[{"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"Elkrewi MN, Vicoso B. 2024. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. 20(8), e1011376.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>, vol. 20, no. 8, e1011376, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>.","ama":"Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. 2024;20(8). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>","ieee":"M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome,” <i>PLoS Genetics</i>, vol. 20, no. 8. Public Library of Science, 2024.","short":"M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024).","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>.","apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>"},"publication":"PLoS Genetics","file":[{"file_id":"18056","file_size":8962687,"relation":"main_file","content_type":"application/pdf","checksum":"f5d96b9af57126fc1063e951440477d6","file_name":"2024_PloSGenetics_Elkrewi.pdf","date_created":"2024-09-11T07:54:12Z","date_updated":"2024-09-11T07:54:12Z","success":1,"access_level":"open_access","creator":"dernst"}],"acknowledgement":"We thank the Vicoso group for their valuable comments on the earlier draft of the manuscript. We would also like to thank the Vienna BioCenter Next Generation Sequencing (NGS) facility staff, and in particular, Thomas Grentzinger for his support with the handling and sequencing of the samples, the scientific computing unit at ISTA for the computational resources, Brittney Wick for the help with hosting our data on the UCSC Cell Browser, and Lora B. Sweeney for her valuable input at the different stages of the project.\r\nThis research was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium https://sfbmeiosis.org/, grant ID FWF SFB F88-10) to BV. ","type":"journal_article","OA_place":"publisher","isi":1,"tmp":{"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)","image":"/images/cc_by.png"},"date_published":"2024-08-30T00:00:00Z","external_id":{"isi":["001304090200001"],"pmid":["39213449"]},"date_updated":"2026-05-27T22:31:20Z","title":"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome","APC_amount":"3145,39 EUR","publication_status":"published","project":[{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"DOAJ_listed":"1","quality_controlled":"1","abstract":[{"lang":"eng","text":"Our understanding of the molecular pathways that regulate oogenesis and define cellular identity in the Arthropod female reproductive system and the extent of their conservation is currently very limited. This is due to the focus on model systems, including Drosophila and Daphnia, which do not reflect the observed diversity of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the adult Artemia franciscana female reproductive system. We map our data to the Fly Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding light on the conserved regulatory programs between the two distantly related Arthropod species. We identify the major cell types known to be present in the Artemia ovary, including germ cells, follicle cells, and ovarian muscle cells. Additionally, we use the germ cells to explore gene regulation and expression of the Z chromosome during meiosis, highlighting its unique regulatory dynamics and allowing us to explore the presence of meiotic sex chromosome silencing in this group."}],"publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"corr_author":"1","language":[{"iso":"eng"}],"year":"2024","OA_type":"gold","license":"https://creativecommons.org/licenses/by/4.0/","day":"30","issue":"8","publisher":"Public Library of Science","article_type":"original","department":[{"_id":"BeVi"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"article_processing_charge":"Yes","intvolume":"        20","scopus_import":"1","doi":"10.1371/journal.pgen.1011376","date_created":"2024-09-08T22:01:11Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"17362"},{"status":"public","id":"19386","relation":"dissertation_contains"}],"link":[{"url":"https://github.com/Melkrewi/Artemia-snRNAseq-Project","relation":"software"}]},"volume":20,"author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"month":"08","oa":1,"article_number":"e1011376","status":"public","oa_version":"Published Version","ddc":["570"],"_id":"17890","file_date_updated":"2024-09-11T07:54:12Z"},{"file":[{"file_name":"2024_GBE_Bett.pdf","date_created":"2024-02-26T09:54:59Z","access_level":"open_access","creator":"dernst","success":1,"date_updated":"2024-02-26T09:54:59Z","file_size":5213306,"file_id":"15029","checksum":"106a40f10443b2e7ba66749844ebbdf1","relation":"main_file","content_type":"application/pdf"}],"type":"journal_article","OA_place":"publisher","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"mla":"Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” <i>Genome Biology and Evolution</i>, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/gbe/evae006\">10.1093/gbe/evae006</a>.","ista":"Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 16(1), evae006.","ieee":"V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” <i>Genome Biology and Evolution</i>, vol. 16, no. 1. Oxford University Press, 2024.","ama":"Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. <i>Genome Biology and Evolution</i>. 2024;16(1). doi:<a href=\"https://doi.org/10.1093/gbe/evae006\">10.1093/gbe/evae006</a>","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","apa":"Bett, V. K., Macon, A., Vicoso, B., &#38; Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evae006\">https://doi.org/10.1093/gbe/evae006</a>","chicago":"Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/gbe/evae006\">https://doi.org/10.1093/gbe/evae006</a>."},"publication":"Genome Biology and Evolution","publication_identifier":{"eissn":["1759-6653"]},"corr_author":"1","isi":1,"tmp":{"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)","image":"/images/cc_by.png"},"date_published":"2024-01-20T00:00:00Z","external_id":{"isi":["001153952800001"],"pmid":["38245839"]},"date_updated":"2026-05-27T22:31:20Z","title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","publication_status":"published","DOAJ_listed":"1","abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"quality_controlled":"1","issue":"1","day":"20","publisher":"Oxford University Press","article_type":"original","department":[{"_id":"BeVi"}],"has_accepted_license":"1","article_processing_charge":"Yes","language":[{"iso":"eng"}],"year":"2024","OA_type":"gold","month":"01","oa":1,"article_number":"evae006","status":"public","oa_version":"Published Version","ddc":["570"],"_id":"15009","file_date_updated":"2024-02-26T09:54:59Z","intvolume":"        16","scopus_import":"1","doi":"10.1093/gbe/evae006","related_material":{"record":[{"id":"14705","relation":"research_data","status":"public"},{"id":"20444","relation":"dissertation_contains","status":"private"},{"id":"20449","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"19386"}]},"date_created":"2024-02-18T23:01:02Z","volume":16,"author":[{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett","full_name":"Bett, Vincent K"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana","last_name":"Macon"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"},{"last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"}]},{"ec_funded":1,"arxiv":1,"publication_identifier":{"eissn":["2691-3399"]},"corr_author":"1","abstract":[{"text":"The photon blockade breakdown in a continuously driven cavity QED system has been proposed as a prime example for a first-order driven-dissipative quantum phase transition. However, the predicted scaling from a microscopic behavior—dominated by quantum fluctuations—to a macroscopic one—characterized by stable phases—and the associated exponents and phase diagram have not been observed so far. In this work we couple a single transmon qubit with a fixed coupling strength 𝑔 to a superconducting cavity that is in situ bandwidth 𝜅 tunable to controllably approach this thermodynamic limit. Even though the system remains microscopic, we observe its behavior becoming increasingly macroscopic as a function of 𝑔/𝜅. For the highest realized 𝑔/𝜅 of approximately 287, the system switches with a characteristic timescale as long as 6 s between a bright coherent state with approximately 8×103 intracavity photons and the vacuum state. This exceeds the microscopic timescales by 6 orders of magnitude and approaches the perfect hysteresis expected between two macroscopic attractors in the thermodynamic limit. These findings and interpretation are qualitatively supported by neoclassical theory and large-scale quantum-jump Monte Carlo simulations. Besides shedding more light on driven-dissipative physics in the limit of strong light-matter coupling, this system might also find applications in quantum sensing and metrology.","lang":"eng"}],"quality_controlled":"1","DOAJ_listed":"1","date_updated":"2026-05-27T22:31:23Z","project":[{"grant_number":"862644","name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"},{"grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"title":"Emergent macroscopic bistability induced by a single superconducting qubit","publication_status":"published","APC_amount":"3782,54","tmp":{"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)","image":"/images/cc_by.png"},"date_published":"2024-02-16T00:00:00Z","external_id":{"arxiv":["2210.14182"],"isi":["001171652500001"]},"isi":1,"acknowledgement":"This work has received funding from the Austrian Science Fund (FWF) through BeyondC (F7105) and the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 862644 (FETopen QUARTET). A.V. acknowledges support from the National Research, Development and Innovation Office of Hungary (NKFIH) within the Quantum Information National Laboratory of Hungary. The authors thank the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility for technical support. We are grateful to HUN-REN Cloud for providing us with suitable computational infrastructure for the simulations.","type":"journal_article","OA_place":"publisher","file":[{"file_size":1443351,"file_id":"17185","content_type":"application/pdf","relation":"main_file","checksum":"0833880d47f74ad1deda93a1d8ffa5a7","date_created":"2024-06-28T12:04:43Z","file_name":"2024_PRXQuantum_Sett.pdf","success":1,"date_updated":"2024-06-28T12:04:43Z","access_level":"open_access","creator":"cchlebak"}],"publication":"PRX Quantum","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, PRX Quantum 5 (2024).","apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., &#38; Fink, J. M. (2024). Emergent macroscopic bistability induced by a single superconducting qubit. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.5.010327\">https://doi.org/10.1103/prxquantum.5.010327</a>","chicago":"Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” <i>PRX Quantum</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/prxquantum.5.010327\">https://doi.org/10.1103/prxquantum.5.010327</a>.","ista":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. 5(1), 010327.","mla":"Sett, Riya, et al. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” <i>PRX Quantum</i>, vol. 5, no. 1, 010327, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/prxquantum.5.010327\">10.1103/prxquantum.5.010327</a>.","ieee":"R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Emergent macroscopic bistability induced by a single superconducting qubit,” <i>PRX Quantum</i>, vol. 5, no. 1. American Physical Society, 2024.","ama":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Emergent macroscopic bistability induced by a single superconducting qubit. <i>PRX Quantum</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1103/prxquantum.5.010327\">10.1103/prxquantum.5.010327</a>"},"oa_version":"Published Version","status":"public","_id":"17183","ddc":["530"],"file_date_updated":"2024-06-28T12:04:43Z","article_number":"010327","oa":1,"month":"02","author":[{"last_name":"Sett","full_name":"Sett, Riya","orcid":"0000-0001-7641-8348","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","first_name":"Riya"},{"first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","last_name":"Hassani","full_name":"Hassani, Farid"},{"full_name":"Phan, Duc T","last_name":"Phan","first_name":"Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423"},{"first_name":"Andras","last_name":"Vukics","full_name":"Vukics, Andras"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"18978"},{"status":"public","relation":"dissertation_contains","id":"19533"}]},"date_created":"2024-06-27T10:58:06Z","volume":5,"scopus_import":"1","doi":"10.1103/prxquantum.5.010327","intvolume":"         5","has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"}],"article_processing_charge":"Yes","department":[{"_id":"JoFi"},{"_id":"AnHi"}],"publisher":"American Physical Society","article_type":"original","day":"16","issue":"1","OA_type":"gold","language":[{"iso":"eng"}],"year":"2024"},{"OA_type":"green","language":[{"iso":"eng"}],"year":"2024","page":"114-119","article_type":"original","publisher":"American Association for the Advancement of Science","day":"05","issue":"6678","article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"scopus_import":"1","doi":"10.1126/science.adi2982","intvolume":"       383","main_file_link":[{"open_access":"1","url":"https://figshare.com/articles/journal_contribution/The_genetic_basis_of_a_recent_transition_to_live-bearing_in_marine_snails/26356054?file=47868241"}],"author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"first_name":"Zuzanna B.","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B."},{"first_name":"Martin D.","last_name":"Garlovsky","full_name":"Garlovsky, Martin D."},{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka","last_name":"Pal","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469"},{"first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","last_name":"Shipilina","full_name":"Shipilina, Daria"},{"full_name":"Garcia Castillo, Diego Fernando","last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando"},{"first_name":"Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","full_name":"Lifchitz, Hila","last_name":"Lifchitz"},{"first_name":"Alan","full_name":"Le Moan, Alan","last_name":"Le Moan"},{"first_name":"Erica","full_name":"Leder, Erica","last_name":"Leder"},{"full_name":"Reeve, James","last_name":"Reeve","first_name":"James"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"date_created":"2024-01-14T23:00:56Z","related_material":{"record":[{"relation":"research_data","id":"14812","status":"public"},{"relation":"dissertation_contains","id":"20694","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/the-snail-or-the-egg/","relation":"press_release","description":"News on ISTA Website"}]},"volume":383,"oa":1,"month":"01","status":"public","oa_version":"Submitted Version","_id":"14796","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.adi2982\">https://doi.org/10.1126/science.adi2982</a>.","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adi2982\">https://doi.org/10.1126/science.adi2982</a>","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” <i>Science</i>, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:<a href=\"https://doi.org/10.1126/science.adi2982\">10.1126/science.adi2982</a>.","ieee":"S. Stankowski <i>et al.</i>, “The genetic basis of a recent transition to live-bearing in marine snails,” <i>Science</i>, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024.","ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. <i>Science</i>. 2024;383(6678):114-119. doi:<a href=\"https://doi.org/10.1126/science.adi2982\">10.1126/science.adi2982</a>"},"pmid":1,"publication":"Science","acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","type":"journal_article","OA_place":"repository","date_updated":"2026-05-27T22:31:22Z","publication_status":"published","title":"The genetic basis of a recent transition to live-bearing in marine snails","isi":1,"external_id":{"isi":["001138156400003"],"pmid":["38175895"]},"date_published":"2024-01-05T00:00:00Z","abstract":[{"text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.","lang":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1095-9203"]},"corr_author":"1"},{"tmp":{"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)","image":"/images/cc_by.png"},"date_published":"2024-01-16T00:00:00Z","doi":"10.5281/ZENODO.10518320","title":"Data Analysis files for \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\"","date_updated":"2026-05-27T22:31:23Z","date_created":"2025-01-30T08:30:03Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"17183"},{"id":"19533","relation":"used_in_publication","status":"public"}]},"author":[{"id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","first_name":"Riya","full_name":"Sett, Riya","last_name":"Sett","orcid":"0000-0001-7641-8348"},{"last_name":"Hassani","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid"},{"id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T","last_name":"Phan","full_name":"Phan, Duc T"},{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir"},{"first_name":"Andras","full_name":"Vukics, Andras","last_name":"Vukics"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.10518320"}],"abstract":[{"lang":"eng","text":"Data analysis files for the manuscript \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\".\r\n\r\nThis contains the raw data and the data analysis files for generating the figures in the manuscript.\r\n\r\n Figure1 file - The raw data of cavity transmission spectra for 6 different kappas are there. They are fitted with input-output theory in the python file.\r\n Figure2 file - The raw data at 8 MHz kappa are included. all hte figures in figure 2 are generated in the python file\r\n Figure3 file - The raw data of PBB single shot measurements at all kappas are included. The detailed analysis and the Figure3 generated for the paper are all in the python analysis file. Also, thefiles containing the time-evolution of the intensity from Master Equation solution are included.\r\nFigure4 file - The raw data at 2.6 MHz for different drive detunings and the corresponding analyses are included. And the python file includes the analysis of the experimental data as well as approximate neoclassical equations solutions for 2-level and 3-level transmons are included.  "}],"month":"01","corr_author":"1","oa":1,"_id":"18978","ddc":["530"],"status":"public","oa_version":"Published Version","year":"2024","citation":{"short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, (2024).","chicago":"Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Data Analysis Files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.10518320\">https://doi.org/10.5281/ZENODO.10518320</a>.","apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., &#38; Fink, J. M. (2024). Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.10518320\">https://doi.org/10.5281/ZENODO.10518320</a>","mla":"Sett, Riya, et al. <i>Data Analysis Files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.”</i> Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.10518320\">10.5281/ZENODO.10518320</a>.","ista":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.10518320\">10.5281/ZENODO.10518320</a>.","ieee":"R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024.","ama":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.10518320\">10.5281/ZENODO.10518320</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"gold","day":"16","publisher":"Zenodo","department":[{"_id":"JoFi"},{"_id":"AnHi"}],"article_processing_charge":"No","OA_place":"repository","type":"research_data_reference","has_accepted_license":"1"},{"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"d4d6fa9ddf36643af994a6a757919afb","file_id":"12685","file_size":2269822,"date_updated":"2023-02-27T07:10:17Z","success":1,"creator":"dernst","access_level":"open_access","file_name":"2023_EvolutionaryApplications_DeJode.pdf","date_created":"2023-02-27T07:10:17Z"}],"acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","type":"journal_article","citation":{"ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” <i>Evolutionary Applications</i>, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>.","ieee":"A. De Jode <i>et al.</i>, “Ten years of demographic modelling of divergence and speciation in the sea,” <i>Evolutionary Applications</i>, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. 2023;16(2):542-559. doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” <i>Evolutionary Applications</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/eva.13428\">https://doi.org/10.1111/eva.13428</a>.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. Wiley. <a href=\"https://doi.org/10.1111/eva.13428\">https://doi.org/10.1111/eva.13428</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication":"Evolutionary Applications","publication_identifier":{"eissn":["1752-4571"]},"publication_status":"published","title":"Ten years of demographic modelling of divergence and speciation in the sea","date_updated":"2025-04-23T08:49:14Z","tmp":{"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)","image":"/images/cc_by.png"},"isi":1,"date_published":"2023-02-01T00:00:00Z","external_id":{"pmid":["36793688"],"isi":["000815663700001"]},"abstract":[{"text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.","lang":"eng"}],"quality_controlled":"1","publisher":"Wiley","article_type":"original","day":"01","issue":"2","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"year":"2023","language":[{"iso":"eng"}],"page":"542-559","oa":1,"month":"02","ddc":["576"],"_id":"11479","file_date_updated":"2023-02-27T07:10:17Z","oa_version":"Published Version","status":"public","doi":"10.1111/eva.13428","scopus_import":"1","intvolume":"        16","author":[{"first_name":"Aurélien","full_name":"De Jode, Aurélien","last_name":"De Jode"},{"full_name":"Le Moan, Alan","last_name":"Le Moan","first_name":"Alan"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"volume":16,"date_created":"2022-07-03T22:01:33Z"},{"month":"07","oa":1,"oa_version":"Published Version","status":"public","_id":"11706","ddc":["510"],"file_date_updated":"2023-10-04T09:37:26Z","intvolume":"        62","scopus_import":"1","doi":"10.1002/rsa.21106","date_created":"2022-07-31T22:01:49Z","volume":62,"author":[{"first_name":"Anita","full_name":"Liebenau, Anita","last_name":"Liebenau"},{"first_name":"Letícia","last_name":"Mattos","full_name":"Mattos, Letícia"},{"first_name":"Walner","id":"12c6bd4d-2cd0-11ec-a0da-e28f42f65ebd","full_name":"Mendonca Dos Santos, Walner","last_name":"Mendonca Dos Santos"},{"last_name":"Skokan","full_name":"Skokan, Jozef","first_name":"Jozef"}],"issue":"4","day":"01","publisher":"Wiley","article_type":"original","department":[{"_id":"MaKw"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"year":"2023","page":"1035-1055","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_identifier":{"issn":["1042-9832"],"eissn":["1098-2418"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"date_published":"2023-07-01T00:00:00Z","isi":1,"external_id":{"isi":["000828530400001"]},"date_updated":"2023-10-04T09:38:45Z","publication_status":"published","title":"Asymmetric Ramsey properties of random graphs involving cliques and cycles","abstract":[{"text":"We say that (Formula presented.) if, in every edge coloring (Formula presented.), we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy of (Formula presented.). The well-known states that the threshold for the property (Formula presented.) is equal to (Formula presented.), where (Formula presented.) is given by (Formula presented.) for any pair of graphs (Formula presented.) and (Formula presented.) with (Formula presented.). In this article, we show the 0-statement of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques. ","lang":"eng"}],"quality_controlled":"1","file":[{"access_level":"open_access","creator":"dernst","date_updated":"2023-10-04T09:37:26Z","success":1,"file_name":"2023_RandomStructureAlgorithms_Liebenau.pdf","date_created":"2023-10-04T09:37:26Z","checksum":"3a5969d0c512aef01c30f3dc81c6d59b","relation":"main_file","content_type":"application/pdf","file_id":"14389","file_size":1362334}],"type":"journal_article","acknowledgement":"This work was started at the thematic program GRAPHS@IMPA (January–March 2018), in Rio de Janeiro. We thank IMPA and the organisers for the hospitality and for providing a pleasant research environment. We thank Rob Morris for helpful discussions, and the anonymous referees for their careful reading and many helpful suggestions. Open Access funding enabled and organized by Projekt DEAL.\r\nA. Liebenau was supported by an ARC DECRA Fellowship Grant DE170100789. L. Mattos was supported by CAPES and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – The Berlin Mathematics Research Center MATH+ (EXC-2046/1, project ID: 390685689). W. Mendonça was supported by CAPES project 88882.332408/2010-01.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. 2023. Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. 62(4), 1035–1055.","mla":"Liebenau, Anita, et al. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” <i>Random Structures and Algorithms</i>, vol. 62, no. 4, Wiley, 2023, pp. 1035–55, doi:<a href=\"https://doi.org/10.1002/rsa.21106\">10.1002/rsa.21106</a>.","ieee":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, and J. Skokan, “Asymmetric Ramsey properties of random graphs involving cliques and cycles,” <i>Random Structures and Algorithms</i>, vol. 62, no. 4. Wiley, pp. 1035–1055, 2023.","ama":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. Asymmetric Ramsey properties of random graphs involving cliques and cycles. <i>Random Structures and Algorithms</i>. 2023;62(4):1035-1055. doi:<a href=\"https://doi.org/10.1002/rsa.21106\">10.1002/rsa.21106</a>","short":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, J. Skokan, Random Structures and Algorithms 62 (2023) 1035–1055.","chicago":"Liebenau, Anita, Letícia Mattos, Walner Mendonca dos Santos, and Jozef Skokan. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” <i>Random Structures and Algorithms</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/rsa.21106\">https://doi.org/10.1002/rsa.21106</a>.","apa":"Liebenau, A., Mattos, L., Mendonca dos Santos, W., &#38; Skokan, J. (2023). Asymmetric Ramsey properties of random graphs involving cliques and cycles. <i>Random Structures and Algorithms</i>. Wiley. <a href=\"https://doi.org/10.1002/rsa.21106\">https://doi.org/10.1002/rsa.21106</a>"},"publication":"Random Structures and Algorithms"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Cipolloni, Giorgio, et al. “Quenched Universality for Deformed Wigner Matrices.” <i>Probability Theory and Related Fields</i>, vol. 185, Springer Nature, 2023, pp. 1183–1218, doi:<a href=\"https://doi.org/10.1007/s00440-022-01156-7\">10.1007/s00440-022-01156-7</a>.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 185, 1183–1218.","ama":"Cipolloni G, Erdös L, Schröder DJ. Quenched universality for deformed Wigner matrices. <i>Probability Theory and Related Fields</i>. 2023;185:1183–1218. doi:<a href=\"https://doi.org/10.1007/s00440-022-01156-7\">10.1007/s00440-022-01156-7</a>","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Quenched universality for deformed Wigner matrices,” <i>Probability Theory and Related Fields</i>, vol. 185. Springer Nature, pp. 1183–1218, 2023.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields 185 (2023) 1183–1218.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2023). Quenched universality for deformed Wigner matrices. <i>Probability Theory and Related Fields</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00440-022-01156-7\">https://doi.org/10.1007/s00440-022-01156-7</a>","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Quenched Universality for Deformed Wigner Matrices.” <i>Probability Theory and Related Fields</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00440-022-01156-7\">https://doi.org/10.1007/s00440-022-01156-7</a>."},"publication":"Probability Theory and Related Fields","file":[{"content_type":"application/pdf","relation":"main_file","checksum":"b9247827dae5544d1d19c37abe547abc","file_size":782278,"file_id":"14054","success":1,"date_updated":"2023-08-14T12:47:32Z","creator":"dernst","access_level":"open_access","date_created":"2023-08-14T12:47:32Z","file_name":"2023_ProbabilityTheory_Cipolloni.pdf"}],"type":"journal_article","acknowledgement":"The authors are indebted to Sourav Chatterjee for forwarding the very inspiring question that Stephen Shenker originally addressed to him which initiated the current paper. They are also grateful that the authors of [23] kindly shared their preliminary numerical results in June 2021.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","isi":1,"tmp":{"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)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2106.10200"],"isi":["000830344500001"]},"date_published":"2023-04-01T00:00:00Z","date_updated":"2024-10-09T21:03:02Z","publication_status":"published","title":"Quenched universality for deformed Wigner matrices","abstract":[{"text":"Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble.","lang":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"corr_author":"1","arxiv":1,"language":[{"iso":"eng"}],"year":"2023","page":"1183–1218","day":"01","article_type":"original","publisher":"Springer Nature","department":[{"_id":"LaEr"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","intvolume":"       185","scopus_import":"1","doi":"10.1007/s00440-022-01156-7","date_created":"2022-08-07T22:02:00Z","volume":185,"author":[{"first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László"},{"orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","last_name":"Schröder","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"month":"04","oa":1,"oa_version":"Published Version","status":"public","ddc":["510"],"_id":"11741","file_date_updated":"2023-08-14T12:47:32Z"},{"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","article_type":"original","day":"01","page":"745–770","language":[{"iso":"eng"}],"year":"2023","status":"public","oa_version":"Published Version","_id":"11999","ddc":["510"],"file_date_updated":"2022-08-29T11:23:15Z","oa":1,"month":"04","author":[{"full_name":"Arroyo Guevara, Alan M","last_name":"Arroyo Guevara","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M"},{"full_name":"Klute, Fabian","last_name":"Klute","first_name":"Fabian"},{"last_name":"Parada","full_name":"Parada, Irene","first_name":"Irene"},{"first_name":"Birgit","full_name":"Vogtenhuber, Birgit","last_name":"Vogtenhuber"},{"full_name":"Seidel, Raimund","last_name":"Seidel","first_name":"Raimund"},{"first_name":"Tilo","full_name":"Wiedera, Tilo","last_name":"Wiedera"}],"date_created":"2022-08-28T22:02:01Z","volume":69,"scopus_import":"1","doi":"10.1007/s00454-022-00394-9","intvolume":"        69","type":"journal_article","acknowledgement":"This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.","file":[{"checksum":"def7ae3b28d9fd6aec16450e40090302","content_type":"application/pdf","relation":"main_file","file_size":1002218,"file_id":"12006","creator":"alisjak","access_level":"open_access","date_updated":"2022-08-29T11:23:15Z","success":1,"date_created":"2022-08-29T11:23:15Z","file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf"}],"publication":"Discrete and Computational Geometry","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770.","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., &#38; Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00394-9\">https://doi.org/10.1007/s00454-022-00394-9</a>","chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-022-00394-9\">https://doi.org/10.1007/s00454-022-00394-9</a>.","mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” <i>Discrete and Computational Geometry</i>, vol. 69, Springer Nature, 2023, pp. 745–770, doi:<a href=\"https://doi.org/10.1007/s00454-022-00394-9\">10.1007/s00454-022-00394-9</a>.","ista":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770.","ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. <i>Discrete and Computational Geometry</i>. 2023;69:745–770. doi:<a href=\"https://doi.org/10.1007/s00454-022-00394-9\">10.1007/s00454-022-00394-9</a>","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” <i>Discrete and Computational Geometry</i>, vol. 69. Springer Nature, pp. 745–770, 2023."},"ec_funded":1,"arxiv":1,"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"abstract":[{"text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.","lang":"eng"}],"quality_controlled":"1","date_updated":"2025-04-14T07:43:59Z","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"title":"Inserting one edge into a simple drawing is hard","publication_status":"published","isi":1,"tmp":{"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)","image":"/images/cc_by.png"},"date_published":"2023-04-01T00:00:00Z","external_id":{"arxiv":["1909.07347"],"isi":["000840292800001"]}},{"ec_funded":1,"publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"corr_author":"1","quality_controlled":"1","abstract":[{"lang":"eng","text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets."}],"isi":1,"tmp":{"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)","image":"/images/cc_by.png"},"date_published":"2023-01-01T00:00:00Z","external_id":{"isi":["000846967100001"],"pmid":["36687803"]},"date_updated":"2025-04-23T08:46:48Z","title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","project":[{"grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended"},{"call_identifier":"FWF","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"},{"name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35"}],"publication_status":"published","type":"journal_article","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","file":[{"file_id":"12322","file_size":911017,"checksum":"71685ca5121f4c837f40c3f8eb50c915","content_type":"application/pdf","relation":"main_file","date_created":"2023-01-20T10:02:48Z","file_name":"2023_Algorithmica_Edelsbrunner.pdf","creator":"dernst","access_level":"open_access","date_updated":"2023-01-20T10:02:48Z","success":1}],"publication":"Algorithmica","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Edelsbrunner, H., &#38; Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. <i>Algorithmica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00453-022-01027-6\">https://doi.org/10.1007/s00453-022-01027-6</a>","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” <i>Algorithmica</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00453-022-01027-6\">https://doi.org/10.1007/s00453-022-01027-6</a>.","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” <i>Algorithmica</i>, vol. 85. Springer Nature, pp. 277–295, 2023.","ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. <i>Algorithmica</i>. 2023;85:277-295. doi:<a href=\"https://doi.org/10.1007/s00453-022-01027-6\">10.1007/s00453-022-01027-6</a>","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” <i>Algorithmica</i>, vol. 85, Springer Nature, 2023, pp. 277–95, doi:<a href=\"https://doi.org/10.1007/s00453-022-01027-6\">10.1007/s00453-022-01027-6</a>.","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295."},"oa_version":"Published Version","status":"public","_id":"12086","file_date_updated":"2023-01-20T10:02:48Z","ddc":["510"],"month":"01","oa":1,"date_created":"2022-09-11T22:01:57Z","volume":85,"author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"orcid":"0000-0002-8882-5116","last_name":"Osang","full_name":"Osang, Georg F","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        85","scopus_import":"1","doi":"10.1007/s00453-022-01027-6","department":[{"_id":"HeEd"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","article_type":"original","publisher":"Springer Nature","page":"277-295","language":[{"iso":"eng"}],"year":"2023"},{"author":[{"first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","full_name":"Wirth, Melchior","last_name":"Wirth"},{"last_name":"Zhang","full_name":"Zhang, Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","first_name":"Haonan"}],"date_created":"2022-09-11T22:01:57Z","volume":24,"scopus_import":"1","doi":"10.1007/s00023-022-01220-x","intvolume":"        24","status":"public","oa_version":"Published Version","file_date_updated":"2023-08-14T11:38:28Z","_id":"12087","ddc":["510"],"oa":1,"month":"03","page":"717-750","language":[{"iso":"eng"}],"year":"2023","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"JaMa"}],"article_type":"original","publisher":"Springer Nature","day":"01","quality_controlled":"1","abstract":[{"text":"Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups.","lang":"eng"}],"date_updated":"2025-04-23T08:53:05Z","publication_status":"published","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"M03337","_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","name":"Curvature-dimension in noncommutative analysis"},{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"title":"Curvature-dimension conditions for symmetric quantum Markov semigroups","tmp":{"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)","image":"/images/cc_by.png"},"date_published":"2023-03-01T00:00:00Z","isi":1,"external_id":{"arxiv":["2105.08303"],"isi":["000837499800002"],"pmid":["36950223"]},"ec_funded":1,"arxiv":1,"publication_identifier":{"issn":["1424-0637"]},"corr_author":"1","publication":"Annales Henri Poincare","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov semigroups. <i>Annales Henri Poincare</i>. 2023;24:717-750. doi:<a href=\"https://doi.org/10.1007/s00023-022-01220-x\">10.1007/s00023-022-01220-x</a>","ieee":"M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum Markov semigroups,” <i>Annales Henri Poincare</i>, vol. 24. Springer Nature, pp. 717–750, 2023.","mla":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” <i>Annales Henri Poincare</i>, vol. 24, Springer Nature, 2023, pp. 717–50, doi:<a href=\"https://doi.org/10.1007/s00023-022-01220-x\">10.1007/s00023-022-01220-x</a>.","ista":"Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 24, 717–750.","apa":"Wirth, M., &#38; Zhang, H. (2023). Curvature-dimension conditions for symmetric quantum Markov semigroups. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-022-01220-x\">https://doi.org/10.1007/s00023-022-01220-x</a>","chicago":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” <i>Annales Henri Poincare</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00023-022-01220-x\">https://doi.org/10.1007/s00023-022-01220-x</a>.","short":"M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750."},"pmid":1,"type":"journal_article","acknowledgement":"H.Z. is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. M.W. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117) and from the Austrian Science Fund (FWF) through grant number F65. Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. Open access funding provided by Austrian Science Fund (FWF).","file":[{"content_type":"application/pdf","relation":"main_file","checksum":"8c7b185eba5ccd92ef55c120f654222c","file_id":"14051","file_size":554871,"success":1,"date_updated":"2023-08-14T11:38:28Z","access_level":"open_access","creator":"dernst","date_created":"2023-08-14T11:38:28Z","file_name":"2023_AnnalesHenriPoincare_Wirth.pdf"}]},{"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","department":[{"_id":"JaMa"}],"article_type":"original","publisher":"Springer Nature","day":"01","issue":"1","year":"2023","language":[{"iso":"eng"}],"_id":"12104","file_date_updated":"2023-01-20T10:45:06Z","ddc":["510"],"oa_version":"Published Version","status":"public","article_number":"9","oa":1,"month":"01","author":[{"full_name":"Dello Schiavo, Lorenzo","last_name":"Dello Schiavo","orcid":"0000-0002-9881-6870","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo"},{"id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","first_name":"Melchior","full_name":"Wirth, Melchior","last_name":"Wirth","orcid":"0000-0002-0519-4241"}],"volume":23,"date_created":"2023-01-08T23:00:53Z","doi":"10.1007/s00028-022-00859-7","scopus_import":"1","intvolume":"        23","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","type":"journal_article","file":[{"file_id":"12325","file_size":422612,"checksum":"1f34f3e2cb521033de6154f274ea3a4e","content_type":"application/pdf","relation":"main_file","date_created":"2023-01-20T10:45:06Z","file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","access_level":"open_access","creator":"dernst","success":1,"date_updated":"2023-01-20T10:45:06Z"}],"publication":"Journal of Evolution Equations","citation":{"short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” <i>Journal of Evolution Equations</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00028-022-00859-7\">https://doi.org/10.1007/s00028-022-00859-7</a>.","apa":"Dello Schiavo, L., &#38; Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. <i>Journal of Evolution Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00028-022-00859-7\">https://doi.org/10.1007/s00028-022-00859-7</a>","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” <i>Journal of Evolution Equations</i>, vol. 23, no. 1, 9, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00028-022-00859-7\">10.1007/s00028-022-00859-7</a>.","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. <i>Journal of Evolution Equations</i>. 2023;23(1). doi:<a href=\"https://doi.org/10.1007/s00028-022-00859-7\">10.1007/s00028-022-00859-7</a>","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” <i>Journal of Evolution Equations</i>, vol. 23, no. 1. Springer Nature, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"ec_funded":1,"corr_author":"1","publication_identifier":{"eissn":["1424-3202"],"issn":["1424-3199"]},"abstract":[{"lang":"eng","text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces."}],"quality_controlled":"1","publication_status":"published","title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"name":"Configuration Spaces over Non-Smooth Spaces","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","grant_number":"E208"},{"_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833","name":"Gradient flow techniques for quantum Markov semigroups","grant_number":"ESP156_N"}],"date_updated":"2025-04-23T08:45:56Z","tmp":{"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)","image":"/images/cc_by.png"},"isi":1,"external_id":{"pmid":["36597554"],"isi":["000906214600004"]},"date_published":"2023-01-01T00:00:00Z"},{"type":"journal_article","acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society.","file":[{"date_updated":"2023-08-16T11:30:45Z","success":1,"access_level":"open_access","creator":"dernst","file_name":"2023_NatureBioTech_Yeung.pdf","date_created":"2023-08-16T11:30:45Z","relation":"main_file","content_type":"application/pdf","checksum":"668447a1c8d360b68f8aaf9e08ed644f","file_id":"14066","file_size":12040976}],"publication":"Nature Biotechnology","citation":{"ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” <i>Nature Biotechnology</i>, vol. 41. Springer Nature, pp. 813–823, 2023.","ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. <i>Nature Biotechnology</i>. 2023;41:813–823. doi:<a href=\"https://doi.org/10.1038/s41587-022-01560-3\">10.1038/s41587-022-01560-3</a>","mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” <i>Nature Biotechnology</i>, vol. 41, Springer Nature, 2023, pp. 813–823, doi:<a href=\"https://doi.org/10.1038/s41587-022-01560-3\">10.1038/s41587-022-01560-3</a>.","ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823.","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., &#38; Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-022-01560-3\">https://doi.org/10.1038/s41587-022-01560-3</a>","chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” <i>Nature Biotechnology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41587-022-01560-3\">https://doi.org/10.1038/s41587-022-01560-3</a>.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"corr_author":"1","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"abstract":[{"text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.","lang":"eng"}],"quality_controlled":"1","title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","publication_status":"published","date_updated":"2025-04-23T08:45:24Z","tmp":{"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)","image":"/images/cc_by.png"},"date_published":"2023-06-01T00:00:00Z","isi":1,"external_id":{"isi":["000909067600003"],"pmid":["36593403"]},"article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"ScienComp"}],"publisher":"Springer Nature","article_type":"original","day":"01","page":"813–823","year":"2023","language":[{"iso":"eng"}],"ddc":["570"],"_id":"12106","file_date_updated":"2023-08-16T11:30:45Z","status":"public","oa_version":"Published Version","oa":1,"month":"06","author":[{"id":"123012b2-db30-11eb-b4d8-a35840c0551b","first_name":"Jake","full_name":"Yeung, Jake","last_name":"Yeung","orcid":"0000-0003-1732-1559"},{"full_name":"Florescu, Maria","last_name":"Florescu","first_name":"Maria"},{"last_name":"Zeller","full_name":"Zeller, Peter","first_name":"Peter"},{"first_name":"Buys Anton","last_name":"De Barbanson","full_name":"De Barbanson, Buys Anton"},{"first_name":"Max D.","full_name":"Wellenstein, Max D.","last_name":"Wellenstein"},{"first_name":"Alexander","last_name":"Van Oudenaarden","full_name":"Van Oudenaarden, Alexander"}],"volume":41,"date_created":"2023-01-08T23:00:53Z","doi":"10.1038/s41587-022-01560-3","scopus_import":"1","intvolume":"        41"},{"publication":"Journal of Structural Biology: X","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","mla":"Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” <i>Journal of Structural Biology: X</i>, vol. 7, 100079, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">10.1016/j.yjsbx.2022.100079</a>.","ieee":"D. F. Gauto <i>et al.</i>, “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” <i>Journal of Structural Biology: X</i>, vol. 7. Elsevier, 2023.","ama":"Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. <i>Journal of Structural Biology: X</i>. 2023;7. doi:<a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">10.1016/j.yjsbx.2022.100079</a>","short":"D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).","chicago":"Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” <i>Journal of Structural Biology: X</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">https://doi.org/10.1016/j.yjsbx.2022.100079</a>.","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., &#38; Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. <i>Journal of Structural Biology: X</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">https://doi.org/10.1016/j.yjsbx.2022.100079</a>"},"acknowledgement":"The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”.","type":"journal_article","file":[{"file_id":"14064","file_size":5132322,"checksum":"b4b1c10a31018aafe053b7d55a470e54","content_type":"application/pdf","relation":"main_file","date_created":"2023-08-16T09:36:28Z","file_name":"2023_JourStrucBiologyX_Gauto.pdf","creator":"dernst","access_level":"open_access","date_updated":"2023-08-16T09:36:28Z","success":1}],"abstract":[{"text":"Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.","lang":"eng"}],"quality_controlled":"1","external_id":{"pmid":["36578472"]},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"date_published":"2023-01-01T00:00:00Z","date_updated":"2024-10-09T21:04:02Z","publication_status":"published","title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","publication_identifier":{"issn":["2590-1524"]},"corr_author":"1","keyword":["Structural Biology"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","language":[{"iso":"eng"}],"year":"2023","department":[{"_id":"PaSc"}],"has_accepted_license":"1","article_processing_charge":"No","day":"01","publisher":"Elsevier","article_type":"original","date_created":"2023-01-12T11:55:38Z","volume":7,"author":[{"full_name":"Gauto, Diego F.","last_name":"Gauto","first_name":"Diego F."},{"first_name":"Olga O.","last_name":"Lebedenko","full_name":"Lebedenko, Olga O."},{"id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie","full_name":"Becker, Lea Marie","last_name":"Becker","orcid":"0000-0002-6401-5151"},{"first_name":"Isabel","full_name":"Ayala, Isabel","last_name":"Ayala"},{"full_name":"Lichtenecker, Roman","last_name":"Lichtenecker","first_name":"Roman"},{"last_name":"Skrynnikov","full_name":"Skrynnikov, Nikolai R.","first_name":"Nikolai R."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"}],"intvolume":"         7","scopus_import":"1","doi":"10.1016/j.yjsbx.2022.100079","article_number":"100079","oa_version":"Published Version","status":"public","ddc":["570"],"_id":"12114","file_date_updated":"2023-08-16T09:36:28Z","month":"01","oa":1},{"publication":"Annals of Surgical Oncology","citation":{"apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. <i>Annals of Surgical Oncology</i>. Springer Nature. <a href=\"https://doi.org/10.1245/s10434-022-12681-z\">https://doi.org/10.1245/s10434-022-12681-z</a>","chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” <i>Annals of Surgical Oncology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1245/s10434-022-12681-z\">https://doi.org/10.1245/s10434-022-12681-z</a>.","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 46–47.","ieee":"J. Glajzer <i>et al.</i>, “ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium,” <i>Annals of Surgical Oncology</i>, vol. 30. Springer Nature, pp. 46–47, 2023.","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. <i>Annals of Surgical Oncology</i>. 2023;30:46-47. doi:<a href=\"https://doi.org/10.1245/s10434-022-12681-z\">10.1245/s10434-022-12681-z</a>","ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 46–47.","mla":"Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” <i>Annals of Surgical Oncology</i>, vol. 30, Springer Nature, 2023, pp. 46–47, doi:<a href=\"https://doi.org/10.1245/s10434-022-12681-z\">10.1245/s10434-022-12681-z</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).","type":"journal_article","quality_controlled":"1","date_published":"2023-01-01T00:00:00Z","isi":1,"external_id":{"isi":["000879151800001"]},"publication_status":"published","title":"ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium","date_updated":"2025-04-23T08:43:43Z","publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"keyword":["Oncology","Surgery"],"page":"46-47","year":"2023","language":[{"iso":"eng"}],"department":[{"_id":"JoDa"}],"article_processing_charge":"No","day":"01","publisher":"Springer Nature","article_type":"original","volume":30,"related_material":{"record":[{"status":"public","id":"12205","relation":"other"}]},"date_created":"2023-01-12T11:56:22Z","author":[{"full_name":"Glajzer, Jacek","last_name":"Glajzer","first_name":"Jacek"},{"first_name":"Dan Cacsire","last_name":"Castillo-Tong","full_name":"Castillo-Tong, Dan Cacsire"},{"first_name":"Rolf","full_name":"Richter, Rolf","last_name":"Richter"},{"first_name":"Ignace","last_name":"Vergote","full_name":"Vergote, Ignace"},{"last_name":"Kulbe","full_name":"Kulbe, Hagen","first_name":"Hagen"},{"last_name":"Vanderstichele","full_name":"Vanderstichele, Adriaan","first_name":"Adriaan"},{"first_name":"Ilary","full_name":"Ruscito, Ilary","last_name":"Ruscito"},{"first_name":"Fabian","full_name":"Trillsch, Fabian","last_name":"Trillsch"},{"full_name":"Mustea, Alexander","last_name":"Mustea","first_name":"Alexander"},{"first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger"},{"first_name":"Charlie","last_name":"Gourley","full_name":"Gourley, Charlie"},{"first_name":"Hani","last_name":"Gabra","full_name":"Gabra, Hani"},{"full_name":"Taube, Eliane T.","last_name":"Taube","first_name":"Eliane T."},{"full_name":"Dorigo, Oliver","last_name":"Dorigo","first_name":"Oliver"},{"first_name":"David","last_name":"Horst","full_name":"Horst, David"},{"full_name":"Keunecke, Carlotta","last_name":"Keunecke","first_name":"Carlotta"},{"first_name":"Joanna","last_name":"Baum","full_name":"Baum, Joanna"},{"full_name":"Angelotti, Timothy","last_name":"Angelotti","first_name":"Timothy"},{"last_name":"Sehouli","full_name":"Sehouli, Jalid","first_name":"Jalid"},{"full_name":"Braicu, Elena Ioana","last_name":"Braicu","first_name":"Elena Ioana"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1245/s10434-022-12681-z"}],"intvolume":"        30","doi":"10.1245/s10434-022-12681-z","scopus_import":"1","_id":"12115","oa_version":"Published Version","status":"public","month":"01","oa":1},{"title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","publication_status":"published","date_updated":"2025-04-23T08:45:00Z","date_published":"2023-02-01T00:00:00Z","tmp":{"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)","image":"/images/cc_by.png"},"external_id":{"pmid":["36539617"]},"quality_controlled":"1","abstract":[{"text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages.","lang":"eng"}],"publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"citation":{"ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. <i>Nature Genetics</i>. 2023;55:333-345. doi:<a href=\"https://doi.org/10.1038/s41588-022-01260-3\">10.1038/s41588-022-01260-3</a>","ieee":"P. Zeller <i>et al.</i>, “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” <i>Nature Genetics</i>, vol. 55. Springer Nature, pp. 333–345, 2023.","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” <i>Nature Genetics</i>, vol. 55, Springer Nature, 2023, pp. 333–45, doi:<a href=\"https://doi.org/10.1038/s41588-022-01260-3\">10.1038/s41588-022-01260-3</a>.","ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” <i>Nature Genetics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41588-022-01260-3\">https://doi.org/10.1038/s41588-022-01260-3</a>.","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-022-01260-3\">https://doi.org/10.1038/s41588-022-01260-3</a>","short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication":"Nature Genetics","file":[{"access_level":"open_access","creator":"dernst","success":1,"date_updated":"2023-02-27T07:46:45Z","date_created":"2023-02-27T07:46:45Z","file_name":"2023_NatureGenetics_Zeller.pdf","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e","content_type":"application/pdf","relation":"main_file","file_size":21484855,"file_id":"12688"}],"type":"journal_article","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","doi":"10.1038/s41588-022-01260-3","scopus_import":"1","intvolume":"        55","author":[{"first_name":"Peter","full_name":"Zeller, Peter","last_name":"Zeller"},{"id":"123012b2-db30-11eb-b4d8-a35840c0551b","first_name":"Jake","last_name":"Yeung","full_name":"Yeung, Jake","orcid":"0000-0003-1732-1559"},{"first_name":"Helena","full_name":"Viñas Gaza, Helena","last_name":"Viñas Gaza"},{"first_name":"Buys Anton","full_name":"de Barbanson, Buys Anton","last_name":"de Barbanson"},{"first_name":"Vivek","last_name":"Bhardwaj","full_name":"Bhardwaj, Vivek"},{"last_name":"Florescu","full_name":"Florescu, Maria","first_name":"Maria"},{"first_name":"Reinier","full_name":"van der Linden, Reinier","last_name":"van der Linden"},{"full_name":"van Oudenaarden, Alexander","last_name":"van Oudenaarden","first_name":"Alexander"}],"volume":55,"date_created":"2023-01-12T12:09:09Z","oa":1,"month":"02","file_date_updated":"2023-02-27T07:46:45Z","_id":"12158","ddc":["570","000"],"status":"public","oa_version":"Published Version","year":"2023","language":[{"iso":"eng"}],"keyword":["Genetics"],"page":"333-345","article_type":"review","publisher":"Springer Nature","day":"01","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"ScienComp"}]},{"language":[{"iso":"eng"}],"year":"2023","page":"58-65","keyword":["Cell Biology","Developmental Biology"],"day":"02","publisher":"Elsevier","article_type":"review","department":[{"_id":"EdHa"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","doi":"10.1016/j.semcdb.2022.11.005","date_created":"2023-01-12T12:09:47Z","volume":"150-151","author":[{"full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B"}],"month":"12","oa":1,"oa_version":"Published Version","status":"public","file_date_updated":"2024-01-08T10:16:04Z","_id":"12162","ddc":["570"],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Corominas-Murtra, Bernat, and Edouard B Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” <i>Seminars in Cell &#38; Developmental Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">https://doi.org/10.1016/j.semcdb.2022.11.005</a>.","apa":"Corominas-Murtra, B., &#38; Hannezo, E. B. (2023). Modelling the dynamics of mammalian gut homeostasis. <i>Seminars in Cell &#38; Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">https://doi.org/10.1016/j.semcdb.2022.11.005</a>","short":"B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell &#38; Developmental Biology 150–151 (2023) 58–65.","ama":"Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis. <i>Seminars in Cell &#38; Developmental Biology</i>. 2023;150-151:58-65. doi:<a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">10.1016/j.semcdb.2022.11.005</a>","ieee":"B. Corominas-Murtra and E. B. Hannezo, “Modelling the dynamics of mammalian gut homeostasis,” <i>Seminars in Cell &#38; Developmental Biology</i>, vol. 150–151. Elsevier, pp. 58–65, 2023.","ista":"Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell &#38; Developmental Biology. 150–151, 58–65.","mla":"Corominas-Murtra, Bernat, and Edouard B. Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” <i>Seminars in Cell &#38; Developmental Biology</i>, vol. 150–151, Elsevier, 2023, pp. 58–65, doi:<a href=\"https://doi.org/10.1016/j.semcdb.2022.11.005\">10.1016/j.semcdb.2022.11.005</a>."},"publication":"Seminars in Cell & Developmental Biology","file":[{"checksum":"c619887cf130f4649bf3035417186004","relation":"main_file","content_type":"application/pdf","file_id":"14741","file_size":1343750,"creator":"dernst","access_level":"open_access","date_updated":"2024-01-08T10:16:04Z","success":1,"file_name":"2023_SeminarsCellDevBiology_CorominasMurtra.pdf","date_created":"2024-01-08T10:16:04Z"}],"acknowledgement":"This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.).\r\nB. C-M wants to acknowledge the support of the field of excellence Complexity of Life, in Basic Research and Innovation of the University of Graz.","type":"journal_article","isi":1,"tmp":{"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)","image":"/images/cc_by.png"},"external_id":{"isi":["001053522200001"],"pmid":["36470715"]},"date_published":"2023-12-02T00:00:00Z","date_updated":"2025-04-14T07:52:27Z","title":"Modelling the dynamics of mammalian gut homeostasis","publication_status":"published","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"abstract":[{"text":"Homeostatic balance in the intestinal epithelium relies on a fast cellular turnover, which is coordinated by an intricate interplay between biochemical signalling, mechanical forces and organ geometry. We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues.","lang":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["1084-9521"]},"corr_author":"1","ec_funded":1},{"type":"journal_article","acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints.","file":[{"date_created":"2023-08-16T08:31:04Z","file_name":"2023_FEBSLetters_Loose.pdf","creator":"dernst","access_level":"open_access","success":1,"date_updated":"2023-08-16T08:31:04Z","file_size":3148143,"file_id":"14063","checksum":"7492244d3f9c5faa1347ef03f6e5bc84","content_type":"application/pdf","relation":"main_file"}],"publication":"FEBS Letters","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. 2023;597(6):762-777. doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>","ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” <i>FEBS Letters</i>, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>.","apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., &#38; Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>","chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>.","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777."},"publication_identifier":{"eissn":["1873-3468"],"issn":["0014-5793"]},"corr_author":"1","quality_controlled":"1","abstract":[{"lang":"eng","text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time."}],"date_published":"2023-03-01T00:00:00Z","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"isi":1,"external_id":{"isi":["000891573000001"],"pmid":["36448231"]},"date_updated":"2024-10-09T21:03:42Z","title":"In vitro reconstitution of small GTPase regulation","publication_status":"published","department":[{"_id":"MaLo"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","issue":"6","article_type":"review","publisher":"Wiley","page":"762-777","keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"language":[{"iso":"eng"}],"year":"2023","oa_version":"Published Version","status":"public","_id":"12163","ddc":["570"],"file_date_updated":"2023-08-16T08:31:04Z","month":"03","oa":1,"date_created":"2023-01-12T12:09:58Z","volume":597,"author":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Loose, Martin","last_name":"Loose","orcid":"0000-0001-7309-9724"},{"last_name":"Auer","full_name":"Auer, Albert","orcid":"0000-0002-3580-2906","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","first_name":"Albert"},{"first_name":"Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425","full_name":"Brognara, Gabriel","last_name":"Brognara"},{"first_name":"Hanifatul R","id":"55380f95-15b2-11ec-abd3-aff8e230696b","last_name":"Budiman","full_name":"Budiman, Hanifatul R"},{"last_name":"Kowalski","full_name":"Kowalski, Lukasz M","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","first_name":"Lukasz M"},{"last_name":"Matijevic","full_name":"Matijevic, Ivana","first_name":"Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd"}],"intvolume":"       597","scopus_import":"1","doi":"10.1002/1873-3468.14540"},{"citation":{"ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic amortized step complexity. <i>Distributed Computing</i>. 2023;36:29-43. doi:<a href=\"https://doi.org/10.1007/s00446-022-00439-5\">10.1007/s00446-022-00439-5</a>","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with polylogarithmic amortized step complexity,” <i>Distributed Computing</i>, vol. 36. Springer Nature, pp. 29–43, 2023.","ista":"Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 29–43.","mla":"Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” <i>Distributed Computing</i>, vol. 36, Springer Nature, 2023, pp. 29–43, doi:<a href=\"https://doi.org/10.1007/s00446-022-00439-5\">10.1007/s00446-022-00439-5</a>.","apa":"Baig, M. A., Hendler, D., Milani, A., &#38; Travers, C. (2023). Long-lived counters with polylogarithmic amortized step complexity. <i>Distributed Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00446-022-00439-5\">https://doi.org/10.1007/s00446-022-00439-5</a>","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” <i>Distributed Computing</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00446-022-00439-5\">https://doi.org/10.1007/s00446-022-00439-5</a>.","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023) 29–43."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Distributed Computing","type":"journal_article","acknowledgement":"A preliminary version of this work appeared in DISC’19. Mirza Ahad Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported by the Israel Science Foundation (Grants 380/18 and 1425/22).","external_id":{"isi":["000890138700001"]},"isi":1,"date_published":"2023-03-01T00:00:00Z","title":"Long-lived counters with polylogarithmic amortized step complexity","publication_status":"published","date_updated":"2023-08-16T08:39:36Z","quality_controlled":"1","abstract":[{"lang":"eng","text":"A shared-memory counter is a widely-used and well-studied concurrent object. It supports two operations: An Inc operation that increases its value by 1 and a Read operation that returns its current value. In Jayanti et al (SIAM J Comput, 30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case step complexity of obstruction-free implementations, from read-write registers, of a large class of shared objects that includes counters. The lower bound leaves open the question of finding counter implementations with sub-linear amortized step complexity. In this work, we address this gap. We show that n-process, wait-free and linearizable counters can be implemented from read-write registers with O(log2n) amortized step complexity. This is the first counter algorithm from read-write registers that provides sub-linear amortized step complexity in executions of arbitrary length. Since a logarithmic lower bound on the amortized step complexity of obstruction-free counter implementations exists, our upper bound is within a logarithmic factor of the optimal. The worst-case step complexity of the construction remains linear, which is optimal. This is obtained thanks to a new max register construction with O(logn) amortized step complexity in executions of arbitrary length in which the value stored in the register does not grow too quickly. We then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel [1] in which we “plug” our max register implementation to show that it remains linearizable while achieving O(log2n) amortized step complexity."}],"publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]},"year":"2023","language":[{"iso":"eng"}],"keyword":["Computational Theory and Mathematics","Computer Networks and Communications","Hardware and Architecture","Theoretical Computer Science"],"page":"29-43","day":"01","article_type":"original","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"article_processing_charge":"No","intvolume":"        36","doi":"10.1007/s00446-022-00439-5","scopus_import":"1","volume":36,"date_created":"2023-01-12T12:10:08Z","author":[{"id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad","last_name":"Baig","full_name":"Baig, Mirza Ahad"},{"first_name":"Danny","last_name":"Hendler","full_name":"Hendler, Danny"},{"first_name":"Alessia","last_name":"Milani","full_name":"Milani, Alessia"},{"first_name":"Corentin","last_name":"Travers","full_name":"Travers, Corentin"}],"main_file_link":[{"open_access":"1","url":"https://drops.dagstuhl.de/opus/volltexte/2019/11310/"}],"month":"03","oa":1,"_id":"12164","oa_version":"Preprint","status":"public"},{"page":"26-29","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"OA_type":"free access","language":[{"iso":"eng"}],"year":"2023","article_processing_charge":"No","department":[{"_id":"NiBa"}],"publisher":"Wiley","article_type":"editorial","issue":"1","day":"01","main_file_link":[{"url":"https://doi.org/10.1111/mec.16779","open_access":"1"}],"author":[{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"date_created":"2023-01-12T12:10:28Z","volume":32,"scopus_import":"1","doi":"10.1111/mec.16779","intvolume":"        32","oa_version":"Published Version","status":"public","_id":"12166","oa":1,"month":"01","publication":"Molecular Ecology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>.","apa":"Westram, A. M., &#38; Butlin, R. (2023). Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>","short":"A.M. Westram, R. Butlin, Molecular Ecology 32 (2023) 26–29.","ama":"Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. 2023;32(1):26-29. doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>","ieee":"A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize,” <i>Molecular Ecology</i>, vol. 32, no. 1. Wiley, pp. 26–29, 2023.","ista":"Westram AM, Butlin R. 2023. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.","mla":"Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>, vol. 32, no. 1, Wiley, 2023, pp. 26–29, doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>."},"pmid":1,"type":"journal_article","abstract":[{"text":"Kerstin Johannesson is a marine ecologist and evolutionary biologist based at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated in the beautiful Kosterhavet National Park on the Swedish west coast. Her work, using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main model systems, has made a remarkable contribution to marine evolutionary biology and our understanding of local adaptation and its genetic underpinnings.","lang":"eng"}],"quality_controlled":"1","date_updated":"2025-04-23T08:44:33Z","title":"Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize","publication_status":"published","external_id":{"pmid":["36443277"],"isi":["000892168800001"]},"isi":1,"date_published":"2023-01-01T00:00:00Z","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"corr_author":"1"}]