Genome Biology Department

Publications

0
Publications in 2021
L, Moniot-Perron, Moindrot B, Manceau L, Edouard J, Jaszczyszyn Y, Gilardi-Hebenstreit P, Hernandez C, Bloyer S, and Noordermeer D. 2023. “The Drosophila Fab-7 Boundary Modulates Abd-B Gene Activity by Guiding an Inversion of Collinear Chromatin Organization and Alternate Promoter Use.” Cell Reports 42 (1). https://doi.org/10.1016/j.celrep.2022.111967.
Oliveira, Leonor, Nicolas Chevrollier, Jean-Felix Dallery, Richard J. O’Connell, Marc-Henri Lebrun, Muriel Viaud, and Olivier Lespinet. 2023. “CusProSe: A Customizable Protein Annotation Software with an Application to the Prediction of Fungal Secondary Metabolism Genes.” Scientific Reports 13 (1): 1417. https://doi.org/10.1038/s41598-023-27813-y.
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.
Barkova, Anastasia, Indranil Adhya, Christine Conesa, Amna Asif-Laidin, Amandine Bonnet, Elise Rabut, Carine Chagneau, Pascale Lesage, and Joël Acker. 2022. “A Proteomic Screen of Ty1 Integrase Partners Identifies the Protein Kinase CK2 as a Regulator of Ty1 Retrotransposition.” Mobile DNA 13 (1): 26. https://doi.org/10.1186/s13100-022-00284-0.
Bastide, Paul, Charlotte Soneson, David B Stern, Olivier Lespinet, and Mélina Gallopin. 2022. “A Phylogenetic Framework to Simulate Synthetic Inter-Species RNA-Seq Data.” Molecular Biology and Evolution, December, msac269. https://doi.org/10.1093/molbev/msac269.
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.
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.
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 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. “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. “Basic Bacteriological Routines.” Cold Spring Harbor Protocols, August. https://doi.org/10.1101/pdb.prot107849.
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, 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, 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.
Franck, Coste, Goffinont Stéphane, Cros Julien, Gaudon Virginie, Guérin Martine, Garnier Norbert, Fabrice Confalonieri, Flament Didier, Suskiewicz Marcin Josef, and Castaing Bertrand. 2022. “Structural and Functional Determinants of the Archaeal 8-Oxoguanine-DNA Glycosylase AGOG for DNA Damage Recognition and Processing.” Nucleic Acids Research, October, gkac932. https://doi.org/10.1093/nar/gkac932.
Gianfrotta, Coline, Vladimir Reinharz, Olivier Lespinet, Dominique Barth, and Alain Denise. 2022. “On the Predictibility of A-Minor Motifs from Their Local Contexts.” RNA Biology 19 (1): 1208–27. https://doi.org/10.1080/15476286.2022.2144611.
González-Alemán, Roy, Daniel Platero-Rochart, Alejandro Rodríguez-Serradet, Erix W Hernández-Rodríguez, Julio Caballero, Fabrice Leclerc, and Luis Montero-Cabrera. 2022. “MDSCAN: RMSD-Based HDBSCAN Clustering of Long Molecular Dynamics.” Bioinformatics, October, btac666. https://doi.org/10.1093/bioinformatics/btac666.
Gosset, Simon, Annie Glatigny, Mélina Gallopin, Zhou Yi, Marion Salé, and Marie-Hélène Mucchielli-Giorgi. 2022. “APPINetwork: An R Package for Building and Computational Analysis of Protein–Protein Interaction Networks.” PeerJ 10 (November): e14204. https://doi.org/10.7717/peerj.14204.
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.
L’Hôte, Valentin, Carl Mann, and Jean-Yves Thuret. 2022. “From the Divergence of Senescent Cell Fates to Mechanisms and Selectivity of Senolytic Drugs.” Open Biology 12 (9): 220171. https://doi.org/10.1098/rsob.220171.
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.
Lelandais, Gaëlle, Damien Remy, Fabienne Malagnac, and Pierre Grognet. 2022. “New Insights into Genome Annotation in Podospora Anserina through Re-Exploiting Multiple RNA-Seq Data.” BMC Genomics 23 (1): 859. https://doi.org/10.1186/s12864-022-09085-4.
Lorenzi, Jean-Noël, Annabelle Thibessard, Virginia S Lioy, Frédéric Boccard, Pierre Leblond, Jean-Luc Pernodet, and Stéphanie Bury-Moné. 2022. “Ribosomal RNA Operons Define a Central Functional Compartment in the Streptomyces Chromosome.” Nucleic Acids Research, November, gkac1076. https://doi.org/10.1093/nar/gkac1076.
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.
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.
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.
Pranke, Iwona M., Jessica Varilh, Aurélie Hatton, Caroline Faucon, Emmanuelle Girodon, Elise Dreano, Benoit Chevalier, et al. 2022. “The U UGA C Sequence Provides a Favorable Context to ELX-02 Induced CFTR Readthrough.” Journal of Cystic Fibrosis 0 (0). https://doi.org/10.1016/j.jcf.2022.10.010.
Pronier, Elodie, Aygun Imanci, Dorothée Selimoglu-Buet, Bouchra Badaoui, Raphael Itzykson, Thierry Roger, Chloé Jego, et al. 2022. “Macrophage Migration Inhibitory Factor Is Overproduced through EGR1 in TET2low Resting Monocytes.” Communications Biology 5 (1): 110. https://doi.org/10.1038/s42003-022-03057-w.
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.
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.
Shevtsov, Alexandr, Zabida Aushakhmetova, Asylulan Amirgazin, Olga Khegay, Dinara Kamalova, Bibiaisha Sanakulova, Askar Abdaliyev, et al. 2022. “Whole Genome Sequence Analysis of Neisseria Meningitidis Strains Circulating in Kazakhstan, 2017–2018.” PLOS ONE 17 (12): e0279536. https://doi.org/10.1371/journal.pone.0279536.
Timofeev, Vitalii, Irina Bakhteeva, Alexander Mokrievich, Galina Vakhrameeva, Elena Gritskova, Yuriy Anisimov, Evgeny Rozhdestvensky, et al. 2022. “The First Finding of Francisella Tularensis Subsp. Mediasiatica in Krasnoyarsk Territory, Siberia, and an Update of the Subspecies Genetic Diversity.” Bacteria 1 (4): 242–49. https://doi.org/10.3390/bacteria1040018.
Uribe-Calvillo, Tannia, Laetitia Maestroni, Marie-Claude Marsolier, Basheer Khadaroo, Christine Arbiol, Jonathan Schott, and Bertrand Llorente. 2022. “Comprehensive Analysis of Cis- and Trans-Acting Factors Affecting Ectopic Break-Induced Replication.” PLOS Genetics 18 (6): e1010124. https://doi.org/10.1371/journal.pgen.1010124.
Veller, Carl, Shunxin Wang, Denise Zickler, Liangran Zhang, and Nancy Kleckner. 2022. “Limitations of Gamete Sequencing for Crossover Analysis.” Nature 606 (7913): E1–3. https://doi.org/10.1038/s41586-022-04693-2.
Wang, Yucheng, Ana Prohaska, Haoran Dong, Adriana Alberti, Inger Greve Alsos, David W. Beilman, Anders A. Bjørk, et al. 2022. “Reply to: When Did Mammoths Go Extinct?” Nature 612 (7938): E4–6. https://doi.org/10.1038/s41586-022-05417-2.
Wang, Yunfeng, Haoliang Xue, Marine Aglave, Antoine Lainé, Mélina Gallopin, and Daniel Gautheret. 2022. “The Contribution of Uncharted RNA Sequences to Tumor Identity in Lung Adenocarcinoma.” NAR Cancer 4 (1): zcac001. https://doi.org/10.1093/narcan/zcac001.
Willems, Patrick, Pitter F. Huesgen, Iris Finkemeier, Emmanuelle Graciet, Thierry Meinnel, and Frank Van Breusegem. 2022. “Editorial: Plant Protein Termini: Their Generation, Modification and Function.” Frontiers in Plant Science 13 (September). https://www.frontiersin.org/articles/10.3389/fpls.2022.1040392.
Zangarelli, Coralie, Olivier Arnaiz, Mickael Bourge, Kevin Gorrichon, Yan Jaszczyszyn, Nathalie Mathy, Loic Escoriza, Mireille Betermier, and Vinciane Regnier. 2022. “Developmental Timing of Programmed DNA Elimination in Paramecium Tetraurelia Recapitulates Germline Transposon Evolutionary Dynamics.” Genome Research, November, gr.277027.122. https://doi.org/10.1101/gr.277027.122.
Zeitler, Leo, Cyril Denby Wilkes, Arach Goldar, and Julie Soutourina. 2022. “A Quantitative Modelling Approach for DNA Repair on a Population Scale.” PLOS Computational Biology 18 (9): e1010488. https://doi.org/10.1371/journal.pcbi.1010488.
“Gel-like Inclusions of C-Terminal Fragments of TDP-43 Sequester Stalled Proteasomes in Neurons.” 2022. EMBO Reports n/a (n/a): e53890. https://doi.org/10.15252/embr.202153890.
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