Publications

  • Efficient indexing and querying of annotations in a pangenome graph. bioRxiv 2024.
    AM Novak, D Chung, G Hickey, S Djebali, TT Yokoyama, E Garrison, G Narzisi, B Paten, J Monlong
  • Personalized pangenome references. Nature Methods 2024.
    J Sirén, P Eskandar, MT Ungaro, G Hickey, JM Eizenga, AM Novak, X Chang, PC Chang, M Kolmogorov, A Carroll, J Monlong, B Paten
    Preprint
  • Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection. medRxiv 2024.
    S Negi, SL Stenton, SI Berger, B McNulty, I Violich, J Gardner, …, E Vilain, A O-Luria, E Délot, KH Miga, J Monlong, B Paten
  • Mapping the scientific output of organoids for animal and human modeling infectious diseases: a bibliometric assessment. Veterinary Research 2024.
    J Yan, J Monlong, C Cougoule, S Lacroix-Lamandé, A Wiedemann
  • Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Genome Research 2024.
    R Lorig-Roach, M Meredith, J Monlong, …, P Carnevali, K Miga, B Paten
    Preprint
  • Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References. Annual Review of Genomics and Human Genetics 2024.
    DJ Taylor, JM Eizenga, Q Li, A Das, KM Jenike, EE Kenny, KH Miga, J Monlong, RC McCoy, B Paten, MC Schatz
  • Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring. Cell Reports 2024.
    E Kuzmin, TM Baker, T Lesluyes, J Monlong, KT Abe, PP Coelho, M Schwartz, …, J Ragoussis, G Bourque, P Van Loo, M Park
  • Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nature Methods 2023.
    M Kolmogorov, KJ Billingsley, M Mastoras, M Meredith, J Monlong, …, C Blauwendraat, B Paten
    Preprint
  • A draft human pangenome reference. Nature 2023.
    W Liao, M Asri, J Ebler, D Doerr, M Haukness, G Hickey, S Lu, JK Lucas, J Monlong, …, G Bourque, MJP Chaisson, P Flicek, AM Phillippy, JM Zook, EE Eichler, D Haussler, T Wang, ED Jarvis, KH Miga, E Garrison, T Marschall, IM Hall, H Li, B Paten
    Preprint Press
  • Pangenome graph construction from genome alignments with Minigraph-Cactus. Nature Biotechnology 2023.
    G Hickey*, J Monlong*, J Ebler, AM Novak, JM Eizenga, Y Gao, Human Pangenome Reference Consortium, H Li, B Paten
    Preprint Data/Code
  • Glioblastoma scRNAseq Shows Treatment-induced, Immune-dependent Rise In Mesenchymal Cancer Cells, and Structural Variants in Distal Neural Stem Cells. Neuro-Oncology 2022.
    CP Couturier, J Nadaf, Z Li, S Baig, G Riva, P Le, DJ Kloosterman, J Monlong, A Nkili Meyong, R Allache, T Degenhard, M Al-Rashid, M Guiot, G Bourque, J Ragoussis, L Akkari, FJ Quintana, K Petrecca
  • Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nature Biotechnology 2022.
    SD Goenka, JE Gorzynski, K Shafin, DG Fisk, T Pesout, TD Jensen, J Monlong, P Chang, G Baid, …, B Paten, EA Ashley
    PubMed Central Press
  • Ultra-Rapid Nanopore Whole Genome Genetic Diagnosis of Dilated Cardiomyopathy in an Adolescent With Cardiogenic Shock. Circulation: Genomic and Precision Medicine 2022.
    JE Gorzynski, SD Goenka, K Shafin, TD Jensen, DG Fisk, ME Grove, E Spiteri, T Pesout, J Monlong, JA Bernstein, …, B Paten, EA Ashley
    Press
  • Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting. New England Journal of Medicine 2022.
    JE Gorzynski, SD Goenka, K Shafin, TD Jensen, DG Fisk, ME Grove, E Spiteri, T Pesout, J Monlong, …, B Paten, EA Ashley
    Press
  • Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science 2021.
    J Sirén*, J Monlong*, X Chang*, AM Novak*, JM Eizenga*, C Markello, JA Sibbesen, G Hickey, P Chang, A Carroll, N Gupta, S Gabriel, TW Blackwell, A Ratan, KD Taylor, SS Rich, JI Rotter, D Haussler, E Garrison, B Paten
    PubMed Central Preprint Data/Code Press
  • Inferring Copy Number from Triple-Negative Breast Cancer Patient Derived Xenograft scRNAseq Data Using scCNA. Mapping Genetic Interactions 2021.
    E Kuzmin, J Monlong, C Martinez, H Kuasne, CL Kleinman, J Ragoussis, G Bourque, M Park
  • Invasive growth associated with cold-inducible RNA-binding protein expression drives recurrence of surgically resected brain metastases. Neuro-Oncology 2021.
    M Dankner, M Caron, T Al-Saadi, W Yu, V Ouellet, R Ezzeddine, SM Maritan, MG Annis, PU Le, J Nadaf, NS Neubarth, P Savage, D Zuo, CP Couturier, J Monlong, H Djambazian, H Altoukhi, G Bourque, J Ragoussis, RJ Diaz, M Park, M Guiot, S Lam, K Petrecca, PM Siegel
    PubMed Central
  • A Preclinical Trial and Molecularly Annotated Patient Cohort Identify Predictive Biomarkers in Homologous RecombinationDeficient Pancreatic Cancer. Clinical Cancer Research 2020.
    Y Wang, JYP Park, A Pacis, RE Denroche, GH Jang, A Zhang, A Cuggia, C Domecq, J Monlong, …, G Zogopoulos
  • Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy. Nature Communications 2020.
    CP Couturier, S Ayyadhury, PU Le, J Nadaf, J Monlong, …, J Antel, G Bourque, J Ragoussis, K Petrecca
    PubMed Central Preprint Press
  • Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology 2020.
    K Shafin, T Pesout, R Lorig-Roach, M Haukness, HE Olsen, …, J Monlong, …, KH Miga, P Carnevali, M Jain, B Paten
    PubMed Central Preprint
  • Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics 2020.
    B Rodriguez-Martin, EG Alvarez, A Baez-Ortega, …, J Monlong, …, HH Kazazian, KH Burns, PJ Campbell, JMC Tubio
    PubMed Central Preprint
  • Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biology 2020.
    G Hickey*, D Heller*, J Monlong*, JA Sibbesen, J Siren, J Eizenga, ET Dawson, E Garrison, AM Novak, B Paten
    PubMed Central Preprint Data/Code Press
  • Stalled developmental programs at the root of pediatric brain tumors. Nature Genetics 2019.
    S Jessa, A Blanchet-Cohen, B Krug, M Vladoiu, M Coutelier, D Faury, B Poreau, N De Jay, S Hébert, J Monlong, …, G Bourque, J Ragoussis, L Garzia, MD Taylor, N Jabado, CL Kleinman
    PubMed Central Press
  • Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations. Nature Communications 2019.
    J Grajcarek, J Monlong, Y Nishinaka-Arai, M Nakamura, M Nagai, S Matsuo, D Lougheed, H Sakurai, MK Saito, G Bourque, K Woltjen
    PubMed Central Data/Code Press
  • Human copy number variants are enriched in regions of low mappability. Nucleic Acids Research 2018.
    J Monlong, P Cossette, C Meloche, G Rouleau, SL Girard, G Bourque
    PubMed Central Preprint Data/Code
  • Global characterization of copy number variants in epilepsy patients from whole genome sequencing. PLOS Genetics 2018.
    J Monlong*, SL Girard*, …, JL Michaud, G Rouleau, BA Minassian, G Bourque, P Cossette
    PubMed Central Preprint Data/Code
  • High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies. American journal of human genetics 2017.
    F Hamdan, CT Myers, P Cossette, P Lemay, D Spiegelman, A Dionne-Laporte, C Nassif, O Diallo, J Monlong, …, BA Minassian, JL Michaud
    PubMed Central Press
  • Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma. Scientific Reports 2017.
    M Arseneault*, J Monlong*, …, M Lathrop, G Bourque, Y Riazalhosseini
    PubMed Central
  • The human transcriptome across tissues and individuals. Science 2015.
    M Melé, PG Ferreira, F Reverter, DS DeLuca, J Monlong, M Sammeth, …, The GTEx Consortium
    PubMed Central
  • The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science 2015.
    The GTEx Consortium
    PubMed Central
  • Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nature Communications 2015.
    D Pervouchine, S Djebali, A Breschi, CA Davis, PP Barja, A Dobin, A Tanzer, J Lagarde, C Zaleski, L See, M Fastuca, J Drenkow, H Wang, G Bussotti, B Pei, S Balasubramanian, J Monlong, …, C Notredame, R Guigo, TR Gingeras
    PubMed Central
  • Identification of genetic variants associated with alternative splicing using sQTLseekeR. Nature Communications 2014.
    J Monlong, M Calvo, PG Ferreira, R Guigó
    PubMed Central
  • Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia. Genome research 2014.
    PG Ferreira, P Jares, D Rico, G Gomez-Lopez, A Martinez-Trillos, N Villamor, S Ecker, A Gonzalez-Perez, DG Knowles, J Monlong, …, E Campo, R Guigo
    PubMed Central
  • Transcriptome and genome sequencing uncovers functional variation in humans. Nature 2013.
    T Lappalainen, M Sammeth*, MR Friedlander*, PA t Hoen*, J Monlong*, MA Rivas*, et al.
    PubMed Central
  • Overdiagnosis from non-progressive cancer detected by screening mammography: stochastic simulation study with calibration to population based registry data. BMJ 2011.
    A Seigneurin, O Francois, J Labarere, P Oudeville, J Monlong, M Colonna
    PubMed Central

And here is the PDF of my PhD thesis on “Population-Based Approaches to Characterize Copy Number Variation from Whole-Genome Sequencing in Healthy Individuals and Disease Cohorts” (LaTeX source).

Presentations

2024

  • Characterising the CYP21A2 gene with Parakit

    Jul 2, 2024, International Genome Graph Symposium
    Ascona, Switzerland Details PDF

  • Pangenome graph construction from genome alignments with Minigraph-Cactus

    Jun 26, 2024, Journées Ouvertes en Biologie, Informatique, et Mathématiques
    Toulouse, France Details PDF

2022

  • Pangenomes: incorporating diversity into genomic analyses

    Oct 4, 2022, Google Genomics Deep Dive
    Palo Alto, CA, USA Details

  • Accurate short variant calling from sequencing data with pangenomes and DeepVariant

    Sep 9, 2022, AGBT Precision Health
    San Diego, CA, USA Details PDF

2020

  • Genotyping structural variants in human cohorts using pangenome graphs

    Dec 11, 2020, Voice of the Researcher
    Genomics Institute, UC Santa Cruz, CA, USA Details PDF

  • Genotyping structural variants in TOPMed using pangenome graphs

    Feb 12, 2020, GSP-TOPMed Analysis Workshop
    New York City, NY, USA Details PDF

2019

  • Genotyping structural variants in pangenome graphs using the vg toolkit

    Nov 7, 2019, Genome Informatics
    Cold Spring Harbor Laboratory, NY, USA Details PDF Slides

  • Genome variation graphs with the vg toolkit

    Oct 15, 2019, GRC-GIAB Workshop (ASHG19)
    Houston, TX, USA Details PDF

  • Genotyping structural variants in pangenome graphs using the vg toolkit

    Oct 12, 2019, Northern California Computational Biology Symposium
    UC Davis, CA, USA Details PDF

2017

  • Genome-wide characterization of copy number variants in epilepsy patients

    May 18, 2017, Human Genetics Research Day, McGill University
    Montreal, Canada Details PDF

  • Genome-wide characterization of copy number variants in epilepsy patients

    Apr 24, 2017, Canadian Human and Statistical Genetics Meeting
    Quebec, Canada Details PDF

2016

  • Global patterns of copy number variation in humans from a population-based analysis

    Apr 5, 2016, International Congress of Human Genetics
    Kyoto, Japan Details PDF

2015

  • Population-based Detection of Structural Variants in Normal and Aberrant Genomes

    Apr 19, 2015, Canadian Human and Statistical Genetics Meeting
    Vancouver, Canada Details PDF

2014

  • Population-based Detection of Structural Variants in Normal and Aberrant Genomes

    Sep 21, 2014, Genome Informatics
    Cambridge, UK Details PDF

  • Population-based detection of Structural Variants in normal and aberrant genomes.

    Jun 5, 2014, Human Genetics Research Day, McGill University
    Montreal, Canada Details PDF

Teaching

Between 2013 and 2018, I organized eight R workshops for the students of the Human Genetics department. Slides can be found here. For these workshops, I received a Certificate of Appreciation from the department.

Other teaching experiences include:

2024

  • HPRC workshop

    Apr 8, 2024, Human Genome Meeting (HUGO)
    Rome, Italy Slides

2023

  • HPRC workshop

    Mar 14, 2023, ACMG Annual Clinical Genetics Meeting
    Salt Lake City, USA Slides

2019

  • GRC-GIAB workshop

    Oct 15, 2019, American Society of Human Genetics (ASHG) Annual Meeting
    Houston, USA

2018

  • Introduction to R Markdown

    May 9, 2018, Montreal Bioinformatics User Group
    Montreal, Canada Slides

2017

  • Genomic Region Visualization in R with the Gviz package

    Jan 25, 2017, Montreal Bioinformatics User Group
    Montreal, Canada Slides

2016

  • Instructor at the 4th Kyoto Course and Symposium on Bioinformatics for Next Generation Sequencing with Applications in Human Genetics.

    Mar 29, 2016, Human Genetics Dpt., McGill University
    Kyoto, Japan Slides

2014

  • Teaching Assistant for the Advanced Statistical Concepts in Genetic and Genomic Analysis course.

    Sep 1, 2014, Human Genetics Dpt., McGill University
    Montreal, Canada

  • Four-days R and Bioinformatics workshop for graduate students.

    Jul 21, 2014, System Biology Dpt., McGill University
    Montreal, Canada

Notes

I regularly write down notes about the tools and programming languages I use in a separate website. There are instructions to setup my working environment (Emacs-based) or things I don’t use often enough to remember but enough to collectively waste my time re-googling. I also put some exploratory analyses that might be helpful or interesting to some.

HippocamPlus: my second memory

Contact

  • jean.monlong@gmail.com
  • B522, INSERM IRSD U1220, CHU PURPAN, Place du Docteur Baylac, CS 60039, 31024 TOULOUSE CEDEX 3, ​FRANCE