[{"publisher":"Institute of Science and Technology Austria","corr_author":"1","oa":1,"author":[{"first_name":"Yunzhe","id":"41cb05d3-f128-11eb-9611-e4e2b3cfba31","full_name":"Li, Yunzhe","last_name":"Li"}],"acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"CampIT"}],"year":"2026","date_updated":"2026-07-20T14:58:23Z","title":"Spectral rigidity and nonrigidity of dynamical systems","doi":"10.15479/AT-ISTA-22255","has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","degree_awarded":"PhD","_id":"22255","date_created":"2026-07-08T12:44:31Z","supervisor":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin","full_name":"Kaloshin, Vadim"}],"OA_place":"publisher","article_processing_charge":"No","month":"07","department":[{"_id":"GradSch"},{"_id":"VaKa"}],"publication_status":"published","fulldoi":"https://doi.org/10.15479/AT-ISTA-22255","date_published":"2026-07-11T00:00:00Z","type":"dissertation","related_material":{"record":[{"status":"public","id":"22340","relation":"part_of_dissertation"},{"status":"public","id":"22341","relation":"part_of_dissertation"}]},"ddc":["515"],"license":"https://creativecommons.org/licenses/by/4.0/","page":"131","doi_confirm":"1","ec_funded":1,"abstract":[{"text":"This thesis studies spectral rigidity and nonrigidity phenomena in dynamical systems. The central question is whether a dynamical system can be determined, up to a natural conjugacy, from its spectrum. We consider three related spectra: the length spectrum, the action spectrum, and the Lyapunov spectrum.\r\n\r\nThe first part of the thesis concerns Liouville metrics on the two-dimensional torus. It is a long-standing folklore conjecture that Liouville metrics are the only integrable metrics on the torus. We prove a length-spectral rigidity result for linear conformal deformations of Liouville metrics by exploiting the dynamical properties of the rational tori -- analogues of the resonant convex caustics in billiards. We also establish a complementary classification result showing that marked-length-isospectral Liouville metrics are characterized by rearrangements of the one-dimensional functions appearing in their conformal factors, generalizing a theorem of Abbondandolo-Mazzucchelli. In particular, the second result gives nonrigidity examples within the class of Liouville metrics.\r\n\r\nThe second part of the thesis studies the standard map from the viewpoint of action and Lyapunov spectra. We construct nontrivial deformations of the standard map which preserve the symplectic actions (respectively, the Lyapunov exponents) of infinitely many periodic orbits accumulating on an invariant curve. The proof combines a resonant normal form construction with Picard iteration schemes to obtain a sequence of periodic orbits accumulating on an invariant curve with a Liouville rotation number. Within the resonant normal forms we capture the dependence of these periodic orbits on the resonant Fourier coefficients of the dynamics on the invariant curve and, using the contraction mapping principle, obtain a suitable deformation achieving the prescribed spectral data associated with this sequence of orbits. The result can be viewed as a symplectic twist-map analogue of a length-spectral nonrigidity phenomenon for Riemannian manifolds and convex billiards, and it motivates the existence problem for similar 'partially length-isospectral' deformations of strictly convex billiard tables.\r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"day":"11","project":[{"grant_number":"885707","name":"Spectral rigidity and integrability for billiards and geodesic flows","call_identifier":"H2020","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A"}],"citation":{"ieee":"Y. Li, “Spectral rigidity and nonrigidity of dynamical systems,” Institute of Science and Technology Austria, 2026.","chicago":"Li, Yunzhe. “Spectral Rigidity and Nonrigidity of Dynamical Systems.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22255\">https://doi.org/10.15479/AT-ISTA-22255</a>.","short":"Y. Li, Spectral Rigidity and Nonrigidity of Dynamical Systems, Institute of Science and Technology Austria, 2026.","apa":"Li, Y. (2026). <i>Spectral rigidity and nonrigidity of dynamical systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22255\">https://doi.org/10.15479/AT-ISTA-22255</a>","mla":"Li, Yunzhe. <i>Spectral Rigidity and Nonrigidity of Dynamical Systems</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22255\">10.15479/AT-ISTA-22255</a>.","ista":"Li Y. 2026. Spectral rigidity and nonrigidity of dynamical systems. Institute of Science and Technology Austria.","ama":"Li Y. Spectral rigidity and nonrigidity of dynamical systems. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22255\">10.15479/AT-ISTA-22255</a>"},"publication_identifier":{"issn":["2663-337X"]},"file":[{"content_type":"application/pdf","date_created":"2026-07-14T10:48:45Z","checksum":"8201cb5a427656a41828ecde8a85c04b","file_name":"2026_Li_Yunzhe_Thesis.pdf","creator":"yli","file_id":"22337","relation":"main_file","file_size":1260717,"date_updated":"2026-07-14T10:48:45Z","access_level":"open_access"},{"file_name":"2026_Li_Yunzhe_Thesis.zip","checksum":"19ee8461ed77f5b7980fc9461f778b6f","date_created":"2026-07-14T11:07:18Z","content_type":"application/x-zip-compressed","access_level":"closed","date_updated":"2026-07-20T14:00:33Z","file_size":418752,"relation":"source_file","file_id":"22339","creator":"yli"}],"file_date_updated":"2026-07-20T14:00:33Z","language":[{"iso":"eng"}],"acknowledgement":"The financial support of the ERC grant SPERIG #885707 is gratefully acknowledged.\r\n","oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","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"}},{"degree_awarded":"PhD","_id":"22873","title":"Biological functionality without biochemistry: Designing nanomachines for target behavior","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"year":"2026","date_updated":"2026-09-18T11:28:29Z","doi":"10.15479/AT-ISTA-22873","status":"public","has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","author":[{"id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2","first_name":"Andreas","orcid":"0000-0002-0997-5678","last_name":"Ehrmann","full_name":"Ehrmann, Andreas"}],"corr_author":"1","date_published":"2026-09-04T00:00:00Z","type":"dissertation","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"22893"},{"id":"22892","relation":"part_of_dissertation","status":"public"}]},"das_tickbox":"0","fulldoi":"https://doi.org/10.15479/AT-ISTA-22873","OA_place":"publisher","article_processing_charge":"No","month":"09","department":[{"_id":"GradSch"},{"_id":"CaGo"},{"_id":"EdHa"}],"publication_status":"published","date_created":"2026-09-09T12:18:24Z","supervisor":[{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"researchdata_availability":"upon request","project":[{"grant_number":"PAT 8537123","name":"Functional bio-inspired nanomachines from sticky colloids","_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d"}],"alternative_title":["ISTA Thesis"],"supplementarymaterial":"not applicable","day":"04","doi_confirm":"1","ddc":["530","600","621","004","005"],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","page":"168","oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"language":[{"iso":"eng"}],"acknowledgement":"I acknowledge funding by the Austrian Science Fund (FWF) [10.55776/PAT8537123].","file":[{"date_created":"2026-09-11T07:23:57Z","checksum":"a5e3d79e0e5f3f4fb3c414e48116dc9e","file_name":"2026_Ehrmann_Andreas_Thesis.pdf","content_type":"application/pdf","embargo":"2027-01-15","date_updated":"2026-09-17T08:59:39Z","access_level":"closed","embargo_to":"open_access","creator":"aehrmann","relation":"main_file","file_id":"22901","file_size":14782662},{"content_type":"application/zip","date_created":"2026-09-11T07:24:14Z","file_name":"thesis_latex_files.zip","checksum":"0235b9c52fee0c97f402f1c3d4efc1eb","creator":"aehrmann","file_size":155228,"relation":"source_file","description":"All LaTeX files to compile my PhD Thesis.","file_id":"22902","date_updated":"2026-09-11T07:24:14Z","access_level":"closed"}],"file_date_updated":"2026-09-17T08:59:39Z","citation":{"chicago":"Ehrmann, Andreas. “Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22873\">https://doi.org/10.15479/AT-ISTA-22873</a>.","ieee":"A. Ehrmann, “Biological functionality without biochemistry: Designing nanomachines for target behavior,” Institute of Science and Technology Austria, 2026.","short":"A. Ehrmann, Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior, Institute of Science and Technology Austria, 2026.","apa":"Ehrmann, A. (2026). <i>Biological functionality without biochemistry: Designing nanomachines for target behavior</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22873\">https://doi.org/10.15479/AT-ISTA-22873</a>","mla":"Ehrmann, Andreas. <i>Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22873\">10.15479/AT-ISTA-22873</a>.","ista":"Ehrmann A. 2026. Biological functionality without biochemistry: Designing nanomachines for target behavior. Institute of Science and Technology Austria.","ama":"Ehrmann A. Biological functionality without biochemistry: Designing nanomachines for target behavior. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22873\">10.15479/AT-ISTA-22873</a>"},"keyword":["PhD Thesis","functional nanomachines","biological functionality","nanotechnology","energy delivery","target behavior","dynamics","design principles","optimization","differentiable statistical physics","machine learning"],"publication_identifier":{"isbn":["978-3-99078-092-3"],"issn":["2663-337X"]}},{"project":[{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"},{"name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"}],"day":"18","alternative_title":["ISTA Thesis"],"doi_confirm":"1","page":"289","ddc":["580"],"license":"https://creativecommons.org/licenses/by-sa/4.0/","oa_version":"Published Version","tmp":{"image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","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)"},"acknowledgement":"European Research Council (101142681 CYNIPS), Cyclic nucleotides as second messengers \r\nin plants, DOI: https://doi.org/10.3030/101142681 \r\nAustrian Science Fund (P 37051-B), Guanylate cyclase activity of TIR1/AFBs auxin receptors, \r\nDOI: https://doi.org/10.55776/P37051 ","language":[{"iso":"eng"}],"file_date_updated":"2026-10-20T11:48:37Z","file":[{"creator":"mranduch","file_id":"23176","relation":"source_file","file_size":89544771,"date_updated":"2026-10-20T11:48:37Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2026-10-20T09:17:28Z","checksum":"4ace20ba4f1bb0f8dcc3f8eb45eb68fa","file_name":"2026_Marek_Randuch_Thesis.docx"},{"embargo":"2027-10-20","content_type":"application/pdf","file_name":"2026_Marek_Randuch_Thesis.pdf","checksum":"fc630c7e8d795e7f13000cbb428424b3","date_created":"2026-10-20T09:17:20Z","file_size":28321059,"relation":"main_file","file_id":"23177","embargo_to":"open_access","creator":"mranduch","access_level":"closed","date_updated":"2026-10-20T11:48:37Z"}],"publication_identifier":{"issn":["2663-337X"]},"citation":{"ieee":"M. Randuch, “Fast growth responses in plants: Growth regulation and phospho-proteomic ,” Institute of Science and Technology Austria, 2026.","chicago":"Randuch, Marek. “Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic .” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-23145\">https://doi.org/10.15479/AT-ISTA-23145</a>.","short":"M. Randuch, Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic , Institute of Science and Technology Austria, 2026.","apa":"Randuch, M. (2026). <i>Fast growth responses in plants: Growth regulation and phospho-proteomic </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-23145\">https://doi.org/10.15479/AT-ISTA-23145</a>","mla":"Randuch, Marek. <i>Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic </i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-23145\">10.15479/AT-ISTA-23145</a>.","ista":"Randuch M. 2026. Fast growth responses in plants: Growth regulation and phospho-proteomic . Institute of Science and Technology Austria.","ama":"Randuch M. Fast growth responses in plants: Growth regulation and phospho-proteomic . 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-23145\">10.15479/AT-ISTA-23145</a>"},"_id":"23145","degree_awarded":"PhD","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","date_updated":"2026-10-22T09:15:44Z","year":"2026","title":"Fast growth responses in plants: Growth regulation and phospho-proteomic ","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"},{"_id":"Bio"}],"doi":"10.15479/AT-ISTA-23145","author":[{"full_name":"Randuch, Marek","last_name":"Randuch","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek"}],"corr_author":"1","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"id":"12291","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"21763"},{"id":"23175","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"23174","status":"public"},{"id":"20656","relation":"part_of_dissertation","status":"public"}]},"date_published":"2026-10-18T00:00:00Z","type":"dissertation","fulldoi":"https://doi.org/10.15479/AT-ISTA-23145","publication_status":"published","article_processing_charge":"No","OA_place":"publisher","month":"10","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"date_created":"2026-10-16T17:14:40Z","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}]},{"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-070-1"]},"citation":{"ama":"Ishida S. Symplectic-prequantum structures and dynamics on the codimension-2 shape space. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20551\">10.15479/AT-ISTA-20551</a>","ista":"Ishida S. 2025. Symplectic-prequantum structures and dynamics on the codimension-2 shape space. Institute of Science and Technology Austria.","mla":"Ishida, Sadashige. <i>Symplectic-Prequantum Structures and Dynamics on the Codimension-2 Shape Space</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20551\">10.15479/AT-ISTA-20551</a>.","apa":"Ishida, S. (2025). <i>Symplectic-prequantum structures and dynamics on the codimension-2 shape space</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20551\">https://doi.org/10.15479/AT-ISTA-20551</a>","short":"S. Ishida, Symplectic-Prequantum Structures and Dynamics on the Codimension-2 Shape Space, Institute of Science and Technology Austria, 2025.","chicago":"Ishida, Sadashige. “Symplectic-Prequantum Structures and Dynamics on the Codimension-2 Shape Space.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20551\">https://doi.org/10.15479/AT-ISTA-20551</a>.","ieee":"S. Ishida, “Symplectic-prequantum structures and dynamics on the codimension-2 shape space,” Institute of Science and Technology Austria, 2025."},"file_date_updated":"2025-11-10T08:45:05Z","file":[{"file_name":"Thesis_tex.zip","checksum":"4eef80afcb67691cbb6549c4756fa534","date_created":"2025-11-01T18:26:14Z","content_type":"application/zip","access_level":"open_access","date_updated":"2025-11-01T18:26:14Z","file_size":72487812,"file_id":"20583","relation":"source_file","creator":"sishida"},{"date_updated":"2025-11-10T08:45:05Z","access_level":"open_access","success":1,"creator":"sishida","file_size":8945141,"file_id":"20623","relation":"main_file","date_created":"2025-11-10T08:45:05Z","file_name":"Thesis_Sadashige_Ishida_PDFA.pdf","checksum":"1e5a557900bf2dce01966b211b15d0fe","content_type":"application/pdf"}],"acknowledgement":"Projects contained in this thesis were financially supported in part by the\r\nEuropean Research Council with grants 1. ERC Consolidator Grant 101045083 CoDiNA,\r\nand 2. the European Union’s Horizon 2020 research and innovation programme under grant\r\nagreement No. 638176.","language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","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"},"oa_version":"Published Version","page":"141","ddc":["516"],"ec_funded":1,"day":"31","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The space of codimension-2 shapes, such as curves in 3D and surfaces in 4D, is an infinite-dimensional manifold. This thesis explores geometric structures and dynamics on this space, with emphasis on their implications for physics, particularly hydrodynamics.\r\n\r\nOur investigation ranges from theoretical studies of infinite-dimensional symplectic and prequantum geometry to numerical computation of the time evolution of shapes. The thesis presents four main contributions.\r\n\r\nIn the first part, we introduce implicit representations of codimension-2 shapes using a class of complex-valued functions, and prove that the space of these implicit representations forms a prequantum bundle over the codimension-2 shape space. This reveals a new geometric interpretation of the canonical symplectic structure on the codimension-2 shape space.\r\n\r\nIn the second part, we use implicit representations to develop a simulation method for the dynamics of space curves. To handle chaotic systems such as vortex filaments in hydrodynamics, we exploit the infinite degrees of freedom, hidden in both the configuration and dynamics of implicit representations.\r\n\r\nIn the third part, we introduce new symplectic structures on the space of space curves, which generalize the only previously known symplectic structure on this space, allowing for new Hamiltonian dynamics of space curves.\r\n\r\nIn the fourth part, we apply a symplectic viewpoint to a differential geometric problem with practical applications. We derive a new area formula for spherical polygons via prequantization. "}],"project":[{"call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"date_created":"2025-10-27T10:28:52Z","supervisor":[{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"},{"full_name":"Chern, Albert","last_name":"Chern","first_name":"Albert"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"article_processing_charge":"No","OA_place":"publisher","month":"10","fulldoi":"https://doi.org/10.15479/AT-ISTA-20551","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12431"},{"id":"20580","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"17361","relation":"part_of_dissertation"},{"status":"public","id":"12846","relation":"part_of_dissertation"}]},"date_published":"2025-10-31T00:00:00Z","type":"dissertation","oa":1,"author":[{"last_name":"Ishida","full_name":"Ishida, Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige","orcid":"0000-0002-3121-3100"}],"corr_author":"1","publisher":"Institute of Science and Technology Austria","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","doi":"10.15479/AT-ISTA-20551","year":"2025","acknowledged_ssus":[{"_id":"CampIT"}],"date_updated":"2026-10-02T11:17:04Z","title":"Symplectic-prequantum structures and dynamics on the codimension-2 shape space","degree_awarded":"PhD","_id":"20551"},{"publisher":"Institute of Science and Technology Austria","oa":1,"corr_author":"1","author":[{"full_name":"Maslov, Mikhail","last_name":"Maslov","orcid":"0000-0003-4074-2570","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"doi":"10.15479/at:ista:19048","date_updated":"2026-10-02T11:36:24Z","acknowledged_ssus":[{"_id":"CampIT"},{"_id":"E-Lib"},{"_id":"SSU"}],"year":"2025","title":"Emergent physics of rotating quantum impurities in many-body environments","status":"public","has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","_id":"19048","date_created":"2025-02-18T01:41:27Z","supervisor":[{"orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"}],"department":[{"_id":"GradSch"},{"_id":"MiLe"}],"article_processing_charge":"No","OA_place":"publisher","month":"02","publication_status":"published","fulldoi":"https://doi.org/10.15479/at:ista:19048","type":"dissertation","date_published":"2025-02-18T00:00:00Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"10845","status":"public"},{"id":"7933","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"18087","status":"public"}]},"ddc":["539","535","541"],"page":"86","ec_funded":1,"alternative_title":["ISTA Thesis"],"abstract":[{"text":"Rotations are found in physics problems at all scales: from spatial motion of celestial bodies, to transitions between quantum states of atoms and molecules. Mathematically, they represent a fundamental class of transformations and symmetries. Unlike spatial displacements, rotational transformations in three-dimensional space  are non-commutative: the result of applying a sequence of rotations depends on the order of these operations. This feature makes the emergent physics that involves rotations rather intricate, but instrumental for studies of highly-interconnected many-body systems. In the presence of an environment, rotational properties of an object change, due to the interaction with particles of the environment. Owing to the complexity of this interaction, it can be engineered to exhibit certain properties of interest. In this Thesis, we examine several scenarios of how the rotational behavior of an impurity can be modified by interactions with its environment.","lang":"eng"}],"day":"18","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"},{"_id":"7c040762-9f16-11ee-852c-dd79eeee4ab3","name":"Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions","grant_number":"F100403"}],"citation":{"ieee":"M. Maslov, “Emergent physics of rotating quantum impurities in many-body environments,” Institute of Science and Technology Austria, 2025.","chicago":"Maslov, Mikhail. “Emergent Physics of Rotating Quantum Impurities in Many-Body Environments.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/at:ista:19048\">https://doi.org/10.15479/at:ista:19048</a>.","short":"M. Maslov, Emergent Physics of Rotating Quantum Impurities in Many-Body Environments, Institute of Science and Technology Austria, 2025.","apa":"Maslov, M. (2025). <i>Emergent physics of rotating quantum impurities in many-body environments</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:19048\">https://doi.org/10.15479/at:ista:19048</a>","mla":"Maslov, Mikhail. <i>Emergent Physics of Rotating Quantum Impurities in Many-Body Environments</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/at:ista:19048\">10.15479/at:ista:19048</a>.","ista":"Maslov M. 2025. Emergent physics of rotating quantum impurities in many-body environments. Institute of Science and Technology Austria.","ama":"Maslov M. Emergent physics of rotating quantum impurities in many-body environments. 2025. doi:<a href=\"https://doi.org/10.15479/at:ista:19048\">10.15479/at:ista:19048</a>"},"publication_identifier":{"issn":["2663-337X"]},"file":[{"file_size":7779825,"relation":"main_file","file_id":"19061","creator":"mmaslov","access_level":"open_access","date_updated":"2025-02-18T14:25:59Z","content_type":"application/pdf","file_name":"thesis_Maslov.pdf","checksum":"5822a4dd31724c512b37c658af1787ab","date_created":"2025-02-18T14:25:59Z"},{"content_type":"application/zip","checksum":"89bdce4774406d26ceca88a8bbcd6a9a","file_name":"thesis_Maslov_source.zip","date_created":"2025-02-18T14:25:59Z","file_id":"19062","relation":"source_file","file_size":14453726,"creator":"mmaslov","access_level":"open_access","date_updated":"2025-02-18T14:25:59Z"}],"file_date_updated":"2025-02-18T14:25:59Z","language":[{"iso":"eng"}],"acknowledgement":"I am grateful to the European Research Council (ERC) [10.3030/801770] and Austrian\r\nScience Fund (FWF) [10.55776/F1004] for funding my research and to the Physical\r\nReview journals for publishing it. I also want to thank the VCQ (previously CoQuS) and\r\nIQOQI for organizing wonderful networking events for the physics community in Vienna\r\nand Innsbruck, respectively. Moreover, I thank Austrian Science Fund (FWF) for the\r\ncontinuous support for quantum research.","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"oa_version":"Published Version"},{"arxiv":1,"type":"conference","date_published":"2024-12-20T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2408.17163"}],"publication_status":"published","OA_place":"repository","month":"12","article_processing_charge":"No","department":[{"_id":"DaAl"},{"_id":"MaMo"}],"OA_type":"green","conference":{"location":"Vancouver, Canada","start_date":"2024-12-09","name":"NeurIPS: Neural Information Processing Systems","end_date":"2024-12-15"},"external_id":{"arxiv":["2408.17163"]},"date_created":"2025-04-06T22:01:32Z","_id":"19518","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","title":"The iterative optimal brain surgeon: Faster sparse recovery by leveraging second-order information","acknowledged_ssus":[{"_id":"CampIT"}],"year":"2024","date_updated":"2025-05-14T11:37:10Z","corr_author":"1","oa":1,"author":[{"id":"1a5914c2-896a-11ed-bdf8-fb80621a0635","first_name":"Diyuan","last_name":"Wu","full_name":"Wu, Diyuan"},{"last_name":"Modoranu","full_name":"Modoranu, Ionut-Vlad","first_name":"Ionut-Vlad","id":"449f7a18-f128-11eb-9611-9b430c0c6333"},{"first_name":"Mher","id":"dd546b39-0804-11ed-9c55-ef075c39778d","last_name":"Safaryan","full_name":"Safaryan, Mher"},{"first_name":"Denis","last_name":"Kuznedelev","full_name":"Kuznedelev, Denis"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"intvolume":"        37","publisher":"Neural Information Processing Systems Foundation","oa_version":"Preprint","acknowledgement":"The authors thank the anonymous NeurIPS reviewers for their useful comments and feedback, the IT department from the Institute of Science and Technology Austria for the hardware support, and Weights and Biases for the infrastructure to track all our experiments. Mher Safaryan has received funding from the European Union’s Horizon 2020 research and innovation program under the Maria Skłodowska-Curie grant agreement No 101034413.","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1049-5258"]},"citation":{"apa":"Wu, D., Modoranu, I.-V., Safaryan, M., Kuznedelev, D., &#38; Alistarh, D.-A. (2024). The iterative optimal brain surgeon: Faster sparse recovery by leveraging second-order information. In <i>38th Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","short":"D. Wu, I.-V. Modoranu, M. Safaryan, D. Kuznedelev, D.-A. Alistarh, in:, 38th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024.","ieee":"D. Wu, I.-V. Modoranu, M. Safaryan, D. Kuznedelev, and D.-A. Alistarh, “The iterative optimal brain surgeon: Faster sparse recovery by leveraging second-order information,” in <i>38th Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37.","chicago":"Wu, Diyuan, Ionut-Vlad Modoranu, Mher Safaryan, Denis Kuznedelev, and Dan-Adrian Alistarh. “The Iterative Optimal Brain Surgeon: Faster Sparse Recovery by Leveraging Second-Order Information.” In <i>38th Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024.","ama":"Wu D, Modoranu I-V, Safaryan M, Kuznedelev D, Alistarh D-A. The iterative optimal brain surgeon: Faster sparse recovery by leveraging second-order information. In: <i>38th Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024.","ista":"Wu D, Modoranu I-V, Safaryan M, Kuznedelev D, Alistarh D-A. 2024. The iterative optimal brain surgeon: Faster sparse recovery by leveraging second-order information. 38th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.","mla":"Wu, Diyuan, et al. “The Iterative Optimal Brain Surgeon: Faster Sparse Recovery by Leveraging Second-Order Information.” <i>38th Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024."},"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"scopus_import":"1","day":"20","abstract":[{"text":"The rising footprint of machine learning has led to a focus on imposing model\r\nsparsity as a means of reducing computational and memory costs. For deep neural\r\nnetworks (DNNs), the state-of-the-art accuracy-vs-sparsity is achieved by heuristics\r\ninspired by the classical Optimal Brain Surgeon (OBS) framework [LeCun et al.,\r\n1989, Hassibi and Stork, 1992, Hassibi et al., 1993], which leverages loss curvature\r\ninformation to make better pruning decisions. Yet, these results still lack a solid\r\ntheoretical understanding, and it is unclear whether they can be improved by\r\nleveraging connections to the wealth of work on sparse recovery algorithms. In this\r\npaper, we draw new connections between these two areas and present new sparse\r\nrecovery algorithms inspired by the OBS framework that comes with theoretical\r\nguarantees under reasonable assumptions and have strong practical performance.\r\nSpecifically, our work starts from the observation that we can leverage curvature\r\ninformation in OBS-like fashion upon the projection step of classic iterative sparse\r\nrecovery algorithms such as IHT. We show for the first time that this leads both\r\nto improved convergence bounds under standard assumptions. Furthermore, we\r\npresent extensions of this approach to the practical task of obtaining accurate sparse\r\nDNNs, and validate it experimentally at scale for Transformer-based models on\r\nvision and language tasks.","lang":"eng"}],"alternative_title":["Advances in Neural Information Processing Systems"],"volume":37,"ec_funded":1,"publication":"38th Conference on Neural Information Processing Systems"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","status":"public","year":"2024","acknowledged_ssus":[{"_id":"CampIT"}],"date_updated":"2026-10-01T09:33:07Z","title":"Error feedback can accurately compress preconditioners","_id":"18975","author":[{"first_name":"Ionut-Vlad","id":"449f7a18-f128-11eb-9611-9b430c0c6333","last_name":"Modoranu","full_name":"Modoranu, Ionut-Vlad"},{"last_name":"Kalinov","full_name":"Kalinov, Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","first_name":"Aleksei","orcid":"0000-0003-2189-3904"},{"last_name":"Kurtic","full_name":"Kurtic, Eldar","first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218"},{"last_name":"Frantar","full_name":"Frantar, Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","first_name":"Elias"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"corr_author":"1","oa":1,"publisher":"ML Research Press","intvolume":"       235","das_tickbox":"0","arxiv":1,"type":"conference","date_published":"2024-07-30T00:00:00Z","external_id":{"arxiv":["2306.06098"]},"conference":{"location":"Vienna, Austria","start_date":"2024-07-21","end_date":"2024-07-27","name":"ICML: International Conference on Machine Learning"},"date_created":"2025-01-30T07:53:22Z","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.06098","open_access":"1"}],"OA_place":"repository","article_processing_charge":"No","month":"07","OA_type":"green","department":[{"_id":"DaAl"}],"scopus_import":"1","day":"30","abstract":[{"lang":"eng","text":"Leveraging second-order information about the loss at the scale of deep networks is one of the main lines of approach for improving the performance of current optimizers for deep learning. Yet, existing approaches for accurate full-matrix preconditioning, such as Full-Matrix Adagrad (GGT) or Matrix-Free Approximate Curvature (M-FAC) suffer from massive storage costs when applied even to small-scale models, as they must store a sliding window of gradients, whose memory requirements are multiplicative in the model dimension. In this paper, we address this issue via a novel and efficient error-feedback technique that can be applied to compress preconditioners by up to two orders of magnitude in practice, without loss of convergence. Specifically, our approach compresses the gradient information via sparsification or low-rank compression before it is fed into the preconditioner, feeding the compression error back into future iterations. Extensive experiments on deep neural networks show that this approach can compress full-matrix preconditioners to up to 99% sparsity without accuracy loss, effectively removing the memory overhead of fullmatrix preconditioners such as GGT and M-FAC."}],"alternative_title":["PMLR"],"volume":235,"supplementarymaterial":"no","researchdata_availability":"yes","page":"35910-35933","publication":"41st International Conference on Machine Learning","acknowledgement":"The authors thank Adrian Vladu, Razvan Pascanu, Alexandra Peste, Mher Safaryan for their valuable feedback, the IT department from Institute of Science and Technology Austria for the hardware support and Weights and Biases for the infrastructure to track all our experiments.","language":[{"iso":"eng"}],"oa_version":"Preprint","publication_identifier":{"eissn":["2640-3498"]},"citation":{"ama":"Modoranu I-V, Kalinov A, Kurtic E, Frantar E, Alistarh D-A. Error feedback can accurately compress preconditioners. In: <i>41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:35910-35933.","mla":"Modoranu, Ionut-Vlad, et al. “Error Feedback Can Accurately Compress Preconditioners.” <i>41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 35910–33.","ista":"Modoranu I-V, Kalinov A, Kurtic E, Frantar E, Alistarh D-A. 2024. Error feedback can accurately compress preconditioners. 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 35910–35933.","short":"I.-V. Modoranu, A. Kalinov, E. Kurtic, E. Frantar, D.-A. Alistarh, in:, 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 35910–35933.","apa":"Modoranu, I.-V., Kalinov, A., Kurtic, E., Frantar, E., &#38; Alistarh, D.-A. (2024). Error feedback can accurately compress preconditioners. In <i>41st International Conference on Machine Learning</i> (Vol. 235, pp. 35910–35933). Vienna, Austria: ML Research Press.","chicago":"Modoranu, Ionut-Vlad, Aleksei Kalinov, Eldar Kurtic, Elias Frantar, and Dan-Adrian Alistarh. “Error Feedback Can Accurately Compress Preconditioners.” In <i>41st International Conference on Machine Learning</i>, 235:35910–33. ML Research Press, 2024.","ieee":"I.-V. Modoranu, A. Kalinov, E. Kurtic, E. Frantar, and D.-A. Alistarh, “Error feedback can accurately compress preconditioners,” in <i>41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 35910–35933."}},{"publication_identifier":{"issn":["1049-5258"]},"citation":{"chicago":"Modoranu, Ionut-Vlad, Mher Safaryan, Grigory Malinovsky, Eldar Kurtic, Thomas Robert, Peter Richtárik, and Dan-Adrian Alistarh. “MICROADAM: Accurate Adaptive Optimization with Low Space Overhead and Provable Convergence.” In <i>38th Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024. <a href=\"https://doi.org/10.52202/079017-0001\">https://doi.org/10.52202/079017-0001</a>.","ieee":"I.-V. Modoranu <i>et al.</i>, “MICROADAM: Accurate adaptive optimization with low space overhead and provable convergence,” in <i>38th Conference on Neural Information Processing Systems</i>, 2024, vol. 37.","short":"I.-V. Modoranu, M. Safaryan, G. Malinovsky, E. Kurtic, T. Robert, P. Richtárik, D.-A. Alistarh, in:, 38th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024.","apa":"Modoranu, I.-V., Safaryan, M., Malinovsky, G., Kurtic, E., Robert, T., Richtárik, P., &#38; Alistarh, D.-A. (2024). MICROADAM: Accurate adaptive optimization with low space overhead and provable convergence. In <i>38th Conference on Neural Information Processing Systems</i> (Vol. 37). Neural Information Processing Systems Foundation. <a href=\"https://doi.org/10.52202/079017-0001\">https://doi.org/10.52202/079017-0001</a>","mla":"Modoranu, Ionut-Vlad, et al. “MICROADAM: Accurate Adaptive Optimization with Low Space Overhead and Provable Convergence.” <i>38th Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024, doi:<a href=\"https://doi.org/10.52202/079017-0001\">10.52202/079017-0001</a>.","ista":"Modoranu I-V, Safaryan M, Malinovsky G, Kurtic E, Robert T, Richtárik P, Alistarh D-A. 2024. MICROADAM: Accurate adaptive optimization with low space overhead and provable convergence. 38th Conference on Neural Information Processing Systems. , Advances in Neural Information Processing Systems, vol. 37.","ama":"Modoranu I-V, Safaryan M, Malinovsky G, et al. MICROADAM: Accurate adaptive optimization with low space overhead and provable convergence. In: <i>38th Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024. doi:<a href=\"https://doi.org/10.52202/079017-0001\">10.52202/079017-0001</a>"},"acknowledgement":"The authors thank Razvan Pascanu, Mahdi Nikdan and Soroush Tabesh for their valuable feedback, the IT department from Institute of Science and Technology Austria for the hardware support and Weights and Biases for the infrastructure to track all our experiments. Mher Safaryan has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 101034413.","language":[{"iso":"eng"}],"oa_version":"Preprint","publication":"38th Conference on Neural Information Processing Systems","ec_funded":1,"day":"20","scopus_import":"1","volume":37,"alternative_title":["Advances in Neural Information Processing Systems"],"abstract":[{"lang":"eng","text":"We propose a new variant of the Adam optimizer [Kingma and Ba, 2014] called\r\nMICROADAM that specifically minimizes memory overheads, while maintaining\r\ntheoretical convergence guarantees. We achieve this by compressing the gradient\r\ninformation before it is fed into the optimizer state, thereby reducing its memory\r\nfootprint significantly. We control the resulting compression error via a novel\r\ninstance of the classical error feedback mechanism from distributed optimization [Seide et al., 2014, Alistarh et al., 2018, Karimireddy et al., 2019] in which\r\nthe error correction information is itself compressed to allow for practical memory\r\ngains. We prove that the resulting approach maintains theoretical convergence\r\nguarantees competitive to those of AMSGrad, while providing good practical performance. Specifically, we show that MICROADAM can be implemented efficiently\r\non GPUs: on both million-scale (BERT) and billion-scale (LLaMA) models, MICROADAM provides practical convergence competitive to that of the uncompressed\r\nAdam baseline, with lower memory usage and similar running time. Our code is\r\navailable at https://github.com/IST-DASLab/MicroAdam."}],"project":[{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"external_id":{"arxiv":["2405.15593"]},"date_created":"2025-04-06T22:01:32Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.15593","open_access":"1"}],"publication_status":"published","OA_type":"green","department":[{"_id":"DaAl"}],"month":"12","article_processing_charge":"No","OA_place":"repository","fulldoi":"https://doi.org/10.52202/079017-0001","related_material":{"link":[{"url":"https://github.com/IST-DASLab/MicroAdam","relation":"software"}]},"arxiv":1,"type":"conference","date_published":"2024-12-20T00:00:00Z","author":[{"last_name":"Modoranu","full_name":"Modoranu, Ionut-Vlad","id":"449f7a18-f128-11eb-9611-9b430c0c6333","first_name":"Ionut-Vlad"},{"full_name":"Safaryan, Mher","last_name":"Safaryan","id":"dd546b39-0804-11ed-9c55-ef075c39778d","first_name":"Mher"},{"full_name":"Malinovsky, Grigory","last_name":"Malinovsky","first_name":"Grigory"},{"full_name":"Kurtic, Eldar","last_name":"Kurtic","first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218"},{"id":"de632733-1457-11f0-ae22-b5914b8c1c41","first_name":"Thomas","last_name":"Robert","full_name":"Robert, Thomas"},{"last_name":"Richtárik","full_name":"Richtárik, Peter","first_name":"Peter"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"corr_author":"1","intvolume":"        37","publisher":"Neural Information Processing Systems Foundation","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.52202/079017-0001","title":"MICROADAM: Accurate adaptive optimization with low space overhead and provable convergence","year":"2024","date_updated":"2026-10-15T09:49:27Z","acknowledged_ssus":[{"_id":"CampIT"}],"_id":"19510"},{"language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa_version":"Published Version","keyword":["Sex chromosomes","evolution","selection","sheltering"],"citation":{"ama":"Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>","mla":"Mrnjavac, Andrea. <i>Early Stages of Sex Chromosome Evolution</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>.","ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria.","short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024.","apa":"Mrnjavac, A. (2024). <i>Early stages of sex chromosome evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>","chicago":"Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>.","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024."},"publication_identifier":{"issn":["2663-337X"]},"file":[{"file_size":26870629,"file_id":"18551","relation":"source_file","creator":"amrnjava","embargo_to":"open_access","access_level":"closed","date_updated":"2025-05-11T22:30:04Z","title":"Early stages of sex chromosome evolution","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"AMrnjavac_thesis_library.docx","checksum":"3e48b163c22114ef5d5371f758668289","date_created":"2024-11-13T12:15:28Z"},{"access_level":"open_access","title":"Early stages of sex chromosome evolution","date_updated":"2025-05-11T22:30:04Z","file_id":"18552","relation":"main_file","file_size":4228766,"creator":"amrnjava","checksum":"3ead60c1b678e7dcf018043aef3b5db2","file_name":"AMrnjavac_thesis_library.pdf","date_created":"2024-11-13T12:15:54Z","embargo":"2025-05-11","content_type":"application/pdf"}],"file_date_updated":"2025-05-11T22:30:04Z","supplementarymaterial":"unclear","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. ","lang":"eng"}],"day":"11","researchdata_availability":"unclear","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ddc":["576"],"page":"181","doi_confirm":"1","fulldoi":"https://doi.org/10.15479/at:ista:18531","type":"dissertation","date_published":"2024-11-11T00:00:00Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"12521","status":"public"},{"status":"public","id":"18549","relation":"part_of_dissertation"}]},"date_created":"2024-11-11T08:40:45Z","supervisor":[{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"OA_embargo":"6","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"article_processing_charge":"No","OA_place":"publisher","month":"11","publication_status":"published","doi":"10.15479/at:ista:18531","title":"Early stages of sex chromosome evolution","date_updated":"2026-10-02T11:14:08Z","year":"2024","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"has_accepted_license":"1","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","degree_awarded":"PhD","_id":"18531","publisher":"Institute of Science and Technology Austria","corr_author":"1","oa":1,"author":[{"last_name":"Mrnjavac","full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"}]},{"file_date_updated":"2023-03-08T15:08:46Z","file":[{"file_id":"12717","relation":"source_file","file_size":23029260,"creator":"lburnett","access_level":"closed","date_updated":"2023-03-08T15:08:46Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","file_name":"Burnett_Thesis_2023.docx","date_created":"2023-03-08T15:08:46Z"},{"creator":"lburnett","file_id":"12718","relation":"main_file","file_size":11959869,"date_updated":"2023-03-08T15:08:46Z","success":1,"access_level":"open_access","content_type":"application/pdf","date_created":"2023-03-08T15:08:46Z","checksum":"cebc77705288bf4382db9b3541483cd0","file_name":"Burnett_Thesis_2023_pdfA.pdf"}],"publication_identifier":{"issn":["2663-337X"]},"citation":{"ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12716\">10.15479/at:ista:12716</a>","mla":"Burnett, Laura. <i>To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12716\">10.15479/at:ista:12716</a>.","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","apa":"Burnett, L. (2023). <i>To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12716\">https://doi.org/10.15479/at:ista:12716</a>","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12716\">https://doi.org/10.15479/at:ista:12716</a>."},"oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1,"page":"178","ddc":["599","573"],"project":[{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Circuits of Visual Attention","grant_number":"756502"}],"day":"10","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism.","lang":"eng"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"OA_place":"publisher","article_processing_charge":"No","month":"03","supervisor":[{"last_name":"Jösch","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","orcid":"0000-0002-3937-1330"}],"date_created":"2023-03-08T15:19:45Z","type":"dissertation","date_published":"2023-03-10T00:00:00Z","fulldoi":"https://doi.org/10.15479/at:ista:12716","author":[{"orcid":"0000-0002-8937-410X","first_name":"Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","full_name":"Burnett, Laura","last_name":"Burnett"}],"corr_author":"1","oa":1,"publisher":"Institute of Science and Technology Austria","_id":"12716","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","status":"public","doi":"10.15479/at:ista:12716","year":"2023","date_updated":"2026-04-07T13:25:15Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism"},{"type":"dissertation","date_published":"2023-11-30T00:00:00Z","fulldoi":"https://doi.org/10.15479/at:ista:14641","das_tickbox":"1","publication_status":"published","article_processing_charge":"No","OA_place":"publisher","month":"11","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"supervisor":[{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn"}],"date_created":"2023-12-04T13:17:37Z","degree_awarded":"PhD","_id":"14641","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","has_accepted_license":"1","date_updated":"2026-07-13T10:55:56Z","year":"2023","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"title":"Adaptive mutation in E. coli modulated by luxS","doi":"10.15479/at:ista:14641","author":[{"full_name":"Hennessey-Wesen, Mike","last_name":"Hennessey-Wesen","first_name":"Mike","id":"3F338C72-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","language":[{"iso":"eng"}],"file_date_updated":"2026-07-13T10:55:56Z","file":[{"content_type":"application/vnd.oasis.opendocument.text","file_name":"mike_thesis_v06-12-2023.odt","checksum":"4127c285b34f4bf7fb31ef24f9d14c25","date_created":"2023-12-06T13:13:26Z","file_size":46405919,"relation":"source_file","file_id":"14648","embargo_to":"open_access","creator":"mhenness","access_level":"closed","date_updated":"2024-11-30T23:30:05Z"},{"date_updated":"2026-07-13T10:55:56Z","access_level":"closed","embargo_to":"open_access","creator":"mhenness","relation":"main_file","file_id":"14649","file_size":21282155,"date_created":"2023-12-06T13:14:15Z","checksum":"f5203a61eddaf35235bbc51904d73982","file_name":"mike_thesis_v06-12-2023.pdf","content_type":"application/pdf","embargo":"2026-11-18"},{"access_level":"closed","date_updated":"2025-05-20T22:31:34Z","title":"Print version","relation":"other","description":"for printing purposes only","file_id":"19720","file_size":45847968,"embargo_to":"open_access","creator":"cchlebak","checksum":"902102d26d30e74dbd6cdd70a65820c3","file_name":"2023_Hennessey_Michael_Thesis_print.pdf","date_created":"2025-05-20T12:59:12Z","content_type":"application/pdf"}],"publication_identifier":{"issn":["2663-337X"]},"citation":{"ista":"Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria.","mla":"Hennessey-Wesen, Mike. <i>Adaptive Mutation in E. Coli Modulated by LuxS</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>.","ama":"Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>","chicago":"Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>.","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023.","apa":"Hennessey-Wesen, M. (2023). <i>Adaptive mutation in E. coli modulated by luxS</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>","short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023."},"keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"day":"30","abstract":[{"text":"Mutation rates represent the net result of complex interactions among various\r\ncellular processes and can dramatically influence the evolutionary fate of\r\nmicrobial populations. However, many popular techniques used to study\r\nmutations are subject to the confounding effects of heredity and the subtleties\r\nof adaptation to selection, all of which make it difficult to observe any dynamic\r\nresponses of mutation rates to fitness challenges. Furthermore, in spite of the\r\nubiquity of quorum sensing systems across the bacterial domain and relevance\r\nfor many physiological behaviors, the effects of such mechanisms on mutation\r\nrate and adaptation remain poorly understood. In the following work, I\r\npresent the development of a microfluidic droplet-based method to measure\r\nsingle base-pair mutation rates in growing populations of the bacterium\r\nEscherichia coli. I use this method to observe a stress-induced increase in\r\nmutation rate that is mediated by luxS, a highly conserved bacterial quorum\r\nsensing component. I also show that the aforementioned increase in mutation\r\nrate, and its associated control by luxS, corresponds to a higher degree of\r\nadaptability under competitive environments.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"ec_funded":1,"doi_confirm":"1","page":"104","ddc":["570"]},{"date_created":"2021-05-24T13:06:23Z","supervisor":[{"full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"month":"05","article_processing_charge":"No","OA_place":"publisher","fulldoi":"https://doi.org/10.15479/AT:ISTA:9418","related_material":{"record":[{"status":"deleted","id":"7435","relation":"part_of_dissertation"},{"status":"public","id":"7481","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"9416"},{"status":"public","relation":"part_of_dissertation","id":"7479"}]},"type":"dissertation","date_published":"2021-05-30T00:00:00Z","author":[{"full_name":"Bui Thi Mai, Phuong","last_name":"Bui Thi Mai","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong"}],"oa":1,"corr_author":"1","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","doi":"10.15479/AT:ISTA:9418","year":"2021","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"date_updated":"2026-07-30T05:33:52Z","title":"Underspecification in deep learning","_id":"9418","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"citation":{"ama":"Phuong M. Underspecification in deep learning. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9418\">10.15479/AT:ISTA:9418</a>","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","mla":"Phuong, Mary. <i>Underspecification in Deep Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9418\">10.15479/AT:ISTA:9418</a>.","apa":"Phuong, M. (2021). <i>Underspecification in deep learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9418\">https://doi.org/10.15479/AT:ISTA:9418</a>","short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9418\">https://doi.org/10.15479/AT:ISTA:9418</a>.","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021."},"file_date_updated":"2021-05-24T11:56:02Z","file":[{"content_type":"application/pdf","date_created":"2021-05-24T11:22:29Z","checksum":"4f0abe64114cfed264f9d36e8d1197e3","file_name":"mph-thesis-v519-pdfimages.pdf","creator":"bphuong","relation":"main_file","file_id":"9419","file_size":2673905,"date_updated":"2021-05-24T11:22:29Z","success":1,"access_level":"open_access"},{"date_updated":"2021-05-24T11:56:02Z","access_level":"closed","creator":"bphuong","file_size":92995100,"relation":"source_file","file_id":"9420","date_created":"2021-05-24T11:56:02Z","file_name":"thesis.zip","checksum":"f5699e876bc770a9b0df8345a77720a2","content_type":"application/zip"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","page":"125","ddc":["000"],"doi_confirm":"1","day":"30","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models.","lang":"eng"}]},{"degree_awarded":"PhD","_id":"8032","has_accepted_license":"1","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"CampIT"}],"year":"2020","title":"Combinatorial width parameters for 3-dimensional manifolds","date_updated":"2026-04-08T07:21:28Z","doi":"10.15479/AT:ISTA:8032","author":[{"id":"33C26278-F248-11E8-B48F-1D18A9856A87","first_name":"Kristóf","orcid":"0000-0002-5445-5057","last_name":"Huszár","full_name":"Huszár, Kristóf"}],"corr_author":"1","oa":1,"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"relation":"dissertation_contains","id":"6556","status":"public"},{"status":"public","relation":"dissertation_contains","id":"7093"}]},"date_published":"2020-06-26T00:00:00Z","type":"dissertation","fulldoi":"https://doi.org/10.15479/AT:ISTA:8032","publication_status":"published","article_processing_charge":"No","month":"06","OA_place":"publisher","department":[{"_id":"UlWa"}],"date_created":"2020-06-26T10:00:36Z","supervisor":[{"full_name":"Wagner, Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"},{"last_name":"Spreer","full_name":"Spreer, Jonathan","first_name":"Jonathan"}],"day":"26","abstract":[{"text":"Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”\r\nIn this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"page":"xviii+120","ddc":["514"],"oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","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"},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:08Z","file":[{"file_name":"Kristof_Huszar-Thesis.pdf","checksum":"bd8be6e4f1addc863dfcc0fad29ee9c3","date_created":"2020-06-26T10:03:58Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:08Z","file_size":2637562,"relation":"main_file","file_id":"8034","creator":"khuszar"},{"file_size":7163491,"file_id":"8035","relation":"source_file","creator":"khuszar","access_level":"closed","date_updated":"2020-07-14T12:48:08Z","content_type":"application/x-zip-compressed","file_name":"Kristof_Huszar-Thesis-source.zip","checksum":"d5f8456202b32f4a77552ef47a2837d1","date_created":"2020-06-26T10:10:06Z"}],"publication_identifier":{"isbn":["978-3-99078-006-0"],"issn":["2663-337X"]},"citation":{"ama":"Huszár K. Combinatorial width parameters for 3-dimensional manifolds. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8032\">10.15479/AT:ISTA:8032</a>","mla":"Huszár, Kristóf. <i>Combinatorial Width Parameters for 3-Dimensional Manifolds</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8032\">10.15479/AT:ISTA:8032</a>.","ista":"Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria.","short":"K. Huszár, Combinatorial Width Parameters for 3-Dimensional Manifolds, Institute of Science and Technology Austria, 2020.","apa":"Huszár, K. (2020). <i>Combinatorial width parameters for 3-dimensional manifolds</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8032\">https://doi.org/10.15479/AT:ISTA:8032</a>","ieee":"K. Huszár, “Combinatorial width parameters for 3-dimensional manifolds,” Institute of Science and Technology Austria, 2020.","chicago":"Huszár, Kristóf. “Combinatorial Width Parameters for 3-Dimensional Manifolds.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8032\">https://doi.org/10.15479/AT:ISTA:8032</a>."}},{"oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","language":[{"iso":"eng"}],"file_date_updated":"2020-09-14T13:39:17Z","file":[{"content_type":"application/pdf","date_created":"2020-09-14T13:39:14Z","checksum":"c914d2f88846032f3d8507734861b6ee","file_name":"2020_Thesis_Royer.pdf","creator":"dernst","file_id":"8391","relation":"main_file","file_size":30224591,"date_updated":"2020-09-14T13:39:14Z","success":1,"access_level":"open_access"},{"date_updated":"2020-09-14T13:39:17Z","access_level":"closed","creator":"dernst","file_size":74227627,"file_id":"8392","relation":"main_file","date_created":"2020-09-14T13:39:17Z","file_name":"thesis_sources.zip","checksum":"ae98fb35d912cff84a89035ae5794d3c","content_type":"application/x-zip-compressed"}],"publication_identifier":{"isbn":["978-3-99078-007-7"],"issn":["2663-337X"]},"citation":{"chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8390\">https://doi.org/10.15479/AT:ISTA:8390</a>.","ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","apa":"Royer, A. (2020). <i>Leveraging structure in Computer Vision tasks for flexible Deep Learning models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8390\">https://doi.org/10.15479/AT:ISTA:8390</a>","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria.","mla":"Royer, Amélie. <i>Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8390\">10.15479/AT:ISTA:8390</a>.","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8390\">10.15479/AT:ISTA:8390</a>"},"day":"14","abstract":[{"lang":"eng","text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. "}],"alternative_title":["ISTA Thesis"],"page":"197","ddc":["000"],"related_material":{"record":[{"id":"7936","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"8092","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"911"},{"status":"public","id":"8193","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"7937"}]},"type":"dissertation","date_published":"2020-09-14T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:8390","publication_status":"published","OA_place":"publisher","month":"09","article_processing_charge":"No","department":[{"_id":"ChLa"}],"supervisor":[{"full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-09-14T13:42:09Z","degree_awarded":"PhD","_id":"8390","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","status":"public","year":"2020","title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"date_updated":"2026-04-08T07:26:44Z","doi":"10.15479/AT:ISTA:8390","author":[{"orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","full_name":"Royer, Amélie","last_name":"Royer"}],"corr_author":"1","oa":1,"publisher":"Institute of Science and Technology Austria"},{"day":"30","abstract":[{"lang":"eng","text":"Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers."}],"alternative_title":["ISTA Thesis"],"page":"141","ddc":["570"],"acknowledgement":"Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria.","language":[{"iso":"eng"}],"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"citation":{"ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>","mla":"Emtenani, Shamsi. <i>Metabolic Regulation of Drosophila Macrophage Tissue Invasion</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>.","ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria.","short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020.","apa":"Emtenani, S. (2020). <i>Metabolic regulation of Drosophila macrophage tissue invasion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>","ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","chicago":"Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>."},"file_date_updated":"2021-12-31T23:30:04Z","file":[{"file_size":10848175,"relation":"main_file","file_id":"8984","creator":"semtenan","access_level":"open_access","date_updated":"2021-12-31T23:30:04Z","embargo":"2021-12-30","content_type":"application/pdf","file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf","checksum":"ec2797ab7a6f253b35df0572b36d1b43","date_created":"2020-12-30T15:34:01Z"},{"content_type":"application/pdf","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","checksum":"cc30e6608a9815414024cf548dff3b3a","date_created":"2020-12-30T15:37:36Z","file_size":10073648,"relation":"source_file","file_id":"8985","embargo_to":"open_access","creator":"semtenan","access_level":"closed","date_updated":"2021-12-31T23:30:04Z"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","has_accepted_license":"1","title":"Metabolic regulation of Drosophila macrophage tissue invasion","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}],"date_updated":"2026-04-08T07:28:54Z","year":"2020","doi":"10.15479/AT:ISTA:8983","_id":"8983","degree_awarded":"PhD","corr_author":"1","oa":1,"author":[{"orcid":"0000-0001-6981-6938","id":"49D32318-F248-11E8-B48F-1D18A9856A87","first_name":"Shamsi","full_name":"Emtenani, Shamsi","last_name":"Emtenani"}],"publisher":"Institute of Science and Technology Austria","fulldoi":"https://doi.org/10.15479/AT:ISTA:8983","related_material":{"record":[{"status":"public","id":"8557","relation":"part_of_dissertation"},{"id":"6187","relation":"part_of_dissertation","status":"public"}]},"date_published":"2020-12-30T00:00:00Z","type":"dissertation","date_created":"2020-12-30T15:41:26Z","supervisor":[{"last_name":"Siekhaus","full_name":"Siekhaus, Daria E","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"}],"publication_status":"published","month":"12","OA_place":"publisher","article_processing_charge":"No","department":[{"_id":"DaSi"}]},{"article_processing_charge":"No","month":"07","department":[{"_id":"BeVi"}],"publication_status":"published","date_created":"2019-08-04T21:59:18Z","external_id":{"pmid":["31273378"],"isi":["000484039500018"]},"date_published":"2019-07-01T00:00:00Z","type":"journal_article","pmid":1,"fulldoi":"https://doi.org/10.1093/gbe/evz133","intvolume":"        11","publisher":"Oxford University Press","author":[{"orcid":"0000-0002-8101-2518","first_name":"Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Picard, Marion A L","last_name":"Picard"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"},{"first_name":"David","full_name":"Roquis, David","last_name":"Roquis"},{"full_name":"Bulla, Ingo","last_name":"Bulla","first_name":"Ingo"},{"last_name":"Augusto","full_name":"Augusto, Ronaldo C.","first_name":"Ronaldo C."},{"full_name":"Arancibia, Nathalie","last_name":"Arancibia","first_name":"Nathalie"},{"full_name":"Grunau, Christoph","last_name":"Grunau","first_name":"Christoph"},{"full_name":"Boissier, Jérôme","last_name":"Boissier","first_name":"Jérôme"},{"first_name":"Céline","last_name":"Cosseau","full_name":"Cosseau, Céline"}],"oa":1,"_id":"6755","isi":1,"title":"Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome","acknowledged_ssus":[{"_id":"CampIT"}],"year":"2019","date_updated":"2025-05-14T11:08:50Z","doi":"10.1093/gbe/evz133","has_accepted_license":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:39Z","file_size":580205,"file_id":"6765","relation":"main_file","creator":"dernst","file_name":"2019_GenomeBiology_Picard.pdf","checksum":"f9e8f6863a406dcc5a36b2be001c138c","date_created":"2019-08-05T07:55:02Z","content_type":"application/pdf"}],"file_date_updated":"2020-07-14T12:47:39Z","citation":{"short":"M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia, C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922.","apa":"Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia, N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz133\">https://doi.org/10.1093/gbe/evz133</a>","ieee":"M. A. L. Picard <i>et al.</i>, “Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 7. Oxford University Press, pp. 1909–1922, 2019.","chicago":"Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz133\">https://doi.org/10.1093/gbe/evz133</a>.","ama":"Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. <i>Genome biology and evolution</i>. 2019;11(7):1909-1922. doi:<a href=\"https://doi.org/10.1093/gbe/evz133\">10.1093/gbe/evz133</a>","mla":"Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 7, Oxford University Press, 2019, pp. 1909–22, doi:<a href=\"https://doi.org/10.1093/gbe/evz133\">10.1093/gbe/evz133</a>.","ista":"Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 11(7), 1909–1922."},"publication_identifier":{"eissn":["1759-6653"]},"oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","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"},"language":[{"iso":"eng"}],"issue":"7","publication":"Genome biology and evolution","ddc":["570"],"page":"1909-1922","abstract":[{"text":"Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.","lang":"eng"}],"volume":11,"scopus_import":"1","day":"01","article_type":"original"},{"tmp":{"short":"CC BY (4.0)","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"},"oa_version":"Published Version","acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:43Z","file":[{"creator":"dernst","file_size":3158125,"file_id":"5695","relation":"main_file","date_updated":"2020-07-14T12:44:43Z","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-17T11:55:05Z","file_name":"2018_eLife_Picard.pdf","checksum":"d6331d4385b1fffd6b47b45d5949d841"}],"citation":{"ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>","mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>, vol. 7, e35684, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>.","ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684.","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., &#38; Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>","ieee":"M. A. L. Picard <i>et al.</i>, “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>."},"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"day":"13","article_type":"original","scopus_import":"1","volume":7,"abstract":[{"lang":"eng","text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. "}],"ddc":["570"],"publication":"eLife","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5586"}]},"type":"journal_article","date_published":"2018-08-13T00:00:00Z","fulldoi":"https://doi.org/10.7554/eLife.35684","das_tickbox":"1","publication_status":"published","department":[{"_id":"BeVi"}],"month":"08","article_processing_charge":"No","article_number":"e35684","external_id":{"isi":["000441388200001"]},"date_created":"2018-12-11T11:44:47Z","_id":"131","isi":1,"quality_controlled":"1","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","doi":"10.7554/eLife.35684","year":"2018","title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","date_updated":"2026-07-28T09:45:56Z","acknowledged_ssus":[{"_id":"CampIT"}],"author":[{"last_name":"Picard","full_name":"Picard, Marion A","first_name":"Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518"},{"first_name":"Celine","full_name":"Cosseau, Celine","last_name":"Cosseau"},{"full_name":"Ferré, Sabrina","last_name":"Ferré","first_name":"Sabrina"},{"first_name":"Thomas","full_name":"Quack, Thomas","last_name":"Quack"},{"last_name":"Grevelding","full_name":"Grevelding, Christoph","first_name":"Christoph"},{"last_name":"Couté","full_name":"Couté, Yohann","first_name":"Yohann"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"oa":1,"publist_id":"7792","publisher":"eLife Sciences Publications","intvolume":"         7"}]