Team leaders: Sarah DJEBALI & Jean MONLONG

Research Programs

 
The Bioinformatics Research In Disease Genomics (BRIDGe) team studies the functional impact of genomic variations on diseases. While the core of our research is hypothesis-free, our goal is to apply our methods and analyses primarily to digestive health conditions studied in the lab in order to leverage the lab’s expertise and validate our findings.

If many genome-wide association studies have identified thousands of variants associated with common diseases, two important problems hinder a thorough understanding of the biological mechanisms underlying these diseases and the development of new treatments: 1) the actual causal variants very often remain unknown, 2) the set of identified variants do not entirely explain the heritability of the disease. In reality, these two problems stem from the fact that 1) only small variants (SNPs) are tested for the association with the disease and that 2) the vast majority of associated variants are located in non-coding regulatory regions of the genome. For these reasons, we are focusing our efforts on:
  • Extending association studies to longer and more complex variants, Structural Variants (SVs such as duplications, deletions, insertions, translocations) using pangenomic approaches
  • Deriving cell-type-specific functional genomic annotations and incorporate them into disease studies
  • Integrating structural variants and functional annotation to improve the molecular diagnosis in rare genetic disease studies.

Keywords: Genomics, Gene-Enhancer relationship, Structural Variants, Pangenome.

Members

 

Past Members

Tools & Methods

 
  • Transcriptome sequencing nalysis (RNA-seq, miRNA-seq)
  • 3D DNA conformation analysis (Hi-C, promoter capture Hi-C)
  • Integrative multi-omics methods (e.g. mixOmics)
  • Genome sequencing analysis from short-read (Illumina) or long-read (Oxford Nanopore) data
  • Sequencing data analysis using human pangenomes (pangenome construction, read alignment, variant calling)
  • Genome-wide association tests (GWAS)
  • Rare disease variant calling from long-read data (phased de novo assembly, structural variants, annotation), including for complex regions (e.g. RCCX module)

Members of the team contributed to several public softwares, some of them highlighted below:

Recruitment

 
We are actively looking to expand and welcome new researchers in genomics and bioinformatics to join our team. Some projects could benefit from new expertise: advanced statistical skills to help with variant imputation, single-cell transcriptomics to enrich our cell-specific characterization of gene regulation, or machine learning to assist in the prediction of functional elements in the genome or functional non-coding variants. Complementary research could also include approaches that would benefit from integrating more variants (e.g. structural variants) or variants with better functional annotation (e.g. in cell-specific regulatory regions), for example developing finer evolutionary metrics or polygenic risk scores. Don’t hesitate to reach out to Sarah and Jean if you are interested in joining the team!

Selected Publications

 
Polygenic risk score prediction accuracy convergence
Henches L, Kim J, Yang Z, Rubinacci S, Pires G, Albiñana C, Boetto C, Julienne H, Frouin A, Auvergne A, Suzuki, Y, Djebali S, Delaneau O, Ganna A, Vilhjálmsson B, Privé F, Aschard H
Human Genetics and Genomics Advances. 2025

Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets
Chalabi S, Loonen L, Boekhorst J, Li, Fang L, Harrison PW, Lakhal W, Lluch J, Sokolov A, Djebali S, Rau A, Giuffra E, Wells J
Genomics. 2025

Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection
Negi S, Stenton S, Berger S, McNulty B, Violich I, Gardner J, Hillaker T, O'Rourke S, O'Leary M, Carbonell E, Austin-Tse C, Lemire G, Serrano J, Mangilog B, VanNoy G, Kolmogorov M, Vilain E, O'Donnell-Luria A, Délot E, Miga K, Monlong JC, Paten BC
The American Journal of Human Genetics. 2025

PaintorPipe: a pipeline for genetic variant fine-mapping using functional annotations.
Gerber Z, Fisun M, Aschard H, Djebali SC.
Bioinformatics Advances. 2024

Pangenome graph construction from genome alignments with Minigraph-Cactus
Hickey G*, Monlong J*, Ebler J, Novak A, Eizenga J, Gao Y, Marschall T, Li H, Paten B
Nature Biotechnology. 2024

Personalized pangenome references
Sirén J, Eskandar P, Ungaro M, Hickey G, Eizenga J, Novak A, Chang X, Chang P, Kolmogorov M, Carroll A, Monlong J, Paten B
Nature Methods. 2024

TAGADA: a scalable pipeline to improve genome annotations with RNA-seq data.
Kurylo C, Guyomar C, Foissac SC, Djebali S.
NAR Genomics and Bioinformatics. 2023

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
Kolmogorov M, Billingsley K, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Alvarez Jerez P, Malik L, Dewan R, Reed X, Genner R, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz S, Traynor B, Miga K, Jain M, Timp W, Phillippy A, Chaisson M, Sedlazeck F, Blauwendraat C, Paten B
Nature Methods. 2023

Enhancer/gene relationships: Need for more reliable genome-wide reference sets.
Hoellinger T, Mestre C, Aschard H, Le Goff W, Foissac S, Faraut T, Djebali SC.
Frontiers in Bioinformatics. 2023

A draft human pangenome reference
Liao W, Asri M, Ebler J, et al.
Nature. 2023

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing
Goenka S, Gorzynski J, Shafin K, Fisk D, Pesout T, Jensen T, Monlong J, Chang P, Baid G, Bernstein J, Christle J, Dalton K, Garalde D, Grove M, Guillory J, Kolesnikov A, Nattestad M, Ruzhnikov M, Samadi M, Sethia A, Spiteri E, Wright C, Xiong K, Zhu T, Jain M, Sedlazeck F, Carroll A, Paten B, Ashley E
Nature Biotechnology. 2022

Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting
Gorzynski J, Goenka S, Shafin K, Jensen T, Fisk D, Grove M, Spiteri E, Pesout T, Monlong J, Baid G, Bernstein J, Ceresnak S, Chang P, Christle J, Chubb H, Dalton K, Dunn K, Garalde D, Guillory J, Knowles J, Kolesnikov A, Ma M, Moscarello T, Nattestad M, Perez M, Ruzhnikov M, Samadi M, Setia A, Wright C, Wusthoff C, Xiong K, Zhu T, Jain M, Sedlazeck F, Carroll A, Paten B, Ashley E
The New England Journal of Medicine. 2022

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes
Sirén J*, Monlong J*, Chang X*, Novak A*, Eizenga J*, et al.
Science. 2021

RNA-Seq data for reliable SNP detection and genotype calling: interest for coding variant characterization and cis-regulation analysis by allele-specific expression in livestock species
Jehl F, Degalez F, Bernard M, Lecerf F, Lagoutte L, Désert C, Coulée M, Bouchez O, Leroux S, Abasht B, Tixier-Boichard M, Bed'hom B, Burlot T, Gourichon D, Bardou P, Acloque H, Foissac S, Djebali S, Giuffra E, Zerjal T, Pitel F, Klopp C, Lagarrigue S.
Frontiers in Genetics. 2021

An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues
Jehl F, Muret K, Bernard M, Boutin M, Lagoutte L, Désert C, Dehais P, Esquerré D, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Pitel F, Zerjal T, Klopp C, Lagarrigue S.
Scientific reports. 2020

A limited set of transcriptional programs define major cell types
Breschi A, Muñoz-Aguirre M, Wucher V, Davis CA, Garrido-Martín D, Djebali S, Gillis J, Pervouchine DD, Vlasova A, Dobin A, Zaleski C.
Genome research. 2020

Genotyping structural variants in pangenome graphs using the vg toolkit
Hickey G*, Heller D*, Monlong J*, Sibbesen J, Sirén J, Eizenga J, Dawson E, Garrison E, Novak A, Paten B
Genome Biology. 2020

Multi-species annotation of transcriptome and chromatin structure in domesticated animals.
Foissac S*, Djebali S*, et al.
BMC biology. 2019
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