[{"external_id":{"isi":["000456958800017"]},"day":"01","publisher":"Springer","scopus_import":"1","citation":{"ieee":"N. Nikolic, “Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system,” Current Genetics, vol. 65, no. 1. Springer, pp. 133–138, 2019.","ista":"Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.","mla":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics, vol. 65, no. 1, Springer, 2019, pp. 133–38, doi:10.1007/s00294-018-0879-8.","chicago":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics. Springer, 2019. https://doi.org/10.1007/s00294-018-0879-8.","apa":"Nikolic, N. (2019). Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. Springer. https://doi.org/10.1007/s00294-018-0879-8","ama":"Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 2019;65(1):133-138. doi:10.1007/s00294-018-0879-8","short":"N. Nikolic, Current Genetics 65 (2019) 133–138."},"publication":"Current Genetics","oa_version":"Published Version","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publist_id":"7785","oa":1,"department":[{"_id":"CaGu"}],"issue":"1","publication_status":"published","file":[{"access_level":"open_access","file_id":"5930","creator":"dernst","checksum":"6779708b0b632a1a6ed28c56f5161142","file_name":"2019_CurrentGenetics_Nikolic.pdf","relation":"main_file","date_created":"2019-02-06T07:50:58Z","content_type":"application/pdf","file_size":776399,"date_updated":"2020-07-14T12:44:47Z"}],"ddc":["570"],"has_accepted_license":"1","author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela","last_name":"Nikolic","orcid":"0000-0001-9068-6090","first_name":"Nela"}],"volume":65,"isi":1,"date_published":"2019-02-01T00:00:00Z","ec_funded":1,"page":"133-138","intvolume":" 65","doi":"10.1007/s00294-018-0879-8","_id":"138","month":"02","title":"Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:44:47Z","type":"journal_article","date_created":"2018-12-11T11:44:50Z","abstract":[{"lang":"eng","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."}],"year":"2019","date_updated":"2023-09-08T13:23:42Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"status":"public","oa_version":"Published Version","publication":"Proceedings of the National Academy of Sciences","citation":{"ama":"Baykusheva DR, Zindel D, Svoboda V, et al. Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. 2019;116(48):23923-23929. doi:10.1073/pnas.1907189116","apa":"Baykusheva, D. R., Zindel, D., Svoboda, V., Bommeli, E., Ochsner, M., Tehlar, A., & Wörner, H. J. (2019). Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1907189116","chicago":"Baykusheva, Denitsa Rangelova, Daniel Zindel, Vít Svoboda, Elias Bommeli, Manuel Ochsner, Andres Tehlar, and Hans Jakob Wörner. “Real-Time Probing of Chirality during a Chemical Reaction.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1907189116.","mla":"Baykusheva, Denitsa Rangelova, et al. “Real-Time Probing of Chirality during a Chemical Reaction.” Proceedings of the National Academy of Sciences, vol. 116, no. 48, Proceedings of the National Academy of Sciences, 2019, pp. 23923–29, doi:10.1073/pnas.1907189116.","ieee":"D. R. Baykusheva et al., “Real-time probing of chirality during a chemical reaction,” Proceedings of the National Academy of Sciences, vol. 116, no. 48. Proceedings of the National Academy of Sciences, pp. 23923–23929, 2019.","ista":"Baykusheva DR, Zindel D, Svoboda V, Bommeli E, Ochsner M, Tehlar A, Wörner HJ. 2019. Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. 116(48), 23923–23929.","short":"D.R. Baykusheva, D. Zindel, V. Svoboda, E. Bommeli, M. Ochsner, A. Tehlar, H.J. Wörner, Proceedings of the National Academy of Sciences 116 (2019) 23923–23929."},"scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publisher":"Proceedings of the National Academy of Sciences","day":"13","arxiv":1,"external_id":{"pmid":["31723044"],"arxiv":["1906.10818"]},"pmid":1,"publication_status":"published","issue":"48","oa":1,"_id":"14001","title":"Real-time probing of chirality during a chemical reaction","month":"11","intvolume":" 116","doi":"10.1073/pnas.1907189116","page":"23923-23929","date_published":"2019-11-13T00:00:00Z","author":[{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva"},{"first_name":"Daniel","full_name":"Zindel, Daniel","last_name":"Zindel"},{"first_name":"Vít","full_name":"Svoboda, Vít","last_name":"Svoboda"},{"first_name":"Elias","last_name":"Bommeli","full_name":"Bommeli, Elias"},{"first_name":"Manuel","full_name":"Ochsner, Manuel","last_name":"Ochsner"},{"full_name":"Tehlar, Andres","last_name":"Tehlar","first_name":"Andres"},{"last_name":"Wörner","full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob"}],"extern":"1","volume":116,"article_type":"original","date_updated":"2023-08-22T07:40:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","type":"journal_article","date_created":"2023-08-09T13:10:36Z","abstract":[{"text":"Chiral molecules interact and react differently with other chiral objects, depending on their handedness. Therefore, it is essential to understand and ultimately control the evolution of molecular chirality during chemical reactions. Although highly sophisticated techniques for the controlled synthesis of chiral molecules have been developed, the observation of chirality on the natural femtosecond time scale of a chemical reaction has so far remained out of reach in the gas phase. Here, we demonstrate a general experimental technique, based on high-harmonic generation in tailored laser fields, and apply it to probe the time evolution of molecular chirality during the photodissociation of 2-iodobutane. These measurements show a change in sign and a pronounced increase in the magnitude of the chiral response over the first 100 fs, followed by its decay within less than 500 fs, revealing the photodissociation to achiral products. The observed time evolution is explained in terms of the variation of the electric and magnetic transition-dipole moments between the lowest electronic states of the cation as a function of the reaction coordinate. These results open the path to investigations of the chirality of molecular-reaction pathways, light-induced chirality in chemical processes, and the control of molecular chirality through tailored laser pulses.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1907189116","open_access":"1"}],"quality_controlled":"1","keyword":["Multidisciplinary"],"article_processing_charge":"No","language":[{"iso":"eng"}]},{"year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-22T09:32:56Z","article_number":"8871819","abstract":[{"lang":"eng","text":"The advancement of attosecond chronoscopy has made it possible to reveal ultrashort time dynamics of photoionization [1]. Ionization delay measurements in atomic targets provide a wealth of information about the timing of the photoelectric effect [2], resonances, electron correlations and transport. The extension of this approach to molecules, however, presents great challenges. In addition to the difficulty of identifying correct ionization channels, it is hard to disentangle the role of the anisotropic molecular landscape from the delays inherent to the excitation process itself. Here, we present the measurements of ionization delays from ethyl iodide around the 4d giant dipole resonance of iodine. We employ attosecond streaking spectroscopy, which enables to disentangle the contribution to the delay from the functional ethyl group, being responsible for the characteristic chemical reactivity of the molecule. An attosecond extreme ultraviolet (XUV) pulse ionizes the molecule around the energy of the giant resonance and the released electron is exposed to the ponderomotive force of a synchronized near-infrared (NIR) field, which yields a streaking spectrogram (see figure). Comparative phase analysis of the spectrograms corresponding to iodine 4d and neon 2p emission permits extracting overall photoemission delays for ethyl iodide. The data is recorded for multiple photon energies around the iodine 4d resonance and compared to classical Wigner propagation [3] and quantum scattering [4] calculations. Here the outgoing electron, produced via inner shell ionization of the iodine atom in ethyl iodide, and thereby hardly influenced by the molecular potential during the birth process, acquires the necessary information about the influence of the functional ethyl group during its propagation. We find significant delay contributions that can distinguish between different functional groups, providing a sensitive probe of the local molecular environment [5]. This would stimulate to perform further angle resolved measurements in molecules to probe the potential landscape in three dimension."}],"type":"conference","date_created":"2023-08-09T13:10:49Z","publication_status":"published","quality_controlled":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","doi":"10.1109/cleoe-eqec.2019.8871819","oa_version":"None","title":"Probing molecular influence on photoemission delays","_id":"14002","month":"10","status":"public","publication_identifier":{"isbn":["9781728104706"],"eisbn":["9781728104690"]},"date_published":"2019-10-17T00:00:00Z","citation":{"ieee":"S. Biswas et al., “Probing molecular influence on photoemission delays,” in 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, Munich, Germany, 2019.","ista":"Biswas S, Liontos I, Kamal AM, Kling NG, Alharbi AF, Alharbi M, Azzeer AM, Worner HJ, Landsman AS, Kling MF, Forg B, Schotz J, Schweinberger W, Ortmann L, Zimmermann T, Pi L-W, Baykusheva DR, Masood HA. 2019. Probing molecular influence on photoemission delays. 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. CLEO: European Conference on Lasers and Electro-Optics, 8871819.","mla":"Biswas, Shubhadeep, et al. “Probing Molecular Influence on Photoemission Delays.” 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, 8871819, Institute of Electrical and Electronics Engineers, 2019, doi:10.1109/cleoe-eqec.2019.8871819.","apa":"Biswas, S., Liontos, I., Kamal, A. M., Kling, N. G., Alharbi, A. F., Alharbi, M., … Masood, H. A. (2019). Probing molecular influence on photoemission delays. In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Munich, Germany: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/cleoe-eqec.2019.8871819","chicago":"Biswas, Shubhadeep, I. Liontos, A. M. Kamal, N. G. Kling, A. F. Alharbi, M. Alharbi, A. M. Azzeer, et al. “Probing Molecular Influence on Photoemission Delays.” In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Institute of Electrical and Electronics Engineers, 2019. https://doi.org/10.1109/cleoe-eqec.2019.8871819.","ama":"Biswas S, Liontos I, Kamal AM, et al. Probing molecular influence on photoemission delays. In: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Institute of Electrical and Electronics Engineers; 2019. doi:10.1109/cleoe-eqec.2019.8871819","short":"S. Biswas, I. Liontos, A.M. Kamal, N.G. Kling, A.F. Alharbi, M. Alharbi, A.M. Azzeer, H.J. Worner, A.S. Landsman, M.F. Kling, B. Forg, J. Schotz, W. Schweinberger, L. Ortmann, T. Zimmermann, L.-W. Pi, D.R. Baykusheva, H.A. Masood, in:, 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, Institute of Electrical and Electronics Engineers, 2019."},"scopus_import":"1","publication":"2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference","publisher":"Institute of Electrical and Electronics Engineers","day":"17","extern":"1","conference":{"end_date":"2019-06-27","name":"CLEO: European Conference on Lasers and Electro-Optics","location":"Munich, Germany","start_date":"2019-06-23"},"author":[{"last_name":"Biswas","full_name":"Biswas, Shubhadeep","first_name":"Shubhadeep"},{"last_name":"Liontos","full_name":"Liontos, I.","first_name":"I."},{"first_name":"A. M.","last_name":"Kamal","full_name":"Kamal, A. M."},{"first_name":"N. G.","last_name":"Kling","full_name":"Kling, N. G."},{"first_name":"A. F.","full_name":"Alharbi, A. F.","last_name":"Alharbi"},{"first_name":"M.","last_name":"Alharbi","full_name":"Alharbi, M."},{"first_name":"A. M.","full_name":"Azzeer, A. M.","last_name":"Azzeer"},{"first_name":"H. J.","full_name":"Worner, H. J.","last_name":"Worner"},{"first_name":"A. S.","full_name":"Landsman, A. S.","last_name":"Landsman"},{"full_name":"Kling, M. F.","last_name":"Kling","first_name":"M. F."},{"first_name":"B.","full_name":"Forg, B.","last_name":"Forg"},{"first_name":"J.","last_name":"Schotz","full_name":"Schotz, J."},{"last_name":"Schweinberger","full_name":"Schweinberger, W.","first_name":"W."},{"first_name":"L.","last_name":"Ortmann","full_name":"Ortmann, L."},{"first_name":"T.","last_name":"Zimmermann","full_name":"Zimmermann, T."},{"last_name":"Pi","full_name":"Pi, L.-W.","first_name":"L.-W."},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"first_name":"H. A.","full_name":"Masood, H. A.","last_name":"Masood"}]},{"citation":{"short":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, O. Bachem, in:, 8th International Conference on Learning Representations, 2019.","mla":"Locatello, Francesco, et al. “Disentangling Factors of Variation Using Few Labels.” 8th International Conference on Learning Representations, 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.","ieee":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, and O. Bachem, “Disentangling factors of variation using few labels,” in 8th International Conference on Learning Representations, Virtual, 2019.","ama":"Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. Disentangling factors of variation using few labels. In: 8th International Conference on Learning Representations. ; 2019.","chicago":"Locatello, Francesco, Michael Tschannen, Stefan Bauer, Gunnar Rätsch, Bernhard Schölkopf, and Olivier Bachem. “Disentangling Factors of Variation Using Few Labels.” In 8th International Conference on Learning Representations, 2019.","apa":"Locatello, F., Tschannen, M., Bauer, S., Rätsch, G., Schölkopf, B., & Bachem, O. (2019). Disentangling factors of variation using few labels. In 8th International Conference on Learning Representations. Virtual."},"scopus_import":"1","date_published":"2019-12-20T00:00:00Z","publication":"8th International Conference on Learning Representations","oa_version":"Preprint","title":"Disentangling factors of variation using few labels","_id":"14184","month":"12","status":"public","arxiv":1,"external_id":{"arxiv":["1905.01258"]},"author":[{"first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Michael","full_name":"Tschannen, Michael","last_name":"Tschannen"},{"full_name":"Bauer, Stefan","last_name":"Bauer","first_name":"Stefan"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"}],"day":"20","conference":{"start_date":"2020-04-26","end_date":"2020-05-01","location":"Virtual","name":"ICLR: International Conference on Learning Representations"},"extern":"1","type":"conference","date_created":"2023-08-22T14:06:37Z","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","date_updated":"2023-09-12T07:01:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"oa":1,"article_processing_charge":"No","department":[{"_id":"FrLo"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.01258"}],"publication_status":"published"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.06642"}],"quality_controlled":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-12T08:07:38Z","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."}],"date_created":"2023-08-22T14:08:35Z","type":"conference","volume":115,"extern":"1","author":[{"first_name":"Luigi","full_name":"Gresele, Luigi","last_name":"Gresele"},{"last_name":"Rubenstein","full_name":"Rubenstein, Paul K.","first_name":"Paul K."},{"last_name":"Mehrjou","full_name":"Mehrjou, Arash","first_name":"Arash"},{"orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"}],"intvolume":" 115","title":"The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA","_id":"14189","month":"05","date_published":"2019-05-16T00:00:00Z","page":"217-227","publication_status":"published","alternative_title":["PMLR"],"department":[{"_id":"FrLo"}],"oa":1,"publisher":"ML Research Press","conference":{"start_date":"2019-07-22","location":"Tel Aviv, Israel","name":"UAI: Uncertainty in Artificial Intelligence","end_date":"2019-07-25"},"day":"16","external_id":{"arxiv":["1905.06642"]},"arxiv":1,"oa_version":"Preprint","status":"public","scopus_import":"1","citation":{"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 Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, Tel Aviv, Israel, 2019, vol. 115, pp. 217–227.","mla":"Gresele, Luigi, et al. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, vol. 115, ML Research Press, 2019, pp. 217–27.","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 Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, 115:217–27. ML Research Press, 2019.","apa":"Gresele, L., Rubenstein, P. K., Mehrjou, A., Locatello, F., & Schölkopf, B. (2019). The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence (Vol. 115, pp. 217–227). Tel Aviv, Israel: ML Research Press.","ama":"Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In: Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence. 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."},"publication":"Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence"},{"date_updated":"2023-09-13T09:46:38Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","type":"conference","date_created":"2023-08-22T14:09:13Z","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"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.03292"}],"publication_status":"published","article_processing_charge":"No","oa":1,"department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"_id":"14190","month":"06","title":"On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset","status":"public","oa_version":"Preprint","intvolume":" 32","publication":"Advances in Neural Information Processing Systems","citation":{"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.","ieee":"M. W. Gondal et al., “On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32.","mla":"Gondal, Muhammad Waleed, et al. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” Advances in Neural Information Processing Systems, 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 Advances in Neural Information Processing Systems, Vol. 32, 2019.","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 Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada.","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: Advances in Neural Information Processing Systems. Vol 32. ; 2019."},"publication_identifier":{"isbn":["9781713807933"]},"date_published":"2019-06-07T00:00:00Z","author":[{"first_name":"Muhammad Waleed","full_name":"Gondal, Muhammad Waleed","last_name":"Gondal"},{"first_name":"Manuel","full_name":"Wüthrich, Manuel","last_name":"Wüthrich"},{"first_name":"Đorđe","full_name":"Miladinović, Đorđe","last_name":"Miladinović"},{"first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Martin","last_name":"Breidt","full_name":"Breidt, Martin"},{"first_name":"Valentin","last_name":"Volchkov","full_name":"Volchkov, Valentin"},{"first_name":"Joel","last_name":"Akpo","full_name":"Akpo, Joel"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"}],"day":"07","conference":{"end_date":"2019-12-14","name":"NeurIPS: Neural Information Processing Systems","location":"Vancouver, Canada","start_date":"2019-12-08"},"extern":"1","volume":32,"arxiv":1,"external_id":{"arxiv":["1906.03292"]}},{"language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10348"}],"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"}],"type":"conference","date_created":"2023-08-22T14:09:35Z","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-12T08:48:45Z","volume":32,"extern":"1","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","first_name":"Francesco"},{"full_name":"Yurtsever, Alp","last_name":"Yurtsever","first_name":"Alp"},{"last_name":"Fercoq","full_name":"Fercoq, Olivier","first_name":"Olivier"},{"first_name":"Volkan","full_name":"Cevher, Volkan","last_name":"Cevher"}],"date_published":"2019-12-29T00:00:00Z","page":"14291–14301","intvolume":" 32","_id":"14191","title":"Stochastic Frank-Wolfe for composite convex minimization","month":"12","department":[{"_id":"FrLo"}],"oa":1,"publication_status":"published","external_id":{"arxiv":["1901.10348"]},"arxiv":1,"day":"29","conference":{"end_date":"2019-12-14","name":"NeurIPS: Neural Information Processing Systems","location":"Vancouver, Canada","start_date":"2019-12-08"},"publication_identifier":{"isbn":["9781713807933"]},"scopus_import":"1","citation":{"short":"F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 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.","ieee":"F. Locatello, A. Yurtsever, O. Fercoq, and V. Cevher, “Stochastic Frank-Wolfe for composite convex minimization,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14291–14301.","mla":"Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14291–14301.","chicago":"Locatello, Francesco, Alp Yurtsever, Olivier Fercoq, and Volkan Cevher. “Stochastic Frank-Wolfe for Composite Convex Minimization.” In Advances in Neural Information Processing Systems, 32:14291–14301, 2019.","apa":"Locatello, F., Yurtsever, A., Fercoq, O., & Cevher, V. (2019). Stochastic Frank-Wolfe for composite convex minimization. In Advances in Neural Information Processing Systems (Vol. 32, pp. 14291–14301). Vancouver, Canada.","ama":"Locatello F, Yurtsever A, Fercoq O, Cevher V. Stochastic Frank-Wolfe for composite convex minimization. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019:14291–14301."},"publication":"Advances in Neural Information Processing Systems","oa_version":"Preprint","status":"public"},{"intvolume":" 32","oa_version":"Preprint","_id":"14193","status":"public","month":"05","title":"Are disentangled representations helpful for abstract visual reasoning?","publication_identifier":{"isbn":["9781713807933"]},"date_published":"2019-05-29T00:00:00Z","citation":{"short":"S. van Steenkiste, F. Locatello, J. Schmidhuber, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019.","mla":"Steenkiste, Sjoerd van, et al. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” Advances in Neural Information Processing Systems, vol. 32, 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 Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32.","ama":"Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. Are disentangled representations helpful for abstract visual reasoning? In: Advances in Neural Information Processing Systems. Vol 32. ; 2019.","chicago":"Steenkiste, Sjoerd van, Francesco Locatello, Jürgen Schmidhuber, and Olivier Bachem. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” In Advances in Neural Information Processing Systems, Vol. 32, 2019.","apa":"Steenkiste, S. van, Locatello, F., Schmidhuber, J., & Bachem, O. (2019). Are disentangled representations helpful for abstract visual reasoning? In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada."},"publication":"Advances in Neural Information Processing Systems","extern":"1","conference":{"end_date":"2019-12-14","name":"NeurIPS: Neural Information Processing Systems","location":"Vancouver, Canada","start_date":"2019-12-08"},"day":"29","volume":32,"author":[{"first_name":"Sjoerd van","full_name":"Steenkiste, Sjoerd van","last_name":"Steenkiste"},{"first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Schmidhuber, Jürgen","last_name":"Schmidhuber","first_name":"Jürgen"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"}],"external_id":{"arxiv":["1905.12506"]},"arxiv":1,"year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-12T09:02:43Z","abstract":[{"lang":"eng","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."}],"type":"conference","date_created":"2023-08-22T14:09:53Z","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.12506","open_access":"1"}],"quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"article_processing_charge":"No","oa":1},{"status":"public","oa_version":"Preprint","publication":"Advances in Neural Information Processing Systems","citation":{"ieee":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, and O. Bachem, “On the fairness of disentangled representations,” in Advances in Neural Information Processing Systems, 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.","mla":"Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14611–14624.","apa":"Locatello, F., Abbati, G., Rainforth, T., Bauer, S., Schölkopf, B., & Bachem, O. (2019). On the fairness of disentangled representations. In Advances in Neural Information Processing Systems (Vol. 32, pp. 14611–14624). Vancouver, Canada.","chicago":"Locatello, Francesco, Gabriele Abbati, Tom Rainforth, Stefan Bauer, Bernhard Schölkopf, and Olivier Bachem. “On the Fairness of Disentangled Representations.” In Advances in Neural Information Processing Systems, 32:14611–14624, 2019.","ama":"Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. On the fairness of disentangled representations. In: Advances in Neural Information Processing Systems. 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."},"scopus_import":"1","publication_identifier":{"isbn":["9781713807933"]},"conference":{"start_date":"2019-12-08","end_date":"2019-12-14","name":"NeurIPS: Neural Information Processing Systems","location":"Vancouver, Canada"},"day":"08","arxiv":1,"external_id":{"arxiv":["1905.13662"]},"publication_status":"published","oa":1,"department":[{"_id":"FrLo"}],"_id":"14197","title":"On the fairness of disentangled representations","month":"12","intvolume":" 32","page":"14611–14624","date_published":"2019-12-08T00:00:00Z","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","first_name":"Francesco"},{"first_name":"Gabriele","full_name":"Abbati, Gabriele","last_name":"Abbati"},{"first_name":"Tom","last_name":"Rainforth","full_name":"Rainforth, Tom"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"}],"extern":"1","volume":32,"date_updated":"2023-09-12T09:37:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","date_created":"2023-08-22T14:12:28Z","type":"conference","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1905.13662","open_access":"1"}],"article_processing_charge":"No","language":[{"iso":"eng"}]},{"date_published":"2019-06-09T00:00:00Z","page":"4114-4124","intvolume":" 97","month":"06","_id":"14200","title":"Challenging common assumptions in the unsupervised learning of disentangled representations","author":[{"first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"},{"last_name":"Lucic","full_name":"Lucic, Mario","first_name":"Mario"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"full_name":"Gelly, Sylvain","last_name":"Gelly","first_name":"Sylvain"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"last_name":"Bachem","full_name":"Bachem, Olivier","first_name":"Olivier"}],"volume":97,"extern":"1","date_created":"2023-08-22T14:13:08Z","type":"conference","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."}],"year":"2019","date_updated":"2023-09-13T07:45:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1811.12359","open_access":"1"}],"citation":{"ama":"Locatello F, Bauer S, Lucic M, et al. Challenging common assumptions in the unsupervised learning of disentangled representations. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:4114-4124.","apa":"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. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 4114–4124). Long Beach, CA, United States: ML Research Press.","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 Proceedings of the 36th International Conference on Machine Learning, 97:4114–24. ML Research Press, 2019.","mla":"Locatello, Francesco, et al. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 4114–24.","ieee":"F. Locatello et al., “Challenging common assumptions in the unsupervised learning of disentangled representations,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, United States, 2019, vol. 97, 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.","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."},"scopus_import":"1","publication":"Proceedings of the 36th International Conference on Machine Learning","oa_version":"Preprint","status":"public","arxiv":1,"external_id":{"arxiv":["1811.12359"]},"day":"09","conference":{"end_date":"2019-06-15","location":"Long Beach, CA, United States","name":"International Conference on Machine Learning","start_date":"2019-06-10"},"publisher":"ML Research Press","oa":1,"department":[{"_id":"FrLo"}],"publication_status":"published"},{"year":"2019","date_updated":"2023-11-07T12:17:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_created":"2023-09-06T12:48:47Z","abstract":[{"text":"DNA origami nano-objects are usually designed around generic single-stranded “scaffolds”. Many properties of the target object are determined by details of those generic scaffold sequences. Here, we enable designers to fully specify the target structure not only in terms of desired 3D shape but also in terms of the sequences used. To this end, we built design tools to construct scaffold sequences de novo based on strand diagrams, and we developed scalable production methods for creating design-specific scaffold strands with fully user-defined sequences. We used 17 custom scaffolds having different lengths and sequence properties to study the influence of sequence redundancy and sequence composition on multilayer DNA origami assembly and to realize efficient one-pot assembly of multiscaffold DNA origami objects. Furthermore, as examples for functionalized scaffolds, we created a scaffold that enables direct, covalent cross-linking of DNA origami via UV irradiation, and we built DNAzyme-containing scaffolds that allow postfolding DNA origami domain separation.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1021/acsnano.9b01025","open_access":"1"}],"quality_controlled":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":" 13","doi":"10.1021/acsnano.9b01025","_id":"14299","title":"Custom-size, functional, and durable DNA origami with design-specific scaffolds","month":"04","date_published":"2019-04-16T00:00:00Z","page":"5015-5027","article_type":"original","author":[{"last_name":"FAS","full_name":"FAS, Engelhardt","first_name":"Engelhardt"},{"first_name":"Florian M","last_name":"Praetorius","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"last_name":"Wachauf","full_name":"Wachauf, CH","first_name":"CH"},{"first_name":"G","last_name":"Brüggenthies","full_name":"Brüggenthies, G"},{"last_name":"Kohler","full_name":"Kohler, F","first_name":"F"},{"first_name":"B","full_name":"Kick, B","last_name":"Kick"},{"full_name":"Kadletz, KL","last_name":"Kadletz","first_name":"KL"},{"first_name":"PN","full_name":"Pham, PN","last_name":"Pham"},{"last_name":"Behler","full_name":"Behler, KL","first_name":"KL"},{"last_name":"Gerling","full_name":"Gerling, T","first_name":"T"},{"first_name":"H","full_name":"Dietz, H","last_name":"Dietz"}],"volume":13,"extern":"1","pmid":1,"issue":"5","publication_status":"published","oa":1,"oa_version":"Published Version","status":"public","citation":{"ama":"FAS E, Praetorius FM, Wachauf C, et al. Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. 2019;13(5):5015-5027. doi:10.1021/acsnano.9b01025","chicago":"FAS, Engelhardt, Florian M Praetorius, CH Wachauf, G Brüggenthies, F Kohler, B Kick, KL Kadletz, et al. “Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds.” ACS Nano. ACS Publications, 2019. https://doi.org/10.1021/acsnano.9b01025.","apa":"FAS, E., Praetorius, F. M., Wachauf, C., Brüggenthies, G., Kohler, F., Kick, B., … Dietz, H. (2019). Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. ACS Publications. https://doi.org/10.1021/acsnano.9b01025","mla":"FAS, Engelhardt, et al. “Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds.” ACS Nano, vol. 13, no. 5, ACS Publications, 2019, pp. 5015–27, doi:10.1021/acsnano.9b01025.","ieee":"E. FAS et al., “Custom-size, functional, and durable DNA origami with design-specific scaffolds,” ACS Nano, vol. 13, no. 5. ACS Publications, pp. 5015–5027, 2019.","ista":"FAS E, Praetorius FM, Wachauf C, Brüggenthies G, Kohler F, Kick B, Kadletz K, Pham P, Behler K, Gerling T, Dietz H. 2019. Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. 13(5), 5015–5027.","short":"E. FAS, F.M. Praetorius, C. Wachauf, G. Brüggenthies, F. Kohler, B. Kick, K. Kadletz, P. Pham, K. Behler, T. Gerling, H. Dietz, ACS Nano 13 (2019) 5015–5027."},"scopus_import":"1","publication_identifier":{"eissn":["1936-086x"],"issn":["1936-0851"]},"publication":"ACS Nano","day":"16","publisher":"ACS Publications","external_id":{"pmid":["30990672"]}},{"publication":"ChemBioChem","citation":{"short":"M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein, A.J. Wilson, ChemBioChem 20 (2019) 891–895.","ieee":"M. M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein, and A. J. Wilson, “Recognition of ASF1 by using hydrocarbon‐constrained peptides,” ChemBioChem, vol. 20, no. 7. Wiley, pp. 891–895, 2019.","ista":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. 2019. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 20(7), 891–895.","mla":"Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” ChemBioChem, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:10.1002/cbic.201800633.","chicago":"Bakail, May M, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin, Françoise Ochsenbein, and Andrew J. Wilson. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” ChemBioChem. Wiley, 2019. https://doi.org/10.1002/cbic.201800633.","apa":"Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein, F., & Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. Wiley. https://doi.org/10.1002/cbic.201800633","ama":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 2019;20(7):891-895. doi:10.1002/cbic.201800633"},"publication_identifier":{"issn":["1439-4227","1439-7633"]},"status":"public","oa_version":"Published Version","day":"01","publisher":"Wiley","oa":1,"publication_status":"published","issue":"7","page":"891-895","date_published":"2019-04-01T00:00:00Z","_id":"9016","title":"Recognition of ASF1 by using hydrocarbon‐constrained peptides","month":"04","intvolume":" 20","doi":"10.1002/cbic.201800633","author":[{"first_name":"May M","orcid":"0000-0002-9592-1587","full_name":"Bakail, May M","last_name":"Bakail","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E"},{"first_name":"Silvia","full_name":"Rodriguez‐Marin, Silvia","last_name":"Rodriguez‐Marin"},{"last_name":"Hegedüs","full_name":"Hegedüs, Zsófia","first_name":"Zsófia"},{"first_name":"Marie E.","last_name":"Perrin","full_name":"Perrin, Marie E."},{"full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein","first_name":"Françoise"},{"last_name":"Wilson","full_name":"Wilson, Andrew J.","first_name":"Andrew J."}],"volume":20,"extern":"1","article_type":"original","date_created":"2021-01-19T10:59:14Z","type":"journal_article","abstract":[{"lang":"eng","text":"Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135) is a strategy through which chemical probes might be elaborated to test this hypothesis. In this work, variant H3118–135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy–entropy compensation occurs."}],"date_updated":"2023-02-23T13:46:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","article_processing_charge":"No","language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.1002/cbic.201800633","open_access":"1"}]},{"article_processing_charge":"No","language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.chembiol.2019.09.002","open_access":"1"}],"keyword":["Clinical Biochemistry","Molecular Medicine","Biochemistry","Molecular Biology","Pharmacology","Drug Discovery"],"abstract":[{"lang":"eng","text":"Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy."}],"date_created":"2021-01-19T11:04:50Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T13:46:53Z","year":"2019","volume":26,"extern":"1","author":[{"full_name":"Bakail, May M","last_name":"Bakail","orcid":"0000-0002-9592-1587","first_name":"May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E"},{"full_name":"Gaubert, Albane","last_name":"Gaubert","first_name":"Albane"},{"full_name":"Andreani, Jessica","last_name":"Andreani","first_name":"Jessica"},{"full_name":"Moal, Gwenaëlle","last_name":"Moal","first_name":"Gwenaëlle"},{"last_name":"Pinna","full_name":"Pinna, Guillaume","first_name":"Guillaume"},{"last_name":"Boyarchuk","full_name":"Boyarchuk, Ekaterina","first_name":"Ekaterina"},{"first_name":"Marie-Cécile","last_name":"Gaillard","full_name":"Gaillard, Marie-Cécile"},{"first_name":"Regis","last_name":"Courbeyrette","full_name":"Courbeyrette, Regis"},{"first_name":"Carl","full_name":"Mann, Carl","last_name":"Mann"},{"first_name":"Jean-Yves","full_name":"Thuret, Jean-Yves","last_name":"Thuret"},{"last_name":"Guichard","full_name":"Guichard, Bérengère","first_name":"Bérengère"},{"first_name":"Brice","full_name":"Murciano, Brice","last_name":"Murciano"},{"last_name":"Richet","full_name":"Richet, Nicolas","first_name":"Nicolas"},{"last_name":"Poitou","full_name":"Poitou, Adeline","first_name":"Adeline"},{"first_name":"Claire","full_name":"Frederic, Claire","last_name":"Frederic"},{"last_name":"Le Du","full_name":"Le Du, Marie-Hélène","first_name":"Marie-Hélène"},{"first_name":"Morgane","last_name":"Agez","full_name":"Agez, Morgane"},{"first_name":"Caroline","full_name":"Roelants, Caroline","last_name":"Roelants"},{"full_name":"Gurard-Levin, Zachary A.","last_name":"Gurard-Levin","first_name":"Zachary A."},{"full_name":"Almouzni, Geneviève","last_name":"Almouzni","first_name":"Geneviève"},{"full_name":"Cherradi, Nadia","last_name":"Cherradi","first_name":"Nadia"},{"full_name":"Guerois, Raphael","last_name":"Guerois","first_name":"Raphael"},{"last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise","first_name":"Françoise"}],"article_type":"original","page":"1573-1585.e10","date_published":"2019-11-21T00:00:00Z","_id":"9018","title":"Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1","month":"11","doi":"10.1016/j.chembiol.2019.09.002","intvolume":" 26","oa":1,"publication_status":"published","issue":"11","pmid":1,"external_id":{"pmid":["31543461"]},"publisher":"Elsevier","day":"21","publication":"Cell Chemical Biology","publication_identifier":{"issn":["2451-9456"]},"citation":{"short":"M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C. Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N. Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin, G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26 (2019) 1573–1585.e10.","chicago":"Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology. Elsevier, 2019. https://doi.org/10.1016/j.chembiol.2019.09.002.","apa":"Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E., … Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. Elsevier. https://doi.org/10.1016/j.chembiol.2019.09.002","ama":"Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 2019;26(11):1573-1585.e10. doi:10.1016/j.chembiol.2019.09.002","ieee":"M. M. Bakail et al., “Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1,” Cell Chemical Biology, vol. 26, no. 11. Elsevier, p. 1573–1585.e10, 2019.","ista":"Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C, Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11), 1573–1585.e10.","mla":"Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology, vol. 26, no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:10.1016/j.chembiol.2019.09.002."},"status":"public","oa_version":"Published Version"},{"external_id":{"pmid":["31358762"],"arxiv":["1909.07382"]},"arxiv":1,"day":"29","publisher":"Springer Nature","publication_identifier":{"issn":["2041-1723"]},"scopus_import":"1","citation":{"ieee":"S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing of colloidal monolayers,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","ista":"Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing of colloidal monolayers. Nature Communications. 10(1), 3380.","mla":"Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.” Nature Communications, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:10.1038/s41467-019-11362-y.","chicago":"Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled Annealing of Colloidal Monolayers.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-11362-y.","apa":"Ramananarivo, S., Ducrot, E., & Palacci, J. A. (2019). Activity-controlled annealing of colloidal monolayers. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-11362-y","ama":"Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal monolayers. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-11362-y","short":"S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019)."},"publication":"Nature Communications","oa_version":"Published Version","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"issue":"1","publication_status":"published","pmid":1,"file":[{"checksum":"70c6e5d6fbea0932b0669505ab6633ec","success":1,"creator":"cziletti","file_id":"9061","access_level":"open_access","date_updated":"2021-02-02T13:47:21Z","file_size":2820337,"content_type":"application/pdf","date_created":"2021-02-02T13:47:21Z","relation":"main_file","file_name":"2019_NatureComm_Ramananarivo.pdf"}],"ddc":["530"],"has_accepted_license":"1","article_type":"original","extern":"1","volume":10,"author":[{"full_name":"Ramananarivo, Sophie","last_name":"Ramananarivo","first_name":"Sophie"},{"first_name":"Etienne","last_name":"Ducrot","full_name":"Ducrot, Etienne"},{"full_name":"Palacci, Jérémie A","last_name":"Palacci","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"}],"date_published":"2019-07-29T00:00:00Z","doi":"10.1038/s41467-019-11362-y","intvolume":" 10","_id":"9060","title":"Activity-controlled annealing of colloidal monolayers","month":"07","language":[{"iso":"eng"}],"article_processing_charge":"No","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"quality_controlled":"1","file_date_updated":"2021-02-02T13:47:21Z","abstract":[{"lang":"eng","text":"Molecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium."}],"type":"journal_article","date_created":"2021-02-02T13:43:36Z","year":"2019","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_updated":"2023-02-23T13:47:59Z","article_number":"3380"},{"article_processing_charge":"No","department":[{"_id":"BeBi"}],"language":[{"iso":"eng"}],"quality_controlled":"1","publication_status":"published","date_created":"2021-03-21T23:01:21Z","type":"conference","abstract":[{"lang":"eng","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."}],"date_updated":"2023-09-08T11:21:54Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","external_id":{"isi":["000563497600059"]},"author":[{"last_name":"Laccone","full_name":"Laccone, Francesco","first_name":"Francesco"},{"last_name":"Malomo","full_name":"Malomo, Luigi","first_name":"Luigi"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez","full_name":"Perez Rodriguez, Jesus","first_name":"Jesus"},{"first_name":"Nico","full_name":"Pietroni, Nico","last_name":"Pietroni"},{"last_name":"Ponchio","full_name":"Ponchio, Federico","first_name":"Federico"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Paolo","full_name":"Cignoni, Paolo","last_name":"Cignoni"}],"conference":{"start_date":"2019-10-07","name":"IASS: International Association for Shell and Spatial Structures","location":"Barcelona, Spain","end_date":"2019-10-10"},"day":"10","publisher":"International Center for Numerical Methods in Engineering","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","page":"509-515","citation":{"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., & Cignoni, P. (2019). FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. 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 (pp. 509–515). Barcelona, Spain: International Center for Numerical Methods in Engineering.","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 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, 509–15. International Center for Numerical Methods in Engineering, 2019.","ama":"Laccone F, Malomo L, Perez Rodriguez J, et al. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. 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; 2019:509-515.","ieee":"F. Laccone et al., “FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels,” 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, Barcelona, Spain, 2019, pp. 509–515.","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.","mla":"Laccone, Francesco, et al. “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, International Center for Numerical Methods in Engineering, 2019, pp. 509–15."},"scopus_import":"1","isi":1,"publication_identifier":{"issn":["2518-6582"],"isbn":["9788412110104"]},"date_published":"2019-10-10T00:00:00Z","title":"FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels","_id":"9261","status":"public","month":"10","oa_version":"None"},{"language":[{"iso":"eng"}],"article_processing_charge":"No","keyword":["Multidisciplinary"],"quality_controlled":"1","file_date_updated":"2021-06-04T12:50:47Z","type":"journal_article","date_created":"2021-06-04T12:38:20Z","abstract":[{"lang":"eng","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."}],"year":"2019","date_updated":"2021-12-14T07:52:30Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["580"],"has_accepted_license":"1","article_type":"original","author":[{"last_name":"Kim","full_name":"Kim, M. Yvonne","first_name":"M. Yvonne"},{"first_name":"Akemi","last_name":"Ono","full_name":"Ono, Akemi"},{"full_name":"Scholten, Stefan","last_name":"Scholten","first_name":"Stefan"},{"last_name":"Kinoshita","full_name":"Kinoshita, Tetsu","first_name":"Tetsu"},{"first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Takashi","last_name":"Okamoto","full_name":"Okamoto, Takashi"},{"last_name":"Fischer","full_name":"Fischer, Robert L.","first_name":"Robert L."}],"extern":"1","volume":116,"date_published":"2019-05-07T00:00:00Z","page":"9652-9657","intvolume":" 116","doi":"10.1073/pnas.1821435116","_id":"9460","month":"05","title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa":1,"department":[{"_id":"DaZi"}],"issue":"19","publication_status":"published","pmid":1,"file":[{"date_created":"2021-06-04T12:50:47Z","file_name":"2019_PNAS_Kim.pdf","relation":"main_file","date_updated":"2021-06-04T12:50:47Z","file_size":1142540,"content_type":"application/pdf","file_id":"9461","access_level":"open_access","checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","success":1,"creator":"asandaue"}],"external_id":{"pmid":["31000601"]},"day":"07","publisher":"National Academy of Sciences","scopus_import":"1","citation":{"mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116.","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.","ieee":"M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” Proceedings of the National Academy of Sciences, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.","ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., & Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116","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.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.","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."},"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication":"Proceedings of the National Academy of Sciences","oa_version":"Published Version","status":"public"},{"publisher":"Springer Nature","day":"10","external_id":{"pmid":["31601251"]},"status":"public","oa_version":"Published Version","publication":"Epigenetics and Chromatin","publication_identifier":{"eissn":["1756-8935"]},"citation":{"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.” Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4.","apa":"Harris, K. D., Lloyd, J. P. B., 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. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4","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. Epigenetics and Chromatin. 2019;12. doi:10.1186/s13072-019-0307-4","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.","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,” Epigenetics and Chromatin, vol. 12. Springer Nature, 2019.","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.” Epigenetics and Chromatin, vol. 12, 62, Springer Nature, 2019, doi:10.1186/s13072-019-0307-4.","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019)."},"scopus_import":"1","publication_status":"published","department":[{"_id":"DaZi"}],"oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"creator":"asandaue","success":1,"checksum":"86ff50a7517891511af2733c76c81b67","access_level":"open_access","file_id":"9531","content_type":"application/pdf","date_updated":"2021-06-08T09:29:19Z","file_size":3221067,"relation":"main_file","file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","date_created":"2021-06-08T09:29:19Z"}],"pmid":1,"extern":"1","volume":12,"author":[{"full_name":"Harris, Keith D.","last_name":"Harris","first_name":"Keith D."},{"last_name":"Lloyd","full_name":"Lloyd, James P. B.","first_name":"James P. B."},{"first_name":"Katherine","last_name":"Domb","full_name":"Domb, Katherine"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","first_name":"Daniel"},{"first_name":"Assaf","last_name":"Zemach","full_name":"Zemach, Assaf"}],"article_type":"original","has_accepted_license":"1","ddc":["570"],"_id":"9530","month":"10","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","intvolume":" 12","date_published":"2019-10-10T00:00:00Z","quality_controlled":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_number":"62","date_updated":"2021-12-14T07:53:00Z","year":"2019","abstract":[{"lang":"eng","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."}],"date_created":"2021-06-08T09:21:51Z","type":"journal_article","file_date_updated":"2021-06-08T09:29:19Z"},{"publication_status":"published","issue":"1","oa":1,"day":"01","publisher":"Springer","arxiv":1,"external_id":{"arxiv":["1803.08462"]},"status":"public","oa_version":"Preprint","publication":"Israel Journal of Mathematics","citation":{"mla":"Conlon, David, et al. “Hypergraph Cuts above the Average.” Israel Journal of Mathematics, vol. 233, no. 1, Springer, 2019, pp. 67–111, doi:10.1007/s11856-019-1897-z.","ista":"Conlon D, Fox J, Kwan MA, Sudakov B. 2019. Hypergraph cuts above the average. Israel Journal of Mathematics. 233(1), 67–111.","ieee":"D. Conlon, J. Fox, M. A. Kwan, and B. Sudakov, “Hypergraph cuts above the average,” Israel Journal of Mathematics, vol. 233, no. 1. Springer, pp. 67–111, 2019.","ama":"Conlon D, Fox J, Kwan MA, Sudakov B. Hypergraph cuts above the average. Israel Journal of Mathematics. 2019;233(1):67-111. doi:10.1007/s11856-019-1897-z","apa":"Conlon, D., Fox, J., Kwan, M. A., & Sudakov, B. (2019). Hypergraph cuts above the average. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-019-1897-z","chicago":"Conlon, David, Jacob Fox, Matthew Alan Kwan, and Benny Sudakov. “Hypergraph Cuts above the Average.” Israel Journal of Mathematics. Springer, 2019. https://doi.org/10.1007/s11856-019-1897-z.","short":"D. Conlon, J. Fox, M.A. Kwan, B. Sudakov, Israel Journal of Mathematics 233 (2019) 67–111."},"scopus_import":"1","publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.08462","open_access":"1"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"date_updated":"2023-02-23T14:01:41Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","date_created":"2021-06-21T13:36:02Z","type":"journal_article","abstract":[{"lang":"eng","text":"An r-cut of a k-uniform hypergraph H is a partition of the vertex set of H into r parts and the size of the cut is the number of edges which have a vertex in each part. A classical result of Edwards says that every m-edge graph has a 2-cut of size m/2+Ω)(m−−√) and this is best possible. That is, there exist cuts which exceed the expected size of a random cut by some multiple of the standard deviation. We study analogues of this and related results in hypergraphs. First, we observe that similarly to graphs, every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m−−√) larger than the expected size of a random r-cut. Moreover, in the case where k = 3 and r = 2 this bound is best possible and is attained by Steiner triple systems. Surprisingly, for all other cases (that is, if k ≥ 4 or r ≥ 3), we show that every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m5/9) larger than the expected size of a random r-cut. This is a significant difference in behaviour, since the amount by which the size of the largest cut exceeds the expected size of a random cut is now considerably larger than the standard deviation."}],"author":[{"first_name":"David","last_name":"Conlon","full_name":"Conlon, David"},{"first_name":"Jacob","full_name":"Fox, Jacob","last_name":"Fox"},{"full_name":"Kwan, Matthew Alan","last_name":"Kwan","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sudakov","full_name":"Sudakov, Benny","first_name":"Benny"}],"volume":233,"extern":"1","article_type":"original","month":"08","_id":"9580","title":"Hypergraph cuts above the average","doi":"10.1007/s11856-019-1897-z","intvolume":" 233","page":"67-111","date_published":"2019-08-01T00:00:00Z"},{"publication_status":"published","issue":"8","oa":1,"publisher":"American Mathematical Society","day":"15","arxiv":1,"external_id":{"arxiv":["1712.05656"]},"status":"public","oa_version":"Submitted Version","publication":"Transactions of the American Mathematical Society","citation":{"short":"M.A. Kwan, B. Sudakov, Transactions of the American Mathematical Society 372 (2019) 5571–5594.","apa":"Kwan, M. A., & Sudakov, B. (2019). Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7729","chicago":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7729.","ama":"Kwan MA, Sudakov B. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 2019;372(8):5571-5594. doi:10.1090/tran/7729","ista":"Kwan MA, Sudakov B. 2019. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 372(8), 5571–5594.","ieee":"M. A. Kwan and B. Sudakov, “Proof of a conjecture on induced subgraphs of Ramsey graphs,” Transactions of the American Mathematical Society, vol. 372, no. 8. American Mathematical Society, pp. 5571–5594, 2019.","mla":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society, vol. 372, no. 8, American Mathematical Society, 2019, pp. 5571–94, doi:10.1090/tran/7729."},"scopus_import":"1","publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"main_file_link":[{"url":"https://doi.org/10.1090/tran/7729","open_access":"1"}],"quality_controlled":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"date_updated":"2023-02-23T14:01:50Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","date_created":"2021-06-22T09:31:45Z","type":"journal_article","abstract":[{"text":"An n-vertex graph is called C-Ramsey if it has no clique or independent set of size C log n. All known constructions of Ramsey graphs involve randomness in an essential way, and there is an ongoing line of research towards showing that in fact all Ramsey graphs must obey certain “richness” properties characteristic of random graphs. More than 25 years ago, Erdős, Faudree and Sós conjectured that in any C-Ramsey graph there are Ω(n^5/2) induced subgraphs, no pair of which have the same numbers of vertices and edges. Improving on earlier results of Alon, Balogh, Kostochka and Samotij, in this paper we prove this conjecture.","lang":"eng"}],"author":[{"orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","last_name":"Kwan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"full_name":"Sudakov, Benny","last_name":"Sudakov","first_name":"Benny"}],"volume":372,"extern":"1","article_type":"original","_id":"9585","month":"10","title":"Proof of a conjecture on induced subgraphs of Ramsey graphs","intvolume":" 372","doi":"10.1090/tran/7729","page":"5571-5594","date_published":"2019-10-15T00:00:00Z"},{"status":"public","oa_version":"Preprint","publication":"Journal of the London Mathematical Society","scopus_import":"1","citation":{"chicago":"Kwan, Matthew Alan, Benny Sudakov, and Tuan Tran. “Anticoncentration for Subgraph Statistics.” Journal of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12192.","apa":"Kwan, M. A., Sudakov, B., & Tran, T. (2019). Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12192","ama":"Kwan MA, Sudakov B, Tran T. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 2019;99(3):757-777. doi:10.1112/jlms.12192","ieee":"M. A. Kwan, B. Sudakov, and T. Tran, “Anticoncentration for subgraph statistics,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 757–777, 2019.","ista":"Kwan MA, Sudakov B, Tran T. 2019. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 99(3), 757–777.","mla":"Kwan, Matthew Alan, et al. “Anticoncentration for Subgraph Statistics.” Journal of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 757–77, doi:10.1112/jlms.12192.","short":"M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society 99 (2019) 757–777."},"publication_identifier":{"issn":["0024-6107"],"eissn":["1469-7750"]},"day":"03","publisher":"Wiley","arxiv":1,"external_id":{"arxiv":["1807.05202"]},"publication_status":"published","issue":"3","oa":1,"_id":"9586","title":"Anticoncentration for subgraph statistics","month":"05","intvolume":" 99","doi":"10.1112/jlms.12192","page":"757-777","date_published":"2019-05-03T00:00:00Z","author":[{"orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sudakov","full_name":"Sudakov, Benny","first_name":"Benny"},{"last_name":"Tran","full_name":"Tran, Tuan","first_name":"Tuan"}],"extern":"1","volume":99,"article_type":"original","date_updated":"2023-02-23T14:01:53Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","type":"journal_article","date_created":"2021-06-22T09:46:03Z","abstract":[{"text":"Consider integers 𝑘,ℓ such that 0⩽ℓ⩽(𝑘2) . Given a large graph 𝐺 , what is the fraction of 𝑘 -vertex subsets of 𝐺 which span exactly ℓ edges? When 𝐺 is empty or complete, and ℓ is zero or (𝑘2) , this fraction can be exactly 1. On the other hand, if ℓ is far from these extreme values, one might expect that this fraction is substantially smaller than 1. This was recently proved by Alon, Hefetz, Krivelevich, and Tyomkyn who initiated the systematic study of this question and proposed several natural conjectures.\r\nLet ℓ∗=min{ℓ,(𝑘2)−ℓ} . Our main result is that for any 𝑘 and ℓ , the fraction of 𝑘 -vertex subsets that span ℓ edges is at most log𝑂(1)(ℓ∗/𝑘)√ 𝑘/ℓ∗, which is best-possible up to the logarithmic factor. This improves on multiple results of Alon, Hefetz, Krivelevich, and Tyomkyn, and resolves one of their conjectures. In addition, we also make some first steps towards some analogous questions for hypergraphs.\r\nOur proofs involve some Ramsey-type arguments, and a number of different probabilistic tools, such as polynomial anticoncentration inequalities, hypercontractivity, and a coupling trick for random variables defined on a ‘slice’ of the Boolean hypercube.","lang":"eng"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1807.05202","open_access":"1"}],"article_processing_charge":"No","language":[{"iso":"eng"}]}]