Integrative Bio Informatics

Ceppi, Ilaria, Maria Rosaria Dello Stritto, Martin Mütze, Stefan Braunshier, Valentina Mengoli, Giordano Reginato, Hồ Mỹ Phúc Võ, et al. 2024. “Mechanism of BRCA1-BARD1 Function in DNA End Resection and DNA Protection.” Nature, September. https://doi.org/10.1038/s41586-024-07909-9.

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.

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.

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.

Nicolas, Yoann, Hélène Bret, Elda Cannavo, Ananya Acharya, Petr Cejka, Valérie Borde, and Raphaël Guerois. 2024. “Molecular Insights into the Activation of Mre11-Rad50 Endonuclease Activity by Sae2/CtIP.” Molecular Cell, June, S1097-2765(24)00442-8. https://doi.org/10.1016/j.molcel.2024.05.019.

Haas, Drago, Matthieu Barba, Cláudia M. Vicente, Šarká Nezbedová, Amélie Garénaux, Stéphanie Bury-Moné, Jean-Noël Lorenzi, et al. 2024. “Synteruptor: Mining Genomic Islands for Non-Classical Specialized Metabolite Gene Clusters.” NAR Genomics and Bioinformatics 6 (2): lqae069. https://doi.org/10.1093/nargab/lqae069.

Acharya, Ananya, Hélène Bret, Jen-Wei Huang, Martin Mütze, Martin Göse, Vera Maria Kissling, Ralf Seidel, Alberto Ciccia, Raphaël Guérois, and Petr Cejka. 2024. “Mechanism of DNA Unwinding by MCM8-9 in Complex with HROB.” Nature Communications 15 (1): 3584. https://doi.org/10.1038/s41467-024-47936-8.

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.

Ouasti, Fouad, Maxime Audin, Karine Fréon, Jean-Pierre Quivy, Mehdi Tachekort, Elizabeth Cesard, Aurélien Thureau, et al. 2024. “Disordered Regions and Folded Modules in CAF-1 Promote Histone Deposition in Schizosaccharomyces Pombe.” ELife 12 (February):RP91461. https://doi.org/10.7554/eLife.91461.

Leuzzi, Giuseppe, Alessandro Vasciaveo, Angelo Taglialatela, Xiao Chen, Tessa M. Firestone, Allison R. Hickman, Wendy Mao, et al. 2024. “SMARCAL1 Is a Dual Regulator of Innate Immune Signaling and PD-L1 Expression That Promotes Tumor Immune Evasion.” Cell, January, S0092-8674(24)00010-2. https://doi.org/10.1016/j.cell.2024.01.008.

Bret, Hélène, Jinmei Gao, Diego Javier Zea, Jessica Andreani, and Raphaël Guerois. 2024. “From Interaction Networks to Interfaces, Scanning Intrinsically Disordered Regions Using AlphaFold2.” Nature Communications 15 (1): 597. https://doi.org/10.1038/s41467-023-44288-7.

Liu, Siyu, Judith Miné-Hattab, Marie Villemeur, Raphaël Guerois, Henrik Dahl Pinholt, Leonid A. Mirny, and Angela Taddei. 2023. “Author Correction: In Vivo Tracking of Functionally Tagged Rad51 Unveils a Robust Strategy of Homology Search.” Nature Structural & Molecular Biology, November. https://doi.org/10.1038/s41594-023-01180-8.

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.

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.

Schweke, Hugo, Qifang Xu, Gerardo Tauriello, Lorenzo Pantolini, Torsten Schwede, Frédéric Cazals, Alix Lhéritier, et al. 2023. “Discriminating Physiological from Non-Physiological Interfaces in Structures of Protein Complexes: A Community-Wide Study.” Proteomics, June, e2200323. https://doi.org/10.1002/pmic.202200323.

Wang, Yanan, Giovanni Chiappetta, Raphaël Guérois, Yijun Liu, Stéphane Romero, Daniel J. Boesch, Matthias Krause, et al. 2023. “PPP2R1A Regulates Migration Persistence through the NHSL1-Containing WAVE Shell Complex.” Nature Communications 14 (1): 3541. https://doi.org/10.1038/s41467-023-39276-w.

Ceppi, Ilaria, Elda Cannavo, Hélène Bret, Rosa Camarillo, Francesca Vivalda, Roshan Singh Thakur, Amador Romero-Franco, et al. 2023. “PLK1 Regulates CtIP and DNA2 Interplay in Long-Range DNA End Resection.” Genes & Development, February. https://doi.org/10.1101/gad.349981.122.

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.

Singh, Dipesh Kumar, Rigel Salinas Gamboa, Avinash Kumar Singh, Birgit Walkemeier, Jelle Van Leene, Geert De Jaeger, Imran Siddiqi, Raphael Guerois, Wayne Crismani, and Raphael Mercier. 2023. “The FANCC-FANCE-FANCF Complex Is Evolutionarily Conserved and Regulates Meiotic Recombination.” Nucleic Acids Research, January, gkac1244. https://doi.org/10.1093/nar/gkac1244.

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.

Kissling, Vera M., Giordano Reginato, Eliana Bianco, Kristina Kasaciunaite, Janny Tilma, Gea Cereghetti, Natalie Schindler, et al. 2022. “Mre11-Rad50 Oligomerization Promotes DNA Double-Strand Break Repair.” Nature Communications 13 (1): 2374. https://doi.org/10.1038/s41467-022-29841-0.

Acharya, Ananya, Kristina Kasaciunaite, Martin Göse, Vera Kissling, Raphaël Guérois, Ralf Seidel, and Petr Cejka. 2021. “Distinct RPA Domains Promote Recruitment and the Helicase-Nuclease Activities of Dna2.” Nature Communications 12 (1): 6521. https://doi.org/10.1038/s41467-021-26863-y.

Porro, Antonio, Mohiuddin Mohiuddin, Christina Zurfluh, Vincent Spegg, Jingqi Dai, Florence Iehl, Virginie Ropars, et al. 2021. “FAN1-MLH1 Interaction Affects Repair of DNA Interstrand Cross-Links and Slipped-CAG/CTG Repeats.” Science Advances 7 (31): eabf7906. https://doi.org/10.1126/sciadv.abf7906.

Quignot, Chloé, Guillaume Postic, Hélène Bret, Julien Rey, Pierre Granger, Samuel Murail, Pablo Chacón, Jessica Andreani, Pierre Tufféry, and Raphaël Guerois. 2021. “InterEvDock3: A Combined Template-Based and Free Docking Server with Increased Performance through Explicit Modeling of Complex Homologs and Integration of Covariation-Based Contact Maps.” Nucleic Acids Research 49 (W1): W277–84. https://doi.org/10.1093/nar/gkab358.

Postic, Guillaume, Jessica Andreani, Julien Marcoux, Victor Reys, Raphaël Guerois, Julien Rey, Emmanuelle Mouton-Barbosa, et al. 2021. “Proteo3Dnet: A Web Server for the Integration of Structural Information with Interactomics Data.” Nucleic Acids Research 49 (W1): W567–72. https://doi.org/10.1093/nar/gkab332.

Riquier, Sébastien, Chloé Bessiere, Benoit Guibert, Anne-Laure Bouge, Anthony Boureux, Florence Ruffle, Jérôme Audoux, et al. 2021. “Kmerator Suite: Design of Specific k-Mer Signatures and Automatic Metadata Discovery in Large RNA-Seq Datasets.” NAR Genomics and Bioinformatics 3 (3): lqab058. https://doi.org/10.1093/nargab/lqab058.

Dai, Jingqi, Aurore Sanchez, Céline Adam, Lepakshi Ranjha, Giordano Reginato, Pierre Chervy, Carine Tellier-Lebegue, et al. 2021. “Molecular Basis of the Dual Role of the Mlh1-Mlh3 Endonuclease in MMR and in Meiotic Crossover Formation.” Proceedings of the National Academy of Sciences of the United States of America 118 (23): e2022704118. https://doi.org/10.1073/pnas.2022704118.

Wang, Yunfeng, Haoliang Xue, Christine Pourcel, Yang Du, and Daniel Gautheret. 2021. “2-Kupl: Mapping-Free Variant Detection from DNA-Seq Data of Matched Samples.” BMC Bioinformatics 22 (1): 304. https://doi.org/10.1186/s12859-021-04185-6.

Ma, Emilie, Laurent Maloisel, Léa Le Falher, Raphaël Guérois, and Eric Coïc. 2021. “Rad52 Oligomeric N-Terminal Domain Stabilizes Rad51 Nucleoprotein Filaments and Contributes to Their Protection against Srs2.” Cells 10 (6). https://doi.org/10.3390/cells10061467.

Ribeiro, Jonathan, Pauline Dupaigne, Cynthia Petrillo, Cécile Ducrot, Clotilde Duquenne, Xavier Veaute, Carole Saintomé, et al. 2021. “The Meiosis-Specific MEIOB-SPATA22 Complex Cooperates with RPA to Form a Compacted Mixed MEIOB/SPATA22/RPA/SsDNA Complex.” DNA Repair 102 (June):103097. https://doi.org/10.1016/j.dnarep.2021.103097.

Vernekar, Dipti Vinayak, Giordano Reginato, Céline Adam, Lepakshi Ranjha, Florent Dingli, Marie-Claude Marsolier, Damarys Loew, et al. 2021. “The Pif1 Helicase Is Actively Inhibited during Meiotic Recombination Which Restrains Gene Conversion Tract Length.” Nucleic Acids Research 49 (8): 4522–33. https://doi.org/10.1093/nar/gkab232.

Lecoq, Lauriane, Shishan Wang, Marie Dujardin, Peter Zimmermann, Leonard Schuster, Marie-Laure Fogeron, Mathilde Briday, et al. 2021. “A Pocket-Factor-Triggered Conformational Switch in the Hepatitis B Virus Capsid.” Proceedings of the National Academy of Sciences of the United States of America 118 (17): e2022464118. https://doi.org/10.1073/pnas.2022464118.

Quignot, Chloé, Pierre Granger, Pablo Chacón, Raphael Guerois, and Jessica Andreani. 2021. “Atomic-Level Evolutionary Information Improves Protein-Protein Interface Scoring.” Bioinformatics (Oxford, England), April, btab254. https://doi.org/10.1093/bioinformatics/btab254.

Nguyen, Ha T. N., Haoliang Xue, Virginie Firlej, Yann Ponty, Melina Gallopin, and Daniel Gautheret. 2021. “Reference-Free Transcriptome Signatures for Prostate Cancer Prognosis.” BMC Cancer 21 (1): 394. https://doi.org/10.1186/s12885-021-08021-1.

Kuksin, Maria, Daphné Morel, Marine Aglave, François-Xavier Danlos, Aurélien Marabelle, Andrei Zinovyev, Daniel Gautheret, and Loïc Verlingue. 2021. “Applications of Single-Cell and Bulk RNA Sequencing in Onco-Immunology.” European Journal of Cancer (Oxford, England: 1990) 149 (April):193–210. https://doi.org/10.1016/j.ejca.2021.03.005.

Mbianda, Johanne, May Bakail, Christophe André, Gwenaëlle Moal, Marie E. Perrin, Guillaume Pinna, Raphaël Guerois, et al. 2021. “Optimal Anchoring of a Foldamer Inhibitor of ASF1 Histone Chaperone through Backbone Plasticity.” Science Advances 7 (12): eabd9153. https://doi.org/10.1126/sciadv.abd9153.

Boudry, Pierre, Emma Piattelli, Emilie Drouineau, Johann Peltier, Anaïs Boutserin, Maxence Lejars, Eliane Hajnsdorf, et al. 2021. “Identification of RNAs Bound by Hfq Reveals Widespread RNA Partners and a Sporulation Regulator in the Human Pathogen Clostridioides Difficile.” RNA Biology, February, 1–22. https://doi.org/10.1080/15476286.2021.1882180.

Öz, Robin, Jing L. Wang, Raphael Guerois, Gaurav Goyal, Sriram Kk, Virginie Ropars, Rajhans Sharma, et al. 2021. “Dynamics of Ku and Bacterial Non-Homologous End-Joining Characterized Using Single DNA Molecule Analysis.” Nucleic Acids Research, February. https://doi.org/10.1093/nar/gkab083.

Kalvari, Ioanna, Eric P Nawrocki, Nancy Ontiveros-Palacios, Joanna Argasinska, Kevin Lamkiewicz, Manja Marz, Sam Griffiths-Jones, et al. 2021. “Rfam 14: Expanded Coverage of Metagenomic, Viral and MicroRNA Families.” Nucleic Acids Research 49 (D1): D192–200. https://doi.org/10.1093/nar/gkaa1047.

Wang, Ji, Claire Toffano-Nioche, Florence Lorieux, Daniel Gautheret, and Jean Lehmann. 2021. “Accurate Characterization of Escherichia Coli TRNA Modifications with a Simple Method of Deep-Sequencing Library Preparation.” RNA Biology 18 (1): 33–46. https://doi.org/10.1080/15476286.2020.1790871.

Rahman, Md Maminur, Mohiuddin Mohiuddin, Islam Shamima Keka, Kousei Yamada, Masataka Tsuda, Hiroyuki Sasanuma, Jessica Andreani, et al. 2020. “Genetic Evidence for the Involvement of Mismatch Repair Proteins, PMS2 and MLH3, in a Late Step of Homologous Recombination.” The Journal of Biological Chemistry 295 (51): 17460–75. https://doi.org/10.1074/jbc.RA120.013521.

Sanchez, Aurore, Céline Adam, Felix Rauh, Yann Duroc, Lepakshi Ranjha, Bérangère Lombard, Xiaojing Mu, et al. 2020. “Exo1 Recruits Cdc5 Polo Kinase to MutLγ to Ensure Efficient Meiotic Crossover Formation.” Proceedings of the National Academy of Sciences of the United States of America 117 (48): 30577–88. https://doi.org/10.1073/pnas.2013012117.

Marchet, Camille, Zamin Iqbal, Daniel Gautheret, Mikaël Salson, and Rayan Chikhi. 2020. “REINDEER: Efficient Indexing of k-Mer Presence and Abundance in Sequencing Datasets.” Bioinformatics 36 (Supplement_1): i177–85. https://doi.org/10.1093/bioinformatics/btaa487.

Postic, Guillaume, Julien Marcoux, Victor Reys, Jessica Andreani, Yves Vandenbrouck, Marie-Pierre Bousquet, Emmanuelle Mouton-Barbosa, et al. 2020. “Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration.” Journal of Proteome Research 19 (7): 2807–20. https://doi.org/10.1021/acs.jproteome.0c00066.

Phongsavanh, Xaysongkhame, Noha Al-Qatabi, Mohammed Samer Shaban, Fawzi Khoder-Agha, Merwan El Asri, Martine Comisso, Raphaël Guérois, and Marc Mirande. 2020. “How HIV-1 Integrase Associates with Human Mitochondrial Lysyl-TRNA Synthetase.” Viruses 12 (10): 1202. https://doi.org/10.3390/v12101202.

Pourcel, Christine, Marie Touchon, Nicolas Villeriot, Jean-Philippe Vernadet, David Couvin, Claire Toffano-Nioche, and Gilles Vergnaud. 2020. “CRISPRCasdb a Successor of CRISPRdb Containing CRISPR Arrays and Cas Genes from Complete Genome Sequences, and Tools to Download and Query Lists of Repeats and Spacers.” Nucleic Acids Research 48 (D1): D535–44. https://doi.org/10.1093/nar/gkz915.

Nadaradjane, Aravindan Arun, Chloé Quignot, Seydou Traoré, Jessica Andreani, and Raphaël Guerois. 2020. “Docking Proteins and Peptides under Evolutionary Constraints in Critical Assessment of PRediction of Interactions Rounds 38 to 45.” Proteins: Structure, Function, and Bioinformatics 88 (8): 986–98. https://doi.org/https://doi.org/10.1002/prot.25857.

Andreani, Jessica, Chloe Quignot, and Raphael Guerois. 2020. “Structural Prediction of Protein Interactions and Docking Using Conservation and Coevolution.” Wiley Interdisciplinary Reviews-Computational Molecular Science 10 (6): e1470. https://doi.org/10.1002/wcms.1470.

Tidjani, Abdoul-Razak, Jean-Noël Lorenzi, Maxime Toussaint, Erwin van Dijk, Delphine Naquin, Olivier Lespinet, Cyril Bontemps, and Pierre Leblond. 2019. “Genome Sequences of 11 Conspecific Streptomyces Sp. Strains.” Microbiology Resource Announcements 8 (38): e00863-19. https://doi.org/10.1128/MRA.00863-19.

Tidjani, Abdoul-Razak, Jean-Noël Lorenzi, Maxime Toussaint, Erwin van Dijk, Delphine Naquin, Olivier Lespinet, Cyril Bontemps, and Pierre Leblond. 2019. “Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics.” MBio 10 (5): e01533-19. https://doi.org/10.1128/mBio.01533-19.