Rotation Projects: Academic Year 2025-26
Below are the rotation projects that are suitable for incoming graduate students in multiple Options / Divisions. If you are a G1 graduate student at Caltech interested in doing a rotation with Ismagilov Lab on one of these topics, please reach out to the student or postdoc associated with the project for more details.
Areas: global health, cancer
Project: Development of novel single-cell analysis tools for studying and detecting cancer
Contact: Matt Ratanapanichkich, mratanap at caltech.edu
Skills to use and/or to learn: qPCR, basic mammalian cell handling, mammalian cell culture (optional)
Areas: global health, environment
Projects (2): Technology to understand bacterial-viral-plasmid-interactions in antibiotic resistance, human health, carbon cycling, and environment
Contact: Matt Ratanapanichkich, mratanap at caltech.edu
Skills to use and/or to learn: synthetic hydrogel chemistry, qPCR, basic biochem manipulations; basic bacterial cell handling,
Area: Tool development for exploration of low-biomass microbiomes
Project: Development of the first rigorous quantitative method for low-biomass bacterial RNA sequencing
Contact: Matt Cooper, mattcooper at caltech.edu
Skills to use and/or to learn: Computational analysis with stochastic math and pipeline development -or- NGS, qPCR, basic data analysis, assay design and optimization
Area: Tool development for human microbiome exploration
Project: Development of tools for detection of single biomarker molecules in complex clinical matrices
Contact: Matt Cooper, mattcooper at caltech.edu
Skills to use and/or to learn: qPCR, basic data analysis, assay design and optimization
Area: The plant microbiome and agriculture
Project: Investigating the plant endosphere
Contact: Chris Neimeth, cneimeth at caltech.edu
Skills to use and/or to learn: qPCR, basic data analysis
Area: Exploring the mycobiome (fungal microbiome)
Project: Investigating fungal mRNA expression in human cells
Contact: Chris Neimeth, cneimeth at caltech.edu
Skills to use and/or to learn: Fungal culture, qPCR, RT, DNase treatment, RNA clean-up, extraction, basic data analysis
Area: Role of the microbiome in human disease and health
Project: Microbial impacts on Parkinson's disease
Contact: Natalie Wu-Woods, nwuwoods at caltech.edu
Skills to be taught: NGS, computational biology
Prerequisites: Strong working knowledge of Python
Reference: Natalie J. Wu-Woods, Jacob T. Barlow, Florian Trigodet, Dustin G. Shaw, Anna E. Romano, Bana Jabri, A. Murat Eren, and Rustem F. Ismagilov. 2023. "Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples." Nature Methods 20: 1672–1682. doi: 10.1038/s41592-023-02025-4. Manuscript
Area: Understanding microbe-host interactions in infection (COVID-19) to inform mucosal vaccine development
Project: Studying the dynamics and influence of the microbial ecosystem on human mucosal immune function
Contact: Dr. Alex Viloria Winnett, awinnett at caltech.edu
Skills to be taught: Computational genomics, bacterial taxonomy, timeseries analysis, systems biology (Note: this is a dry lab project working with transcriptomic data from human samples)
Prerequisites: Strong computational skills (Python, bash) and familiarity with high performance computing
Reference: https://covid-study.caltech.edu/publications
Area: Microbe-host interactions in infection (COVID-19) to inform mucosal vaccine development
Project: Role of non-coding RNAs (e.g. lncRNA, mirRNA, snoRNA) in regulation of the mucosal immune response to acute viral infection
Contact: Dr. Alex Viloria Winnett, awinnett at caltech.edu
Skills to be taught: Computational genomics, network analysis, timeseries analysis (Note: this is a dry lab project working with transcriptomic data from human samples)
Prerequisites: Strong computational skills (Python, bash) and familiarity with high performance computing
Reference: https://covid-study.caltech.edu/publications
Area: Microbe-host interactions in infection and re-activation of latent infection
Project: Viral element reactivation during acute infection (transcriptional control in humans, non-coding regulatory RNA)
Contact: Dr. Alex Viloria Winnett, awinnett at caltech.edu
Skills to be taught: Computational genomics, timeseries analysis, innate immunology, mucosal immunology (Note: this is a dry lab project working with transcriptomic data from human samples)
Prerequisites: Strong computational skills (Python, bash) and familiarity with high performance computing
Reference: https://covid-study.caltech.edu/publications
Area: Diagnostics for Global Health
Project: Development of advanced diagnostic devices for limited resource settings
Contact: Dr. Si Hyung Jin, shjin at caltech.edu
Skills to be taught: microfluidics, device fabrication
Prerequisites: Enthusiasm for global-health research and translational research. One of the following academic backgrounds: Microfluidics, fluid dynamics, electrical engineering, chemical engineering, biomedical engineering; Experience with one of the following device fabrication techniques (or wet lab experience): Photolithography, soft lithography, laser cutting, 3D printing, milling, any plastic molding techniques, electrical circuit design/programming.
Reference: /research/diagnostics-for-global-health