Academic lineage
- Bernhard Ø Palsson - Ph.D. student
A Phase 1b Safety Study of SER-287, a Spore-Based Microbiome Therapeutic, for Active Mild to Moderate Ulcerative Colitis
- Matthew R Henn, Edward J O’Brien, Liyang Diao, …, Bharat K Misra, John G AuninÅ¡, Michele Trucksis
- Gastroenterology, 10.1053/j.gastro.2020.07.048
SER-109, an Investigational Microbiome Drug to Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial
- Barbara H McGovern, Christopher B Ford, Matthew R Henn, …, Roger J Pomerantz, John G AuninÅ¡, Michele Trucksis
- Clin Infect Dis, 10.1093/cid/ciaa387
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
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
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
Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation
- Ke Chen, Ye Gao, Nathan Mih, Edward J O’Brien, Laurence Yang, Bernhard O Palsson
- Proc Natl Acad Sci U S A, 10.1073/pnas.1705524114
Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion
- Zachary A King, Edward J O’Brien, Adam M Feist, Bernhard O Palsson
- Metab Eng, 10.1016/j.ymben.2016.12.004
Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments
- Edward J O’Brien, Jose Utrilla, Bernhard O Palsson
- PLoS Comput Biol, 10.1371/journal.pcbi.1004998
Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution
- Jose Utrilla, Edward J O’Brien, Ke Chen, …, Dagoberto Armenta-Medina, Adam M Feist, Bernhard O Palsson
- Cell Syst, 10.1016/j.cels.2016.04.003
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
Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli
- Sang Woo Seo, Donghyuk Kim, Edward J O’Brien, Richard Szubin, Bernhard O Palsson
- Nat Commun, 10.1038/ncomms8970
Using Genome-scale Models to Predict Biological Capabilities
- Edward J O’Brien, Jonathan M Monk, Bernhard O Palsson
- Cell, 10.1016/j.cell.2015.05.019
Computing the functional proteome: recent progress and future prospects for genome-scale models
- Edward J O’Brien, Bernhard O Palsson
- Curr Opin Biotechnol, 10.1016/j.copbio.2014.12.017
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale
- Joanne K Liu, Edward J O’Brien, Joshua A Lerman, Karsten Zengler, Bernhard O Palsson, Adam M Feist
- None, 10.1186/s12918-014-0110-6
Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli
- Sang Woo Seo, Donghyuk Kim, Haythem Latif, Edward J O’Brien, Richard Szubin, Bernhard O Palsson
- Nat Commun, 10.1038/ncomms5910