| Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2. 0 J Schellenberger, R Que, RMT Fleming, I Thiele, JD Orth, AM Feist, ... Nature protocols 6 (9), 1290-1307, 2011 | 1621 | 2011 |
| Recon3D enables a three-dimensional view of gene variation in human metabolism E Brunk, S Sahoo, DC Zielinski, A Altunkaya, A Dräger, N Mih, F Gatto, ... Nature biotechnology 36 (3), 272-281, 2018 | 631 | 2018 |
| Recon 2.2: from reconstruction to model of human metabolism N Swainston, K Smallbone, H Hefzi, PD Dobson, J Brewer, M Hanscho, ... Metabolomics 12, 1-7, 2016 | 310 | 2016 |
| Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli AM Feist, DC Zielinski, JD Orth, J Schellenberger, MJ Herrgard, ... Metabolic engineering 12 (3), 173-186, 2010 | 293 | 2010 |
| A consensus genome-scale reconstruction of Chinese hamster ovary cell metabolism H Hefzi, KS Ang, M Hanscho, A Bordbar, D Ruckerbauer, M Lakshmanan, ... Cell systems 3 (5), 434-443. e8, 2016 | 242 | 2016 |
| A systematic evaluation of methods for tailoring genome-scale metabolic models S Opdam, A Richelle, B Kellman, S Li, DC Zielinski, NE Lewis Cell systems 4 (3), 318-329. e6, 2017 | 208 | 2017 |
| Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models D Heckmann, CJ Lloyd, N Mih, Y Ha, DC Zielinski, ZB Haiman, ... Nature communications 9 (1), 5252, 2018 | 181 | 2018 |
| Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic … C Zuñiga, CT Li, T Huelsman, J Levering, DC Zielinski, BO McConnell, ... Plant physiology 172 (1), 589-602, 2016 | 118 | 2016 |
| 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 | 114 | 2015 |
| Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism DC Zielinski, N Jamshidi, AJ Corbett, A Bordbar, A Thomas, BO Palsson Scientific reports 7 (1), 41241, 2017 | 103 | 2017 |
| A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks H Nam, M Campodonico, A Bordbar, DR Hyduke, S Kim, DC Zielinski, ... PLoS computational biology 10 (9), e1003837, 2014 | 80 | 2014 |
| Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks JT Yurkovich, DC Zielinski, L Yang, G Paglia, O Rolfsson, ... Journal of Biological Chemistry 292 (48), 19556-19564, 2017 | 57 | 2017 |
| Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis DC Zielinski, FV Filipp, A Bordbar, K Jensen, JW Smith, MJ Herrgard, ... Nature communications 6 (1), 7101, 2015 | 53 | 2015 |
| COBRA Toolbox 2.0 D Hyduke, J Schellenberger, R Que, R Fleming, I Thiele, J Orth, A Feist, ... | 45 | 2011 |
| Temperature-dependent estimation of Gibbs energies using an updated group-contribution method B Du, Z Zhang, S Grubner, JT Yurkovich, BO Palsson, DC Zielinski Biophysical journal 114 (11), 2691-2702, 2018 | 44 | 2018 |
| Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling J Schellenberger, DC Zielinski, W Choi, S Madireddi, V Portnoy, DA Scott, ... BMC systems biology 6, 1-14, 2012 | 41 | 2012 |
| Evaluation of rate law approximations in bottom-up kinetic models of metabolism B Du, DC Zielinski, ES Kavvas, A Dräger, J Tan, Z Zhang, KE Ruggiero, ... BMC systems biology 10, 1-15, 2016 | 38 | 2016 |
| Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice B Du, DC Zielinski, JM Monk, BO Palsson Proceedings of the National Academy of Sciences 115 (44), 11339-11344, 2018 | 36 | 2018 |
| SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks A Dräger, DC Zielinski, R Keller, M Rall, J Eichner, BO Palsson, A Zell BMC systems biology 9, 1-17, 2015 | 31 | 2015 |
| MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics ZB Haiman, DC Zielinski, Y Koike, JT Yurkovich, BO Palsson PLoS computational biology 17 (1), e1008208, 2021 | 26 | 2021 |
