Genome Biology Department

Publications

0
Publications in 2022
2020 - 2022
2015 - 2019
Andjus, Sara, Ugo Szachnowski, Nicolas Vogt, Stamatia Gioftsidi, Isabelle Hatin, David Cornu, Chris Papadopoulos, et al. 2024. “Pervasive Translation of Xrn1-Sensitive Unstable Long Non-Coding RNAs in Yeast.” RNA (New York, N.Y.), March, rna.079903.123. https://doi.org/10.1261/rna.079903.123.
Bischerour, Julien, Olivier Arnaiz, Coralie Zangarelli, Vinciane Régnier, Florence Iehl, Virginie Ropars, Jean-Baptiste Charbonnier, and Mireille Bétermier. 2024. “Uncoupling Programmed DNA Cleavage and Repair Scrambles the Paramecium Somatic Genome.” Cell Reports 43 (4): 114001. https://doi.org/10.1016/j.celrep.2024.114001.
Buggiani, Julia, Thierry Meinnel, Carmela Giglione, and Frédéric Frottin. 2024. “Advances in Nuclear Proteostasis of Metazoans.” Biochimie, April, S0300-9084(24)00081-6. https://doi.org/10.1016/j.biochi.2024.04.006.
Farhadova, Sabina, Amani Ghousein, François Charon, Caroline Surcis, Melisa Gomez-Velazques, Clara Roidor, Flavio Di Michele, et al. 2024. “The Long Non-Coding RNA Meg3 Mediates Imprinted Gene Expression during Stem Cell Differentiation.” Nucleic Acids Research, April, gkae247. https://doi.org/10.1093/nar/gkae247.
Figueroa-Bossi, Nara, Rocío Fernández-Fernández, Patricia Kerboriou, Philippe Bouloc, Josep Casadesús, María Antonia Sánchez-Romero, and Lionello Bossi. 2024. “Transcription-Driven DNA Supercoiling Counteracts H-NS-Mediated Gene Silencing in Bacterial Chromatin.” Nature Communications 15 (1): 2787. https://doi.org/10.1038/s41467-024-47114-w.
Gong, Xiaodi, Jean-Baptiste Boyer, Simone Gierlich, Marlena Pożoga, Jonas Weidenhausen, Irmgard Sinning, Thierry Meinnel, et al. 2024. “HYPK Controls Stability and Catalytic Activity of the N-Terminal Acetyltransferase A in Arabidopsis Thaliana.” Cell Reports 43 (2): 113768. https://doi.org/10.1016/j.celrep.2024.113768.
Leiba, Jade, Tamara Sipka, Christina Begon-Pescia, Matteo Bernardello, Sofiane Tairi, Lionello Bossi, Anne-Alicia Gonzalez, et al. 2024. “Dynamics of Macrophage Polarization Support Salmonella Persistence in a Whole Living Organism.” ELife 13 (January): e89828. https://doi.org/10.7554/eLife.89828.
Monteagudo-Sánchez, Ana, Daan Noordermeer, and Maxim V. C. Greenberg. 2024. “The Impact of DNA Methylation on CTCF-Mediated 3D Genome Organization.” Nature Structural & Molecular Biology 31 (3): 404–12. https://doi.org/10.1038/s41594-024-01241-6.
Rossier, Ombeline, Cécile Labarre, Anne Lopes, Monique Auberdiac, Kevin Tambosco, Daniel Delaruelle, Hakima Abes, et al. 2024. “Genome Sequence of PSonyx, a Singleton Bacteriophage Infecting Corynebacterium Glutamicum.” Microbiology Resource Announcements, January, e0115523. https://doi.org/10.1128/mra.01155-23.
Seba, Mohammed, Frederic Boccard, and Stéphane Duigou. 2024. “Activity of MukBEF for Chromosome Management in E. Coli and Its Inhibition by MatP.” ELife 12 (February): RP91185. https://doi.org/10.7554/eLife.91185.
Wu, Xiaofen, Anca M. Segall, Carmela Giglione, and Thierry Meinnel. 2024. “The Complete Genome of Vibrio Sp. 16 Unveils Two Circular Chromosomes and a Distinctive 46-Kb Plasmid.” Microbiology Resource Announcements, February, e0122223. https://doi.org/10.1128/mra.01222-23.
Xue, Haoliang, Mélina Gallopin, Camille Marchet, Ha N. Nguyen, Yunfeng Wang, Antoine Lainé, Chloé Bessiere, and Daniel Gautheret. 2024. “KaMRaT: A C ++ Toolkit for k-Mer Count Matrix Dimension Reduction.” Bioinformatics (Oxford, England), March, btae090. https://doi.org/10.1093/bioinformatics/btae090.
Zeitler, Leo, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, and Arach Goldar. 2024. “A Genome-Wide Comprehensive Analysis of Nucleosome Positioning in Yeast.” PLoS Computational Biology 20 (1): e1011799. https://doi.org/10.1371/journal.pcbi.1011799.
Abd Al-Razaq, Mutaz A., Benjamin M. Freyter, Anna Isermann, Gargi Tewary, Adèle Mangelinck, Carl Mann, and Claudia E. Rübe. 2023. “Role of Histone Variant H2A.J in Fine-Tuning Chromatin Organization for the Establishment of Ionizing Radiation-Induced Senescence.” Cells 12 (6): 916. https://doi.org/10.3390/cells12060916.
Abdelli, Mehdi, Charlotte Falaise, Valérie Morineaux-Hilaire, Amélie Cumont, Laurent Taysse, Françoise Raynaud, and Vincent Ramisse. 2023. “Get to Know Your Neighbors: Characterization of Close Bacillus Anthracis Isolates and Toxin Profile Diversity in the Bacillus Cereus Group.” Microorganisms 11 (11): 2721. https://doi.org/10.3390/microorganisms11112721.
André, Kévin M., Nathalie Giordanengo Aiach, Veronica Martinez-Fernandez, Leo Zeitler, Adriana Alberti, Arach Goldar, Michel Werner, Cyril Denby Wilkes, and Julie Soutourina. 2023. “Functional Interplay between Mediator and RSC Chromatin Remodeling Complex Controls Nucleosome-Depleted Region Maintenance at Promoters.” Cell Reports 42 (5): 112465. https://doi.org/10.1016/j.celrep.2023.112465.
Arbona, Jean-Michel, Hadi Kabalane, Jeremy Barbier, Arach Goldar, Olivier Hyrien, and Benjamin Audit. 2023. “Neural Network and Kinetic Modelling of Human Genome Replication Reveal Replication Origin Locations and Strengths.” PLoS Computational Biology 19 (5): e1011138. https://doi.org/10.1371/journal.pcbi.1011138.
Arnesen, Thomas, Henriette Aksnes, and Carmela Giglione. 2023. “Protein Termini 2022: Central Roles of Protein Ends.” Trends in Biochemical Sciences, March, S0968-0004(23)00075-0. https://doi.org/10.1016/j.tibs.2023.02.008.
Arnould, Coline, Vincent Rocher, Florian Saur, Aldo S. Bader, Fernando Muzzopappa, Sarah Collins, Emma Lesage, et al. 2023. “Chromatin Compartmentalization Regulates the Response to DNA Damage.” Nature, October. https://doi.org/10.1038/s41586-023-06635-y.
Arnould, Coline, Vincent Rocher, Florian Saur, Aldo S. Bader, Fernando Muzzopappa, Sarah Collins, Emma Lesage, et al. 2023. “Author Correction: Chromatin Compartmentalization Regulates the Response to DNA Damage.” Nature, November. https://doi.org/10.1038/s41586-023-06841-8.
Balbontín, Roberto, Nara Figueroa-Bossi, and Lionello Bossi. 2023. “Construction of Single-Copy Fluorescent Protein Fusions by One-Step Recombineering.” Cold Spring Harbor Protocols, February. https://doi.org/10.1101/pdb.prot107950.
Balbontín, Roberto, Mathilde Ratel, Nara Figueroa-Bossi, and Lionello Bossi. 2023. “Converting an FRT-Tagged Gene into a Fluorescent Protein Gene Fusion by Flp-Mediated Site-Specific Recombination.” Cold Spring Harbor Protocols, February. https://doi.org/10.1101/pdb.prot107951.
Barone, M., Y. Ramayo-Caldas, J. Estellé, K. Tambosco, S. Chadi, F. Maillard, M. Gallopin, et al. 2023. “Gut Barrier-Microbiota Imbalances in Early Life Lead to Higher Sensitivity to Inflammation in a Murine Model of C-Section Delivery.” Microbiome 11 (1): 140. https://doi.org/10.1186/s40168-023-01584-0.
Bazin-Gélis, Mélanie, Evangelia Eleftheriou, Coralie Zangarelli, Gaëlle Lelandais, Linda Sperling, Olivier Arnaiz, and Mireille Bétermier. 2023. “Inter-Generational Nuclear Crosstalk Links the Control of Gene Expression to Programmed Genome Rearrangement during the Paramecium Sexual Cycle.” Nucleic Acids Research, November, gkad1006. https://doi.org/10.1093/nar/gkad1006.
Belser, Caroline, Julie Poulain, Karine Labadie, Frederick Gavory, Adriana Alberti, Julie Guy, Quentin Carradec, et al. 2023. “Integrative Omics Framework for Characterization of Coral Reef Ecosystems from the Tara Pacific Expedition.” Scientific Data 10 (1): 326. https://doi.org/10.1038/s41597-023-02204-0.
Bétermier, Mireille, Lawrence A. Klobutcher, and Eduardo Orias. 2023. “Programmed Chromosome Fragmentation in Ciliated Protozoa: Multiple Means to Chromosome Ends.” Microbiology and Molecular Biology Reviews: MMBR, November, e0018422. https://doi.org/10.1128/mmbr.00184-22.
Bonaud, Amélie, Pierre Larraufie, Mélanie Khamyath, Ugo Szachnowski, Shaun M. Flint, Nadège Brunel-Meunier, François Delhommeau, et al. 2023. “Transinteractome Analysis Reveals Distinct Niche Requirements for Isotype-Based Plasma Cell Subsets in the Bone Marrow.” European Journal of Immunology, June, e2250334. https://doi.org/10.1002/eji.202250334.
Braetz, Sebastian, Peter Schwerk, Nara Figueroa-Bossi, Karsten Tedin, and Marcus Fulde. 2023. “Prophage Gifsy-1 Induction in Salmonella Enterica Serovar Typhimurium Reduces Persister Cell Formation after Ciprofloxacin Exposure.” Microbiology Spectrum, June, e0187423. https://doi.org/10.1128/spectrum.01874-23.
Bury-Moné, Stéphanie, Annabelle Thibessard, Virginia S. Lioy, and Pierre Leblond. 2023. “Dynamics of the Streptomyces Chromosome: Chance and Necessity.” Trends in Genetics: TIG, September, S0168-9525(23)00166-X. https://doi.org/10.1016/j.tig.2023.07.008.
Camus, Adrien, Elena Espinosa, Pénélope Zapater Baras, Parul Singh, Nicole Quenech’Du, Elise Vickridge, Mauro Modesti, François Xavier Barre, and Olivier Espéli. 2023. “The SMC-like RecN Protein Is at the Crossroads of Several Genotoxic Stress Responses in Escherichia Coli.” Frontiers in Microbiology 14: 1146496. https://doi.org/10.3389/fmicb.2023.1146496.
Challal, Drice, Alexandra Menant, Can Goksal, Estelle Leroy, Bassem Al-Sady, and Mathieu Rougemaille. 2023. “A Dual, Catalytic Role for the Fission Yeast Ccr4-Not Complex in Gene Silencing and Heterochromatin Spreading.” Genetics, June, iyad108. https://doi.org/10.1093/genetics/iyad108.
Clerissi, Camille, Xing Luo, Aude Lucasson, Shogofa Mortaza, Julien de Lorgeril, Eve Toulza, Bruno Petton, et al. 2023. “A Core of Functional Complementary Bacteria Infects Oysters in Pacific Oyster Mortality Syndrome.” Animal Microbiome 5 (1): 26. https://doi.org/10.1186/s42523-023-00246-8.
Costa-Nunes, José A. da, and Daan Noordermeer. 2023. “TADs: Dynamic Structures to Create Stable Regulatory Functions.” Current Opinion in Structural Biology 81 (June): 102622. https://doi.org/10.1016/j.sbi.2023.102622.
Etherington, Ross D., Mark Bailey, Jean-Baptiste Boyer, Laura Armbruster, Xulyu Cao, Juliet C. Coates, Thierry Meinnel, Markus Wirtz, Carmela Giglione, and Daniel J. Gibbs. 2023. “Nt-Acetylation-Independent Turnover of SQUALENE EPOXIDASE 1 by Arabidopsis DOA10-like E3 Ligases.” Plant Physiology, July, kiad406. https://doi.org/10.1093/plphys/kiad406.
Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2023. “DNA Recombineering Applications.” Cold Spring Harbor Protocols, February. https://doi.org/10.1101/pdb.top107855.
Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2023. “Recombineering 101: Making an in-Frame Deletion Mutant.” Cold Spring Harbor Protocols, February. https://doi.org/10.1101/pdb.prot107856.
Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2023. “Scarless DNA Recombineering.” Cold Spring Harbor Protocols, February. https://doi.org/10.1101/pdb.prot107857.
Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2023. “Generating Libraries of Random LacZY or GFP Gene Fusions in the Bacterial Chromosome: Screening for Differentially Expressed Fusions.” Cold Spring Harbor Protocols, May. https://doi.org/10.1101/pdb.prot108196.
Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2023. “Use of Transposable Reporters in the Analysis of Bacterial Regulatory Networks.” Cold Spring Harbor Protocols, May. https://doi.org/10.1101/pdb.top108327.
Figueroa-Bossi, Nara, Roberto Balbontín, and Lionello Bossi. 2023. “Mapping Transposon Insertion Sites by Inverse Polymerase Chain Reaction and Sanger Sequencing.” Cold Spring Harbor Protocols, May. https://doi.org/10.1101/pdb.prot108197.
Girard, Chloe, David Zwicker, and Raphael Mercier. 2023. “The Regulation of Meiotic Crossover Distribution: A Coarse Solution to a Century-Old Mystery?” Biochemical Society Transactions, May, BST20221329. https://doi.org/10.1042/BST20221329.
Goudin, Anthony, Jean-Luc Ferat, Christophe Possoz, François-Xavier Barre, and Elisa Galli. 2023. “Recovery of Vibrio Cholerae Polarized Cellular Organization after Exit from a Non-Proliferating Spheroplast State.” PloS One 18 (10): e0293276. https://doi.org/10.1371/journal.pone.0293276.
Gout, Jean-Francois, Yue Hao, Parul Johri, Olivier Arnaiz, Thomas G. Doak, Simran Bhullar, Arnaud Couloux, et al. 2023. “Dynamics of Gene Loss Following Ancient Whole-Genome Duplication in the Cryptic Paramecium Complex.” Molecular Biology and Evolution, May, msad107. https://doi.org/10.1093/molbev/msad107.
Haccard, Olivier, Diletta Ciardo, Hemalatha Narrissamprakash, Odile Bronchain, Akiko Kumagai, William G. Dunphy, Arach Goldar, and Kathrin Marheineke. 2023. “Rif1 Restrains the Rate of Replication Origin Firing in Xenopus Laevis.” Communications Biology 6 (1): 788. https://doi.org/10.1038/s42003-023-05172-8.
Hensen, Noah, Lucas Bonometti, Ivar Westerberg, Ioana Onut Brännström, Sonia Guillou, Sandrine Cros-Aarteil, Sara Calhoun, et al. 2023. “Genome-Scale Phylogeny and Comparative Genomics of the Fungal Order Sordariales.” Molecular Phylogenetics and Evolution, October, 107938. https://doi.org/10.1016/j.ympev.2023.107938.
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.
Lo, Ying-Chu, Jade Bruxaux, Ricardo C. Rodríguez de la Vega, Samuel O’Donnell, Alodie Snirc, Monika Coton, Mélanie Le Piver, et al. 2023. “Domestication in Dry-Cured Meat Penicillium Fungi: Convergent Specific Phenotypes and Horizontal Gene Transfers without Strong Genetic Subdivision.” Evolutionary Applications 16 (9): 1637–60. https://doi.org/10.1111/eva.13591.
Meinnel, Thierry, Jean-Baptiste Boyer, and Carmela Giglione. 2023. “The Global Acetylation Profiling Pipeline for Quick Assessment of Protein N-Acetyltransferase Specificity In Cellulo.” Methods in Molecular Biology (Clifton, N.J.) 2718: 137–50. https://doi.org/10.1007/978-1-0716-3457-8_8.
Monassa, Paul, Frédéric Rivière, Cyril Dian, Frédéric Frottin, Carmela Giglione, and Thierry Meinnel. 2023. “Biochemical and Structural Analysis of N-Myristoyltransferase Mediated Protein Tagging.” Methods in Enzymology 684: 135–66. https://doi.org/10.1016/bs.mie.2023.02.016.
Nguyen, Phong Quoc, Sonia Huecas, Amna Asif-Laidin, Adrián Plaza-Pegueroles, Beatrice Capuzzi, Noé Palmic, Christine Conesa, et al. 2023. “Structural Basis of Ty1 Integrase Tethering to RNA Polymerase III for Targeted Retrotransposon Integration.” Nature Communications 14 (1): 1729. https://doi.org/10.1038/s41467-023-37109-4.
Noordermeer, Daan. 2023. “RNA Pol II Enters the Ring of Cohesin-Mediated Loop Extrusion.” Nature Genetics, July. https://doi.org/10.1038/s41588-023-01463-2.
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.
Penzo, Arianna, Marion Dubarry, Clémentine Brocas, Myriam Zheng, Raphaël M. Mangione, Mathieu Rougemaille, Coralie Goncalves, et al. 2023. “A R-Loop Sensing Pathway Mediates the Relocation of Transcribed Genes to Nuclear Pore Complexes.” Nature Communications 14 (1): 5606. https://doi.org/10.1038/s41467-023-41345-z.
Poinsignon, Thibault, Mélina Gallopin, Pierre Grognet, Fabienne Malagnac, Gaëlle Lelandais, and Pierre Poulain. 2023. “3D Models of Fungal Chromosomes to Enhance Visual Integration of Omics Data.” NAR Genomics and Bioinformatics 5 (4): lqad104. https://doi.org/10.1093/nargab/lqad104.
Pourcel, Christine, Malika Ouldali, Paulo Tavares, and Christiane Essoh. 2023. “The Saclayvirus Aci01-1 Very Long and Complex Fiber and Its Receptor at the Acinetobacter Baumannii Surface.” Archives of Virology 168 (7): 187. https://doi.org/10.1007/s00705-023-05817-3.
Pradat, Yoann, Julien Viot, Andrey A. Yurchenko, Konstantin Gunbin, Luigi Cerbone, Marc Deloger, Guillaume Grisay, et al. 2023. “Integrative Pan-Cancer Genomic and Transcriptomic Analyses of Refractory Metastatic Cancer.” Cancer Discovery 13 (5): 1116–43. https://doi.org/10.1158/2159-8290.CD-22-0966.
Rivière, Frédéric, Paul Monassa, Carmela Giglione, and Thierry Meinnel. 2023. “Kinetic and Catalytic Features of N-Myristoyltransferases.” Methods in Enzymology 684: 167–90. https://doi.org/10.1016/bs.mie.2023.02.018.
Rollo, Filipe, Guilherme D. Martins, André G. Gouveia, Solenne Ithurbide, Pascale Servant, Célia V. Romão, and Elin Moe. 2023. “Insights into the Role of Three Endonuclease III Enzymes for Oxidative Stress Resistance in the Extremely Radiation Resistant Bacterium Deinococcus Radiodurans.” Frontiers in Microbiology 14: 1266785. https://doi.org/10.3389/fmicb.2023.1266785.
Shen, Minjia, Kelly Goldlust, Sandra Daniel, Christian Lesterlin, and Yoshiharu Yamaichi. 2023. “Recipient UvrD Helicase Is Involved in Single- to Double-Stranded DNA Conversion during Conjugative Plasmid Transfer.” Nucleic Acids Research, February, gkad075. https://doi.org/10.1093/nar/gkad075.
Shevtsov, Alexandr, Axel Cloeckaert, Kalysh Berdimuratova, Elena Shevtsova, Alexandr V. Shustov, Asylulan Amirgazin, Talgat Karibayev, et al. 2023. “Brucella Abortus in Kazakhstan, Population Structure and Comparison with Worldwide Genetic Diversity.” Frontiers in Microbiology 14: 1106994. https://doi.org/10.3389/fmicb.2023.1106994.
Sun, Dongchang, Xingmin Sun, Yongfei Hu, and Yoshiharu Yamaichi. 2023. “Editorial: Horizontal Gene Transfer Mediated Bacterial Antibiotic Resistance, Volume II.” Frontiers in Microbiology 14: 1221606. https://doi.org/10.3389/fmicb.2023.1221606.
Tewary, Gargi, Benjamin Freyter, Mutaz Abd Al-Razaq, Hendrik Auerbach, Matthias W. Laschke, Tanja Kübelbeck, Antonia Kolb, et al. 2023. “Immunomodulatory Effects of Histone Variant H2A.J in Ionizing Radiation Dermatitis.” International Journal of Radiation Oncology, Biology, Physics, September, S0360-3016(23)07934-8. https://doi.org/10.1016/j.ijrobp.2023.09.022.
Timofeev, Vitalii, Irina Bakhteeva, Kseniya Khlopova, Raisa Mironova, Galina Titareva, Yulia Goncharova, Viktor Solomentsev, Tatiana Kravchenko, Ivan Dyatlov, and Gilles Vergnaud. 2023. “New Research on the Bacillus Anthracis Genetic Diversity in Siberia.” Pathogens (Basel, Switzerland) 12 (10): 1257. https://doi.org/10.3390/pathogens12101257.
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. “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. “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, 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.
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.
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.
García-Del Portillo, Francisco, Nara Figueroa-Bossi, and Lionello Bossi. 2022. “Remembering Pepe Casadesús.” MicroLife 3: uqac016. https://doi.org/10.1093/femsml/uqac016.
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.
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