[{"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"}],"external_id":{"arxiv":["1905.12506"]},"publication_identifier":{"isbn":["9781713807933"]},"_id":"14193","status":"public","extern":"1","author":[{"first_name":"Sjoerd van","full_name":"Steenkiste, Sjoerd van","last_name":"Steenkiste"},{"last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"last_name":"Schmidhuber","first_name":"Jürgen","full_name":"Schmidhuber, Jürgen"},{"last_name":"Bachem","full_name":"Bachem, Olivier","first_name":"Olivier"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Steenkiste, Sjoerd van, Francesco Locatello, Jürgen Schmidhuber, and Olivier Bachem. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” In <i>Advances in Neural Information Processing Systems</i>, Vol. 32, 2019.","short":"S. van Steenkiste, F. Locatello, J. Schmidhuber, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019.","ama":"Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. Are disentangled representations helpful for abstract visual reasoning? In: <i>Advances in Neural Information Processing Systems</i>. Vol 32. ; 2019.","ieee":"S. van Steenkiste, F. Locatello, J. Schmidhuber, and O. Bachem, “Are disentangled representations helpful for abstract visual reasoning?,” in <i>Advances in Neural Information Processing Systems</i>, Vancouver, Canada, 2019, vol. 32.","apa":"Steenkiste, S. van, Locatello, F., Schmidhuber, J., &#38; Bachem, O. (2019). Are disentangled representations helpful for abstract visual reasoning? In <i>Advances in Neural Information Processing Systems</i> (Vol. 32). Vancouver, Canada.","mla":"Steenkiste, Sjoerd van, et al. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” <i>Advances in Neural Information Processing Systems</i>, vol. 32, 2019.","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."},"day":"29","department":[{"_id":"FrLo"}],"oa_version":"Preprint","publication_status":"published","date_updated":"2023-09-12T09:02:43Z","month":"05","type":"conference","quality_controlled":"1","title":"Are disentangled representations helpful for abstract visual reasoning?","date_published":"2019-05-29T00:00:00Z","conference":{"end_date":"2019-12-14","location":"Vancouver, Canada","start_date":"2019-12-08","name":"NeurIPS: Neural Information Processing Systems"},"volume":32,"arxiv":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","publication":"Advances in Neural Information Processing Systems","year":"2019","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1905.12506"}],"intvolume":"        32","date_created":"2023-08-22T14:09:53Z"},{"publication":"Advances in Neural Information Processing Systems","article_processing_charge":"No","volume":32,"year":"2019","main_file_link":[{"url":"https://arxiv.org/abs/1905.13662","open_access":"1"}],"date_created":"2023-08-22T14:12:28Z","quality_controlled":"1","date_published":"2019-12-08T00:00:00Z","title":"On the fairness of disentangled representations","conference":{"end_date":"2019-12-14","location":"Vancouver, Canada","start_date":"2019-12-08","name":"NeurIPS: Neural Information Processing Systems"},"citation":{"ieee":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, and O. Bachem, “On the fairness of disentangled representations,” in <i>Advances in Neural Information Processing Systems</i>, 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 <i>Advances in Neural Information Processing Systems</i>, 32:14611–14624, 2019.","ama":"Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. On the fairness of disentangled representations. In: <i>Advances in Neural Information Processing Systems</i>. Vol 32. ; 2019:14611–14624.","short":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019, pp. 14611–14624.","mla":"Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.” <i>Advances in Neural Information Processing Systems</i>, vol. 32, 2019, pp. 14611–14624.","apa":"Locatello, F., Abbati, G., Rainforth, T., Bauer, S., Schölkopf, B., &#38; Bachem, O. (2019). On the fairness of disentangled representations. In <i>Advances in Neural Information Processing Systems</i> (Vol. 32, pp. 14611–14624). Vancouver, Canada.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","last_name":"Locatello"},{"first_name":"Gabriele","full_name":"Abbati, Gabriele","last_name":"Abbati"},{"full_name":"Rainforth, Tom","first_name":"Tom","last_name":"Rainforth"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"full_name":"Bachem, Olivier","first_name":"Olivier","last_name":"Bachem"}],"date_updated":"2023-09-12T09:37:22Z","oa_version":"Preprint","department":[{"_id":"FrLo"}],"type":"conference","scopus_import":"1","external_id":{"arxiv":["1905.13662"]},"_id":"14197","language":[{"iso":"eng"}],"arxiv":1,"page":"14611–14624","intvolume":"        32","day":"08","extern":"1","publication_status":"published","month":"12","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."}],"publication_identifier":{"isbn":["9781713807933"]},"status":"public"},{"publication_status":"published","day":"09","extern":"1","month":"06","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","arxiv":1,"language":[{"iso":"eng"}],"intvolume":"        97","page":"4114-4124","publisher":"ML Research Press","date_updated":"2023-09-13T07:45:30Z","oa_version":"Preprint","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Locatello, Francesco, et al. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” <i>Proceedings of the 36th International Conference on Machine Learning</i>, vol. 97, ML Research Press, 2019, pp. 4114–24.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., &#38; Bachem, O. (2019). Challenging common assumptions in the unsupervised learning of disentangled representations. In <i>Proceedings of the 36th International Conference on Machine Learning</i> (Vol. 97, pp. 4114–4124). Long Beach, CA, United States: ML Research Press.","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.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” In <i>Proceedings of the 36th International Conference on Machine Learning</i>, 97:4114–24. ML Research Press, 2019.","ama":"Locatello F, Bauer S, Lucic M, et al. Challenging common assumptions in the unsupervised learning of disentangled representations. In: <i>Proceedings of the 36th International Conference on Machine Learning</i>. Vol 97. ML Research Press; 2019:4114-4124.","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.","ieee":"F. Locatello <i>et al.</i>, “Challenging common assumptions in the unsupervised learning of disentangled representations,” in <i>Proceedings of the 36th International Conference on Machine Learning</i>, Long Beach, CA, United States, 2019, vol. 97, pp. 4114–4124."},"oa":1,"author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"last_name":"Bauer","first_name":"Stefan","full_name":"Bauer, Stefan"},{"last_name":"Lucic","first_name":"Mario","full_name":"Lucic, Mario"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"last_name":"Gelly","first_name":"Sylvain","full_name":"Gelly, Sylvain"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"last_name":"Bachem","first_name":"Olivier","full_name":"Bachem, Olivier"}],"type":"conference","external_id":{"arxiv":["1811.12359"]},"scopus_import":"1","_id":"14200","year":"2019","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.12359"}],"publication":"Proceedings of the 36th International Conference on Machine Learning","article_processing_charge":"No","volume":97,"date_created":"2023-08-22T14:13:08Z","date_published":"2019-06-09T00:00:00Z","title":"Challenging common assumptions in the unsupervised learning of disentangled representations","quality_controlled":"1","conference":{"name":"International Conference on Machine Learning","start_date":"2019-06-10","location":"Long Beach, CA, United States","end_date":"2019-06-15"}},{"publisher":"ACS Publications","intvolume":"        13","article_type":"original","page":"5015-5027","language":[{"iso":"eng"}],"status":"public","pmid":1,"publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086x"]},"issue":"5","abstract":[{"lang":"eng","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."}],"doi":"10.1021/acsnano.9b01025","month":"04","publication_status":"published","day":"16","extern":"1","title":"Custom-size, functional, and durable DNA origami with design-specific scaffolds","date_published":"2019-04-16T00:00:00Z","quality_controlled":"1","date_created":"2023-09-06T12:48:47Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsnano.9b01025"}],"year":"2019","publication":"ACS Nano","article_processing_charge":"No","volume":13,"_id":"14299","external_id":{"pmid":["30990672"]},"scopus_import":"1","type":"journal_article","oa_version":"Published Version","date_updated":"2023-11-07T12:17:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.” <i>ACS Nano</i>. ACS Publications, 2019. <a href=\"https://doi.org/10.1021/acsnano.9b01025\">https://doi.org/10.1021/acsnano.9b01025</a>.","ama":"FAS E, Praetorius FM, Wachauf C, et al. Custom-size, functional, and durable DNA origami with design-specific scaffolds. <i>ACS Nano</i>. 2019;13(5):5015-5027. doi:<a href=\"https://doi.org/10.1021/acsnano.9b01025\">10.1021/acsnano.9b01025</a>","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.","ieee":"E. FAS <i>et al.</i>, “Custom-size, functional, and durable DNA origami with design-specific scaffolds,” <i>ACS Nano</i>, vol. 13, no. 5. ACS Publications, pp. 5015–5027, 2019.","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. <i>ACS Nano</i>. ACS Publications. <a href=\"https://doi.org/10.1021/acsnano.9b01025\">https://doi.org/10.1021/acsnano.9b01025</a>","mla":"FAS, Engelhardt, et al. “Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds.” <i>ACS Nano</i>, vol. 13, no. 5, ACS Publications, 2019, pp. 5015–27, doi:<a href=\"https://doi.org/10.1021/acsnano.9b01025\">10.1021/acsnano.9b01025</a>.","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."},"author":[{"last_name":"FAS","first_name":"Engelhardt","full_name":"FAS, Engelhardt"},{"first_name":"Florian M","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius"},{"full_name":"Wachauf, CH","first_name":"CH","last_name":"Wachauf"},{"first_name":"G","full_name":"Brüggenthies, G","last_name":"Brüggenthies"},{"last_name":"Kohler","full_name":"Kohler, F","first_name":"F"},{"last_name":"Kick","first_name":"B","full_name":"Kick, B"},{"last_name":"Kadletz","full_name":"Kadletz, KL","first_name":"KL"},{"last_name":"Pham","full_name":"Pham, PN","first_name":"PN"},{"last_name":"Behler","full_name":"Behler, KL","first_name":"KL"},{"full_name":"Gerling, T","first_name":"T","last_name":"Gerling"},{"last_name":"Dietz","first_name":"H","full_name":"Dietz, H"}],"oa":1},{"publisher":"Wiley","page":"891-895","article_type":"original","intvolume":"        20","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1439-4227","1439-7633"]},"status":"public","doi":"10.1002/cbic.201800633","abstract":[{"text":"Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135) is a strategy through which chemical probes might be elaborated to test this hypothesis. In this work, variant H3118–135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy–entropy compensation occurs.","lang":"eng"}],"issue":"7","month":"04","day":"01","extern":"1","publication_status":"published","quality_controlled":"1","date_published":"2019-04-01T00:00:00Z","title":"Recognition of ASF1 by using hydrocarbon‐constrained peptides","date_created":"2021-01-19T10:59:14Z","publication":"ChemBioChem","article_processing_charge":"No","volume":20,"main_file_link":[{"url":" https://doi.org/10.1002/cbic.201800633","open_access":"1"}],"year":"2019","_id":"9016","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bakail, May M, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin, Françoise Ochsenbein, and Andrew J. Wilson. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” <i>ChemBioChem</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cbic.201800633\">https://doi.org/10.1002/cbic.201800633</a>.","short":"M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein, A.J. Wilson, ChemBioChem 20 (2019) 891–895.","ama":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. Recognition of ASF1 by using hydrocarbon‐constrained peptides. <i>ChemBioChem</i>. 2019;20(7):891-895. doi:<a href=\"https://doi.org/10.1002/cbic.201800633\">10.1002/cbic.201800633</a>","ieee":"M. M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein, and A. J. Wilson, “Recognition of ASF1 by using hydrocarbon‐constrained peptides,” <i>ChemBioChem</i>, vol. 20, no. 7. Wiley, pp. 891–895, 2019.","apa":"Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein, F., &#38; Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained peptides. <i>ChemBioChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cbic.201800633\">https://doi.org/10.1002/cbic.201800633</a>","mla":"Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” <i>ChemBioChem</i>, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:<a href=\"https://doi.org/10.1002/cbic.201800633\">10.1002/cbic.201800633</a>.","ista":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. 2019. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 20(7), 891–895."},"oa":1,"author":[{"last_name":"Bakail","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M","full_name":"Bakail, May M","orcid":"0000-0002-9592-1587"},{"last_name":"Rodriguez‐Marin","first_name":"Silvia","full_name":"Rodriguez‐Marin, Silvia"},{"last_name":"Hegedüs","full_name":"Hegedüs, Zsófia","first_name":"Zsófia"},{"first_name":"Marie E.","full_name":"Perrin, Marie E.","last_name":"Perrin"},{"last_name":"Ochsenbein","first_name":"Françoise","full_name":"Ochsenbein, Françoise"},{"last_name":"Wilson","full_name":"Wilson, Andrew J.","first_name":"Andrew J."}],"oa_version":"Published Version","date_updated":"2023-02-23T13:46:48Z"},{"citation":{"apa":"Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E., … Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. <i>Cell Chemical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">https://doi.org/10.1016/j.chembiol.2019.09.002</a>","mla":"Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” <i>Cell Chemical Biology</i>, vol. 26, no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:<a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">10.1016/j.chembiol.2019.09.002</a>.","ista":"Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C, Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11), 1573–1585.e10.","chicago":"Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” <i>Cell Chemical Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">https://doi.org/10.1016/j.chembiol.2019.09.002</a>.","ama":"Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. <i>Cell Chemical Biology</i>. 2019;26(11):1573-1585.e10. doi:<a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">10.1016/j.chembiol.2019.09.002</a>","short":"M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C. Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N. Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin, G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26 (2019) 1573–1585.e10.","ieee":"M. M. Bakail <i>et al.</i>, “Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1,” <i>Cell Chemical Biology</i>, vol. 26, no. 11. Elsevier, p. 1573–1585.e10, 2019."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"full_name":"Bakail, May M","first_name":"May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","orcid":"0000-0002-9592-1587","last_name":"Bakail"},{"full_name":"Gaubert, Albane","first_name":"Albane","last_name":"Gaubert"},{"full_name":"Andreani, Jessica","first_name":"Jessica","last_name":"Andreani"},{"first_name":"Gwenaëlle","full_name":"Moal, Gwenaëlle","last_name":"Moal"},{"last_name":"Pinna","full_name":"Pinna, Guillaume","first_name":"Guillaume"},{"first_name":"Ekaterina","full_name":"Boyarchuk, Ekaterina","last_name":"Boyarchuk"},{"last_name":"Gaillard","first_name":"Marie-Cécile","full_name":"Gaillard, Marie-Cécile"},{"full_name":"Courbeyrette, Regis","first_name":"Regis","last_name":"Courbeyrette"},{"first_name":"Carl","full_name":"Mann, Carl","last_name":"Mann"},{"full_name":"Thuret, Jean-Yves","first_name":"Jean-Yves","last_name":"Thuret"},{"last_name":"Guichard","full_name":"Guichard, Bérengère","first_name":"Bérengère"},{"last_name":"Murciano","full_name":"Murciano, Brice","first_name":"Brice"},{"last_name":"Richet","full_name":"Richet, Nicolas","first_name":"Nicolas"},{"full_name":"Poitou, Adeline","first_name":"Adeline","last_name":"Poitou"},{"first_name":"Claire","full_name":"Frederic, Claire","last_name":"Frederic"},{"full_name":"Le Du, Marie-Hélène","first_name":"Marie-Hélène","last_name":"Le Du"},{"first_name":"Morgane","full_name":"Agez, Morgane","last_name":"Agez"},{"last_name":"Roelants","first_name":"Caroline","full_name":"Roelants, Caroline"},{"full_name":"Gurard-Levin, Zachary A.","first_name":"Zachary A.","last_name":"Gurard-Levin"},{"full_name":"Almouzni, Geneviève","first_name":"Geneviève","last_name":"Almouzni"},{"full_name":"Cherradi, Nadia","first_name":"Nadia","last_name":"Cherradi"},{"first_name":"Raphael","full_name":"Guerois, Raphael","last_name":"Guerois"},{"last_name":"Ochsenbein","first_name":"Françoise","full_name":"Ochsenbein, Françoise"}],"oa_version":"Published Version","date_updated":"2023-02-23T13:46:53Z","type":"journal_article","external_id":{"pmid":["31543461"]},"_id":"9018","publication":"Cell Chemical Biology","volume":26,"article_processing_charge":"No","year":"2019","main_file_link":[{"url":"https://doi.org/10.1016/j.chembiol.2019.09.002","open_access":"1"}],"date_created":"2021-01-19T11:04:50Z","quality_controlled":"1","title":"Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1","keyword":["Clinical Biochemistry","Molecular Medicine","Biochemistry","Molecular Biology","Pharmacology","Drug Discovery"],"date_published":"2019-11-21T00:00:00Z","day":"21","extern":"1","publication_status":"published","month":"11","abstract":[{"text":"Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.","lang":"eng"}],"doi":"10.1016/j.chembiol.2019.09.002","issue":"11","publication_identifier":{"issn":["2451-9456"]},"pmid":1,"status":"public","language":[{"iso":"eng"}],"article_type":"original","page":"1573-1585.e10","intvolume":"        26","publisher":"Elsevier"},{"external_id":{"pmid":["31358762"],"arxiv":["1909.07382"]},"file_date_updated":"2021-02-02T13:47:21Z","scopus_import":"1","_id":"9060","oa_version":"Published Version","date_updated":"2023-02-23T13:47:59Z","file":[{"creator":"cziletti","relation":"main_file","checksum":"70c6e5d6fbea0932b0669505ab6633ec","success":1,"date_created":"2021-02-02T13:47:21Z","file_id":"9061","access_level":"open_access","file_size":2820337,"content_type":"application/pdf","date_updated":"2021-02-02T13:47:21Z","file_name":"2019_NatureComm_Ramananarivo.pdf"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","has_accepted_license":"1","citation":{"ama":"Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal monolayers. <i>Nature Communications</i>. 2019;10(1). doi:<a href=\"https://doi.org/10.1038/s41467-019-11362-y\">10.1038/s41467-019-11362-y</a>","short":"S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019).","chicago":"Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled Annealing of Colloidal Monolayers.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-11362-y\">https://doi.org/10.1038/s41467-019-11362-y</a>.","ieee":"S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing of colloidal monolayers,” <i>Nature Communications</i>, vol. 10, no. 1. Springer Nature, 2019.","ista":"Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing of colloidal monolayers. Nature Communications. 10(1), 3380.","apa":"Ramananarivo, S., Ducrot, E., &#38; Palacci, J. A. (2019). Activity-controlled annealing of colloidal monolayers. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-11362-y\">https://doi.org/10.1038/s41467-019-11362-y</a>","mla":"Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.” <i>Nature Communications</i>, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-11362-y\">10.1038/s41467-019-11362-y</a>."},"author":[{"first_name":"Sophie","full_name":"Ramananarivo, Sophie","last_name":"Ramananarivo"},{"last_name":"Ducrot","first_name":"Etienne","full_name":"Ducrot, Etienne"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci"}],"oa":1,"type":"journal_article","title":"Activity-controlled annealing of colloidal monolayers","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"date_published":"2019-07-29T00:00:00Z","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2019","publication":"Nature Communications","article_processing_charge":"No","volume":10,"ddc":["530"],"date_created":"2021-02-02T13:43:36Z","issue":"1","abstract":[{"text":"Molecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium.","lang":"eng"}],"doi":"10.1038/s41467-019-11362-y","status":"public","pmid":1,"publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","day":"29","extern":"1","month":"07","publisher":"Springer Nature","arxiv":1,"language":[{"iso":"eng"}],"article_number":"3380","intvolume":"        10","article_type":"original"},{"type":"conference","isi":1,"month":"10","date_updated":"2023-09-08T11:21:54Z","oa_version":"None","publication_status":"published","department":[{"_id":"BeBi"}],"citation":{"chicago":"Laccone, Francesco, Luigi Malomo, Jesus Perez Rodriguez, Nico Pietroni, Federico Ponchio, Bernd Bickel, and Paolo Cignoni. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” In <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>, 509–15. International Center for Numerical Methods in Engineering, 2019.","ama":"Laccone F, Malomo L, Perez Rodriguez J, et al. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In: <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>. International Center for Numerical Methods in Engineering; 2019:509-515.","short":"F. Laccone, L. Malomo, J. Perez Rodriguez, N. Pietroni, F. Ponchio, B. Bickel, P. Cignoni, in:, IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, International Center for Numerical Methods in Engineering, 2019, pp. 509–515.","ieee":"F. Laccone <i>et al.</i>, “FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels,” in <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>, Barcelona, Spain, 2019, pp. 509–515.","mla":"Laccone, Francesco, et al. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>, International Center for Numerical Methods in Engineering, 2019, pp. 509–15.","apa":"Laccone, F., Malomo, L., Perez Rodriguez, J., Pietroni, N., Ponchio, F., Bickel, B., &#38; Cignoni, P. (2019). FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i> (pp. 509–515). Barcelona, Spain: International Center for Numerical Methods in Engineering.","ista":"Laccone F, Malomo L, Perez Rodriguez J, Pietroni N, Ponchio F, Bickel B, Cignoni P. 2019. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE. IASS: International Association for Shell and Spatial Structures, 509–515."},"day":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Laccone, Francesco","first_name":"Francesco","last_name":"Laccone"},{"full_name":"Malomo, Luigi","first_name":"Luigi","last_name":"Malomo"},{"last_name":"Perez Rodriguez","first_name":"Jesus","full_name":"Perez Rodriguez, Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"},{"last_name":"Ponchio","first_name":"Federico","full_name":"Ponchio, Federico"},{"last_name":"Bickel","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"last_name":"Cignoni","first_name":"Paolo","full_name":"Cignoni, Paolo"}],"status":"public","_id":"9261","publication_identifier":{"issn":["2518-6582"],"isbn":["9788412110104"]},"external_id":{"isi":["000563497600059"]},"abstract":[{"text":"Bending-active structures are able to efficiently produce complex curved shapes starting from flat panels. The desired deformation of the panels derives from the proper selection of their elastic properties. Optimized panels, called FlexMaps, are designed such that, once they are bent and assembled, the resulting static equilibrium configuration matches a desired input 3D shape. The FlexMaps elastic properties are controlled by locally varying spiraling geometric mesostructures, which are optimized in size and shape to match the global curvature (i.e., bending requests) of the target shape. The design pipeline starts from a quad mesh representing the input 3D shape, which defines the edge size and the total amount of spirals: every quad will embed one spiral. Then, an optimization algorithm tunes the geometry of the spirals by using a simplified pre-computed rod model. This rod model is derived from a non-linear regression algorithm which approximates the non-linear behavior of solid FEM spiral models subject to hundreds of load combinations. This innovative pipeline has been applied to the project of a lightweight plywood pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted arc that fits a bounding box of 3.90x3.96x3.25 meters.","lang":"eng"}],"scopus_import":"1","date_created":"2021-03-21T23:01:21Z","page":"509-515","year":"2019","publication":"IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE","article_processing_charge":"No","language":[{"iso":"eng"}],"conference":{"name":"IASS: International Association for Shell and Spatial Structures","start_date":"2019-10-07","location":"Barcelona, Spain","end_date":"2019-10-10"},"publisher":"International Center for Numerical Methods in Engineering","title":"FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels","date_published":"2019-10-10T00:00:00Z","quality_controlled":"1"},{"language":[{"iso":"eng"}],"article_type":"original","page":"9652-9657","intvolume":"       116","publisher":"National Academy of Sciences","extern":"1","day":"07","publication_status":"published","month":"05","doi":"10.1073/pnas.1821435116","abstract":[{"text":"Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"19","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"pmid":1,"status":"public","article_processing_charge":"No","volume":116,"publication":"Proceedings of the National Academy of Sciences","year":"2019","date_created":"2021-06-04T12:38:20Z","ddc":["580"],"quality_controlled":"1","title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","keyword":["Multidisciplinary"],"date_published":"2019-05-07T00:00:00Z","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa":1,"author":[{"last_name":"Kim","full_name":"Kim, M. Yvonne","first_name":"M. Yvonne"},{"last_name":"Ono","first_name":"Akemi","full_name":"Ono, Akemi"},{"first_name":"Stefan","full_name":"Scholten, Stefan","last_name":"Scholten"},{"first_name":"Tetsu","full_name":"Kinoshita, Tetsu","last_name":"Kinoshita"},{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel"},{"last_name":"Okamoto","first_name":"Takashi","full_name":"Okamoto, Takashi"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"}],"citation":{"ista":"Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.","mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>.","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., &#38; Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>","ieee":"M. Y. Kim <i>et al.</i>, “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.","ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. 2019;116(19):9652-9657. doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>","short":"M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.","chicago":"Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>."},"has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"file":[{"file_name":"2019_PNAS_Kim.pdf","file_size":1142540,"date_updated":"2021-06-04T12:50:47Z","content_type":"application/pdf","access_level":"open_access","date_created":"2021-06-04T12:50:47Z","success":1,"file_id":"9461","relation":"main_file","checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","creator":"asandaue"}],"date_updated":"2021-12-14T07:52:30Z","oa_version":"Published Version","type":"journal_article","scopus_import":"1","file_date_updated":"2021-06-04T12:50:47Z","external_id":{"pmid":["31000601"]},"_id":"9460"},{"title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","date_published":"2019-10-10T00:00:00Z","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2019","publication":"Epigenetics and Chromatin","volume":12,"article_processing_charge":"No","ddc":["570"],"date_created":"2021-06-08T09:21:51Z","external_id":{"pmid":["31601251"]},"file_date_updated":"2021-06-08T09:29:19Z","scopus_import":"1","_id":"9530","oa_version":"Published Version","date_updated":"2021-12-14T07:53:00Z","department":[{"_id":"DaZi"}],"file":[{"file_id":"9531","date_created":"2021-06-08T09:29:19Z","success":1,"access_level":"open_access","date_updated":"2021-06-08T09:29:19Z","content_type":"application/pdf","file_size":3221067,"file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","creator":"asandaue","checksum":"86ff50a7517891511af2733c76c81b67","relation":"main_file"}],"has_accepted_license":"1","citation":{"ista":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62.","mla":"Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” <i>Epigenetics and Chromatin</i>, vol. 12, 62, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1186/s13072-019-0307-4\">10.1186/s13072-019-0307-4</a>.","apa":"Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., &#38; Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. <i>Epigenetics and Chromatin</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13072-019-0307-4\">https://doi.org/10.1186/s13072-019-0307-4</a>","ama":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. <i>Epigenetics and Chromatin</i>. 2019;12. doi:<a href=\"https://doi.org/10.1186/s13072-019-0307-4\">10.1186/s13072-019-0307-4</a>","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019).","chicago":"Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” <i>Epigenetics and Chromatin</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1186/s13072-019-0307-4\">https://doi.org/10.1186/s13072-019-0307-4</a>.","ieee":"K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” <i>Epigenetics and Chromatin</i>, vol. 12. Springer Nature, 2019."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"author":[{"last_name":"Harris","first_name":"Keith D.","full_name":"Harris, Keith D."},{"full_name":"Lloyd, James P. B.","first_name":"James P. B.","last_name":"Lloyd"},{"first_name":"Katherine","full_name":"Domb, Katherine","last_name":"Domb"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"},{"last_name":"Zemach","first_name":"Assaf","full_name":"Zemach, Assaf"}],"type":"journal_article","publisher":"Springer Nature","language":[{"iso":"eng"}],"article_number":"62","intvolume":"        12","article_type":"original","abstract":[{"text":"Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems.","lang":"eng"}],"doi":"10.1186/s13072-019-0307-4","pmid":1,"status":"public","publication_identifier":{"eissn":["1756-8935"]},"publication_status":"published","day":"10","extern":"1","month":"10"},{"month":"08","extern":"1","day":"01","publication_status":"published","publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"status":"public","doi":"10.1007/s11856-019-1897-z","abstract":[{"text":"An r-cut of a k-uniform hypergraph H is a partition of the vertex set of H into r parts and the size of the cut is the number of edges which have a vertex in each part. A classical result of Edwards says that every m-edge graph has a 2-cut of size m/2+Ω)(m−−√) and this is best possible. That is, there exist cuts which exceed the expected size of a random cut by some multiple of the standard deviation. We study analogues of this and related results in hypergraphs. First, we observe that similarly to graphs, every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m−−√) larger than the expected size of a random r-cut. Moreover, in the case where k = 3 and r = 2 this bound is best possible and is attained by Steiner triple systems. Surprisingly, for all other cases (that is, if k ≥ 4 or r ≥ 3), we show that every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m5/9) larger than the expected size of a random r-cut. This is a significant difference in behaviour, since the amount by which the size of the largest cut exceeds the expected size of a random cut is now considerably larger than the standard deviation.","lang":"eng"}],"issue":"1","article_type":"original","page":"67-111","intvolume":"       233","language":[{"iso":"eng"}],"arxiv":1,"publisher":"Springer","type":"journal_article","oa":1,"author":[{"full_name":"Conlon, David","first_name":"David","last_name":"Conlon"},{"last_name":"Fox","full_name":"Fox, Jacob","first_name":"Jacob"},{"last_name":"Kwan","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567"},{"full_name":"Sudakov, Benny","first_name":"Benny","last_name":"Sudakov"}],"citation":{"ieee":"D. Conlon, J. Fox, M. A. Kwan, and B. Sudakov, “Hypergraph cuts above the average,” <i>Israel Journal of Mathematics</i>, vol. 233, no. 1. Springer, pp. 67–111, 2019.","chicago":"Conlon, David, Jacob Fox, Matthew Alan Kwan, and Benny Sudakov. “Hypergraph Cuts above the Average.” <i>Israel Journal of Mathematics</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s11856-019-1897-z\">https://doi.org/10.1007/s11856-019-1897-z</a>.","ama":"Conlon D, Fox J, Kwan MA, Sudakov B. Hypergraph cuts above the average. <i>Israel Journal of Mathematics</i>. 2019;233(1):67-111. doi:<a href=\"https://doi.org/10.1007/s11856-019-1897-z\">10.1007/s11856-019-1897-z</a>","short":"D. Conlon, J. Fox, M.A. Kwan, B. Sudakov, Israel Journal of Mathematics 233 (2019) 67–111.","apa":"Conlon, D., Fox, J., Kwan, M. A., &#38; Sudakov, B. (2019). Hypergraph cuts above the average. <i>Israel Journal of Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s11856-019-1897-z\">https://doi.org/10.1007/s11856-019-1897-z</a>","mla":"Conlon, David, et al. “Hypergraph Cuts above the Average.” <i>Israel Journal of Mathematics</i>, vol. 233, no. 1, Springer, 2019, pp. 67–111, doi:<a href=\"https://doi.org/10.1007/s11856-019-1897-z\">10.1007/s11856-019-1897-z</a>.","ista":"Conlon D, Fox J, Kwan MA, Sudakov B. 2019. Hypergraph cuts above the average. Israel Journal of Mathematics. 233(1), 67–111."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Preprint","date_updated":"2023-02-23T14:01:41Z","_id":"9580","scopus_import":"1","external_id":{"arxiv":["1803.08462"]},"date_created":"2021-06-21T13:36:02Z","volume":233,"article_processing_charge":"No","publication":"Israel Journal of Mathematics","year":"2019","main_file_link":[{"url":"https://arxiv.org/abs/1803.08462","open_access":"1"}],"quality_controlled":"1","date_published":"2019-08-01T00:00:00Z","title":"Hypergraph cuts above the average"},{"_id":"9585","scopus_import":"1","external_id":{"arxiv":["1712.05656"]},"type":"journal_article","citation":{"chicago":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2019. <a href=\"https://doi.org/10.1090/tran/7729\">https://doi.org/10.1090/tran/7729</a>.","short":"M.A. Kwan, B. Sudakov, Transactions of the American Mathematical Society 372 (2019) 5571–5594.","ama":"Kwan MA, Sudakov B. Proof of a conjecture on induced subgraphs of Ramsey graphs. <i>Transactions of the American Mathematical Society</i>. 2019;372(8):5571-5594. doi:<a href=\"https://doi.org/10.1090/tran/7729\">10.1090/tran/7729</a>","ieee":"M. A. Kwan and B. Sudakov, “Proof of a conjecture on induced subgraphs of Ramsey graphs,” <i>Transactions of the American Mathematical Society</i>, vol. 372, no. 8. American Mathematical Society, pp. 5571–5594, 2019.","mla":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” <i>Transactions of the American Mathematical Society</i>, vol. 372, no. 8, American Mathematical Society, 2019, pp. 5571–94, doi:<a href=\"https://doi.org/10.1090/tran/7729\">10.1090/tran/7729</a>.","apa":"Kwan, M. A., &#38; Sudakov, B. (2019). Proof of a conjecture on induced subgraphs of Ramsey graphs. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/7729\">https://doi.org/10.1090/tran/7729</a>","ista":"Kwan MA, Sudakov B. 2019. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 372(8), 5571–5594."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"author":[{"last_name":"Kwan","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567"},{"full_name":"Sudakov, Benny","first_name":"Benny","last_name":"Sudakov"}],"oa_version":"Submitted Version","date_updated":"2023-02-23T14:01:50Z","quality_controlled":"1","date_published":"2019-10-15T00:00:00Z","title":"Proof of a conjecture on induced subgraphs of Ramsey graphs","date_created":"2021-06-22T09:31:45Z","publication":"Transactions of the American Mathematical Society","volume":372,"article_processing_charge":"No","year":"2019","main_file_link":[{"url":"https://doi.org/10.1090/tran/7729","open_access":"1"}],"publication_identifier":{"issn":["0002-9947"],"eissn":["1088-6850"]},"status":"public","abstract":[{"lang":"eng","text":"An n-vertex graph is called C-Ramsey if it has no clique or independent set of size C log n. All known constructions of Ramsey graphs involve randomness in an essential way, and there is an ongoing line of research towards showing that in fact all Ramsey graphs must obey certain “richness” properties characteristic of random graphs. More than 25 years ago, Erdős, Faudree and Sós conjectured that in any C-Ramsey graph there are Ω(n^5/2) induced subgraphs, no pair of which have the same numbers of vertices and edges. Improving on earlier results of Alon, Balogh, Kostochka and Samotij, in this paper we prove this conjecture."}],"doi":"10.1090/tran/7729","issue":"8","month":"10","day":"15","extern":"1","publication_status":"published","publisher":"American Mathematical Society","page":"5571-5594","article_type":"original","intvolume":"       372","language":[{"iso":"eng"}],"arxiv":1},{"publisher":"Wiley","arxiv":1,"language":[{"iso":"eng"}],"intvolume":"        99","page":"757-777","article_type":"original","issue":"3","doi":"10.1112/jlms.12192","abstract":[{"lang":"eng","text":"Consider integers  𝑘,ℓ  such that  0⩽ℓ⩽(𝑘2) . Given a large graph  𝐺 , what is the fraction of  𝑘 -vertex subsets of  𝐺  which span exactly  ℓ  edges? When  𝐺  is empty or complete, and  ℓ  is zero or  (𝑘2) , this fraction can be exactly 1. On the other hand, if  ℓ  is far from these extreme values, one might expect that this fraction is substantially smaller than 1. This was recently proved by Alon, Hefetz, Krivelevich, and Tyomkyn who initiated the systematic study of this question and proposed several natural conjectures.\r\nLet  ℓ∗=min{ℓ,(𝑘2)−ℓ} . Our main result is that for any  𝑘  and  ℓ , the fraction of  𝑘 -vertex subsets that span  ℓ  edges is at most  log𝑂(1)(ℓ∗/𝑘)√ 𝑘/ℓ∗, which is best-possible up to the logarithmic factor. This improves on multiple results of Alon, Hefetz, Krivelevich, and Tyomkyn, and resolves one of their conjectures. In addition, we also make some first steps towards some analogous questions for hypergraphs.\r\nOur proofs involve some Ramsey-type arguments, and a number of different probabilistic tools, such as polynomial anticoncentration inequalities, hypercontractivity, and a coupling trick for random variables defined on a ‘slice’ of the Boolean hypercube."}],"status":"public","publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"publication_status":"published","day":"03","extern":"1","month":"05","title":"Anticoncentration for subgraph statistics","date_published":"2019-05-03T00:00:00Z","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1807.05202","open_access":"1"}],"year":"2019","publication":"Journal of the London Mathematical Society","volume":99,"article_processing_charge":"No","date_created":"2021-06-22T09:46:03Z","external_id":{"arxiv":["1807.05202"]},"scopus_import":"1","_id":"9586","oa_version":"Preprint","date_updated":"2023-02-23T14:01:53Z","citation":{"chicago":"Kwan, Matthew Alan, Benny Sudakov, and Tuan Tran. “Anticoncentration for Subgraph Statistics.” <i>Journal of the London Mathematical Society</i>. Wiley, 2019. <a href=\"https://doi.org/10.1112/jlms.12192\">https://doi.org/10.1112/jlms.12192</a>.","ama":"Kwan MA, Sudakov B, Tran T. Anticoncentration for subgraph statistics. <i>Journal of the London Mathematical Society</i>. 2019;99(3):757-777. doi:<a href=\"https://doi.org/10.1112/jlms.12192\">10.1112/jlms.12192</a>","short":"M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society 99 (2019) 757–777.","ieee":"M. A. Kwan, B. Sudakov, and T. Tran, “Anticoncentration for subgraph statistics,” <i>Journal of the London Mathematical Society</i>, vol. 99, no. 3. Wiley, pp. 757–777, 2019.","apa":"Kwan, M. A., Sudakov, B., &#38; Tran, T. (2019). Anticoncentration for subgraph statistics. <i>Journal of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/jlms.12192\">https://doi.org/10.1112/jlms.12192</a>","mla":"Kwan, Matthew Alan, et al. “Anticoncentration for Subgraph Statistics.” <i>Journal of the London Mathematical Society</i>, vol. 99, no. 3, Wiley, 2019, pp. 757–77, doi:<a href=\"https://doi.org/10.1112/jlms.12192\">10.1112/jlms.12192</a>.","ista":"Kwan MA, Sudakov B, Tran T. 2019. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 99(3), 757–777."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"author":[{"last_name":"Kwan","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sudakov","full_name":"Sudakov, Benny","first_name":"Benny"},{"last_name":"Tran","first_name":"Tuan","full_name":"Tran, Tuan"}],"type":"journal_article"},{"language":[{"iso":"eng"}],"arxiv":1,"intvolume":"       236","page":"214-223","article_type":"original","publisher":"Elsevier","publication_status":"published","day":"01","extern":"1","month":"03","doi":"10.1016/j.cpc.2018.09.020","abstract":[{"lang":"eng","text":"Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born–Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code (Ceriotti et al., 2014) was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives."}],"status":"public","publication_identifier":{"issn":["0010-4655"]},"year":"2019","main_file_link":[{"url":"https://arxiv.org/abs/1808.03824","open_access":"1"}],"publication":"Computer Physics Communications","volume":236,"article_processing_charge":"No","date_created":"2021-07-16T08:53:01Z","title":"i-PI 2.0: A universal force engine for advanced molecular simulations","date_published":"2019-03-01T00:00:00Z","quality_controlled":"1","date_updated":"2021-08-09T12:37:16Z","oa_version":"Preprint","citation":{"ieee":"V. Kapil <i>et al.</i>, “i-PI 2.0: A universal force engine for advanced molecular simulations,” <i>Computer Physics Communications</i>, vol. 236. Elsevier, pp. 214–223, 2019.","ama":"Kapil V, Rossi M, Marsalek O, et al. i-PI 2.0: A universal force engine for advanced molecular simulations. <i>Computer Physics Communications</i>. 2019;236:214-223. doi:<a href=\"https://doi.org/10.1016/j.cpc.2018.09.020\">10.1016/j.cpc.2018.09.020</a>","short":"V. Kapil, M. Rossi, O. Marsalek, R. Petraglia, Y. Litman, T. Spura, B. Cheng, A. Cuzzocrea, R.H. Meißner, D.M. Wilkins, B.A. Helfrecht, P. Juda, S.P. Bienvenue, W. Fang, J. Kessler, I. Poltavsky, S. Vandenbrande, J. Wieme, C. Corminboeuf, T.D. Kühne, D.E. Manolopoulos, T.E. Markland, J.O. Richardson, A. Tkatchenko, G.A. Tribello, V. Van Speybroeck, M. Ceriotti, Computer Physics Communications 236 (2019) 214–223.","chicago":"Kapil, Venkat, Mariana Rossi, Ondrej Marsalek, Riccardo Petraglia, Yair Litman, Thomas Spura, Bingqing Cheng, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations.” <i>Computer Physics Communications</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cpc.2018.09.020\">https://doi.org/10.1016/j.cpc.2018.09.020</a>.","ista":"Kapil V, Rossi M, Marsalek O, Petraglia R, Litman Y, Spura T, Cheng B, Cuzzocrea A, Meißner RH, Wilkins DM, Helfrecht BA, Juda P, Bienvenue SP, Fang W, Kessler J, Poltavsky I, Vandenbrande S, Wieme J, Corminboeuf C, Kühne TD, Manolopoulos DE, Markland TE, Richardson JO, Tkatchenko A, Tribello GA, Van Speybroeck V, Ceriotti M. 2019. i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. 236, 214–223.","apa":"Kapil, V., Rossi, M., Marsalek, O., Petraglia, R., Litman, Y., Spura, T., … Ceriotti, M. (2019). i-PI 2.0: A universal force engine for advanced molecular simulations. <i>Computer Physics Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cpc.2018.09.020\">https://doi.org/10.1016/j.cpc.2018.09.020</a>","mla":"Kapil, Venkat, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations.” <i>Computer Physics Communications</i>, vol. 236, Elsevier, 2019, pp. 214–23, doi:<a href=\"https://doi.org/10.1016/j.cpc.2018.09.020\">10.1016/j.cpc.2018.09.020</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Venkat","full_name":"Kapil, Venkat","last_name":"Kapil"},{"full_name":"Rossi, Mariana","first_name":"Mariana","last_name":"Rossi"},{"full_name":"Marsalek, Ondrej","first_name":"Ondrej","last_name":"Marsalek"},{"full_name":"Petraglia, Riccardo","first_name":"Riccardo","last_name":"Petraglia"},{"last_name":"Litman","first_name":"Yair","full_name":"Litman, Yair"},{"full_name":"Spura, Thomas","first_name":"Thomas","last_name":"Spura"},{"orcid":"0000-0002-3584-9632","first_name":"Bingqing","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng"},{"full_name":"Cuzzocrea, Alice","first_name":"Alice","last_name":"Cuzzocrea"},{"first_name":"Robert H.","full_name":"Meißner, Robert H.","last_name":"Meißner"},{"last_name":"Wilkins","full_name":"Wilkins, David M.","first_name":"David M."},{"last_name":"Helfrecht","first_name":"Benjamin A.","full_name":"Helfrecht, Benjamin A."},{"first_name":"Przemysław","full_name":"Juda, Przemysław","last_name":"Juda"},{"last_name":"Bienvenue","full_name":"Bienvenue, Sébastien P.","first_name":"Sébastien P."},{"full_name":"Fang, Wei","first_name":"Wei","last_name":"Fang"},{"first_name":"Jan","full_name":"Kessler, Jan","last_name":"Kessler"},{"full_name":"Poltavsky, Igor","first_name":"Igor","last_name":"Poltavsky"},{"last_name":"Vandenbrande","first_name":"Steven","full_name":"Vandenbrande, Steven"},{"full_name":"Wieme, Jelle","first_name":"Jelle","last_name":"Wieme"},{"full_name":"Corminboeuf, Clemence","first_name":"Clemence","last_name":"Corminboeuf"},{"first_name":"Thomas D.","full_name":"Kühne, Thomas D.","last_name":"Kühne"},{"last_name":"Manolopoulos","full_name":"Manolopoulos, David E.","first_name":"David E."},{"first_name":"Thomas E.","full_name":"Markland, Thomas E.","last_name":"Markland"},{"full_name":"Richardson, Jeremy O.","first_name":"Jeremy O.","last_name":"Richardson"},{"last_name":"Tkatchenko","first_name":"Alexandre","full_name":"Tkatchenko, Alexandre"},{"full_name":"Tribello, Gareth A.","first_name":"Gareth A.","last_name":"Tribello"},{"full_name":"Van Speybroeck, Veronique","first_name":"Veronique","last_name":"Van Speybroeck"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"oa":1,"type":"journal_article","external_id":{"arxiv":["1808.03824"]},"scopus_import":"1","_id":"9677"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1911.01140"}],"year":"2019","article_processing_charge":"No","volume":16,"publication":"Journal of Chemical Theory and Computation","date_created":"2021-07-19T06:56:45Z","title":"Iterative unbiasing of quasi-equilibrium sampling","date_published":"2019-01-14T00:00:00Z","quality_controlled":"1","oa_version":"Preprint","date_updated":"2021-08-09T12:37:37Z","oa":1,"author":[{"first_name":"F.","full_name":"Giberti, F.","last_name":"Giberti"},{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng"},{"first_name":"G. A.","full_name":"Tribello, G. A.","last_name":"Tribello"},{"last_name":"Ceriotti","first_name":"M.","full_name":"Ceriotti, M."}],"citation":{"ista":"Giberti F, Cheng B, Tribello GA, Ceriotti M. 2019. Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 16(1), 100–107.","mla":"Giberti, F., et al. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” <i>Journal of Chemical Theory and Computation</i>, vol. 16, no. 1, American Chemical Society, 2019, pp. 100–07, doi:<a href=\"https://doi.org/10.1021/acs.jctc.9b00907\">10.1021/acs.jctc.9b00907</a>.","apa":"Giberti, F., Cheng, B., Tribello, G. A., &#38; Ceriotti, M. (2019). Iterative unbiasing of quasi-equilibrium sampling. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.9b00907\">https://doi.org/10.1021/acs.jctc.9b00907</a>","ama":"Giberti F, Cheng B, Tribello GA, Ceriotti M. Iterative unbiasing of quasi-equilibrium sampling. <i>Journal of Chemical Theory and Computation</i>. 2019;16(1):100-107. doi:<a href=\"https://doi.org/10.1021/acs.jctc.9b00907\">10.1021/acs.jctc.9b00907</a>","short":"F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory and Computation 16 (2019) 100–107.","chicago":"Giberti, F., Bingqing Cheng, G. A. Tribello, and M. Ceriotti. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/acs.jctc.9b00907\">https://doi.org/10.1021/acs.jctc.9b00907</a>.","ieee":"F. Giberti, B. Cheng, G. A. Tribello, and M. Ceriotti, “Iterative unbiasing of quasi-equilibrium sampling,” <i>Journal of Chemical Theory and Computation</i>, vol. 16, no. 1. American Chemical Society, pp. 100–107, 2019."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"journal_article","external_id":{"pmid":["31743021"],"arxiv":["1911.01140"]},"scopus_import":"1","_id":"9680","language":[{"iso":"eng"}],"arxiv":1,"intvolume":"        16","page":"100-107","article_type":"original","publisher":"American Chemical Society","publication_status":"published","extern":"1","day":"14","month":"01","issue":"1","doi":"10.1021/acs.jctc.9b00907","abstract":[{"lang":"eng","text":"Atomistic modeling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an appropriately chosen set of collective variables can significantly accelerate the exploration of phase space, albeit at the price of distorting the distribution of microstates. Efficient reweighting to recover the unbiased distribution can be nontrivial when employing adaptive sampling techniques such as metadynamics, variationally enhanced sampling, or parallel bias metadynamics, in which the system evolves in a quasi-equilibrium manner under a time-dependent bias. We introduce an iterative unbiasing scheme that makes efficient use of all the trajectory data and that does not require the distribution to be evaluated on a grid. The method can thus be used even when the bias has a high dimensionality. We benchmark this approach against some of the existing schemes on model systems with different complexity and dimensionality."}],"status":"public","pmid":1,"publication_identifier":{"issn":["1549-9618"],"eissn":["1549-9626"]}},{"date_created":"2021-07-19T10:17:09Z","article_processing_charge":"No","volume":116,"publication":"Proceedings of the National Academy of Sciences","year":"2019","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1815117116","open_access":"1"}],"quality_controlled":"1","title":"Ab initio thermodynamics of liquid and solid water","date_published":"2019-01-22T00:00:00Z","type":"journal_article","oa":1,"author":[{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing","last_name":"Cheng"},{"full_name":"Engel, Edgar A.","first_name":"Edgar A.","last_name":"Engel"},{"last_name":"Behler","full_name":"Behler, Jörg","first_name":"Jörg"},{"last_name":"Dellago","full_name":"Dellago, Christoph","first_name":"Christoph"},{"first_name":"Michele","full_name":"Ceriotti, Michele","last_name":"Ceriotti"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4), 1110–1115.","mla":"Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1110–15, doi:<a href=\"https://doi.org/10.1073/pnas.1815117116\">10.1073/pnas.1815117116</a>.","apa":"Cheng, B., Engel, E. A., Behler, J., Dellago, C., &#38; Ceriotti, M. (2019). Ab initio thermodynamics of liquid and solid water. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1815117116\">https://doi.org/10.1073/pnas.1815117116</a>","ieee":"B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio thermodynamics of liquid and solid water,” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115, 2019.","short":"B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of the National Academy of Sciences 116 (2019) 1110–1115.","ama":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics of liquid and solid water. <i>Proceedings of the National Academy of Sciences</i>. 2019;116(4):1110-1115. doi:<a href=\"https://doi.org/10.1073/pnas.1815117116\">10.1073/pnas.1815117116</a>","chicago":"Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1815117116\">https://doi.org/10.1073/pnas.1815117116</a>."},"date_updated":"2023-02-23T14:05:08Z","oa_version":"Published Version","_id":"9689","scopus_import":"1","external_id":{"pmid":["30610171"],"arxiv":["1811.08630"]},"page":"1110-1115","article_type":"original","intvolume":"       116","language":[{"iso":"eng"}],"arxiv":1,"publisher":"National Academy of Sciences","month":"01","extern":"1","day":"22","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"pmid":1,"status":"public","doi":"10.1073/pnas.1815117116","abstract":[{"lang":"eng","text":"A central goal of computational physics and chemistry is to predict material properties by using first-principles methods based on the fundamental laws of quantum mechanics. However, the high computational costs of these methods typically prevent rigorous predictions of macroscopic quantities at finite temperatures, such as heat capacity, density, and chemical potential. Here, we enable such predictions by marrying advanced free-energy methods with data-driven machine-learning interatomic potentials. We show that, for the ubiquitous and technologically essential system of water, a first-principles thermodynamic description not only leads to excellent agreement with experiments, but also reveals the crucial role of nuclear quantum fluctuations in modulating the thermodynamic stabilities of different phases of water."}],"issue":"4"},{"arxiv":1,"language":[{"iso":"eng"}],"article_number":"1910.05841","abstract":[{"lang":"eng","text":"We study double quantum dots in a Ge/SiGe heterostructure and test their maturity towards singlet-triplet ($S-T_0$) qubits. We demonstrate a large range of tunability, from two single quantum dots to a double quantum dot. We measure Pauli spin blockade and study the anisotropy of the $g$-factor. We use an adjacent quantum dot for sensing charge transitions in the double quantum dot at interest. In conclusion, Ge/SiGe possesses all ingredients necessary for building a singlet-triplet qubit."}],"doi":"10.48550/arXiv.1910.05841","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"status":"public","ec_funded":1,"day":"13","publication_status":"submitted","acknowledgement":"We thank Matthias Brauns for helpful discussions and careful proofreading of the manuscript. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 844511 and from the FWF project P30207. The research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA machine shop and the nanofabrication\r\nfacility.","related_material":{"record":[{"relation":"dissertation_contains","id":"10058","status":"public"}]},"month":"10","title":"Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits","date_published":"2019-10-13T00:00:00Z","project":[{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Majorana bound states in Ge/SiGe heterostructures","grant_number":"844511"},{"_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","grant_number":"P30207"}],"article_processing_charge":"No","publication":"arXiv","main_file_link":[{"url":"https://arxiv.org/abs/1910.05841","open_access":"1"}],"year":"2019","date_created":"2021-10-01T12:14:51Z","external_id":{"arxiv":["1910.05841"]},"_id":"10065","oa":1,"author":[{"last_name":"Hofmann","first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C"},{"last_name":"Jirovec","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Jirovec, Daniel"},{"last_name":"Borovkov","first_name":"Maxim","full_name":"Borovkov, Maxim"},{"orcid":"0000-0002-7370-5357","first_name":"Ivan","full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez"},{"full_name":"Ballabio, Andrea","first_name":"Andrea","last_name":"Ballabio"},{"first_name":"Jacopo","full_name":"Frigerio, Jacopo","last_name":"Frigerio"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"full_name":"Isella, Giovanni","first_name":"Giovanni","last_name":"Isella"},{"first_name":"Georgios","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. C. Hofmann <i>et al.</i>, “Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits,” <i>arXiv</i>. .","ama":"Hofmann AC, Jirovec D, Borovkov M, et al. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1910.05841\">10.48550/arXiv.1910.05841</a>","short":"A.C. Hofmann, D. Jirovec, M. Borovkov, I. Prieto Gonzalez, A. Ballabio, J. Frigerio, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","chicago":"Hofmann, Andrea C, Daniel Jirovec, Maxim Borovkov, Ivan Prieto Gonzalez, Andrea Ballabio, Jacopo Frigerio, Daniel Chrastina, Giovanni Isella, and Georgios Katsaros. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1910.05841\">https://doi.org/10.48550/arXiv.1910.05841</a>.","ista":"Hofmann AC, Jirovec D, Borovkov M, Prieto Gonzalez I, Ballabio A, Frigerio J, Chrastina D, Isella G, Katsaros G. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv, 1910.05841.","apa":"Hofmann, A. C., Jirovec, D., Borovkov, M., Prieto Gonzalez, I., Ballabio, A., Frigerio, J., … Katsaros, G. (n.d.). Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1910.05841\">https://doi.org/10.48550/arXiv.1910.05841</a>","mla":"Hofmann, Andrea C., et al. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” <i>ArXiv</i>, 1910.05841, doi:<a href=\"https://doi.org/10.48550/arXiv.1910.05841\">10.48550/arXiv.1910.05841</a>."},"department":[{"_id":"GeKa"}],"oa_version":"Preprint","date_updated":"2024-03-25T23:30:14Z","type":"preprint"},{"project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"date_published":"2019-10-10T00:00:00Z","title":"Value-centric dynamic partial order reduction","keyword":["safety","risk","reliability and quality","software"],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"end_date":"2019-10-25","start_date":"2019-10-23","location":"Athens, Greece","name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications"},"year":"2019","main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3360550","open_access":"1"}],"publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications","volume":3,"article_processing_charge":"No","ddc":["000"],"date_created":"2021-10-27T14:57:06Z","external_id":{"arxiv":["1909.00989"]},"file_date_updated":"2021-11-12T11:41:56Z","_id":"10190","oa_version":"Published Version","date_updated":"2025-07-14T09:10:15Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"file":[{"relation":"main_file","checksum":"2149979c46964c4d117af06ccb6c0834","creator":"cchlebak","file_name":"2019_ACM_Chatterjee.pdf","file_size":570829,"content_type":"application/pdf","date_updated":"2021-11-12T11:41:56Z","access_level":"open_access","success":1,"date_created":"2021-11-12T11:41:56Z","file_id":"10278"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","citation":{"ama":"Chatterjee K, Pavlogiannis A, Toman V. Value-centric dynamic partial order reduction. In: <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>. Vol 3. ACM; 2019. doi:<a href=\"https://doi.org/10.1145/3360550\">10.1145/3360550</a>","short":"K. Chatterjee, A. Pavlogiannis, V. Toman, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, ACM, 2019.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Viktor Toman. “Value-Centric Dynamic Partial Order Reduction.” In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, Vol. 3. ACM, 2019. <a href=\"https://doi.org/10.1145/3360550\">https://doi.org/10.1145/3360550</a>.","ieee":"K. Chatterjee, A. Pavlogiannis, and V. Toman, “Value-centric dynamic partial order reduction,” in <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, Athens, Greece, 2019, vol. 3.","ista":"Chatterjee K, Pavlogiannis A, Toman V. 2019. Value-centric dynamic partial order reduction. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 124.","mla":"Chatterjee, Krishnendu, et al. “Value-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, vol. 3, 124, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3360550\">10.1145/3360550</a>.","apa":"Chatterjee, K., Pavlogiannis, A., &#38; Toman, V. (2019). Value-centric dynamic partial order reduction. In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i> (Vol. 3). Athens, Greece: ACM. <a href=\"https://doi.org/10.1145/3360550\">https://doi.org/10.1145/3360550</a>"},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","orcid":"0000-0002-8943-0722"},{"first_name":"Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X","last_name":"Toman"}],"oa":1,"type":"conference","publisher":"ACM","arxiv":1,"language":[{"iso":"eng"}],"article_number":"124","intvolume":"         3","abstract":[{"lang":"eng","text":"The verification of concurrent programs remains an open challenge, as thread interaction has to be accounted for, which leads to state-space explosion. Stateless model checking battles this problem by exploring traces rather than states of the program. As there are exponentially many traces, dynamic partial-order reduction (DPOR) techniques are used to partition the trace space into equivalence classes, and explore a few representatives from each class. The standard equivalence that underlies most DPOR techniques is the happens-before equivalence, however recent works have spawned a vivid interest towards coarser equivalences. The efficiency of such approaches is a product of two parameters: (i) the size of the partitioning induced by the equivalence, and (ii) the time spent by the exploration algorithm in each class of the partitioning. In this work, we present a new equivalence, called value-happens-before and show that it has two appealing features. First, value-happens-before is always at least as coarse as the happens-before equivalence, and can be even exponentially coarser. Second, the value-happens-before partitioning is efficiently explorable when the number of threads is bounded. We present an algorithm called value-centric DPOR (VCDPOR), which explores the underlying partitioning using polynomial time per class. Finally, we perform an experimental evaluation of VCDPOR on various benchmarks, and compare it against other state-of-the-art approaches. Our results show that value-happens-before typically induces a significant reduction in the size of the underlying partitioning, which leads to a considerable reduction in the running time for exploring the whole partitioning."}],"doi":"10.1145/3360550","status":"public","publication_identifier":{"eissn":["2475-1421"]},"acknowledgement":"The authors would also like to thank anonymous referees for their valuable comments and helpful suggestions. This work is supported by the Austrian Science Fund (FWF) NFN grants S11407-N23 (RiSE/SHiNE) and S11402-N23 (RiSE/SHiNE), by the Vienna Science and Technology Fund (WWTF) Project ICT15-003, and by the Austrian Science Fund (FWF) Schrodinger grant J-4220.\r\n","publication_status":"published","day":"10","related_material":{"record":[{"id":"10199","relation":"dissertation_contains","status":"public"}]},"month":"10"},{"publication_identifier":{"issn":["1741-7007"]},"pmid":1,"status":"public","doi":"10.1186/s12915-019-0700-2","abstract":[{"lang":"eng","text":"Background\r\nESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filaments do not consume energy themselves, but work in conjunction with another ATP-consuming complex. Despite rapid progress in describing the cell biology of ESCRT-III, we lack an understanding of the physical mechanisms behind its force production and membrane remodelling.\r\nResults\r\nHere we present a minimal coarse-grained model that captures all the experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of downward and upward cones and tubules. This model suggests that a change in the geometry of membrane bound ESCRT-III filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then show that such repetitive filament geometry transitions can induce the fission of cargo-containing vesicles.\r\nConclusions\r\nOur model provides a general physical mechanism that explains the full range of ESCRT-III-dependent membrane remodelling and scission events observed in cells. This mechanism for filament force production is distinct from the mechanisms described for other cytoskeletal elements discovered so far. The mechanistic principles revealed here suggest new ways of manipulating ESCRT-III-driven processes in cells and could be used to guide the engineering of synthetic membrane-sculpting systems."}],"issue":"1","month":"10","extern":"1","day":"22","publication_status":"published","acknowledgement":"We thank Jeremy Carlton, Mike Staddon, Geraint Harker, and the Wellcome Trust Consortium “Archaeal Origins of Eukaryotic Cell Organisation” for fruitful conversations. We thank Peter Wirnsberger and Tine Curk for discussions about the membrane model implementation.","publisher":"Springer Nature","article_type":"original","intvolume":"        17","article_number":"82","language":[{"iso":"eng"}],"_id":"10354","scopus_import":"1","file_date_updated":"2021-11-26T11:37:54Z","external_id":{"pmid":["31640700"]},"type":"journal_article","oa":1,"author":[{"last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena","first_name":"Lena"},{"first_name":"Buzz","full_name":"Baum, Buzz","last_name":"Baum"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","citation":{"ama":"Harker-Kirschneck L, Baum B, Šarić A. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. <i>BMC Biology</i>. 2019;17(1). doi:<a href=\"https://doi.org/10.1186/s12915-019-0700-2\">10.1186/s12915-019-0700-2</a>","short":"L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019).","chicago":"Harker-Kirschneck, Lena, Buzz Baum, and Anđela Šarić. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” <i>BMC Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1186/s12915-019-0700-2\">https://doi.org/10.1186/s12915-019-0700-2</a>.","ieee":"L. Harker-Kirschneck, B. Baum, and A. Šarić, “Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico,” <i>BMC Biology</i>, vol. 17, no. 1. Springer Nature, 2019.","ista":"Harker-Kirschneck L, Baum B, Šarić A. 2019. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 17(1), 82.","mla":"Harker-Kirschneck, Lena, et al. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” <i>BMC Biology</i>, vol. 17, no. 1, 82, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1186/s12915-019-0700-2\">10.1186/s12915-019-0700-2</a>.","apa":"Harker-Kirschneck, L., Baum, B., &#38; Šarić, A. (2019). Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. <i>BMC Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12915-019-0700-2\">https://doi.org/10.1186/s12915-019-0700-2</a>"},"file":[{"relation":"main_file","checksum":"31d8bae55a376d30925f53f7e1a02396","creator":"cchlebak","access_level":"open_access","date_created":"2021-11-26T11:37:54Z","success":1,"file_id":"10356","file_name":"2019_BMCBio_Harker_Kirschneck.pdf","file_size":1648926,"date_updated":"2021-11-26T11:37:54Z","content_type":"application/pdf"}],"oa_version":"Published Version","date_updated":"2021-11-26T11:54:29Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","keyword":["cell biology"],"title":"Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico","date_published":"2019-10-22T00:00:00Z","date_created":"2021-11-26T11:25:03Z","ddc":["570"],"volume":17,"article_processing_charge":"No","publication":"BMC Biology","year":"2019","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/559898","open_access":"1"}]},{"volume":58,"article_processing_charge":"No","publication":"Current Opinion in Structural Biology","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.09349"}],"year":"2019","date_created":"2021-11-26T11:33:21Z","quality_controlled":"1","title":"Minimal coarse-grained models for molecular self-organisation in biology","keyword":["molecular biology","structural biology"],"date_published":"2019-06-18T00:00:00Z","author":[{"full_name":"Hafner, Anne E","first_name":"Anne E","last_name":"Hafner"},{"full_name":"Krausser, Johannes","first_name":"Johannes","last_name":"Krausser"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Hafner, A. E., Krausser, J., &#38; Šarić, A. (2019). Minimal coarse-grained models for molecular self-organisation in biology. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2019.05.018\">https://doi.org/10.1016/j.sbi.2019.05.018</a>","mla":"Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” <i>Current Opinion in Structural Biology</i>, vol. 58, Elsevier, 2019, pp. 43–52, doi:<a href=\"https://doi.org/10.1016/j.sbi.2019.05.018\">10.1016/j.sbi.2019.05.018</a>.","ista":"Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52.","chicago":"Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.sbi.2019.05.018\">https://doi.org/10.1016/j.sbi.2019.05.018</a>.","short":"A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology 58 (2019) 43–52.","ama":"Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. <i>Current Opinion in Structural Biology</i>. 2019;58:43-52. doi:<a href=\"https://doi.org/10.1016/j.sbi.2019.05.018\">10.1016/j.sbi.2019.05.018</a>","ieee":"A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for molecular self-organisation in biology,” <i>Current Opinion in Structural Biology</i>, vol. 58. Elsevier, pp. 43–52, 2019."},"date_updated":"2021-11-26T11:54:25Z","oa_version":"Preprint","type":"journal_article","scopus_import":"1","external_id":{"pmid":["31226513"]},"_id":"10355","language":[{"iso":"eng"}],"article_type":"original","page":"43-52","intvolume":"        58","publisher":"Elsevier","extern":"1","day":"18","publication_status":"published","acknowledgement":"We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations.","month":"06","doi":"10.1016/j.sbi.2019.05.018","abstract":[{"lang":"eng","text":"The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments."}],"publication_identifier":{"issn":["0959-440X"]},"pmid":1,"status":"public"}]