Opportunity Information: Apply for RFA AI 12 028
Apply for RFA AI 12 028
- The National Institutes of Health in the health sector is offering a public funding opportunity titled "Understanding the Functions of Uncharacterized Genes in Infectious Disease Pathogens (U19)" and is now available to receive applicants.
- Interested and eligible applicants and submit their applications by referencing the CFDA number(s): 93.855 Allergy and Infectious Diseases Research 93.856 Microbiology and Infectious Diseases Research.
- This funding opportunity was created on Jul 20, 2012 and posted on Jul 20, 2012.
- Applicants must submit their applications by Nov 13, 2012. (Agency may still review applications by suitable applicants for the remaining/unused allocated funding in 2026.)
- The funding agency has allocated a total of $7,100,000.00 to eligible and selected applicants.
- Eligible applicants include: State governments Nonprofits having a 501(c)(3) status with the IRS, other than institutions of higher education Independent school districts Small businesses Native American tribal governments (Federally recognized) County governments City or township governments Public and State controlled institutions of higher education Private institutions of higher education Special district governments Native American tribal organizations (other than Federally recognized tribal governments) Others (see text field entitled Additional Information on Eligibility for clarification) For profit organizations other than small businesses Nonprofits that do not have a 501(c)(3) status with the IRS, other than institutions of higher education Public housing authorities/Indian housing authorities.
- Other Eligible Applicants include the following Alaska Native and Native Hawaiian Serving Institutions Faith based or Community based Organizations Hispanic serving Institutions Historically Black Colleges and Universities (HBCUs) Indian/Native American Tribal Governments (Other than Federally Recognized) Regional Organizations Tribally Controlled Colleges and Universities (TCCUs) U.S. Territory or Possession Non domestic (non U.S.) Entities (Foreign Institutions) are eligible to apply. Non domestic (non U.S.) components of U.S. Organizations are eligible to apply. Foreign components, as defined in the NIH Grants Policy Statement, are allowed.
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Opportunity Summary:
The funding opportunity titled "Understanding the Functions of Uncharacterized Genes in Infectious Disease Pathogens (U19)" (Funding Opportunity Number RFA-AI-12-028) is a National Institutes of Health (NIH) initiative designed to build a coordinated research program focused on functional genomics in infectious disease pathogens. The central goal is to move beyond genome sequencing and annotation by experimentally determining what poorly understood genetic elements actually do. In practical terms, the FOA targets three major categories of "known unknowns" that remain common even in well-studied pathogen genomes: hypothetical genes (genes predicted from sequence but lacking functional evidence), unknown open reading frames (ORFs) that may encode proteins but have unclear roles, and noncoding RNAs whose regulatory or biological functions have not been defined. By supporting projects that assign specific biochemical functions and clarify biological roles for these elements, the program aims to produce knowledge that can strengthen the broader infectious disease research pipeline, including better understanding of pathogen biology, virulence, survival strategies, and potential vulnerabilities that could inform diagnostics, therapeutics, and vaccines.
This opportunity uses the U19 cooperative agreement mechanism, which signals that NIH expects substantial scientific or programmatic involvement during the life of the award. A U19 typically supports multi-project, team-based efforts rather than a single standalone research project, and it is structured to enable coordination across complementary research components. The emphasis on a "program" indicates that applicants are generally expected to propose integrated, collaborative research plans that can systematically tackle functional characterization at scale, rather than only addressing one gene at a time. Functional genomics approaches that fit this purpose commonly include high-throughput genetics, phenotypic screening, transcriptomics, proteomics, metabolomics, structural biology, computational function prediction paired with experimental validation, and other strategies that can connect sequence to biochemical activity and pathogen behavior. The FOA frames success in terms of increasing knowledge of specific biochemical functions, which suggests a preference for mechanistic, experimentally supported functional assignments over purely descriptive analyses.
The award falls under NIH funding activity categories related to health, and it is associated with CFDA numbers 93.855 (Allergy and Infectious Diseases Research) and 93.856 (Microbiology and Infectious Diseases Research). There is no cost sharing or matching requirement, which means applicants are not required to contribute non-federal funds as a condition of the award. The estimated total program funding listed is $7,100,000, reflecting the overall amount NIH anticipated committing under this announcement rather than a guaranteed amount per award. The FOA was posted and created on July 20, 2012, with an original and current closing date of November 13, 2012, and an archive date of December 14, 2012, indicating it is no longer open for applications but remains part of the historical NIH funding record.
Eligibility is broad and includes many U.S. organizational types across government, education, nonprofit, and for-profit sectors. Eligible applicants include state governments, county and local governments, city or township governments, special district governments, independent school districts, and public housing authorities/Indian housing authorities. Higher education institutions are eligible, including both public/state-controlled and private institutions of higher education. The FOA also allows participation from nonprofit organizations with 501(c)(3) status and nonprofits without 501(c)(3) status, as well as for-profit organizations (including those other than small businesses) and small businesses. It explicitly includes Native American tribal governments (federally recognized) and tribal organizations (other than federally recognized tribal governments), as well as regional organizations and tribally controlled colleges and universities. In addition, the eligibility language highlights participation from various mission-focused institution types such as Historically Black Colleges and Universities (HBCUs), Hispanic-serving institutions, Alaska Native and Native Hawaiian-serving institutions, and faith-based or community-based organizations. Importantly, the FOA permits non-U.S. entities (foreign institutions) to apply, allows non-U.S. components of U.S. organizations, and allows foreign components as defined in the NIH Grants Policy Statement. This global eligibility aligns with the reality that many high-impact infectious disease research programs involve international pathogens, international field sites, and specialized expertise distributed across countries.
From a programmatic standpoint, the FOA is essentially addressing a bottleneck created by the gap between rapidly generated pathogen genome sequences and the much slower pace of experimentally validated gene function. Even when a pathogen genome is "annotated," a significant fraction of genes are often labeled as hypothetical proteins or assigned only vague, similarity-based predictions. Noncoding RNAs add another layer of complexity because they can control gene expression, stress responses, host adaptation, or persistence without encoding proteins, and their functions are frequently missed by conventional annotation pipelines. By funding coordinated functional genomics work to characterize these unassigned or ambiguous genome features, NIH is aiming to help the field build a more complete and actionable map of pathogen biology that can support future hypothesis-driven studies and translational advances.
The administering agency is NIH, and the full announcement was made available through an NIH Grants Guide link. For technical issues accessing the announcement, the contact listed is the NIH Office of Extramural Research (OER) Webmaster at FBOWebmaster@OD.NIH.GOV, which reflects the standard NIH practice for handling access and linking problems related to archived or web-hosted funding notices.
Frequently Asked Questions (FAQs)
What is the title and funding opportunity number for this grant?
The opportunity is titled "Understanding the Functions of Uncharacterized Genes in Infectious Disease Pathogens (U19)" and the Funding Opportunity Number is RFA-AI-12-028.
Which agency is administering this funding opportunity?
The administering agency is the National Institutes of Health (NIH).
What is the main purpose of this funding opportunity?
The central purpose is to build a coordinated research program focused on functional genomics in infectious disease pathogens, specifically moving beyond genome sequencing and annotation by experimentally determining the functions of genetic elements that are poorly understood.
What problem or bottleneck is NIH trying to address with this program?
The FOA targets the gap between the rapid pace of pathogen genome sequencing and the slower pace of experimentally validated gene function. Even in well-studied pathogens, many genes remain labeled as hypothetical or only weakly predicted, and many noncoding RNAs lack defined biological roles.
What kinds of "uncharacterized" genetic elements does the FOA emphasize?
The FOA highlights three major categories of "known unknowns": hypothetical genes (predicted from sequence but lacking functional evidence), unknown open reading frames (ORFs) that may encode proteins but have unclear roles, and noncoding RNAs whose regulatory or biological functions have not been defined.
What does the FOA mean by moving beyond sequencing and annotation?
It means the program is focused on experimental work that assigns specific biochemical functions and clarifies biological roles for genes, ORFs, and noncoding RNAs, rather than stopping at sequence-based predictions or descriptive genome annotation.
What outcomes is the program trying to produce?
The program aims to generate experimentally supported functional assignments that strengthen the broader infectious disease research pipeline by improving understanding of pathogen biology, virulence, survival strategies, and potential vulnerabilities that could inform diagnostics, therapeutics, and vaccines.
What funding mechanism is used, and what does it imply?
This opportunity uses the U19 cooperative agreement mechanism. This indicates NIH expects substantial scientific or programmatic involvement during the life of the award and that the effort is generally intended to be multi-project and team-based rather than a single standalone project.
Does the FOA favor individual projects or coordinated, program-style applications?
The FOA emphasizes a coordinated "program" and is structured to support integrated, collaborative research plans that can systematically tackle functional characterization at scale rather than focusing only on one gene at a time.
What types of research approaches are consistent with the FOA's functional genomics goals?
The FOA describes functional genomics approaches such as high-throughput genetics, phenotypic screening, transcriptomics, proteomics, metabolomics, structural biology, and computational function prediction paired with experimental validation, as well as other strategies that connect sequence features to biochemical activity and pathogen behavior.
Does the FOA indicate a preference for any kind of scientific evidence?
Yes. The FOA frames success in terms of increasing knowledge of specific biochemical functions, suggesting a preference for mechanistic, experimentally supported functional assignments rather than purely descriptive analyses.
Which NIH-related funding activity categories and CFDA numbers are associated with this opportunity?
The opportunity is associated with NIH funding activity categories related to health and lists CFDA numbers 93.855 (Allergy and Infectious Diseases Research) and 93.856 (Microbiology and Infectious Diseases Research).
Is cost sharing or matching required?
No. The FOA states there is no cost sharing or matching requirement, meaning applicants are not required to contribute non-federal funds as a condition of the award.
How much total funding was estimated under this announcement?
The FOA lists an estimated total program funding level of $7,100,000. This reflects the overall amount NIH anticipated committing under the announcement rather than a guaranteed amount per award.
When was the FOA posted, and what were the closing and archive dates?
The FOA was posted and created on July 20, 2012. The original and current closing date is November 13, 2012, and the archive date is December 14, 2012.
Is this funding opportunity still open for applications?
No. Based on the closing and archive dates provided, the FOA is no longer open for applications and remains part of the historical NIH funding record.
Who is eligible to apply?
Eligibility is broad and includes many U.S. organizational types across government, education, nonprofit, and for-profit sectors, including small businesses and organizations other than small businesses.
Are U.S. government entities eligible (state, local, and tribal)?
Yes. Eligible applicants include state governments, county and local governments, city or township governments, special district governments, independent school districts, and public housing authorities/Indian housing authorities. The FOA also explicitly includes Native American tribal governments (federally recognized) and tribal organizations (other than federally recognized tribal governments).
Are colleges and universities eligible?
Yes. Eligible applicants include public/state-controlled institutions of higher education and private institutions of higher education, including tribally controlled colleges and universities.
Are nonprofit organizations eligible?
Yes. Eligibility includes nonprofit organizations with 501(c)(3) status and nonprofit organizations without 501(c)(3) status.
Are for-profit organizations and small businesses eligible?
Yes. The FOA includes for-profit organizations (including those other than small businesses) and small businesses.
Are foreign institutions or non-U.S. components allowed to apply?
Yes. The FOA permits non-U.S. entities (foreign institutions) to apply, allows non-U.S. components of U.S. organizations, and allows foreign components as defined in the NIH Grants Policy Statement.
Does the FOA encourage participation by specific institution types (for example, minority-serving institutions)?
The eligibility language highlights participation from Historically Black Colleges and Universities (HBCUs), Hispanic-serving institutions, Alaska Native and Native Hawaiian-serving institutions, and faith-based or community-based organizations.
Where was the full announcement made available?
The full announcement was made available through an NIH Grants Guide link (as described in the FOA summary provided).
Who should be contacted for technical issues accessing the announcement?
For technical issues accessing the announcement, the listed contact is the NIH Office of Extramural Research (OER) Webmaster at FBOWebmaster@OD.NIH.GOV.
What is the practical scientific focus of the work expected under this FOA?
The practical focus is to connect pathogen genome sequence features to experimentally validated function, including defining biochemical activities and biological roles that can clarify how pathogens survive, cause disease, and potentially expose vulnerabilities relevant to diagnostics, therapeutics, or vaccines.
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