Aside

I’m a microbiome-focused data scientist and bioinformatician with 10 years of experience developing workflows for processing raw sequencing data. I work as a resource in a large research group developing and running pipelines, integrating datasets with thousands of samples and several modalities, and training and advising other researchers on data generation and analysis, all with the goal of understanding how the microbes in the human vagina protect or disrupt mucosal immunity.

Contact

Skills

Programming:

Bioinformatics:

Data Analysis:

Disclaimer

Made with the R package pagedown.
Forked from wjakethompson/cv

Main

Joseph Elsherbini, PhD

Bioinformatician & Data Scientist

Education

PhD., Microbiology

Massachussetts Institute of Technology (MIT)

Cambridge, MA, USA

2021 - 2014

B.S., Biology

Georgia Institute of Technology (Georgia Tech)

Atlanta, GA, USA

2013 - 2008

Employment

Bioinformatician and Data Scientist | Kwon Lab

Ragon Institute of MGB, MIT, and Harvard

Cambridge, MA, USA

present - 2021

  • Supported bioinformatics needs in a lab of over 30 researchers and staff based both in the US and South Africa studying vaginal microbiome. Integrated and analyzed multi-omics datasets comprising thousands specimens assayed in many modalities.
  • Developed pipelines using Snakemake and Nextflow and trained the group on how to use the pipelines and how to analyze data further. Created documentation website and group github repository.
  • Managed two bioinformatics technicians who assisted researchers in the group and conducted independent research.
  • Developed and conducted workshops in the United States and in South Africa to support collaborators and group members.

Graduate Research Assistant | Polz Lab

MIT

Cambridge, MA, USA

2021 - 2015

  • Studied microbial ecology and evolution with a focus on Vibrio, microeukaryotes, and viruses in the coastal ocean.
  • Built Snakemake pipelines for genome assembly and annotation, amplicon processing with dada2, and others as needed.
  • Processed and analyzed large amplicon datasets, shotgun metagenomics, and bacterial transcriptomics.

Undergraduate Researcher | Hammer Lab

Georgia Tech

Atlanta, GA, USA

2013 - 2008

  • Studied quorum-sensing in Vibrio cholerae using genetic tools and molecular methods.
  • Developed a computational tool for predicting sRNA binding based on sequence.

Teaching

Data Science for Biology Workshop Series | Durban Data Science

Vaginal Microbiome Research Consortium

Durban, KZN, South Africa

2025 - 2023

  • Led a three-part workshop series to address computational needs with collaborators in South Africa.
  • Created the curriculum, produced the website, coordinated with other instructors, and provisioned AWS-based cloud instances for the participants.
  • Details at https://elsherbini.github.io/durban-data-science-for-biology/

Consultant | BE Data Lab

MIT

Cambridge, MA, USA

2022 - 2020

  • Created and delivered short Snakemake and basic R modules targetted at graduate researchers.
  • Established a framework for biological data science education with a focus on four key areas: (1) Raw data processing, (2) Exploratory data analysis, (3) Simulation, uncertainty, and inference, and (4) Computation and data management.

Team Leader | Hands On Atlanta

AmeriCorps

Atlanta, GA, USA

2011 - 2009

  • Served in a program aimed at increasing high school graduation rates.
  • Managed a team of two to provide classroom support and after-school programming for elementary and middle-school children.

Selected Publications

Effect of the vaginal live biotherapeutic LACTIN-V (Lactobacillus crispatus CTV-05) on vaginal microbiota and genital tract inflammation among women at high risk of HIV acquisition in South Africa: a phase 2, randomised, placebo-controlled trial

Hemmerling, A., Mitchell, C. M., Demby, S., Gebremichael, M., Elsherbini, J., Xu, J., Xulu, N., Shih, J., Dong, K., Govender, V., & others, (2024). Effect of the vaginal live biotherapeutic LACTIN-V (Lactobacillus crispatus CTV-05) on vaginal microbiota and genital tract inflammation among women at high risk of HIV acquisition in South Africa: a phase 2, randomised, placebo-controlled trial. The Lancet Microbe. https://doi.org/10.1016/j.lanmic.2024.101037

N/A

2024

Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages

Hussain, F. A., Dubert, J., Elsherbini, J., Murphy, M., VanInsberghe, D., Arevalo, P., Kauffman, K., Rodino-Janeiro, B. K., Gavin, H., Gomez, A., & others, (2021). Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages. Science, 374(6566), 488–492. https://doi.org/10.1126/science.abb1083

N/A

2021

Evolution of a vegetarian Vibrio: metabolic specialization of Vibrio breoganii to macroalgal substrates

Corzett, C. H., Elsherbini, J., Chien, D. M., Hehemann, J., Henschel, A., Preheim, S. P., Yu, X., Alm, E. J., & Polz, M. F. (2018). Evolution of a vegetarian Vibrio: metabolic specialization of Vibrio breoganii to macroalgal substrates. Journal of Bacteriology, 200(15), 10–1128. https://doi.org/10.1128/jb.00020

N/A

2018