Authors: Cyril Matthey-Doret, Morgan J. Colp, Pedro Escoll, Agnès Thierry, Pierrick Moreau, Bruce Curtis, Tobias Sahr, Matt Sarrasin, Michael W. Gray, B. Franz Lang, John M. Archibald, Carmen Buchrieser, Romain Koszul

Source: Genome Research. 32:1698-1710

Subject Terms: Genetics (clinical), Genetics

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_________::1fd84e1335c51304c2246e05359eb63b
https://doi.org/10.1101/gr.276375.121

Authors: Daniel Schindler, Roy S.K. Walker, Shuangying Jiang, Aaron N. Brooks, Yun Wang, Carolin A. Müller, Charlotte Cockram, Yisha Luo, Alicia García, Daniel Schraivogel, Julien Mozziconacci, Benjamin A. Blount, Jitong Cai, Lois Ogunlana, Wei Liu, Katarina Jönsson, Dariusz Abramczyk, Eva Garcia-Ruiz, Tomasz W. Turowski, Reem Swidah, Tom Ellis, Francisco Antequera, Yue Shen, Conrad A. Nieduszynski, Romain Koszul, Junbiao Dai, Lars M. Steinmetz, Jef D. Boeke, Yizhi Cai

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_________::cc49c630d11fb6cf58c3ffb12496ed73
https://doi.org/10.1101/2022.10.03.510608

Authors: Jonay Garcia-Luis, Hélène Bordelet, Agnès Thierry, Romain Koszul, Luis Aragon

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_________::4fc41a7c4b58908050b9a26e3d7867a0
https://doi.org/10.7554/elife.80147.sa2

Authors: Amaury Bignaud, Charlotte Cockram, Eric Allemand, Julien Mozziconnacci, Olivier Espeli, Romain Koszul

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_________::6859bf226312eb2ccab81472a8fc0d01
https://doi.org/10.1101/2022.09.16.507559

Authors: Giovanni Stracquadanio, Kun Yang, Jef D. Boeke, Romain Koszul, Joel S. Bader

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_________::ba3601f3ffde3f35ed305cbae46caccc
https://doi.org/10.1101/2022.09.14.507906

Authors: Brenna Conin, Ingrid Billault-Chaumartin, Hafez El Sayyed, Nicole Quenech’Du, Charlotte Cockram, Romain Koszul, Olivier Espéli

Contributors: Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Sorbonne Université (SU), European Research Council under the 7th Framework Program [ERC Grant Agreement 771813 to R.K.], ANR [HiResBac ANR-15-CE11-0023-03 to R.K. and O.E.]. Fondation Bettencourt Schueller. Funding for open access charge: CNRS., ANR-15-CE11-0023,HiResBaCS,Structure des chromosomes bactériens revélée a haute résolution(2015), European Project: 771813,ERC-2017-COG,SynarchiC(2018)

Source: Nucleic Acids Research
Nucleic Acids Research, Oxford University Press, 2022, 50 (5), pp.2635-2650. ⟨10.1093/nar/gkac105⟩

Subject Terms: Genetics, MESH: Chromatids, MESH: Chromosomal Proteins, Non-Histone, MESH: Chromosome Segregation, MESH: Chromosomes, Bacterial, MESH: DNA Replication, MESH: DNA Topoisomerase IV, MESH: DNA Topoisomerases, Type I, MESH: Escherichia coli, MESH: Escherichia coli Proteins, [SDV]Life Sciences [q-bio], [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC]

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1270dd02c811c9d23313576efbeaf944
https://doi.org/10.1093/nar/gkac105

Authors: Guilherme Dias de Melo, Victoire Perraud, Flavio Alvarez, Alba Vieites-Prado, Seonhee Kim, Lauriane Kergoat, Bettina Salome Trüeb, Magali Tichit, Aurèle Piazza, Agnès Thierry, David Hardy, Nicolas Wolff, Sandie Munier, Romain Koszul, Etienne Simon-Lorière, Volker Thiel, Marc Lecuit, Pierre-Marie Lledo, Nicolas Renier, Florence Larrous, Hervé Bourhy

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_________::2db1c655e34f5f9b18c040bc84beb688
https://doi.org/10.1101/2022.08.31.505985

Authors: Hugo Darras, Natalia De Souza Araujo, Lyam Baudry, Nadège Guiglielmoni, Pedro Lorite, Martial Marbouty, Fernando Rodriguez, Irina Arkhipova, Romain Koszul, Jean-François Flot, Serge Aron

Source: bioRxiv-biorxiv;2022.01.07.475286v2

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7d6b2721d861c65ea886c7934b2bda00
https://doi.org/10.24072/pcjournal.140

Authors: Sébastien Bloyer, Romain Koszul

Source: Peer Community In Genomics.

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_________::734bfc33b55b1133a14ee2060fb9bc8c
https://doi.org/10.24072/pci.genomics.100014

Authors: Isabelle Boutet, Homère J. Alves Monteiro, Lyam Baudry, Takeshi Takeuchi, Eric Bonnivard, Bernard Billoud, Sarah Farhat, Ricardo Gonzales-Haraya, Benoit Salaun, Ann Andersen, Jean-Yves Toullec, François Lallier, Jean-François Flot, Nadège Guiglielmoni, Ximing Guo, Li Cui, Bassem Allam, Emmanuelle Pales-Espinoza, Jakob Hemmer-Hansen, Martial Marbouty, Romain Koszul, Arnaud Tanguy

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_________::82c00e06deae64c2be0f6def404b64aa
https://doi.org/10.1101/2022.06.26.497643

Authors: Philipp H. Schiffer, Paschalis Natsidis, Daniel J. Leite, Helen E. Robertson, François Lapraz, Ferdinand Marlétaz, Bastian Fromm, Liam Baudry, Fraser Simpson, Eirik Høye, Anne-C. Zakrzewski, Paschalia Kapli, Katharina J. Hoff, Steven Mueller, Martial Marbouty, Heather Marlow, Richard R. Copley, Romain Koszul, Peter Sarkies, Maximilian J. Telford

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_________::eab7784782934a52ce63d796dc542535
https://doi.org/10.1101/2022.06.24.497508

Authors: Quentin Lamy-Besnier, Amaury Bignaud, Julian R. Garneau, Marie Titecat, Devon Conti, Alexandra Von Strempel, Marc Monot, Bärbel Stecher, Romain Koszul, Laurent Debarbieux, Martial Marbouty

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_________::2b7be870df3432c286006745cbf80700
https://doi.org/10.1101/2022.05.18.492453

Authors: Romain Koszul, Nadège Guiglielmoni, Ramón Rivera-Vicéns, Jean-François Flot

Subject Terms: genetics, Vertebrate Animals, Evolutionary biology, Genome, Deep dive, Biology, Sequence assembly

File Description: application/pdf

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3d290b4d243619dcf9b41823e0763014

Authors: Isabelle Boutet, Homère J. Alves Monteiro, Lyam Baudry, Takeshi Takeuchi, Eric Bonnivard, Bernard Billoud, Sarah Farhat, Ricardo Gonzales‐Araya, Benoit Salaun, Ann C. Andersen, Jean‐Yves Toullec, François H. Lallier, Jean‐François Flot, Nadège Guiglielmoni, Ximing Guo, Cui Li, Bassem Allam, Emmanuelle Pales‐Espinosa, Jakob Hemmer‐Hansen, Pierrick Moreau, Martial Marbouty, Romain Koszul, Arnaud Tanguy

Source: Boutet, I, Monteiro, H J A, Baudry, L, Takeuchi, T, Bonnivard, E, Billoud, B, Farhat, S, Gonzales-Araya, R, Salaun, B, Andersen, A C, Toullec, J-Y, Lallier, F H, Flot, J-F, Guiglielmoni, N, Guo, X, Li, C, Allam, B, Pales-Espinosa, E, Hemmer-Hansen, J, Moreau, P, Marbouty, M, Koszul, R & Tanguy, A 2022, ' Chromosomal assembly of the flat oyster ( Ostrea edulis L.) genome as a new genetic resource for aquaculture ', Evolutionary Applications, vol. 15, no. 11, pp. 1730-1748 . https://doi.org/10.1111/eva.13462

Subject Terms: Aquaculture, Flat oyster, Genome, Martelia, Transposable elements, General Agricultural and Biological Sciences, Genetics, Ecology, Evolution, Behavior and Systematics

File Description: application/pdf

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c4699edab01477d9cfa7a36593b889b5
https://orbit.dtu.dk/en/publications/3ace1df4-7de6-4bd3-89a7-c48282d7b729

Authors: Nathalie Bastié, Christophe Chapard, Lise Dauban, Olivier Gadal, Frédéric Beckouët, Romain Koszul

Contributors: Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)

Source: Nature Structural and Molecular Biology
Nature Structural and Molecular Biology, Nature Publishing Group, 2022, 29 (6), pp.575-585. ⟨10.1038/s41594-022-00780-0⟩

Subject Terms: MESH: Acetylation, MESH: Cell Cycle Proteins, MESH: Chromatin, MESH: Chromosomal Proteins, Non-Histone, MESH: Saccharomyces cerevisiae, MESH: Saccharomyces cerevisiae Proteins, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV]Life Sciences [q-bio], [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], biological phenomena, cell phenomena, and immunity, Molecular Biology, Structural Biology

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4c9faa8f8b958ec0e0af3221a3948838
https://hal.archives-ouvertes.fr/hal-03697578

Authors: Romain Koszul, Charlotte Cockram, Agnès Thierry

Contributors: Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This research was supported by funding to Romain Koszul from the European Research Council under the Horizon 2020 program (ERC grant agreement: 771813)., We thank Roxane Lestini, Aurore Gorlas, and Pierrick Moreau and the members of the RSG laboratory for insightful discussions regarding the development of this protocol., European Project: 771813,SynarchiC, European Project: 771813,ERC-2017-COG,SynarchiC(2018)

Source: STAR Protocols
STAR Protocols, Elsevier, 2021, 2 (2), pp.100512. ⟨10.1016/j.xpro.2021.100512⟩
STAR Protocols, Vol 2, Iss 2, Pp 100512-(2021)

Subject Terms: Genetics, Genomics, Microbiology, Molecular Biology, Sequencing, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Protocol, General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Neuroscience, Genome, Biology, Chromosome conformation capture, Resolution (electron density), Computational biology, Gene, Chromosome, Bacteria, biology.organism_classification, Archaea, Science (General), Q1-390

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::037267e015a4fe36397b892d1386777d
https://hal-pasteur.archives-ouvertes.fr/pasteur-03376845

Authors: Luciana Lazar-Stefanita, Jingchuan Luo, Remi Montagne, Agnes Thierry, Xiaoji Sun, Guillaume Mercy, Julien Mozziconacci, Romain Koszul, Jef D. Boeke

Source: Cell Genomics. 2:100163

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_________::f9e08c05858e9f0fb4d0674c0a977917
https://doi.org/10.1016/j.xgen.2022.100163

Authors: Luciana Lazar-Stefanita, Myriam Ruault, Angela Taddei, Antoine Hocher, Romain Koszul, Isabelle Loïodice, Vittore F. Scolari

Contributors: Dynamique du noyau [Institut Curie], Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Laboratoire Cogitamus, A.T. team was financially supported by funding from the Labex DEEP (ANR-11-LABEX-0044 DEEP and ANR-10-IDEX-0001-02 PSL), from the ANR DNA-Life (ANR-15-CE12-0007), Fondation pour la Recherche Médicale (DEP20151234398), and CNRS grant 80prime PhONeS.The authors greatly acknowledge the PICT-IBiSA@Pasteur Imaging Facility of the Institut Curie, member of the France Bioimaging National Infrastructure (ANR-10-INBS-04).V.F.S. is the recipient of a Roux-Cantarini Pasteur fellowship. L.L.S. was supported in part by a fellowship from the Fondation pour la Recherche Médicale. This research was supported by funding to R.K. from the European Research Council under the Horizon 2020 Program (ERC grant agreement 771813)., ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-15-CE12-0007,DNA-Life,Impact de l'achitecture nucléaire sur la longévité(2015), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), European Project: 771813,SynarchiC, Collège Doctoral, European Project: 771813,ERC-2017-COG,SynarchiC(2018)

Source: Genome Research
Genome Research, Cold Spring Harbor Laboratory Press, 2021, 31 (3), pp.411-425. ⟨10.1101/gr.267872.120⟩
Genome Research, 2021, 31 (3), pp.411-425. ⟨10.1101/gr.267872.120⟩
Genome Res

Subject Terms: Genetics (clinical), Genetics, Function (biology), Chromosome, Subtelomere, Heterochromatin, Telomere, Context (language use), Genome, Rap1, Biology, heterochromatin, yeast, nuclear organization, telomeres, nucleolus, Hi-C, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Research

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::67054d04d3dd938b7be5b6df0c10e56b
https://doi.org/10.1101/gr.267872.120

Authors: J. M. Cock, Romain Koszul, Mie Yl, Olivier Godfroy, Martial Marbouty, Susana M. Coelho, Lyam Baudry, Christophe Zimmer, Komlan Avia, Hervé Marie-Nelly, Nadège Guiglielmoni, Alexandre Cormier, Sterck L

Contributors: Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Collège Doctoral, Sorbonne Université (SU), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université libre de Bruxelles (ULB), Imagerie et Modélisation - Imaging and Modeling, This research was supported by funding to R.K. and S.M.C. from the European Research Council under the Horizon 2020 Program (ERC grant agreements 260822 and 638240, respectively) and from Agence Nationale pour la Recherche (JPI-EC-AMR STARCS ANR-16-JPEC-0003-05) to R.K. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 764840, ANR-16-JPEC-0003,STARCS,Selection and Transmission of Antimicrobial Resistance in Complex Systems(2016), European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), European Project: 638240,H2020,ERC-2014-STG,SEXSEA(2015), European Project: 764840,IGNITE, Collège doctoral [Sorbonne universités]

Source: BioRxiv
BioRxiv, 2019, ⟨10.1101/2019.12.22.882084⟩

Subject Terms: Ectocarpus, Hi-C scaffolding, Hi-C genome assembly, MCMC, GPU, parallel computing, Desmarestia herbacea, [SDV]Life Sciences [q-bio], Scaffold, Genome, Locus (genetics), Quality (business), media_common.quotation_subject, media_common, Chromosome (genetic algorithm), Computational biology, Sequence assembly, Computer science, Ligation, Chromosome, biology.organism_classification, biology, Modular design, business.industry, business, Contig

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c0b86c022fb37ce1ecc37ad319a9614b
https://hal.inrae.fr/hal-02947625

Authors: B. Franz Lang, Michael W. Gray, Morgan Colp, John M. Archibald, Romain Koszul, Pedro Escoll, Cyril Matthey-Doret, Bruce A. Curtis, Matt Sarrasin, Carmen Buchrieser, Agnès Thierry

Subject Terms: Comparative genomics, Organelle assembly, Genetics, Cytoskeleton organization, Biology, Legionella pneumophila, biology.organism_classification, Gene, Chromatin, Genome, Acanthamoeba castellanii

Access URL: https://explore.openaire.eu/search/publication?articleId=doi_________::0d965e041072c3be69ead834475b6f1b
https://doi.org/10.1101/2021.10.26.465878