[{"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9437"},{"status":"public","id":"612","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8532","status":"public"},{"relation":"part_of_dissertation","id":"9756","status":"public"}]},"type":"dissertation","publication_status":"published","doi":"10.15479/at:ista:9562","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-06-01T00:00:00Z","file":[{"access_level":"open_access","file_id":"9563","checksum":"659df5518db495f679cb1df9e9bd1d94","date_updated":"2022-07-02T22:30:04Z","date_created":"2021-06-17T14:03:14Z","creator":"dkleindienst","embargo":"2022-07-01","file_size":77299142,"content_type":"application/pdf","relation":"main_file","file_name":"Thesis.pdf"},{"file_name":"Thesis_source.zip","relation":"source_file","file_size":369804895,"content_type":"application/zip","creator":"dkleindienst","date_updated":"2022-07-02T22:30:04Z","date_created":"2021-06-17T14:04:30Z","checksum":"3bcf63a2b19e5b6663be051bea332748","embargo_to":"open_access","access_level":"closed","file_id":"9564"}],"page":"124","day":"01","OA_place":"publisher","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.","lang":"eng"}],"supervisor":[{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"}],"corr_author":"1","fulldoi":"https://doi.org/10.15479/at:ista:9562","publication_identifier":{"issn":["2663-337X"]},"author":[{"first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","full_name":"Kleindienst, David"}],"year":"2021","oa_version":"Published Version","ddc":["570"],"date_updated":"2026-07-06T13:11:44Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"month":"06","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","_id":"9562","publisher":"Institute of Science and Technology Austria","citation":{"apa":"Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","mla":"Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021."},"date_created":"2021-06-17T14:10:47Z","article_processing_charge":"No","status":"public","file_date_updated":"2022-07-02T22:30:04Z","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","oa":1},{"type":"book_chapter","quality_controlled":"1","publication_status":"published","das_tickbox":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-1-0716-1522-5_19","scopus_import":"1","place":"New York","publication":"Receptor and Ion Channel Detection in the Brain","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"9562","relation":"dissertation_contains","status":"public"}]},"fulldoi":"https://doi.org/10.1007/978-1-0716-1522-5_19","corr_author":"1","ec_funded":1,"keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"name":"Human Brain Project Specific Grant Agreement 1","grant_number":"720270","call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425"}],"series_title":"Neuromethods","publication_identifier":{"eisbn":["9781071615225"],"isbn":["9781071615218"]},"page":"267-283","date_published":"2021-07-27T00:00:00Z","abstract":[{"lang":"eng","text":"High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms."}],"day":"27","month":"07","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"has_accepted_license":"1","alternative_title":["Neuromethods"],"oa_version":"None","year":"2021","acknowledgement":"This work was supported by the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.) and the Austrian Academy of Sciences (DOC fellowship to D.K.).","author":[{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","first_name":"Walter"},{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","first_name":"David"},{"first_name":"Harumi","orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada"},{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"}],"date_updated":"2026-09-25T22:31:02Z","ddc":["573"],"status":"public","intvolume":" 169","title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","_id":"9756","date_created":"2021-07-30T09:34:56Z","citation":{"mla":"Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” Receptor and Ion Channel Detection in the Brain, vol. 169, Humana Press, 2021, pp. 267–83, doi:10.1007/978-1-0716-1522-5_19.","ista":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Neuromethods, vol. 169, 267–283.","ama":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Vol 169. Neuromethods. New York: Humana Press; 2021:267-283. doi:10.1007/978-1-0716-1522-5_19","short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Humana Press, New York, 2021, pp. 267–283.","apa":"Kaufmann, W., Kleindienst, D., Harada, H., & Shigemoto, R. (2021). High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In Receptor and Ion Channel Detection in the Brain (Vol. 169, pp. 267–283). New York: Humana Press. https://doi.org/10.1007/978-1-0716-1522-5_19","ieee":"W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL),” in Receptor and Ion Channel Detection in the Brain, vol. 169, New York: Humana Press, 2021, pp. 267–283.","chicago":"Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In Receptor and Ion Channel Detection in the Brain, 169:267–83. Neuromethods. New York: Humana Press, 2021. https://doi.org/10.1007/978-1-0716-1522-5_19."},"article_processing_charge":"No","volume":169,"publisher":"Humana Press"},{"article_type":"original","_id":"10299","external_id":{"arxiv":["2103.00023"],"pmid":[" 34732570"],"isi":["000720926900019"]},"article_processing_charge":"No","volume":118,"date_created":"2021-11-17T13:24:24Z","citation":{"ieee":"G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 45. National Academy of Sciences, 2021.","chicago":"Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118.","ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences of the United States of America. 2021;118(45). doi:10.1073/pnas.2102350118","ista":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences of the United States of America. 118(45), e2102350118.","mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:10.1073/pnas.2102350118.","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2102350118"},"publisher":"National Academy of Sciences","pmid":1,"status":"public","arxiv":1,"title":"Experimental observation of the origin and structure of elastoinertial turbulence","intvolume":" 118","oa":1,"oa_version":"Preprint","year":"2021","author":[{"last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H","first_name":"George H"},{"last_name":"Lopez Alonso","id":"40770848-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022","first_name":"Jose M"},{"first_name":"Atul","orcid":"0000-0002-3072-5999","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","full_name":"Varshney, Atul"},{"last_name":"Sankar","full_name":"Sankar, Sarath","first_name":"Sarath"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754"}],"acknowledgement":"We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688.","date_updated":"2026-09-25T22:31:05Z","article_number":"e2102350118","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.00023"}],"month":"11","isi":1,"department":[{"_id":"BjHo"}],"issue":"45","date_published":"2021-11-03T00:00:00Z","abstract":[{"text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number.","lang":"eng"}],"day":"03","corr_author":"1","fulldoi":"https://doi.org/10.1073/pnas.2102350118","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"project":[{"_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF","grant_number":"I04188","name":"Instabilities in pulsating pipe flow in complex fluids"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19906"}]},"type":"journal_article","quality_controlled":"1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1073/pnas.2102350118","scopus_import":"1"},{"author":[{"orcid":"0000-0001-5400-8508","first_name":"Stefan","full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"}],"acknowledgement":"We would like to thank D. Abanin and R. Medina for fruitful discussions and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","year":"2021","oa_version":"Published Version","ddc":["530"],"date_updated":"2026-09-25T22:31:11Z","article_number":"491","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"month":"07","isi":1,"has_accepted_license":"1","external_id":{"isi":["000669830600001"],"arxiv":["2101.05742"]},"article_type":"original","_id":"9760","publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","citation":{"short":"S. Sack, M. Serbyn, Quantum 5 (2021).","apa":"Sack, S., & Serbyn, M. (2021). Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/Q-2021-07-01-491","ama":"Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 2021;5. doi:10.22331/Q-2021-07-01-491","mla":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” Quantum, vol. 5, 491, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:10.22331/Q-2021-07-01-491.","ista":"Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 5, 491.","chicago":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021. https://doi.org/10.22331/Q-2021-07-01-491.","ieee":"S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate optimization algorithm,” Quantum, vol. 5. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021."},"article_processing_charge":"Yes","volume":5,"date_created":"2021-08-01T22:01:21Z","status":"public","arxiv":1,"file_date_updated":"2021-08-06T06:44:31Z","title":"Quantum annealing initialization of the quantum approximate optimization algorithm","intvolume":" 5","oa":1,"publication":"Quantum","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14622"}]},"type":"journal_article","quality_controlled":"1","publication_status":"published","doi":"10.22331/Q-2021-07-01-491","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-07-01T00:00:00Z","file":[{"checksum":"9706c2bb8e748e9b5b138381995a7f6f","access_level":"open_access","file_id":"9774","date_updated":"2021-08-06T06:44:31Z","date_created":"2021-08-06T06:44:31Z","creator":"cchlebak","relation":"main_file","file_name":"2021_Quantum_Sack.pdf","file_size":2312482,"content_type":"application/pdf"}],"day":"01","abstract":[{"text":"The quantum approximate optimization algorithm (QAOA) is a prospective near-term quantum algorithm due to its modest circuit depth and promising benchmarks. However, an external parameter optimization required in the QAOA could become a performance bottleneck. This motivates studies of the optimization landscape and search for heuristic ways of parameter initialization. In this work we visualize the optimization landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating that random initialization of the QAOA is prone to converging to local minima with suboptimal performance. We introduce the initialization of QAOA parameters based on the Trotterized quantum annealing (TQA) protocol, parameterized by the Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe issue of false minima for a broad range of time steps, yielding the same performance as the best result out of an exponentially scaling number of random initializations. Moreover, we demonstrate that the optimal value of the time step coincides with the point of proliferation of Trotter errors in quantum annealing. Our results suggest practical ways of initializing QAOA protocols on near-term quantum devices and reveal new connections between QAOA and quantum annealing.","lang":"eng"}],"ec_funded":1,"fulldoi":"https://doi.org/10.22331/Q-2021-07-01-491","corr_author":"1","publication_identifier":{"eissn":["2521-327X"]},"project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}]},{"publication":"Molecular Biology and Evolution","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"related_material":{"record":[{"status":"public","id":"19386","relation":"dissertation_contains"}]},"quality_controlled":"1","type":"journal_article","publication_status":"published","das_tickbox":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1093/molbev/msab178","scopus_import":"1","page":"5345-58","date_published":"2021-06-19T00:00:00Z","file":[{"content_type":"application/pdf","file_size":1008594,"relation":"main_file","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","creator":"dernst","success":1,"date_created":"2022-05-06T09:47:18Z","date_updated":"2022-05-06T09:47:18Z","file_id":"11352","access_level":"open_access","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"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.","lang":"eng"}],"day":"19","fulldoi":"https://doi.org/10.1093/molbev/msab178","corr_author":"1","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","call_identifier":"FWF"}],"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"oa_version":"Published Version","year":"2021","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.","author":[{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"},{"orcid":"0000-0002-8876-6494","first_name":"Mikhail A.","last_name":"Moldovan","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A."},{"orcid":"0000-0002-8101-2518","first_name":"Marion A L","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Picard, Marion A L"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"date_updated":"2026-09-25T22:31:14Z","ddc":["610"],"month":"06","isi":1,"department":[{"_id":"BeVi"}],"has_accepted_license":"1","issue":"12","article_type":"original","_id":"10167","external_id":{"isi":["000741368600009"],"pmid":["34146097"]},"volume":138,"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. Molecular Biology and Evolution. 2021;138(12):5345-5358. doi:10.1093/molbev/msab178","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.","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and Evolution, vol. 138, no. 12, Oxford University Press, 2021, pp. 5345–58, doi:10.1093/molbev/msab178.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., & Vicoso, B. (2021). Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msab178","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution 138 (2021) 5345–58.","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,” Molecular Biology and Evolution, vol. 138, no. 12. Oxford University Press, pp. 5345–58, 2021.","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.” Molecular Biology and Evolution. Oxford University Press, 2021. https://doi.org/10.1093/molbev/msab178."},"article_processing_charge":"No","publisher":"Oxford University Press","file_date_updated":"2022-05-06T09:47:18Z","pmid":1,"status":"public","title":"Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","intvolume":" 138","oa":1},{"page":"741-758","date_published":"2020-08-03T00:00:00Z","abstract":[{"text":"We introduce in this paper AMT2.0, a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended signal temporal logic, which integrates timed regular expressions within signal temporal logic. The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal. We demonstrate the tool functionality on several running examples and case studies, and evaluate its performance.","lang":"eng"}],"day":"03","fulldoi":"https://doi.org/10.1007/s10009-020-00582-z","keyword":["Information Systems","Software"],"publication_identifier":{"eissn":["1433-2787"],"issn":["1433-2779"]},"publication":"International Journal on Software Tools for Technology Transfer","related_material":{"record":[{"relation":"earlier_version","id":"299","status":"public"}]},"language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","doi":"10.1007/s10009-020-00582-z","_id":"10861","article_type":"original","external_id":{"isi":["000555398600001"]},"volume":22,"article_processing_charge":"No","citation":{"ieee":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6. Springer Nature, pp. 741–758, 2020.","chicago":"Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer. Springer Nature, 2020. https://doi.org/10.1007/s10009-020-00582-z.","mla":"Nickovic, Dejan, et al. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6, Springer Nature, 2020, pp. 741–58, doi:10.1007/s10009-020-00582-z.","ista":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2020. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 22(6), 741–758.","ama":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 2020;22(6):741-758. doi:10.1007/s10009-020-00582-z","apa":"Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2020). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. Springer Nature. https://doi.org/10.1007/s10009-020-00582-z","short":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, International Journal on Software Tools for Technology Transfer 22 (2020) 741–758."},"date_created":"2022-03-18T10:10:53Z","publisher":"Springer Nature","status":"public","intvolume":" 22","title":"AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic","year":"2020","oa_version":"None","author":[{"first_name":"Dejan","last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan"},{"first_name":"Olivier","last_name":"Lebeltel","full_name":"Lebeltel, Olivier"},{"last_name":"Maler","full_name":"Maler, Oded","first_name":"Oded"},{"first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","full_name":"Ferrere, Thomas"},{"first_name":"Dogan","full_name":"Ulus, Dogan","last_name":"Ulus"}],"date_updated":"2024-10-09T20:58:18Z","isi":1,"month":"08","department":[{"_id":"ToHe"}],"issue":"6"},{"publication":"Journal of Functional Analysis","language":[{"iso":"eng"}],"publication_status":"published","type":"journal_article","quality_controlled":"1","scopus_import":"1","doi":"10.1016/j.jfa.2020.108639","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-10-15T00:00:00Z","day":"15","abstract":[{"lang":"eng","text":"We consider the sum of two large Hermitian matrices A and B with a Haar unitary conjugation bringing them into a general relative position. We prove that the eigenvalue density on the scale slightly above the local eigenvalue spacing is asymptotically given by the free additive convolution of the laws of A and B as the dimension of the matrix increases. This implies optimal rigidity of the eigenvalues and optimal rate of convergence in Voiculescu's theorem. Our previous works [4], [5] established these results in the bulk spectrum, the current paper completely settles the problem at the spectral edges provided they have the typical square-root behavior. The key element of our proof is to compensate the deterioration of the stability of the subordination equations by sharp error estimates that properly account for the local density near the edge. Our results also hold if the Haar unitary matrix is replaced by the Haar orthogonal matrix."}],"ec_funded":1,"fulldoi":"https://doi.org/10.1016/j.jfa.2020.108639","corr_author":"1","publication_identifier":{"issn":["0022-1236"]},"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"keyword":["Analysis"],"author":[{"full_name":"Bao, Zhigang","last_name":"Bao","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","orcid":"0000-0003-3036-1475"},{"first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Schnelli, Kevin","last_name":"Schnelli","first_name":"Kevin"}],"acknowledgement":"Partially supported by ERC Advanced Grant RANMAT No. 338804.","year":"2020","oa_version":"Preprint","article_number":"108639","date_updated":"2025-04-15T08:05:01Z","department":[{"_id":"LaEr"}],"isi":1,"month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01597"}],"issue":"7","external_id":{"isi":["000559623200009"],"arxiv":["1708.01597"]},"_id":"10862","article_type":"original","publisher":"Elsevier","volume":279,"date_created":"2022-03-18T10:18:59Z","citation":{"short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 279 (2020).","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2020). Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2020.108639","mla":"Bao, Zhigang, et al. “Spectral Rigidity for Addition of Random Matrices at the Regular Edge.” Journal of Functional Analysis, vol. 279, no. 7, 108639, Elsevier, 2020, doi:10.1016/j.jfa.2020.108639.","ista":"Bao Z, Erdös L, Schnelli K. 2020. Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. 279(7), 108639.","ama":"Bao Z, Erdös L, Schnelli K. Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. 2020;279(7). doi:10.1016/j.jfa.2020.108639","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Spectral Rigidity for Addition of Random Matrices at the Regular Edge.” Journal of Functional Analysis. Elsevier, 2020. https://doi.org/10.1016/j.jfa.2020.108639.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Spectral rigidity for addition of random matrices at the regular edge,” Journal of Functional Analysis, vol. 279, no. 7. Elsevier, 2020."},"article_processing_charge":"No","arxiv":1,"status":"public","oa":1,"title":"Spectral rigidity for addition of random matrices at the regular edge","intvolume":" 279"},{"title":"Waist of balls in hyperbolic and spherical spaces","intvolume":" 2020","oa":1,"status":"public","arxiv":1,"date_created":"2022-03-18T11:39:30Z","citation":{"ama":"Akopyan A, Karasev R. Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. 2020;2020(3):669-697. doi:10.1093/imrn/rny037","mla":"Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical Spaces.” International Mathematics Research Notices, vol. 2020, no. 3, Oxford University Press, 2020, pp. 669–97, doi:10.1093/imrn/rny037.","ista":"Akopyan A, Karasev R. 2020. Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. 2020(3), 669–697.","apa":"Akopyan, A., & Karasev, R. (2020). Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rny037","short":"A. Akopyan, R. Karasev, International Mathematics Research Notices 2020 (2020) 669–697.","ieee":"A. Akopyan and R. Karasev, “Waist of balls in hyperbolic and spherical spaces,” International Mathematics Research Notices, vol. 2020, no. 3. Oxford University Press, pp. 669–697, 2020.","chicago":"Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical Spaces.” International Mathematics Research Notices. Oxford University Press, 2020. https://doi.org/10.1093/imrn/rny037."},"article_processing_charge":"No","volume":2020,"publisher":"Oxford University Press","article_type":"original","_id":"10867","external_id":{"isi":["000522852700002"],"arxiv":["1702.07513"]},"issue":"3","month":"02","main_file_link":[{"url":"https://arxiv.org/abs/1702.07513","open_access":"1"}],"isi":1,"department":[{"_id":"HeEd"}],"date_updated":"2023-08-24T14:19:55Z","year":"2020","oa_version":"Preprint","author":[{"orcid":"0000-0002-2548-617X","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","full_name":"Akopyan, Arseniy"},{"last_name":"Karasev","full_name":"Karasev, Roman","first_name":"Roman"}],"acknowledgement":" Supported by the Russian Foundation for Basic Research grant 18-01-00036.","keyword":["General Mathematics"],"publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"fulldoi":"https://doi.org/10.1093/imrn/rny037","abstract":[{"lang":"eng","text":"In this paper we find a tight estimate for Gromov’s waist of the balls in spaces of constant curvature, deduce the estimates for the balls in Riemannian manifolds with upper bounds on the curvature (CAT(ϰ)-spaces), and establish similar result for normed spaces."}],"day":"01","page":"669-697","date_published":"2020-02-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1093/imrn/rny037","scopus_import":"1","quality_controlled":"1","type":"journal_article","publication_status":"published","language":[{"iso":"eng"}],"publication":"International Mathematics Research Notices"},{"status":"public","pmid":1,"file_date_updated":"2023-02-07T11:29:55Z","oa":1,"intvolume":" 117","title":"The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2","external_id":{"pmid":["32601198"]},"_id":"12188","article_type":"original","publisher":"Proceedings of the National Academy of Sciences","citation":{"ieee":"R. H. Bloomer et al., “The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2,” Proceedings of the National Academy of Sciences, vol. 117, no. 28. Proceedings of the National Academy of Sciences, pp. 16660–16666, 2020.","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.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1920621117.","ama":"Bloomer RH, Hutchison CE, Bäurle I, et al. The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. 2020;117(28):16660-16666. doi:10.1073/pnas.1920621117","mla":"Bloomer, Rebecca H., et al. “The Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the National Academy of Sciences, vol. 117, no. 28, Proceedings of the National Academy of Sciences, 2020, pp. 16660–66, doi:10.1073/pnas.1920621117.","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.","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.","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. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1920621117"},"article_processing_charge":"No","date_created":"2023-01-16T09:15:44Z","volume":117,"extern":"1","department":[{"_id":"XiFe"}],"month":"05","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/"}],"issue":"28","has_accepted_license":"1","author":[{"full_name":"Bloomer, Rebecca H.","last_name":"Bloomer","first_name":"Rebecca H."},{"first_name":"Claire E.","last_name":"Hutchison","full_name":"Hutchison, Claire E."},{"full_name":"Bäurle, Isabel","last_name":"Bäurle","first_name":"Isabel"},{"full_name":"Walker, James","last_name":"Walker","first_name":"James"},{"last_name":"Fang","full_name":"Fang, Xiaofeng","first_name":"Xiaofeng"},{"last_name":"Perera","full_name":"Perera, Pumi","first_name":"Pumi"},{"full_name":"Velanis, Christos N.","last_name":"Velanis","first_name":"Christos N."},{"last_name":"Gümüs","full_name":"Gümüs, Serin","first_name":"Serin"},{"first_name":"Christos","last_name":"Spanos","full_name":"Spanos, Christos"},{"first_name":"Juri","full_name":"Rappsilber, Juri","last_name":"Rappsilber"},{"full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"last_name":"Goodrich","full_name":"Goodrich, Justin","first_name":"Justin"},{"full_name":"Dean, Caroline","last_name":"Dean","first_name":"Caroline"}],"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).","oa_version":"Published Version","year":"2020","ddc":["580"],"date_updated":"2023-05-08T10:53:55Z","fulldoi":"https://doi.org/10.1073/pnas.1920621117","publication_identifier":{"issn":["0027-8424","1091-6490"]},"keyword":["Multidisciplinary"],"file":[{"file_name":"2020_PNAS_Bloomer.pdf","relation":"main_file","file_size":1105414,"content_type":"application/pdf","success":1,"creator":"alisjak","date_updated":"2023-02-07T11:29:55Z","date_created":"2023-02-07T11:29:55Z","checksum":"cedee184cb12f454f2fba4158ff47db9","access_level":"open_access","file_id":"12526"}],"date_published":"2020-05-22T00:00:00Z","page":"16660-16666","day":"22","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."}],"publication_status":"published","type":"journal_article","quality_controlled":"1","scopus_import":"1","doi":"10.1073/pnas.1920621117","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the National Academy of Sciences","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}]},{"intvolume":" 16","title":"AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization","oa":1,"status":"public","pmid":1,"publisher":"Public Library of Science (PLoS)","date_created":"2023-01-16T09:16:10Z","volume":16,"article_processing_charge":"No","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.","mla":"Christophorou, Nicolas, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” PLOS Genetics, vol. 16, no. 6, e1008894, Public Library of Science (PLoS), 2020, doi:10.1371/journal.pgen.1008894.","ama":"Christophorou N, She W, Long J, et al. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. 2020;16(6). doi:10.1371/journal.pgen.1008894","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).","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. PLOS Genetics. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1008894","ieee":"N. Christophorou et al., “AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization,” PLOS Genetics, vol. 16, no. 6. Public Library of Science (PLoS), 2020.","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.” PLOS Genetics. Public Library of Science (PLoS), 2020. https://doi.org/10.1371/journal.pgen.1008894."},"external_id":{"pmid":["32598340"]},"article_type":"original","_id":"12189","issue":"6","department":[{"_id":"XiFe"}],"extern":"1","month":"06","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/","open_access":"1"}],"date_updated":"2023-05-08T10:54:39Z","article_number":"e1008894","acknowledgement":"The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript.","author":[{"first_name":"Nicolas","full_name":"Christophorou, Nicolas","last_name":"Christophorou"},{"last_name":"She","full_name":"She, Wenjing","first_name":"Wenjing"},{"last_name":"Long","full_name":"Long, Jincheng","first_name":"Jincheng"},{"last_name":"Hurel","full_name":"Hurel, Aurélie","first_name":"Aurélie"},{"first_name":"Sébastien","full_name":"Beaubiat, Sébastien","last_name":"Beaubiat"},{"first_name":"Yassir","last_name":"Idir","full_name":"Idir, Yassir"},{"first_name":"Marina","full_name":"Tagliaro-Jahns, Marina","last_name":"Tagliaro-Jahns"},{"first_name":"Aurélie","last_name":"Chambon","full_name":"Chambon, Aurélie"},{"full_name":"Solier, Victor","last_name":"Solier","first_name":"Victor"},{"first_name":"Daniel","last_name":"Vezon","full_name":"Vezon, Daniel"},{"full_name":"Grelon, Mathilde","last_name":"Grelon","first_name":"Mathilde"},{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"},{"full_name":"Bouché, Nicolas","last_name":"Bouché","first_name":"Nicolas"},{"full_name":"Mézard, Christine","last_name":"Mézard","first_name":"Christine"}],"oa_version":"Published Version","year":"2020","publication_identifier":{"issn":["1553-7404"]},"keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"fulldoi":"https://doi.org/10.1371/journal.pgen.1008894","day":"29","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"}],"date_published":"2020-06-29T00:00:00Z","doi":"10.1371/journal.pgen.1008894","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","type":"journal_article","publication_status":"published","language":[{"iso":"eng"}],"publication":"PLOS Genetics"},{"author":[{"orcid":"0000-0003-1397-7876","first_name":"Georg M","last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M"},{"orcid":"0000-0001-6613-1378","first_name":"Matthias","full_name":"Wulf, Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","first_name":"Shabir"},{"first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"first_name":"Alfredo R","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez"},{"orcid":"0000-0001-9868-2166","first_name":"William J","full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease"},{"orcid":"0000-0001-6937-5773","first_name":"Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid"},{"full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X"}],"year":"2020","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"8529","relation":"used_in_publication"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ddc":["530"],"date_updated":"2025-06-12T07:03:01Z","department":[{"_id":"JoFi"}],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3961562","open_access":"1"}],"type":"research_data_reference","month":"07","doi":"10.5281/ZENODO.3961561","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-07-27T00:00:00Z","_id":"13056","publisher":"Zenodo","day":"27","citation":{"apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020).","mla":"Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561.","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561.","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561.","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020."},"date_created":"2023-05-23T13:37:41Z","article_processing_charge":"No","abstract":[{"text":"This datasets comprises all data shown in plots of the submitted article \"Converting microwave and telecom photons with a silicon photonic nanomechanical interface\". Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"corr_author":"1","fulldoi":"https://doi.org/10.5281/ZENODO.3961561","status":"public","oa":1,"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface"},{"corr_author":"1","fulldoi":"https://doi.org/10.5061/DRYAD.CRJDFN318","status":"public","oa":1,"title":"Social immunity modulates competition between coinfecting pathogens","date_published":"2020-12-19T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","_id":"13060","day":"19","publisher":"Dryad","article_processing_charge":"No","citation":{"apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Dryad. https://doi.org/10.5061/DRYAD.CRJDFN318","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, (2020).","mla":"Milutinovic, Barbara, et al. Social Immunity Modulates Competition between Coinfecting Pathogens. Dryad, 2020, doi:10.5061/DRYAD.CRJDFN318.","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens, Dryad, 10.5061/DRYAD.CRJDFN318.","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. 2020. doi:10.5061/DRYAD.CRJDFN318","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Dryad, 2020. https://doi.org/10.5061/DRYAD.CRJDFN318.","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens.” Dryad, 2020."},"date_created":"2023-05-23T16:11:22Z","abstract":[{"lang":"eng","text":"Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level."}],"department":[{"_id":"SyCr"},{"_id":"KrCh"}],"month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.crjdfn318"}],"type":"research_data_reference","doi":"10.5061/DRYAD.CRJDFN318","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Barbara","orcid":"0000-0002-8214-4758","full_name":"Milutinovic, Barbara","last_name":"Milutinovic","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stock, Miriam","last_name":"Stock","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V"},{"id":"31757262-F248-11E8-B48F-1D18A9856A87","last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth","first_name":"Elisabeth"},{"orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"year":"2020","oa_version":"Published Version","tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"ddc":["570"],"related_material":{"record":[{"relation":"used_in_publication","id":"7343","status":"public"}]},"date_updated":"2025-06-12T07:32:35Z"},{"date_updated":"2026-06-18T19:37:16Z","tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"ddc":["570"],"related_material":{"link":[{"url":"https://github.com/starnoux/arnoux_et_al_2019","relation":"software"}],"record":[{"relation":"used_in_publication","id":"8928","status":"public"}]},"oa_version":"Published Version","year":"2020","author":[{"last_name":"Arnoux","full_name":"Arnoux, Stephanie","first_name":"Stephanie"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"first_name":"Christopher","last_name":"Sauvage","full_name":"Sauvage, Christopher"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.5061/DRYAD.Q2BVQ83HD","month":"10","type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.q2bvq83hd"}],"department":[{"_id":"NiBa"}],"citation":{"mla":"Arnoux, Stephanie, et al. VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species. Dryad, 2020, doi:10.5061/DRYAD.Q2BVQ83HD.","ama":"Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:10.5061/DRYAD.Q2BVQ83HD","ista":"Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, 10.5061/DRYAD.Q2BVQ83HD.","apa":"Arnoux, S., Fraisse, C., & Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83HD","short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020).","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020.","chicago":"Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. https://doi.org/10.5061/DRYAD.Q2BVQ83HD."},"date_created":"2023-05-23T16:30:20Z","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available."}],"day":"19","publisher":"Dryad","_id":"13065","date_published":"2020-10-19T00:00:00Z","oa":1,"title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","fulldoi":"https://doi.org/10.5061/DRYAD.Q2BVQ83HD","status":"public"},{"_id":"13070","date_published":"2020-09-27T00:00:00Z","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Surpassing the resistance quantum with a geometric superinductor\". Additional raw data are available from the corresponding author on reasonable request."}],"citation":{"chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4052882.","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020.","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020).","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. https://doi.org/10.5281/ZENODO.4052882","mla":"Peruzzo, Matilda, et al. Surpassing the Resistance Quantum with a Geometric Superinductor. Zenodo, 2020, doi:10.5281/ZENODO.4052882.","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, 10.5281/ZENODO.4052882.","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:10.5281/ZENODO.4052882"},"date_created":"2023-05-23T16:42:30Z","article_processing_charge":"No","day":"27","publisher":"Zenodo","status":"public","fulldoi":"https://doi.org/10.5281/ZENODO.4052882","corr_author":"1","title":"Surpassing the resistance quantum with a geometric superinductor","oa":1,"oa_version":"Published Version","year":"2020","author":[{"full_name":"Peruzzo, Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","first_name":"Matilda"},{"first_name":"Andrea","last_name":"Trioni","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","full_name":"Trioni, Andrea"},{"full_name":"Hassani, Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid","orcid":"0000-0001-6937-5773"},{"first_name":"Martin","orcid":"0009-0005-0878-3032","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"date_updated":"2026-04-15T06:43:02Z","related_material":{"record":[{"relation":"used_in_publication","id":"8755","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ddc":["530"],"month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4052883"}],"type":"research_data_reference","department":[{"_id":"JoFi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.5281/ZENODO.4052882"},{"oa":1,"title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","fulldoi":"https://doi.org/10.5281/ZENODO.4266025","corr_author":"1","status":"public","publisher":"Zenodo","day":"10","article_processing_charge":"No","citation":{"ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. 2020. doi:10.5281/ZENODO.4266025","ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel H, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state, Zenodo, 10.5281/ZENODO.4266025.","mla":"Hease, William J., et al. Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State. Zenodo, 2020, doi:10.5281/ZENODO.4266025.","short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H. Schwefel, J.M. Fink, (2020).","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H., & Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. Zenodo. https://doi.org/10.5281/ZENODO.4266025","ieee":"W. J. Hease et al., “Bidirectional electro-optic wavelength conversion in the quantum ground state.” Zenodo, 2020.","chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4266025."},"date_created":"2023-05-23T16:44:11Z","abstract":[{"text":"This dataset comprises all data shown in the plots of the main part of the submitted article \"Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State\". Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"date_published":"2020-11-10T00:00:00Z","_id":"13071","doi":"10.5281/ZENODO.4266025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoFi"}],"month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4266026"}],"type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"related_material":{"record":[{"status":"public","id":"9114","relation":"used_in_publication"}]},"ddc":["530"],"date_updated":"2026-04-15T06:43:26Z","author":[{"full_name":"Hease, William J","last_name":"Hease","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","first_name":"William J"},{"last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","orcid":"0000-0001-6249-5860"},{"full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","last_name":"Sahu","first_name":"Rishabh","orcid":"0000-0001-6264-2162"},{"first_name":"Matthias","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold","first_name":"Georg M","orcid":"0000-0003-1397-7876"},{"last_name":"Schwefel","full_name":"Schwefel, Harald","first_name":"Harald"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"oa_version":"Published Version","year":"2020"},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8708"}]},"tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"ddc":["570"],"date_updated":"2025-07-10T12:01:22Z","author":[{"last_name":"Simon","full_name":"Simon, Alexis","first_name":"Alexis"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","first_name":"Christelle"},{"last_name":"El Ayari","full_name":"El Ayari, Tahani","first_name":"Tahani"},{"last_name":"Liautard-Haag","full_name":"Liautard-Haag, Cathy","first_name":"Cathy"},{"last_name":"Strelkov","full_name":"Strelkov, Petr","first_name":"Petr"},{"last_name":"Welch","full_name":"Welch, John","first_name":"John"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"year":"2020","oa_version":"Published Version","doi":"10.5061/DRYAD.R4XGXD29N","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"type":"research_data_reference","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r4xgxd29n"}],"publisher":"Dryad","day":"22","date_created":"2023-05-23T16:48:27Z","citation":{"ista":"Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, 10.5061/DRYAD.R4XGXD29N.","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:10.5061/DRYAD.R4XGXD29N","mla":"Simon, Alexis, et al. How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels. Dryad, 2020, doi:10.5061/DRYAD.R4XGXD29N.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., & Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. https://doi.org/10.5061/DRYAD.R4XGXD29N","ieee":"A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. https://doi.org/10.5061/DRYAD.R4XGXD29N."},"article_processing_charge":"No","abstract":[{"text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.","lang":"eng"}],"date_published":"2020-09-22T00:00:00Z","_id":"13073","oa":1,"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","fulldoi":"https://doi.org/10.5061/DRYAD.R4XGXD29N","status":"public"},{"author":[{"last_name":"Stark","full_name":"Stark, Stefan G","first_name":"Stefan G"},{"first_name":"Joanna","full_name":"Ficek, Joanna","last_name":"Ficek"},{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683"},{"full_name":"Bonilla, Ximena","last_name":"Bonilla","first_name":"Ximena"},{"first_name":"Stéphane","full_name":"Chevrier, Stéphane","last_name":"Chevrier"},{"first_name":"Franziska","full_name":"Singer, Franziska","last_name":"Singer"},{"full_name":"Aebersold, Rudolf","last_name":"Aebersold","first_name":"Rudolf"},{"first_name":"Faisal S","full_name":"Al-Quaddoomi, Faisal S","last_name":"Al-Quaddoomi"},{"first_name":"Jonas","full_name":"Albinus, Jonas","last_name":"Albinus"},{"last_name":"Alborelli","full_name":"Alborelli, Ilaria","first_name":"Ilaria"},{"first_name":"Sonali","full_name":"Andani, Sonali","last_name":"Andani"},{"first_name":"Per-Olof","last_name":"Attinger","full_name":"Attinger, Per-Olof"},{"last_name":"Bacac","full_name":"Bacac, Marina","first_name":"Marina"},{"first_name":"Daniel","full_name":"Baumhoer, Daniel","last_name":"Baumhoer"},{"full_name":"Beck-Schimmer, Beatrice","last_name":"Beck-Schimmer","first_name":"Beatrice"},{"last_name":"Beerenwinkel","full_name":"Beerenwinkel, Niko","first_name":"Niko"},{"first_name":"Christian","last_name":"Beisel","full_name":"Beisel, Christian"},{"first_name":"Lara","full_name":"Bernasconi, Lara","last_name":"Bernasconi"},{"full_name":"Bertolini, Anne","last_name":"Bertolini","first_name":"Anne"},{"first_name":"Bernd","last_name":"Bodenmiller","full_name":"Bodenmiller, Bernd"},{"last_name":"Bonilla","full_name":"Bonilla, Ximena","first_name":"Ximena"},{"first_name":"Ruben","full_name":"Casanova, Ruben","last_name":"Casanova"},{"first_name":"Stéphane","last_name":"Chevrier","full_name":"Chevrier, Stéphane"},{"full_name":"Chicherova, Natalia","last_name":"Chicherova","first_name":"Natalia"},{"last_name":"D'Costa","full_name":"D'Costa, Maya","first_name":"Maya"},{"full_name":"Danenberg, Esther","last_name":"Danenberg","first_name":"Esther"},{"last_name":"Davidson","full_name":"Davidson, Natalie","first_name":"Natalie"},{"first_name":"Monica-Andreea Dră","last_name":"gan","full_name":"gan, Monica-Andreea Dră"},{"last_name":"Dummer","full_name":"Dummer, Reinhard","first_name":"Reinhard"},{"first_name":"Stefanie","last_name":"Engler","full_name":"Engler, Stefanie"},{"first_name":"Martin","last_name":"Erkens","full_name":"Erkens, Martin"},{"full_name":"Eschbach, Katja","last_name":"Eschbach","first_name":"Katja"},{"first_name":"Cinzia","full_name":"Esposito, Cinzia","last_name":"Esposito"},{"full_name":"Fedier, André","last_name":"Fedier","first_name":"André"},{"last_name":"Ferreira","full_name":"Ferreira, Pedro","first_name":"Pedro"},{"last_name":"Ficek","full_name":"Ficek, Joanna","first_name":"Joanna"},{"full_name":"Frei, Anja L","last_name":"Frei","first_name":"Anja L"},{"first_name":"Bruno","full_name":"Frey, Bruno","last_name":"Frey"},{"first_name":"Sandra","full_name":"Goetze, Sandra","last_name":"Goetze"},{"first_name":"Linda","last_name":"Grob","full_name":"Grob, Linda"},{"last_name":"Gut","full_name":"Gut, Gabriele","first_name":"Gabriele"},{"last_name":"Günther","full_name":"Günther, Detlef","first_name":"Detlef"},{"last_name":"Haberecker","full_name":"Haberecker, Martina","first_name":"Martina"},{"first_name":"Pirmin","last_name":"Haeuptle","full_name":"Haeuptle, Pirmin"},{"first_name":"Viola","last_name":"Heinzelmann-Schwarz","full_name":"Heinzelmann-Schwarz, Viola"},{"first_name":"Sylvia","last_name":"Herter","full_name":"Herter, Sylvia"},{"last_name":"Holtackers","full_name":"Holtackers, Rene","first_name":"Rene"},{"first_name":"Tamara","last_name":"Huesser","full_name":"Huesser, Tamara"},{"last_name":"Irmisch","full_name":"Irmisch, Anja","first_name":"Anja"},{"first_name":"Francis","full_name":"Jacob, Francis","last_name":"Jacob"},{"last_name":"Jacobs","full_name":"Jacobs, Andrea","first_name":"Andrea"},{"first_name":"Tim M","full_name":"Jaeger, Tim M","last_name":"Jaeger"},{"first_name":"Katharina","full_name":"Jahn, Katharina","last_name":"Jahn"},{"full_name":"James, Alva R","last_name":"James","first_name":"Alva R"},{"full_name":"Jermann, Philip M","last_name":"Jermann","first_name":"Philip M"},{"first_name":"André","last_name":"Kahles","full_name":"Kahles, André"},{"full_name":"Kahraman, Abdullah","last_name":"Kahraman","first_name":"Abdullah"},{"first_name":"Viktor H","last_name":"Koelzer","full_name":"Koelzer, Viktor H"},{"first_name":"Werner","full_name":"Kuebler, Werner","last_name":"Kuebler"},{"first_name":"Jack","last_name":"Kuipers","full_name":"Kuipers, Jack"},{"last_name":"Kunze","full_name":"Kunze, Christian P","first_name":"Christian P"},{"first_name":"Christian","last_name":"Kurzeder","full_name":"Kurzeder, Christian"},{"first_name":"Kjong-Van","full_name":"Lehmann, Kjong-Van","last_name":"Lehmann"},{"first_name":"Mitchell","last_name":"Levesque","full_name":"Levesque, Mitchell"},{"full_name":"Lugert, Sebastian","last_name":"Lugert","first_name":"Sebastian"},{"last_name":"Maass","full_name":"Maass, Gerd","first_name":"Gerd"},{"first_name":"Markus","full_name":"Manz, Markus","last_name":"Manz"},{"first_name":"Philipp","full_name":"Markolin, Philipp","last_name":"Markolin"},{"full_name":"Mena, Julien","last_name":"Mena","first_name":"Julien"},{"first_name":"Ulrike","last_name":"Menzel","full_name":"Menzel, Ulrike"},{"first_name":"Julian M","last_name":"Metzler","full_name":"Metzler, Julian M"},{"full_name":"Miglino, Nicola","last_name":"Miglino","first_name":"Nicola"},{"full_name":"Milani, Emanuela S","last_name":"Milani","first_name":"Emanuela S"},{"last_name":"Moch","full_name":"Moch, Holger","first_name":"Holger"},{"first_name":"Simone","full_name":"Muenst, Simone","last_name":"Muenst"},{"first_name":"Riccardo","last_name":"Murri","full_name":"Murri, Riccardo"},{"first_name":"Charlotte KY","full_name":"Ng, Charlotte KY","last_name":"Ng"},{"first_name":"Stefan","last_name":"Nicolet","full_name":"Nicolet, Stefan"},{"full_name":"Nowak, Marta","last_name":"Nowak","first_name":"Marta"},{"full_name":"Pedrioli, Patrick GA","last_name":"Pedrioli","first_name":"Patrick GA"},{"first_name":"Lucas","last_name":"Pelkmans","full_name":"Pelkmans, Lucas"},{"first_name":"Salvatore","full_name":"Piscuoglio, Salvatore","last_name":"Piscuoglio"},{"first_name":"Michael","full_name":"Prummer, Michael","last_name":"Prummer"},{"first_name":"Mathilde","last_name":"Ritter","full_name":"Ritter, Mathilde"},{"last_name":"Rommel","full_name":"Rommel, Christian","first_name":"Christian"},{"first_name":"María L","full_name":"Rosano-González, María L","last_name":"Rosano-González"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"full_name":"Santacroce, Natascha","last_name":"Santacroce","first_name":"Natascha"},{"first_name":"Jacobo Sarabia del","full_name":"Castillo, Jacobo Sarabia del","last_name":"Castillo"},{"first_name":"Ramona","last_name":"Schlenker","full_name":"Schlenker, Ramona"},{"first_name":"Petra C","full_name":"Schwalie, Petra C","last_name":"Schwalie"},{"first_name":"Severin","full_name":"Schwan, Severin","last_name":"Schwan"},{"first_name":"Tobias","full_name":"Schär, Tobias","last_name":"Schär"},{"full_name":"Senti, Gabriela","last_name":"Senti","first_name":"Gabriela"},{"first_name":"Franziska","last_name":"Singer","full_name":"Singer, Franziska"},{"first_name":"Sujana","full_name":"Sivapatham, Sujana","last_name":"Sivapatham"},{"last_name":"Snijder","full_name":"Snijder, Berend","first_name":"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"},{"full_name":"Stekhoven, Daniel J","last_name":"Stekhoven","first_name":"Daniel J"},{"first_name":"Alexandre PA","full_name":"Theocharides, Alexandre PA","last_name":"Theocharides"},{"first_name":"Tinu M","full_name":"Thomas, Tinu M","last_name":"Thomas"},{"first_name":"Markus","last_name":"Tolnay","full_name":"Tolnay, Markus"},{"full_name":"Tosevski, Vinko","last_name":"Tosevski","first_name":"Vinko"},{"last_name":"Toussaint","full_name":"Toussaint, Nora C","first_name":"Nora C"},{"last_name":"Tuncel","full_name":"Tuncel, Mustafa A","first_name":"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"},{"last_name":"Vlajnic","full_name":"Vlajnic, Tatjana","first_name":"Tatjana"},{"first_name":"Sandra","last_name":"Weber","full_name":"Weber, Sandra"},{"full_name":"Weber, Walter P","last_name":"Weber","first_name":"Walter P"},{"last_name":"Wegmann","full_name":"Wegmann, Rebekka","first_name":"Rebekka"},{"last_name":"Weller","full_name":"Weller, Michael","first_name":"Michael"},{"full_name":"Wendt, Fabian","last_name":"Wendt","first_name":"Fabian"},{"first_name":"Norbert","full_name":"Wey, Norbert","last_name":"Wey"},{"full_name":"Wicki, Andreas","last_name":"Wicki","first_name":"Andreas"},{"last_name":"Wollscheid","full_name":"Wollscheid, Bernd","first_name":"Bernd"},{"last_name":"Yu","full_name":"Yu, Shuqing","first_name":"Shuqing"},{"full_name":"Ziegler, Johanna","last_name":"Ziegler","first_name":"Johanna"},{"last_name":"Zimmermann","full_name":"Zimmermann, Marc","first_name":"Marc"},{"full_name":"Zoche, Martin","last_name":"Zoche","first_name":"Martin"},{"last_name":"Zuend","full_name":"Zuend, Gregor","first_name":"Gregor"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"first_name":"Kjong-Van","last_name":"Lehmann","full_name":"Lehmann, Kjong-Van"}],"oa_version":"Published Version","year":"2020","date_updated":"2023-09-11T10:21:00Z","extern":"1","department":[{"_id":"FrLo"}],"month":"12","main_file_link":[{"url":"https://doi.org/10.1093/bioinformatics/btaa843","open_access":"1"}],"issue":"Supplement_2","external_id":{"pmid":["33381818"]},"_id":"14125","article_type":"original","publisher":"Oxford University Press","article_processing_charge":"No","citation":{"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.” Bioinformatics. Oxford University Press, 2020. https://doi.org/10.1093/bioinformatics/btaa843.","ieee":"S. G. Stark et al., “SCIM: Universal single-cell matching with unpaired feature sets,” Bioinformatics, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.","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. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaa843","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.","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.” Bioinformatics, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:10.1093/bioinformatics/btaa843.","ama":"Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 2020;36(Supplement_2):i919-i927. doi:10.1093/bioinformatics/btaa843"},"date_created":"2023-08-21T12:28:20Z","volume":36,"status":"public","pmid":1,"oa":1,"title":"SCIM: Universal single-cell matching with unpaired feature sets","intvolume":" 36","publication":"Bioinformatics","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://github.com/ratschlab/scim","relation":"software"}]},"publication_status":"published","quality_controlled":"1","type":"journal_article","scopus_import":"1","doi":"10.1093/bioinformatics/btaa843","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-12-01T00:00:00Z","page":"i919-i927","day":"01","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"}],"fulldoi":"https://doi.org/10.1093/bioinformatics/btaa843","publication_identifier":{"eissn":["1367-4811"]},"keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"]},{"publication_status":"published","type":"conference","quality_controlled":"1","scopus_import":"1","doi":"10.1609/aaai.v34i09.7120","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"The 34th AAAI Conference on Artificial Intelligence","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1609/aaai.v34i09.7120","publication_identifier":{"eissn":["2374-3468"],"isbn":["9781577358350"]},"date_published":"2020-07-28T00:00:00Z","page":"13681-13684","conference":{"location":"New York, NY, United States","start_date":"2020-02-07","name":"AAAI: Conference on Artificial Intelligence","end_date":"2020-02-12"},"day":"28","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."}],"extern":"1","department":[{"_id":"FrLo"}],"month":"07","main_file_link":[{"url":"https://arxiv.org/abs/2007.14184","open_access":"1"}],"issue":"9","author":[{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","first_name":"Francesco"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"},{"last_name":"Lucic","full_name":"Lucic, Mario","first_name":"Mario"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"full_name":"Gelly, Sylvain","last_name":"Gelly","first_name":"Sylvain"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"}],"oa_version":"Preprint","year":"2020","date_updated":"2023-09-12T07:44:48Z","arxiv":1,"status":"public","oa":1,"intvolume":" 34","title":"A commentary on the unsupervised learning of disentangled representations","external_id":{"arxiv":["2007.14184"]},"_id":"14186","publisher":"Association for the Advancement of Artificial Intelligence","citation":{"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 The 34th AAAI Conference on Artificial Intelligence, 34:13681–84. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i09.7120.","ieee":"F. Locatello et al., “A commentary on the unsupervised learning of disentangled representations,” in The 34th AAAI Conference on Artificial Intelligence, New York, NY, United States, 2020, vol. 34, no. 9, pp. 13681–13684.","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.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A commentary on the unsupervised learning of disentangled representations. In The 34th AAAI Conference on Artificial Intelligence (Vol. 34, pp. 13681–13684). New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i09.7120","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.","ama":"Locatello F, Bauer S, Lucic M, et al. A commentary on the unsupervised learning of disentangled representations. In: The 34th AAAI Conference on Artificial Intelligence. Vol 34. Association for the Advancement of Artificial Intelligence; 2020:13681-13684. doi:10.1609/aaai.v34i09.7120","mla":"Locatello, Francesco, et al. “A Commentary on the Unsupervised Learning of Disentangled Representations.” The 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 9, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–84, doi:10.1609/aaai.v34i09.7120."},"article_processing_charge":"No","date_created":"2023-08-22T14:07:26Z","volume":34},{"oa":1,"intvolume":" 119","title":"Stochastic Frank-Wolfe for constrained finite-sum minimization","arxiv":1,"status":"public","volume":119,"article_processing_charge":"No","date_created":"2023-08-22T14:07:52Z","citation":{"ieee":"G. Négiar et al., “Stochastic Frank-Wolfe for constrained finite-sum minimization,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 7253–7262.","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 Proceedings of the 37th International Conference on Machine Learning, 119:7253–62, 2020.","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: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:7253-7262.","mla":"Négiar, Geoffrey, et al. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 7253–62.","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.","apa":"Négiar, G., Dresdner, G., Tsai, A., Ghaoui, L. E., Locatello, F., Freund, R. M., & Pedregosa, F. (2020). Stochastic Frank-Wolfe for constrained finite-sum minimization. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 7253–7262). Virtual."},"_id":"14187","external_id":{"arxiv":["2002.11860"]},"alternative_title":["PMLR"],"month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.11860"}],"department":[{"_id":"FrLo"}],"extern":"1","date_updated":"2023-09-12T08:03:40Z","oa_version":"Preprint","year":"2020","author":[{"last_name":"Négiar","full_name":"Négiar, Geoffrey","first_name":"Geoffrey"},{"full_name":"Dresdner, Gideon","last_name":"Dresdner","first_name":"Gideon"},{"last_name":"Tsai","full_name":"Tsai, Alicia","first_name":"Alicia"},{"first_name":"Laurent El","full_name":"Ghaoui, Laurent El","last_name":"Ghaoui"},{"orcid":"0000-0002-4850-0683","first_name":"Francesco","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"first_name":"Robert M.","full_name":"Freund, Robert M.","last_name":"Freund"},{"first_name":"Fabian","full_name":"Pedregosa, Fabian","last_name":"Pedregosa"}],"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."}],"conference":{"location":"Virtual","start_date":"2020-07-13","end_date":"2020-07-18","name":"International Conference on Machine Learning"},"day":"27","page":"7253-7262","date_published":"2020-07-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the 37th International Conference on Machine Learning"},{"date_published":"2020-07-07T00:00:00Z","page":"6348–6359","conference":{"end_date":"2020-07-18","name":"International Conference on Machine Learning","start_date":"2020-07-13","location":"Virtual"},"day":"07","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."}],"publication_status":"published","quality_controlled":"1","type":"conference","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the 37th International Conference on Machine Learning","language":[{"iso":"eng"}],"arxiv":1,"status":"public","oa":1,"title":"Weakly-supervised disentanglement without compromises","intvolume":" 119","external_id":{"arxiv":["2002.02886"]},"_id":"14188","article_processing_charge":"No","volume":119,"date_created":"2023-08-22T14:08:14Z","citation":{"apa":"Locatello, F., Poole, B., Rätsch, G., Schölkopf, B., Bachem, O., & Tschannen, M. (2020). Weakly-supervised disentanglement without compromises. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 6348–6359). Virtual.","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.","ama":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. Weakly-supervised disentanglement without compromises. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:6348–6359.","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.","mla":"Locatello, Francesco, et al. “Weakly-Supervised Disentanglement without Compromises.” Proceedings of the 37th International Conference on Machine Learning, 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 Proceedings of the 37th International Conference on Machine Learning, 119:6348–6359, 2020.","ieee":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, and M. Tschannen, “Weakly-supervised disentanglement without compromises,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 6348–6359."},"extern":"1","department":[{"_id":"FrLo"}],"month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.02886"}],"alternative_title":["PMLR"],"author":[{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","first_name":"Francesco"},{"first_name":"Ben","full_name":"Poole, Ben","last_name":"Poole"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"},{"full_name":"Tschannen, Michael","last_name":"Tschannen","first_name":"Michael"}],"oa_version":"Preprint","year":"2020","date_updated":"2024-10-14T12:28:02Z"}]