Timothy J. Straub

Senior Data Scientist · Remote

Leading development and validation of novel microbiome metrics using machine learning on large-scale metagenomic and health data; building scalable, reproducible analysis frameworks in R and Python and supporting clinical study design.

Senior Data Scientist, Computational Microbiome Sciences · Cambridge, MA

Drove multi-omic computational analyses for microbiome therapeutics from preclinical development through Phase 3 clinical evaluation (SER-109/VOWST®); developed and maintained a proprietary R package.

Senior Computational Associate, Bacterial Genomics · Cambridge, MA

Analyzed large omics/NGS datasets (16S, metagenomics, RNA-seq) in the Infectious Disease and Microbiome Program; developed and maintained NGS pipelines including the software suite StrainGE.

Visiting Scientist, Neafsey Lab · Boston, MA

Computational research on sequencing data from malaria parasites and their vectors, including single-cell and amplicon sequencing analysis that led to the AmpSeQC tool.

• Bryant JA, Straub TJ, et al. Comparability of Gastrointestinal Microbiome and Bile Acid Profiles in Patients With First or Multiply Recurrent Clostridioides difficile Infection. The Journal of Infectious Diseases, 2025. doi:10.1093/infdis/jiaf408
• Bryant JA, et al. The impact of an oral purified microbiome therapeutic on the gastrointestinal microbiome. Nature Medicine, 2026. doi:10.1038/s41591-025-04076-w
• Straub TJ, Lombardo M-J, Bryant JA, et al. Impact of a purified microbiome therapeutic on abundance of antimicrobial resistance genes in patients with recurrent Clostridioides difficile infection. Clinical Infectious Diseases, 2023. doi:10.1093/cid/ciad636
• Young MG*, Straub TJ*, et al. Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection. Nature Communications, 2024. doi:10.1038/s41467-024-53829-7
• Worby CJ, Schreiber HL, Straub TJ, et al. Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women. Nature Microbiology, 2022. doi:10.1038/s41564-022-01107-x
• van Dijk LR, Walker BJ, Straub TJ, et al. StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities. Genome Biology, 2022. doi:10.1186/s13059-022-02630-0
• Straub TJ*, Chou WC*, et al. Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections. BMC Microbiology, 2021. doi:10.1186/s12866-021-02106-4
• Straub TJ, Shaw WR, Marcenac P, et al. The Anopheles coluzzii microbiome and its interaction with the intracellular parasite Wolbachia. Scientific Reports, 2020. doi:10.1038/s41598-020-70745-0
• Brancucci NMB*, De Niz M*, Straub TJ*, et al. Probing Plasmodium falciparum sexual commitment at the single-cell level. Wellcome Open Research, 2018. doi:10.12688/wellcomeopenres.14645.4
• Straub TJ, Zhaxybayeva O. A null model for microbial diversification. PNAS, 2017. doi:10.1073/pnas.1619993114

A toolkit to track and characterize low-abundance strains in complex microbial communities. Published in Genome Biology (2022).

Amplicon sequencing quality control pipeline, developed from work on malaria parasites and their vectors. Published in Molecular Ecology Resources (2022). Read the paper.

M.Sc. in Biological Sciences

Thesis published as “A null model for microbial diversification,” PNAS 2017.

B.S. in Biology and Chemistry

A web app I built for designing gallery walls — plan, arrange, and preview picture layouts before you put a single nail in the wall.

An AI coding agent orchestrator I'm building. More to come soon.