Library of Integrated Network Based Cellular Signatures (LINCS) Perturbation Induced Data and Signature Generation Centers (U54) | Apply Online

Frequently Asked Questions (FAQs)

What is RFA-RM-13-013?

RFA-RM-13-013 is an NIH funding opportunity announcement titled "Library of Integrated Network Based Cellular Signatures (LINCS) Perturbation Induced Data and Signature Generation Centers (U54)." It supports centers that generate large-scale perturbation-response data in human cells and convert those responses into interpretable cellular "signatures" that can be compared across experiments and biological contexts.

What is the main purpose of this funding opportunity?

The main purpose is to expand and strengthen LINCS as a long-term, community-facing biomedical resource by building a systematic, high-throughput data production effort. The program focuses on measuring how human cells respond to many kinds of perturbations and producing standardized signatures that enable mechanism-based comparisons between different perturbations.

What does LINCS stand for and what is LINCS in this context?

LINCS stands for Library of Integrated Network Based Cellular Signatures. In this opportunity, LINCS refers to a program and resource that organizes perturbation-response measurements and derived signatures so researchers can compare cellular responses, infer mechanisms, and connect perturbations to pathways and gene networks.

What type of NIH award mechanism is used?

This opportunity uses a U54 cooperative agreement mechanism, meaning it is a discretionary NIH award with substantial NIH programmatic involvement and coordination with awardees compared with standard grant mechanisms.

What kinds of work are the funded centers expected to do?

Funded centers are expected to (1) generate high-throughput perturbation-response datasets in selected human cell types, (2) convert those responses into robust and interpretable cellular signatures, (3) support multidimensional integration across different data types and readouts, and (4) deliver usable datasets and interfaces so the broader biomedical community can access and apply the resource.

What is meant by "perturbation-response" data?

Perturbation-response data are measurements of how cells change after being exposed to an intervention or condition that alters cellular state. The FOA emphasizes capturing cellular responses to many different biological perturbations in a systematic way.

What types of perturbations are highlighted?

The announcement highlights siRNAs, small bioactive molecules, and environmental or culture manipulations. It also signals a broader intent to cover a wide range of agents and conditions that alter cellular state.

Why does the FOA emphasize using human cell types?

A key scientific emphasis is generating perturbation-response datasets across carefully selected human cell types, because mechanisms and responses can depend strongly on cellular context. Expanding cell type coverage is presented as a concrete way to enhance the LINCS resource.

What are "cellular signatures" in this program?

Cellular signatures are interpretable summaries of complex cellular responses to perturbations. They are meant to enable comparisons, clustering, and inference about pathways, gene networks, and mechanisms of action across experiments, perturbation types, and biological contexts.

What kinds of outputs are expected from awardees?

Outputs are expected to include molecular activity measurements and cellular response features, along with derived cellular signatures that can be integrated computationally. The FOA also emphasizes producing user-facing interfaces that typical biomedical scientists can use.

What does "multidimensional data integration" mean here?

It refers to integrating data across different modalities and readouts (different assay types and response measurements). Applicants are expected not only to generate data, but also to support integration so patterns and signatures can be compared and interpreted across assays and contexts.

Does the FOA encourage development of new technologies?

Yes. It encourages some new technology development where needed to improve throughput, data quality, or the interpretability of the resulting signatures.

How important is usability and access for non-specialists?

Usability is a stated emphasis. The FOA explicitly mentions user interfaces needed by the typical biomedical scientist, indicating the resource should be accessible to non-specialists and not only to computational experts.

What broader impact is NIH seeking through these LINCS centers?

The announcement frames LINCS signatures as a bridge between perturbations and biological meaning. The intended impact includes enabling mechanism-based connections between different perturbations (such as genetic knockdowns and drug treatments), supporting disease biology research, and promoting broad reuse and combination with external datasets.

How can LINCS outputs help with drug research?

According to the FOA, the outcomes are positioned to clarify mechanisms of action for known drugs, which can support drug repurposing, target identification, and understanding off-target effects.

How can LINCS outputs help with disease biology?

The FOA indicates the resulting knowledge base should help researchers associate disease states with detailed molecular and cellular phenotypes, including phenotypes driven by specific genetic variants, and map diseases to changes in specific gene networks.

Is the program intended to be used alongside other research programs and datasets?

Yes. The FOA notes the outcomes should be synergistic with other research programs, reflecting an expectation that LINCS data and tools will be reused broadly and combined with external datasets.

How much funding is available under this opportunity?

The total estimated funding is $10,000,000, and the award ceiling is $1,700,000.

Is cost sharing or matching required?

No. Cost sharing or matching is not required.

When was the opportunity posted and what were the key dates?

The opportunity was posted on August 19, 2013. The original and current closing date is December 19, 2013. The archive date is January 19, 2014.

Who is eligible to apply?

Eligibility is broad across U.S.-based organizations and governments. Eligible applicants include public and private institutions of higher education; nonprofits (including 501(c)(3) and other nonprofit categories); for-profit organizations (including categories explicitly listed, with small businesses also listed separately); and government entities such as state, county, city or township, and special district governments. Certain tribal governments and tribal organizations are also included, along with eligible federal agencies.

Are minority-serving institutions included in the eligible applicant types?

Yes. The FOA explicitly includes various minority-serving institution categories, such as HBCUs, Hispanic-serving institutions, AANAPISIs, TCCUs, and others listed in the eligibility description.

Are faith-based or community-based organizations eligible?

Yes. The FOA explicitly includes faith-based or community-based organizations among eligible applicants.

Are foreign institutions eligible to apply?

No. Foreign institutions are not eligible.

Are foreign components allowed as part of an application?

No. Foreign components, as defined by NIH policy, are not allowed. This includes non-U.S. components of U.S. organizations.

What is the overall goal of the centers being funded?

The overall goal is to create and scale centers that can produce high-throughput, high-quality perturbation-response data in human cells, transform those data into robust cellular signatures, integrate the results across multiple assay types, and deliver durable datasets and interfaces as a widely usable scientific resource.