[{"has_accepted_license":"1","corr_author":"1","abstract":[{"text":"Across the tree of life, distinct designs of cellular membranes have evolved that are both stable\r\nand flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids\r\nthat self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess\r\nboth bilayer and double-headed, monolayer spanning bolalipids. This composition is believed\r\nto enable extremophile archaea to survive harsh environments. Here, through the creation of a\r\nminimal computational model for bolalipid membranes, we discover trade-offs when forming\r\nmembranes using lipids of a single type. Similar to living archaea, we can tune the stiffness of\r\nbolalipid molecules. We find that membranes made out of flexible bolalipid molecules resemble\r\nbilayer membranes as they can adopt U-shaped conformations to enable higher curvatures.\r\nConversely, rigid bolalipid molecules, like those found in archaea at higher temperatures,\r\npreferentially take on a straight conformation to self-assemble into liquid membranes that are\r\nstable, stiff, prone to pore formation, and which tear during membrane reshaping. Strikingly,\r\nhowever, our analysis reveals that it is possible to achieve the best of both worlds – membranes\r\nthat are fluid, stable at high temperatures and flexible enough to be reshaped without leaking –\r\nthrough the inclusion of a small fraction of bilayer lipids into a bolalipid membrane. Additionally,\r\nthe curvature-dependent softening of bolalipid membranes made of lipids with tension-sensitive\r\nconformation can also enable high rigidity at low curvatures while softening at high curvatures,\r\nmaking the membrane effectively a plastic material. Taken together, our study compares the\r\ndifferent membrane designs across the tree of life and indicates how combining lipids can be\r\nused to resolve trade-offs when generating membranes for (bio)technological applications.\r\n","lang":"eng"}],"type":"dissertation","degree_awarded":"PhD","file":[{"file_id":"18671","relation":"source_file","file_size":19161387,"embargo_to":"open_access","content_type":"application/zip","checksum":"eca06497a29078558395455c890a32d9","date_updated":"2025-06-18T22:30:03Z","date_created":"2024-12-18T12:27:01Z","file_name":"2024_msfa_thesis.zip","access_level":"closed","creator":"mamaral"},{"file_id":"18672","relation":"main_file","file_size":16530084,"content_type":"application/pdf","checksum":"2dc30ea46c5daf48d07e4cccb3c3de00","file_name":"2024_msfa_thesis.pdf","date_updated":"2025-06-18T22:30:03Z","date_created":"2024-12-18T12:26:30Z","access_level":"open_access","embargo":"2025-06-18","creator":"mamaral"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"AnSa"}],"file_date_updated":"2025-06-18T22:30:03Z","doi":"10.15479/at:ista:18661","publication_status":"published","tmp":{"short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"17","title":"Archaeal membranes : In silico modelling and design","ddc":["572","530"],"status":"public","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-046-6"]},"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"18670","status":"public"}]},"page":"57","alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"}],"date_updated":"2026-04-07T13:22:29Z","date_created":"2024-12-16T10:53:39Z","oa":1,"date_published":"2024-12-17T00:00:00Z","_id":"18661","citation":{"ista":"Santana de Freitas Amaral M. 2024. Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria.","short":"M. Santana de Freitas Amaral, Archaeal Membranes : In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.","apa":"Santana de Freitas Amaral, M. (2024). Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18661","chicago":"Santana de Freitas Amaral, Miguel. “Archaeal Membranes : In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18661.","ama":"Santana de Freitas Amaral M. Archaeal membranes : In silico modelling and design. 2024. doi:10.15479/at:ista:18661","mla":"Santana de Freitas Amaral, Miguel. Archaeal Membranes : In Silico Modelling and Design. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18661.","ieee":"M. Santana de Freitas Amaral, “Archaeal membranes : In silico modelling and design,” Institute of Science and Technology Austria, 2024."},"article_processing_charge":"No","year":"2024","month":"12","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","author":[{"full_name":"Santana de Freitas Amaral, Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","first_name":"Miguel","last_name":"Santana de Freitas Amaral"}]},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.10.18.619072"}],"language":[{"iso":"eng"}],"status":"public","abstract":[{"lang":"eng","text":"Across the tree of life, distinct designs of cellular membranes have evolved. In bacteria and eukaryotes single-headed lipids self-assemble into flexible bilayer membranes. By contrast, archaea often possess double-headed, monolayer spanning bolalipids, mixed with bilayer lipids, enabling them to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we discover trade-offs when forming membranes. We find that membranes made out of flexible bolalipids resemble bilayer membranes as bolalipids exhibit conformational switch into U-shaped conformations to enable higher curvatures. Conversely, stiffer bolalipids, resembling those in extremophile archaea, take on straight conformations and form liquid membranes that are stiff, and prone to pore formation during membrane reshaping. Strikingly, we show how to achieve fluid bolalipid membranes that are both stable and flexible – by including small amounts of bilayer lipids, as archaea do. Our study explains how different organisms resolve trade-offs when generating membranes of desired material properties."}],"corr_author":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"18661"}]},"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"}],"type":"preprint","ec_funded":1,"oa":1,"department":[{"_id":"AnSa"}],"OA_place":"repository","date_updated":"2026-05-31T22:30:31Z","date_created":"2024-12-18T10:07:45Z","_id":"18670","date_published":"2024-11-27T00:00:00Z","doi":"10.1101/2024.10.18.619072","citation":{"chicago":"Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” BioRxiv, n.d. https://doi.org/10.1101/2024.10.18.619072.","apa":"Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., & Šarić, A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv. https://doi.org/10.1101/2024.10.18.619072","mla":"Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” BioRxiv, doi:10.1101/2024.10.18.619072.","ieee":"M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Stability vs flexibility: Reshaping archaeal membranes in silico,” bioRxiv. .","ama":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv. doi:10.1101/2024.10.18.619072","ista":"Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, 10.1101/2024.10.18.619072.","short":"M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv (n.d.)."},"article_processing_charge":"No","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"draft","day":"27","year":"2024","acknowledgement":"MA, BB, and AŠ acknowledge funding by the\r\nVolkswagen Foundation Grant Az 96727. FF\r\nacknowledges fnancial support by the NOMIS\r\nfoundation. AŠ acknowledges funding by ERC\r\nStarting Grant “NEPA” 802960. We thank\r\nClaudia Flandoli for help with illustrations.","month":"11","oa_version":"Preprint","title":"Stability vs flexibility: Reshaping archaeal membranes in silico","publication":"bioRxiv","author":[{"full_name":"Santana de Freitas Amaral, Miguel","first_name":"Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","last_name":"Santana de Freitas Amaral"},{"orcid":"0000-0001-8501-6017","full_name":"Frey, Felix F","last_name":"Frey","first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3"},{"first_name":"Xiuyun","last_name":"Jiang","full_name":"Jiang, Xiuyun"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"}]},{"article_processing_charge":"No","doi":"10.1101/2024.07.02.601697","citation":{"short":"A. Mrnjavac, B. Vicoso, BioRxiv (n.d.).","ista":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv, 10.1101/2024.07.02.601697.","mla":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” BioRxiv, doi:10.1101/2024.07.02.601697.","ieee":"A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,” bioRxiv. .","ama":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv. doi:10.1101/2024.07.02.601697","chicago":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” BioRxiv, n.d. https://doi.org/10.1101/2024.07.02.601697.","apa":"Mrnjavac, A., & Vicoso, B. (n.d.). Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv. https://doi.org/10.1101/2024.07.02.601697"},"date_published":"2024-07-04T00:00:00Z","_id":"18549","date_created":"2024-11-13T09:12:08Z","OA_place":"repository","date_updated":"2026-05-31T22:30:30Z","department":[{"_id":"BeVi"}],"oa":1,"publication":"bioRxiv","author":[{"full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","last_name":"Mrnjavac"},{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"title":"Evidence of a Slower-Z effect in Schistosoma japonicum","oa_version":"Preprint","month":"07","day":"04","year":"2024","publication_status":"draft","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"corr_author":"1","abstract":[{"lang":"eng","text":"Sex-linked and autosomal loci experience different selective pressures and\r\nevolutionary dynamics. X (or Z) chromosomes are often hemizygous, as Y (or W)\r\nchromosomes often degenerate. Such hemizygous regions can be under greater\r\nefficacy of selection, as recessive mutations are immediately exposed to selection in\r\nthe heterogametic sex (the so-called Faster-X or Faster-Z effect). However, in young\r\nnon-recombining regions, Y/W chromosomes often have many functional genes, and\r\nmany X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on\r\nthe X/Z by the Y/W homolog is expected to drive a Slower-X (Slower-Z) effect for\r\ndiploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect\r\nhas been studied extensively, much less is known empirically about the evolutionary\r\ndynamics of diploid X or Z chromosomes. Here, we took advantage of published\r\npopulation genomic data in the female-heterogametic human parasite Schistosoma\r\njaponicum to characterize the gene content and diversity levels of the diploid and\r\nhemizygous regions of the Z chromosome. We used different metrics of selective\r\npressures acting on genes to test for differences in the efficacy of selection in\r\nhemizygous and diploid Z regions, relative to autosomes. We found consistent\r\npatterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both\r\nhemizygous and diploid Z regions. Moreover, relaxed selection was particularly\r\npronounced for female-biased genes on the diploid Z, as predicted by Slower-Z\r\ntheory.\r\n"}],"status":"public","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.07.02.601697"}],"type":"preprint","related_material":{"record":[{"status":"public","id":"19370","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"18531"}]}},{"degree_awarded":"PhD","type":"dissertation","abstract":[{"lang":"eng","text":"We introduce a new all-electric platform, that strong couples light to mechanical motion\r\nby ensuring that the external environmental coupling dominates over internal mechanical\r\ndissipation. The system only has three everyday components: AC, DC, and a fip-chip, in which\r\na metallized silicon nitride membrane is fipped on top of the device under test. This everyday\r\nelectromechanical device can be operated at low or room temperature and has 10000× lower\r\ninsertion loss than a comparable commercial quartz crystal, achieves a position imprecision\r\nmatching state-of-the-art optical interferometer, and enables remote cooling of mechanical\r\nmotion. The spatial properties of higher order mechanical modes are a promising feature for\r\nreconstructing unknown charge distributions.\r\n"}],"has_accepted_license":"1","corr_author":"1","ddc":["530"],"title":"Everyday electromechanics: Capacitive strong coupling to mechanical motion","day":"20","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","doi":"10.15479/at:ista:18104","file_date_updated":"2025-05-20T22:30:05Z","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nc/4.0/","file":[{"file_name":"PhD_DPuglia_Final.pdf","date_updated":"2025-05-20T22:30:05Z","content_type":"application/pdf","date_created":"2024-09-20T12:07:48Z","checksum":"7969263451b2356bfa0924725aa9de10","embargo":"2025-05-20","access_level":"open_access","creator":"cchlebak","file_id":"18105","relation":"main_file","file_size":10778238},{"access_level":"closed","date_updated":"2025-05-20T22:30:05Z","content_type":"application/x-zip-compressed","checksum":"98dfe7675775e30efffa03f7ff7c091b","date_created":"2024-09-20T12:13:09Z","file_name":"PhD_DPuglia_Thesis.zip","creator":"cchlebak","relation":"source_file","file_id":"18106","embargo_to":"open_access","file_size":385419748}],"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","id":"18143","relation":"part_of_dissertation"}]},"page":"63","project":[{"name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"},{"name":"Surface Charge and Tunneling Multi-Mode Imaging","grant_number":"26088","_id":"62843413-2b32-11ec-9570-c4ec6eabfae7"}],"language":[{"iso":"eng"}],"status":"public","publication_identifier":{"issn":["2663-337X"]},"author":[{"first_name":"Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","last_name":"Puglia","orcid":"0000-0003-1144-2763","full_name":"Puglia, Denise"}],"publisher":"Institute of Science and Technology Austria","month":"09","oa_version":"Published Version","year":"2024","citation":{"chicago":"Puglia, Denise. “Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18104.","apa":"Puglia, D. (2024). Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18104","mla":"Puglia, Denise. Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18104.","ieee":"D. Puglia, “Everyday electromechanics: Capacitive strong coupling to mechanical motion,” Institute of Science and Technology Austria, 2024.","ama":"Puglia D. Everyday electromechanics: Capacitive strong coupling to mechanical motion. 2024. doi:10.15479/at:ista:18104","ista":"Puglia D. 2024. Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria.","short":"D. Puglia, Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion, Institute of Science and Technology Austria, 2024."},"article_processing_charge":"No","_id":"18104","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"date_published":"2024-09-20T00:00:00Z","oa":1,"date_created":"2024-09-20T12:13:30Z","date_updated":"2026-04-07T13:22:10Z","supervisor":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"}]},{"corr_author":"1","abstract":[{"text":"Strong optomechanical coupling -- a regime where mechanical motion is damped\r\nby environmental radiation -- has traditionally required demanding experimental\r\ningredients such as superconducting resonators, high-quality optical cavities,\r\nor large magnetic fields. Here we demonstrate a room temperature, cavity-free,\r\nall-electric device reaching this regime at radio frequencies, enabled by a\r\nmechanically compliant parallel-plate capacitor with a nanoscale plate\r\nseparation and an aspect ratio exceeding 1,000. The device has four orders of\r\nmagnitude lower insertion loss than a comparable commercial quartz crystal, and\r\nachieves a position imprecision rivaling an optical interferometer. With the\r\nhelp of a back-action isolation scheme, we observe radiative cooling of\r\nmechanical motion by a remote cryogenic load. This work provides a\r\ntechnologically accessible route to high-precision sensing, transduction, and\r\nsignal processing.","lang":"eng"}],"status":"public","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2407.15314","open_access":"1"}],"external_id":{"arxiv":["2407.15314"]},"article_number":"2407.15314","arxiv":1,"type":"preprint","project":[{"name":"Surface Charge and Tunneling Multi-Mode Imaging","_id":"62843413-2b32-11ec-9570-c4ec6eabfae7","grant_number":"26088"},{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"}],"related_material":{"record":[{"id":"19026","relation":"later_version","status":"public"},{"id":"18104","relation":"dissertation_contains","status":"public"}]},"article_processing_charge":"No","doi":"10.48550/arXiv.2407.15314","citation":{"short":"D. Puglia, R.H. Odessey, P.S. Burns, N. Luhmann, S. Schmid, A.P. Higginbotham, ArXiv (n.d.).","ista":"Puglia D, Odessey RH, Burns PS, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical motion. arXiv, 2407.15314.","ieee":"D. Puglia, R. H. Odessey, P. S. Burns, N. Luhmann, S. Schmid, and A. P. Higginbotham, “Room temperature, cavity-free capacitive strong coupling to mechanical motion,” arXiv. .","mla":"Puglia, Denise, et al. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical Motion.” ArXiv, 2407.15314, doi:10.48550/arXiv.2407.15314.","ama":"Puglia D, Odessey RH, Burns PS, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical motion. arXiv. doi:10.48550/arXiv.2407.15314","chicago":"Puglia, Denise, Rachel H Odessey, Peter S. Burns, Niklas Luhmann, Silvan Schmid, and Andrew P Higginbotham. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical Motion.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2407.15314.","apa":"Puglia, D., Odessey, R. H., Burns, P. S., Luhmann, N., Schmid, S., & Higginbotham, A. P. (n.d.). Room temperature, cavity-free capacitive strong coupling to mechanical motion. arXiv. https://doi.org/10.48550/arXiv.2407.15314"},"date_published":"2024-08-24T00:00:00Z","_id":"18143","date_created":"2024-09-26T06:58:27Z","OA_place":"repository","department":[{"_id":"AnHi"}],"date_updated":"2026-05-31T22:30:32Z","oa":1,"author":[{"id":"4D495994-AE37-11E9-AC72-31CAE5697425","first_name":"Denise","last_name":"Puglia","full_name":"Puglia, Denise","orcid":"0000-0003-1144-2763"},{"last_name":"Odessey","id":"9a7a5123-8972-11ed-ae7b-dd1f2af457bd","first_name":"Rachel H","full_name":"Odessey, Rachel H"},{"full_name":"Burns, Peter S.","first_name":"Peter S.","last_name":"Burns"},{"full_name":"Luhmann, Niklas","last_name":"Luhmann","first_name":"Niklas"},{"first_name":"Silvan","last_name":"Schmid","full_name":"Schmid, Silvan"},{"last_name":"Higginbotham","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"}],"title":"Room temperature, cavity-free capacitive strong coupling to mechanical motion","publication":"arXiv","month":"08","oa_version":"Preprint","year":"2024","day":"24","publication_status":"draft","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_identifier":{"issn":["2663-337X"]},"status":"public","language":[{"iso":"eng"}],"project":[{"grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"18648","status":"public"},{"relation":"part_of_dissertation","id":"8707","status":"public"}]},"page":"138","alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson"}],"date_created":"2024-12-10T13:49:15Z","date_updated":"2026-04-07T13:23:06Z","oa":1,"date_published":"2024-12-11T00:00:00Z","_id":"18642","citation":{"mla":"Machnik, Nick N. Algorithms for Causal Learning and Comparative Analysis for Genomic Data. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18642.","ieee":"N. N. Machnik, “Algorithms for causal learning and comparative analysis for genomic data,” Institute of Science and Technology Austria, 2024.","ama":"Machnik NN. Algorithms for causal learning and comparative analysis for genomic data. 2024. doi:10.15479/at:ista:18642","chicago":"Machnik, Nick N. “Algorithms for Causal Learning and Comparative Analysis for Genomic Data.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18642.","apa":"Machnik, N. N. (2024). Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18642","short":"N.N. Machnik, Algorithms for Causal Learning and Comparative Analysis for Genomic Data, Institute of Science and Technology Austria, 2024.","ista":"Machnik NN. 2024. Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria."},"article_processing_charge":"No","year":"2024","month":"12","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","author":[{"orcid":"0000-0001-6617-9742","full_name":"Machnik, Nick N","last_name":"Machnik","first_name":"Nick N","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","has_accepted_license":"1","abstract":[{"text":"This thesis consists of two pieces of work in the broader feld of computational biology,\r\nboth of which are methods for the analysis of large scale biological data, implemented in\r\nefcient software.\r\nChapter 2 introduces a statistical software for causal discovery and inference from observed\r\ngenetic marker and phenotypic trait data. We explore in simulation how well the method\r\ncan fne-map genetic efects, fnd the correct causal structure among tens of traits and\r\nmillions of genetic markers, and infer the causal efect size for the discovered causal\r\nrelations. We then apply the method to 8 million markers and 17 traits from the UK\r\nBiobank and show that many relationships found with other methods are likely due to\r\nthe efects of hidden confounders.\r\nChapter 3 describes how this method can be applied to longitudinal data. I show how one\r\ncan incorporate the background knowledge present in the known order of measurements to\r\nimprove the accuracy of the causal discovery process, and explore the method’s ability to\r\nidentify age specifc genetic efects, and how the error rates of this recovery are infuenced\r\nby missing data due to diferent censoring mechanisms.\r\nChapter 4 introduces a statistical software for the comparison of chromatin contact maps\r\nbased on the structural similarity index. We explore the robustness of the method to\r\nnoise and size diferences of the compared maps, show how it can measure evolutionary\r\nconservation of topological features by providing a similarity ranking of syntenic regions,\r\nand fnally how it can detect alterations in 3D genome structure due to genetic mutations\r\nin samples of medical relevance.\r\n","lang":"eng"}],"type":"dissertation","degree_awarded":"PhD","file":[{"content_type":"application/pdf","checksum":"d45e4d170f9a70a1f69b44b99bd058e4","file_name":"NickMachnikThesisFinal_pdfa_conv.pdf","date_updated":"2025-06-12T22:30:02Z","date_created":"2024-12-11T11:59:54Z","access_level":"open_access","embargo":"2025-06-12","creator":"nmachnik","file_id":"18649","relation":"main_file","file_size":12845009},{"access_level":"closed","content_type":"application/zip","checksum":"f88c9acc62002395ec4dcbdb5eea8b82","date_created":"2024-12-11T11:59:34Z","date_updated":"2025-06-12T22:30:02Z","file_name":"thesis.zip","creator":"nmachnik","relation":"source_file","file_id":"18650","file_size":14189810,"embargo_to":"open_access"}],"department":[{"_id":"GradSch"},{"_id":"MaRo"}],"OA_place":"publisher","file_date_updated":"2025-06-12T22:30:02Z","doi":"10.15479/at:ista:18642","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"11","acknowledgement":"I would like to thank the Swiss National Science Foundation for funding parts of this work\r\nthrough the Eccellenza Grant \"Improving estimation and prediction of common complex\r\ndisease risk\" with grant number PCEGP3_181181.","ddc":["576"],"title":"Algorithms for causal learning and comparative analysis for genomic data"},{"status":"public","language":[{"iso":"eng"}],"project":[{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk"},{"grant_number":"590359","_id":"bd936e6f-d553-11ed-ba76-a82299f63e8c","name":"Advanced statistical modelling to facilitate more accurate characterisation of disease phenotypes, improved genetic mapping, and effective therapeutic hypothesis generation"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"18642","status":"public"}]},"article_processing_charge":"No","citation":{"ieee":"N. N. Machnik, S. M. Mahmoudi, M. Borczyk, I. Krätschmer, M. J. Bauer, and M. R. Robinson, “Causal inference for multiple risk factors and diseases from genomics data,” bioRxiv. 2024.","mla":"Machnik, Nick N., et al. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” BioRxiv, 2024, doi:10.1101/2023.12.06.570392.","ama":"Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv. 2024. doi:10.1101/2023.12.06.570392","chicago":"Machnik, Nick N, Seyed Mahdi Mahmoudi, Malgorzata Borczyk, Ilse Krätschmer, Markus J. Bauer, and Matthew Richard Robinson. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” BioRxiv, 2024. https://doi.org/10.1101/2023.12.06.570392.","apa":"Machnik, N. N., Mahmoudi, S. M., Borczyk, M., Krätschmer, I., Bauer, M. J., & Robinson, M. R. (2024). Causal inference for multiple risk factors and diseases from genomics data. bioRxiv. https://doi.org/10.1101/2023.12.06.570392","short":"N.N. Machnik, S.M. Mahmoudi, M. Borczyk, I. Krätschmer, M.J. Bauer, M.R. Robinson, BioRxiv (2024).","ista":"Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. 2024. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv, 10.1101/2023.12.06.570392."},"date_published":"2024-08-10T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"18648","date_created":"2024-12-11T10:42:59Z","date_updated":"2026-05-31T22:30:34Z","oa":1,"author":[{"full_name":"Machnik, Nick N","orcid":"0000-0001-6617-9742","last_name":"Machnik","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","first_name":"Nick N"},{"full_name":"Mahmoudi, Seyed Mahdi","id":"b9f6d5ef-7774-11eb-a47f-df2c75c02ee7","first_name":"Seyed Mahdi","last_name":"Mahmoudi"},{"full_name":"Borczyk, Malgorzata","last_name":"Borczyk","first_name":"Malgorzata"},{"id":"30d4014e-7753-11eb-b44b-db6d61112e73","first_name":"Ilse","last_name":"Krätschmer","full_name":"Krätschmer, Ilse","orcid":"0000-0002-5636-9259"},{"last_name":"Bauer","first_name":"Markus J.","full_name":"Bauer, Markus J."},{"last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"}],"month":"08","oa_version":"Preprint","year":"2024","corr_author":"1","abstract":[{"text":"Statistical causal learning in genomics relies on the instrumental variable method of\r\nMendelian Randomization (MR). Currently, an overwhelming number of MR studies\r\npurport to show causal relationships among a wide range of risk factors and outcomes.\r\nHere, we show that selecting instrument variables from genome-wide association study\r\nestimates leads to high false discovery rates for many MR approaches, which can be\r\ngreatly reduced by employing a graphical inference approach which: (i) explicitly tests\r\ninstrumental variable assumptions; (ii) distinguishes direct from indirect factors in very\r\nhigh-dimensional data; (iii) discriminates pleiotropic from trait-specific markers, controlling for LD genome-wide; (iv) accommodates rare variants and binary outcomes in a\r\nprincipled way; and (v) identifies potential unobserved latent confounding. For 17 traits\r\nand 8.4M variants recorded for 458,747 individuals in the UK Biobank, we show that\r\nstandard MR analysis gives an abundance of findings that disappear under stringent\r\nassumption checks, with many relationships reflecting potential unmeasured confounding. This implies that mixtures of temporal precedence and potential for reverse-causality\r\nprohibit understanding the underlying nature of phenotypic and genetic correlations in\r\nbiobank data. We propose that well-curated longitudinal records are likely needed and\r\nthat our approach provides a first-step toward robust principled screening for potential\r\ncausal links.\r\n","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1101/2023.12.06.570392","open_access":"1"}],"type":"preprint","doi":"10.1101/2023.12.06.570392","OA_type":"free access","department":[{"_id":"MaRo"}],"OA_place":"repository","title":"Causal inference for multiple risk factors and diseases from genomics data","publication":"bioRxiv","day":"10","acknowledgement":"We thank Zoltan Kutalik and members of the Robinson group \r\nat ISTA for their comments, which improved this manuscript. This work was funded \r\nby a research collaboration agreement between Boehringer Ingelheim and the research \r\ngroup of MRR at the Institute of Science and Technology Austria. Additional funding \r\nwas also provided by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by \r\ncore funding from the Institute of Science and Technology Austria. We would like \r\nto acknowledge the participants and investigators of the UK Biobank study. High- \r\nperformance computing was supported by the Scientific Service Units (SSU) of IST \r\nAustria through resources provided by Scientific Computing (SciComp). ","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"}},{"language":[{"iso":"eng"}],"status":"public","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-050-3"]},"alternative_title":["ISTA Thesis"],"page":"86","related_material":{"record":[{"id":"12349","relation":"part_of_dissertation","status":"public"},{"id":"12370","relation":"research_data","status":"public"}]},"project":[{"name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","grant_number":"101086580","_id":"bdaf81a8-d553-11ed-ba76-c95961984540"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502","name":"Circuits of Visual Attention"}],"article_processing_charge":"No","citation":{"chicago":"Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18574.","apa":"Gupta, D. (2024). Visual adaptations to natural statistics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18574","mla":"Gupta, Divyansh. Visual Adaptations to Natural Statistics. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18574.","ieee":"D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024.","ama":"Gupta D. Visual adaptations to natural statistics. 2024. doi:10.15479/at:ista:18574","ista":"Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria.","short":"D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024."},"_id":"18574","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"date_published":"2024-11-22T00:00:00Z","oa":1,"date_created":"2024-11-20T21:30:44Z","date_updated":"2026-04-07T13:24:48Z","supervisor":[{"orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","last_name":"Jösch","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"author":[{"full_name":"Gupta, Divyansh","orcid":"0000-0001-7400-6665","last_name":"Gupta","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","first_name":"Divyansh"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","month":"11","year":"2024","abstract":[{"lang":"eng","text":"Biological vision is unlike a camera; rather than transmitting light information faithfully, early\r\nvisual circuits process the visual scene to convey only the relevant information in an efficient\r\nmanner. Consequentially, the nature of this visual processing then depends on what is the\r\nrelevant information in a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing is modulated by two different variations in the visual scene. First, I discovered that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual\r\nfield have differences in the center surround structure of their receptive fields. Comparison\r\nwith models of efficient coding show that this adaptation likely evolved to cope with the\r\nbrightness gradient from the sky to the ground that is pervasive in natural scenes. In the\r\nsecond project, I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs the scene gets darker or when the animal is is less aroused, the neuronal responses get\r\nlaggier, while still maintaining their relative timing with respect to the population. Overall, this\r\nwork emphasises the need to understand visual processing in the context of specific demands\r\nof the animal in its the environment. The adaptive changes in the visual system, from the\r\nretinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological\r\nvision optimizes the processing of visual information.\r\n"}],"has_accepted_license":"1","corr_author":"1","degree_awarded":"PhD","type":"dissertation","OA_embargo":"12","doi":"10.15479/at:ista:18574","file_date_updated":"2025-11-11T23:30:02Z","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file":[{"relation":"source_file","file_id":"18589","embargo_to":"open_access","file_size":75512262,"access_level":"closed","date_updated":"2025-11-11T23:30:02Z","file_name":"PhD Thesis - Divyansh Gupta.zip","date_created":"2024-11-25T14:44:03Z","checksum":"ebb000d361c36b22ed6e639a931c6b7c","content_type":"application/zip","creator":"dgupta"},{"embargo":"2025-11-11","access_level":"open_access","file_name":"PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf","date_updated":"2025-11-11T23:30:02Z","date_created":"2024-11-26T11:43:19Z","checksum":"1282401eb71598bc311058b0fcefc6a1","content_type":"application/pdf","creator":"dgupta","relation":"main_file","file_id":"18591","file_size":6412619}],"ec_funded":1,"title":"Visual adaptations to natural statistics","ddc":["573"],"day":"22","acknowledgement":"This work would have been impossible without the Scientific Service Units of IST Austria. The resources and expertise provided by Scientific Computing (especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility and the Imaging and Optics Facility were the essential bedrock I could build upon. I would also like to thank IT support at ISTA for powering through remote work and a cyberattack.\r\nI am grateful for having been funded initially by the European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian Joesch's the European Research Council Starting (756502) and Consolidator (101086580) Grants.","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published"},{"ddc":["570"],"title":"Visualizing the neuronal transcriptional landscape with tissue context","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"28","file_date_updated":"2025-05-05T22:30:04Z","doi":"10.15479/at:ista:18471","file":[{"access_level":"closed","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx","date_created":"2024-10-26T22:29:06Z","date_updated":"2025-05-05T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"6d7c7725d040d8debc070dcb35ac965d","creator":"nagudelo","relation":"source_file","file_id":"18475","embargo_to":"open_access","file_size":183077763},{"access_level":"open_access","embargo":"2025-05-05","checksum":"52f9c0bf2bdafa3baf827b73814a53ff","content_type":"application/pdf","date_created":"2024-10-26T23:13:33Z","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf","date_updated":"2025-05-05T22:30:04Z","creator":"nagudelo","relation":"main_file","file_id":"18476","file_size":47027710}],"ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"OA_place":"publisher","degree_awarded":"PhD","type":"dissertation","has_accepted_license":"1","corr_author":"1","abstract":[{"text":"Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. ","lang":"eng"}],"month":"10","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","author":[{"full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas"}],"year":"2024","date_published":"2024-10-28T00:00:00Z","_id":"18471","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"citation":{"short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024.","ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria.","ama":"Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:10.15479/at:ista:18471","mla":"Agudelo Duenas, Nathalie. Visualizing the Neuronal Transcriptional Landscape with Tissue Context. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18471.","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024.","apa":"Agudelo Duenas, N. (2024). Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18471","chicago":"Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18471."},"article_processing_charge":"No","supervisor":[{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}],"date_created":"2024-10-26T20:02:42Z","date_updated":"2026-04-14T08:34:37Z","oa":1,"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"call_identifier":"FWF","grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"page":"97","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-044-2"]},"status":"public","language":[{"iso":"eng"}]},{"OA_place":"publisher","department":[{"_id":"AnKi"}],"file":[{"file_size":6249076,"file_id":"18841","relation":"main_file","success":1,"creator":"dernst","content_type":"application/pdf","file_name":"2024_DevelopmentalCell_Krammer.pdf","checksum":"fefdea9c02862b4bb74de49b65ce638a","date_created":"2025-01-13T10:59:12Z","date_updated":"2025-01-13T10:59:12Z","access_level":"open_access"}],"doi":"10.1016/j.devcel.2024.04.021","pmid":1,"OA_type":"hybrid","file_date_updated":"2025-01-13T10:59:12Z","acknowledgement":"We thank P. Pasierbek, A.C. Moreno, T. Lendl, and K. Aumayr for microscopy support; G. Schmauss for FACS support; M. Novatchkova for assistance with Bioinformatic analyses; J. Ahel, A. Polikarpova, S. Horer, E. Cesare, and E. Norouzi for technical assistance; A. Meinhardt for supervision; DRESDEN-concept Genome Center, A. Vogt, A. Sommer, and the Vienna BioCenter NGS facility for RNA sequencing. We are grateful to M. Placzek and E. Martí for discussions about the floorplate; to S. Shvartsman for valuable input; to A. Aszodi, W. Masselink, and S. Raiders for advice on statistical analyses; to J. Cornwall Scoones, G. Martello, and Tanaka lab members for critical reading of the manuscript; E. Bassat and E. Chatzidaki for contributing schematics; and to K. Lust for support. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC AdG 742046) to E.M.T. This research was funded in whole or in part by the Austrian Science Fund (FWF) (10.55776/F7803-B) (Stem Cell Modulation) to E.M.T. and A.K., Sir Henry Wellcome postdoctoral fellowship to H.T.S., ELBE fellowship to K.I., and National Science Foundation (US) Phy 2013131 to E.S. The A.K. lab is also supported by ISTA and the European Research Council under Horizon Europe grant 101044579, and S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. This work was supported in part by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript (AAM) version arising from this submission.","day":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"publication_status":"published","ddc":["570"],"publication":"Developmental Cell","title":"Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition","abstract":[{"text":"During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering.","lang":"eng"}],"has_accepted_license":"1","quality_controlled":"1","type":"journal_article","scopus_import":"1","volume":59,"oa":1,"date_updated":"2026-05-31T22:31:10Z","date_created":"2024-06-16T22:01:07Z","citation":{"chicago":"Krammer, Teresa, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Dillon Cislo, Manuela Melchionda, Fernando Becerril Perez, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” Developmental Cell. Elsevier, 2024. https://doi.org/10.1016/j.devcel.2024.04.021.","apa":"Krammer, T., Stuart, H. T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., … Tanaka, E. M. (2024). Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2024.04.021","ieee":"T. Krammer et al., “Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition,” Developmental Cell, vol. 59, no. 15. Elsevier, p. 1940–1953.e10, 2024.","mla":"Krammer, Teresa, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” Developmental Cell, vol. 59, no. 15, Elsevier, 2024, p. 1940–1953.e10, doi:10.1016/j.devcel.2024.04.021.","ama":"Krammer T, Stuart HT, Gromberg E, et al. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 2024;59(15):1940-1953.e10. doi:10.1016/j.devcel.2024.04.021","ista":"Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Rus S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. 2024. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 59(15), 1940–1953.e10.","short":"T. Krammer, H.T. Stuart, E. Gromberg, K. Ishihara, D. Cislo, M. Melchionda, F. Becerril Perez, J. Wang, E. Costantini, S. Rus, L. Arbanas, A. Hörmann, R.A. Neumüller, N. Elvassore, E. Siggia, J. Briscoe, A. Kicheva, E.M. Tanaka, Developmental Cell 59 (2024) 1940–1953.e10."},"article_processing_charge":"Yes (in subscription journal)","_id":"17148","date_published":"2024-08-01T00:00:00Z","year":"2024","isi":1,"article_type":"original","author":[{"full_name":"Krammer, Teresa","first_name":"Teresa","last_name":"Krammer"},{"first_name":"Hannah T.","last_name":"Stuart","full_name":"Stuart, Hannah T."},{"full_name":"Gromberg, Elena","first_name":"Elena","last_name":"Gromberg"},{"full_name":"Ishihara, Keisuke","first_name":"Keisuke","last_name":"Ishihara"},{"last_name":"Cislo","first_name":"Dillon","full_name":"Cislo, Dillon"},{"last_name":"Melchionda","first_name":"Manuela","full_name":"Melchionda, Manuela"},{"full_name":"Becerril Perez, Fernando","first_name":"Fernando","last_name":"Becerril Perez"},{"first_name":"Jingkui","last_name":"Wang","full_name":"Wang, Jingkui"},{"last_name":"Costantini","first_name":"Elena","full_name":"Costantini, Elena"},{"orcid":"0000-0001-8703-1093","full_name":"Rus, Stefanie","first_name":"Stefanie","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","last_name":"Rus"},{"last_name":"Arbanas","first_name":"Laura","full_name":"Arbanas, Laura"},{"last_name":"Hörmann","first_name":"Alexandra","full_name":"Hörmann, Alexandra"},{"last_name":"Neumüller","first_name":"Ralph A.","full_name":"Neumüller, Ralph A."},{"first_name":"Nicola","last_name":"Elvassore","full_name":"Elvassore, Nicola"},{"last_name":"Siggia","first_name":"Eric","full_name":"Siggia, Eric"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Kicheva"},{"full_name":"Tanaka, Elly M.","first_name":"Elly M.","last_name":"Tanaka"}],"publisher":"Elsevier","oa_version":"Published Version","month":"08","external_id":{"isi":["001289684800001"],"pmid":["38776925"]},"issue":"15","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"status":"public","page":"1940-1953.e10","related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"project":[{"name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579"},{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"intvolume":" 59"},{"doi":"10.1016/j.xpro.2024.103187","pmid":1,"file_date_updated":"2024-12-03T10:53:23Z","OA_type":"gold","department":[{"_id":"AnKi"},{"_id":"NanoFab"}],"OA_place":"publisher","file":[{"creator":"dernst","success":1,"file_name":"2024_STARProtoc_Lehr.pdf","date_created":"2024-12-03T10:53:23Z","content_type":"application/pdf","date_updated":"2024-12-03T10:53:23Z","checksum":"0c61a6f9978608a103865905e06f4581","access_level":"open_access","file_size":4989169,"file_id":"18610","relation":"main_file"}],"publication":"STAR Protocols","title":"Protocol for fabricating elastomeric stencils for patterned stem cell differentiation","ddc":["570"],"day":"20","acknowledgement":"We thank the nanofabrication facility at ISTA for technical assistance. Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78). S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.\r\nFor complete details on the use and execution of this protocol, please refer to Lehr et al.1"}],"scopus_import":"1","type":"journal_article","quality_controlled":"1","volume":5,"citation":{"ista":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 5(4), 103187.","short":"S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols 5 (2024).","chicago":"Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington, and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103187.","apa":"Rus, S., Merrin, J., Kulig, M. A., Minchington, T., & Kicheva, A. (2024). Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103187","mla":"Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” STAR Protocols, vol. 5, no. 4, 103187, Elsevier, 2024, doi:10.1016/j.xpro.2024.103187.","ieee":"S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol for fabricating elastomeric stencils for patterned stem cell differentiation,” STAR Protocols, vol. 5, no. 4. Elsevier, 2024.","ama":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 2024;5(4). doi:10.1016/j.xpro.2024.103187"},"article_processing_charge":"Yes","date_published":"2024-12-20T00:00:00Z","acknowledged_ssus":[{"_id":"NanoFab"}],"_id":"18601","date_created":"2024-12-01T23:01:53Z","date_updated":"2026-05-31T22:31:10Z","oa":1,"APC_amount":"804 EUR","DOAJ_listed":"1","author":[{"id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","last_name":"Rus","full_name":"Rus, Stefanie","orcid":"0000-0001-8703-1093"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"full_name":"Kulig, Monika Aleksandra","id":"3331f5ae-e896-11ec-af79-eeb79769bcb7","first_name":"Monika Aleksandra","last_name":"Kulig"},{"full_name":"Minchington, Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","first_name":"Thomas","last_name":"Minchington"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"oa_version":"Published Version","publisher":"Elsevier","month":"12","year":"2024","article_type":"original","publication_identifier":{"eissn":["2666-1667"]},"status":"public","language":[{"iso":"eng"}],"issue":"4","external_id":{"pmid":["39602310"]},"intvolume":" 5","article_number":"103187","project":[{"name":"Mechanisms of tissue size regulation in spinal cord development","grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"related_material":{"record":[{"id":"19763","relation":"dissertation_contains","status":"public"}]}},{"article_type":"original","year":"2024","isi":1,"oa_version":"Published Version","publisher":"Public Library of Science","month":"08","author":[{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"DOAJ_listed":"1","APC_amount":"3145,39 EUR","date_updated":"2026-05-31T22:31:20Z","date_created":"2024-09-08T22:01:11Z","oa":1,"date_published":"2024-08-30T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"17890","citation":{"short":"M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024).","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.","ama":"Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. 2024;20(8). doi:10.1371/journal.pgen.1011376","ieee":"M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome,” PLoS Genetics, vol. 20, no. 8. Public Library of Science, 2024.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” PLoS Genetics, vol. 20, no. 8, e1011376, Public Library of Science, 2024, doi:10.1371/journal.pgen.1011376.","apa":"Elkrewi, M. N., & Vicoso, B. (2024). Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1011376","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” PLoS Genetics. Public Library of Science, 2024. https://doi.org/10.1371/journal.pgen.1011376."},"article_processing_charge":"Yes","project":[{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"17362"},{"status":"public","relation":"dissertation_contains","id":"19386"}],"link":[{"url":"https://github.com/Melkrewi/Artemia-snRNAseq-Project","relation":"software"}]},"article_number":"e1011376","intvolume":" 20","issue":"8","external_id":{"isi":["001304090200001"],"pmid":["39213449"]},"publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"status":"public","language":[{"iso":"eng"}],"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"30","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. ","publication":"PLoS Genetics","title":"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome","ddc":["570"],"file":[{"creator":"dernst","success":1,"content_type":"application/pdf","checksum":"f5d96b9af57126fc1063e951440477d6","date_updated":"2024-09-11T07:54:12Z","date_created":"2024-09-11T07:54:12Z","file_name":"2024_PloSGenetics_Elkrewi.pdf","access_level":"open_access","file_size":8962687,"file_id":"18056","relation":"main_file"}],"OA_place":"publisher","department":[{"_id":"BeVi"}],"pmid":1,"file_date_updated":"2024-09-11T07:54:12Z","OA_type":"gold","doi":"10.1371/journal.pgen.1011376","volume":20,"scopus_import":"1","quality_controlled":"1","type":"journal_article","has_accepted_license":"1","corr_author":"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."}]},{"article_processing_charge":"Yes","citation":{"apa":"Bett, V. K., Macon, A., Vicoso, B., & Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evae006","chicago":"Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution. Oxford University Press, 2024. https://doi.org/10.1093/gbe/evae006.","ama":"Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 2024;16(1). doi:10.1093/gbe/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,” Genome Biology and Evolution, vol. 16, no. 1. Oxford University Press, 2024.","mla":"Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:10.1093/gbe/evae006.","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.","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024)."},"_id":"15009","date_published":"2024-01-20T00:00:00Z","oa":1,"date_updated":"2026-05-31T22:31:20Z","date_created":"2024-02-18T23:01:02Z","DOAJ_listed":"1","author":[{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K","last_name":"Bett","full_name":"Bett, Vincent K"},{"full_name":"Macon, Ariana","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"},{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"}],"publisher":"Oxford University Press","oa_version":"Published Version","month":"01","year":"2024","isi":1,"article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1759-6653"]},"status":"public","external_id":{"isi":["001153952800001"],"pmid":["38245839"]},"issue":"1","intvolume":" 16","article_number":"evae006","related_material":{"record":[{"id":"14705","relation":"research_data","status":"public"},{"id":"20444","relation":"dissertation_contains","status":"private"},{"status":"public","id":"20449","relation":"dissertation_contains"},{"status":"public","id":"19386","relation":"dissertation_contains"}]},"doi":"10.1093/gbe/evae006","pmid":1,"file_date_updated":"2024-02-26T09:54:59Z","OA_type":"gold","OA_place":"publisher","department":[{"_id":"BeVi"}],"file":[{"creator":"dernst","success":1,"access_level":"open_access","checksum":"106a40f10443b2e7ba66749844ebbdf1","content_type":"application/pdf","date_updated":"2024-02-26T09:54:59Z","date_created":"2024-02-26T09:54:59Z","file_name":"2024_GBE_Bett.pdf","file_size":5213306,"relation":"main_file","file_id":"15029"}],"ddc":["570"],"publication":"Genome Biology and Evolution","title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","day":"20","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","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"}],"corr_author":"1","has_accepted_license":"1","type":"journal_article","quality_controlled":"1","scopus_import":"1","volume":16},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"16","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.","title":"Emergent macroscopic bistability induced by a single superconducting qubit","publication":"PRX Quantum","ddc":["530"],"file":[{"relation":"main_file","file_id":"17185","file_size":1443351,"access_level":"open_access","checksum":"0833880d47f74ad1deda93a1d8ffa5a7","content_type":"application/pdf","file_name":"2024_PRXQuantum_Sett.pdf","date_updated":"2024-06-28T12:04:43Z","date_created":"2024-06-28T12:04:43Z","success":1,"creator":"cchlebak"}],"ec_funded":1,"OA_place":"publisher","department":[{"_id":"JoFi"},{"_id":"AnHi"}],"OA_type":"gold","file_date_updated":"2024-06-28T12:04:43Z","doi":"10.1103/prxquantum.5.010327","volume":5,"scopus_import":"1","quality_controlled":"1","type":"journal_article","corr_author":"1","has_accepted_license":"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"}],"article_type":"original","year":"2024","isi":1,"publisher":"American Physical Society","oa_version":"Published Version","month":"02","author":[{"first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","last_name":"Sett","orcid":"0000-0001-7641-8348","full_name":"Sett, Riya"},{"orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani"},{"last_name":"Phan","first_name":"Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan, Duc T"},{"full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","last_name":"Barzanjeh"},{"full_name":"Vukics, Andras","last_name":"Vukics","first_name":"Andras"},{"last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"DOAJ_listed":"1","APC_amount":"3782,54","date_created":"2024-06-27T10:58:06Z","date_updated":"2026-05-31T22:31:24Z","oa":1,"date_published":"2024-02-16T00:00:00Z","acknowledged_ssus":[{"_id":"M-Shop"}],"_id":"17183","citation":{"short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, PRX Quantum 5 (2024).","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.","ama":"Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. 2024;5(1). doi:10.1103/prxquantum.5.010327","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,” PRX Quantum, vol. 5, no. 1. American Physical Society, 2024.","mla":"Sett, Riya, et al. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” PRX Quantum, vol. 5, no. 1, 010327, American Physical Society, 2024, doi:10.1103/prxquantum.5.010327.","apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., & Fink, J. M. (2024). Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. American Physical Society. https://doi.org/10.1103/prxquantum.5.010327","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.” PRX Quantum. American Physical Society, 2024. https://doi.org/10.1103/prxquantum.5.010327."},"article_processing_charge":"Yes","project":[{"call_identifier":"H2020","name":"Quantum readout techniques and technologies","grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"related_material":{"record":[{"id":"18978","relation":"research_data","status":"public"},{"relation":"dissertation_contains","id":"19533","status":"public"}]},"arxiv":1,"article_number":"010327","intvolume":" 5","issue":"1","external_id":{"isi":["001171652500001"],"arxiv":["2210.14182"]},"publication_identifier":{"eissn":["2691-3399"]},"status":"public","language":[{"iso":"eng"}]},{"article_type":"original","year":"2024","isi":1,"oa_version":"Submitted Version","month":"01","publisher":"American Association for the Advancement of Science","author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"},{"last_name":"Zagrodzka","first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B."},{"full_name":"Garlovsky, Martin D.","first_name":"Martin D.","last_name":"Garlovsky"},{"full_name":"Pal, Arka","orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka","last_name":"Pal"},{"last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria","full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226"},{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando","last_name":"Garcia Castillo","full_name":"Garcia Castillo, Diego Fernando"},{"id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","first_name":"Hila","last_name":"Lifchitz","full_name":"Lifchitz, Hila"},{"full_name":"Le Moan, Alan","first_name":"Alan","last_name":"Le Moan"},{"first_name":"Erica","last_name":"Leder","full_name":"Leder, Erica"},{"first_name":"James","last_name":"Reeve","full_name":"Reeve, James"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"oa":1,"date_created":"2024-01-14T23:00:56Z","date_updated":"2026-05-31T22:31:23Z","_id":"14796","date_published":"2024-01-05T00:00:00Z","citation":{"mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982.","ieee":"S. Stankowski et al., “The genetic basis of a recent transition to live-bearing in marine snails,” Science, 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. Science. 2024;383(6678):114-119. doi:10.1126/science.adi2982","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.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982.","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. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adi2982","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.","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."},"article_processing_charge":"No","page":"114-119","related_material":{"record":[{"status":"public","id":"14812","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"20694"}],"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/the-snail-or-the-egg/","relation":"press_release"}]},"intvolume":" 383","external_id":{"isi":["001138156400003"],"pmid":["38175895"]},"issue":"6678","language":[{"iso":"eng"}],"status":"public","publication_identifier":{"eissn":["1095-9203"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","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.).","day":"05","publication":"Science","title":"The genetic basis of a recent transition to live-bearing in marine snails","OA_place":"repository","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"OA_type":"green","pmid":1,"doi":"10.1126/science.adi2982","volume":383,"type":"journal_article","quality_controlled":"1","scopus_import":"1","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"}],"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"}],"corr_author":"1"},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"17183"},{"status":"public","relation":"used_in_publication","id":"19533"}]},"type":"research_data_reference","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.10518320","open_access":"1"}],"status":"public","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. "}],"corr_author":"1","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2024","day":"16","publisher":"Zenodo","oa_version":"Published Version","month":"01","title":"Data Analysis files for \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\"","author":[{"full_name":"Sett, Riya","orcid":"0000-0001-7641-8348","last_name":"Sett","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","first_name":"Riya"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid","last_name":"Hassani","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"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","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"},{"full_name":"Vukics, Andras","first_name":"Andras","last_name":"Vukics"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"ddc":["530"],"oa":1,"date_updated":"2026-05-31T22:31:24Z","department":[{"_id":"JoFi"},{"_id":"AnHi"}],"date_created":"2025-01-30T08:30:03Z","OA_place":"repository","_id":"18978","OA_type":"gold","date_published":"2024-01-16T00:00:00Z","citation":{"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:10.5281/ZENODO.10518320","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.","mla":"Sett, Riya, et al. Data Analysis Files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” Zenodo, 2024, doi:10.5281/ZENODO.10518320.","apa":"Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., & Fink, J. M. (2024). Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” Zenodo. https://doi.org/10.5281/ZENODO.10518320","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. https://doi.org/10.5281/ZENODO.10518320.","short":"R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, (2024).","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, 10.5281/ZENODO.10518320."},"doi":"10.5281/ZENODO.10518320","article_processing_charge":"No"},{"page":"542-559","intvolume":" 16","external_id":{"isi":["000815663700001"],"pmid":["36793688"]},"issue":"2","language":[{"iso":"eng"}],"status":"public","publication_identifier":{"eissn":["1752-4571"]},"year":"2023","isi":1,"article_type":"original","author":[{"full_name":"De Jode, Aurélien","first_name":"Aurélien","last_name":"De Jode"},{"full_name":"Le Moan, Alan","first_name":"Alan","last_name":"Le Moan"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"}],"month":"02","oa_version":"Published Version","publisher":"Wiley","oa":1,"date_updated":"2025-04-23T08:49:14Z","date_created":"2022-07-03T22:01:33Z","citation":{"ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428","ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428.","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. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","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.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428.","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.","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."},"article_processing_charge":"No","_id":"11479","date_published":"2023-02-01T00:00:00Z","type":"journal_article","quality_controlled":"1","scopus_import":"1","volume":16,"abstract":[{"lang":"eng","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."}],"has_accepted_license":"1","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).","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","title":"Ten years of demographic modelling of divergence and speciation in the sea","ddc":["576"],"publication":"Evolutionary Applications","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"file":[{"file_name":"2023_EvolutionaryApplications_DeJode.pdf","content_type":"application/pdf","checksum":"d4d6fa9ddf36643af994a6a757919afb","date_updated":"2023-02-27T07:10:17Z","date_created":"2023-02-27T07:10:17Z","access_level":"open_access","success":1,"creator":"dernst","file_id":"12685","relation":"main_file","file_size":2269822}],"doi":"10.1111/eva.13428","file_date_updated":"2023-02-27T07:10:17Z","pmid":1},{"quality_controlled":"1","type":"journal_article","scopus_import":"1","volume":62,"abstract":[{"lang":"eng","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. "}],"has_accepted_license":"1","ddc":["510"],"publication":"Random Structures and Algorithms","title":"Asymmetric Ramsey properties of random graphs involving cliques and cycles","day":"01","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.","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","doi":"10.1002/rsa.21106","file_date_updated":"2023-10-04T09:37:26Z","department":[{"_id":"MaKw"}],"file":[{"creator":"dernst","success":1,"access_level":"open_access","date_updated":"2023-10-04T09:37:26Z","file_name":"2023_RandomStructureAlgorithms_Liebenau.pdf","content_type":"application/pdf","date_created":"2023-10-04T09:37:26Z","checksum":"3a5969d0c512aef01c30f3dc81c6d59b","file_size":1362334,"relation":"main_file","file_id":"14389"}],"intvolume":" 62","page":"1035-1055","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1098-2418"],"issn":["1042-9832"]},"status":"public","external_id":{"isi":["000828530400001"]},"issue":"4","author":[{"full_name":"Liebenau, Anita","first_name":"Anita","last_name":"Liebenau"},{"full_name":"Mattos, Letícia","first_name":"Letícia","last_name":"Mattos"},{"last_name":"Mendonca Dos Santos","id":"12c6bd4d-2cd0-11ec-a0da-e28f42f65ebd","first_name":"Walner","full_name":"Mendonca Dos Santos, Walner"},{"last_name":"Skokan","first_name":"Jozef","full_name":"Skokan, Jozef"}],"oa_version":"Published Version","month":"07","publisher":"Wiley","isi":1,"year":"2023","article_type":"original","citation":{"short":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, J. Skokan, Random Structures and Algorithms 62 (2023) 1035–1055.","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.” Random Structures and Algorithms, vol. 62, no. 4, Wiley, 2023, pp. 1035–55, doi:10.1002/rsa.21106.","ieee":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, and J. Skokan, “Asymmetric Ramsey properties of random graphs involving cliques and cycles,” Random Structures and Algorithms, 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. Random Structures and Algorithms. 2023;62(4):1035-1055. doi:10.1002/rsa.21106","chicago":"Liebenau, Anita, Letícia Mattos, Walner Mendonca dos Santos, and Jozef Skokan. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” Random Structures and Algorithms. Wiley, 2023. https://doi.org/10.1002/rsa.21106.","apa":"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. Wiley. https://doi.org/10.1002/rsa.21106"},"article_processing_charge":"Yes (in subscription journal)","_id":"11706","date_published":"2023-07-01T00:00:00Z","oa":1,"date_created":"2022-07-31T22:01:49Z","date_updated":"2023-10-04T09:38:45Z"},{"month":"04","oa_version":"Published Version","publisher":"Springer Nature","author":[{"orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J"}],"article_type":"original","year":"2023","isi":1,"date_published":"2023-04-01T00:00:00Z","_id":"11741","citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 2023;185:1183–1218. doi:10.1007/s00440-022-01156-7","mla":"Cipolloni, Giorgio, et al. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields, vol. 185, Springer Nature, 2023, pp. 1183–1218, doi:10.1007/s00440-022-01156-7.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Quenched universality for deformed Wigner matrices,” Probability Theory and Related Fields, vol. 185. Springer Nature, pp. 1183–1218, 2023.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-022-01156-7","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields. Springer Nature, 2023. https://doi.org/10.1007/s00440-022-01156-7.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields 185 (2023) 1183–1218.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 185, 1183–1218."},"article_processing_charge":"Yes (via OA deal)","date_updated":"2024-10-09T21:03:02Z","date_created":"2022-08-07T22:02:00Z","oa":1,"arxiv":1,"intvolume":" 185","page":"1183–1218","status":"public","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"language":[{"iso":"eng"}],"external_id":{"isi":["000830344500001"],"arxiv":["2106.10200"]},"title":"Quenched universality for deformed Wigner matrices","publication":"Probability Theory and Related Fields","ddc":["510"],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","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).","file_date_updated":"2023-08-14T12:47:32Z","doi":"10.1007/s00440-022-01156-7","file":[{"file_id":"14054","relation":"main_file","file_size":782278,"checksum":"b9247827dae5544d1d19c37abe547abc","content_type":"application/pdf","file_name":"2023_ProbabilityTheory_Cipolloni.pdf","date_updated":"2023-08-14T12:47:32Z","date_created":"2023-08-14T12:47:32Z","access_level":"open_access","success":1,"creator":"dernst"}],"department":[{"_id":"LaEr"}],"volume":185,"scopus_import":"1","type":"journal_article","quality_controlled":"1","has_accepted_license":"1","corr_author":"1","abstract":[{"lang":"eng","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."}]},{"department":[{"_id":"UlWa"}],"ec_funded":1,"file":[{"file_size":1002218,"relation":"main_file","file_id":"12006","success":1,"creator":"alisjak","access_level":"open_access","file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","content_type":"application/pdf","checksum":"def7ae3b28d9fd6aec16450e40090302","date_updated":"2022-08-29T11:23:15Z","date_created":"2022-08-29T11:23:15Z"}],"doi":"10.1007/s00454-022-00394-9","file_date_updated":"2022-08-29T11:23:15Z","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.","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","ddc":["510"],"title":"Inserting one edge into a simple drawing is hard","publication":"Discrete and Computational Geometry","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"}],"has_accepted_license":"1","quality_controlled":"1","type":"journal_article","scopus_import":"1","volume":69,"oa":1,"date_created":"2022-08-28T22:02:01Z","date_updated":"2025-04-14T07:43:59Z","citation":{"ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 2023;69:745–770. doi:10.1007/s00454-022-00394-9","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,” Discrete and Computational Geometry, vol. 69. Springer Nature, pp. 745–770, 2023.","mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry, vol. 69, Springer Nature, 2023, pp. 745–770, doi:10.1007/s00454-022-00394-9.","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., & Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00394-9","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.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00394-9.","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770.","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."},"article_processing_charge":"Yes (in subscription journal)","_id":"11999","date_published":"2023-04-01T00:00:00Z","isi":1,"year":"2023","article_type":"original","author":[{"orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M","first_name":"Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","last_name":"Arroyo Guevara"},{"last_name":"Klute","first_name":"Fabian","full_name":"Klute, Fabian"},{"full_name":"Parada, Irene","first_name":"Irene","last_name":"Parada"},{"full_name":"Vogtenhuber, Birgit","first_name":"Birgit","last_name":"Vogtenhuber"},{"full_name":"Seidel, Raimund","first_name":"Raimund","last_name":"Seidel"},{"last_name":"Wiedera","first_name":"Tilo","full_name":"Wiedera, Tilo"}],"month":"04","oa_version":"Published Version","publisher":"Springer Nature","external_id":{"arxiv":["1909.07347"],"isi":["000840292800001"]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"status":"public","page":"745–770","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"intvolume":" 69","arxiv":1}]