Genome Biology Department
3888256
DBG
2024
chicago-author-date
50
creator
asc
year
7443
https://www.i2bc.paris-saclay.fr/wp-content/plugins/zotpress/
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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.
Barrault, Maxime, Svetlana Chabelskaya, Rodrigo H. Coronel-Tellez, Claire Toffano-Nioche, Eric Jacquet, and Philippe Bouloc. 2024. “Staphylococcal Aconitase Expression during Iron Deficiency Is Controlled by an SRNA-Driven Feedforward Loop and Moonlighting Activity.” Nucleic Acids Research, June, gkae506. https://doi.org/10.1093/nar/gkae506.
Barrault, Maxime, Elise Leclair, Etornam Kofi Kumeko, Eric Jacquet, and Philippe Bouloc. 2024. “Staphylococcal SRNA IsrR Downregulates Methylthiotransferase MiaB under Iron-Deficient Conditions.” Microbiology Spectrum, August, e0388823. https://doi.org/10.1128/spectrum.03888-23.
Besombes, Amelie, Yazid Adam, Christophe Possoz, Ivan Junier, Francois-Xavier Barre, and Jean-Luc Ferat. 2024. “DciA Secures Bidirectional Replication Initiation in Vibrio Cholerae.” Nucleic Acids Research, September, gkae795. https://doi.org/10.1093/nar/gkae795.
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.
Brünje, Annika, Magdalena Füßl, Jürgen Eirich, Jean-Baptiste Boyer, Paulina Heinkow, Ulla Neumann, Minna Konert, et al. 2024. “The Plastidial Protein Acetyltransferase GNAT1 Forms a Complex with GNAT2, yet Their Interaction Is Dispensable for State Transitions.” Molecular & Cellular Proteomics: MCP, September, 100850. https://doi.org/10.1016/j.mcpro.2024.100850.
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.
Campese, Lucia, Luca Russo, Maria Abagnale, Adriana Alberti, Giancarlo Bachi, Cecilia Balestra, Daniele Bellardini, et al. 2024. “The NEREA Augmented Observatory: An Integrative Approach to Marine Coastal Ecology.” Scientific Data 11 (1): 989. https://doi.org/10.1038/s41597-024-03787-y.
Chang, Li-Hsin, and Daan Noordermeer. 2024. “Permeable TAD Boundaries and Their Impact on Genome-Associated Functions.” BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology, August, e2400137. https://doi.org/10.1002/bies.202400137.
Coux, Olivier, Rosa Farràs, and Core Group of ProteoCure. 2024. “ProteoCure : An European Network to Fine-Tune the Proteome.” Biochimie, June, S0300-9084(24)00140-8. https://doi.org/10.1016/j.biochi.2024.06.004.
Delaleau, Mildred, Nara Figueroa-Bossi, Thuy Duong Do, Patricia Kerboriou, Eric Eveno, Lionello Bossi, and Marc Boudvillain. 2024. “Rho-Dependent Transcriptional Switches Regulate the Bacterial Response to Cold Shock.” Molecular Cell, August, S1097-2765(24)00632-4. https://doi.org/10.1016/j.molcel.2024.07.034.
Dubois, Emeline, Stéphanie Boisnard, Henri-Marc Bourbon, Kenza Yefsah, Karine Budin, Robert Debuchy, Liangran Zhang, Nancy Kleckner, Denise Zickler, and Eric Espagne. 2024. “Canonical and Noncanonical Roles of Hop1 Are Crucial for Meiotic Prophase in the Fungus Sordaria Macrospora.” PLoS Biology 22 (7): e3002705. https://doi.org/10.1371/journal.pbio.3002705.
Eirich, Jürgen, Jean-Baptiste Boyer, Laura Armbruster, Aiste Ivanauskaite, Carolina De La Torre, Thierry Meinnel, Markus Wirtz, Paula Mulo, Iris Finkemeier, and Carmela Giglione. 2024. “Light Changes Promote Distinct Responses of Plastid Protein Acetylation Marks.” Molecular & Cellular Proteomics: MCP, September, 100845. https://doi.org/10.1016/j.mcpro.2024.100845.
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.
Guedes, Joana P., Jean Baptiste Boyer, Jasmine Elurbide, Beatriz Carte, Virginie Redeker, Laila Sago, Thierry Meinnel, Manuela Côrte-Real, Carmela Giglione, and Rafael Aldabe. 2024. “NatB Protects Procaspase-8 from UBR4-Mediated Degradation and Is Required for Full Induction of the Extrinsic Apoptosis Pathway.” Molecular and Cellular Biology, August, 1–14. https://doi.org/10.1080/10985549.2024.2382453.
Gutiérrez-Santiago, Francisco, Verónica Martínez-Fernández, Ana Isabel Garrido-Godino, Cristina Colino-Palomino, Andrés Clemente-Blanco, Christine Conesa, Joël Acker, and Francisco Navarro. 2024. “Maf1 Phosphorylation Is Regulated through the Action of Prefoldin-like Bud27 on PP4 Phosphatase in Saccharomyces Cerevisiae.” Nucleic Acids Research, May, gkae414. https://doi.org/10.1093/nar/gkae414.
Jaffal, Hoda, Mounia Kortebi, Pauline Misson, Paulo Tavares, Malika Ouldali, Hervé Leh, Sylvie Lautru, Virginia S. Lioy, François Lecointe, and Stéphanie G. Bury-Moné. 2024. “Prophage Induction Can Facilitate the in Vitro Dispersal of Multicellular Streptomyces Structures.” PLoS Biology 22 (7): e3002725. https://doi.org/10.1371/journal.pbio.3002725.
Jones, Gareth, Nancy Kleckner, and Denise Zickler. 2024. “Meiosis through Three Centuries.” Chromosoma, May. https://doi.org/10.1007/s00412-024-00822-0.
Karri, Sabrina, David Cornu, Claudia Serot, Lynda Biri, Aurélie Hatton, Elise Dréanot, Camille Rullaud, et al. 2024. “TLN468 Changes the Pattern of TRNA Used to Read through Premature Termination Codons in CFTR.” Journal of Cystic Fibrosis: Official Journal of the European Cystic Fibrosis Society, August, S1569-1993(24)00802-6. https://doi.org/10.1016/j.jcf.2024.07.017.
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.
Lekota, Kgaugelo Edward, Ayesha Hassim, Maphuti Betty Ledwaba, Barbara A. Glover, Edgar H. Dekker, Louis Ockert van Schalkwyk, Jennifer Rossouw, Wolfgang Beyer, Gilles Vergnaud, and Henriette van Heerden. 2024. “Bacillus Anthracis in South Africa, 1975-2013: Are Some Lineages Vanishing?” BMC Genomics 25 (1): 742. https://doi.org/10.1186/s12864-024-10631-5.
Maalouf, Christelle A., Adriana Alberti, and Julie Soutourina. 2024. “Mediator Complex in Transcription Regulation and DNA Repair: Relevance for Human Diseases.” DNA Repair 141 (June):103714. https://doi.org/10.1016/j.dnarep.2024.103714.
Moindrot, Benoit, Yui Imaizumi, and Robert Feil. 2024. “Differential 3D Genome Architecture and Imprinted Gene Expression: Cause or Consequence?” Biochemical Society Transactions, May, BST20230143. https://doi.org/10.1042/BST20230143.
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.
Monteagudo-Sánchez, Ana, Julien Richard Albert, Margherita Scarpa, Daan Noordermeer, and Maxim V. C. Greenberg. 2024. “The Impact of the Embryonic DNA Methylation Program on CTCF-Mediated Genome Regulation.” Nucleic Acids Research, August, gkae724. https://doi.org/10.1093/nar/gkae724.
Nocente, Marina C., Anida Mesihovic Karamitsos, Emilie Drouineau, Manon Soleil, Waad Albawardi, Cécile Dulary, Florence Ribierre, et al. 2024. “CBAF Generates Subnucleosomes That Expand OCT4 Binding and Function beyond DNA Motifs at Enhancers.” Nature Structural & Molecular Biology, July. https://doi.org/10.1038/s41594-024-01344-0.
O, Saatci, Alam R, Huynh-Dam Kt, Isik A, Uner M, Belder N, Ersan Pg, et al. 2024. “Targeting LINC00152 Activates CAMP/Ca2+/Ferroptosis Axis and Overcomes Tamoxifen Resistance in ER+ Breast Cancer.” Cell Death & Disease 15 (6). https://doi.org/10.1038/s41419-024-06814-3.
Ponndara, Sokrich, Mounia Kortebi, Frédéric Boccard, Stéphanie Bury-Moné, and Virginia S. Lioy. 2024. “Principles of Bacterial Genome Organization, a Conformational Point of View.” Molecular Microbiology, June. https://doi.org/10.1111/mmi.15290.
Pourcel, Christine, Christiane Essoh, Malika Ouldali, and Paulo Tavares. 2024. “Acinetobacter Baumannii Satellite Phage Aci01-2-Phanie Depends on a Helper Myophage for Its Multiplication.” Journal of Virology, June, e0066724. https://doi.org/10.1128/jvi.00667-24.
Riemenschneider, Henrick, Qiang Guo, Jakob Bader, Frédéric Frottin, Daniel Farny, Gernot Kleinberger, Christian Haass, et al. 2024. “Author Correction: Gel-like Inclusions of C-Terminal Fragments of TDP-43 Sequester Stalled Proteasomes in Neurons.” EMBO Reports, June. https://doi.org/10.1038/s44319-024-00163-0.
Rivière, Frédéric, Cyril Dian, Rémi F. Dutheil, Paul Monassa, Carmela Giglione, and Thierry Meinnel. 2024. “Novel, Tightly Structurally Related N-Myristoyltransferase Inhibitors Display Equally Potent yet Distinct Inhibitory Mechanisms.” Structure (London, England: 1993), August, S0969-2126(24)00318-6. https://doi.org/10.1016/j.str.2024.08.001.
Roginski, Paul, Anna Grandchamp, Chloé Quignot, and Anne Lopes. 2024. “De Novo Emerged Gene Search in Eukaryotes with DENSE.” Genome Biology and Evolution 16 (8): evae159. https://doi.org/10.1093/gbe/evae159.
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.
Sebastià, C., M. Gallopin, Y. Ramayo-Caldas, J. Estellé, J. Valdés-Hernández, A. Castelló, A. Sánchez, D. Crespo-Piazuelo, and J. M. Folch. 2024. “Gene Co-Expression Network Analysis for Porcine Intramuscular Fatty Acid Composition.” Animal: An International Journal of Animal Bioscience 18 (9): 101259. https://doi.org/10.1016/j.animal.2024.101259.
Shevtsov, Alexandr, Uinkul Izbanova, Asylulan Amirgazin, Alma Kairzhanova, Ayan Dauletov, Vladimir Kiyan, and Gilles Vergnaud. 2024. “Genetic Homogeneity of Francisella Tularensis Subsp. Mediasiatica Strains in Kazakhstan.” Pathogens (Basel, Switzerland) 13 (7): 581. https://doi.org/10.3390/pathogens13070581.
Timofeev, Vitalii, Irina Bakhteeva, Galina Titareva, Raisa Mironova, Vera Evseeva, Tatiana Kravchenko, Angelika Sizova, et al. 2024. “Avirulence of a Spontaneous Francisella Tularensis Subsp. Mediasiatica PrmA Mutant.” PloS One 19 (6): e0305569. https://doi.org/10.1371/journal.pone.0305569.
Vauclare, Pierre, Jip Wulffelé, Françoise Lacroix, Pascale Servant, Fabrice Confalonieri, Jean-Philippe Kleman, Dominique Bourgeois, and Joanna Timmins. 2024. “Stress-Induced Nucleoid Remodeling in Deinococcus Radiodurans Is Associated with Major Changes in Heat Unstable (HU) Protein Dynamics.” Nucleic Acids Research, May, gkae379. https://doi.org/10.1093/nar/gkae379.
Vergnaud, Gilles, Michel S. Zygmunt, Roland T. Ashford, Adrian M. Whatmore, and Axel Cloeckaert. 2024. “Genomic Diversity and Zoonotic Potential of Brucella Neotomae.” Emerging Infectious Diseases 30 (1): 155–58. https://doi.org/10.3201/eid3001.221783.
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.
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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.
Chang, Li-Hsin, Sourav Ghosh, Andrea Papale, Jennifer M. Luppino, Mélanie Miranda, Vincent Piras, Jéril Degrouard, et al. 2023. “Multi-Feature Clustering of CTCF Binding Creates Robustness for Loop Extrusion Blocking and Topologically Associating Domain Boundaries.” Nature Communications 14 (1): 5615. https://doi.org/10.1038/s41467-023-41265-y.
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.
Couturier, Agathe, Chloé Virolle, Kelly Goldlust, Annick Berne-Dedieu, Audrey Reuter, Sophie Nolivos, Yoshiharu Yamaichi, Sarah Bigot, and Christian Lesterlin. 2023. “Real-Time Visualisation of the Intracellular Dynamics of Conjugative Plasmid Transfer.” Nature Communications 14 (1): 294. https://doi.org/10.1038/s41467-023-35978-3.
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.
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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.
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.
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.
Moindrot, Benoit, and Daan Noordermeer. 2022. “Open for Connections: HiCAR Reveals the Interactions of Accessible DNA.” Cell Genomics 2 (4): 100121. https://doi.org/10.1016/j.xgen.2022.100121.
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.
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.
Vigueras-Meneses, Liliana Guadalupe, Ximena Escalera-Fanjul, Mohammed El-Hafidi, Javier Montalvo-Arredondo, Nicolás Gómez-Hernández, Maritrini Colón, Estefany Granados, et al. 2022. “Two Alpha Isopropylmalate Synthase Isozymes with Similar Kinetic Properties Are Extant in the Yeast Lachancea Kluyveri.” FEMS Yeast Research 22 (1): foac016. https://doi.org/10.1093/femsyr/foac016.
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.