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Jesse Gillis

Jesse Gillis

Associate Professor

Ph.D., University of Toronto, 2007

jgillis@cshl.edu | (516) 422-4041

Gillis Lab

Of the tens of thousand of protein-coding genes in the human genome, only a small portion have an experimentally defined function. For the rest, how can we determine what they do? My lab develops computational predictions based on co-expression networks. We are applying our predictions to understand neuropsychiatric disorders.

There has been a growing appreciation in recent years that gene function is frequently context-dependent, with a large part of that context provided by the activities of other genes. But trying to understand how genes interact to produce function is a hugely complicated problem and one that appears likely to become more so as genomic information becomes more detailed. Jesse Gillis and colleagues are computational biologists who are presently challenging an oft-taken approach to the problem in which the functions of genes are interpreted in the context of networks derived from gene association data. Such networks consist of millions of interactions across thousands of genes, derived from protein-binding assays, RNA coexpression analysis, and other sources. Historically, many attempts to understand gene function through networks have leveraged a biological principle known as “guilt by association.” It suggests that genes with related functions tend to share properties (e.g., physical interactions). In the past decade, this approach has been scaled up for application to large gene networks, becoming a favored way to grapple with the complex interdependencies of gene functions in the face of floods of genomics and proteomics data. Gillis’ work centers on identifying the limits of the approach and making fundamental improvements to its operation, as well as applying those improvements to neuropsychiatric gene network data.

    NIH grant awarded for interneuron research

    NIH grant awarded for interneuron research

    April 4, 2019

    Dr. Maggie Crow, a CSHL postdoctoral researcher in quantitative biology, has been awarded a National Institutes of Health (NIH) grant for her research at the intersection of genomics, neuroscience, and computer science. Crow, who is affiliated with Associate Professor Jesse Gillis’ lab, will use the grant for her project studying interneurons, which she likens to...


    Genetic ‘usual suspects’ identified in researchers’ new list

    Genetic ‘usual suspects’ identified in researchers’ new list

    March 4, 2019

    Cold Spring Harbor, NY — It’s no secret that our genes are what makes us… us! But genes are often also the basis for debilitating diseases. One of the major clues to understanding any illness is seeing which genes are acting unusually during disease onset. But it’s not often clear if unusual gene activity is...


    Portrait of a Neuroscience Powerhouse

    Portrait of a Neuroscience Powerhouse

    April 27, 2018

    At noon every Tuesday from September through June, scenes from a revolution in neuroscience are playing out at Cold Spring Harbor Laboratory. Week after week, over 100 scientists cram themselves into a ground-floor meeting room in the Beckman Laboratory. It’s standing-room only as everyone in the Neuroscience Program settles in to hear details of the...


    New leadership roles in BRAIN Initiative and International Brain Lab reflect CSHL’s excellence in neuroscience

    New leadership roles in BRAIN Initiative and International Brain Lab reflect CSHL’s excellence in neuroscience

    October 24, 2017

    Cold Spring Harbor, NY — The National Institute of Mental Health (NIMH) yesterday announced multiple grant awards totaling $50 million per year for five years to fund cutting-edge research on the brain. The project, part of the BRAIN Initiative Cell Census Network (BICCN) of the National Institutes of Health (NIH), establishes a Center and a...


Crow, M. and Lim, N. and Ballouz, S. and Pavlidis, P. and Gillis, J. (2019) Predictability of human differential gene expression. Proc Natl Acad Sci U S A,

Crow, M. and Gillis, J. (2018) Co-expression in Single-Cell Analysis: Saving Grace or Original Sin?. Trends Genet, 34(11) pp. 823-831.

Ballouz, S. and Dobin, A. and Gingeras, T. R. and Gillis, J. (2018) The fractured landscape of RNA-seq alignment: the default in our STARs. Nucleic Acids Res,

Crow, M. and Paul, A. and Ballouz, S. and Huang, Z. J. and Gillis, J. (2018) Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. Nat Commun, 9(1) pp. 884.

Ballouz, S. and Gillis, J. (2017) Strength of functional signature correlates with effect size in autism. Genome Med, 9(1) pp. 64.

Additional materials of the author at
CSHL Institutional Repository