RNA Sequence, Structure & Function

Cossu, Carlo Andrea, Giuliano Garofolo, Anna Janowicz, Fabrizio De Massis, Jeanette Wentzel, Maphuti Betty Ledwaba, Claude Sabeta, et al. 2025. “Phylogenomics of Brucella Abortus Isolated from African Buffalo in Kruger National Park: New Perspectives on Wildlife-Cattle Disease Dynamics.” Veterinary Microbiology 304 (March):110493. https://doi.org/10.1016/j.vetmic.2025.110493.

Kreis, Victor, Claire Toffano-Nioche, Cécile Denève-Larrazet, Jean-Christophe Marvaud, Julian R. Garneau, Florent Dumont, Erwin L. van Dijk, et al. 2024. “Dual RNA-Seq Study of the Dynamics of Coding and Non-Coding RNA Expression during Clostridioides Difficile Infection in a Mouse Model.” MSystems 9 (12): e00863-24. https://doi.org/10.1128/msystems.00863-24.

Shevtsov, Alexandr, Ayan Dauletov, Uinkul Izbanova, Alma Kairzhanova, Nailya Tursunbay, Vladimir Kiyan, and Gilles Vergnaud. 2024. “Development of a Real-Time PCR Assay for the Detection of Francisella Spp. and the Identification of F. Tularensis Subsp. Mediasiatica.” Microorganisms 12 (11): 2345. https://doi.org/10.3390/microorganisms12112345.

Essoh, Christiane, Yolande Hauck, Timothée Ouassa, Daouda Touré, Richmond Djatchi, Guillaume Yao Loukou, Simon-Pierre Assanvo N’Guetta, Gilles Vergnaud, and Christine Pourcel. 2024. “Molecular Typing of Pseudomonas Aeruginosa Isolates Collected in Abidjan Hospitals (Côte d’Ivoire) Using the Multiple-Locus Variable Number of Tandem Repeats Method.” Diagnostics (Basel, Switzerland) 14 (20): 2284. https://doi.org/10.3390/diagnostics14202284.

Kadyrova, Madina, Alexandr Ostrovskii, Kassym Mukanov, Amirkhan Kassen, Elena Shevtsova, Maxat Berdikulov, Gilles Vergnaud, and Alexandr Shevtsov. 2024. “Molecular Characterization of Anaplasma Spp. in Cattle from Kazakhstan.” Pathogens (Basel, Switzerland) 13 (10): 894. https://doi.org/10.3390/pathogens13100894.

Bessière, Chloé, Haoliang Xue, Benoit Guibert, Anthony Boureux, Florence Rufflé, Julien Viot, Rayan Chikhi, et al. 2024. “Transipedia.Org: K-Mer-Based Exploration of Large RNA Sequencing Datasets and Application to Cancer Data.” Genome Biology 25 (1): 266. https://doi.org/10.1186/s13059-024-03413-5.

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 52 (14): 8241–53. https://doi.org/10.1093/nar/gkae506.

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.

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.

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.

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.

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 13 (2): e01155-23. https://doi.org/10.1128/mra.01155-23.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Fasemore, Akinyemi M., Andrea Helbich, Mathias C. Walter, Thomas Dandekar, Gilles Vergnaud, Konrad U. Förstner, and Dimitrios Frangoulidis. 2021. “CoxBase: An Online Platform for Epidemiological Surveillance, Visualization, Analysis, and Typing of Coxiella Burnetii Genomic Sequences.” MSystems, December. https://doi.org/10.1128/mSystems.00403-21.

Jia, Bin, Tianlong Wang, and Jean Lehmann. 2021. “Peptidyl Transferase Center Decompaction and Structural Constraints during Early Protein Elongation on the Ribosome.” Scientific Reports 11 (1): 24061. https://doi.org/10.1038/s41598-021-02985-7.

Monachello, Dario, Marc Lauraine, Sandra Gillot, François Michel, and Maria Costa. 2021. “A New RNA-DNA Interaction Required for Integration of Group II Intron Retrotransposons into DNA Targets.” Nucleic Acids Research, November, gkab1031. https://doi.org/10.1093/nar/gkab1031.

González-Alemán, Roy, Daniel Platero-Rochart, David Hernández-Castillo, Erix W. Hernández-Rodríguez, Julio Caballero, Fabrice Leclerc, and Luis Montero-Cabrera. 2021. “BitQT: A Graph-Based Approach to the Quality Threshold Clustering of Molecular Dynamics.” Bioinformatics (Oxford, England), August, btab595. https://doi.org/10.1093/bioinformatics/btab595.

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.

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.

Shevtsov, Vladislav, Alma Kairzhanova, Alexandr Shevtsov, Alexandr Shustov, Ruslan Kalendar, Sarsenbay Abdrakhmanov, Larissa Lukhnova, Uinkul Izbanova, Yerlan Ramankulov, and Gilles Vergnaud. 2021. “Genetic Diversity of Francisella Tularensis Subsp. Holarctica in Kazakhstan.” PLoS Neglected Tropical Diseases 15 (5): e0009419. https://doi.org/10.1371/journal.pntd.0009419.

Zygmunt, Michel S., Gilles Vergnaud, and Axel Cloeckaert. 2021. “Whole-Genome Sequence of a Brucella Pinnipedialis Sequence Type 54 Strain Isolated from a Hooded Seal (Cystophora Cristata) from the North Atlantic Ocean, Norway.” Microbiology Resource Announcements 10 (18): e00271-21. https://doi.org/10.1128/MRA.00271-21.

González-Alemán, Roy, Nicolas Chevrollier, Manuel Simoes, Luis Montero-Cabrera, and Fabrice Leclerc. 2021. “MCSS-Based Predictions of Binding Mode and Selectivity of Nucleotide Ligands.” Journal of Chemical Theory and Computation 17 (4): 2599–2618. https://doi.org/10.1021/acs.jctc.0c01339.

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.

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.

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.

Shevtsov, Alexandr, Larissa Lukhnova, Uinkul Izbanova, Jean-Philippe Vernadet, Marat Kuibagarov, Asylulan Amirgazin, Yerlan Ramankulov, and Gilles Vergnaud. 2021. “Bacillus Anthracis Phylogeography: New Clues From Kazakhstan, Central Asia.” Frontiers in Microbiology 12:3797. https://doi.org/10.3389/fmicb.2021.778225.

Shevtsov, Alexandr, Gilles Vergnaud, Asylulan Amirgazin, Larissa Lukhnova, Uinkul Izbanova, Vladislav Shevtsov, and Yerlan Ramankulov. 2020. “Retrospective Analysis of the Relationship between Two Anthrax Outbreaks in Kazakhstan Based on Genomic Data.” Microbiology Resource Announcements 9 (50). https://doi.org/10.1128/MRA.01126-20.

Pourcel, Christine. 2020. “New Insights into CRISPR Arrays.” The CRISPR Journal 3 (6): 422–24. https://doi.org/10.1089/crispr.2020.29111.cpo.

Amirgazin, Asylulan, Gilles Vergnaud, Kasym Mukanov, Marat Kuibagarov, Talgat Karibaev, Yerlan Ramankulov, and Alexandr Shevtsov. 2020. “Draft Genome Sequences of Three Pasteurella Multocida Strains Isolated from Domestic Animals in Kazakhstan.” Microbiology Resource Announcements 9 (32): e00487-20. https://doi.org/10.1128/MRA.00487-20.

Kuibagarov, Marat, Alma Kairzhanova, Gilles Vergnaud, Asylulan Amirgazin, Larissa Lukhnova, Uinkul Izbanova, Yerlan Ramankulov, and Alexandr Shevtsov. 2020. “Draft Genome Sequence of the Strain Francisella Tularensis Subsp. Mediasiatica 240, Isolated in Kazakhstan.” Microbiology Resource Announcements 9 (35): e00766-20. https://doi.org/10.1128/MRA.00766-20.

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.

Kuibagarov, Marat, Asylulan Amirgazin, Gilles Vergnaud, Alexandr Shustov, Anara Ryskeldina, Yerlan Ramankulov, and Alexandr Shevtsov. 2020. “Draft Genome Sequence of Moraxella Bovoculi Strain KZ-1, Isolated from Cattle in North Kazakhstan.” Microbiology Resource Announcements 9 (30): e00670-20. https://doi.org/10.1128/MRA.00670-20.

Xu, Xi, Chaoju Gong, Yunfeng Wang, Yanyan Hu, Hong Liu, and Zejun Fang. 2020. “Multi-Omics Analysis to Identify Driving Factors in Colorectal Cancer.” Epigenomics 12 (18): 1633–50. https://doi.org/10.2217/epi-2020-0073.

Pourcel, Christine, Cédric Midoux, Gilles Vergnaud, and Libera Latino. 2020. “The Basis for Natural Multiresistance to Phage in Pseudomonas Aeruginosa.” Antibiotics (Basel, Switzerland) 9 (6): 339. https://doi.org/10.3390/antibiotics9060339.