Transformative Collaborative Pilot Project Initiative


Letter of Interest Due Date:  March 22nd, 2019

The Center for Epigenomics – Transformative Collaborative Pilot Project Initiative 2019

The Center for Epigenomics at UC San Diego is pleased to invite academic investigators to partner with us as part of our Transformative Collaborative Pilot Project Initiative. The goal of this program is to stimulate groundbreaking and collaborative research between San Diego investigators and the Center for Epigenomics. This research will use epigenomic concepts and technologies to make transformative discoveries which advance science and human health. To this end, we are now taking applications for three or more collaborative projects; these projects are expected to lead to joint large-scale grant applications and publications. 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 likewise be expected to commit considerable resources. Early stage investigators are strongly encouraged to apply.

Investigators are invited to submit letters of interest describing potential collaborative pilot projects; deadline for submission is March 22nd, 2019.

A downloadable version of this RFA is available here.

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 and histone modifications in a wide variety of sample types and at single-cell resolution. Specific technologies routinely employed at the Center include ATAC-seq, ChIP-seq, single-cell RNA-seq, and single-cell ATAC-seq. For more information, see

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 strengths to collaboratively achieve results beyond the capabilities of any single participant.  The ideal collaborative project with the Center for Epigenomics will:

  • Address an important problem or answering an impactful question related to biomedical science and human health.
  • Be feasible within the 1-year timeframe.
  • Have strong potential to yield 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 three collaborative pilot projects will be initiated in 2019.

HOW TO EXPRESS INTEREST: Investigators are invited to submit letters of interest, which will be reviewed by the Center for Epigenomics leadership to ensure alignment with the Center's mission and capabilities. 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 references may also be submitted but is not required. All documents should be sent as one PDF to by March 22nd, 2019. The letter should clearly and succinctly describe:
  1. The question to be answered or the problem to be solved (including background and significance).
  2. A description of the specific goals for the pilot phase of the project.
  3. 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 year), 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: 1) the specific technologies and associated analytical tools routinely employed at the Center for Epigenomics (see 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 the Center's single-cell RNA-seq and single-cell ATAC-seq capabilities. Projects involving the development or implementation of particularly promising new technologies will also be considered. 2) Data analysis, with mention of key avenues to be pursued and thought given to bioinformatics expertise and resources.   

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 and timeline. 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
  • The potential for large-scale extramural funding and future growth
  • Feasibility of the proposed research given the budget, timeline, and relevant qualifications of the investigative team. Reviewers will consider the feasibility of plans for both wet bench experimentation and data analysis.

Based on this review, 3 or more pilot projects will be selected. We will provide further details regarding phase II of this process 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; Rady Children's Hospital; and J. Craig Venter Institute. Extra consideration will be given to early stage investigators.

All phase I documents should be submitted as one PDF to <> by 5:00 PM, Friday, March 22nd, 2019

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