Academic lineage
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
- Joanne K Liu, Colton Lloyd, Mahmoud M Al-Bassam, …, Alexander Aksenov, Pieter Dorrestein, Karsten Zengler
- PLoS Comput Biol, 10.1371/journal.pcbi.1006848
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
ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions
- Haythem Latif, Stephen Federowicz, Ali Ebrahim, …, Jose Utrilla, Karsten Zengler, Bernhard O Palsson
- PLoS One, 10.1371/journal.pone.0197272
Principles of proteome allocation are revealed using proteomic data and genome-scale models
- Laurence Yang, James T Yurkovich, Colton J Lloyd, Ali Ebrahim, Michael A Saunders, Bernhard O Palsson
- Sci Rep, 10.1038/srep36734
solveME: fast and reliable solution of nonlinear ME models
- Laurence Yang, Ding Ma, Ali Ebrahim, Colton J Lloyd, Michael A Saunders, Bernhard O Palsson
- BMC Bioinformatics, 10.1186/s12859-016-1240-1
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
- Zachary A King, Justin Lu, Andreas Dräger, …, Ali Ebrahim, Bernhard O Palsson, Nathan E Lewis
- Nucleic Acids Res, 10.1093/nar/gkv1049
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
- Zachary A King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E Lewis, Bernhard O Palsson
- PLoS Comput Biol, 10.1371/journal.pcbi.1004321
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
- Laurence Yang, Justin Tan, Edward J O’Brien, …, Yuekai Sun, Michael A Saunders, Bernhard O Palsson
- Proc Natl Acad Sci U S A, 10.1073/pnas.1501384112
Model-driven discovery of underground metabolic functions in Escherichia coli
- Gabriela I Guzmán, José Utrilla, Sergey Nurk, …, Ali Ebrahim, Bernhard O Palsson, Adam M Feist
- Proc Natl Acad Sci U S A, 10.1073/pnas.1414218112
Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium
- Ryan A LaCroix, Troy E Sandberg, Edward J O’Brien, …, Richard Szubin, Bernhard O Palsson, Adam M Feist
- Appl Environ Microbiol, 10.1128/aem.02246-14
Minimal metabolic pathway structure is consistent with associated biomolecular interactions
- Aarash Bordbar, Harish Nagarajan, Nathan E Lewis, …, Stephen Federowicz, Jan Schellenberger, Bernhard O Palsson
- Mol Syst Biol, 10.15252/msb.20145243