Microbial Genomics

Genomics has become a mainstream tool yet and the amount of data produced by sequencing instruments or available on public databases presents challenges and opportunities for discovery. BCBB has expertise on many types of genomics methods applied to metagenomics, microbial genomics, transcriptomics, phylogenomics and others. See below for examples of microbial genomics collaboration areas and tools and visit pages for clinical genomics page and metagenomics page to learn more.

We are available to engage in research collaborations, offer you consultations, assist you with pipeline development, and even provide you with custom training on a method or tool as needed. Some collaborations with NIAID investigators have also led to the development of bioinformatics tools and pipelines for public use. See the Relevant Tools section (right panel) to learn about some of these tools.

For assistance with a NIAID bioinformatics or computational biology project, please LOGIN and return to this page

Microbial Genomics Collaboration Areas

  • Assembly of viral, bacterial and eukaryotic genomes.
  • Structural and functional annotation of genomic and transcriptomics datasets.
  • Comparative genomics, identification and characterization of gene families and mobile genetic elements.
  • Genome diversity studies, including identification, annotation, and analysis of single and multiple nucleotide polymorphisms.
  • Phylogenetic analysis and molecular evolution.
  • Single-cell and bulk RNA-seq, ChIP-seq, and ATAC-seq analysis and integration using longitudinal and cross-sectional experimental designs.
  • Gene ontology and gene enrichment analyses, functional gene clustering and network studies.
  • Host-pathogen interaction studies.
  • Development of custom bioinformatic analysis pipelines.

Microbial Genomics Team

  • Kurt Wollenberg, Ph.D. (Group coordinator)
  • Madeline Galac, Ph.D.
  • Brendan Jeffrey, Ph.D.
  • Janet Chang, Ph.D.
  • Margaret Ho, Ph.D.

Selected Publications

  • Beare, P. A., Jeffrey, B. M., Long, C. M., Martens, C. M. and Heinzen, R. A. Genetic mechanisms of Coxiella burnetii lipopolysaccharide phase variation. PLoS Pathog, 14, 3 (Mar 2018), e1006922. https://doi.org/10.1371/journal.ppat.1006922. PMID: 29481553
  • Cooper, K. G., Chong, A., Kari, L., Jeffrey, B., Starr, T., Martens, C., McClurg, M., Posada, V. R., Laughlin, R. C., Whitfield-Cargile, C., Garry Adams, L., Bryan, L. K., Little, S. V., Krath, M., Lawhon, S. D. and Steele-Mortimer, O. Regulatory protein HilD stimulates Salmonella Typhimurium invasiveness by promoting smooth swimming via the methyl-accepting chemotaxis protein McpC. Nat Commun, 12, 1 (Jan 13 2021), 348. https://doi.org/10.1038/s41467-020-20558-6. PMID: 33441540.
  • Larson, C. L., Martinez, E., Beare, P. A., Jeffrey, B. M., Heinzen, R. A. and Bonazzi, M. Right on Q: genetics begin to unravel Coxiella burnetii host cell interactions. Future Microbiol, 11 (Jul 2016), 919-939. https://doi.org/10.2217/fmb-2016-0044. PMID: 27418426
  • Schureck, M. A., Darling, J. E., Merk, A., Shao, J., Daggupati, G., Srinivasan, P., Olinares, P. D. B., Rout, M. P., Chait, B. T., Wollenberg, K., Subramaniam, S. and Desai, S. A. Malaria parasites use a soluble RhopH complex for erythrocyte invasion and an integral form for nutrient uptake. Elife, 10 (Jan 4 2021). https://doi.org/10.7554/eLife.65282. PMID: 33393463
  • Srivastava, K., Wollenberg, K. R. and Flegel, W. A. The phylogeny of 48 alleles, experimentally verified at 21 kb, and its application to clinical allele detection. J Transl Med, 17, 1 (Feb 11 2019), 43. https://doi.org/10.1186/s12967-019-1791-9. PMID: 30744658.
  • Wollenberg, K., Harris, M., Gabrielian, A., Ciobanu, N., Chesov, D., Long, A., Taaffe, J., Hurt, D., Rosenthal, A., Tartakovsky, M. and Crudu, V. A retrospective genomic analysis of drug-resistant strains of M. tuberculosis in a high-burden setting, with an emphasis on comparative diagnostics and reactivation and reinfection status. BMC Infect Dis, 20, 1 (Jan 7 2020), 17. https://doi.org/10.1186/s12879-019-4739-z. PMID: 31910804.
Related tools developed by BCBB

TB Portals 

Open, web-based database that integrates clinical, bacterial genomic, and medical imaging data from tuberculosis patients to facilitate meta-domain and domain-specific TB data exploration and analysis.


SARS-CoV-2 pipeline: pipeline for variant calling and consensus sequence generation


Cloud application for metadata annotation and SRA submission of sequence data


Pamillomavirus episteme database and tools