Bioinformatics

Leader: Valérie COGNAT

Description

The bioinformatics core facility provides bioinformatics services for all IBMP researchers, especially in high throughput data analyses. The platform has a dedicated computing server that is open in partnership to the GMGM and the LNCA.

Missions :

– Provide an expertise in biological data analysis for researchers
– Give access to a dedicated computing and storage infrastructure
– Develop tools or workflows
– Organize bioinformatics trainings for biologists and/or bioinformaticians. (Access to the trainings)

To request access to the cluster: Web account form  – or – PDF account form (to send at ibmp-servers@unistra.fr).

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 collaborates with the AEG platform to assist biologists from the experimental design to the results exploration.

Provision of a dedicated computing and storage infrastructure

With the SSI team, the bioinformatics provides a dedicated server of 256 cores, 1,2 Tb RAM and 70 To of working space for the IBMP and our 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 installed 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

  • GIRAUDO P., SIMONNOT Q., PFLIEGER D., PETER J., GAGLIARDI D. and ZUBER H.

    Nano3'RACE: A Method to Analyze Poly(A) Tail Length and Nucleotide Additions at the 3' Extremity of Selected mRNAs Using Nanopore Sequencing.

    In: Eugene Valkov, Aaron C. Goldstrohm (eds) Deadenylation. Methods in Molecular Biology, vol 2723. Humana New York, NY., 2024. | DOI : doi: 10.1007/978-1-0716-3481-3_14DOI logo

  • ELSER D., PFLIEGER D., VILLETTE C., MOEGLE B., MIESCH L. and GAQUEREL E.

    Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights N-acylnornicotine innovations

    Science Advances, 9(34), 2023. | DOI : 10.1126/sciadv.ade8984DOI logo

  • KRIEGER C., HALTER D., BALTENWECK R., COGNAT V., BOISSINOT S., MAIA-GRONDARD A., ERDINGER M., BOGAERT F., PICHON E., HUGUENEY P., BRAULT V. and ZIEGLER-GRAFF V.

    An aphid-transmitted virus reduces the host plant response to its vector to promote its transmission

    Phytopathology, 113(9):1745-1760, 2023. | DOI : 10.1094/PHYTO-12-22-0454-FIDOI logo

  • ARRIVÉ M., BRUGGEMAN M., SCALTSOYIANNES V., COUDRAY L., QUAN Y.F.P., SCHELCHER C., COGNAT V., HAMMANN P., CHICHER J., WOLFF P., GOBERT A. and GIEGÉ P.

    A tRNA modifying enzyme facilitates RNase P activity in Arabidopsis nuclei.

    Nature Plants, 9, 2031-2041, 2023.

  • GRAINDORGE S., VILLETTE C., KOECHLER S., GROH C., COMTET-MARRE S., MERCIER P., MAGERAND R., PEYRET P., HEINTZ D., SCHALLER H. and ARSÈNE-PLOETZE F.

    The Arabidopsis thaliana–Streptomyces Interaction Is Controlled by the Metabolic Status of the Holobiont

    International Journal of Molecular Sciences, 23:12952, 2022.