[{"doi":"10.1016/j.chembiol.2019.09.002","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.chembiol.2019.09.002","open_access":"1"}],"external_id":{"pmid":["31543461"]},"oa":1,"quality_controlled":"1","month":"11","publication_identifier":{"issn":["2451-9456"]},"author":[{"orcid":"0000-0002-9592-1587","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","last_name":"Bakail","first_name":"May M","full_name":"Bakail, May M"},{"full_name":"Gaubert, Albane","first_name":"Albane","last_name":"Gaubert"},{"last_name":"Andreani","first_name":"Jessica","full_name":"Andreani, Jessica"},{"last_name":"Moal","first_name":"Gwenaëlle","full_name":"Moal, Gwenaëlle"},{"full_name":"Pinna, Guillaume","first_name":"Guillaume","last_name":"Pinna"},{"last_name":"Boyarchuk","first_name":"Ekaterina","full_name":"Boyarchuk, Ekaterina"},{"last_name":"Gaillard","first_name":"Marie-Cécile","full_name":"Gaillard, Marie-Cécile"},{"full_name":"Courbeyrette, Regis","first_name":"Regis","last_name":"Courbeyrette"},{"full_name":"Mann, Carl","first_name":"Carl","last_name":"Mann"},{"last_name":"Thuret","first_name":"Jean-Yves","full_name":"Thuret, Jean-Yves"},{"full_name":"Guichard, Bérengère","first_name":"Bérengère","last_name":"Guichard"},{"last_name":"Murciano","first_name":"Brice","full_name":"Murciano, Brice"},{"first_name":"Nicolas","last_name":"Richet","full_name":"Richet, Nicolas"},{"full_name":"Poitou, Adeline","first_name":"Adeline","last_name":"Poitou"},{"full_name":"Frederic, Claire","first_name":"Claire","last_name":"Frederic"},{"full_name":"Le Du, Marie-Hélène","first_name":"Marie-Hélène","last_name":"Le Du"},{"full_name":"Agez, Morgane","last_name":"Agez","first_name":"Morgane"},{"first_name":"Caroline","last_name":"Roelants","full_name":"Roelants, Caroline"},{"last_name":"Gurard-Levin","first_name":"Zachary A.","full_name":"Gurard-Levin, Zachary A."},{"full_name":"Almouzni, Geneviève","last_name":"Almouzni","first_name":"Geneviève"},{"full_name":"Cherradi, Nadia","first_name":"Nadia","last_name":"Cherradi"},{"full_name":"Guerois, Raphael","first_name":"Raphael","last_name":"Guerois"},{"full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein","first_name":"Françoise"}],"date_created":"2021-01-19T11:04:50Z","date_updated":"2023-02-23T13:46:53Z","volume":26,"year":"2019","pmid":1,"publication_status":"published","publisher":"Elsevier","extern":"1","date_published":"2019-11-21T00:00:00Z","publication":"Cell Chemical Biology","citation":{"ista":"Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C, Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11), 1573–1585.e10.","apa":"Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E., … Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. Elsevier. https://doi.org/10.1016/j.chembiol.2019.09.002","ieee":"M. M. Bakail et al., “Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1,” Cell Chemical Biology, vol. 26, no. 11. Elsevier, p. 1573–1585.e10, 2019.","ama":"Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 2019;26(11):1573-1585.e10. doi:10.1016/j.chembiol.2019.09.002","chicago":"Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology. Elsevier, 2019. https://doi.org/10.1016/j.chembiol.2019.09.002.","mla":"Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology, vol. 26, no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:10.1016/j.chembiol.2019.09.002.","short":"M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C. Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N. Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin, G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26 (2019) 1573–1585.e10."},"article_type":"original","page":"1573-1585.e10","day":"21","article_processing_charge":"No","keyword":["Clinical Biochemistry","Molecular Medicine","Biochemistry","Molecular Biology","Pharmacology","Drug Discovery"],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9018","status":"public","title":"Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1","intvolume":" 26","abstract":[{"text":"Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.","lang":"eng"}],"issue":"11","type":"journal_article"},{"date_published":"2019-10-10T00:00:00Z","article_type":"original","publication":"Epigenetics and Chromatin","citation":{"ama":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 2019;12. doi:10.1186/s13072-019-0307-4","ista":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62.","apa":"Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., & Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4","ieee":"K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” Epigenetics and Chromatin, vol. 12. Springer Nature, 2019.","mla":"Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin, vol. 12, 62, Springer Nature, 2019, doi:10.1186/s13072-019-0307-4.","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019).","chicago":"Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4."},"day":"10","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"asandaue","file_size":3221067,"content_type":"application/pdf","file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","access_level":"open_access","date_created":"2021-06-08T09:29:19Z","date_updated":"2021-06-08T09:29:19Z","success":1,"checksum":"86ff50a7517891511af2733c76c81b67","file_id":"9531","relation":"main_file"}],"title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","status":"public","ddc":["570"],"intvolume":" 12","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9530","abstract":[{"lang":"eng","text":"Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1186/s13072-019-0307-4","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31601251"]},"oa":1,"month":"10","publication_identifier":{"eissn":["1756-8935"]},"date_created":"2021-06-08T09:21:51Z","date_updated":"2021-12-14T07:53:00Z","volume":12,"author":[{"full_name":"Harris, Keith D.","last_name":"Harris","first_name":"Keith D."},{"full_name":"Lloyd, James P. B.","first_name":"James P. B.","last_name":"Lloyd"},{"first_name":"Katherine","last_name":"Domb","full_name":"Domb, Katherine"},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"},{"full_name":"Zemach, Assaf","first_name":"Assaf","last_name":"Zemach"}],"publication_status":"published","department":[{"_id":"DaZi"}],"publisher":"Springer Nature","year":"2019","pmid":1,"license":"https://creativecommons.org/licenses/by/4.0/","extern":"1","file_date_updated":"2021-06-08T09:29:19Z","article_number":"62"},{"extern":"1","author":[{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","last_name":"Kwan","full_name":"Kwan, Matthew Alan"},{"full_name":"Sudakov, Benny","first_name":"Benny","last_name":"Sudakov"},{"last_name":"Tran","first_name":"Tuan","full_name":"Tran, Tuan"}],"volume":99,"date_updated":"2023-02-23T14:01:53Z","date_created":"2021-06-22T09:46:03Z","year":"2019","publisher":"Wiley","publication_status":"published","publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"month":"05","doi":"10.1112/jlms.12192","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1807.05202","open_access":"1"}],"external_id":{"arxiv":["1807.05202"]},"oa":1,"quality_controlled":"1","issue":"3","abstract":[{"text":"Consider integers 𝑘,ℓ such that 0⩽ℓ⩽(𝑘2) . Given a large graph 𝐺 , what is the fraction of 𝑘 -vertex subsets of 𝐺 which span exactly ℓ edges? When 𝐺 is empty or complete, and ℓ is zero or (𝑘2) , this fraction can be exactly 1. On the other hand, if ℓ is far from these extreme values, one might expect that this fraction is substantially smaller than 1. This was recently proved by Alon, Hefetz, Krivelevich, and Tyomkyn who initiated the systematic study of this question and proposed several natural conjectures.\r\nLet ℓ∗=min{ℓ,(𝑘2)−ℓ} . Our main result is that for any 𝑘 and ℓ , the fraction of 𝑘 -vertex subsets that span ℓ edges is at most log𝑂(1)(ℓ∗/𝑘)√ 𝑘/ℓ∗, which is best-possible up to the logarithmic factor. This improves on multiple results of Alon, Hefetz, Krivelevich, and Tyomkyn, and resolves one of their conjectures. In addition, we also make some first steps towards some analogous questions for hypergraphs.\r\nOur proofs involve some Ramsey-type arguments, and a number of different probabilistic tools, such as polynomial anticoncentration inequalities, hypercontractivity, and a coupling trick for random variables defined on a ‘slice’ of the Boolean hypercube.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9586","intvolume":" 99","status":"public","title":"Anticoncentration for subgraph statistics","article_processing_charge":"No","day":"03","scopus_import":"1","date_published":"2019-05-03T00:00:00Z","citation":{"short":"M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society 99 (2019) 757–777.","mla":"Kwan, Matthew Alan, et al. “Anticoncentration for Subgraph Statistics.” Journal of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 757–77, doi:10.1112/jlms.12192.","chicago":"Kwan, Matthew Alan, Benny Sudakov, and Tuan Tran. “Anticoncentration for Subgraph Statistics.” Journal of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12192.","ama":"Kwan MA, Sudakov B, Tran T. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 2019;99(3):757-777. doi:10.1112/jlms.12192","ieee":"M. A. Kwan, B. Sudakov, and T. Tran, “Anticoncentration for subgraph statistics,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 757–777, 2019.","apa":"Kwan, M. A., Sudakov, B., & Tran, T. (2019). Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12192","ista":"Kwan MA, Sudakov B, Tran T. 2019. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 99(3), 757–777."},"publication":"Journal of the London Mathematical Society","page":"757-777","article_type":"original"},{"date_published":"2019-08-01T00:00:00Z","publication":"Israel Journal of Mathematics","citation":{"chicago":"Conlon, David, Jacob Fox, Matthew Alan Kwan, and Benny Sudakov. “Hypergraph Cuts above the Average.” Israel Journal of Mathematics. Springer, 2019. https://doi.org/10.1007/s11856-019-1897-z.","mla":"Conlon, David, et al. “Hypergraph Cuts above the Average.” Israel Journal of Mathematics, vol. 233, no. 1, Springer, 2019, pp. 67–111, doi:10.1007/s11856-019-1897-z.","short":"D. Conlon, J. Fox, M.A. Kwan, B. Sudakov, Israel Journal of Mathematics 233 (2019) 67–111.","ista":"Conlon D, Fox J, Kwan MA, Sudakov B. 2019. Hypergraph cuts above the average. Israel Journal of Mathematics. 233(1), 67–111.","ieee":"D. Conlon, J. Fox, M. A. Kwan, and B. Sudakov, “Hypergraph cuts above the average,” Israel Journal of Mathematics, vol. 233, no. 1. Springer, pp. 67–111, 2019.","apa":"Conlon, D., Fox, J., Kwan, M. A., & Sudakov, B. (2019). Hypergraph cuts above the average. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-019-1897-z","ama":"Conlon D, Fox J, Kwan MA, Sudakov B. Hypergraph cuts above the average. Israel Journal of Mathematics. 2019;233(1):67-111. doi:10.1007/s11856-019-1897-z"},"article_type":"original","page":"67-111","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9580","title":"Hypergraph cuts above the average","status":"public","intvolume":" 233","abstract":[{"lang":"eng","text":"An r-cut of a k-uniform hypergraph H is a partition of the vertex set of H into r parts and the size of the cut is the number of edges which have a vertex in each part. A classical result of Edwards says that every m-edge graph has a 2-cut of size m/2+Ω)(m−−√) and this is best possible. That is, there exist cuts which exceed the expected size of a random cut by some multiple of the standard deviation. We study analogues of this and related results in hypergraphs. First, we observe that similarly to graphs, every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m−−√) larger than the expected size of a random r-cut. Moreover, in the case where k = 3 and r = 2 this bound is best possible and is attained by Steiner triple systems. Surprisingly, for all other cases (that is, if k ≥ 4 or r ≥ 3), we show that every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m5/9) larger than the expected size of a random r-cut. This is a significant difference in behaviour, since the amount by which the size of the largest cut exceeds the expected size of a random cut is now considerably larger than the standard deviation."}],"issue":"1","type":"journal_article","doi":"10.1007/s11856-019-1897-z","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.08462"}],"external_id":{"arxiv":["1803.08462"]},"oa":1,"quality_controlled":"1","month":"08","publication_identifier":{"issn":["0021-2172"],"eissn":["1565-8511"]},"author":[{"first_name":"David","last_name":"Conlon","full_name":"Conlon, David"},{"full_name":"Fox, Jacob","last_name":"Fox","first_name":"Jacob"},{"orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan"},{"first_name":"Benny","last_name":"Sudakov","full_name":"Sudakov, Benny"}],"date_updated":"2023-02-23T14:01:41Z","date_created":"2021-06-21T13:36:02Z","volume":233,"year":"2019","publication_status":"published","publisher":"Springer","extern":"1"},{"day":"15","article_processing_charge":"No","scopus_import":"1","date_published":"2019-10-15T00:00:00Z","publication":"Transactions of the American Mathematical Society","citation":{"short":"M.A. Kwan, B. Sudakov, Transactions of the American Mathematical Society 372 (2019) 5571–5594.","mla":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society, vol. 372, no. 8, American Mathematical Society, 2019, pp. 5571–94, doi:10.1090/tran/7729.","chicago":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7729.","ama":"Kwan MA, Sudakov B. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 2019;372(8):5571-5594. doi:10.1090/tran/7729","apa":"Kwan, M. A., & Sudakov, B. (2019). Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7729","ieee":"M. A. Kwan and B. Sudakov, “Proof of a conjecture on induced subgraphs of Ramsey graphs,” Transactions of the American Mathematical Society, vol. 372, no. 8. American Mathematical Society, pp. 5571–5594, 2019.","ista":"Kwan MA, Sudakov B. 2019. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 372(8), 5571–5594."},"article_type":"original","page":"5571-5594","abstract":[{"lang":"eng","text":"An n-vertex graph is called C-Ramsey if it has no clique or independent set of size C log n. All known constructions of Ramsey graphs involve randomness in an essential way, and there is an ongoing line of research towards showing that in fact all Ramsey graphs must obey certain “richness” properties characteristic of random graphs. More than 25 years ago, Erdős, Faudree and Sós conjectured that in any C-Ramsey graph there are Ω(n^5/2) induced subgraphs, no pair of which have the same numbers of vertices and edges. Improving on earlier results of Alon, Balogh, Kostochka and Samotij, in this paper we prove this conjecture."}],"issue":"8","type":"journal_article","oa_version":"Submitted Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9585","title":"Proof of a conjecture on induced subgraphs of Ramsey graphs","status":"public","intvolume":" 372","month":"10","publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"doi":"10.1090/tran/7729","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1712.05656"]},"main_file_link":[{"url":"https://doi.org/10.1090/tran/7729","open_access":"1"}],"quality_controlled":"1","extern":"1","author":[{"first_name":"Matthew Alan","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan"},{"full_name":"Sudakov, Benny","first_name":"Benny","last_name":"Sudakov"}],"date_created":"2021-06-22T09:31:45Z","date_updated":"2023-02-23T14:01:50Z","volume":372,"year":"2019","publication_status":"published","publisher":"American Mathematical Society"}]