Transformative Collaborative Pilot Project Initiative

We are no longer accepting letters of interest for 2018. Thank you to those who submitted.

The Center for Epigenomics at the University of California San Diego (UCSD) is pleased to invite academic investigators to partner with us as part of our Transformative Collaborative Pilot Project initiative. The goal of which is to stimulate groundbreaking and collaborative research, between San Diego investigators and the newly founded Center for Epigenomics. This research will use epigenomic concepts and technologies to make transformative discoveries which advance science and human health.

Each calendar year, the center will partner with academic investigators from the San Diego research community to initiate three or more transformative collaborative pilot projects. As part of this program, the Center for Epigenomics will commit up to $100,000 in resources to each collaborative pilot project (in the form of epigenomic assays, reagents, personnel effort, etc.). We are pleased to announce that we are now taking applications for collaborative pilot projects for 2018. Investigators are invited to submit letters of interest describing potential collaborative pilot projects; deadline for submission is March 9th, 2018. Download a copy of this RFA. View frequently asked questions.

ABOUT THE CENTER FOR EPIGENOMICS: The Center for Epigenomics, founded in 2017, applies cutting-edge epigenomic technologies to make transformative discoveries which advance science and human health. The Center examines multiple aspects of the epigenome, including chromatin accessibility, transcription factor binding, histone modification, and 3D chromatin architecture, in a wide variety of sample types and at single-cell resolution. Specific technologies routinely employed at the Center include ATAC-seq, ChIP-seq, Hi-C, PLACseq, single-cell RNA-seq, and single-cell ATAC-seq.

ABOUT THE COLLABORATIVE PILOT PROJECTS: Collaborative pilot projects between the Center for Epigenomics and investigators in the San Diego area will seek to answer important questions related to biomedical science and human health. These projects should build on each participant's unique strengths to collaboratively achieve results beyond the capabilities of any single participant. The Center for Epigenomics will commit up to $100,000 in resources to each collaborative pilot project (in the form of epigenomic assays, reagents, personnel effort, etc.). In accordance with the collaborative nature of these projects, successful applicants will be expected to likewise commit considerable resources. The ideal collaborative project with the Center for Epigenomics will:

  • Focus on solving an important problem or answering an impactful question related to biomedical science and/or human health.
  • Have strong potential to develop into joint large-scale external funding applications and publications within 1-2 years.
  • Require significant intellectual and material investment from both the collaborator and the Center.
    Take advantage of new research opportunities created by collaboration with the Center for Epigenomics.

At least 3 collaborative pilot projects will be initiated in 2018.

HOW TO EXPRESS INTEREST: Investigators are invited to submit letters of interest, which will be reviewed by Center for Epigenomics leadership to ensure alignment with the Center’s mission and capabilities. Letter of interest should be sent to by 5 PM, March 9th, 2018. Up to 10 Investigators will then be invited to construct short proposals, with feedback from the Center's staff; these proposals will then be reviewed by an external committee for final selection.

Phase I – Letter of Interest

A letter of interest should not exceed one page in length and should be accompanied by an NIH Biosketch(es) of the investigator(s). Up to one additional page of figures, tables, and/or references may also be submitted but is not required. The letter should clearly and succinctly describe:

  • The question to be answered or problem to be solved (including background and significance). 
  • A description of specific goals for the pilot phase of the project.
  • A brief mention of why collaboration with the Center for Epigenomics is important. 
  • A succinct discussion of the current stage of the project and potential growth beyond the pilot phase (1-2 years), if successful. 

A budget is not required at the time of the letter of interest, but the scope of the pilot project should reflect the resources available at this stage: the Center for Epigenomics will invest up to $100K in resources, and expects substantial – and, if possible, roughly equivalent – resources committed by the collaborator.

The letter should also consider the specific technologies and associated analytical tools routinely employed at the Center for Epigenomics. Extra consideration will be given to projects that take advantage of the Center’s automated ATAC-seq platform capable of processing up to 96 samples in parallel, and/or the Center’s single-cell RNA-seq and single-cell ATAC-seq capabilities.

Letters of Interest will be reviewed by the Center’s executive committee consisting of the Center’s Director and Associate Directors based on the following criteria:

  • Alignment with the mission of the Center for Epigenomics
  • Leveraging of Center for Epigenomics resources

Phase II – Full application

Between 5 and 10 Letters of Interest will be selected, and these investigators will be invited to submit a 3-4-page NIH style expanded application as well as a budget. During the preparation of these applications, applicants will work with investigators at the Center for Epigenomics who will provide feedback and consultation. This application will be reviewed by an external review committee based on the same criteria as above as well as additional criteria detailed below:

  • Scientific merit
  • Innovation and potential impact
  • Potential for large-scale extramural funding
  • Feasibility of the proposed research given the budget and relevant qualifications of the investigative team

Based on this review, 3 or more pilot projects will be selected. Further details regarding phase II of this process will be provided at the time of selection.

ELIGIBILITY: Applicants must be full-time faculty members at UC San Diego, or at one of the UC San Diego partner institutions, including but not limited to the Salk Institute; Sanford Burnham Prebys Medical Discovery Institute; Scripps Research Institute; La Jolla Institute for Allergy and Immunology; and Rady Children's Hospital.

QUESTIONS: For additional information or assistance with questions regarding this program and letters of interest, please contact Dr. Allen Wang.

All documents should be submitted as one PDF to by 5:00 PM, Friday, March 9th, 2018