[{"quality_controlled":"1","doi":"10.1364/QUANTUM.2020.QTu8A.1","date_published":"2020-01-01T00:00:00Z","publication_identifier":{"isbn":["9-781-5575-2820-9"]},"publication_status":"published","citation":{"mla":"Lambert, Nicholas J., et al. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” <i>OSA Quantum 2.0 Conference</i>, QTu8A.1, Optica Publishing Group, 2020, doi:<a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">10.1364/QUANTUM.2020.QTu8A.1</a>.","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.","apa":"Lambert, N. J., Mobassem, S., Rueda Sanchez, A. R., &#38; Schwefel, H. G. L. (2020). New designs and noise channels in electro-optic microwave to optical up-conversion. In <i>OSA Quantum 2.0 Conference</i>. Washington, DC, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">https://doi.org/10.1364/QUANTUM.2020.QTu8A.1</a>","ama":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. New designs and noise channels in electro-optic microwave to optical up-conversion. In: <i>OSA Quantum 2.0 Conference</i>. Optica Publishing Group; 2020. doi:<a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">10.1364/QUANTUM.2020.QTu8A.1</a>","short":"N.J. Lambert, S. Mobassem, A.R. Rueda Sanchez, H.G.L. Schwefel, in:, OSA Quantum 2.0 Conference, Optica Publishing Group, 2020.","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 <i>OSA Quantum 2.0 Conference</i>, Washington, DC, United States, 2020.","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 <i>OSA Quantum 2.0 Conference</i>. Optica Publishing Group, 2020. <a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">https://doi.org/10.1364/QUANTUM.2020.QTu8A.1</a>."},"language":[{"iso":"eng"}],"conference":{"end_date":"2020-09-17","name":"OSA: Optical Society of America","location":"Washington, DC, United States","start_date":"2020-09-14"},"status":"public","alternative_title":["OSA Technical Digest"],"date_created":"2021-11-21T23:01:31Z","article_number":"QTu8A.1","title":"New designs and noise channels in electro-optic microwave to optical up-conversion","month":"01","oa_version":"None","type":"conference","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-10-18T08:32:34Z","day":"01","author":[{"full_name":"Lambert, Nicholas J.","last_name":"Lambert","first_name":"Nicholas J."},{"last_name":"Mobassem","first_name":"Sonia","full_name":"Mobassem, Sonia"},{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R"},{"last_name":"Schwefel","first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L."}],"article_processing_charge":"No","scopus_import":"1","_id":"10328","publication":"OSA Quantum 2.0 Conference","year":"2020","department":[{"_id":"JoFi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Optica Publishing Group"},{"date_created":"2021-12-16T13:23:27Z","page":"1751–1767","date_updated":"2024-02-22T13:10:45Z","abstract":[{"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+1<k łe 2f+1, which is of independent interest. Our High-threshold-AVSS (HAVSS) uses an asymmetric bivariate polynomial to encode the secret. This enables the reconstruction of the secret only if a set of k nodes contribute while allowing an honest node that did not participate in the sharing phase to recover his share with the help of f+1 honest parties. Once we have HAVSS we can use it to bootstrap scalable partially synchronous consensus protocols, but the question on how to get a DKG in asynchrony remains as we need a way to produce common randomness. The solution comes from a novel Eventually Perfect Common Coin (EPCC) abstraction that enables the generation of a common coin from n concurrent HAVSS invocations. EPCC's key property is that it is eventually reliable, as it might fail to agree at most f times (even if invoked a polynomial number of times). Using EPCC we implement an Eventually Efficient Asynchronous Binary Agreement (EEABA) which is optimal when the EPCC agrees and protects safety when EPCC fails. Finally, using EEABA we construct the first ADKG which has the same overhead and expected runtime as the best partially-synchronous DKG (O(n4) words, O(f) rounds). As a corollary of our ADKG, we can also create the first Validated Asynchronous Byzantine Agreement (VABA) that does not need a trusted dealer to setup threshold signatures of degree n-f. Our VABA has an overhead of expected O(n2) words and O(1) time per instance, after an initial O(n4) words and O(f) time bootstrap via ADKG.","lang":"eng"}],"oa_version":"Preprint","type":"conference","month":"10","_id":"10556","acknowledgement":"We would like to thank Ittai Abraham for the discussions and guidance during the initial conception of the project, especially for HAVSS. Furthermore, we would like to thank the anonymous reviewers for pointing out the relevance of this work to MPC protocols.","year":"2020","date_published":"2020-10-30T00:00:00Z","main_file_link":[{"url":"https://eprint.iacr.org/2019/1015","open_access":"1"}],"publication_status":"published","oa":1,"citation":{"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.","ieee":"E. Kokoris Kogias, D. Malkhi, and A. Spiegelman, “Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures,” in <i>Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security</i>, Virtual, United States, 2020, pp. 1751–1767.","chicago":"Kokoris Kogias, Eleftherios, Dahlia Malkhi, and Alexander Spiegelman. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” In <i>Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security</i>, 1751–1767. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3372297.3423364\">https://doi.org/10.1145/3372297.3423364</a>.","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.” <i>Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security</i>, Association for Computing Machinery, 2020, pp. 1751–1767, doi:<a href=\"https://doi.org/10.1145/3372297.3423364\">10.1145/3372297.3423364</a>.","apa":"Kokoris Kogias, E., Malkhi, D., &#38; Spiegelman, A. (2020). Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In <i>Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security</i> (pp. 1751–1767). Virtual, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3372297.3423364\">https://doi.org/10.1145/3372297.3423364</a>","ama":"Kokoris Kogias E, Malkhi D, Spiegelman A. Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In: <i>Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security</i>. Association for Computing Machinery; 2020:1751–1767. doi:<a href=\"https://doi.org/10.1145/3372297.3423364\">10.1145/3372297.3423364</a>"},"status":"public","external_id":{"isi":["000768470400104"]},"title":"Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures","author":[{"first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Malkhi, Dahlia","last_name":"Malkhi","first_name":"Dahlia"},{"first_name":"Alexander","last_name":"Spiegelman","full_name":"Spiegelman, Alexander"}],"day":"30","publication":"Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security","article_processing_charge":"No","scopus_import":"1","publisher":"Association for Computing Machinery","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ElKo"}],"doi":"10.1145/3372297.3423364","quality_controlled":"1","publication_identifier":{"isbn":["978-1-4503-7089-9"]},"isi":1,"conference":{"end_date":"2020-11-13","start_date":"2020-11-09","name":"CCS: Computer and Communications Security","location":"Virtual, United States"},"language":[{"iso":"eng"}]},{"related_material":{"link":[{"relation":"earlier_version","url":"https://patents.google.com/patent/US20180359096A1/en"}]},"extern":"1","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., &#38; Jovanovic, P. (2020). Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods.","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. <i>Cryptographically Verifiable Data Structure Having Multi-Hop Forward and Backwards Links and Associated Systems and Methods</i>. 2020.","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.","short":"B. Ford, L. Gasse, E. Kokoris Kogias, P. Jovanovic, (2020)."},"application_date":"2017-06-09","ipc":" H04L9/3247 ; G06Q20/29 ; G06Q20/382 ; H04L9/3236","ipn":"10581613","status":"public","date_published":"2020-03-03T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://patents.google.com/patent/US10581613B2/en"}],"oa":1,"publication_date":"2020-03-03","_id":"10557","article_processing_charge":"No","applicant":["Ecole Polytechnique Federale de Lausanne"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2020","department":[{"_id":"ElKo"}],"title":"Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods","date_created":"2021-12-16T13:28:59Z","author":[{"first_name":"Bryan","last_name":"Ford","full_name":"Ford, Bryan"},{"full_name":"Gasse, Linus","first_name":"Linus","last_name":"Gasse"},{"last_name":"Kokoris Kogias","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Jovanovic, Philipp","first_name":"Philipp","last_name":"Jovanovic"}],"date_updated":"2021-12-21T10:04:50Z","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."}],"day":"03","type":"patent","oa_version":"Published Version","month":"03"},{"author":[{"last_name":"Bloomer","first_name":"Rebecca H.","full_name":"Bloomer, Rebecca H."},{"full_name":"Hutchison, Claire E.","first_name":"Claire E.","last_name":"Hutchison"},{"full_name":"Bäurle, Isabel","first_name":"Isabel","last_name":"Bäurle"},{"last_name":"Walker","first_name":"James","full_name":"Walker, James"},{"full_name":"Fang, Xiaofeng","last_name":"Fang","first_name":"Xiaofeng"},{"full_name":"Perera, Pumi","first_name":"Pumi","last_name":"Perera"},{"first_name":"Christos N.","last_name":"Velanis","full_name":"Velanis, Christos N."},{"full_name":"Gümüs, Serin","first_name":"Serin","last_name":"Gümüs"},{"full_name":"Spanos, Christos","last_name":"Spanos","first_name":"Christos"},{"first_name":"Juri","last_name":"Rappsilber","full_name":"Rappsilber, Juri"},{"full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng"},{"full_name":"Goodrich, Justin","first_name":"Justin","last_name":"Goodrich"},{"last_name":"Dean","first_name":"Caroline","full_name":"Dean, Caroline"}],"license":"https://creativecommons.org/licenses/by/4.0/","file":[{"creator":"alisjak","relation":"main_file","content_type":"application/pdf","file_size":1105414,"success":1,"file_name":"2020_PNAS_Bloomer.pdf","access_level":"open_access","date_created":"2023-02-07T11:29:55Z","checksum":"cedee184cb12f454f2fba4158ff47db9","date_updated":"2023-02-07T11:29:55Z","file_id":"12526"}],"day":"22","title":"The  Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2","publisher":"Proceedings of the National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"department":[{"_id":"XiFe"}],"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","scopus_import":"1","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_identifier":{"issn":["0027-8424","1091-6490"]},"doi":"10.1073/pnas.1920621117","quality_controlled":"1","keyword":["Multidisciplinary"],"language":[{"iso":"eng"}],"issue":"28","page":"16660-16666","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."}],"date_updated":"2023-05-08T10:53:55Z","oa_version":"Published Version","month":"05","type":"journal_article","volume":117,"file_date_updated":"2023-02-07T11:29:55Z","date_created":"2023-01-16T09:15:44Z","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).","year":"2020","_id":"12188","oa":1,"publication_status":"published","has_accepted_license":"1","date_published":"2020-05-22T00:00:00Z","ddc":["580"],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/","open_access":"1"}],"external_id":{"pmid":["32601198"]},"status":"public","extern":"1","intvolume":"       117","citation":{"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.” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 28, Proceedings of the National Academy of Sciences, 2020, pp. 16660–66, doi:<a href=\"https://doi.org/10.1073/pnas.1920621117\">10.1073/pnas.1920621117</a>.","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. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1920621117\">https://doi.org/10.1073/pnas.1920621117</a>","ama":"Bloomer RH, Hutchison CE, Bäurle I, et al. The  Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. <i>Proceedings of the National Academy of Sciences</i>. 2020;117(28):16660-16666. doi:<a href=\"https://doi.org/10.1073/pnas.1920621117\">10.1073/pnas.1920621117</a>","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.","ieee":"R. H. Bloomer <i>et al.</i>, “The  Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2,” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 28. Proceedings of the National Academy of Sciences, pp. 16660–16666, 2020.","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.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1920621117\">https://doi.org/10.1073/pnas.1920621117</a>."}},{"department":[{"_id":"XiFe"}],"pmid":1,"publisher":"Public Library of Science (PLoS)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","scopus_import":"1","article_processing_charge":"No","publication":"PLOS Genetics","day":"29","author":[{"first_name":"Nicolas","last_name":"Christophorou","full_name":"Christophorou, Nicolas"},{"first_name":"Wenjing","last_name":"She","full_name":"She, Wenjing"},{"full_name":"Long, Jincheng","first_name":"Jincheng","last_name":"Long"},{"first_name":"Aurélie","last_name":"Hurel","full_name":"Hurel, Aurélie"},{"full_name":"Beaubiat, Sébastien","last_name":"Beaubiat","first_name":"Sébastien"},{"full_name":"Idir, Yassir","last_name":"Idir","first_name":"Yassir"},{"full_name":"Tagliaro-Jahns, Marina","last_name":"Tagliaro-Jahns","first_name":"Marina"},{"first_name":"Aurélie","last_name":"Chambon","full_name":"Chambon, Aurélie"},{"last_name":"Solier","first_name":"Victor","full_name":"Solier, Victor"},{"last_name":"Vezon","first_name":"Daniel","full_name":"Vezon, Daniel"},{"last_name":"Grelon","first_name":"Mathilde","full_name":"Grelon, Mathilde"},{"first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234"},{"first_name":"Nicolas","last_name":"Bouché","full_name":"Bouché, Nicolas"},{"full_name":"Mézard, Christine","last_name":"Mézard","first_name":"Christine"}],"article_number":"e1008894","title":"AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization","issue":"6","language":[{"iso":"eng"}],"keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"publication_identifier":{"issn":["1553-7404"]},"quality_controlled":"1","doi":"10.1371/journal.pgen.1008894","year":"2020","acknowledgement":"The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript.","_id":"12189","oa_version":"Published Version","type":"journal_article","month":"06","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-05-08T10:54:39Z","date_created":"2023-01-16T09:16:10Z","volume":16,"status":"public","external_id":{"pmid":["32598340"]},"citation":{"mla":"Christophorou, Nicolas, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” <i>PLOS Genetics</i>, vol. 16, no. 6, e1008894, Public Library of Science (PLoS), 2020, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008894\">10.1371/journal.pgen.1008894</a>.","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.","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. <i>PLOS Genetics</i>. Public Library of Science (PLoS). <a href=\"https://doi.org/10.1371/journal.pgen.1008894\">https://doi.org/10.1371/journal.pgen.1008894</a>","ama":"Christophorou N, She W, Long J, et al. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. <i>PLOS Genetics</i>. 2020;16(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008894\">10.1371/journal.pgen.1008894</a>","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).","ieee":"N. Christophorou <i>et al.</i>, “AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization,” <i>PLOS Genetics</i>, vol. 16, no. 6. Public Library of Science (PLoS), 2020.","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.” <i>PLOS Genetics</i>. Public Library of Science (PLoS), 2020. <a href=\"https://doi.org/10.1371/journal.pgen.1008894\">https://doi.org/10.1371/journal.pgen.1008894</a>."},"intvolume":"        16","extern":"1","publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/"}],"date_published":"2020-06-29T00:00:00Z"},{"date_created":"2021-07-23T08:59:15Z","title":"Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","day":"09","date_updated":"2023-08-22T07:55:36Z","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)."}],"oa_version":"Published Version","type":"research_data_reference","month":"07","author":[{"last_name":"Hillary","first_name":"Robert F.","full_name":"Hillary, Robert F."},{"first_name":"Daniel","last_name":"Trejo-Banos","full_name":"Trejo-Banos, Daniel"},{"full_name":"Kousathanas, Athanasios","last_name":"Kousathanas","first_name":"Athanasios"},{"last_name":"McCartney","first_name":"Daniel L.","full_name":"McCartney, Daniel L."},{"full_name":"Harris, Sarah E.","first_name":"Sarah E.","last_name":"Harris"},{"last_name":"Stevenson","first_name":"Anna J.","full_name":"Stevenson, Anna J."},{"full_name":"Patxot, Marion","first_name":"Marion","last_name":"Patxot"},{"first_name":"Sven Erik","last_name":"Ojavee","full_name":"Ojavee, Sven Erik"},{"full_name":"Zhang, Qian","first_name":"Qian","last_name":"Zhang"},{"first_name":"David C.","last_name":"Liewald","full_name":"Liewald, David C."},{"last_name":"Ritchie","first_name":"Craig W.","full_name":"Ritchie, Craig W."},{"last_name":"Evans","first_name":"Kathryn L.","full_name":"Evans, Kathryn L."},{"full_name":"Tucker-Drob, Elliot M.","last_name":"Tucker-Drob","first_name":"Elliot M."},{"last_name":"Wray","first_name":"Naomi R.","full_name":"Wray, Naomi R."},{"full_name":"McRae, Allan F. ","last_name":"McRae","first_name":"Allan F. "},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"first_name":"Ian J.","last_name":"Deary","full_name":"Deary, Ian J."},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard"},{"last_name":"Marioni","first_name":"Riccardo E. ","full_name":"Marioni, Riccardo E. "}],"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9706","department":[{"_id":"MaRo"}],"year":"2020","publisher":"Springer Nature","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.12629697.v1","open_access":"1"}],"doi":"10.6084/m9.figshare.12629697.v1","date_published":"2020-07-09T00:00:00Z","has_accepted_license":"1","oa":1,"citation":{"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).","ieee":"R. F. Hillary <i>et al.</i>, “Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Springer Nature, 2020.","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. <a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">https://doi.org/10.6084/m9.figshare.12629697.v1</a>.","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, <a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">10.6084/m9.figshare.12629697.v1</a>.","mla":"Hillary, Robert F., et al. <i>Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults</i>. Springer Nature, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">10.6084/m9.figshare.12629697.v1</a>.","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. <a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">https://doi.org/10.6084/m9.figshare.12629697.v1</a>","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:<a href=\"https://doi.org/10.6084/m9.figshare.12629697.v1\">10.6084/m9.figshare.12629697.v1</a>"},"other_data_license":"CC0 + CC BY (4.0)","related_material":{"record":[{"relation":"used_in_publication","id":"8133","status":"public"}]},"status":"public"},{"abstract":[{"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.","lang":"eng"}],"day":"29","date_updated":"2023-08-21T07:06:48Z","type":"research_data_reference","oa_version":"Published Version","month":"05","author":[{"full_name":"Hartstein, Mate","first_name":"Mate","last_name":"Hartstein"},{"full_name":"Hsu, Yu-Te","first_name":"Yu-Te","last_name":"Hsu"},{"first_name":"Kimberly A","last_name":"Modic","full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"},{"full_name":"Porras, Juan","first_name":"Juan","last_name":"Porras"},{"full_name":"Loew, Toshinao","last_name":"Loew","first_name":"Toshinao"},{"last_name":"Le Tacon","first_name":"Matthieu","full_name":"Le Tacon, Matthieu"},{"first_name":"Huakun","last_name":"Zuo","full_name":"Zuo, Huakun"},{"first_name":"Jinhua","last_name":"Wang","full_name":"Wang, Jinhua"},{"full_name":"Zhu, Zengwei","first_name":"Zengwei","last_name":"Zhu"},{"full_name":"Chan, Mun","last_name":"Chan","first_name":"Mun"},{"full_name":"McDonald, Ross","first_name":"Ross","last_name":"McDonald"},{"full_name":"Lonzarich, Gilbert","last_name":"Lonzarich","first_name":"Gilbert"},{"last_name":"Keimer","first_name":"Bernhard","full_name":"Keimer, Bernhard"},{"first_name":"Suchitra","last_name":"Sebastian","full_name":"Sebastian, Suchitra"},{"last_name":"Harrison","first_name":"Neil","full_name":"Harrison, Neil"}],"date_created":"2021-07-23T10:00:35Z","title":"Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'","year":"2020","department":[{"_id":"KiMo"}],"publisher":"Apollo - University of Cambridge","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9708","has_accepted_license":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.17863/CAM.50169"}],"doi":"10.17863/cam.50169","date_published":"2020-05-29T00:00:00Z","status":"public","citation":{"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. <a href=\"https://doi.org/10.17863/cam.50169\">https://doi.org/10.17863/cam.50169</a>.","ieee":"M. Hartstein <i>et al.</i>, “Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.’” Apollo - University of Cambridge, 2020.","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).","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:<a href=\"https://doi.org/10.17863/cam.50169\">10.17863/cam.50169</a>","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. <a href=\"https://doi.org/10.17863/cam.50169\">https://doi.org/10.17863/cam.50169</a>","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, <a href=\"https://doi.org/10.17863/cam.50169\">10.17863/cam.50169</a>.","mla":"Hartstein, Mate, et al. <i>Accompanying Dataset for “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.”</i> Apollo - University of Cambridge, 2020, doi:<a href=\"https://doi.org/10.17863/cam.50169\">10.17863/cam.50169</a>."},"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7942"}]}},{"title":"Supporting information","date_created":"2021-07-23T12:02:39Z","author":[{"first_name":"Chitrak","last_name":"Gupta","full_name":"Gupta, Chitrak"},{"first_name":"Umesh","last_name":"Khaniya","full_name":"Khaniya, Umesh"},{"first_name":"Chun Kit","last_name":"Chan","full_name":"Chan, Chun Kit"},{"full_name":"Dehez, Francois","last_name":"Dehez","first_name":"Francois"},{"full_name":"Shekhar, Mrinal","last_name":"Shekhar","first_name":"Mrinal"},{"full_name":"Gunner, M.R.","last_name":"Gunner","first_name":"M.R."},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A"},{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"},{"first_name":"Abhishek","last_name":"Singharoy","full_name":"Singharoy, Abhishek"}],"type":"research_data_reference","month":"05","oa_version":"Published Version","day":"20","abstract":[{"lang":"eng","text":"Additional analyses of the trajectories"}],"date_updated":"2023-08-22T07:49:38Z","_id":"9713","article_processing_charge":"No","publisher":"American Chemical Society ","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2020","department":[{"_id":"LeSa"}],"date_published":"2020-05-20T00:00:00Z","doi":"10.1021/jacs.9b13450.s001","related_material":{"record":[{"status":"public","id":"8040","relation":"used_in_publication"}]},"citation":{"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 , <a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">10.1021/jacs.9b13450.s001</a>.","mla":"Gupta, Chitrak, et al. <i>Supporting Information</i>. American Chemical Society , 2020, doi:<a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">10.1021/jacs.9b13450.s001</a>.","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Supporting information. American Chemical Society . <a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">https://doi.org/10.1021/jacs.9b13450.s001</a>","ama":"Gupta C, Khaniya U, Chan CK, et al. Supporting information. 2020. doi:<a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">10.1021/jacs.9b13450.s001</a>","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ieee":"C. Gupta <i>et al.</i>, “Supporting information.” American Chemical Society , 2020.","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. <a href=\"https://doi.org/10.1021/jacs.9b13450.s001\">https://doi.org/10.1021/jacs.9b13450.s001</a>."},"status":"public"},{"ec_funded":1,"article_processing_charge":"No","_id":"9750","publication":"bioRxiv","year":"2020","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"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.","publisher":"Cold Spring Harbor Laboratory","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2021-07-29T11:29:50Z","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion","oa_version":"Preprint","type":"preprint","month":"11","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."}],"date_updated":"2024-03-25T23:30:10Z","day":"20","author":[{"last_name":"Slovakova","first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K","last_name":"Sikora","first_name":"Mateusz K"},{"last_name":"Caballero Mancebo","first_name":"Silvia","full_name":"Caballero Mancebo, Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346"},{"first_name":"Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter"},{"first_name":"Karla","last_name":"Huljev","full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"page":"41","citation":{"ieee":"J. Slovakova <i>et al.</i>, “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2020.","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.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2020. <a href=\"https://doi.org/10.1101/2020.11.20.391284\">https://doi.org/10.1101/2020.11.20.391284</a>.","short":"J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K. Huljev, C.-P.J. Heisenberg, BioRxiv (2020).","ama":"Slovakova J, Sikora MK, Caballero Mancebo S, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. <i>bioRxiv</i>. 2020. doi:<a href=\"https://doi.org/10.1101/2020.11.20.391284\">10.1101/2020.11.20.391284</a>","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, <a href=\"https://doi.org/10.1101/2020.11.20.391284\">10.1101/2020.11.20.391284</a>.","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2020, doi:<a href=\"https://doi.org/10.1101/2020.11.20.391284\">10.1101/2020.11.20.391284</a>.","apa":"Slovakova, J., Sikora, M. K., Caballero Mancebo, S., Krens, G., Kaufmann, W., Huljev, K., &#38; Heisenberg, C.-P. J. (2020). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.11.20.391284\">https://doi.org/10.1101/2020.11.20.391284</a>"},"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"10766"},{"status":"public","id":"9623","relation":"dissertation_contains"}]},"status":"public","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"_id":"2521E28E-B435-11E9-9278-68D0E5697425","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","grant_number":"187-2013"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"SSU"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.11.20.391284"}],"doi":"10.1101/2020.11.20.391284","date_published":"2020-11-20T00:00:00Z","publication_status":"published","oa":1},{"author":[{"full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","last_name":"Grah"},{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"}],"month":"02","type":"research_data_reference","oa_version":"Published Version","date_updated":"2023-08-18T06:47:47Z","day":"25","title":"Supporting information","date_created":"2021-08-06T07:15:04Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"year":"2020","_id":"9776","article_processing_charge":"No","doi":"10.1371/journal.pcbi.1007642.s001","date_published":"2020-02-25T00:00:00Z","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7569"}]},"citation":{"apa":"Grah, R., &#38; Friedlander, T. 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Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 605–622.","ieee":"D. Feliciangeli and R. Seiringer, “Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 1. Society for Industrial &#38; Applied Mathematics , pp. 605–622, 2020.","chicago":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial &#38; Applied Mathematics , 2020. <a href=\"https://doi.org/10.1137/19m126284x\">https://doi.org/10.1137/19m126284x</a>.","mla":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 1, Society for Industrial &#38; Applied Mathematics , 2020, pp. 605–22, doi:<a href=\"https://doi.org/10.1137/19m126284x\">10.1137/19m126284x</a>.","ista":"Feliciangeli D, Seiringer R. 2020. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 52(1), 605–622.","apa":"Feliciangeli, D., &#38; Seiringer, R. (2020). Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial &#38; Applied Mathematics . <a href=\"https://doi.org/10.1137/19m126284x\">https://doi.org/10.1137/19m126284x</a>","ama":"Feliciangeli D, Seiringer R. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. <i>SIAM Journal on Mathematical Analysis</i>. 2020;52(1):605-622. doi:<a href=\"https://doi.org/10.1137/19m126284x\">10.1137/19m126284x</a>"},"page":"605-622","abstract":[{"lang":"eng","text":"We consider the Pekar functional on a ball in ℝ3. We prove uniqueness of minimizers, and a quadratic lower bound in terms of the distance to the minimizer. The latter follows from nondegeneracy of the Hessian at the minimum."}],"date_updated":"2023-09-07T13:30:11Z","month":"02","oa_version":"Preprint","type":"journal_article","volume":52,"date_created":"2021-08-06T07:34:16Z","acknowledgement":"We are grateful for the hospitality at the Mittag-Leffler Institute, where part of this work has been done. The work of the authors was supported by the European Research Council (ERC)under the European Union's Horizon 2020 research and innovation programme grant 694227.","year":"2020","_id":"9781"},{"publisher":"Royal Society of London","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2020","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"_id":"9798","article_processing_charge":"No","author":[{"last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"day":"15","date_updated":"2023-08-25T10:34:41Z","abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. 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Amberg, S. Laukoter, and S. Hippenmeyer, “Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex,” <i>Journal of Neurochemistry</i>, vol. 149, no. 1. Wiley, pp. 12–26, 2019.","chicago":"Amberg, Nicole, Susanne Laukoter, and Simon Hippenmeyer. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” <i>Journal of Neurochemistry</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/jnc.14601\">https://doi.org/10.1111/jnc.14601</a>.","short":"N. Amberg, S. Laukoter, S. Hippenmeyer, Journal of Neurochemistry 149 (2019) 12–26.","ama":"Amberg N, Laukoter S, Hippenmeyer S. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. <i>Journal of Neurochemistry</i>. 2019;149(1):12-26. doi:<a href=\"https://doi.org/10.1111/jnc.14601\">10.1111/jnc.14601</a>","mla":"Amberg, Nicole, et al. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” <i>Journal of Neurochemistry</i>, vol. 149, no. 1, Wiley, 2019, pp. 12–26, doi:<a href=\"https://doi.org/10.1111/jnc.14601\">10.1111/jnc.14601</a>.","ista":"Amberg N, Laukoter S, Hippenmeyer S. 2019. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. 149(1), 12–26.","apa":"Amberg, N., Laukoter, S., &#38; Hippenmeyer, S. (2019). Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. <i>Journal of Neurochemistry</i>. Wiley. <a href=\"https://doi.org/10.1111/jnc.14601\">https://doi.org/10.1111/jnc.14601</a>"},"intvolume":"       149","has_accepted_license":"1","publication_status":"published","oa":1,"ddc":["570"],"date_published":"2019-04-01T00:00:00Z","year":"2019","acknowledgement":" This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung \r\nn[f+b]   (C13-002)   to   SH;   a   program   grant   from   the   Human   Frontiers   Science   Program (RGP0053/2014)  to SH;  the  People  Programme  (Marie  Curie  Actions)  of  the  European  Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No 618444 to SH, and the  European  Research  Council  (ERC)  under  the  European  Union’s  Horizon  2020  research  and innovation programme (grant agreement No 725780 LinPro)to SH.\r\n","_id":"27","oa_version":"Published Version","month":"04","type":"journal_article","date_updated":"2023-09-11T13:40:26Z","abstract":[{"text":"The cerebral cortex is composed of a large variety of distinct cell-types including projection neurons, interneurons and glial cells which emerge from distinct neural stem cell (NSC) lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells (RGPs) in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that NSC and RGP lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell-type diversity during cortical development. This article is protected by copyright. All rights reserved.","lang":"eng"}],"page":"12-26","date_created":"2018-12-11T11:44:14Z","file_date_updated":"2020-07-14T12:45:45Z","volume":149,"project":[{"grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0053/2014","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444"},{"grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"issue":"1","language":[{"iso":"eng"}],"isi":1,"quality_controlled":"1","doi":"10.1111/jnc.14601","department":[{"_id":"SiHi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","article_type":"review","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","ec_funded":1,"publication":"Journal of Neurochemistry","day":"01","file":[{"checksum":"db027721a95d36f5de36aadcd0bdf7e6","date_updated":"2020-07-14T12:45:45Z","file_id":"7239","access_level":"open_access","date_created":"2020-01-07T13:35:52Z","file_name":"2019_Wiley_Amberg.pdf","creator":"kschuh","relation":"main_file","content_type":"application/pdf","file_size":889709}],"author":[{"first_name":"Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole"},{"id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","first_name":"Susanne","last_name":"Laukoter"},{"last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"title":"Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex"}]