Microbial Genomics at BCBB

Genomics has become a mainstream tool, yet the amount of data produced by sequencing instruments or available on public databases presents challenges and opportunities for discovery. Bioinformatics and Computational Biosciences Branch (BCBB) has expertise in many types of genomics methods applied to metagenomics, microbial genomics, transcriptomics, phylogenomics and others. Areas of collaboration include:

• 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

Technologies

• Nephele
• TB Portals
• PaVE
• METAGENOTE

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.