Bioinformatics Resource Centers (BRCs) for Infectious Diseases

The NIAID-funded Bioinformatics Resource Centers provide data-driven, production-level, sustainable computational platforms to enable sharing and access to data, portable computational tools, and standards that support interoperability for the infectious diseases research community.

Laboratory of Immune System Biology

Ronald N. Germain, M.D., Ph.D., Chief

The major research activities of Laboratory of Immune System Biology (LISB) are focused on the basic genetics, molecular biology, and cell biology of the immune system, as well as on human disease informed by these more basic studies. How dysregulation of the immune system results in immunodeficiencies, autoimmunity, inflammation, allergy, chronic infections, and lymphoproliferative diseases and what strategies might be valuable for therapeutic or vaccine development related to these conditions as well as cancer are important topics of interest, as is the behavior of the meta-organism (the combination of the host and the commensal microbiota).

A key aspect of LISB research is the development and application of systems and quantitative approaches to dissect how the molecules, cells, and commensals studied by LISB investigators together shape emergent immune system behavior. Modern technology now allows the analysis of immune responses and host-pathogen interactions at a global level, across scales ranging from molecular interactions to intracellular signaling and gene regulatory networks to individual cell behavior to the functioning of a tissue, an organ, and the whole organism. The challenge is to organize and integrate this information to extract biological insights that can help enhance our understanding of how the immune system operates in health or disease or how pathogens affect their hosts. To move towards these goals, LISB scientists seek to collect detailed quantitative as well as qualitative data on the state, organization, and operation of the immune system to develop computational models (mechanistic, statistical, and machine-learning) that can be used to predict the behavior of a complex biological system, uncover the components involved, and help explain the mechanistic basis for physiological and pathological responses to infection or vaccination or to design new therapies or vaccines.

Achieving this goal requires an interdisciplinary effort, and LISB is designed to address this challenge. Although it is composed of independent laboratories, the LISB is intended to operate in many of its research efforts as an integrated group of scientists and support staff. Although it has been established within NIAID, it is expected to play a major role in fostering the growth of immunology and systems biology efforts across the National Institutes of Health (NIH) through its development of software tools for complex systems modeling, new experimental paradigms, advanced imaging modalities, high-throughput screening efforts, and novel approaches to microbiome analysis. LISB members are involved in an extensive web of formal and informal interactions with other intramural NIH scientists and with extramural groups in the United States and abroad that have a common interest in a systems approach to biology in general and immunology in particular.

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Major Areas of Research

  • Quantitative systems-level studies of humans and of animal models
  • Development, differentiation, and plasticity of immune cells, including T cells, B cells, and innate lymphoid cells
  • Transcriptional and post-transcriptional regulation of lymphocyte differentiation and function
  • Regulation of primary and secondary immune responses
  • Mechanisms of pattern recognition and antigen receptor signaling and transcriptional control
  • Gene expression profiling, high-content imaging of immune signaling pathways, RNAi and CRISPR/Cas9 for the discovery of pathway components, high-throughput proteomic and genomic analysis
  • Translational immunogenomics: integrative analysis of the human immune system’s response to vaccines, medications, and disease states, in vitro and in vivo
  • Detection and analysis of gene defects and pathogenetic mechanisms in human inborn errors of immunity
  • Single-cell biology: quantitative and functional analysis of cellular heterogeneity and stochastic gene expression
  • Advanced dynamic and static multiplex imaging of mouse and human tissues
  • RNA-binding protein and miRNA-mediated regulation of immune cells
  • Host-pathogen interactions
  • Immune-microbiota interactions
  • Role of nutrition on the immune system
  • Tissue-specific immunity
  • Fetal hematopoietic stem cells
  • Programmed cell death and autophagy
  • Biology of regulatory T cells and their role in autoimmunity and chronic infection
  • Induction of T-cell tolerance and treatment of autoimmunity
  • Structural and functional studies of macromolecules involved in antigen processing and presentation, adaptive and innate immune recognition, and viral immunoevasion
  • Detection and analysis of gene defects pathogenetic mechanisms in human inborn errors of immunity

See a playlist of videos of LISB research.

Simmune Project

Simmune is a suite of software tools that guides the user through the multiple hierarchical scales of cellular behavior, facilitating the generation of comprehensive models. It was originally created to simulate immunological phenomena—hence its name, Simmune—but it is applicable to a very broad class of cell biological models.


Read more about the Simmune Project

Laboratory of Infectious Diseases

Jeffrey I. Cohen, M.D., Chief

Established in 1942, the Laboratory of Infectious Diseases (LID) has a long history of vaccine development and identification of new agents of viral diseases. LID is noted for undertaking high-risk, high-re​ward programs that require extraordinary time and resource commitments, such as programs to develop vaccines for viral hepatitis, severe childhood respiratory diseases, viral gastroenteritis, flaviviruses, and herpesviruses.

Clinical studies complement LID’s major areas of research, including testing candidate vaccines in clinical trials, human challenge studies with influenza and respiratory syncytial virus to study pathogenesis and immune correlates for protection against these viruses, and studies of severe virus infections in persons without known immune deficiency.

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Examples of LID Accomplishments

  • The first approved hepatitis A vaccine in the US (Havrix) and a monoclonal antibody to respiratory syncytial virus (RSV) (Synagis).
  • A live, attenuated influenza vaccine, FluMist (Medimmune) developed by LID with participation of extramural NIAID.
  • Vaccines against potential pandemic influenza strains in collaboration with Medimmune tested in Phase I clinical trials.
  • The first approved rotavirus vaccine in the US (RotaShield). 
  • A bovine-human reassortant rotavirus vaccine, RotaSIIL used in India. A USPTO Patents for Humanity award to NIAID for RotaSIIL in 2018.
  • A recombinant live, attenuated RSV vaccine shown to be safe and immunogenic in 1- to 2-month-old infants and continuing in clinical trials.
  • A hepatitis E vaccine, licensed to GlaxoSmithKline, proved highly effective in preventing hepatitis E in a field trial in Nepal.
  • A vaccine candidate for West Nile virus was shown to be safe and immunogenic in young adults and in the elderly.
  • A tetravalent live, attenuated dengue virus vaccine in a Phase III clinical trial and licensed throughout the world.
  • A live, attenuated PIV3 vaccine passed Phase II safety trials in infants; PIV1 and PIV2 vaccine candidates generated.
  • A diagnostic for norovirus, RIDASCREEN, licensed.
  • Human volunteer influenza and respiratory syncytial virus challenge models developed for testing vaccines, immunotherapeutics, and antivirals.

Former Senior Investigators

Listing of former Senior Investigators with the Laboratory of Infectious Diseases


Former Senior Investigators

Systems Biology Consortium Resources

The Systems Biology Consortium for Infectious Diseases is a community of systems biologists who integrate experimental biology, computational tools and modeling across temporal and spatial scales to improve our understanding of infectious diseases. Through collaborative efforts, scientists test and validate hypotheses that drive innovation and discovery. The Consortium seeks to develop strategies that predict and alleviate disease severity and ultimately provide solutions to the world's most important health challenges.

Therapeutic Development Services

The Therapeutic Development Services program offers a collection of preclinical services to support the development of products intended for use in the cure, mitigation, diagnosis, or treatment of disease caused by a pathogen or certain toxins.

This is one of several programs provided by NIAID's Division of Microbiology and Infectious Diseases to support infectious disease product developers.

Vaccine and Treatment Evaluation Units (VTEUs) Services

The Vaccine and Treatment Evaluation Units (VTEUs), supported by the Division of Microbiology and Infectious Diseases (DMID) since the 1960s, provide a ready resource for the conduct of clinical trials to evaluate promising vaccines, treatments, and diagnostics for infectious diseases. The sites are part of DMID's Infectious Diseases Clinical Research Consortium (IDCRC).

Centers for Research on Structural Biology of Infectious Diseases (CRSTAL-ID)—Resources

The Centers for Research on Structural Biology of Infectious Diseases (CRSTAL-ID) provide the research community with: 3-D protein structures and protein-ligand complexes; Sequence-verified clones and peptides; Services that deliver requested 3-D structure determination; and Molecular screening of proteins in complex with inhibitors, cofactors and substrate analogs

Vaccine Development Services

The Vaccine Development Services program offers a collection of preclinical services to support the development of vaccines intended for use in the investigation, control, prevention, and treatment of a wide range of infectious agents (other than HIV).

This is one of several programs provided by NIAID's Division of Microbiology and Infectious Diseases to support infectious disease product developers.

Early Phase Clinical Trial Units

The Early Phase Clinical Trial Units (EPCTUs) support the design, development, implementation, and conduct of Phase 0 to Phase 2 clinical trials, including proof-of-concept studies in healthy, special, and disease-specific populations, carried out in an expeditious and efficient manner, aided by bioanalysis when necessary, against viral, bacterial, parasitic, and fungal pathogens and emerging and re-emerging infectious diseases. The candidate products assessed through the EPCTUs may include licensed or investigational products such as small molecules, monoclonal antibodies, i

Therapeutic Development Services - Interventional Agents

Therapeutic Development Services - Interventional Agents program provides services to facilitate preclinical development of therapeutics and new in vivo diagnostics for infectious pathogens, including bacteria, viruses, parasites, fungi, and toxins. Services will be conducted at the appropriate regulatory compliance level dependent on the stage of product development.

Note: Devices are excluded.