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.

Operating rules

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

  • SCHEER H., DE ALMEIDA C., FERRIER E., SIMONNOT Q., POIRIER L., PFLIEGER D., SEMENT F., KOECHLER S., PIERMARIA C., KRAWCZYK P., MROCZEK S., CHICHER J., KUHN L., DZIEMBOWSKI A., HAMMANN P., ZUBER H. and GAGLIARDI D.

    The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis

    Nature Communications, 12:1298, 2021. | DOI : 10.1038/s41467-021-21382-2DOI logo

  • FERTET A., GRAINDORGE S., KOECHLER S., DE BOER G.J., GUILLOTEAU-FONTENY E. and GUALBERTO J.M.

    Sequence of the mitochondrial genome of Lactuca virosa suggests an unexpected role in Lactuca sativa’s evolution

    Frontiers in Plant Science, , 2021. | DOI : doi: 10.3389/fpls.2021.697136DOI logo

  • 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

    In: Heinlein M. (ed) RNA tagging. Methods in Molecular Biology, vol 2166. Humana New York, NY., 2020. | DOI : 10.1007/978-1-0716-0712-1_23DOI logo

  • 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, 2013-2025, 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 : https://doi.org/10.1104/pp.20.00188DOI logo