Epigenetics Boot Camp: Planning and Analyzing DNA Methylation Studies


Epigenetics Boot Camp Training 1080The most recent live-stream Epigenetics Boot Camp was June 22-23, 2020. Join the email list below to hear about the next training


The Epigenetics Boot Camp is a two-day intensive boot camp of seminars and hands-on analytical sessions to provide an overview of concepts, techniques, and data analysis methods utilized in human epigenetics studies.       

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Summer 2020 dates: Live-stream, online training June 22-23, 2020; 10:00am EDT - 5:00pm EDT

This two-day intensive boot camp integrates the principle concepts of epigenetics and the effects of risk factors on the epigenome as we step through the key components of designing and executing DNA methylation studies. Led by a team of scientists with more than 40 years of combined expertise in the field of environmental epigenetics, this epigenetics training will integrate seminar lectures with hands-on computer sessions to put concepts into practice. Emphasis will be given to leveraging existing resources from ongoing studies and initiating new investigations. The afternoon lab sessions will provide an opportunity to work hands-on with real methylation data generated by the Illumina Infinium MethylationEPIC (850k) BeadChip platform. Participants will learn and practice data handling, cleaning, and basic analysis of epigenome-wide DNA methylation data.

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

  • Principles of epigenetics
  • Concept ideation and study design
  • Sample collection and processing
  • Laboratory methods and platforms for analysis
  • Data handling and cleaning
  • Data analysis
  • Study design advantages and pitfalls
  • Emerging epigenetic topics and laboratory platforms

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


  1. Each participant is required to bring a personal laptop as all lab sessions will be done on your personal laptop. Tablets and ipads will not work with the platform being used.

  2. The Boot Camp will use data sets in R, therefore participants must have a basic understanding of this platform prior to attending the Boot Camp. If you have never used this platform before, make sure to step through all the tutorials outlined below so you have the basic skills needed for Boot Camp success.


Knowing basic R platform and commands is required for the Boot Camp as noted in prerequisites above. If you are new to R or need a refresher, you can review the below tutorials to be well prepared:

If you have any specific questions about R and R studio in the context of the Epigenetics Boot Camp, please email us.


John Greally, DMed, PhD, Center for Epigenomics, Albert Einstein College of Medicine.


Andrea Baccarelli, MD, MPH, PhD, Mailman School of Public Health, Columbia University 

Andres Cardenas, PhD, MPH, School of Public Health, University of California, Berkeley

Elena Colicino, PhD, Icahn School of Medicine at Mount Sinai

Jonathan Heiss, PhD, Icahn School of Medicine at Mount Sinai

Allison Kupsco, PhD, Mailman School of Public Health, Columbia University 

Learn more about each instructor here.


Allan Just, PhD, Icahn School of Medicine at Mount Sinai, 2017-2019.

Chris Mason, PhD, Weill Cornell Medical College. Keynote Speaker, 2017.

John Greally, DMed, PhD, Center for Epigenomics, Albert Einstein College of Medicine. Keynote Speaker, 2017-2018.

Cavin Ward-Caviness, PhD, Environmental Public Health Division, US Environmental Protection Agency. Instructor, 2017.

Kasey Brennan, MS, Mailman School of Public Health, Columbia University. Instructor, 2017-2018.


Scholarships are available for the Epigenetics Boot Camp. 


COVID-19 Update: The Epigenetics Boot Camp will no longer take place in person due to the COVID-19 pandemic. The Boot Camp will instead be a live-stream, remote training that takes place over live, online video on June 22-23, 2020 from 10am EDT - 5pm EDT. Please note this training is not a self-paced, pre-recorded online training. 


The level of knowledge and experience as well as careful planning by all instructors made the entire two-day experience worthwhile. Best applied training I have been to, I now feel equipped to work with my own data and collaborate with bioinformatics colleagues in cleaning and analyzing our data.​ Dr. Kristen M., Faculty Member at University of Wisconsin-Madison, 2017 

Overall, I found the Epigenetics Boot Camp to be a very useful and comprehensive tool for learning basic principles surrounding DNA methylation analysis and interpretation. It provided a good foundation from which to build upon as I advance my knowledge in this field. - Postdoc at Emory University, 2017

I feel like I was catapulted to the forefront of the field of epigenetics for a stunning view of where the field is going. The workshop gave me clear tools and a roadmap of how to follow the brilliant minds who are leading the way. - Postdoc at Columbia University Medical Center, 2018

The Boot Camp gives a very comprehensive overview of the epigenetic research with enough technical details that all levels of participants will find informative and educational. I especially appreciate how knowledgeable the speakers are. Thank you for putting such a great workshop together! - Staff Member at Harvard University, 2017 

The Epigenetics Boot Camp was an inspiring and very helpful introduction enabling me to grasp the basics of both planning and analyzing epigenetic data. Because of the excellent instructors, one-to-one attention, and clear materials for the lectures and data-labs it was a brilliant learning experience. I would definitely recommend the epigenetics Boot Camp for anyone starting in the field of epigenetics! - Elize V., Student at Erasmus Medical Center, Rotterdam, the Netherlands, 2017  

As someone new to epigenetics, this workshop provided a great introduction to key concepts and strategies that will allow me to effectively implement epigenetic data into my research. - Student at Virginia Commonwealth University, 2018

The Boot Camp offers a great balance of introductory concepts in epigenetics with detailed strategies in data analysis. The presentation content is well organized, and the tools provided by the course are practical and helpful to conduct epigenetic studies, even for those new to epigenetics. - Lisa S., Faculty Member at Emory University, 2017

This was a very useful, all-encompassing dive into the epidemiologic methods required for epigenome-wide DNA methylation analyses.  The instruction was high-quality, and there was a strong lab component that supported application of skills to real-world data.  I would only hope for a part 2 to this quick course. - Alonzo F., Faculty Member at Cincinnati Children's Hospital Medical Center, 2018

Impressive bootcamp that included a helpful overview for newbies like myself, but also tons of detail for more experienced users. - Anonymous Faculty member, 2019

The Epigenetics Boot Camp was a great intro to epigenetics and how to work with epigenetic data. I am so much more confident heading into my dissertation, and working on the epigentics aim, after this program. - Jennifer W., UW-Milwaukee, PhD Candidate - Epidemiology, 2019

This bootcamp was extremely well-organized and presenters were incredibly knowledgeable about the topics they discussed. It is a deep dive into the technical details of DNA methylation assays, as well as the data gathering and analysis from these assays. I plan to return next year in hopes that I can understand and utilize even more of what was presented. - Anna R., University of Cincinnati, Postdoc Fellow, 2019

The instructors were friendly and enthusiastic. The material and activities were accessible and the format allowed participants to engage at their desired level. - Dawn M., Wayne State University, Professor, 2019

The boot camp provided a great overview of important considerations from study conception through design, analysis, and interpretation. The provided information would be useful to researchers with all levels of experience in methylome analyses. -  Mark G., American Cancer Society, Postdoc Fellow


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

  Early-Bird Rate (through 4/15/20 4/22/20) Regular Rate (4/16/20 4/23/20-5/31/20) 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 Columbia.EBC@gmail.com 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 Columbia.EBC@gmail.com with details.

Registration Fee: Fee includes course material. Course material 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 Columbia.EBC@gmail.com. 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 Columbia.EBC@gmail.com. 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 Epigenetics Boot Camp is hosted by Columbia University's Department of Environmental Health Sciences in the Mailman School of Public Health with additional support from Zymo ResearchDiagenode, and Illumina, Inc.

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