[{"external_id":{"pmid":["30444575"]},"quality_controlled":"1","doi":"10.1002/cphc.201800935","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1439-4235"]},"month":"01","pmid":1,"year":"2019","publisher":"Wiley","publication_status":"published","author":[{"last_name":"Marion","first_name":"Dominique","full_name":"Marion, Dominique"},{"last_name":"Gauto","first_name":"Diego F.","full_name":"Gauto, Diego F."},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"full_name":"Giandoreggio-Barranco, Karine","first_name":"Karine","last_name":"Giandoreggio-Barranco"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"}],"volume":20,"date_created":"2020-09-17T10:29:36Z","date_updated":"2021-01-12T08:19:06Z","extern":"1","citation":{"ista":"Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. 2019. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 20(2), 276–284.","ieee":"D. Marion, D. F. Gauto, I. Ayala, K. Giandoreggio-Barranco, and P. Schanda, “Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 276–284, 2019.","apa":"Marion, D., Gauto, D. F., Ayala, I., Giandoreggio-Barranco, K., & Schanda, P. (2019). Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800935","ama":"Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 2019;20(2):276-284. doi:10.1002/cphc.201800935","chicago":"Marion, Dominique, Diego F. Gauto, Isabel Ayala, Karine Giandoreggio-Barranco, and Paul Schanda. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800935.","mla":"Marion, Dominique, et al. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 276–84, doi:10.1002/cphc.201800935.","short":"D. Marion, D.F. Gauto, I. Ayala, K. Giandoreggio-Barranco, P. Schanda, ChemPhysChem 20 (2019) 276–284."},"publication":"ChemPhysChem","page":"276-284","article_type":"original","date_published":"2019-01-21T00:00:00Z","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"article_processing_charge":"No","day":"21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8411","intvolume":" 20","status":"public","title":"Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR","oa_version":"Submitted Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Studying protein dynamics on microsecond‐to‐millisecond (μs‐ms) time scales can provide important insight into protein function. In magic‐angle‐spinning (MAS) NMR, μs dynamics can be visualized by R1p rotating‐frame relaxation dispersion experiments in different regimes of radio‐frequency field strengths: at low RF field strength, isotropic‐chemical‐shift fluctuation leads to “Bloch‐McConnell‐type” relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R1p rate constants (“Near‐Rotary‐Resonance Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical‐shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin."}]},{"extern":"1","year":"2019","publication_status":"published","publisher":"Springer Nature","author":[{"last_name":"Bálint","first_name":"Péter","full_name":"Bálint, Péter"},{"full_name":"De Simoi, Jacopo","last_name":"De Simoi","first_name":"Jacopo"},{"full_name":"Kaloshin, Vadim","first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628"},{"last_name":"Leguil","first_name":"Martin","full_name":"Leguil, Martin"}],"date_updated":"2021-01-12T08:19:08Z","date_created":"2020-09-17T10:41:27Z","volume":374,"month":"05","publication_identifier":{"issn":["0010-3616","1432-0916"]},"external_id":{"arxiv":["1809.08947"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1809.08947","open_access":"1"}],"quality_controlled":"1","doi":"10.1007/s00220-019-03448-x","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We consider billiards obtained by removing three strictly convex obstacles satisfying the non-eclipse condition on the plane. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift on three symbols that provides a natural labeling of all periodic orbits. We study the following inverse problem: does the Marked Length Spectrum (i.e., the set of lengths of periodic orbits together with their labeling), determine the geometry of the billiard table? We show that from the Marked Length Spectrum it is possible to recover the curvature at periodic points of period two, as well as the Lyapunov exponent of each periodic orbit."}],"issue":"3","_id":"8415","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards","intvolume":" 374","oa_version":"Preprint","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"day":"09","article_processing_charge":"No","publication":"Communications in Mathematical Physics","citation":{"mla":"Bálint, Péter, et al. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics, vol. 374, no. 3, Springer Nature, 2019, pp. 1531–75, doi:10.1007/s00220-019-03448-x.","short":"P. Bálint, J. De Simoi, V. Kaloshin, M. Leguil, Communications in Mathematical Physics 374 (2019) 1531–1575.","chicago":"Bálint, Péter, Jacopo De Simoi, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03448-x.","ama":"Bálint P, De Simoi J, Kaloshin V, Leguil M. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 2019;374(3):1531-1575. doi:10.1007/s00220-019-03448-x","ista":"Bálint P, De Simoi J, Kaloshin V, Leguil M. 2019. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 374(3), 1531–1575.","apa":"Bálint, P., De Simoi, J., Kaloshin, V., & Leguil, M. (2019). Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03448-x","ieee":"P. Bálint, J. De Simoi, V. Kaloshin, and M. Leguil, “Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards,” Communications in Mathematical Physics, vol. 374, no. 3. Springer Nature, pp. 1531–1575, 2019."},"article_type":"original","page":"1531-1575","date_published":"2019-05-09T00:00:00Z"},{"publication_identifier":{"issn":["1047-8477"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1016/j.jsb.2018.07.009","quality_controlled":"1","external_id":{"pmid":["30031884"]},"extern":"1","volume":206,"date_created":"2020-09-17T10:29:10Z","date_updated":"2021-01-12T08:19:05Z","author":[{"first_name":"Catherine","last_name":"Bougault","full_name":"Bougault, Catherine"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"last_name":"Vollmer","first_name":"Waldemar","full_name":"Vollmer, Waldemar"},{"first_name":"Jean-Pierre","last_name":"Simorre","full_name":"Simorre, Jean-Pierre"},{"full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2019","article_processing_charge":"No","day":"01","keyword":["Structural Biology"],"date_published":"2019-04-01T00:00:00Z","page":"66-72","article_type":"original","citation":{"short":"C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, P. Schanda, Journal of Structural Biology 206 (2019) 66–72.","mla":"Bougault, Catherine, et al. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology, vol. 206, no. 1, Elsevier, 2019, pp. 66–72, doi:10.1016/j.jsb.2018.07.009.","chicago":"Bougault, Catherine, Isabel Ayala, Waldemar Vollmer, Jean-Pierre Simorre, and Paul Schanda. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.jsb.2018.07.009.","ama":"Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 2019;206(1):66-72. doi:10.1016/j.jsb.2018.07.009","ieee":"C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, and P. Schanda, “Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency,” Journal of Structural Biology, vol. 206, no. 1. Elsevier, pp. 66–72, 2019.","apa":"Bougault, C., Ayala, I., Vollmer, W., Simorre, J.-P., & Schanda, P. (2019). Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2018.07.009","ista":"Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. 2019. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 206(1), 66–72."},"publication":"Journal of Structural Biology","issue":"1","abstract":[{"lang":"eng","text":"The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer that maintains the integrity of the bacterial cell. Due to its multi-gigadalton size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex. Solid-state NMR is an important technique to gain insight into its structure, dynamics and interactions. Here, we explore the possibilities to study the PG with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly resolved spectra can be obtained, and show strategies to obtain site-specific resonance assignments and distance information. We also explore the use of proton-proton correlation experiments, thus opening the way for NMR studies of intact cell walls without the need for isotope labeling."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 206","status":"public","title":"Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8409"},{"type":"journal_article","extern":"1","_id":"8407","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","pmid":1,"status":"public","title":"Relaxing with liquids and solids – A perspective on biomolecular dynamics","publication_status":"published","intvolume":" 306","publisher":"Elsevier","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"}],"date_updated":"2021-01-12T08:19:04Z","date_created":"2020-09-17T10:28:47Z","volume":306,"oa_version":"Submitted Version","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"month":"09","day":"01","article_processing_charge":"No","publication_identifier":{"issn":["1090-7807"]},"publication":"Journal of Magnetic Resonance","citation":{"short":"P. Schanda, Journal of Magnetic Resonance 306 (2019) 180–186.","mla":"Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” Journal of Magnetic Resonance, vol. 306, Elsevier, 2019, pp. 180–86, doi:10.1016/j.jmr.2019.07.025.","chicago":"Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” Journal of Magnetic Resonance. Elsevier, 2019. https://doi.org/10.1016/j.jmr.2019.07.025.","ama":"Schanda P. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 2019;306:180-186. doi:10.1016/j.jmr.2019.07.025","ieee":"P. Schanda, “Relaxing with liquids and solids – A perspective on biomolecular dynamics,” Journal of Magnetic Resonance, vol. 306. Elsevier, pp. 180–186, 2019.","apa":"Schanda, P. (2019). Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2019.07.025","ista":"Schanda P. 2019. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 306, 180–186."},"external_id":{"pmid":["31350165"]},"quality_controlled":"1","article_type":"original","page":"180-186","doi":"10.1016/j.jmr.2019.07.025","date_published":"2019-09-01T00:00:00Z","language":[{"iso":"eng"}]},{"day":"21","article_processing_charge":"No","date_published":"2019-01-21T00:00:00Z","publication":"ChemPhysChem","citation":{"short":"P. Schanda, E.Y. Chekmenev, ChemPhysChem 20 (2019) 177–177.","mla":"Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 177–177, doi:10.1002/cphc.201801100.","chicago":"Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201801100.","ama":"Schanda P, Chekmenev EY. NMR for Biological Systems. ChemPhysChem. 2019;20(2):177-177. doi:10.1002/cphc.201801100","apa":"Schanda, P., & Chekmenev, E. Y. (2019). NMR for Biological Systems. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201801100","ieee":"P. Schanda and E. Y. Chekmenev, “NMR for Biological Systems,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 177–177, 2019.","ista":"Schanda P, Chekmenev EY. 2019. NMR for Biological Systems. ChemPhysChem. 20(2), 177–177."},"article_type":"letter_note","page":"177-177","issue":"2","type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8410","status":"public","title":"NMR for Biological Systems","intvolume":" 20","month":"01","publication_identifier":{"issn":["1439-4235"]},"doi":"10.1002/cphc.201801100","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["30556633"]},"main_file_link":[{"url":"https://doi.org/10.1002/cphc.201801100","open_access":"1"}],"quality_controlled":"1","extern":"1","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"},{"full_name":"Chekmenev, Eduard Y.","last_name":"Chekmenev","first_name":"Eduard Y."}],"date_created":"2020-09-17T10:29:26Z","date_updated":"2021-01-12T08:19:05Z","volume":20,"year":"2019","pmid":1,"publication_status":"published","publisher":"Wiley"},{"abstract":[{"lang":"eng","text":"This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been applied to solve six different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date."}],"type":"conference","date_updated":"2021-01-12T08:20:05Z","date_created":"2020-09-26T14:23:54Z","volume":61,"oa_version":"Published Version","author":[{"full_name":"Althoff, Matthias","last_name":"Althoff","first_name":"Matthias"},{"full_name":"Bak, Stanley","first_name":"Stanley","last_name":"Bak"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"last_name":"Kochdumper","first_name":"Niklas","full_name":"Kochdumper, Niklas"},{"last_name":"Ray","first_name":"Rajarshi","full_name":"Ray, Rajarshi"},{"full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065"},{"full_name":"Schupp, Stefan","last_name":"Schupp","first_name":"Stefan"}],"publication_status":"published","status":"public","title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics","department":[{"_id":"ToHe"}],"intvolume":" 61","publisher":"EasyChair","year":"2019","_id":"8570","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"25","month":"05","article_processing_charge":"No","publication_identifier":{"eissn":["23987340"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2019-04-15","start_date":"2019-04-15","location":"Montreal, Canada","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"date_published":"2019-05-25T00:00:00Z","doi":"10.29007/bj1w","quality_controlled":"1","page":"14-40","publication":"EPiC Series in Computing","oa":1,"citation":{"short":"M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling, S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40.","mla":"Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” EPiC Series in Computing, vol. 61, EasyChair, 2019, pp. 14–40, doi:10.29007/bj1w.","chicago":"Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper, Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” In EPiC Series in Computing, 61:14–40. EasyChair, 2019. https://doi.org/10.29007/bj1w.","ama":"Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In: EPiC Series in Computing. Vol 61. EasyChair; 2019:14-40. doi:10.29007/bj1w","apa":"Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp, S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In EPiC Series in Computing (Vol. 61, pp. 14–40). Montreal, Canada: EasyChair. https://doi.org/10.29007/bj1w","ieee":"M. Althoff et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 14–40.","ista":"Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40."},"main_file_link":[{"open_access":"1","url":"https://easychair.org/publications/open/1gbP"}]},{"article_processing_charge":"No","day":"01","date_published":"2019-04-01T00:00:00Z","citation":{"ama":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 2019;20(7):891-895. doi:10.1002/cbic.201800633","ieee":"M. M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein, and A. J. Wilson, “Recognition of ASF1 by using hydrocarbon‐constrained peptides,” ChemBioChem, vol. 20, no. 7. Wiley, pp. 891–895, 2019.","apa":"Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein, F., & Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. Wiley. https://doi.org/10.1002/cbic.201800633","ista":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. 2019. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 20(7), 891–895.","short":"M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein, A.J. Wilson, ChemBioChem 20 (2019) 891–895.","mla":"Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” ChemBioChem, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:10.1002/cbic.201800633.","chicago":"Bakail, May M, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin, Françoise Ochsenbein, and Andrew J. Wilson. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” ChemBioChem. Wiley, 2019. https://doi.org/10.1002/cbic.201800633."},"publication":"ChemBioChem","page":"891-895","article_type":"original","issue":"7","abstract":[{"lang":"eng","text":"Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135) is a strategy through which chemical probes might be elaborated to test this hypothesis. In this work, variant H3118–135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy–entropy compensation occurs."}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9016","intvolume":" 20","status":"public","title":"Recognition of ASF1 by using hydrocarbon‐constrained peptides","publication_identifier":{"issn":["1439-4227","1439-7633"]},"month":"04","doi":"10.1002/cbic.201800633","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":" https://doi.org/10.1002/cbic.201800633","open_access":"1"}],"quality_controlled":"1","extern":"1","author":[{"orcid":"0000-0002-9592-1587","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","last_name":"Bakail","first_name":"May M","full_name":"Bakail, May M"},{"first_name":"Silvia","last_name":"Rodriguez‐Marin","full_name":"Rodriguez‐Marin, Silvia"},{"full_name":"Hegedüs, Zsófia","first_name":"Zsófia","last_name":"Hegedüs"},{"last_name":"Perrin","first_name":"Marie E.","full_name":"Perrin, Marie E."},{"last_name":"Ochsenbein","first_name":"Françoise","full_name":"Ochsenbein, Françoise"},{"full_name":"Wilson, Andrew J.","last_name":"Wilson","first_name":"Andrew J."}],"volume":20,"date_updated":"2023-02-23T13:46:48Z","date_created":"2021-01-19T10:59:14Z","year":"2019","publisher":"Wiley","publication_status":"published"},{"extern":"1","file_date_updated":"2021-02-02T13:47:21Z","article_number":"3380","date_updated":"2023-02-23T13:47:59Z","date_created":"2021-02-02T13:43:36Z","volume":10,"author":[{"first_name":"Sophie","last_name":"Ramananarivo","full_name":"Ramananarivo, Sophie"},{"last_name":"Ducrot","first_name":"Etienne","full_name":"Ducrot, Etienne"},{"full_name":"Palacci, Jérémie A","last_name":"Palacci","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"}],"publication_status":"published","publisher":"Springer Nature","year":"2019","pmid":1,"month":"07","publication_identifier":{"issn":["2041-1723"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-11362-y","quality_controlled":"1","external_id":{"arxiv":["1909.07382"],"pmid":["31358762"]},"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"},"oa":1,"abstract":[{"lang":"eng","text":"Molecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium."}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2021-02-02T13:47:21Z","date_updated":"2021-02-02T13:47:21Z","checksum":"70c6e5d6fbea0932b0669505ab6633ec","success":1,"relation":"main_file","file_id":"9061","content_type":"application/pdf","file_size":2820337,"creator":"cziletti","file_name":"2019_NatureComm_Ramananarivo.pdf","access_level":"open_access"}],"ddc":["530"],"status":"public","title":"Activity-controlled annealing of colloidal monolayers","intvolume":" 10","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9060","day":"29","has_accepted_license":"1","article_processing_charge":"No","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"scopus_import":"1","date_published":"2019-07-29T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"ista":"Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing of colloidal monolayers. Nature Communications. 10(1), 3380.","apa":"Ramananarivo, S., Ducrot, E., & Palacci, J. A. (2019). Activity-controlled annealing of colloidal monolayers. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-11362-y","ieee":"S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing of colloidal monolayers,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","ama":"Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal monolayers. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-11362-y","chicago":"Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled Annealing of Colloidal Monolayers.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-11362-y.","mla":"Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.” Nature Communications, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:10.1038/s41467-019-11362-y.","short":"S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019)."}},{"type":"journal_article","issue":"19","abstract":[{"text":"Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion.","lang":"eng"}],"intvolume":" 116","title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","ddc":["580"],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9460","file":[{"creator":"asandaue","content_type":"application/pdf","file_size":1142540,"access_level":"open_access","file_name":"2019_PNAS_Kim.pdf","success":1,"checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","date_updated":"2021-06-04T12:50:47Z","date_created":"2021-06-04T12:50:47Z","file_id":"9461","relation":"main_file"}],"oa_version":"Published Version","keyword":["Multidisciplinary"],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"07","page":"9652-9657","article_type":"original","citation":{"mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116.","short":"M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.","chicago":"Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.","ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116","ista":"Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., & Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116","ieee":"M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” Proceedings of the National Academy of Sciences, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019."},"publication":"Proceedings of the National Academy of Sciences","date_published":"2019-05-07T00:00:00Z","extern":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2021-06-04T12:50:47Z","publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}],"publication_status":"published","pmid":1,"year":"2019","volume":116,"date_updated":"2021-12-14T07:52:30Z","date_created":"2021-06-04T12:38:20Z","author":[{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"first_name":"Akemi","last_name":"Ono","full_name":"Ono, Akemi"},{"last_name":"Scholten","first_name":"Stefan","full_name":"Scholten, Stefan"},{"full_name":"Kinoshita, Tetsu","last_name":"Kinoshita","first_name":"Tetsu"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman"},{"last_name":"Okamoto","first_name":"Takashi","full_name":"Okamoto, Takashi"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"05","quality_controlled":"1","external_id":{"pmid":["31000601"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1821435116"},{"day":"22","article_processing_charge":"No","scopus_import":"1","date_published":"2019-01-22T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","citation":{"chicago":"Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1815117116.","short":"B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of the National Academy of Sciences 116 (2019) 1110–1115.","mla":"Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings of the National Academy of Sciences, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1110–15, doi:10.1073/pnas.1815117116.","apa":"Cheng, B., Engel, E. A., Behler, J., Dellago, C., & Ceriotti, M. (2019). Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1815117116","ieee":"B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio thermodynamics of liquid and solid water,” Proceedings of the National Academy of Sciences, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115, 2019.","ista":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4), 1110–1115.","ama":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 2019;116(4):1110-1115. doi:10.1073/pnas.1815117116"},"article_type":"original","page":"1110-1115","abstract":[{"text":"A central goal of computational physics and chemistry is to predict material properties by using first-principles methods based on the fundamental laws of quantum mechanics. However, the high computational costs of these methods typically prevent rigorous predictions of macroscopic quantities at finite temperatures, such as heat capacity, density, and chemical potential. Here, we enable such predictions by marrying advanced free-energy methods with data-driven machine-learning interatomic potentials. We show that, for the ubiquitous and technologically essential system of water, a first-principles thermodynamic description not only leads to excellent agreement with experiments, but also reveals the crucial role of nuclear quantum fluctuations in modulating the thermodynamic stabilities of different phases of water.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9689","status":"public","title":"Ab initio thermodynamics of liquid and solid water","intvolume":" 116","month":"01","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.1815117116","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1815117116","open_access":"1"}],"external_id":{"pmid":["30610171"],"arxiv":["1811.08630"]},"quality_controlled":"1","extern":"1","author":[{"last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"},{"last_name":"Engel","first_name":"Edgar A.","full_name":"Engel, Edgar A."},{"full_name":"Behler, Jörg","last_name":"Behler","first_name":"Jörg"},{"last_name":"Dellago","first_name":"Christoph","full_name":"Dellago, Christoph"},{"last_name":"Ceriotti","first_name":"Michele","full_name":"Ceriotti, Michele"}],"date_updated":"2023-02-23T14:05:08Z","date_created":"2021-07-19T10:17:09Z","volume":116,"year":"2019","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences"},{"scopus_import":1,"day":"08","article_processing_charge":"No","has_accepted_license":"1","publication":"BMC Research Notes","citation":{"chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes. BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, BMC Research Notes 12 (2019).","mla":"Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol. 12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells,” BMC Research Notes, vol. 12. BioMed Central, 2019.","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 12, 494.","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3"},"date_published":"2019-08-08T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome."}],"ddc":["570"],"title":"Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","status":"public","intvolume":" 12","_id":"6819","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-23T11:10:35Z","checksum":"4a2bb7994b7f2c432bf44f5127ea3102","relation":"main_file","file_id":"6829","content_type":"application/pdf","file_size":1177482,"creator":"dernst","file_name":"2019_BMC_Antoniou.pdf","access_level":"open_access"}],"oa_version":"Published Version","month":"08","publication_identifier":{"eissn":["1756-0500"]},"quality_controlled":"1","external_id":{"pmid":["31395095"]},"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"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1186/s13104-019-4534-3","article_number":"494","file_date_updated":"2020-07-14T12:47:40Z","publication_status":"published","department":[{"_id":"LifeSc"}],"publisher":"BioMed Central","year":"2019","pmid":1,"date_created":"2019-08-18T22:00:39Z","date_updated":"2023-02-23T14:08:14Z","volume":12,"author":[{"full_name":"Antoniou, Michael N.","last_name":"Antoniou","first_name":"Michael N."},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas","first_name":"Armel","full_name":"Nicolas, Armel"},{"full_name":"Mesnage, Robin","last_name":"Mesnage","first_name":"Robin"},{"first_name":"Martina","last_name":"Biserni","full_name":"Biserni, Martina"},{"first_name":"Francesco V.","last_name":"Rao","full_name":"Rao, Francesco V."},{"first_name":"Cristina Vazquez","last_name":"Martin","full_name":"Martin, Cristina Vazquez"}],"related_material":{"record":[{"id":"9784","relation":"research_data","status":"public"}]}},{"type":"research_data_reference","abstract":[{"text":"Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures.","lang":"eng"}],"status":"public","title":"MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","department":[{"_id":"LifeSc"}],"publisher":"Springer Nature","year":"2019","_id":"9784","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-06T08:14:05Z","date_updated":"2023-02-23T12:52:29Z","oa_version":"Published Version","author":[{"full_name":"Antoniou, Michael N.","first_name":"Michael N.","last_name":"Antoniou"},{"last_name":"Nicolas","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"full_name":"Mesnage, Robin","last_name":"Mesnage","first_name":"Robin"},{"first_name":"Martina","last_name":"Biserni","full_name":"Biserni, Martina"},{"first_name":"Francesco V.","last_name":"Rao","full_name":"Rao, Francesco V."},{"full_name":"Martin, Cristina Vazquez","last_name":"Martin","first_name":"Cristina Vazquez"}],"related_material":{"record":[{"id":"6819","relation":"used_in_publication","status":"public"}]},"month":"08","day":"09","article_processing_charge":"No","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9411761.v1"}],"citation":{"ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:10.6084/m9.figshare.9411761.v1","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1.","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1","mla":"Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature, 2019, doi:10.6084/m9.figshare.9411761.v1.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019).","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9411761.v1."},"date_published":"2019-08-09T00:00:00Z","doi":"10.6084/m9.figshare.9411761.v1"},{"type":"research_data_reference","abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"year":"2019","_id":"9839","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"}],"publisher":"Dryad","status":"public","title":"Data from: Is the sky the limit? On the expansion threshold of a species' range","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"315"}]},"author":[{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka"}],"oa_version":"Published Version","date_updated":"2023-02-23T11:14:30Z","date_created":"2021-08-09T13:07:28Z","article_processing_charge":"No","day":"22","month":"06","oa":1,"citation":{"chicago":"Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.","short":"J. Polechova, (2019).","mla":"Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.","apa":"Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37","ieee":"J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019.","ista":"Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, 10.5061/dryad.5vv37.","ama":"Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:10.5061/dryad.5vv37"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.5vv37","open_access":"1"}],"date_published":"2019-06-22T00:00:00Z","doi":"10.5061/dryad.5vv37"},{"oa_version":"Submitted Version","_id":"8408","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 141","title":"Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR","status":"public","issue":"28","abstract":[{"lang":"eng","text":"Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artefact-free dynamics measurements, and allows probing motions effectively without molecular-weight limitations. The application to the TET2 enzyme assembly of ~0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (ps-ms). We quantitatively probe ring flip motions, and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples."}],"type":"journal_article","date_published":"2019-06-14T00:00:00Z","citation":{"mla":"Gauto, Diego F., et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” Journal of the American Chemical Society, vol. 141, no. 28, American Chemical Society, 2019, pp. 11183–95, doi:10.1021/jacs.9b04219.","short":"D.F. Gauto, P. Macek, A. Barducci, H. Fraga, A. Hessel, T. Terauchi, D. Gajan, Y. Miyanoiri, J. Boisbouvier, R. Lichtenecker, M. Kainosho, P. Schanda, Journal of the American Chemical Society 141 (2019) 11183–11195.","chicago":"Gauto, Diego F., Pavel Macek, Alessandro Barducci, Hugo Fraga, Audrey Hessel, Tsutomu Terauchi, David Gajan, et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.9b04219.","ama":"Gauto DF, Macek P, Barducci A, et al. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. 2019;141(28):11183-11195. doi:10.1021/jacs.9b04219","ista":"Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. 2019. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. 141(28), 11183–11195.","ieee":"D. F. Gauto et al., “Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR,” Journal of the American Chemical Society, vol. 141, no. 28. American Chemical Society, pp. 11183–11195, 2019.","apa":"Gauto, D. F., Macek, P., Barducci, A., Fraga, H., Hessel, A., Terauchi, T., … Schanda, P. (2019). Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b04219"},"publication":"Journal of the American Chemical Society","page":"11183-11195","article_type":"original","article_processing_charge":"No","day":"14","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"author":[{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"first_name":"Pavel","last_name":"Macek","full_name":"Macek, Pavel"},{"first_name":"Alessandro","last_name":"Barducci","full_name":"Barducci, Alessandro"},{"full_name":"Fraga, Hugo","first_name":"Hugo","last_name":"Fraga"},{"full_name":"Hessel, Audrey","first_name":"Audrey","last_name":"Hessel"},{"full_name":"Terauchi, Tsutomu","first_name":"Tsutomu","last_name":"Terauchi"},{"first_name":"David","last_name":"Gajan","full_name":"Gajan, David"},{"last_name":"Miyanoiri","first_name":"Yohei","full_name":"Miyanoiri, Yohei"},{"full_name":"Boisbouvier, Jerome","last_name":"Boisbouvier","first_name":"Jerome"},{"full_name":"Lichtenecker, Roman","last_name":"Lichtenecker","first_name":"Roman"},{"first_name":"Masatsune","last_name":"Kainosho","full_name":"Kainosho, Masatsune"},{"last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"volume":141,"date_created":"2020-09-17T10:29:00Z","date_updated":"2021-01-12T08:19:04Z","pmid":1,"year":"2019","publisher":"American Chemical Society","publication_status":"published","extern":"1","doi":"10.1021/jacs.9b04219","language":[{"iso":"eng"}],"external_id":{"pmid":["31199882"]},"quality_controlled":"1","publication_identifier":{"issn":["0002-7863","1520-5126"]},"month":"06"},{"keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"day":"12","article_processing_charge":"No","publication":"Archive for Rational Mechanics and Analysis","citation":{"chicago":"Guardia, Marcel, Vadim Kaloshin, and Jianlu Zhang. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” Archive for Rational Mechanics and Analysis. Springer Nature, 2019. https://doi.org/10.1007/s00205-019-01368-7.","mla":"Guardia, Marcel, et al. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” Archive for Rational Mechanics and Analysis, vol. 233, no. 2, Springer Nature, 2019, pp. 799–836, doi:10.1007/s00205-019-01368-7.","short":"M. Guardia, V. Kaloshin, J. Zhang, Archive for Rational Mechanics and Analysis 233 (2019) 799–836.","ista":"Guardia M, Kaloshin V, Zhang J. 2019. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. 233(2), 799–836.","apa":"Guardia, M., Kaloshin, V., & Zhang, J. (2019). Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-019-01368-7","ieee":"M. Guardia, V. Kaloshin, and J. Zhang, “Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem,” Archive for Rational Mechanics and Analysis, vol. 233, no. 2. Springer Nature, pp. 799–836, 2019.","ama":"Guardia M, Kaloshin V, Zhang J. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. 2019;233(2):799-836. doi:10.1007/s00205-019-01368-7"},"article_type":"original","page":"799-836","date_published":"2019-03-12T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"For the Restricted Circular Planar 3 Body Problem, we show that there exists an open set U in phase space of fixed measure, where the set of initial points which lead to collision is O(μ120) dense as μ→0."}],"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8418","status":"public","title":"Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem","intvolume":" 233","oa_version":"Published Version","month":"03","publication_identifier":{"issn":["0003-9527","1432-0673"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1007/s00205-019-01368-7","open_access":"1"}],"quality_controlled":"1","doi":"10.1007/s00205-019-01368-7","language":[{"iso":"eng"}],"extern":"1","year":"2019","publication_status":"published","publisher":"Springer Nature","author":[{"full_name":"Guardia, Marcel","last_name":"Guardia","first_name":"Marcel"},{"first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"},{"last_name":"Zhang","first_name":"Jianlu","full_name":"Zhang, Jianlu"}],"date_created":"2020-09-17T10:41:51Z","date_updated":"2021-01-12T08:19:09Z","volume":233},{"extern":"1","author":[{"first_name":"Guan","last_name":"Huang","full_name":"Huang, Guan"},{"orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim"}],"volume":19,"date_created":"2020-09-17T10:41:36Z","date_updated":"2021-01-12T08:19:08Z","year":"2019","publisher":"American Mathematical Society","publication_status":"published","publication_identifier":{"issn":["1609-4514"]},"month":"04","doi":"10.17323/1609-4514-2019-19-2-307-327","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1809.09341","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1809.09341"]},"quality_controlled":"1","issue":"2","abstract":[{"text":"In this paper, we show that any smooth one-parameter deformations of a strictly convex integrable billiard table Ω0 preserving the integrability near the boundary have to be tangent to a finite dimensional space passing through Ω0.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"8416","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 19","status":"public","title":"On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables","article_processing_charge":"No","day":"01","date_published":"2019-04-01T00:00:00Z","citation":{"short":"G. Huang, V. Kaloshin, Moscow Mathematical Journal 19 (2019) 307–327.","mla":"Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical Journal, vol. 19, no. 2, American Mathematical Society, 2019, pp. 307–27, doi:10.17323/1609-4514-2019-19-2-307-327.","chicago":"Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical Journal. American Mathematical Society, 2019. https://doi.org/10.17323/1609-4514-2019-19-2-307-327.","ama":"Huang G, Kaloshin V. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. 2019;19(2):307-327. doi:10.17323/1609-4514-2019-19-2-307-327","ieee":"G. Huang and V. Kaloshin, “On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables,” Moscow Mathematical Journal, vol. 19, no. 2. American Mathematical Society, pp. 307–327, 2019.","apa":"Huang, G., & Kaloshin, V. (2019). On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. American Mathematical Society. https://doi.org/10.17323/1609-4514-2019-19-2-307-327","ista":"Huang G, Kaloshin V. 2019. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. 19(2), 307–327."},"publication":"Moscow Mathematical Journal","page":"307-327","article_type":"original"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We review V. I. Arnold’s 1963 celebrated paper [1] Proof of A. N. Kolmogorov’s Theorem on the Conservation of Conditionally Periodic Motions with a Small Variation in the Hamiltonian, and prove that, optimising Arnold’s scheme, one can get “sharp” asymptotic quantitative conditions (as ε → 0, ε being the strength of the perturbation). All constants involved are explicitly computed."}],"extern":"1","year":"2019","_id":"8693","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 24","publisher":"Springer","publication_status":"published","title":"V. I. Arnold’s “pointwise” KAM theorem","status":"public","author":[{"full_name":"Chierchia, Luigi","first_name":"Luigi","last_name":"Chierchia"},{"id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","orcid":"0000-0003-2640-4049","first_name":"Edmond","last_name":"Koudjinan","full_name":"Koudjinan, Edmond"}],"volume":24,"oa_version":"Preprint","date_updated":"2021-01-12T08:20:34Z","date_created":"2020-10-21T15:25:45Z","article_processing_charge":"No","month":"12","day":"10","main_file_link":[{"url":"https://arxiv.org/abs/1908.02523","open_access":"1"}],"citation":{"short":"L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 24 (2019) 583–606.","mla":"Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” Regular and Chaotic Dynamics, vol. 24, Springer, 2019, pp. 583–606, doi:10.1134/S1560354719060017.","chicago":"Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” Regular and Chaotic Dynamics. Springer, 2019. https://doi.org/10.1134/S1560354719060017.","ama":"Chierchia L, Koudjinan E. V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. 2019;24:583–606. doi:10.1134/S1560354719060017","apa":"Chierchia, L., & Koudjinan, E. (2019). V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. Springer. https://doi.org/10.1134/S1560354719060017","ieee":"L. Chierchia and E. Koudjinan, “V. I. Arnold’s ‘pointwise’ KAM theorem,” Regular and Chaotic Dynamics, vol. 24. Springer, pp. 583–606, 2019.","ista":"Chierchia L, Koudjinan E. 2019. V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. 24, 583–606."},"external_id":{"arxiv":["1908.02523"]},"oa":1,"publication":"Regular and Chaotic Dynamics","page":"583–606","quality_controlled":"1","article_type":"original","date_published":"2019-12-10T00:00:00Z","doi":"10.1134/S1560354719060017","language":[{"iso":"eng"}]},{"page":"1573-1585.e10","article_type":"original","citation":{"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","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.","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","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.","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.","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.","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."},"publication":"Cell Chemical Biology","date_published":"2019-11-21T00:00:00Z","keyword":["Clinical Biochemistry","Molecular Medicine","Biochemistry","Molecular Biology","Pharmacology","Drug Discovery"],"article_processing_charge":"No","day":"21","intvolume":" 26","title":"Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1","status":"public","_id":"9018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","issue":"11","abstract":[{"text":"Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.","lang":"eng"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chembiol.2019.09.002"}],"external_id":{"pmid":["31543461"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.chembiol.2019.09.002","publication_identifier":{"issn":["2451-9456"]},"month":"11","publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2019","volume":26,"date_updated":"2023-02-23T13:46:53Z","date_created":"2021-01-19T11:04:50Z","author":[{"first_name":"May M","last_name":"Bakail","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","orcid":"0000-0002-9592-1587","full_name":"Bakail, May M"},{"first_name":"Albane","last_name":"Gaubert","full_name":"Gaubert, Albane"},{"full_name":"Andreani, Jessica","last_name":"Andreani","first_name":"Jessica"},{"full_name":"Moal, Gwenaëlle","first_name":"Gwenaëlle","last_name":"Moal"},{"first_name":"Guillaume","last_name":"Pinna","full_name":"Pinna, Guillaume"},{"last_name":"Boyarchuk","first_name":"Ekaterina","full_name":"Boyarchuk, Ekaterina"},{"first_name":"Marie-Cécile","last_name":"Gaillard","full_name":"Gaillard, Marie-Cécile"},{"first_name":"Regis","last_name":"Courbeyrette","full_name":"Courbeyrette, Regis"},{"full_name":"Mann, Carl","last_name":"Mann","first_name":"Carl"},{"full_name":"Thuret, Jean-Yves","first_name":"Jean-Yves","last_name":"Thuret"},{"full_name":"Guichard, Bérengère","first_name":"Bérengère","last_name":"Guichard"},{"first_name":"Brice","last_name":"Murciano","full_name":"Murciano, Brice"},{"first_name":"Nicolas","last_name":"Richet","full_name":"Richet, Nicolas"},{"last_name":"Poitou","first_name":"Adeline","full_name":"Poitou, Adeline"},{"full_name":"Frederic, Claire","first_name":"Claire","last_name":"Frederic"},{"full_name":"Le Du, Marie-Hélène","last_name":"Le Du","first_name":"Marie-Hélène"},{"last_name":"Agez","first_name":"Morgane","full_name":"Agez, Morgane"},{"full_name":"Roelants, Caroline","first_name":"Caroline","last_name":"Roelants"},{"first_name":"Zachary A.","last_name":"Gurard-Levin","full_name":"Gurard-Levin, Zachary A."},{"first_name":"Geneviève","last_name":"Almouzni","full_name":"Almouzni, Geneviève"},{"first_name":"Nadia","last_name":"Cherradi","full_name":"Cherradi, Nadia"},{"first_name":"Raphael","last_name":"Guerois","full_name":"Guerois, Raphael"},{"full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein","first_name":"Françoise"}],"extern":"1"},{"pmid":1,"year":"2019","department":[{"_id":"DaZi"}],"publisher":"Springer Nature","publication_status":"published","author":[{"last_name":"Harris","first_name":"Keith D.","full_name":"Harris, Keith D."},{"last_name":"Lloyd","first_name":"James P. B.","full_name":"Lloyd, James P. B."},{"last_name":"Domb","first_name":"Katherine","full_name":"Domb, Katherine"},{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"},{"first_name":"Assaf","last_name":"Zemach","full_name":"Zemach, Assaf"}],"volume":12,"date_updated":"2021-12-14T07:53:00Z","date_created":"2021-06-08T09:21:51Z","article_number":"62","file_date_updated":"2021-06-08T09:29:19Z","extern":"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"},"oa":1,"external_id":{"pmid":["31601251"]},"quality_controlled":"1","doi":"10.1186/s13072-019-0307-4","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1756-8935"]},"month":"10","_id":"9530","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 12","status":"public","title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","ddc":["570"],"file":[{"date_created":"2021-06-08T09:29:19Z","date_updated":"2021-06-08T09:29:19Z","success":1,"checksum":"86ff50a7517891511af2733c76c81b67","file_id":"9531","relation":"main_file","creator":"asandaue","file_size":3221067,"content_type":"application/pdf","file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems.","lang":"eng"}],"citation":{"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.","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (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.","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.","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.","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"},"publication":"Epigenetics and Chromatin","article_type":"original","date_published":"2019-10-10T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"10"},{"article_processing_charge":"No","day":"03","scopus_import":"1","date_published":"2019-05-03T00:00:00Z","page":"757-777","article_type":"original","citation":{"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.","short":"M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society 99 (2019) 757–777.","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","ista":"Kwan MA, Sudakov B, Tran T. 2019. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 99(3), 757–777.","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","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."},"publication":"Journal of the London Mathematical Society","issue":"3","abstract":[{"lang":"eng","text":"Consider integers 𝑘,ℓ such that 0⩽ℓ⩽(𝑘2) . Given a large graph 𝐺 , what is the fraction of 𝑘 -vertex subsets of 𝐺 which span exactly ℓ edges? When 𝐺 is empty or complete, and ℓ is zero or (𝑘2) , this fraction can be exactly 1. On the other hand, if ℓ is far from these extreme values, one might expect that this fraction is substantially smaller than 1. This was recently proved by Alon, Hefetz, Krivelevich, and Tyomkyn who initiated the systematic study of this question and proposed several natural conjectures.\r\nLet ℓ∗=min{ℓ,(𝑘2)−ℓ} . Our main result is that for any 𝑘 and ℓ , the fraction of 𝑘 -vertex subsets that span ℓ edges is at most log𝑂(1)(ℓ∗/𝑘)√ 𝑘/ℓ∗, which is best-possible up to the logarithmic factor. This improves on multiple results of Alon, Hefetz, Krivelevich, and Tyomkyn, and resolves one of their conjectures. In addition, we also make some first steps towards some analogous questions for hypergraphs.\r\nOur proofs involve some Ramsey-type arguments, and a number of different probabilistic tools, such as polynomial anticoncentration inequalities, hypercontractivity, and a coupling trick for random variables defined on a ‘slice’ of the Boolean hypercube."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 99","status":"public","title":"Anticoncentration for subgraph statistics","_id":"9586","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publication_identifier":{"issn":["0024-6107"],"eissn":["1469-7750"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1112/jlms.12192","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.05202"}],"external_id":{"arxiv":["1807.05202"]},"oa":1,"extern":"1","volume":99,"date_updated":"2023-02-23T14:01:53Z","date_created":"2021-06-22T09:46:03Z","author":[{"last_name":"Kwan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan"},{"full_name":"Sudakov, Benny","first_name":"Benny","last_name":"Sudakov"},{"full_name":"Tran, Tuan","first_name":"Tuan","last_name":"Tran"}],"publisher":"Wiley","publication_status":"published","year":"2019"}]