[{"has_accepted_license":"1","year":"2019","ec_funded":1,"oa":1,"article_processing_charge":"Yes (via OA deal)","title":"Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system","doi":"10.1007/s00294-018-0879-8","isi":1,"external_id":{"isi":["000456958800017"]},"day":"01","date_updated":"2023-09-08T13:23:42Z","page":"133-138","issue":"1","language":[{"iso":"eng"}],"_id":"138","file_date_updated":"2020-07-14T12:44:47Z","month":"02","file":[{"file_name":"2019_CurrentGenetics_Nikolic.pdf","relation":"main_file","creator":"dernst","checksum":"6779708b0b632a1a6ed28c56f5161142","content_type":"application/pdf","access_level":"open_access","date_created":"2019-02-06T07:50:58Z","date_updated":"2020-07-14T12:44:47Z","file_size":776399,"file_id":"5930"}],"author":[{"orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","first_name":"Nela","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ista":"Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.","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.","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.","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."},"ddc":["570"],"volume":65,"type":"journal_article","department":[{"_id":"CaGu"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","publication_status":"published","publisher":"Springer","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."}],"date_published":"2019-02-01T00:00:00Z","status":"public","publication":"Current Genetics","publist_id":"7785","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 65","oa_version":"Published Version","scopus_import":"1","date_created":"2018-12-11T11:44:50Z"},{"issue":"48","page":"23923-23929","_id":"14001","language":[{"iso":"eng"}],"month":"11","author":[{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"first_name":"Daniel","last_name":"Zindel","full_name":"Zindel, Daniel"},{"first_name":"Vít","last_name":"Svoboda","full_name":"Svoboda, Vít"},{"last_name":"Bommeli","first_name":"Elias","full_name":"Bommeli, Elias"},{"full_name":"Ochsner, Manuel","first_name":"Manuel","last_name":"Ochsner"},{"first_name":"Andres","last_name":"Tehlar","full_name":"Tehlar, Andres"},{"full_name":"Wörner, Hans Jakob","last_name":"Wörner","first_name":"Hans Jakob"}],"keyword":["Multidisciplinary"],"arxiv":1,"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","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.","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.","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.","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."},"article_type":"original","year":"2019","article_processing_charge":"No","oa":1,"external_id":{"pmid":["31723044"],"arxiv":["1906.10818"]},"title":"Real-time probing of chirality during a chemical reaction","doi":"10.1073/pnas.1907189116","date_updated":"2023-08-22T07:40:05Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"day":"13","status":"public","date_published":"2019-11-13T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","abstract":[{"lang":"eng","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."}],"intvolume":" 116","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2023-08-09T13:10:36Z","extern":"1","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1907189116","open_access":"1"}],"volume":116,"type":"journal_article","pmid":1,"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","publication_status":"published"},{"date_updated":"2023-08-22T09:32:56Z","publisher":"Institute of Electrical and Electronics Engineers","day":"17","publication_identifier":{"isbn":["9781728104706"],"eisbn":["9781728104690"]},"publication_status":"published","quality_controlled":"1","doi":"10.1109/cleoe-eqec.2019.8871819","title":"Probing molecular influence on photoemission delays","article_processing_charge":"No","type":"conference","year":"2019","conference":{"location":"Munich, Germany","name":"CLEO: European Conference on Lasers and Electro-Optics","start_date":"2019-06-23","end_date":"2019-06-27"},"citation":{"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.","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","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","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.","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.","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.","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."},"date_created":"2023-08-09T13:10:49Z","extern":"1","scopus_import":"1","author":[{"full_name":"Biswas, Shubhadeep","last_name":"Biswas","first_name":"Shubhadeep"},{"first_name":"I.","last_name":"Liontos","full_name":"Liontos, I."},{"first_name":"A. M.","last_name":"Kamal","full_name":"Kamal, A. M."},{"full_name":"Kling, N. G.","first_name":"N. G.","last_name":"Kling"},{"full_name":"Alharbi, A. F.","last_name":"Alharbi","first_name":"A. F."},{"full_name":"Alharbi, M.","last_name":"Alharbi","first_name":"M."},{"full_name":"Azzeer, A. M.","first_name":"A. M.","last_name":"Azzeer"},{"full_name":"Worner, H. J.","first_name":"H. J.","last_name":"Worner"},{"last_name":"Landsman","first_name":"A. S.","full_name":"Landsman, A. S."},{"full_name":"Kling, M. F.","first_name":"M. F.","last_name":"Kling"},{"full_name":"Forg, B.","last_name":"Forg","first_name":"B."},{"last_name":"Schotz","first_name":"J.","full_name":"Schotz, J."},{"first_name":"W.","last_name":"Schweinberger","full_name":"Schweinberger, W."},{"first_name":"L.","last_name":"Ortmann","full_name":"Ortmann, L."},{"full_name":"Zimmermann, T.","last_name":"Zimmermann","first_name":"T."},{"full_name":"Pi, L.-W.","last_name":"Pi","first_name":"L.-W."},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova"},{"full_name":"Masood, H. A.","first_name":"H. A.","last_name":"Masood"}],"oa_version":"None","month":"10","article_number":"8871819","_id":"14002","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference","date_published":"2019-10-17T00:00:00Z","status":"public","abstract":[{"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.","lang":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"14184","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."}],"publication":"8th International Conference on Learning Representations","status":"public","date_published":"2019-12-20T00:00:00Z","scopus_import":"1","extern":"1","date_created":"2023-08-22T14:06:37Z","citation":{"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.","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.","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.","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.","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.","mla":"Locatello, Francesco, et al. “Disentangling Factors of Variation Using Few Labels.” 8th International Conference on Learning Representations, 2019.","short":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, O. Bachem, in:, 8th International Conference on Learning Representations, 2019."},"arxiv":1,"author":[{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Tschannen, Michael","last_name":"Tschannen","first_name":"Michael"},{"full_name":"Bauer, Stefan","first_name":"Stefan","last_name":"Bauer"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"},{"last_name":"Bachem","first_name":"Olivier","full_name":"Bachem, Olivier"}],"oa_version":"Preprint","month":"12","type":"conference","oa":1,"article_processing_charge":"No","conference":{"name":"ICLR: International Conference on Learning Representations","location":"Virtual","end_date":"2020-05-01","start_date":"2020-04-26"},"main_file_link":[{"url":"https://arxiv.org/abs/1905.01258","open_access":"1"}],"year":"2019","day":"20","publication_status":"published","date_updated":"2023-09-12T07:01:34Z","title":"Disentangling factors of variation using few labels","department":[{"_id":"FrLo"}],"external_id":{"arxiv":["1905.01258"]},"quality_controlled":"1"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.06642"}],"type":"conference","volume":115,"department":[{"_id":"FrLo"}],"quality_controlled":"1","publication_status":"published","publisher":"ML Research Press","abstract":[{"lang":"eng","text":"We consider the problem of recovering a common latent source with independent\r\ncomponents from multiple views. This applies to settings in which a variable is\r\nmeasured with multiple experimental modalities, and where the goal is to\r\nsynthesize the disparate measurements into a single unified representation. We\r\nconsider the case that the observed views are a nonlinear mixing of\r\ncomponent-wise corruptions of the sources. When the views are considered\r\nseparately, this reduces to nonlinear Independent Component Analysis (ICA) for\r\nwhich it is provably impossible to undo the mixing. We present novel\r\nidentifiability proofs that this is possible when the multiple views are\r\nconsidered jointly, showing that the mixing can theoretically be undone using\r\nfunction approximators such as deep neural networks. In contrast to known\r\nidentifiability results for nonlinear ICA, we prove that independent latent\r\nsources with arbitrary mixing can be recovered as long as multiple,\r\nsufficiently different noisy views are available."}],"publication":"Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence","date_published":"2019-05-16T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 115","oa_version":"Preprint","scopus_import":"1","extern":"1","alternative_title":["PMLR"],"date_created":"2023-08-22T14:08:35Z","conference":{"location":"Tel Aviv, Israel","name":"UAI: Uncertainty in Artificial Intelligence","start_date":"2019-07-22","end_date":"2019-07-25"},"year":"2019","oa":1,"article_processing_charge":"No","title":"The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA","external_id":{"arxiv":["1905.06642"]},"day":"16","date_updated":"2023-09-12T08:07:38Z","page":"217-227","language":[{"iso":"eng"}],"_id":"14189","author":[{"full_name":"Gresele, Luigi","first_name":"Luigi","last_name":"Gresele"},{"full_name":"Rubenstein, Paul K.","last_name":"Rubenstein","first_name":"Paul K."},{"full_name":"Mehrjou, Arash","last_name":"Mehrjou","first_name":"Arash"},{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"}],"month":"05","arxiv":1,"citation":{"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.","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.","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.","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.","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.","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.","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."}},{"day":"07","publication_status":"published","publication_identifier":{"isbn":["9781713807933"]},"date_updated":"2023-09-13T09:46:38Z","department":[{"_id":"FrLo"}],"title":"On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset","quality_controlled":"1","external_id":{"arxiv":["1906.03292"]},"type":"conference","volume":32,"article_processing_charge":"No","oa":1,"conference":{"end_date":"2019-12-14","start_date":"2019-12-08","name":"NeurIPS: Neural Information Processing Systems","location":"Vancouver, Canada"},"main_file_link":[{"url":"https://arxiv.org/abs/1906.03292","open_access":"1"}],"year":"2019","extern":"1","arxiv":1,"citation":{"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.","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.","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.","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.","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.","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."},"date_created":"2023-08-22T14:09:13Z","oa_version":"Preprint","author":[{"full_name":"Gondal, Muhammad Waleed","last_name":"Gondal","first_name":"Muhammad Waleed"},{"full_name":"Wüthrich, Manuel","last_name":"Wüthrich","first_name":"Manuel"},{"full_name":"Miladinović, Đorđe","first_name":"Đorđe","last_name":"Miladinović"},{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"last_name":"Breidt","first_name":"Martin","full_name":"Breidt, Martin"},{"last_name":"Volchkov","first_name":"Valentin","full_name":"Volchkov, Valentin"},{"full_name":"Akpo, Joel","first_name":"Joel","last_name":"Akpo"},{"last_name":"Bachem","first_name":"Olivier","full_name":"Bachem, Olivier"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"}],"month":"06","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"14190","intvolume":" 32","language":[{"iso":"eng"}],"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"}],"publication":"Advances in Neural Information Processing Systems","status":"public","date_published":"2019-06-07T00:00:00Z"},{"language":[{"iso":"eng"}],"_id":"14191","page":"14291–14301","arxiv":1,"citation":{"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.","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.","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.","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.","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.","short":"F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 14291–14301."},"author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Alp","last_name":"Yurtsever","full_name":"Yurtsever, Alp"},{"full_name":"Fercoq, Olivier","last_name":"Fercoq","first_name":"Olivier"},{"full_name":"Cevher, Volkan","last_name":"Cevher","first_name":"Volkan"}],"month":"12","article_processing_charge":"No","oa":1,"conference":{"end_date":"2019-12-14","start_date":"2019-12-08","name":"NeurIPS: Neural Information Processing Systems","location":"Vancouver, Canada"},"year":"2019","day":"29","publication_identifier":{"isbn":["9781713807933"]},"date_updated":"2023-09-12T08:48:45Z","title":"Stochastic Frank-Wolfe for composite convex minimization","external_id":{"arxiv":["1901.10348"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 32","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"}],"publication":"Advances in Neural Information Processing Systems","status":"public","date_published":"2019-12-29T00:00:00Z","scopus_import":"1","extern":"1","date_created":"2023-08-22T14:09:35Z","oa_version":"Preprint","type":"conference","volume":32,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10348"}],"publication_status":"published","department":[{"_id":"FrLo"}],"quality_controlled":"1"},{"date_updated":"2023-09-12T09:02:43Z","publication_identifier":{"isbn":["9781713807933"]},"publication_status":"published","day":"29","quality_controlled":"1","external_id":{"arxiv":["1905.12506"]},"title":"Are disentangled representations helpful for abstract visual reasoning?","department":[{"_id":"FrLo"}],"oa":1,"article_processing_charge":"No","volume":32,"type":"conference","year":"2019","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.12506","open_access":"1"}],"conference":{"location":"Vancouver, Canada","name":"NeurIPS: Neural Information Processing Systems","start_date":"2019-12-08","end_date":"2019-12-14"},"citation":{"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.","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.","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.","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.","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.","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."},"arxiv":1,"date_created":"2023-08-22T14:09:53Z","extern":"1","month":"05","oa_version":"Preprint","author":[{"full_name":"Steenkiste, Sjoerd van","last_name":"Steenkiste","first_name":"Sjoerd van"},{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Schmidhuber","first_name":"Jürgen","full_name":"Schmidhuber, Jürgen"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"_id":"14193","intvolume":" 32","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2019-05-29T00:00:00Z","publication":"Advances in Neural Information Processing Systems","abstract":[{"text":"A disentangled representation encodes information about the salient factors\r\nof variation in the data independently. Although it is often argued that this\r\nrepresentational format is useful in learning to solve many real-world\r\ndown-stream tasks, there is little empirical evidence that supports this claim.\r\nIn this paper, we conduct a large-scale study that investigates whether\r\ndisentangled representations are more suitable for abstract reasoning tasks.\r\nUsing two new tasks similar to Raven's Progressive Matrices, we evaluate the\r\nusefulness of the representations learned by 360 state-of-the-art unsupervised\r\ndisentanglement models. Based on these representations, we train 3600 abstract\r\nreasoning models and observe that disentangled representations do in fact lead\r\nto better down-stream performance. In particular, they enable quicker learning\r\nusing fewer samples.","lang":"eng"}]},{"conference":{"location":"Vancouver, Canada","name":"NeurIPS: Neural Information Processing Systems","start_date":"2019-12-08","end_date":"2019-12-14"},"year":"2019","article_processing_charge":"No","oa":1,"title":"On the fairness of disentangled representations","external_id":{"arxiv":["1905.13662"]},"publication_identifier":{"isbn":["9781713807933"]},"day":"08","date_updated":"2023-09-12T09:37:22Z","page":"14611–14624","_id":"14197","language":[{"iso":"eng"}],"month":"12","author":[{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"last_name":"Abbati","first_name":"Gabriele","full_name":"Abbati, Gabriele"},{"last_name":"Rainforth","first_name":"Tom","full_name":"Rainforth, Tom"},{"last_name":"Bauer","first_name":"Stefan","full_name":"Bauer, Stefan"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"arxiv":1,"citation":{"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.","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.","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.","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.","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.","mla":"Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 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."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.13662"}],"volume":32,"type":"conference","department":[{"_id":"FrLo"}],"quality_controlled":"1","publication_status":"published","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."}],"date_published":"2019-12-08T00:00:00Z","status":"public","publication":"Advances in Neural Information Processing Systems","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 32","oa_version":"Preprint","scopus_import":"1","extern":"1","date_created":"2023-08-22T14:12:28Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 97","abstract":[{"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.","lang":"eng"}],"status":"public","date_published":"2019-06-09T00:00:00Z","publication":"Proceedings of the 36th International Conference on Machine Learning","extern":"1","scopus_import":"1","date_created":"2023-08-22T14:13:08Z","oa_version":"Preprint","volume":97,"type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1811.12359","open_access":"1"}],"publication_status":"published","publisher":"ML Research Press","department":[{"_id":"FrLo"}],"quality_controlled":"1","language":[{"iso":"eng"}],"_id":"14200","page":"4114-4124","citation":{"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.","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.","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.","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.","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."},"arxiv":1,"month":"06","author":[{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"full_name":"Bauer, Stefan","first_name":"Stefan","last_name":"Bauer"},{"first_name":"Mario","last_name":"Lucic","full_name":"Lucic, Mario"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"full_name":"Gelly, Sylvain","first_name":"Sylvain","last_name":"Gelly"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"full_name":"Bachem, Olivier","first_name":"Olivier","last_name":"Bachem"}],"article_processing_charge":"No","oa":1,"conference":{"name":"International Conference on Machine Learning","location":"Long Beach, CA, United States","end_date":"2019-06-15","start_date":"2019-06-10"},"year":"2019","day":"09","date_updated":"2023-09-13T07:45:30Z","title":"Challenging common assumptions in the unsupervised learning of disentangled representations","external_id":{"arxiv":["1811.12359"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","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"}],"publication":"ACS Nano","date_published":"2019-04-16T00:00:00Z","status":"public","scopus_import":"1","extern":"1","date_created":"2023-09-06T12:48:47Z","oa_version":"Published Version","type":"journal_article","volume":13,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsnano.9b01025"}],"publication_status":"published","publisher":"ACS Publications","quality_controlled":"1","pmid":1,"_id":"14299","language":[{"iso":"eng"}],"page":"5015-5027","issue":"5","article_type":"original","citation":{"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.","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.","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.","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.","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","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"},"author":[{"full_name":"FAS, Engelhardt","last_name":"FAS","first_name":"Engelhardt"},{"full_name":"Praetorius, Florian M","first_name":"Florian M","last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"last_name":"Wachauf","first_name":"CH","full_name":"Wachauf, CH"},{"first_name":"G","last_name":"Brüggenthies","full_name":"Brüggenthies, G"},{"last_name":"Kohler","first_name":"F","full_name":"Kohler, F"},{"first_name":"B","last_name":"Kick","full_name":"Kick, B"},{"full_name":"Kadletz, KL","last_name":"Kadletz","first_name":"KL"},{"first_name":"PN","last_name":"Pham","full_name":"Pham, PN"},{"full_name":"Behler, KL","first_name":"KL","last_name":"Behler"},{"first_name":"T","last_name":"Gerling","full_name":"Gerling, T"},{"full_name":"Dietz, H","last_name":"Dietz","first_name":"H"}],"month":"04","article_processing_charge":"No","oa":1,"year":"2019","day":"16","publication_identifier":{"eissn":["1936-086x"],"issn":["1936-0851"]},"date_updated":"2023-11-07T12:17:31Z","doi":"10.1021/acsnano.9b01025","title":"Custom-size, functional, and durable DNA origami with design-specific scaffolds","external_id":{"pmid":["30990672"]}},{"date_updated":"2023-09-07T12:07:12Z","publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"day":"01","isi":1,"external_id":{"arxiv":["1709.09380"],"isi":["000494042900008"]},"title":"Poisson–Delaunay Mosaics of Order k","doi":"10.1007/s00454-018-0049-2","article_processing_charge":"Yes (via OA deal)","oa":1,"ec_funded":1,"year":"2019","has_accepted_license":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"6287","status":"public"}]},"citation":{"chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Poisson–Delaunay Mosaics of Order K.” Discrete and Computational Geometry. Springer, 2019. https://doi.org/10.1007/s00454-018-0049-2.","ieee":"H. Edelsbrunner and A. Nikitenko, “Poisson–Delaunay Mosaics of Order k,” Discrete and Computational Geometry, vol. 62, no. 4. Springer, pp. 865–878, 2019.","short":"H. Edelsbrunner, A. Nikitenko, Discrete and Computational Geometry 62 (2019) 865–878.","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Poisson–Delaunay Mosaics of Order K.” Discrete and Computational Geometry, vol. 62, no. 4, Springer, 2019, pp. 865–878, doi:10.1007/s00454-018-0049-2.","ama":"Edelsbrunner H, Nikitenko A. Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. 2019;62(4):865–878. doi:10.1007/s00454-018-0049-2","ista":"Edelsbrunner H, Nikitenko A. 2019. Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. 62(4), 865–878.","apa":"Edelsbrunner, H., & Nikitenko, A. (2019). Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. Springer. https://doi.org/10.1007/s00454-018-0049-2"},"arxiv":1,"ddc":["516"],"article_type":"original","file_date_updated":"2020-07-14T12:47:10Z","month":"12","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"first_name":"Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton"}],"file":[{"content_type":"application/pdf","file_name":"2018_DiscreteCompGeometry_Edelsbrunner.pdf","relation":"main_file","creator":"dernst","checksum":"f9d00e166efaccb5a76bbcbb4dcea3b4","file_size":599339,"file_id":"5932","access_level":"open_access","date_created":"2019-02-06T10:10:46Z","date_updated":"2020-07-14T12:47:10Z"}],"_id":"5678","language":[{"iso":"eng"}],"issue":"4","page":"865–878","publisher":"Springer","publication_status":"published","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020"},{"name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","department":[{"_id":"HeEd"}],"volume":62,"type":"journal_article","date_created":"2018-12-16T22:59:20Z","scopus_import":"1","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 62","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2019-12-01T00:00:00Z","publication":"Discrete and Computational Geometry","abstract":[{"text":"The order-k Voronoi tessellation of a locally finite set 𝑋⊆ℝ𝑛 decomposes ℝ𝑛 into convex domains whose points have the same k nearest neighbors in X. Assuming X is a stationary Poisson point process, we give explicit formulas for the expected number and total area of faces of a given dimension per unit volume of space. We also develop a relaxed version of discrete Morse theory and generalize by counting only faces, for which the k nearest points in X are within a given distance threshold.","lang":"eng"}]},{"type":"journal_article","volume":166,"quality_controlled":"1","department":[{"_id":"NiBa"}],"publisher":"Taylor and Francis","publication_status":"published","publication":"Botany Letters","date_published":"2019-01-01T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones."}],"intvolume":" 166","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","date_created":"2018-12-16T22:59:20Z","scopus_import":"1","year":"2019","article_processing_charge":"No","external_id":{"isi":["000463802800009"]},"isi":1,"doi":"10.1080/23818107.2018.1545142","title":"Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone","date_updated":"2023-08-24T14:34:12Z","day":"01","publication_identifier":{"issn":["23818107"],"eissn":["23818115"]},"issue":"1","page":"80-92","_id":"5680","language":[{"iso":"eng"}],"author":[{"last_name":"Andalo","first_name":"Christophe","full_name":"Andalo, Christophe"},{"full_name":"Burrus, Monique","first_name":"Monique","last_name":"Burrus"},{"last_name":"Paute","first_name":"Sandrine","full_name":"Paute, Sandrine"},{"last_name":"Lauzeral","first_name":"Christine","full_name":"Lauzeral, Christine"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"}],"month":"01","citation":{"ama":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 2019;166(1):80-92. doi:10.1080/23818107.2018.1545142","ista":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 166(1), 80–92.","apa":"Andalo, C., Burrus, M., Paute, S., Lauzeral, C., & Field, D. (2019). Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. Taylor and Francis. https://doi.org/10.1080/23818107.2018.1545142","chicago":"Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral, and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters. Taylor and Francis, 2019. https://doi.org/10.1080/23818107.2018.1545142.","ieee":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone,” Botany Letters, vol. 166, no. 1. Taylor and Francis, pp. 80–92, 2019.","short":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92.","mla":"Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:10.1080/23818107.2018.1545142."}},{"acknowledged_ssus":[{"_id":"Bio"}],"publisher":"Nature Publishing Group","publication_status":"published","quality_controlled":"1","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020"},{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants (EMBO fellowship)","grant_number":"ALTF710-2016"}],"pmid":1,"department":[{"_id":"CaHe"},{"_id":"EdHa"}],"type":"journal_article","volume":21,"date_created":"2018-12-30T22:59:15Z","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 21","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Nature Cell Biology","status":"public","date_published":"2019-02-01T00:00:00Z","abstract":[{"text":"Tissue morphogenesis is driven by mechanical forces that elicit changes in cell size, shape and motion. The extent by which forces deform tissues critically depends on the rheological properties of the recipient tissue. Yet, whether and how dynamic changes in tissue rheology affect tissue morphogenesis and how they are regulated within the developing organism remain unclear. Here, we show that blastoderm spreading at the onset of zebrafish morphogenesis relies on a rapid, pronounced and spatially patterned tissue fluidization. Blastoderm fluidization is temporally controlled by mitotic cell rounding-dependent cell–cell contact disassembly during the last rounds of cell cleavages. Moreover, fluidization is spatially restricted to the central blastoderm by local activation of non-canonical Wnt signalling within the blastoderm margin, increasing cell cohesion and thereby counteracting the effect of mitotic rounding on contact disassembly. Overall, our results identify a fluidity transition mediated by loss of cell cohesion as a critical regulator of embryo morphogenesis.","lang":"eng"}],"date_updated":"2023-09-11T14:03:28Z","day":"01","publication_identifier":{"issn":["14657392"]},"external_id":{"pmid":["30559456"],"isi":["000457468300011"]},"isi":1,"doi":"10.1038/s41556-018-0247-4","title":"Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling","article_processing_charge":"No","oa":1,"ec_funded":1,"year":"2019","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/when-a-fish-becomes-fluid/"}]},"has_accepted_license":"1","ddc":["570"],"citation":{"ista":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. 2019. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 21, 169–178.","apa":"Petridou, N., Grigolon, S., Salbreux, G., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0247-4","ama":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 2019;21:169–178. doi:10.1038/s41556-018-0247-4","short":"N. Petridou, S. Grigolon, G. Salbreux, E.B. Hannezo, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 169–178.","mla":"Petridou, Nicoletta, et al. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology, vol. 21, Nature Publishing Group, 2019, pp. 169–178, doi:10.1038/s41556-018-0247-4.","chicago":"Petridou, Nicoletta, Silvia Grigolon, Guillaume Salbreux, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology. Nature Publishing Group, 2019. https://doi.org/10.1038/s41556-018-0247-4.","ieee":"N. Petridou, S. Grigolon, G. Salbreux, E. B. Hannezo, and C.-P. J. Heisenberg, “Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling,” Nature Cell Biology, vol. 21. Nature Publishing Group, pp. 169–178, 2019."},"article_type":"original","file":[{"date_updated":"2020-10-21T07:18:35Z","date_created":"2020-10-21T07:18:35Z","access_level":"open_access","success":1,"file_id":"8685","file_size":71590590,"checksum":"e38523787b3bc84006f2793de99ad70f","creator":"dernst","file_name":"2018_NatureCellBio_Petridou_accepted.pdf","relation":"main_file","content_type":"application/pdf"}],"author":[{"first_name":"Nicoletta","last_name":"Petridou","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8451-1195","full_name":"Petridou, Nicoletta"},{"full_name":"Grigolon, Silvia","last_name":"Grigolon","first_name":"Silvia"},{"full_name":"Salbreux, Guillaume","last_name":"Salbreux","first_name":"Guillaume"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"month":"02","file_date_updated":"2020-10-21T07:18:35Z","_id":"5789","language":[{"iso":"eng"}],"page":"169–178"},{"date_published":"2019-08-01T00:00:00Z","status":"public","publication":"Journal of Graph Theory","abstract":[{"lang":"eng","text":"The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest."}],"intvolume":" 91","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","date_created":"2018-12-30T22:59:15Z","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1309.2399","open_access":"1"}],"volume":91,"type":"journal_article","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","department":[{"_id":"UlWa"}],"publisher":"Wiley","publication_status":"published","issue":"4","page":"365-394","language":[{"iso":"eng"}],"_id":"5790","month":"08","author":[{"full_name":"Chaplick, Steven","last_name":"Chaplick","first_name":"Steven"},{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"last_name":"Klavík","first_name":"Pavel","full_name":"Klavík, Pavel"}],"citation":{"short":"S. Chaplick, R. Fulek, P. Klavík, Journal of Graph Theory 91 (2019) 365–394.","mla":"Chaplick, Steven, et al. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory, vol. 91, no. 4, Wiley, 2019, pp. 365–94, doi:10.1002/jgt.22436.","chicago":"Chaplick, Steven, Radoslav Fulek, and Pavel Klavík. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory. Wiley, 2019. https://doi.org/10.1002/jgt.22436.","ieee":"S. Chaplick, R. Fulek, and P. Klavík, “Extending partial representations of circle graphs,” Journal of Graph Theory, vol. 91, no. 4. Wiley, pp. 365–394, 2019.","ista":"Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of circle graphs. Journal of Graph Theory. 91(4), 365–394.","apa":"Chaplick, S., Fulek, R., & Klavík, P. (2019). Extending partial representations of circle graphs. Journal of Graph Theory. Wiley. https://doi.org/10.1002/jgt.22436","ama":"Chaplick S, Fulek R, Klavík P. Extending partial representations of circle graphs. Journal of Graph Theory. 2019;91(4):365-394. doi:10.1002/jgt.22436"},"arxiv":1,"article_type":"original","ec_funded":1,"year":"2019","oa":1,"article_processing_charge":"No","isi":1,"external_id":{"isi":["000485392800004"],"arxiv":["1309.2399"]},"title":"Extending partial representations of circle graphs","doi":"10.1002/jgt.22436","date_updated":"2023-08-24T14:30:43Z","publication_identifier":{"issn":["03649024"]},"day":"01"},{"editor":[{"first_name":"Alexander","last_name":"Hergovich","full_name":"Hergovich, Alexander"}],"doi":"10.1007/978-1-4939-8910-2_14","department":[{"_id":"CaHe"}],"title":"Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids","quality_controlled":"1","day":"01","publication_identifier":{"isbn":["978-1-4939-8909-6"]},"publication_status":"published","date_updated":"2021-01-12T08:03:30Z","publisher":"Springer","series_title":"Methods in Molecular Biology","year":"2019","type":"book_chapter","volume":1893,"author":[{"full_name":"Asaoka, Yoichi","first_name":"Yoichi","last_name":"Asaoka"},{"full_name":"Morita, Hitoshi","first_name":"Hitoshi","last_name":"Morita"},{"last_name":"Furumoto","first_name":"Hiroko","full_name":"Furumoto, Hiroko"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Furutani-Seiki","first_name":"Makoto","full_name":"Furutani-Seiki, Makoto"}],"oa_version":"None","month":"01","scopus_import":1,"alternative_title":["MIMB"],"date_created":"2019-01-06T22:59:11Z","citation":{"short":"Y. Asaoka, H. Morita, H. Furumoto, C.-P.J. Heisenberg, M. Furutani-Seiki, in:, A. Hergovich (Ed.), The Hippo Pathway, Springer, 2019, pp. 167–181.","mla":"Asaoka, Yoichi, et al. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” The Hippo Pathway, edited by Alexander Hergovich, vol. 1893, Springer, 2019, pp. 167–81, doi:10.1007/978-1-4939-8910-2_14.","ieee":"Y. Asaoka, H. Morita, H. Furumoto, C.-P. J. Heisenberg, and M. Furutani-Seiki, “Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids,” in The hippo pathway, vol. 1893, A. Hergovich, Ed. Springer, 2019, pp. 167–181.","chicago":"Asaoka, Yoichi, Hitoshi Morita, Hiroko Furumoto, Carl-Philipp J Heisenberg, and Makoto Furutani-Seiki. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” In The Hippo Pathway, edited by Alexander Hergovich, 1893:167–81. Methods in Molecular Biology. Springer, 2019. https://doi.org/10.1007/978-1-4939-8910-2_14.","apa":"Asaoka, Y., Morita, H., Furumoto, H., Heisenberg, C.-P. J., & Furutani-Seiki, M. (2019). Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In A. Hergovich (Ed.), The hippo pathway (Vol. 1893, pp. 167–181). Springer. https://doi.org/10.1007/978-1-4939-8910-2_14","ista":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. 2019.Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: The hippo pathway. MIMB, vol. 1893, 167–181.","ama":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: Hergovich A, ed. The Hippo Pathway. Vol 1893. Methods in Molecular Biology. Springer; 2019:167-181. doi:10.1007/978-1-4939-8910-2_14"},"page":"167-181","abstract":[{"lang":"eng","text":"The transcription coactivator, Yes-associated protein (YAP), which is a nuclear effector of the Hippo signaling pathway, has been shown to be a mechano-transducer. By using mutant fish and human 3D spheroids, we have recently demonstrated that YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis of organ and global body shape by controlling actomyosin-mediated tissue tension. In this chapter, we present a platform that links the findings in fish embryos with human cells. The protocols for analyzing tissue tension-mediated global body shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in vitro using human cell spheroids represent useful tools for unraveling the molecular mechanisms by which YAP functions in regulating global body/organ morphogenesis."}],"publication":"The hippo pathway","date_published":"2019-01-01T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5793","language":[{"iso":"eng"}],"intvolume":" 1893"},{"status":"public","date_published":"2019-01-10T00:00:00Z","publication":"Soft Matter","abstract":[{"lang":"eng","text":"We theoretically study the shapes of lipid vesicles confined to a spherical cavity, elaborating a framework based on the so-called limiting shapes constructed from geometrically simple structural elements such as double-membrane walls and edges. Partly inspired by numerical results, the proposed non-compartmentalized and compartmentalized limiting shapes are arranged in the bilayer-couple phase diagram which is then compared to its free-vesicle counterpart. We also compute the area-difference-elasticity phase diagram of the limiting shapes and we use it to interpret shape transitions experimentally observed in vesicles confined within another vesicle. The limiting-shape framework may be generalized to theoretically investigate the structure of certain cell organelles such as the mitochondrion."}],"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","intvolume":" 15","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","short":"CC BY-NC-ND (3.0)"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","date_created":"2019-01-11T07:37:47Z","scopus_import":"1","volume":15,"type":"journal_article","pmid":1,"quality_controlled":"1","department":[{"_id":"GaTk"}],"publisher":"Royal Society of Chemistry","publication_status":"published","issue":"4","page":"602-614","language":[{"iso":"eng"}],"_id":"5817","month":"01","file_date_updated":"2020-10-09T11:00:05Z","author":[{"last_name":"Kavcic","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor"},{"full_name":"Sakashita, A.","last_name":"Sakashita","first_name":"A."},{"full_name":"Noguchi, H.","last_name":"Noguchi","first_name":"H."},{"full_name":"Ziherl, P.","first_name":"P.","last_name":"Ziherl"}],"file":[{"file_name":"lmt_sftmtr_V8.pdf","relation":"main_file","checksum":"614c337d6424ccd3d48d1b1f9513510d","creator":"bkavcic","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-10-09T11:00:05Z","date_created":"2020-10-09T11:00:05Z","file_size":5370762,"success":1,"file_id":"8641"}],"citation":{"chicago":"Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8sm01956h.","ieee":"B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” Soft Matter, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019.","mla":"Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:10.1039/c8sm01956h.","short":"B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.","ama":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. Soft Matter. 2019;15(4):602-614. doi:10.1039/c8sm01956h","ista":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614.","apa":"Kavcic, B., Sakashita, A., Noguchi, H., & Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c8sm01956h"},"ddc":["530"],"article_type":"original","year":"2019","has_accepted_license":"1","article_processing_charge":"No","oa":1,"isi":1,"external_id":{"isi":["000457329700003"],"pmid":["30629082"]},"title":"Limiting shapes of confined lipid vesicles","doi":"10.1039/c8sm01956h","date_updated":"2023-09-13T08:47:16Z","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"day":"10"},{"main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.1016/j.neuron.2018.11.015"}],"volume":101,"type":"journal_article","department":[{"_id":"JoCs"}],"project":[{"call_identifier":"FP7","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"}],"quality_controlled":"1","publication_status":"published","publisher":"Elsevier","abstract":[{"text":"Hippocampus is needed for both spatial working and reference memories. Here, using a radial eight-arm maze, we examined how the combined demand on these memories influenced CA1 place cell assemblies while reference memories were partially updated. This was contrasted with control tasks requiring only working memory or the update of reference memory. Reference memory update led to the reward-directed place field shifts at newly rewarded arms and to the gradual strengthening of firing in passes between newly rewarded arms but not between those passes that included a familiar-rewarded arm. At the maze center, transient network synchronization periods preferentially replayed trajectories of the next chosen arm in reference memory tasks but the previously visited arm in the working memory task. Hence, reference memory demand was uniquely associated with a gradual, goal novelty-related reorganization of place cell assemblies and with trajectory replay that reflected the animal's decision of which arm to visit next.","lang":"eng"}],"status":"public","date_published":"2019-01-02T00:00:00Z","publication":"Neuron","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 101","oa_version":"Published Version","scopus_import":"1","date_created":"2019-01-13T22:59:10Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/reading-rats-minds/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"relation":"dissertation_contains","id":"837","status":"public"}]},"year":"2019","ec_funded":1,"oa":1,"article_processing_charge":"No","title":"Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze","doi":"10.1016/j.neuron.2018.11.015","isi":1,"external_id":{"isi":["000454791500014"]},"publication_identifier":{"issn":["10974199"]},"day":"02","date_updated":"2023-09-07T12:06:37Z","page":"119-132.e4","issue":"1","_id":"5828","language":[{"iso":"eng"}],"month":"01","author":[{"id":"310349D0-F248-11E8-B48F-1D18A9856A87","first_name":"Haibing","last_name":"Xu","full_name":"Xu, Haibing"},{"id":"361CC00E-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Baracskay","full_name":"Baracskay, Peter"},{"last_name":"O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","full_name":"O'Neill, Joseph"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari"}],"article_type":"original","citation":{"short":"H. Xu, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 101 (2019) 119–132.e4.","mla":"Xu, Haibing, et al. “Assembly Responses of Hippocampal CA1 Place Cells Predict Learned Behavior in Goal-Directed Spatial Tasks on the Radial Eight-Arm Maze.” Neuron, vol. 101, no. 1, Elsevier, 2019, p. 119–132.e4, doi:10.1016/j.neuron.2018.11.015.","ieee":"H. Xu, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze,” Neuron, vol. 101, no. 1. Elsevier, p. 119–132.e4, 2019.","chicago":"Xu, Haibing, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Assembly Responses of Hippocampal CA1 Place Cells Predict Learned Behavior in Goal-Directed Spatial Tasks on the Radial Eight-Arm Maze.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2018.11.015.","apa":"Xu, H., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.11.015","ista":"Xu H, Baracskay P, O’Neill J, Csicsvari JL. 2019. Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. 101(1), 119–132.e4.","ama":"Xu H, Baracskay P, O’Neill J, Csicsvari JL. Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. 2019;101(1):119-132.e4. doi:10.1016/j.neuron.2018.11.015"}},{"oa_version":"Published Version","date_created":"2019-01-20T22:59:17Z","scopus_import":"1","publication":"Annales Henri Poincare","status":"public","date_published":"2019-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"We give a bound on the ground-state energy of a system of N non-interacting fermions in a three-dimensional cubic box interacting with an impurity particle via point interactions. We show that the change in energy compared to the system in the absence of the impurity is bounded in terms of the gas density and the scattering length of the interaction, independently of N. Our bound holds as long as the ratio of the mass of the impurity to the one of the gas particles is larger than a critical value m∗ ∗≈ 0.36 , which is the same regime for which we recently showed stability of the system."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 20","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"department":[{"_id":"RoSe"}],"publisher":"Springer","publication_status":"published","type":"journal_article","volume":20,"author":[{"full_name":"Moser, Thomas","first_name":"Thomas","last_name":"Moser","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"file":[{"content_type":"application/pdf","checksum":"255e42f957a8e2b10aad2499c750a8d6","creator":"dernst","file_name":"2019_Annales_Moser.pdf","relation":"main_file","file_id":"5894","file_size":859846,"date_updated":"2020-07-14T12:47:12Z","date_created":"2019-01-28T15:27:17Z","access_level":"open_access"}],"file_date_updated":"2020-07-14T12:47:12Z","month":"04","ddc":["530"],"arxiv":1,"citation":{"ieee":"T. Moser and R. Seiringer, “Energy contribution of a point-interacting impurity in a Fermi gas,” Annales Henri Poincare, vol. 20, no. 4. Springer, pp. 1325–1365, 2019.","chicago":"Moser, Thomas, and Robert Seiringer. “Energy Contribution of a Point-Interacting Impurity in a Fermi Gas.” Annales Henri Poincare. Springer, 2019. https://doi.org/10.1007/s00023-018-00757-0.","mla":"Moser, Thomas, and Robert Seiringer. “Energy Contribution of a Point-Interacting Impurity in a Fermi Gas.” Annales Henri Poincare, vol. 20, no. 4, Springer, 2019, pp. 1325–1365, doi:10.1007/s00023-018-00757-0.","short":"T. Moser, R. Seiringer, Annales Henri Poincare 20 (2019) 1325–1365.","ama":"Moser T, Seiringer R. Energy contribution of a point-interacting impurity in a Fermi gas. Annales Henri Poincare. 2019;20(4):1325–1365. doi:10.1007/s00023-018-00757-0","apa":"Moser, T., & Seiringer, R. (2019). Energy contribution of a point-interacting impurity in a Fermi gas. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-00757-0","ista":"Moser T, Seiringer R. 2019. Energy contribution of a point-interacting impurity in a Fermi gas. Annales Henri Poincare. 20(4), 1325–1365."},"article_type":"original","issue":"4","page":"1325–1365","_id":"5856","language":[{"iso":"eng"}],"external_id":{"arxiv":["1807.00739"],"isi":["000462444300008"]},"isi":1,"doi":"10.1007/s00023-018-00757-0","title":"Energy contribution of a point-interacting impurity in a Fermi gas","date_updated":"2023-09-07T12:37:42Z","day":"01","publication_identifier":{"issn":["14240637"]},"ec_funded":1,"year":"2019","related_material":{"record":[{"relation":"dissertation_contains","id":"52","status":"public"}]},"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","oa":1},{"scopus_import":"1","date_created":"2019-01-20T22:59:17Z","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 259","abstract":[{"text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is [Formula presented](n−1), and that this bound is best possible for infinitely many values of n.","lang":"eng"}],"date_published":"2019-04-30T00:00:00Z","status":"public","publication":"Discrete Applied Mathematics","publication_status":"published","publisher":"Elsevier","department":[{"_id":"UlWa"}],"project":[{"name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","call_identifier":"FWF"}],"quality_controlled":"1","volume":259,"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1708.08037","open_access":"1"}],"article_type":"original","arxiv":1,"citation":{"mla":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics, vol. 259, no. 4, Elsevier, 2019, pp. 266–231, doi:10.1016/j.dam.2018.12.025.","short":"R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231.","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” Discrete Applied Mathematics, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.","chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.dam.2018.12.025.","apa":"Fulek, R., & Pach, J. (2019). Thrackles: An improved upper bound. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2018.12.025","ista":"Fulek R, Pach J. 2019. Thrackles: An improved upper bound. Discrete Applied Mathematics. 259(4), 266–231.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. Discrete Applied Mathematics. 2019;259(4):266-231. doi:10.1016/j.dam.2018.12.025"},"month":"04","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"full_name":"Pach, János","first_name":"János","last_name":"Pach"}],"_id":"5857","language":[{"iso":"eng"}],"page":"266-231","issue":"4","publication_identifier":{"issn":["0166218X"]},"day":"30","date_updated":"2023-08-24T14:39:33Z","title":"Thrackles: An improved upper bound","doi":"10.1016/j.dam.2018.12.025","isi":1,"external_id":{"isi":["000466061100020"],"arxiv":["1708.08037"]},"article_processing_charge":"No","oa":1,"related_material":{"record":[{"id":"433","relation":"earlier_version","status":"public"}]},"year":"2019"}]