[{"month":"07","supervisor":[{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn"}],"keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","type":"dissertation","publication_status":"published","degree_awarded":"PhD","_id":"9728","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","acknowledged_ssus":[{"_id":"M-Shop"}],"date_updated":"2026-04-16T08:43:20Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Transition to turbulence and drag reduction in particle-laden pipe flows","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"author":[{"id":"469E6004-F248-11E8-B48F-1D18A9856A87","last_name":"Agrawal","full_name":"Agrawal, Nishchal","first_name":"Nishchal"}],"date_published":"2021-07-29T00:00:00Z","file":[{"file_id":"9744","embargo_to":"open_access","creator":"nagrawal","relation":"source_file","date_updated":"2022-07-29T22:30:05Z","checksum":"77436be3563a90435024307b1b5ee7e8","date_created":"2021-07-28T13:32:02Z","content_type":"application/x-zip-compressed","access_level":"closed","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","file_size":22859658},{"creator":"nagrawal","file_id":"9745","embargo":"2022-07-28","relation":"main_file","date_updated":"2022-07-29T22:30:05Z","checksum":"72a891d7daba85445c29b868c22575ed","content_type":"application/pdf","access_level":"open_access","date_created":"2021-07-28T13:32:05Z","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","file_size":18658048}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","year":"2021","language":[{"iso":"eng"}],"page":"118","doi":"10.15479/at:ista:9728","related_material":{"record":[{"id":"6189","status":"public","relation":"part_of_dissertation"}]},"corr_author":"1","day":"29","alternative_title":["ISTA Thesis"],"citation":{"apa":"Agrawal, N. (2021). <i>Transition to turbulence and drag reduction in particle-laden pipe flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>","chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>.","mla":"Agrawal, Nishchal. <i>Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>.","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria.","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>"},"date_created":"2021-07-27T13:40:30Z","has_accepted_license":"1","article_processing_charge":"No","oa":1,"file_date_updated":"2022-07-29T22:30:05Z","ddc":["532"],"abstract":[{"lang":"eng","text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work."}]},{"publication":"Wiley Interdisciplinary Reviews: Developmental Biology","language":[{"iso":"eng"}],"year":"2021","acknowledgement":"Austrian Academy of Sciences, Grant/Award Number: DOC fellowship for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037","status":"public","date_published":"2021-04-15T00:00:00Z","file":[{"relation":"main_file","file_id":"8800","creator":"dernst","date_updated":"2020-11-24T13:11:39Z","date_created":"2020-11-24T13:11:39Z","access_level":"open_access","content_type":"application/pdf","checksum":"f0a7745d48afa09ea7025e876a0145a8","file_size":2527276,"success":1,"file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000531419400001"],"pmid":["32391980"]},"author":[{"first_name":"Katarzyna","full_name":"Kuzmicz-Kowalska, Katarzyna","last_name":"Kuzmicz-Kowalska","id":"4CED352A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","first_name":"Anna"}],"ddc":["570"],"abstract":[{"text":"All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species‐specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior–posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue‐scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue‐scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern.","lang":"eng"}],"oa":1,"file_date_updated":"2020-11-24T13:11:39Z","article_number":"e383","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","date_created":"2020-05-24T22:01:00Z","citation":{"short":"K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021).","ieee":"K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate spinal cord development,” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021.","ama":"Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. 2021. doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>","ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.","mla":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>, e383, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>.","chicago":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>.","apa":"Kuzmicz-Kowalska, K., &#38; Kicheva, A. (2021). Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>"},"quality_controlled":"1","scopus_import":"1","corr_author":"1","day":"15","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14323"}]},"doi":"10.1002/wdev.383","publication_status":"published","publisher":"Wiley","type":"journal_article","oa_version":"Published Version","OA_type":"hybrid","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"},{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802"}],"month":"04","article_type":"original","title":"Regulation of size and scale in vertebrate spinal cord development","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"AnKi"}],"date_updated":"2026-06-19T22:31:02Z","OA_place":"publisher","isi":1,"publication_identifier":{"issn":["1759-7684"],"eissn":["1759-7692"]},"_id":"7883","ec_funded":1,"pmid":1},{"article_number":"041501","article_processing_charge":"No","has_accepted_license":"1","abstract":[{"lang":"eng","text":"The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development."}],"ddc":["570"],"oa":1,"file_date_updated":"2021-04-27T08:38:35Z","related_material":{"record":[{"id":"13081","status":"public","relation":"dissertation_contains"}]},"intvolume":"        18","doi":"10.1088/1478-3975/abd0db","quality_controlled":"1","citation":{"ama":"Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical biology</i>. 2021;18(4). doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>","short":"P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi, A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A. Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B. Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia, B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021).","ieee":"P. F. Lenne <i>et al.</i>, “Roadmap for the multiscale coupling of biochemical and mechanical signals during development,” <i>Physical biology</i>, vol. 18, no. 4. IOP Publishing, 2021.","apa":"Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi, K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical Biology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>","mla":"Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>, vol. 18, no. 4, 041501, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>.","chicago":"Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>.","ista":"Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 18(4), 041501."},"date_created":"2021-04-25T22:01:29Z","scopus_import":"1","day":"14","year":"2021","language":[{"iso":"eng"}],"publication":"Physical biology","issue":"4","date_published":"2021-04-14T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":6296324,"success":1,"file_name":"2021_PhysBio_Lenne.pdf","date_created":"2021-04-27T08:38:35Z","access_level":"open_access","content_type":"application/pdf","checksum":"4f52082549d3561c4c15d4d8d84ca5d8","date_updated":"2021-04-27T08:38:35Z","relation":"main_file","file_id":"9355","creator":"cziletti"}],"volume":18,"external_id":{"pmid":["33276350"],"isi":["000640396400001"]},"author":[{"full_name":"Lenne, Pierre François","last_name":"Lenne","first_name":"Pierre François"},{"last_name":"Munro","full_name":"Munro, Edwin","first_name":"Edwin"},{"last_name":"Heemskerk","full_name":"Heemskerk, Idse","first_name":"Idse"},{"first_name":"Aryeh","full_name":"Warmflash, Aryeh","last_name":"Warmflash"},{"full_name":"Bocanegra, Laura","last_name":"Bocanegra","id":"4896F754-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"},{"first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","last_name":"Kishi","full_name":"Kishi, Kasumi","orcid":"0000-0001-6060-4795"},{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"},{"first_name":"Yuchen","full_name":"Long, Yuchen","last_name":"Long"},{"full_name":"Fruleux, Antoine","last_name":"Fruleux","first_name":"Antoine"},{"full_name":"Boudaoud, Arezki","last_name":"Boudaoud","first_name":"Arezki"},{"full_name":"Saunders, Timothy E.","last_name":"Saunders","first_name":"Timothy E."},{"first_name":"Paolo","last_name":"Caldarelli","full_name":"Caldarelli, Paolo"},{"first_name":"Arthur","last_name":"Michaut","full_name":"Michaut, Arthur"},{"first_name":"Jerome","full_name":"Gros, Jerome","last_name":"Gros"},{"last_name":"Maroudas-Sacks","full_name":"Maroudas-Sacks, Yonit","first_name":"Yonit"},{"last_name":"Keren","full_name":"Keren, Kinneret","first_name":"Kinneret"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo"},{"last_name":"Gartner","full_name":"Gartner, Zev J.","first_name":"Zev J."},{"first_name":"Benjamin","full_name":"Stormo, Benjamin","last_name":"Stormo"},{"first_name":"Amy","full_name":"Gladfelter, Amy","last_name":"Gladfelter"},{"last_name":"Rodrigues","full_name":"Rodrigues, Alan","first_name":"Alan"},{"full_name":"Shyer, Amy","last_name":"Shyer","first_name":"Amy"},{"first_name":"Nicolas","last_name":"Minc","full_name":"Minc, Nicolas"},{"first_name":"Jean Léon","last_name":"Maître","full_name":"Maître, Jean Léon"},{"first_name":"Stefano","last_name":"Di Talia","full_name":"Di Talia, Stefano"},{"first_name":"Bassma","last_name":"Khamaisi","full_name":"Khamaisi, Bassma"},{"full_name":"Sprinzak, David","last_name":"Sprinzak","first_name":"David"},{"first_name":"Sham","full_name":"Tlili, Sham","last_name":"Tlili"}],"acknowledgement":"The AK group is supported by IST Austria and by the ERC under European Union Horizon 2020 research and innovation programme Grant 680037. Apologies to those whose work could not be mentioned due to limited space. We thank all my lab members, both past and present, for stimulating discussion. This work was funded by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis Corson for continuous discussion and collaboration contributing to these views and for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665807. Research in JG's laboratory is funded by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi for help with figure 5. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for fruitful discussions on these topics—and apologize for not being able to cite many very relevant publications due to the strict 10-reference limit. EH acknowledges the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreements (851288). The authors acknowledge the inspiring scientists whose work could not be cited in this perspective due to space constraints; the members of the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation, the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health, and the Centre for Cellular Construction, an NSF Science and Technology Centre. The Minc laboratory is currently funded by the CNRS and the European Research Council (CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche via the Fondation pour la Recherche Médicale, the European Research Council Starting Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas (HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005) grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02). We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported by NIH-R01GM122936. The authors acknowledge the support by a grant from the European Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements d'Avenir' French Government programme managed by the French National Research Agency (ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX, and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).","status":"public","date_updated":"2026-06-19T22:31:03Z","department":[{"_id":"AnKi"},{"_id":"EdHa"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Roadmap for the multiscale coupling of biochemical and mechanical signals during development","_id":"9349","ec_funded":1,"pmid":1,"isi":1,"publication_identifier":{"eissn":["1478-3975"]},"type":"journal_article","publisher":"IOP Publishing","publication_status":"published","oa_version":"Published Version","month":"04","project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","call_identifier":"H2020"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton"},{"grant_number":"851288","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"article_type":"original"},{"article_processing_charge":"No","has_accepted_license":"1","abstract":[{"text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.","lang":"eng"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","ddc":["005"],"file_date_updated":"2021-12-23T23:30:04Z","oa":1,"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6490"},{"status":"public","relation":"part_of_dissertation","id":"6780"},{"relation":"part_of_dissertation","status":"public","id":"7158"},{"id":"66","relation":"part_of_dissertation","status":"public"},{"id":"6378","status":"public","relation":"part_of_dissertation"},{"id":"311","relation":"part_of_dissertation","status":"public"},{"id":"6175","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6340"},{"relation":"part_of_dissertation","status":"public","id":"7014"},{"relation":"part_of_dissertation","status":"public","id":"6009"},{"id":"1437","status":"public","relation":"part_of_dissertation"},{"id":"8728","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8089"},{"id":"6380","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"5977"},{"id":"6056","relation":"part_of_dissertation","status":"public"},{"id":"639","relation":"part_of_dissertation","status":"public"},{"id":"1386","relation":"part_of_dissertation","status":"public"},{"id":"6918","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"7810"},{"id":"949","status":"public","relation":"part_of_dissertation"}]},"doi":"10.15479/AT:ISTA:8934","date_created":"2020-12-10T12:17:07Z","citation":{"ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","apa":"Goharshady, A. K. (2021). <i>Parameterized and algebro-geometric advances in static program analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>","mla":"Goharshady, Amir Kafshdar. <i>Parameterized and Algebro-Geometric Advances in Static Program Analysis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8934\">10.15479/AT:ISTA:8934</a>.","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:8934\">https://doi.org/10.15479/AT:ISTA:8934</a>.","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"day":"01","corr_author":"1","year":"2021","language":[{"iso":"eng"}],"page":"278","date_published":"2021-01-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"date_updated":"2021-12-23T23:30:04Z","file_id":"8969","creator":"akafshda","embargo":"2021-12-22","relation":"main_file","file_name":"Thesis-pdfa.pdf","file_size":5251507,"checksum":"d1b9db3725aed34dadd81274aeb9426c","date_created":"2020-12-22T20:08:44Z","access_level":"open_access","content_type":"application/pdf"},{"access_level":"closed","content_type":"application/zip","date_created":"2020-12-22T20:08:50Z","checksum":"1661df7b393e6866d2460eba3c905130","file_size":10636756,"file_name":"source.zip","relation":"source_file","embargo_to":"open_access","creator":"akafshda","file_id":"8970","date_updated":"2021-03-04T23:30:04Z"}],"author":[{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar"}],"status":"public","acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","date_updated":"2026-04-16T10:07:18Z","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"title":"Parameterized and algebro-geometric advances in static program analysis","_id":"8934","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","publisher":"Institute of Science and Technology Austria","publication_status":"published","oa_version":"Published Version","degree_awarded":"PhD","project":[{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"month":"01","supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}]},{"publication_identifier":{"issn":["0168-9452"]},"isi":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"pmid":1,"ec_funded":1,"_id":"8931","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"JiFr"},{"_id":"Bio"}],"title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","date_updated":"2026-06-19T22:31:09Z","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"article_type":"original","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"month":"02","oa_version":"Published Version","publisher":"Elsevier","publication_status":"published","type":"journal_article","corr_author":"1","day":"01","scopus_import":"1","quality_controlled":"1","citation":{"ieee":"Z. Gelová <i>et al.</i>, “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” <i>Plant Science</i>, vol. 303. Elsevier, 2021.","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. 2021;303. doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>, vol. 303, 110750, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>.","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>."},"date_created":"2020-12-09T14:48:28Z","doi":"10.1016/j.plantsci.2020.110750","intvolume":"       303","related_material":{"record":[{"id":"11626","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","status":"public","id":"10083"}]},"file_date_updated":"2021-02-04T07:49:25Z","oa":1,"ddc":["580"],"abstract":[{"text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.","lang":"eng"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","article_number":"110750","acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","status":"public","external_id":{"isi":["000614154500001"],"pmid":["33487339"]},"author":[{"last_name":"Gelová","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","first_name":"Zuzana"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","first_name":"Michelle C"},{"last_name":"Pernisová","full_name":"Pernisová, Markéta","first_name":"Markéta"},{"first_name":"Géraldine","full_name":"Brunoud, Géraldine","last_name":"Brunoud"},{"first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","first_name":"Matous"},{"orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin"},{"full_name":"Michalko, Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","last_name":"Michalko","first_name":"Jaroslav"},{"full_name":"Pavlovicova, Zlata","last_name":"Pavlovicova","first_name":"Zlata"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","first_name":"Huibin"},{"first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert"},{"last_name":"Čovanová","full_name":"Čovanová, Milada","first_name":"Milada"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","first_name":"Lukas"},{"first_name":"Matyas","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xu","full_name":"Xu, Tongda","first_name":"Tongda"},{"first_name":"Teva","full_name":"Vernoux, Teva","last_name":"Vernoux"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"}],"volume":303,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-02-01T00:00:00Z","file":[{"success":1,"file_name":"2021_PlantScience_Gelova.pdf","file_size":12563728,"checksum":"a7f2562bdca62d67dfa88e271b62a629","access_level":"open_access","content_type":"application/pdf","date_created":"2021-02-04T07:49:25Z","date_updated":"2021-02-04T07:49:25Z","creator":"dernst","file_id":"9083","relation":"main_file"}],"language":[{"iso":"eng"}],"publication":"Plant Science","year":"2021"},{"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"isi":1,"publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"_id":"9287","ec_funded":1,"pmid":1,"department":[{"_id":"JiFr"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","date_updated":"2026-06-19T22:31:09Z","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630"}],"month":"06","article_type":"original","publisher":"Oxford University Press","publication_status":"published","type":"journal_article","oa_version":"Published Version","citation":{"ista":"Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142.","chicago":"Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>.","apa":"Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>","mla":"Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>.","ieee":"M. Narasimhan <i>et al.</i>, “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” <i>Plant Physiology</i>, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021.","short":"M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142.","ama":"Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. 2021;186(2):1122–1142. doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>"},"quality_controlled":"1","date_created":"2021-03-26T12:08:38Z","scopus_import":"1","corr_author":"1","day":"01","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11626"},{"id":"10083","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1093/plphys/kiab380"}]},"intvolume":"       186","doi":"10.1093/plphys/kiab134","abstract":[{"lang":"eng","text":"The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its\r\npolarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. "}],"ddc":["580"],"oa":1,"file_date_updated":"2021-11-11T15:07:51Z","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","acknowledgement":"We thank Ivan Kulik for developing the Chip’n’Dale apparatus with Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help; Barbara Casillas-Perez for her help with statistics. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 742985). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. ","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"date_created":"2021-11-11T15:07:51Z","access_level":"open_access","content_type":"application/pdf","checksum":"532bb9469d3b665907f06df8c383eade","file_size":2289127,"success":1,"file_name":"2021_PlantPhysio_Narasimhan.pdf","relation":"main_file","file_id":"10273","creator":"cziletti","date_updated":"2021-11-11T15:07:51Z"}],"date_published":"2021-06-01T00:00:00Z","volume":186,"external_id":{"isi":["000671555900031"],"pmid":["33734402"]},"author":[{"first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","last_name":"Narasimhan","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha"},{"orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","first_name":"Michelle C"},{"first_name":"Shutang","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","first_name":"Inge"},{"first_name":"Lanxin","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey"},{"first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"first_name":"E","full_name":"Himschoot, E","last_name":"Himschoot"},{"first_name":"R","full_name":"Wang, R","last_name":"Wang"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"first_name":"J","full_name":"Sánchez-Simarro, J","last_name":"Sánchez-Simarro"},{"last_name":"Aniento","full_name":"Aniento, F","first_name":"F"},{"orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"language":[{"iso":"eng"}],"page":"1122–1142","publication":"Plant Physiology","issue":"2","year":"2021"},{"file":[{"checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","date_created":"2021-10-14T08:00:07Z","access_level":"open_access","content_type":"application/pdf","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","file_size":8616142,"file_id":"10138","creator":"cchlebak","embargo":"2022-10-14","relation":"main_file","date_updated":"2022-12-20T23:30:03Z"},{"relation":"source_file","file_id":"10139","creator":"cchlebak","embargo_to":"open_access","date_updated":"2022-12-20T23:30:03Z","date_created":"2021-10-14T08:00:13Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","checksum":"f23ed258ca894f6aabf58b0c128bf242","file_size":15058499,"file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx"}],"date_published":"2021-10-06T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin"}],"status":"public","year":"2021","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"442","relation":"part_of_dissertation","status":"public"},{"id":"6627","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8931"},{"relation":"part_of_dissertation","status":"public","id":"8986"},{"id":"10095","status":"public","relation":"part_of_dissertation"},{"id":"8283","relation":"part_of_dissertation","status":"public"},{"id":"9287","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10015"}]},"doi":"10.15479/at:ista:10083","citation":{"ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria.","apa":"Li, L. (2021). <i>Rapid cell growth regulation in Arabidopsis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>","chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>.","mla":"Li, Lanxin. <i>Rapid Cell Growth Regulation in Arabidopsis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>."},"date_created":"2021-10-04T13:33:10Z","day":"06","corr_author":"1","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that  vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. "}],"ddc":["575"],"oa":1,"file_date_updated":"2022-12-20T23:30:03Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"month":"10","supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"type":"dissertation","publication_status":"published","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","degree_awarded":"PhD","_id":"10083","ec_funded":1,"OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-16T12:20:41Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"title":"Rapid cell growth regulation in Arabidopsis"},{"publication_identifier":{"issn":["2073-4409"]},"isi":1,"pmid":1,"ec_funded":1,"_id":"10015","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"JiFr"}],"title":"The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators","date_updated":"2026-06-19T22:31:09Z","keyword":["primary root","(phospho)proteomics","auxin","(receptor) kinase"],"article_type":"original","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"month":"07","oa_version":"Published Version","type":"journal_article","publication_status":"published","publisher":"MDPI","alternative_title":["Protein Phosphorylation and Cell Signaling in Plants"],"day":"02","scopus_import":"1","quality_controlled":"1","date_created":"2021-09-14T11:36:20Z","citation":{"ieee":"N. Nikonorova <i>et al.</i>, “The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators,” <i>Cells</i>, vol. 10. MDPI, 2021.","short":"N. Nikonorova, E. Murphy, C. Fonseca de Lima, S. Zhu, B. van de Cotte, L. Vu, D. Balcerowicz, L. Li, X. Kong, G. De Rop, T. Beeckman, J. Friml, K. Vissenberg, P. Morris, Z. Ding, I. De Smet, Cells 10 (2021).","ama":"Nikonorova N, Murphy E, Fonseca de Lima C, et al. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. <i>Cells</i>. 2021;10. doi:<a href=\"https://doi.org/10.3390/cells10071665\">10.3390/cells10071665</a>","ista":"Nikonorova N, Murphy E, Fonseca de Lima C, Zhu S, van de Cotte B, Vu L, Balcerowicz D, Li L, Kong X, De Rop G, Beeckman T, Friml J, Vissenberg K, Morris P, Ding Z, De Smet I. 2021. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 10, 1665.","apa":"Nikonorova, N., Murphy, E., Fonseca de Lima, C., Zhu, S., van de Cotte, B., Vu, L., … De Smet, I. (2021). The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells10071665\">https://doi.org/10.3390/cells10071665</a>","chicago":"Nikonorova, N, E Murphy, CF Fonseca de Lima, S Zhu, B van de Cotte, LD Vu, D Balcerowicz, et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” <i>Cells</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/cells10071665\">https://doi.org/10.3390/cells10071665</a>.","mla":"Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” <i>Cells</i>, vol. 10, 1665, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/cells10071665\">10.3390/cells10071665</a>."},"doi":"10.3390/cells10071665","intvolume":"        10","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10083"}]},"file_date_updated":"2021-09-16T09:07:06Z","oa":1,"abstract":[{"lang":"eng","text":"Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31 phosphorylation site for growth regulation in the Arabidopsis root tip."}],"ddc":["575"],"has_accepted_license":"1","article_processing_charge":"Yes","article_number":"1665 ","status":"public","acknowledgement":"We thank the Nottingham Stock Centre for seeds, Frank Van Breusegem for the phb3 mutant, and Herman Höfte for the the1 mutant. Open Access Funding by the Austrian Science Fund (FWF).","external_id":{"pmid":["34359847"],"isi":["000676604700001"]},"author":[{"full_name":"Nikonorova, N","last_name":"Nikonorova","first_name":"N"},{"full_name":"Murphy, E","last_name":"Murphy","first_name":"E"},{"first_name":"CF","full_name":"Fonseca de Lima, CF","last_name":"Fonseca de Lima"},{"full_name":"Zhu, S","last_name":"Zhu","first_name":"S"},{"first_name":"B","full_name":"van de Cotte, B","last_name":"van de Cotte"},{"full_name":"Vu, LD","last_name":"Vu","first_name":"LD"},{"full_name":"Balcerowicz, D","last_name":"Balcerowicz","first_name":"D"},{"first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X"},{"first_name":"X","full_name":"Kong, X","last_name":"Kong"},{"first_name":"G","last_name":"De Rop","full_name":"De Rop, G"},{"first_name":"T","last_name":"Beeckman","full_name":"Beeckman, T"},{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"K","full_name":"Vissenberg, K","last_name":"Vissenberg"},{"first_name":"PC","full_name":"Morris, PC","last_name":"Morris"},{"first_name":"Z","last_name":"Ding","full_name":"Ding, Z"},{"first_name":"I","last_name":"De Smet","full_name":"De Smet, I"}],"volume":10,"date_published":"2021-07-02T00:00:00Z","file":[{"success":1,"file_name":"2021_Cells_Nikonorova.pdf","file_size":2667848,"checksum":"2a9f534b9c2200e72e2cde95afaf4eed","date_created":"2021-09-16T09:07:06Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-09-16T09:07:06Z","file_id":"10021","creator":"cchlebak","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Cells","language":[{"iso":"eng"}],"year":"2021"},{"related_material":{"record":[{"id":"10223","relation":"later_version","status":"public"},{"id":"10083","relation":"dissertation_contains","status":"public"}]},"doi":"10.21203/rs.3.rs-266395/v3","date_created":"2021-10-06T08:56:22Z","citation":{"ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>.","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, 266395, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” <i>Research Square</i>. .","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.)."},"corr_author":"1","day":"09","article_number":"266395","article_processing_charge":"No","abstract":[{"text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment.","lang":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-09-09T00:00:00Z","author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin"},{"first_name":"Inge","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Roosjen","full_name":"Roosjen, Mark","first_name":"Mark"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","first_name":"Lesia"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"first_name":"Jian","full_name":"Chen, Jian","last_name":"Chen"},{"last_name":"Shabala","full_name":"Shabala, Lana","first_name":"Lana"},{"first_name":"Wouter","full_name":"Smet, Wouter","last_name":"Smet"},{"full_name":"Ren, Hong","last_name":"Ren","first_name":"Hong"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"last_name":"Shabala","full_name":"Shabala, Sergey","first_name":"Sergey"},{"last_name":"De Rybel","full_name":"De Rybel, Bert","first_name":"Bert"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"},{"last_name":"Kinoshita","full_name":"Kinoshita, Toshinori","first_name":"Toshinori"},{"last_name":"Gray","full_name":"Gray, William M.","first_name":"William M."},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"status":"public","acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910),  the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","year":"2021","publication":"Research Square","language":[{"iso":"eng"}],"_id":"10095","ec_funded":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"publication_identifier":{"issn":["2693-5015"]},"date_updated":"2026-06-19T22:31:09Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"month":"09","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"type":"preprint","publication_status":"draft","oa_version":"Preprint"},{"external_id":{"isi":["000741368600009"],"pmid":["34146097"]},"author":[{"orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"},{"last_name":"Moldovan","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A.","orcid":"0000-0002-8876-6494","first_name":"Mikhail A."},{"last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Picard, Marion A L","orcid":"0000-0002-8101-2518","first_name":"Marion A L"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz"}],"volume":138,"file":[{"creator":"dernst","file_id":"11352","relation":"main_file","date_updated":"2022-05-06T09:47:18Z","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","content_type":"application/pdf","access_level":"open_access","date_created":"2022-05-06T09:47:18Z","success":1,"file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","file_size":1008594}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-06-19T00:00:00Z","acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","status":"public","year":"2021","issue":"12","page":"5345-58","publication":"Molecular Biology and Evolution","language":[{"iso":"eng"}],"doi":"10.1093/molbev/msab178","intvolume":"       138","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19386"}]},"day":"19","corr_author":"1","scopus_import":"1","date_created":"2021-10-21T07:49:12Z","citation":{"ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021;138(12):5345-5358. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12. Oxford University Press , pp. 5345–58, 2021.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution 138 (2021) 5345–58.","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12, Oxford University Press , 2021, pp. 5345–58, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press . <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 138(12), 5345–58."},"quality_controlled":"1","has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2022-05-06T09:47:18Z","oa":1,"ddc":["610"],"abstract":[{"lang":"eng","text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group."}],"article_type":"original","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"month":"06","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"oa_version":"Published Version","publication_status":"published","publisher":"Oxford University Press ","type":"journal_article","pmid":1,"_id":"10167","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"isi":1,"date_updated":"2026-06-19T22:31:10Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","department":[{"_id":"BeVi"}]},{"external_id":{"isi":["000613273900009"],"pmid":["33321104"]},"author":[{"first_name":"Shayan","full_name":"Shamipour, Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Silvia","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"volume":56,"date_published":"2021-01-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","acknowledgement":"We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript.","year":"2021","issue":"2","publication":"Developmental Cell","language":[{"iso":"eng"}],"page":"P213-226","doi":"10.1016/j.devcel.2020.12.002","intvolume":"        56","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9623"}]},"day":"25","corr_author":"1","scopus_import":"1","quality_controlled":"1","date_created":"2021-01-17T23:01:10Z","citation":{"ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. <i>Developmental Cell</i>. 2021;56(2):P213-226. doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226.","ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” <i>Developmental Cell</i>, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>.","mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” <i>Developmental Cell</i>, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">10.1016/j.devcel.2020.12.002</a>.","apa":"Shamipour, S., Caballero Mancebo, S., &#38; Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2020.12.002\">https://doi.org/10.1016/j.devcel.2020.12.002</a>","ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226."},"article_processing_charge":"No","oa":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species."}],"article_type":"original","month":"01","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2020.12.002","open_access":"1"}],"oa_version":"Published Version","publisher":"Elsevier","publication_status":"published","type":"journal_article","pmid":1,"_id":"9006","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"isi":1,"date_updated":"2026-06-19T22:31:25Z","title":"Cytoplasm's got moves","department":[{"_id":"CaHe"}]},{"month":"07","supervisor":[{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"oa_version":"Published Version","type":"dissertation","publication_status":"published","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","_id":"9623","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-012-1"]},"OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"date_updated":"2026-06-18T19:38:50Z","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","author":[{"first_name":"Silvia","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2021-07-01T00:00:00Z","file":[{"checksum":"e039225a47ef32666d59bf35ddd30ecf","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2021-07-01T14:48:54Z","file_name":"PhDThesis_SCM.docx","file_size":131946790,"embargo_to":"open_access","creator":"scaballe","file_id":"9624","relation":"source_file","date_updated":"2022-07-02T22:30:06Z"},{"date_updated":"2022-07-02T22:30:06Z","embargo":"2022-07-01","relation":"main_file","creator":"scaballe","file_id":"9625","file_size":17094958,"file_name":"PhDThesis_SCM.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2021-07-01T14:46:25Z","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","year":"2021","page":"111","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:9623","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9750"},{"id":"9006","relation":"part_of_dissertation","status":"public"}]},"corr_author":"1","alternative_title":["ISTA Thesis"],"citation":{"ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","apa":"Caballero Mancebo, S. (2021). <i>Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>","mla":"Caballero Mancebo, Silvia. <i>Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>.","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>."},"date_created":"2021-07-01T14:50:17Z","has_accepted_license":"1","article_processing_charge":"No","oa":1,"file_date_updated":"2022-07-02T22:30:06Z","abstract":[{"lang":"eng","text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n"}],"ddc":["570"]},{"day":"22","citation":{"short":"R.H. Bloomer, C.E. Hutchison, I. Bäurle, J. Walker, X. Fang, P. Perera, C.N. Velanis, S. Gümüs, C. Spanos, J. Rappsilber, X. Feng, J. Goodrich, C. Dean, Proceedings of the National Academy of Sciences 117 (2020) 16660–16666.","ieee":"R. H. Bloomer <i>et al.</i>, “The  Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2,” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 28. Proceedings of the National Academy of Sciences, pp. 16660–16666, 2020.","ama":"Bloomer RH, Hutchison CE, Bäurle I, et al. The  Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. <i>Proceedings of the National Academy of Sciences</i>. 2020;117(28):16660-16666. doi:<a href=\"https://doi.org/10.1073/pnas.1920621117\">10.1073/pnas.1920621117</a>","ista":"Bloomer RH, Hutchison CE, Bäurle I, Walker J, Fang X, Perera P, Velanis CN, Gümüs S, Spanos C, Rappsilber J, Feng X, Goodrich J, Dean C. 2020. The  Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. 117(28), 16660–16666.","mla":"Bloomer, Rebecca H., et al. “The  Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 28, Proceedings of the National Academy of Sciences, 2020, pp. 16660–66, doi:<a href=\"https://doi.org/10.1073/pnas.1920621117\">10.1073/pnas.1920621117</a>.","apa":"Bloomer, R. H., Hutchison, C. E., Bäurle, I., Walker, J., Fang, X., Perera, P., … Dean, C. (2020). The  Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1920621117\">https://doi.org/10.1073/pnas.1920621117</a>","chicago":"Bloomer, Rebecca H., Claire E. Hutchison, Isabel Bäurle, James Walker, Xiaofeng Fang, Pumi Perera, Christos N. Velanis, et al. “The  Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1920621117\">https://doi.org/10.1073/pnas.1920621117</a>."},"date_created":"2023-01-16T09:15:44Z","quality_controlled":"1","scopus_import":"1","doi":"10.1073/pnas.1920621117","intvolume":"       117","oa":1,"file_date_updated":"2023-02-07T11:29:55Z","abstract":[{"lang":"eng","text":"Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states."}],"ddc":["580"],"has_accepted_license":"1","article_processing_charge":"No","acknowledgement":"We would like to thank Scott Berry for help with ICU-GFP nuclear localization microscopy, Hao Yu and Lisha Shen for assistance with 6mA DNA methylation analysis, Donna Gibson for graphic design assistance, and members of the C.D. and Howard laboratories for helpful discussions. This work was funded by the European Research Council grants to “MEXTIM” (to C.D.) and “SexMeth” (to X. Feng), by the Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic Programmes GRO (BB/J004588/1), GEN (BB/P013511/1), BBSRC grant (to X. Feng) (BB/S009620/1), and the Marie Sklodowska–Curie Postdoctoral Fellowships “UNRAVEL” (to R.H.B.) and \"WISDOM\" (to X. Fang). Additional funding via the Wellcome Trust through a Senior Research Fellowship (to J.R.) (103139) and a multiuser equipment grant (108504). The Wellcome Centre for Cell Biology is supported by core funding from the Wellcome Trust (203149).","status":"public","volume":117,"extern":"1","author":[{"first_name":"Rebecca H.","last_name":"Bloomer","full_name":"Bloomer, Rebecca H."},{"first_name":"Claire E.","last_name":"Hutchison","full_name":"Hutchison, Claire E."},{"last_name":"Bäurle","full_name":"Bäurle, Isabel","first_name":"Isabel"},{"first_name":"James","last_name":"Walker","full_name":"Walker, James"},{"full_name":"Fang, Xiaofeng","last_name":"Fang","first_name":"Xiaofeng"},{"first_name":"Pumi","full_name":"Perera, Pumi","last_name":"Perera"},{"last_name":"Velanis","full_name":"Velanis, Christos N.","first_name":"Christos N."},{"last_name":"Gümüs","full_name":"Gümüs, Serin","first_name":"Serin"},{"first_name":"Christos","last_name":"Spanos","full_name":"Spanos, Christos"},{"full_name":"Rappsilber, Juri","last_name":"Rappsilber","first_name":"Juri"},{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"first_name":"Justin","last_name":"Goodrich","full_name":"Goodrich, Justin"},{"first_name":"Caroline","last_name":"Dean","full_name":"Dean, Caroline"}],"external_id":{"pmid":["32601198"]},"date_published":"2020-05-22T00:00:00Z","file":[{"date_updated":"2023-02-07T11:29:55Z","relation":"main_file","creator":"alisjak","file_id":"12526","file_size":1105414,"success":1,"file_name":"2020_PNAS_Bloomer.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2023-02-07T11:29:55Z","checksum":"cedee184cb12f454f2fba4158ff47db9"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"28","page":"16660-16666","publication":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"year":"2020","publication_identifier":{"issn":["0027-8424","1091-6490"]},"pmid":1,"_id":"12188","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"The  Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2","department":[{"_id":"XiFe"}],"date_updated":"2023-05-08T10:53:55Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/"}],"keyword":["Multidisciplinary"],"article_type":"original","month":"05","oa_version":"Published Version","type":"journal_article","publisher":"Proceedings of the National Academy of Sciences","publication_status":"published"},{"year":"2020","issue":"6","publication":"PLOS Genetics","language":[{"iso":"eng"}],"author":[{"first_name":"Nicolas","full_name":"Christophorou, Nicolas","last_name":"Christophorou"},{"first_name":"Wenjing","last_name":"She","full_name":"She, Wenjing"},{"full_name":"Long, Jincheng","last_name":"Long","first_name":"Jincheng"},{"last_name":"Hurel","full_name":"Hurel, Aurélie","first_name":"Aurélie"},{"full_name":"Beaubiat, Sébastien","last_name":"Beaubiat","first_name":"Sébastien"},{"first_name":"Yassir","full_name":"Idir, Yassir","last_name":"Idir"},{"last_name":"Tagliaro-Jahns","full_name":"Tagliaro-Jahns, Marina","first_name":"Marina"},{"last_name":"Chambon","full_name":"Chambon, Aurélie","first_name":"Aurélie"},{"last_name":"Solier","full_name":"Solier, Victor","first_name":"Victor"},{"first_name":"Daniel","last_name":"Vezon","full_name":"Vezon, Daniel"},{"full_name":"Grelon, Mathilde","last_name":"Grelon","first_name":"Mathilde"},{"first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"},{"full_name":"Bouché, Nicolas","last_name":"Bouché","first_name":"Nicolas"},{"last_name":"Mézard","full_name":"Mézard, Christine","first_name":"Christine"}],"external_id":{"pmid":["32598340"]},"volume":16,"extern":"1","date_published":"2020-06-29T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","acknowledgement":"The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript.","article_processing_charge":"No","article_number":"e1008894","oa":1,"abstract":[{"text":"Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells.","lang":"eng"}],"doi":"10.1371/journal.pgen.1008894","intvolume":"        16","day":"29","scopus_import":"1","date_created":"2023-01-16T09:16:10Z","quality_controlled":"1","citation":{"ista":"Christophorou N, She W, Long J, Hurel A, Beaubiat S, Idir Y, Tagliaro-Jahns M, Chambon A, Solier V, Vezon D, Grelon M, Feng X, Bouché N, Mézard C. 2020. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. 16(6), e1008894.","chicago":"Christophorou, Nicolas, Wenjing She, Jincheng Long, Aurélie Hurel, Sébastien Beaubiat, Yassir Idir, Marina Tagliaro-Jahns, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” <i>PLOS Genetics</i>. Public Library of Science (PLoS), 2020. <a href=\"https://doi.org/10.1371/journal.pgen.1008894\">https://doi.org/10.1371/journal.pgen.1008894</a>.","mla":"Christophorou, Nicolas, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” <i>PLOS Genetics</i>, vol. 16, no. 6, e1008894, Public Library of Science (PLoS), 2020, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008894\">10.1371/journal.pgen.1008894</a>.","apa":"Christophorou, N., She, W., Long, J., Hurel, A., Beaubiat, S., Idir, Y., … Mézard, C. (2020). AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. <i>PLOS Genetics</i>. Public Library of Science (PLoS). <a href=\"https://doi.org/10.1371/journal.pgen.1008894\">https://doi.org/10.1371/journal.pgen.1008894</a>","ieee":"N. Christophorou <i>et al.</i>, “AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization,” <i>PLOS Genetics</i>, vol. 16, no. 6. Public Library of Science (PLoS), 2020.","short":"N. Christophorou, W. She, J. Long, A. Hurel, S. Beaubiat, Y. Idir, M. Tagliaro-Jahns, A. Chambon, V. Solier, D. Vezon, M. Grelon, X. Feng, N. Bouché, C. Mézard, PLOS Genetics 16 (2020).","ama":"Christophorou N, She W, Long J, et al. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. <i>PLOS Genetics</i>. 2020;16(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008894\">10.1371/journal.pgen.1008894</a>"},"oa_version":"Published Version","type":"journal_article","publisher":"Public Library of Science (PLoS)","publication_status":"published","article_type":"original","month":"06","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/"}],"keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"date_updated":"2023-05-08T10:54:39Z","department":[{"_id":"XiFe"}],"title":"AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization","pmid":1,"_id":"12189","publication_identifier":{"issn":["1553-7404"]}},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bioinformatics/btaa843"}],"keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"article_type":"original","month":"12","oa_version":"Published Version","type":"journal_article","publication_status":"published","publisher":"Oxford University Press","publication_identifier":{"eissn":["1367-4811"]},"pmid":1,"_id":"14125","department":[{"_id":"FrLo"}],"title":"SCIM: Universal single-cell matching with unpaired feature sets","date_updated":"2023-09-11T10:21:00Z","status":"public","author":[{"first_name":"Stefan G","last_name":"Stark","full_name":"Stark, Stefan G"},{"full_name":"Ficek, Joanna","last_name":"Ficek","first_name":"Joanna"},{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"first_name":"Ximena","last_name":"Bonilla","full_name":"Bonilla, Ximena"},{"full_name":"Chevrier, Stéphane","last_name":"Chevrier","first_name":"Stéphane"},{"first_name":"Franziska","last_name":"Singer","full_name":"Singer, Franziska"},{"first_name":"Rudolf","full_name":"Aebersold, Rudolf","last_name":"Aebersold"},{"first_name":"Faisal S","last_name":"Al-Quaddoomi","full_name":"Al-Quaddoomi, Faisal S"},{"full_name":"Albinus, Jonas","last_name":"Albinus","first_name":"Jonas"},{"full_name":"Alborelli, Ilaria","last_name":"Alborelli","first_name":"Ilaria"},{"last_name":"Andani","full_name":"Andani, Sonali","first_name":"Sonali"},{"first_name":"Per-Olof","full_name":"Attinger, Per-Olof","last_name":"Attinger"},{"first_name":"Marina","last_name":"Bacac","full_name":"Bacac, Marina"},{"first_name":"Daniel","full_name":"Baumhoer, Daniel","last_name":"Baumhoer"},{"last_name":"Beck-Schimmer","full_name":"Beck-Schimmer, Beatrice","first_name":"Beatrice"},{"first_name":"Niko","last_name":"Beerenwinkel","full_name":"Beerenwinkel, Niko"},{"first_name":"Christian","full_name":"Beisel, Christian","last_name":"Beisel"},{"first_name":"Lara","last_name":"Bernasconi","full_name":"Bernasconi, Lara"},{"last_name":"Bertolini","full_name":"Bertolini, Anne","first_name":"Anne"},{"first_name":"Bernd","last_name":"Bodenmiller","full_name":"Bodenmiller, Bernd"},{"full_name":"Bonilla, Ximena","last_name":"Bonilla","first_name":"Ximena"},{"last_name":"Casanova","full_name":"Casanova, Ruben","first_name":"Ruben"},{"first_name":"Stéphane","last_name":"Chevrier","full_name":"Chevrier, Stéphane"},{"last_name":"Chicherova","full_name":"Chicherova, Natalia","first_name":"Natalia"},{"last_name":"D'Costa","full_name":"D'Costa, Maya","first_name":"Maya"},{"first_name":"Esther","last_name":"Danenberg","full_name":"Danenberg, Esther"},{"first_name":"Natalie","full_name":"Davidson, Natalie","last_name":"Davidson"},{"first_name":"Monica-Andreea Dră","full_name":"gan, Monica-Andreea Dră","last_name":"gan"},{"last_name":"Dummer","full_name":"Dummer, Reinhard","first_name":"Reinhard"},{"first_name":"Stefanie","full_name":"Engler, Stefanie","last_name":"Engler"},{"last_name":"Erkens","full_name":"Erkens, Martin","first_name":"Martin"},{"first_name":"Katja","last_name":"Eschbach","full_name":"Eschbach, Katja"},{"full_name":"Esposito, Cinzia","last_name":"Esposito","first_name":"Cinzia"},{"first_name":"André","full_name":"Fedier, André","last_name":"Fedier"},{"first_name":"Pedro","full_name":"Ferreira, Pedro","last_name":"Ferreira"},{"first_name":"Joanna","last_name":"Ficek","full_name":"Ficek, Joanna"},{"first_name":"Anja L","full_name":"Frei, Anja L","last_name":"Frei"},{"first_name":"Bruno","full_name":"Frey, Bruno","last_name":"Frey"},{"last_name":"Goetze","full_name":"Goetze, Sandra","first_name":"Sandra"},{"first_name":"Linda","full_name":"Grob, Linda","last_name":"Grob"},{"first_name":"Gabriele","full_name":"Gut, Gabriele","last_name":"Gut"},{"first_name":"Detlef","full_name":"Günther, Detlef","last_name":"Günther"},{"last_name":"Haberecker","full_name":"Haberecker, Martina","first_name":"Martina"},{"last_name":"Haeuptle","full_name":"Haeuptle, Pirmin","first_name":"Pirmin"},{"last_name":"Heinzelmann-Schwarz","full_name":"Heinzelmann-Schwarz, Viola","first_name":"Viola"},{"full_name":"Herter, Sylvia","last_name":"Herter","first_name":"Sylvia"},{"full_name":"Holtackers, Rene","last_name":"Holtackers","first_name":"Rene"},{"first_name":"Tamara","last_name":"Huesser","full_name":"Huesser, Tamara"},{"last_name":"Irmisch","full_name":"Irmisch, Anja","first_name":"Anja"},{"full_name":"Jacob, Francis","last_name":"Jacob","first_name":"Francis"},{"first_name":"Andrea","full_name":"Jacobs, Andrea","last_name":"Jacobs"},{"last_name":"Jaeger","full_name":"Jaeger, Tim M","first_name":"Tim M"},{"first_name":"Katharina","last_name":"Jahn","full_name":"Jahn, Katharina"},{"last_name":"James","full_name":"James, Alva R","first_name":"Alva R"},{"first_name":"Philip M","last_name":"Jermann","full_name":"Jermann, Philip M"},{"first_name":"André","full_name":"Kahles, André","last_name":"Kahles"},{"last_name":"Kahraman","full_name":"Kahraman, Abdullah","first_name":"Abdullah"},{"first_name":"Viktor H","last_name":"Koelzer","full_name":"Koelzer, Viktor H"},{"first_name":"Werner","last_name":"Kuebler","full_name":"Kuebler, Werner"},{"first_name":"Jack","last_name":"Kuipers","full_name":"Kuipers, Jack"},{"last_name":"Kunze","full_name":"Kunze, Christian P","first_name":"Christian P"},{"full_name":"Kurzeder, Christian","last_name":"Kurzeder","first_name":"Christian"},{"first_name":"Kjong-Van","full_name":"Lehmann, Kjong-Van","last_name":"Lehmann"},{"first_name":"Mitchell","last_name":"Levesque","full_name":"Levesque, Mitchell"},{"first_name":"Sebastian","last_name":"Lugert","full_name":"Lugert, Sebastian"},{"last_name":"Maass","full_name":"Maass, Gerd","first_name":"Gerd"},{"full_name":"Manz, Markus","last_name":"Manz","first_name":"Markus"},{"first_name":"Philipp","full_name":"Markolin, Philipp","last_name":"Markolin"},{"first_name":"Julien","full_name":"Mena, Julien","last_name":"Mena"},{"last_name":"Menzel","full_name":"Menzel, Ulrike","first_name":"Ulrike"},{"full_name":"Metzler, Julian M","last_name":"Metzler","first_name":"Julian M"},{"full_name":"Miglino, Nicola","last_name":"Miglino","first_name":"Nicola"},{"full_name":"Milani, Emanuela S","last_name":"Milani","first_name":"Emanuela S"},{"first_name":"Holger","last_name":"Moch","full_name":"Moch, Holger"},{"first_name":"Simone","last_name":"Muenst","full_name":"Muenst, Simone"},{"first_name":"Riccardo","last_name":"Murri","full_name":"Murri, Riccardo"},{"full_name":"Ng, Charlotte KY","last_name":"Ng","first_name":"Charlotte KY"},{"last_name":"Nicolet","full_name":"Nicolet, Stefan","first_name":"Stefan"},{"last_name":"Nowak","full_name":"Nowak, Marta","first_name":"Marta"},{"first_name":"Patrick GA","last_name":"Pedrioli","full_name":"Pedrioli, Patrick GA"},{"last_name":"Pelkmans","full_name":"Pelkmans, Lucas","first_name":"Lucas"},{"first_name":"Salvatore","last_name":"Piscuoglio","full_name":"Piscuoglio, Salvatore"},{"last_name":"Prummer","full_name":"Prummer, Michael","first_name":"Michael"},{"last_name":"Ritter","full_name":"Ritter, Mathilde","first_name":"Mathilde"},{"full_name":"Rommel, Christian","last_name":"Rommel","first_name":"Christian"},{"first_name":"María L","last_name":"Rosano-González","full_name":"Rosano-González, María L"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"first_name":"Natascha","full_name":"Santacroce, Natascha","last_name":"Santacroce"},{"last_name":"Castillo","full_name":"Castillo, Jacobo Sarabia del","first_name":"Jacobo Sarabia del"},{"full_name":"Schlenker, Ramona","last_name":"Schlenker","first_name":"Ramona"},{"first_name":"Petra C","last_name":"Schwalie","full_name":"Schwalie, Petra C"},{"full_name":"Schwan, Severin","last_name":"Schwan","first_name":"Severin"},{"first_name":"Tobias","last_name":"Schär","full_name":"Schär, Tobias"},{"full_name":"Senti, Gabriela","last_name":"Senti","first_name":"Gabriela"},{"last_name":"Singer","full_name":"Singer, Franziska","first_name":"Franziska"},{"first_name":"Sujana","last_name":"Sivapatham","full_name":"Sivapatham, Sujana"},{"first_name":"Berend","last_name":"Snijder","full_name":"Snijder, Berend"},{"full_name":"Sobottka, Bettina","last_name":"Sobottka","first_name":"Bettina"},{"last_name":"Sreedharan","full_name":"Sreedharan, Vipin T","first_name":"Vipin T"},{"full_name":"Stark, Stefan","last_name":"Stark","first_name":"Stefan"},{"first_name":"Daniel J","full_name":"Stekhoven, Daniel J","last_name":"Stekhoven"},{"first_name":"Alexandre PA","full_name":"Theocharides, Alexandre PA","last_name":"Theocharides"},{"last_name":"Thomas","full_name":"Thomas, Tinu M","first_name":"Tinu M"},{"last_name":"Tolnay","full_name":"Tolnay, Markus","first_name":"Markus"},{"first_name":"Vinko","last_name":"Tosevski","full_name":"Tosevski, Vinko"},{"first_name":"Nora C","full_name":"Toussaint, Nora C","last_name":"Toussaint"},{"first_name":"Mustafa A","last_name":"Tuncel","full_name":"Tuncel, Mustafa A"},{"first_name":"Marina","last_name":"Tusup","full_name":"Tusup, Marina"},{"first_name":"Audrey Van","last_name":"Drogen","full_name":"Drogen, Audrey Van"},{"last_name":"Vetter","full_name":"Vetter, Marcus","first_name":"Marcus"},{"first_name":"Tatjana","full_name":"Vlajnic, Tatjana","last_name":"Vlajnic"},{"last_name":"Weber","full_name":"Weber, Sandra","first_name":"Sandra"},{"full_name":"Weber, Walter P","last_name":"Weber","first_name":"Walter P"},{"first_name":"Rebekka","last_name":"Wegmann","full_name":"Wegmann, Rebekka"},{"first_name":"Michael","last_name":"Weller","full_name":"Weller, Michael"},{"first_name":"Fabian","last_name":"Wendt","full_name":"Wendt, Fabian"},{"first_name":"Norbert","full_name":"Wey, Norbert","last_name":"Wey"},{"last_name":"Wicki","full_name":"Wicki, Andreas","first_name":"Andreas"},{"first_name":"Bernd","full_name":"Wollscheid, Bernd","last_name":"Wollscheid"},{"last_name":"Yu","full_name":"Yu, Shuqing","first_name":"Shuqing"},{"last_name":"Ziegler","full_name":"Ziegler, Johanna","first_name":"Johanna"},{"first_name":"Marc","last_name":"Zimmermann","full_name":"Zimmermann, Marc"},{"last_name":"Zoche","full_name":"Zoche, Martin","first_name":"Martin"},{"last_name":"Zuend","full_name":"Zuend, Gregor","first_name":"Gregor"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"first_name":"Kjong-Van","last_name":"Lehmann","full_name":"Lehmann, Kjong-Van"}],"external_id":{"pmid":["33381818"]},"volume":36,"extern":"1","date_published":"2020-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"Supplement_2","language":[{"iso":"eng"}],"page":"i919-i927","publication":"Bioinformatics","year":"2020","day":"01","scopus_import":"1","date_created":"2023-08-21T12:28:20Z","citation":{"ieee":"S. G. Stark <i>et al.</i>, “SCIM: Universal single-cell matching with unpaired feature sets,” <i>Bioinformatics</i>, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.","short":"S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R. Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger, M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi, A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova, M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens, K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey, S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz, S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger, K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler, J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G. Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S. Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli, L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González, G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan, T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan, S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski, N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S. Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid, S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann, Bioinformatics 36 (2020) i919–i927.","ama":"Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. <i>Bioinformatics</i>. 2020;36(Supplement_2):i919-i927. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">10.1093/bioinformatics/btaa843</a>","ista":"Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927.","mla":"Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” <i>Bioinformatics</i>, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">10.1093/bioinformatics/btaa843</a>.","chicago":"Stark, Stefan G, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Rudolf Aebersold, et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” <i>Bioinformatics</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">https://doi.org/10.1093/bioinformatics/btaa843</a>.","apa":"Stark, S. G., Ficek, J., Locatello, F., Bonilla, X., Chevrier, S., Singer, F., … Lehmann, K.-V. (2020). SCIM: Universal single-cell matching with unpaired feature sets. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">https://doi.org/10.1093/bioinformatics/btaa843</a>"},"quality_controlled":"1","doi":"10.1093/bioinformatics/btaa843","intvolume":"        36","related_material":{"link":[{"url":"https://github.com/ratschlab/scim","relation":"software"}]},"oa":1,"abstract":[{"text":"Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.\r\nResults: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively.","lang":"eng"}],"article_processing_charge":"No"},{"date_updated":"2023-09-12T07:44:48Z","title":"A commentary on the unsupervised learning of disentangled representations","department":[{"_id":"FrLo"}],"_id":"14186","publication_identifier":{"eissn":["2374-3468"],"isbn":["9781577358350"]},"publication_status":"published","type":"conference","publisher":"Association for the Advancement of Artificial Intelligence","oa_version":"Preprint","arxiv":1,"month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.14184"}],"conference":{"end_date":"2020-02-12","name":"AAAI: Conference on Artificial Intelligence","location":"New York, NY, United States","start_date":"2020-02-07"},"article_processing_charge":"No","abstract":[{"lang":"eng","text":"The goal of the unsupervised learning of disentangled representations is to\r\nseparate the independent explanatory factors of variation in the data without\r\naccess to supervision. In this paper, we summarize the results of Locatello et\r\nal., 2019, and focus on their implications for practitioners. We discuss the\r\ntheoretical result showing that the unsupervised learning of disentangled\r\nrepresentations is fundamentally impossible without inductive biases and the\r\npractical challenges it entails. Finally, we comment on our experimental\r\nfindings, highlighting the limitations of state-of-the-art approaches and\r\ndirections for future research."}],"oa":1,"intvolume":"        34","doi":"10.1609/aaai.v34i09.7120","quality_controlled":"1","date_created":"2023-08-22T14:07:26Z","citation":{"ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A commentary on the unsupervised learning of disentangled representations. The 34th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 34, 13681–13684.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Commentary on the Unsupervised Learning of Disentangled Representations.” In <i>The 34th AAAI Conference on Artificial Intelligence</i>, 34:13681–84. Association for the Advancement of Artificial Intelligence, 2020. <a href=\"https://doi.org/10.1609/aaai.v34i09.7120\">https://doi.org/10.1609/aaai.v34i09.7120</a>.","mla":"Locatello, Francesco, et al. “A Commentary on the Unsupervised Learning of Disentangled Representations.” <i>The 34th AAAI Conference on Artificial Intelligence</i>, vol. 34, no. 9, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–84, doi:<a href=\"https://doi.org/10.1609/aaai.v34i09.7120\">10.1609/aaai.v34i09.7120</a>.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., &#38; Bachem, O. (2020). A commentary on the unsupervised learning of disentangled representations. In <i>The 34th AAAI Conference on Artificial Intelligence</i> (Vol. 34, pp. 13681–13684). New York, NY, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v34i09.7120\">https://doi.org/10.1609/aaai.v34i09.7120</a>","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, The 34th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–13684.","ieee":"F. Locatello <i>et al.</i>, “A commentary on the unsupervised learning of disentangled representations,” in <i>The 34th AAAI Conference on Artificial Intelligence</i>, New York, NY, United States, 2020, vol. 34, no. 9, pp. 13681–13684.","ama":"Locatello F, Bauer S, Lucic M, et al. A commentary on the unsupervised learning of disentangled representations. In: <i>The 34th AAAI Conference on Artificial Intelligence</i>. Vol 34. Association for the Advancement of Artificial Intelligence; 2020:13681-13684. doi:<a href=\"https://doi.org/10.1609/aaai.v34i09.7120\">10.1609/aaai.v34i09.7120</a>"},"scopus_import":"1","day":"28","year":"2020","publication":"The 34th AAAI Conference on Artificial Intelligence","page":"13681-13684","language":[{"iso":"eng"}],"issue":"9","date_published":"2020-07-28T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","volume":34,"external_id":{"arxiv":["2007.14184"]},"author":[{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"},{"last_name":"Lucic","full_name":"Lucic, Mario","first_name":"Mario"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"full_name":"Gelly, Sylvain","last_name":"Gelly","first_name":"Sylvain"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"}],"status":"public"},{"title":"Stochastic Frank-Wolfe for constrained finite-sum minimization","department":[{"_id":"FrLo"}],"date_updated":"2023-09-12T08:03:40Z","_id":"14187","arxiv":1,"oa_version":"Preprint","publication_status":"published","type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/2002.11860","open_access":"1"}],"month":"07","oa":1,"abstract":[{"lang":"eng","text":"We propose a novel Stochastic Frank-Wolfe (a.k.a. conditional gradient)\r\nalgorithm for constrained smooth finite-sum minimization with a generalized\r\nlinear prediction/structure. This class of problems includes empirical risk\r\nminimization with sparse, low-rank, or other structured constraints. The\r\nproposed method is simple to implement, does not require step-size tuning, and\r\nhas a constant per-iteration cost that is independent of the dataset size.\r\nFurthermore, as a byproduct of the method we obtain a stochastic estimator of\r\nthe Frank-Wolfe gap that can be used as a stopping criterion. Depending on the\r\nsetting, the proposed method matches or improves on the best computational\r\nguarantees for Stochastic Frank-Wolfe algorithms. Benchmarks on several\r\ndatasets highlight different regimes in which the proposed method exhibits a\r\nfaster empirical convergence than related methods. Finally, we provide an\r\nimplementation of all considered methods in an open-source package."}],"article_processing_charge":"No","conference":{"end_date":"2020-07-18","name":"International Conference on Machine Learning","location":"Virtual","start_date":"2020-07-13"},"alternative_title":["PMLR"],"day":"27","quality_controlled":"1","date_created":"2023-08-22T14:07:52Z","citation":{"apa":"Négiar, G., Dresdner, G., Tsai, A., Ghaoui, L. E., Locatello, F., Freund, R. M., &#38; Pedregosa, F. (2020). Stochastic Frank-Wolfe for constrained finite-sum minimization. In <i>Proceedings of the 37th International Conference on Machine Learning</i> (Vol. 119, pp. 7253–7262). Virtual.","chicago":"Négiar, Geoffrey, Gideon Dresdner, Alicia Tsai, Laurent El Ghaoui, Francesco Locatello, Robert M. Freund, and Fabian Pedregosa. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” In <i>Proceedings of the 37th International Conference on Machine Learning</i>, 119:7253–62, 2020.","mla":"Négiar, Geoffrey, et al. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” <i>Proceedings of the 37th International Conference on Machine Learning</i>, vol. 119, 2020, pp. 7253–62.","ista":"Négiar G, Dresdner G, Tsai A, Ghaoui LE, Locatello F, Freund RM, Pedregosa F. 2020. Stochastic Frank-Wolfe for constrained finite-sum minimization. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 7253–7262.","ama":"Négiar G, Dresdner G, Tsai A, et al. Stochastic Frank-Wolfe for constrained finite-sum minimization. In: <i>Proceedings of the 37th International Conference on Machine Learning</i>. Vol 119. ; 2020:7253-7262.","short":"G. Négiar, G. Dresdner, A. Tsai, L.E. Ghaoui, F. Locatello, R.M. Freund, F. Pedregosa, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 7253–7262.","ieee":"G. Négiar <i>et al.</i>, “Stochastic Frank-Wolfe for constrained finite-sum minimization,” in <i>Proceedings of the 37th International Conference on Machine Learning</i>, Virtual, 2020, vol. 119, pp. 7253–7262."},"intvolume":"       119","language":[{"iso":"eng"}],"publication":"Proceedings of the 37th International Conference on Machine Learning","page":"7253-7262","year":"2020","status":"public","external_id":{"arxiv":["2002.11860"]},"author":[{"last_name":"Négiar","full_name":"Négiar, Geoffrey","first_name":"Geoffrey"},{"full_name":"Dresdner, Gideon","last_name":"Dresdner","first_name":"Gideon"},{"first_name":"Alicia","last_name":"Tsai","full_name":"Tsai, Alicia"},{"first_name":"Laurent El","last_name":"Ghaoui","full_name":"Ghaoui, Laurent El"},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"last_name":"Freund","full_name":"Freund, Robert M.","first_name":"Robert M."},{"first_name":"Fabian","full_name":"Pedregosa, Fabian","last_name":"Pedregosa"}],"extern":"1","volume":119,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-07-27T00:00:00Z"},{"author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"first_name":"Ben","last_name":"Poole","full_name":"Poole, Ben"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"},{"first_name":"Michael","last_name":"Tschannen","full_name":"Tschannen, Michael"}],"external_id":{"arxiv":["2002.02886"]},"extern":"1","volume":119,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-07-07T00:00:00Z","status":"public","year":"2020","page":"6348–6359","publication":"Proceedings of the 37th International Conference on Machine Learning","language":[{"iso":"eng"}],"intvolume":"       119","alternative_title":["PMLR"],"day":"07","scopus_import":"1","citation":{"ama":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. Weakly-supervised disentanglement without compromises. In: <i>Proceedings of the 37th International Conference on Machine Learning</i>. Vol 119. ; 2020:6348–6359.","ieee":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, and M. Tschannen, “Weakly-supervised disentanglement without compromises,” in <i>Proceedings of the 37th International Conference on Machine Learning</i>, Virtual, 2020, vol. 119, pp. 6348–6359.","short":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, M. Tschannen, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 6348–6359.","apa":"Locatello, F., Poole, B., Rätsch, G., Schölkopf, B., Bachem, O., &#38; Tschannen, M. (2020). Weakly-supervised disentanglement without compromises. In <i>Proceedings of the 37th International Conference on Machine Learning</i> (Vol. 119, pp. 6348–6359). Virtual.","mla":"Locatello, Francesco, et al. “Weakly-Supervised Disentanglement without Compromises.” <i>Proceedings of the 37th International Conference on Machine Learning</i>, vol. 119, 2020, pp. 6348–6359.","chicago":"Locatello, Francesco, Ben Poole, Gunnar Rätsch, Bernhard Schölkopf, Olivier Bachem, and Michael Tschannen. “Weakly-Supervised Disentanglement without Compromises.” In <i>Proceedings of the 37th International Conference on Machine Learning</i>, 119:6348–6359, 2020.","ista":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. 2020. Weakly-supervised disentanglement without compromises. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 6348–6359."},"date_created":"2023-08-22T14:08:14Z","quality_controlled":"1","article_processing_charge":"No","conference":{"start_date":"2020-07-13","end_date":"2020-07-18","location":"Virtual","name":"International Conference on Machine Learning"},"oa":1,"abstract":[{"lang":"eng","text":"Intelligent agents should be able to learn useful representations by\r\nobserving changes in their environment. We model such observations as pairs of\r\nnon-i.i.d. images sharing at least one of the underlying factors of variation.\r\nFirst, we theoretically show that only knowing how many factors have changed,\r\nbut not which ones, is sufficient to learn disentangled representations.\r\nSecond, we provide practical algorithms that learn disentangled representations\r\nfrom pairs of images without requiring annotation of groups, individual\r\nfactors, or the number of factors that have changed. Third, we perform a\r\nlarge-scale empirical study and show that such pairs of observations are\r\nsufficient to reliably learn disentangled representations on several benchmark\r\ndata sets. Finally, we evaluate our learned representations and find that they\r\nare simultaneously useful on a diverse suite of tasks, including generalization\r\nunder covariate shifts, fairness, and abstract reasoning. Overall, our results\r\ndemonstrate that weak supervision enables learning of useful disentangled\r\nrepresentations in realistic scenarios."}],"month":"07","main_file_link":[{"url":"https://arxiv.org/abs/2002.02886","open_access":"1"}],"oa_version":"Preprint","publication_status":"published","type":"conference","arxiv":1,"_id":"14188","date_updated":"2024-10-14T12:28:02Z","department":[{"_id":"FrLo"}],"title":"Weakly-supervised disentanglement without compromises"},{"article_number":"209","article_processing_charge":"No","has_accepted_license":"1","abstract":[{"text":"The idea behind the unsupervised learning of disentangled representations is that real-world data is generated by a few explanatory factors of variation which can be recovered by unsupervised learning algorithms. In this paper, we provide a sober look at recent progress in the field and challenge some common assumptions. We first theoretically show that the unsupervised learning of disentangled representations is fundamentally impossible without inductive biases on both the models and the data. Then, we train over 14000\r\n models covering most prominent methods and evaluation metrics in a reproducible large-scale experimental study on eight data sets. We observe that while the different methods successfully enforce properties “encouraged” by the corresponding losses, well-disentangled models seemingly cannot be identified without supervision. Furthermore, different evaluation metrics do not always agree on what should be considered “disentangled” and exhibit systematic differences in the estimation. Finally, increased disentanglement does not seem to necessarily lead to a decreased sample complexity of learning for downstream tasks. Our results suggest that future work on disentanglement learning should be explicit about the role of inductive biases and (implicit) supervision, investigate concrete benefits of enforcing disentanglement of the learned representations, and consider a reproducible experimental setup covering several data sets.","lang":"eng"}],"ddc":["000"],"oa":1,"intvolume":"        21","quality_controlled":"1","citation":{"ieee":"F. Locatello <i>et al.</i>, “A sober look at the unsupervised learning of disentangled representations and their evaluation,” <i>Journal of Machine Learning Research</i>, vol. 21. MIT Press, 2020.","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, Journal of Machine Learning Research 21 (2020).","ama":"Locatello F, Bauer S, Lucic M, et al. A sober look at the unsupervised learning of disentangled representations and their evaluation. <i>Journal of Machine Learning Research</i>. 2020;21.","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 21, 209.","mla":"Locatello, Francesco, et al. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” <i>Journal of Machine Learning Research</i>, vol. 21, 209, MIT Press, 2020.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., &#38; Bachem, O. (2020). A sober look at the unsupervised learning of disentangled representations and their evaluation. <i>Journal of Machine Learning Research</i>. MIT Press.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” <i>Journal of Machine Learning Research</i>. MIT Press, 2020."},"date_created":"2023-08-22T14:10:34Z","scopus_import":"1","day":"01","year":"2020","publication":"Journal of Machine Learning Research","language":[{"iso":"eng"}],"date_published":"2020-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","volume":21,"author":[{"first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"},{"full_name":"Lucic, Mario","last_name":"Lucic","first_name":"Mario"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"last_name":"Gelly","full_name":"Gelly, Sylvain","first_name":"Sylvain"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"last_name":"Bachem","full_name":"Bachem, Olivier","first_name":"Olivier"}],"external_id":{"arxiv":["2010.14766"]},"status":"public","date_updated":"2024-10-14T12:28:26Z","title":"A sober look at the unsupervised learning of disentangled representations and their evaluation","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"FrLo"}],"_id":"14195","publication_status":"published","type":"journal_article","publisher":"MIT Press","oa_version":"Published Version","arxiv":1,"month":"09","article_type":"original","main_file_link":[{"open_access":"1","url":"https://jmlr.csail.mit.edu/papers/v21/19-976.html"}]},{"title":"Object-centric learning with slot attention","department":[{"_id":"FrLo"}],"date_updated":"2025-07-10T11:50:47Z","publication_identifier":{"eissn":["1049-5258"],"isbn":["9781713829546"]},"_id":"14326","arxiv":1,"type":"conference","publication_status":"published","publisher":"Neural Information Processing Systems Foundation","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2006.15055"}],"month":"12","abstract":[{"text":"Learning object-centric representations of complex scenes is a promising step towards enabling efficient abstract reasoning from low-level perceptual features. Yet, most deep learning approaches learn distributed representations that do not capture the compositional properties of natural scenes. In this paper, we present the Slot Attention module, an architectural component that interfaces with perceptual representations such as the output of a convolutional neural network and produces a set of task-dependent abstract representations which we call slots. These slots are exchangeable and can bind to any object in the input by specializing through a competitive procedure over multiple rounds of attention. We empirically demonstrate that Slot Attention can extract object-centric representations that enable generalization to unseen compositions when trained on unsupervised object discovery and supervised property prediction tasks.\r\n\r\n","lang":"eng"}],"oa":1,"conference":{"start_date":"2020-12-06","end_date":"2020-12-12","name":"NeurIPS: Neural Information Processing Systems","location":"Virtual"},"article_processing_charge":"No","date_created":"2023-09-13T12:03:46Z","quality_controlled":"1","citation":{"ista":"Locatello F, Weissenborn D, Unterthiner T, Mahendran A, Heigold G, Uszkoreit J, Dosovitskiy A, Kipf T. 2020. Object-centric learning with slot attention. 34th International Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 33, 11525–11538.","mla":"Locatello, Francesco, et al. “Object-Centric Learning with Slot Attention.” <i>34th International Conference on Neural Information Processing Systems</i>, vol. 33, Neural Information Processing Systems Foundation, 2020, pp. 11525–38.","chicago":"Locatello, Francesco, Dirk Weissenborn, Thomas Unterthiner, Aravindh Mahendran, Georg Heigold, Jakob Uszkoreit, Alexey Dosovitskiy, and Thomas Kipf. “Object-Centric Learning with Slot Attention.” In <i>34th International Conference on Neural Information Processing Systems</i>, 33:11525–38. Neural Information Processing Systems Foundation, 2020.","apa":"Locatello, F., Weissenborn, D., Unterthiner, T., Mahendran, A., Heigold, G., Uszkoreit, J., … Kipf, T. (2020). Object-centric learning with slot attention. In <i>34th International Conference on Neural Information Processing Systems</i> (Vol. 33, pp. 11525–11538). Virtual: Neural Information Processing Systems Foundation.","ama":"Locatello F, Weissenborn D, Unterthiner T, et al. Object-centric learning with slot attention. In: <i>34th International Conference on Neural Information Processing Systems</i>. Vol 33. Neural Information Processing Systems Foundation; 2020:11525-11538.","short":"F. Locatello, D. Weissenborn, T. Unterthiner, A. Mahendran, G. Heigold, J. Uszkoreit, A. Dosovitskiy, T. Kipf, in:, 34th International Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2020, pp. 11525–11538.","ieee":"F. Locatello <i>et al.</i>, “Object-centric learning with slot attention,” in <i>34th International Conference on Neural Information Processing Systems</i>, Virtual, 2020, vol. 33, pp. 11525–11538."},"day":"20","alternative_title":["Advances in Neural Information Processing Systems"],"intvolume":"        33","page":"11525-11538","publication":"34th International Conference on Neural Information Processing Systems","language":[{"iso":"eng"}],"year":"2020","status":"public","date_published":"2020-12-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","volume":33,"external_id":{"arxiv":["2006.15055"]},"author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Weissenborn, Dirk","last_name":"Weissenborn","first_name":"Dirk"},{"first_name":"Thomas","full_name":"Unterthiner, Thomas","last_name":"Unterthiner"},{"first_name":"Aravindh","full_name":"Mahendran, Aravindh","last_name":"Mahendran"},{"last_name":"Heigold","full_name":"Heigold, Georg","first_name":"Georg"},{"first_name":"Jakob","full_name":"Uszkoreit, Jakob","last_name":"Uszkoreit"},{"last_name":"Dosovitskiy","full_name":"Dosovitskiy, Alexey","first_name":"Alexey"},{"first_name":"Thomas","full_name":"Kipf, Thomas","last_name":"Kipf"}]}]