Jeremy Schwartzentruber
Jeremy Schwartzentruber

Postdoctoral Fellow in neurodegenerative disease genetics at European Bioinformatics Institute

Cambridge, United Kingdom

  • Focus: Contributions are valued by peers
  • Accountability: Thoroughly contributes in all areas
  • Sense of Urgency: Consistently responds in a timely fashion
  • Team: Frequently supports and responds to peers

Awards earned:





Level: LEVEL 01

12 month points: 5 ptsView details

Lifetime points: 10 pts

Gene expression regulation
QTL mapping
fine mapping
R programming
BASH scripting
Cluster Computing
Exome-seq data analysis
Cancer Genomics
Rare Diseases


I am a genomic scientist with broad experience across different technologies and disease areas. My PhD at the Wellcome Sanger Institute focused on using iPSC-derived cells as models for complex diseases, as well as statistical modelling to predict causal genetic variants influencing gene expression in human tissues. Prior to this I was the lead bioinformatician for the Canada-wide rare disease sequencing projects FORGE and Care4Rare, where we identified causal gene disruptions for over 50 rare diseases. As a postdoctoral fellow at EMBL-EBI, I now work to fine-map causal genetic variants for Alzheimer's and Parkinson's diseases, using gene expression, epigenomic annotations, and iPSC-derived cell models. Having previously studied computer science and worked as a software engineer, I maintain an interest in machine learning and follow developments in the field of relevance to genomics and health.


Postdoctoral Fellow

European Bioinformatics Institute | EMBL-EBI

October 2017 - Present

As a postdoctoral fellow at EBI, I work as part of a collaboration between academic and industrial partners to use genomics to identify potential therapeutic targets for Alzheimer's and Parkinson's diseases. Specifically I integrate genomic and epigenomic datasets to identify causal genetic variants and genes leading to neurodegenerative disease risk. For variants that I identify, members of the team use CRISPR-Cas9 genome editing to investigate the causal effects of these variants on gene expression or other molecular phenotypes.

Ph.D. in Genomics

Wellcome Sanger Institute

October 2013 - October 2017

Thesis: "Using molecular QTLs to identify cell types and causal variants for complex traits"
Among projects during my PhD, I analyzed RNA-sequencing from 123 cell lines differentiated from iPSCs to sensory neurons, and identified genetic variants influencing gene expression in this cell type. I discovered factors in the iPSCs which led to differential gene expression in the derived neurons, and determined how the variability in expression among the neurons impacted on power to detect genetic effects of common gene regulatory variants. I identified gene regulatory variants that were also associated with complex traits from prior genome-wide association studies. This work was published in Nature Genetics. In addition to this, I developed a machine-learning model that uses summary statistics from gene expression studies, along with genetic and epigenetic annotations, to predict the location of causal gene regulatory variants. I then applied these cell type-specific genome-wide regulatory scores to determine strongly associated cell types for a number of complex diseases.

Lead Bioinformatician

Genome Quebec & McGill University

December 2010 - September 2013

As lead Bioinformatician for the Canada-wide rare disease projects FORGE and Care4Rare, I analyzed human exome sequencing data from rare disease patients and unaffected family members to identify the disease-causing mutations. I worked across many stages of the analysis, from developing software pipelines to process sequencing data, to annotating genetic variants and causal genes, to communicating with the medical genetic teams responsible for the patients. In addition to rare diseases, I worked with specific collaborators to analyze cancer genomes from pediatric cancer patients. One of our key findings was the discovery of mutations at specific sites in histone proteins in pediatric glioblastoma and other brain cancers, published in Nature (2012).

Lead Bioinformatician

Wellcome Sanger Institute

October 2012 - September 2013

In the group of Eleftheria Zeggini, I worked (part-time) on variant calling and imputation pipelines for complex trait association studies using very low depth whole genome sequencing in thousands of individuals

M.Sc. in Biophysics

McGill University

September 2008 - August 2010

Thesis title: "Fourier-space analysis methods for measuring molecular diffusion and flow from fluorescence microscopy image time series." Supervised by Prof. Paul Wiseman.

Undergraduate studies in biology & chemistry

McGill University

September 2006 - May 2008

I spent 2 years in additional full-time undergraduate studies in biology and chemistry, achieving a 4.0 GPA.

Lead software engineer

Action Engine Corp, Redmond, WA

May 2003 - January 2006

Led a team of five engineers and graphic designers creating applications to deliver data services to smart phones. Wrote server-based code using C#, XML, XSLT.

Lead software engineer

HealtheTech Inc.

January 2001 - April 2003

Developed applications for PalmOS devices using C++, which were optimized for quick data retrieval from a large database on resource-limited mobile devices.

Software engineer

RealNetworks, Seattle, WA

January 2000 - December 2000

Developed a multi-threaded HTTP communications module used by the RealPlayer.

Software Engineer

Golder Associates, Redmond, WA

June 1998 - October 1999

Developed the core user-interface features and data structures for a Monte-Carlo simulation program to model contaminant transport.

B.Sc. (honours) in Computer Science

University of Victoria

September 1994 - August 1998

I did an honours B.Sc. in computer science, while doing a co-op internship program, and completed the program 8 months ahead of schedule, achieving a 4.0 GPA. I received the inaugural Department of Computer Science graduation medal.