--- OA_place: publisher OA_type: hybrid _id: '18605' abstract: - lang: eng text: The response of clouds and moist-convective processes to heat loss to space by long-wave radiative cooling is an important feedback in the Earth's atmosphere. It is known that moist convection increases roughly in equilibrium with radiative cooling, an assumption often made in simplified models of the tropical atmosphere. In this study, we use an idealised two-dimensional model of the atmosphere introduced by Vallis et. al. and incorporate a bulk-cooling term, which is an idealisation of radiative cooling in the atmosphere. We comment briefly on the static stability of the system to dry and moist convection and characteris its moist convective response to changes in the bulk cooling. We find that, while the clear-sky regions of the model respond directly to the change in the cooling term, the regions dominated by moist convective plumes are insensitive to changes in cooling. Similar to previous findings from cloud-resolving models, we too find in our idealised setting that the majority of the increase in convection occurs via an increase in the areal coverage of convection, rather than its intensity. We argue that these small-scale convective processes are an upper bound on how quickly convective intensity can change to stay in equilibrium with radiative cooling. acknowledged_ssus: - _id: ScienComp acknowledgement: "The authors gratefully acknowledge the help of Julian Renaud and Alzbeta “Bety” Pechacova. Julian went through the relevant literature on the topic in the initial stages of the study in a very thorough manner and allowed the authors to understand the various types of idealised models that have been studied and the various approaches used. Bety ran simulations and performed analysis of the outputs of several simulations, which were crucial to bringing the article to its final form.\r\n\r\nThe authors also acknowledge the input of Prof. Martin Singh (Monash University, Australia) and discussions with Gregory Dritschel, Prof. Steven Tobias, and Prof. Douglas Parker (Leeds University, United Kingdom).\r\n\r\nThis project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 101034413. C. Muller gratefully acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp)." article_number: e4902 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lokahith N full_name: Agasthya, Lokahith N id: cd100965-0804-11ed-9c55-f4878ff4e877 last_name: Agasthya - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Mathis full_name: Cheve, Mathis id: c2cdb722-b15c-11ef-9e63-db902a30b40d last_name: Cheve citation: ama: 'Agasthya LN, Muller CJ, Cheve M. Moist convective scaling: Insights from an idealised model. Quarterly Journal of the Royal Meteorological Society. 2025;151(766). doi:10.1002/qj.4902' apa: 'Agasthya, L. N., Muller, C. J., & Cheve, M. (2025). Moist convective scaling: Insights from an idealised model. Quarterly Journal of the Royal Meteorological Society. Wiley. https://doi.org/10.1002/qj.4902' chicago: 'Agasthya, Lokahith N, Caroline J Muller, and Mathis Cheve. “Moist Convective Scaling: Insights from an Idealised Model.” Quarterly Journal of the Royal Meteorological Society. Wiley, 2025. https://doi.org/10.1002/qj.4902.' ieee: 'L. N. Agasthya, C. J. Muller, and M. Cheve, “Moist convective scaling: Insights from an idealised model,” Quarterly Journal of the Royal Meteorological Society, vol. 151, no. 766. Wiley, 2025.' ista: 'Agasthya LN, Muller CJ, Cheve M. 2025. Moist convective scaling: Insights from an idealised model. Quarterly Journal of the Royal Meteorological Society. 151(766), e4902.' mla: 'Agasthya, Lokahith N., et al. “Moist Convective Scaling: Insights from an Idealised Model.” Quarterly Journal of the Royal Meteorological Society, vol. 151, no. 766, e4902, Wiley, 2025, doi:10.1002/qj.4902.' short: L.N. Agasthya, C.J. Muller, M. Cheve, Quarterly Journal of the Royal Meteorological Society 151 (2025). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The data that support the findings of this study are available from the corresponding author, Lokahith Agasthya, upon reasonable request. date_created: 2024-12-01T23:01:54Z date_published: 2025-01-01T00:00:00Z date_updated: 2026-10-01T09:23:20Z day: '01' ddc: - '550' department: - _id: CaMu doi: 10.1002/qj.4902 ec_funded: 1 external_id: isi: - '001363135200001' file: - access_level: open_access checksum: 2b4968f1c794da56d1eb7b856a406de7 content_type: application/pdf creator: dernst date_created: 2025-07-03T06:46:27Z date_updated: 2025-07-03T06:46:27Z file_id: '19958' file_name: 2025_QuartJRMS_Agasthya.pdf file_size: 5924105 relation: main_file success: 1 file_date_updated: 2025-07-03T06:46:27Z fulldoi: https://doi.org/10.1002/qj.4902 has_accepted_license: '1' intvolume: ' 151' isi: 1 issue: '766' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '01' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: 629205d8-2b32-11ec-9570-e1356ff73576 call_identifier: H2020 grant_number: '805041' name: Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate publication: Quarterly Journal of the Royal Meteorological Society publication_identifier: eissn: - 1477-870X issn: - 0035-9009 publication_status: published publisher: Wiley quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: 'Moist convective scaling: Insights from an idealised model' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 151 year: '2025' ... --- APC_amount: 12348 EUR OA_place: publisher OA_type: hybrid _id: '17884' abstract: - lang: eng 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. 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Mathias full_name: Percipalle, Mathias id: 4986e21c-eb97-11eb-a6c2-a4ef0b629971 last_name: Percipalle - first_name: Darya full_name: Chernikova, Darya id: 7dbaf460-fa9e-11eb-b0ca-bc7c7ff21ad0 last_name: Chernikova - first_name: Huixin full_name: Yang, Huixin last_name: Yang - first_name: Andreas full_name: Thader, Andreas id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87 last_name: Thader - first_name: Gergely full_name: Pinke, Gergely id: 4D5303E6-F248-11E8-B48F-1D18A9856A87 last_name: Pinke - first_name: Dario J full_name: Porley, Dario J id: 2FD6EA6C-F248-11E8-B48F-1D18A9856A87 last_name: Porley - first_name: Louis M. full_name: Mansky, Louis M. last_name: Mansky - first_name: Robert A. full_name: Dick, Robert A. last_name: Dick - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Obr M, Percipalle M, Chernikova D, et al. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. Nature Structural & Molecular Biology. 2025;32:268-276. doi:10.1038/s41594-024-01390-8 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. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-024-01390-8 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.” Nature Structural & Molecular Biology. Springer Nature, 2025. https://doi.org/10.1038/s41594-024-01390-8. ieee: M. Obr et al., “Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice,” Nature Structural & Molecular Biology, vol. 32. Springer Nature, pp. 268–276, 2025. 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 & Molecular Biology. 32, 268–276. mla: Obr, Martin, et al. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” Nature Structural & Molecular Biology, vol. 32, Springer Nature, 2025, pp. 268–76, doi:10.1038/s41594-024-01390-8. 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 & Molecular Biology 32 (2025) 268–276. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The EM density maps and models for the immature HTLV-1 CA-NTD lattice and representative tomograms were deposited to the EM Data Bank under accession codes EMD-17929, EMD-17930, EMD-17931, EMD-17932, EMD-17933, EMD-17934, EMD-17935, EMD-17936, EMD-17937, EMD-17938, EMD-17939, EMD-17940, EMD-17941, EMD-17942 and EMD-17943 and the PDB under accession codes 8PU6, 8PU7, 8PU8, 8PU9, 8PUA, 8PUB, 8PUC, 8PUD, 8PUE, 8PUF, 8PUG and 8PUH. PDB 1QRJ was used as starting model to derive a refined model of the HTLV-1 CA-NTD. The models used to generate Fig. 3 and Extended Data Fig. 3 were PDB 5L93 (HIV-1), PDB 5A9E (RSV), PDB 6HWI (M-PMV) and PDB 6HWW (MLV). The UniProt codes for the protein sequences used for generating Extended Data Fig. 9 were P03345 (GAG_HTL1A), P03346 (GAG_HTLV2), Q0R5R4 (GAG_HTL32), P25058 (GAG_BLVAU), P04585 (POL_HV1H2), P15832 (GAG_HV2D2), P16087 (GAG_FIVPE), P69732 (GAG_EIAVY), P03322 (GAG_RSVP), P0C776 (GAG_ALVA), P07567 (GAG_MPMV), P31622 (GAG_JSRV), P10258 (GAG_MMTVB), P03355 (POL_MLVMS), P10262 (GAG_FLV) and Q9TTC2 (GAG_KORV). Source data are provided with this paper. date_created: 2024-09-08T10:29:06Z date_published: 2025-02-01T00:00:00Z date_updated: 2026-10-01T11:23:34Z day: '01' ddc: - '570' department: - _id: FlSc - _id: LeSa doi: 10.1038/s41594-024-01390-8 external_id: isi: - '001306564000001' oaworkid: - W4402316284 pmid: - '39242978' file: - access_level: open_access checksum: c641ad94afb28917b20425db676fc3ee content_type: application/pdf creator: dernst date_created: 2025-04-23T07:02:33Z date_updated: 2025-04-23T07:02:33Z file_id: '19608' file_name: 2025_NatureStrucBio_Obr.pdf file_size: 13724041 relation: main_file success: 1 file_date_updated: 2025-04-23T07:02:33Z fulldoi: https://doi.org/10.1038/s41594-024-01390-8 has_accepted_license: '1' intvolume: ' 32' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version oaworkid: 1 page: 268-276 pmid: 1 project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid - _id: 9B9C98E0-BA93-11EA-9121-9846C619BF3A grant_number: '25762' name: Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms publication: Nature Structural & Molecular Biology publication_identifier: eissn: - 1545-9985 issn: - 1545-9993 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 32 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '19704' abstract: - lang: eng text: The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution1,2 with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules, but dense, synapse-level circuit reconstruction by light microscopy has been out of reach, owing to limitations in resolution, contrast and volumetric imaging capability. Here we describe light-microscopy-based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning-based segmentation and analysis of connectivity, thereby directly incorporating molecular information into synapse-level reconstructions of brain tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological experiments in a readily adoptable manner. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: ScienComp - _id: PreCl - _id: M-Shop - _id: E-Lib acknowledgement: 'We thank S. Dorkenwald and P. Li for critical reading of the manuscript, S. Loomba for discussions and E. Miguel for support with data handling. We acknowledge support from ISTA’s scientific service units: Imaging and Optics, Lab Support, Scientific Computing, the preclinical facility, the Miba Machine Shop and the library. We acknowledge funding from the following sources: Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and M.R.T.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); the European Union’s Horizon 2020 research and innovation programme and Marie Skłodowska-Curie Actions Fellowship 665385 (J.L.); and the European Union’s Horizon 2020 research and innovation programme and European Research Council (ERC) grant 101044865 ‘SecretAutism’ (G.N.).Open access funding provided by Institute of Science and Technology (IST Austria).' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Michał full_name: Januszewski, Michał last_name: Januszewski - first_name: Vitali full_name: Vistunou, Vitali id: 7e146587-8972-11ed-ae7b-d7a32ea86a81 last_name: Vistunou - first_name: Nathalie full_name: Agudelo Duenas, Nathalie id: 40E7F008-F248-11E8-B48F-1D18A9856A87 last_name: Agudelo Duenas - first_name: Jakob full_name: Vorlaufer, Jakob id: 937696FA-C996-11E9-8C7C-CF13E6697425 last_name: Vorlaufer orcid: 0009-0000-7590-3501 - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Caroline full_name: Kreuzinger, Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger - first_name: Bárbara full_name: Oliveira, Bárbara id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87 last_name: Oliveira - first_name: Alban full_name: Cenameri, Alban id: 9ac8f577-2357-11eb-997a-e566c5550886 last_name: Cenameri - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Viren full_name: Jain, Viren last_name: Jain - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Nature. 2025;642:398-410. doi:10.1038/s41586-025-08985-1 apa: Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (2025). Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-08985-1 chicago: Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” Nature. Springer Nature, 2025. https://doi.org/10.1038/s41586-025-08985-1. ieee: M. Tavakoli et al., “Light-microscopy-based connectomic reconstruction of mammalian brain tissue,” Nature, vol. 642. Springer Nature, pp. 398–410, 2025. ista: Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. 2025. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Nature. 642, 398–410. mla: Tavakoli, Mojtaba, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” Nature, vol. 642, Springer Nature, 2025, pp. 398–410, doi:10.1038/s41586-025-08985-1. short: M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, Nature 642 (2025) 398–410. corr_author: '1' date_created: 2025-05-18T22:02:51Z date_published: 2025-06-12T00:00:00Z date_updated: 2026-10-02T09:59:44Z day: '12' ddc: - '570' department: - _id: JoDa - _id: GradSch - _id: Bio - _id: GaNo doi: 10.1038/s41586-025-08985-1 ec_funded: 1 external_id: isi: - '001483477000001' pmid: - '40335689' file: - access_level: open_access checksum: ebc99d7108e728f46db0a009292675ef content_type: application/pdf creator: dernst date_created: 2025-07-03T06:55:20Z date_updated: 2025-07-03T06:55:20Z file_id: '19959' file_name: 2025_Nature_Tavakoli.pdf file_size: 133201290 relation: main_file success: 1 file_date_updated: 2025-07-03T06:55:20Z fulldoi: https://doi.org/10.1038/s41586-025-08985-1 has_accepted_license: '1' intvolume: ' 642' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 398-410 pmid: 1 project: - _id: 6285a163-2b32-11ec-9570-8e204ca2dba5 grant_number: '26137' name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6 grant_number: '101044865' name: Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders - _id: 26AA4EF2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/piecing-together-the-brain-puzzle/ record: - id: '18697' relation: research_data status: public - id: '18677' relation: earlier_version status: public scopus_import: '1' status: public title: Light-microscopy-based connectomic reconstruction of mammalian brain tissue tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 642 year: '2025' ... --- OA_place: publisher _id: '19630' abstract: - lang: eng text: "This thesis consists of three chapters, each corresponding to one publication. While each of these projects tackles a topic in a different area of research, they all share a common thread in the type of topological structure they handle - a partition of space into volumes separated by interfaces that meet in non-manifold junctions.\r\n\r\nIn Chapter 2, we study clusters of soap bubbles from a simulation perspective. In particular, we develop a surface-only algorithm that couples large scale motion and shape deformation of soap bubble clusters with the small scale evolution of the thin film's thickness, which is responsible for visual phenomena like surface vortices, Newton's interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. We model film thickness as a reduced degree of freedom in the Navier-Stokes equations and from them derive three sets of equations governing normal and tangential motion of the soap film surface, as well as the evolution of the thin film thickness. We discretize these equations on a non-manifold triangle mesh, extending and adapting operators to handle complex topology. We also present an incompressible fluid solver for 2.5D films and an advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film.\r\n\r\nIn Chapter 3, we introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts mesh defects, such as overlaps, self-intersections, and inversions into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations, such as those presented in Chapter 2, but with an order of magnitude more interacting bubbles than what we could achieve before, and Boolean unions of non-manifold meshes consisting of millions of triangles.\r\n\r\nLastly, in Chapter 4, we utilize developments in the theory of random geometric complexes facilitated by observations from Discrete Morse theory. We survey the methods and results obtained with this new approach, and discuss some of its shortcomings. We use simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics." acknowledged_ssus: - _id: ScienComp acknowledgement: The project in Chapter 2 has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme under grant agreement No. 638176. The project in Chapter 3 was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA). The project in Chapter 4 has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreements No 78818 Alpha and No 638176). It was also partially supported by the DFG Collaborative Research Center TRR 109, 'Discretization in Geometry and Dynamics', through grant no. I02979-N35 of the Austrian Science Fund (FWF). Thank you for providing funds to support my work. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Peter full_name: Synak, Peter id: 331776E2-F248-11E8-B48F-1D18A9856A87 last_name: Synak citation: ama: Synak P. Methods for fluid simulation, surface tracking, and statistics of non-manifold structures. 2025. doi:10.15479/AT-ISTA-19630 apa: Synak, P. (2025). Methods for fluid simulation, surface tracking, and statistics of non-manifold structures. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19630 chicago: Synak, Peter. “Methods for Fluid Simulation, Surface Tracking, and Statistics of Non-Manifold Structures.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19630. ieee: P. Synak, “Methods for fluid simulation, surface tracking, and statistics of non-manifold structures,” Institute of Science and Technology Austria, 2025. ista: Synak P. 2025. Methods for fluid simulation, surface tracking, and statistics of non-manifold structures. Institute of Science and Technology Austria. mla: Synak, Peter. Methods for Fluid Simulation, Surface Tracking, and Statistics of Non-Manifold Structures. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19630. short: P. Synak, Methods for Fluid Simulation, Surface Tracking, and Statistics of Non-Manifold Structures, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-04-29T09:39:34Z date_published: 2025-04-29T00:00:00Z date_updated: 2026-10-02T11:19:03Z day: '29' ddc: - '519' - '006' degree_awarded: PhD department: - _id: ChWo - _id: GradSch doi: 10.15479/AT-ISTA-19630 ec_funded: 1 file: - access_level: closed checksum: f00b519c27529daa0c3b2d4102b4fa7b content_type: application/x-zip-compressed creator: cchlebak date_created: 2025-04-30T14:02:25Z date_updated: 2025-04-30T14:02:25Z file_id: '19633' file_name: Thesis_source_Heiss_Synak.zip file_size: 60670543 relation: source_file - access_level: open_access checksum: 6e40a2fd3b1b881af1385670854a682e content_type: application/pdf creator: cchlebak date_created: 2025-04-30T14:02:42Z date_updated: 2025-04-30T15:49:16Z file_id: '19634' file_name: Thesis_PDFA_Heiss_Synak.pdf file_size: 21319043 relation: main_file file_date_updated: 2025-04-30T15:49:16Z fulldoi: https://doi.org/10.15479/AT-ISTA-19630 has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '106' project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales' - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales' - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8135' relation: part_of_dissertation status: public - id: '8384' relation: part_of_dissertation status: public - id: '17219' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 title: Methods for fluid simulation, surface tracking, and statistics of non-manifold structures type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20705' abstract: - lang: eng 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. acknowledged_ssus: - _id: M-Shop - _id: ScienComp 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. article_number: '218202' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Andrea full_name: Stöllner, Andrea id: 4bdcf7f6-eb97-11eb-a6c2-9981bbdc3bed last_name: Stöllner orcid: 0000-0002-0464-8440 - first_name: Isaac C full_name: Lenton, Isaac C id: a550210f-223c-11ec-8182-e2d45e817efb last_name: Lenton orcid: 0000-0002-5010-6984 - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 - first_name: James full_name: Millen, James last_name: Millen - first_name: Renjiro full_name: Shibuya, Renjiro last_name: Shibuya - first_name: Hisao full_name: Ishii, Hisao last_name: Ishii - first_name: Dmytro full_name: Rak, Dmytro id: 70313b46-47c2-11ec-9e88-cd79101918fe last_name: Rak - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 - first_name: Grégory full_name: David, Grégory last_name: David - first_name: Ruth full_name: Signorell, Ruth last_name: Signorell - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: 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. Physical Review Letters. 2025;135(21). doi:10.1103/5xd9-4tjj 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. Physical Review Letters. American Physical Society. https://doi.org/10.1103/5xd9-4tjj 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.” Physical Review Letters. American Physical Society, 2025. https://doi.org/10.1103/5xd9-4tjj. ieee: A. Stöllner et al., “Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air,” Physical Review Letters, vol. 135, no. 21. American Physical Society, 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.” Physical Review Letters, vol. 135, no. 21, 218202, American Physical Society, 2025, doi:10.1103/5xd9-4tjj. 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). corr_author: '1' date_created: 2025-11-30T23:02:07Z date_published: 2025-11-21T00:00:00Z date_updated: 2026-10-09T11:09:09Z day: '21' ddc: - '530' - '550' department: - _id: ZhAl - _id: CaMu - _id: ScWa doi: 10.1103/5xd9-4tjj ec_funded: 1 external_id: arxiv: - '2507.17591' file: - access_level: open_access checksum: a5f76b1230cc7b039ecd0dbd6f99e775 content_type: application/pdf creator: dernst date_created: 2025-12-01T08:19:46Z date_updated: 2025-12-01T08:19:46Z file_id: '20717' file_name: 2025_PhysReviewLetters_Stoellner.pdf file_size: 1761373 relation: main_file success: 1 file_date_updated: 2025-12-01T08:19:46Z fulldoi: https://doi.org/10.1103/5xd9-4tjj has_accepted_license: '1' intvolume: ' 135' issue: '21' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' - _id: 629205d8-2b32-11ec-9570-e1356ff73576 call_identifier: H2020 grant_number: '805041' name: Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/trapping-particles-to-explain-lightning/ record: - id: '23033' relation: dissertation_contains status: public scopus_import: '1' status: public title: Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 135 year: '2025' ... --- OA_place: publisher _id: '19557' acknowledged_ssus: - _id: Bio - _id: PreCl - _id: ScienComp acknowledgement: "The work presented in this doctoral thesis was performed at the Institute of Science\r\nand Technology (ISTA) and financially supported by a European Research Council\r\n(ERC) Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the\r\nAustrian Science Fund (FWF) to Gaia Novarino (PE1028W1232). I am very thankful\r\nto the Doctoral Program “Molecular Drug Targets” (MolTag) for offering me financial\r\nsupport to perform essential experiments during my PhD studies and to participate in\r\ninternational conferences and courses." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lena A full_name: Schwarz, Lena A id: 29A8453C-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz citation: ama: Schwarz LA. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. 2025. doi:10.15479/AT-ISTA-19557 apa: Schwarz, L. A. (2025). Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19557 chicago: Schwarz, Lena A. “Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19557. ieee: L. A. Schwarz, “Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution,” Institute of Science and Technology Austria, 2025. ista: Schwarz LA. 2025. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. Institute of Science and Technology Austria. mla: Schwarz, Lena A. Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19557. short: L.A. Schwarz, Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-04-14T06:59:06Z date_published: 2025-04-14T00:00:00Z date_updated: 2026-10-15T22:30:03Z day: '14' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: GaNo doi: 10.15479/AT-ISTA-19557 file: - access_level: closed checksum: 50290a8604edb0a720387f01e9d59fe4 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lschwarz date_created: 2025-04-15T08:43:36Z date_updated: 2026-10-15T22:30:02Z embargo_to: open_access file_id: '19561' file_name: Schwarz_Thesis_2025_FINAL.docx file_size: 21783427 relation: source_file - access_level: open_access checksum: ed028488180ac4901e018ef1c330cf01 content_type: application/pdf creator: lschwarz date_created: 2025-04-15T08:43:42Z date_updated: 2026-10-15T22:30:02Z embargo: 2026-10-15 file_id: '19562' file_name: Schwarz_Thesis_2025_FINALpdfa.pdf file_size: 11432175 relation: main_file file_date_updated: 2026-10-15T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19557 has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '124' project: - _id: 9B91375C-BA93-11EA-9121-9846C619BF3A grant_number: '707964' name: Critical windows and reversibility of ASD associated with mutations in chromatin remodelers - _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6 grant_number: '101044865' name: Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12802' relation: part_of_dissertation status: public - id: '9429' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 title: Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '19431' abstract: - lang: eng 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." acknowledged_ssus: - _id: LifeSc - _id: EM-Fac - _id: ScienComp 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 article_processing_charge: No author: - first_name: Annamaria full_name: Hlavata, Annamaria id: 36062FEC-F248-11E8-B48F-1D18A9856A87 last_name: Hlavata citation: ama: Hlavata A. Regulation of Cytoplasmic RNA Polymerase II. 2025. doi:10.15479/10.15479/AT-ISTA-19431 apa: Hlavata, A. (2025). Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria. https://doi.org/10.15479/10.15479/AT-ISTA-19431 chicago: Hlavata, Annamaria. “Regulation of Cytoplasmic RNA Polymerase II.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/10.15479/AT-ISTA-19431. ieee: A. Hlavata, “Regulation of Cytoplasmic RNA Polymerase II,” Institute of Science and Technology Austria, 2025. ista: Hlavata A. 2025. Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria. mla: Hlavata, Annamaria. Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria, 2025, doi:10.15479/10.15479/AT-ISTA-19431. short: A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-03-20T12:52:47Z date_published: 2025-03-20T00:00:00Z date_updated: 2026-04-07T11:46:32Z day: '20' ddc: - '572' degree_awarded: PhD department: - _id: GradSch - _id: CaBe doi: 10.15479/10.15479/AT-ISTA-19431 file: - access_level: closed checksum: b7ddf424ffe95f8c767c53c8bb62d4f3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ahlavata date_created: 2025-03-24T12:48:36Z date_updated: 2026-03-20T23:30:04Z embargo_to: open_access file_id: '19448' file_name: PhD_Thesis_Hlavata_final_submission.docx file_size: 23506747 relation: source_file - access_level: open_access checksum: 6c5a59c9bac467c3d0b3ffb8ea6d9fd4 content_type: application/pdf creator: ahlavata date_created: 2025-03-24T12:51:10Z date_updated: 2026-03-20T23:30:04Z embargo: 2026-03-20 file_id: '19449' file_name: PhD_Thesis_Hlavata_final_submission_update.pdf file_size: 9478591 relation: main_file file_date_updated: 2026-03-20T23:30:04Z fulldoi: https://doi.org/10.15479/10.15479/AT-ISTA-19431 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '83' publication_identifier: eissn: - 2663-337X isbn: - 978-3-99078-055-8 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 title: Regulation of Cytoplasmic RNA Polymerase II type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '20694' 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." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Arka full_name: Pal, Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal orcid: 0000-0002-4530-8469 citation: ama: Pal A. Using genealogies to study the genomic basis of species divergence. 2025. doi:10.15479/AT-ISTA-20694 apa: Pal, A. (2025). Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20694 chicago: Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20694. ieee: A. Pal, “Using genealogies to study the genomic basis of species divergence,” Institute of Science and Technology Austria, 2025. ista: Pal A. 2025. Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria. mla: Pal, Arka. Using Genealogies to Study the Genomic Basis of Species Divergence. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20694. short: A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-11-25T13:19:11Z date_published: 2025-11-25T00:00:00Z date_updated: 2026-04-28T13:20:36Z day: '25' ddc: - '576' - '578' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/AT-ISTA-20694 file: - access_level: open_access checksum: 7a10a738d58524aebb5dcbd9b34c21c5 content_type: application/pdf creator: apal date_created: 2025-12-01T13:53:36Z date_updated: 2026-03-01T23:30:03Z embargo: 2026-03-01 file_id: '20721' file_name: 2025_Pal_Arka_Thesis.pdf file_size: 42723135 relation: main_file - access_level: closed checksum: 166d832b08d0434ce407f8f3cb930fe5 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: apal date_created: 2025-12-01T13:53:39Z date_updated: 2026-03-01T23:30:03Z embargo_to: open_access file_id: '20722' file_name: 2025_Pal_Arka_Thesis.docx file_size: 60632116 relation: source_file file_date_updated: 2026-03-01T23:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-20694 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '11' oa: 1 oa_version: Published Version page: '268' project: - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: Snapdragon Speciation publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12159' relation: part_of_dissertation status: public - id: '14796' relation: part_of_dissertation status: public - id: '20190' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Using genealogies to study the genomic basis of species divergence tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20190' 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.' acknowledged_ssus: - _id: ScienComp 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. ' article_number: e70067 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Arka full_name: Pal, Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal orcid: 0000-0002-4530-8469 - first_name: Daria full_name: Shipilina, Daria id: 428A94B0-F248-11E8-B48F-1D18A9856A87 last_name: Shipilina orcid: 0000-0002-1145-9226 - first_name: Alan full_name: Le Moan, Alan last_name: Le Moan - first_name: Adrian J. full_name: Mcnairn, Adrian J. last_name: Mcnairn - first_name: Jennifer K. full_name: Grenier, Jennifer K. last_name: Grenier - first_name: Marek full_name: Kucka, Marek last_name: Kucka - first_name: Graham full_name: Coop, Graham last_name: Coop - first_name: Yingguang Frank full_name: Chan, Yingguang Frank last_name: Chan - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski citation: ama: Pal A, Shipilina D, Le Moan A, et al. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. 2025;34(22). doi:10.1111/mec.70067 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. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.70067 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.” Molecular Ecology. Wiley, 2025. https://doi.org/10.1111/mec.70067. ieee: A. Pal et al., “Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum,” Molecular Ecology, vol. 34, no. 22. Wiley, 2025. 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. mla: Pal, Arka, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” Molecular Ecology, vol. 34, no. 22, e70067, Wiley, 2025, doi:10.1111/mec.70067. 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). corr_author: '1' date_created: 2025-08-17T22:01:37Z date_published: 2025-11-01T00:00:00Z date_updated: 2026-10-16T22:30:39Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/mec.70067 external_id: isi: - '001546622100001' file: - access_level: open_access checksum: c586fc674df4e7dd6e43aef87a52c6f6 content_type: application/pdf creator: dernst date_created: 2026-01-05T13:47:47Z date_updated: 2026-01-05T13:47:47Z file_id: '20958' file_name: 2025_MolecEcology_Pal.pdf file_size: 9886694 relation: main_file success: 1 file_date_updated: 2026-01-05T13:47:47Z fulldoi: https://doi.org/10.1111/mec.70067 has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '22' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: Snapdragon Speciation - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes publication: Molecular Ecology publication_identifier: eissn: - 1365-294X issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/snapdragon-secrets/ record: - id: '20694' relation: dissertation_contains status: public scopus_import: '1' status: public title: Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 34 year: '2025' ... --- OA_embargo: '12' OA_place: publisher _id: '19386' 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. " acknowledged_ssus: - _id: ScienComp 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 article_processing_charge: No author: - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 citation: ama: Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. 2025. doi:10.15479/AT-ISTA-19386 apa: Elkrewi, M. N. (2025). Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19386 chicago: Elkrewi, Marwan N. “Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19386. ieee: M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025. ista: Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. Institute of Science and Technology Austria. mla: Elkrewi, Marwan N. Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19386. short: M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-03-11T12:54:31Z date_published: 2025-03-14T00:00:00Z date_updated: 2026-09-24T11:17:37Z day: '14' ddc: - '570' - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/AT-ISTA-19386 file: - access_level: closed checksum: 5549a8216c07e4c39281648912d72246 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: melkrewi date_created: 2025-03-26T07:06:56Z date_updated: 2026-03-26T23:30:03Z embargo_to: open_access file_id: '19462' file_name: Thesis_Marwan_Elkrewi.docx file_size: 25019680 relation: source_file - access_level: open_access checksum: aed2ba9965aa89b3414deae1ae9f4321 content_type: application/pdf creator: melkrewi date_created: 2025-03-26T07:06:22Z date_updated: 2026-03-26T23:30:03Z embargo: 2026-03-26 file_id: '19463' file_name: Thesis_Marwan_Elkrewi.pdf file_size: 17294844 relation: main_file file_date_updated: 2026-03-26T23:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-19386 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '170' project: - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication_identifier: eissn: - 2663-337X isbn: - '9783990780534' publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12248' relation: part_of_dissertation status: public - id: '10767' relation: part_of_dissertation status: public - id: '14613' relation: part_of_dissertation status: public - id: '10167' relation: part_of_dissertation status: public - id: '15009' relation: part_of_dissertation status: public - id: '17890' relation: part_of_dissertation status: public status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 title: Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20449' abstract: - lang: eng 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. " acknowledged_ssus: - _id: ScienComp acknowledgement: "This work was supported by the Austrian Science Fund (FWF) through grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Vincent K full_name: Bett, Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett citation: ama: Bett VK. Evolution and regulation of the Z chromosome. 2025. doi:10.15479/AT-ISTA-20449 apa: Bett, V. K. (2025). Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20449 chicago: Bett, Vincent K. “Evolution and Regulation of the Z Chromosome.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20449. ieee: V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science and Technology Austria, 2025. ista: Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria. mla: Bett, Vincent K. Evolution and Regulation of the Z Chromosome. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20449. short: V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-11T08:18:51Z date_published: 2025-10-10T00:00:00Z date_updated: 2026-09-24T11:11:01Z day: '10' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/AT-ISTA-20449 file: - access_level: open_access checksum: 26905c22bca417198a733d792d8ce422 content_type: application/pdf creator: vbett date_created: 2025-10-20T13:32:29Z date_updated: 2026-06-01T22:30:04Z embargo: 2026-06-01 file_id: '20507' file_name: 2025_Bett_Vincent_Thesis.pdf file_size: 18507283 relation: main_file - access_level: closed checksum: 6a09a8d126d3628bfd8a35202735f267 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: vbett date_created: 2025-10-20T13:35:34Z date_updated: 2026-06-01T22:30:04Z embargo_to: open_access file_id: '20508' file_name: 2025_Bett_Vincent_Thesis.docx file_size: 17163921 relation: source_file file_date_updated: 2026-06-01T22:30:04Z fulldoi: https://doi.org/10.15479/AT-ISTA-20449 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '114' project: - _id: 8ed82125-16d5-11f0-9cad-fbcae312235b grant_number: PAT 8748323 name: Sex chromosomes in evolution and development - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19735' relation: part_of_dissertation status: public - id: '15009' relation: part_of_dissertation status: public status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 title: Evolution and regulation of the Z chromosome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19735' 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. acknowledged_ssus: - _id: ScienComp 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. article_number: msaf085 article_processing_charge: Yes article_type: original author: - first_name: Vincent K full_name: Bett, Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett - first_name: Minerva S full_name: Trejo Arellano, Minerva S id: 2b681148-eed5-11eb-b81b-ae229e8620f8 last_name: Trejo Arellano orcid: 0000-0002-1982-3475 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: 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. Molecular Biology and Evolution. 2025;42(5). doi:10.1093/molbev/msaf085 apa: Bett, V. K., Trejo Arellano, M. S., & 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. Oxford University Press. https://doi.org/10.1093/molbev/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.” Molecular Biology and Evolution. Oxford University Press, 2025. https://doi.org/10.1093/molbev/msaf085. 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,” Molecular Biology and Evolution, vol. 42, no. 5. Oxford University Press, 2025. 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. 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.” Molecular Biology and Evolution, vol. 42, no. 5, msaf085, Oxford University Press, 2025, doi:10.1093/molbev/msaf085. short: V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025). corr_author: '1' date_created: 2025-05-25T22:16:56Z date_published: 2025-05-01T00:00:00Z date_updated: 2026-10-16T22:31:15Z day: '01' ddc: - '570' department: - _id: BeVi - _id: DaZi doi: 10.1093/molbev/msaf085 external_id: isi: - '001483460200001' pmid: - '40202086' file: - access_level: open_access checksum: 6c14b03f94b4aadf8869be2c4366d077 content_type: application/pdf creator: dernst date_created: 2025-05-28T09:34:36Z date_updated: 2025-05-28T09:34:36Z file_id: '19756' file_name: 2025_MBE_Bett.pdf file_size: 1282772 relation: main_file success: 1 file_date_updated: 2025-05-28T09:34:36Z fulldoi: https://doi.org/10.1093/molbev/msaf085 has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 8ed82125-16d5-11f0-9cad-fbcae312235b grant_number: PAT 8748323 name: Sex chromosomes in evolution and development - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication: Molecular Biology and Evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git record: - id: '20449' relation: dissertation_contains status: public - id: '20444' relation: dissertation_contains status: deleted scopus_import: '1' status: public title: Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 42 year: '2025' ... --- OA_place: publisher _id: '20357' acknowledged_ssus: - _id: ScienComp - _id: E-Lib 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Natalia full_name: Ruzickova, Natalia id: D2761128-D73D-11E9-A1BF-BA0DE6697425 last_name: Ruzickova citation: ama: Ruzickova N. Effect propagation in biological networks. 2025. doi:10.15479/AT-ISTA-20357 apa: Ruzickova, N. (2025). Effect propagation in biological networks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20357 chicago: Ruzickova, Natalia. “Effect Propagation in Biological Networks.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20357. ieee: N. Ruzickova, “Effect propagation in biological networks,” Institute of Science and Technology Austria, 2025. ista: Ruzickova N. 2025. Effect propagation in biological networks. Institute of Science and Technology Austria. mla: Ruzickova, Natalia. Effect Propagation in Biological Networks. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20357. short: N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-09-15T17:04:48Z date_published: 2025-09-15T00:00:00Z date_updated: 2026-10-02T10:15:31Z day: '15' ddc: - '570' - '530' degree_awarded: PhD department: - _id: GradSch - _id: GaTk doi: 10.15479/AT-ISTA-20357 doi_confirm: '1' file: - access_level: closed checksum: 0582508d439b233497384f83a8307398 content_type: application/x-zip-compressed creator: cchlebak date_created: 2026-08-07T10:57:05Z date_updated: 2026-09-15T22:30:02Z embargo_to: open_access file_id: '22661' file_name: 2025_Ruzickova_Natalia_Thesis.zip file_size: 56464803 relation: source_file - access_level: open_access checksum: b722289fd550abede63adc27b9c61784 content_type: application/pdf creator: cchlebak date_created: 2026-08-07T10:57:34Z date_updated: 2026-09-15T22:30:02Z embargo: 2026-09-15 file_id: '22662' file_name: 2025_Ruzickova_Natalia_Thesis.pdf file_size: 30634378 relation: main_file file_date_updated: 2026-09-15T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20357 has_accepted_license: '1' keyword: - gene regulation - networks - omnigenic model - pancreas - collective behaviour language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '156' project: - _id: 7bec9174-9f16-11ee-852c-ded9fe5f810e name: Collective behaviour of cells in pancreatic Islets of Langerhans publication_identifier: isbn: - 978-3-99078-066-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18525' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 title: Effect propagation in biological networks type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '19533' 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" acknowledged_ssus: - _id: ScienComp - _id: M-Shop - _id: NanoFab - _id: LifeSc - _id: SSU 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett orcid: 0000-0001-7641-8348 citation: ama: Sett R. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. 2025. doi:10.15479/AT-ISTA-19533 apa: Sett, R. (2025). Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19533 chicago: Sett, Riya. “Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19533. ieee: R. Sett, “Quantum remote sensing and non-equilibrium phase transitions in the microwave regime,” Institute of Science and Technology Austria, 2025. 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. Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19533. short: R. Sett, Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-04-09T16:44:26Z date_published: 2025-04-01T00:00:00Z date_updated: 2026-10-15T09:08:00Z day: '1' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/AT-ISTA-19533 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: ba6cd2289d0141a160a14fc97df1632f content_type: application/pdf creator: rsett date_created: 2025-04-10T11:33:22Z date_updated: 2025-10-11T22:30:02Z embargo: 2025-10-11 file_id: '19538' file_name: PhD_Thesis_Riya_Sett_pdfa.pdf file_size: 4129208 relation: main_file - access_level: closed checksum: ee63a94cb8f7adf5e766903028b81ed6 content_type: application/x-zip-compressed creator: rsett date_created: 2025-04-10T11:34:08Z date_updated: 2025-10-11T22:30:02Z embargo_to: open_access file_id: '19539' file_name: PhD Thesis Riya Sett.zip file_size: 6646110 relation: source_file file_date_updated: 2025-10-11T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19533 has_accepted_license: '1' 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 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '109' project: - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18978' relation: research_data status: public - id: '19280' relation: part_of_dissertation status: public - id: '13117' relation: part_of_dissertation status: public - id: '17183' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: Quantum remote sensing and non-equilibrium phase transitions in the microwave regime tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '15375' abstract: - lang: eng text: In the eukaryotic nucleus, heterochromatin forms highly condensed, visible foci known as heterochromatin foci (HF). These HF are enriched with linker histone H1, a key player in heterochromatin condensation and silencing. However, it is unknown how H1 aggregates HF and condenses heterochromatin. In this study, we established that H1 facilitates heterochromatin condensation by enhancing inter- and intrachromosomal interactions between and within heterochromatic regions of the Arabidopsis (Arabidopsis thaliana) genome. We demonstrated that H1 drives HF formation via phase separation, which requires its C-terminal intrinsically disordered region (C-IDR). A truncated H1 lacking the C-IDR fails to form foci or recover HF in the h1 mutant background, whereas C-IDR with a short stretch of the globular domain (18 out of 71 amino acids) is sufficient to rescue both defects. In addition, C-IDR is essential for H1's roles in regulating nucleosome repeat length and DNA methylation in Arabidopsis, indicating that phase separation capability is required for chromatin functions of H1. Our data suggest that bacterial H1-like proteins, which have been shown to condense DNA, are intrinsically disordered and capable of mediating phase separation. Therefore, we propose that phase separation mediated by H1 or H1-like proteins may represent an ancient mechanism for condensing chromatin and DNA. acknowledged_ssus: - _id: Bio - _id: ScienComp acknowledgement: "This work was funded by ISTA core support (Y.Y. and X.F.) and grants from the National Natural Science Foundation of China (31871443 to L.W. and P.L.; 32100417 to L.W.).\r\nWe thank the ISTA Imaging and Optics Facility for assistance with microscopy and the ISTA Scientific Computing Facility for high-performance computing resources." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Shengbo full_name: He, Shengbo last_name: He - first_name: Yiming full_name: Yu, Yiming id: 318e643b-8b61-11ed-b69e-aafa103ec8dd last_name: Yu - first_name: Liang full_name: Wang, Liang last_name: Wang - first_name: Jingyi full_name: Zhang, Jingyi last_name: Zhang - first_name: Zhengyong full_name: Bai, Zhengyong last_name: Bai - first_name: Guohong full_name: Li, Guohong last_name: Li - first_name: Pilong full_name: Li, Pilong last_name: Li - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 citation: ama: He S, Yu Y, Wang L, et al. Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. The Plant Cell. 2024;36(5):1829-1843. doi:10.1093/plcell/koae034 apa: He, S., Yu, Y., Wang, L., Zhang, J., Bai, Z., Li, G., … Feng, X. (2024). Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koae034 chicago: He, Shengbo, Yiming Yu, Liang Wang, Jingyi Zhang, Zhengyong Bai, Guohong Li, Pilong Li, and Xiaoqi Feng. “Linker Histone H1 Drives Heterochromatin Condensation via Phase Separation in Arabidopsis.” The Plant Cell. Oxford University Press, 2024. https://doi.org/10.1093/plcell/koae034. ieee: S. He et al., “Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis,” The Plant Cell, vol. 36, no. 5. Oxford University Press, pp. 1829–1843, 2024. ista: He S, Yu Y, Wang L, Zhang J, Bai Z, Li G, Li P, Feng X. 2024. Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. The Plant Cell. 36(5), 1829–1843. mla: He, Shengbo, et al. “Linker Histone H1 Drives Heterochromatin Condensation via Phase Separation in Arabidopsis.” The Plant Cell, vol. 36, no. 5, Oxford University Press, 2024, pp. 1829–43, doi:10.1093/plcell/koae034. short: S. He, Y. Yu, L. Wang, J. Zhang, Z. Bai, G. Li, P. Li, X. Feng, The Plant Cell 36 (2024) 1829–1843. corr_author: '1' date_created: 2024-05-12T22:01:01Z date_published: 2024-05-01T00:00:00Z date_updated: 2025-09-08T07:21:17Z day: '01' ddc: - '580' department: - _id: XiFe doi: 10.1093/plcell/koae034 external_id: isi: - '001180817000001' pmid: - '38309957' file: - access_level: open_access checksum: eed76c848fe3d8fe9a53943181aaa53c content_type: application/pdf creator: dernst date_created: 2025-04-23T07:43:12Z date_updated: 2025-04-23T07:43:12Z file_id: '19611' file_name: 2024_PlantCell_He.pdf file_size: 50791962 relation: main_file success: 1 file_date_updated: 2025-04-23T07:43:12Z fulldoi: https://doi.org/10.1093/plcell/koae034 has_accepted_license: '1' intvolume: ' 36' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1829-1843 pmid: 1 publication: The Plant Cell publication_identifier: eissn: - 1532-298X publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 36 year: '2024' ... --- OA_place: publisher _id: '18579' abstract: - lang: eng text: 'Electrophysiological, calcium two-photon recordings and behavioral data for Vega-Zuniga et al. Relevant information can be found in the ''README.txt'' files. ' acknowledged_ssus: - _id: ScienComp - _id: PreCl - _id: M-Shop - _id: Bio - _id: LifeSc acknowledgement: Freyja Lange, Michael Schunn, and Todor Asenov article_processing_charge: No author: - first_name: Tomas A full_name: Vega Zuniga, Tomas A id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87 last_name: Vega Zuniga - first_name: Anton L full_name: Sumser, Anton L id: 3320A096-F248-11E8-B48F-1D18A9856A87 last_name: Sumser orcid: 0000-0002-4792-1881 - first_name: Olga full_name: Symonova, Olga id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87 last_name: Symonova orcid: 0000-0003-2012-9947 - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Florian full_name: Schmidt, Florian id: A2EF226A-AF19-11E9-924C-0525E6697425 last_name: Schmidt - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 citation: ama: Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. 2024. doi:10.15479/AT:ISTA:18579 apa: Vega Zuniga, T. A., Sumser, A. L., Symonova, O., Koppensteiner, P., Schmidt, F., & Jösch, M. A. (2024). A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:18579 chicago: Vega Zuniga, Tomas A, Anton L Sumser, Olga Symonova, Peter Koppensteiner, Florian Schmidt, and Maximilian A Jösch. “A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:18579. ieee: T. A. Vega Zuniga, A. L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, and M. A. Jösch, “A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics.” Institute of Science and Technology Austria, 2024. ista: Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA. 2024. A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics, Institute of Science and Technology Austria, 10.15479/AT:ISTA:18579. mla: Vega Zuniga, Tomas A., et al. A Thalamic Hub-and-Spoke Network Enables Visual Perception during Action by Coordinating Visuomotor Dynamics. Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:18579. short: T.A. Vega Zuniga, A.L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt, M.A. Jösch, (2024). corr_author: '1' date_created: 2024-11-22T13:48:12Z date_published: 2024-12-09T00:00:00Z date_updated: 2026-06-18T18:12:08Z day: '09' ddc: - '570' department: - _id: MaJö doi: 10.15479/AT:ISTA:18579 ec_funded: 1 file: - access_level: open_access checksum: 8b13990ca1a458ae3f3ae54c2e888564 content_type: application/x-zip-compressed creator: symonova date_created: 2024-12-06T13:28:18Z date_updated: 2024-12-09T10:24:25Z file_id: '18625' file_name: electro_physiology_data.zip file_size: 800647957 relation: main_file - access_level: open_access checksum: c5a4d71c5f29c009c3d96a3244532afa content_type: application/x-zip-compressed creator: symonova date_created: 2024-12-09T10:21:10Z date_updated: 2024-12-09T10:21:10Z file_id: '18636' file_name: NN_vLGN_Ca_data.zip file_size: 828410832 relation: main_file success: 1 - access_level: open_access checksum: 63651df0186196969553dc48b467f6ab content_type: text/plain creator: symonova date_created: 2024-12-09T12:54:55Z date_updated: 2024-12-09T12:54:55Z file_id: '18637' file_name: readme.txt file_size: 505 relation: main_file success: 1 file_date_updated: 2024-12-09T12:54:55Z fulldoi: https://doi.org/10.15479/AT:ISTA:18579 has_accepted_license: '1' month: '12' oa: 1 oa_version: Published Version project: - _id: 264FEA02-B435-11E9-9278-68D0E5697425 grant_number: ALTF 1098-2017 name: Connecting sensory with motor processing in the superior colliculus - _id: 266D407A-B435-11E9-9278-68D0E5697425 grant_number: LT000256 name: Neuronal networks of salience and spatial detection in the murine superior colliculus - _id: 2634E9D2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '756502' name: Circuits of Visual Attention - _id: bdaf81a8-d553-11ed-ba76-c95961984540 grant_number: '101086580' name: 'Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses' publisher: Institute of Science and Technology Austria related_material: record: - id: '19076' relation: used_in_publication status: public status: public title: A thalamic hub-and-spoke network enables visual perception during action by coordinating visuomotor dynamics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- _id: '17344' abstract: - lang: eng text: 'This file contains the Mathematica notebook associated with the paper Effect of assortative mating and sexual selection on polygenic barriers to gene flow. It contains the numerical approximations, analyses, and simulations used in the study. ' acknowledged_ssus: - _id: ScienComp article_processing_charge: No author: - first_name: Parvathy full_name: Surendranadh, Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh orcid: 0000-0001-6395-386X - first_name: Himani full_name: Sachdeva, Himani last_name: Sachdeva citation: ama: Surendranadh P, Sachdeva H. Mathematica notebook for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” 2024. doi:10.15479/AT:ISTA:17344 apa: Surendranadh, P., & Sachdeva, H. (2024). Mathematica notebook for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17344 chicago: Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook for ‘Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17344. ieee: P. Surendranadh and H. Sachdeva, “Mathematica notebook for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow.’” Institute of Science and Technology Austria, 2024. ista: Surendranadh P, Sachdeva H. 2024. Mathematica notebook for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17344. mla: Surendranadh, Parvathy, and Himani Sachdeva. Mathematica Notebook for “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17344. short: P. Surendranadh, H. Sachdeva, (2024). date_created: 2024-07-29T14:01:43Z date_published: 2024-07-01T00:00:00Z date_updated: 2025-01-14T13:02:59Z ddc: - '576' department: - _id: GradSch - _id: NiBa doi: 10.15479/AT:ISTA:17344 file: - access_level: open_access checksum: 75bdbc7ad7cc6afe4459bc4a8824a302 content_type: application/octet-stream creator: psurendr date_created: 2024-07-29T13:51:11Z date_updated: 2024-07-29T13:51:11Z file_id: '17345' file_name: Submission.nb file_size: 726132 relation: main_file success: 1 file_date_updated: 2024-07-29T13:51:11Z fulldoi: https://doi.org/10.15479/AT:ISTA:17344 has_accepted_license: '1' month: '07' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria status: public title: Mathematica notebook for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '19063' abstract: - lang: eng text: "Instruction-tuned Large Language Models (LLMs) show impressive results in numerous practical applications, but they lack essential safety features that are common in other areas of computer science, particularly an explicit separation of instructions and data. This makes them vulnerable to manipulations such as indirect prompt injections and generally unsuitable for safety-critical tasks. Surprisingly, there is currently no established definition or benchmark to quantify this phenomenon. In this work, we close this gap by introducing a formal measure for instruction-data separation and an empirical variant that is calculable from a model's outputs. We also present a new dataset, SEP, that allows estimating the measure for real-world models. Our results on various LLMs show that the problem of instruction-data separation is real: all models fail to achieve high separation, and canonical mitigation techniques, such as prompt engineering and fine-tuning, either fail to substantially improve separation or reduce model utility. The source code and SEP dataset are openly accessible at https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed.\r\n" acknowledged_ssus: - _id: ScienComp acknowledgement: The authors would like to sincerely thank Juan Rocamonde for valuable feedback to our manuscript. We acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We thank Dan Alistarh for providing us with computational resources. This work was partially funded by the German Federal Ministry of Education and Research (BMBF) under the grant AIgenCY (16KIS2012) and ELSA – European Lighthouse on Secure and Safe AI funded by the European Union under grant agreement No. 101070617. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or European Commission. Neither the European Union nor the European Commission can be held responsible for them. article_number: '2403.06833' article_processing_charge: No arxiv: 1 author: - first_name: Egor full_name: Zverev, Egor id: 05162b19-1340-11ed-8f02-fa94e0e8c3bc last_name: Zverev - first_name: Sahar full_name: Abdelnabi, Sahar last_name: Abdelnabi - first_name: Soroush full_name: Tabesh, Soroush id: 06000900-6068-11ef-8d61-c2472ef2e752 last_name: Tabesh orcid: 0009-0003-4119-6281 - first_name: Mario full_name: Fritz, Mario last_name: Fritz - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions from data? And what do we even mean by that? arXiv. doi:10.48550/arXiv.2403.06833 apa: Zverev, E., Abdelnabi, S., Tabesh, S., Fritz, M., & Lampert, C. (n.d.). Can LLMs separate instructions from data? And what do we even mean by that? arXiv. https://doi.org/10.48550/arXiv.2403.06833 chicago: Zverev, Egor, Sahar Abdelnabi, Soroush Tabesh, Mario Fritz, and Christoph Lampert. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” ArXiv, n.d. https://doi.org/10.48550/arXiv.2403.06833. ieee: E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, and C. Lampert, “Can LLMs separate instructions from data? And what do we even mean by that?,” arXiv. . ista: Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions from data? And what do we even mean by that? arXiv, 2403.06833. mla: Zverev, Egor, et al. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” ArXiv, 2403.06833, doi:10.48550/arXiv.2403.06833. short: E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, C. Lampert, ArXiv (n.d.). corr_author: '1' date_created: 2025-02-20T10:13:42Z date_published: 2024-03-01T00:00:00Z date_updated: 2026-08-13T07:26:54Z day: '01' ddc: - '000' department: - _id: GradSch - _id: ChLa doi: 10.48550/arXiv.2403.06833 external_id: arxiv: - '2403.06833' file: - access_level: open_access checksum: 35eb43968684b87be59144603ef10af0 content_type: application/pdf creator: ezverev date_created: 2025-02-20T10:11:45Z date_updated: 2025-02-20T10:11:45Z file_id: '19064' file_name: 2403.06833v3.pdf file_size: 530972 relation: main_file success: 1 file_date_updated: 2025-02-20T10:11:45Z fulldoi: https://doi.org/10.48550/arXiv.2403.06833 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted related_material: link: - relation: software url: ' https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed' status: public title: Can LLMs separate instructions from data? And what do we even mean by that? tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- _id: '17373' abstract: - lang: eng text: Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating the electrostatic properties of material surfaces, enabling the imaging of variations in work function, topology, surface charge density, or combinations thereof. Regardless of the underlying signal source, SKPM results in a voltage image, which is spatially distorted due to the finite size of the probe, long-range electrostatic interactions, mechanical and electrical noise, and the finite response time of the electronics. In order to recover the underlying signal, it is necessary to deconvolve the measurement with an appropriate point spread function (PSF) that accounts the aforementioned distortions, but determining this PSF is difficult. Here, we describe how such PSFs can be determined experimentally and show how they can be used to recover the underlying information of interest. We first consider the physical principles that enable SKPM and discuss how these affect the system PSF. We then show how one can experimentally measure PSFs by looking at well-defined features, and that these compare well to simulated PSFs, provided scans are performed extremely slowly and carefully. Next, we work at realistic scan speeds and show that the idealized PSFs fail to capture temporal distortions in the scan direction. While simulating PSFs for these situations would be quite challenging, we show that measuring PSFs with similar scan conditions works well. Our approach clarifies the basic principles and inherent challenges to SKPM measurements and gives practical methods to improve results. acknowledged_ssus: - _id: M-Shop - _id: NanoFab - _id: LifeSc - _id: ScienComp acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (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 the contributions of the whole Waitukaitis Group for useful discussions and feedback. article_number: '045305' article_processing_charge: No article_type: original author: - first_name: Isaac C full_name: Lenton, Isaac C id: a550210f-223c-11ec-8182-e2d45e817efb last_name: Lenton orcid: 0000-0002-5010-6984 - first_name: Felix full_name: Pertl, Felix id: 6313aec0-15b2-11ec-abd3-ed67d16139af last_name: Pertl orcid: 0000-0003-0463-5794 - first_name: Lubuna B full_name: Shafeek, Lubuna B id: 3CD37A82-F248-11E8-B48F-1D18A9856A87 last_name: Shafeek orcid: 0000-0001-7180-6050 - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: 'Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. Journal of Applied Physics. 2024;136(4). doi:10.1063/5.0215151' apa: 'Lenton, I. C., Pertl, F., Shafeek, L. B., & Waitukaitis, S. R. (2024). Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. Journal of Applied Physics. AIP Publishing. https://doi.org/10.1063/5.0215151' chicago: 'Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” Journal of Applied Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0215151.' ieee: 'I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging,” Journal of Applied Physics, vol. 136, no. 4. AIP Publishing, 2024.' ista: 'Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2024. Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging. Journal of Applied Physics. 136(4), 045305.' mla: 'Lenton, Isaac C., et al. “Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” Journal of Applied Physics, vol. 136, no. 4, 045305, AIP Publishing, 2024, doi:10.1063/5.0215151.' short: I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied Physics 136 (2024). corr_author: '1' date_created: 2024-08-04T22:01:21Z date_published: 2024-07-28T00:00:00Z date_updated: 2026-08-27T11:42:44Z day: '28' ddc: - '530' department: - _id: ScWa - _id: NanoFab doi: 10.1063/5.0215151 ec_funded: 1 external_id: isi: - '001281681100003' file: - access_level: open_access checksum: 6141d05cd68d540a7446dce9490975db content_type: application/pdf creator: dernst date_created: 2024-08-05T08:19:58Z date_updated: 2024-08-05T08:19:58Z file_id: '17386' file_name: 2024_JourApplPhysics_Lenton.pdf file_size: 2537502 relation: main_file success: 1 file_date_updated: 2024-08-05T08:19:58Z fulldoi: https://doi.org/10.1063/5.0215151 has_accepted_license: '1' intvolume: ' 136' isi: 1 issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication: Journal of Applied Physics publication_identifier: eissn: - 1089-7550 issn: - 0021-8979 publication_status: published publisher: AIP Publishing quality_controlled: '1' related_material: record: - id: '22684' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 136 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18761' abstract: - lang: eng text: Termites, together with cockroaches, belong to the Blattodea. They possess an XX/XY sex determination system which has evolved from an XX/X0 system present in other Blattodean species, such as cockroaches and wood roaches. Little is currently known about the sex chromosomes of termites, their gene content, or their evolution. We here investigate the X chromosome of multiple termite species and compare them with the X chromosome of cockroaches using genomic and transcriptomic data. We find that the X chromosome of the termite Macrotermes natalensis is large and differentiated showing hall marks of sex chromosome evolution such as dosage compensation, while this does not seem to be the case in the other two termite species investigated here where sex chromosomes may be evolutionary younger. Furthermore, the X chromosome in M. natalensis is different from the X chromosome found in the cockroach Blattella germanica indicating that sex chromosome turn-over events may have happened during termite evolution. acknowledged_ssus: - _id: ScienComp acknowledgement: "urthermore, we thank all lab members and collaborators for feedback on the project. Specifically, Dino McMahon provided R. flavipes males and females, Judith Korb provided C. secundus males and females, gave feedback on the project and discussed questions on termite reproduction, Mireille Vasseur-Cognet provided M. natalensis males and females, Ariana Macon performed the lab work for sequencing and the Vicoso group gave critical feedback on the project. We furthermore thank the HPC group at IST Austria and Christian Meesters at JGU Mainz for their technical support.\r\nThis work was supported by a Österreichischer Wissenschaftsfonds (FWF) grant of the Meitner Programme to A.K.H. (project number M 2484), funding by the Deutsche Forschungsgemeinschaft (DFG) of the Research Training Group GenEvo (project number 407023052) to A.K.H., R.F., and A.D., and funding of the DFG within the Schwerpunktprogramm Gevol to A.K.H. and R.M. (project number 503256468)." article_number: evae265 article_processing_charge: Yes article_type: original author: - first_name: Roxanne full_name: Fraser, Roxanne last_name: Fraser - first_name: Ruth full_name: Moraa, Ruth last_name: Moraa - first_name: Annika full_name: Djolai, Annika last_name: Djolai - first_name: Nils full_name: Meisenheimer, Nils last_name: Meisenheimer - first_name: Sophie full_name: Laube, Sophie last_name: Laube - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 citation: ama: Fraser R, Moraa R, Djolai A, et al. Evidence for a novel X chromosome in termites. Genome Biology and Evolution. 2024;16(12). doi:10.1093/gbe/evae265 apa: Fraser, R., Moraa, R., Djolai, A., Meisenheimer, N., Laube, S., Vicoso, B., & Huylmans, A. K. (2024). Evidence for a novel X chromosome in termites. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evae265 chicago: Fraser, Roxanne, Ruth Moraa, Annika Djolai, Nils Meisenheimer, Sophie Laube, Beatriz Vicoso, and Ann K Huylmans. “Evidence for a Novel X Chromosome in Termites.” Genome Biology and Evolution. Oxford University Press, 2024. https://doi.org/10.1093/gbe/evae265. ieee: R. Fraser et al., “Evidence for a novel X chromosome in termites,” Genome Biology and Evolution, vol. 16, no. 12. Oxford University Press, 2024. ista: Fraser R, Moraa R, Djolai A, Meisenheimer N, Laube S, Vicoso B, Huylmans AK. 2024. Evidence for a novel X chromosome in termites. Genome Biology and Evolution. 16(12), evae265. mla: Fraser, Roxanne, et al. “Evidence for a Novel X Chromosome in Termites.” Genome Biology and Evolution, vol. 16, no. 12, evae265, Oxford University Press, 2024, doi:10.1093/gbe/evae265. short: R. Fraser, R. Moraa, A. Djolai, N. Meisenheimer, S. Laube, B. Vicoso, A.K. Huylmans, Genome Biology and Evolution 16 (2024). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: Male and female DNAseq reads for the termites C. secundus, M. natalensis, and R. flavipes can be found in the NCBI SRA under accession codes SRR30467421-SRR30467422, SRR30467423-SRR30467424, and SRR30467425-SRR30467426, respectively (all BioProject PRJNA1153745) date_created: 2025-01-05T23:01:58Z date_published: 2024-12-01T00:00:00Z date_updated: 2026-09-24T11:16:00Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/gbe/evae265 external_id: isi: - '001380841100001' pmid: - '39658246' file: - access_level: open_access checksum: 9cf8fd14580dd694dd810ccca808ad0e content_type: application/pdf creator: dernst date_created: 2025-01-08T08:28:07Z date_updated: 2025-01-08T08:28:07Z file_id: '18772' file_name: 2024_GBE_Fraser.pdf file_size: 795106 relation: main_file success: 1 file_date_updated: 2025-01-08T08:28:07Z fulldoi: https://doi.org/10.1093/gbe/evae265 has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '12' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26641CAC-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02484 name: Sex Determination in Termites publication: Genome Biology and Evolution publication_identifier: eissn: - 1759-6653 publication_status: published publisher: Oxford University Press quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Evidence for a novel X chromosome in termites tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 16 year: '2024' ...