Next Generation Sequencing

Publications

Wu, Xia, Yaqun Liu, Yves d’Aubenton-Carafa, Claude Thermes, Olivier Hyrien, Chun-Long Chen, and Nataliya Petryk. 2023. “Genome-Wide Measurement of DNA Replication Fork Directionality and Quantification of DNA Replication Initiation and Termination with Okazaki Fragment Sequencing.” Nature Protocols, January. https://doi.org/10.1038/s41596-022-00793-5.
Liu, Yaqun, Xia Wu, Yves d’Aubenton-Carafa, Claude Thermes, and Chun-Long Chen. 2023. “OKseqHMM: A Genome-Wide Replication Fork Directionality Analysis Toolkit.” Nucleic Acids Research, January, gkac1239. https://doi.org/10.1093/nar/gkac1239.
Torres, Marta, Almudena Gonzalez-Mula, Delphine Naquin, and Denis Faure. 2022. “Construction of a Transposon Mutant Library in the Pathogen Agrobacterium Tumefaciens C58 and Identification of Genes Involved in Gall Niche Exploitation and Colonization.” In Microbial Environmental Genomics (MEG), edited by Francis Martin and Stephane Uroz, 209–26. Methods in Molecular Biology. New York, NY: Springer US. https://doi.org/10.1007/978-1-0716-2871-3_11.
Carceller-Zazo, Elena, Lisa M. Sevilla, Omar Pons-Alonso, Álvaro Chiner-Oms, Larbi Amazit, Thi An Vu, Géraldine Vitellius, et al. 2022. “The Mineralocorticoid Receptor Modulates Timing and Location of Genomic Binding by Glucocorticoid Receptor in Response to Synthetic Glucocorticoids in Keratinocytes.” The FASEB Journal 37 (1): e22709. https://doi.org/10.1096/fj.202201199RR.
Marion-Poll, Lucile, Jean-Pierre Roussarie, Lieng Taing, Cloelia Dard-Dascot, Nicolas Servant, Yan Jaszczyszyn, Emmanuelle Jordi, et al. 2022. “DNA Methylation and Hydroxymethylation Characterize the Identity of D1 and D2 Striatal Projection Neurons.” Communications Biology 5 (1): 1–16. https://doi.org/10.1038/s42003-022-04269-w.
Via y Rada, Romina, Nathalie Daniel, Catherine Archilla, Anne Frambourg, Luc Jouneau, Yan Jaszczyszyn, Gilles Charpigny, Véronique Duranthon, and Sophie Calderari. 2022. “Identification of the Inner Cell Mass and the Trophectoderm Responses after an In Vitro Exposure to Glucose and Insulin during the Preimplantation Period in the Rabbit Embryo.” Cells 11 (23): 3766. https://doi.org/10.3390/cells11233766.
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.
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.
Hernandez, Céline, Gabriele Cancila, Olivier Ayrault, Andrei Zinovyev, and Loredana Martignetti. 2022. “ClustMMRA v2: A Scalable Computational Pipeline for the Identification of MicroRNA Clusters Acting Cooperatively on Tumor Molecular Subgroups.” In Systems Biology of MicroRNAs in Cancer, edited by Ulf Schmitz, Olaf Wolkenhauer, and Julio Vera-González, 259–79. Advances in Experimental Medicine and Biology. Cham: Springer International Publishing. https://doi.org/10.1007/978-3-031-08356-3_10.
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.
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.
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