[{"year":"2024","supervisor":[{"last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","orcid":"0000-0001-8559-3973"}],"citation":{"apa":"Lyudchik, J. (2024). <i>Image analysis for brain tissue reconstruction with super-resolution light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>","mla":"Lyudchik, Julia. <i>Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>.","short":"J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy, Institute of Science and Technology Austria, 2024.","chicago":"Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>.","ista":"Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution light microscopy. Institute of Science and Technology Austria.","ieee":"J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution light microscopy,” Institute of Science and Technology Austria, 2024.","ama":"Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":[" 978-3-99078-051-0"],"issn":["2663-337X"]},"article_processing_charge":"No","date_updated":"2026-04-14T08:34:35Z","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"11160","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18677"},{"status":"public","relation":"part_of_dissertation","id":"13267"},{"relation":"part_of_dissertation","id":"14257","status":"public"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Lyudchik, Julia","last_name":"Lyudchik","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"}],"title":"Image analysis for brain tissue reconstruction with super-resolution light microscopy","OA_place":"publisher","date_created":"2024-12-18T14:24:43Z","doi":"10.15479/at:ista:18674","file_date_updated":"2024-12-18T14:41:53Z","date_published":"2024-12-18T00:00:00Z","abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue requires volumetric imaging at nanoscale spatial resolution. While light microscopy excels at visualizing specific molecules and individual cells, achieving dense, synapse-level circuit reconstruction has not been possible with any light microscopy technique. Thus, the goal of my work was to develop image and data analysis pipelines for brain tissue visualization and reconstruction with light microscopy. To achieve dense circuit reconstruction with single-synapse resolution, I developed both conventional and deep-learning-based synapse detection algorithms, as well as connectivity analysis pipelines that integrate synapse detection with volumetric segmentation of brain tissue."}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"type":"dissertation","publication_status":"published","corr_author":"1","file":[{"file_name":"18122024_PhDthesis_corrected_final_pdfa.pdf","file_size":160536833,"date_created":"2024-12-18T14:17:34Z","checksum":"1b42b8073e2bc09fc504da52372248c1","file_id":"18675","success":1,"date_updated":"2024-12-18T14:17:34Z","content_type":"application/pdf","creator":"jlyudchi","relation":"main_file","access_level":"open_access"},{"date_created":"2024-12-18T14:21:06Z","checksum":"b4da84624060745519723698f7ddf54b","file_size":99172203,"file_name":"18122024_PhDthesis_corrected_final_JL_markup.docx","file_id":"18676","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-12-18T14:41:53Z","creator":"jlyudchi","relation":"source_file","access_level":"closed"}],"month":"12","status":"public","oa":1,"ddc":["004"],"page":"217","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"}],"has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"day":"18","ec_funded":1,"_id":"18674"},{"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","abstract":[{"text":"An ideal quantum computer relies on qubits capable of performing fast gate operations and\r\nmaintaining strong interconnections while preserving their quantum coherence. Since the\r\ninception of experimental eforts toward building a quantum computer, the community has\r\nfaced challenges in engineering such a system. Among the various methods of implementing a\r\nquantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith high coherence require isolation from the environment, while fast operation necessitates\r\nstrong coupling of the qubit. This thesis approaches this issue by proposing the idea of\r\nengineering superconducting qubits capable of transitioning between operating in a protected\r\nregime, where the qubit is completely isolated from the environment, and coupling to the\r\ncommunication channels as needed. In this direction, we use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices, searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier\r\nseparating the local ground states of each quantum well. In this regime, although it is\r\nanticipated that the two quantum wells would be isolated from each other, we observe single\r\nfuxon tunneling between them. The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical system, containing resonance conditions that allow the preparation of the\r\nfuxon ground or excited states. This enables us to study the relaxation rate of such transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling the barrier height\r\nbetween the two quantum wells allows for controllable coupling, which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe 0-π qubit is one of the very few known superconducting circuit types that ofers exponential\r\nprotection from both relaxation and dephasing simultaneously. However, this qubit is not\r\nexempt from the fact that such protection comes at the expense of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably break the circuit symmetry, the\r\nkey reason for the protection, to momentarily restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling of the protected state to the thermally occupied parasitic mode\r\nof the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand show that this can be used as a tunable coupler between the protected states. In the\r\nfuture, this should allow to perform gate operations by dynamically controlling the asymmetry\r\ninstead of driving the protected transition with microwave pulses. Therefore, we believe that\r\nthe proposed method can make the use of protected qubits more practical in experimental\r\nrealizations of quantum computing.","lang":"eng"}],"date_published":"2024-06-11T00:00:00Z","file_date_updated":"2024-06-20T11:52:22Z","doi":"10.15479/at:ista:17133","date_created":"2024-06-11T18:20:05Z","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Superconducting qubits capable of dynamic switching between protected and high-speed control regimes","author":[{"first_name":"Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid","last_name":"Hassani"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13227"},{"id":"9928","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"8755","status":"public"}]},"degree_awarded":"PhD","date_updated":"2026-04-15T06:43:02Z","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-040-4"]},"language":[{"iso":"eng"}],"citation":{"ieee":"F. Hassani, “Superconducting qubits capable of dynamic switching between protected and high-speed control regimes,” Institute of Science and Technology Austria, 2024.","ama":"Hassani F. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>","apa":"Hassani, F. (2024). <i>Superconducting qubits capable of dynamic switching between protected and high-speed control regimes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>","mla":"Hassani, Farid. <i>Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>.","short":"F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024.","ista":"Hassani F. 2024. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria.","chicago":"Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>."},"supervisor":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"}],"year":"2024","_id":"17133","day":"11","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"oa_version":"Published Version","has_accepted_license":"1","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"publisher":"Institute of Science and Technology Austria","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105"}],"page":"161","ddc":["530"],"status":"public","oa":1,"month":"06","file":[{"file_size":28370759,"checksum":"258c353d47fa37ea63ea43b1e10a34a0","date_created":"2024-06-12T07:53:19Z","file_name":"Thesis_main_final.pdf","file_id":"17137","creator":"fhassani","content_type":"application/pdf","date_updated":"2024-06-20T11:52:22Z","access_level":"open_access","relation":"main_file"},{"access_level":"closed","relation":"source_file","creator":"fhassani","content_type":"text/x-tex","date_updated":"2024-06-12T07:54:27Z","file_id":"17138","date_created":"2024-06-12T07:54:27Z","file_size":445735,"checksum":"deffa5d0db88093f74812fa71520d5e1","file_name":"Thesis_main.tex"}],"corr_author":"1","publication_status":"published","type":"dissertation","keyword":["Quantum information","Qubits","Superconducting devices"]},{"file_date_updated":"2024-09-26T13:12:55Z","date_created":"2024-09-24T10:56:25Z","doi":"10.15479/at:ista:18135","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"license":"https://creativecommons.org/licenses/by/4.0/","date_published":"2024-09-23T00:00:00Z","abstract":[{"lang":"eng","text":"This thesis consists of two separate parts. In the first part we consider a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$. Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion principle plays a key role. We show that, at zero temperature, the ground state energy density of the interacting spin-polarized gas differs (to leading order) from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$  with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$ the density. Further, we extend this to positive temperature and show that the pressure of an interacting spin-polarized gas differs from that of the free gas by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly, we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions and show that here, as an upper bound, the ground state energy density differs from that of the free system by a term of order $a_s \\rho^2$ with an error smaller than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$ is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese asymptotic formulas complement the similar formulas in the literature for the dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies or pressures differ from that of the corresponding free systems by a term of order $a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections, of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular its associated critical temperature and energy gap. We prove that the ratio of the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$. This complements the proofs in the literature of this universal behaviour in the limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$ approaches a universal function of the relative temperature $T/T_c$ in the limit of weak coupling in dimensions $d=1,2,3$."}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-042-8"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","supervisor":[{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"year":"2024","citation":{"chicago":"Lauritsen, Asbjørn Bækgaard. “Energies of Dilute Fermi Gases and Universalities in BCS Theory.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>.","short":"A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS Theory, Institute of Science and Technology Austria, 2024.","ista":"Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria.","mla":"Lauritsen, Asbjørn Bækgaard. <i>Energies of Dilute Fermi Gases and Universalities in BCS Theory</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>.","apa":"Lauritsen, A. B. (2024). <i>Energies of dilute Fermi gases and universalities in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>","ama":"Lauritsen AB. Energies of dilute Fermi gases and universalities in BCS theory. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>","ieee":"A. B. Lauritsen, “Energies of dilute Fermi gases and universalities in BCS theory,” Institute of Science and Technology Austria, 2024."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Energies of dilute Fermi gases and universalities in BCS theory","author":[{"first_name":"Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen"}],"OA_place":"publisher","date_updated":"2026-04-16T08:17:55Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11732"},{"status":"public","relation":"part_of_dissertation","id":"14542"},{"id":"18107","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"17240","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14931","status":"public"}]},"degree_awarded":"PhD","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","project":[{"grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","name":"Mathematical Challenges in BCS Theory of Superconductivity"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"day":"23","_id":"18135","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","month":"09","file":[{"relation":"main_file","access_level":"open_access","date_updated":"2024-09-26T13:11:24Z","content_type":"application/pdf","creator":"alaurits","file_id":"18147","success":1,"file_name":"Lauritsen-thesis-final.pdf","checksum":"c7bc3b31e430d57c65393051ca439575","date_created":"2024-09-26T13:11:24Z","file_size":3648831},{"file_name":"Lauritsen-thesis-source.zip","checksum":"39f6b1b7f83e25a3bf9f933f1ea0bc06","date_created":"2024-09-26T13:12:55Z","file_size":1625888,"file_id":"18148","creator":"alaurits","date_updated":"2024-09-26T13:12:55Z","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file"}],"corr_author":"1","type":"dissertation","publication_status":"published","page":"353","oa":1,"ddc":["515","539"],"status":"public"},{"author":[{"last_name":"Sagi","full_name":"Sagi, Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver"},{"full_name":"Crippa, Alessandro","last_name":"Crippa","first_name":"Alessandro","orcid":"0000-0002-2968-611X","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425"},{"full_name":"Valentini, Marco","last_name":"Valentini","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"},{"first_name":"Marian","orcid":"0009-0003-9037-8831","id":"396A1950-F248-11E8-B48F-1D18A9856A87","full_name":"Janik, Marian","last_name":"Janik"},{"id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","first_name":"Levon","last_name":"Baghumyan","full_name":"Baghumyan, Levon"},{"full_name":"Fabris, Giorgio","last_name":"Fabris","first_name":"Giorgio","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352"},{"full_name":"Kapoor, Lucky","last_name":"Kapoor","orcid":"0000-0001-8319-2148","first_name":"Lucky","id":"84b9700b-15b2-11ec-abd3-831089e67615"},{"last_name":"Hassani","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid","orcid":"0000-0001-6937-5773"},{"full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Calcaterra","full_name":"Calcaterra, Stefano","first_name":"Stefano"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"A gate tunable transmon qubit in planar Ge","OA_place":"publisher","date_updated":"2026-04-07T13:01:55Z","isi":1,"related_material":{"record":[{"status":"public","id":"17196","relation":"research_data"},{"relation":"dissertation_contains","id":"18076","status":"public"}],"link":[{"url":"https://doi.org/10.1038/s41467-024-53910-1","relation":"erratum"}]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"article_processing_charge":"Yes","DOAJ_listed":"1","year":"2024","APC_amount":"6828 EUR","citation":{"ama":"Sagi O, Crippa A, Valentini M, et al. A gate tunable transmon qubit in planar Ge. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-50763-6\">10.1038/s41467-024-50763-6</a>","ieee":"O. Sagi <i>et al.</i>, “A gate tunable transmon qubit in planar Ge,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","short":"O. Sagi, A. Crippa, M. Valentini, M. Janik, L. Baghumyan, G. Fabris, L. Kapoor, F. Hassani, J.M. Fink, S. Calcaterra, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024).","chicago":"Sagi, Oliver, Alessandro Crippa, Marco Valentini, Marian Janik, Levon Baghumyan, Giorgio Fabris, Lucky Kapoor, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-50763-6\">https://doi.org/10.1038/s41467-024-50763-6</a>.","ista":"Sagi O, Crippa A, Valentini M, Janik M, Baghumyan L, Fabris G, Kapoor L, Hassani F, Fink JM, Calcaterra S, Chrastina D, Isella G, Katsaros G. 2024. A gate tunable transmon qubit in planar Ge. Nature Communications. 15, 6400.","mla":"Sagi, Oliver, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” <i>Nature Communications</i>, vol. 15, 6400, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-50763-6\">10.1038/s41467-024-50763-6</a>.","apa":"Sagi, O., Crippa, A., Valentini, M., Janik, M., Baghumyan, L., Fabris, G., … Katsaros, G. (2024). A gate tunable transmon qubit in planar Ge. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-50763-6\">https://doi.org/10.1038/s41467-024-50763-6</a>"},"department":[{"_id":"GeKa"},{"_id":"JoFi"},{"_id":"GradSch"}],"date_published":"2024-07-30T00:00:00Z","arxiv":1,"abstract":[{"text":"Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for hybrid quantum circuits. In this study, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material.","lang":"eng"}],"file_date_updated":"2024-08-05T08:38:01Z","article_type":"original","quality_controlled":"1","scopus_import":"1","intvolume":"        15","date_created":"2024-07-04T11:40:45Z","OA_type":"gold","doi":"10.1038/s41467-024-50763-6","acknowledgement":"We acknowledge Lucas Casparis, Jeroen Danon, Valla Fatemi, Morten Kjaergard and Javad Shabani for their valuable insights and comments. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop\r\nand the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the FWF Projects with DOI:10.55776/I5060 and DOI:10.55776/P36507. We also acknowledge the NextGenerationEU PRIN project\r\n2022A8CJP3 (GAMESQUAD) for partial financial support.","ddc":["530"],"status":"public","oa":1,"volume":15,"corr_author":"1","file":[{"file_id":"17388","success":1,"file_name":"2024_NatureComm_Sagi.pdf","checksum":"ddf5361dcb6c543e2cea818501c09910","date_created":"2024-08-05T08:38:01Z","file_size":1928001,"relation":"main_file","access_level":"open_access","date_updated":"2024-08-05T08:38:01Z","content_type":"application/pdf","creator":"dernst"}],"month":"07","publication_status":"published","type":"journal_article","publication":"Nature Communications","day":"30","article_number":"6400","_id":"17202","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pmid":1,"has_accepted_license":"1","external_id":{"pmid":["39080279"],"arxiv":["2403.16774"],"isi":["001281271000022"]},"project":[{"name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"publisher":"Springer Nature","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"}]},{"year":"2024","citation":{"apa":"Maslov, M., Koutentakis, G., Hrast, M., Heckl, O. H., &#38; Lemeshko, M. (2024). Theory of angular momentum transfer from light to molecules. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">https://doi.org/10.1103/physrevresearch.6.033277</a>","chicago":"Maslov, Mikhail, Georgios Koutentakis, Mateja Hrast, Oliver H. Heckl, and Mikhail Lemeshko. “Theory of Angular Momentum Transfer from Light to Molecules.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">https://doi.org/10.1103/physrevresearch.6.033277</a>.","ista":"Maslov M, Koutentakis G, Hrast M, Heckl OH, Lemeshko M. 2024. Theory of angular momentum transfer from light to molecules. Physical Review Research. 6(3), 033277.","short":"M. Maslov, G. Koutentakis, M. Hrast, O.H. Heckl, M. Lemeshko, Physical Review Research 6 (2024).","mla":"Maslov, Mikhail, et al. “Theory of Angular Momentum Transfer from Light to Molecules.” <i>Physical Review Research</i>, vol. 6, no. 3, 033277, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">10.1103/physrevresearch.6.033277</a>.","ama":"Maslov M, Koutentakis G, Hrast M, Heckl OH, Lemeshko M. Theory of angular momentum transfer from light to molecules. <i>Physical Review Research</i>. 2024;6(3). doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">10.1103/physrevresearch.6.033277</a>","ieee":"M. Maslov, G. Koutentakis, M. Hrast, O. H. Heckl, and M. Lemeshko, “Theory of angular momentum transfer from light to molecules,” <i>Physical Review Research</i>, vol. 6, no. 3. American Physical Society, 2024."},"APC_amount":"3028,31 EUR","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2643-1564"]},"article_processing_charge":"Yes","DOAJ_listed":"1","date_updated":"2026-04-07T11:52:53Z","related_material":{"record":[{"id":"19048","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0003-4074-2570","last_name":"Maslov","full_name":"Maslov, Mikhail"},{"first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","full_name":"Koutentakis, Georgios","last_name":"Koutentakis"},{"id":"48dbb294-2a9c-11ef-905d-f56be71f0e5d","first_name":"Mateja","last_name":"Hrast","full_name":"Hrast, Mateja"},{"first_name":"Oliver H.","last_name":"Heckl","full_name":"Heckl, Oliver H."},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail"}],"title":"Theory of angular momentum transfer from light to molecules","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","intvolume":"         6","date_created":"2024-09-18T11:43:16Z","OA_type":"gold","doi":"10.1103/physrevresearch.6.033277","file_date_updated":"2024-09-23T09:46:20Z","issue":"3","article_type":"original","quality_controlled":"1","scopus_import":"1","date_published":"2024-09-10T00:00:00Z","arxiv":1,"abstract":[{"lang":"eng","text":"We present a theory describing the interaction of structured light, such as light carrying orbital angular momentum, with molecules. The light-matter interaction Hamiltonian we derive is expressed through couplings between spherical gradients of the electric field and the (transition) electric multipole moments of a particle of any nontrivial rotation point group. Our model can therefore accommodate an arbitrary complexity of the molecular and electric field structure, and it can be straightforwardly extended to atoms or nanostructures. Applying this framework to rovibrational spectroscopy of molecules, we uncover the general mechanism of angular momentum exchange between the spin and orbital angular momenta of light, molecular rotation, and its center-of-mass motion. We show that the nonzero vorticity of Laguerre-Gaussian beams can strongly enhance certain rovibrational transitions that are considered forbidden in the case of nonhelical light. We discuss the experimental requirements for the observation of these forbidden transitions in state-of-the-art spatially resolved spectroscopy measurements."}],"department":[{"_id":"GradSch"},{"_id":"MiLe"}],"publication_status":"published","type":"journal_article","volume":6,"corr_author":"1","file":[{"date_created":"2024-09-23T09:46:20Z","checksum":"8f744d94956a1683b473b1cf9b411a37","file_size":1563824,"file_name":"2024_PhysicalReviewResearch_Maslov.pdf","success":1,"file_id":"18125","creator":"dernst","content_type":"application/pdf","date_updated":"2024-09-23T09:46:20Z","access_level":"open_access","relation":"main_file"}],"month":"09","oa":1,"ddc":["530"],"status":"public","acknowledgement":"We are grateful to Emilio Pisanty and Philipp Lunt for valuable discussions. This research was funded wholly or in part by the Austrian Science Fund (FWF) [10.55776/F1004]. G.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). O.H.H. acknowledges support by the Austrian Science Fund (FWF) [10.55776/P36040]. Furthermore, the financial support by the Austrian Federal Ministry for Digital and Economic Affairs, the National Foundation for Research, Technology and Development, and the Christian Doppler Research Association is gratefully acknowledged.","external_id":{"arxiv":["2310.00095"]},"project":[{"name":"Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions","grant_number":"F100403","_id":"7c040762-9f16-11ee-852c-dd79eeee4ab3"},{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"publisher":"American Physical Society","has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_number":"033277","day":"10","publication":"Physical Review Research","ec_funded":1,"_id":"18087"},{"corr_author":"1","month":"09","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2024-09-18T14:13:01Z","creator":"osagi","file_id":"18093","success":1,"date_created":"2024-09-18T14:13:01Z","file_size":86679095,"checksum":"d01d0e2846c2f3ac5bb14d321554a4cd","file_name":"OliverSagi_Thesis_pdfa.pdf"},{"creator":"osagi","content_type":"application/x-zip-compressed","date_updated":"2024-09-19T09:20:33Z","access_level":"local","relation":"source_file","checksum":"0543f473d509ee545f4ed3a56f742f4b","date_created":"2024-09-18T14:14:02Z","file_size":172098524,"file_name":"Thesis_OliverSagi.zip","file_id":"18094"}],"type":"dissertation","publication_status":"published","page":"111","ddc":["539"],"oa":1,"status":"public","has_accepted_license":"1","project":[{"grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","name":"Merging spin and superconducting qubits in planar Ge"},{"grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"}],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"day":"18","ec_funded":1,"_id":"18076","oa_version":"Published Version","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","year":"2024","supervisor":[{"last_name":"Katsaros","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X"}],"citation":{"ieee":"O. 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Gate-tunable transmons (gatemons) employing semiconductor Josephson\r\njunctions have recently emerged as building blocks for such hybrid quantum circuits. In this\r\nthesis, we present a gatemon fabricated in planar Germanium. We induce superconductivity\r\nin a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates\r\nthe superconductor from the Ge quantum well. The Josephson junction is then integrated\r\ninto an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase\r\nthe qubit tunability in a broad frequency range with resonator and two-tone spectroscopy.\r\nTime-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our\r\nresults, combined with the recent advances in the spin qubit field, pave the way towards novel\r\nhybrid and protected qubits in a group IV, CMOS-compatible material.","lang":"eng"}]},{"ddc":["530"],"oa":1,"status":"public","acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. 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Sagi, “A gate-tunable transmon in planar Ge.” Institute of Science and Technology Austria, 2024.","ama":"Sagi O. A gate-tunable transmon in planar Ge. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17196\">10.15479/AT:ISTA:17196</a>","apa":"Sagi, O. (2024). A gate-tunable transmon in planar Ge. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17196\">https://doi.org/10.15479/AT:ISTA:17196</a>","mla":"Sagi, Oliver. <i>A Gate-Tunable Transmon in Planar Ge</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17196\">10.15479/AT:ISTA:17196</a>.","ista":"Sagi O. 2024. 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An additional Jupyter Notebook is attached that walks through the data analysis.","lang":"eng"}],"date_published":"2024-07-04T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"GeKa"},{"_id":"JoFi"}],"doi":"10.15479/AT:ISTA:17196","date_created":"2024-07-04T10:14:34Z","file_date_updated":"2024-07-04T10:11:40Z"},{"file":[{"creator":"melkrewi","content_type":"text/plain","date_updated":"2024-08-05T22:24:18Z","access_level":"open_access","relation":"main_file","date_created":"2024-08-05T22:24:18Z","file_size":2465,"checksum":"26b5d41b3103f4284dd97d56e370a5b6","file_name":"README.txt","success":1,"file_id":"17394"},{"success":1,"file_id":"17395","file_size":2526735400,"date_created":"2024-08-05T23:28:52Z","checksum":"95adab5e36148015da313505e3910707","file_name":"Data_artemia_single_nucleus_atlas.zip","access_level":"open_access","relation":"main_file","creator":"melkrewi","content_type":"application/x-zip-compressed","date_updated":"2024-08-05T23:28:52Z"}],"month":"08","corr_author":"1","article_processing_charge":"No","citation":{"ama":"Elkrewi MN, Vicoso B. Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>","ieee":"M. N. Elkrewi and B. Vicoso, “Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.’” Institute of Science and Technology Austria, 2024.","ista":"Elkrewi MN, Vicoso B. 2024. Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>.","short":"M.N. Elkrewi, B. Vicoso, (2024).","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Data for: ‘Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">https://doi.org/10.15479/AT:ISTA:17362</a>.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. <i>Data for: “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>.","apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">https://doi.org/10.15479/AT:ISTA:17362</a>"},"type":"research_data","year":"2024","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"title":"Data for: \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\"","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"17890","relation":"used_in_publication"}]},"status":"public","oa":1,"ddc":["576"],"date_updated":"2026-04-16T12:20:41Z","file_date_updated":"2024-08-05T23:28:52Z","has_accepted_license":"1","doi":"10.15479/AT:ISTA:17362","acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2024-08-02T07:27:45Z","publisher":"Institute of Science and Technology Austria","project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"_id":"17362","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"day":"05","abstract":[{"text":"This is the supplementary data for the paper titled \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\", where we described the generation and analysis of single-nucleus expression and chromatin-accessibility data from the female reproductive system of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus data (over 400 million years of divergence) and highlighted the extreme conservation of several of the molecular pathways of oogenesis and meiosis. We found evidence of global transcriptional quiescence and chromatin condensation in late germ cells, highlighting the conserved role of this repressive stage in arthropod oogenesis. Additionally, we explored the expression patterns of the ZW sex chromosomes during oogenesis. Our data shows that the Z-chromosome is consistently downregulated in germline cells. While this is partly driven by a lack of dosage compensation in the germline, a subset of cells show stronger repression of the Z chromosome.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2024-08-05T00:00:00Z","oa_version":"Published Version"},{"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"},{"name":"Vienna Graduate School on Computational Optimization","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","grant_number":"W1260-N35"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"day":"29","_id":"17465","oa_version":"Published Version","month":"08","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2024-10-04","date_updated":"2024-10-05T22:30:05Z","creator":"ashevche","file_id":"17482","checksum":"da6dd3166078934577f6af93d27000e2","date_created":"2024-09-02T09:23:32Z","file_size":4468610,"file_name":"thesis_a2b.pdf"},{"file_name":"Thesis Alex - ISTA.zip","date_created":"2024-09-02T09:23:46Z","checksum":"76a39ef252239560923cdda4ce0a31a4","file_size":15930999,"file_id":"17483","creator":"ashevche","date_updated":"2024-10-05T22:30:05Z","content_type":"application/zip","access_level":"closed","embargo_to":"open_access","relation":"source_file"}],"corr_author":"1","publication_status":"published","type":"dissertation","page":"232","oa":1,"status":"public","ddc":["519"],"file_date_updated":"2024-10-05T22:30:05Z","date_created":"2024-08-28T15:14:25Z","doi":"10.15479/at:ista:17465","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"alternative_title":["ISTA Thesis"],"date_published":"2024-08-29T00:00:00Z","abstract":[{"text":"In the modern age of machine learning, artificial neural networks have become an integral part\r\nof many practical systems. One of the key ingredients of the success of the deep learning\r\napproach is recent computational advances which allowed the training of models with billions\r\nof parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical analysis of modern models since “classical” statistical wisdom\r\nis no longer applicable. In this view, it is paramount to extend or develop new machinery\r\nthat will allow tackling the neural network analysis under new challenging asymptotic regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems are usually optimized via “local” search algorithms, such\r\nas stochastic gradient descent (SGD). However, given the high-dimensional nature of the\r\nparameter space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe landscape of the SGD training dynamics exhibits a few beneficial properties for the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized network\r\nis dropout stable. The emergence of dropout stability allows to conclude that the minima\r\nfound by SGD are connected via a continuous path of small loss. This in turn means that\r\nthe high-dimensional landscape of the neural network optimization problem is provably not so\r\nunfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized network tends to find solutions that are functionally more “simple”.\r\nThis in turn means that the SGD minima are more robust, since a less complicated solution\r\nwill less likely overfit the data. More formally, for a prototypical example of a wide two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in\r\nits choice of an interpolating solution. Namely, at convergence the neural network implements\r\na piece-wise linear function with the number of linear regions depending only on the amount\r\nof training data. This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven such a severe over-parameterization of the model.\r\nDiverging from the generic supervised setting of classification and regression problems, we\r\nanalyze an auto-encoder model that is commonly used for representation learning and data\r\ncompression. Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding of their behaviour is limited even in the simplistic shallow case. The related\r\nwork is restricted to extreme asymptotic regimes in which the auto-encoder is either severely\r\nover-parameterized or under-parameterized. In contrast, we provide a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the\r\ninput dimension and the size of the compressed representation obey the same asymptotics.\r\nWe also show that gradient-based methods are able to find a globally optimal solution and\r\nthat the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof natural images. Next, we relax the Gaussian assumption and study more structured input\r\nsources. We show that the shallow model is sometimes agnostic to the structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We prove that making the decoding component\r\nslightly less shallow is already enough to escape the “curse” of Gaussian performance.\r\n","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2024","supervisor":[{"first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"citation":{"mla":"Shevchenko, Alexander. <i>High-Dimensional Limits in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>.","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024.","ista":"Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria.","chicago":"Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>.","apa":"Shevchenko, A. (2024). <i>High-dimensional limits in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>","ieee":"A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024.","ama":"Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"High-dimensional limits in artificial neural networks","author":[{"last_name":"Shevchenko","full_name":"Shevchenko, Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr"}],"OA_place":"repository","date_updated":"2025-04-25T10:32:06Z","related_material":{"record":[{"status":"public","id":"11420","relation":"part_of_dissertation"},{"id":"17469","relation":"part_of_dissertation","status":"public"},{"id":"14459","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"9198","relation":"part_of_dissertation"}]},"degree_awarded":"PhD"},{"department":[{"_id":"NiBa"},{"_id":"GradSch"}],"abstract":[{"text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.","lang":"eng"}],"date_published":"2024-01-05T00:00:00Z","scopus_import":"1","quality_controlled":"1","issue":"6678","article_type":"original","doi":"10.1126/science.adi2982","intvolume":"       383","OA_type":"green","date_created":"2024-01-14T23:00:56Z","OA_place":"repository","author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"full_name":"Zagrodzka, Zuzanna B.","last_name":"Zagrodzka","first_name":"Zuzanna B."},{"last_name":"Garlovsky","full_name":"Garlovsky, Martin D.","first_name":"Martin D."},{"full_name":"Pal, Arka","last_name":"Pal","orcid":"0000-0002-4530-8469","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"last_name":"Shipilina","full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria","orcid":"0000-0002-1145-9226"},{"last_name":"Garcia Castillo","full_name":"Garcia Castillo, Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando"},{"last_name":"Lifchitz","full_name":"Lifchitz, Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","first_name":"Hila"},{"first_name":"Alan","full_name":"Le Moan, Alan","last_name":"Le Moan"},{"first_name":"Erica","last_name":"Leder","full_name":"Leder, Erica"},{"first_name":"James","last_name":"Reeve","full_name":"Reeve, James"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"The genetic basis of a recent transition to live-bearing in marine snails","related_material":{"record":[{"status":"public","relation":"research_data","id":"14812"},{"status":"public","relation":"dissertation_contains","id":"20694"}],"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/the-snail-or-the-egg/","relation":"press_release"}]},"isi":1,"date_updated":"2026-04-21T22:30:13Z","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"]},"citation":{"ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. <i>Science</i>. 2024;383(6678):114-119. doi:<a href=\"https://doi.org/10.1126/science.adi2982\">10.1126/science.adi2982</a>","ieee":"S. Stankowski <i>et al.</i>, “The genetic basis of a recent transition to live-bearing in marine snails,” <i>Science</i>, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024.","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.adi2982\">https://doi.org/10.1126/science.adi2982</a>.","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” <i>Science</i>, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:<a href=\"https://doi.org/10.1126/science.adi2982\">10.1126/science.adi2982</a>.","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adi2982\">https://doi.org/10.1126/science.adi2982</a>"},"year":"2024","_id":"14796","day":"05","publication":"Science","pmid":1,"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://figshare.com/articles/journal_contribution/The_genetic_basis_of_a_recent_transition_to_live-bearing_in_marine_snails/26356054?file=47868241"}],"external_id":{"isi":["001138156400003"],"pmid":["38175895"]},"publisher":"American Association for the Advancement of Science","page":"114-119","acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","oa":1,"status":"public","corr_author":"1","month":"01","volume":383,"type":"journal_article","publication_status":"published"},{"date_published":"2024-07-05T00:00:00Z","abstract":[{"lang":"eng","text":"Males and females exhibit numerous differences, from the initial stages of sex determination to the\r\ndevelopment of secondary sexual characteristics. In Drosophila, these differences have been\r\nthoroughly studied. Extensive research has been performed to understand the role and molecular\r\nmode of action of central sex in determining switch genes, such as transformer (tra) and Sex-lethal\r\n(Sxl). Furthermore, studies have highlighted differential gene expression as an essential mechanism to\r\ncreate sexual dimorphism. An alternative path to sexual dimorphism that has been less explored is\r\nalternative splicing, the mechanism through which genes can produce multiple transcripts with\r\ndistinct properties and functions. The primary switch sex-determining gene Sxl is a good example of\r\nthe role of alternative splicing for sex-specific functions: the inclusion of a specific exon determines\r\nthe male or female form of the protein, which in turn switches on either the male or female\r\ndevelopmental pathway. The genes that act upstream of Sxl and determine which form is expressed -\r\nthe counter genes - have received less attention. This thesis addresses two critical questions about\r\nthe molecular encoding of sexes in the Drosophila melanogaster genome: First, the use of splice forms\r\nin male and female tissues in D. melanogaster is examined, inferring the molecular and evolutionary\r\nparameters shaping the diversity of the splicing landscape. Second, the behaviour of counter genes in\r\nDrosophila-related species is investigated, shedding light on potential changes leading to their\r\nincorporation into the sex-determination pathway.\r\nFor the alternative splicing analyses, long-read RNA sequencing of testes, ovaries, female and male\r\nmidguts, heads, and whole bodies was performed. A novel pipeline was developed to assign unique\r\ntranscript identifiers for each sequence of exons and introns in the read, enabling detailed\r\ncomparisons of splicing variants in each tissue/sex. Alternative splicing was found to be more\r\npervasive in females than males (22,201 exclusive splice forms in females versus 12,631 in males),\r\nespecially when comparing ovaries to other tissues. The ovaries alone displayed 15,299 exclusive\r\nsplice forms, suggesting most female exclusive splice forms originate there. Genome location and gene\r\nage were also correlated with the number of splice forms per gene. In particular, the X and 4th\r\nchromosomes (Muller elements A and F) showed more splice forms per gene than other\r\nchromosomes. Additionally, genes older than 63 million years exhibited more splice forms per gene\r\nthan younger genes. Our results suggest that alternative splicing is more prevalent than previously\r\nbelieved, with numerous female-exclusive forms, age, and location playing significant roles in shaping\r\nits prevalence.\r\nFor the counter genes analyses, we combined published gene expression, genomic, and gene\r\ninteraction data from various clades (Bactrocera jarvisi, B. oleae, Ceratitis capitata, Mus musculus,\r\nCaenorhabditis elegans, Homo sapiens, and D. melanogaster). The counter genes scute (sc), extra\r\nmacrochaetae (emc), groucho (gro), deadpan (dpn), daughterless (da), runt (run), Sxl, hermaphrodite\r\n(her), and tra maintain conserved Muller element locations between C. capitata and D. melanogaster,\r\nwhich are most of the counter genes identified in the C. capitata genome. Their expression patterns\r\nduring early embryogenesis in B. jarvisi and D. melanogaster are also similar for counter genes dpn,\r\ngro, da, and emc. However, Sxl and sc are also found to have more extreme expression ratios between\r\nthe species. Lastly, gene interactions within the counter genes are conserved, with da-sc and gro-dpn\r\ninteractions occurring in Drosophila, worms, humans, and mice. Interactions such as dpn-sc, dpn-da,\r\nda-emc, and gro-run are present in Drosophila, mice, and humans, suggesting these genes were\r\nrecruited by ancestral characteristics, primarily during embryogenesis. The conserved expression,\r\nlocation, and interactions of counter genes suggest serendipitous recruitment of such genes instead\r\nof a change in those characteristics as they were recruited for this function. "}],"department":[{"_id":"BeVi"},{"_id":"GradSch"}],"alternative_title":["ISTA Thesis"],"license":"https://creativecommons.org/licenses/by-sa/4.0/","date_created":"2024-07-05T14:15:29Z","doi":"10.15479/at:ista:17206","file_date_updated":"2025-01-11T23:30:04Z","date_updated":"2026-04-07T13:03:22Z","degree_awarded":"PhD","title":"Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination","author":[{"id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Raices","full_name":"Raices, Julia"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","supervisor":[{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"year":"2024","citation":{"ama":"Raices J. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>","ieee":"J. Raices, “Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination,” Institute of Science and Technology Austria, 2024.","chicago":"Raices, Julia. “Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>.","short":"J. Raices, Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination, Institute of Science and Technology Austria, 2024.","ista":"Raices J. 2024. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. Institute of Science and Technology Austria.","mla":"Raices, Julia. <i>Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>.","apa":"Raices, J. (2024). <i>Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>"},"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)"},"oa_version":"Published Version","day":"05","_id":"17206","ec_funded":1,"publisher":"Institute of Science and Technology Austria","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","status":"public","ddc":["570"],"oa":1,"page":"82","publication_status":"published","type":"dissertation","month":"07","file":[{"file_id":"17223","checksum":"d5e9234bde8667b005a8cfe18bb467d3","file_size":13788479,"date_created":"2024-07-11T07:18:01Z","file_name":"ThesisRaices2024_postDefense.docx","relation":"source_file","embargo_to":"open_access","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-01-11T23:30:04Z","creator":"cchlebak"},{"date_updated":"2025-01-11T23:30:04Z","embargo":"2025-01-11","content_type":"application/pdf","creator":"cchlebak","relation":"main_file","access_level":"open_access","file_name":"ThesisRaices2024_nosignature.pdf","checksum":"f5ed0139aa3e11ce58369f0915647c5c","file_size":5580296,"date_created":"2024-07-11T07:22:32Z","file_id":"17224"}],"corr_author":"1"},{"citation":{"apa":"Porley Esteves, D. (2024). <i>Structural characterization of spumavirus capsid assemblies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>","mla":"Porley Esteves, Darío. <i>Structural Characterization of Spumavirus Capsid Assemblies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>.","ista":"Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria.","short":"D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024.","chicago":"Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>.","ieee":"D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024.","ama":"Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>"},"supervisor":[{"full_name":"Schur, Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"year":"2024","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-041-1"]},"degree_awarded":"PhD","date_updated":"2026-04-07T13:21:01Z","OA_place":"publisher","title":"Structural characterization of spumavirus capsid assemblies","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"Dario J","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87","full_name":"Porley, Dario J","last_name":"Porley"}],"doi":"10.15479/at:ista:18101","date_created":"2024-09-20T10:21:03Z","file_date_updated":"2025-03-25T23:30:03Z","abstract":[{"text":"The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the\r\nSpumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the\r\nhuman immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which\r\nare regularly used as model systems to study the retroviral life cycle. The main structural\r\ncomponent of the retroviruses, is the Gag protein and its truncation derivatives occurring\r\nduring viral maturation. Orthoretroviral Gag assemblies have been extensively studied to\r\nunderstand the interactions that confer stability and morphology to viral particles.\r\nThe Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.\r\nIts members, the Foamy viruses (FV), share most of the conventional features found in\r\nretroviruses. However, they also possess multiple characteristics that make them unique. In\r\nparticular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag\r\narchitecture deviates from the canonical domain arrangement in FV. They also exhibit a\r\npeculiar particle morphology, having no apparent immature state and a seemingly\r\nicosahedral mature particle. Due to this, many fundamental questions on FV structural\r\nassembly mechanisms remain open. To answer these questions, was the main focus of this\r\nthesis.\r\nMainly, it is not known how FV assemble their core in a virus particle and what are the\r\nimportant assembly interaction sites within said core. What is the minimum assembly\r\ncompetent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be\r\ninteresting to know what is the evolutionary relationship between FV and the rest of the\r\nretrotranscribing elements, from a structural point of view?\r\nTo answer these questions, membrane-enveloped mammalian cell-derived FV virus-like\r\nparticles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested\r\nthese FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with\r\nearlier observations. To further evaluate FV Gag assembly competence and morphology,\r\nthe first bacterial cell-derived in vitro VLP assembly system was designed and optimized.\r\nUsing this system with different truncation variants, the minimum assembly competent\r\ndomain of FV Gag was found to be the putative CA300-477 domain. Varying VLP\r\nmorphologies were also observed and strongly suggested residues upstream of CA300-477\r\nplay a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal\r\nassembly competent domain. This revealed an unexpectedly unique non-canonical\r\nassembly architecture. Three novel lattice stabilizing interfaces were described which\r\nproved to be as unique as the lattice arrangement. Comparison to a newly published FV CA\r\ncore structure revealed the CA-CA interactions in the atypical assembly do not recapitulate\r\nwhat is described for the FV core lattice. However, the new in vitro VLP assembly system\r\nobtained in this thesis also provides an exciting opportunity to study still unresolved FV\r\nassembly features in a potentially facilitated approach compared to conventional methods.\r\nIn summary, this work provided a deeper understanding of the basic FV Gag assembly unit,\r\nas well as presenting the first FV Gag-derived in vitro VLP assembly system. This system\r\nreveals a novel and unique assembly architecture among retroviral in vitro assemblies.","lang":"eng"}],"date_published":"2024-09-26T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","type":"dissertation","corr_author":"1","file":[{"file_id":"18149","checksum":"3b8b0bacfe61112f3852744f3170e468","file_size":14213128,"date_created":"2024-09-26T13:40:33Z","file_name":"PhD_thesis_DPorley_final_20240919.docx","access_level":"closed","embargo_to":"open_access","relation":"source_file","creator":"dporley","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-03-25T23:30:03Z"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2025-03-25T23:30:03Z","embargo":"2025-03-25","creator":"dporley","file_id":"18150","date_created":"2024-09-26T13:41:39Z","file_size":18583031,"checksum":"6c3a652a8eede874118e11d66a63652f","file_name":"PhD_thesis_DPorley_final_20240926_pdfa1.pdf"}],"month":"09","status":"public","oa":1,"ddc":["570"],"page":"131","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"},{"grant_number":"25762","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A","name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","oa_version":"Published Version","_id":"18101","ec_funded":1,"day":"26"},{"isi":1,"date_updated":"2026-04-21T22:30:16Z","related_material":{"record":[{"status":"public","id":"20563","relation":"dissertation_contains"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Portinale","full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo"},{"full_name":"Quattrocchi, Filippo","last_name":"Quattrocchi","orcid":"0009-0000-9773-1931","first_name":"Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308"}],"title":"Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs","OA_place":"publisher","year":"2024","citation":{"apa":"Portinale, L., &#38; Quattrocchi, F. (2024). Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. <i>European Journal of Applied Mathematics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/s0956792524000810\">https://doi.org/10.1017/s0956792524000810</a>","mla":"Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” <i>European Journal of Applied Mathematics</i>, Cambridge University Press, 2024, pp. 1–29, doi:<a href=\"https://doi.org/10.1017/s0956792524000810\">10.1017/s0956792524000810</a>.","chicago":"Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” <i>European Journal of Applied Mathematics</i>. Cambridge University Press, 2024. <a href=\"https://doi.org/10.1017/s0956792524000810\">https://doi.org/10.1017/s0956792524000810</a>.","short":"L. Portinale, F. Quattrocchi, European Journal of Applied Mathematics (2024) 1–29.","ista":"Portinale L, Quattrocchi F. 2024. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics., 1–29.","ieee":"L. Portinale and F. Quattrocchi, “Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs,” <i>European Journal of Applied Mathematics</i>. Cambridge University Press, pp. 1–29, 2024.","ama":"Portinale L, Quattrocchi F. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. <i>European Journal of Applied Mathematics</i>. 2024:1-29. doi:<a href=\"https://doi.org/10.1017/s0956792524000810\">10.1017/s0956792524000810</a>"},"publication_identifier":{"issn":["0956-7925"],"eissn":["1469-4425"]},"language":[{"iso":"eng"}],"DOAJ_listed":"1","article_processing_charge":"Yes","date_published":"2024-12-20T00:00:00Z","abstract":[{"text":"We prove discrete-to-continuum convergence for dynamical optimal transport on  Zd\r\n -periodic graphs with cost functional having linear growth at infinity. This result provides an answer to a problem left open by Gladbach, Kopfer, Maas, and Portinale (Calc Var Partial Differential Equations 62(5), 2023), where the convergence behaviour of discrete boundary-value dynamical transport problems is proved under the stronger assumption of superlinear growth. Our result extends the known literature to some important classes of examples, such as scaling limits of  1 -Wasserstein transport problems. Similarly to what happens in the quadratic case, the geometry of the graph plays a crucial role in the structure of the limit cost function, as we discuss in the final part of this work, which includes some visual representations.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JaMa"}],"date_created":"2024-12-23T11:03:59Z","OA_type":"gold","doi":"10.1017/s0956792524000810","article_type":"original","scopus_import":"1","quality_controlled":"1","oa":1,"status":"public","acknowledgement":"L.P. gratefully acknowledges fundings from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – GZ 2047/1, Projekt-ID 390685813. F.Q. gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.","page":"1-29","type":"journal_article","publication_status":"epub_ahead","month":"12","oa_version":"Published Version","publication":"European Journal of Applied Mathematics","day":"20","_id":"18706","publisher":"Cambridge University Press","project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"external_id":{"isi":["001381435800001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/S0956792524000810"}]},{"oa_version":"Preprint","_id":"20571","article_number":"2403.07803","day":"09","publication":"arXiv","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2403.07803","open_access":"1"}],"project":[{"_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":"F06504","call_identifier":"FWF","name":"Taming Complexity in Partial Differential Systems"}],"external_id":{"arxiv":["2403.07803"]},"oa":1,"status":"public","acknowledgement":"The author would like to thank Jan Maas for suggesting this project and for many helpful\r\ncomments, Antonio Agresti, Lorenzo Dello Schiavo and Julian Fischer for several fruitful discussions, and Oliver Tse for pointing out the reference [15]. He also gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.\r\n","type":"preprint","publication_status":"draft","keyword":["gradient flows","Jordan–Kinderlehrer–Otto scheme","curves of maximal slope","optimal transport","Dirichlet boundary conditions","Fokker–Planck equation"],"month":"04","corr_author":"1","abstract":[{"lang":"eng","text":"We prove the convergence of a modified Jordan--Kinderlehrer--Otto scheme to a solution to the Fokker--Planck equation in $\\Omega \\Subset \\mathbb{R}^d$ with general, positive and temporally constant, Dirichlet boundary conditions. We work under mild assumptions on the domain, the drift, and the initial datum.   In the special case where $\\Omega$ is an interval in $\\mathbb{R}^1$, we prove that such a solution is a gradient flow -- curve of maximal slope -- within a suitable space of measures, endowed with a modified Wasserstein distance.\r\nOur discrete scheme and modified distance draw inspiration from contributions by A. Figalli and N. Gigli [J. Math. Pures Appl. 94, (2010), pp. 107--130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41--88] on an optimal-transport approach to evolution equations with Dirichlet boundary conditions. Similarly to these works, we allow the mass to flow from/to the boundary $\\partial \\Omega$ throughout the evolution. However, our leading idea is to also keep track of the mass at the boundary by working with measures defined on the whole closure $\\overline \\Omega$. The driving functional is a modification of the classical relative entropy that also makes use of the information at the boundary. As an intermediate result, when $\\Omega$ is an interval in $\\mathbb{R}^1$, we find a formula for the descending slope of this geodesically nonconvex functional. "}],"arxiv":1,"date_published":"2024-04-09T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"doi":"10.48550/arXiv.2403.07803","date_created":"2025-10-28T13:12:56Z","OA_type":"green","related_material":{"record":[{"status":"public","id":"20865","relation":"later_version"},{"id":"20563","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-04-21T22:30:16Z","OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Filippo","orcid":"0009-0000-9773-1931","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","full_name":"Quattrocchi, Filippo","last_name":"Quattrocchi"}],"title":"Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions","citation":{"ama":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2403.07803\">10.48550/arXiv.2403.07803</a>","ieee":"F. Quattrocchi, “Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions,” <i>arXiv</i>. .","apa":"Quattrocchi, F. (n.d.). Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2403.07803\">https://doi.org/10.48550/arXiv.2403.07803</a>","short":"F. Quattrocchi, ArXiv (n.d.).","ista":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv, 2403.07803.","chicago":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2403.07803\">https://doi.org/10.48550/arXiv.2403.07803</a>.","mla":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” <i>ArXiv</i>, 2403.07803, doi:<a href=\"https://doi.org/10.48550/arXiv.2403.07803\">10.48550/arXiv.2403.07803</a>."},"year":"2024","article_processing_charge":"No","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"We investigate the minimal error in approximating a general probability\r\nmeasure $\\mu$ on $\\mathbb{R}^d$ by the uniform measure on a finite set with\r\nprescribed cardinality $n$. The error is measured in the $p$-Wasserstein\r\ndistance. In particular, when $1\\le p<d$, we establish asymptotic upper and\r\nlower bounds as $n \\to \\infty$ on the rescaled minimal error that have the\r\nsame, explicit dependency on $\\mu$.\r\n  In some instances, we prove that the rescaled minimal error has a limit.\r\nThese include general measures in dimension $d = 2$ with $1 \\le p < 2$, and\r\nuniform measures in arbitrary dimension with $1 \\le p < d$. For some uniform\r\nmeasures, we prove the limit existence for $p \\ge d$ as well.\r\n  For a class of compactly supported measures with H\\\"older densities, we\r\ndetermine the convergence speed of the minimal error for every $p \\ge 1$.\r\n  Furthermore, we establish a new Pierce-type (i.e., nonasymptotic) upper\r\nestimate of the minimal error when $1 \\le p < d$.\r\n  In the initial sections, we survey the state of the art and draw connections\r\nwith similar problems, such as classical and random quantization."}],"date_published":"2024-08-23T00:00:00Z","arxiv":1,"department":[{"_id":"GradSch"},{"_id":"JaMa"}],"doi":"10.48550/arXiv.2408.12924","date_created":"2025-10-28T13:12:22Z","OA_type":"green","related_material":{"record":[{"id":"20563","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-04-21T22:30:16Z","OA_place":"repository","title":"Asymptotics for optimal empirical quantization of measures","author":[{"id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","first_name":"Filippo","orcid":"0009-0000-9773-1931","last_name":"Quattrocchi","full_name":"Quattrocchi, Filippo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” <i>ArXiv</i>, 2408.12924, doi:<a href=\"https://doi.org/10.48550/arXiv.2408.12924\">10.48550/arXiv.2408.12924</a>.","ista":"Quattrocchi F. Asymptotics for optimal empirical quantization of measures. arXiv, 2408.12924.","chicago":"Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2408.12924\">https://doi.org/10.48550/arXiv.2408.12924</a>.","short":"F. Quattrocchi, ArXiv (n.d.).","apa":"Quattrocchi, F. (n.d.). Asymptotics for optimal empirical quantization of measures. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2408.12924\">https://doi.org/10.48550/arXiv.2408.12924</a>","ieee":"F. Quattrocchi, “Asymptotics for optimal empirical quantization of measures,” <i>arXiv</i>. .","ama":"Quattrocchi F. Asymptotics for optimal empirical quantization of measures. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2408.12924\">10.48550/arXiv.2408.12924</a>"},"year":"2024","article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Preprint","_id":"20570","day":"23","article_number":"2408.12924","publication":"arXiv","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2408.12924","open_access":"1"}],"external_id":{"arxiv":["2408.12924"]},"project":[{"_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":"F06504","call_identifier":"FWF","name":"Taming Complexity in Partial Differential Systems"}],"oa":1,"status":"public","acknowledgement":"The author is thankful to Nicolas Clozeau, Lorenzo Dello Schiavo, Jan Maas, Dejan Slepčev,\r\nand Dario Trevisan for many fruitful discussions and comments. The author gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.","publication_status":"draft","type":"preprint","keyword":["optimal empirical quantization","vector quantization","Wasserstein distance","semidiscrete optimal transport","Zador’s Theorem","Pierce’s Lemma"],"corr_author":"1","month":"08"},{"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Genomes are shaped by natural selection at the level of the organism, as genomic variants that\r\nhave a beneficial effect on the viability or fecundity of their carriers are on average expected\r\nto be passed on to more offspring than less beneficial alleles. However, selection also favors\r\ngenomic variants that drive their own transmission to the next generation above the mendelian\r\nexpectation of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As\r\nmeiotic drivers often require multiple genes and sequences for transmission ratio distortion,\r\nthey are often found in regions of low recombination, such as inversions, which prevent their\r\nrecombination with the non-driving homologous regions. Reduced recombination rates are\r\nexpected to lead to the accumulation of deleterious mutations, which may affect hundreds\r\nof genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates of recombination between driving and non-driving haplotypes have limited the power of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers, and made the\r\nthe identification of the genes causing transmission ratio distortion difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that\r\nmake use of next generation sequencing data to characterize the sequence and expression\r\nevolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is\r\ntransmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of\r\nsequence degeneration counteracted by occasional recombination with the non-driving homolog\r\nover large parts of the meiotic driver, proposing an explanation for its long-term survival.\r\nChapter 3 investigates the sequence and expression evolution of genes on the t-haplotype,\r\nand finds widespread expression and copy number changes and signs of less efficient purifying\r\nselection compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand which acquired novel sequence and testis-specific expression on the t-haplotype. Finally,\r\nChapter 4 provides unprecedented insights into the gene expression landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression changes along spermatogenesis. This study shows\r\nthe timing of previously found drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes that may underlie the complex biology of transmission ratio distortion of\r\nthe t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in\r\nthe context of the current state of meiotic drive research."}],"date_published":"2024-06-20T00:00:00Z","file_date_updated":"2025-01-10T23:30:10Z","doi":"10.15479/at:ista:17119","date_created":"2024-06-07T16:14:13Z","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","author":[{"id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","first_name":"Réka K","orcid":"0000-0002-8489-9281","last_name":"Kelemen","full_name":"Kelemen, Réka K"}],"related_material":{"record":[{"id":"542","relation":"part_of_dissertation","status":"public"},{"id":"10767","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","date_updated":"2026-04-07T13:21:37Z","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-039-8"],"issn":["2663-337X"]},"citation":{"ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024.","ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>","apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>.","short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024.","chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>.","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria."},"year":"2024","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"_id":"17119","ec_funded":1,"day":"20","oa_version":"Published Version","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"has_accepted_license":"1","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","call_identifier":"H2020"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"publisher":"Institute of Science and Technology Austria","page":"105","status":"public","ddc":["576"],"oa":1,"corr_author":"1","month":"06","file":[{"file_name":"thesis.zip","file_size":180557931,"checksum":"fab59146e3b3dc2e5d214576984a2a63","date_created":"2024-06-07T16:09:17Z","file_id":"17121","creator":"rkelemen","date_updated":"2025-01-10T23:30:10Z","content_type":"application/zip","access_level":"closed","relation":"source_file","embargo_to":"open_access"},{"access_level":"open_access","relation":"main_file","creator":"rkelemen","content_type":"application/pdf","date_updated":"2025-01-10T23:30:10Z","embargo":"2025-01-10","file_id":"17213","checksum":"91cc4c25a792239e8a7688e8aec7c62a","date_created":"2024-07-10T08:00:20Z","file_size":19405484,"file_name":"thesis_to_archive.pdf"}],"publication_status":"published","type":"dissertation","keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"]},{"file_date_updated":"2025-10-29T23:30:02Z","doi":"10.15479/at:ista:18477","date_created":"2024-10-27T07:35:13Z","department":[{"_id":"GradSch"},{"_id":"CaBe"}],"alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"ADAR1 is broadly expressed across various tissues and is vital in regulating pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing autoimmunity and maintaining\r\nimmune tolerance. This editing process has been detected at millions of sites across the\r\nhuman genome. However, the mechanism underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear, with much of the current knowledge derived from\r\ncomparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates and applying a combination of biochemical techniques and structural\r\nstudies using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the\r\nfirst report in the literature to achieve high protein purity and activity. This advancement\r\nenabled the investigation of complex formation between ADAR1 and various RNA substrates,\r\nleading to the identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the\r\ndesired quality, highlighting the need for similar rigorous optimization of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex. The study was complemented by\r\nAlphaFold predictions, which provided some insights into this mechanism.\r\nMoreover, during this project I established a collaboration with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it\r\nwas further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable of detecting modified nucleotides without the need for reverse transcription. The\r\ncollaborators initiated optimization of this nanopore-based approach. However, current\r\ntechnological limitations still constrain the reliable detection of modified nucleotides.\r\nThe project also examined the impact of RNA editing on RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target\r\nof ADAR1's editing activity is RNA derived from repetitive elements present in the genome,\r\nparticularly Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was successfully established. This was\r\nachieved through the testing of different RNA variants and the evaluation of filament\r\nformation using binding techniques and electron microscopy imaging. This groundwork has\r\nset the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch that has provided new insights into MDA5's interaction with dsRNA, it is essential to\r\nrevise the experimental setup to integrate these findings before moving forward with the\r\nCryoEM sample analysis."}],"date_published":"2024-10-29T00:00:00Z","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-045-9"]},"language":[{"iso":"eng"}],"citation":{"ama":"Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>","ieee":"B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,” Institute of Science and Technology Austria, 2024.","apa":"Kaczmarek, B. M. (2024). <i>Biochemical and structural insights into ADAR1 RNA editing</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>","chicago":"Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>.","short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024.","ista":"Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria.","mla":"Kaczmarek, Beata M. <i>Biochemical and Structural Insights into ADAR1 RNA Editing</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>."},"supervisor":[{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky","full_name":"Bernecky, Carrie A"}],"year":"2024","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Biochemical and structural insights into ADAR1 RNA editing","author":[{"last_name":"Kaczmarek","full_name":"Kaczmarek, Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","first_name":"Beata M"}],"degree_awarded":"PhD","date_updated":"2026-04-07T13:23:59Z","has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"publisher":"Institute of Science and Technology Austria","_id":"18477","day":"29","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","month":"10","file":[{"access_level":"closed","embargo_to":"open_access","relation":"source_file","creator":"bkaczmar","date_updated":"2025-10-29T23:30:02Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"18485","file_name":"20241029_PhD_thesis_BKaczmarek.docx","checksum":"2053294ea4d770c495e4cc501e2a218b","file_size":23136626,"date_created":"2024-10-29T11:56:36Z"},{"file_id":"18486","file_name":"20241029_PhD_thesis_BKaczmarek.pdf","date_created":"2024-10-29T11:56:44Z","file_size":11707360,"checksum":"8ce857a4cd44b776791eaf180ac9dbb3","relation":"main_file","access_level":"open_access","embargo":"2025-10-29","date_updated":"2025-10-29T23:30:02Z","content_type":"application/pdf","creator":"bkaczmar"}],"corr_author":"1","type":"dissertation","publication_status":"published","page":"124","oa":1,"ddc":["572"],"status":"public"},{"degree_awarded":"PhD","date_updated":"2026-04-07T13:20:44Z","OA_place":"publisher","author":[{"orcid":"0000-0003-1581-881X","first_name":"Kristina","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","full_name":"Lukic, Kristina","last_name":"Lukic"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku'amide B","citation":{"apa":"Lukic, K. (2024). <i>Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17319\">https://doi.org/10.15479/at:ista:17319</a>","mla":"Lukic, Kristina. <i>Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17319\">10.15479/at:ista:17319</a>.","ista":"Lukic K. 2024. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. Institute of Science and Technology Austria.","short":"K. Lukic, Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B, Institute of Science and Technology Austria, 2024.","chicago":"Lukic, Kristina. “Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17319\">https://doi.org/10.15479/at:ista:17319</a>.","ieee":"K. Lukic, “Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B,” Institute of Science and Technology Austria, 2024.","ama":"Lukic K. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17319\">10.15479/at:ista:17319</a>"},"supervisor":[{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"year":"2024","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"This thesis comprises two distinct projects, each offering unique insights into fundamental\r\ncellular processes. While distinct in their focus, these different perspectives have a common\r\ntheme: chemiosmotic theory and utilisation of the proton gradient for driving the essential\r\nprocesses like auxin efflux and ATP synthesis, effectively bridging the membrane protein\r\nstructure and function from the realms of plant biology and cellular bioenergetics.\r\nThe first project of this thesis centres on the characterisation of PIN proteins, a class of\r\ntransmembrane transporters pivotal in the regulation of auxin transport and distribution in\r\nplants. PINs form a conserved and phylogenetically abundant group of transporters present in\r\nland plants and certain algae. Despite their great importance, they were one of the few elusive\r\nproteins essential for plant development not to be structurally and mechanistically\r\ncharacterised since their discovery almost 30 years ago. This work aimed to uncover the\r\nstructural and functional dynamics of the PIN protein-mediated auxin transport using an array\r\nof experimental techniques, including protein purification, biochemical assays and structural\r\nanalysis. Through an exhaustive screening process that took several years and included testing\r\ndifferent PIN homologues, expression systems, constructs, and purification conditions, we\r\ndeveloped a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein.\r\nMoreover, utilising biophysical methods and buffer screening, we demonstrated that PIN8\r\nexhibits detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and 6.0)\r\nbeing optimal for the stability of the protein. Using SEC-MALS and crosslinking, we\r\ndetermined that PIN8 forms dimers, which was confirmed by our structural studies. We\r\nobtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently published structures,\r\nour map implies major pH-dependent conformational changes and possibly utilisation of the\r\nproton gradient in the transport mechanism.\r\nThe subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental\r\nto cellular energy metabolism. Through an approach integrating biochemical assays and\r\nstructural analysis, this research aimed to unveil the molecular mechanism of inhibition of ATP\r\nsynthase by yaku´amide, a bioactive compound with potential therapeutic implications. Using\r\nsubmitochondrial particles and purified F1Fo-ATP synthase, we demonstrated that, contrary to\r\npublished data, yaku´amide inhibits both ATP hydrolysis and ATP synthesis reactions.\r\nMoreover, we found that yaku´amide inhibitory activity is proton motive force (pmf)\r\ndependent, with lower inhibition in a more coupled system. Utilising cryo-EM, we obtained\r\nmaps and models for the three main rotational states of murine ATP synthase (State 1 at 3.0 Å,\r\n8\r\nState 2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in our maps;\r\nhowever, we cannot definitively determine the exact mechanism of yaku amide’s inhibition on\r\nthe protein due to either resolution limits or suboptimal binding of the inhibitor."}],"date_published":"2024-07-26T00:00:00Z","department":[{"_id":"LeSa"},{"_id":"GradSch"}],"alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:17319","date_created":"2024-07-26T09:05:55Z","file_date_updated":"2025-01-26T23:30:04Z","status":"public","ddc":["580"],"oa":1,"page":"224","publication_status":"published","type":"dissertation","month":"07","file":[{"checksum":"95517e697ea6a87e267e649cad560989","date_created":"2024-07-26T13:14:24Z","file_size":24639084,"file_name":"Thesis_Kristina_Lukic.pdf","file_id":"17320","content_type":"application/pdf","date_updated":"2025-01-26T23:30:04Z","embargo":"2025-01-26","creator":"cchlebak","relation":"main_file","access_level":"open_access"},{"access_level":"closed","relation":"source_file","embargo_to":"open_access","creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-01-26T23:30:04Z","file_id":"17321","checksum":"74325746a9a05078fb9935dbf2aef752","date_created":"2024-07-26T13:14:50Z","file_size":96334272,"file_name":"Thesis_Kristina_Lukic.docx"}],"corr_author":"1","oa_version":"Published Version","_id":"17319","day":"26","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1"},{"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"day":"02","_id":"15352","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","file":[{"file_id":"15354","checksum":"095817a6c944954ac3f277e547031a33","file_size":5936142,"date_created":"2024-05-02T12:26:13Z","file_name":"Murmann_Thesis_final_2024_2.pdf","access_level":"open_access","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","embargo":"2025-05-02","date_updated":"2025-05-02T22:30:04Z"},{"file_id":"15355","checksum":"43b632255372973a437ac87739cfd4db","date_created":"2024-05-02T12:37:56Z","file_size":20645510,"file_name":"Murmann_Thesis_final_2024.zip","access_level":"closed","relation":"source_file","embargo_to":"open_access","creator":"cchlebak","content_type":"application/x-zip-compressed","date_updated":"2025-05-02T22:30:04Z"}],"month":"05","corr_author":"1","publication_status":"published","type":"dissertation","page":"54","ddc":["570"],"status":"public","oa":1,"file_date_updated":"2025-05-02T22:30:04Z","date_created":"2024-05-02T08:31:38Z","doi":"10.15479/at:ista:15352","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"alternative_title":["ISTA Master's Thesis"],"date_published":"2024-05-02T00:00:00Z","abstract":[{"text":"Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological\r\ndisorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common\r\nassumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have\r\nproven unsuccessful in treating seizure progression. One potential reason could be that the therapies\r\nonly focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons\r\nhave been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship\r\nbetween microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo\r\nstudies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term\r\nconsequences on microglia activity leaving out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to\r\ndirectly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,\r\nwe take advantage of the kainic acid (KA) model, which represents similar neuropathological and\r\nelectroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we\r\ninvestigated whether these changes also reached the primary visual cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that microglia changed their morphology at high doses\r\nof KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,\r\nour initial attempts under the microscope suffered from extensive electrical noise, which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia, we had to optimize the imaging parameters, so that we would be able to detect microglial\r\nprocesses in a sufficient resolution to track their process changes. Finally, we combined both\r\nmethodologies with the KA model. We confirmed that KA induced seizure activity and found first\r\nindication that those correlate with microglia volume changes.\r\nOverall, we have developed a first methodological approach, which allows the analysis of the acute\r\neffects of seizure onset on microglia. Future studies will have to continue to optimize the drift during\r\nimaging recording and the post-image analysis. ","lang":"eng"}],"publication_identifier":{"issn":["2791-4585"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","supervisor":[{"full_name":"Siegert, Sandra","last_name":"Siegert","first_name":"Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"year":"2024","citation":{"mla":"Murmann, Julie Stefanie. <i>Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>.","short":"J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and Technology Austria, 2024.","chicago":"Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>.","ista":"Murmann JS. 2024. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria.","apa":"Murmann, J. S. (2024). <i>Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>","ieee":"J. S. Murmann, “Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and Technology Austria, 2024.","ama":"Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>"},"author":[{"full_name":"Murmann, Julie Stefanie","last_name":"Murmann","first_name":"Julie Stefanie","id":"1d390868-f128-11eb-9611-a0ca5f7833b5"}],"title":"Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","date_updated":"2026-04-07T13:05:00Z","degree_awarded":"MS"},{"department":[{"_id":"GradSch"},{"_id":"MaRo"}],"alternative_title":["ISTA Master's Thesis"],"abstract":[{"lang":"eng","text":"Recent advancements in molecular diagnostic techniques have enabled the collection of\r\nmultiple types of omics data from patients, including genomics, epigenomics, proteomics,\r\nand transcriptomics. However, we lack effective methods for integrating all these different\r\ndata types and combining them with clinical outcomes to study the molecular mechanisms\r\nthat govern pathological phenotypes. We present multi-omics BayesW, a penalized Bayesian\r\nregression method that can handle general omics data for survival analysis of time-to-event\r\nphenotypes. Our method can: (1) accommodate incomplete data by allowing censored\r\nindividuals, (2) use continuous time-to-event data to test associations of markers with a\r\nphenotype and (3) estimate effects jointly while allowing for independent groups of biological\r\nmarkers. Extensive simulations using planted signals on real data demonstrate that our model\r\naccurately retrieves the true parameters of the model while controlling for false discoveries\r\nand maintaining the expected prediction accuracy. We address data correlations by estimating\r\nthe effects jointly, even between omic groups, while also estimating the individual variance\r\nexplained by each group. We apply our model to two datasets. Using 18,000 individuals from\r\nthe Generation Scotland study we model the association of time at onset of Type 2 Diabetes,\r\nStroke, Ischemic Disease, and Osteoarthritis from baseline study entry, with 831,724 CpG\r\nmethylation probes. We find that large proportions of variation in disease onset times can\r\nbe attributed to methylation as measured in whole blood at baseline in individuals without\r\ndisease symptoms. We then apply our model to The Cancer Genome Atlas (TCGA) pan-cancer\r\ndataset, in which we use 5 types of omics: copy number variation, epigenetics, somatic\r\nmutations, miRNA, and gene expression. For cancer survival age-at-onset we find that, when\r\nfitting the 5 groups together, almost all variation attributable to \"omics\" data is explained by\r\nDNA methylation. When considering progression times, both methylation and gene expression\r\nexplain a large part of the variance. We found 2 genes that are significantly associated (95%\r\nposterior inclusion probability) with cancer survival time, conditional on all other genome-wide\r\nomics data variation. Owing to the vast variability of mechanisms characterizing different\r\ncancers, there are likely few specific genes with a strong signal in a pan-cancer setting. Taken\r\ntogether, we showed the applicability of our multi-omics BayesW model to a wide-range of\r\nbiological questions in multi-omics data.\r\n"}],"date_published":"2024-08-13T00:00:00Z","file_date_updated":"2025-02-14T23:30:03Z","doi":"10.15479/at:ista:17368","date_created":"2024-08-02T10:52:40Z","OA_place":"publisher","author":[{"id":"e0ae4864-133f-11ed-8f02-adaa8dd27540","first_name":"Ariadna","last_name":"Villanueva Marijuan","full_name":"Villanueva Marijuan, Ariadna"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Bayesian linear regression for analyzing general omics data with time-to-event phenotypes","degree_awarded":"MS","date_updated":"2026-04-07T13:03:41Z","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2791-4585"]},"citation":{"ama":"Villanueva Marijuan A. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17368\">10.15479/at:ista:17368</a>","ieee":"A. Villanueva Marijuan, “Bayesian linear regression for analyzing general omics data with time-to-event phenotypes,” Institute of Science and Technology Austria, 2024.","short":"A. Villanueva Marijuan, Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes, Institute of Science and Technology Austria, 2024.","chicago":"Villanueva Marijuan, Ariadna. “Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17368\">https://doi.org/10.15479/at:ista:17368</a>.","ista":"Villanueva Marijuan A. 2024. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria.","mla":"Villanueva Marijuan, Ariadna. <i>Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17368\">10.15479/at:ista:17368</a>.","apa":"Villanueva Marijuan, A. (2024). <i>Bayesian linear regression for analyzing general omics data with time-to-event phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17368\">https://doi.org/10.15479/at:ista:17368</a>"},"supervisor":[{"orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","last_name":"Robinson"}],"year":"2024","_id":"17368","day":"13","oa_version":"Published Version","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","page":"60","status":"public","ddc":["610"],"oa":1,"corr_author":"1","month":"08","file":[{"file_id":"17433","file_name":"Masters_thesis_AriadnaVillanueva.pdf","file_size":13052436,"checksum":"0c2daa174609f0c00919dccc5701d375","date_created":"2024-08-14T11:51:24Z","access_level":"open_access","relation":"main_file","creator":"avillanu","date_updated":"2025-02-14T23:30:03Z","embargo":"2025-02-14","content_type":"application/pdf"},{"date_created":"2024-08-14T11:51:57Z","checksum":"e9ed4465dfa539ac4c3a8d4d0b6271a1","file_size":45642547,"file_name":"Masters thesis-AriadnaVillanueva.zip","file_id":"17434","content_type":"application/zip","date_updated":"2025-02-14T23:30:03Z","creator":"avillanu","embargo_to":"open_access","relation":"source_file","access_level":"closed"}],"type":"dissertation","publication_status":"published","keyword":["Epigenetics","Multi-omics","Bayesian regression"]}]