Center for Computational and Integrative Biology
Our Mission
The mission of our Center is to understand the biological mechanisms that shape health and disease and translate this knowledge into strategies that improve human health by integrating mechanistic, genetic, and microbial research with patient-focused studies and therapeutic development.
By examining how molecular and cellular networks respond to environmental, nutritional, and inflammatory signals—using systems that range from microbes and plants to mammalian tissues we reveal processes that drive resilience or dysfunction. These insights support the development of small molecules, biologics, and host-directed therapies, connecting fundamental discovery with clinically informed strategies that improve human health.
CCIB is a Nexus for Basic Science and Clinical Investigators
We serve as both a hub and active partner in major research programs.
The Center for the Study of Inflammatory Bowel Disease (CSIBD) identifies microbial and molecular markers of disease risk and therapy response, developing predictive models to guide patient-focused strategies.
The Center for Integrated Solutions for Infectious Diseases (CISID) examines the mechanisms of infection and its complications to improve diagnosis, treatment, and management.
The Gene Lay Institute (GLI), advancing research in aging and immunity, cancer immunology, and tissue inflammation while fostering interdisciplinary collaboration and linking mechanistic discovery with clinical impact.
News and Events
Workshop: Gene Lay Institute Aging & Immunity – December 8, 2025. Hear the latest on how immune system-tissue interactions are perturbed during aging and how these perturbations impact physiology, immune regulation, and disease development. Speakers include long time CCIB collaborator Naomi Habib, who recently described her work on implementation and validation of single-cell genomics experiments in neuroscience (Nature Neurosci). Learn more and register here.
Open to CCIB researchers: Tapestri Tutorial - December 19, 2025. This hands-on tutorial will cover experimental design and applications of the Tapestri Single Cell Multiomics Platform led Kai Liu at the Broad Institute. If you are interested in attending, please register using this Google Form. To learn more about Tapestri applications, see Kai’s recent bioRxiv preprint describing STAG-seq, a high-throughput approach integrating Tapestri with HyPR-seq to enable simultaneous single-cell DNA and RNA profiling.
Applying AI To Transform Biomedical Research - January 28, 2026. The AI4ID: Bridging Infection and Artificial Intelligence Symposium, jointly hosted by CISID and the Eric and Wendy Schmidt Center, will bring together leading infectious disease scientists and clinicians with AI experts to think creatively about how AI technologies can solve the most pressing challenges in infection research. More information and registration here.
Gut Check: How the Microbiome Shapes Inflammation and Depression. A recent collaboration between investigators in CCIB and the HMS Blavatnik Institute revealed that the gut bacterium Morganella morganii may contribute to major depressive disorder by incorporating an environmental contaminant into a molecule that triggers inflammation. This contaminant could serve as a biomarker and supports links between depression and autoimmune processes. Read more in the HMS news story.
Publications
Reference-based chemical-genetic interaction profiling to elucidate small molecule mechanism of action in Mycobacterium tuberculosis. Nat Commun. 2025;16(1):9673
Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes. Nat Microbiol. 2025;10(11):2720-2735
Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation. Science. 2025;390(6772):eadr3545
Kmo restricts Salmonella in a whole organism infection model by promoting macrophage lysosomal acidification through kainate receptor antagonism. PLoS Pathog. 2025;21(10):e1013273
Single-cell transcriptomic characterization of microscopic colitis. Nat Commun. 2025;16(1):4618
Decreased SynMuv B gene activity in response to viral infection leads to activation of the antiviral RNAi pathway in C. elegans. PLoS Biol. 2025;23(1):e3002748
Hydrogen sulfide mediates the interaction between C. elegans and Actinobacteria from its natural microbial environment. Cell Rep. 2025;44(1):115170
Development of an FKBP12-recruiting chemical-induced proximity DNA-encoded library and its application to discover an autophagy potentiator. Cell Chem Biol. 2025;32(3):498-510.e35
Discovery of a Pseudomonas aeruginosa-specific small molecule targeting outer membrane protein OprH-LPS interaction by a multiplexed screen. Cell Chem Biol. 2024;32(2):307-324.e15
ABA-activated low-nanomolar Ca2+-CPK signalling controls root cap cycle plasticity and stress adaptation. Nat Plants. 2024;11(1):90-104
