[{"date_published":"2025-08-01T00:00:00Z","date_updated":"2025-09-30T14:25:57Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"20274","success":1,"date_created":"2025-09-02T07:47:32Z","creator":"dernst","access_level":"open_access","file_size":1239841,"content_type":"application/pdf","file_name":"2025_MolecularBioEvolution_Mrnjavac.pdf","checksum":"f40abffa56cb1e9ff65800f2a7d7b39a","date_updated":"2025-09-02T07:47:32Z","relation":"main_file"}],"external_id":{"isi":["001547617100001"],"pmid":["40713898"]},"day":"01","year":"2025","pmid":1,"doi":"10.1093/molbev/msaf177","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"link":[{"url":"https://git.ista.ac.at/bvicoso/xydegenerate","relation":"software"}]},"scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"We thank Filip Ruzicka, Colin Olito, Akane Uesugi, Melissa Toups, Daniel Jeffries, the Associate Editor, and anonymous reviewers, for comments and suggestions on earlier versions of the paper. We are particularly grateful to Deborah Charlesworth and Brian Charlesworth for extensive comments on two different drafts of the manuscript. We also thank Aneil Agrawal and Thomas Lenormand for email correspondence about the data on dominance and ways to interpret it. Technical support was provided by ISTA Scientific Computing Unit.","isi":1,"issue":"8","department":[{"_id":"BeVi"}],"intvolume":"        42","_id":"20223","oa_version":"Published Version","type":"journal_article","title":"An extension of Muller's sheltering hypothesis for the evolution of sex chromosome gene content","publication_status":"published","citation":{"ista":"Mrnjavac A, Vicoso B, Connallon T. 2025. An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. Molecular Biology and Evolution. 42(8), msaf177.","short":"A. Mrnjavac, B. Vicoso, T. Connallon, Molecular Biology and Evolution 42 (2025).","chicago":"Mrnjavac, Andrea, Beatriz Vicoso, and Tim Connallon. “An Extension of Muller’s Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/molbev/msaf177\">https://doi.org/10.1093/molbev/msaf177</a>.","mla":"Mrnjavac, Andrea, et al. “An Extension of Muller’s Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content.” <i>Molecular Biology and Evolution</i>, vol. 42, no. 8, msaf177, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/molbev/msaf177\">10.1093/molbev/msaf177</a>.","ieee":"A. Mrnjavac, B. Vicoso, and T. Connallon, “An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content,” <i>Molecular Biology and Evolution</i>, vol. 42, no. 8. Oxford University Press, 2025.","apa":"Mrnjavac, A., Vicoso, B., &#38; Connallon, T. (2025). An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msaf177\">https://doi.org/10.1093/molbev/msaf177</a>","ama":"Mrnjavac A, Vicoso B, Connallon T. An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. <i>Molecular Biology and Evolution</i>. 2025;42(8). doi:<a href=\"https://doi.org/10.1093/molbev/msaf177\">10.1093/molbev/msaf177</a>"},"author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"},{"full_name":"Connallon, Tim","last_name":"Connallon","first_name":"Tim"}],"OA_place":"publisher","license":"https://creativecommons.org/licenses/by/4.0/","month":"08","abstract":[{"text":"The first influential hypothesis for sex chromosome evolution was proposed in 1914 by H. J. Muller, who argued that once recombination was suppressed between the X and Y chromosomes, Y-linked genes become “sheltered” from selection, leading to accumulation of recessive loss-of-function (LOF) mutations and decay of Y-linked genes. The hypothesis fell out of favor in the 1970s because early mathematical models failed to support it and data on the dominance of lethal mutations were viewed as incompatible with the hypothesis. We reevaluate the main arguments against Muller's hypothesis and find that they do not conclusively exclude a role for sheltering in sex chromosome evolution. By relaxing restrictive assumptions of earlier models, we show that sheltering promotes fixation of LOF mutations with sexually dimorphic fitness effects, resulting in decay of X-linked genes that are exclusively expressed by males and Y-linked genes that are primarily, though not necessarily exclusively, expressed by females. We further show that drift and other processes contributing to Y degeneration (i.e. selective interference and regulatory evolution) expand conditions of Y-linked gene loss by sheltering. The actual contribution of sheltering to sex chromosome evolution hinges upon the distribution of dominance and sex-specific fitness effects of LOF mutations, which we discuss.","lang":"eng"}],"status":"public","date_created":"2025-08-24T22:01:31Z","oa":1,"OA_type":"gold","PlanS_conform":"1","quality_controlled":"1","volume":42,"article_processing_charge":"Yes","article_type":"original","file_date_updated":"2025-09-02T07:47:32Z","publisher":"Oxford University Press","article_number":"msaf177","ddc":["570"],"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"DOAJ_listed":"1","publication":"Molecular Biology and Evolution"},{"volume":12,"article_processing_charge":"Yes","quality_controlled":"1","OA_type":"gold","PlanS_conform":"1","oa":1,"date_created":"2025-09-07T22:01:33Z","article_number":"e00521","ddc":["530"],"publisher":"Wiley","article_type":"original","file_date_updated":"2025-12-30T09:31:11Z","status":"public","abstract":[{"lang":"eng","text":"Scanning Kelvin probe microscopy (SKPM) is a powerful technique for macroscopic imaging of the electrostatic potential above a surface. Though most often used to image work-function variations of conductive surfaces, it can also be used to probe the surface charge on insulating surfaces. In both cases, relating the measured potential to the underlying signal is non-trivial. Here, general relationships are derived between the measured SKPM voltage and the underlying source, revealing either can be cast as a convolution with an appropriately scaled point spread function (PSF). For charge that exists on a thin insulating layer above a conductor, the PSF has the same shape as what would occur from a work-function variation alone, differing by a simple scaling factor. This relationship is confirmed by: (1) backing it out from finite-element simulations of work-function and charge signals, and (2) experimentally comparing the measured PSF from a small work-function target to that from a small charge spot. This scaling factor is further validated by comparing SKPM charge measurements with Faraday cup measurements for highly charged samples from contact-charging experiments. These results highlight a heretofore unappreciated connection between SKPM voltage and charge signals, offering a rigorous recipe to extract either from experimental data."}],"month":"10","publication_identifier":{"eissn":["2196-7350"]},"DOAJ_listed":"1","publication":"Advanced Materials Interfaces","ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","issue":"19","isi":1,"acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant agreement No. 949120). This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing Facility, and Lab Support Facility. The authors wish to thank Dmytro Rak and Juan Carlos Sobarzo for letting us use their equipment. The authors wish to thank Evgeniia Volobueva for advice in preparing PFIB samples. The authors wish to thank the contributions of the whole Waitukaitis group for useful discussions and feedback.","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"arxiv":["2506.07187"],"isi":["001560163400001"]},"file":[{"file_name":"2025_AdvMaterialsInterfaces_Lenton.pdf","checksum":"906fcc7733be8ce8a83600427b82cd5a","content_type":"application/pdf","file_size":1830117,"relation":"main_file","date_updated":"2025-12-30T09:31:11Z","success":1,"file_id":"20908","access_level":"open_access","creator":"dernst","date_created":"2025-12-30T09:31:11Z"}],"date_updated":"2025-12-30T09:31:25Z","date_published":"2025-10-01T00:00:00Z","doi":"10.1002/admi.202500521","year":"2025","day":"01","project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","grant_number":"949120"}],"corr_author":"1","OA_place":"publisher","citation":{"apa":"Lenton, I. C., Pertl, F., Shafeek, L. B., &#38; Waitukaitis, S. R. (2025). A duality between surface charge and work function in scanning Kelvin probe microscopy. <i>Advanced Materials Interfaces</i>. Wiley. <a href=\"https://doi.org/10.1002/admi.202500521\">https://doi.org/10.1002/admi.202500521</a>","ieee":"I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “A duality between surface charge and work function in scanning Kelvin probe microscopy,” <i>Advanced Materials Interfaces</i>, vol. 12, no. 19. Wiley, 2025.","ama":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. A duality between surface charge and work function in scanning Kelvin probe microscopy. <i>Advanced Materials Interfaces</i>. 2025;12(19). doi:<a href=\"https://doi.org/10.1002/admi.202500521\">10.1002/admi.202500521</a>","mla":"Lenton, Isaac C., et al. “A Duality between Surface Charge and Work Function in Scanning Kelvin Probe Microscopy.” <i>Advanced Materials Interfaces</i>, vol. 12, no. 19, e00521, Wiley, 2025, doi:<a href=\"https://doi.org/10.1002/admi.202500521\">10.1002/admi.202500521</a>.","ista":"Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2025. A duality between surface charge and work function in scanning Kelvin probe microscopy. Advanced Materials Interfaces. 12(19), e00521.","chicago":"Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis. “A Duality between Surface Charge and Work Function in Scanning Kelvin Probe Microscopy.” <i>Advanced Materials Interfaces</i>. Wiley, 2025. <a href=\"https://doi.org/10.1002/admi.202500521\">https://doi.org/10.1002/admi.202500521</a>.","short":"I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Advanced Materials Interfaces 12 (2025)."},"publication_status":"published","author":[{"last_name":"Lenton","id":"a550210f-223c-11ec-8182-e2d45e817efb","first_name":"Isaac C","full_name":"Lenton, Isaac C","orcid":"0000-0002-5010-6984"},{"full_name":"Pertl, Felix","orcid":"0000-0003-0463-5794","last_name":"Pertl","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","first_name":"Felix"},{"first_name":"Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","last_name":"Shafeek","full_name":"Shafeek, Lubuna B","orcid":"0000-0001-7180-6050"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"}],"title":"A duality between surface charge and work function in scanning Kelvin probe microscopy","arxiv":1,"_id":"20295","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"intvolume":"        12","type":"journal_article","oa_version":"Published Version"},{"article_number":"26","ddc":["000"],"file_date_updated":"2025-09-09T08:10:13Z","publisher":"ML Research Press","volume":288,"article_processing_charge":"No","oa":1,"date_created":"2025-09-07T22:01:34Z","OA_type":"diamond","quality_controlled":"1","abstract":[{"text":"Learning-based systems are increasingly deployed across various domains, yet the complexity of traditional neural networks poses significant challenges for formal verification. Unlike conventional neural networks, learned Logic Gate Networks (LGNs) replace multiplications with Boolean logic gates, yielding a sparse, netlist-like architecture that is inherently more amenable to symbolic verification, while still delivering promising performance. In this paper, we introduce a SAT encoding for verifying global robustness and fairness in LGNs. We evaluate our method on five benchmark datasets, including a newly constructed 5-class variant, and find that LGNs are both verification-friendly and maintain strong predictive performance.","lang":"eng"}],"status":"public","month":"06","publication":"2nd International Conferenceon Neuro-Symbolic Systems","ec_funded":1,"publication_identifier":{"eissn":["2640-3498"]},"conference":{"name":"NeuS: International Conferenceon Neuro-Symbolic Systems","start_date":"2025-05-28","location":"Philadephia, PA, United States","end_date":"2025-05-30"},"alternative_title":["PMLR"],"language":[{"iso":"eng"}],"acknowledgement":"This work is supported in part by the ERC grant under Grant No. ERC-2020-AdG 101020093 and\r\nthe Austrian Science Fund (FWF) [10.55776/COE12]. This research was supported by the Scientific\r\nService Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).","acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","year":"2025","day":"01","file":[{"date_updated":"2025-09-09T08:10:13Z","relation":"main_file","file_size":295466,"file_name":"2025_NeuS_Kresse.pdf","checksum":"90a32defed34787e771a5c1623b6b0d2","content_type":"application/pdf","creator":"dernst","date_created":"2025-09-09T08:10:13Z","access_level":"open_access","file_id":"20314","success":1}],"external_id":{"arxiv":["2505.19932"]},"date_updated":"2025-09-09T08:12:44Z","date_published":"2025-06-01T00:00:00Z","arxiv":1,"publication_status":"published","citation":{"mla":"Kresse, Fabian, et al. “Logic Gate Neural Networks Are Good for Verification.” <i>2nd International Conferenceon Neuro-Symbolic Systems</i>, vol. 288, 26, ML Research Press, 2025.","ista":"Kresse F, Yu E, Lampert C, Henzinger TA. 2025. Logic gate neural networks are good for verification. 2nd International Conferenceon Neuro-Symbolic Systems. NeuS: International Conferenceon Neuro-Symbolic Systems, PMLR, vol. 288, 26.","short":"F. Kresse, E. Yu, C. Lampert, T.A. Henzinger, in:, 2nd International Conferenceon Neuro-Symbolic Systems, ML Research Press, 2025.","chicago":"Kresse, Fabian, Emily Yu, Christoph Lampert, and Thomas A Henzinger. “Logic Gate Neural Networks Are Good for Verification.” In <i>2nd International Conferenceon Neuro-Symbolic Systems</i>, Vol. 288. ML Research Press, 2025.","apa":"Kresse, F., Yu, E., Lampert, C., &#38; Henzinger, T. A. (2025). Logic gate neural networks are good for verification. In <i>2nd International Conferenceon Neuro-Symbolic Systems</i> (Vol. 288). Philadephia, PA, United States: ML Research Press.","ieee":"F. Kresse, E. Yu, C. Lampert, and T. A. Henzinger, “Logic gate neural networks are good for verification,” in <i>2nd International Conferenceon Neuro-Symbolic Systems</i>, Philadephia, PA, United States, 2025, vol. 288.","ama":"Kresse F, Yu E, Lampert C, Henzinger TA. Logic gate neural networks are good for verification. In: <i>2nd International Conferenceon Neuro-Symbolic Systems</i>. Vol 288. ML Research Press; 2025."},"author":[{"last_name":"Kresse","id":"faff3c84-23f6-11ef-9085-e5187b51c604","first_name":"Fabian","full_name":"Kresse, Fabian"},{"first_name":"Zhengqi","last_name":"Yu","id":"20aa2ae8-f2f1-11ed-bbfa-8205053f1342","full_name":"Yu, Zhengqi"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"OA_place":"publisher","corr_author":"1","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"title":"Logic gate neural networks are good for verification","type":"conference","oa_version":"Published Version","_id":"20296","department":[{"_id":"ChLa"},{"_id":"ToHe"}],"intvolume":"       288"},{"status":"public","abstract":[{"lang":"eng","text":"The time needed by deep convection to bring the atmosphere back to equilibrium is called convective adjustment timescale or simply adjustment timescale, typically denoted by . In the Community Atmospheric Model|Community Atmosphere Model (CAM),  is the convective available potential energy (CAPE) relaxation timescale and is 1 hr, worldwide. Observational evidence suggests that  is generally longer than 1 hr. Further, continental and oceanic convection are different in terms of the vigor of updrafts and can have different longevities. So using  hour worldwide in CAM has two potential caveats. A longer  improves the simulation of the mean climate. However, it does not address the land‐ocean heterogeneity of atmospheric deep convection. We investigate the prescription of two different CAPE relaxation timescales for land ( hr) and ocean ( to 4 hr). It is arguably an extremely crude parameterization of boundary layer control on atmospheric convection. We contrast a suite of 5‐year‐long simulations with two different  for land and ocean to having one  globally. The choice of longer  over ocean is guided by previous studies and inspired by observational pieces of evidence. Nonetheless, to complement our variable  experiments, we perform a simulation with  hr and  hrs. Most importantly, our key findings are immune to the exact values of prescribed  and . The CAM model, with two  values , improves convective‐stratiform rainfall partitioning and the Madden–Julian oscillation propagation characteristics."}],"month":"09","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_number":"e2025MS005035","ddc":["550"],"publisher":"Wiley","file_date_updated":"2025-09-10T08:12:34Z","article_type":"original","volume":17,"article_processing_charge":"Yes","quality_controlled":"1","oa":1,"date_created":"2025-09-10T05:36:16Z","OA_type":"gold","publication":"Journal of Advances in Modeling Earth Systems","ec_funded":1,"DOAJ_listed":"1","publication_identifier":{"eissn":["1942-2466"]},"doi":"10.1029/2025ms005035","year":"2025","day":"01","file":[{"date_created":"2025-09-10T08:12:34Z","creator":"dernst","access_level":"open_access","file_id":"20338","success":1,"date_updated":"2025-09-10T08:12:34Z","relation":"main_file","file_size":2143025,"content_type":"application/pdf","checksum":"5961d6290432c5ac0e8587ef07f30c9b","file_name":"2025_JAMES_Goswami.pdf"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"date_updated":"2025-09-10T08:14:28Z","date_published":"2025-09-01T00:00:00Z","issue":"9","acknowledgement":"The authors gratefully acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant 805041). This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We would like to thank Prof. Courtney Schumacher and Dr. Aaron Funk of Texas A&M University for their help in understanding the TRMM Radar data. The authors are grateful to two anonymous reviewers who helped improve the quality of this paper.","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa_version":"Published Version","_id":"20319","intvolume":"        17","department":[{"_id":"CaMu"}],"OA_place":"publisher","corr_author":"1","project":[{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020","grant_number":"805041"}],"citation":{"ista":"GOSWAMI BB, Polesello A, Muller CJ. 2025. An assessment of representing land‐ocean heterogeneity via CAPE relaxation timescale in the Community Atmospheric Model 6 (CAM6). Journal of Advances in Modeling Earth Systems. 17(9), e2025MS005035.","chicago":"GOSWAMI, BIDYUT B, Andrea Polesello, and Caroline J Muller. “An Assessment of Representing Land‐ocean Heterogeneity via CAPE Relaxation Timescale in the Community Atmospheric Model 6 (CAM6).” <i>Journal of Advances in Modeling Earth Systems</i>. Wiley, 2025. <a href=\"https://doi.org/10.1029/2025ms005035\">https://doi.org/10.1029/2025ms005035</a>.","short":"B.B. GOSWAMI, A. Polesello, C.J. Muller, Journal of Advances in Modeling Earth Systems 17 (2025).","mla":"GOSWAMI, BIDYUT B., et al. “An Assessment of Representing Land‐ocean Heterogeneity via CAPE Relaxation Timescale in the Community Atmospheric Model 6 (CAM6).” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 17, no. 9, e2025MS005035, Wiley, 2025, doi:<a href=\"https://doi.org/10.1029/2025ms005035\">10.1029/2025ms005035</a>.","apa":"GOSWAMI, B. B., Polesello, A., &#38; Muller, C. J. (2025). An assessment of representing land‐ocean heterogeneity via CAPE relaxation timescale in the Community Atmospheric Model 6 (CAM6). <i>Journal of Advances in Modeling Earth Systems</i>. Wiley. <a href=\"https://doi.org/10.1029/2025ms005035\">https://doi.org/10.1029/2025ms005035</a>","ieee":"B. B. GOSWAMI, A. Polesello, and C. J. Muller, “An assessment of representing land‐ocean heterogeneity via CAPE relaxation timescale in the Community Atmospheric Model 6 (CAM6),” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 17, no. 9. Wiley, 2025.","ama":"GOSWAMI BB, Polesello A, Muller CJ. An assessment of representing land‐ocean heterogeneity via CAPE relaxation timescale in the Community Atmospheric Model 6 (CAM6). <i>Journal of Advances in Modeling Earth Systems</i>. 2025;17(9). doi:<a href=\"https://doi.org/10.1029/2025ms005035\">10.1029/2025ms005035</a>"},"author":[{"last_name":"GOSWAMI","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"BIDYUT B","orcid":"0000-0001-8602-3083","full_name":"GOSWAMI, BIDYUT B"},{"full_name":"Polesello, Andrea","id":"74c777f4-32da-11ee-b498-874db0835561","last_name":"Polesello","first_name":"Andrea"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350"}],"publication_status":"published","title":"An assessment of representing land‐ocean heterogeneity via CAPE relaxation timescale in the Community Atmospheric Model 6 (CAM6)"},{"type":"dissertation","oa_version":"Published Version","_id":"20357","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"supervisor":[{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"OA_place":"publisher","corr_author":"1","project":[{"_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e","name":"Collective behaviour of cells in pancreatic Islets of Langerhans"}],"publication_status":"published","citation":{"mla":"Ruzickova, Natalia. <i>Effect Propagation in Biological Networks</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20357\">10.15479/AT-ISTA-20357</a>.","short":"N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science and Technology Austria, 2025.","chicago":"Ruzickova, Natalia. “Effect Propagation in Biological Networks.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20357\">https://doi.org/10.15479/AT-ISTA-20357</a>.","ista":"Ruzickova N. 2025. Effect propagation in biological networks. Institute of Science and Technology Austria.","ama":"Ruzickova N. Effect propagation in biological networks. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20357\">10.15479/AT-ISTA-20357</a>","apa":"Ruzickova, N. (2025). <i>Effect propagation in biological networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20357\">https://doi.org/10.15479/AT-ISTA-20357</a>","ieee":"N. Ruzickova, “Effect propagation in biological networks,” Institute of Science and Technology Austria, 2025."},"author":[{"full_name":"Ruzickova, Natalia","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","last_name":"Ruzickova"}],"title":"Effect propagation in biological networks","doi":"10.15479/AT-ISTA-20357","year":"2025","day":"15","file":[{"access_level":"closed","date_created":"2025-09-16T12:56:06Z","title":"Effect propagation in biological networks","creator":"nruzicko","file_id":"20360","relation":"main_file","date_updated":"2025-11-27T10:00:25Z","content_type":"application/pdf","embargo_to":"open_access","embargo":"2026-09-14","checksum":"991e81bc16a76b4e0c352567728fd2c5","file_name":"2025_Ruzickova_Natalia_Thesis.pdf","file_size":43518367},{"relation":"source_file","date_updated":"2025-09-16T12:59:23Z","content_type":"application/zip","checksum":"c4ab257adad116083d8a97fac69b2dde","file_name":"2025_Ruzickova_Natalia_Thesis_source.zip","file_size":53464789,"access_level":"closed","date_created":"2025-09-16T12:59:23Z","creator":"nruzicko","file_id":"20361"}],"date_published":"2025-09-15T00:00:00Z","date_updated":"2026-04-07T12:02:39Z","alternative_title":["ISTA Thesis"],"acknowledgement":"I would also like to acknowledge the Austrian Academy of Sciences for funding through the\r\nDOC Fellowship program (fellowship number 26917), the Grants Office at ISTA for their\r\nassistance with the application, and the Scientific Computing Unit for their support regarding\r\nhigh-performance computation.\r\n","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"E-Lib"}],"keyword":["gene regulation","networks","omnigenic model","pancreas","collective behaviour"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"18525","status":"public"}]},"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-066-4"],"issn":["2663-337X"]},"status":"public","month":"09","page":"160","ddc":["570","530"],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2025-11-27T10:00:25Z","article_processing_charge":"No","date_created":"2025-09-15T17:04:48Z"},{"ec_funded":1,"publication":"Proceedings of the National Academy of Sciences","publication_identifier":{"eissn":["1091-6490"]},"month":"10","abstract":[{"lang":"eng","text":"The glassy thermal conductivities observed in crystalline inorganic perovskites such as Cs3Bi2I6Cl3 are perplexing and lacking theoretical explanations. Here, we first experimentally measure its thermal transport behavior from 20 to 300 K, after synthesizing Cs3Bi2I6Cl3 single crystals. Using path-integral molecular dynamics simulations driven by machine learning potentials, we reveal that Cs3Bi2I6Cl3 has large lattice distortions at low temperatures, which may be related to the large atomic size mismatch. Employing the Wigner formulation of thermal transport, we reproduce theexperimental thermal conductivities based on lattice-distorted structures. This studythus provides a framework for predicting and understanding glassy thermal transportin materials with strong lattice disorder."}],"status":"public","page":"e2415664122","file_date_updated":"2025-10-21T10:02:15Z","article_type":"original","publisher":"National Academy of Sciences","ddc":["540"],"PlanS_conform":"1","OA_type":"hybrid","oa":1,"date_created":"2025-10-19T22:01:31Z","quality_controlled":"1","article_processing_charge":"No","volume":122,"oa_version":"Published Version","type":"journal_article","intvolume":"       122","department":[{"_id":"BiCh"}],"_id":"20492","title":"Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3","author":[{"full_name":"Zeng, Zezhu","orcid":"0000-0001-5126-4928","last_name":"Zeng","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu"},{"full_name":"Fan, Zheyong","last_name":"Fan","first_name":"Zheyong"},{"full_name":"Simoncelli, Michele","last_name":"Simoncelli","first_name":"Michele"},{"last_name":"Chen","first_name":"Chen","full_name":"Chen, Chen"},{"full_name":"Liang, Ting","first_name":"Ting","last_name":"Liang"},{"first_name":"Yue","last_name":"Chen","full_name":"Chen, Yue"},{"full_name":"Thornton, Geoff","first_name":"Geoff","last_name":"Thornton"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"}],"publication_status":"published","citation":{"short":"Z. Zeng, Z. Fan, M. Simoncelli, C. Chen, T. Liang, Y. Chen, G. Thornton, B. Cheng, Proceedings of the National Academy of Sciences 122 (2025) e2415664122.","chicago":"Zeng, Zezhu, Zheyong Fan, Michele Simoncelli, Chen Chen, Ting Liang, Yue Chen, Geoff Thornton, and Bingqing Cheng. “Lattice Distortion Leads to Glassy Thermal Transport in Crystalline Cs3Bi2I6Cl3.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2415664122\">https://doi.org/10.1073/pnas.2415664122</a>.","ista":"Zeng Z, Fan Z, Simoncelli M, Chen C, Liang T, Chen Y, Thornton G, Cheng B. 2025. Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3. Proceedings of the National Academy of Sciences. 122(41), e2415664122.","mla":"Zeng, Zezhu, et al. “Lattice Distortion Leads to Glassy Thermal Transport in Crystalline Cs3Bi2I6Cl3.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 41, National Academy of Sciences, 2025, p. e2415664122, doi:<a href=\"https://doi.org/10.1073/pnas.2415664122\">10.1073/pnas.2415664122</a>.","ama":"Zeng Z, Fan Z, Simoncelli M, et al. Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(41):e2415664122. doi:<a href=\"https://doi.org/10.1073/pnas.2415664122\">10.1073/pnas.2415664122</a>","apa":"Zeng, Z., Fan, Z., Simoncelli, M., Chen, C., Liang, T., Chen, Y., … Cheng, B. (2025). Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2415664122\">https://doi.org/10.1073/pnas.2415664122</a>","ieee":"Z. Zeng <i>et al.</i>, “Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 41. National Academy of Sciences, p. e2415664122, 2025."},"OA_place":"publisher","project":[{"grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"corr_author":"1","year":"2025","day":"14","pmid":1,"doi":"10.1073/pnas.2415664122","date_published":"2025-10-14T00:00:00Z","date_updated":"2026-02-16T12:32:11Z","file":[{"relation":"main_file","date_updated":"2025-10-21T10:02:15Z","checksum":"3f9cd0d67ffe9110fb238407671584b7","file_name":"2025_PNAS_Zeng.pdf","content_type":"application/pdf","file_size":12244843,"access_level":"open_access","creator":"dernst","date_created":"2025-10-21T10:02:15Z","success":1,"file_id":"20513"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"external_id":{"pmid":["41052324"],"isi":["001600415200001"]},"language":[{"iso":"eng"}],"acknowledgement":"Z.Z. acknowledges the European Union’s Horizon2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. We acknowledge the high-performance computing facilities offered by Institute of Science and Technology Austria and The University of Hong Kong.","isi":1,"issue":"41","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","scopus_import":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/ZengZezhu/Cs3Bi2I6Cl3_heat_conductivity"}]},"acknowledged_ssus":[{"_id":"ScienComp"}]},{"type":"journal_article","oa_version":"None","_id":"20704","intvolume":"        21","department":[{"_id":"BiCh"},{"_id":"DaAl"}],"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"corr_author":"1","citation":{"apa":"Tuo, P., Zeng, Z., Chen, J., &#38; Cheng, B. (2025). Scalable multitemperature free energy sampling of classical Ising spin states. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.5c01248\">https://doi.org/10.1021/acs.jctc.5c01248</a>","ieee":"P. Tuo, Z. Zeng, J. Chen, and B. Cheng, “Scalable multitemperature free energy sampling of classical Ising spin states,” <i>Journal of Chemical Theory and Computation</i>, vol. 21, no. 22. American Chemical Society, pp. 11427–11435, 2025.","ama":"Tuo P, Zeng Z, Chen J, Cheng B. Scalable multitemperature free energy sampling of classical Ising spin states. <i>Journal of Chemical Theory and Computation</i>. 2025;21(22):11427-11435. doi:<a href=\"https://doi.org/10.1021/acs.jctc.5c01248\">10.1021/acs.jctc.5c01248</a>","mla":"Tuo, Ping, et al. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” <i>Journal of Chemical Theory and Computation</i>, vol. 21, no. 22, American Chemical Society, 2025, pp. 11427–35, doi:<a href=\"https://doi.org/10.1021/acs.jctc.5c01248\">10.1021/acs.jctc.5c01248</a>.","ista":"Tuo P, Zeng Z, Chen J, Cheng B. 2025. Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. 21(22), 11427–11435.","chicago":"Tuo, Ping, Zezhu Zeng, Jiale Chen, and Bingqing Cheng. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/acs.jctc.5c01248\">https://doi.org/10.1021/acs.jctc.5c01248</a>.","short":"P. Tuo, Z. Zeng, J. Chen, B. Cheng, Journal of Chemical Theory and Computation 21 (2025) 11427–11435."},"publication_status":"published","author":[{"full_name":"Tuo, Ping","last_name":"Tuo","id":"6e5644c0-c180-11ed-a2da-facc4c9f4f09","first_name":"Ping"},{"first_name":"Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","last_name":"Zeng","orcid":"0000-0001-5126-4928","full_name":"Zeng, Zezhu"},{"full_name":"Chen, Jiale","orcid":"0000-0001-5337-5875","last_name":"Chen","id":"4d0a9064-1ff6-11ee-9fa6-ec046c604785","first_name":"Jiale"},{"last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"}],"title":"Scalable multitemperature free energy sampling of classical Ising spin states","doi":"10.1021/acs.jctc.5c01248","pmid":1,"day":"31","year":"2025","external_id":{"pmid":["41172130"],"isi":["001605927900001"]},"date_updated":"2025-12-01T15:40:27Z","date_published":"2025-10-31T00:00:00Z","issue":"22","isi":1,"acknowledgement":"P.T. acknowledges funding from FFG MAGNIFICO and the BIDMaP Postdoctoral Fellowship. Z.Z. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. The authors acknowledge the research computing facilities provided by the Institute of Science and Technology Austria (ISTA), and resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy Office of Science User Facility using NERSC award DOEERCAP0031751 ’GenAI@NERSC’. P.T. acknowledges valued discussions with Dr. Daniel King, Dr. Lei Wang, and Dr. Fuzhi Dai.","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/tuoping/alchemicalFES"}]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Chemical Theory and Computation","ec_funded":1,"publication_identifier":{"eissn":["1549-9626"],"issn":["1549-9618"]},"status":"public","abstract":[{"lang":"eng","text":"Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In this work, we introduce a discrete flow matching model, tailored for systems with discrete phase-space coordinates (e.g., the Ising model or a multicomponent system on a lattice). This approach enables a single model to sample free energy surfaces over a wide temperature range with minimal training overhead, and the model generation is scalable to larger lattice sizes than those in the training set. We demonstrate our approach on the 2D Ising model, showing efficient and reliable free energy sampling. These results highlight the potential of flow matching for low-cost, scalable free energy sampling in discrete systems and suggest promising extensions to alchemical degrees of freedom in crystalline materials. The codebase developed for this work is openly available at https://github.com/tuoping/alchemicalFES."}],"month":"10","page":"11427-11435","publisher":"American Chemical Society","article_type":"original","volume":21,"article_processing_charge":"No","quality_controlled":"1","date_created":"2025-11-30T23:02:06Z","OA_type":"closed access"},{"acknowledgement":"We thank Todor Asenov and Abdulhamid Baghdadi for their outstanding technical support and Dr. Michael Gleichweit and Mercede Azizbaig Mohajer for the helpful discussions. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreements No. 949120 and No. 805041) and the Swiss National Science Foundation (SNSF, Project No. 200021-236446). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop and the Scientific Computing service unit.","language":[{"iso":"eng"}],"issue":"21","scopus_import":"1","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/trapping-particles-to-explain-lightning/","relation":"press_release"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"day":"21","year":"2025","doi":"10.1103/5xd9-4tjj","date_published":"2025-11-21T00:00:00Z","date_updated":"2026-04-28T13:09:27Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"arxiv":["2507.17591"]},"file":[{"success":1,"file_id":"20717","access_level":"open_access","creator":"dernst","date_created":"2025-12-01T08:19:46Z","file_name":"2025_PhysReviewLetters_Stoellner.pdf","checksum":"a5f76b1230cc7b039ecd0dbd6f99e775","content_type":"application/pdf","file_size":1761373,"relation":"main_file","date_updated":"2025-12-01T08:19:46Z"}],"arxiv":1,"title":"Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air","OA_place":"publisher","project":[{"grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020"},{"grant_number":"805041","call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"corr_author":"1","citation":{"chicago":"Stöllner, Andrea, Isaac C Lenton, Artem Volosniev, James Millen, Renjiro Shibuya, Hisao Ishii, Dmytro Rak, et al. “Using Optical Tweezers to Simultaneously Trap, Charge, and Measure the Charge of a Microparticle in Air.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/5xd9-4tjj\">https://doi.org/10.1103/5xd9-4tjj</a>.","short":"A. Stöllner, I.C. Lenton, A. Volosniev, J. Millen, R. Shibuya, H. Ishii, D. Rak, Z. Alpichshev, G. David, R. Signorell, C.J. Muller, S.R. Waitukaitis, Physical Review Letters 135 (2025).","ista":"Stöllner A, Lenton IC, Volosniev A, Millen J, Shibuya R, Ishii H, Rak D, Alpichshev Z, David G, Signorell R, Muller CJ, Waitukaitis SR. 2025. Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air. Physical Review Letters. 135(21), 218202.","mla":"Stöllner, Andrea, et al. “Using Optical Tweezers to Simultaneously Trap, Charge, and Measure the Charge of a Microparticle in Air.” <i>Physical Review Letters</i>, vol. 135, no. 21, 218202, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/5xd9-4tjj\">10.1103/5xd9-4tjj</a>.","ama":"Stöllner A, Lenton IC, Volosniev A, et al. Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air. <i>Physical Review Letters</i>. 2025;135(21). doi:<a href=\"https://doi.org/10.1103/5xd9-4tjj\">10.1103/5xd9-4tjj</a>","apa":"Stöllner, A., Lenton, I. C., Volosniev, A., Millen, J., Shibuya, R., Ishii, H., … Waitukaitis, S. R. (2025). Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/5xd9-4tjj\">https://doi.org/10.1103/5xd9-4tjj</a>","ieee":"A. Stöllner <i>et al.</i>, “Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air,” <i>Physical Review Letters</i>, vol. 135, no. 21. American Physical Society, 2025."},"author":[{"orcid":"0000-0002-0464-8440","full_name":"Stöllner, Andrea","first_name":"Andrea","last_name":"Stöllner","id":"4bdcf7f6-eb97-11eb-a6c2-9981bbdc3bed"},{"last_name":"Lenton","id":"a550210f-223c-11ec-8182-e2d45e817efb","first_name":"Isaac C","full_name":"Lenton, Isaac C","orcid":"0000-0002-5010-6984"},{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev"},{"first_name":"James","last_name":"Millen","full_name":"Millen, James"},{"first_name":"Renjiro","last_name":"Shibuya","full_name":"Shibuya, Renjiro"},{"first_name":"Hisao","last_name":"Ishii","full_name":"Ishii, Hisao"},{"full_name":"Rak, Dmytro","id":"70313b46-47c2-11ec-9e88-cd79101918fe","last_name":"Rak","first_name":"Dmytro"},{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek"},{"first_name":"Grégory","last_name":"David","full_name":"David, Grégory"},{"last_name":"Signorell","first_name":"Ruth","full_name":"Signorell, Ruth"},{"full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J"},{"first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"}],"publication_status":"published","oa_version":"Published Version","type":"journal_article","intvolume":"       135","department":[{"_id":"ZhAl"},{"_id":"CaMu"},{"_id":"ScWa"}],"_id":"20705","publisher":"American Physical Society","article_type":"original","file_date_updated":"2025-12-01T08:19:46Z","ddc":["530","550"],"article_number":"218202","quality_controlled":"1","oa":1,"PlanS_conform":"1","date_created":"2025-11-30T23:02:07Z","OA_type":"hybrid","volume":135,"article_processing_charge":"Yes (via OA deal)","month":"11","status":"public","abstract":[{"text":"Optical tweezers are widely used as a highly sensitive tool to measure forces on micron-scale particles. One such application is the measurement of the electric charge of a particle, which can be done with high precision in liquids, air, or vacuum. We experimentally investigate how the trapping laser itself can electrically charge such a particle, in our case a ∼1  μ⁢m SiO2 sphere in air. We model the charging mechanism as a two-photon process which reproduces the experimental data with high fidelity.","lang":"eng"}],"ec_funded":1,"publication":"Physical Review Letters","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]}},{"title":"Causes and consequences of sex-chromosome turnovers in Diptera","corr_author":"1","author":[{"last_name":"Layana Franco","id":"02814589-eb8f-11eb-b029-a70074f3f18f","first_name":"Lorena Alexandra","full_name":"Layana Franco, Lorena Alexandra","orcid":"0000-0002-1253-6297"},{"first_name":"Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"citation":{"mla":"Layana Franco, Lorena Alexandra, et al. <i>Causes and Consequences of Sex-Chromosome Turnovers in Diptera</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20780\">10.15479/AT-ISTA-20780</a>.","chicago":"Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20780\">https://doi.org/10.15479/AT-ISTA-20780</a>.","short":"L.A. Layana Franco, M.A. Toups, B. Vicoso, (2025).","ista":"Layana Franco LA, Toups MA, Vicoso B. 2025. Causes and consequences of sex-chromosome turnovers in Diptera, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-20780\">10.15479/AT-ISTA-20780</a>.","ama":"Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome turnovers in Diptera. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20780\">10.15479/AT-ISTA-20780</a>","ieee":"L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria, 2025.","apa":"Layana Franco, L. A., Toups, M. A., &#38; Vicoso, B. (2025). Causes and consequences of sex-chromosome turnovers in Diptera. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20780\">https://doi.org/10.15479/AT-ISTA-20780</a>"},"oa_version":"Published Version","type":"research_data","department":[{"_id":"BeVi"}],"_id":"20780","publisher":"Institute of Science and Technology Austria","file_date_updated":"2025-12-11T11:00:53Z","keyword":["Schizophora","sex chromosomes","sex-chromosome turnover","Diptera","genomic features","out-of-X movement."],"oa":1,"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","has_accepted_license":"1","date_created":"2025-12-10T23:40:14Z","acknowledged_ssus":[{"_id":"ScienComp"}],"article_processing_charge":"No","year":"2025","month":"12","status":"public","abstract":[{"lang":"eng","text":"Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analysed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on the F element (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes."}],"doi":"10.15479/AT-ISTA-20780","date_updated":"2026-06-10T08:27:48Z","date_published":"2025-12-01T00:00:00Z","file":[{"access_level":"open_access","date_created":"2025-12-11T10:47:15Z","creator":"llayanaf","success":1,"file_id":"20799","relation":"main_file","date_updated":"2025-12-11T10:47:15Z","content_type":"application/zip","checksum":"251e7aab01917c2ad2fbccf465492ea1","file_name":"Perl_scripts.zip","file_size":4575},{"date_created":"2025-12-11T10:52:17Z","creator":"llayanaf","access_level":"open_access","file_id":"20800","success":1,"date_updated":"2025-12-11T10:52:17Z","relation":"main_file","file_size":19052849,"content_type":"application/zip","file_name":"Supplementary_Datasets.zip","checksum":"daf1c03149dd170b14e5c8e109ee3c77"},{"content_type":"application/zip","file_name":"Supplementary_Tables.zip","checksum":"658d6e95a361b0a3db058b7b4e1733d4","file_size":566476,"relation":"main_file","date_updated":"2025-12-11T10:52:11Z","success":1,"file_id":"20801","access_level":"open_access","date_created":"2025-12-11T10:52:11Z","creator":"llayanaf"},{"checksum":"2a2b92eb9fade0015719190596a8c5b7","file_name":"README.txt","content_type":"text/plain","file_size":1204,"relation":"main_file","date_updated":"2025-12-11T11:00:53Z","success":1,"file_id":"20802","access_level":"open_access","creator":"llayanaf","date_created":"2025-12-11T11:00:53Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"page":"53757-53790","month":"05","status":"public","abstract":[{"lang":"eng","text":"Clustering is a cornerstone of data analysis that is particularly suited to identifying coherent subgroups or substructures in unlabeled data, as are generated continuously in large amounts these days. However, in many cases traditional clustering methods are not applicable, because data are increasingly being produced and stored in a distributed way, e.g. on edge devices, and privacy concerns prevent it from being transferred to a central server. To address this challenge, we present FedDP-KMeans, a new algorithm for \r\n-means clustering that is fully-federated as well as differentially private. Our approach leverages (potentially small and out-of-distribution) server-side data to overcome the primary challenge of differentially private clustering methods: the need for a good initialization. Combining our initialization with a simple federated DP-Lloyds algorithm we obtain an algorithm that achieves excellent results on synthetic and real-world benchmark tasks. We also provide a theoretical analysis of our method that provides bounds on the convergence speed and cluster identification success."}],"quality_controlled":"1","OA_type":"gold","oa":1,"date_created":"2025-12-14T23:02:05Z","article_processing_charge":"No","volume":267,"publisher":"ML Research Press","file_date_updated":"2025-12-16T12:38:29Z","ddc":["000"],"conference":{"location":"Vancouver, Canada","end_date":"2025-07-19","start_date":"2025-07-13","name":"ICML: International Conference on Machine Learning"},"publication_identifier":{"eissn":["2640-3498"]},"publication":"42nd International Conference on Machine Learning","date_published":"2025-05-01T00:00:00Z","date_updated":"2026-04-07T11:46:11Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"arxiv":["2506.05408"]},"file":[{"creator":"dernst","date_created":"2025-12-16T12:38:29Z","access_level":"open_access","file_id":"20829","success":1,"date_updated":"2025-12-16T12:38:29Z","relation":"main_file","file_size":746612,"checksum":"815b32b463023ca21e569c2158745c15","file_name":"2025_ICML_Scott.pdf","content_type":"application/pdf"}],"day":"01","year":"2025","scopus_import":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"21198","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"acknowledgement":"This research was funded in part by the Austrian Science Fund (FWF) [10.55776/COE12] and supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).\r\n","language":[{"iso":"eng"}],"alternative_title":["PMLR"],"department":[{"_id":"ChLa"},{"_id":"MoHe"}],"intvolume":"       267","_id":"20819","oa_version":"Published Version","type":"conference","title":"Differentially private federated k-means clustering with server-side data","OA_place":"publisher","corr_author":"1","publication_status":"published","citation":{"ama":"Scott JA, Lampert C, Saulpic D. Differentially private federated k-means clustering with server-side data. In: <i>42nd International Conference on Machine Learning</i>. Vol 267. ML Research Press; 2025:53757-53790.","apa":"Scott, J. A., Lampert, C., &#38; Saulpic, D. (2025). Differentially private federated k-means clustering with server-side data. In <i>42nd International Conference on Machine Learning</i> (Vol. 267, pp. 53757–53790). Vancouver, Canada: ML Research Press.","ieee":"J. A. Scott, C. Lampert, and D. Saulpic, “Differentially private federated k-means clustering with server-side data,” in <i>42nd International Conference on Machine Learning</i>, Vancouver, Canada, 2025, vol. 267, pp. 53757–53790.","short":"J.A. Scott, C. Lampert, D. Saulpic, in:, 42nd International Conference on Machine Learning, ML Research Press, 2025, pp. 53757–53790.","chicago":"Scott, Jonathan A, Christoph Lampert, and David Saulpic. “Differentially Private Federated K-Means Clustering with Server-Side Data.” In <i>42nd International Conference on Machine Learning</i>, 267:53757–90. ML Research Press, 2025.","ista":"Scott JA, Lampert C, Saulpic D. 2025. Differentially private federated k-means clustering with server-side data. 42nd International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 267, 53757–53790.","mla":"Scott, Jonathan A., et al. “Differentially Private Federated K-Means Clustering with Server-Side Data.” <i>42nd International Conference on Machine Learning</i>, vol. 267, ML Research Press, 2025, pp. 53757–90."},"author":[{"last_name":"Scott","id":"e499926b-f6e0-11ea-865d-9c63db0031e8","first_name":"Jonathan A","full_name":"Scott, Jonathan A"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Saulpic, David","id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","last_name":"Saulpic","first_name":"David"}],"arxiv":1},{"quality_controlled":"1","date_created":"2024-08-29T10:40:23Z","oa":1,"PlanS_conform":"1","OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","volume":646,"publisher":"Springer Nature","file_date_updated":"2025-10-20T10:26:13Z","article_type":"original","ddc":["540"],"page":"601–605","month":"10","status":"public","abstract":[{"lang":"eng","text":"Oxygen redox chemistry is central to life1 and many human-made technologies, such as in energy storage2,3,4. The large energy gain from oxygen redox reactions is often connected with the occurrence of harmful reactive oxygen species3,5,6. Key species are superoxide and the highly reactive singlet oxygen3,4,5,6,7, which may evolve from superoxide. However, the factors determining the formation of singlet oxygen, rather than the relatively unreactive triplet oxygen, are unknown. Here we report that the release of triplet or singlet oxygen is governed by individual Marcus normal and inverted region behaviour. We found that as the driving force for the reaction increases, the initially dominant evolution of triplet oxygen slows down, and singlet oxygen evolution becomes predominant with higher maximum kinetics. This behaviour also applies to the widely observed superoxide disproportionation, in which one superoxide is oxidized by another, in both non-aqueous and aqueous systems, with Lewis and Brønsted acidity controlling the driving forces. Singlet oxygen yields governed by these conditions are relevant, for example, in batteries or cellular organelles in which superoxide forms. Our findings suggest ways to understand and control spin states and kinetics in oxygen redox chemistry, with implications for fields, including life sciences, pure chemistry and energy storage."}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication":"Nature","scopus_import":"1","related_material":{"link":[{"url":"https://ista.ac.at/en/news/taming-the-bad-oxygen/","relation":"press_release","description":"News on ISTA website"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"acknowledgement":"S.A.F. thanks the Institute of Science and Technology Austria (ISTA) for the support. The Scientific Service Units of ISTA supported this research through resources provided by the Imaging and Optics Facility, the Lab Support Facility, the Miba Machine Shop and Scientific Computing. This research was partly funded by the Austrian Science Fund (FWF) (10.55776/P37169 and 10.55776/COE5). For open access purposes, the author has applied for a CC BY public copyright licence to any author-accepted manuscript version arising from this submission. R.H. acknowledges funding through CZI grant DAF2020-225401 (10.37921/120055ratwvi) from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (10.13039/100014989). H.T.K.N. acknowledges funding by the European Commission Erasmus Mundus Joint Masters programme. We thank M. Sixt and M. Chinon for the discussions about O-redox in life and R. Jethwa for proofreading. Open access funding was provided by ISTA.","language":[{"iso":"eng"}],"issue":"8085","isi":1,"date_updated":"2026-04-28T13:18:33Z","date_published":"2025-10-16T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["001586378900001"],"pmid":["41044415"]},"file":[{"file_size":3809247,"content_type":"application/pdf","checksum":"b507ddd23df0388aa65d04dc9b00fe3d","file_name":"2025_Nature_Mondal.pdf","date_updated":"2025-10-20T10:26:13Z","relation":"main_file","file_id":"20500","success":1,"date_created":"2025-10-20T10:26:13Z","creator":"dernst","access_level":"open_access"}],"pmid":1,"day":"16","year":"2025","doi":"10.1038/s41586-025-09587-7","title":"Marcus kinetics control singlet and triplet oxygen evolving from superoxide","corr_author":"1","OA_place":"publisher","project":[{"name":"Singlet oxygen in non-aqueous oxygen redox chemistry","_id":"8df062be-16d5-11f0-9cad-f559b6612c7e","grant_number":"P37169"},{"name":"Tools for automation and feedback microscopy","_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","grant_number":"CZI01"}],"author":[{"full_name":"Mondal, Soumyadip","first_name":"Soumyadip","last_name":"Mondal","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48"},{"first_name":"Huyen T.K.","last_name":"Nguyen","full_name":"Nguyen, Huyen T.K."},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger"}],"citation":{"ama":"Mondal S, Nguyen HTK, Hauschild R, Freunberger SA. Marcus kinetics control singlet and triplet oxygen evolving from superoxide. <i>Nature</i>. 2025;646(8085):601–605. doi:<a href=\"https://doi.org/10.1038/s41586-025-09587-7\">10.1038/s41586-025-09587-7</a>","ieee":"S. Mondal, H. T. K. Nguyen, R. Hauschild, and S. A. Freunberger, “Marcus kinetics control singlet and triplet oxygen evolving from superoxide,” <i>Nature</i>, vol. 646, no. 8085. Springer Nature, pp. 601–605, 2025.","apa":"Mondal, S., Nguyen, H. T. K., Hauschild, R., &#38; Freunberger, S. A. (2025). Marcus kinetics control singlet and triplet oxygen evolving from superoxide. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-09587-7\">https://doi.org/10.1038/s41586-025-09587-7</a>","chicago":"Mondal, Soumyadip, Huyen T.K. Nguyen, Robert Hauschild, and Stefan Alexander Freunberger. “Marcus Kinetics Control Singlet and Triplet Oxygen Evolving from Superoxide.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-09587-7\">https://doi.org/10.1038/s41586-025-09587-7</a>.","short":"S. Mondal, H.T.K. Nguyen, R. Hauschild, S.A. Freunberger, Nature 646 (2025) 601–605.","ista":"Mondal S, Nguyen HTK, Hauschild R, Freunberger SA. 2025. Marcus kinetics control singlet and triplet oxygen evolving from superoxide. Nature. 646(8085), 601–605.","mla":"Mondal, Soumyadip, et al. “Marcus Kinetics Control Singlet and Triplet Oxygen Evolving from Superoxide.” <i>Nature</i>, vol. 646, no. 8085, Springer Nature, 2025, pp. 601–605, doi:<a href=\"https://doi.org/10.1038/s41586-025-09587-7\">10.1038/s41586-025-09587-7</a>."},"publication_status":"published","intvolume":"       646","department":[{"_id":"StFr"},{"_id":"Bio"}],"_id":"17468","oa_version":"Published Version","type":"journal_article"},{"department":[{"_id":"FlSc"},{"_id":"LeSa"}],"intvolume":"        32","_id":"17884","oa_version":"Published Version","type":"journal_article","title":"Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice","corr_author":"1","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","grant_number":"P31445"},{"grant_number":"25762","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A","name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms"}],"OA_place":"publisher","publication_status":"published","author":[{"last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0003-1756-6564","full_name":"Obr, Martin"},{"first_name":"Mathias","last_name":"Percipalle","id":"4986e21c-eb97-11eb-a6c2-a4ef0b629971","full_name":"Percipalle, Mathias"},{"id":"7dbaf460-fa9e-11eb-b0ca-bc7c7ff21ad0","last_name":"Chernikova","first_name":"Darya","full_name":"Chernikova, Darya"},{"full_name":"Yang, Huixin","first_name":"Huixin","last_name":"Yang"},{"full_name":"Thader, Andreas","first_name":"Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pinke, Gergely","first_name":"Gergely","id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","last_name":"Pinke"},{"first_name":"Dario J","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87","last_name":"Porley","full_name":"Porley, Dario J"},{"first_name":"Louis M.","last_name":"Mansky","full_name":"Mansky, Louis M."},{"full_name":"Dick, Robert A.","last_name":"Dick","first_name":"Robert A."},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"citation":{"mla":"Obr, Martin, et al. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32, Springer Nature, 2025, pp. 268–76, doi:<a href=\"https://doi.org/10.1038/s41594-024-01390-8\">10.1038/s41594-024-01390-8</a>.","ista":"Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley Esteves D, Mansky LM, Dick RA, Schur FK. 2025. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. Nature Structural &#38; Molecular Biology. 32, 268–276.","short":"M. Obr, M. Percipalle, D. Chernikova, H. Yang, A. Thader, G. Pinke, D. Porley Esteves, L.M. Mansky, R.A. Dick, F.K. Schur, Nature Structural &#38; Molecular Biology 32 (2025) 268–276.","chicago":"Obr, Martin, Mathias Percipalle, Darya Chernikova, Huixin Yang, Andreas Thader, Gergely Pinke, Darío Porley Esteves, Louis M. Mansky, Robert A. Dick, and Florian KM Schur. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41594-024-01390-8\">https://doi.org/10.1038/s41594-024-01390-8</a>.","apa":"Obr, M., Percipalle, M., Chernikova, D., Yang, H., Thader, A., Pinke, G., … Schur, F. K. (2025). Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01390-8\">https://doi.org/10.1038/s41594-024-01390-8</a>","ieee":"M. Obr <i>et al.</i>, “Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32. Springer Nature, pp. 268–276, 2025.","ama":"Obr M, Percipalle M, Chernikova D, et al. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. <i>Nature Structural &#38; Molecular Biology</i>. 2025;32:268-276. doi:<a href=\"https://doi.org/10.1038/s41594-024-01390-8\">10.1038/s41594-024-01390-8</a>"},"date_published":"2025-02-01T00:00:00Z","date_updated":"2026-03-16T12:55:18Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["001306564000001"],"pmid":["39242978"],"oaworkid":["W4402316284"]},"file":[{"file_id":"19608","success":1,"creator":"dernst","date_created":"2025-04-23T07:02:33Z","access_level":"open_access","file_size":13724041,"checksum":"c641ad94afb28917b20425db676fc3ee","file_name":"2025_NatureStrucBio_Obr.pdf","content_type":"application/pdf","date_updated":"2025-04-23T07:02:33Z","relation":"main_file"}],"pmid":1,"day":"01","year":"2025","doi":"10.1038/s41594-024-01390-8","scopus_import":"1","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"acknowledgement":"This work was funded by the Institute of Science and Technology Austria (ISTA) and the Austrian Science Fund (grant P31445 to F.K.M.S.). Access to high-resolution cryo-ET data acquisition at European Molecular Biology Laboratory (EMBL) Heidelberg was supported through the EMBL cryo-EM platform. We thank V.-V. Hodirnau at ISTA and W. Hagen and F. Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This research was also supported by the scientific service units of ISTA through resources provided by Scientific Computing, the Life Science Facility, and the EM Facility. L.M.M. was supported by National Institutes of Health grants R01 GM151775 and R21 DE032878 and by the University of Minnesota Masonic Cancer Center. D.P. was supported by the DOC doctoral fellowship program of the Austrian Academy of Sciences. R.A.D was supported by the National Institute of Allergy and Infectious Diseases (grant R01AI147890). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Specifically, we also want to thank A. Schlögl for computational support and J. Hansen and V. Vogt for critical comments on the manuscript. We also thank the other members of the Schur lab for helpful discussions and experimental advice.","APC_amount":"12348 EUR","language":[{"iso":"eng"}],"isi":1,"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"publication":"Nature Structural & Molecular Biology","page":"268-276","month":"02","status":"public","abstract":[{"text":"Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology from other retroviruses, suggesting a distinct way of assembly. Here we report the results of cryo-electron tomography studies of HTLV-1 virus-like particles assembled in vitro, as well as derived from cells. This work shows that HTLV-1 uses a distinct mechanism of Gag–Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature capsid (CA) tubular arrays reveals that the primary stabilizing component in HTLV-1 is the N-terminal domain of CA. Mutagenesis analysis supports this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the C-terminal domain of CA. These results provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus and this helps explain why HTLV-1 particles are morphologically distinct.","lang":"eng"}],"quality_controlled":"1","date_created":"2024-09-08T10:29:06Z","oa":1,"OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","volume":32,"oaworkid":1,"publisher":"Springer Nature","article_type":"original","file_date_updated":"2025-04-23T07:02:33Z","ddc":["570"]},{"publication":"bioRxiv","article_processing_charge":"No","date_created":"2025-12-11T13:33:27Z","OA_type":"green","oa":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"RNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters the nucleus, where it transcribes protein-coding genes. Although transcription by Pol II is intensively studied, how this central multi-subunit enzyme is made and the role of dedicated factors remains unclear. Here, we report the integrative structural analysis of a native human Pol II from the cytoplasm captured near the end of biogenesis. The complex contained Gdown1 and three biogenesis factors – RPAP2 and the critical small GTPases GPN1 and GPN3. Cryo-EM analysis of the complex revealed how Gdown1 and RPAP2 associate with Pol II and prevent the premature association of transcription factors. Further biochemical and cryo-EM analysis revealed how RPAP2 recruits GPN1–GPN3 to the complex, and how the assembly of the RPAP2–GPN1–GPN3 complex is controlled by GTP hydrolysis. The combined results uncover a network of interactions that chaperone cytoplasmic Pol II to prevent aberrant interactions, reveal a GTP-controlled switch during the final stages of Pol II biogenesis, and suggest a general mechanism for the action of GPN-loop GTPase family of enzymes."}],"status":"public","month":"12","publication_status":"published","author":[{"full_name":"Hlavata, Annamaria","first_name":"Annamaria","last_name":"Hlavata","id":"36062FEC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin","last_name":"Neuditschko","full_name":"Neuditschko, Benjamin"},{"last_name":"Schellhaas","first_name":"Ulla","full_name":"Schellhaas, Ulla"},{"full_name":"Plaschka, Clemens","first_name":"Clemens","last_name":"Plaschka"},{"full_name":"Herzog, Franz","last_name":"Herzog","first_name":"Franz"},{"first_name":"Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036"}],"citation":{"mla":"Hlavata, Annamaria, et al. “Structure of Cytoplasmic RNA Polymerase II.” <i>BioRxiv</i>, 2025, doi:<a href=\"https://doi.org/10.64898/2025.12.10.692585\">10.64898/2025.12.10.692585</a>.","ista":"Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. 2025. Structure of cytoplasmic RNA polymerase II. bioRxiv, <a href=\"https://doi.org/10.64898/2025.12.10.692585\">10.64898/2025.12.10.692585</a>.","short":"A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, C. Bernecky, BioRxiv (2025).","chicago":"Hlavata, Annamaria, Benjamin Neuditschko, Ulla Schellhaas, Clemens Plaschka, Franz Herzog, and Carrie Bernecky. “Structure of Cytoplasmic RNA Polymerase II.” <i>BioRxiv</i>, 2025. <a href=\"https://doi.org/10.64898/2025.12.10.692585\">https://doi.org/10.64898/2025.12.10.692585</a>.","ieee":"A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, and C. Bernecky, “Structure of cytoplasmic RNA polymerase II,” <i>bioRxiv</i>. 2025.","apa":"Hlavata, A., Neuditschko, B., Schellhaas, U., Plaschka, C., Herzog, F., &#38; Bernecky, C. (2025). Structure of cytoplasmic RNA polymerase II. <i>bioRxiv</i>. <a href=\"https://doi.org/10.64898/2025.12.10.692585\">https://doi.org/10.64898/2025.12.10.692585</a>","ama":"Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. Structure of cytoplasmic RNA polymerase II. <i>bioRxiv</i>. 2025. doi:<a href=\"https://doi.org/10.64898/2025.12.10.692585\">10.64898/2025.12.10.692585</a>"},"OA_place":"repository","corr_author":"1","title":"Structure of cytoplasmic RNA polymerase II","_id":"20804","department":[{"_id":"CaBe"}],"type":"preprint","oa_version":"Preprint","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"PreCl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.64898/2025.12.10.692585"}],"language":[{"iso":"eng"}],"acknowledgement":"We thank A. Salmazo for assistance with Pol II purification. We thank staff at the VBCF Proteomics facility for immunoprecipitation-mass spectrometry analysis, and J.A. Stopp for assistance with IP-MS data visualization. This research was further supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF).","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"biorxivid":["10.64898/2025.12.10.692585"]},"date_updated":"2026-07-22T06:51:50Z","date_published":"2025-12-10T00:00:00Z","biorxivid":1,"doi":"10.64898/2025.12.10.692585","day":"10","year":"2025"},{"month":"03","abstract":[{"text":"Gene expression is crucial for cell differentiation, development and survival of\r\norganisms. It consists of several steps, starting with transcription that is mediated by\r\nRNA polymerases. These are protein machineries transcribing and producing different\r\ntypes of RNAs. Although, the individual steps of transcription by RNA polymerase II\r\n(Pol II) as well as the structure of Pol II has been extensively studied, surprisingly,\r\nthere is still little known about its regulation and assembly in cytoplasm. Among the\r\nproteins that are important in biogenesis of Pol II are RNA polymerase II associating\r\nproteins (RPAP) and small GPN-loop GTPases (GPN). Both of these protein groups\r\nwere shown to take essential part in assembly of Pol II.\r\nThe aim of this project was to deepen our knowledge in regulation of Pol II in\r\nthe cytoplasm as well as the proteins involved in this process. Techniques of structural\r\nbiology, biochemistry and cell biology were employed to study and characterize cytoplasmic Pol II and its interacting partners.\r\nThis study shows for the first time the structure of cytoplasmic Pol II at high\r\nresolution. The structure also reveals proteins interacting with Pol II in cytoplasm,\r\nnamely GDOWN1, RPAP2. Comparing the structure of cytoplasmic Pol II with transcribing Pol II revealed striking difference in clamp region that is not in closed state.\r\nFurthermore, GDOWN1 and RPAP2 make steric clashes with various transcription\r\nfactors bound to Pol II during different stages of transcription. Even though GPN1 and\r\nGPN3 proteins were not resolved in the cytoplasmic Pol II structure, they are part of\r\nthe complex and their interaction with Pol II was confirmed in vitro. RPAP2 stabilizes\r\nthese proteins on Pol II and several experiments suggest that they interact with the\r\nclamp region. In addition, GDOWN1, RPAP2 and GPNs might keep clamp in open or\r\npartially open state. Based on these results I propose a novel model of regulation of\r\nPol II in cytoplasm. GDOWN1, RPAP2, GPN1 and GPN3 bind to Pol II in cytoplasm\r\nand doing so they can prevent pre-mature binding of DNA or RNA and different transcription factors to Pol II in cytoplasm or before engaging in transcription nucleus.\r\nThis research contributes to the current knowledge of molecular mechanisms\r\nof Pol II regulation in cytoplasm.","lang":"eng"}],"status":"public","page":"83","file_date_updated":"2026-03-20T23:30:04Z","publisher":"Institute of Science and Technology Austria","ddc":["572"],"oa":1,"date_created":"2025-03-20T12:52:47Z","article_processing_charge":"No","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-055-8"],"eissn":["2663-337X"]},"day":"20","year":"2025","doi":"10.15479/10.15479/AT-ISTA-19431","date_published":"2025-03-20T00:00:00Z","date_updated":"2026-04-07T11:46:32Z","file":[{"file_id":"19448","creator":"ahlavata","date_created":"2025-03-24T12:48:36Z","access_level":"closed","file_size":23506747,"checksum":"b7ddf424ffe95f8c767c53c8bb62d4f3","embargo_to":"open_access","file_name":"PhD_Thesis_Hlavata_final_submission.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2026-03-20T23:30:04Z","relation":"source_file"},{"file_size":9478591,"file_name":"PhD_Thesis_Hlavata_final_submission_update.pdf","embargo":"2026-03-20","checksum":"6c5a59c9bac467c3d0b3ffb8ea6d9fd4","content_type":"application/pdf","date_updated":"2026-03-20T23:30:04Z","relation":"main_file","file_id":"19449","creator":"ahlavata","date_created":"2025-03-24T12:51:10Z","access_level":"open_access"}],"language":[{"iso":"eng"}],"acknowledgement":"I would also like to acknowledge the ISTA Facilities: Lab Support Facility, Protein Services and Electron Microscopy Facility (EMF) and Scientific Computing. EMF for their support during data collections and troubleshooting, especially Valentin. Scientific Computing for solving quickly any issues related with cluster.","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"oa_version":"Published Version","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"CaBe"}],"supervisor":[{"first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A"}],"_id":"19431","title":"Regulation of Cytoplasmic RNA Polymerase II","citation":{"mla":"Hlavata, Annamaria. <i>Regulation of Cytoplasmic RNA Polymerase II</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">10.15479/10.15479/AT-ISTA-19431</a>.","ista":"Hlavata A. 2025. Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria.","chicago":"Hlavata, Annamaria. “Regulation of Cytoplasmic RNA Polymerase II.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">https://doi.org/10.15479/10.15479/AT-ISTA-19431</a>.","short":"A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science and Technology Austria, 2025.","ieee":"A. Hlavata, “Regulation of Cytoplasmic RNA Polymerase II,” Institute of Science and Technology Austria, 2025.","apa":"Hlavata, A. (2025). <i>Regulation of Cytoplasmic RNA Polymerase II</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">https://doi.org/10.15479/10.15479/AT-ISTA-19431</a>","ama":"Hlavata A. Regulation of Cytoplasmic RNA Polymerase II. 2025. doi:<a href=\"https://doi.org/10.15479/10.15479/AT-ISTA-19431\">10.15479/10.15479/AT-ISTA-19431</a>"},"publication_status":"published","author":[{"first_name":"Annamaria","last_name":"Hlavata","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","full_name":"Hlavata, Annamaria"}],"OA_place":"publisher","corr_author":"1"},{"publication_status":"published","author":[{"first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","last_name":"Sett","orcid":"0000-0001-7641-8348","full_name":"Sett, Riya"}],"citation":{"ama":"Sett R.  Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19533\">10.15479/AT-ISTA-19533</a>","ieee":"R. Sett, “ Quantum remote sensing and non-equilibrium phase transitions in the microwave regime,” Institute of Science and Technology Austria, 2025.","apa":"Sett, R. (2025). <i> Quantum remote sensing and non-equilibrium phase transitions in the microwave regime</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19533\">https://doi.org/10.15479/AT-ISTA-19533</a>","short":"R. Sett,  Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime, Institute of Science and Technology Austria, 2025.","chicago":"Sett, Riya. “ Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19533\">https://doi.org/10.15479/AT-ISTA-19533</a>.","ista":"Sett R. 2025.  Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria.","mla":"Sett, Riya. <i> Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19533\">10.15479/AT-ISTA-19533</a>."},"corr_author":"1","project":[{"grant_number":"862644","name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"OA_place":"publisher","title":" Quantum remote sensing and non-equilibrium phase transitions in the microwave regime","type":"dissertation","oa_version":"Published Version","_id":"19533","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"supervisor":[{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}],"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"acknowledgement":"I acknowledge the generous financial support of the Austrian Science Fund (FWF) via BeyondC\r\n(F7105) and the European Union’s Horizon 2020 research and innovation program (FETopen\r\nQUARTET, Grant Agreement No. 862644), which made this research possible. I also extend\r\nmy sincere appreciation to the MIBA workshop and the Institute of Science and Technology\r\nAustria nanofabrication facility for their technical assistance, which was instrumental in realizing\r\nthis work.","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"SSU"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","related_material":{"record":[{"id":"18978","relation":"research_data","status":"public"},{"id":"19280","relation":"part_of_dissertation","status":"public"},{"id":"17183","relation":"part_of_dissertation","status":"public"},{"id":"13117","relation":"part_of_dissertation","status":"public"}]},"keyword":["phase transition","open quantum system","phase diagram","cavity quantum electrodynamics","superconducting qubits","semiclassical physics","quantum optics","josephson junction","parametric converter","phase conjugation","quantum radar","quantum entanglement","correlation","quantum sensing"],"doi":"10.15479/AT-ISTA-19533","year":"2025","day":"1","file":[{"creator":"rsett","date_created":"2025-04-10T11:33:22Z","access_level":"open_access","file_id":"19538","date_updated":"2025-10-11T22:30:02Z","relation":"main_file","file_size":4129208,"checksum":"ba6cd2289d0141a160a14fc97df1632f","embargo":"2025-10-11","file_name":"PhD_Thesis_Riya_Sett_pdfa.pdf","content_type":"application/pdf"},{"file_id":"19539","date_created":"2025-04-10T11:34:08Z","creator":"rsett","access_level":"closed","file_size":6646110,"content_type":"application/x-zip-compressed","checksum":"ee63a94cb8f7adf5e766903028b81ed6","file_name":"PhD Thesis Riya Sett.zip","embargo_to":"open_access","date_updated":"2025-10-11T22:30:02Z","relation":"source_file"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2025-04-01T00:00:00Z","date_updated":"2026-06-03T07:16:05Z","degree_awarded":"PhD","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"ddc":["530"],"file_date_updated":"2025-10-11T22:30:02Z","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","oa":1,"date_created":"2025-04-09T16:44:26Z","abstract":[{"lang":"eng","text":"This thesis explores advancements in quantum remote sensing and non-equilibrium phase\r\ntransitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing.\r\nIn the first project, I experimentally studied photon blockade breakdown as a dissipative phase\r\ntransition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic\r\nlimit, we demonstrated that the observed bistability is a genuine signature of a first-order\r\nphase transition in this system. This work provides insight into non-equilibrium quantum\r\ndynamics and phase transitions in driven-dissipative open quantum systems.\r\nThe second project focuses on the experimental realization of a phase-conjugate receiver for\r\nquantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy\r\nenvironments using entangled light. While an ideal spontaneous parametric down-conversion\r\n(SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical\r\nillumination, no such ideal receiver exists. Instead, we explore an experimental realization of a\r\nphase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a\r\nJosephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled\r\nsignal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate\r\nkey experimental limitations that constrain practical QI performance, contributing to the\r\ndevelopment of quantum-enhanced sensing.\r\nAdditionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These\r\nmethods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been\r\nessential in data acquisition, noise filtering, and correlation analysis across multiple research\r\nprojects. Although not real-time, these DSP techniques significantly enhance the accuracy of\r\nquantum measurements.\r\nOverall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic\r\nlimit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver\r\nfor QI. These findings contribute to quantum metrology, particularly for weak signal detection\r\nand remote sensing in noisy environments.\r\n"}],"status":"public","month":"04","page":"109"},{"publication":"Molecular Biology and Evolution","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"DOAJ_listed":"1","abstract":[{"lang":"eng","text":"The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome."}],"status":"public","month":"05","article_number":"msaf085","ddc":["570"],"file_date_updated":"2025-05-28T09:34:36Z","article_type":"original","publisher":"Oxford University Press","article_processing_charge":"Yes","volume":42,"OA_type":"gold","date_created":"2025-05-25T22:16:56Z","oa":1,"quality_controlled":"1","type":"journal_article","oa_version":"Published Version","_id":"19735","department":[{"_id":"BeVi"},{"_id":"DaZi"}],"intvolume":"        42","author":[{"last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K","full_name":"Bett, Vincent K"},{"first_name":"Minerva S","id":"2b681148-eed5-11eb-b81b-ae229e8620f8","last_name":"Trejo Arellano","full_name":"Trejo Arellano, Minerva S","orcid":"0000-0002-1982-3475"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","citation":{"apa":"Bett, V. K., Trejo Arellano, M. S., &#38; Vicoso, B. (2025). Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>","ieee":"V. K. Bett, M. S. Trejo Arellano, and B. Vicoso, “Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana,” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5. Oxford University Press, 2025.","ama":"Bett VK, Trejo Arellano MS, Vicoso B. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. 2025;42(5). doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>","mla":"Bett, Vincent K., et al. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5, msaf085, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>.","ista":"Bett VK, Trejo Arellano MS, Vicoso B. 2025. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. Molecular Biology and Evolution. 42(5), msaf085.","chicago":"Bett, Vincent K, Minerva S Trejo Arellano, and Beatriz Vicoso. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>.","short":"V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025)."},"corr_author":"1","OA_place":"publisher","project":[{"grant_number":"PAT 8748323","name":"Sex chromosomes in evolution and development","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b"},{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"title":"Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana","doi":"10.1093/molbev/msaf085","year":"2025","day":"01","pmid":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"19756","success":1,"creator":"dernst","date_created":"2025-05-28T09:34:36Z","access_level":"open_access","file_size":1282772,"file_name":"2025_MBE_Bett.pdf","checksum":"6c14b03f94b4aadf8869be2c4366d077","content_type":"application/pdf","date_updated":"2025-05-28T09:34:36Z","relation":"main_file"}],"external_id":{"isi":["001483460200001"],"pmid":["40202086"]},"date_updated":"2026-07-25T22:30:33Z","date_published":"2025-05-01T00:00:00Z","isi":1,"issue":"5","language":[{"iso":"eng"}],"acknowledgement":"We thank the Vicoso lab for their help in maintaining Artemia and for their valuable feedback and suggestions. We thank Marwan Elkrewi for his useful technical advice and discussions. We are also grateful to the Scientific Unit at ISTA Austria for computational resources and assistance. This work was supported by Austrian science fund (FWF) grants PAT8748323 and SFB F88-10 (as part of the SFB Meiosis consortium https://sfbmeiosis.org) to BV and Swedish Research Council (Vetenskapsrådet, grant number 2020-06424) to MSTA.","acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","related_material":{"record":[{"id":"20449","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","id":"20444","status":"deleted"}],"link":[{"relation":"software","url":"https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git"}]}},{"corr_author":"1","project":[{"_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","name":"Sex chromosomes in evolution and development","grant_number":"PAT 8748323"},{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"}],"OA_place":"publisher","publication_status":"published","citation":{"mla":"Bett, Vincent K. <i>Evolution and Regulation of the Z Chromosome</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20449\">10.15479/AT-ISTA-20449</a>.","ista":"Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria.","short":"V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science and Technology Austria, 2025.","chicago":"Bett, Vincent K. “Evolution and Regulation of the Z Chromosome.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20449\">https://doi.org/10.15479/AT-ISTA-20449</a>.","apa":"Bett, V. K. (2025). <i>Evolution and regulation of the Z chromosome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20449\">https://doi.org/10.15479/AT-ISTA-20449</a>","ieee":"V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science and Technology Austria, 2025.","ama":"Bett VK. Evolution and regulation of the Z chromosome. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20449\">10.15479/AT-ISTA-20449</a>"},"author":[{"full_name":"Bett, Vincent K","first_name":"Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425"}],"title":"Evolution and regulation of the Z chromosome","type":"dissertation","oa_version":"Published Version","_id":"20449","supervisor":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"alternative_title":["ISTA Thesis"],"acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso.","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"status":"public","id":"19735","relation":"part_of_dissertation"},{"id":"15009","relation":"part_of_dissertation","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","doi":"10.15479/AT-ISTA-20449","day":"10","year":"2025","file":[{"file_size":18507283,"content_type":"application/pdf","file_name":"2025_Bett_Vincent_Thesis.pdf","checksum":"26905c22bca417198a733d792d8ce422","embargo":"2026-06-01","date_updated":"2026-06-01T22:30:04Z","relation":"main_file","file_id":"20507","date_created":"2025-10-20T13:32:29Z","creator":"vbett","access_level":"open_access"},{"creator":"vbett","date_created":"2025-10-20T13:35:34Z","access_level":"closed","file_id":"20508","date_updated":"2026-06-01T22:30:04Z","relation":"source_file","file_size":17163921,"file_name":"2025_Bett_Vincent_Thesis.docx","checksum":"6a09a8d126d3628bfd8a35202735f267","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-06-12T08:32:16Z","date_published":"2025-10-10T00:00:00Z","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"ddc":["576"],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2026-06-01T22:30:04Z","article_processing_charge":"No","oa":1,"date_created":"2025-10-11T08:18:51Z","status":"public","abstract":[{"text":"Males and females of many  species differ in morphology, physiology, and behavior. In taxa\r\nwith genetic sex determination, sexual differentiation arises largely from sex-biased gene\r\nexpression, which varies across tissues, developmental stages, and lineages. Increasing\r\nevidence highlights chromatin configuration, which can exist in open or closed states, and can\r\nbe shaped by sex-determination path ways, as a key regulatory layer of this dimorphism.\r\nDegeneration of the Y or W chromosome further contributes to sex -specific differences by\r\naltering gene copy numbers relative to autosomes in heterogametic sex. To mitigate these\r\nimbalances, many eukaryotes have independently evolved dosage compensation mechanisms,\r\noften mediated through chromatin -level regulation. In this thesis, we investigate the\r\nevolutionary dynamics of sex chromosome differentiation in two species, Artemia franciscana\r\nand Cameraria  ohridella , with a particular focus on the extent of dosage compensation\r\nfollowing gene loss in the heterogametic sex and the potential chromatin-based mechanisms\r\nunderlying this process. We further characterize sex -biased gene expression and its regulation\r\nthrough histone modifications. Our analyses also reveal that the A. franciscana genome is\r\nhighly repetitive, with many genes containing intronic transposable elements. We find that\r\nenrichment of histonemo difications associated with constitutive heterochromatin, positively\r\ncorrelates with variation in gene expression levels. Collectively, these findings underscore role\r\nof chromatin regulation in shaping the evolution of sex chromosomes and sexual\r\ndifferentiation. ","lang":"eng"}],"month":"10","page":"114"},{"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"ddc":["576","578"],"file_date_updated":"2026-03-01T23:30:03Z","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","date_created":"2025-11-25T13:19:11Z","oa":1,"abstract":[{"lang":"eng","text":"Understanding the mechanisms underlying speciation is a central aim of evolutionary biology.\r\nA persistent challenge in the field is to identify loci that contribute to reproductive isolation,\r\nwhile disentangling signals of selection from demography, linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches that rely on site-based statistics in\r\narbitrary fixed windows face inherent limitations, as they conflate historical and\r\ncontemporary processes of divergence and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce and recombine through time. By directly analysing haplotype clustering by species\r\nor phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow, and tracing their evolutionary history.\r\nIn this thesis, I explore the utility of genealogical approaches for studying species\r\ndivergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks\r\nthrough the structure of the ARG, using simulations and empirical data to highlight how\r\ngenealogical processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter 3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails Littorina. These snails offer a unique opportunity to study an innovation because they\r\ninclude a very recent transition from egg-laying to live bearing, yet snails with the different\r\nreproductive modes are not reciprocally monophyletic. I exploited this by using topology\r\nclustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying\r\nto live-bearing involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale, phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging, then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy combines molecular phasing with statistical phasing to generate phased whole\r\ngenome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn chapter 5, I analyse hybridising populations from two replicate hybrid zones to find\r\na parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape\r\ndriven by variation in demographic history. While outlier genome scans of FST failed to dissect\r\nthe causes of differentiation, ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes across hybrid zones. In addition to the biological insight, this chapter\r\nalso presents a comparison of the latest ARG inference tools, showing that signals of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods, despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association studies of floral pigmentation with genealogical\r\ninference, to test for additional colour loci, and confirm the effect of previously described loci.\r\nThis work demonstrates that flower colour variation is driven by a small number of large effect\r\nloci, while also hinting at the presence of a new candidate regulatory factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary origins. My results show that it\r\nconsists of 5 highly divergent loci, each of which is associated with flower colour. Using\r\npatterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent localized barrier to gene flow within an otherwise permeable genome.\r\nTogether, these chapters add to the increasing pool of studies using genealogical\r\napproaches to complement and extend site-based statistics to use haplotype structures in\r\nspeciation research. By tracking haplotypes directly and connecting genealogical clustering to\r\npopulation processes, ARG-based inference promises to provide new insights into how local\r\nselective pressures, demographic history, and long-term barriers interact to shape the\r\ngenomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about\r\nthe benefits of using genealogical inference to learn more than what site-based statistics\r\ncould tell us."}],"status":"public","month":"11","page":"268","publication_status":"published","citation":{"mla":"Pal, Arka. <i>Using Genealogies to Study the Genomic Basis of Species Divergence</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>.","ista":"Pal A. 2025. Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria.","chicago":"Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20694\">https://doi.org/10.15479/AT-ISTA-20694</a>.","short":"A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025.","apa":"Pal, A. (2025). <i>Using genealogies to study the genomic basis of species divergence</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20694\">https://doi.org/10.15479/AT-ISTA-20694</a>","ieee":"A. Pal, “Using genealogies to study the genomic basis of species divergence,” Institute of Science and Technology Austria, 2025.","ama":"Pal A. Using genealogies to study the genomic basis of species divergence. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>"},"author":[{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","first_name":"Arka","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469"}],"OA_place":"publisher","project":[{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"},{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"}],"corr_author":"1","title":"Using genealogies to study the genomic basis of species divergence","type":"dissertation","oa_version":"Published Version","_id":"20694","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"id":"12159","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"14796","relation":"part_of_dissertation"},{"id":"20190","relation":"part_of_dissertation","status":"public"}]},"doi":"10.15479/AT-ISTA-20694","day":"25","year":"2025","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"file":[{"content_type":"application/pdf","file_name":"2025_Pal_Arka_Thesis.pdf","embargo":"2026-03-01","checksum":"7a10a738d58524aebb5dcbd9b34c21c5","file_size":42723135,"relation":"main_file","date_updated":"2026-03-01T23:30:03Z","file_id":"20721","access_level":"open_access","date_created":"2025-12-01T13:53:36Z","creator":"apal"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2025_Pal_Arka_Thesis.docx","embargo_to":"open_access","checksum":"166d832b08d0434ce407f8f3cb930fe5","file_size":60632116,"relation":"source_file","date_updated":"2026-03-01T23:30:03Z","file_id":"20722","access_level":"closed","date_created":"2025-12-01T13:53:39Z","creator":"apal"}],"date_updated":"2026-04-28T13:20:36Z","date_published":"2025-11-25T00:00:00Z"},{"publication":"Molecular Ecology","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"article_number":"e70067","ddc":["570"],"publisher":"Wiley","file_date_updated":"2026-01-05T13:47:47Z","article_type":"original","volume":34,"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","date_created":"2025-08-17T22:01:37Z","oa":1,"OA_type":"hybrid","PlanS_conform":"1","status":"public","abstract":[{"lang":"eng","text":"A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying replicated population contrasts, including multiple incidences of secondary contact, can strengthen inferences. In this paper, we use linked-read sequencing (haplotagging), FST scans and genealogical methods to characterise the genomic landscape associated with replicate hybrid zone formation. We studied two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies majus, that form secondary hybrid zones in multiple independent valleys in the Pyrenees. Consistent with past work, we found very low differentiation at one well-studied zone (Planoles). However, at a second zone (Avellanet), we found stronger differentiation and greater heterogeneity, which we argue is due to differences in the amount of introgression following secondary contact. Topology weighting of genealogical trees identified loci where haplotype diversity was associated with the two snapdragon varieties. Two of the strongest associations were at previously identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta, two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence times provides additional evidence for selective sweeps at these loci and barriers to gene flow. Our study highlights the impact of demographic history on the differentiation landscape, emphasising the need to distinguish between historical divergence and recent introgression."}],"month":"11","OA_place":"publisher","project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"},{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"corr_author":"1","citation":{"mla":"Pal, Arka, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” <i>Molecular Ecology</i>, vol. 34, no. 22, e70067, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70067\">10.1111/mec.70067</a>.","short":"A. Pal, D. Shipilina, A. Le Moan, A.J. Mcnairn, J.K. Grenier, M. Kucka, G. Coop, Y.F. Chan, N.H. Barton, D. Field, S. Stankowski, Molecular Ecology 34 (2025).","chicago":"Pal, Arka, Daria Shipilina, Alan Le Moan, Adrian J. Mcnairn, Jennifer K. Grenier, Marek Kucka, Graham Coop, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70067\">https://doi.org/10.1111/mec.70067</a>.","ista":"Pal A, Shipilina D, Le Moan A, Mcnairn AJ, Grenier JK, Kucka M, Coop G, Chan YF, Barton NH, Field D, Stankowski S. 2025. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. 34(22), e70067.","ama":"Pal A, Shipilina D, Le Moan A, et al. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. <i>Molecular Ecology</i>. 2025;34(22). doi:<a href=\"https://doi.org/10.1111/mec.70067\">10.1111/mec.70067</a>","apa":"Pal, A., Shipilina, D., Le Moan, A., Mcnairn, A. J., Grenier, J. K., Kucka, M., … Stankowski, S. (2025). Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70067\">https://doi.org/10.1111/mec.70067</a>","ieee":"A. Pal <i>et al.</i>, “Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum,” <i>Molecular Ecology</i>, vol. 34, no. 22. Wiley, 2025."},"author":[{"last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","first_name":"Arka","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka"},{"first_name":"Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226"},{"full_name":"Le Moan, Alan","first_name":"Alan","last_name":"Le Moan"},{"full_name":"Mcnairn, Adrian J.","first_name":"Adrian J.","last_name":"Mcnairn"},{"first_name":"Jennifer K.","last_name":"Grenier","full_name":"Grenier, Jennifer K."},{"full_name":"Kucka, Marek","last_name":"Kucka","first_name":"Marek"},{"full_name":"Coop, Graham","last_name":"Coop","first_name":"Graham"},{"full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank","last_name":"Chan"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"}],"publication_status":"published","title":"Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum","type":"journal_article","oa_version":"Published Version","_id":"20190","intvolume":"        34","department":[{"_id":"NiBa"}],"issue":"22","isi":1,"acknowledgement":"We thank ESEB Godfrey Hewitt Mobility Award for supporting AP’s research stay at UC Davis. We thank Tom Ellis, Parvathy Surendranadh, and other Barton Group and Coop Lab members for stimulating discussions. We are grateful to all the interns and volunteers who have helped us with fieldwork. We thank Eva Salmerón Mateu for her assistance in fieldwork logistics at the field station, El Serrat. We are grateful to Enrico Coen and his research group for providing the Antirrhinum molle PoolSeq data used in the allele polarisation. We are also thankful to Enrico Coen and Cristophe Thébaud for discovering the Avellanet hybrid zone, followed up with sampling led by D.L.F. in 2017. The study was supported by Austrian Science Fund (FWF) Grant (Snapdragon Speciation P32166, awarded to D.L.F.); ERC (Advanced Grant HaplotypeStructure 101055327, awarded to NHB); ERC (POC Grant 101069216, awarded to Y.F.C.) and the National Institutes of Health (NIH R35 GM136290, awarded to G.C.). Y.F.C. was supported by the Max Planck Society. Computing infrastructure for bioinformatics and analyses was provided by ISTA High Performance Cluster. ","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","related_material":{"record":[{"status":"public","id":"20694","relation":"dissertation_contains"}],"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/snapdragon-secrets/"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","doi":"10.1111/mec.70067","year":"2025","day":"01","file":[{"file_id":"20958","success":1,"creator":"dernst","date_created":"2026-01-05T13:47:47Z","access_level":"open_access","file_size":9886694,"file_name":"2025_MolecEcology_Pal.pdf","checksum":"c586fc674df4e7dd6e43aef87a52c6f6","content_type":"application/pdf","date_updated":"2026-01-05T13:47:47Z","relation":"main_file"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["001546622100001"]},"date_updated":"2026-07-25T22:30:33Z","date_published":"2025-11-01T00:00:00Z"},{"supervisor":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"_id":"19386","oa_version":"Published Version","type":"dissertation","OA_embargo":"12","title":"Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp","author":[{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N"}],"publication_status":"published","citation":{"ista":"Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. Institute of Science and Technology Austria.","short":"M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025.","chicago":"Elkrewi, Marwan N. “Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>.","mla":"Elkrewi, Marwan N. <i>Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>.","ieee":"M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025.","apa":"Elkrewi, M. N. (2025). <i>Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>","ama":"Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>"},"corr_author":"1","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"OA_place":"publisher","date_updated":"2026-07-06T13:48:33Z","date_published":"2025-03-14T00:00:00Z","file":[{"file_id":"19462","date_created":"2025-03-26T07:06:56Z","creator":"melkrewi","access_level":"closed","file_size":25019680,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Marwan_Elkrewi.docx","checksum":"5549a8216c07e4c39281648912d72246","embargo_to":"open_access","date_updated":"2026-03-26T23:30:03Z","relation":"source_file"},{"file_id":"19463","access_level":"open_access","date_created":"2025-03-26T07:06:22Z","creator":"melkrewi","content_type":"application/pdf","checksum":"aed2ba9965aa89b3414deae1ae9f4321","embargo":"2026-03-26","file_name":"Thesis_Marwan_Elkrewi.pdf","file_size":17294844,"relation":"main_file","date_updated":"2026-03-26T23:30:03Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2025","day":"14","doi":"10.15479/AT-ISTA-19386","has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","id":"12248","relation":"part_of_dissertation"},{"status":"public","id":"10767","relation":"part_of_dissertation"},{"id":"15009","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"14613","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"17890","status":"public"},{"id":"10167","relation":"part_of_dissertation","status":"public"}]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"My PhD work was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium (https://sfbmeiosis.org/, grant ID FWF SFB F88-10).","alternative_title":["ISTA Thesis"],"publication_identifier":{"eissn":["2663-337X"],"isbn":["9783990780534"]},"degree_awarded":"PhD","page":"170","month":"03","abstract":[{"lang":"eng","text":"Crustaceans are a large group of arthropods with a great diversity of species and\r\ndifferent types of sex determination systems and reproductive modes (Subramoniam, 2017).\r\nThis makes them a great model for exploring the evolution of sex chromosomes and sexual\r\ndimorphism and investigating the evolutionary mechanisms driving and maintaining the\r\ndiversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a\r\nbranchiopod crustacean, are well suited for such explorations, as they have both highly\r\ndimorphic traits and closely related sexual and asexual species. Although brine shrimp are\r\nknown to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex\r\nchromosomes are still not well characterized at the genomic level, the sex-determination gene\r\nis unknown, and it is still unclear whether the same sex chromosomes as shared by the\r\ndifferent species.\r\nThe first part of this thesis was to characterize the Z and W chromosomes in Artemia\r\nusing an array of methods, from generating multiple chromosome and contig level genome\r\nassemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer\r\nbased approaches.\r\nThe second part tackles the conservation of the cell type specific regulatory pathways\r\nin the female reproductive system between Artemia and Drosophila, and the expression of the\r\nZ-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show\r\nthat germline cells lack dosage compensation, with a subset of cells showing evidence of\r\nextreme repression of the Z chromosome.\r\nWith multiple sexual species and several asexual lineages of parthenogenetic females\r\nthat produce rare males at low frequencies, Brine shrimp present the perfect opportunity to\r\nexplore the transition to asexuality and shed light on the prerequisites and repercussions of\r\nthe form of modified meiosis maintaining the asexual lineages. The last chapter is an\r\ninvestigation of the molecular pathways involved in asexual reproduction in Artemia using\r\nnewly generated single nucleus RNAseq and WGS data and previously published data. "}],"status":"public","date_created":"2025-03-11T12:54:31Z","oa":1,"article_processing_charge":"No","file_date_updated":"2026-03-26T23:30:03Z","publisher":"Institute of Science and Technology Austria","ddc":["570","576"]}]