NP-Complete Breakfast

James T Webber



Senior Computational Scientist

September 2022 - present

Methods Development Lab, Broad Institute

  • Developing new sequencing methods, particularly those involving long released
  • Learning about all kinds of stuff, TBD…

Computational Scientist

January 2021 - August 2022

Macosko Lab, Broad Institute

  • Single-cell biology, this time in the brain
  • Learned a lot about GCP

Bioinformatics Scientist

July 2017 - December 2020

Data Sciences, Chan-Zuckerberg Biohub

  • Learned a lot about single-cell RNA sequencing
  • Learned a lot about AWS
  • Learned far too much about NovaSeq raw data. See here for details.

Graduate Research Assistant

September 2011 – July 2017

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