation is still unknown. The aim of our study was to gain new insights into the high-resolution localization of elements in the bodies of acanthocephalans, thus taking an initial step towards elucidating metal uptake and accumulation in organisms under real environmental conditions. For the first time, nanoscale secondary ion mass spectrometry (NanoSIMS) was used for high-resolution mapping of 12 elements (C, Ca, Cu, Fe, N, Na, O, P, Pb, S, Se, and Tl) in three selected body parts (trunk spines, inner part of the proboscis receptacle and inner surface of the tegument) of Dentitruncus truttae, a parasite of brown trout (Salmo trutta) from the Krka River in Croatia. In addition, the same body parts were examined using transmission electron microscopy (TEM) and correlated with NanoSIMS images. Metal concentrations determined using HR ICP-MS confirmed higher accumulation in D. truttae than in the fish intestine. The chemical composition of the acanthocephalan body showed the highest density of C, Ca, N, Na, O, S, as important and constitutive elements in living cells in all studied structures, while Fe was predominant among trace elements. In general, higher element density was found in trunk spines and tegument, as body structures responsible for substance absorption in parasites. The results obtained with NanoSIMS and TEM-NanoSIMS correlative imaging represent pilot data for mapping of elements at nanoscale resolution in the ultrastructure of various body parts of acanthocephalans and generally provide a contribution for further application of this technique in all parasite species.","lang":"eng"}],"volume":887,"quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"pmid":1,"main_file_link":[{"open_access":"1","url":"https://hal.science/hal-04296657/document"}],"day":"20","type":"journal_article","year":"2023","oa_version":"Submitted Version","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.scitotenv.2023.164010","article_number":"164010","status":"public","OA_type":"green","intvolume":"       887","date_published":"2023-08-20T00:00:00Z","month":"08","date_updated":"2025-04-24T11:35:33Z","author":[{"last_name":"Filipović Marijić","full_name":"Filipović Marijić, Vlatka","first_name":"Vlatka"},{"last_name":"Subirana","full_name":"Subirana, Maria Angels","first_name":"Maria Angels"},{"first_name":"Dirk","full_name":"Schaumlöffel, Dirk","last_name":"Schaumlöffel"},{"last_name":"Barišić","first_name":"Josip","full_name":"Barišić, Josip"},{"last_name":"Gontier","first_name":"Etienne","full_name":"Gontier, Etienne"},{"last_name":"Krasnici","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","first_name":"Nesrete","full_name":"Krasnici, Nesrete"},{"first_name":"Tatjana","full_name":"Mijošek, Tatjana","last_name":"Mijošek"},{"last_name":"Hernández-Orts","full_name":"Hernández-Orts, Jesús S.","first_name":"Jesús S."},{"full_name":"Scholz, Tomáš","first_name":"Tomáš","last_name":"Scholz"},{"full_name":"Erk, Marijana","first_name":"Marijana","last_name":"Erk"}],"citation":{"short":"V. Filipović Marijić, M.A. Subirana, D. Schaumlöffel, J. Barišić, E. Gontier, N. Krasnici, T. Mijošek, J.S. Hernández-Orts, T. Scholz, M. Erk, Science of The Total Environment 887 (2023).","ieee":"V. Filipović Marijić <i>et al.</i>, “First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS,” <i>Science of The Total Environment</i>, vol. 887. Elsevier, 2023.","ista":"Filipović Marijić V, Subirana MA, Schaumlöffel D, Barišić J, Gontier E, Krasnici N, Mijošek T, Hernández-Orts JS, Scholz T, Erk M. 2023. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. 887, 164010.","chicago":"Filipović Marijić, Vlatka, Maria Angels Subirana, Dirk Schaumlöffel, Josip Barišić, Etienne Gontier, Nesrete Krasnici, Tatjana Mijošek, Jesús S. Hernández-Orts, Tomáš Scholz, and Marijana Erk. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” <i>Science of The Total Environment</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">https://doi.org/10.1016/j.scitotenv.2023.164010</a>.","ama":"Filipović Marijić V, Subirana MA, Schaumlöffel D, et al. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. <i>Science of The Total Environment</i>. 2023;887. doi:<a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">10.1016/j.scitotenv.2023.164010</a>","mla":"Filipović Marijić, Vlatka, et al. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” <i>Science of The Total Environment</i>, vol. 887, 164010, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">10.1016/j.scitotenv.2023.164010</a>.","apa":"Filipović Marijić, V., Subirana, M. A., Schaumlöffel, D., Barišić, J., Gontier, E., Krasnici, N., … Erk, M. (2023). First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. <i>Science of The Total Environment</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">https://doi.org/10.1016/j.scitotenv.2023.164010</a>"},"OA_place":"repository","date_created":"2024-01-10T10:43:08Z","language":[{"iso":"eng"}],"keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"publication_identifier":{"issn":["0048-9697"]},"scopus_import":"1","department":[{"_id":"LifeSc"}],"title":"First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS","article_processing_charge":"No","external_id":{"isi":["001002645100001"],"pmid":["37169189"]},"acknowledgement":"The authors thank the Czech Science Foundation (project No. 19-28399X) and the Czech Academy of Sciences (RVO: 60077344) and are sincerely grateful to the Bordeaux Imaging Centre (member of the France BioImaging national infrastructure, ANR-10-INBS-04) for help with TEM and to members of the Laboratory of Biological Effects of Metals and Laboratory of Aquaculture and Pathology of Aquatic Organisms (Ruđer Bošković Institute, Croatia) for the assistance with fieldwork.","article_type":"original"},{"isi":1,"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1111/mec.16849","status":"public","intvolume":"        32","main_file_link":[{"url":"https://doi.org/10.1101/2022.01.28.478139","open_access":"1"}],"day":"01","year":"2023","type":"journal_article","publisher":"Wiley","oa_version":"Preprint","_id":"14787","publication":"Molecular Ecology","publication_status":"published","abstract":[{"text":"Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes of<jats:italic>Mimulus aurantiacus</jats:italic>. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system.","lang":"eng"}],"doi":"10.1111/mec.16849","volume":32,"quality_controlled":"1","oa":1,"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"department":[{"_id":"NiBa"}],"title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","article_processing_charge":"No","date_created":"2024-01-10T10:44:45Z","language":[{"iso":"eng"}],"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"article_type":"original","acknowledgement":"We thank Julian Catchen for making modifications to Stacks to aid this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and Nicholas H. Barton provided advice, stimulating discussion and critical feedback. The project was supported by National Science Foundation grant DEB-1258199.","external_id":{"isi":["000919244600001"],"pmid":["36651268"]},"month":"04","page":"2041-2054","date_published":"2023-04-01T00:00:00Z","citation":{"apa":"Stankowski, S., Chase, M. A., McIntosh, H., &#38; Streisfeld, M. A. (2023). Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16849\">https://doi.org/10.1111/mec.16849</a>","ama":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. <i>Molecular Ecology</i>. 2023;32(8):2041-2054. doi:<a href=\"https://doi.org/10.1111/mec.16849\">10.1111/mec.16849</a>","mla":"Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” <i>Molecular Ecology</i>, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:<a href=\"https://doi.org/10.1111/mec.16849\">10.1111/mec.16849</a>.","chicago":"Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16849\">https://doi.org/10.1111/mec.16849</a>.","ista":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.","ieee":"S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone,” <i>Molecular Ecology</i>, vol. 32, no. 8. Wiley, pp. 2041–2054, 2023.","short":"S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054."},"issue":"8","date_updated":"2024-01-16T10:10:00Z","author":[{"full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"first_name":"Madeline A.","full_name":"Chase, Madeline A.","last_name":"Chase"},{"last_name":"McIntosh","first_name":"Hanna","full_name":"McIntosh, Hanna"},{"first_name":"Matthew A.","full_name":"Streisfeld, Matthew A.","last_name":"Streisfeld"}]},{"day":"03","oa_version":"Published Version","publisher":"Rockefeller University Press","year":"2023","type":"journal_article","status":"public","article_number":"e202206038","fulldoi":"https://doi.org/10.1083/jcb.202206038","intvolume":"       222","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","isi":1,"pmid":1,"volume":222,"oa":1,"file":[{"date_updated":"2024-01-16T10:15:09Z","checksum":"505d5cac36c14b073b68c7fed1a92bd3","relation":"main_file","creator":"dernst","file_id":"14811","content_type":"application/pdf","success":1,"date_created":"2024-01-16T10:15:09Z","file_size":5678069,"access_level":"open_access","file_name":"2023_JCB_Mund.pdf"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publication":"Journal of Cell Biology","_id":"14788","publication_status":"published","doi":"10.1083/jcb.202206038","abstract":[{"text":"Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane.","lang":"eng"}],"external_id":{"isi":["000978065000001"],"pmid":["36734980"]},"acknowledgement":"We thank the entire Ries and Kaksonen labs for fruitful discussions and support. This work was supported by the European Research Council (ERC CoG-724489 to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND (Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund, A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant 310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent of the Miriam Berman Presidential Development Chair.","article_type":"original","language":[{"iso":"eng"}],"date_created":"2024-01-10T10:45:55Z","keyword":["Cell Biology"],"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"article_processing_charge":"No","title":"Clathrin coats partially preassemble and subsequently bend during endocytosis","file_date_updated":"2024-01-16T10:15:09Z","department":[{"_id":"AnSa"}],"date_updated":"2024-01-16T10:17:05Z","author":[{"full_name":"Mund, Markus","first_name":"Markus","last_name":"Mund"},{"first_name":"Aline","full_name":"Tschanz, Aline","last_name":"Tschanz"},{"last_name":"Wu","first_name":"Yu-Le","full_name":"Wu, Yu-Le"},{"orcid":"0000-0001-8501-6017","first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F","last_name":"Frey"},{"last_name":"Mehl","full_name":"Mehl, Johanna L.","first_name":"Johanna L."},{"last_name":"Kaksonen","full_name":"Kaksonen, Marko","first_name":"Marko"},{"full_name":"Avinoam, Ori","first_name":"Ori","last_name":"Avinoam"},{"last_name":"Schwarz","first_name":"Ulrich S.","full_name":"Schwarz, Ulrich S."},{"first_name":"Jonas","full_name":"Ries, Jonas","last_name":"Ries"}],"citation":{"short":"M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam, U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).","chicago":"Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2023. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>.","ista":"Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 222(3), e202206038.","ieee":"M. Mund <i>et al.</i>, “Clathrin coats partially preassemble and subsequently bend during endocytosis,” <i>Journal of Cell Biology</i>, vol. 222, no. 3. Rockefeller University Press, 2023.","mla":"Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>, vol. 222, no. 3, e202206038, Rockefeller University Press, 2023, doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>.","ama":"Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. 2023;222(3). doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>","apa":"Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., … Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>"},"issue":"3","ddc":["570"],"date_published":"2023-02-03T00:00:00Z","month":"02"},{"project":[{"name":"Perception-Aware Appearance Fabrication","grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027"}],"abstract":[{"lang":"eng","text":"A faithful reproduction of gloss is inherently difficult because of the limited dynamic range, peak luminance, and 3D capabilities of display devices. This work investigates how the display capabilities affect gloss appearance with respect to a real-world reference object. To this end, we employ an accurate imaging pipeline to achieve a perceptual gloss match between a virtual and real object presented side-by-side on an augmented-reality high-dynamic-range (HDR) stereoscopic display, which has not been previously attained to this extent. Based on this precise gloss reproduction, we conduct a series of gloss matching experiments to study how gloss perception degrades based on individual factors: object albedo, display luminance, dynamic range, stereopsis, and tone mapping. We support the study with a detailed analysis of individual factors, followed by an in-depth discussion on the observed perceptual effects. Our experiments demonstrate that stereoscopic presentation has a limited effect on the gloss matching task on our HDR display. However, both reduced luminance and dynamic range of the display reduce the perceived gloss. This means that the visual system cannot compensate for the changes in gloss appearance across luminance (lack of gloss constancy), and the tone mapping operator should be carefully selected when reproducing gloss on a low dynamic range (LDR) display."}],"doi":"10.1145/3610548.3618226","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"_id":"14798","publication_status":"published","publication":"Proceedings of the SIGGRAPH Asia 2023 Conference","oa":1,"file":[{"creator":"dernst","relation":"main_file","checksum":"8abe27432ed222b50d1af9b3388db1b0","date_updated":"2024-01-17T08:33:06Z","success":1,"file_id":"14823","content_type":"application/pdf","date_created":"2024-01-17T08:33:06Z","file_name":"2023_SA_Chen.pdf","access_level":"open_access","file_size":95967451}],"quality_controlled":"1","isi":1,"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","article_number":"90","fulldoi":"https://doi.org/10.1145/3610548.3618226","oa_version":"Published Version","publisher":"Association for Computing Machinery","year":"2023","type":"conference","day":"10","month":"12","ddc":["000"],"date_published":"2023-12-10T00:00:00Z","citation":{"short":"B. Chen, A. Jindal, M. Piovarci, C. Wang, H.P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, R.K. Mantiuk, in:, Proceedings of the SIGGRAPH Asia 2023 Conference, Association for Computing Machinery, 2023.","ista":"Chen B, Jindal A, Piovarci M, Wang C, Seidel HP, Didyk P, Myszkowski K, Serrano A, Mantiuk RK. 2023. The effect of display capabilities on the gloss consistency between real and virtual objects. Proceedings of the SIGGRAPH Asia 2023 Conference. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 90.","chicago":"Chen, Bin, Akshay Jindal, Michael Piovarci, Chao Wang, Hans Peter Seidel, Piotr Didyk, Karol Myszkowski, Ana Serrano, and Rafał K. Mantiuk. “The Effect of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.” In <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3610548.3618226\">https://doi.org/10.1145/3610548.3618226</a>.","ieee":"B. Chen <i>et al.</i>, “The effect of display capabilities on the gloss consistency between real and virtual objects,” in <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>, Sydney, Australia, 2023.","ama":"Chen B, Jindal A, Piovarci M, et al. The effect of display capabilities on the gloss consistency between real and virtual objects. In: <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>. Association for Computing Machinery; 2023. doi:<a href=\"https://doi.org/10.1145/3610548.3618226\">10.1145/3610548.3618226</a>","mla":"Chen, Bin, et al. “The Effect of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.” <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>, 90, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3610548.3618226\">10.1145/3610548.3618226</a>.","apa":"Chen, B., Jindal, A., Piovarci, M., Wang, C., Seidel, H. P., Didyk, P., … Mantiuk, R. K. (2023). The effect of display capabilities on the gloss consistency between real and virtual objects. In <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>. Sydney, Australia: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3610548.3618226\">https://doi.org/10.1145/3610548.3618226</a>"},"author":[{"last_name":"Chen","first_name":"Bin","full_name":"Chen, Bin"},{"last_name":"Jindal","full_name":"Jindal, Akshay","first_name":"Akshay"},{"orcid":"0000-0002-5062-4474","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael","full_name":"Piovarci, Michael","last_name":"Piovarci"},{"last_name":"Wang","first_name":"Chao","full_name":"Wang, Chao"},{"full_name":"Seidel, Hans Peter","first_name":"Hans Peter","last_name":"Seidel"},{"last_name":"Didyk","first_name":"Piotr","full_name":"Didyk, Piotr"},{"full_name":"Myszkowski, Karol","first_name":"Karol","last_name":"Myszkowski"},{"first_name":"Ana","full_name":"Serrano, Ana","last_name":"Serrano"},{"last_name":"Mantiuk","full_name":"Mantiuk, Rafał K.","first_name":"Rafał K."}],"date_updated":"2025-09-09T14:20:50Z","article_processing_charge":"Yes (in subscription journal)","title":"The effect of display capabilities on the gloss consistency between real and virtual objects","file_date_updated":"2024-01-17T08:33:06Z","department":[{"_id":"BeBi"}],"scopus_import":"1","publication_identifier":{"isbn":["9798400703157"]},"conference":{"end_date":"2023-12-15","location":"Sydney, Australia","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2023-12-12"},"language":[{"iso":"eng"}],"date_created":"2024-01-14T23:00:57Z","acknowledgement":"This work is supported by FWF Lise Meitner (Grant M 3319), Spanish Agencia Estatal de Investigación (project PID2022-141539NBI00), European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement\r\nN◦ 725253–EyeCode), Swiss National Science Foundation (Grant no. 200502), and academic gifts from Meta. We thank Dmitry Lubyako and Ali Özgür Yöntem for building the turntable for our experiment.","external_id":{"isi":["001278296700090"]}},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"_id":"14812","ddc":["570"],"date_published":"2023-09-05T00:00:00Z","doi":"10.5281/ZENODO.8318995","abstract":[{"text":"This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode","lang":"eng"}],"month":"09","related_material":{"record":[{"id":"14796","status":"public","relation":"used_in_publication"}]},"date_updated":"2025-09-04T11:38:30Z","oa":1,"author":[{"full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"}],"citation":{"short":"S. Stankowski, (2023).","ista":"Stankowski S. 2023. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8318995\">10.5281/ZENODO.8318995</a>.","chicago":"Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8318995\">https://doi.org/10.5281/ZENODO.8318995</a>.","ieee":"S. Stankowski, “Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails.” Zenodo, 2023.","mla":"Stankowski, Sean. <i>Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8318995\">10.5281/ZENODO.8318995</a>.","ama":"Stankowski S. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8318995\">10.5281/ZENODO.8318995</a>","apa":"Stankowski, S. (2023). Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8318995\">https://doi.org/10.5281/ZENODO.8318995</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-01-16T10:23:01Z","has_accepted_license":"1","article_processing_charge":"No","title":"Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails","department":[{"_id":"NiBa"}],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8318995","open_access":"1"}],"day":"05","contributor":[{"first_name":"Zusanna","last_name":"Zagrodzka"},{"first_name":"Martin","last_name":"Garlovsky"},{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka","orcid":"0000-0002-4530-8469","last_name":"Pal"},{"first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","last_name":"Shipilina"},{"first_name":"Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","last_name":"Garcia Castillo"},{"first_name":"Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","last_name":"Lifchitz"},{"first_name":"Alan","last_name":"Le Moan"},{"last_name":"Leder","first_name":"Erica"},{"first_name":"James","last_name":"Reeve"},{"last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Roger","last_name":"Butlin"}],"publisher":"Zenodo","oa_version":"Published Version","corr_author":"1","type":"research_data_reference","year":"2023","status":"public","fulldoi":"https://doi.org/10.5281/ZENODO.8318995"},{"file":[{"file_id":"14816","content_type":"application/pdf","success":1,"date_updated":"2024-01-16T12:13:27Z","relation":"main_file","checksum":"c50f2b9db53938b755e30a085f464059","creator":"dernst","access_level":"open_access","file_size":1510993,"file_name":"2023_JMLR_Beznosikov.pdf","date_created":"2024-01-16T12:13:27Z"}],"quality_controlled":"1","oa":1,"volume":24,"abstract":[{"lang":"eng","text":"In the last few years, various communication compression techniques have emerged as an indispensable tool helping to alleviate the communication bottleneck in distributed learning. However, despite the fact biased compressors often show superior performance in practice when compared to the much more studied and understood unbiased compressors, very little is known about them. In this work we study three classes of biased compression operators, two of which are new, and their performance when applied to (stochastic) gradient descent and distributed (stochastic) gradient descent. We show for the first time that biased compressors can lead to linear convergence rates both in the single node and distributed settings. We prove that distributed compressed SGD method, employed with error feedback mechanism, enjoys the ergodic rate O(δLexp[−μKδL]+(C+δD)Kμ), where δ≥1 is a compression parameter which grows when more compression is applied, L and μ are the smoothness and strong convexity constants, C captures stochastic gradient noise (C=0 if full gradients are computed on each node) and D captures the variance of the gradients at the optimum (D=0 for over-parameterized models). Further, via a theoretical study of several synthetic and empirical distributions of communicated gradients, we shed light on why and by how much biased compressors outperform their unbiased variants. Finally, we propose several new biased compressors with promising theoretical guarantees and practical performance."}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publication":"Journal of Machine Learning Research","_id":"14815","publication_status":"published","type":"journal_article","year":"2023","oa_version":"Published Version","publisher":"Journal of Machine Learning Research","day":"01","intvolume":"        24","status":"public","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"author":[{"full_name":"Beznosikov, Aleksandr","first_name":"Aleksandr","last_name":"Beznosikov"},{"last_name":"Horvath","first_name":"Samuel","full_name":"Horvath, Samuel"},{"last_name":"Richtarik","full_name":"Richtarik, Peter","first_name":"Peter"},{"id":"dd546b39-0804-11ed-9c55-ef075c39778d","first_name":"Mher","full_name":"Safaryan, Mher","last_name":"Safaryan"}],"date_updated":"2024-10-09T21:07:52Z","arxiv":1,"citation":{"apa":"Beznosikov, A., Horvath, S., Richtarik, P., &#38; Safaryan, M. (2023). On biased compression for distributed learning. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","mla":"Beznosikov, Aleksandr, et al. “On Biased Compression for Distributed Learning.” <i>Journal of Machine Learning Research</i>, vol. 24, Journal of Machine Learning Research, 2023, pp. 1–50.","ama":"Beznosikov A, Horvath S, Richtarik P, Safaryan M. On biased compression for distributed learning. <i>Journal of Machine Learning Research</i>. 2023;24:1-50.","chicago":"Beznosikov, Aleksandr, Samuel Horvath, Peter Richtarik, and Mher Safaryan. “On Biased Compression for Distributed Learning.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2023.","ista":"Beznosikov A, Horvath S, Richtarik P, Safaryan M. 2023. On biased compression for distributed learning. Journal of Machine Learning Research. 24, 1–50.","ieee":"A. Beznosikov, S. Horvath, P. Richtarik, and M. Safaryan, “On biased compression for distributed learning,” <i>Journal of Machine Learning Research</i>, vol. 24. Journal of Machine Learning Research, pp. 1–50, 2023.","short":"A. Beznosikov, S. Horvath, P. Richtarik, M. Safaryan, Journal of Machine Learning Research 24 (2023) 1–50."},"date_published":"2023-10-01T00:00:00Z","ddc":["000"],"month":"10","page":"1-50","corr_author":"1","external_id":{"isi":["001111578500001"],"arxiv":["2002.12410"]},"acknowledgement":"The work in Sections 1-5 was conducted while A. Beznosikov was a research intern in the Optimizationand Machine Learning Lab of Peter Richtárik at KAUST; this visit was funded by the KAUST Baseline Research Funding Scheme. The work of A. Beznosikov in Section 6 was conducted in Skoltech and was supported by Ministry of Science and Higher Education grant No. 075-10-2021-068. ","article_type":"original","date_created":"2024-01-16T12:13:36Z","language":[{"iso":"eng"}],"department":[{"_id":"DaAl"}],"file_date_updated":"2024-01-16T12:13:27Z","title":"On biased compression for distributed learning","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1533-7928"]}},{"conference":{"start_date":"2023-05-01","end_date":"2023-05-05","location":"Bol, Brac, Croatia","name":"FC: Financial Cryptography and Data Security"},"date_created":"2024-01-18T07:41:12Z","language":[{"iso":"eng"}],"department":[{"_id":"ElKo"}],"title":"Proof of availability and retrieval in a modular blockchain architecture","article_processing_charge":"No","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031477508"],"eisbn":["9783031477515"],"eissn":["1611-3349"]},"scopus_import":"1","external_id":{"isi":["001150231600003"]},"acknowledgement":"This work is partially supported by Meta. Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N. Shir Cohen is supported by the Adams Fellowship Program of the Israel Academy of Sciences and Humanities.","date_published":"2023-12-01T00:00:00Z","month":"12","page":"36-53","author":[{"last_name":"Cohen","full_name":"Cohen, Shir","first_name":"Shir"},{"first_name":"Guy","full_name":"Goren, Guy","last_name":"Goren"},{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"first_name":"Alberto","full_name":"Sonnino, Alberto","last_name":"Sonnino"},{"full_name":"Spiegelman, Alexander","first_name":"Alexander","last_name":"Spiegelman"}],"date_updated":"2025-09-09T14:22:38Z","citation":{"chicago":"Cohen, Shir, Guy Goren, Eleftherios Kokoris Kogias, Alberto Sonnino, and Alexander Spiegelman. “Proof of Availability and Retrieval in a Modular Blockchain Architecture.” In <i>27th International Conference on Financial Cryptography and Data Security</i>, 13951:36–53. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-47751-5_3\">https://doi.org/10.1007/978-3-031-47751-5_3</a>.","ista":"Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. 2023. Proof of availability and retrieval in a modular blockchain architecture. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13951, 36–53.","ieee":"S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, and A. Spiegelman, “Proof of availability and retrieval in a modular blockchain architecture,” in <i>27th International Conference on Financial Cryptography and Data Security</i>, Bol, Brac, Croatia, 2023, vol. 13951, pp. 36–53.","short":"S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 36–53.","apa":"Cohen, S., Goren, G., Kokoris Kogias, E., Sonnino, A., &#38; Spiegelman, A. (2023). Proof of availability and retrieval in a modular blockchain architecture. In <i>27th International Conference on Financial Cryptography and Data Security</i> (Vol. 13951, pp. 36–53). Bol, Brac, Croatia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-47751-5_3\">https://doi.org/10.1007/978-3-031-47751-5_3</a>","ama":"Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. Proof of availability and retrieval in a modular blockchain architecture. In: <i>27th International Conference on Financial Cryptography and Data Security</i>. Vol 13951. Springer Nature; 2023:36-53. doi:<a href=\"https://doi.org/10.1007/978-3-031-47751-5_3\">10.1007/978-3-031-47751-5_3</a>","mla":"Cohen, Shir, et al. “Proof of Availability and Retrieval in a Modular Blockchain Architecture.” <i>27th International Conference on Financial Cryptography and Data Security</i>, vol. 13951, Springer Nature, 2023, pp. 36–53, doi:<a href=\"https://doi.org/10.1007/978-3-031-47751-5_3\">10.1007/978-3-031-47751-5_3</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"type":"conference","year":"2023","publisher":"Springer Nature","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://fc23.ifca.ai/preproceedings/150.pdf"}],"day":"01","intvolume":"     13951","fulldoi":"https://doi.org/10.1007/978-3-031-47751-5_3","status":"public","abstract":[{"lang":"eng","text":"This paper explores a modular design architecture aimed at helping blockchains (and other SMR implementation) to scale to a very large number of processes. This comes in contrast to existing monolithic architectures that interleave transaction dissemination, ordering, and execution in a single functionality. To achieve this we first split the monolith to multiple layers which can use existing distributed computing primitives. The exact specifications of the data dissemination part are formally defined by the Proof of Availability & Retrieval (PoA &R) abstraction. Solutions to the PoA &R problem contain two related sub-protocols: one that “pushes” information into the network and another that “pulls” this information. Regarding the latter, there is a dearth of research literature which is rectified in this paper. We present a family of pulling sub-protocols and rigorously analyze them. Extensive simulations support the theoretical claims of efficiency and robustness in case of a very large number of players. Finally, actual implementation and deployment on a small number of machines (roughly the size of several industrial systems) demonstrates the viability of the architecture’s paradigm."}],"doi":"10.1007/978-3-031-47751-5_3","project":[{"_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","name":"Security and Privacy by Design for Complex Systems","grant_number":"F8512"}],"_id":"14829","publication":"27th International Conference on Financial Cryptography and Data Security","publication_status":"published","quality_controlled":"1","oa":1,"alternative_title":["LNCS"],"volume":13951},{"date_created":"2024-01-18T07:44:31Z","language":[{"iso":"eng"}],"keyword":["General Medicine"],"conference":{"location":"Washington, DC, United States","end_date":"2023-02-14","name":"AAAI: Conference on Artificial Intelligence","start_date":"2023-02-07"},"publication_identifier":{"issn":["2159-5399"],"eissn":["2374-3468"]},"scopus_import":"1","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"article_processing_charge":"No","title":"Learning control policies for stochastic systems with reach-avoid guarantees","external_id":{"arxiv":["2210.05308"]},"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","corr_author":"1","date_published":"2023-06-26T00:00:00Z","month":"06","related_material":{"record":[{"relation":"earlier_version","id":"14600","status":"public"}]},"page":"11926-11935","date_updated":"2025-07-03T11:38:12Z","author":[{"orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","last_name":"Zikelic"},{"last_name":"Lechner","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"}],"citation":{"ieee":"D. Zikelic, M. Lechner, T. A. Henzinger, and K. Chatterjee, “Learning control policies for stochastic systems with reach-avoid guarantees,” in <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, Washington, DC, United States, 2023, vol. 37, no. 10, pp. 11926–11935.","ista":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. 2023. Learning control policies for stochastic systems with reach-avoid guarantees. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 11926–11935.","chicago":"Zikelic, Dorde, Mathias Lechner, Thomas A Henzinger, and Krishnendu Chatterjee. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” In <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, 37:11926–35. Association for the Advancement of Artificial Intelligence, 2023. <a href=\"https://doi.org/10.1609/aaai.v37i10.26407\">https://doi.org/10.1609/aaai.v37i10.26407</a>.","short":"D. Zikelic, M. Lechner, T.A. Henzinger, K. Chatterjee, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2023, pp. 11926–11935.","apa":"Zikelic, D., Lechner, M., Henzinger, T. A., &#38; Chatterjee, K. (2023). Learning control policies for stochastic systems with reach-avoid guarantees. In <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i> (Vol. 37, pp. 11926–11935). Washington, DC, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v37i10.26407\">https://doi.org/10.1609/aaai.v37i10.26407</a>","mla":"Zikelic, Dorde, et al. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, vol. 37, no. 10, Association for the Advancement of Artificial Intelligence, 2023, pp. 11926–35, doi:<a href=\"https://doi.org/10.1609/aaai.v37i10.26407\">10.1609/aaai.v37i10.26407</a>.","ama":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. In: <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>. Vol 37. Association for the Advancement of Artificial Intelligence; 2023:11926-11935. doi:<a href=\"https://doi.org/10.1609/aaai.v37i10.26407\">10.1609/aaai.v37i10.26407</a>"},"issue":"10","OA_place":"repository","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/2210.05308","open_access":"1"}],"day":"26","ec_funded":1,"year":"2023","type":"conference","publisher":"Association for the Advancement of Artificial Intelligence","oa_version":"Preprint","fulldoi":"https://doi.org/10.1609/aaai.v37i10.26407","OA_type":"green","status":"public","intvolume":"        37","publication_status":"published","_id":"14830","publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","doi":"10.1609/aaai.v37i10.26407","abstract":[{"text":"We study the problem of learning controllers for discrete-time non-linear stochastic dynamical systems with formal reach-avoid guarantees. This work presents the first method for providing formal reach-avoid guarantees, which combine and generalize stability and safety guarantees, with a tolerable probability threshold p in [0,1] over the infinite time horizon. Our method leverages advances in machine learning literature and it represents formal certificates as neural networks. In particular, we learn a certificate in the form of a reach-avoid supermartingale (RASM), a novel notion that we introduce in this work. Our RASMs provide reachability and avoidance guarantees by imposing constraints on what can be viewed as a stochastic extension of level sets of Lyapunov functions for deterministic systems. Our approach solves several important problems -- it can be used to learn a control policy from scratch, to verify a reach-avoid specification for a fixed control policy, or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification. We validate our approach on 3 stochastic non-linear reinforcement learning tasks.","lang":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"},{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"volume":37,"quality_controlled":"1","oa":1},{"citation":{"apa":"Sakref, Y., Muñoz Basagoiti, M., Zeravcic, Z., &#38; Rivoire, O. (2023). On kinetic constraints that catalysis imposes on elementary processes. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">https://doi.org/10.1021/acs.jpcb.3c04627</a>","mla":"Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” <i>The Journal of Physical Chemistry B</i>, vol. 127, no. 51, American Chemical Society, 2023, pp. 10950–59, doi:<a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">10.1021/acs.jpcb.3c04627</a>.","ama":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints that catalysis imposes on elementary processes. <i>The Journal of Physical Chemistry B</i>. 2023;127(51):10950-10959. doi:<a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">10.1021/acs.jpcb.3c04627</a>","ieee":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints that catalysis imposes on elementary processes,” <i>The Journal of Physical Chemistry B</i>, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023.","chicago":"Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">https://doi.org/10.1021/acs.jpcb.3c04627</a>.","ista":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. 2023. On kinetic constraints that catalysis imposes on elementary processes. The Journal of Physical Chemistry B. 127(51), 10950–10959.","short":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical Chemistry B 127 (2023) 10950–10959."},"arxiv":1,"issue":"51","date_updated":"2025-04-23T13:15:17Z","author":[{"last_name":"Sakref","first_name":"Yann","full_name":"Sakref, Yann"},{"first_name":"Maitane","full_name":"Muñoz Basagoiti, Maitane","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607","orcid":"0000-0003-1483-1457","last_name":"Muñoz Basagoiti"},{"full_name":"Zeravcic, Zorana","first_name":"Zorana","last_name":"Zeravcic"},{"full_name":"Rivoire, Olivier","first_name":"Olivier","last_name":"Rivoire"}],"page":"10950-10959","month":"12","date_published":"2023-12-13T00:00:00Z","article_type":"original","external_id":{"arxiv":["2312.15940"],"pmid":["38091487"],"isi":["001134068000001"]},"acknowledgement":"We acknowledge funding from ANR-22-CE06-0037-02. This work has received funding from the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754387.","scopus_import":"1","publication_identifier":{"issn":["1520-6106"],"eissn":["1520-5207"]},"article_processing_charge":"No","title":"On kinetic constraints that catalysis imposes on elementary processes","department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"date_created":"2024-01-18T07:47:11Z","keyword":["Materials Chemistry","Surfaces","Coatings and Films","Physical and Theoretical Chemistry"],"volume":127,"oa":1,"quality_controlled":"1","publication_status":"published","_id":"14831","publication":"The Journal of Physical Chemistry B","doi":"10.1021/acs.jpcb.3c04627","abstract":[{"lang":"eng","text":"Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the products. While efforts to design catalysts are often focused on accelerating the chemical reaction on the catalyst, catalysis is a global property of the catalytic cycle that involves all processes. These are controlled by both intrinsic parameters such as the composition and shape of the catalyst and extrinsic parameters such as the concentration of the chemical species at play. We examine here the conditions that catalysis imposes on the different steps of a reaction cycle and the respective role of intrinsic and extrinsic parameters of the system on the emergence of catalysis by using an approach based on first-passage times. We illustrate this approach for various decompositions of a catalytic cycle into elementary steps, including non-Markovian decompositions, which are useful when the presence and nature of intermediate states are a priori unknown. Our examples cover different types of reactions and clarify the constraints on elementary steps and the impact of species concentrations on catalysis."}],"status":"public","fulldoi":"https://doi.org/10.1021/acs.jpcb.3c04627","intvolume":"       127","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.15940","open_access":"1"}],"day":"13","oa_version":"Preprint","publisher":"American Chemical Society","type":"journal_article","year":"2023","isi":1,"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Oxford University Press","oa_version":"Published Version","year":"2023","type":"journal_article","day":"17","intvolume":"         2","status":"public","fulldoi":"https://doi.org/10.1093/evolinnean/kzad002","article_number":"kzad002","has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","file":[{"creator":"dernst","checksum":"ba6f9102d3a9fe6631c4fa398c5e4313","relation":"main_file","date_updated":"2024-01-23T08:10:00Z","file_id":"14875","content_type":"application/pdf","success":1,"date_created":"2024-01-23T08:10:00Z","file_name":"2023_EvolJourLinneanSociety_Stankowski.pdf","file_size":3408944,"access_level":"open_access"}],"volume":2,"abstract":[{"lang":"eng","text":"Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies."}],"doi":"10.1093/evolinnean/kzad002","_id":"14833","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"publication_status":"published","publication":"Evolutionary Journal of the Linnean Society","corr_author":"1","acknowledgement":"Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield high-performance computing cluster, ShARC. Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council (ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00).","article_type":"original","language":[{"iso":"eng"}],"date_created":"2024-01-18T07:54:10Z","article_processing_charge":"Yes","title":"Whole-genome phylogeography of the intertidal snail Littorina saxatilis","department":[{"_id":"NiBa"}],"file_date_updated":"2024-01-23T08:10:00Z","publication_identifier":{"eissn":["2752-938X"]},"author":[{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","full_name":"Stankowski, Sean"},{"last_name":"Zagrodzka","first_name":"Zuzanna B","full_name":"Zagrodzka, Zuzanna B"},{"last_name":"Galindo","full_name":"Galindo, Juan","first_name":"Juan"},{"last_name":"Montaño-Rendón","first_name":"Mauricio","full_name":"Montaño-Rendón, Mauricio"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"last_name":"Mikhailova","full_name":"Mikhailova, Natalia","first_name":"Natalia"},{"last_name":"Blakeslee","full_name":"Blakeslee, April M H","first_name":"April M H"},{"first_name":"Einar","full_name":"Arnason, Einar","last_name":"Arnason"},{"first_name":"Thomas","full_name":"Broquet, Thomas","last_name":"Broquet"},{"first_name":"Hernán E","full_name":"Morales, Hernán E","last_name":"Morales"},{"first_name":"John W","full_name":"Grahame, John W","last_name":"Grahame"},{"last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"full_name":"Butlin, Roger K","first_name":"Roger K","last_name":"Butlin"}],"date_updated":"2024-10-09T21:07:54Z","issue":"1","citation":{"short":"S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N. Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame, A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean Society 2 (2023).","ieee":"S. Stankowski <i>et al.</i>, “Whole-genome phylogeography of the intertidal snail Littorina saxatilis,” <i>Evolutionary Journal of the Linnean Society</i>, vol. 2, no. 1. Oxford University Press, 2023.","ista":"Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002.","chicago":"Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón, Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolinnean/kzad002\">https://doi.org/10.1093/evolinnean/kzad002</a>.","mla":"Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” <i>Evolutionary Journal of the Linnean Society</i>, vol. 2, no. 1, kzad002, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evolinnean/kzad002\">10.1093/evolinnean/kzad002</a>.","ama":"Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. <i>Evolutionary Journal of the Linnean Society</i>. 2023;2(1). doi:<a href=\"https://doi.org/10.1093/evolinnean/kzad002\">10.1093/evolinnean/kzad002</a>","apa":"Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R., Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal snail Littorina saxatilis. <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolinnean/kzad002\">https://doi.org/10.1093/evolinnean/kzad002</a>"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","ddc":["570"],"date_published":"2023-08-17T00:00:00Z","month":"08"},{"article_number":"e202219314","fulldoi":"https://doi.org/10.1002/ange.202219314","status":"public","intvolume":"       135","day":"02","year":"2023","type":"journal_article","publisher":"Wiley","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","volume":135,"file":[{"success":1,"file_id":"14876","content_type":"application/pdf","date_updated":"2024-01-23T08:57:01Z","relation":"main_file","checksum":"98e68d370159f7be52a3d7c8a8ee1198","creator":"dernst","access_level":"open_access","file_size":1004676,"file_name":"2023_AngewChem_Becker.pdf","date_created":"2024-01-23T08:57:01Z"}],"quality_controlled":"1","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"publication":"Angewandte Chemie","_id":"14835","publication_status":"published","doi":"10.1002/ange.202219314","abstract":[{"lang":"ger","text":"Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen. Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen Cross‐β‐Amyloidstruktur hervorgeht."}],"article_type":"original","acknowledgement":"Wir danken Albert A. Smith (Leipzig) für aufschlussreiche Diskussionen. Diese Arbeit wurde mit Mitteln des Europäischen Forschungsrats (StG-2012-311318 an P.S.) unterstützt und nutzte die Plattformen des Grenoble Instruct-ERIC Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) im Rahmen der Grenoble Partnership for Structural Biology (PSB) sowie die Einrichtungen und das Fachwissen der Biophysical and Structural Chemistry Platform (BPCS) am IECB, CNRS UAR3033, INSERM US001 und der Universität Bordeaux.","corr_author":"1","publication_identifier":{"eissn":["1521-3757"],"issn":["0044-8249"]},"file_date_updated":"2024-01-23T08:57:01Z","department":[{"_id":"PaSc"}],"article_processing_charge":"Yes (in subscription journal)","title":"Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten","date_created":"2024-01-18T10:01:01Z","language":[{"iso":"ger"}],"keyword":["General Medicine"],"citation":{"ama":"Becker LM, Berbon M, Vallet A, et al. Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. <i>Angewandte Chemie</i>. 2023;135(19). doi:<a href=\"https://doi.org/10.1002/ange.202219314\">10.1002/ange.202219314</a>","mla":"Becker, Lea Marie, et al. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” <i>Angewandte Chemie</i>, vol. 135, no. 19, e202219314, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/ange.202219314\">10.1002/ange.202219314</a>.","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. <i>Angewandte Chemie</i>. Wiley. <a href=\"https://doi.org/10.1002/ange.202219314\">https://doi.org/10.1002/ange.202219314</a>","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie 135 (2023).","ieee":"L. M. Becker <i>et al.</i>, “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten,” <i>Angewandte Chemie</i>, vol. 135, no. 19. Wiley, 2023.","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte Chemie. 135(19), e202219314.","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” <i>Angewandte Chemie</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/ange.202219314\">https://doi.org/10.1002/ange.202219314</a>."},"issue":"19","date_updated":"2024-10-09T21:07:55Z","author":[{"full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie","orcid":"0000-0002-6401-5151","last_name":"Becker"},{"last_name":"Berbon","full_name":"Berbon, Mélanie","first_name":"Mélanie"},{"last_name":"Vallet","full_name":"Vallet, Alicia","first_name":"Alicia"},{"last_name":"Grelard","full_name":"Grelard, Axelle","first_name":"Axelle"},{"full_name":"Morvan, Estelle","first_name":"Estelle","last_name":"Morvan"},{"last_name":"Bardiaux","first_name":"Benjamin","full_name":"Bardiaux, Benjamin"},{"last_name":"Lichtenecker","first_name":"Roman","full_name":"Lichtenecker, Roman"},{"full_name":"Ernst, Matthias","first_name":"Matthias","last_name":"Ernst"},{"last_name":"Loquet","full_name":"Loquet, Antoine","first_name":"Antoine"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"}],"month":"05","date_published":"2023-05-02T00:00:00Z","ddc":["540"]},{"doi":"10.1039/bk9781839165986-00136","abstract":[{"text":"Understanding the mechanisms of chaperones at the atomic level generally requires producing chaperone–client complexes in vitro. This task comes with significant challenges, because one needs to find conditions in which the client protein is presented to the chaperone in a state that binds and at the same time avoid the pitfalls of protein aggregation that are often inherent to such states. The strategy differs significantly for different client proteins and chaperones, but there are common underlying principles. Here, we discuss these principles and deduce the strategies that can be successfully applied for different chaperone–client complexes. We review successful biochemical strategies applied to making the client protein “binding competent” and illustrate the different strategies with examples of recent biophysical and biochemical studies.","lang":"eng"}],"_id":"14847","publication_status":"published","publication":"Biophysics of Molecular Chaperones","quality_controlled":"1","oa":1,"alternative_title":["New Developments in NMR"],"volume":29,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","year":"2023","oa_version":"Preprint","publisher":"Royal Society of Chemistry","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv-2023-rpn28"}],"day":"01","intvolume":"        29","fulldoi":"https://doi.org/10.1039/bk9781839165986-00136","status":"public","date_published":"2023-11-01T00:00:00Z","month":"11","page":"136-161","author":[{"last_name":"Sučec","first_name":"I.","full_name":"Sučec, I."},{"full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda"}],"date_updated":"2024-10-09T21:07:57Z","citation":{"mla":"Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies.” <i>Biophysics of Molecular Chaperones</i>, edited by Sebastian Hiller et al., vol. 29, Royal Society of Chemistry, 2023, pp. 136–61, doi:<a href=\"https://doi.org/10.1039/bk9781839165986-00136\">10.1039/bk9781839165986-00136</a>.","ama":"Sučec I, Schanda P. Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In: Hiller S, Liu M, He L, eds. <i>Biophysics of Molecular Chaperones</i>. Vol 29. Royal Society of Chemistry; 2023:136-161. doi:<a href=\"https://doi.org/10.1039/bk9781839165986-00136\">10.1039/bk9781839165986-00136</a>","apa":"Sučec, I., &#38; Schanda, P. (2023). Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In S. Hiller, M. Liu, &#38; L. He (Eds.), <i>Biophysics of Molecular Chaperones</i> (Vol. 29, pp. 136–161). Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/bk9781839165986-00136\">https://doi.org/10.1039/bk9781839165986-00136</a>","short":"I. Sučec, P. Schanda, in:, S. Hiller, M. Liu, L. He (Eds.), Biophysics of Molecular Chaperones, Royal Society of Chemistry, 2023, pp. 136–161.","ieee":"I. Sučec and P. Schanda, “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies,” in <i>Biophysics of Molecular Chaperones</i>, vol. 29, S. Hiller, M. Liu, and L. He, Eds. Royal Society of Chemistry, 2023, pp. 136–161.","chicago":"Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies.” In <i>Biophysics of Molecular Chaperones</i>, edited by Sebastian Hiller, Maili Liu, and Lichun He, 29:136–61. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/bk9781839165986-00136\">https://doi.org/10.1039/bk9781839165986-00136</a>.","ista":"Sučec I, Schanda P. 2023.Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In: Biophysics of Molecular Chaperones. New Developments in NMR, vol. 29, 136–161."},"date_created":"2024-01-22T08:04:57Z","language":[{"iso":"eng"}],"department":[{"_id":"PaSc"}],"title":"Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies","article_processing_charge":"No","publication_identifier":{"isbn":["9781839162824"],"eisbn":["9781839165993"]},"corr_author":"1","editor":[{"first_name":"Sebastian","full_name":"Hiller, Sebastian","last_name":"Hiller"},{"last_name":"Liu","full_name":"Liu, Maili","first_name":"Maili"},{"first_name":"Lichun","full_name":"He, Lichun","last_name":"He"}]},{"_id":"14849","publication":"The Annals of Probability","publication_status":"published","doi":"10.1214/23-aop1643","abstract":[{"text":"We establish a precise three-term asymptotic expansion, with an optimal estimate of the error term, for the rightmost eigenvalue of an n×n random matrix with independent identically distributed complex entries as n tends to infinity. All terms in the expansion are universal.","lang":"eng"}],"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","grant_number":"101020331"}],"volume":51,"quality_controlled":"1","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"day":"01","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.04448","open_access":"1"}],"type":"journal_article","ec_funded":1,"year":"2023","publisher":"Institute of Mathematical Statistics","oa_version":"Preprint","fulldoi":"https://doi.org/10.1214/23-aop1643","status":"public","intvolume":"        51","date_published":"2023-11-01T00:00:00Z","month":"11","page":"2192-2242","date_updated":"2025-09-09T14:23:34Z","author":[{"orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio","first_name":"Giorgio","last_name":"Cipolloni"},{"last_name":"Erdös","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"last_name":"Schröder","full_name":"Schröder, Dominik J","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856"},{"first_name":"Yuanyuan","full_name":"Xu, Yuanyuan","last_name":"Xu"}],"citation":{"mla":"Cipolloni, Giorgio, et al. “On the Rightmost Eigenvalue of Non-Hermitian Random Matrices.” <i>The Annals of Probability</i>, vol. 51, no. 6, Institute of Mathematical Statistics, 2023, pp. 2192–242, doi:<a href=\"https://doi.org/10.1214/23-aop1643\">10.1214/23-aop1643</a>.","ama":"Cipolloni G, Erdös L, Schröder DJ, Xu Y. On the rightmost eigenvalue of non-Hermitian random matrices. <i>The Annals of Probability</i>. 2023;51(6):2192-2242. doi:<a href=\"https://doi.org/10.1214/23-aop1643\">10.1214/23-aop1643</a>","apa":"Cipolloni, G., Erdös, L., Schröder, D. J., &#38; Xu, Y. (2023). On the rightmost eigenvalue of non-Hermitian random matrices. <i>The Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-aop1643\">https://doi.org/10.1214/23-aop1643</a>","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Y. Xu, The Annals of Probability 51 (2023) 2192–2242.","ieee":"G. Cipolloni, L. Erdös, D. J. Schröder, and Y. Xu, “On the rightmost eigenvalue of non-Hermitian random matrices,” <i>The Annals of Probability</i>, vol. 51, no. 6. Institute of Mathematical Statistics, pp. 2192–2242, 2023.","ista":"Cipolloni G, Erdös L, Schröder DJ, Xu Y. 2023. On the rightmost eigenvalue of non-Hermitian random matrices. The Annals of Probability. 51(6), 2192–2242.","chicago":"Cipolloni, Giorgio, László Erdös, Dominik J Schröder, and Yuanyuan Xu. “On the Rightmost Eigenvalue of Non-Hermitian Random Matrices.” <i>The Annals of Probability</i>. Institute of Mathematical Statistics, 2023. <a href=\"https://doi.org/10.1214/23-aop1643\">https://doi.org/10.1214/23-aop1643</a>."},"issue":"6","arxiv":1,"date_created":"2024-01-22T08:08:41Z","language":[{"iso":"eng"}],"keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"publication_identifier":{"issn":["0091-1798"]},"scopus_import":"1","department":[{"_id":"LaEr"}],"title":"On the rightmost eigenvalue of non-Hermitian random matrices","article_processing_charge":"No","external_id":{"arxiv":["2206.04448"],"isi":["001112165000004"]},"acknowledgement":"The second and the fourth author were supported by the ERC Advanced Grant\r\n“RMTBeyond” No. 101020331. The third author was supported by Dr. Max Rössler, the\r\nWalter Haefner Foundation and the ETH Zürich Foundation.","corr_author":"1","article_type":"original"},{"article_type":"original","external_id":{"arxiv":["2211.03606"]},"corr_author":"1","scopus_import":"1","publication_identifier":{"eissn":["2578-5885"],"issn":["2578-5893"]},"article_processing_charge":"No","title":"Ubiquity of bound states for the strongly coupled polaron","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"date_created":"2024-01-22T08:24:23Z","keyword":["General Medicine"],"citation":{"short":"D.J. Mitrouskas, R. Seiringer, Pure and Applied Analysis 5 (2023) 973–1008.","chicago":"Mitrouskas, David Johannes, and Robert Seiringer. “Ubiquity of Bound States for the Strongly Coupled Polaron.” <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers, 2023. <a href=\"https://doi.org/10.2140/paa.2023.5.973\">https://doi.org/10.2140/paa.2023.5.973</a>.","ista":"Mitrouskas DJ, Seiringer R. 2023. Ubiquity of bound states for the strongly coupled polaron. Pure and Applied Analysis. 5(4), 973–1008.","ieee":"D. J. Mitrouskas and R. Seiringer, “Ubiquity of bound states for the strongly coupled polaron,” <i>Pure and Applied Analysis</i>, vol. 5, no. 4. Mathematical Sciences Publishers, pp. 973–1008, 2023.","ama":"Mitrouskas DJ, Seiringer R. Ubiquity of bound states for the strongly coupled polaron. <i>Pure and Applied Analysis</i>. 2023;5(4):973-1008. doi:<a href=\"https://doi.org/10.2140/paa.2023.5.973\">10.2140/paa.2023.5.973</a>","mla":"Mitrouskas, David Johannes, and Robert Seiringer. “Ubiquity of Bound States for the Strongly Coupled Polaron.” <i>Pure and Applied Analysis</i>, vol. 5, no. 4, Mathematical Sciences Publishers, 2023, pp. 973–1008, doi:<a href=\"https://doi.org/10.2140/paa.2023.5.973\">10.2140/paa.2023.5.973</a>.","apa":"Mitrouskas, D. J., &#38; Seiringer, R. (2023). Ubiquity of bound states for the strongly coupled polaron. <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/paa.2023.5.973\">https://doi.org/10.2140/paa.2023.5.973</a>"},"arxiv":1,"OA_place":"repository","issue":"4","date_updated":"2025-04-23T14:21:39Z","author":[{"last_name":"Mitrouskas","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","full_name":"Mitrouskas, David Johannes"},{"last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"page":"973-1008","month":"12","date_published":"2023-12-15T00:00:00Z","OA_type":"green","status":"public","fulldoi":"https://doi.org/10.2140/paa.2023.5.973","intvolume":"         5","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.03606","open_access":"1"}],"day":"15","oa_version":"Preprint","publisher":"Mathematical Sciences Publishers","year":"2023","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":5,"oa":1,"quality_controlled":"1","publication_status":"published","_id":"14854","publication":"Pure and Applied Analysis","abstract":[{"text":"We study the spectrum of the Fröhlich Hamiltonian for the polaron at fixed total momentum. We prove the existence of excited eigenvalues between the ground state energy and the essential spectrum at strong coupling. In fact, our main result shows that the number of excited energy bands diverges in the strong coupling limit. To prove this we derive upper bounds for the min-max values of the corresponding fiber Hamiltonians and compare them with the bottom of the essential spectrum, a lower bound on which was recently obtained by Brooks and Seiringer (Comm. Math. Phys. 404:1 (2023), 287–337). The upper bounds are given in terms of the ground state energy band shifted by momentum-independent excitation energies determined by an effective Hamiltonian of Bogoliubov type.","lang":"eng"}],"doi":"10.2140/paa.2023.5.973"},{"corr_author":"1","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"department":[{"_id":"PaSc"}],"title":"Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues","article_processing_charge":"No","date_created":"2024-01-22T11:54:34Z","language":[{"iso":"eng"}],"keyword":["General Chemistry","Catalysis"],"citation":{"ama":"Becker LM, Berbon M, Vallet A, et al. <i>Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues</i>. Vol 62. Wiley; 2023. doi:<a href=\"https://doi.org/10.1002/anie.202304138\">10.1002/anie.202304138</a>","mla":"Becker, Lea Marie, et al. “Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues.” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 19, e202304138, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/anie.202304138\">10.1002/anie.202304138</a>.","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). <i>Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues</i>. <i>Angewandte Chemie International Edition</i> (Vol. 62). Wiley. <a href=\"https://doi.org/10.1002/anie.202304138\">https://doi.org/10.1002/anie.202304138</a>","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. 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Extreme precipitation in tropical squall lines. EGU General Assembly 2023. EGU General Assembly, EGU23-15870.","ieee":"S. Abramian, C. J. Muller, and C. Risi, “Extreme precipitation in tropical squall lines,” in <i>EGU General Assembly 2023</i>, Vienna, Austria &#38; Virtual, 2023."},"date_updated":"2024-10-09T21:08:04Z","author":[{"first_name":"Sophie","full_name":"Abramian, Sophie","last_name":"Abramian"},{"last_name":"Muller","orcid":"0000-0001-5836-5350","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J"},{"full_name":"Risi, Camille","first_name":"Camille","last_name":"Risi"}],"article_processing_charge":"No","title":"Extreme precipitation in tropical squall lines","department":[{"_id":"CaMu"}],"file_date_updated":"2024-02-05T08:10:43Z","language":[{"iso":"eng"}],"date_created":"2024-01-22T12:10:52Z","conference":{"start_date":"2023-04-23","name":"EGU General Assembly","location":"Vienna, Austria & Virtual","end_date":"2023-04-28"},"corr_author":"1","publication":"EGU General Assembly 2023","publication_status":"published","_id":"14866","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"doi":"10.5194/egusphere-egu23-15870","oa":1,"file":[{"success":1,"content_type":"application/pdf","file_id":"14935","checksum":"8cd5bb8bf3d48ceefb395b6875819147","relation":"main_file","date_updated":"2024-02-05T08:10:43Z","creator":"dernst","access_level":"open_access","file_size":294690,"file_name":"2023_EGU_Abramian.pdf","date_created":"2024-02-05T08:10:43Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","status":"public","fulldoi":"https://doi.org/10.5194/egusphere-egu23-15870","article_number":"EGU23-15870","day":"23","publisher":"European Geosciences Union","oa_version":"Published Version","year":"2023","type":"conference_abstract"},{"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.\r\n","external_id":{"isi":["001448447300005"],"arxiv":["2209.09860"]},"corr_author":"1","publication_identifier":{"eissn":["2788-3116"]},"department":[{"_id":"MaKw"}],"file_date_updated":"2024-01-24T09:34:43Z","title":"Constructing Hamilton cycles and perfect matchings efficiently","article_processing_charge":"No","date_created":"2024-01-22T12:20:15Z","language":[{"iso":"eng"}],"conference":{"start_date":"2023-08-28","name":"EUROCOMB: European Conference on Combinatorics, Graph Theory and Applications","location":"Prague, Czech Republic","end_date":"2023-09-01"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","citation":{"apa":"Anastos, M. (2023). Constructing Hamilton cycles and perfect matchings efficiently. In <i>Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications</i> (pp. 36–41). Prague, Czech Republic: Masaryk University Press. <a href=\"https://doi.org/10.5817/cz.muni.eurocomb23-005\">https://doi.org/10.5817/cz.muni.eurocomb23-005</a>","mla":"Anastos, Michael. “Constructing Hamilton Cycles and Perfect Matchings Efficiently.” <i>Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications</i>, Masaryk University Press, 2023, pp. 36–41, doi:<a href=\"https://doi.org/10.5817/cz.muni.eurocomb23-005\">10.5817/cz.muni.eurocomb23-005</a>.","ama":"Anastos M. Constructing Hamilton cycles and perfect matchings efficiently. In: <i>Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications</i>. Masaryk University Press; 2023:36-41. doi:<a href=\"https://doi.org/10.5817/cz.muni.eurocomb23-005\">10.5817/cz.muni.eurocomb23-005</a>","ieee":"M. Anastos, “Constructing Hamilton cycles and perfect matchings efficiently,” in <i>Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications</i>, Prague, Czech Republic, 2023, pp. 36–41.","ista":"Anastos M. 2023. Constructing Hamilton cycles and perfect matchings efficiently. Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications. EUROCOMB: European Conference on Combinatorics, Graph Theory and Applications, 36–41.","chicago":"Anastos, Michael. “Constructing Hamilton Cycles and Perfect Matchings Efficiently.” In <i>Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications</i>, 36–41. Masaryk University Press, 2023. <a href=\"https://doi.org/10.5817/cz.muni.eurocomb23-005\">https://doi.org/10.5817/cz.muni.eurocomb23-005</a>.","short":"M. Anastos, in:, Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications, Masaryk University Press, 2023, pp. 36–41."},"arxiv":1,"date_updated":"2025-09-09T14:24:21Z","author":[{"first_name":"Michael","full_name":"Anastos, Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos"}],"month":"09","page":"36-41","date_published":"2023-09-01T00:00:00Z","ddc":["510"],"fulldoi":"https://doi.org/10.5817/cz.muni.eurocomb23-005","status":"public","day":"01","type":"conference","year":"2023","ec_funded":1,"publisher":"Masaryk University Press","oa_version":"Published Version","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","quality_controlled":"1","file":[{"content_type":"application/pdf","file_id":"14881","success":1,"creator":"dernst","relation":"main_file","date_updated":"2024-01-24T09:34:43Z","checksum":"fb1d9a1e7389d90ec0e5e76934373cf8","file_name":"2023_Eurocomb_Anastos.pdf","file_size":464230,"access_level":"open_access","date_created":"2024-01-24T09:34:43Z"}],"oa":1,"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"publication_status":"published","_id":"14867","publication":"Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications","abstract":[{"lang":"eng","text":"<jats:p>Starting with the empty graph on $[n]$, at each round, a set of $K=K(n)$ edges is presented chosen uniformly at random from the ones that have not been presented yet. We are then asked to choose at most one of the presented edges and add it to the current graph. Our goal is to construct a Hamiltonian graph with $(1+o(1))n$ edges within as few rounds as possible. We show that in this process, one can build a Hamiltonian graph of size $(1+o(1))n$ in $(1+o(1))(1+(\\log n)/2K) n$ rounds w.h.p. The case $K=1$ implies that w.h.p. one can build a Hamiltonian graph by choosing $(1+o(1))n$ edges in an online fashion as they appear along the first $(0.5+o(1))n\\log n$ rounds of the random graph process. This answers a question of Frieze, Krivelevich and Michaeli. Observe that the number of rounds is asymptotically optimal as the first $0.5n\\log n$ edges do not span a Hamilton cycle w.h.p. The case $K=\\Theta(\\log n)$ implies that the Hamiltonicity threshold of the corresponding Achlioptas process is at most $(1+o(1))(1+(\\log n)/2K) n$. This matches the $(1-o(1))(1+(\\log n)/2K) n$ lower bound due to Krivelevich, Lubetzky and Sudakov and resolves the problem of determining the Hamiltonicity threshold of the Achlioptas process with $K=\\Theta(\\log n)$. We also show that in the above process one can construct a graph $G$ that spans a matching of size $\\lfloor V(G)/2) \\rfloor$ and $(0.5+o(1))n$ edges within $(1+o(1))(0.5+(\\log n)/2K) n$ rounds w.h.p. Our proof relies on a robust Hamiltonicity property of the strong $4$-core of the binomial random graph which we use as a black-box. This property allows it to absorb paths covering vertices outside the strong $4$-core into a cycle.</jats:p>"}],"doi":"10.5817/cz.muni.eurocomb23-005","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}]},{"type":"journal_article","year":"2023","publisher":"eLife Sciences Publications","oa_version":"Submitted Version","corr_author":"1","acknowledgement":"This work was supported by M.H.’s NIH R01 grants (NS096786, GM126829) and Salk Cancer Center Support Grant P30 CA014195. M.H. also received financial support from the W.M. Keck Foundation and the NOMIS Foundation. Further, M.H. received support from the AHA-Allen Initiative in Brain Health and Cognitive Impairment award made jointly through the American Heart Association and The Paul G. Allen Frontiers Group (19PABH134610000).\r\n\r\nS.T. and J.C. were supported by Salk’s Women & Science Awards. S.T. also received financial support from the Hewitt Foundation fellowship, and J.C. is a Paul F. Glenn Biology of Aging fellow. J.H. was supported by the National Natural Science Foundation of China (31871317 and 32070635).\r\n\r\nWe thank Roberta Schulte for assistance with in vitro transport assays, for comments that greatly improved the manuscript, and for helping refine the figures presented in this work. We thank Shefali Krishna for creating the diagram for the NPC-DamID method, for her input on super-resolution microscopy analysis, and her insightful comments on this manuscript. We thank all members of the Hetzer lab for helpful discussions of these research ideas and their thoughtful comments on this manuscript. We are also grateful to Salk’s core facilities for their assistance. Specifically, we thank the Next Generation Sequencing Core (NGS) for sequencing our DamID and RNA NGS libraries, the Advanced Biophotonics Core for assistance with super-resolution microscopy, and the Razavi Newman Integrative Genomics and Bioinformatics Core (IGC) for their input on analysis methods for DamID experiments.","day":"23","main_file_link":[{"url":"https://doi.org/10.7554/eLife.87462.1","open_access":"1"}],"fulldoi":"https://doi.org/10.7554/elife.87462","status":"public","article_type":"original","date_created":"2024-01-22T12:21:56Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaHe"}],"title":"High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope","article_processing_charge":"Yes","author":[{"first_name":"Swati","full_name":"Tyagi, Swati","last_name":"Tyagi"},{"first_name":"Juliana S.","full_name":"Capitanio, Juliana S.","last_name":"Capitanio"},{"first_name":"Jiawei","full_name":"Xu, Jiawei","last_name":"Xu"},{"last_name":"Chen","first_name":"Fei","full_name":"Chen, Fei"},{"last_name":"Sharma","full_name":"Sharma, Rahul","first_name":"Rahul"},{"full_name":"Huang, Jialiang","first_name":"Jialiang","last_name":"Huang"},{"last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"oa":1,"date_updated":"2024-07-31T11:56:25Z","citation":{"ista":"Tyagi S, Capitanio JS, Xu J, Chen F, Sharma R, Huang J, Hetzer M. 2023. High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope. eLife.","chicago":"Tyagi, Swati, Juliana S. Capitanio, Jiawei Xu, Fei Chen, Rahul Sharma, Jialiang Huang, and Martin Hetzer. “High-Precision Mapping of Nuclear Pore-Chromatin Interactions Reveals New Principles of Genome Organization at the Nuclear Envelope.” <i>ELife</i>. eLife Sciences Publications, 2023. <a href=\"https://doi.org/10.7554/elife.87462\">https://doi.org/10.7554/elife.87462</a>.","ieee":"S. Tyagi <i>et al.</i>, “High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope,” <i>eLife</i>. eLife Sciences Publications, 2023.","short":"S. Tyagi, J.S. Capitanio, J. Xu, F. Chen, R. Sharma, J. Huang, M. Hetzer, ELife (2023).","apa":"Tyagi, S., Capitanio, J. S., Xu, J., Chen, F., Sharma, R., Huang, J., &#38; Hetzer, M. (2023). High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.87462\">https://doi.org/10.7554/elife.87462</a>","mla":"Tyagi, Swati, et al. “High-Precision Mapping of Nuclear Pore-Chromatin Interactions Reveals New Principles of Genome Organization at the Nuclear Envelope.” <i>ELife</i>, eLife Sciences Publications, 2023, doi:<a href=\"https://doi.org/10.7554/elife.87462\">10.7554/elife.87462</a>.","ama":"Tyagi S, Capitanio JS, Xu J, et al. High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope. <i>eLife</i>. 2023. doi:<a href=\"https://doi.org/10.7554/elife.87462\">10.7554/elife.87462</a>"},"date_published":"2023-06-23T00:00:00Z","doi":"10.7554/elife.87462","abstract":[{"text":"The role of nuclear pore complexes (NPCs) in genome organization remains poorly characterized due to technical limitations in probing genome-wide protein-DNA interactions specific to the nuclear periphery. Here, we developed a new sensitive method, NPC-DamID, which combines in vitro reconstitution of nuclear import and DamID technology. The fixation-free method identifies chromatin interactions at the NPCs in intact nuclei from cells and tissues. We found that NPCs are preferentially associated with common and hierarchically arranged super-enhancers (SEs) across multiple cell types. We also uncovered phase-separated condensates at NPCs that compartmentalize and concentrate transcriptional coactivators and structural proteins at SE-regulated genes. Our results support NPCs as anchoring sites for SE regulatory hubs and cell-type-specific transcriptional control.","lang":"eng"}],"_id":"14868","publication_status":"epub_ahead","publication":"eLife","month":"06"}]