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

We regret to announce the Functional Genetics Boot Camp will not be offered in summer 2021. We recommend you check out our upcoming Quantitative Genomics training, or subscribe for updates to hear when the Functional Genetics Boot Camp will be offered again.


Functional genetics genomics boot camp trainingThe 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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Jump to:  Overview  |  Prerequisites  |   Instructors  | Testimonials  |  Additional Information


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 training, 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.


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.

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.


"The Functional Genetics Boot Camp was extremely helpful and complete.  I was pleasantly surprised by the well-organized program and interesting talks.  Dr. Lappalainen and her team made a wonderful job! I'm happy that I had the chance to attend this course." - Postdoc at the University of California, San Francisco, 2020

"The Columbia Functional Genetics Boot camp had a great mix of conceptual lectures and practical tutorials and labs. The instructors all communicated clearly and encouraged questions from participants." - Student at the University of Kentucky, 2020

"I appreciated the presenters' ability to speak clearly and explain concepts clearly. Usually trainings like these feel as if they are taught in a different language. As a non-geneticist, I was able to learn a few things. Great job!" - Postdoc at the UNC Chapel Hill, 2020

"This workshop provides very nice insight of eQTL analysis, allele specific expression analysis, GWAS and eQTL co-localization analysis, and very extensive introduction of GTEx resources. It also included keynote speakers who discussed how these techniques were used for their specific areas." - Academic Staff at the University of Maryland, 2020

"The Functional Genetics Boot Camp was a really well run course, with an outstanding dive into eQTL analysis by Dr Lappalainen that was as informative as it was entertaining. The instructors did a great job of walking you through the field from basic concepts, all the way up through advanced topics." - Academic Staff at Columbia University Irving Medical Center, 2020

"The Functional Genetics Bootcamp was an excellent crash course to the fundamentals of eQTL, ASE, and co-localization analyses. It was also an excellent opportunity to interact with other researchers interested in functional genomics and to ask questions from the leading researcher on the field. I feel very confident in continuing analyzing my own datasets!" - Postdoc attendee, 2019

"This is a great general overview on the functional genomics and various methodology, challenges, and advances. I thought it was great and I didn't have a deep background in functional genomic analyses." - Haotian W., Postdoc at Columbia Mailman School of Public Health, 2019

"I thoroughly enjoyed the Functional Genomics Bootcamp. The material was highly engaging and relevant, and the lecturers were fantastic." - William Z., MD/PhD student at the Icahn School of Medicine at Mount Sinai, 2019





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Questions? Email the Boot Camp team here.

The Functional Genetics Boot Camp is hosted by Columbia University's SHARP Program in the Mailman School of Public Health.