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



Functional genetics genomics boot camp trainingCourse at capacity! Join the waitlist below for the next live-stream, remote Functional Genetics Boot Camp: July 9-10, 2020!


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 2020 dates: Live-stream, online training July 9-10, 2020; 10:00am - 5:00pm EDT

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.


Towfique Raj, PhD, Icahn School of Medicine at Mount Sinai. Dr. Raj is an Assistant Professor at Icahn School of Medicine at Mount Sinai. His research focuses on integration of genomic and functional genomics data to understand molecular mechanisms of Alzheimer’s disease and other neurological diseases.


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.

FORmer Keynote speakers and Instructors

Christopher (Casey) Brown, PhD, University of Pennsylvania; Keynote Speaker, 2019.

Sarah Kim-Hellmuth, PhD, Columbia University & New York Genome Center; Instructor, 2019.

David Knowles, PhD, Columbia University & New York Genome Center; Instructor, 2019.


Scholarships are available for the Functional Genetics Boot Camp. 


COVID-19 Update: The Functional Genetics Boot Camp will no longer take place in person due to the COVID-19 pandemic. The training will instead be a live-stream, remote training that takes place over live, online video on July 9-10, 2020 from 10am EDT - 5pm EDT. Please note this training is not a self-paced, pre-recorded online training.  


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


COVID-19 Update: With the training being offered virtually, we are passing along any and all costs saved to attendees.

  Early-Bird Rate (through 5/15/20 5/22/20) Regular Rate (5/16/20 5/23/20- 6/25/20) Columbia Discount*
Student/Postdoc/Trainee      $1,150  $825 $1,350 $975  10%
Faculty/Academic Staff/Non-Profit Organizations $1,350 $975  $1,550 $1,125 10%
Corporate/For-Profit Organizations $1,550 $1,125 $1,750 $1,275 NA

*Columbia Discount: This discount is valid for any active student, postdoc, staff, or faculty at Columbia University. To access Columbia discount, email​ for instructions and specify if you are paying by credit card, or internal transfer within Columbia.

Invoice Payment and Group Registrations: If you would prefer to pay by invoice/check, or would like to pay for a group of registrants, please email with details.

Registration Fee: includes course material, which will be available to all students after the workshop. 

Cancellations: For summer 2020, no administrative fees will be assessed due to the evolving COVID-19 situation. Cancellation notices must be received via email at least 14 days prior to the workshop start date in order to receive a full refund. Please email your cancellation notice to Due to workshop capacity and preparation, we regret that we are unable to refund registration fees for cancellations after these dates, unless a new COVID-19 restriction is implemented that impedes virtual attendance, in which case any registration cancellation <14 days prior to a training related to COVID-19 restriction beyond your control (institutional policy, shift in work responsibilities, etc.) will be fully refunded and no administrative fee will be assessed. Because of the significant resources required to develop these trainings, you will be asked to submit supporting documentation (e.g. employer email notice, local regulations, etc.) for any COVID-19 related cancellation <14 days before a given training.

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 In the event Columbia must cancel the event, your registration fee will be fully refunded. 




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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.