[{"external_id":{"arxiv":["2110.06399"]},"year":"2021","title":"Dynamic inference with neural interpreters","arxiv":1,"_id":"14180","date_published":"2021-10-12T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2110.06399"}],"volume":34,"language":[{"iso":"eng"}],"intvolume":"        34","type":"conference","date_created":"2023-08-22T14:04:55Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","author":[{"last_name":"Rahaman","first_name":"Nasim","full_name":"Rahaman, Nasim"},{"first_name":"Muhammad Waleed","full_name":"Gondal, Muhammad Waleed","last_name":"Gondal"},{"full_name":"Joshi, Shruti","first_name":"Shruti","last_name":"Joshi"},{"last_name":"Gehler","first_name":"Peter","full_name":"Gehler, Peter"},{"last_name":"Bengio","full_name":"Bengio, Yoshua","first_name":"Yoshua"},{"full_name":"Locatello, Francesco","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"}],"date_updated":"2024-10-14T12:27:25Z","citation":{"mla":"Rahaman, Nasim, et al. “Dynamic Inference with Neural Interpreters.” <i>Advances in Neural Information Processing Systems</i>, vol. 34, 2021, pp. 10985–98.","ama":"Rahaman N, Gondal MW, Joshi S, et al. Dynamic inference with neural interpreters. In: <i>Advances in Neural Information Processing Systems</i>. Vol 34. ; 2021:10985-10998.","apa":"Rahaman, N., Gondal, M. W., Joshi, S., Gehler, P., Bengio, Y., Locatello, F., &#38; Schölkopf, B. (2021). Dynamic inference with neural interpreters. In <i>Advances in Neural Information Processing Systems</i> (Vol. 34, pp. 10985–10998). Virtual.","short":"N. Rahaman, M.W. Gondal, S. Joshi, P. Gehler, Y. Bengio, F. Locatello, B. Schölkopf, in:, Advances in Neural Information Processing Systems, 2021, pp. 10985–10998.","chicago":"Rahaman, Nasim, Muhammad Waleed Gondal, Shruti Joshi, Peter Gehler, Yoshua Bengio, Francesco Locatello, and Bernhard Schölkopf. “Dynamic Inference with Neural Interpreters.” In <i>Advances in Neural Information Processing Systems</i>, 34:10985–98, 2021.","ieee":"N. Rahaman <i>et al.</i>, “Dynamic inference with neural interpreters,” in <i>Advances in Neural Information Processing Systems</i>, Virtual, 2021, vol. 34, pp. 10985–10998.","ista":"Rahaman N, Gondal MW, Joshi S, Gehler P, Bengio Y, Locatello F, Schölkopf B. 2021. Dynamic inference with neural interpreters. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 34, 10985–10998."},"quality_controlled":"1","publication":"Advances in Neural Information Processing Systems","publication_identifier":{"isbn":["9781713845393"]},"status":"public","oa":1,"day":"12","conference":{"end_date":"2021-12-10","start_date":"2021-12-07","location":"Virtual","name":"NeurIPS: Neural Information Processing Systems"},"department":[{"_id":"FrLo"}],"extern":"1","oa_version":"Preprint","publication_status":"published","page":"10985-10998","abstract":[{"text":"Modern neural network architectures can leverage large amounts of data to generalize well within the training distribution. However, they are less capable of systematic generalization to data drawn from unseen but related distributions, a feat that is hypothesized to require compositional reasoning and reuse of knowledge. In this work, we present Neural Interpreters, an architecture that factorizes inference in a self-attention network as a system of modules, which we call \\emph{functions}. Inputs to the model are routed through a sequence of functions in a way that is end-to-end learned. The proposed architecture can flexibly compose computation along width and depth, and lends itself well to capacity extension after training. To demonstrate the versatility of Neural Interpreters, we evaluate it in two distinct settings: image classification and visual abstract reasoning on Raven Progressive Matrices. In the former, we show that Neural Interpreters perform on par with the vision transformer using fewer parameters, while being transferrable to a new task in a sample efficient manner. In the latter, we find that Neural Interpreters are competitive with respect to the state-of-the-art in terms of systematic generalization. ","lang":"eng"}]},{"publication_status":"published","abstract":[{"lang":"eng","text":"Variational Inference makes a trade-off between the capacity of the variational family and the tractability of finding an approximate posterior distribution. Instead, Boosting Variational Inference allows practitioners to obtain increasingly good posterior approximations by spending more compute. The main obstacle to widespread adoption of Boosting Variational Inference is the amount of resources necessary to improve over a strong Variational Inference baseline. In our work, we trace this limitation back to the global curvature of the KL-divergence. We characterize how the global curvature impacts time and memory consumption, address the problem with the notion of local curvature, and provide a novel approximate backtracking algorithm for estimating local curvature. We give new theoretical convergence rates for our algorithms and provide experimental validation on synthetic and real-world datasets."}],"page":"2337-2343","oa_version":"Published Version","conference":{"location":"Montreal, Canada","name":"IJCAI: International Joint Conference on Artificial Intelligence","end_date":"2021-08-27","start_date":"2021-08-19"},"extern":"1","department":[{"_id":"FrLo"}],"day":"19","doi":"10.24963/ijcai.2021/322","status":"public","publication_identifier":{"eisbn":["9780999241196"]},"oa":1,"publication":"Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence","quality_controlled":"1","author":[{"last_name":"Dresdner","full_name":"Dresdner, Gideon","first_name":"Gideon"},{"first_name":"Saurav","full_name":"Shekhar, Saurav","last_name":"Shekhar"},{"first_name":"Fabian","full_name":"Pedregosa, Fabian","last_name":"Pedregosa"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","first_name":"Francesco","full_name":"Locatello, Francesco"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"}],"date_updated":"2023-09-11T11:14:30Z","citation":{"mla":"Dresdner, Gideon, et al. “Boosting Variational Inference with Locally Adaptive Step-Sizes.” <i>Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence</i>, International Joint Conferences on Artificial Intelligence, 2021, pp. 2337–43, doi:<a href=\"https://doi.org/10.24963/ijcai.2021/322\">10.24963/ijcai.2021/322</a>.","ama":"Dresdner G, Shekhar S, Pedregosa F, Locatello F, Rätsch G. Boosting variational inference with locally adaptive step-sizes. In: <i>Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence</i>. International Joint Conferences on Artificial Intelligence; 2021:2337-2343. doi:<a href=\"https://doi.org/10.24963/ijcai.2021/322\">10.24963/ijcai.2021/322</a>","short":"G. Dresdner, S. Shekhar, F. Pedregosa, F. Locatello, G. Rätsch, in:, Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2021, pp. 2337–2343.","apa":"Dresdner, G., Shekhar, S., Pedregosa, F., Locatello, F., &#38; Rätsch, G. (2021). Boosting variational inference with locally adaptive step-sizes. In <i>Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence</i> (pp. 2337–2343). Montreal, Canada: International Joint Conferences on Artificial Intelligence. <a href=\"https://doi.org/10.24963/ijcai.2021/322\">https://doi.org/10.24963/ijcai.2021/322</a>","chicago":"Dresdner, Gideon, Saurav Shekhar, Fabian Pedregosa, Francesco Locatello, and Gunnar Rätsch. “Boosting Variational Inference with Locally Adaptive Step-Sizes.” In <i>Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence</i>, 2337–43. International Joint Conferences on Artificial Intelligence, 2021. <a href=\"https://doi.org/10.24963/ijcai.2021/322\">https://doi.org/10.24963/ijcai.2021/322</a>.","ista":"Dresdner G, Shekhar S, Pedregosa F, Locatello F, Rätsch G. 2021. Boosting variational inference with locally adaptive step-sizes. Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence, 2337–2343.","ieee":"G. Dresdner, S. Shekhar, F. Pedregosa, F. Locatello, and G. Rätsch, “Boosting variational inference with locally adaptive step-sizes,” in <i>Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence</i>, Montreal, Canada, 2021, pp. 2337–2343."},"publisher":"International Joint Conferences on Artificial Intelligence","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","month":"05","type":"conference","date_created":"2023-08-22T14:05:14Z","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2105.09240"}],"_id":"14181","date_published":"2021-05-19T00:00:00Z","year":"2021","arxiv":1,"title":"Boosting variational inference with locally adaptive step-sizes","external_id":{"arxiv":["2105.09240"]}},{"oa_version":"Preprint","publication_status":"published","abstract":[{"lang":"eng","text":"When machine learning systems meet real world applications, accuracy is only\r\none of several requirements. In this paper, we assay a complementary\r\nperspective originating from the increasing availability of pre-trained and\r\nregularly improving state-of-the-art models. While new improved models develop\r\nat a fast pace, downstream tasks vary more slowly or stay constant. Assume that\r\nwe have a large unlabelled data set for which we want to maintain accurate\r\npredictions. Whenever a new and presumably better ML models becomes available,\r\nwe encounter two problems: (i) given a limited budget, which data points should\r\nbe re-evaluated using the new model?; and (ii) if the new predictions differ\r\nfrom the current ones, should we update? Problem (i) is about compute cost,\r\nwhich matters for very large data sets and models. Problem (ii) is about\r\nmaintaining consistency of the predictions, which can be highly relevant for\r\ndownstream applications; our demand is to avoid negative flips, i.e., changing\r\ncorrect to incorrect predictions. In this paper, we formalize the Prediction\r\nUpdate Problem and present an efficient probabilistic approach as answer to the\r\nabove questions. In extensive experiments on standard classification benchmark\r\ndata sets, we show that our method outperforms alternative strategies along key\r\nmetrics for backward-compatible prediction updates."}],"page":"116-128","day":"02","conference":{"start_date":"2021-12-07","end_date":"2021-12-10","name":"NeurIPS: Neural Information Processing Systems","location":"Virtual"},"extern":"1","department":[{"_id":"FrLo"}],"publication":"35th Conference on Neural Information Processing Systems","status":"public","publication_identifier":{"isbn":["9781713845393"]},"oa":1,"author":[{"first_name":"Frederik","full_name":"Träuble, Frederik","last_name":"Träuble"},{"last_name":"Kügelgen","full_name":"Kügelgen, Julius von","first_name":"Julius von"},{"last_name":"Kleindessner","full_name":"Kleindessner, Matthäus","first_name":"Matthäus"},{"last_name":"Locatello","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"first_name":"Peter","full_name":"Gehler, Peter","last_name":"Gehler"}],"date_updated":"2023-09-11T11:31:59Z","citation":{"mla":"Träuble, Frederik, et al. “Backward-Compatible Prediction Updates: A Probabilistic Approach.” <i>35th Conference on Neural Information Processing Systems</i>, vol. 34, 2021, pp. 116–28.","ama":"Träuble F, Kügelgen J von, Kleindessner M, Locatello F, Schölkopf B, Gehler P. Backward-compatible prediction updates: A probabilistic approach. In: <i>35th Conference on Neural Information Processing Systems</i>. Vol 34. ; 2021:116-128.","short":"F. Träuble, J. von Kügelgen, M. Kleindessner, F. Locatello, B. Schölkopf, P. Gehler, in:, 35th Conference on Neural Information Processing Systems, 2021, pp. 116–128.","apa":"Träuble, F., Kügelgen, J. von, Kleindessner, M., Locatello, F., Schölkopf, B., &#38; Gehler, P. (2021). Backward-compatible prediction updates: A probabilistic approach. In <i>35th Conference on Neural Information Processing Systems</i> (Vol. 34, pp. 116–128). Virtual.","ista":"Träuble F, Kügelgen J von, Kleindessner M, Locatello F, Schölkopf B, Gehler P. 2021. Backward-compatible prediction updates: A probabilistic approach. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 34, 116–128.","chicago":"Träuble, Frederik, Julius von Kügelgen, Matthäus Kleindessner, Francesco Locatello, Bernhard Schölkopf, and Peter Gehler. “Backward-Compatible Prediction Updates: A Probabilistic Approach.” In <i>35th Conference on Neural Information Processing Systems</i>, 34:116–28, 2021.","ieee":"F. Träuble, J. von Kügelgen, M. Kleindessner, F. Locatello, B. Schölkopf, and P. Gehler, “Backward-compatible prediction updates: A probabilistic approach,” in <i>35th Conference on Neural Information Processing Systems</i>, Virtual, 2021, vol. 34, pp. 116–128."},"quality_controlled":"1","type":"conference","date_created":"2023-08-22T14:05:41Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.01057"}],"volume":34,"language":[{"iso":"eng"}],"intvolume":"        34","_id":"14182","date_published":"2021-07-02T00:00:00Z","external_id":{"arxiv":["2107.01057"]},"year":"2021","arxiv":1,"title":"Backward-compatible prediction updates: A probabilistic approach"},{"year":"2021","applicant":["Google LLC"],"arxiv":1,"title":"Object-centric learning with slot attention","date_updated":"2025-01-31T11:35:46Z","author":[{"last_name":"Weissenborn","first_name":"Dirk","full_name":"Weissenborn, Dirk"},{"last_name":"Uszkoreit","full_name":"Uszkoreit, Jakob","first_name":"Jakob"},{"last_name":"Unterthiner","full_name":"Unterthiner, Thomas","first_name":"Thomas"},{"first_name":"Aravindh","full_name":"Mahendran, Aravindh","last_name":"Mahendran"},{"first_name":"Francesco","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683"},{"last_name":"Kipf","full_name":"Kipf, Thomas","first_name":"Thomas"},{"last_name":"Heigold","first_name":"Georg","full_name":"Heigold, Georg"},{"last_name":"Dosovitskiy","full_name":"Dosovitskiy, Alexey","first_name":"Alexey"}],"external_id":{"arxiv":["2006.15055"]},"citation":{"ieee":"D. Weissenborn <i>et al.</i>, “Object-centric learning with slot attention.” 2021.","ista":"Weissenborn D, Uszkoreit J, Unterthiner T, Mahendran A, Locatello F, Kipf T, Heigold G, Dosovitskiy A. 2021. Object-centric learning with slot attention.","chicago":"Weissenborn, Dirk, Jakob Uszkoreit, Thomas Unterthiner, Aravindh Mahendran, Francesco Locatello, Thomas Kipf, Georg Heigold, and Alexey Dosovitskiy. “Object-Centric Learning with Slot Attention,” 2021.","apa":"Weissenborn, D., Uszkoreit, J., Unterthiner, T., Mahendran, A., Locatello, F., Kipf, T., … Dosovitskiy, A. (2021). Object-centric learning with slot attention.","short":"D. Weissenborn, J. Uszkoreit, T. Unterthiner, A. Mahendran, F. Locatello, T. Kipf, G. Heigold, A. Dosovitskiy, (2021).","ama":"Weissenborn D, Uszkoreit J, Unterthiner T, et al. Object-centric learning with slot attention. 2021.","mla":"Weissenborn, Dirk, et al. <i>Object-Centric Learning with Slot Attention</i>. 2021."},"status":"public","application_number":"16 / 927,018 ","oa":1,"ipc":"G06N 3/063 ; G06N 3/08 ; G06F 17/16","_id":"14185","date_published":"2021-12-09T00:00:00Z","extern":"1","department":[{"_id":"FrLo"}],"main_file_link":[{"url":"https://patents.google.com/patent/US20210383199A1/en","open_access":"1"}],"day":"09","OA_place":"repository","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","publication_date":"2021-12-09","abstract":[{"lang":"eng","text":"A method involves receiving a perceptual representation including a plurality of feature vectors, and initializing a plurality of slot vectors represented by a neural network memory unit. Each respective slot vector is configured to represent a corresponding entity in the perceptual representation. The method also involves determining an attention matrix based on a product of the plurality of feature vectors transformed by a key function and the plurality of slot vectors transformed by a query function. Each respective value of a plurality of values along each respective dimension of the attention matrix is normalized with respect to the plurality of values. The method additionally involves determining an update matrix based on the plurality of feature vectors transformed by a value function and the attention matrix, and updating the plurality of slot vectors based on the update matrix by way of the neural network memory unit."}],"ipn":"US20210383199A1","month":"12","type":"patent","application_date":"2020-07-13","oa_version":"Published Version","date_created":"2023-08-22T14:07:06Z"},{"publication_status":"submitted","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","month":"11","abstract":[{"text":"The world is structured in countless ways. It may be prudent to enforce corresponding structural properties to a learning algorithm's solution, such as incorporating prior beliefs, natural constraints, or causal structures. Doing so may translate to faster, more accurate, and more flexible models, which may directly relate to real-world impact. In this dissertation, we consider two different research areas that concern structuring a learning algorithm's solution: when the structure is known and when it has to be discovered.","lang":"eng"}],"type":"preprint","date_created":"2023-08-22T14:23:35Z","oa_version":"Preprint","department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"extern":"1","day":"26","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2111.13693","open_access":"1"}],"doi":"10.48550/arXiv.2111.13693","article_number":"2111.13693","status":"public","oa":1,"_id":"14221","publication":"arXiv","date_published":"2021-11-26T00:00:00Z","year":"2021","title":"Enforcing and discovering structure in machine learning","arxiv":1,"author":[{"full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683"}],"date_updated":"2024-10-14T12:27:49Z","citation":{"mla":"Locatello, Francesco. “Enforcing and Discovering Structure in Machine Learning.” <i>ArXiv</i>, 2111.13693, doi:<a href=\"https://doi.org/10.48550/arXiv.2111.13693\">10.48550/arXiv.2111.13693</a>.","ama":"Locatello F. Enforcing and discovering structure in machine learning. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2111.13693\">10.48550/arXiv.2111.13693</a>","apa":"Locatello, F. (n.d.). Enforcing and discovering structure in machine learning. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2111.13693\">https://doi.org/10.48550/arXiv.2111.13693</a>","short":"F. Locatello, ArXiv (n.d.).","ista":"Locatello F. Enforcing and discovering structure in machine learning. arXiv, 2111.13693.","chicago":"Locatello, Francesco. “Enforcing and Discovering Structure in Machine Learning.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2111.13693\">https://doi.org/10.48550/arXiv.2111.13693</a>.","ieee":"F. Locatello, “Enforcing and discovering structure in machine learning,” <i>arXiv</i>. ."},"external_id":{"arxiv":["2111.13693"]}},{"title":"Representation learning for out-of-distribution generalization in reinforcement learning","quality_controlled":"1","year":"2021","citation":{"short":"F. Träuble, A. Dittadi, M. Wuthrich, F. Widmaier, P.V. Gehler, O. Winther, F. Locatello, O. Bachem, B. Schölkopf, S. Bauer, in:, ICML 2021 Workshop on Unsupervised Reinforcement Learning, 2021.","apa":"Träuble, F., Dittadi, A., Wuthrich, M., Widmaier, F., Gehler, P. V., Winther, O., … Bauer, S. (2021). Representation learning for out-of-distribution generalization in reinforcement learning. In <i>ICML 2021 Workshop on Unsupervised Reinforcement Learning</i>. Virtual.","ista":"Träuble F, Dittadi A, Wuthrich M, Widmaier F, Gehler PV, Winther O, Locatello F, Bachem O, Schölkopf B, Bauer S. 2021. Representation learning for out-of-distribution generalization in reinforcement learning. ICML 2021 Workshop on Unsupervised Reinforcement Learning. ICML: International Conference on Machine Learning.","chicago":"Träuble, Frederik, Andrea Dittadi, Manuel Wuthrich, Felix Widmaier, Peter Vincent Gehler, Ole Winther, Francesco Locatello, Olivier Bachem, Bernhard Schölkopf, and Stefan Bauer. “Representation Learning for Out-of-Distribution Generalization in Reinforcement Learning.” In <i>ICML 2021 Workshop on Unsupervised Reinforcement Learning</i>, 2021.","ieee":"F. Träuble <i>et al.</i>, “Representation learning for out-of-distribution generalization in reinforcement learning,” in <i>ICML 2021 Workshop on Unsupervised Reinforcement Learning</i>, Virtual, 2021.","mla":"Träuble, Frederik, et al. “Representation Learning for Out-of-Distribution Generalization in Reinforcement Learning.” <i>ICML 2021 Workshop on Unsupervised Reinforcement Learning</i>, 2021.","ama":"Träuble F, Dittadi A, Wuthrich M, et al. Representation learning for out-of-distribution generalization in reinforcement learning. In: <i>ICML 2021 Workshop on Unsupervised Reinforcement Learning</i>. ; 2021."},"date_updated":"2023-09-13T12:44:00Z","author":[{"full_name":"Träuble, Frederik","first_name":"Frederik","last_name":"Träuble"},{"full_name":"Dittadi, Andrea","first_name":"Andrea","last_name":"Dittadi"},{"full_name":"Wuthrich, Manuel","first_name":"Manuel","last_name":"Wuthrich"},{"first_name":"Felix","full_name":"Widmaier, Felix","last_name":"Widmaier"},{"last_name":"Gehler","first_name":"Peter Vincent","full_name":"Gehler, Peter Vincent"},{"last_name":"Winther","full_name":"Winther, Ole","first_name":"Ole"},{"first_name":"Francesco","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"full_name":"Bachem, Olivier","first_name":"Olivier","last_name":"Bachem"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"},{"last_name":"Bauer","first_name":"Stefan","full_name":"Bauer, Stefan"}],"status":"public","publication":"ICML 2021 Workshop on Unsupervised Reinforcement Learning","date_published":"2021-07-23T00:00:00Z","_id":"14332","language":[{"iso":"eng"}],"extern":"1","department":[{"_id":"FrLo"}],"conference":{"start_date":"2021-07-23","end_date":"2021-07-23","name":"ICML: International Conference on Machine Learning","location":"Virtual"},"day":"23","abstract":[{"text":"Learning data representations that are useful for various downstream tasks is a cornerstone of artificial intelligence. While existing methods are typically evaluated on downstream tasks such as classification or generative image quality, we propose to assess representations through their usefulness in downstream control tasks, such as reaching or pushing objects. By training over 10,000 reinforcement learning policies, we extensively evaluate to what extent different representation properties affect out-of-distribution (OOD) generalization. Finally, we demonstrate zero-shot transfer of these policies from simulation to the real world, without any domain randomization or fine-tuning. This paper aims to establish the first systematic characterization of the usefulness of learned representations for real-world OOD downstream tasks.","lang":"eng"}],"month":"07","publication_status":"published","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_created":"2023-09-13T12:43:14Z","type":"conference"},{"type":"journal_article","date_created":"2024-01-14T23:00:58Z","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"10","article_type":"review","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3866/PKU.WHXB202108017"}],"issue":"12","volume":37,"intvolume":"        37","language":[{"iso":"eng"}],"_id":"14800","date_published":"2021-10-13T00:00:00Z","external_id":{"isi":["000731879300002"]},"year":"2021","title":"Recent progress on two-dimensional materials","oa_version":"Submitted Version","publication_status":"published","abstract":[{"lang":"eng","text":"Research on two-dimensional (2D) materials has been explosively increasing in last seventeen years in varying subjects including condensed matter physics, electronic engineering, materials science, and chemistry since the mechanical exfoliation of graphene in 2004. Starting from graphene, 2D materials now have become a big family with numerous members and diverse categories. The unique structural features and physicochemical properties of 2D materials make them one class of the most appealing candidates for a wide range of potential applications. In particular, we have seen some major breakthroughs made in the field of 2D materials in last five years not only in developing novel synthetic methods and exploring new structures/properties but also in identifying innovative applications and pushing forward commercialisation. In this review, we provide a critical summary on the recent progress made in the field of 2D materials with a particular focus on last five years. After a brief background introduction, we first discuss the major synthetic methods for 2D materials, including the mechanical exfoliation, liquid exfoliation, vapor phase deposition, and wet-chemical synthesis as well as phase engineering of 2D materials belonging to the field of phase engineering of nanomaterials (PEN). We then introduce the superconducting/optical/magnetic properties and chirality of 2D materials along with newly emerging magic angle 2D superlattices. Following that, the promising applications of 2D materials in electronics, optoelectronics, catalysis, energy storage, solar cells, biomedicine, sensors, environments, etc. are described sequentially. Thereafter, we present the theoretic calculations and simulations of 2D materials. Finally, after concluding the current progress, we provide some personal discussions on the existing challenges and future outlooks in this rapidly developing field. "}],"day":"13","doi":"10.3866/PKU.WHXB202108017","article_number":"2108017","department":[{"_id":"MaIb"}],"isi":1,"publication":"Acta Physico-Chimica Sinica","scopus_import":"1","publication_identifier":{"issn":["1001-4861"]},"status":"public","oa":1,"date_updated":"2025-09-10T10:12:25Z","author":[{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","first_name":"Cheng"},{"full_name":"Chen, Wei","first_name":"Wei","last_name":"Chen"},{"last_name":"Chen","first_name":"Ye","full_name":"Chen, Ye"},{"last_name":"Chen","full_name":"Chen, Yonghua","first_name":"Yonghua"},{"full_name":"Chen, Yu","first_name":"Yu","last_name":"Chen"},{"last_name":"Ding","full_name":"Ding, Feng","first_name":"Feng"},{"last_name":"Fan","full_name":"Fan, Chunhai","first_name":"Chunhai"},{"last_name":"Fan","first_name":"Hong Jin","full_name":"Fan, Hong Jin"},{"full_name":"Fan, Zhanxi","first_name":"Zhanxi","last_name":"Fan"},{"full_name":"Gong, 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Minghua"},{"last_name":"Liu","first_name":"Nan","full_name":"Liu, Nan"},{"last_name":"Liu","full_name":"Liu, Zhuang","first_name":"Zhuang"},{"last_name":"Loh","first_name":"Kian Ping","full_name":"Loh, Kian Ping"},{"first_name":"Jianmin","full_name":"Ma, Jianmin","last_name":"Ma"},{"first_name":"Feng","full_name":"Miao, Feng","last_name":"Miao"},{"first_name":"Hailin","full_name":"Peng, Hailin","last_name":"Peng"},{"last_name":"Shao","full_name":"Shao, Mingfei","first_name":"Mingfei"},{"last_name":"Song","full_name":"Song, Li","first_name":"Li"},{"last_name":"Su","first_name":"Shao","full_name":"Su, Shao"},{"last_name":"Sun","full_name":"Sun, Shuo","first_name":"Shuo"},{"full_name":"Tan, Chaoliang","first_name":"Chaoliang","last_name":"Tan"},{"last_name":"Tang","full_name":"Tang, Zhiyong","first_name":"Zhiyong"},{"last_name":"Wang","first_name":"Dingsheng","full_name":"Wang, Dingsheng"},{"last_name":"Wang","full_name":"Wang, Huan","first_name":"Huan"},{"last_name":"Wang","full_name":"Wang, Jinlan","first_name":"Jinlan"},{"full_name":"Wang, Xin","first_name":"Xin","last_name":"Wang"},{"first_name":"Xinran","full_name":"Wang, Xinran","last_name":"Wang"},{"full_name":"Wee, Andrew T.S.","first_name":"Andrew T.S.","last_name":"Wee"},{"first_name":"Zhongming","full_name":"Wei, Zhongming","last_name":"Wei"},{"last_name":"Wu","first_name":"Yuen","full_name":"Wu, Yuen"},{"full_name":"Wu, Zhong Shuai","first_name":"Zhong Shuai","last_name":"Wu"},{"first_name":"Jie","full_name":"Xiong, Jie","last_name":"Xiong"},{"first_name":"Qihua","full_name":"Xiong, Qihua","last_name":"Xiong"},{"first_name":"Weigao","full_name":"Xu, Weigao","last_name":"Xu"},{"full_name":"Yin, Peng","first_name":"Peng","last_name":"Yin"},{"last_name":"Zeng","full_name":"Zeng, Haibo","first_name":"Haibo"},{"full_name":"Zeng, Zhiyuan","first_name":"Zhiyuan","last_name":"Zeng"},{"last_name":"Zhai","full_name":"Zhai, Tianyou","first_name":"Tianyou"},{"last_name":"Zhang","full_name":"Zhang, Han","first_name":"Han"},{"last_name":"Zhang","full_name":"Zhang, Hui","first_name":"Hui"},{"full_name":"Zhang, Qichun","first_name":"Qichun","last_name":"Zhang"},{"full_name":"Zhang, Tierui","first_name":"Tierui","last_name":"Zhang"},{"first_name":"Xiang","full_name":"Zhang, Xiang","last_name":"Zhang"},{"last_name":"Zhao","first_name":"Li Dong","full_name":"Zhao, Li Dong"},{"first_name":"Meiting","full_name":"Zhao, Meiting","last_name":"Zhao"},{"last_name":"Zhao","full_name":"Zhao, Weijie","first_name":"Weijie"},{"full_name":"Zhao, Yunxuan","first_name":"Yunxuan","last_name":"Zhao"},{"last_name":"Zhou","first_name":"Kai Ge","full_name":"Zhou, Kai Ge"},{"first_name":"Xing","full_name":"Zhou, Xing","last_name":"Zhou"},{"first_name":"Yu","full_name":"Zhou, Yu","last_name":"Zhou"},{"full_name":"Zhu, Hongwei","first_name":"Hongwei","last_name":"Zhu"},{"last_name":"Zhang","first_name":"Hua","full_name":"Zhang, Hua"},{"full_name":"Liu, Zhongfan","first_name":"Zhongfan","last_name":"Liu"}],"publisher":"Peking University","citation":{"mla":"Chang, Cheng, et al. “Recent Progress on Two-Dimensional Materials.” <i>Acta Physico-Chimica Sinica</i>, vol. 37, no. 12, 2108017, Peking University, 2021, doi:<a href=\"https://doi.org/10.3866/PKU.WHXB202108017\">10.3866/PKU.WHXB202108017</a>.","ama":"Chang C, Chen W, Chen Y, et al. Recent progress on two-dimensional materials. <i>Acta Physico-Chimica Sinica</i>. 2021;37(12). doi:<a href=\"https://doi.org/10.3866/PKU.WHXB202108017\">10.3866/PKU.WHXB202108017</a>","short":"C. Chang, W. Chen, Y. Chen, Y. Chen, Y. Chen, F. Ding, C. Fan, H.J. Fan, Z. Fan, C. Gong, Y. Gong, Q. He, X. Hong, S. Hu, W. Hu, W. Huang, Y. Huang, W. Ji, D. Li, L.J. Li, Q. Li, L. Lin, C. Ling, M. Liu, N. Liu, Z. Liu, K.P. Loh, J. Ma, F. Miao, H. Peng, M. Shao, L. Song, S. Su, S. Sun, C. Tan, Z. Tang, D. Wang, H. Wang, J. Wang, X. Wang, X. Wang, A.T.S. Wee, Z. Wei, Y. Wu, Z.S. Wu, J. Xiong, Q. Xiong, W. Xu, P. Yin, H. Zeng, Z. Zeng, T. Zhai, H. Zhang, H. Zhang, Q. Zhang, T. Zhang, X. Zhang, L.D. Zhao, M. Zhao, W. Zhao, Y. Zhao, K.G. Zhou, X. Zhou, Y. Zhou, H. Zhu, H. Zhang, Z. Liu, Acta Physico-Chimica Sinica 37 (2021).","apa":"Chang, C., Chen, W., Chen, Y., Chen, Y., Chen, Y., Ding, F., … Liu, Z. (2021). Recent progress on two-dimensional materials. <i>Acta Physico-Chimica Sinica</i>. Peking University. <a href=\"https://doi.org/10.3866/PKU.WHXB202108017\">https://doi.org/10.3866/PKU.WHXB202108017</a>","ieee":"C. Chang <i>et al.</i>, “Recent progress on two-dimensional materials,” <i>Acta Physico-Chimica Sinica</i>, vol. 37, no. 12. Peking University, 2021.","ista":"Chang C, Chen W, Chen Y, Chen Y, Chen Y, Ding F, Fan C, Fan HJ, Fan Z, Gong C, Gong Y, He Q, Hong X, Hu S, Hu W, Huang W, Huang Y, Ji W, Li D, Li LJ, Li Q, Lin L, Ling C, Liu M, Liu N, Liu Z, Loh KP, Ma J, Miao F, Peng H, Shao M, Song L, Su S, Sun S, Tan C, Tang Z, Wang D, Wang H, Wang J, Wang X, Wang X, Wee ATS, Wei Z, Wu Y, Wu ZS, Xiong J, Xiong Q, Xu W, Yin P, Zeng H, Zeng Z, Zhai T, Zhang H, Zhang H, Zhang Q, Zhang T, Zhang X, Zhao LD, Zhao M, Zhao W, Zhao Y, Zhou KG, Zhou X, Zhou Y, Zhu H, Zhang H, Liu Z. 2021. Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica. 37(12), 2108017.","chicago":"Chang, Cheng, Wei Chen, Ye Chen, Yonghua Chen, Yu Chen, Feng Ding, Chunhai Fan, et al. “Recent Progress on Two-Dimensional Materials.” <i>Acta Physico-Chimica Sinica</i>. Peking University, 2021. <a href=\"https://doi.org/10.3866/PKU.WHXB202108017\">https://doi.org/10.3866/PKU.WHXB202108017</a>."},"quality_controlled":"1"},{"publication_identifier":{"eissn":["2578-5885"],"issn":["2578-5893"]},"status":"public","oa":1,"acknowledgement":"Financial support by the European Union’s Horizon 2020 research and innovation programme\r\nunder the Marie Skłodowska-Curie grant agreement No. 754411 (S.R.) and the European\r\nResearch Council under grant agreement No. 694227 (N.L. and R.S.), as well as by the SNSF\r\nEccellenza project PCEFP2 181153 (N.L.), the NCCR SwissMAP (N.L. and B.S.) and by the\r\nDeutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral\r\nTheory and Dynamics of Quantum Systems (D.M.) is gratefully acknowledged. B.S. gratefully\r\nacknowledges financial support from the Swiss National Science Foundation through the Grant\r\n“Dynamical and energetic properties of Bose-Einstein condensates” and from the European\r\nResearch Council through the ERC-AdG CLaQS (grant agreement No 834782). D.M. thanks\r\nMarcel Griesemer for helpful discussions.","publication":"Pure and Applied Analysis","scopus_import":"1","quality_controlled":"1","ec_funded":1,"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"date_updated":"2025-04-14T07:27:00Z","author":[{"id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","last_name":"Leopold","orcid":"0000-0002-0495-6822","first_name":"Nikolai K","full_name":"Leopold, Nikolai K"},{"id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","first_name":"David Johannes"},{"first_name":"Simone Anna Elvira","full_name":"Rademacher, Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425","last_name":"Rademacher","orcid":"0000-0001-5059-4466"},{"last_name":"Schlein","first_name":"Benjamin","full_name":"Schlein, Benjamin"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"publisher":"Mathematical Sciences Publishers","citation":{"ama":"Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. <i>Pure and Applied Analysis</i>. 2021;3(4):653-676. doi:<a href=\"https://doi.org/10.2140/paa.2021.3.653\">10.2140/paa.2021.3.653</a>","mla":"Leopold, Nikolai K., et al. “Landau–Pekar Equations and Quantum Fluctuations for the Dynamics of a Strongly Coupled Polaron.” <i>Pure and Applied Analysis</i>, vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 653–76, doi:<a href=\"https://doi.org/10.2140/paa.2021.3.653\">10.2140/paa.2021.3.653</a>.","ieee":"N. K. Leopold, D. J. Mitrouskas, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron,” <i>Pure and Applied Analysis</i>, vol. 3, no. 4. Mathematical Sciences Publishers, pp. 653–676, 2021.","chicago":"Leopold, Nikolai K, David Johannes Mitrouskas, Simone Anna Elvira Rademacher, Benjamin Schlein, and Robert Seiringer. “Landau–Pekar Equations and Quantum Fluctuations for the Dynamics of a Strongly Coupled Polaron.” <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers, 2021. <a href=\"https://doi.org/10.2140/paa.2021.3.653\">https://doi.org/10.2140/paa.2021.3.653</a>.","ista":"Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. 2021. Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. Pure and Applied Analysis. 3(4), 653–676.","short":"N.K. Leopold, D.J. Mitrouskas, S.A.E. Rademacher, B. Schlein, R. Seiringer, Pure and Applied Analysis 3 (2021) 653–676.","apa":"Leopold, N. K., Mitrouskas, D. J., Rademacher, S. A. E., Schlein, B., &#38; Seiringer, R. (2021). Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron. <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/paa.2021.3.653\">https://doi.org/10.2140/paa.2021.3.653</a>"},"publication_status":"published","page":"653-676","corr_author":"1","abstract":[{"text":"We consider the Fröhlich Hamiltonian with large coupling constant α. For initial data of Pekar product form with coherent phonon field and with the electron minimizing the corresponding energy, we provide a norm approximation of the evolution, valid up to times of order α2. The approximation is given in terms of a Pekar product state, evolved through the Landau-Pekar equations, corrected by a Bogoliubov dynamics taking quantum fluctuations into account. This allows us to show that the Landau-Pekar equations approximately describe the evolution of the electron- and one-phonon reduced density matrices under the Fröhlich dynamics up to times of order α2.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"RoSe"}],"day":"01","doi":"10.2140/paa.2021.3.653","_id":"14889","date_published":"2021-10-01T00:00:00Z","year":"2021","title":"Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron","arxiv":1,"external_id":{"arxiv":["2005.02098"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","month":"10","article_type":"original","type":"journal_article","date_created":"2024-01-28T23:01:43Z","volume":3,"intvolume":"         3","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2005.02098","open_access":"1"}],"issue":"4"},{"day":"01","doi":"10.2140/paa.2021.3.677","department":[{"_id":"RoSe"}],"oa_version":"Preprint","publication_status":"published","corr_author":"1","abstract":[{"text":"We consider a system of N interacting bosons in the mean-field scaling regime and construct corrections to the Bogoliubov dynamics that approximate the true N-body dynamics in norm to arbitrary precision. The N-independent corrections are given in terms of the solutions of the Bogoliubov and Hartree equations and satisfy a generalized form of Wick's theorem. We determine the n-point correlation functions of the excitations around the condensate, as well as the reduced densities of the N-body system, to arbitrary accuracy, given only the knowledge of the two-point functions of a quasi-free state and the solution of the Hartree equation. In this way, the complex problem of computing all n-point correlation functions for an interacting N-body system is essentially reduced to the problem of solving the Hartree equation and the PDEs for the Bogoliubov two-point functions.","lang":"eng"}],"page":"677-726","author":[{"orcid":"0000-0002-6854-1343","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","last_name":"Bossmann","full_name":"Bossmann, Lea","first_name":"Lea"},{"last_name":"Petrat","orcid":"0000-0002-9166-5889","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","first_name":"Sören P","full_name":"Petrat, Sören P"},{"last_name":"Pickl","full_name":"Pickl, Peter","first_name":"Peter"},{"last_name":"Soffer","full_name":"Soffer, Avy","first_name":"Avy"}],"project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"date_updated":"2025-04-14T07:44:02Z","citation":{"ieee":"L. Bossmann, S. P. Petrat, P. Pickl, and A. Soffer, “Beyond Bogoliubov dynamics,” <i>Pure and Applied Analysis</i>, vol. 3, no. 4. Mathematical Sciences Publishers, pp. 677–726, 2021.","ista":"Bossmann L, Petrat SP, Pickl P, Soffer A. 2021. Beyond Bogoliubov dynamics. Pure and Applied Analysis. 3(4), 677–726.","chicago":"Bossmann, Lea, Sören P Petrat, Peter Pickl, and Avy Soffer. “Beyond Bogoliubov Dynamics.” <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers, 2021. <a href=\"https://doi.org/10.2140/paa.2021.3.677\">https://doi.org/10.2140/paa.2021.3.677</a>.","short":"L. Bossmann, S.P. Petrat, P. Pickl, A. Soffer, Pure and Applied Analysis 3 (2021) 677–726.","apa":"Bossmann, L., Petrat, S. P., Pickl, P., &#38; Soffer, A. (2021). Beyond Bogoliubov dynamics. <i>Pure and Applied Analysis</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/paa.2021.3.677\">https://doi.org/10.2140/paa.2021.3.677</a>","ama":"Bossmann L, Petrat SP, Pickl P, Soffer A. Beyond Bogoliubov dynamics. <i>Pure and Applied Analysis</i>. 2021;3(4):677-726. doi:<a href=\"https://doi.org/10.2140/paa.2021.3.677\">10.2140/paa.2021.3.677</a>","mla":"Bossmann, Lea, et al. “Beyond Bogoliubov Dynamics.” <i>Pure and Applied Analysis</i>, vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 677–726, doi:<a href=\"https://doi.org/10.2140/paa.2021.3.677\">10.2140/paa.2021.3.677</a>."},"publisher":"Mathematical Sciences Publishers","ec_funded":1,"quality_controlled":"1","publication":"Pure and Applied Analysis","scopus_import":"1","status":"public","publication_identifier":{"issn":["2578-5893"],"eissn":["2578-5885"]},"oa":1,"acknowledgement":"We are grateful for the hospitality of Central China Normal University (CCNU),\r\nwhere parts of this work were done, and thank Phan Th`anh Nam, Simone\r\nRademacher, Robert Seiringer and Stefan Teufel for helpful discussions. L.B. gratefully acknowledges the support by the German Research Foundation (DFG) within the Research\r\nTraining Group 1838 “Spectral Theory and Dynamics of Quantum Systems”, and the funding\r\nfrom the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSk lodowska-Curie Grant Agreement No. 754411.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1912.11004"}],"issue":"4","volume":3,"language":[{"iso":"eng"}],"intvolume":"         3","type":"journal_article","date_created":"2024-01-28T23:01:43Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","article_type":"original","external_id":{"arxiv":["1912.11004"]},"year":"2021","arxiv":1,"title":"Beyond Bogoliubov dynamics","_id":"14890","date_published":"2021-10-01T00:00:00Z"},{"publication":"Encyclopedia of Life Sciences","date_published":"2021-05-28T00:00:00Z","_id":"14984","series_title":"eLS","publication_identifier":{"eisbn":["9780470015902"],"isbn":["9780470016176"]},"status":"public","citation":{"chicago":"Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.” In <i>Encyclopedia of Life Sciences</i>, Vol. 2. ELS. Wiley, 2021. <a href=\"https://doi.org/10.1002/9780470015902.a0029355\">https://doi.org/10.1002/9780470015902.a0029355</a>.","ista":"Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2.","ieee":"S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in <i>Encyclopedia of Life Sciences</i>, vol. 2, Wiley, 2021.","apa":"Stankowski, S., Shipilina, D., &#38; Westram, A. M. (2021). Hybrid Zones. In <i>Encyclopedia of Life Sciences</i> (Vol. 2). Wiley. <a href=\"https://doi.org/10.1002/9780470015902.a0029355\">https://doi.org/10.1002/9780470015902.a0029355</a>","short":"S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021.","ama":"Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: <i>Encyclopedia of Life Sciences</i>. Vol 2. eLS. Wiley; 2021. doi:<a href=\"https://doi.org/10.1002/9780470015902.a0029355\">10.1002/9780470015902.a0029355</a>","mla":"Stankowski, Sean, et al. “Hybrid Zones.” <i>Encyclopedia of Life Sciences</i>, vol. 2, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/9780470015902.a0029355\">10.1002/9780470015902.a0029355</a>."},"publisher":"Wiley","author":[{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean"},{"first_name":"Daria","full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","last_name":"Shipilina"},{"first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"}],"date_updated":"2024-10-09T21:08:11Z","title":"Hybrid Zones","year":"2021","quality_controlled":"1","date_created":"2024-02-14T12:05:50Z","oa_version":"None","type":"book_chapter","month":"05","corr_author":"1","abstract":[{"text":"Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species, with hybrid zones having been described as ‘natural laboratories’. This is because they allow us to study,in situ, the conditions and evolutionary forces that enable divergent taxa to remain distinct despite some ongoing gene exchange between them.","lang":"eng"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","doi":"10.1002/9780470015902.a0029355","day":"28","department":[{"_id":"NiBa"}],"intvolume":"         2","language":[{"iso":"eng"}],"volume":2},{"department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"edition":"2","doi":"10.1007/978-3-030-63416-2_874","day":"13","page":"1395-1397","month":"10","abstract":[{"text":"The goal of zero-shot learning is to construct a classifier that can identify object classes for which no training examples are available. When training data for some of the object classes is available but not for others, the name generalized zero-shot learning is commonly used.\r\nIn a wider sense, the phrase zero-shot is also used to describe other machine learning-based approaches that require no training data from the problem of interest, such as zero-shot action recognition or zero-shot machine translation.","lang":"eng"}],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_status":"published","date_created":"2024-02-14T14:05:32Z","oa_version":"None","type":"book_chapter","title":"Zero-Shot Learning","year":"2021","quality_controlled":"1","editor":[{"last_name":"Ikeuchi","first_name":"Katsushi","full_name":"Ikeuchi, Katsushi"}],"publisher":"Springer","citation":{"mla":"Lampert, Christoph. “Zero-Shot Learning.” <i>Computer Vision</i>, edited by Katsushi Ikeuchi, 2nd ed., Springer, 2021, pp. 1395–97, doi:<a href=\"https://doi.org/10.1007/978-3-030-63416-2_874\">10.1007/978-3-030-63416-2_874</a>.","ama":"Lampert C. Zero-Shot Learning. In: Ikeuchi K, ed. <i>Computer Vision</i>. 2nd ed. Cham: Springer; 2021:1395-1397. doi:<a href=\"https://doi.org/10.1007/978-3-030-63416-2_874\">10.1007/978-3-030-63416-2_874</a>","short":"C. Lampert, in:, K. Ikeuchi (Ed.), Computer Vision, 2nd ed., Springer, Cham, 2021, pp. 1395–1397.","apa":"Lampert, C. (2021). Zero-Shot Learning. In K. Ikeuchi (Ed.), <i>Computer Vision</i> (2nd ed., pp. 1395–1397). Cham: Springer. <a href=\"https://doi.org/10.1007/978-3-030-63416-2_874\">https://doi.org/10.1007/978-3-030-63416-2_874</a>","ieee":"C. Lampert, “Zero-Shot Learning,” in <i>Computer Vision</i>, 2nd ed., K. Ikeuchi, Ed. Cham: Springer, 2021, pp. 1395–1397.","chicago":"Lampert, Christoph. “Zero-Shot Learning.” In <i>Computer Vision</i>, edited by Katsushi Ikeuchi, 2nd ed., 1395–97. Cham: Springer, 2021. <a href=\"https://doi.org/10.1007/978-3-030-63416-2_874\">https://doi.org/10.1007/978-3-030-63416-2_874</a>.","ista":"Lampert C. 2021.Zero-Shot Learning. In: Computer Vision. , 1395–1397."},"date_updated":"2024-10-09T21:08:12Z","author":[{"last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","full_name":"Lampert, Christoph"}],"publication_identifier":{"eisbn":["9783030634162"],"isbn":["9783030634155"]},"status":"public","publication":"Computer Vision","date_published":"2021-10-13T00:00:00Z","_id":"14987","place":"Cham"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Raw data from Johnson et al, PNAS, 2021","year":"2021","citation":{"mla":"Johnson, Alexander J. <i>Raw Data from Johnson et Al, PNAS, 2021</i>. Zenodo, 2021, doi:<a href=\"https://doi.org/10.5281/ZENODO.5747100\">10.5281/ZENODO.5747100</a>.","ama":"Johnson AJ. Raw data from Johnson et al, PNAS, 2021. 2021. doi:<a href=\"https://doi.org/10.5281/ZENODO.5747100\">10.5281/ZENODO.5747100</a>","short":"A.J. Johnson, (2021).","apa":"Johnson, A. J. (2021). Raw data from Johnson et al, PNAS, 2021. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5747100\">https://doi.org/10.5281/ZENODO.5747100</a>","chicago":"Johnson, Alexander J. “Raw Data from Johnson et Al, PNAS, 2021.” Zenodo, 2021. <a href=\"https://doi.org/10.5281/ZENODO.5747100\">https://doi.org/10.5281/ZENODO.5747100</a>.","ieee":"A. J. Johnson, “Raw data from Johnson et al, PNAS, 2021.” Zenodo, 2021.","ista":"Johnson AJ. 2021. Raw data from Johnson et al, PNAS, 2021, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5747100\">10.5281/ZENODO.5747100</a>."},"publisher":"Zenodo","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9887"}]},"date_updated":"2025-05-14T09:25:33Z","author":[{"full_name":"Johnson, Alexander J","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843"}],"oa":1,"status":"public","date_published":"2021-12-01T00:00:00Z","_id":"14988","department":[{"_id":"JiFr"}],"doi":"10.5281/ZENODO.5747100","day":"01","has_accepted_license":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5747100"}],"month":"12","corr_author":"1","abstract":[{"text":"Raw data generated from the publication - The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In PNAS","lang":"eng"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["580"],"date_created":"2024-02-14T14:13:48Z","oa_version":"Published Version","type":"research_data_reference"},{"quality_controlled":"1","ec_funded":1,"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"author":[{"full_name":"Alt, Johannes","first_name":"Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"László","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","first_name":"Torben H","full_name":"Krüger, Torben H"}],"date_updated":"2025-04-15T08:05:02Z","publisher":"Mathematical Sciences Publishers","citation":{"ista":"Alt J, Erdös L, Krüger TH. 2021. Spectral radius of random matrices with independent entries. Probability and Mathematical Physics. 2(2), 221–280.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Spectral radius of random matrices with independent entries,” <i>Probability and Mathematical Physics</i>, vol. 2, no. 2. Mathematical Sciences Publishers, pp. 221–280, 2021.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Spectral Radius of Random Matrices with Independent Entries.” <i>Probability and Mathematical Physics</i>. Mathematical Sciences Publishers, 2021. <a href=\"https://doi.org/10.2140/pmp.2021.2.221\">https://doi.org/10.2140/pmp.2021.2.221</a>.","short":"J. Alt, L. Erdös, T.H. Krüger, Probability and Mathematical Physics 2 (2021) 221–280.","apa":"Alt, J., Erdös, L., &#38; Krüger, T. H. (2021). Spectral radius of random matrices with independent entries. <i>Probability and Mathematical Physics</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/pmp.2021.2.221\">https://doi.org/10.2140/pmp.2021.2.221</a>","ama":"Alt J, Erdös L, Krüger TH. Spectral radius of random matrices with independent entries. <i>Probability and Mathematical Physics</i>. 2021;2(2):221-280. doi:<a href=\"https://doi.org/10.2140/pmp.2021.2.221\">10.2140/pmp.2021.2.221</a>","mla":"Alt, Johannes, et al. “Spectral Radius of Random Matrices with Independent Entries.” <i>Probability and Mathematical Physics</i>, vol. 2, no. 2, Mathematical Sciences Publishers, 2021, pp. 221–80, doi:<a href=\"https://doi.org/10.2140/pmp.2021.2.221\">10.2140/pmp.2021.2.221</a>."},"publication_identifier":{"issn":["2690-0998"],"eissn":["2690-1005"]},"status":"public","oa":1,"acknowledgement":"Partially supported by ERC Starting Grant RandMat No. 715539 and the SwissMap grant of Swiss National Science Foundation. Partially supported by ERC Advanced Grant RanMat No. 338804. Partially supported by the Hausdorff Center for Mathematics in Bonn.","scopus_import":"1","publication":"Probability and Mathematical Physics","department":[{"_id":"LaEr"}],"day":"21","doi":"10.2140/pmp.2021.2.221","publication_status":"published","page":"221-280","abstract":[{"text":"We consider random n×n matrices X with independent and centered entries and a general variance profile. We show that the spectral radius of X converges with very high probability to the square root of the spectral radius of the variance matrix of X when n tends to infinity. We also establish the optimal rate of convergence, that is a new result even for general i.i.d. matrices beyond the explicitly solvable Gaussian cases. The main ingredient is the proof of the local inhomogeneous circular law [arXiv:1612.07776] at the spectral edge.","lang":"eng"}],"corr_author":"1","oa_version":"Preprint","year":"2021","title":"Spectral radius of random matrices with independent entries","arxiv":1,"external_id":{"arxiv":["1907.13631"]},"_id":"15013","date_published":"2021-05-21T00:00:00Z","volume":2,"intvolume":"         2","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1907.13631","open_access":"1"}],"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","article_type":"original","month":"05","type":"journal_article","date_created":"2024-02-18T23:01:03Z"},{"type":"journal_article","date_created":"2024-03-20T10:42:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","month":"08","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-021-25337-5"}],"volume":12,"language":[{"iso":"eng"}],"intvolume":"        12","_id":"15137","date_published":"2021-08-19T00:00:00Z","external_id":{"pmid":["34413302"]},"year":"2021","title":"SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation","oa_version":"Published Version","publication_status":"published","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"abstract":[{"lang":"eng","text":"Characteristic properties of type III CRISPR-Cas systems include recognition of target RNA and the subsequent induction of a multifaceted immune response. This involves sequence-specific cleavage of the target RNA and production of cyclic oligoadenylate (cOA) molecules. Here we report that an exposed seed region at the 3′ end of the crRNA is essential for target RNA binding and cleavage, whereas cOA production requires base pairing at the 5′ end of the crRNA. Moreover, we uncover that the variation in the size and composition of type III complexes within a single host results in variable seed regions. This may prevent escape by invading genetic elements, while controlling cOA production tightly to prevent unnecessary damage to the host. Lastly, we use these findings to develop a new diagnostic tool, SCOPE, for the specific detection of SARS-CoV-2 from human nasal swab samples, revealing sensitivities in the atto-molar range."}],"day":"19","doi":"10.1038/s41467-021-25337-5","article_number":"5033","extern":"1","scopus_import":"1","publication":"Nature Communications","publication_identifier":{"issn":["2041-1723"]},"status":"public","oa":1,"date_updated":"2024-06-04T06:11:54Z","author":[{"last_name":"Steens","first_name":"Jurre A.","full_name":"Steens, Jurre A."},{"last_name":"Zhu","full_name":"Zhu, Yifan","first_name":"Yifan"},{"last_name":"Taylor","full_name":"Taylor, David W.","first_name":"David W."},{"first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo"},{"last_name":"Prinsen","first_name":"Stijn H. P.","full_name":"Prinsen, Stijn H. P."},{"full_name":"Schoen, Cor D.","first_name":"Cor D.","last_name":"Schoen"},{"first_name":"Bart J. F.","full_name":"Keijser, Bart J. F.","last_name":"Keijser"},{"last_name":"Ossendrijver","full_name":"Ossendrijver, Michel","first_name":"Michel"},{"first_name":"L. Marije","full_name":"Hofstra, L. Marije","last_name":"Hofstra"},{"first_name":"Stan J. J.","full_name":"Brouns, Stan J. J.","last_name":"Brouns"},{"last_name":"Shinkai","first_name":"Akeo","full_name":"Shinkai, Akeo"},{"first_name":"John","full_name":"van der Oost, John","last_name":"van der Oost"},{"full_name":"Staals, Raymond H. J.","first_name":"Raymond H. J.","last_name":"Staals"}],"citation":{"mla":"Steens, Jurre A., et al. “SCOPE Enables Type III CRISPR-Cas Diagnostics Using Flexible Targeting and Stringent CARF Ribonuclease Activation.” <i>Nature Communications</i>, vol. 12, 5033, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-25337-5\">10.1038/s41467-021-25337-5</a>.","ama":"Steens JA, Zhu Y, Taylor DW, et al. SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-25337-5\">10.1038/s41467-021-25337-5</a>","apa":"Steens, J. A., Zhu, Y., Taylor, D. W., Bravo, J. P. K., Prinsen, S. H. P., Schoen, C. D., … Staals, R. H. J. (2021). SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-25337-5\">https://doi.org/10.1038/s41467-021-25337-5</a>","short":"J.A. Steens, Y. Zhu, D.W. Taylor, J.P.K. Bravo, S.H.P. Prinsen, C.D. Schoen, B.J.F. Keijser, M. Ossendrijver, L.M. Hofstra, S.J.J. Brouns, A. Shinkai, J. van der Oost, R.H.J. Staals, Nature Communications 12 (2021).","chicago":"Steens, Jurre A., Yifan Zhu, David W. Taylor, Jack Peter Kelly Bravo, Stijn H. P. Prinsen, Cor D. Schoen, Bart J. F. Keijser, et al. “SCOPE Enables Type III CRISPR-Cas Diagnostics Using Flexible Targeting and Stringent CARF Ribonuclease Activation.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-25337-5\">https://doi.org/10.1038/s41467-021-25337-5</a>.","ieee":"J. A. Steens <i>et al.</i>, “SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","ista":"Steens JA, Zhu Y, Taylor DW, Bravo JPK, Prinsen SHP, Schoen CD, Keijser BJF, Ossendrijver M, Hofstra LM, Brouns SJJ, Shinkai A, van der Oost J, Staals RHJ. 2021. SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation. Nature Communications. 12, 5033."},"publisher":"Springer Nature","quality_controlled":"1","pmid":1},{"article_type":"original","month":"11","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-03-20T10:42:39Z","type":"journal_article","intvolume":"        40","language":[{"iso":"eng"}],"volume":40,"issue":"21","main_file_link":[{"url":"https://doi.org/10.15252/embj.2021107711","open_access":"1"}],"date_published":"2021-11-02T00:00:00Z","_id":"15138","title":"Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses","year":"2021","external_id":{"pmid":["34524703"]},"abstract":[{"lang":"eng","text":"RNA viruses induce the formation of subcellular organelles that provide microenvironments conducive to their replication. Here we show that replication factories of rotaviruses represent protein‐RNA condensates that are formed via liquid–liquid phase separation of the viroplasm‐forming proteins NSP5 and rotavirus RNA chaperone NSP2. Upon mixing, these proteins readily form condensates at physiologically relevant low micromolar concentrations achieved in the cytoplasm of virus‐infected cells. Early infection stage condensates could be reversibly dissolved by 1,6‐hexanediol, as well as propylene glycol that released rotavirus transcripts from these condensates. During the early stages of infection, propylene glycol treatments reduced viral replication and phosphorylation of the condensate‐forming protein NSP5. During late infection, these condensates exhibited altered material properties and became resistant to propylene glycol, coinciding with hyperphosphorylation of NSP5. Some aspects of the assembly of cytoplasmic rotavirus replication factories mirror the formation of other ribonucleoprotein granules. Such viral RNA‐rich condensates that support replication of multi‐segmented genomes represent an attractive target for developing novel therapeutic approaches."}],"publication_status":"published","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology","General Neuroscience"],"oa_version":"Published Version","extern":"1","doi":"10.15252/embj.2021107711","article_number":"e107711","day":"02","oa":1,"publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"status":"public","scopus_import":"1","publication":"The EMBO Journal","pmid":1,"quality_controlled":"1","publisher":"Embo Press","citation":{"mla":"Geiger, Florian, et al. “Liquid–Liquid Phase Separation Underpins the Formation of Replication Factories in Rotaviruses.” <i>The EMBO Journal</i>, vol. 40, no. 21, e107711, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2021107711\">10.15252/embj.2021107711</a>.","ama":"Geiger F, Acker J, Papa G, et al. Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses. <i>The EMBO Journal</i>. 2021;40(21). doi:<a href=\"https://doi.org/10.15252/embj.2021107711\">10.15252/embj.2021107711</a>","short":"F. Geiger, J. Acker, G. Papa, X. Wang, W.E. Arter, K.L. Saar, N.A. Erkamp, R. Qi, J.P.K. Bravo, S. Strauss, G. Krainer, O.R. Burrone, R. Jungmann, T.P. Knowles, H. Engelke, A. Borodavka, The EMBO Journal 40 (2021).","apa":"Geiger, F., Acker, J., Papa, G., Wang, X., Arter, W. E., Saar, K. L., … Borodavka, A. (2021). Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses. <i>The EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2021107711\">https://doi.org/10.15252/embj.2021107711</a>","ista":"Geiger F, Acker J, Papa G, Wang X, Arter WE, Saar KL, Erkamp NA, Qi R, Bravo JPK, Strauss S, Krainer G, Burrone OR, Jungmann R, Knowles TP, Engelke H, Borodavka A. 2021. Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses. The EMBO Journal. 40(21), e107711.","ieee":"F. Geiger <i>et al.</i>, “Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses,” <i>The EMBO Journal</i>, vol. 40, no. 21. Embo Press, 2021.","chicago":"Geiger, Florian, Julia Acker, Guido Papa, Xinyu Wang, William E Arter, Kadi L Saar, Nadia A Erkamp, et al. “Liquid–Liquid Phase Separation Underpins the Formation of Replication Factories in Rotaviruses.” <i>The EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2021107711\">https://doi.org/10.15252/embj.2021107711</a>."},"author":[{"first_name":"Florian","full_name":"Geiger, Florian","last_name":"Geiger"},{"first_name":"Julia","full_name":"Acker, Julia","last_name":"Acker"},{"first_name":"Guido","full_name":"Papa, Guido","last_name":"Papa"},{"first_name":"Xinyu","full_name":"Wang, Xinyu","last_name":"Wang"},{"first_name":"William E","full_name":"Arter, William E","last_name":"Arter"},{"first_name":"Kadi L","full_name":"Saar, Kadi L","last_name":"Saar"},{"full_name":"Erkamp, Nadia A","first_name":"Nadia A","last_name":"Erkamp"},{"last_name":"Qi","full_name":"Qi, Runzhang","first_name":"Runzhang"},{"id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","last_name":"Bravo","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly"},{"full_name":"Strauss, Sebastian","first_name":"Sebastian","last_name":"Strauss"},{"first_name":"Georg","full_name":"Krainer, Georg","last_name":"Krainer"},{"first_name":"Oscar R","full_name":"Burrone, Oscar R","last_name":"Burrone"},{"last_name":"Jungmann","first_name":"Ralf","full_name":"Jungmann, Ralf"},{"first_name":"Tuomas PJ","full_name":"Knowles, Tuomas PJ","last_name":"Knowles"},{"last_name":"Engelke","full_name":"Engelke, Hanna","first_name":"Hanna"},{"last_name":"Borodavka","full_name":"Borodavka, Alexander","first_name":"Alexander"}],"date_updated":"2024-06-04T06:08:16Z"},{"pmid":1,"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","citation":{"mla":"Bravo, Jack Peter Kelly, et al. “Structural Basis of Rotavirus RNA Chaperone Displacement and RNA Annealing.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 41, e2100198118, Proceedings of the National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2100198118\">10.1073/pnas.2100198118</a>.","ama":"Bravo JPK, Bartnik K, Venditti L, et al. Structural basis of rotavirus RNA chaperone displacement and RNA annealing. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(41). doi:<a href=\"https://doi.org/10.1073/pnas.2100198118\">10.1073/pnas.2100198118</a>","apa":"Bravo, J. P. K., Bartnik, K., Venditti, L., Acker, J., Gail, E. H., Colyer, A., … Borodavka, A. (2021). Structural basis of rotavirus RNA chaperone displacement and RNA annealing. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2100198118\">https://doi.org/10.1073/pnas.2100198118</a>","short":"J.P.K. Bravo, K. Bartnik, L. Venditti, J. Acker, E.H. Gail, A. Colyer, C. Davidovich, D.C. Lamb, R. Tuma, A.N. Calabrese, A. Borodavka, Proceedings of the National Academy of Sciences 118 (2021).","chicago":"Bravo, Jack Peter Kelly, Kira Bartnik, Luca Venditti, Julia Acker, Emma H. Gail, Alice Colyer, Chen Davidovich, et al. “Structural Basis of Rotavirus RNA Chaperone Displacement and RNA Annealing.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2100198118\">https://doi.org/10.1073/pnas.2100198118</a>.","ista":"Bravo JPK, Bartnik K, Venditti L, Acker J, Gail EH, Colyer A, Davidovich C, Lamb DC, Tuma R, Calabrese AN, Borodavka A. 2021. Structural basis of rotavirus RNA chaperone displacement and RNA annealing. Proceedings of the National Academy of Sciences. 118(41), e2100198118.","ieee":"J. P. K. Bravo <i>et al.</i>, “Structural basis of rotavirus RNA chaperone displacement and RNA annealing,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 41. Proceedings of the National Academy of Sciences, 2021."},"date_updated":"2024-06-04T06:04:07Z","author":[{"id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","last_name":"Bravo","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly"},{"first_name":"Kira","full_name":"Bartnik, Kira","last_name":"Bartnik"},{"first_name":"Luca","full_name":"Venditti, Luca","last_name":"Venditti"},{"first_name":"Julia","full_name":"Acker, Julia","last_name":"Acker"},{"full_name":"Gail, Emma H.","first_name":"Emma H.","last_name":"Gail"},{"full_name":"Colyer, Alice","first_name":"Alice","last_name":"Colyer"},{"last_name":"Davidovich","full_name":"Davidovich, Chen","first_name":"Chen"},{"full_name":"Lamb, Don C.","first_name":"Don C.","last_name":"Lamb"},{"last_name":"Tuma","full_name":"Tuma, Roman","first_name":"Roman"},{"last_name":"Calabrese","full_name":"Calabrese, Antonio N.","first_name":"Antonio N."},{"last_name":"Borodavka","first_name":"Alexander","full_name":"Borodavka, Alexander"}],"oa":1,"status":"public","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication":"Proceedings of the National Academy of Sciences","scopus_import":"1","extern":"1","article_number":"e2100198118","doi":"10.1073/pnas.2100198118","day":"06","abstract":[{"lang":"eng","text":"Rotavirus genomes are distributed between 11 distinct RNA molecules, all of which must be selectively copackaged during virus assembly. This likely occurs through sequence-specific RNA interactions facilitated by the RNA chaperone NSP2. Here, we report that NSP2 autoregulates its chaperone activity through its C-terminal region (CTR) that promotes RNA–RNA interactions by limiting its helix-unwinding activity. Unexpectedly, structural proteomics data revealed that the CTR does not directly interact with RNA, while accelerating RNA release from NSP2. Cryo–electron microscopy reconstructions of an NSP2–RNA complex reveal a highly conserved acidic patch on the CTR, which is poised toward the bound RNA. Virus replication was abrogated by charge-disrupting mutations within the acidic patch but completely restored by charge-preserving mutations. Mechanistic similarities between NSP2 and the unrelated bacterial RNA chaperone Hfq suggest that accelerating RNA dissociation while promoting intermolecular RNA interactions may be a widespread strategy of RNA chaperone recycling."}],"publication_status":"published","oa_version":"Published Version","title":"Structural basis of rotavirus RNA chaperone displacement and RNA annealing","year":"2021","external_id":{"pmid":["34615715"]},"date_published":"2021-10-06T00:00:00Z","_id":"15139","language":[{"iso":"eng"}],"intvolume":"       118","volume":118,"issue":"41","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2100198118"}],"article_type":"original","month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_created":"2024-03-20T10:42:45Z","type":"journal_article"},{"year":"2021","title":"Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication","external_id":{"pmid":["33631104"]},"_id":"15140","date_published":"2021-04-01T00:00:00Z","volume":81,"intvolume":"        81","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1101/2020.12.14.422718 ","open_access":"1"}],"issue":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","article_type":"original","month":"04","type":"journal_article","date_created":"2024-03-20T10:42:53Z","quality_controlled":"1","pmid":1,"date_updated":"2024-06-04T06:00:56Z","author":[{"first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","last_name":"Bravo"},{"full_name":"Dangerfield, Tyler L.","first_name":"Tyler L.","last_name":"Dangerfield"},{"full_name":"Taylor, David W.","first_name":"David W.","last_name":"Taylor"},{"last_name":"Johnson","full_name":"Johnson, Kenneth A.","first_name":"Kenneth A."}],"publisher":"Elsevier","citation":{"chicago":"Bravo, Jack Peter Kelly, Tyler L. Dangerfield, David W. Taylor, and Kenneth A. Johnson. “Remdesivir Is a Delayed Translocation Inhibitor of SARS-CoV-2 Replication.” <i>Molecular Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.molcel.2021.01.035\">https://doi.org/10.1016/j.molcel.2021.01.035</a>.","ista":"Bravo JPK, Dangerfield TL, Taylor DW, Johnson KA. 2021. Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication. Molecular Cell. 81(7), 1548–1552.e4.","ieee":"J. P. K. Bravo, T. L. Dangerfield, D. W. Taylor, and K. A. Johnson, “Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication,” <i>Molecular Cell</i>, vol. 81, no. 7. Elsevier, p. 1548–1552.e4, 2021.","apa":"Bravo, J. P. K., Dangerfield, T. L., Taylor, D. W., &#38; Johnson, K. A. (2021). Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2021.01.035\">https://doi.org/10.1016/j.molcel.2021.01.035</a>","short":"J.P.K. Bravo, T.L. Dangerfield, D.W. Taylor, K.A. Johnson, Molecular Cell 81 (2021) 1548–1552.e4.","ama":"Bravo JPK, Dangerfield TL, Taylor DW, Johnson KA. Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication. <i>Molecular Cell</i>. 2021;81(7):1548-1552.e4. doi:<a href=\"https://doi.org/10.1016/j.molcel.2021.01.035\">10.1016/j.molcel.2021.01.035</a>","mla":"Bravo, Jack Peter Kelly, et al. “Remdesivir Is a Delayed Translocation Inhibitor of SARS-CoV-2 Replication.” <i>Molecular Cell</i>, vol. 81, no. 7, Elsevier, 2021, p. 1548–1552.e4, doi:<a href=\"https://doi.org/10.1016/j.molcel.2021.01.035\">10.1016/j.molcel.2021.01.035</a>."},"status":"public","publication_identifier":{"issn":["1097-2765"]},"oa":1,"scopus_import":"1","publication":"Molecular Cell","extern":"1","day":"01","doi":"10.1016/j.molcel.2021.01.035","keyword":["Cell Biology","Molecular Biology"],"publication_status":"published","abstract":[{"lang":"eng","text":"Remdesivir is a nucleoside analog approved by the US FDA for treatment of COVID-19. Here, we present a 3.9-Å-resolution cryo-EM reconstruction of a remdesivir-stalled RNA-dependent RNA polymerase complex, revealing full incorporation of 3 copies of remdesivir monophosphate (RMP) and a partially incorporated fourth RMP in the active site. The structure reveals that RMP blocks RNA translocation after incorporation of 3 bases following RMP, resulting in delayed chain termination, which can guide the rational design of improved antiviral drugs."}],"page":"1548-1552.e4","oa_version":"Preprint"},{"external_id":{"pmid":["33733066"]},"title":"Structure of a type IV CRISPR-Cas ribonucleoprotein complex","year":"2021","date_published":"2021-03-19T00:00:00Z","_id":"15141","issue":"3","main_file_link":[{"url":"https://doi.org/10.1016/j.isci.2021.102201","open_access":"1"}],"intvolume":"        24","language":[{"iso":"eng"}],"volume":24,"date_created":"2024-03-20T10:43:00Z","type":"journal_article","month":"03","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","publisher":"Elsevier","citation":{"apa":"Zhou, Y., Bravo, J. P. K., Taylor, H. N., Steens, J. A., Jackson, R. N., Staals, R. H. J., &#38; Taylor, D. W. (2021). Structure of a type IV CRISPR-Cas ribonucleoprotein complex. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2021.102201\">https://doi.org/10.1016/j.isci.2021.102201</a>","short":"Y. Zhou, J.P.K. Bravo, H.N. Taylor, J.A. Steens, R.N. Jackson, R.H.J. Staals, D.W. Taylor, IScience 24 (2021).","ista":"Zhou Y, Bravo JPK, Taylor HN, Steens JA, Jackson RN, Staals RHJ, Taylor DW. 2021. Structure of a type IV CRISPR-Cas ribonucleoprotein complex. iScience. 24(3), 102201.","ieee":"Y. Zhou <i>et al.</i>, “Structure of a type IV CRISPR-Cas ribonucleoprotein complex,” <i>iScience</i>, vol. 24, no. 3. Elsevier, 2021.","chicago":"Zhou, Yi, Jack Peter Kelly Bravo, Hannah N. Taylor, Jurre A. Steens, Ryan N. Jackson, Raymond H.J. Staals, and David W. Taylor. “Structure of a Type IV CRISPR-Cas Ribonucleoprotein Complex.” <i>IScience</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.isci.2021.102201\">https://doi.org/10.1016/j.isci.2021.102201</a>.","mla":"Zhou, Yi, et al. “Structure of a Type IV CRISPR-Cas Ribonucleoprotein Complex.” <i>IScience</i>, vol. 24, no. 3, 102201, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.isci.2021.102201\">10.1016/j.isci.2021.102201</a>.","ama":"Zhou Y, Bravo JPK, Taylor HN, et al. Structure of a type IV CRISPR-Cas ribonucleoprotein complex. <i>iScience</i>. 2021;24(3). doi:<a href=\"https://doi.org/10.1016/j.isci.2021.102201\">10.1016/j.isci.2021.102201</a>"},"date_updated":"2024-06-04T05:56:45Z","author":[{"last_name":"Zhou","first_name":"Yi","full_name":"Zhou, Yi"},{"full_name":"Bravo, Jack Peter Kelly","first_name":"Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","last_name":"Bravo"},{"first_name":"Hannah N.","full_name":"Taylor, Hannah N.","last_name":"Taylor"},{"last_name":"Steens","first_name":"Jurre A.","full_name":"Steens, Jurre A."},{"last_name":"Jackson","first_name":"Ryan N.","full_name":"Jackson, Ryan N."},{"first_name":"Raymond H.J.","full_name":"Staals, Raymond H.J.","last_name":"Staals"},{"last_name":"Taylor","full_name":"Taylor, David W.","first_name":"David W."}],"pmid":1,"quality_controlled":"1","publication":"iScience","oa":1,"status":"public","publication_identifier":{"issn":["2589-0042"]},"article_number":"102201","doi":"10.1016/j.isci.2021.102201","day":"19","extern":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We reveal the cryo-electron microscopy structure of a type IV-B CRISPR ribonucleoprotein (RNP) complex (Csf) at 3.9-Å resolution. The complex best resembles the type III-A CRISPR Csm effector complex, consisting of a Cas7-like (Csf2) filament intertwined with a small subunit (Cas11) filament, but the complex lacks subunits for RNA processing and target DNA cleavage. Surprisingly, instead of assembling around a CRISPR-derived RNA (crRNA), the complex assembles upon heterogeneous RNA of a regular length arranged in a pseudo-A-form configuration. These findings provide a high-resolution glimpse into the assembly and function of enigmatic type IV CRISPR systems, expanding our understanding of class I CRISPR-Cas system architecture, and suggesting a function for type IV-B RNPs that may be distinct from other class 1 CRISPR-associated systems."}],"keyword":["Multidisciplinary"],"publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_status":"published","article_type":"original","month":"08","page":"133-137","abstract":[{"lang":"eng","text":"The majority of gene transcripts generated by RNA polymerase II in mammalian genomes initiate at CpG island (CGI) promoters1,2, yet our understanding of their regulation remains limited. This is in part due to the incomplete information that we have on transcription factors, their DNA-binding motifs and which genomic binding sites are functional in any given cell type3,4,5. In addition, there are orphan motifs without known binders, such as the CGCG element, which is associated with highly expressed genes across human tissues and enriched near the transcription start site of a subset of CGI promoters6,7,8. Here we combine single-molecule footprinting with interaction proteomics to identify BTG3-associated nuclear protein (BANP) as the transcription factor that binds this element in the mouse and human genome. We show that BANP is a strong CGI activator that controls essential metabolic genes in pluripotent stem and terminally differentiated neuronal cells. BANP binding is repelled by DNA methylation of its motif in vitro and in vivo, which epigenetically restricts most binding to CGIs and accounts for differential binding at aberrantly methylated CGI promoters in cancer cells. Upon binding to an unmethylated motif, BANP opens chromatin and phases nucleosomes. These findings establish BANP as a critical activator of a set of essential genes and suggest a model in which the activity of CGI promoters relies on methylation-sensitive transcription factors that are capable of chromatin opening."}],"type":"journal_article","date_created":"2024-03-21T07:53:48Z","oa_version":"None","volume":596,"language":[{"iso":"eng"}],"intvolume":"       596","extern":"1","day":"05","doi":"10.1038/s41586-021-03689-8","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"status":"public","_id":"15150","publication":"Nature","scopus_import":"1","date_published":"2021-08-05T00:00:00Z","quality_controlled":"1","year":"2021","title":"BANP opens chromatin and activates CpG-island-regulated genes","date_updated":"2024-03-25T12:34:31Z","author":[{"first_name":"Ralph S.","full_name":"Grand, Ralph S.","last_name":"Grand"},{"first_name":"Lukas","full_name":"Burger, Lukas","last_name":"Burger"},{"full_name":"Gräwe, Cathrin","first_name":"Cathrin","last_name":"Gräwe"},{"full_name":"Michael, Alicia","first_name":"Alicia","last_name":"Michael","orcid":"0000-0002-6080-839X","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"last_name":"Isbel","full_name":"Isbel, Luke","first_name":"Luke"},{"last_name":"Hess","first_name":"Daniel","full_name":"Hess, Daniel"},{"last_name":"Hoerner","first_name":"Leslie","full_name":"Hoerner, Leslie"},{"last_name":"Iesmantavicius","first_name":"Vytautas","full_name":"Iesmantavicius, Vytautas"},{"first_name":"Sevi","full_name":"Durdu, Sevi","last_name":"Durdu"},{"first_name":"Marco","full_name":"Pregnolato, Marco","last_name":"Pregnolato"},{"last_name":"Krebs","first_name":"Arnaud R.","full_name":"Krebs, Arnaud R."},{"full_name":"Smallwood, Sébastien A.","first_name":"Sébastien A.","last_name":"Smallwood"},{"last_name":"Thomä","full_name":"Thomä, Nicolas","first_name":"Nicolas"},{"first_name":"Michiel","full_name":"Vermeulen, Michiel","last_name":"Vermeulen"},{"last_name":"Schübeler","first_name":"Dirk","full_name":"Schübeler, Dirk"}],"publisher":"Springer Nature","citation":{"apa":"Grand, R. S., Burger, L., Gräwe, C., Michael, A. K., Isbel, L., Hess, D., … Schübeler, D. (2021). BANP opens chromatin and activates CpG-island-regulated genes. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-03689-8\">https://doi.org/10.1038/s41586-021-03689-8</a>","short":"R.S. Grand, L. Burger, C. Gräwe, A.K. Michael, L. Isbel, D. Hess, L. Hoerner, V. Iesmantavicius, S. Durdu, M. Pregnolato, A.R. Krebs, S.A. Smallwood, N. Thomä, M. Vermeulen, D. Schübeler, Nature 596 (2021) 133–137.","chicago":"Grand, Ralph S., Lukas Burger, Cathrin Gräwe, Alicia K. Michael, Luke Isbel, Daniel Hess, Leslie Hoerner, et al. “BANP Opens Chromatin and Activates CpG-Island-Regulated Genes.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-03689-8\">https://doi.org/10.1038/s41586-021-03689-8</a>.","ista":"Grand RS, Burger L, Gräwe C, Michael AK, Isbel L, Hess D, Hoerner L, Iesmantavicius V, Durdu S, Pregnolato M, Krebs AR, Smallwood SA, Thomä N, Vermeulen M, Schübeler D. 2021. BANP opens chromatin and activates CpG-island-regulated genes. Nature. 596, 133–137.","ieee":"R. S. Grand <i>et al.</i>, “BANP opens chromatin and activates CpG-island-regulated genes,” <i>Nature</i>, vol. 596. Springer Nature, pp. 133–137, 2021.","mla":"Grand, Ralph S., et al. “BANP Opens Chromatin and Activates CpG-Island-Regulated Genes.” <i>Nature</i>, vol. 596, Springer Nature, 2021, pp. 133–37, doi:<a href=\"https://doi.org/10.1038/s41586-021-03689-8\">10.1038/s41586-021-03689-8</a>.","ama":"Grand RS, Burger L, Gräwe C, et al. BANP opens chromatin and activates CpG-island-regulated genes. <i>Nature</i>. 2021;596:133-137. doi:<a href=\"https://doi.org/10.1038/s41586-021-03689-8\">10.1038/s41586-021-03689-8</a>"}},{"publication":"Cell","scopus_import":"1","oa":1,"publication_identifier":{"issn":["0092-8674"]},"status":"public","publisher":"Elsevier","citation":{"mla":"Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.” <i>Cell</i>, vol. 184, no. 14, Elsevier, 2021, pp. 3599–611, doi:<a href=\"https://doi.org/10.1016/j.cell.2021.05.029\">10.1016/j.cell.2021.05.029</a>.","ama":"Michael AK, Thomä NH. Reading the chromatinized genome. <i>Cell</i>. 2021;184(14):3599-3611. doi:<a href=\"https://doi.org/10.1016/j.cell.2021.05.029\">10.1016/j.cell.2021.05.029</a>","apa":"Michael, A. K., &#38; Thomä, N. H. (2021). Reading the chromatinized genome. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2021.05.029\">https://doi.org/10.1016/j.cell.2021.05.029</a>","short":"A.K. Michael, N.H. Thomä, Cell 184 (2021) 3599–3611.","ista":"Michael AK, Thomä NH. 2021. Reading the chromatinized genome. Cell. 184(14), 3599–3611.","chicago":"Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.” <i>Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cell.2021.05.029\">https://doi.org/10.1016/j.cell.2021.05.029</a>.","ieee":"A. K. Michael and N. H. Thomä, “Reading the chromatinized genome,” <i>Cell</i>, vol. 184, no. 14. Elsevier, pp. 3599–3611, 2021."},"date_updated":"2024-03-25T12:31:39Z","author":[{"first_name":"Alicia","full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael"},{"full_name":"Thomä, Nicolas H.","first_name":"Nicolas H.","last_name":"Thomä"}],"quality_controlled":"1","oa_version":"Published Version","page":"3599-3611","abstract":[{"lang":"eng","text":"Eukaryotic DNA-binding proteins operate in the context of chromatin, where nucleosomes are the elementary building blocks. Nucleosomal DNA is wrapped around a histone core, thereby rendering a large fraction of the DNA surface inaccessible to DNA-binding proteins. Nevertheless, first responders in DNA repair and sequence-specific transcription factors bind DNA target sites obstructed by chromatin. While early studies examined protein binding to histone-free DNA, it is only now beginning to emerge how DNA sequences are interrogated on nucleosomes. These readout strategies range from the release of nucleosomal DNA from histones, to rotational/translation register shifts of the DNA motif, and nucleosome-specific DNA binding modes that differ from those observed on naked DNA. Since DNA motif engagement on nucleosomes strongly depends on position and orientation, we argue that motif location and nucleosome positioning co-determine protein access to DNA in transcription and DNA repair."}],"publication_status":"published","keyword":["General Biochemistry","Genetics and Molecular Biology"],"doi":"10.1016/j.cell.2021.05.029","day":"08","extern":"1","date_published":"2021-07-08T00:00:00Z","_id":"15151","title":"Reading the chromatinized genome","year":"2021","date_created":"2024-03-21T07:54:19Z","type":"journal_article","month":"07","article_type":"review","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","issue":"14","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2021.05.029"}],"intvolume":"       184","language":[{"iso":"eng"}],"volume":184}]