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List of works by Daniel Gautheret

2-kupl: mapping-free variant detection from DNA-seq data of matched samples

scientific article published on 05 June 2021

A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events

scientific article published on 20 November 2015

A benchmark study of scoring methods for non-coding mutations.

scientific article published on 11 January 2018

A secondary and tertiary structure editor for nucleic acids.

scientific article published in March 1988

A survey of metazoan selenocysteine insertion sequences.

scientific article

A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders.

scientific article

ARNold: a web tool for the prediction of Rho-independent transcription terminators.

scientific article published in January 2011

ASTD: The Alternative Splicing and Transcript Diversity database

scientific article

Accurate characterization of Escherichia coli tRNA modifications with a simple method of deep sequencing library preparation

scientific article published on 03 July 2020

Acquired initiating mutations in early hematopoietic cells of CLL patients

scientific article

AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation.

scientific article

Alternate Polyadenylation in Human mRNAs: A Large-Scale Analysis by EST Clustering ⬇️

scientific article published on May 1, 1998

An RNA pattern matching program with enhanced performance and portability.

scientific article published in April 1994

An assessment of bacterial small RNA target prediction programs

scientific article

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

scientific article (publication date: 2012)

Beyond the 3' end: experimental validation of extended transcript isoforms

scientific article published on 4 March 2007

Bridging the gap between reference and real transcriptomes

scientific article published on 03 June 2019

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins.

scientific article published in July 2018

Characterization of novel genomic alterations and therapeutic approaches using acute megakaryoblastic leukemia xenograft models

scientific article

Computer modeling and display of RNA secondary and tertiary structures.

scientific article published on January 1990

Computing expectation values for RNA motifs using discrete convolutions

scientific article

Conservation of alternative polyadenylation patterns in mammalian genes

scientific article

CsfG, a sporulation-specific, small non-coding RNA highly conserved in endospore formers

scientific article (publication date: 2011)

DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

scientific article published on 28 December 2017

Detection of generic differential RNA processing events from RNA-seq data

scientific article

Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline

scientific article published on 25 June 2013

Differential repression of alternative transcripts: a screen for miRNA targets

scientific article

Entropy measures quantify global splicing disorders in cancer

scientific article

Erratum: The Non-Coding RNA Journal Club: Highlights on Recent Papers-4. Non-Coding RNA 2016, 2, 9.

scientific article

Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism

scientific article

Expression profiling in mouse fetal thymus reveals clusters of coordinately expressed genes that mark individual stages of T-cell ontogeny

scientific article published on 10 August 2002

Fitting the structurally diverse animal mitochondrial tRNAs(Ser) to common three-dimensional constraints.

scientific article published in March 1994

Gene structure, expression pattern, and biological activity of mouse killer cell activating receptor-associated protein (KARAP)/DAP-12

scientific journal article

Genome-wide discovery and analysis of microRNAs and other small RNAs from rice embryogenic callus

scientific article

Genome-wide translational changes induced by the prion [PSI+].

scientific article published on 17 July 2014

Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen <i>Clostridioides difficile</i>

scientific article published on 25 February 2021

Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data.

scientific article

Identification of base-triples in RNA using comparative sequence analysis.

scientific article published in April 1995

Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing

scientific article

In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs

scientific article

Metagenome annotation using a distributed grid of undergraduate students

scientific article

Mining the coding and non-coding genome for cancer drivers

scientific article published on 30 September 2015

Modeling the three-dimensional structure of RNA using discrete nucleotide conformational sets.

scientific article published in February 1993

Modeling the three-dimensional structure of RNA.

scientific article

NAPP: the Nucleic Acid Phylogenetic Profile Database

scientific article

Native Elongating Transcript Sequencing reveals global anti-correlation between sense and antisense nascent transcription in fission yeast

scientific article published on 7 November 2017

New Functional Signatures for Understanding Melanoma Biology from Tumor Cell Lineage-Specific Analysis.

scientific article published on 13 October 2015

No tRNA3Lys unwinding in a complex with HIV NCp7

scientific article published on 01 October 1997

Nonsense-Mediated Decay Restricts LncRNA Levels in Yeast Unless Blocked by Double-Stranded RNA Structure

scientific article published on 19 January 2016

Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA ⬇️

scientific article published on October 1, 1990

Predicting U-turns in ribosomal RNA with comparative sequence analysis

scientific article published on 01 July 2000

Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation ⬇️

scientific article published on September 29, 2010

Profile-based detection of microRNA precursors in animal genomes.

scientific article

Quantitative Analysis of the T Cell Repertoire Selected by a Single Peptide–Major Histocompatibility Complex ⬇️

scientific article published on June 1, 1998

RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi

scientific article (publication date: July 2013)

RNAML: a standard syntax for exchanging RNA information.

scientific article

RNAMotif, an RNA secondary structure definition and search algorithm

scientific article

RNAcentral: A vision for an international database of RNA sequences

scientific article (publication date: November 2011)

RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.

scientific article published on 23 September 2011

Reference-free transcriptome exploration reveals novel RNAs for prostate cancer diagnosis

scientific article published on 15 November 2019

Relative amplification efficiency of differently sized templates by long-distance PCR

scientific article published on 01 March 1998

Reproducing the three-dimensional structure of a tRNA molecule from structural constraints.

scientific article published on October 1993

Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea

scientific article published on 3 August 2015

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

scientific article published on 19 November 2020

RsaOG, a new staphylococcal family of highly transcribed non-coding RNA.

scientific article

Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles

scientific article

The ERPIN server: an interface to profile-based RNA motif identification

scientific article

The Non-Coding RNA Journal Club: Highlights on Recent Papers-4.

scientific article

The Non-Coding RNA Journal Club: Highlights on Recent Papers.

scientific article

The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus

scientific article published on 28 September 2018

The contribution of uncharted RNA sequences to tumor identity in lung adenocarcinoma

scientific article published on 01 February 2022

The disparate nature of "intergenic" polyadenylation sites

scientific article

The genome sequence of the model ascomycete fungus Podospora anserina

scientific article

Transcription attenuation in bacteria: theme and variations

scientific article published on 01 March 2010

Transcription attenuation in bacteria: theme and variations.

scientific article

Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus

scientific article (publication date: December 2012)

Using Alu elements as polyadenylation sites: A case of retroposon exaptation.

scientific article

VING: a software for visualization of deep sequencing signals

scientific article published on 7 September 2015

Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq.

scientific article published on 21 March 2013

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