Bioinformatic Analysis of Cell-Cell Interaction Networks
Iain Clark, Professor
Bioengineering
Closed. This professor is continuing with Fall 2024 apprentices on this project; no new apprentices needed for Spring 2025.
We recently developed a molecular method that categorizes the cellular connections and transcriptional profiles of glial cells in the mouse brain. The data from this technique can be represented as a highly connected network. The goal of this project is to discover ligand-receptor interactions that promote inflammation in the brain using network analysis. Keywords: CNS, neuroinflammation, single-cell sequencing, genomics, transcriptomics, bioinformatics, computational biology
Role: We are currently seeking an undergraduate to work in a remote, independent position mentored weekly by a graduate student on this project. Remote workers are expected to attend weekly check-ins and lab meetings in-person. The goal of the project includes continuing development of a bioinformatic pipeline and investigation of ligand-receptor pairs within real cell-cell interaction data from viral tracing experiments.
Qualifications: Preferred qualifications include: strong computational skills (At least 3 semesters in computational or statistics major or equivalent), Python, familiarity with Savio, desire to learn and familiarize with bioinformatic skills, packages, and programs, desire to learn basic molecular biology concepts. Must be available 10 or more hours per week (8 or more hours remote, 2-3 hours in-person)
Day-to-day supervisor for this project: Kevin Joslin, Graduate Student
Hours: 9-11 hrs
Related website: https://clarklab.berkeley.edu/
Related website: https://www.science.org/doi/10.1126/science.abf1230?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed