| Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells CA Lewis, SJ Parker, BP Fiske, D McCloskey, DY Gui, CR Green, ... Molecular cell 55 (2), 253-263, 2014 | 630 | 2014 |
| Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli D McCloskey, BØ Palsson, AM Feist Molecular systems biology 9 (1), 661, 2013 | 424 | 2013 |
| A white-box machine learning approach for revealing antibiotic mechanisms of action JH Yang, SN Wright, M Hamblin, D McCloskey, MA Alcantar, ... Cell 177 (6), 1649-1661. e9, 2019 | 305 | 2019 |
| Antibiotic-induced changes to the host metabolic environment inhibit drug efficacy and alter immune function JH Yang, P Bhargava, D McCloskey, N Mao, BO Palsson, JJ Collins Cell host & microbe 22 (6), 757-765. e3, 2017 | 259 | 2017 |
| Personalized whole-cell kinetic models of metabolism for discovery in genomics and pharmacodynamics A Bordbar, D McCloskey, DC Zielinski, N Sonnenschein, N Jamshidi, ... Cell systems 1 (4), 283-292, 2015 | 120 | 2015 |
| 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 | 118 | 2016 |
| AMPD2 regulates GTP synthesis and is mutated in a potentially treatable neurodegenerative brainstem disorder N Akizu, V Cantagrel, J Schroth, N Cai, K Vaux, D McCloskey, ... Cell 154 (3), 505-517, 2013 | 118 | 2013 |
| 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 | 102 | 2016 |
| Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism D McCloskey, S Xu, TE Sandberg, E Brunk, Y Hefner, R Szubin, AM Feist, ... Nature communications 9 (1), 3796, 2018 | 71 | 2018 |
| A model‐driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K‐12 MG1655 that is biochemically and thermodynamically … D McCloskey, JA Gangoiti, ZA King, RK Naviaux, BA Barshop, ... Biotechnology and bioengineering 111 (4), 803-815, 2014 | 71 | 2014 |
| MID Max: LC–MS/MS method for measuring the precursor and product mass isotopomer distributions of metabolic intermediates and cofactors for metabolic flux analysis applications D McCloskey, JD Young, S Xu, BO Palsson, AM Feist Analytical chemistry 88 (2), 1362-1370, 2016 | 59 | 2016 |
| A pH and solvent optimized reverse-phase ion-paring-LC–MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites D McCloskey, JA Gangoiti, BO Palsson, AM Feist Metabolomics 11, 1338-1350, 2015 | 51 | 2015 |
| Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the phosphotransferase system D McCloskey, S Xu, TE Sandberg, E Brunk, Y Hefner, R Szubin, AM Feist, ... Metabolic engineering 48, 233-242, 2018 | 49 | 2018 |
| Oral supplementation of nicotinamide riboside alters intestinal microbial composition in rats and mice, but not humans AA Peluso, AT Lundgaard, P Babaei, F Mousovich-Neto, AL Rocha, ... npj Aging 9 (1), 7, 2023 | 47 | 2023 |
| Automating the design-build-test-learn cycle towards next-generation bacterial cell factories N Gurdo, DC Volke, D McCloskey, PI Nikel New Biotechnology 74, 1-15, 2023 | 43 | 2023 |
| Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes D McCloskey, S Xu, TE Sandberg, E Brunk, Y Hefner, R Szubin, AM Feist, ... Metabolic engineering 48, 82-93, 2018 | 43 | 2018 |
| 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 |
| Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica J Dahlin, C Holkenbrink, ER Marella, G Wang, U Liebal, C Lieven, ... Frontiers in genetics 10, 747, 2019 | 40 | 2019 |
| Modeling method for increased precision and scope of directly measurable fluxes at a genome-scale D McCloskey, JD Young, S Xu, BO Palsson, AM Feist Analytical chemistry 88 (7), 3844-3852, 2016 | 38 | 2016 |
| Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media D McCloskey, J Utrilla, RK Naviaux, BO Palsson, AM Feist Metabolomics 11, 198-209, 2015 | 36 | 2015 |
