Jean Monlong
Mini-CV
- I graduated from the École nationale supérieure d’informatique et de mathématiques appliquées (ENSIMAG) in Grenoble with a specialization in bioinformatics.
- My engineering school studies ended with a research project studying alternative splicing from RNA sequencing data at the Center for Genomic Regulation (CRG) in Barcelona (Spain) under the supervision of Dr. Roderic Guigó
- For my PhD, I developed methods to detect and study copy-number variation in human cohorts with whole-genome sequencing data in the laboratory of Dr. Guillaume Bourque, at McGill University, in Montreal (Canada).
- As a postdoc, I combined my interest for structural variation with the new pangenomic methods that were being developed at the University of California, Santa Cruz (UCSC) in the Computational Genomics Lab of Dr. Benedict Paten, in Santa Cruz (USA).
- I joined as a CRCN INSERM in May 2023. I will continue developing and using pangenomic approaches to study structural variation, with more focus toward characterizing their functional impact, especially in the disease context.
More up-to-date informations, publications, … at jmonlong.github.io/.
Expertise: Genomics, variant analysis, pangenomics.
Research projects
Structural variants (SVs) are defined as genomic variations involving 50 nucleotides or more. They can take multiple forms, from simple deletions and insertions to complex rearrangements formed by multiple SV types like inversions, translocations and duplications. Most SVs are under-studied because of the technical challenges to identify them. Their impact is also more difficult to predict, as they often affect multiple functional elements or can trigger epigenetic changes.
Although the sequencing of short DNA fragments of about 300 nucleotides (short read sequencing) is widely used today, it cannot identify many types of SVs. Long read sequencing, in contrast, can sequence longer DNA fragments (thousands of nucleotides) and detect SVs at much higher resolution, but remains costly. We have shown that short read sequencing data can be analyzed with pangenomes to accurately genotype SVs that had been discovered with long read sequencing. A pangenome represents multiple genomes and provides a framework to enhance a reference genome by integrating known variants.
My research goal is to develop pangenome-oriented tools to better detect SVs, integrate them into genome-wide association studies (GWAS), and predict their functional impact. With those tools, the aim is to identify novel disease genetic factors or identify the causal variant of known disease associations.
Publications
Article type:
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation. Julian Lucas, Prajna Hebbar, ..., Jean Monlong, et al., bioRxiv 2026. DOI: 10.64898/2026.07.21.739710
vgteam/vg: vg 1.71.0 - Cera. Adam Novak, Erik Garrison, ..., Jean Monlong, et al., 2026. DOI: 10.5281/zenodo.18164686
vgteam/vg: vg 1.71.0 - Cera. Adam Novak, Erik Garrison, ..., Jean Monlong, et al., 2026. DOI: 10.5281/zenodo.18163949
Surmonter la complexité de CYP21A2 : une stratégie NGS optimisée pour le diagnostic moléculaire du déficit en 21-hydroxylase – à propos d’un cas clinique. Julie Milandri, Jean Monlong, et al., Annales d'Endocrinologie 2026. DOI: 10.1016/j.ando.2026.102540
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection. Shloka Negi, Sarah L. Stenton, ..., Jean Monlong, et al., The American Journal of Human Genetics 2025. DOI: 10.1016/j.ajhg.2025.01.002
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe. Xian Chang, Adam M. Novak, ..., Jean Monlong, et al., bioRxiv 2025. DOI: 10.1101/2025.09.29.678807
Long-read sequencing resolves the clinically relevant *CYP21A2* locus, supporting a new clinical test for Congenital Adrenal Hyperplasia. Jean Monlong, Xiao Chen, et al., medRxiv 2025. DOI: 10.1101/2025.02.07.25321404
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe. Benedict Paten, Xian Chang, ..., Jean Monlong, et al., Research Square 2025. DOI: 10.21203/rs.3.rs-7747403/v1
Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References. Dylan J. Taylor, Jordan M. Eizenga, ..., Jean Monlong, et al., Annual Review of Genomics and Human Genetics 2024. DOI: 10.1146/annurev-genom-021623-081639
Personalized pangenome references. Jouni Sirén, Parsa Eskandar, ..., Jean Monlong, et al., Nature Methods 2024. DOI: 10.1038/s41592-024-02407-2
Mapping the scientific output of organoids for animal and human modeling infectious diseases: a bibliometric assessment. Yan Jin, Jean Monlong, ..., Agnès Wiedemann, Veterinary Research 2024. DOI: 10.1186/s13567-024-01333-7
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection. Shloka Negi, Sarah L. Stenton, ..., Jean Monlong, et al., medRxiv 2024. DOI: 10.1101/2024.08.22.24312327
Efficient indexing and querying of annotations in a pangenome graph. Adam M. Novak, Dickson Chung, ..., Sarah Djebali, ..., Jean Monlong, bioRxiv 2024. DOI: 10.1101/2024.10.12.618009
Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring. Elena Kuzmin, Toby M. Baker, ..., Jean Monlong, et al., Cell Reports 2024. DOI: 10.1016/j.celrep.2024.113988
Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Ryan Lorig-Roach, Melissa Meredith, Jean Monlong, et al., Genome Research 2024. DOI: 10.1101/gr.278268.123
Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation. Kimberley J. Billingsley, Melissa Meredith, ..., Jean Monlong, et al., bioRxiv 2024. DOI: 10.1101/2024.12.16.628723
P821: Long-read sequencing resolves CYP21A2 alleles in congenital adrenal hyperplasia*. Emmanuèle C. Délot, Jean Monlong, et al., Genetics in Medicine Open 2024. DOI: 10.1016/j.gimo.2024.101732
A draft human pangenome reference. Wen‐Wei Liao, Mobin Asri, ..., Jean Monlong, et al., Nature 2023. DOI: 10.1038/s41586-023-05896-x
Pangenome graph construction from genome alignments with Minigraph-Cactus. Glenn Hickey, Jean Monlong, et al., Nature Biotechnology 2023. DOI: 10.1038/s41587-023-01793-w
Recombination between heterologous human acrocentric chromosomes. Andrea Guarracino, Silvia Buonaiuto, ..., Jean Monlong, et al., Nature 2023. DOI: 10.1038/s41586-023-05976-y
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Mikhail Kolmogorov, Kimberley J. Billingsley, ..., Jean Monlong, et al., Nature Methods 2023. DOI: 10.1038/s41592-023-01993-x
Increased mutation and gene conversion within human segmental duplications. Mitchell R. Vollger, Philip C. Dishuck, ..., Jean Monlong, et al., Nature 2023. DOI: 10.1038/s41586-023-05895-y
A draft human pangenome reference. Wen‐Wei Liao, Mobin Asri, ..., Jean Monlong, et al., Yearbook of Paediatric Endocrinology 2023. DOI: 10.1530/ey.20.12.1
Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting. John E. Gorzynski, Sneha D. Goenka, ..., Jean Monlong, et al., New England Journal of Medicine 2022. DOI: 10.1056/nejmc2112090
Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Sneha D. Goenka, John E. Gorzynski, ..., Jean Monlong, et al., Nature Biotechnology 2022. DOI: 10.1038/s41587-022-01221-5
Glioblastoma scRNA-seq shows treatment-induced, immune-dependent increase in mesenchymal cancer cells and structural variants in distal neural stem cells. Charles Couturier, Javad Nadaf, ..., Jean Monlong, et al., Neuro-Oncology 2022. DOI: 10.1093/neuonc/noac085
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Jouni Sirén, Jean Monlong, et al., Science 2021. DOI: 10.1126/science.abg8871
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Kishwar Shafin, Trevor Pesout, ..., Jean Monlong, et al., Nature Biotechnology 2020. DOI: 10.1038/s41587-020-0503-6
Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy. Charles Couturier, Shamini Ayyadhury, ..., Jean Monlong, et al., Nature Communications 2020. DOI: 10.1038/s41467-020-17186-5
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Bernardo Rodríguez–Martín, Eva G. Alvarez, ..., Jean Monlong, et al., Nature Genetics 2020. DOI: 10.1038/s41588-019-0562-0
Genotyping structural variants in pangenome graphs using the vg toolkit. Glenn Hickey, David N. Heller, Jean Monlong, et al., Genome Biology 2020. DOI: 10.1186/s13059-020-1941-7
Genetic effects on gene expression across human tissues. Eric Haugen, Yuan He, ..., Jean Monlong, et al., 2020. DOI: 10.17615/p82n-gb73
Stalled developmental programs at the root of pediatric brain tumors. Selin Jessa, Alexis Blanchet-Cohen, ..., Jean Monlong, et al., Nature Genetics 2019. DOI: 10.1038/s41588-019-0531-7
Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. Alvaro Barbeira, Scott Dickinson, ..., Jean Monlong, et al., Nature Communications 2018. DOI: 10.1038/s41467-018-03621-1
Global characterization of copy number variants in epilepsy patients from whole genome sequencing. Jean Monlong, Simon Girard, et al., PLOS Genetics 2018. DOI: 10.1371/journal.pgen.1007285
Human copy number variants are enriched in regions of low mappability. Jean Monlong, Patrick Cossette, et al., Nucleic Acids Research 2018. DOI: 10.1093/nar/gky538
