Rotation Projects: Academic Year 2026-27
Below are some of the many potential rotation projects 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 / Oncogene enrichment (via in-nuclei linear DNA degradation)
Contact: Matt Ratanapanichkich, mratanap at caltech.edu
Skills to use and/or to learn: qPCR, basic mammalian cell handling, mammalian cell culture (optional)
Prerequisites: Good general wet lab skills
Areas: global health, environment
Project: 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 low numbers of 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: Diagnostics for Global Health
Project: Development of advanced diagnostic devices for limited resource settings
Subprojects: 1) [ChemE, MedE, MechE] Evaluation and optimization of fluidic-physics-based device functionalities; 2) [Ch, ChemE, MedE] Development of chemistries to improve device functionalities, e.g., heat control, pressure control, readout; 3) [EE] Development of low-complexity electronic modules for cartridge readout and/or operation
Contact: Dr. Si Hyung Jin, shjin at caltech.edu
Skills to use and/or to learn: 1) Fluidic device design and fabrication; 2) General chemical reactions, nucleic acid handling, and isothermal amplification; 3) Circuit design and fabrication
Prerequisites: (1) Enthusiasm for global-health research and translational research; (2) Strong academic background in at least one of the following areas: Microfluidics, Fluid dynamics, Electrical engineering, Chemistry, Chemical engineering, Biomedical engineering, Mechanical engineering; (3) Experience with at least one of the following device fabrication techniques or wet-lab workflows: Photolithography, Soft lithography, Laser cutting, 3D printing, Milling, Plastic molding techniques, Electrical circuit design/programming, General chemical reactions
Reference: /research/diagnostics-for-global-health
Areas: Human virome, method benchmarking, NIH HVP consortium activities
Project: Benchmarking in-house viral enrichment methods against current VLP approaches. Project will interface with wider NIH Human Virome Program (HVP) consortium and should cumulate in a small benchmarking paper
Contacts: Chris Neimeth, cneimeth at caltech.edu and Natalie Wu-Woods, nwuwoods at caltech.edu
Skills to be taught/applied: viral handling, in-house viral enrichment strategies, DNA/RNA extractions, RT, qPCR, ddPCR, NGS, basic data analysis.
Areas: Microbiome, metatranscriptomics, colorectal cancer, host-microbe interactions
Project: Illuminating Microbial Tumor-Hypoxia Relationships in Rectal Cancer Patients Undergoing Curative Therapy
Contact: Chris Neimeth, cneimeth at caltech.edu
Skills to be taught/applied: BSL2 tissue handling, low biomass handling, extractions, in-house bacterial enrichment methods (RNA-MEM), NGS library preparation, data analysis
Rotation project goals: Learn how to process BSL2 human tissue samples using in-house low biomass practices; learn in-house bacterial enrichment method (RNA-MEM); demonstrate RNA-MEM performance in tumoral samples from rectal adenocarcinoma patients through RT-qPCR/RT-ddPCR of host and bacterial markers.
Area: Microbial shapers of the immune activity
Project: Illuminating the microbial functional activity that drives Th17 immune activation in a mouse model (COH collaboration)
Contact: Veronica Chen, mchen3 at caltech.edu
Skills to be taught/applied: BSL1 sample processing/handling, in-house bacterial enrichment strategies (RNA-MEM), DNA/RNA extractions, RT, qPCR/ddPCR, NGS library preparation, basic data analysis
Rotation project goals: Learn how to process BSL1 mouse tissue samples using best practices; learn in-house bacterial enrichment method (RNA-MEM); demonstrate RNA-MEM performance in SFB monocolonized mice tissue from the Honda group (City of Hope); learn NGS library prep; prepare NGS libraries for sequencing from a small set of pilot samples
Areas: Automation, liquid handlers, assay design and validation
Project: Developing and validating high-priority automated workflows in the lab to enable higher throughput studies on a liquid handler (epMotion)
Contact: rustem.admin at caltech.edu
Skills to be taught/applied: liquid handlers, assay design/optimization/validation, NGS library preparation, plate reader, high throughput experimental design and readouts