Functional Genetics Boot Camp: Computational Integration of Genome and Transcriptome Data

Most recent Functional Genetics Boot Camp in NYC: June 27-28, 2019. Join our email list below to hear about the next training!


The Functional Genetics Boot Camp is a two-day intensive boot camp of seminars and hands-on analytical sessions to provide an overview of concepts and data analysis methods for computational integration of genome and transcriptome data to characterize molecular effects of genetic variants.     



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Summer 2019 dates: June 27-28, 2019; 9:00am - 5:00pm

Genetic studies in humans have led to discovery of thousands of loci and variants that associate to diverse traits and diseases. However, especially for variants in the noncoding genome, interpretation of functional effects of these variants has been a challenge. One of the approaches to address this challenge has been large-scale analysis of functional genomics data from human samples.

This two-day intensive workshop will provide a rigorous introduction to concepts and analytical methods to map and characterize molecular effects of genetic variants by integration of large-scale genetic and transcriptome data. Led by world experts in functional genomics, human genetics, and statistical methods development, the workshop will integrate seminar lectures with hands-on computer lab sessions to put concepts into practice. The workshop will focus on genetic effects on gene regulation, and guide the participants not only in analytical methods but also the use of major resource data sets like GTEx. 

By the end of the workshop, participants will be familiar with the following topics:

  • Genetic association to gene expression by eQTL analysis
  • Allele-specific expression analysis
  • Basics of processing of population-scale RNA-seq data sets
  • Integration of GWAS and eQTL data
  • Genetic effects on other epigenomic and transcriptomic traits
  • Functional interpretation of rare disease-associated variants

Investigators at all career stages are welcome to attend, and we particularly encourage trainees and early-stage investigators to participate.


There are three prerequisites/requirements to attend this training:

  1. Each participant must have an introductory background in human genetics and genomics (genetic variants, GWAS, gene expression)
  2. Each participant must be familiar with R.
  3. Each participant must bring a laptop with R downloaded and installed prior to the first day of the workshop. R is available for free download and installation on Mac, PC, and Linux devices.   

If you have any specific questions about R in the context of the Functional Genetics Boot Camp, please email us.


The Functional Genetics Boot Camp will take place on the Columbia University Medical Center (CUMC) Campus in New York City, specifically at Columbia Mailman School of Public Health, 722 W. 168th Street, Allan Rosenfield Building 8th Floor Auditorium. Please note that the entrance to the building is on the 10th floor (training is located two floors below entrance).

General transportation and lodging information can be found in the Getting Around sectionA PDF map of the 2019 Boot Camp location on the CUMC campus will be available closer to training dates. 


Christopher (Casey) Brown, PhD, University of Pennsylvania. Dr. Brown is an Assistant Professor at the Department of Genetics at University of Pennsylvania. He is a leading expert in analysis of functional human non-coding sequence variation using both experimental and computational approaches.


Training Director: Tuuli Lappalainen, PhD, Columbia University & New York Genome Center. Dr. Lappalainen is an Assistant Professor at the Department of Systems Biology at Columbia University and at the New York Genome Center. Her research focuses on molecular effects of genetic variants by integration of genome and transcriptome data sets.

François Aguet, PhD, Broad Institute. Dr Aguet is a postdoctoral researcher at the Broad Institute. He is a lead analyst of the Genotype Tissue Expression project, and a specialist in processing very large data sets in human genomics.

Sarah Kim-Hellmuth, PhD, Columbia University & New York Genome Center. Dr. Kim-Hellmuth is a Postdoctoral Research Scientist at the Department of Systems Biology at Columbia University and at the New York Genome Center. Her research focuses on human genetic variation and its effects on cellular functions linked to infectious and autoimmune disease. 

David Knowles, PhD, Columbia University & New York Genome Center. Dr. Knowles is an Assistant Professor at the Department of Computer Science at Columbia University and at the New York Genome Center. He develops statistical machine learning methods for interpretation of molecular effects of genetic variants.

Yufeng Shen, PhD, Columbia University. Dr Shen is an Assistant Professor at the Department of Systems Biology at Columbia University. He is an expert in computational and statistical methods to study rare disease variation in human genomes.


 Early-Bird Rate (through 4/15/19)Regular Rate (4/16/19 - 6/15/19)Columbia Discount*
Student/Postdoc/Trainee     $975$1,17510%
Faculty/Academic Staff/Non-Profit Organizations$1,175 $1,37510%
Corporate/For-Profit Organizations$1,375$1,575NA

*Columbia Discount: This discount is valid for any active student, postdoc, staff, or faculty at Columbia University. To access Columbia discount, email​ for instructions.

Registration Fee: includes course material, breakfast, lunch, and refreshment breaks. Course material will be available to all students after the workshop. Lodging and transportation are not included.  

Cancellations: Cancellation notices must be received via email at least 30 days prior to the workshop start date in order to receive a full refund, minus a $50 administrative fee. Cancellation notices received via email 14-29 days prior to the workshop will receive a 50% refund, minus a $50 administrative fee. Please email your cancellation notice to​. Due to workshop capacity, we regret that we are unable to refund registration fees for cancellations after these dates. 

If you are unable to attend the training, we encourage you to send a substitute within the same registration category. Please inform us of the substitute via email at least one week prior to the training to include them on attendee communications, updated registration forms, and materials. Should the substitute fall within a different registration category your credit card will be credited/charged respectively. Please email substitute inquiries to



Want updates on new Boot Camp details or registration deadlines? Subscribe here.

Questions? Email the Boot Camp team here.

The Functional Genetics Boto Camp is hosted by Columbia University's Department of Environmental Health Sciences in the Mailman School of Public Health.