• Supplemental data for "A dual model for prioritizing cancer mutations"
    Jia Li et al.. submitted

  • Supplemental data for "An Assesment of Bacterial Small RNA Target Prediction Programs"
    Adrien Pain, Alban Ott, Hamza Amine, Tatiana Rochat, Philippe Bouloc, Daniel Gautheret. RNA Biol. 2015, 12:509.

  • Supplemental data for "RNA at 92 C: the Non-Coding Transcriptome of the Hyperthermophile Archaea Pyrococcus abyssi"
    Toffano-Nioche et al. RNA Biol. 2013; 10:1211-20
    Lists of ncRNA and extended annotations based on transcription units (gff files), features of ncRNA (xls file).

  • Supplemental data for "Detection of non-coding RNA in Bacteria and Archaea using the DETR'PROK Galaxy pipeline"
    Toffano-Nioche et al. Methods. 2013; 63:60-5.
    Data files to launch the workflow based on an RNAseq of Vibrio splendidus: alignments (bam and bai files), annotations and sequences of the 2 chromosomes (gff and fna files), and files for a toy example (first 60000 nt of the 2nd chromosome).

  • Supplemental data for "Screening Genome Sequences for Known RNA genes and motifs"
    Gautheret D. Handbook of RNA Biochemistry: Second, Completely Revised and Enlarged Edition, Hartmann, Bindereif, Schon and Westhof, Eds. Wiley, 2014.
    Warning: one big file herein! (2.5Gb uncompressed)

  • Supplemental data for "Genome-wide discovery and analysis of microRNAs and other small RNAs from rice embryogenic callus. .
    Chen CJ, Liu Q, Zhang YC, Qu LH, Chen YQ, Gautheret D. RNA Biol. 8(3). 2011.

  • Supplemental data for "Transcription attenuation in Bacteria: Theme and Variations".
    Naville & Gautheret, Brief Funct Genomic Proteomic. 9: 178-89. 2010.
    Includes supplemental methods (supp_data.doc), Table S1 and S2.

  • Supplemental data for "Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles."
    Marchais et al, Genome Res. 6:1084-92, 2009.
    Contains genomic coordinates, names and flanking genes of all CNEs (conserved non-coding elements) and protein-coding genes in ncRNA-enriched clusters. One file per species.