Leader: Valérie COGNAT
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.
To request access to the cluster: Web account form – or – PDF account form (to send at ibmp-servers@unistra.fr).
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.
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.
The facility has expertise in programming (R, python, bash, perl) and develops some visualisation tools and databases on request.
Ingénieur de recherche / Research engineer
Ingénieur d'études / Engineer
Ingénieur d'études / Engineer
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/s41467-021-21382-2
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,
12:697136,
2021.
| DOI : doi: 10.3389/fpls.2021.697136
CLAVEL M., LECHNER E., INCARBONE M., VINCENT T., COGNAT V., SMIRNOVA E., LECORBEILLER M., BRAULT V., ZIEGLER-GRAFF V. and GENSCHIK P.
Atypical molecular features of RNA silencing against the phloem-restricted polerovirus TuYV
Nucleic Acid Research,
in press,
2021.
| DOI : 10.1093/nar/gkab802
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_23
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.2020.03.059
