Dennis Goldfarb, PhD

Assistant Professor
Cell Biology and Physiology
Institute for Informatics

Biomedical Informatics and Data Science Program
Computational and Systems Biology Program
Molecular Cell Biology Program
Biochemistry, Biophysics, and Structural Biology Program


  • Mass Spectrometry, Proteomics, Bioinformatics

  • Computational mass spectrometry and proteomics

Research Abstract:

Our laboratory develops proteomic technologies to study mechanisms in cellular biology and disease. Specifically, our objective is to achieve full proteome quantification using mass spectrometry by developing novel data acquisition strategies and bioinformatics tools in conjunction with informative data visualization.

Data Acquisition: Using machine learning, statistical modeling, and computer science we develop algorithms that control and optimize the instrument’s data acquisition strategy in real-time to improve identification, quantification, and create novel analytical capabilities.

Bioinformatics: We create data analysis and visualization tools tailored to the challenges of unique experiments. We aim to increase the throughput and reproducibility of large-scale projects with automated pipelines that leverage high-performance computing.

Protein Complexes: The complexome is the catalogue of all protein complexes in a cell. What are their members, subunits, and stoichiometries? How do they interact with each other? How do they change under different conditions? Our lab is developing the tools to answer these questions in high-throughput.

Selected Publications:

Discovering the Microbial Enzymes Driving Drug Toxicity with Activity-Based Protein Profiling.
Jariwala PB, Pellock SJ, Goldfarb D, Cloer EW, Artola M, Simpson JB, Bhatt AP, Walton WG, Roberts LR, Major MB, Davies GJ, Overkleeft HS, Redinbo MR.
ACS Chem Biol. 2020 Jan 17;15(1):217-225.

NRF2 Activation in Cancer: From DNA to Protein.
Cloer EW, Goldfarb D, Schrank TP, Weissman BE, Major MB.
Cancer Res. 2019 Mar 1;79(5):889-898. doi: 10.1158/0008-5472.CAN-18-2723. Epub 2019 Feb 13. Review.
PMID: 30760522 Free PMC Article
Similar articles
Select item 30288463

Approximating Isotope Distributions of Biomolecule Fragments.
Goldfarb D, Lafferty MJ, Herring LE, Wang W, Major MB.
ACS Omega. 2018 Sep 30;3(9):11383-11391.

Competitive Kinase Enrichment Proteomics Reveals that Abemaciclib Inhibits GSK3β and Activates WNT Signaling.
Cousins EM, Goldfarb D, Yan F, Roques J, Darr D, Johnson GL, Major MB.
Mol Cancer Res. 2018 Feb;16(2):333-344

MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics.
Goldfarb D, Wang W, Major MB.
Bioinformatics. 2016 Apr 15;32(8):1269-71.

Last Updated: 11/7/2022 11:33:40 AM

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