Bioinformatician & Data Scientist

PhD., Microbiology

Massachussetts Institute of Technology (MIT)

Cambridge, MA, USA

2021 - 2014

• Dissertation: High-resolution time series reveals differential behaviors of closely-related microbes in coastal communities.
• Advisor: Martin Polz
• Emphasis: Bioinformatics and statistics of microbial community sequencing

B.S., Biology

Georgia Institute of Technology (Georgia Tech)

Atlanta, GA, USA

2013 - 2008

• Thesis: Characterizing a novel direct target of the quorum-sensing controlled small RNAs in V. cholerae.
• Advisor: Brian Hammer
• Emphasis: Bacterial genetics and microbial metabolism

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.
• 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.

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.

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