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D. Gautheret · SciRah

Researcher profile · Semantic Scholar

D. Gautheret

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D. Gautheret — researcher profile on SciRah

h-index: 46
Works: 132
Citations: 9,469

Most-cited papers

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
D. Couvin, A. Bernheim, C. Toffano-Nioche, M. Touchon +6 more
2018Nucleic Acids Res.1,437 citations Open access
Semantic Scholar
Rfam 14: expanded coverage of metagenomic, viral and microRNA families
Ioanna Kalvari, Eric P. Nawrocki, Nancy Ontiveros-Palacios, Joanna Argasinska +11 more
2020Nucleic Acids Res.924 citations Open access
Semantic Scholar
The genome sequence of the model ascomycete fungus Podospora anserina
E. Espagne, O. Lespinet, F. Malagnac, C. da Silva +31 more
2008Genome Biology334 citations Open access
Semantic Scholar
Acquired initiating mutations in early hematopoietic cells of CLL patients.
F. Damm, E. Mylonas, A. Cosson, K. Yoshida +23 more
2014Cancer Discovery260 citations Open access
Semantic Scholar
Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism
C. Bohn, Candice Rigoulay, S. Chabelskaya, C. Sharma +10 more
2010Nucleic Acids Research187 citations Open access
Semantic Scholar
Sequence determinants in human polyadenylation site selection
M. Legendre, D. Gautheret
2003BMC Genomics152 citations Open access
Semantic Scholar
Applications of single-cell and bulk RNA sequencing in onco-immunology.
M. Kuksin, D. Morel, Marine Aglave, F. Danlos +4 more
2021European Journal of Cancer133 citations Open access
Semantic Scholar
Genome-wide discovery and analysis of microRNAs and other small RNAs from rice embryogenic callus
Chongjian Chen, Qing Liu, Yu-Chan Zhang, L. Qu +2 more
2011RNA Biology125 citations Open access
Semantic Scholar
Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing
Coline Billerey, M. Boussaha, D. Esquerré, E. Rebours +5 more
2014BMC Genomics123 citations Open access
Semantic Scholar
Characterization of novel genomic alterations and therapeutic approaches using acute megakaryoblastic leukemia xenograft models
C. Thiollier, Cécile K. Lopez, B. Gerby, C. Ignacimouttou +26 more
2012Journal of Experimental Medicine119 citations Open access
Semantic Scholar
In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs
Á. E. Martínez de Alba, A. B. Moreno, M. Gabriel, A. Mallory +8 more
2015bioRxiv116 citations Open access
Semantic Scholar
Nonsense-Mediated Decay Restricts LncRNA Levels in Yeast Unless Blocked by Double-Stranded RNA Structure
M. Wéry, M. Descrimes, N. Vogt, Anne-Sophie Dallongeville +2 more
2016Molecules and Cells110 citations Open access
Semantic Scholar
ASTD: The Alternative Splicing and Transcript Diversity database.
Gautier Koscielny, Vincent Le Texier, C. Gopalakrishnan, V. Kumanduri +25 more
2009Genomics110 citations Open access
Semantic Scholar
Using Alu elements as polyadenylation sites: A case of retroposon exaptation.
Chongjian Chen, Takeshi Ara, D. Gautheret
2009Molecular biology and evolution104 citations
Semantic Scholar
Profile-based detection of microRNA precursors in animal genomes
M. Legendre, André Lambert, D. Gautheret
2005Bioinform.104 citations Open access
Semantic Scholar
New Functional Signatures for Understanding Melanoma Biology from Tumor Cell Lineage-Specific Analysis
F. Rambow, B. Job, V. Petit, F. Gesbert +10 more
2015Cell Reports93 citations Open access
Semantic Scholar
The ERPIN server: an interface to profile-based RNA motif identification
André Lambert, Jean-Fred Fontaine, M. Legendre, Fabrice Leclerc +6 more
2004Nucleic Acids Res.91 citations Open access
Semantic Scholar
An assessment of bacterial small RNA target prediction programs
A. Pain, Alban Ott, Hamza Amine, T. Rochat +2 more
2015RNA Biology79 citations Open access
Semantic Scholar
SINGLE‐PASS CLASSIFICATION OF ALL NON‐CODING SEQUENCES IN A BACTERIAL GENOME USING PHYLOGENETIC PROFILES
A. Marchais, M. Naville, C. Bohn, P. Bouloc +1 more
2009Genome Research79 citations Open access
Semantic Scholar
RNA stem-loops: to be or not to be cleaved by RNAse III.
W. Ritchie, M. Legendre, D. Gautheret
2007RNA: A publication of the RNA Society79 citations Open access
Semantic Scholar
Differential Repression of Alternative Transcripts: A Screen for miRNA Targets
M. Legendre, W. Ritchie, F. Lopez, D. Gautheret
2006PLoS Comput. Biol.77 citations Open access
Semantic Scholar
RNAcentral: A vision for an international database of RNA sequences.
A. Bateman, Shipra Agrawal, E. Birney, E. Bruford +26 more
2011RNA: A publication of the RNA Society76 citations Open access
Semantic Scholar
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
Camille Marchet, Z. Iqbal, D. Gautheret, Mikaël Salson +1 more
2020bioRxiv71 citations Open access
Semantic Scholar
Entropy Measures Quantify Global Splicing Disorders in Cancer
W. Ritchie, S. Granjeaud, D. Puthier, D. Gautheret
2008PLoS Comput. Biol.70 citations Open access
Semantic Scholar
Transcription attenuation in bacteria: theme and variations.
M. Naville, D. Gautheret
2009Briefings in Functional Genomics & Proteomics67 citations Open access
Semantic Scholar
Genome-wide translational changes induced by the prion [PSI+].
Agnès Baudin-Baillieu, R. Legendre, Claire Kuchly, I. Hatin +4 more
2014Cell Reports61 citations Open access
Semantic Scholar
Conservation of alternative polyadenylation patterns in mammalian genes
Takeshi Ara, F. Lopez, W. Ritchie, P. Benech +1 more
2006BMC Genomics54 citations Open access
Semantic Scholar
Bridging the gap between reference and real transcriptomes
A. Morillon, D. Gautheret
2019Genome Biology52 citations Open access
Semantic Scholar
Native elongating transcript sequencing reveals global anti-correlation between sense and antisense nascent transcription in fission yeast
M. Wéry, Camille Gautier, M. Descrimes, Mayuko Yoda +5 more
2018RNA: A publication of the RNA Society50 citations Open access
Semantic Scholar
Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus.
C. Toffano-Nioche, A. Nguyen, Claire Kuchly, Alban Ott +3 more
2012RNA: A publication of the RNA Society49 citations Open access
Semantic Scholar
A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders
Jean Lehmann, F. Jossinet, D. Gautheret
2013Nucleic Acids Research47 citations Open access
Semantic Scholar
The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus
T. Rochat, C. Bohn, C. Morvan, Thao Nguyen Le Lam +9 more
2018Nucleic Acids Research46 citations Open access
Semantic Scholar
Integrative Pan-Cancer Genomic and Transcriptomic Analyses of Refractory Metastatic Cancer
Y. Pradat, J. Viot, A. Yurchenko, K. Gunbin +19 more
2023Cancer Discovery42 citations Open access
Semantic Scholar
Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation
M. Naville, D. Gautheret
2010Genome Biology41 citations Open access
Semantic Scholar
Mireval: a web tool for simple microRNA prediction in genome sequences
W. Ritchie, F. Théodule, D. Gautheret
2008Bioinform.41 citations Open access
Semantic Scholar
AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation
Vincent Le Texier, J. Riethoven, V. Kumanduri, C. Gopalakrishnan +3 more
2006BMC Bioinformatics41 citations Open access
Semantic Scholar
DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition
J. Audoux, N. Philippe, R. Chikhi, Mikaël Salson +6 more
2017Genome Biology40 citations Open access
Semantic Scholar
Transcription attenuation in bacteria: theme and variations.
M. Naville, D. Gautheret
2009Briefings in Functional Genomics39 citations Open access
Semantic Scholar
RNA at 92°C
C. Toffano-Nioche, Alban Ott, Estelle Crozat, A. Nguyen +5 more
2013RNA Biology37 citations Open access
Semantic Scholar
Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq.
M. Wéry, M. Descrimes, C. Thermes, D. Gautheret +1 more
2013Methods33 citations
Semantic Scholar
CsfG, a sporulation-specific, small non-coding RNA highly conserved in endospore formers
A. Marchais, S. Duperrier, Sylvain Durand, D. Gautheret +1 more
2011RNA Biology31 citations Open access
Semantic Scholar
Metagenome Annotation Using a Distributed Grid of Undergraduate Students
P. Hingamp, C. Brochier, E. Talla, D. Gautheret +2 more
2008PLoS Biology30 citations Open access
Semantic Scholar
The disparate nature of "intergenic" polyadenylation sites.
F. Lopez, S. Granjeaud, Takeshi Ara, B. Ghattas +1 more
2006RNA: A publication of the RNA Society30 citations Open access
Semantic Scholar
Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation1
T. Blein, Coline Balzergue, Thomas Roulé, M. Gabriel +12 more
2020Plant Physiology28 citations Open access
Semantic Scholar
RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.
M. Cros, A. de Monte, J. Mariette, P. Bardou +4 more
2011RNA: A publication of the RNA Society28 citations Open access
Semantic Scholar
Detection of generic differential RNA processing events from RNA-seq data
Van Du T. Tran, Oussema Souiai, Natali Romero-Barrios, M. Crespi +1 more
2016RNA Biology23 citations Open access
Semantic Scholar
Macrophage migration inhibitory factor is overproduced through EGR1 in TET2low resting monocytes
E. Pronier, Aygun Imanci, D. Selimoglu-Buet, Bouchra Badaoui +16 more
2022Communications Biology22 citations Open access
Semantic Scholar
Beyond the 3′ end: experimental validation of extended transcript isoforms
Virginie Moucadel, F. Lopez, Takeshi Ara, P. Benech +1 more
2007Nucleic Acids Research22 citations Open access
Semantic Scholar
Genomic profiling of metastatic castration-resistant prostate cancer samples resistant to androgen-receptor pathway inhibitors.
N. Menssouri, L. Poiraudeau, C. Helissey, L. Bigot +32 more
2023Clinical Cancer Research21 citations Open access
Semantic Scholar
Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile
P. Boudry, Emma Piattelli, Emilie Drouineau, J. Peltier +9 more
2020bioRxiv21 citations Open access
Semantic Scholar

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