| Using genome-scale models to predict biological capabilities EJ O’Brien, JM Monk, BO Palsson Cell 161 (5), 971-987, 2015 | 734 | 2015 |
| Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction EJ O'brien, JA Lerman, RL Chang, DR Hyduke, BØ Palsson Molecular systems biology 9 (1), 693, 2013 | 537 | 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 | 461 | 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), 4910, 2014 | 316 | 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 | 261 | 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), 13091, 2016 | 171 | 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 | 156 | 2018 |
| 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 | 138 | 2021 |
| 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 | 132 | 2016 |
| 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 | 115 | 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, 1-15, 2014 | 113 | 2014 |
| 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), 7970, 2015 | 108 | 2015 |
| 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 | 99 | 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 | 93 | 2017 |
| A phase 1b safety study of SER-287, a spore-based microbiome therapeutic, for active mild to moderate ulcerative colitis MR Henn, EJ O’Brien, L Diao, BG Feagan, WJ Sandborn, C Huttenhower, ... Gastroenterology 160 (1), 115-127. e30, 2021 | 77 | 2021 |
| 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 | 76 | 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, 1-16, 2016 | 61 | 2016 |
| 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 | 46 | 2015 |
| 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 | 41 | 2019 |
| 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 | 41 | 2017 |
