The Encyclopedia of DNA Elements (ENCODE) (original) (raw)

ENCODE is a public research consortium aimed at identifying all functional elements in the human and mouse genomes.

Overview

ENCODE has produced vast amounts of data that can be accessed through the project's freely accessible database, the ENCODE Portal. The ENCODE "Encyclopedia" organizes these data into two levels of annotations: 1) integrative-level annotations, including a registry of candidate cis-regulatory elements and 2) ground-level annotations derived directly from experimental data.

As a result of outreach and collaboration, ENCODE data are widely used. Lists of publications using ENCODE resources can be found on the ENCODE Portal. (See ENCODE-funded Publications and Community Publications.) The ENCODE Portal also hosts data from modENCODE as well as data from the RoadMap Epigenomics and Genomics of Gene Regulation projects. Additional information about data standards and guidelines and uniform data processing can also be found on the ENCODE Portal.

The ENCODE Project started in 2003 with the ENCODE Pilot Project, which focused on 1% of the human genome and subsequently completed two additional phases (ENCODE 2 and ENCODE 3) which conducted whole-genome analyses on the human and mouse genomes. A parallel effort was devoted to whole-genome analyses of the C. elegans and D. melanogaster genomes under the modENCODE Project. In recognition of the need for new approaches, methods and technologies to achieve the goals of ENCODE, NHGRI has also funded four rounds of technology development initiatives since 2003. A number of these efforts have been incorporated into subsequent phases of ENCODE data production and analysis.

With the success of these three phases of the ENCODE Project and the recognition that additional effort was needed to complete and understand the catalog of candidate regulatory elements compiled, NHGRI funded the fourth phase of ENCODE (ENCODE 4) in February 2017 to continue and expand on its work to understand the human and mouse genomes.

• Overview
  ENCODE has produced vast amounts of data that can be accessed through the project's freely accessible database, the ENCODE Portal. The ENCODE "Encyclopedia" organizes these data into two levels of annotations: 1) integrative-level annotations, including a registry of candidate cis-regulatory elements and 2) ground-level annotations derived directly from experimental data.
  As a result of outreach and collaboration, ENCODE data are widely used. Lists of publications using ENCODE resources can be found on the ENCODE Portal. (See ENCODE-funded Publications and Community Publications.) The ENCODE Portal also hosts data from modENCODE as well as data from the RoadMap Epigenomics and Genomics of Gene Regulation projects. Additional information about data standards and guidelines and uniform data processing can also be found on the ENCODE Portal.
  The ENCODE Project started in 2003 with the ENCODE Pilot Project, which focused on 1% of the human genome and subsequently completed two additional phases (ENCODE 2 and ENCODE 3) which conducted whole-genome analyses on the human and mouse genomes. A parallel effort was devoted to whole-genome analyses of the C. elegans and D. melanogaster genomes under the modENCODE Project. In recognition of the need for new approaches, methods and technologies to achieve the goals of ENCODE, NHGRI has also funded four rounds of technology development initiatives since 2003. A number of these efforts have been incorporated into subsequent phases of ENCODE data production and analysis.
  With the success of these three phases of the ENCODE Project and the recognition that additional effort was needed to complete and understand the catalog of candidate regulatory elements compiled, NHGRI funded the fourth phase of ENCODE (ENCODE 4) in February 2017 to continue and expand on its work to understand the human and mouse genomes.

ENCODE 4

ENCODE 4 seeks to expand the catalog of candidate regulatory elements in the human and mouse genomes through the study of a broader diversity of biological samples including those associated with disease as well as by employing novel assays not used previously in ENCODE. To maximize access to ENCODE data by the research community, all data is shared in databases without controlled access. All newly obtained human biological samples are consented for unrestricted data sharing. To study the biological function of candidate regulatory elements already compiled by ENCODE, a new component, functional element characterization, has been added in ENCODE 4.

ENCODE 4 includes the following components:

• Functional Element Mapping Centers
  • Conduct high-throughput experiments that map biochemical activities to identify candidate functional elements in the human and mouse genomes.
• Functional Element Characterization Centers
  • Develop and apply generalizable approaches to characterize the role of candidate functional elements in specific biological contexts.
• Computational Analysis Groups
  • Pilot new applications of ENCODE data
• Data Coordination Center (DCC)
  • Processes and shares ENCODE metadata and data, and provide a portal for the community to visualize and download data.
• Data Analysis Center (DAC)
  • Specifies data processing pipelines and quality metrics for major data types, design and perform integrative analysis of ENCODE data to update and refine the Encyclopedia.

Read about the ENCODE Pilot Project.

• ENCODE 4
  ENCODE 4 seeks to expand the catalog of candidate regulatory elements in the human and mouse genomes through the study of a broader diversity of biological samples including those associated with disease as well as by employing novel assays not used previously in ENCODE. To maximize access to ENCODE data by the research community, all data is shared in databases without controlled access. All newly obtained human biological samples are consented for unrestricted data sharing. To study the biological function of candidate regulatory elements already compiled by ENCODE, a new component, functional element characterization, has been added in ENCODE 4.

ENCODE 4 includes the following components:

• Functional Element Mapping Centers
  * Conduct high-throughput experiments that map biochemical activities to identify candidate functional elements in the human and mouse genomes.
• Functional Element Characterization Centers
  * Develop and apply generalizable approaches to characterize the role of candidate functional elements in specific biological contexts.
• Computational Analysis Groups
  * Pilot new applications of ENCODE data
• Data Coordination Center (DCC)
  * Processes and shares ENCODE metadata and data, and provide a portal for the community to visualize and download data.
• Data Analysis Center (DAC)
  * Specifies data processing pipelines and quality metrics for major data types, design and perform integrative analysis of ENCODE data to update and refine the Encyclopedia.

Read about the ENCODE Pilot Project.

Participants and Projects

Phase 4 (Current)

Affiliate Members

Brenton Graveley,
University of Connecticut Health Center

Gene Yeo
University of California, San Diego

Guo-Cheng Yuan
Icahn School of Medicine at Mount Sinai

Alexander Dobin
Cold Spring Harbor Laboratory

Melissa Fullwood
Nanyang Technological University and Cancer Science Institute

Nir Yosef
University of California, Berkeley

Jesse Engreitz
Stanford University

Adam Siepel
Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory

Douglas Phanstiel
University of North Carolina at Chapel Hill

Feng Yue
Northwestern University

Max Libbrecht
Simon Fraser University

Jian Ma
Carnegie Mellon University

Katie Pollard
University of California, San Francisco

Past Participants and Projects

• Phase 3
• Phase 2
• Pilot

Membership

The ENCODE Consortium is composed primarily of scientists who were funded under RFAs released by NHGRI. Other participants have been identified and brought into the Consortium or Analysis Working Group (which leads the integrative analysis of ENCODE data) as appropriate. The Consortium and Analysis Working Group are open to any investigator willing to abide by the criteria for participation established for the ENCODE Project by NHGRI. The ENCODE External Consultants Panel oversees the activities of the Consortium and provides advice and feedback on the Consortium's goals, progress and membership.

Those interested in applying for membership to the ENCODE Consortium or to the ENCODE Analysis Working Group should review the criteria for participation and contact Elise Feingold, Ph.D., Dan Gilchrist, Ph.D. or Mike Pazin, Ph.D. (See: Program Staff).

• ENCODE Consortium Criteria for Participation

• ENCODE External Consultants Panel

• Projects and Partcipants (Pilot, Phase 2, Phase 3, Phase 4)

• Membership
  The ENCODE Consortium is composed primarily of scientists who were funded under RFAs released by NHGRI. Other participants have been identified and brought into the Consortium or Analysis Working Group (which leads the integrative analysis of ENCODE data) as appropriate. The Consortium and Analysis Working Group are open to any investigator willing to abide by the criteria for participation established for the ENCODE Project by NHGRI. The ENCODE External Consultants Panel oversees the activities of the Consortium and provides advice and feedback on the Consortium's goals, progress and membership.
  Those interested in applying for membership to the ENCODE Consortium or to the ENCODE Analysis Working Group should review the criteria for participation and contact Elise Feingold, Ph.D., Dan Gilchrist, Ph.D. or Mike Pazin, Ph.D. (See: Program Staff).

  • ENCODE Consortium Criteria for Participation
  • ENCODE External Consultants Panel
  • Projects and Partcipants (Pilot, Phase 2, Phase 3, Phase 4)

Informed Consent

As the ENCODE Project has increased its study of primary cells and tissues, it has begun working on human biological samples that have been explicitly consented for genomic research and unrestricted sharing of genomic data, in order to maximize the accessibility and utility of ENCODE data. This means that data can be deposited in freely accessible databases, e.g., GEO and the ENCODE Portal and shared without registration or prior approval.

The ENCODE Consortium has developed sample informed consent language that explicitly asks for 1) consent to genomic research and 2) consent to unrestricted sharing of genomic data. Below are links to this sample language as well as two examples of IRB-approved consents allowing for release of genomic data to unrestricted, public databases:

• Sample consent for unrestricted access to genomic data
• IRB-approved consent for unrestricted access to ENCODE data
• IRB-approved consent for unrestricted access to ENCODE data as addendum to consent for pre-existing project

These examples provide the research community with information and examples to assist with the development of informed consent processes and consent forms for genomics-related research projects. They are not provided as guidance or as a template promoted by NHGRI, but as a reference to inform investigators and IRBs considering these issues. It is important to tailor consent documents for each individual study.

For general information from NHGRI about the informed consent process in genomics research, including additional sample consent forms, see: www.genome.gov/informedconsent.

• Informed Consent
  As the ENCODE Project has increased its study of primary cells and tissues, it has begun working on human biological samples that have been explicitly consented for genomic research and unrestricted sharing of genomic data, in order to maximize the accessibility and utility of ENCODE data. This means that data can be deposited in freely accessible databases, e.g., GEO and the ENCODE Portal and shared without registration or prior approval.
  The ENCODE Consortium has developed sample informed consent language that explicitly asks for 1) consent to genomic research and 2) consent to unrestricted sharing of genomic data. Below are links to this sample language as well as two examples of IRB-approved consents allowing for release of genomic data to unrestricted, public databases:
  • Sample consent for unrestricted access to genomic data
  • IRB-approved consent for unrestricted access to ENCODE data
  • IRB-approved consent for unrestricted access to ENCODE data as addendum to consent for pre-existing project
    These examples provide the research community with information and examples to assist with the development of informed consent processes and consent forms for genomics-related research projects. They are not provided as guidance or as a template promoted by NHGRI, but as a reference to inform investigators and IRBs considering these issues. It is important to tailor consent documents for each individual study.
    For general information from NHGRI about the informed consent process in genomics research, including additional sample consent forms, see: www.genome.gov/informedconsent.

Data Policy

NHGRI has designated the ENCODE Project as a community resource project to accelerate access to and use of the data by the entire scientific community. Accordingly, the data release policy is based on the principle of rapid data release to the scientific community.

External data users may freely download, analyze and publish results based on any ENCODE data without restrictions as soon as they are released. This applies to all datasets, regardless of type or size, and includes no grace period for ENCODE data producers, either as individual members or as part of the Consortium. Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. The Consortium will continue to publish the results of its own analysis efforts in independent publications. ?We request that researchers who use ENCODE datasets (published or unpublished) in publications and talks cite the ENCODE Consortium in all of the following ways:

1. Cite the Consortium's most recent integrative publication (PMID: 22955616; PMC: PMC3439153);
2. Reference the ENCODE Data Coordination Center (DCC) or GEO accession numbers of the datasets; and
3. Acknowledge the ENCODE Consortium and the ENCODE production laboratory(s) generating the particular dataset(s).

Data Release Policies

• Current ENCODE Consortium Data Release Policy (2014-present)
• ENCODE-modENCODE Consortia Data Release Policy (2008-2014)
• ENCODE Pilot Project Data Release Policy (2003-2007)
• Ft. Lauderdale Agreement on Sharing Data from Large-scale Biological Research Projects: A System of Tripartite Responsibility

The data produced by ENCODE Consortium members are deposited to public databases, including the ENCODE Portal and are available for all to use without restriction. Data users are asked to abide by the ENCODE Data Release Policy when using data produced by ENCODE Consortium members, acknowledging the ENCODE Consortium as specified in the policy.

• Data Policy
  NHGRI has designated the ENCODE Project as a community resource project to accelerate access to and use of the data by the entire scientific community. Accordingly, the data release policy is based on the principle of rapid data release to the scientific community.
  External data users may freely download, analyze and publish results based on any ENCODE data without restrictions as soon as they are released. This applies to all datasets, regardless of type or size, and includes no grace period for ENCODE data producers, either as individual members or as part of the Consortium. Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. The Consortium will continue to publish the results of its own analysis efforts in independent publications. ?We request that researchers who use ENCODE datasets (published or unpublished) in publications and talks cite the ENCODE Consortium in all of the following ways:
  1. Cite the Consortium's most recent integrative publication (PMID: 22955616; PMC: PMC3439153);
  2. Reference the ENCODE Data Coordination Center (DCC) or GEO accession numbers of the datasets; and
  3. Acknowledge the ENCODE Consortium and the ENCODE production laboratory(s) generating the particular dataset(s).

Data Release Policies

• Current ENCODE Consortium Data Release Policy (2014-present)
• ENCODE-modENCODE Consortia Data Release Policy (2008-2014)
• ENCODE Pilot Project Data Release Policy (2003-2007)
• Ft. Lauderdale Agreement on Sharing Data from Large-scale Biological Research Projects: A System of Tripartite Responsibility
  The data produced by ENCODE Consortium members are deposited to public databases, including the ENCODE Portal and are available for all to use without restriction. Data users are asked to abide by the ENCODE Data Release Policy when using data produced by ENCODE Consortium members, acknowledging the ENCODE Consortium as specified in the policy.

Tutorials

These tutorials were prepared for biologists using human and/or mouse genetic data to study disease, gene regulation, and basic biology. They explain what data are available, what they mean, how they can be displayed and downloaded and how they can be used in genetic research on human disease.

• ENCODE 2020: Research Applications and Users Meeting, Sept 30 - Oct 2, 2020

• ENCODE Data Utilization Workshop, October 2018, ASHG

• Navigating the ENCODE Encyclopedia: Exploring Candidate Regulatory Elements, Linked Genes and Genetic Variation with SCREEN, October 2017, ASHG

• ENCODE 2016: Research Applications and Users Meeting

• American Society of Human Genetics 2016: ENCODE DCC Uniform Processing Pipelines

• American Society of Human Genetics 2016: 3D Genome Organization and Chromatin Interaction

• ENCODE: Getting Started

• 2016 Society of Toxicology Annual Meeting Workshop

• ENCODE/Roadmap Epigenomics Tutorial, October 2015, ASHG

• ENCODE 2015: Research Applications and Users Meeting

• ENCODE Workshop, April 2015, Keystone Symposia

• Using the ENCODE Resource for Functional Annotation of Genetic Variants, January - March 2015

• Roadmap Epigenomics Tutorial, March 2015, Keystone Symposia

• Roadmap Epigenomics Tutorial, October 2014, ASHG

• ENCODE Workshop Tutorial, October 2014, ASHG

• ENCODE/Roadmap Epigenomics Tutorial, October 2013, ASHG

• ENCODE Tutorial May 2013, Biology of Genomes, CSHL

• ENCODE/Roadmap Epigenomics Tutorial, November 2012, ASHG

• ENCODE Portal Tutorials

• Tutorials
  These tutorials were prepared for biologists using human and/or mouse genetic data to study disease, gene regulation, and basic biology. They explain what data are available, what they mean, how they can be displayed and downloaded and how they can be used in genetic research on human disease.

  • ENCODE 2020: Research Applications and Users Meeting, Sept 30 - Oct 2, 2020
  • ENCODE Data Utilization Workshop, October 2018, ASHG
  • Navigating the ENCODE Encyclopedia: Exploring Candidate Regulatory Elements, Linked Genes and Genetic Variation with SCREEN, October 2017, ASHG
  • ENCODE 2016: Research Applications and Users Meeting
  • American Society of Human Genetics 2016: ENCODE DCC Uniform Processing Pipelines
  • American Society of Human Genetics 2016: 3D Genome Organization and Chromatin Interaction
  • ENCODE: Getting Started
  • 2016 Society of Toxicology Annual Meeting Workshop
  • ENCODE/Roadmap Epigenomics Tutorial, October 2015, ASHG
  • ENCODE 2015: Research Applications and Users Meeting
  • ENCODE Workshop, April 2015, Keystone Symposia
  • Using the ENCODE Resource for Functional Annotation of Genetic Variants, January - March 2015
  • Roadmap Epigenomics Tutorial, March 2015, Keystone Symposia
  • Roadmap Epigenomics Tutorial, October 2014, ASHG
  • ENCODE Workshop Tutorial, October 2014, ASHG
  • ENCODE/Roadmap Epigenomics Tutorial, October 2013, ASHG
  • ENCODE Tutorial May 2013, Biology of Genomes, CSHL
  • ENCODE/Roadmap Epigenomics Tutorial, November 2012, ASHG
  • ENCODE Portal Tutorials

News

Features/Profiles

• Elise Feingold retires after spearheading program to build encyclopedia of DNA elements, ENCODE
  February 10, 2023
• Reddit "Ask Me Anything" Recap: The ENCODE Project
  February 17, 2017
• NHGRI to host symposium on model organism Encyclopedia of DNA Elements project
  June 20-21, 2012
• ENCODE RFAs Expand Effort to Understand the Genome
  October 5, 2011
• Funding Now Available for Technology Development to Catalog and Analyze Function of Genomes
  May 25, 2011
• New user's guide and tutorial helps disease researchers interpret human genome
  April 19, 2011

Press Releases

• NHGRI-funded project creates an encyclopedia detailing the inner workings of the human and mouse genomes
  July 29, 2020
• NIH to expand critical catalog for genomics research
  February 2, 2017
• NIH ENCODE grants advance effort to survey entire human instruction book
  September 24, 2012
• ENCODE data describes function of human genome
  September 5, 2012
• NHGRI to develop revolutionary technologies for exploring genome function
  April 25, 2012
• Researchers Expand Efforts to Explore Functional Landscape of the Human Genome
  October 9, 2007
• New Findings Challenge Established Views on Human Genome
  June 13, 2007
• ENCODE Consortium Publishes Scientific Strategy
  October 21, 2004
• Beyond Genes: Scientists Venture Deeper Into the Human Genome: ENCODE Project Seeks to Identify All Functional Elements in Human DNA
  October 9, 2003
• Launch of Pilot Project to Identify All Functional Elements in Human DNA
  March 4, 2003

Publications

• Defining functional DNA elements in the Human Genome
  Proceedings of the National Academy of Sciences, April 21, 2014

• Nature ENCODE explorer
  A series of coordinated scientific reports published in the Nature, Sept. 5, 2012 online issue

• A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
  PLoS Biology, April 19, 2011

• Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
  Nature, June 13, 2007

• ENCODE Web Focus
  Related articles on ENCODE from Nature, June 2007

• Special Issue on ENCODE from Genome Research
  June 2007

• The ENCODE (ENCylopedia Of DNA Elements) Project.
  Science, Vol. 306, Issue 5696, 636-640, 22 October 2004.

• News

Features/Profiles

• Elise Feingold retires after spearheading program to build encyclopedia of DNA elements, ENCODE
  February 10, 2023
• Reddit "Ask Me Anything" Recap: The ENCODE Project
  February 17, 2017
• NHGRI to host symposium on model organism Encyclopedia of DNA Elements project
  June 20-21, 2012
• ENCODE RFAs Expand Effort to Understand the Genome
  October 5, 2011
• Funding Now Available for Technology Development to Catalog and Analyze Function of Genomes
  May 25, 2011
• New user's guide and tutorial helps disease researchers interpret human genome
  April 19, 2011

Press Releases

• NHGRI-funded project creates an encyclopedia detailing the inner workings of the human and mouse genomes
  July 29, 2020
• NIH to expand critical catalog for genomics research
  February 2, 2017
• NIH ENCODE grants advance effort to survey entire human instruction book
  September 24, 2012
• ENCODE data describes function of human genome
  September 5, 2012
• NHGRI to develop revolutionary technologies for exploring genome function
  April 25, 2012
• Researchers Expand Efforts to Explore Functional Landscape of the Human Genome
  October 9, 2007
• New Findings Challenge Established Views on Human Genome
  June 13, 2007
• ENCODE Consortium Publishes Scientific Strategy
  October 21, 2004
• Beyond Genes: Scientists Venture Deeper Into the Human Genome: ENCODE Project Seeks to Identify All Functional Elements in Human DNA
  October 9, 2003
• Launch of Pilot Project to Identify All Functional Elements in Human DNA
  March 4, 2003

Publications

• Defining functional DNA elements in the Human Genome
  Proceedings of the National Academy of Sciences, April 21, 2014
• Nature ENCODE explorer
  A series of coordinated scientific reports published in the Nature, Sept. 5, 2012 online issue
• A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
  PLoS Biology, April 19, 2011
• Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
  Nature, June 13, 2007
• ENCODE Web Focus
  Related articles on ENCODE from Nature, June 2007
• Special Issue on ENCODE from Genome Research
  June 2007
• The ENCODE (ENCylopedia Of DNA Elements) Project.
  Science, Vol. 306, Issue 5696, 636-640, 22 October 2004.

Funding Opportunities

Current ENCODE RFAs

At this time, there are no current ENCODE RFAs.

Recently Expired RFAs

• ENCODE FOA Webinar Information
  NOT-HG-16-007 Notice of Applicant Information Webinar for NHGRI ENCODE RFAs: RFA-HG-16-002, RFA-HG-16-003, RFA-HG-16-004, RFA-HG-16-005, and RFA-HG-16-006
  This notice applies to the following ENCODE RFAs:
  • RFA-HG-16-002 Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Mouse (UM1)
  • RFA-HG-16-003 Characterizing the Functional Elements in the Encyclopedia of DNA Elements (ENCODE) Catalog (UM1)
  • RFA-HG-16-004 Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01)
  • RFA-HG-16-005 ENCODE Data Coordinating Center (U24)
  • RFA-HG-16-006 ENCODE Data Analysis Center (U24)
  • NOT-HG-15-034 Notice of Intent to Publish a Funding Opportunity Announcement for Functional Element Mapping Centers (UM1)
• NOT-HG-15-035 Notice of Intent to Publish a Funding Opportunity Announcement for Functional Element Characterization Centers (UM1)
• NOT-HG-15-036 Notice of Intent to Publish a Funding Opportunity Announcement for Computational Analysis Research Projects (U01)
• NOT-HG-15-037 Notice of Intent to Publish a Funding Opportunity Announcement for ENCODE Data Coordination and Analysis Center (U24)

Past ENCODE RFAs

• NOT-HG-12-002 Notice of Change in the Receipt Date: RFA-HG-11-024, Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Model Organisms (U54) and RFA-HG-11-025, Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01) (Expired)

• RFA-HG-11-024 Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Model Organisms (U54) (Expired)

• RFA-HG-11-025 Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01) (Expired)

• RFA-HG-11-026 Data Analysis and Coordination Center for the Encyclopedia of DNA Elements (ENCODE) (U41) (Expired)

• RFA-HG-11-013 Technology Development for High-Throughput Functional Genomics (R01) (Expired)

• RFA-HG-11-014 Technology Development for High-Throughput Functional Genomics (R21) (Expired)

• RFA-HG-11-015 Technology Development for High-Throughput Functional Genomics (R43/44) (Expired)

• RFA-HG-07-030 Creating the Encyclopedia of DNA Elements (ENCODE) in the Human Genome (U01 and U54) (Expired)
  NOT-07-007: Clarification and Additional Information to HG-07-030 and HG-07-031
  Slides from Applicant Information Meeting - HG-07-030

• RFA-HG-07-031 A Data Coordination Center for the Encyclopedia of DNA Elements (ENCODE) Project (U41)(Expired)
  NOT-07-007: Clarification and Additional Information to HG-07-030 and HG-07-031
  Slides from Applicant Information Meeting - HG-07-031

• RFA-HG-07-010: A Data Analysis Center for the Encyclopedia of DNA Elements (ENCODE) Project (U01) (Expired)

• RFA HG-03-003 Determination of All Functional Elements in Human DNA (Expired)

• RFA HG-03-004 Technologies to Find Functional Elements in Genomic DNA (Expired)

• RFA-HG-04-001 Technologies to Find Functional Elements in Genomic DNA. (Expired)

• RFA-HG-07-028 Technology Development for the Comprehensive Determination of Functional Elements in Eukaryotic Genomes (R21) (Expired)

• RFA HG-07-029 Technology Development for the Comprehensive Determination of Functional Elements in Eukaryotic Genomes (R01) (Expired)

• Funding Opportunities

Current ENCODE RFAs

At this time, there are no current ENCODE RFAs.

Recently Expired RFAs

• ENCODE FOA Webinar Information
  NOT-HG-16-007 Notice of Applicant Information Webinar for NHGRI ENCODE RFAs: RFA-HG-16-002, RFA-HG-16-003, RFA-HG-16-004, RFA-HG-16-005, and RFA-HG-16-006
  This notice applies to the following ENCODE RFAs:
  * RFA-HG-16-002 Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Mouse (UM1)
  * RFA-HG-16-003 Characterizing the Functional Elements in the Encyclopedia of DNA Elements (ENCODE) Catalog (UM1)
  * RFA-HG-16-004 Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01)
  * RFA-HG-16-005 ENCODE Data Coordinating Center (U24)
  * RFA-HG-16-006 ENCODE Data Analysis Center (U24)
  * NOT-HG-15-034 Notice of Intent to Publish a Funding Opportunity Announcement for Functional Element Mapping Centers (UM1)
• NOT-HG-15-035 Notice of Intent to Publish a Funding Opportunity Announcement for Functional Element Characterization Centers (UM1)
• NOT-HG-15-036 Notice of Intent to Publish a Funding Opportunity Announcement for Computational Analysis Research Projects (U01)
• NOT-HG-15-037 Notice of Intent to Publish a Funding Opportunity Announcement for ENCODE Data Coordination and Analysis Center (U24)

Past ENCODE RFAs

• NOT-HG-12-002 Notice of Change in the Receipt Date: RFA-HG-11-024, Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Model Organisms (U54) and RFA-HG-11-025, Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01) (Expired)
• RFA-HG-11-024 Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Model Organisms (U54) (Expired)
• RFA-HG-11-025 Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01) (Expired)
• RFA-HG-11-026 Data Analysis and Coordination Center for the Encyclopedia of DNA Elements (ENCODE) (U41) (Expired)
• RFA-HG-11-013 Technology Development for High-Throughput Functional Genomics (R01) (Expired)
• RFA-HG-11-014 Technology Development for High-Throughput Functional Genomics (R21) (Expired)
• RFA-HG-11-015 Technology Development for High-Throughput Functional Genomics (R43/44) (Expired)
• RFA-HG-07-030 Creating the Encyclopedia of DNA Elements (ENCODE) in the Human Genome (U01 and U54) (Expired)
  NOT-07-007: Clarification and Additional Information to HG-07-030 and HG-07-031
  Slides from Applicant Information Meeting - HG-07-030
• RFA-HG-07-031 A Data Coordination Center for the Encyclopedia of DNA Elements (ENCODE) Project (U41)(Expired)
  NOT-07-007: Clarification and Additional Information to HG-07-030 and HG-07-031
  Slides from Applicant Information Meeting - HG-07-031
• RFA-HG-07-010: A Data Analysis Center for the Encyclopedia of DNA Elements (ENCODE) Project (U01) (Expired)
• RFA HG-03-003 Determination of All Functional Elements in Human DNA (Expired)
• RFA HG-03-004 Technologies to Find Functional Elements in Genomic DNA (Expired)
• RFA-HG-04-001 Technologies to Find Functional Elements in Genomic DNA. (Expired)
• RFA-HG-07-028 Technology Development for the Comprehensive Determination of Functional Elements in Eukaryotic Genomes (R21) (Expired)
• RFA HG-07-029 Technology Development for the Comprehensive Determination of Functional Elements in Eukaryotic Genomes (R01) (Expired)

Program Staff

Program Directors

Last updated: September 17, 2023