BiBs : Bioinformatics and Biostatistics

The Epigenetics and Cell Fate lab BiBs facility provides a broad range of services related to bioinformatics.

Picture from Gerd Altmann, source: Pixabay.

Presentation

We develop and provide standardized protocols for the analysis of NGS data in epigenomics. We support staff in their bioinformatics and biostatistics analyses, promoting their skills development and developing their autonomy. Our services include technology watch, specific analyses, as well as personalized training for our users. We also maintain access to a local compute resource. Finally, an important part of our job is to promote good practices in data analysis and management.
The BiBs platform is part of and actively contributes to the development of the iPOP-UP platform which federates and promotes bioinformatics at the level of the Université Paris Cité.
The facility includes two permanent staff and regularly welcomes trainees or apprentices.

Expertise

Our expertise is about the analysis of high-throughput sequencing data (Illumina and Oxford Nanopore). We can guide you on analyzing different types of omics data:

  • Transcriptome (RNA-seq)
  • Methylome (bisulphite sequencing, or direct long-read detection by nanopore)
  • Genomic localization of transcription factors or histone marks (ChIP-seq or CUT&RUN)
  • Chromatin accessibility (ATAC-seq)
  • Chromosome conformation (Hi-C)

In addition to ‘bulk’ analyses, we are strengthening our skills in the analysis of ‘single-cell’ data, in particular thanks to the iPOP-UP network.

We are also experts in the integration of different bioinformatics tools within workflows (Snakemake), which makes analyzes reproducible and accessible to a wide audience of researchers. Our workflows are compatible with the high performance computing clusters of the Université Paris Cité (iPOP-UP, hosted by RPBS) and the French Institute of Bioinformatics.

Finally, we have expertise in data management (drafting of data management plans, FAIR principles).

Services

  • Experimental design: advice on the choice of sequencing technique, the necessary depth, the controls, the number of biological replicates…

  • Development of high throughput sequencing data analysis workflows and support in their use.

  • Support in the use of the iPOP-UP high-performance computing cluster and organization of dedicated training.

  • Maintenance and promotion of the bioinformatics tools developed by members of the laboratory.

  • On-demand training on the use of bioinformatics tools to develop user autonomy.

  • Proofreading of articles or funding requests concerning projects using NGS analyses.

  • Assistance in the recruitment of interns, doctoral students, post-doctoral fellow or engineers in charge of omics data analysis.

  • Best practice recommendations for data management and analysis based on the FAIR principles.

Members

Magali Hennion

Head, IR CNRS

Olivier Kirsh

Assistant professor, Université Paris Cité

Elouan Bethuel

Trainee, master M1-BI

Resources

Website of the facility

All tutorials and related documentation written by BiBs are available on https://parisepigenetics.github.io/bibs/.

GitHub

All codes developed by EDC lab members are available on https://github.com/parisepigenetics.

 

 

Contact

BiBs

Lamarck B building, room 366b

35 rue Hélène Brion, 75013 Paris

e-mail: bibs@parisepigenetics.com

 

 

 

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