Academic lineage
ImmCellFie: A user-friendly web-based platform to infer metabolic function from omics data
- Helen O Masson, David Borland, Jason Reilly, …, Anne Richelle, Nathan E Lewis, Kimberly Robasky
- STAR Protoc, 10.1016/j.xpro.2023.102069
Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data
- Avi Kumar, Jack Mitchener, Zachary A King, Christian M Metallo
- BMC Bioinformatics, 10.1186/s12859-020-03632-0
Visualizing metabolic network dynamics through time-series metabolomic data
- Lea F Buchweitz, James T Yurkovich, Christoph Blessing, …, Óttar Rolfsson, Julian Heinrich, Andreas Dräger
- BMC Bioinformatics, 10.1186/s12859-020-3415-z
MEMOTE for standardized genome-scale metabolic model testing
- Christian Lieven, Moritz E Beber, Brett G Olivier, …, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang
- Nat Biotechnol, 10.1038/s41587-020-0446-y
The Escherichia coli transcriptome mostly consists of independently regulated modules
- Anand V Sastry, Ye Gao, Richard Szubin, …, Laurence Yang, Zachary A King, Bernhard O Palsson
- Nat Commun, 10.1038/s41467-019-13483-w
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
- Charles J Norsigian, Neha Pusarla, John Luke McConn, …, Andreas Dräger, Bernhard O Palsson, Zachary King
- Nucleic Acids Res, 10.1093/nar/gkz1054
Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism
- Chuankai Cheng, Edward J O’Brien, Douglas McCloskey, …, Adam M Feist, Bernhard O Palsson, Zachary A King
- PLoS Comput Biol, 10.1371/journal.pcbi.1007066
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
- Jean-Christophe Lachance, Colton J Lloyd, Jonathan M Monk, …, Adam M Feist, Zachary A King, Pierre-Étienne Jacques
- PLoS Comput Biol, 10.1371/journal.pcbi.1006971
Enzyme promiscuity shapes adaptation to novel growth substrates
- Gabriela I Guzmán, Troy E Sandberg, Ryan A LaCroix, …, Bernhard O Palsson, Balázs Papp, Adam M Feist
- Mol Syst Biol, 10.15252/msb.20188462
The genetic basis for adaptation of model-designed syntrophic co-cultures
- Colton J Lloyd, Zachary A King, Troy E Sandberg, …, Gregory Humphrey, Rob Knight, Adam M Feist
- PLoS Comput Biol, 10.1371/journal.pcbi.1006213
The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function
- Sankha Ghatak, Zachary A King, Anand Sastry, Bernhard O Palsson
- Nucleic Acids Res, 10.1093/nar/gkz030
Identification of growth-coupled production strains considering protein costs and kinetic variability
- Hoang V Dinh, Zachary A King, Bernhard O Palsson, Adam M Feist
- Metab Eng, 10.1016/j.mec.2018.e00080
Escher-FBA: a web application for interactive flux balance analysis
- Elliot Rowe, Bernhard O Palsson, Zachary A King
- None, 10.1186/s12918-018-0607-5
COBRAme: A computational framework for genome-scale models of metabolism and gene expression
- Colton J Lloyd, Ali Ebrahim, Laurence Yang, …, Edward J O’Brien, Joanne K Liu, Bernhard O Palsson
- PLoS Comput Biol, 10.1371/journal.pcbi.1006302
Modeling the multi-scale mechanisms of macromolecular resource allocation
- Laurence Yang, James T Yurkovich, Zachary A King, Bernhard O Palsson
- Curr Opin Microbiol, 10.1016/j.mib.2018.01.002