Next Generation Sequencing

Publications

Blin, Pauline, Kévin Robic, Slimane Khayi, Jérémy Cigna, Euphrasie Munier, Pauline Dewaegeneire, Angélique Laurent, et al. 2022. “Pattern and Causes of the Establishment of the Invasive Bacterial Potato Pathogen Dickeya Solani and of the Maintenance of the Resident Pathogen D. Dianthicola.” Molecular Ecology 30 (2): 608–24. https://doi.org/https://doi.org/10.1111/mec.15751.
Bouchereau, Wilhelm, Luc Jouneau, Catherine Archilla, Irène Aksoy, Anais Moulin, Nathalie Daniel, Nathalie Peynot, et al. 2022. “Major Transcriptomic, Epigenetic and Metabolic Changes Underly the Pluripotency Continuum in Rabbit Preimplantation Embryos.” Development, August, dev.200538. https://doi.org/10.1242/dev.200538.
Banerjee, Payel, Paul Joly, Luc Jouneau, Yan Jaszczyszyn, Mickaël Bourge, Pierre Affaticati, Jean-Pierre Levraud, Pierre Boudinot, and Jean-Stéphane Joly. 2022. “Molecular and Cellular Analysis of the Repair of Zebrafish Optic Tectum Meninges Following Laser Injury.” Cells 11 (13): 2016. https://doi.org/10.3390/cells11132016.
Derisoud, Emilie, Luc Jouneau, Cédric Dubois, Catherine Archilla, Yan Jaszczyszyn, Rachel Legendre, Nathalie Daniel, et al. 2022. “Maternal Age Affects Equine Day 8 Embryo Gene Expression Both in Trophoblast and Inner Cell Mass.” BMC Genomics 23 (1): 443. https://doi.org/10.1186/s12864-022-08593-7.
Miró-Pina, Caridad, Olivia Charmant, Takayuki Kawaguchi, Daniel Holoch, Audrey Michaud, Isadora Cohen, Adeline Humbert, et al. 2022. “Paramecium Polycomb Repressive Complex 2 Physically Interacts with the Small RNA-Binding PIWI Protein to Repress Transposable Elements.” Developmental Cell, April. https://doi.org/10.1016/j.devcel.2022.03.014.
Gnan, Stefano, Melody Matelot, Marion Weiman, Olivier Arnaiz, Frederic Guerin, Linda Sperling, Mireille Betermier, Claude Thermes, Chun-Long Chen, and Sandra Duharcourt. 2022. “GC Content but Not Nucleosome Positioning Directly Contributes to Intron-Splicing Efficiency in Paramecium.” Genome Research, March, gr.276125.121. https://doi.org/10.1101/gr.276125.121.
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.
Derisoud, E., L. Jouneau, A. Margat, C. Gourtay, C. Dubois, C. Archilla, Y. Jaszczyszyn, et al. 2021. “52 Equine Embryo Size Does Matter!” Reproduction, Fertility and Development 34 (2): 261–261. https://doi.org/10.1071/RDv34n2Ab52.
Montagné, Nicolas, Muriel Jager, Thomas Chertemps, Emma Persyn, Yan Jaszczyszyn, Camille Meslin, Emmanuelle Jacquin-Joly, and Michaël Manuel. 2021. “The Chemosensory Transcriptome of a Diving Beetle.” Frontiers in Ecology and Evolution 9 (December). https://www.frontiersin.org/article/10.3389/fevo.2021.773915.
Torres, Marta, Audren Jiquel, Etienne Jeanne, Delphine Naquin, Yves Dessaux, and Denis Faure. 2021. “Agrobacterium Tumefaciens Fitness Genes Involved in the Colonization of Plant Tumors and Roots.” New Phytologist 233 (2): 905–18. https://doi.org/10.1111/nph.17810.
Lioy, Virginia S., Jean-Noël Lorenzi, Soumaya Najah, Thibault Poinsignon, Hervé Leh, Corinne Saulnier, Bertrand Aigle, et al. 2021. “Dynamics of the Compartmentalized Streptomyces Chromosome during Metabolic Differentiation.” Nature Communications 12 (1): 5221. https://doi.org/10.1038/s41467-021-25462-1.
Blin, Marion, Laurent Lacroix, Nataliya Petryk, Yan Jaszczyszyn, Chun-Long Chen, Olivier Hyrien, and Benoît Le Tallec. 2021. “DNA Molecular Combing-Based Replication Fork Directionality Profiling.” Nucleic Acids Research 49 (12): e69. https://doi.org/10.1093/nar/gkab219.
Guérin, Cyprien, Bo-Hyung Lee, Benjamin Fradet, Erwin van Dijk, Bogdan Mirauta, Claude Thermes, Jean-François Bernardet, et al. 2021. “Transcriptome Architecture and Regulation at Environmental Transitions in Flavobacteria: The Case of an Important Fish Pathogen.” ISME Communications 1 (1): 1–13. https://doi.org/10.1038/s43705-021-00029-9.
Helou, Laura, Linda Beauclair, Hugues Dardente, Peter Arensburger, Nicolas Buisine, Yan Jaszczyszyn, Florian Guillou, Thierry Lecomte, Alex Kentsis, and Yves Bigot. 2021. “Corrigendum to ‘The C-Terminal Domain of PiggyBac Transposase Is Not Required for DNA Transposition’ [J. Mol. Biol. 433 (2021) 166805].” Journal of Molecular Biology, June, 167089. https://doi.org/10.1016/j.jmb.2021.167089.
Dijk, Erwin L. van, and Claude Thermes. 2021. “A Small RNA-Seq Protocol with Less Bias and Improved Capture of 2’-O-Methyl RNAs.” Methods in Molecular Biology (Clifton, N.J.) 2298 (June): 153–67. https://doi.org/10.1007/978-1-0716-1374-0_10.
Aydin, Malik, Cornelius Weisser, Olivier Rué, Mahendra Mariadassou, Sandra Maaß, Ann-Kathrin Behrendt, Yan Jaszczyszyn, et al. 2021. “The Rhinobiome of Exacerbated Wheezers and Asthmatics: Insights From a German Pediatric Exacerbation Network.” Frontiers in Allergy 2 (May). https://www.frontiersin.org/article/10.3389/falgy.2021.667562.
Prudent, Victoria, Gaëlle Demarre, Emilie Vazeille, Maxime Wery, Nicole Quenech’Du, Antinéa Ravet, Julie Dauverd-Girault, et al. 2021. “The Crohn’s Disease-Related Bacterial Strain LF82 Assembles Biofilm-like Communities to Protect Itself from Phagolysosomal Attack.” Communications Biology 4 (1): 627. https://doi.org/10.1038/s42003-021-02161-7.
Villa, Tommaso, Yan Jaszczyszyn, and Domenico Libri. 2021. “Data from Crosslinking and Analysis of CDNAs (CRAC) of Nab3 in Yeast Cells Expressing a Circular NcRNA Decoy.” Data in Brief 35 (March): 106951. https://doi.org/10.1016/j.dib.2021.106951.
Helou, Laura, Linda Beauclair, Hugues Dardente, Peter Arensburger, Nicolas Buisine, Yan Jaszczyszyn, Florian Guillou, Thierry Lecomte, Alex Kentsis, and Yves Bigot. 2021. “The C-Terminal Domain of PiggyBac Transposase Is Not Required for DNA Transposition.” Journal of Molecular Biology, January, 166805. https://doi.org/10.1016/j.jmb.2020.166805.
Descoeudres, Natalie, Luc Jouneau, Céline Henry, Kevin Gorrichon, Aurélie Derré-Bobillot, Pascale Serror, Laura Lee Gillespie, Cristel Archambaud, Alessandro Pagliuso, and Hélène Bierne. 2021. “An Immunomodulatory Transcriptional Signature Associated With Persistent Listeria Infection in Hepatocytes.” Frontiers in Cellular and Infection Microbiology 11: 761945. https://doi.org/10.3389/fcimb.2021.761945.
Policarpo, Maxime, Julien Fumey, Philippe Lafargeas, Delphine Naquin, Claude Thermes, Magali Naville, Corentin Dechaud, et al. 2020. “Contrasting Gene Decay in Subterranean Vertebrates: Insights from Cavefishes and Fossorial Mammals.” Molecular Biology and Evolution, September. https://doi.org/10.1093/molbev/msaa249.
Benoist, Romain, Claire Capdevielle-Dulac, Célina Chantre, Rémi Jeannette, Paul-André Calatayud, Jean-Michel Drezen, Stéphane Dupas, et al. 2020. “Quantitative Trait Loci Involved in the Reproductive Success of a Parasitoid Wasp.” Molecular Ecology 29 (18): 3476–93. https://doi.org/10.1111/mec.15567.
Jouneau, Luc, David J. Lefebvre, Fleur Costa, Aurore Romey, Sandra Blaise-Boisseau, Anthony Relmy, Yan Jaszczyszyn, et al. 2020. “The Antibody Response Induced FMDV Vaccines in Sheep Correlates with Early Transcriptomic Responses in Blood.” NPJ Vaccines 5: 1. https://doi.org/10.1038/s41541-019-0151-3.
Brison, Olivier, Sami El-Hilali, Dana Azar, Stéphane Koundrioukoff, Mélanie Schmidt, Viola Nähse, Yan Jaszczyszyn, et al. 2019. “Transcription-Mediated Organization of the Replication Initiation Program across Large Genes Sets Common Fragile Sites Genome-Wide.” Nature Communications 10 (1): 5693. https://doi.org/10.1038/s41467-019-13674-5.
Sanz, Guenhaël, Nathalie Daniel, Marie-Christine Aubrière, Catherine Archilla, Luc Jouneau, Yan Jaszczyszyn, Véronique Duranthon, Pascale Chavatte-Palmer, and Alice Jouneau. 2019. “Differentiation of Derived Rabbit Trophoblast Stem Cells under Fluid Shear Stress to Mimic the Trophoblastic Barrier.” Biochimica Et Biophysica Acta. General Subjects 1863 (10): 1608–18. https://doi.org/10.1016/j.bbagen.2019.07.003.
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.
Dijk, Erwin L. van, Evangelia Eleftheriou, and Claude Thermes. 2019. “Improving Small RNA-Seq: Less Bias and Better Detection of 2’-O-Methyl RNAs.” Journal of Visualized Experiments: JoVE, no. 151 (September): e60056. https://doi.org/10.3791/60056.
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.
Raoul des Essarts, Yannick, Jacques Pédron, Pauline Blin, Erwin Van Dijk, Denis Faure, and Frédérique Van Gijsegem. 2019. “Common and Distinctive Adaptive Traits Expressed in Dickeya Dianthicola and Dickeya Solani Pathogens When Exploiting Potato Plant Host.” Environmental Microbiology 21 (3): 1004–18. https://doi.org/10.1111/1462-2920.14519.
Gonzalez-Mula, Almudena, Joy Lachat, Léo Mathias, Delphine Naquin, Florian Lamouche, Peter Mergaert, and Denis Faure. 2019. “The Biotroph Agrobacterium Tumefaciens Thrives in Tumors by Exploiting a Wide Spectrum of Plant Host Metabolites.” The New Phytologist 222 (1): 455–67. https://doi.org/10.1111/nph.15598.
Mellouk, Namya, Christelle Rame, Delphine Naquin, Yan Jaszczyszyn, Jean-Luc Touzé, Eric Briant, Daniel Guillaume, Theodoros Ntallaris, Patrice Humblot, and Joëlle Dupont. 2019. “Impact of the Severity of Negative Energy Balance on Gene Expression in the Subcutaneous Adipose Tissue of Periparturient Primiparous Holstein Dairy Cows: Identification of Potential Novel Metabolic Signals for the Reproductive System.” PloS One 14 (9): e0222954. https://doi.org/10.1371/journal.pone.0222954.
Baroin-Tourancheau, Anne, Yan Jaszczyszyn, Xavier Benigni, and Laurence Amar. 2019. “Evaluating and Correcting Inherent Bias of MicroRNA Expression in Illumina Sequencing Analysis.” Frontiers in Molecular Biosciences 6: 17. https://doi.org/10.3389/fmolb.2019.00017.
Wu, Xia, Hadi Kabalane, Malik Kahli, Nataliya Petryk, Bastien Laperrousaz, Yan Jaszczyszyn, Guenola Drillon, et al. 2018. “Developmental and Cancer-Associated Plasticity of DNA Replication Preferentially Targets GC-Poor, Lowly Expressed and Late-Replicating Regions.” Nucleic Acids Research 46 (19): 10157–72. https://doi.org/10.1093/nar/gky797.
Dijk, Erwin L. van, Yan Jaszczyszyn, Delphine Naquin, and Claude Thermes. 2018. “The Third Revolution in Sequencing Technology.” Trends in Genetics 34 (9): 666–81. https://doi.org/10.1016/j.tig.2018.05.008.
Tubbs, Anthony, Sriram Sridharan, Niek van Wietmarschen, Yaakov Maman, Elsa Callen, Andre Stanlie, Wei Wu, et al. 2018. “Dual Roles of Poly(DA:DT) Tracts in Replication Initiation and Fork Collapse.” Cell 174 (5): 1127-1142.e19. https://doi.org/10.1016/j.cell.2018.07.011.
González-Mula, Almudena, Julien Lang, Catherine Grandclément, Delphine Naquin, Mohammed Ahmar, Laurent Soulère, Yves Queneau, Yves Dessaux, and Denis Faure. 2018. “Lifestyle of the Biotroph Agrobacterium Tumefaciens in the Ecological Niche Constructed on Its Host Plant.” The New Phytologist 219 (1): 350–62. https://doi.org/10.1111/nph.15164.
Agier, Nicolas, Stéphane Delmas, Qing Zhang, Aubin Fleiss, Yan Jaszczyszyn, Erwin van Dijk, Claude Thermes, Martin Weigt, Marco Cosentino-Lagomarsino, and Gilles Fischer. 2018. “The Evolution of the Temporal Program of Genome Replication.” Nature Communications 9 (1): 2199. https://doi.org/10.1038/s41467-018-04628-4.
Fumey, Julien, Hélène Hinaux, Céline Noirot, Claude Thermes, Sylvie Rétaux, and Didier Casane. 2018. “Evidence for Late Pleistocene Origin of Astyanax Mexicanus Cavefish.” BMC Evolutionary Biology 18 (1): 43. https://doi.org/10.1186/s12862-018-1156-7.
Naquin, Delphine, Cristina Panozzo, Genevieve Dujardin, Erwin van Dijk, Yves D’Aubenton-Carafa, and Claude Thermes. 2018. “Complete Sequence of the Intronless Mitochondrial Genome of the Saccharomyces Cerevisiae Strain CW252.” Microbiology Resource Announcements 6 (17): UNSP e00219-18. https://doi.org/10.1128/genomeA.00219-18.
Pranke, Iwona, Laure Bidou, Natacha Martin, Sandra Blanchet, Aurélie Hatton, Sabrina Karri, David Cornu, et al. 2018. “Factors Influencing Readthrough Therapy for Frequent Cystic Fibrosis Premature Termination Codons.” ERJ Open Research 4 (1). https://doi.org/10.1183/23120541.00080-2017.
Dard-Dascot, Cloelia, Delphine Naquin, Yves d’Aubenton-Carafa, Karine Alix, Claude Thermes, and Erwin van Dijk. 2018. “Systematic Comparison of Small RNA Library Preparation Protocols for Next-Generation Sequencing.” BMC Genomics 19 (1): 118. https://doi.org/10.1186/s12864-018-4491-6.
Sinha, Anurag Kumar, Adeline Durand, Jean-Michel Desfontaines, Ielyzaveta Iurchenko, Hélène Auger, David R. F. Leach, François-Xavier Barre, and Bénédicte Michel. 2017. “Division-Induced DNA Double Strand Breaks in the Chromosome Terminus Region of Escherichia Coli Lacking RecBCD DNA Repair Enzyme.” PLoS Genetics 13 (10): e1006895. https://doi.org/10.1371/journal.pgen.1006895.
Arnaiz, Olivier, Erwin Van Dijk, Mireille Bétermier, Maoussi Lhuillier-Akakpo, Augustin de Vanssay, Sandra Duharcourt, Erika Sallet, Jérôme Gouzy, and Linda Sperling. 2017. “Improved Methods and Resources for Paramecium Genomics: Transcription Units, Gene Annotation and Gene Expression.” BMC Genomics 18 (1): 483. https://doi.org/10.1186/s12864-017-3887-z.
Le Lam, Thao Nguyen, Claire Morvan, Wenfeng Liu, Chantal Bohn, Yan Jaszczyszyn, and Philippe Bouloc. 2017. “Finding SRNA-Associated Phenotypes by Competition Assays: An Example with Staphylococcus Aureus.” Methods 117: 21–27. https://doi.org/10.1016/j.ymeth.2016.11.018.
Dambroise, Emilie, Matthieu Simion, Thomas Bourquard, Stéphanie Bouffard, Barbara Rizzi, Yan Jaszczyszyn, Mickaël Bourge, et al. 2017. “Postembryonic Fish Brain Proliferation Zones Exhibit Neuroepithelial-Type Gene Expression Profile: Features of Neuroepithelial Cells in Fish.” STEM CELLS. https://doi.org/10.1002/stem.2588.
Weil, Patrick P., Yan Jaszczyszyn, Anne Baroin-Tourancheau, Jan Postberg, and Laurence Amar. 2017. “Holistic and Affordable Analyses of MicroRNA Expression Profiles Using Tagged CDNA Libraries and a Multiplex Sequencing Strategy.” In Functional Genomics, edited by Michael Kaufmann, Claudia Klinger, and Andreas Savelsbergh, 1654:179–96. New York, NY: Springer New York. https://doi.org/10.1007/978-1-4939-7231-9_12.
Durand, Adeline, Anurag Kumar Sinha, Cloelia Dard-Dascot, and Bénédicte Michel. 2016. “Mutations Affecting Potassium Import Restore the Viability of the Escherichia Coli DNA Polymerase III HolD Mutant.” PLoS Genetics 12 (6): e1006114. https://doi.org/10.1371/journal.pgen.1006114.
Petryk, Nataliya, Malik Kahli, Yves d’Aubenton-Carafa, Yan Jaszczyszyn, Yimin Shen, Maud Silvain, Claude Thermes, Chun-Long Chen, and Olivier Hyrien. 2016. “Replication Landscape of the Human Genome.” Nature Communications 7 (January): 10208. https://doi.org/10.1038/ncomms10208.
Passot, Fanny Marie, Hong Ha Nguyen, Cloelia Dard-Dascot, Claude Thermes, Pascale Servant, Olivier Espéli, and Suzanne Sommer. 2015. “Nucleoid Organization in the Radioresistant Bacterium Deinococcus Radiodurans.” Molecular Microbiology 97 (4): 759–74. https://doi.org/10.1111/mmi.13064.
Kérouanton, Annaëlle, Edouard Hirchaud, Valérie Rose, Emilie Esnault, Delphine Naquin, and Martine Denis. 2015. “First Complete Genome Sequence of a Salmonella Enterica Subsp. Enterica Serovar Derby Strain Associated with Pork in France.” Genome Announcements 3 (4). https://doi.org/10.1128/genomeA.00853-15.
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