Defective efferocytosis, the phagocytic clearance of apoptotic cells, by macrophages is the cause of many human diseases including tumor, autoimmune diseases and atherosclerosis. Enhancing efferocytosis has potential therapeutic benefits. Many key regulators of efferocytosis have been identified, but a systematic approach to map regulators of efferocytosis in an unbiased manner on a genome-wide scale is missing. This project applies innovative genome-wide CRISPR screen to discover novel regulators of macrophage efferocytosis.

The NGS data of the screen have already been analyzed and the ranking/score of the top hits are obtained. The students involved in this project are expected to work on: (1) illustration of the data by generating a variety of plots using R/Bioconductor packages; (2) Interpretation of the data using packages such as GSEA, DEPICT, MAGENTA.; (3) query public resources, including GTEx and GEO, to prioritize tissue-relevant and disease-related hits.

One selected candidate will receive a stipend via the DSI Scholars program. Amount is subject to available funding.

Faculty Advisor

  • Professor Hanrui Zhang
  • Department/School: Medicine/CUMC
  • Location: CUMC
  • The Zhang laboratory is interested in studying the role of macrophages in cardiometabolic diseases using human iPS cells, CRISPR gene editing and screening, and functional genomic approaches including next-gen sequencing.

Project timeline

  • Earliest starting date: 03/01/2019
  • End date: 07/31/2019
  • Number of hours per week of research expected during Spring 2019: ~4
  • Number of hours per week of research expected during Summer 2019: ~4

Candidate requirements

  • Skill sets: R and Bioconductor
  • Student eligibility (as of Spring 2019): freshman, sophomore, junior, senior, master’s
  • International students on F1 or J1 visa: eligible
  • Additional comments: Students should be interested in bioinformatics in a biomedical research setting.