The Trans-NIH Microbiome Working Group (TMWG) was established in 2012 by Dr. Lita Proctor (NHGRI) to provide a forum for coordinating NIH extramural research activities related to the human microbiome. TMWG membership is open to all extramural program staff from NIH institutes and centers (ICs) with an interest in the human microbiome. The TMWG meets monthly.
Main Area of Focus
- To provide a forum for coordinating NIH extramural research activities related to the human microbiome
Points of Contact
Below is a list of extramural program staff who have agreed to serve as the primary point of contact for their Institute for microbiome research related inquiries. They will address general questions and, if needed, will direct your inquiries to the appropriate program director in their Institute
| ICO | Program Staff |
|---|---|
| NIAID | Ryan Ranallo (Co-chair) |
| NCI | Phil Daschner (Co-chair) |
| NCCIH | Hye Sook Kim |
| NEI | Charles Wright |
| NHGRI | Lisa Chadwick |
| NCATS | Pablo Cure |
| NHLBI | Emmanuel Mongodin |
| NIA | Rebecca Fuldner |
| NIAAA | Joe Wang |
| NIAMS | Ricardo R. Cibotti |
| NICHD | Ashley Vargas |
| NIDA | Jag H. Khalsa |
| NIDCR | Tamara McNealy |
| NIDDK | Bob Karp |
| NIEHS | Anika Dzierlenga |
| NIGMS | Andrea Keane-Myers |
| NIMH | Nancy Desmond |
| NIMHD | Michael Sayre |
| ODS | Cindy Davis |
Systems Biology Consortium for Infectious Diseases Working Groups
The NIAID/DMID Systems Biology Consortium for Infectious Diseases established working groups composed to foster collaboration in areas of shared expertise and project milestones. The working groups focus on critical areas of the program: modeling and data dissemination.
Modeling Working Group
The Modeling Working Group involves computational biologists, data scientists, and statistical modeling experts who work together to identify areas of collaboration and share modeling techniques and tools to leverage expertise across the centers.
Working Group publication:
Systems Biology Consortium Pathogens and Infectious Diseases Studied
The NIAID/Division of Microbiology and Infectious Diseases (DMID) Systems Biology Consortium for Infectious Diseases works with a variety of pathogens from bacteria to viruses, antimicrobial resistance and infectious diseases. Several of these pathogens are considered by NIAID as emerging infectious diseases or that are included in the NIAID Category A, B, or C priority pathogens.
Systems Biology Consortium for Infectious Diseases Resources and Data Sharing
Rapid and unrestricted sharing of data and research resources is essential for advancing research on human health and infectious diseases. The utility of data and resources to the scientific community is largely dependent on how quickly these data are deposited into public databases, whether the data are easy to find, accessible, and can be re-used by others.
Systems Biology Consortium for Infectious Diseases Lecture Series and Meetings
The NIAID/DMID Systems Biology Consortium for Infectious Diseases hosts a webinar series to share the expertise, technological advances, and scientific breakthroughs at each of the centers, and serves as a platform to foster collaboration and knowledge sharing. This lecture series includes members of the NIAID/DMID Systems Biology Consortium and other invited scientists. Lectures are given by participating or invited scientists, ranging from senior investigators to graduate student researchers.
Systems Biology Consortium for Infectious Diseases
The NIAID/Division of Microbiology and Infectious Diseases (DMID) Systems Biology Consortium for Infectious Diseases is a group of interdisciplinary scientists that bridge disparate scientific disciplines including microbiology, immunology, infectious diseases, microbiome, mathematics, physics, bioinformatics, computational biology, machine learning, statistical methods, and mathematical modeling. These teams integrate large-scale experimental biological and clinical data across temporal and spatial scales. Scientists iteratively test and validate hypotheses to gain insight into the overall complexity of the biological, biochemical, and biophysical molecular processes within microbial organisms as well as their interaction with the host. The research findings drive innovation and discovery, with the goal of developing novel therapeutic and diagnostic strategies, and predictive signatures of disease to alleviate infectious disease burden and provide solutions to complex public health challenges and disease outbreaks.
Programs
Currently Funded: Systems Biology for Infectious Diseases
In response to RFA-AI-21-065 Centers conduct research to develop and validate predictive models of infectious disease initiation, progression, and outcomes. These models are derived from the study of the architecture and dynamics of systems-wide host/pathogen molecular interaction networks during infection. The research findings will provide a deeper understanding of the overall complexity of the biological, biochemical, and biophysical molecular processes within microbial organisms, as well as their interaction with the host, and help researchers identify targets for the development of diagnostics, vaccines, and therapeutics.
Icahn School of Medicine at Mount Sinai; SARS-CoV adaptations through a Systems Biology Lens (SYBIL)
- Contact PI: Adolfo Garcia-Sastre
- Project PIs: Adolfo Garcia-Sastre, Sumit Chanda, Michael Schotsaert, and Rafael Medina
- Admin Core PIs: Adolfo Garcia-Sastre and Sumit Chanda
- Data Core PI: Lars Pache
- Technology Core PI: Nevan Krogan
- Modeling Core PI: Rafick Sekaly
Northwestern University at Chicago; Successful Clinical Response in Pneumonia Therapy (SCRIPT) Systems Biology Center
- Contact PI: Richard Wunderink
- Project PIs: Richard Wunderink and Alan Hauser
- Admin Core PI: Richard Wunderink
- Data Core PI: Theresa Walunas
- Technology Core PI: Benjamin Singer
- Modeling Core PIs: Alexander Misharin and Thomas Stoeger
Scripps Research Institute; Consortium for Viral Systems Biology (CViSB)
- Contact PI: Kristian Andersen
- Project PIs: Kristian Andersen, Robert Garry, Ryan McNamara and Donald S Grant
- Admin Core PI: Kristian Andersen
- Data Core PI: Karthik Gangavarapu
- Technology Core PI: Bryan Briney
- Modeling Core PI: Douglas Lauffenburger and Marc Suchard
University of California, Los Angeles; Systems Epigenomics of Persistent Bloodstream Infection
- Contact PI: Michael Yeaman
- Project PIs: Michael Yeaman, Scott Filler, Elaine Reed and Melissa Johnson
- Admin Core PI: Michael Yeaman
- Data Core PI: David Gjertson
- Technology Core PI: Monica Cappelletti
- Modeling Core PI: Aaron Meyer
University of California, San Francisco; Host Pathogen Mapping Initiative (HPMI)
- Contact PI: Nevan Krogan
- Project PIs: Nevan Krogan, Jeffrey Cox, Michael Glickman and Melanie Ott
- Admin Core PIs: Nevan Krogan & Jeffrey Cox
- Data Core PI: Andrej Sali
- Technology Core PIs: Danielle Swaney and Jennifer Doudna
- Modeling Core PI: Trey Ideker
Publications
PubMed search for articles from the current Systems Biology for Infectious Diseases Program.
Previously Funded Systems Biology Centers
For more information, please see the Systems Biology Program History page.
The NIAID/DMID Systems Biology Consortium for Infectious Diseases is committed to training the next generation of researchers and informing the community about the approaches and resources (datasets, analysis tools, predictive models) generated by the programs.
Consortium training and outreach activities include workshops, annual meeting postdoctoral networking sessions, and a webinar series.
Clinical and Single-Cell Transcriptomics for Pneumonia Codeathon
The codeathon brought together data science experts to compare and develop computational approaches to better understand pneumonia.
Systems Biology Consortium Resources
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.
Tuberculosis Research Units Network (TBRU-N)
The Tuberculosis Research Units operate as a collaborative network designed to improve the understanding of Mycobacterium tuberculosis (Mtb)-host interactions. During the past 20 years, there has been significant progress in tuberculosis (TB) research to better understand host-pathogen interactions, but much remains to be learned. Effective management of TB continues to be hampered by a limited understanding of the different stages of this complex disease, as well as the mechanisms that control these stages. An improved understanding of the host and pathogen mechanisms underlying heterogeneity, latency and persistence has the potential to inform novel assays to identify persons at increased risk for progression to active disease, new drugs to shorten the duration of treatment, and other interventions to prevent or improve disease outcome. Finally, some comorbidities including diabetes, hypertension, malnutrition and tobacco smoking are risk factors for TB and for poor TB treatment outcomes, and inflammation in the lung is recognized as an important factor for TB pathogenesis. It is therefore important to understand how these comorbidities and inflammation impact TB progression to improve co-management.
Main Areas of Focus
Each TBRU has been established as part of a multi-disciplinary consortium of investigators and institutions with expertise in clinical research, animal models, microbiology, epidemiology, pharmacology, immunology as well as data and statistical management to characterize bacterial and host determinants that are relevant during stages of infection, disease and transmission, and the impact of bacterial and host heterogeneity on disease outcomes.
Contact Information
For more information about the TBRU network, please contact NIAIDTBRU@mail.nih.gov.
- Brigham and Women’s Hospital (Myco3V TBRU)
PI: D. Branch Moody, Kyu Rhee (Weill Cornell Medical College) - Rutgers, The State University of New Jersey TBRU
PIs: David Alland, Jerrold Ellner, Padmini Salgame - University of Washington TBRU
PIs: Thomas Hawn, Jeffery Cox (University of California, Berkeley) - Weill Cornell Medical College (Tri‐I TBRU)
PIs: Sabine Ehrt, Michael Glickman (Sloan Kettering Institute for Cancer Research)
Infectious Diseases Clinical Research Consortium (IDCRC)
Read more about this network: Infectious Diseases Clinical Research Consortium (IDCRC)
Main Areas of Focus
To organize and conduct Phase 1 through 4 vaccine and treatment trials, including clinical studies in collaboration with industry partners.
Contact Information
In 2019, NIAID established the Infectious Diseases Clinical Research Consortium (IDCRC), a clinical trials network that encompasses the Institute’s long-standing Vaccine and Treatment Evaluation Units (VTEUs) and a consortium leadership group.
The consortium leadership group is chaired by David S. Stephens, M.D., of Emory University, and vice-chair James D. Campbell, M.D., M.S, of the University of Maryland School of Medicine. The group, which includes VTEU investigators as well as other scientific experts in infectious diseases, prioritizes candidate vaccines, diagnostics, therapeutics, and other interventions to test in clinical trials.
The VTEUs are located at institutions across the United States. They conduct Phase 1 through 4 vaccine and treatment trials, including clinical studies in collaboration with industry partners. Depending on the disease or condition, the VTEUs may establish study sites and enroll participants at locations outside the United States. Additionally, VTEU sites have the capacity to conduct human challenge trials—where healthy volunteers are exposed to infection under tightly controlled conditions—of influenza, malaria, and other diseases.
The VTEUs are ready resources to help NIAID respond quickly to public health emergencies, including COVID-19. For example, they rapidly enrolled healthy volunteers for NIAID’s mRNA-1273 vaccine study, and enrolled COVID-19 patients for the Adaptive COVID-19 Treatment Trial, meeting rigorous scientific standards and generating high quality data.
Highlights
NIH-Sponsored Trial of Enterovirus D68 Therapeutic Begins
The National Institutes of Health (NIH) is sponsoring a clinical trial to evaluate the safety of an investigational monoclonal antibody to treat enterovirus D68 (EV-D68), which can cause severe respiratory and neurological diseases such as acute flaccid myelitis (AFM) – similar to polio. Scientists are striving to better understand AFM, which has emerged in the United States with spikes in cases every other year, primarily in the late-summer months over the last decade.