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.