[{"publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"status":"public","publication_status":"published","ec_funded":1,"title":"Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion","author":[{"orcid":"0000-0001-5013-2843","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"first_name":"Roger","last_name":"Hasler","full_name":"Hasler, Roger"},{"last_name":"Genç","full_name":"Genç, Aziz","first_name":"Aziz"},{"last_name":"Liu","full_name":"Liu, Yu","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740"},{"last_name":"Kuster","full_name":"Kuster, Beatrice","first_name":"Beatrice"},{"last_name":"Schuster","full_name":"Schuster, Maximilian","first_name":"Maximilian"},{"first_name":"Oleksandr","last_name":"Dobrozhan","full_name":"Dobrozhan, Oleksandr"},{"last_name":"Cadavid","full_name":"Cadavid, Doris","first_name":"Doris"},{"first_name":"Jordi","full_name":"Arbiol, Jordi","last_name":"Arbiol"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"},{"full_name":"Kovalenko, Maksym V.","last_name":"Kovalenko","first_name":"Maksym V."}],"_id":"6586","abstract":[{"lang":"eng","text":"The bottom-up assembly of colloidal nanocrystals is a versatile methodology to produce composite nanomaterials with precisely tuned electronic properties. Beyond the synthetic control over crystal domain size, shape, crystal phase, and composition, solution-processed nanocrystals allow exquisite surface engineering. This provides additional means to modulate the nanomaterial characteristics and particularly its electronic transport properties. For instance, inorganic surface ligands can be used to tune the type and concentration of majority carriers or to modify the electronic band structure. Herein, we report the thermoelectric properties of SnTe nanocomposites obtained from the consolidation of surface-engineered SnTe nanocrystals into macroscopic pellets. A CdSe-based ligand is selected to (i) converge the light and heavy bands through partial Cd alloying and (ii) generate CdSe nanoinclusions as a secondary phase within the SnTe matrix, thereby reducing the thermal conductivity. These SnTe-CdSe nanocomposites possess thermoelectric figures of merit of up to 1.3 at 850 K, which is, to the best of our knowledge, the highest thermoelectric figure of merit reported for solution-processed SnTe."}],"issue":"20","doi":"10.1021/jacs.9b01394","file":[{"file_id":"6587","date_created":"2019-06-25T11:59:00Z","date_updated":"2020-07-14T12:47:34Z","access_level":"open_access","content_type":"application/pdf","checksum":"34d7ec837869cc6a07996b54f75696b7","file_name":"JACS_April2019.pdf","relation":"main_file","creator":"cpetz","file_size":6234004}],"has_accepted_license":"1","volume":141,"article_processing_charge":"No","citation":{"mla":"Ibáñez, Maria, et al. “Ligand-Mediated Band Engineering in Bottom-up Assembled SnTe Nanocomposites for Thermoelectric Energy Conversion.” <i>Journal of the American Chemical Society</i>, vol. 141, no. 20, American Chemical Society, 2019, pp. 8025–29, doi:<a href=\"https://doi.org/10.1021/jacs.9b01394\">10.1021/jacs.9b01394</a>.","chicago":"Ibáñez, Maria, Roger Hasler, Aziz Genç, Yu Liu, Beatrice Kuster, Maximilian Schuster, Oleksandr Dobrozhan, et al. “Ligand-Mediated Band Engineering in Bottom-up Assembled SnTe Nanocomposites for Thermoelectric Energy Conversion.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/jacs.9b01394\">https://doi.org/10.1021/jacs.9b01394</a>.","short":"M. Ibáñez, R. Hasler, A. Genç, Y. Liu, B. Kuster, M. Schuster, O. Dobrozhan, D. Cadavid, J. Arbiol, A. Cabot, M.V. Kovalenko, Journal of the American Chemical Society 141 (2019) 8025–8029.","ista":"Ibáñez M, Hasler R, Genç A, Liu Y, Kuster B, Schuster M, Dobrozhan O, Cadavid D, Arbiol J, Cabot A, Kovalenko MV. 2019. Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. 141(20), 8025–8029.","ama":"Ibáñez M, Hasler R, Genç A, et al. Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. <i>Journal of the American Chemical Society</i>. 2019;141(20):8025-8029. doi:<a href=\"https://doi.org/10.1021/jacs.9b01394\">10.1021/jacs.9b01394</a>","ieee":"M. Ibáñez <i>et al.</i>, “Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion,” <i>Journal of the American Chemical Society</i>, vol. 141, no. 20. American Chemical Society, pp. 8025–8029, 2019.","apa":"Ibáñez, M., Hasler, R., Genç, A., Liu, Y., Kuster, B., Schuster, M., … Kovalenko, M. V. (2019). Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.9b01394\">https://doi.org/10.1021/jacs.9b01394</a>"},"day":"19","month":"04","file_date_updated":"2020-07-14T12:47:34Z","ddc":["540"],"pmid":1,"oa_version":"Published Version","publication":"Journal of the American Chemical Society","date_updated":"2023-09-05T12:03:45Z","page":"8025-8029","article_type":"original","oa":1,"year":"2019","publisher":"American Chemical Society","intvolume":"       141","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","department":[{"_id":"MaIb"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000469292300004"],"pmid":["31017419 "]},"date_published":"2019-04-19T00:00:00Z","date_created":"2019-06-25T11:53:35Z","scopus_import":"1"},{"citation":{"short":"N.H. Konstantinov, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 3488–3498.","ista":"Konstantinov NH, Lampert C. 2019. Robust learning from untrusted sources. Proceedings of the 36th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 97, 3488–3498.","ama":"Konstantinov NH, Lampert C. Robust learning from untrusted sources. In: <i>Proceedings of the 36th International Conference on Machine Learning</i>. Vol 97. ML Research Press; 2019:3488-3498.","apa":"Konstantinov, N. H., &#38; Lampert, C. (2019). Robust learning from untrusted sources. In <i>Proceedings of the 36th International Conference on Machine Learning</i> (Vol. 97, pp. 3488–3498). Long Beach, CA, USA: ML Research Press.","ieee":"N. H. Konstantinov and C. Lampert, “Robust learning from untrusted sources,” in <i>Proceedings of the 36th International Conference on Machine Learning</i>, Long Beach, CA, USA, 2019, vol. 97, pp. 3488–3498.","mla":"Konstantinov, Nikola H., and Christoph Lampert. “Robust Learning from Untrusted Sources.” <i>Proceedings of the 36th International Conference on Machine Learning</i>, vol. 97, ML Research Press, 2019, pp. 3488–98.","chicago":"Konstantinov, Nikola H, and Christoph Lampert. “Robust Learning from Untrusted Sources.” In <i>Proceedings of the 36th International Conference on Machine Learning</i>, 97:3488–98. ML Research Press, 2019."},"day":"01","month":"06","oa_version":"Preprint","conference":{"start_date":"2019-06-10","location":"Long Beach, CA, USA","end_date":"2919-06-15","name":"ICML: International Conference on Machine Learning"},"arxiv":1,"article_processing_charge":"No","volume":97,"title":"Robust learning from untrusted sources","author":[{"full_name":"Konstantinov, Nikola H","last_name":"Konstantinov","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola H"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"_id":"6590","abstract":[{"lang":"eng","text":"Modern machine learning methods often require more data for training than a single expert can provide. Therefore, it has become a standard procedure to collect data from external sources, e.g. via crowdsourcing. Unfortunately, the quality of these sources is not always guaranteed. As additional complications, the data might be stored in a distributed way, or might even have to remain private. In this work, we address the question of how to learn robustly in such scenarios. Studying the problem through the lens of statistical learning theory, we derive a procedure that allows for learning from all available sources, yet automatically suppresses irrelevant or corrupted data. We show by extensive experiments that our method provides significant improvements over alternative approaches from robust statistics and distributed optimization. "}],"project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"publication_status":"published","status":"public","ec_funded":1,"department":[{"_id":"ChLa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1901.10310"]},"date_published":"2019-06-01T00:00:00Z","date_created":"2019-06-27T14:18:23Z","scopus_import":"1","publisher":"ML Research Press","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10310"}],"intvolume":"        97","type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"year":"2019","publication":"Proceedings of the 36th International Conference on Machine Learning","date_updated":"2023-10-17T12:31:55Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10799"}]},"page":"3488-3498"},{"oa":1,"year":"2019","date_updated":"2023-08-28T12:26:22Z","publication":"Results in Mathematics","article_number":"138","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"VlKo"}],"date_created":"2019-06-29T10:11:30Z","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","external_id":{"isi":["000473237500002"],"arxiv":["2101.09068"]},"publisher":"Springer","intvolume":"        74","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"_id":"6596","title":"Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces","author":[{"first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","last_name":"Shehu","full_name":"Shehu, Yekini","orcid":"0000-0001-9224-7139"}],"doi":"10.1007/s00025-019-1061-4","abstract":[{"text":"It is well known that many problems in image recovery, signal processing, and machine learning can be modeled as finding zeros of the sum of maximal monotone and Lipschitz continuous monotone operators. Many papers have studied forward-backward splitting methods for finding zeros of the sum of two monotone operators in Hilbert spaces. Most of the proposed splitting methods in the literature have been proposed for the sum of maximal monotone and inverse-strongly monotone operators in Hilbert spaces. In this paper, we consider splitting methods for finding zeros of the sum of maximal monotone operators and Lipschitz continuous monotone operators in Banach spaces. We obtain weak and strong convergence results for the zeros of the sum of maximal monotone and Lipschitz continuous monotone operators in Banach spaces. Many already studied problems in the literature can be considered as special cases of this paper.","lang":"eng"}],"issue":"4","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication_identifier":{"issn":["1422-6383"],"eissn":["1420-9012"]},"ec_funded":1,"status":"public","publication_status":"published","file_date_updated":"2020-07-14T12:47:34Z","month":"12","ddc":["000"],"citation":{"mla":"Shehu, Yekini. “Convergence Results of Forward-Backward Algorithms for Sum of Monotone Operators in Banach Spaces.” <i>Results in Mathematics</i>, vol. 74, no. 4, 138, Springer, 2019, doi:<a href=\"https://doi.org/10.1007/s00025-019-1061-4\">10.1007/s00025-019-1061-4</a>.","chicago":"Shehu, Yekini. “Convergence Results of Forward-Backward Algorithms for Sum of Monotone Operators in Banach Spaces.” <i>Results in Mathematics</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s00025-019-1061-4\">https://doi.org/10.1007/s00025-019-1061-4</a>.","ista":"Shehu Y. 2019. Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. Results in Mathematics. 74(4), 138.","ama":"Shehu Y. Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. <i>Results in Mathematics</i>. 2019;74(4). doi:<a href=\"https://doi.org/10.1007/s00025-019-1061-4\">10.1007/s00025-019-1061-4</a>","short":"Y. Shehu, Results in Mathematics 74 (2019).","apa":"Shehu, Y. (2019). Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces. <i>Results in Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s00025-019-1061-4\">https://doi.org/10.1007/s00025-019-1061-4</a>","ieee":"Y. Shehu, “Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces,” <i>Results in Mathematics</i>, vol. 74, no. 4. Springer, 2019."},"day":"01","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/","file":[{"file_id":"6605","date_created":"2019-07-03T15:20:40Z","date_updated":"2020-07-14T12:47:34Z","access_level":"open_access","content_type":"application/pdf","checksum":"c6d18cb1e16fc0c36a0e0f30b4ebbc2d","file_name":"Springer_2019_Shehu.pdf","creator":"kschuh","relation":"main_file","file_size":466942}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"volume":74,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"pmid":1,"month":"07","citation":{"mla":"Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” <i>Cell</i>, vol. 178, no. 1, Elsevier, 2019, pp. 12–25, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.05.052\">10.1016/j.cell.2019.05.052</a>.","chicago":"Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.05.052\">https://doi.org/10.1016/j.cell.2019.05.052</a>.","short":"E.B. Hannezo, C.-P.J. Heisenberg, Cell 178 (2019) 12–25.","ama":"Hannezo EB, Heisenberg C-PJ. Mechanochemical feedback loops in development and disease. <i>Cell</i>. 2019;178(1):12-25. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.05.052\">10.1016/j.cell.2019.05.052</a>","ista":"Hannezo EB, Heisenberg C-PJ. 2019. Mechanochemical feedback loops in development and disease. Cell. 178(1), 12–25.","ieee":"E. B. Hannezo and C.-P. J. Heisenberg, “Mechanochemical feedback loops in development and disease,” <i>Cell</i>, vol. 178, no. 1. Elsevier, pp. 12–25, 2019.","apa":"Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2019). Mechanochemical feedback loops in development and disease. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.05.052\">https://doi.org/10.1016/j.cell.2019.05.052</a>"},"day":"27","oa_version":"Published Version","article_processing_charge":"No","volume":178,"_id":"6601","title":"Mechanochemical feedback loops in development and disease","author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"doi":"10.1016/j.cell.2019.05.052","abstract":[{"text":"There is increasing evidence that both mechanical and biochemical signals play important roles in development and disease. The development of complex organisms, in particular, has been proposed to rely on the feedback between mechanical and biochemical patterning events. This feedback occurs at the molecular level via mechanosensation but can also arise as an emergent property of the system at the cellular and tissue level. In recent years, dynamic changes in tissue geometry, flow, rheology, and cell fate specification have emerged as key platforms of mechanochemical feedback loops in multiple processes. Here, we review recent experimental and theoretical advances in understanding how these feedbacks function in development and disease.","lang":"eng"}],"issue":"1","project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639"}],"publication_identifier":{"issn":["00928674"]},"ec_funded":1,"status":"public","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"date_created":"2019-06-30T21:59:11Z","scopus_import":"1","date_published":"2019-07-27T00:00:00Z","external_id":{"isi":["000473002700005"],"pmid":["31251912"]},"publisher":"Elsevier","intvolume":"       178","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.05.052"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"oa":1,"year":"2019","date_updated":"2023-08-28T12:25:21Z","publication":"Cell","page":"12-25","article_type":"review"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":2017352,"relation":"main_file","creator":"kschuh","file_name":"nature_2019_Nguyen.pdf","date_updated":"2020-07-14T12:47:34Z","checksum":"3283522fffadf4b5fc8c7adfe3ba4564","content_type":"application/pdf","access_level":"open_access","date_created":"2019-07-08T15:15:28Z","file_id":"6623"}],"volume":9,"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:34Z","ddc":["576"],"month":"06","day":"24","citation":{"apa":"Nguyen, C. H., Glüxam, T., Schlerka, A., Bauer, K., Grandits, A. M., Hackl, H., … Heller, G. (2019). SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-019-45579-0\">https://doi.org/10.1038/s41598-019-45579-0</a>","ieee":"C. H. Nguyen <i>et al.</i>, “SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness,” <i>Scientific Reports</i>, vol. 9, no. 1. Nature Publishing Group, 2019.","short":"C.H. Nguyen, T. Glüxam, A. Schlerka, K. Bauer, A.M. Grandits, H. Hackl, O. Dovey, S. Zöchbauer-Müller, J.L. Cooper, G.S. Vassiliou, D. Stoiber, R. Wieser, G. Heller, Scientific Reports 9 (2019).","ama":"Nguyen CH, Glüxam T, Schlerka A, et al. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. <i>Scientific Reports</i>. 2019;9(1). doi:<a href=\"https://doi.org/10.1038/s41598-019-45579-0\">10.1038/s41598-019-45579-0</a>","ista":"Nguyen CH, Glüxam T, Schlerka A, Bauer K, Grandits AM, Hackl H, Dovey O, Zöchbauer-Müller S, Cooper JL, Vassiliou GS, Stoiber D, Wieser R, Heller G. 2019. SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness. Scientific Reports. 9(1), 9139.","mla":"Nguyen, Chi Huu, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” <i>Scientific Reports</i>, vol. 9, no. 1, 9139, Nature Publishing Group, 2019, doi:<a href=\"https://doi.org/10.1038/s41598-019-45579-0\">10.1038/s41598-019-45579-0</a>.","chicago":"Nguyen, Chi Huu, Tobias Glüxam, Angela Schlerka, Katharina Bauer, Alexander M. Grandits, Hubert Hackl, Oliver Dovey, et al. “SOCS2 Is Part of a Highly Prognostic 4-Gene Signature in AML and Promotes Disease Aggressiveness.” <i>Scientific Reports</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41598-019-45579-0\">https://doi.org/10.1038/s41598-019-45579-0</a>."},"oa_version":"Published Version","publication_status":"published","status":"public","_id":"6607","author":[{"last_name":"Nguyen","full_name":"Nguyen, Chi Huu","first_name":"Chi Huu"},{"first_name":"Tobias","full_name":"Glüxam, Tobias","last_name":"Glüxam"},{"last_name":"Schlerka","full_name":"Schlerka, Angela","first_name":"Angela"},{"id":"2ED6B14C-F248-11E8-B48F-1D18A9856A87","first_name":"Katharina","full_name":"Bauer, Katharina","last_name":"Bauer"},{"full_name":"Grandits, Alexander M.","last_name":"Grandits","first_name":"Alexander M."},{"full_name":"Hackl, Hubert","last_name":"Hackl","first_name":"Hubert"},{"full_name":"Dovey, Oliver","last_name":"Dovey","first_name":"Oliver"},{"last_name":"Zöchbauer-Müller","full_name":"Zöchbauer-Müller, Sabine","first_name":"Sabine"},{"first_name":"Jonathan L.","full_name":"Cooper, Jonathan L.","last_name":"Cooper"},{"last_name":"Vassiliou","full_name":"Vassiliou, George S.","first_name":"George S."},{"first_name":"Dagmar","full_name":"Stoiber, Dagmar","last_name":"Stoiber"},{"first_name":"Rotraud","last_name":"Wieser","full_name":"Wieser, Rotraud"},{"first_name":"Gerwin","last_name":"Heller","full_name":"Heller, Gerwin"}],"title":"SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness","doi":"10.1038/s41598-019-45579-0","issue":"1","abstract":[{"lang":"eng","text":"Acute myeloid leukemia (AML) is a heterogeneous disease with respect to its genetic and molecular basis and to patients´ outcome. Clinical, cytogenetic, and mutational data are used to classify patients into risk groups with different survival, however, within-group heterogeneity is still an issue. Here, we used a robust likelihood-based survival modeling approach and publicly available gene expression data to identify a minimal number of genes whose combined expression values were prognostic of overall survival. The resulting gene expression signature (4-GES) consisted of 4 genes (SOCS2, IL2RA, NPDC1, PHGDH), predicted patient survival as an independent prognostic parameter in several cohorts of AML patients (total, 1272 patients), and further refined prognostication based on the European Leukemia Net classification. An oncogenic role of the top scoring gene in this signature, SOCS2, was investigated using MLL-AF9 and Flt3-ITD/NPM1c driven mouse models of AML. SOCS2 promoted leukemogenesis as well as the abundance, quiescence, and activity of AML stem cells. Overall, the 4-GES represents a highly discriminating prognostic parameter in AML, whose clinical applicability is greatly enhanced by its small number of genes. The newly established role of SOCS2 in leukemia aggressiveness and stemness raises the possibility that the signature might even be exploitable therapeutically."}],"intvolume":"         9","publisher":"Nature Publishing Group","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"PreCl"}],"scopus_import":"1","date_created":"2019-07-07T21:59:19Z","external_id":{"isi":["000472597400042"]},"date_published":"2019-06-24T00:00:00Z","date_updated":"2023-08-28T12:26:51Z","publication":"Scientific Reports","article_number":"9139","oa":1,"year":"2019"},{"file":[{"content_type":"application/pdf","checksum":"7c99be505dc7533257d42eb1830cef04","access_level":"open_access","date_updated":"2020-07-14T12:47:34Z","relation":"main_file","creator":"kschuh","file_size":2665013,"file_name":"Elsevier_2019_Edelsbrunner.pdf","date_created":"2019-07-08T15:24:26Z","file_id":"6624"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"has_accepted_license":"1","volume":73,"article_processing_charge":"No","day":"01","citation":{"chicago":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Holes and Dependences in an Ordered Complex.” <i>Computer Aided Geometric Design</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cagd.2019.06.003\">https://doi.org/10.1016/j.cagd.2019.06.003</a>.","mla":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Holes and Dependences in an Ordered Complex.” <i>Computer Aided Geometric Design</i>, vol. 73, Elsevier, 2019, pp. 1–15, doi:<a href=\"https://doi.org/10.1016/j.cagd.2019.06.003\">10.1016/j.cagd.2019.06.003</a>.","short":"H. Edelsbrunner, K. Ölsböck, Computer Aided Geometric Design 73 (2019) 1–15.","ama":"Edelsbrunner H, Ölsböck K. Holes and dependences in an ordered complex. <i>Computer Aided Geometric Design</i>. 2019;73:1-15. doi:<a href=\"https://doi.org/10.1016/j.cagd.2019.06.003\">10.1016/j.cagd.2019.06.003</a>","ista":"Edelsbrunner H, Ölsböck K. 2019. Holes and dependences in an ordered complex. Computer Aided Geometric Design. 73, 1–15.","apa":"Edelsbrunner, H., &#38; Ölsböck, K. (2019). Holes and dependences in an ordered complex. <i>Computer Aided Geometric Design</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cagd.2019.06.003\">https://doi.org/10.1016/j.cagd.2019.06.003</a>","ieee":"H. Edelsbrunner and K. Ölsböck, “Holes and dependences in an ordered complex,” <i>Computer Aided Geometric Design</i>, vol. 73. Elsevier, pp. 1–15, 2019."},"month":"08","ddc":["000"],"file_date_updated":"2020-07-14T12:47:34Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"status":"public","publication_status":"published","ec_funded":1,"author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"last_name":"Ölsböck","full_name":"Ölsböck, Katharina","first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4672-8297"}],"title":"Holes and dependences in an ordered complex","_id":"6608","abstract":[{"lang":"eng","text":"We use the canonical bases produced by the tri-partition algorithm in (Edelsbrunner and Ölsböck, 2018) to open and close holes in a polyhedral complex, K. In a concrete application, we consider the Delaunay mosaic of a finite set, we let K be an Alpha complex, and we use the persistence diagram of the distance function to guide the hole opening and closing operations. The dependences between the holes define a partial order on the cells in K that characterizes what can and what cannot be constructed using the operations. The relations in this partial order reveal structural information about the underlying filtration of complexes beyond what is expressed by the persistence diagram."}],"doi":"10.1016/j.cagd.2019.06.003","intvolume":"        73","publisher":"Elsevier","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000485207800001"]},"date_published":"2019-08-01T00:00:00Z","scopus_import":"1","date_created":"2019-07-07T21:59:20Z","publication":"Computer Aided Geometric Design","date_updated":"2023-09-07T13:15:29Z","related_material":{"record":[{"id":"7460","status":"public","relation":"dissertation_contains"}]},"page":"1-15","oa":1,"year":"2019"},{"intvolume":"       570","main_file_link":[{"url":"https://arxiv.org/abs/1809.05865","open_access":"1"}],"publisher":"Nature Publishing Group","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-06-27T00:00:00Z","external_id":{"arxiv":["1809.05865"],"isi":["000472860000042"]},"scopus_import":"1","acknowledged_ssus":[{"_id":"NanoFab"}],"date_created":"2019-07-07T21:59:20Z","publication":"Nature","date_updated":"2024-08-07T07:11:54Z","page":"480-483","oa":1,"year":"2019","arxiv":1,"volume":570,"article_processing_charge":"No","day":"27","citation":{"short":"S. Barzanjeh, E. Redchenko, M. Peruzzo, M. Wulf, D. Lewis, G.M. Arnold, J.M. Fink, Nature 570 (2019) 480–483.","ista":"Barzanjeh S, Redchenko E, Peruzzo M, Wulf M, Lewis D, Arnold GM, Fink JM. 2019. Stationary entangled radiation from micromechanical motion. Nature. 570, 480–483.","ama":"Barzanjeh S, Redchenko E, Peruzzo M, et al. Stationary entangled radiation from micromechanical motion. <i>Nature</i>. 2019;570:480-483. doi:<a href=\"https://doi.org/10.1038/s41586-019-1320-2\">10.1038/s41586-019-1320-2</a>","apa":"Barzanjeh, S., Redchenko, E., Peruzzo, M., Wulf, M., Lewis, D., Arnold, G. M., &#38; Fink, J. M. (2019). Stationary entangled radiation from micromechanical motion. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-019-1320-2\">https://doi.org/10.1038/s41586-019-1320-2</a>","ieee":"S. Barzanjeh <i>et al.</i>, “Stationary entangled radiation from micromechanical motion,” <i>Nature</i>, vol. 570. Nature Publishing Group, pp. 480–483, 2019.","chicago":"Barzanjeh, Shabir, Elena Redchenko, Matilda Peruzzo, Matthias Wulf, Dylan Lewis, Georg M Arnold, and Johannes M Fink. “Stationary Entangled Radiation from Micromechanical Motion.” <i>Nature</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1320-2\">https://doi.org/10.1038/s41586-019-1320-2</a>.","mla":"Barzanjeh, Shabir, et al. “Stationary Entangled Radiation from Micromechanical Motion.” <i>Nature</i>, vol. 570, Nature Publishing Group, 2019, pp. 480–83, doi:<a href=\"https://doi.org/10.1038/s41586-019-1320-2\">10.1038/s41586-019-1320-2</a>."},"month":"06","oa_version":"Preprint","project":[{"_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","call_identifier":"H2020","name":"Hybrid Optomechanical Technologies"},{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"publication_status":"published","status":"public","ec_funded":1,"author":[{"orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir"},{"full_name":"Redchenko, Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda"},{"full_name":"Wulf, Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","orcid":"0000-0001-6613-1378"},{"first_name":"Dylan","full_name":"Lewis, Dylan","last_name":"Lewis"},{"first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876"},{"full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X"}],"title":"Stationary entangled radiation from micromechanical motion","_id":"6609","abstract":[{"lang":"eng","text":"Mechanical systems facilitate the development of a hybrid quantum technology comprising electrical, optical, atomic and acoustic degrees of freedom1, and entanglement is essential to realize quantum-enabled devices. Continuous-variable entangled fields—known as Einstein–Podolsky–Rosen (EPR) states—are spatially separated two-mode squeezed states that can be used for quantum teleportation and quantum communication2. In the optical domain, EPR states are typically generated using nondegenerate optical amplifiers3, and at microwave frequencies Josephson circuits can serve as a nonlinear medium4,5,6. An outstanding goal is to deterministically generate and distribute entangled states with a mechanical oscillator, which requires a carefully arranged balance between excitation, cooling and dissipation in an ultralow noise environment. Here we observe stationary emission of path-entangled microwave radiation from a parametrically driven 30-micrometre-long silicon nanostring oscillator, squeezing the joint field operators of two thermal modes by 3.40 decibels below the vacuum level. The motion of this micromechanical system correlates up to 50 photons per second per hertz, giving rise to a quantum discord that is robust with respect to microwave noise7. Such generalized quantum correlations of separable states are important for quantum-enhanced detection8 and provide direct evidence of the non-classical nature of the mechanical oscillator without directly measuring its state9. This noninvasive measurement scheme allows to infer information about otherwise inaccessible objects, with potential implications for sensing, open-system dynamics and fundamental tests of quantum gravity. In the future, similar on-chip devices could be used to entangle subsystems on very different energy scales, such as microwave and optical photons."}],"doi":"10.1038/s41586-019-1320-2"},{"year":"2019","oa":1,"page":"257 - 311","publication":"Journal of Differential Equations","date_updated":"2023-09-08T13:25:35Z","external_id":{"isi":["000449108500010"],"arxiv":["1408.1587"]},"date_published":"2019-01-05T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:44:54Z","department":[{"_id":"JuFi"}],"publist_id":"7770","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","intvolume":"       266","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1408.1587"}],"publisher":"Elsevier","issue":"1","abstract":[{"text":"We construct planar bi-Sobolev mappings whose local volume distortion is bounded from below by a given function f∈Lp with p&gt;1. More precisely, for any 1&lt;q&lt;(p+1)/2 we construct W1,q-bi-Sobolev maps with identity boundary conditions; for f∈L∞, we provide bi-Lipschitz maps. The basic building block of our construction are bi-Lipschitz maps which stretch a given compact subset of the unit square by a given factor while preserving the boundary. The construction of these stretching maps relies on a slight strengthening of the celebrated covering result of Alberti, Csörnyei, and Preiss for measurable planar sets in the case of compact sets. We apply our result to a model functional in nonlinear elasticity, the integrand of which features fast blowup as the Jacobian determinant of the deformation becomes small. For such functionals, the derivation of the equilibrium equations for minimizers requires an additional regularization of test functions, which our maps provide.","lang":"eng"}],"doi":"10.1016/j.jde.2018.07.045","author":[{"full_name":"Fischer, Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X"},{"full_name":"Kneuss, Olivier","last_name":"Kneuss","first_name":"Olivier"}],"title":"Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity","_id":"151","status":"public","publication_status":"published","oa_version":"Preprint","day":"05","citation":{"apa":"Fischer, J. L., &#38; Kneuss, O. (2019). Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. <i>Journal of Differential Equations</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jde.2018.07.045\">https://doi.org/10.1016/j.jde.2018.07.045</a>","ieee":"J. L. Fischer and O. Kneuss, “Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity,” <i>Journal of Differential Equations</i>, vol. 266, no. 1. Elsevier, pp. 257–311, 2019.","ista":"Fischer JL, Kneuss O. 2019. Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. 266(1), 257–311.","ama":"Fischer JL, Kneuss O. Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. <i>Journal of Differential Equations</i>. 2019;266(1):257-311. doi:<a href=\"https://doi.org/10.1016/j.jde.2018.07.045\">10.1016/j.jde.2018.07.045</a>","short":"J.L. Fischer, O. Kneuss, Journal of Differential Equations 266 (2019) 257–311.","chicago":"Fischer, Julian L, and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.” <i>Journal of Differential Equations</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.jde.2018.07.045\">https://doi.org/10.1016/j.jde.2018.07.045</a>.","mla":"Fischer, Julian L., and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.” <i>Journal of Differential Equations</i>, vol. 266, no. 1, Elsevier, 2019, pp. 257–311, doi:<a href=\"https://doi.org/10.1016/j.jde.2018.07.045\">10.1016/j.jde.2018.07.045</a>."},"month":"01","volume":266,"article_processing_charge":"No","arxiv":1},{"doi":"10.5061/DRYAD.TB2RBNZWK","abstract":[{"lang":"eng","text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of &gt;500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females."}],"year":"2019","_id":"13067","title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","oa":1,"author":[{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna","first_name":"Zuzanna"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7205"}]},"status":"public","date_updated":"2023-09-06T14:48:57Z","date_created":"2023-05-23T16:36:27Z","oa_version":"Published Version","date_published":"2019-12-02T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","ddc":["570"],"citation":{"ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., &#38; Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. <a href=\"https://doi.org/10.5061/DRYAD.TB2RBNZWK\">https://doi.org/10.5061/DRYAD.TB2RBNZWK</a>","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:<a href=\"https://doi.org/10.5061/DRYAD.TB2RBNZWK\">10.5061/DRYAD.TB2RBNZWK</a>","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.TB2RBNZWK\">10.5061/DRYAD.TB2RBNZWK</a>.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. <a href=\"https://doi.org/10.5061/DRYAD.TB2RBNZWK\">https://doi.org/10.5061/DRYAD.TB2RBNZWK</a>.","mla":"Johannesson, Kerstin, et al. <i>Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?</i> Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/DRYAD.TB2RBNZWK\">10.5061/DRYAD.TB2RBNZWK</a>."},"day":"02","department":[{"_id":"NiBa"}],"article_processing_charge":"No","type":"research_data_reference","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.tb2rbnzwk"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"}},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2020-07-14T12:44:47Z","content_type":"application/pdf","checksum":"6779708b0b632a1a6ed28c56f5161142","access_level":"open_access","creator":"dernst","relation":"main_file","file_size":776399,"file_name":"2019_CurrentGenetics_Nikolic.pdf","date_created":"2019-02-06T07:50:58Z","file_id":"5930"}],"has_accepted_license":"1","volume":65,"article_processing_charge":"Yes (via OA deal)","day":"01","citation":{"ista":"Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.","ama":"Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. <i>Current Genetics</i>. 2019;65(1):133-138. doi:<a href=\"https://doi.org/10.1007/s00294-018-0879-8\">10.1007/s00294-018-0879-8</a>","short":"N. Nikolic, Current Genetics 65 (2019) 133–138.","ieee":"N. Nikolic, “Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system,” <i>Current Genetics</i>, vol. 65, no. 1. Springer, pp. 133–138, 2019.","apa":"Nikolic, N. (2019). Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. <i>Current Genetics</i>. Springer. <a href=\"https://doi.org/10.1007/s00294-018-0879-8\">https://doi.org/10.1007/s00294-018-0879-8</a>","mla":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” <i>Current Genetics</i>, vol. 65, no. 1, Springer, 2019, pp. 133–38, doi:<a href=\"https://doi.org/10.1007/s00294-018-0879-8\">10.1007/s00294-018-0879-8</a>.","chicago":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” <i>Current Genetics</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s00294-018-0879-8\">https://doi.org/10.1007/s00294-018-0879-8</a>."},"ddc":["570"],"file_date_updated":"2020-07-14T12:44:47Z","month":"02","oa_version":"Published Version","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"status":"public","publication_status":"published","ec_funded":1,"author":[{"orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","full_name":"Nikolic, Nela","last_name":"Nikolic"}],"title":"Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system","_id":"138","issue":"1","abstract":[{"text":"Autoregulation is the direct modulation of gene expression by the product of the corresponding gene. Autoregulation of bacterial gene expression has been mostly studied at the transcriptional level, when a protein acts as the cognate transcriptional repressor. A recent study investigating dynamics of the bacterial toxin–antitoxin MazEF system has shown how autoregulation at both the transcriptional and post-transcriptional levels affects the heterogeneity of Escherichia coli populations. Toxin–antitoxin systems hold a crucial but still elusive part in bacterial response to stress. This perspective highlights how these modules can also serve as a great model system for investigating basic concepts in gene regulation. However, as the genomic background and environmental conditions substantially influence toxin activation, it is important to study (auto)regulation of toxin–antitoxin systems in well-defined setups as well as in conditions that resemble the environmental niche.","lang":"eng"}],"doi":"10.1007/s00294-018-0879-8","intvolume":"        65","publisher":"Springer","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"CaGu"}],"publist_id":"7785","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000456958800017"]},"date_published":"2019-02-01T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:44:50Z","publication":"Current Genetics","date_updated":"2023-09-08T13:23:42Z","page":"133-138","oa":1,"year":"2019"},{"arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.01258"}],"article_processing_charge":"No","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","citation":{"mla":"Locatello, Francesco, et al. “Disentangling Factors of Variation Using Few Labels.” <i>8th International Conference on Learning Representations</i>, 2019.","chicago":"Locatello, Francesco, Michael Tschannen, Stefan Bauer, Gunnar Rätsch, Bernhard Schölkopf, and Olivier Bachem. “Disentangling Factors of Variation Using Few Labels.” In <i>8th International Conference on Learning Representations</i>, 2019.","ama":"Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. Disentangling factors of variation using few labels. In: <i>8th International Conference on Learning Representations</i>. ; 2019.","ista":"Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. 2019. Disentangling factors of variation using few labels. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","short":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, O. Bachem, in:, 8th International Conference on Learning Representations, 2019.","apa":"Locatello, F., Tschannen, M., Bauer, S., Rätsch, G., Schölkopf, B., &#38; Bachem, O. (2019). Disentangling factors of variation using few labels. In <i>8th International Conference on Learning Representations</i>. Virtual.","ieee":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, and O. Bachem, “Disentangling factors of variation using few labels,” in <i>8th International Conference on Learning Representations</i>, Virtual, 2019."},"department":[{"_id":"FrLo"}],"day":"20","date_created":"2023-08-22T14:06:37Z","oa_version":"Preprint","conference":{"location":"Virtual","start_date":"2020-04-26","end_date":"2020-05-01","name":"ICLR: International Conference on Learning Representations"},"scopus_import":"1","date_published":"2019-12-20T00:00:00Z","external_id":{"arxiv":["1905.01258"]},"extern":"1","date_updated":"2023-09-12T07:01:34Z","publication":"8th International Conference on Learning Representations","status":"public","publication_status":"published","_id":"14184","title":"Disentangling factors of variation using few labels","oa":1,"author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683"},{"last_name":"Tschannen","full_name":"Tschannen, Michael","first_name":"Michael"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"}],"abstract":[{"lang":"eng","text":"Learning disentangled representations is considered a cornerstone problem in\r\nrepresentation learning. Recently, Locatello et al. (2019) demonstrated that\r\nunsupervised disentanglement learning without inductive biases is theoretically\r\nimpossible and that existing inductive biases and unsupervised methods do not\r\nallow to consistently learn disentangled representations. However, in many\r\npractical settings, one might have access to a limited amount of supervision,\r\nfor example through manual labeling of (some) factors of variation in a few\r\ntraining examples. In this paper, we investigate the impact of such supervision\r\non state-of-the-art disentanglement methods and perform a large scale study,\r\ntraining over 52000 models under well-defined and reproducible experimental\r\nconditions. We observe that a small number of labeled examples (0.01--0.5\\% of\r\nthe data set), with potentially imprecise and incomplete labels, is sufficient\r\nto perform model selection on state-of-the-art unsupervised models. Further, we\r\ninvestigate the benefit of incorporating supervision into the training process.\r\nOverall, we empirically validate that with little and imprecise supervision it\r\nis possible to reliably learn disentangled representations."}],"year":"2019"},{"year":"2019","alternative_title":["PMLR"],"oa":1,"page":"217-227","publication":"Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence","date_updated":"2023-09-12T08:07:38Z","date_published":"2019-05-16T00:00:00Z","extern":"1","external_id":{"arxiv":["1905.06642"]},"scopus_import":"1","date_created":"2023-08-22T14:08:35Z","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"       115","main_file_link":[{"url":"https://arxiv.org/abs/1905.06642","open_access":"1"}],"publisher":"ML Research Press","abstract":[{"lang":"eng","text":"We consider the problem of recovering a common latent source with independent\r\ncomponents from multiple views. This applies to settings in which a variable is\r\nmeasured with multiple experimental modalities, and where the goal is to\r\nsynthesize the disparate measurements into a single unified representation. We\r\nconsider the case that the observed views are a nonlinear mixing of\r\ncomponent-wise corruptions of the sources. When the views are considered\r\nseparately, this reduces to nonlinear Independent Component Analysis (ICA) for\r\nwhich it is provably impossible to undo the mixing. We present novel\r\nidentifiability proofs that this is possible when the multiple views are\r\nconsidered jointly, showing that the mixing can theoretically be undone using\r\nfunction approximators such as deep neural networks. In contrast to known\r\nidentifiability results for nonlinear ICA, we prove that independent latent\r\nsources with arbitrary mixing can be recovered as long as multiple,\r\nsufficiently different noisy views are available."}],"author":[{"last_name":"Gresele","full_name":"Gresele, Luigi","first_name":"Luigi"},{"full_name":"Rubenstein, Paul K.","last_name":"Rubenstein","first_name":"Paul K."},{"first_name":"Arash","last_name":"Mehrjou","full_name":"Mehrjou, Arash"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"}],"title":"The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA","_id":"14189","publication_status":"published","status":"public","conference":{"name":"UAI: Uncertainty in Artificial Intelligence","end_date":"2019-07-25","location":"Tel Aviv, Israel","start_date":"2019-07-22"},"oa_version":"Preprint","day":"16","citation":{"chicago":"Gresele, Luigi, Paul K. Rubenstein, Arash Mehrjou, Francesco Locatello, and Bernhard Schölkopf. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” In <i>Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence</i>, 115:217–27. ML Research Press, 2019.","mla":"Gresele, Luigi, et al. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” <i>Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence</i>, vol. 115, ML Research Press, 2019, pp. 217–27.","ama":"Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In: <i>Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence</i>. Vol 115. ML Research Press; 2019:217-227.","short":"L. Gresele, P.K. Rubenstein, A. Mehrjou, F. Locatello, B. Schölkopf, in:, Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence, ML Research Press, 2019, pp. 217–227.","ista":"Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. 2019. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence. UAI: Uncertainty in Artificial Intelligence, PMLR, vol. 115, 217–227.","ieee":"L. Gresele, P. K. Rubenstein, A. Mehrjou, F. Locatello, and B. Schölkopf, “The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA,” in <i>Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence</i>, Tel Aviv, Israel, 2019, vol. 115, pp. 217–227.","apa":"Gresele, L., Rubenstein, P. K., Mehrjou, A., Locatello, F., &#38; Schölkopf, B. (2019). The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In <i>Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence</i> (Vol. 115, pp. 217–227). Tel Aviv, Israel: ML Research Press."},"month":"05","volume":115,"article_processing_charge":"No","arxiv":1},{"language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","volume":32,"article_processing_charge":"No","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.03292"}],"intvolume":"        32","date_published":"2019-06-07T00:00:00Z","external_id":{"arxiv":["1906.03292"]},"extern":"1","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14","location":"Vancouver, Canada","start_date":"2019-12-08"},"date_created":"2023-08-22T14:09:13Z","oa_version":"Preprint","department":[{"_id":"FrLo"}],"day":"07","citation":{"apa":"Gondal, M. W., Wüthrich, M., Miladinović, Đ., Locatello, F., Breidt, M., Volchkov, V., … Bauer, S. (2019). On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In <i>Advances in Neural Information Processing Systems</i> (Vol. 32). Vancouver, Canada.","ieee":"M. W. Gondal <i>et al.</i>, “On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset,” in <i>Advances in Neural Information Processing Systems</i>, Vancouver, Canada, 2019, vol. 32.","short":"M.W. Gondal, M. Wüthrich, Đ. Miladinović, F. Locatello, M. Breidt, V. Volchkov, J. Akpo, O. Bachem, B. Schölkopf, S. Bauer, in:, Advances in Neural Information Processing Systems, 2019.","ista":"Gondal MW, Wüthrich M, Miladinović Đ, Locatello F, Breidt M, Volchkov V, Akpo J, Bachem O, Schölkopf B, Bauer S. 2019. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.","ama":"Gondal MW, Wüthrich M, Miladinović Đ, et al. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In: <i>Advances in Neural Information Processing Systems</i>. Vol 32. ; 2019.","mla":"Gondal, Muhammad Waleed, et al. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” <i>Advances in Neural Information Processing Systems</i>, vol. 32, 2019.","chicago":"Gondal, Muhammad Waleed, Manuel Wüthrich, Đorđe Miladinović, Francesco Locatello, Martin Breidt, Valentin Volchkov, Joel Akpo, Olivier Bachem, Bernhard Schölkopf, and Stefan Bauer. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” In <i>Advances in Neural Information Processing Systems</i>, Vol. 32, 2019."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"06","status":"public","publication_status":"published","publication":"Advances in Neural Information Processing Systems","publication_identifier":{"isbn":["9781713807933"]},"date_updated":"2023-09-13T09:46:38Z","year":"2019","abstract":[{"text":"Learning meaningful and compact representations with disentangled semantic\r\naspects is considered to be of key importance in representation learning. Since\r\nreal-world data is notoriously costly to collect, many recent state-of-the-art\r\ndisentanglement models have heavily relied on synthetic toy data-sets. In this\r\npaper, we propose a novel data-set which consists of over one million images of\r\nphysical 3D objects with seven factors of variation, such as object color,\r\nshape, size and position. In order to be able to control all the factors of\r\nvariation precisely, we built an experimental platform where the objects are\r\nbeing moved by a robotic arm. In addition, we provide two more datasets which\r\nconsist of simulations of the experimental setup. These datasets provide for\r\nthe first time the possibility to systematically investigate how well different\r\ndisentanglement methods perform on real data in comparison to simulation, and\r\nhow simulated data can be leveraged to build better representations of the real\r\nworld. We provide a first experimental study of these questions and our results\r\nindicate that learned models transfer poorly, but that model and hyperparameter\r\nselection is an effective means of transferring information to the real world.","lang":"eng"}],"author":[{"full_name":"Gondal, Muhammad Waleed","last_name":"Gondal","first_name":"Muhammad Waleed"},{"last_name":"Wüthrich","full_name":"Wüthrich, Manuel","first_name":"Manuel"},{"last_name":"Miladinović","full_name":"Miladinović, Đorđe","first_name":"Đorđe"},{"orcid":"0000-0002-4850-0683","last_name":"Locatello","full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Breidt","full_name":"Breidt, Martin","first_name":"Martin"},{"last_name":"Volchkov","full_name":"Volchkov, Valentin","first_name":"Valentin"},{"last_name":"Akpo","full_name":"Akpo, Joel","first_name":"Joel"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"}],"title":"On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset","oa":1,"_id":"14190"},{"abstract":[{"text":"A broad class of convex optimization problems can be formulated as a semidefinite program (SDP), minimization of a convex function over the positive-semidefinite cone subject to some affine constraints. The majority of classical SDP solvers are designed for the deterministic setting where problem data is readily available. In this setting, generalized conditional gradient methods (aka Frank-Wolfe-type methods) provide scalable solutions by leveraging the so-called linear minimization oracle instead of the projection onto the semidefinite cone. Most problems in machine learning and modern engineering applications, however, contain some degree of stochasticity. In this work, we propose the first conditional-gradient-type method for solving stochastic optimization problems under affine constraints. Our method guarantees O(k−1/3) convergence rate in expectation on the objective residual and O(k−5/12) on the feasibility gap.","lang":"eng"}],"author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"full_name":"Yurtsever, Alp","last_name":"Yurtsever","first_name":"Alp"},{"first_name":"Olivier","last_name":"Fercoq","full_name":"Fercoq, Olivier"},{"first_name":"Volkan","full_name":"Cevher, Volkan","last_name":"Cevher"}],"title":"Stochastic Frank-Wolfe for composite convex minimization","_id":"14191","publication_status":"published","status":"public","publication_identifier":{"isbn":["9781713807933"]},"conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2019-12-08","location":"Vancouver, Canada","end_date":"2019-12-14"},"oa_version":"Preprint","day":"29","citation":{"ieee":"F. Locatello, A. Yurtsever, O. Fercoq, and V. Cevher, “Stochastic Frank-Wolfe for composite convex minimization,” in <i>Advances in Neural Information Processing Systems</i>, Vancouver, Canada, 2019, vol. 32, pp. 14291–14301.","apa":"Locatello, F., Yurtsever, A., Fercoq, O., &#38; Cevher, V. (2019). Stochastic Frank-Wolfe for composite convex minimization. In <i>Advances in Neural Information Processing Systems</i> (Vol. 32, pp. 14291–14301). Vancouver, Canada.","short":"F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 14291–14301.","ama":"Locatello F, Yurtsever A, Fercoq O, Cevher V. Stochastic Frank-Wolfe for composite convex minimization. In: <i>Advances in Neural Information Processing Systems</i>. Vol 32. ; 2019:14291–14301.","ista":"Locatello F, Yurtsever A, Fercoq O, Cevher V. 2019. Stochastic Frank-Wolfe for composite convex minimization. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14291–14301.","chicago":"Locatello, Francesco, Alp Yurtsever, Olivier Fercoq, and Volkan Cevher. “Stochastic Frank-Wolfe for Composite Convex Minimization.” In <i>Advances in Neural Information Processing Systems</i>, 32:14291–14301, 2019.","mla":"Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.” <i>Advances in Neural Information Processing Systems</i>, vol. 32, 2019, pp. 14291–14301."},"month":"12","article_processing_charge":"No","volume":32,"arxiv":1,"year":"2019","oa":1,"page":"14291–14301","publication":"Advances in Neural Information Processing Systems","date_updated":"2023-09-12T08:48:45Z","external_id":{"arxiv":["1901.10348"]},"date_published":"2019-12-29T00:00:00Z","extern":"1","scopus_import":"1","date_created":"2023-08-22T14:09:35Z","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","intvolume":"        32","main_file_link":[{"url":"https://arxiv.org/abs/1901.10348","open_access":"1"}]},{"intvolume":"        32","arxiv":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.12506","open_access":"1"}],"article_processing_charge":"No","volume":32,"language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","citation":{"ama":"Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. Are disentangled representations helpful for abstract visual reasoning? In: <i>Advances in Neural Information Processing Systems</i>. Vol 32. ; 2019.","short":"S. van Steenkiste, F. Locatello, J. Schmidhuber, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019.","ista":"Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. 2019. Are disentangled representations helpful for abstract visual reasoning? Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.","ieee":"S. van Steenkiste, F. Locatello, J. Schmidhuber, and O. Bachem, “Are disentangled representations helpful for abstract visual reasoning?,” in <i>Advances in Neural Information Processing Systems</i>, Vancouver, Canada, 2019, vol. 32.","apa":"Steenkiste, S. van, Locatello, F., Schmidhuber, J., &#38; Bachem, O. (2019). Are disentangled representations helpful for abstract visual reasoning? In <i>Advances in Neural Information Processing Systems</i> (Vol. 32). Vancouver, Canada.","mla":"Steenkiste, Sjoerd van, et al. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” <i>Advances in Neural Information Processing Systems</i>, vol. 32, 2019.","chicago":"Steenkiste, Sjoerd van, Francesco Locatello, Jürgen Schmidhuber, and Olivier Bachem. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” In <i>Advances in Neural Information Processing Systems</i>, Vol. 32, 2019."},"day":"29","department":[{"_id":"FrLo"}],"date_created":"2023-08-22T14:09:53Z","oa_version":"Preprint","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14","start_date":"2019-12-08","location":"Vancouver, Canada"},"extern":"1","date_published":"2019-05-29T00:00:00Z","external_id":{"arxiv":["1905.12506"]},"date_updated":"2023-09-12T09:02:43Z","publication":"Advances in Neural Information Processing Systems","publication_identifier":{"isbn":["9781713807933"]},"publication_status":"published","status":"public","_id":"14193","oa":1,"title":"Are disentangled representations helpful for abstract visual reasoning?","author":[{"first_name":"Sjoerd van","last_name":"Steenkiste","full_name":"Steenkiste, Sjoerd van"},{"full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Jürgen","full_name":"Schmidhuber, Jürgen","last_name":"Schmidhuber"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"}],"abstract":[{"text":"A disentangled representation encodes information about the salient factors\r\nof variation in the data independently. Although it is often argued that this\r\nrepresentational format is useful in learning to solve many real-world\r\ndown-stream tasks, there is little empirical evidence that supports this claim.\r\nIn this paper, we conduct a large-scale study that investigates whether\r\ndisentangled representations are more suitable for abstract reasoning tasks.\r\nUsing two new tasks similar to Raven's Progressive Matrices, we evaluate the\r\nusefulness of the representations learned by 360 state-of-the-art unsupervised\r\ndisentanglement models. Based on these representations, we train 3600 abstract\r\nreasoning models and observe that disentangled representations do in fact lead\r\nto better down-stream performance. In particular, they enable quicker learning\r\nusing fewer samples.","lang":"eng"}],"year":"2019"},{"abstract":[{"text":"Recently there has been a significant interest in learning disentangled\r\nrepresentations, as they promise increased interpretability, generalization to\r\nunseen scenarios and faster learning on downstream tasks. In this paper, we\r\ninvestigate the usefulness of different notions of disentanglement for\r\nimproving the fairness of downstream prediction tasks based on representations.\r\nWe consider the setting where the goal is to predict a target variable based on\r\nthe learned representation of high-dimensional observations (such as images)\r\nthat depend on both the target variable and an \\emph{unobserved} sensitive\r\nvariable. We show that in this setting both the optimal and empirical\r\npredictions can be unfair, even if the target variable and the sensitive\r\nvariable are independent. Analyzing the representations of more than\r\n\\num{12600} trained state-of-the-art disentangled models, we observe that\r\nseveral disentanglement scores are consistently correlated with increased\r\nfairness, suggesting that disentanglement may be a useful property to encourage\r\nfairness when sensitive variables are not observed.","lang":"eng"}],"title":"On the fairness of disentangled representations","author":[{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"last_name":"Abbati","full_name":"Abbati, Gabriele","first_name":"Gabriele"},{"first_name":"Tom","full_name":"Rainforth, Tom","last_name":"Rainforth"},{"first_name":"Stefan","full_name":"Bauer, Stefan","last_name":"Bauer"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"last_name":"Bachem","full_name":"Bachem, Olivier","first_name":"Olivier"}],"_id":"14197","publication_status":"published","status":"public","publication_identifier":{"isbn":["9781713807933"]},"oa_version":"Preprint","conference":{"end_date":"2019-12-14","start_date":"2019-12-08","location":"Vancouver, Canada","name":"NeurIPS: Neural Information Processing Systems"},"citation":{"mla":"Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.” <i>Advances in Neural Information Processing Systems</i>, vol. 32, 2019, pp. 14611–14624.","chicago":"Locatello, Francesco, Gabriele Abbati, Tom Rainforth, Stefan Bauer, Bernhard Schölkopf, and Olivier Bachem. “On the Fairness of Disentangled Representations.” In <i>Advances in Neural Information Processing Systems</i>, 32:14611–14624, 2019.","apa":"Locatello, F., Abbati, G., Rainforth, T., Bauer, S., Schölkopf, B., &#38; Bachem, O. (2019). On the fairness of disentangled representations. In <i>Advances in Neural Information Processing Systems</i> (Vol. 32, pp. 14611–14624). Vancouver, Canada.","ieee":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, and O. Bachem, “On the fairness of disentangled representations,” in <i>Advances in Neural Information Processing Systems</i>, Vancouver, Canada, 2019, vol. 32, pp. 14611–14624.","ista":"Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. 2019. On the fairness of disentangled representations. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14611–14624.","ama":"Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. On the fairness of disentangled representations. In: <i>Advances in Neural Information Processing Systems</i>. Vol 32. ; 2019:14611–14624.","short":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019, pp. 14611–14624."},"day":"08","month":"12","volume":32,"article_processing_charge":"No","arxiv":1,"year":"2019","oa":1,"page":"14611–14624","publication":"Advances in Neural Information Processing Systems","date_updated":"2023-09-12T09:37:22Z","date_published":"2019-12-08T00:00:00Z","external_id":{"arxiv":["1905.13662"]},"extern":"1","date_created":"2023-08-22T14:12:28Z","scopus_import":"1","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","intvolume":"        32","main_file_link":[{"url":"https://arxiv.org/abs/1905.13662","open_access":"1"}]},{"article_processing_charge":"No","volume":97,"arxiv":1,"oa_version":"Preprint","conference":{"name":"International Conference on Machine Learning","location":"Long Beach, CA, United States","start_date":"2019-06-10","end_date":"2019-06-15"},"citation":{"mla":"Locatello, Francesco, et al. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” <i>Proceedings of the 36th International Conference on Machine Learning</i>, vol. 97, ML Research Press, 2019, pp. 4114–24.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” In <i>Proceedings of the 36th International Conference on Machine Learning</i>, 97:4114–24. ML Research Press, 2019.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., &#38; Bachem, O. (2019). Challenging common assumptions in the unsupervised learning of disentangled representations. In <i>Proceedings of the 36th International Conference on Machine Learning</i> (Vol. 97, pp. 4114–4124). Long Beach, CA, United States: ML Research Press.","ieee":"F. Locatello <i>et al.</i>, “Challenging common assumptions in the unsupervised learning of disentangled representations,” in <i>Proceedings of the 36th International Conference on Machine Learning</i>, Long Beach, CA, United States, 2019, vol. 97, pp. 4114–4124.","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 4114–4124.","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2019. Challenging common assumptions in the unsupervised learning of disentangled representations. Proceedings of the 36th International Conference on Machine Learning. International Conference on Machine Learning vol. 97, 4114–4124.","ama":"Locatello F, Bauer S, Lucic M, et al. Challenging common assumptions in the unsupervised learning of disentangled representations. In: <i>Proceedings of the 36th International Conference on Machine Learning</i>. Vol 97. ML Research Press; 2019:4114-4124."},"day":"09","month":"06","publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"The key idea behind the unsupervised learning of disentangled representations\r\nis that real-world data is generated by a few explanatory factors of variation\r\nwhich can be recovered by unsupervised learning algorithms. In this paper, we\r\nprovide a sober look at recent progress in the field and challenge some common\r\nassumptions. We first theoretically show that the unsupervised learning of\r\ndisentangled representations is fundamentally impossible without inductive\r\nbiases on both the models and the data. Then, we train more than 12000 models\r\ncovering most prominent methods and evaluation metrics in a reproducible\r\nlarge-scale experimental study on seven different data sets. We observe that\r\nwhile the different methods successfully enforce properties ``encouraged'' by\r\nthe corresponding losses, well-disentangled models seemingly cannot be\r\nidentified without supervision. Furthermore, increased disentanglement does not\r\nseem to lead to a decreased sample complexity of learning for downstream tasks.\r\nOur results suggest that future work on disentanglement learning should be\r\nexplicit about the role of inductive biases and (implicit) supervision,\r\ninvestigate concrete benefits of enforcing disentanglement of the learned\r\nrepresentations, and consider a reproducible experimental setup covering\r\nseveral data sets."}],"title":"Challenging common assumptions in the unsupervised learning of disentangled representations","author":[{"last_name":"Locatello","full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"first_name":"Stefan","full_name":"Bauer, Stefan","last_name":"Bauer"},{"last_name":"Lucic","full_name":"Lucic, Mario","first_name":"Mario"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"first_name":"Sylvain","last_name":"Gelly","full_name":"Gelly, Sylvain"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"}],"_id":"14200","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"publisher":"ML Research Press","intvolume":"        97","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.12359"}],"date_published":"2019-06-09T00:00:00Z","external_id":{"arxiv":["1811.12359"]},"extern":"1","date_created":"2023-08-22T14:13:08Z","scopus_import":"1","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"4114-4124","publication":"Proceedings of the 36th International Conference on Machine Learning","date_updated":"2023-09-13T07:45:30Z","year":"2019","oa":1},{"year":"2019","abstract":[{"text":"Bending-active structures are able to efficiently produce complex curved shapes starting from flat panels. The desired deformation of the panels derives from the proper selection of their elastic properties. Optimized panels, called FlexMaps, are designed such that, once they are bent and assembled, the resulting static equilibrium configuration matches a desired input 3D shape. The FlexMaps elastic properties are controlled by locally varying spiraling geometric mesostructures, which are optimized in size and shape to match the global curvature (i.e., bending requests) of the target shape. The design pipeline starts from a quad mesh representing the input 3D shape, which defines the edge size and the total amount of spirals: every quad will embed one spiral. Then, an optimization algorithm tunes the geometry of the spirals by using a simplified pre-computed rod model. This rod model is derived from a non-linear regression algorithm which approximates the non-linear behavior of solid FEM spiral models subject to hundreds of load combinations. This innovative pipeline has been applied to the project of a lightweight plywood pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted arc that fits a bounding box of 3.90x3.96x3.25 meters.","lang":"eng"}],"author":[{"first_name":"Francesco","last_name":"Laccone","full_name":"Laccone, Francesco"},{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"last_name":"Perez Rodriguez","full_name":"Perez Rodriguez, Jesus","first_name":"Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nico","full_name":"Pietroni, Nico","last_name":"Pietroni"},{"first_name":"Federico","full_name":"Ponchio, Federico","last_name":"Ponchio"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd","last_name":"Bickel"},{"full_name":"Cignoni, Paolo","last_name":"Cignoni","first_name":"Paolo"}],"title":"FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels","_id":"9261","status":"public","publication_status":"published","page":"509-515","publication":"IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE","publication_identifier":{"issn":["2518-6582"],"isbn":["9788412110104"]},"date_updated":"2023-09-08T11:21:54Z","date_published":"2019-10-10T00:00:00Z","external_id":{"isi":["000563497600059"]},"conference":{"end_date":"2019-10-10","start_date":"2019-10-07","location":"Barcelona, Spain","name":"IASS: International Association for Shell and Spatial Structures"},"scopus_import":"1","date_created":"2021-03-21T23:01:21Z","oa_version":"None","day":"10","department":[{"_id":"BeBi"}],"citation":{"mla":"Laccone, Francesco, et al. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>, International Center for Numerical Methods in Engineering, 2019, pp. 509–15.","chicago":"Laccone, Francesco, Luigi Malomo, Jesus Perez Rodriguez, Nico Pietroni, Federico Ponchio, Bernd Bickel, and Paolo Cignoni. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” In <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>, 509–15. International Center for Numerical Methods in Engineering, 2019.","ista":"Laccone F, Malomo L, Perez Rodriguez J, Pietroni N, Ponchio F, Bickel B, Cignoni P. 2019. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE. IASS: International Association for Shell and Spatial Structures, 509–515.","ama":"Laccone F, Malomo L, Perez Rodriguez J, et al. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In: <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>. International Center for Numerical Methods in Engineering; 2019:509-515.","short":"F. Laccone, L. Malomo, J. Perez Rodriguez, N. Pietroni, F. Ponchio, B. Bickel, P. Cignoni, in:, IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, International Center for Numerical Methods in Engineering, 2019, pp. 509–515.","apa":"Laccone, F., Malomo, L., Perez Rodriguez, J., Pietroni, N., Ponchio, F., Bickel, B., &#38; Cignoni, P. (2019). FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i> (pp. 509–515). Barcelona, Spain: International Center for Numerical Methods in Engineering.","ieee":"F. Laccone <i>et al.</i>, “FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels,” in <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>, Barcelona, Spain, 2019, pp. 509–515."},"month":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","article_processing_charge":"No","publisher":"International Center for Numerical Methods in Engineering"},{"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"status":"public","publication_status":"published","author":[{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"last_name":"Ono","full_name":"Ono, Akemi","first_name":"Akemi"},{"last_name":"Scholten","full_name":"Scholten, Stefan","first_name":"Stefan"},{"full_name":"Kinoshita, Tetsu","last_name":"Kinoshita","first_name":"Tetsu"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"full_name":"Okamoto, Takashi","last_name":"Okamoto","first_name":"Takashi"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"}],"title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","_id":"9460","issue":"19","abstract":[{"text":"Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion.","lang":"eng"}],"doi":"10.1073/pnas.1821435116","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"file_id":"9461","date_created":"2021-06-04T12:50:47Z","access_level":"open_access","content_type":"application/pdf","checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","success":1,"date_updated":"2021-06-04T12:50:47Z","file_name":"2019_PNAS_Kim.pdf","relation":"main_file","file_size":1142540,"creator":"asandaue"}],"has_accepted_license":"1","article_processing_charge":"No","volume":116,"day":"07","citation":{"mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>.","chicago":"Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>.","ista":"Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.","ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. 2019;116(19):9652-9657. doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>","short":"M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.","ieee":"M. Y. Kim <i>et al.</i>, “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., &#38; Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>"},"ddc":["580"],"file_date_updated":"2021-06-04T12:50:47Z","pmid":1,"month":"05","oa_version":"Published Version","publication":"Proceedings of the National Academy of Sciences","date_updated":"2021-12-14T07:52:30Z","article_type":"original","page":"9652-9657","oa":1,"year":"2019","keyword":["Multidisciplinary"],"intvolume":"       116","publisher":"National Academy of Sciences","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2019-05-07T00:00:00Z","extern":"1","external_id":{"pmid":["31000601"]},"scopus_import":"1","date_created":"2021-06-04T12:38:20Z"},{"oa":1,"year":"2019","date_updated":"2021-12-14T07:53:00Z","publication":"Epigenetics and Chromatin","article_type":"original","article_number":"62","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"scopus_import":"1","date_created":"2021-06-08T09:21:51Z","date_published":"2019-10-10T00:00:00Z","external_id":{"pmid":["31601251"]},"extern":"1","intvolume":"        12","publisher":"Springer Nature","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"_id":"9530","author":[{"first_name":"Keith D.","full_name":"Harris, Keith D.","last_name":"Harris"},{"first_name":"James P. B.","full_name":"Lloyd, James P. B.","last_name":"Lloyd"},{"first_name":"Katherine","last_name":"Domb","full_name":"Domb, Katherine"},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"},{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"}],"title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","doi":"10.1186/s13072-019-0307-4","abstract":[{"text":"Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems.","lang":"eng"}],"publication_identifier":{"eissn":["1756-8935"]},"status":"public","publication_status":"published","pmid":1,"month":"10","file_date_updated":"2021-06-08T09:29:19Z","ddc":["570"],"day":"10","citation":{"mla":"Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” <i>Epigenetics and Chromatin</i>, vol. 12, 62, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1186/s13072-019-0307-4\">10.1186/s13072-019-0307-4</a>.","chicago":"Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” <i>Epigenetics and Chromatin</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1186/s13072-019-0307-4\">https://doi.org/10.1186/s13072-019-0307-4</a>.","apa":"Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., &#38; Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. <i>Epigenetics and Chromatin</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13072-019-0307-4\">https://doi.org/10.1186/s13072-019-0307-4</a>","ieee":"K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” <i>Epigenetics and Chromatin</i>, vol. 12. Springer Nature, 2019.","ista":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62.","ama":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. <i>Epigenetics and Chromatin</i>. 2019;12. doi:<a href=\"https://doi.org/10.1186/s13072-019-0307-4\">10.1186/s13072-019-0307-4</a>","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019)."},"oa_version":"Published Version","file":[{"date_created":"2021-06-08T09:29:19Z","file_id":"9531","file_size":3221067,"relation":"main_file","creator":"asandaue","file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","checksum":"86ff50a7517891511af2733c76c81b67","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-06-08T09:29:19Z","success":1}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":12,"article_processing_charge":"No","has_accepted_license":"1"}]