--- _id: '9526' abstract: - lang: eng text: DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. In plants and animals with mosaic genomic methylation, functionally mysterious methylation is also common within constitutively active housekeeping genes. Here, we show that H1 is enriched in methylated sequences, including genes, of Arabidopsis thaliana, yet this enrichment is independent of DNA methylation. Loss of H1 disperses heterochromatin, globally alters nucleosome organization, and activates H1-bound genes, but only weakly de-represses transposable elements. However, H1 loss strongly activates transposable elements hypomethylated through mutation of DNA methyltransferase MET1. Hypomethylation of genes also activates antisense transcription, which is modestly enhanced by H1 loss. Our results demonstrate that H1 and DNA methylation jointly maintain transcriptional homeostasis by silencing transposable elements and aberrant intragenic transcripts. Such functionality plausibly explains why DNA methylation, a well-known mutagen, has been maintained within coding sequences of crucial plant and animal genes. article_processing_charge: No article_type: original author: - first_name: Jaemyung full_name: Choi, Jaemyung last_name: Choi - first_name: David B. full_name: Lyons, David B. last_name: Lyons - first_name: M. Yvonne full_name: Kim, M. Yvonne last_name: Kim - first_name: Jonathan D. full_name: Moore, Jonathan D. last_name: Moore - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts. Molecular Cell. 2020;77(2):310-323.e7. doi:10.1016/j.molcel.2019.10.011 apa: Choi, J., Lyons, D. B., Kim, M. Y., Moore, J. D., & Zilberman, D. (2020). DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2019.10.011 chicago: Choi, Jaemyung, David B. Lyons, M. Yvonne Kim, Jonathan D. Moore, and Daniel Zilberman. “DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.” Molecular Cell. Elsevier, 2020. https://doi.org/10.1016/j.molcel.2019.10.011. ieee: J. Choi, D. B. Lyons, M. Y. Kim, J. D. Moore, and D. Zilberman, “DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts,” Molecular Cell, vol. 77, no. 2. Elsevier, p. 310–323.e7, 2020. ista: Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. 2020. DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts. Molecular Cell. 77(2), 310–323.e7. mla: Choi, Jaemyung, et al. “DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.” Molecular Cell, vol. 77, no. 2, Elsevier, 2020, p. 310–323.e7, doi:10.1016/j.molcel.2019.10.011. short: J. Choi, D.B. Lyons, M.Y. Kim, J.D. Moore, D. Zilberman, Molecular Cell 77 (2020) 310–323.e7. date_created: 2021-06-08T06:37:09Z date_published: 2020-01-16T00:00:00Z date_updated: 2021-12-14T07:51:15Z day: '16' department: - _id: DaZi doi: 10.1016/j.molcel.2019.10.011 extern: '1' external_id: pmid: - '31732458' intvolume: ' 77' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.molcel.2019.10.011 month: '01' oa: 1 oa_version: Published Version page: 310-323.e7 pmid: 1 publication: Molecular Cell publication_identifier: eissn: - 1097-4164 issn: - 1097-2765 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 77 year: '2020' ... --- _id: '9630' abstract: - lang: eng text: Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory needed for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context. acknowledgement: This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF). article_processing_charge: Yes article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ziga full_name: Virk, Ziga id: 2E36B656-F248-11E8-B48F-1D18A9856A87 last_name: Virk - first_name: Hubert full_name: Wagner, Hubert id: 379CA8B8-F248-11E8-B48F-1D18A9856A87 last_name: Wagner citation: ama: Edelsbrunner H, Virk Z, Wagner H. Topological data analysis in information space. Journal of Computational Geometry. 2020;11(2):162-182. doi:10.20382/jocg.v11i2a7 apa: Edelsbrunner, H., Virk, Z., & Wagner, H. (2020). Topological data analysis in information space. Journal of Computational Geometry. Carleton University. https://doi.org/10.20382/jocg.v11i2a7 chicago: Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Topological Data Analysis in Information Space.” Journal of Computational Geometry. Carleton University, 2020. https://doi.org/10.20382/jocg.v11i2a7. ieee: H. Edelsbrunner, Z. Virk, and H. Wagner, “Topological data analysis in information space,” Journal of Computational Geometry, vol. 11, no. 2. Carleton University, pp. 162–182, 2020. ista: Edelsbrunner H, Virk Z, Wagner H. 2020. Topological data analysis in information space. Journal of Computational Geometry. 11(2), 162–182. mla: Edelsbrunner, Herbert, et al. “Topological Data Analysis in Information Space.” Journal of Computational Geometry, vol. 11, no. 2, Carleton University, 2020, pp. 162–82, doi:10.20382/jocg.v11i2a7. short: H. Edelsbrunner, Z. Virk, H. Wagner, Journal of Computational Geometry 11 (2020) 162–182. date_created: 2021-07-04T22:01:26Z date_published: 2020-12-14T00:00:00Z date_updated: 2021-08-11T12:26:34Z day: '14' ddc: - '510' - '000' department: - _id: HeEd doi: 10.20382/jocg.v11i2a7 file: - access_level: open_access checksum: f02d0b2b3838e7891a6c417fc34ffdcd content_type: application/pdf creator: asandaue date_created: 2021-08-11T11:55:11Z date_updated: 2021-08-11T11:55:11Z file_id: '9882' file_name: 2020_JournalOfComputationalGeometry_Edelsbrunner.pdf file_size: 1449234 relation: main_file success: 1 file_date_updated: 2021-08-11T11:55:11Z has_accepted_license: '1' intvolume: ' 11' issue: '2' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '12' oa: 1 oa_version: Published Version page: 162-182 project: - _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316 grant_number: I4887 name: Discretization in Geometry and Dynamics publication: Journal of Computational Geometry publication_identifier: eissn: - 1920180X publication_status: published publisher: Carleton University quality_controlled: '1' scopus_import: '1' status: public title: Topological data analysis in information space tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 11 year: '2020' ... --- _id: '9631' abstract: - lang: eng text: The ability to leverage large-scale hardware parallelism has been one of the key enablers of the accelerated recent progress in machine learning. Consequently, there has been considerable effort invested into developing efficient parallel variants of classic machine learning algorithms. However, despite the wealth of knowledge on parallelization, some classic machine learning algorithms often prove hard to parallelize efficiently while maintaining convergence. In this paper, we focus on efficient parallel algorithms for the key machine learning task of inference on graphical models, in particular on the fundamental belief propagation algorithm. We address the challenge of efficiently parallelizing this classic paradigm by showing how to leverage scalable relaxed schedulers in this context. We present an extensive empirical study, showing that our approach outperforms previous parallel belief propagation implementations both in terms of scalability and in terms of wall-clock convergence time, on a range of practical applications. acknowledgement: "We thank Marco Mondelli for discussions related to LDPC decoding, and Giorgi Nadiradze for discussions on analysis of relaxed schedulers. This project has received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML)." article_processing_charge: No arxiv: 1 author: - first_name: Vitaly full_name: Aksenov, Vitaly last_name: Aksenov - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Janne full_name: Korhonen, Janne id: C5402D42-15BC-11E9-A202-CA2BE6697425 last_name: Korhonen citation: ama: 'Aksenov V, Alistarh D-A, Korhonen J. Scalable belief propagation via relaxed scheduling. In: Advances in Neural Information Processing Systems. Vol 33. Curran Associates; 2020:22361-22372.' apa: 'Aksenov, V., Alistarh, D.-A., & Korhonen, J. (2020). Scalable belief propagation via relaxed scheduling. In Advances in Neural Information Processing Systems (Vol. 33, pp. 22361–22372). Vancouver, Canada: Curran Associates.' chicago: Aksenov, Vitaly, Dan-Adrian Alistarh, and Janne Korhonen. “Scalable Belief Propagation via Relaxed Scheduling.” In Advances in Neural Information Processing Systems, 33:22361–72. Curran Associates, 2020. ieee: V. Aksenov, D.-A. Alistarh, and J. Korhonen, “Scalable belief propagation via relaxed scheduling,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 22361–22372. ista: 'Aksenov V, Alistarh D-A, Korhonen J. 2020. Scalable belief propagation via relaxed scheduling. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 33, 22361–22372.' mla: Aksenov, Vitaly, et al. “Scalable Belief Propagation via Relaxed Scheduling.” Advances in Neural Information Processing Systems, vol. 33, Curran Associates, 2020, pp. 22361–72. short: V. Aksenov, D.-A. Alistarh, J. Korhonen, in:, Advances in Neural Information Processing Systems, Curran Associates, 2020, pp. 22361–22372. conference: end_date: 2020-12-12 location: Vancouver, Canada name: 'NeurIPS: Conference on Neural Information Processing Systems' start_date: 2020-12-06 date_created: 2021-07-04T22:01:26Z date_published: 2020-12-06T00:00:00Z date_updated: 2023-02-23T14:03:03Z day: '06' department: - _id: DaAl ec_funded: 1 external_id: arxiv: - '2002.11505' intvolume: ' 33' language: - iso: eng main_file_link: - open_access: '1' url: https://proceedings.neurips.cc/paper/2020/hash/fdb2c3bab9d0701c4a050a4d8d782c7f-Abstract.html month: '12' oa: 1 oa_version: Published Version page: 22361-22372 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781713829546' issn: - '10495258' publication_status: published publisher: Curran Associates quality_controlled: '1' scopus_import: '1' status: public title: Scalable belief propagation via relaxed scheduling type: conference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 33 year: '2020' ... --- _id: '9632' abstract: - lang: eng text: "Second-order information, in the form of Hessian- or Inverse-Hessian-vector products, is a fundamental tool for solving optimization problems. Recently, there has been significant interest in utilizing this information in the context of deep\r\nneural networks; however, relatively little is known about the quality of existing approximations in this context. Our work examines this question, identifies issues with existing approaches, and proposes a method called WoodFisher to compute a faithful and efficient estimate of the inverse Hessian. Our main application is to neural network compression, where we build on the classic Optimal Brain Damage/Surgeon framework. We demonstrate that WoodFisher significantly outperforms popular state-of-the-art methods for oneshot pruning. Further, even when iterative, gradual pruning is allowed, our method results in a gain in test accuracy over the state-of-the-art approaches, for standard image classification datasets such as ImageNet ILSVRC. We examine how our method can be extended to take into account first-order information, as well as\r\nillustrate its ability to automatically set layer-wise pruning thresholds and perform compression in the limited-data regime. The code is available at the following link, https://github.com/IST-DASLab/WoodFisher." acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). Also, we would like to thank Alexander Shevchenko, Alexandra Peste, and other members of the group for fruitful discussions. article_processing_charge: No arxiv: 1 author: - first_name: Sidak Pal full_name: Singh, Sidak Pal id: DD138E24-D89D-11E9-9DC0-DEF6E5697425 last_name: Singh - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Singh SP, Alistarh D-A. WoodFisher: Efficient second-order approximation for neural network compression. In: Advances in Neural Information Processing Systems. Vol 33. Curran Associates; 2020:18098-18109.' apa: 'Singh, S. P., & Alistarh, D.-A. (2020). WoodFisher: Efficient second-order approximation for neural network compression. In Advances in Neural Information Processing Systems (Vol. 33, pp. 18098–18109). Vancouver, Canada: Curran Associates.' chicago: 'Singh, Sidak Pal, and Dan-Adrian Alistarh. “WoodFisher: Efficient Second-Order Approximation for Neural Network Compression.” In Advances in Neural Information Processing Systems, 33:18098–109. Curran Associates, 2020.' ieee: 'S. P. Singh and D.-A. Alistarh, “WoodFisher: Efficient second-order approximation for neural network compression,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 18098–18109.' ista: 'Singh SP, Alistarh D-A. 2020. WoodFisher: Efficient second-order approximation for neural network compression. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 33, 18098–18109.' mla: 'Singh, Sidak Pal, and Dan-Adrian Alistarh. “WoodFisher: Efficient Second-Order Approximation for Neural Network Compression.” Advances in Neural Information Processing Systems, vol. 33, Curran Associates, 2020, pp. 18098–109.' short: S.P. Singh, D.-A. Alistarh, in:, Advances in Neural Information Processing Systems, Curran Associates, 2020, pp. 18098–18109. conference: end_date: 2020-12-12 location: Vancouver, Canada name: 'NeurIPS: Conference on Neural Information Processing Systems' start_date: 2020-12-06 date_created: 2021-07-04T22:01:26Z date_published: 2020-12-06T00:00:00Z date_updated: 2023-02-23T14:03:06Z day: '06' department: - _id: DaAl - _id: ToHe ec_funded: 1 external_id: arxiv: - '2004.14340' intvolume: ' 33' language: - iso: eng main_file_link: - open_access: '1' url: https://proceedings.neurips.cc/paper/2020/hash/d1ff1ec86b62cd5f3903ff19c3a326b2-Abstract.html month: '12' oa: 1 oa_version: Published Version page: 18098-18109 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781713829546' issn: - '10495258' publication_status: published publisher: Curran Associates quality_controlled: '1' scopus_import: '1' status: public title: 'WoodFisher: Efficient second-order approximation for neural network compression' type: conference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 33 year: '2020' ... --- _id: '9633' abstract: - lang: eng text: The search for biologically faithful synaptic plasticity rules has resulted in a large body of models. They are usually inspired by – and fitted to – experimental data, but they rarely produce neural dynamics that serve complex functions. These failures suggest that current plasticity models are still under-constrained by existing data. Here, we present an alternative approach that uses meta-learning to discover plausible synaptic plasticity rules. Instead of experimental data, the rules are constrained by the functions they implement and the structure they are meant to produce. Briefly, we parameterize synaptic plasticity rules by a Volterra expansion and then use supervised learning methods (gradient descent or evolutionary strategies) to minimize a problem-dependent loss function that quantifies how effectively a candidate plasticity rule transforms an initially random network into one with the desired function. We first validate our approach by re-discovering previously described plasticity rules, starting at the single-neuron level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction of most variability of inputs to a neuron (i.e., the first principal component). We expand the problem to the network level and ask the framework to find Oja’s rule together with an anti-Hebbian rule such that an initially random two-layer firing-rate network will recover several principal components of the input space after learning. Next, we move to networks of integrate-and-fire neurons with plastic inhibitory afferents. We train for rules that achieve a target firing rate by countering tuned excitation. Our algorithm discovers a specific subset of the manifold of rules that can solve this task. Our work is a proof of principle of an automated and unbiased approach to unveil synaptic plasticity rules that obey biological constraints and can solve complex functions. acknowledgement: We would like to thank Chaitanya Chintaluri, Georgia Christodoulou, Bill Podlaski and Merima Šabanovic for useful discussions and comments. This work was supported by a Wellcome Trust ´ Senior Research Fellowship (214316/Z/18/Z), a BBSRC grant (BB/N019512/1), an ERC consolidator Grant (SYNAPSEEK), a Leverhulme Trust Project Grant (RPG-2016-446), and funding from École Polytechnique, Paris. article_processing_charge: No author: - first_name: Basile J full_name: Confavreux, Basile J id: C7610134-B532-11EA-BD9F-F5753DDC885E last_name: Confavreux - first_name: Friedemann full_name: Zenke, Friedemann last_name: Zenke - first_name: Everton J. full_name: Agnes, Everton J. last_name: Agnes - first_name: Timothy full_name: Lillicrap, Timothy last_name: Lillicrap - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: 'Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In: Advances in Neural Information Processing Systems. Vol 33. ; 2020:16398-16408.' apa: Confavreux, B. J., Zenke, F., Agnes, E. J., Lillicrap, T., & Vogels, T. P. (2020). A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In Advances in Neural Information Processing Systems (Vol. 33, pp. 16398–16408). Vancouver, Canada. chicago: Confavreux, Basile J, Friedemann Zenke, Everton J. Agnes, Timothy Lillicrap, and Tim P Vogels. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” In Advances in Neural Information Processing Systems, 33:16398–408, 2020. ieee: B. J. Confavreux, F. Zenke, E. J. Agnes, T. Lillicrap, and T. P. Vogels, “A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 16398–16408. ista: 'Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. 2020. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 33, 16398–16408.' mla: Confavreux, Basile J., et al. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” Advances in Neural Information Processing Systems, vol. 33, 2020, pp. 16398–408. short: B.J. Confavreux, F. Zenke, E.J. Agnes, T. Lillicrap, T.P. Vogels, in:, Advances in Neural Information Processing Systems, 2020, pp. 16398–16408. conference: end_date: 2020-12-12 location: Vancouver, Canada name: 'NeurIPS: Conference on Neural Information Processing Systems' start_date: 2020-12-06 date_created: 2021-07-04T22:01:27Z date_published: 2020-12-06T00:00:00Z date_updated: 2023-10-18T09:20:55Z day: '06' department: - _id: TiVo ec_funded: 1 intvolume: ' 33' language: - iso: eng main_file_link: - open_access: '1' url: https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html month: '12' oa: 1 oa_version: Published Version page: 16398-16408 project: - _id: c084a126-5a5b-11eb-8a69-d75314a70a87 grant_number: 214316/Z/18/Z name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks. - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. publication: Advances in Neural Information Processing Systems publication_identifier: issn: - 1049-5258 publication_status: published quality_controlled: '1' related_material: link: - relation: is_continued_by url: https://doi.org/10.1101/2020.10.24.353409 record: - id: '14422' relation: dissertation_contains status: public scopus_import: '1' status: public title: A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network type: conference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 33 year: '2020' ... --- _id: '10012' abstract: - lang: eng text: We prove that in the absence of topological changes, the notion of BV solutions to planar multiphase mean curvature flow does not allow for a mechanism for (unphysical) non-uniqueness. Our approach is based on the local structure of the energy landscape near a classical evolution by mean curvature. Mean curvature flow being the gradient flow of the surface energy functional, we develop a gradient-flow analogue of the notion of calibrations. Just like the existence of a calibration guarantees that one has reached a global minimum in the energy landscape, the existence of a "gradient flow calibration" ensures that the route of steepest descent in the energy landscape is unique and stable. acknowledgement: Parts of the paper were written during the visit of the authors to the Hausdorff Research Institute for Mathematics (HIM), University of Bonn, in the framework of the trimester program “Evolution of Interfaces”. The support and the hospitality of HIM are gratefully acknowledged. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665385. article_number: '2003.05478' article_processing_charge: No arxiv: 1 author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Sebastian full_name: Hensel, Sebastian id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87 last_name: Hensel orcid: 0000-0001-7252-8072 - first_name: Tim full_name: Laux, Tim last_name: Laux - first_name: Thilo full_name: Simon, Thilo last_name: Simon citation: ama: 'Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv.' apa: 'Fischer, J. L., Hensel, S., Laux, T., & Simon, T. (n.d.). The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv.' chicago: 'Fischer, Julian L, Sebastian Hensel, Tim Laux, and Thilo Simon. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” ArXiv, n.d.' ieee: 'J. L. Fischer, S. Hensel, T. Laux, and T. Simon, “The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions,” arXiv. .' ista: 'Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv, 2003.05478.' mla: 'Fischer, Julian L., et al. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” ArXiv, 2003.05478.' short: J.L. Fischer, S. Hensel, T. Laux, T. Simon, ArXiv (n.d.). date_created: 2021-09-13T12:17:11Z date_published: 2020-03-11T00:00:00Z date_updated: 2023-09-07T13:30:45Z day: '11' department: - _id: JuFi ec_funded: 1 external_id: arxiv: - '2003.05478' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2003.05478 month: '03' oa: 1 oa_version: Preprint project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: arXiv publication_status: submitted related_material: record: - id: '10007' relation: dissertation_contains status: public status: public title: 'The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions' type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '10022' abstract: - lang: eng text: We consider finite-volume approximations of Fokker-Planck equations on bounded convex domains in R^d and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker-Planck equation via the method of Evolutionary Γ-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalising the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality. acknowledgement: This work is supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117) and by the Austrian Science Fund (FWF), grants No F65 and W1245. article_number: '2008.10962' article_processing_charge: No arxiv: 1 author: - first_name: Dominik L full_name: Forkert, Dominik L id: 35C79D68-F248-11E8-B48F-1D18A9856A87 last_name: Forkert - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale citation: ama: Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv. apa: Forkert, D. L., Maas, J., & Portinale, L. (n.d.). Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv. chicago: Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, n.d. ieee: D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” arXiv. . ista: Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv, 2008.10962. mla: Forkert, Dominik L., et al. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, 2008.10962. short: D.L. Forkert, J. Maas, L. Portinale, ArXiv (n.d.). date_created: 2021-09-17T10:57:27Z date_published: 2020-08-25T00:00:00Z date_updated: 2023-09-07T13:31:05Z day: '25' department: - _id: JaMa ec_funded: 1 external_id: arxiv: - '2008.10962' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2008.10962 month: '08' oa: 1 oa_version: Preprint page: '33' project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: arXiv publication_status: submitted related_material: record: - id: '11739' relation: later_version status: public - id: '10030' relation: dissertation_contains status: public status: public title: Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '10328' abstract: - lang: eng text: We discus noise channels in coherent electro-optic up-conversion between microwave and optical fields, in particular due to optical heating. We also report on a novel configuration, which promises to be flexible and highly efficient. alternative_title: - OSA Technical Digest article_number: QTu8A.1 article_processing_charge: No author: - first_name: Nicholas J. full_name: Lambert, Nicholas J. last_name: Lambert - first_name: Sonia full_name: Mobassem, Sonia last_name: Mobassem - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: Harald G.L. full_name: Schwefel, Harald G.L. last_name: Schwefel citation: ama: 'Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. New designs and noise channels in electro-optic microwave to optical up-conversion. In: OSA Quantum 2.0 Conference. Optica Publishing Group; 2020. doi:10.1364/QUANTUM.2020.QTu8A.1' apa: 'Lambert, N. J., Mobassem, S., Rueda Sanchez, A. R., & Schwefel, H. G. L. (2020). New designs and noise channels in electro-optic microwave to optical up-conversion. In OSA Quantum 2.0 Conference. Washington, DC, United States: Optica Publishing Group. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1' chicago: Lambert, Nicholas J., Sonia Mobassem, Alfredo R Rueda Sanchez, and Harald G.L. Schwefel. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” In OSA Quantum 2.0 Conference. Optica Publishing Group, 2020. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1. ieee: N. J. Lambert, S. Mobassem, A. R. Rueda Sanchez, and H. G. L. Schwefel, “New designs and noise channels in electro-optic microwave to optical up-conversion,” in OSA Quantum 2.0 Conference, Washington, DC, United States, 2020. ista: 'Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. 2020. New designs and noise channels in electro-optic microwave to optical up-conversion. OSA Quantum 2.0 Conference. OSA: Optical Society of America, OSA Technical Digest, , QTu8A.1.' mla: Lambert, Nicholas J., et al. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” OSA Quantum 2.0 Conference, QTu8A.1, Optica Publishing Group, 2020, doi:10.1364/QUANTUM.2020.QTu8A.1. short: N.J. Lambert, S. Mobassem, A.R. Rueda Sanchez, H.G.L. Schwefel, in:, OSA Quantum 2.0 Conference, Optica Publishing Group, 2020. conference: end_date: 2020-09-17 location: Washington, DC, United States name: 'OSA: Optical Society of America' start_date: 2020-09-14 date_created: 2021-11-21T23:01:31Z date_published: 2020-01-01T00:00:00Z date_updated: 2023-10-18T08:32:34Z day: '01' department: - _id: JoFi doi: 10.1364/QUANTUM.2020.QTu8A.1 language: - iso: eng month: '01' oa_version: None publication: OSA Quantum 2.0 Conference publication_identifier: isbn: - 9-781-5575-2820-9 publication_status: published publisher: Optica Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: New designs and noise channels in electro-optic microwave to optical up-conversion type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '10556' abstract: - lang: eng text: In this paper, we present the first Asynchronous Distributed Key Generation (ADKG) algorithm which is also the first distributed key generation algorithm that can generate cryptographic keys with a dual (f,2f+1)-threshold (where f is the number of faulty parties). As a result, using our ADKG we remove the trusted setup assumption that the most scalable consensus algorithms make. In order to create a DKG with a dual (f,2f+1)- threshold we first answer in the affirmative the open question posed by Cachin et al. [7] on how to create an Asynchronous Verifiable Secret Sharing (AVSS) protocol with a reconstruction threshold of f+1Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security. Association for Computing Machinery; 2020:1751–1767. doi:10.1145/3372297.3423364' apa: 'Kokoris Kogias, E., Malkhi, D., & Spiegelman, A. (2020). Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security (pp. 1751–1767). Virtual, United States: Association for Computing Machinery. https://doi.org/10.1145/3372297.3423364' chicago: Kokoris Kogias, Eleftherios, Dahlia Malkhi, and Alexander Spiegelman. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” In Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, 1751–1767. Association for Computing Machinery, 2020. https://doi.org/10.1145/3372297.3423364. ieee: E. Kokoris Kogias, D. Malkhi, and A. Spiegelman, “Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures,” in Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Virtual, United States, 2020, pp. 1751–1767. ista: 'Kokoris Kogias E, Malkhi D, Spiegelman A. 2020. Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security. CCS: Computer and Communications Security, 1751–1767.' mla: Kokoris Kogias, Eleftherios, et al. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767, doi:10.1145/3372297.3423364. short: E. Kokoris Kogias, D. Malkhi, A. Spiegelman, in:, Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767. conference: end_date: 2020-11-13 location: Virtual, United States name: 'CCS: Computer and Communications Security' start_date: 2020-11-09 date_created: 2021-12-16T13:23:27Z date_published: 2020-10-30T00:00:00Z date_updated: 2024-02-22T13:10:45Z day: '30' department: - _id: ElKo doi: 10.1145/3372297.3423364 external_id: isi: - '000768470400104' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2019/1015 month: '10' oa: 1 oa_version: Preprint page: 1751–1767 publication: Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security publication_identifier: isbn: - 978-1-4503-7089-9 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '10557' abstract: - lang: eng text: Data storage and retrieval systems, methods, and computer-readable media utilize a cryptographically verifiable data structure that facilitates verification of a transaction in a decentralized peer-to-peer environment using multi-hop backwards and forwards links. Backward links are cryptographic hashes of past records. Forward links are cryptographic signatures of future records that are added retroactively to records once the target block has been appended to the data structure. applicant: - Ecole Polytechnique Federale de Lausanne application_date: 2017-06-09 article_processing_charge: No author: - first_name: Bryan full_name: Ford, Bryan last_name: Ford - first_name: Linus full_name: Gasse, Linus last_name: Gasse - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Philipp full_name: Jovanovic, Philipp last_name: Jovanovic citation: ama: Ford B, Gasse L, Kokoris Kogias E, Jovanovic P. Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods. 2020. apa: Ford, B., Gasse, L., Kokoris Kogias, E., & Jovanovic, P. (2020). Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods. chicago: Ford, Bryan, Linus Gasse, Eleftherios Kokoris Kogias, and Philipp Jovanovic. “Cryptographically Verifiable Data Structure Having Multi-Hop Forward and Backwards Links and Associated Systems and Methods,” 2020. ieee: B. Ford, L. Gasse, E. Kokoris Kogias, and P. Jovanovic, “Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods.” 2020. ista: Ford B, Gasse L, Kokoris Kogias E, Jovanovic P. 2020. Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods. mla: Ford, Bryan, et al. Cryptographically Verifiable Data Structure Having Multi-Hop Forward and Backwards Links and Associated Systems and Methods. 2020. short: B. Ford, L. Gasse, E. Kokoris Kogias, P. Jovanovic, (2020). date_created: 2021-12-16T13:28:59Z date_published: 2020-03-03T00:00:00Z date_updated: 2021-12-21T10:04:50Z day: '03' department: - _id: ElKo extern: '1' ipc: ' H04L9/3247 ; G06Q20/29 ; G06Q20/382 ; H04L9/3236' ipn: '10581613' main_file_link: - open_access: '1' url: https://patents.google.com/patent/US10581613B2/en month: '03' oa: 1 oa_version: Published Version publication_date: 2020-03-03 related_material: link: - relation: earlier_version url: https://patents.google.com/patent/US20180359096A1/en status: public title: Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '12188' abstract: - lang: eng text: Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states. acknowledgement: We would like to thank Scott Berry for help with ICU-GFP nuclear localization microscopy, Hao Yu and Lisha Shen for assistance with 6mA DNA methylation analysis, Donna Gibson for graphic design assistance, and members of the C.D. and Howard laboratories for helpful discussions. This work was funded by the European Research Council grants to “MEXTIM” (to C.D.) and “SexMeth” (to X. Feng), by the Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic Programmes GRO (BB/J004588/1), GEN (BB/P013511/1), BBSRC grant (to X. Feng) (BB/S009620/1), and the Marie Sklodowska–Curie Postdoctoral Fellowships “UNRAVEL” (to R.H.B.) and "WISDOM" (to X. Fang). Additional funding via the Wellcome Trust through a Senior Research Fellowship (to J.R.) (103139) and a multiuser equipment grant (108504). The Wellcome Centre for Cell Biology is supported by core funding from the Wellcome Trust (203149). article_processing_charge: No article_type: original author: - first_name: Rebecca H. full_name: Bloomer, Rebecca H. last_name: Bloomer - first_name: Claire E. full_name: Hutchison, Claire E. last_name: Hutchison - first_name: Isabel full_name: Bäurle, Isabel last_name: Bäurle - first_name: James full_name: Walker, James last_name: Walker - first_name: Xiaofeng full_name: Fang, Xiaofeng last_name: Fang - first_name: Pumi full_name: Perera, Pumi last_name: Perera - first_name: Christos N. full_name: Velanis, Christos N. last_name: Velanis - first_name: Serin full_name: Gümüs, Serin last_name: Gümüs - first_name: Christos full_name: Spanos, Christos last_name: Spanos - first_name: Juri full_name: Rappsilber, Juri last_name: Rappsilber - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 - first_name: Justin full_name: Goodrich, Justin last_name: Goodrich - first_name: Caroline full_name: Dean, Caroline last_name: Dean citation: ama: Bloomer RH, Hutchison CE, Bäurle I, et al. The  Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. 2020;117(28):16660-16666. doi:10.1073/pnas.1920621117 apa: Bloomer, R. H., Hutchison, C. E., Bäurle, I., Walker, J., Fang, X., Perera, P., … Dean, C. (2020). The  Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1920621117 chicago: Bloomer, Rebecca H., Claire E. Hutchison, Isabel Bäurle, James Walker, Xiaofeng Fang, Pumi Perera, Christos N. Velanis, et al. “The  Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1920621117. ieee: R. H. Bloomer et al., “The  Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2,” Proceedings of the National Academy of Sciences, vol. 117, no. 28. Proceedings of the National Academy of Sciences, pp. 16660–16666, 2020. ista: Bloomer RH, Hutchison CE, Bäurle I, Walker J, Fang X, Perera P, Velanis CN, Gümüs S, Spanos C, Rappsilber J, Feng X, Goodrich J, Dean C. 2020. The  Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. 117(28), 16660–16666. mla: Bloomer, Rebecca H., et al. “The  Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the National Academy of Sciences, vol. 117, no. 28, Proceedings of the National Academy of Sciences, 2020, pp. 16660–66, doi:10.1073/pnas.1920621117. short: R.H. Bloomer, C.E. Hutchison, I. Bäurle, J. Walker, X. Fang, P. Perera, C.N. Velanis, S. Gümüs, C. Spanos, J. Rappsilber, X. Feng, J. Goodrich, C. Dean, Proceedings of the National Academy of Sciences 117 (2020) 16660–16666. date_created: 2023-01-16T09:15:44Z date_published: 2020-05-22T00:00:00Z date_updated: 2023-05-08T10:53:55Z day: '22' ddc: - '580' department: - _id: XiFe doi: 10.1073/pnas.1920621117 extern: '1' external_id: pmid: - '32601198' file: - access_level: open_access checksum: cedee184cb12f454f2fba4158ff47db9 content_type: application/pdf creator: alisjak date_created: 2023-02-07T11:29:55Z date_updated: 2023-02-07T11:29:55Z file_id: '12526' file_name: 2020_PNAS_Bloomer.pdf file_size: 1105414 relation: main_file success: 1 file_date_updated: 2023-02-07T11:29:55Z has_accepted_license: '1' intvolume: ' 117' issue: '28' keyword: - Multidisciplinary language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/ month: '05' oa: 1 oa_version: Published Version page: 16660-16666 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - 0027-8424 - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 117 year: '2020' ... --- _id: '12189' abstract: - lang: eng text: Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells. acknowledgement: The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript. article_number: e1008894 article_processing_charge: No article_type: original author: - first_name: Nicolas full_name: Christophorou, Nicolas last_name: Christophorou - first_name: Wenjing full_name: She, Wenjing last_name: She - first_name: Jincheng full_name: Long, Jincheng last_name: Long - first_name: Aurélie full_name: Hurel, Aurélie last_name: Hurel - first_name: Sébastien full_name: Beaubiat, Sébastien last_name: Beaubiat - first_name: Yassir full_name: Idir, Yassir last_name: Idir - first_name: Marina full_name: Tagliaro-Jahns, Marina last_name: Tagliaro-Jahns - first_name: Aurélie full_name: Chambon, Aurélie last_name: Chambon - first_name: Victor full_name: Solier, Victor last_name: Solier - first_name: Daniel full_name: Vezon, Daniel last_name: Vezon - first_name: Mathilde full_name: Grelon, Mathilde last_name: Grelon - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 - first_name: Nicolas full_name: Bouché, Nicolas last_name: Bouché - first_name: Christine full_name: Mézard, Christine last_name: Mézard citation: ama: Christophorou N, She W, Long J, et al. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. 2020;16(6). doi:10.1371/journal.pgen.1008894 apa: Christophorou, N., She, W., Long, J., Hurel, A., Beaubiat, S., Idir, Y., … Mézard, C. (2020). AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1008894 chicago: Christophorou, Nicolas, Wenjing She, Jincheng Long, Aurélie Hurel, Sébastien Beaubiat, Yassir Idir, Marina Tagliaro-Jahns, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” PLOS Genetics. Public Library of Science (PLoS), 2020. https://doi.org/10.1371/journal.pgen.1008894. ieee: N. Christophorou et al., “AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization,” PLOS Genetics, vol. 16, no. 6. Public Library of Science (PLoS), 2020. ista: Christophorou N, She W, Long J, Hurel A, Beaubiat S, Idir Y, Tagliaro-Jahns M, Chambon A, Solier V, Vezon D, Grelon M, Feng X, Bouché N, Mézard C. 2020. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. 16(6), e1008894. mla: Christophorou, Nicolas, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” PLOS Genetics, vol. 16, no. 6, e1008894, Public Library of Science (PLoS), 2020, doi:10.1371/journal.pgen.1008894. short: N. Christophorou, W. She, J. Long, A. Hurel, S. Beaubiat, Y. Idir, M. Tagliaro-Jahns, A. Chambon, V. Solier, D. Vezon, M. Grelon, X. Feng, N. Bouché, C. Mézard, PLOS Genetics 16 (2020). date_created: 2023-01-16T09:16:10Z date_published: 2020-06-29T00:00:00Z date_updated: 2023-05-08T10:54:39Z day: '29' department: - _id: XiFe doi: 10.1371/journal.pgen.1008894 extern: '1' external_id: pmid: - '32598340' intvolume: ' 16' issue: '6' keyword: - Cancer Research - Genetics (clinical) - Genetics - Molecular Biology - Ecology - Evolution - Behavior and Systematics language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/ month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: PLOS Genetics publication_identifier: issn: - 1553-7404 publication_status: published publisher: Public Library of Science (PLoS) quality_controlled: '1' scopus_import: '1' status: public title: AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2020' ... --- _id: '9706' abstract: - lang: eng text: 'Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19).' article_processing_charge: No author: - first_name: Robert F. full_name: Hillary, Robert F. last_name: Hillary - first_name: Daniel full_name: Trejo-Banos, Daniel last_name: Trejo-Banos - first_name: Athanasios full_name: Kousathanas, Athanasios last_name: Kousathanas - first_name: Daniel L. full_name: McCartney, Daniel L. last_name: McCartney - first_name: Sarah E. full_name: Harris, Sarah E. last_name: Harris - first_name: Anna J. full_name: Stevenson, Anna J. last_name: Stevenson - first_name: Marion full_name: Patxot, Marion last_name: Patxot - first_name: Sven Erik full_name: Ojavee, Sven Erik last_name: Ojavee - first_name: Qian full_name: Zhang, Qian last_name: Zhang - first_name: David C. full_name: Liewald, David C. last_name: Liewald - first_name: Craig W. full_name: Ritchie, Craig W. last_name: Ritchie - first_name: Kathryn L. full_name: Evans, Kathryn L. last_name: Evans - first_name: Elliot M. full_name: Tucker-Drob, Elliot M. last_name: Tucker-Drob - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: 'Allan F. ' full_name: 'McRae, Allan F. ' last_name: McRae - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Ian J. full_name: Deary, Ian J. last_name: Deary - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: 'Riccardo E. ' full_name: 'Marioni, Riccardo E. ' last_name: Marioni citation: ama: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. 2020. doi:10.6084/m9.figshare.12629697.v1 apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1 chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1. ieee: R. F. Hillary et al., “Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Springer Nature, 2020. ista: Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1. mla: Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults. Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1. short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, (2020). date_created: 2021-07-23T08:59:15Z date_published: 2020-07-09T00:00:00Z date_updated: 2023-08-22T07:55:36Z day: '09' department: - _id: MaRo doi: 10.6084/m9.figshare.12629697.v1 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.12629697.v1 month: '07' oa: 1 oa_version: Published Version other_data_license: CC0 + CC BY (4.0) publisher: Springer Nature related_material: record: - id: '8133' relation: used_in_publication status: public status: public title: Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9708' abstract: - lang: eng text: This research data supports 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file for plotting each figure is provided. article_processing_charge: No author: - first_name: Mate full_name: Hartstein, Mate last_name: Hartstein - first_name: Yu-Te full_name: Hsu, Yu-Te last_name: Hsu - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Juan full_name: Porras, Juan last_name: Porras - first_name: Toshinao full_name: Loew, Toshinao last_name: Loew - first_name: Matthieu full_name: Le Tacon, Matthieu last_name: Le Tacon - first_name: Huakun full_name: Zuo, Huakun last_name: Zuo - first_name: Jinhua full_name: Wang, Jinhua last_name: Wang - first_name: Zengwei full_name: Zhu, Zengwei last_name: Zhu - first_name: Mun full_name: Chan, Mun last_name: Chan - first_name: Ross full_name: McDonald, Ross last_name: McDonald - first_name: Gilbert full_name: Lonzarich, Gilbert last_name: Lonzarich - first_name: Bernhard full_name: Keimer, Bernhard last_name: Keimer - first_name: Suchitra full_name: Sebastian, Suchitra last_name: Sebastian - first_name: Neil full_name: Harrison, Neil last_name: Harrison citation: ama: Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” 2020. doi:10.17863/cam.50169 apa: Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M., … Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” Apollo - University of Cambridge. https://doi.org/10.17863/cam.50169 chicago: Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.’” Apollo - University of Cambridge, 2020. https://doi.org/10.17863/cam.50169. ieee: M. Hartstein et al., “Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.’” Apollo - University of Cambridge, 2020. ista: Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N. 2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University of Cambridge, 10.17863/cam.50169. mla: Hartstein, Mate, et al. Accompanying Dataset for “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Apollo - University of Cambridge, 2020, doi:10.17863/cam.50169. short: M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H. Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian, N. Harrison, (2020). date_created: 2021-07-23T10:00:35Z date_published: 2020-05-29T00:00:00Z date_updated: 2023-08-21T07:06:48Z day: '29' department: - _id: KiMo doi: 10.17863/cam.50169 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.17863/CAM.50169 month: '05' oa: 1 oa_version: Published Version publisher: Apollo - University of Cambridge related_material: record: - id: '7942' relation: used_in_publication status: public status: public title: Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9713' abstract: - lang: eng text: Additional analyses of the trajectories article_processing_charge: No author: - first_name: Chitrak full_name: Gupta, Chitrak last_name: Gupta - first_name: Umesh full_name: Khaniya, Umesh last_name: Khaniya - first_name: Chun Kit full_name: Chan, Chun Kit last_name: Chan - first_name: Francois full_name: Dehez, Francois last_name: Dehez - first_name: Mrinal full_name: Shekhar, Mrinal last_name: Shekhar - first_name: M.R. full_name: Gunner, M.R. last_name: Gunner - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: Abhishek full_name: Singharoy, Abhishek last_name: Singharoy citation: ama: Gupta C, Khaniya U, Chan CK, et al. Supporting information. 2020. doi:10.1021/jacs.9b13450.s001 apa: Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Supporting information. American Chemical Society . https://doi.org/10.1021/jacs.9b13450.s001 chicago: Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Supporting Information.” American Chemical Society , 2020. https://doi.org/10.1021/jacs.9b13450.s001. ieee: C. Gupta et al., “Supporting information.” American Chemical Society , 2020. ista: Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Supporting information, American Chemical Society , 10.1021/jacs.9b13450.s001. mla: Gupta, Chitrak, et al. Supporting Information. American Chemical Society , 2020, doi:10.1021/jacs.9b13450.s001. short: C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020). date_created: 2021-07-23T12:02:39Z date_published: 2020-05-20T00:00:00Z date_updated: 2023-08-22T07:49:38Z day: '20' department: - _id: LeSa doi: 10.1021/jacs.9b13450.s001 month: '05' oa_version: Published Version publisher: 'American Chemical Society ' related_material: record: - id: '8040' relation: used_in_publication status: public status: public title: Supporting information type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9750' abstract: - lang: eng text: Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase, and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension stabilizing E-cadherin-actin complexes at the contact. acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: SSU acknowledgement: We would like to thank Edouard Hannezo for discussions, Shayan Shami Pour and Daniel Capek for help with data analysis, Vanessa Barone and other members of the Heisenberg laboratory for thoughtful discussions and comments on the manuscript. We also thank Jack Merrin for preparing the microwells, and the Scientific Service Units at IST Austria, specifically Bioimaging and Electron Microscopy, and the Zebrafish Facility for continuous support. We acknowledge Hitoshi Morita for the kind gift of VinculinB-GFP plasmid. This research was supported by an ERC Advanced Grant (MECSPEC) to C.-P.H, EMBO Long Term grant (ALTF 187-2013) to M.S and IST Fellow Marie-Curie COFUND No. P_IST_EU01 to J.S. article_processing_charge: No author: - first_name: Jana full_name: Slovakova, Jana id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87 last_name: Slovakova - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora - first_name: Silvia full_name: Caballero Mancebo, Silvia id: 2F1E1758-F248-11E8-B48F-1D18A9856A87 last_name: Caballero Mancebo orcid: 0000-0002-5223-3346 - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Karla full_name: Huljev, Karla id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87 last_name: Huljev - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Slovakova J, Sikora MK, Caballero Mancebo S, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. 2020. doi:10.1101/2020.11.20.391284 apa: Slovakova, J., Sikora, M. K., Caballero Mancebo, S., Krens, G., Kaufmann, W., Huljev, K., & Heisenberg, C.-P. J. (2020). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.20.391284 chicago: Slovakova, Jana, Mateusz K Sikora, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Karla Huljev, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.11.20.391284. ieee: J. Slovakova et al., “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion,” bioRxiv. Cold Spring Harbor Laboratory, 2020. ista: Slovakova J, Sikora MK, Caballero Mancebo S, Krens G, Kaufmann W, Huljev K, Heisenberg C-PJ. 2020. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv, 10.1101/2020.11.20.391284. mla: Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.11.20.391284. short: J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K. Huljev, C.-P.J. Heisenberg, BioRxiv (2020). date_created: 2021-07-29T11:29:50Z date_published: 2020-11-20T00:00:00Z date_updated: 2024-03-25T23:30:10Z day: '20' department: - _id: CaHe - _id: EM-Fac - _id: Bio doi: 10.1101/2020.11.20.391284 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2020.11.20.391284 month: '11' oa: 1 oa_version: Preprint page: '41' project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 2521E28E-B435-11E9-9278-68D0E5697425 grant_number: 187-2013 name: Modulation of adhesion function in cell-cell contact formation by cortical tension publication: bioRxiv publication_status: published publisher: Cold Spring Harbor Laboratory related_material: record: - id: '10766' relation: later_version status: public - id: '9623' relation: dissertation_contains status: public status: public title: Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '9776' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. Supporting information. 2020. doi:10.1371/journal.pcbi.1007642.s001 apa: Grah, R., & Friedlander, T. (2020). Supporting information. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s001 chicago: Grah, Rok, and Tamar Friedlander. “Supporting Information.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s001. ieee: R. Grah and T. Friedlander, “Supporting information.” Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. Supporting information, Public Library of Science, 10.1371/journal.pcbi.1007642.s001. mla: Grah, Rok, and Tamar Friedlander. Supporting Information. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s001. short: R. Grah, T. Friedlander, (2020). date_created: 2021-08-06T07:15:04Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-08-18T06:47:47Z day: '25' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007642.s001 month: '02' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '7569' relation: used_in_publication status: public status: public title: Supporting information type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9777' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002 apa: Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002 chicago: Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002. ieee: R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, 10.1371/journal.pcbi.1007642.s002. mla: Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002. short: R. Grah, T. Friedlander, (2020). date_created: 2021-08-06T07:21:51Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-09-12T11:02:25Z day: '25' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007642.s002 main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pcbi.1007642.s002 month: '02' oa: 1 oa_version: None publisher: Public Library of Science related_material: record: - id: '7569' relation: used_in_publication status: public status: public title: Maximizing crosstalk type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9779' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. Distribution of crosstalk values. 2020. doi:10.1371/journal.pcbi.1007642.s003 apa: Grah, R., & Friedlander, T. (2020). Distribution of crosstalk values. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s003 chicago: Grah, Rok, and Tamar Friedlander. “Distribution of Crosstalk Values.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s003. ieee: R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. Distribution of crosstalk values, Public Library of Science, 10.1371/journal.pcbi.1007642.s003. mla: Grah, Rok, and Tamar Friedlander. Distribution of Crosstalk Values. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s003. short: R. Grah, T. Friedlander, (2020). date_created: 2021-08-06T07:24:37Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-08-18T06:47:47Z day: '25' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007642.s003 month: '02' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '7569' relation: research_data status: public status: public title: Distribution of crosstalk values type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9780' abstract: - lang: eng text: "PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol\r\nSpace Group: C 2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°" article_processing_charge: No author: - first_name: Werner full_name: Schlemmer, Werner last_name: Schlemmer - first_name: Philipp full_name: Nothdurft, Philipp last_name: Nothdurft - first_name: Alina full_name: Petzold, Alina last_name: Petzold - first_name: Gisbert full_name: Riess, Gisbert last_name: Riess - first_name: Philipp full_name: Frühwirt, Philipp last_name: Frühwirt - first_name: Max full_name: Schmallegger, Max last_name: Schmallegger - first_name: Georg full_name: Gescheidt-Demner, Georg last_name: Gescheidt-Demner - first_name: Roland full_name: Fischer, Roland last_name: Fischer - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Wolfgang full_name: Kern, Wolfgang last_name: Kern - first_name: Stefan full_name: Spirk, Stefan last_name: Spirk citation: ama: 'Schlemmer W, Nothdurft P, Petzold A, et al. CCDC 1991959: Experimental Crystal Structure Determination. 2020. doi:10.5517/ccdc.csd.cc24vsrk' apa: 'Schlemmer, W., Nothdurft, P., Petzold, A., Riess, G., Frühwirt, P., Schmallegger, M., … Spirk, S. (2020). CCDC 1991959: Experimental Crystal Structure Determination. CCDC. https://doi.org/10.5517/ccdc.csd.cc24vsrk' chicago: 'Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Gisbert Riess, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, et al. “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020. https://doi.org/10.5517/ccdc.csd.cc24vsrk.' ieee: 'W. Schlemmer et al., “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020.' ista: 'Schlemmer W, Nothdurft P, Petzold A, Riess G, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. CCDC 1991959: Experimental Crystal Structure Determination, CCDC, 10.5517/ccdc.csd.cc24vsrk.' mla: 'Schlemmer, Werner, et al. CCDC 1991959: Experimental Crystal Structure Determination. CCDC, 2020, doi:10.5517/ccdc.csd.cc24vsrk.' short: W. Schlemmer, P. Nothdurft, A. Petzold, G. Riess, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, (2020). date_created: 2021-08-06T07:41:07Z date_published: 2020-03-22T00:00:00Z date_updated: 2023-09-05T16:03:47Z day: '22' department: - _id: StFr doi: 10.5517/ccdc.csd.cc24vsrk main_file_link: - open_access: '1' url: https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk month: '03' oa: 1 oa_version: Published Version publisher: CCDC related_material: record: - id: '8329' relation: used_in_publication status: public status: public title: 'CCDC 1991959: Experimental Crystal Structure Determination' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ...