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…
January 2021 - August 2022
Macosko Lab, Broad Institute
- Single-cell biology, this time in the brain
- Learned a lot about GCP
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
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