Publications

  • 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
    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
    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
  • 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
  • The human transcriptome across tissues and individuals. Science 2015.
    M Melé, P G Ferreira, F Reverter, D S DeLuca, J Monlong, M Sammeth, …, The GTEx Consortium
  • The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science 2015.
    The GTEx Consortium
  • Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nature Communications 2015.
    D Pervouchine, S Djebali, A Breschi, C A Davis, P P 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
  • Identification of genetic variants associated with alternative splicing using sQTLseekeR. Nature Communications 2014.
    J Monlong, M Calvo, P G Ferreira, R Guigó
  • Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia.. Genome research 2014.
    P G Ferreira, P Jares, D Rico, G Gomez-Lopez, A Martinez-Trillos, N Villamor, S Ecker, A Gonzalez-Perez, D G Knowles, J Monlong, …, E Campo, R Guigo
  • Transcriptome and genome sequencing uncovers functional variation in humans. Nature 2013.
    T Lappalainen, M Sammeth*, M R Friedlander*, P A t Hoen*, J Monlong*, M A Rivas*, et al.
  • 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

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).

Talks

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:

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