Center for Computational and Integrative Biology

About our Center

Faculty in the Center for Computational and Integrative Biology (CCIB) apply interdisciplinary approaches and new technologies to answer enduring biological questions and provide insights into human disease. Novel chemical, genomics and computational tools are developed to probe signaling pathways, identify mediators of host-microbe interactions, understand and simulate the conditions associated with the emergence of life, and design therapeutic disease interventions. Center investigators also conduct translational research to explore the potential utility of early-stage drug candidates in phase 1 studies carried out in small populations of individuals with the target disease indication. 

The CCIB provides support for investigators at Mass General Hospital and across the greater Boston area through a variety of autonomous cores that provide services in DNA sequencing, oligonucleotide synthesis and research laboratory automation. 

In the News

The 33rd Annual Center for the Study of Inflammatory Bowel Disease (CSIBD) Workshop will take place on November 2-3, 2023. The workshop will focus on four key areas: proteins and metabolites in immunity, host-microbiome interactions, T cell functional specification, and tissue organization and memory formation.  Confirmed speakers include Giorgio Trinchieri, Aashik Manglik, Marcia Haigis, Vamsi Mootha, Nicholas Polizzi, Wendy Garrett, Curtis Huttenhower, Alexandra Zhernakova, Andrea Reboldi, Meng Wu, Vijay Kuchroo, Rob Rahimi, Carmen Gerlach, David Artis, Judith Agudo, Rob Manguso, Diane Mathis, Moshe Biton, Azucena Salas, Jeffrey Moffitt, Ruth Franklin, Christoph Thaiss, and Ananda Goldrath.

We are hiring: Assistant Professor, Infectious Disease Focus!  The Center for Integrated Solutions to Infectious Diseases (CISID), together with CCIB, is looking for a talented junior investigator.  For more information, please see our ad.

Welcome Jonathan Strecker, new faculty member in CCIB!  A main interest in the Strecker lab will be to investigate diverse immune proteins throughout nature, including phage defense and CRISPR-Cas systems, with the long-term goal of using these basic discoveries to enable new programmable functions in biology.

Congratulations Chris Smillie for being selected to join the Pew Scholars Program in Biomedical Sciences! The Scholars were chosen from 188 applicants nominated by leading academic institutions and researchers throughout the United States. This year’s class includes scientists who are studying how external and internal factors affect the gut microbiome, what causes HIV to re-emerge when treatment is halted, and how living an urban lifestyle affects long-term health.

Celebrating a historic $100M gift to establish the Gene Lay Institute for Immunology and Inflammation! The gift, from eminent biotechnology entrepreneur Gene Lay, founder and CEO of BioLegend, is the largest in Brigham's history. The Gene Lay Institute will be led by Vijay Kuchroo, an immunologist and principal investigator at the Brigham who will serve as inaugural director, Arlene Sharpe, chair of the Department of Immunology at HMS, and Ramnik Xavier, our Center Director. Areas of research will include basic understanding of immune-mediated diseases, aging, and cancer toward the development of new immunotherapies. The Institute will also provide training opportunities for students and fellows to support immunology innovators of the future.

Congratulations Emanuel Burgos-Robles in the Smillie lab, for receiving the prestigious NSF Graduate Research Fellowship! Ema is a graduate student in the MIT Computational and Systems Biology PhD Program (CSB).



  • Small-Molecule Organocatalysis Facilitates In Situ Nucleotide Activation and RNA Copying. J Am Chem Soc. 2023;145(29):16142-16149

  • Identification of host regulators of Mycobacterium tuberculosis phenotypes uncovers a role for the MMGT1-GPR156 lipid droplet axis in persistence. Cell Host Microbe. 2023;31(6):978-992.e5

  • Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan. Nat Microbiol. 2023;8(6):1064-1078

  • Association of distinct microbial signatures with premalignant colorectal adenomas. Cell Host Microbe. 2023;31(5):827-838.e3

  • Genome-wide tiled detection of circulating Mycobacterium tuberculosis cell-free DNA using Cas13. Nat Commun. 2023;14(1):1803

  • Remodeling of colon plasma cell repertoire within ulcerative colitis patients. J Exp Med. 2023;220(4):ePub

  • The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon. Immunity. 2023;56(2):444-458.e5

  • Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states. Cell. 2023;186(4):877-891.e14

  • Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism. Cell. 2022;185(26):4921-4936.e15

  • The Caenorhabditis elegans ARIP-4 DNA helicase couples mitochondrial surveillance to immune, detoxification, and antiviral pathways. Proc Natl Acad Sci U S A. 2022;119(49):e2215966119

  • Phase 2 Trial of Baxdrostat for Treatment-Resistant Hypertension. N Engl J Med. 2022;388(5):395-405

  • A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning. Cell. 2022;185(23):4280-4297.e12

  • Folding and Duplex Formation in Sequence-Defined Aniline Benzaldehyde Oligoarylacetylenes. J Am Chem Soc. 2022;144(40):18350-18358

  • Engineered CRISPR prime editors with compact, untethered reverse transcriptases. Nat Biotechnol. 2022;41(3):337-343

  • NIN-like protein 7 transcription factor is a plant nitrate sensor. Science. 2022;377(6613):1419-1425

  • Glucose-driven TOR-FIE-PRC2 signalling controls plant development. Nature. 2022;609(7929):986-993

See all publications