RNA Sequence, Structure & Function

Publications

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.
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.
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.
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.
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 (May): 193–210. https://doi.org/10.1016/j.ejca.2021.03.005.
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.
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, 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.
Maurel, Marie-Christine, Fabrice Leclerc, and Guy Herve. 2020. “Ribozyme Chemistry: To Be or Not To Be under High Pressure.” Chemical Reviews 120 (11): 4898–4918. https://doi.org/10.1021/acs.chemrev.9b00457.
Gainer, Robert S., Gilles Vergnaud, and Martin E. Hugh-Jones. 2020. “A Review of Arguments for the Existence of Latent Infections OfBacillus Anthracis, and Research Needed to Understand Their Role in the Outbreaks of Anthrax.” Microorganisms 8 (6): 800. https://doi.org/10.3390/microorganisms8060800.
Essoh, Christiane, Jean-Philippe Vernadet, Gilles Vergnaud, Adama Coulibaly, Adèle Kakou-N’Douba, Assavo S.-P. N’Guetta, Thimotée Ouassa, and Christine Pourcel. 2020. “Characterization of Sixteen Achromobacter Xylosoxidans Phages from Abidjan, Côte d’Ivoire, Isolated on a Single Clinical Strain.” Archives of Virology 165 (3): 725–30. https://doi.org/10.1007/s00705-019-04511-7.
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–D544. https://doi.org/10.1093/nar/gkz915.
Vergnaud, Gilles. 2020. “Bacillus Anthracis Evolutionary History: Taking Advantage of the Topology of the Phylogenetic Tree and of Human History to Propose Dating Points.” Erciyes Medical Journal 42 (4): 362–69. https://doi.org/10.14744/etd.2020.64920.
Cloeckaert, Axel, Gilles Vergnaud, and Michel S. Zygmunt. 2020. “Omp2b Porin Alteration in the Course of Evolution of Brucella Spp.” Frontiers in Microbiology 11: 284. https://doi.org/10.3389/fmicb.2020.00284.
Lehmann, Jean, and Shixin Ye. 2019. “D Amino Acids Highlight the Catalytic Power of the Ribosome.” Cell Chemical Biology 26 (12): 1639–41. https://doi.org/10.1016/j.chembiol.2019.10.007.
Vergnaud, Gilles. 2019. “And Then There Were Three: Discovering the Role of CRISPRs.” The CRISPR Journal 2 (6): 359–61. https://doi.org/10.1089/crispr.2019.29073.gve.
Briquet, Anaïs, Rithy Vong, Jean-Baptiste Roseau, Emilie Javelle, Nicolas Cazes, Fréderic Rivière, Marc Aletti, et al. 2019. “Clinical Features of Mycobacterium Canettii Infection: A Retrospective Study of 20 Cases among French Soldiers and Relatives.” Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America 69 (11): 2003–10. https://doi.org/10.1093/cid/ciz107.
Pinskaya, Marina, Zohra Saci, Mélina Gallopin, Marc Gabriel, Ha Tn Nguyen, Virginie Firlej, Marc Descrimes, et al. 2019. “Reference-Free Transcriptome Exploration Reveals Novel RNAs for Prostate Cancer Diagnosis.” Life Science Alliance 2 (6): e201900449. https://doi.org/10.26508/lsa.201900449.
Li, Shuang, Zhaoming Su, Jean Lehmann, Vassiliki Stamatopoulou, Nikoleta Giarimoglou, Frances E. Henderson, Lixin Fan, et al. 2019. “Structural Basis of Amino Acid Surveillance by Higher-Order TRNA-MRNA Interactions.” Nature Structural & Molecular Biology 26 (12): 1094–1105. https://doi.org/10.1038/s41594-019-0326-7.
Latino, Libera, Delphine Patin, Dimitri Cherier, Thierry Touze, Christine Pourcel, Helene Barreteau, and Dominique Mengin-Lecreulx. 2019. “Impact of FiuA Outer Membrane Receptor Polymorphism on the Resistance of Pseudomonas Aeruginosa toward Peptidoglycan Lipid II-Targeting PaeM Pyocins.” Journal of Bacteriology 201 (13): e00164. https://doi.org/10.1128/JB.00164-19.
Morillon, Antonin, and Daniel Gautheret. 2019. “Bridging the Gap between Reference and Real Transcriptomes.” Genome Biology 20 (1): 112. https://doi.org/10.1186/s13059-019-1710-7.
Loiseau, Chloe, Daniela Brites, Irmgard Moser, Francesc Coll, Christine Pourcel, Suelee Robbe-Austerman, Vincent Escuyer, et al. 2019. “Revised Interpretation of the Hain Lifescience GenoType MTBC To Differentiate Mycobacterium Canettii and Members of the Mycobacterium Tuberculosis Complex.” Antimicrobial Agents and Chemotherapy 63 (6): e00159-19. https://doi.org/10.1128/AAC.00159-19.
Ledwaba, Maphuti Betty, Calvin Gomo, Kgaugelo Edward Lekota, Philippe Le Flèche, Ayesha Hassim, Gilles Vergnaud, and Henriette van Heerden. 2019. “Molecular Characterization of Brucella Species from Zimbabwe.” PLoS Neglected Tropical Diseases 13 (5): e0007311. https://doi.org/10.1371/journal.pntd.0007311.
Maurel, Marie-Christine, Fabrice Leclerc, Jacques Vergne, and Giuseppe Zaccai. 2019. “RNA Back and Forth: Looking through Ribozyme and Viroid Motifs.” Viruses 11 (3): 283. https://doi.org/10.3390/v11030283.
Paleiron, N., C. Soler, M. O. Hassan, D. Andriamanantena, R. Vong, C. Pourcel, and J.-B. Roseau. 2019. “First Description of Mycobacterium Tuberculosis and M. Canettii Concomitant Infection: Report of Two Cases.” International Journal of Tuberculosis and Lung Disease 23 (2): 232–35. https://doi.org/10.5588/ijtld.18.0261.
Essoh, Christiane, Jean-Philippe Vernadet, Gilles Vergnaud, Adama Coulibaly, Adèle Kakou-N’Douba, Assanvo S.-P. N’Guetta, Gregory Resch, and Christine Pourcel. 2019. “Complete Genome Sequences of Five Acinetobacter Baumannii Phages from Abidjan, Côte d’Ivoire.” Microbiology Resource Announcements 8 (1): e01358-18. https://doi.org/10.1128/MRA.01358-18.
Shevtsova, Elena, Gilles Vergnaud, Alexandr Shevtsov, Alexandr Shustov, Kalysh Berdimuratova, Kasim Mukanov, Marat Syzdykov, et al. 2019. “Genetic Diversity of Brucella Melitensis in Kazakhstan in Relation to World-Wide Diversity.” Frontiers in Microbiology 10: 1897. https://doi.org/10.3389/fmicb.2019.01897.
Timofeev, Vitalii, Irina Bahtejeva, Raisa Mironova, Galina Titareva, Igor Lev, David Christiany, Alexander Borzilov, Alexander Bogun, and Gilles Vergnaud. 2019. “Insights from Bacillus Anthracis Strains Isolated from Permafrost in the Tundra Zone of Russia.” PloS One 14 (5): e0209140. https://doi.org/10.1371/journal.pone.0209140.
Latino, Libera, Cédric Midoux, Gilles Vergnaud, and Christine Pourcel. 2019. “Investigation of Pseudomonas Aeruginosa Strain PcyII-10 Variants Resisting Infection by N4-like Phage Ab09 in Search for Genes Involved in Phage Adsorption.” PloS One 14 (4): e0215456. https://doi.org/10.1371/journal.pone.0215456.
Rochat, Tatiana, Chantal Bohn, Claire Morvan, Thao Nguyen Le Lam, Fareha Razvi, Adrien Pain, Claire Toffano-Nioche, et al. 2018. “The Conserved Regulatory RNA RsaE Down-Regulates the Arginine Degradation Pathway in Staphylococcus Aureus.” Nucleic Acids Research 46 (17): 8803–16. https://doi.org/10.1093/nar/gky584.
Couvin, David, Aude Bernheim, Claire Toffano-Nioche, Marie Touchon, Juraj Michalik, Bertrand Néron, Eduardo P C Rocha, Gilles Vergnaud, Daniel Gautheret, and Christine Pourcel. 2018. “CRISPRCasFinder, an Update of CRISRFinder, Includes a Portable Version, Enhanced Performance and Integrates Search for Cas Proteins.” Nucleic Acids Research 46 (W1): W246–51. https://doi.org/10.1093/nar/gky425.
Drubay, Damien, Daniel Gautheret, and Stefan Michiels. 2018. “A Benchmark Study of Scoring Methods for Non-Coding Mutations.” Bioinformatics 34 (10): 1635–41. https://doi.org/10.1093/bioinformatics/bty008.
Wery, Maxime, Camille Gautier, Marc Descrimes, Mayuko Yoda, Hervé Vennin-Rendos, Valérie Migeot, Daniel Gautheret, Damien Hermand, and Antonin Morillon. 2018. “Native Elongating Transcript Sequencing Reveals Global Anti-Correlation between Sense and Antisense Nascent Transcription in Fission Yeast.” RNA 24 (2): 196–208. https://doi.org/10.1261/rna.063446.117.
Liu, Wenfeng, Tatiana Rochat, Claire Toffano-Nioche, Thao Nguyen Le Lam, Philippe Bouloc, and Claire Morvan. 2018. “Assessment of Bona Fide SRNAs in Staphylococcus Aureus.” Frontiers in Microbiology 9: 228. https://doi.org/10.3389/fmicb.2018.00228.
Audoux, Jérôme, Nicolas Philippe, Rayan Chikhi, Mikaël Salson, Mélina Gallopin, Marc Gabriel, Jérémy Le Coz, Emilie Drouineau, Thérèse Commes, and Daniel Gautheret. 2017. “DE-Kupl: Exhaustive Capture of Biological Variation in RNA-Seq Data through k-Mer Decomposition.” Genome Biology 18 (1): 243. https://doi.org/10.1186/s13059-017-1372-2.
Lehmann, Jean. 2017. “Induced Fit of the Peptidyl-Transferase Center of the Ribosome and Conformational Freedom of the Esterified Amino Acids.” RNA (New York, N.Y.) 23 (2): 229–39. https://doi.org/10.1261/rna.057273.116.
Wang, J., and J. Lehmann. 2017. “Commaless Code☆.” In Reference Module in Life Sciences. Elsevier. https://doi.org/10.1016/B978-0-12-809633-8.06251-8.
Esnault, Catherine, Denis Leiber, Claire Toffano-Nioche, Zahra Tanfin, and Marie-Joelle Virolle. 2017. “Another Example of Enzymatic Promiscuity: The Polyphosphate Kinase of Streptomyces Lividans Is Endowed with Phospholipase D Activity.” Applied Microbiology and Biotechnology 101 (1): 139–45. https://doi.org/10.1007/s00253-016-7743-x.
Wang, J., and J. Lehmann. 2017. “Commaless Code ☆.” In Reference Module in Life Sciences. Elsevier. https://doi.org/10.1016/B978-0-12-809633-8.06251-8.
Lehmann, Jean, Albert Libchaber, and Benjamin D. Greenbaum. 2016. “Fundamental Amino Acid Mass Distributions and Entropy Costs in Proteomes.” Journal of Theoretical Biology 410 (December): 119–24. https://doi.org/10.1016/j.jtbi.2016.08.011.
Leclerc, Fabrice, Giuseppe Zaccai, Jacques Vergne, Martina Řìhovà, Anne Martel, and Marie-Christine Maurel. 2016. “Self-Assembly Controls Self-Cleavage of HHR from ASBVd (-): A Combined SANS and Modeling Study.” Scientific Reports 6 (July): 30287. https://doi.org/10.1038/srep30287.
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