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Edward J. O'Brien, PhD - Publications

Affiliations: 
2015 Bioinformatics University of California, San Diego, La Jolla, CA 
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19 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Cheng C, O'Brien EJ, McCloskey D, Utrilla J, Olson C, LaCroix RA, Sandberg TE, Feist AM, Palsson BO, King ZA. Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism. Plos Computational Biology. 15: e1007066. PMID 31158228 DOI: 10.1371/Journal.Pcbi.1007066  0.785
2019 Lloyd CJ, King ZA, Sandberg TE, Hefner Y, Olson CA, Phaneuf PV, O'Brien EJ, Sanders JG, Salido RA, Sanders K, Brennan C, Humphrey G, Knight R, Feist AM. The genetic basis for adaptation of model-designed syntrophic co-cultures. Plos Computational Biology. 15: e1006213. PMID 30822347 DOI: 10.1371/Journal.Pcbi.1006213  0.753
2018 Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK, Palsson BO. COBRAme: A computational framework for genome-scale models of metabolism and gene expression. Plos Computational Biology. 14: e1006302. PMID 29975681 DOI: 10.1371/Journal.Pcbi.1006302  0.793
2017 Chen K, Gao Y, Mih N, O'Brien EJ, Yang L, Palsson BO. Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation. Proceedings of the National Academy of Sciences of the United States of America. 114: 11548-11553. PMID 29073085 DOI: 10.1073/Pnas.1705524114  0.807
2016 King ZA, O'Brien EJ, Feist AM, Palsson BO. Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion. Metabolic Engineering. PMID 27986597 DOI: 10.1016/J.Ymben.2016.12.004  0.732
2016 Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson BO. Multi-omic data integration enables discovery of hidden biological regularities. Nature Communications. 7: 13091. PMID 27782110 DOI: 10.1038/Ncomms13091  0.726
2016 O'Brien EJ, Utrilla J, Palsson BO. Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. Plos Computational Biology. 12: e1004998. PMID 27351952 DOI: 10.1371/Journal.Pcbi.1004998  0.482
2016 Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O'Brien EJ, Batth TS, Martin HG, Feist A, Adams PD, et al. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Systems. PMID 27211860 DOI: 10.1016/J.Cels.2016.04.004  0.762
2016 Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO. Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. Cell Systems. 2: 260-271. PMID 27135538 DOI: 10.1016/J.Cels.2016.04.003  0.778
2016 Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO. Systems biology of the structural proteome. Bmc Systems Biology. 10: 26. PMID 26969117 DOI: 10.1186/S12918-016-0271-6  0.775
2015 Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, et al. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proceedings of the National Academy of Sciences of the United States of America. PMID 26261351 DOI: 10.1073/Pnas.1501384112  0.756
2015 Seo SW, Kim D, O'Brien EJ, Szubin R, Palsson BO. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli. Nature Communications. 6: 7970. PMID 26258987 DOI: 10.1038/Ncomms8970  0.772
2015 O'Brien EJ, Monk JM, Palsson BO. Using Genome-scale Models to Predict Biological Capabilities. Cell. 161: 971-987. PMID 26000478 DOI: 10.1016/J.Cell.2015.05.019  0.734
2015 O'Brien EJ, Palsson BO. Computing the functional proteome: recent progress and future prospects for genome-scale models. Current Opinion in Biotechnology. 34: 125-134. PMID 25576845 DOI: 10.1016/J.Copbio.2014.12.017  0.545
2015 LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson BO, Feist AM. Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. Applied and Environmental Microbiology. 81: 17-30. PMID 25304508 DOI: 10.1128/Aem.02246-14  0.785
2014 Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM. Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. Bmc Systems Biology. 8: 110. PMID 25227965 DOI: 10.1186/S12918-014-0110-6  0.798
2014 Seo SW, Kim D, Latif H, O'Brien EJ, Szubin R, Palsson BO. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nature Communications. 5: 4910. PMID 25222563 DOI: 10.1038/Ncomms5910  0.765
2013 O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BØ. Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Molecular Systems Biology. 9: 693. PMID 24084808 DOI: 10.1038/Msb.2013.52  0.806
2013 Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, et al. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nature Biotechnology. 31: 759-65. PMID 23873082 DOI: 10.1038/Nbt.2624  0.736
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