U.S. Department of Energy

Pacific Northwest National Laboratory

Jeremy Zucker

Professional Title: 
Computational Biologist
Phone Number: 
(509) 371-7311
Email: 
Jeremy.Zucker@pnnl.gov
Biography: 

Over 15 years of experience integrating high-throughput systems biology data with computational methods to advance knowledge in the study of symbiosis, circadian rhythms, evolution, biofuels, human health and infectious disease.

Research Interests: 

● Genome Annotation, Constraint-based Metabolic Reconstruction and Analysis, Pathway Engineering
● Transcriptomics, ChIP-Seq, Metabolomics, Proteomics, 13C-Metabolic flux analysis, 
● Convex Optimization, Probabilistic Graphical Models, Deep Reinforcement Learning
● Agile Development, Literate Programming, Reproducible Research

Publications: 

2018

  • Cannon, W., Zucker, J., Baxter, D., Kumar, N., Baker, S., Hurley, J., & Dunlap, J. (2018). Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy-Based Simulations with Application to Central Metabolism of Neurospora crassa. Processes, 6(6), 63. https://doi.org/10.3390/pr6060063

2017

  • White RA, III, JM Brown, SM Colby, CC Overall, JY Lee, JD Zucker, KR Glaesemann, GC Jansson, and JK Jansson. 2017. "ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data." PeerJ Preprints 5:,doi:10.7287/peerj.preprints.2843v1

2016

  • Henry CS, HC Bernstein, P Weisenhorn, RC Taylor, JY Lee, JD Zucker, and HS Song. 2016. "Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction." Journal of Cellular Physiology 231(11):2339-2345.  doi:10.1002/jcp.25428
  • White RA, III, EM Bottos, T Roy Chowdhury, JD Zucker, CJ Brislawn, CD Nicora, SJ Fansler, KR Glaesemann, KA Glass, and JK Jansson. 2016. "Moleculo long-read sequencing facilitates assembly and resolves functionally active genomic bins from complex soil metagenomes." mSystems 1(3):, doi:10.1128/mSystems.00045-16
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