Edward J. O'Brien
Edward J. O'Brien
Sr. Scientist, Seres Therapeutics
Verified email at serestherapeutics.com
Cited by
Cited by
Using genome-scale models to predict biological capabilities
EJ O’Brien, JM Monk, BO Palsson
Cell 161 (5), 971-987, 2015
Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction
EJ O'brien, JA Lerman, RL Chang, DR Hyduke, BŲ Palsson
Molecular systems biology 9 (1), 693, 2013
Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome
NE Lewis, X Liu, Y Li, H Nagarajan, G Yerganian, E O'brien, A Bordbar, ...
Nature biotechnology 31 (8), 759-765, 2013
Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli
SW Seo, D Kim, H Latif, EJ O’Brien, R Szubin, BO Palsson
Nature communications 5 (1), 1-10, 2014
Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium
RA LaCroix, TE Sandberg, EJ O'Brien, J Utrilla, A Ebrahim, GI Guzman, ...
Applied and environmental microbiology 81 (1), 17-30, 2015
Multi-omic data integration enables discovery of hidden biological regularities
A Ebrahim, E Brunk, J Tan, EJ O'brien, D Kim, R Szubin, JA Lerman, ...
Nature communications 7 (1), 1-9, 2016
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale
JK Liu, EJ O’Brien, JA Lerman, K Zengler, BO Palsson, AM Feist
BMC systems biology 8 (1), 1-15, 2014
Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments
EJ O’Brien, J Utrilla, BO Palsson
PLoS computational biology 12 (6), e1004998, 2016
COBRAme: A computational framework for genome-scale models of metabolism and gene expression
CJ Lloyd, A Ebrahim, L Yang, ZA King, E Catoiu, EJ O’Brien, JK Liu, ...
PLoS computational biology 14 (7), e1006302, 2018
Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution
J Utrilla, EJ O’Brien, K Chen, D McCloskey, J Cheung, H Wang, ...
Cell systems 2 (4), 260-271, 2016
Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow
E Brunk, KW George, J Alonso-Gutierrez, M Thompson, E Baidoo, ...
Cell systems 2 (5), 335-346, 2016
Computing the functional proteome: recent progress and future prospects for genome-scale models
EJ O’Brien, BO Palsson
Current opinion in biotechnology 34, 125-134, 2015
Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli
SW Seo, D Kim, EJ O’Brien, R Szubin, BO Palsson
Nature communications 6 (1), 1-8, 2015
Systems biology of the structural proteome
E Brunk, N Mih, J Monk, Z Zhang, EJ O’Brien, SE Bliven, K Chen, ...
BMC systems biology 10 (1), 1-16, 2016
Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation
K Chen, Y Gao, N Mih, EJ O’Brien, L Yang, BO Palsson
Proceedings of the National Academy of Sciences 114 (43), 11548-11553, 2017
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
L Yang, J Tan, EJ O’Brien, JM Monk, D Kim, HJ Li, P Charusanti, ...
Proceedings of the National Academy of Sciences 112 (34), 10810-10815, 2015
Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion
ZA King, EJ O'Brien, AM Feist, BO Palsson
Metabolic engineering 39, 220-227, 2017
SER-109, an Investigational Microbiome Drug to Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial
BH McGovern, CB Ford, MR Henn, DS Pardi, S Khanna, EL Hohmann, ...
Clinical Infectious Diseases 72 (12), 2132-2140, 2021
Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism
C Cheng, EJ O’brien, D McCloskey, J Utrilla, C Olson, RA LaCroix, ...
PLoS computational biology 15 (6), e1007066, 2019
The genetic basis for adaptation of model-designed syntrophic co-cultures
CJ Lloyd, ZA King, TE Sandberg, Y Hefner, CA Olson, PV Phaneuf, ...
PLoS computational biology 15 (3), e1006213, 2019
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