Bioinformatics

Leader: Valérie COGNAT

Description

The bioinformatics core facility provides bioinformatics services for all IBMP researchers, specially in next generation sequencing data analysis.
The platform has a dedicated server that is open in partnership with GMGM and LNCA.

Account form to request access to the cluster.

Expertises

High-throughput sequencing data analysis

The facility has expertise in NGS data analysis, particularly with Illumina and Oxford Nanopore technologies. It covers various topics, including :
– Small genome assembly,
– Transcriptome analysis (RNA-seq and smallRNA-seq)
– 16S metagenomics
– Protein/DNA-RNA interactions (ChIP-seq, …)
– Methylation
Our team collaborate with AEG platform to assist biologist from experimental design to results exploration.

Provision of a dedicated computing and storage infrastructure

With the SSI team, the bioinformatics provided a dedicated server of 192 cores, 864 Gb RAM and 60 To of working space for the IBMP and partners. Private storage volumes for each institute are available for project storage and backup. Several software tools, in particular for high-throughput data analysis, are deployed on the cluster.
Anyone working in a partner lab can ask an account with the Account form. Other people can contact the platform manager to ask a partnership.

Tool and workflow development

The facility has expertise in programming (R, python, bash, perl) and develops some visualisation tools and databases on request.

Members

Recent publications

  • BÖHRER M., RYMEN B., HIMBER C., GERBAUD A., PFLIEGER D., LAUDENCIA-CHINGCUANCO D., CARTWRIGHT A., VOGEL J., SIBOUT R. and BLEVINS T.

    Integrated genome-scale analysis and northern blot detection of retrotransposon siRNAs across plant species

    , , 2020.

  • GOSWAMI R., ASNACIOS A., MILANI P., GRAINDORGE S., HOULNÉ G., MUTTERER J., HAMANT O. and CHABOUTÉ M.E.

    Mechanical shielding in plant nuclei.

    Current Biology, :, 2020. | DOI : 10.1016/j.cub.2020.03.059DOI logo

  • GENTRIC N., MASOUD K., JOURNOT R.P., COGNAT V., CHABOUTÉ M.E., NOIR S. and GENSCHIK P.

    The F-box-like protein FBL17 is a regulator of DNA-damage response and co-localizes with RETINOBLASTOMA RELATED 1 at DNA lesion sites

    Plant Physiology, :20.00188, 2020. | DOI : DOI:10.1104/pp.20.00188DOI logo

  • MEGEL C., HUMMEL G., LALANDE S., UBRIG E., COGNAT V., MORELLE G., SALINAS-GIEGÉ T., DUCHÊNE A.M. and MARÉCHAL-DROUARD L.

    Plant RNases T2, but not Dicer-like proteins, are major players of tRNA-derived fragments biogenesis

    Nucleic Acids Research, 47(2):941-952, 2019. | DOI : 10.1093/nar/gky1156DOI logo

  • LANGE H., NDECKY S., GOMEZ-DIAZ C., PFLIEGER D., BUTEL N., ZUMSTEG J., KUHN L., PIERMARIA C., CHICHER J., CHRISTIE M., KARAASLAN E.S., LANG P.L., WEIGEL D., VAUCHERET H., HAMMANN P. and GAGLIARDI D.

    RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis

    Nature Communications, 10:3871, 2019. | DOI : 10.1038/s41467-019-11807-4DOI logo