Genome Biology Department

Publications

0
Publications in 2021
Adam, Yazid, Pierre Brezellec, Elena Espinosa, Amelie Besombes, Delphine Naquin, Evelyne Paly, Christophe Possoz, Erwin van Dijk, Barre Francois-Xavier, and Ferat Jean-Luc. 2022. “Plesiomonas Shigelloides, an Atypical Enterobacterales with a Vibrio-Related Secondary Chromosome.” Genome Biology and Evolution, January, evac011. https://doi.org/10.1093/gbe/evac011.
Altinoglu, Ipek, Guillaume Abriat, Alexis Carreaux, Lucía Torres-Sánchez, Mickaël Poidevin, Petya Violinova Krasteva, and Yoshiharu Yamaichi. 2022. “Analysis of HubP-Dependent Cell Pole Protein Targeting in Vibrio Cholerae Uncovers Novel Motility Regulators.” PLOS Genetics 18 (1): e1009991. https://doi.org/10.1371/journal.pgen.1009991.
Asensio, Thomas, Cyril Dian, Jean-Baptiste Boyer, Frédéric Rivière, Thierry Meinnel, and Carmela Giglione. 2022. “A Continuous Assay Set to Screen and Characterize Novel Protein N-Acetyltransferases Unveils Rice General Control Non-Repressible 5-Related N-Acetyltransferase2 Activity.” Frontiers in Plant Science 13 (March). https://www.frontiersin.org/article/10.3389/fpls.2022.832144.
Banneville, Anne-Sophie, Claire Bouthier de la Tour, Salvatore De Bonis, Cécilia Hognon, Jacques-Philippe Colletier, Jean-Marie Teulon, Aline Le Roy, et al. 2022. “Structural and Functional Characterization of DdrC, a Novel DNA Damage-Induced Nucleoid Associated Protein Involved in DNA Compaction.” Nucleic Acids Research, July, gkac563. https://doi.org/10.1093/nar/gkac563.
Bidou, Laure, Olivier Bugaud, Goulven Merer, Matthieu Coupet, Isabelle Hatin, Egor Chirkin, Sabrina Karri, et al. 2022. “2-Guanidino-Quinazoline Promotes the Readthrough of Nonsense Mutations Underlying Human Genetic Diseases.” Proceedings of the National Academy of Sciences 119 (35): e2122004119. https://doi.org/10.1073/pnas.2122004119.
Bokor, Eszter, Judit Ámon, Mónika Varga, András Szekeres, Zsófia Hegedűs, Tamás Jakusch, Zsolt Szakonyi, et al. 2022. “A Complete Nicotinate Degradation Pathway in the Microbial Eukaryote Aspergillus Nidulans.” Communications Biology 5 (1): 1–11. https://doi.org/10.1038/s42003-022-03684-3.
Chua, Lingluo, Zheng Zhanga, Maria Mukhinaa, Denise Zicklerc, and Nancy Kleckner. 2022. “Sister Chromatids Separate during Anaphase in a Three-Stage Program as Directed by Interaxis Bridges | PNAS.” March 2, 2022. https://www.pnas.org/doi/full/10.1073/pnas.2123363119.
Coronel-Tellez, Rodrigo H, Mateusz Pospiech, Maxime Barrault, Wenfeng Liu, Valérie Bordeau, Christelle Vasnier, Brice Felden, Bruno Sargueil, and Philippe Bouloc. 2022. “SRNA-Controlled Iron Sparing Response in Staphylococci.” Nucleic Acids Research, July, gkac648. https://doi.org/10.1093/nar/gkac648.
Costa, Maria. 2022. “Group II Introns: Flexibility and Repurposing.” Frontiers in Molecular Biosciences 9 (June). https://www.frontiersin.org/articles/10.3389/fmolb.2022.916157.
Nuez Veulens, Ania de la, Yoanna M. Álvarez Ginarte, Rolando E. Rodríguez Fernandez, Fabrice Leclerc, and Luis A. Montero Cabrera. 2022. “Prediction of Molecular Interactions and Physicochemical Properties Relevant for Vasopressin V2 Receptor Antagonism.” Journal of Molecular Modeling 28 (2): 31. https://doi.org/10.1007/s00894-021-05022-6.
Denecker, Thomas, and Gaëlle Lelandais. 2022. “Omics Analyses: How to Navigate Through a Constant DataData Deluge.” In Yeast Functional Genomics: Methods and Protocols, edited by Frédéric Devaux, 457–71. Methods in Molecular Biology. New York, NY: Springer US. https://doi.org/10.1007/978-1-0716-2257-5_25.
Dos Santos, Matthieu, Stéphanie Backer, Frédéric Auradé, Matthew Man-Kin Wong, Maud Wurmser, Rémi Pierre, Francina Langa, et al. 2022. “A Fast Myosin Super Enhancer Dictates Muscle Fiber Phenotype through Competitive Interactions with Myosin Genes.” Nature Communications 13 (1): 1039. https://doi.org/10.1038/s41467-022-28666-1.
Esberard, Marick, Marc Hallier, Wenfeng Liu, Claire Morvan, Lionello Bossi, Nara Figueroa-Bossi, Brice Felden, and Philippe Bouloc. 2022. “6S RNA-Dependent Susceptibility to RNA Polymerase Inhibitors.” Antimicrobial Agents and Chemotherapy 0 (0): e02435-21. https://doi.org/10.1128/aac.02435-21.
Fekete, Erzsébet, Fruzsina Pénzes, Norbert Ág, Viktória Ág-Rácz, Erzsébet Sándor, Claudio Scazzocchio, Michel Flipphi, and Levente Karaffa. 2022. “Unique and Repeated Stwintrons (Spliceosomal Twin Introns) in the Hypoxylaceae.” Journal of Fungi 8 (4): 397. https://doi.org/10.3390/jof8040397.
Ferrad, Melissa, Nour Ghazzaui, Hussein Issaoui, Emilie Drouineau, Christelle Oblet, Tiffany Marchiol, Jeanne Cook-Moreau, and Yves Denizot. 2022. “Homozygous IMycCα Transgenic Mice as a Model of Plasma B-Cell Lymphomas.” Leukemia & Lymphoma 0 (0): 1–12. https://doi.org/10.1080/10428194.2022.2064989.
Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2022. “Working with Phage P22.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.prot107850.
Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2022. “Preparing Bacterial Genomic DNA.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.prot107853.
Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2022. “Preparing Plasmid DNA from Bacteria.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.prot107852.
Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2022. “Basic Bacteriological Routines.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.prot107849.
Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2022. “Working with Bacteria, Phage, and Plasmids.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.top107848.
Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2022. “Quick Transformation with Plasmid DNA.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.prot107854.
Figueroa-Bossi, Nara, María Antonia Sánchez-Romero, Patricia Kerboriou, Delphine Naquin, Clara Mendes, Philippe Bouloc, Josep Casadesús, and Lionello Bossi. 2022. “Pervasive Transcription Enhances the Accessibility of H-NS–Silenced Promoters and Generates Bistability in Salmonella Virulence Gene Expression.” Proceedings of the National Academy of Sciences 119 (30): e2203011119. https://doi.org/10.1073/pnas.2203011119.
Fontaine, Emeline, Christophe Papin, Guillaume Martinez, Stéphanie Le Gras, Roland Abi Nahed, Patrick Héry, Thierry Buchou, et al. 2022. “Dual Role of Histone Variant H3.3B in Spermatogenesis: Positive Regulation of PiRNA Transcription and Implication in X-Chromosome Inactivation.” Nucleic Acids Research, June, gkac541. https://doi.org/10.1093/nar/gkac541.
Gnan, Stefano, Melody Matelot, Marion Weiman, Olivier Arnaiz, Frederic Guerin, Linda Sperling, Mireille Betermier, Claude Thermes, Chun-Long Chen, and Sandra Duharcourt. 2022. “GC Content but Not Nucleosome Positioning Directly Contributes to Intron-Splicing Efficiency in Paramecium.” Genome Research, March, gr.276125.121. https://doi.org/10.1101/gr.276125.121.
Gopaul, Diyavarshini, Cyril Denby Wilkes, Arach Goldar, Nathalie Giordanengo Aiach, Marie-Benedicte Barrault, Elizaveta Novikova, and Julie Soutourina. 2022. “Genomic Analysis of Rad26 and Rad1-Rad10 Reveals Differences in Their Dependence on Mediator and RNA Polymerase II.” Genome Research, June, gr.276371.121. https://doi.org/10.1101/gr.276371.121.
Grunchec, Héloïse, Jérôme Deraze, Delphine Dardalhon-Cuménal, Valérie Ribeiro, Anne Coléno-Costes, Karine Dias, Sébastien Bloyer, Emmanuèle Mouchel-Vielh, Frédérique Peronnet, and Hélène Thomassin. 2022. “Single Amino-Acid Mutation in a Drosoph Ila Melanogaster Ribosomal Protein: An Insight in UL11 Transcriptional Activity.” PLOS ONE 17 (8): e0273198. https://doi.org/10.1371/journal.pone.0273198.
Guérin, Nina, Marta Ciccarella, Elisa Flamant, Paul Frémont, Sophie Mangenot, Benjamin Istace, Benjamin Noel, et al. 2022. “Genomic Adaptation of the Picoeukaryote Pelagomonas Calceolata to Iron-Poor Oceans Revealed by a Chromosome-Scale Genome Sequence.” Communications Biology 5 (1): 1–14. https://doi.org/10.1038/s42003-022-03939-z.
Lassagne, Alexandre, Sylvain Brun, Fabienne Malagnac, Henri Adreit, Joëlle Milazzo, Elisabeth Fournier, and Didier Tharreau. 2022. “Male Fertility in Pyricularia Oryzae: Microconidia Are Spermatia.” Environmental Microbiology n/a (n/a). https://doi.org/10.1111/1462-2920.16226.
Martín Caballero, Lucía, Matías Capella, Ramón Ramos Barrales, Nikolay Dobrev, Thomas van Emden, Yasuhiro Hirano, Vishnu N. Suma Sreechakram, et al. 2022. “The Inner Nuclear Membrane Protein Lem2 Coordinates RNA Degradation at the Nuclear Periphery.” Nature Structural & Molecular Biology 29 (9): 910–21. https://doi.org/10.1038/s41594-022-00831-6.
Meinnel, Thierry. 2022. “Tracking N-Terminal Protein Processing from the Golgi to the Chromatophore of a Rhizarian Amoeba.” Plant Physiology, April, kiac173. https://doi.org/10.1093/plphys/kiac173.
Meinnel, Thierry, and Carmela Giglione. 2022. “Amino Terminal Modifications, the Associated Processing Machinery, and Their Evolution in Plastid-Containing Organisms.” Journal of Experimental Botany, June, erac290. https://doi.org/10.1093/jxb/erac290.
Meléndez García, Rodrigo, Olivier Haccard, Albert Chesneau, Hemalatha Narassimprakash, Jérôme Roger, Muriel Perron, Kathrin Marheineke, and Odile Bronchain. 2022. “A Non-Transcriptional Function of Yap Regulates the DNA Replication Program in Xenopus Laevis.” Edited by Sigolène M Meilhac and Jessica K Tyler. ELife 11 (July): e75741. https://doi.org/10.7554/eLife.75741.
Miele, Solange, James Iain Provan, Justine Vergne, Christophe Possoz, Françoise Ochsenbein, and François-Xavier Barre. 2022. “The Xer Activation Factor of TLCΦ Expands the Possibilities for Xer Recombination.” Nucleic Acids Research, June, gkac429. https://doi.org/10.1093/nar/gkac429.
Miranda, Mélanie, Daan Noordermeer, and Benoit Moindrot. 2022. “Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-Seq.” In Spatial Genome Organization: Methods and Protocols, edited by Tom Sexton, 15–33. Methods in Molecular Biology. New York, NY: Springer US. https://doi.org/10.1007/978-1-0716-2497-5_2.
Miró-Pina, Caridad, Olivia Charmant, Takayuki Kawaguchi, Daniel Holoch, Audrey Michaud, Isadora Cohen, Adeline Humbert, et al. 2022. “Paramecium Polycomb Repressive Complex 2 Physically Interacts with the Small RNA-Binding PIWI Protein to Repress Transposable Elements.” Developmental Cell, April. https://doi.org/10.1016/j.devcel.2022.03.014.
Nyonda, Mary Akinyi, Jean-Baptiste Boyer, Lucid Belmudes, Aarti Krishnan, Paco Pino, Yohann Couté, Mathieu Brochet, Thierry Meinnel, Dominique Soldati-Favre, and Carmela Giglione. 2022. “N-Acetylation of Secreted Proteins Is Widespread in Apicomplexa and Independent of Acetyl-CoA ER-Transporter AT1.” Journal of Cell Science, May, jcs.259811. https://doi.org/10.1242/jcs.259811.
Owsian, Dawid, Julita Gruchota, Olivier Arnaiz, and Jacek K Nowak. 2022. “The Transient Spt4-Spt5 Complex as an Upstream Regulator of Non-Coding RNAs during Development.” Nucleic Acids Research, February, gkac106. https://doi.org/10.1093/nar/gkac106.
Papadopoulos, Chris, Nicolas Chevrollier, and Anne Lopes. 2022. “Exploring the Peptide Potential of Genomes.” In Computational Peptide Science, edited by Thomas Simonson, 2405:63–82. New York, NY: Springer US. https://doi.org/10.1007/978-1-0716-1855-4_3.
Platero-Rochart, Daniel, Roy González-Alemán, Erix W Hernández-Rodríguez, Fabrice Leclerc, Julio Caballero, and Luis Montero-Cabrera. 2022. “RCDPeaks: Memory-Efficient Density Peaks Clustering of Long Molecular Dynamics.” Bioinformatics, January, btac021. https://doi.org/10.1093/bioinformatics/btac021.
Poinsignon, Thibault, Mélina Gallopin, Jean-Michel Camadro, Pierre Poulain, and Gaëlle Lelandais. 2022. “Additional Insights into the Organization of Transcriptional Regulatory Modules Based on a 3D Model of the Saccharomyces Cerevisiae Genome.” BMC Research Notes 15 (1): 67. https://doi.org/10.1186/s13104-022-05940-5.
Possoz, Christophe, Yoshiharu Yamaichi, Elisa Galli, Jean-Luc Ferat, and Francois-Xavier Barre. 2022. “Vibrio Cholerae Chromosome Partitioning without Polar Anchoring by HubP.” Genes 13 (5): 877. https://doi.org/10.3390/genes13050877.
Repoila, F., F. Le Bohec, C. Guérin, C. Lacoux, S. Tiwari, A. K. Jaiswal, M. Passos Santana, et al. 2022. “Adaptation of the Gut Pathobiont Enterococcus Faecalis to Deoxycholate and Taurocholate Bile Acids.” Scientific Reports 12 (1): 8485. https://doi.org/10.1038/s41598-022-12552-3.
Riemenschneider, Henrick, Qiang Guo, Jakob Bader, Frédéric Frottin, Daniel Farny, Gernot Kleinberger, Christian Haass, et al. 2022. “Gel-like Inclusions of C-Terminal Fragments of TDP-43 Sequester Stalled Proteasomes in Neurons.” EMBO Reports, June.
Rivière, Frédéric, Cyril Dian, Rémi F. Dutheil, Paul Monassa, Carmela Giglione, and Thierry Meinnel. 2022. “Structural and Large-Scale Analysis Unveil the Intertwined Paths Promoting NMT-Catalyzed Lysine and Glycine Myristoylation.” Journal of Molecular Biology, September, 167843. https://doi.org/10.1016/j.jmb.2022.167843.
Robert, Caroline, and Daniel Gautheret. 2022. “Multi-Omics Prediction in Melanoma Immunotherapy: A New Brick in the Wall.” Cancer Cell 40 (1): 14–16. https://doi.org/10.1016/j.ccell.2021.12.008.
Santos, Joana M., and Karine Frénal. 2022. “Dominique Soldati-Favre: Bringing Toxoplasma Gondii to the Molecular World.” Frontiers in Cellular and Infection Microbiology 12 (May). https://www.frontiersin.org/article/10.3389/fcimb.2022.910611.
Schweke, Hugo, Marie-Hélène Mucchielli, Nicolas Chevrollier, Simon Gosset, and Anne Lopes. 2022. “SURFMAP: A Software for Mapping in Two Dimensions Protein Surface Features.” Journal of Chemical Information and Modeling, March. https://doi.org/10.1021/acs.jcim.1c01269.
Segueni, Julie, and Daan Noordermeer. 2022. “CTCF: A Misguided Jack-of-All-Trades in Cancer Cells.” Computational and Structural Biotechnology Journal 20 (January): 2685–98. https://doi.org/10.1016/j.csbj.2022.05.044.
Sénécaut, Nicolas, Pierre Poulain, Laurent Lignières, Samuel Terrier, Véronique Legros, Guillaume Chevreux, Gaëlle Lelandais, and Jean-Michel Camadro. 2022. “Quantitative ProteomicsProteomics in YeastYeasts: From BSLIMBSLIM and Proteome DiscovererProteome Discoverer Outputs to Graphical Assessment of the Significance of Protein QuantificationQuantificationsScores.” In Yeast Functional Genomics: Methods and Protocols, edited by Frédéric Devaux, 275–92. Methods in Molecular Biology. New York, NY: Springer US. https://doi.org/10.1007/978-1-0716-2257-5_16.
Smyčka, Jan, Cristina Roquet, Martí Boleda, Adriana Alberti, Frédéric Boyer, Rolland Douzet, Christophe Perrier, et al. 2022. “Tempo and Drivers of Plant Diversification in the European Mountain System.” Nature Communications 13 (1): 2750. https://doi.org/10.1038/s41467-022-30394-5.
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