Publications

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

  • Current options to index, represent, and visualize annotations in a pangenome with the vg toolkit

    Sep 23, 2024, Methods for Interfacing with Graphs of Genomic Sequences Symposium
    Lille, France Details Event Slides

  • Characterising the CYP21A2 gene with Parakit

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

  • Pangenome graph construction from genome alignments with Minigraph-Cactus

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

2019

  • Genotyping structural variants in pangenome graphs using the vg toolkit

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

  • Genome variation graphs with the vg toolkit

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

  • Genotyping structural variants in pangenome graphs using the vg toolkit

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

2017

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

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

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

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

2014

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

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

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

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

Teaching

2024

  • Recent advances in human pangenomics

    Dec 5, 2024, Journées Pangénomes, BioinfOmics (INRAE)
    Toulouse, France Event

  • Massive Genomic Data: Statistical and Bioinformatic advances

    Sep 16, 2024, Atelier INSERM
    Bordeaux/Brest, France Event Slides Video

  • HPRC workshop

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

2023

  • HPRC workshop

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

2019

  • GRC-GIAB workshop

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

2018

  • Introduction to R Markdown

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

2017

  • Genomic Region Visualization in R with the Gviz package

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

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.

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