Jack Humphrey

I am a geneticist and computational RNA biologist working to understand neurodegeneration. I study the genetic factors that cause diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer’s disease. I develop and apply computational tools to measure gene expression, mRNA splicing, and genetic variation, as well as statistical methods to integrate multiple types of genomic data.

Education

University College London | London, UK
   Ph.D. Clinical Neuroscience | September 2014 - February 2019
      Mentors: Adrian Isaacs, Pietro Fratta & Vincent Plagnol
   MSci Natural Sciences | September 2010 - July 2014
      Mentor: John Wood

Experience

Icahn School of Medicine at Mount Sinai | New York City, USA
   Instructor | November 2021 - Present
   Postdoctoral Fellow | February 2019 - November 2021
      Mentor: Towfique Raj
Inivata | Cambridge, UK
   Computational Scientist | January 2018 - March 2018
Stanford University | Palo Alto, USA
   Visiting Student Researcher, Pritchard Lab | February 2017 - May 2017
Justus Liebig University | Giessen, Germany
  DAAD RISE Scholar, Diener Lab | June 2012 - August 2012

Skills

Programming languages I like:
   R, Python, Bash, AWK
Tools I use a lot:
   ggplot2, dplyr, snakemake, Shiny, STAR, samtools, vcftools, plink, tensorQTL, SQANTI, Inkscape
Software I wrote/co-wrote:
    NYGC ALS Consortium Spinal Cord Browser
    leafcutter
    leafviz
    sqtlviztools
    cryptex

Selected Publications

Humphrey J, Brophy E, Kosoy R, Zeng B, Coccia E, Mattei D, Ravi A, Efthymiou AG, Navarro E, Muller BZ, Snijders GJ, Allan A, Münch A, Kitata RB, Kleopoulos SP, Argyriou S, Shao Z, Francoeur N, Tsai CF, Gritsenko MA, Monroe ME, Paurus VL, Weitz KK, Shi T, Sebra R, Liu T, de Witte LD, Goate AM, Bennett DA, Haroutunian V, Hoffman GE, Fullard JF, Roussos P, Raj T. Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing. (2023) medRxiv

Humphrey J, Venkatesh S, Hasan R, Herb JT, de Paiva Lopes K, Küçükali F, Byrska-Bishop M, Evani US, Narzisi G, Fagegaltier D, NYGC ALS Consortium, Sleegers K, Phatnani H, Knowles DA, Fratta P, Raj T. Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes. (2023) Nature Neuroscience

Brown A, Wilkins OG, Keuss MJ, Hill SE, Zanovello M, Lee WC, Lee FCY, Masino L, Qi YA, Bryce-Smith S, Bampton A, Gatt A, Phatnani H, NYGC ALS Consortium, Schiavo G, Fisher EMC, Raj T, Secrier M, Lashley T, Ule J, Buratti E, Humphrey J, Ward ME, Fratta P. TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A. (2022) Nature

Hasan R†, Humphrey J†, Bettencount C, NYGC ALS Consortium, Lashley T, Fratta P, Raj T. Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions. (2022) Acta Neuropathologica

Lopes KP†, Snijders GJL†, Humphrey J†, Allan A, Sneeboer M, Navarro E, Schilder BM, Vialle RA, Parks M, Missall R, van Zuiden W, Gigase F, Kübler R, van Berlekom AB, Böttcher C, Priller J, Kahn RS, de Witte LD, Raj T. Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies. (2022) Nature Genetics

Jack Humphrey

I am a geneticist and computational RNA biologist working to understand neurodegeneration. I study the genetic factors that cause diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer’s disease. I develop and apply computational tools to measure gene expression, mRNA splicing, and genetic variation, as well as statistical methods to integrate multiple types of genomic data.

Education

University College London | London, UK
   Ph.D. Clinical Neuroscience | September 2014 - February 2019
      Mentors: Adrian Isaacs, Pietro Fratta & Vincent Plagnol
   MSci Natural Sciences | September 2010 - July 2014
      Mentor: John Wood

Experience

Icahn School of Medicine at Mount Sinai | New York City, USA
   Instructor | November 2021 - Present
   Postdoctoral Fellow | February 2019 - November 2021
      Mentor: Towfique Raj
Inivata | Cambridge, UK
   Computational Scientist | January 2018 - March 2018
Stanford University | Palo Alto, USA
   Visiting Student Researcher, Pritchard Lab | February 2017 - May 2017
Justus Liebig University | Giessen, Germany
  DAAD RISE Scholar, Diener Lab | June 2012 - August 2012

Skills

Programming languages I like:
   R, Python, Bash, AWK
Tools I use a lot:
   ggplot2, dplyr, snakemake, Shiny, STAR, samtools, vcftools, plink, tensorQTL, SQANTI, Inkscape
Software I wrote/co-wrote:
    NYGC ALS Consortium Spinal Cord Browser
    leafcutter
    leafviz
    sqtlviztools
    cryptex

Selected Publications

Humphrey J, Brophy E, Kosoy R, Zeng B, Coccia E, Mattei D, Ravi A, Efthymiou AG, Navarro E, Muller BZ, Snijders GJ, Allan A, Münch A, Kitata RB, Kleopoulos SP, Argyriou S, Shao Z, Francoeur N, Tsai CF, Gritsenko MA, Monroe ME, Paurus VL, Weitz KK, Shi T, Sebra R, Liu T, de Witte LD, Goate AM, Bennett DA, Haroutunian V, Hoffman GE, Fullard JF, Roussos P, Raj T. Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing. (2023) medRxiv

Humphrey J, Venkatesh S, Hasan R, Herb JT, de Paiva Lopes K, Küçükali F, Byrska-Bishop M, Evani US, Narzisi G, Fagegaltier D, NYGC ALS Consortium, Sleegers K, Phatnani H, Knowles DA, Fratta P, Raj T. Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes. (2023) Nature Neuroscience

Brown A, Wilkins OG, Keuss MJ, Hill SE, Zanovello M, Lee WC, Lee FCY, Masino L, Qi YA, Bryce-Smith S, Bampton A, Gatt A, Phatnani H, NYGC ALS Consortium, Schiavo G, Fisher EMC, Raj T, Secrier M, Lashley T, Ule J, Buratti E, Humphrey J, Ward ME, Fratta P. TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A. (2022) Nature

Hasan R†, Humphrey J†, Bettencount C, NYGC ALS Consortium, Lashley T, Fratta P, Raj T. Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions. (2022) Acta Neuropathologica

Lopes KP†, Snijders GJL†, Humphrey J†, Allan A, Sneeboer M, Navarro E, Schilder BM, Vialle RA, Parks M, Missall R, van Zuiden W, Gigase F, Kübler R, van Berlekom AB, Böttcher C, Priller J, Kahn RS, de Witte LD, Raj T. Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies. (2022) Nature Genetics