Helen Frankenthaler Foundation

cell signaling research

publis NGS – Institute for Integrative Biology of the Cell

Publications List

2025

Leroy, Estelle, Drice Challal, Stéphane Pelletier, et al. 2025. “A Bifunctional snoRNA with Separable Activities in Guiding rRNA 2’-O-Methylation and Scaffolding Gametogenesis Effectors.” Nature Communications 16 (1): 3250.

Porter, Dean, Catherine Collins, Andrea Mazzolini, et al. 2025. “Divergent B-Cell Repertoire Remodelling by mRNA, DNA and Live Attenuated Vaccines in Fish.” NPJ Vaccines 10 (1): 166.

Naquin, Delphine, Sandra Blanchet, Erwin van Dijk, et al. 2025. “High-Resolution HIV-1 m6A Epitranscriptome Reveals Isoform-Dependent Methylation Clusters and Unique 2-LTR Transcript Modifications.” NAR Genomics and Bioinformatics 7 (4): lqaf200.

2024

Zanetti, Andrea, Gwendal Dujardin, Lucas Fares-Taie, et al. 2024. “GPATCH11 Variants Cause Mis-Splicing and Early-Onset Retinal Dystrophy with Neurological Impairment.” Nature Communications 15 (1): 10096.

2023

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 11, gkac1239.

Wu, Xia, Yaqun Liu, Yves d’Aubenton-Carafa, et al. 2023. “Genome-Wide Measurement of DNA Replication Fork Directionality and Quantification of DNA Replication Initiation and Termination with Okazaki Fragment Sequencing.” Nature Protocols, ahead of print, January 18.

Dijk, Erwin L. van, Delphine Naquin, Kévin Gorrichon, et al. 2023. “Genomics in the Long-Read Sequencing Era.” Trends in Genetics: TIG, May 23, S0168-9525(23)00119-1.

2022

Adam, Yazid, Pierre Brezellec, Elena Espinosa, et al. 2022. “Plesiomonas Shigelloides, an Atypical Enterobacterales with a Vibrio-Related Secondary Chromosome.” Genome Biology and Evolution, January 25, evac011.

Derisoud, Emilie, Luc Jouneau, Cédric Dubois, et al. 2022. “Maternal Age Affects Equine Day 8 Embryo Gene Expression Both in Trophoblast and Inner Cell Mass.” BMC Genomics 23 (1): 443.

Banerjee, Payel, Paul Joly, Luc Jouneau, et al. 2022. “Molecular and Cellular Analysis of the Repair of Zebrafish Optic Tectum Meninges Following Laser Injury.” Cells 11 (13): 2016.

Bouchereau, Wilhelm, Luc Jouneau, Catherine Archilla, et al. 2022. “Major Transcriptomic, Epigenetic and Metabolic Changes Underly the Pluripotency Continuum in Rabbit Preimplantation Embryos.” Development, August 19, dev.200538.

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. Advances in Experimental Medicine and Biology. Springer International Publishing.

Blin, Pauline, Kévin Robic, Slimane Khayi, 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.

Zangarelli, Coralie, Olivier Arnaiz, Mickael Bourge, et al. 2022. “Developmental Timing of Programmed DNA Elimination in Paramecium Tetraurelia Recapitulates Germline Transposon Evolutionary Dynamics.” Genome Research, November 23, gr.277027.122.

Via y Rada, Romina, Nathalie Daniel, Catherine Archilla, et al. 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.

Marion-Poll, Lucile, Jean-Pierre Roussarie, Lieng Taing, et al. 2022. “DNA Methylation and Hydroxymethylation Characterize the Identity of D1 and D2 Striatal Projection Neurons.” Communications Biology 5 (1): 1–16.

Carceller-Zazo, Elena, Lisa M. Sevilla, Omar Pons-Alonso, 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.

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. Methods in Molecular Biology. Springer US.

2021

Helou, Laura, Linda Beauclair, Hugues Dardente, et al. 2021. “The C-Terminal Domain of piggyBac Transposase Is Not Required for DNA Transposition.” Journal of Molecular Biology, January 12, 166805.

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.

Prudent, Victoria, Gaëlle Demarre, Emilie Vazeille, 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.

Aydin, Malik, Cornelius Weisser, Olivier Rué, et al. 2021. “The Rhinobiome of Exacerbated Wheezers and Asthmatics: Insights From a German Pediatric Exacerbation Network.” Frontiers in Allergy 2 (May).

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.

Helou, Laura, Linda Beauclair, Hugues Dardente, et al. 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 11, 167089.

Guérin, Cyprien, Bo-Hyung Lee, Benjamin Fradet, 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.

Blin, Marion, Laurent Lacroix, Nataliya Petryk, et al. 2021. “DNA Molecular Combing-Based Replication Fork Directionality Profiling.” Nucleic Acids Research 49 (12): e69.

Lioy, Virginia S., Jean-Noël Lorenzi, Soumaya Najah, et al. 2021. “Dynamics of the Compartmentalized Streptomyces Chromosome during Metabolic Differentiation.” Nature Communications 12 (1): 5221.

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.

Montagné, Nicolas, Muriel Jager, Thomas Chertemps, et al. 2021. “The Chemosensory Transcriptome of a Diving Beetle.” Frontiers in Ecology and Evolution 9 (December).

Derisoud, E., L. Jouneau, A. Margat, et al. 2021. “52 Equine Embryo Size Does Matter!” Reproduction, Fertility and Development 34 (2): 261–261.

Descoeudres, Natalie, Luc Jouneau, Céline Henry, et al. 2021. “An Immunomodulatory Transcriptional Signature Associated With Persistent Listeria Infection in Hepatocytes.” Frontiers in Cellular and Infection Microbiology 11: 761945.

2020

Policarpo, Maxime, Julien Fumey, Philippe Lafargeas, et al. 2020. “Contrasting Gene Decay in Subterranean Vertebrates: Insights from Cavefishes and Fossorial Mammals.” Molecular Biology and Evolution, ahead of print, September 28.

Benoist, Romain, Claire Capdevielle-Dulac, Célina Chantre, et al. 2020. “Quantitative Trait Loci Involved in the Reproductive Success of a Parasitoid Wasp.” Molecular Ecology 29 (18): 3476–93.

Jouneau, Luc, David J. Lefebvre, Fleur Costa, et al. 2020. “The Antibody Response Induced FMDV Vaccines in Sheep Correlates with Early Transcriptomic Responses in Blood.” NPJ Vaccines 5: 1.

2019

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.

Tidjani, Abdoul-Razak, Jean-Noël Lorenzi, Maxime Toussaint, et al. 2019. “Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics.” mBio 10 (5): e01533-19.

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.

Tidjani, Abdoul-Razak, Jean-Noël Lorenzi, Maxime Toussaint, et al. 2019. “Genome Sequences of 11 Conspecific Streptomyces Sp. Strains.” Microbiology Resource Announcements 8 (38): e00863-19.

Sanz, Guenhaël, Nathalie Daniel, Marie-Christine Aubrière, et al. 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.

Brison, Olivier, Sami El-Hilali, Dana Azar, 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.

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.

Gonzalez-Mula, Almudena, Joy Lachat, Léo Mathias, et al. 2019. “The Biotroph Agrobacterium Tumefaciens Thrives in Tumors by Exploiting a Wide Spectrum of Plant Host Metabolites.” The New Phytologist 222 (1): 455–67.

Mellouk, Namya, Christelle Rame, Delphine Naquin, et al. 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.

2018

Pranke, Iwona, Laure Bidou, Natacha Martin, et al. 2018. “Factors Influencing Readthrough Therapy for Frequent Cystic Fibrosis Premature Termination Codons.” ERJ Open Research 4 (1).

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.

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.

Agier, Nicolas,