NP-Complete Breakfast

James T Webber

Education

Experience

Graduate Research Assistant

September 2011 – present

Dr. Sourav Bandyopadhyay & Dr. Nevan Krogan, UCSF

  • Modeling drug sensitivity in breast cancer by integrating systems-levels ‘omics datasets.
  • Developing methods to integrate genomic and proteomic data from tumor samples and cancer-derived cell lines together with drug response data to identify new biomarkers and subtypes.
  • Analyzing quantitative mass-spectrometry data to characterize the kinase activity profile of breast cancer cell lines after treatment with a panel of targeted inhibitors.
  • Currently developing an ensemble model of drug response based on single-cell heterogeneity data

Bioinformatics Engineer

March 2009 – August 2011

Dr. Jarrod Marto, Dana-Farber Cancer Institute, Boston, MA

  • Main developer for Multiplierz, an open-source Python-based environment for mass-spectrometry based proteomics.
  • Implemented an automated pipeline for data acquisition, storage, analysis and post-processing.
  • Developed a new database-based format and interactive viewer for efficiently sharing the results of proteomic experiments.
  • Assisted in developing a web-based API for sharing mass spectrometry data.
  • Worked with multiple researchers in the lab to write customized data analysis workflows.

Teaching & Outreach

Publications