| Molecular mechanisms driving switch behavior in xylem cell differentiation GM Turco, J Rodriguez-Medina, S Siebert, D Han, ... Cell reports 28 (2), 342-351. e4, 2019 | 102 | 2019 |
| Application of theoretical methods to increase succinate production in engineered strains MA Valderrama-Gomez, D Kreitmayer, S Wolf, A Marin-Sanguino, ... Bioprocess and biosystems engineering 40, 479-497, 2017 | 17 | 2017 |
| Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data S Gopalakrishnan, CJ Joshi, MÁ Valderrama-Gómez, E Icten, P Rolandi, ... Metabolic engineering 75, 181-191, 2023 | 13 | 2023 |
| Phenotype-centric modeling for elucidation of biological design principles MA Valderrama-Gómez, RE Parales, MA Savageau Journal of theoretical biology, 2018 | 13 | 2018 |
| Mechanistic modeling of biochemical systems without a priori parameter values using the design space toolbox v. 3.0 MÁ Valderrama-Gómez, JG Lomnitz, RA Fasani, MA Savageau Iscience 23 (6), 2020 | 9 | 2020 |
| COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling S Gopalakrishnan, W Johnson, MA Valderrama-Gomez, E Icten, J Tat, ... Metabolic Engineering 82, 183-192, 2024 | 7 | 2024 |
| TaxisPy: A Python-based software for the quantitative analysis of bacterial chemotaxis MÁ Valderrama-Gómez, RA Schomer, MA Savageau, RE Parales Journal of Microbiological Methods 175, 105918, 2020 | 5 | 2020 |
| Multi-omic characterization of antibody-producing CHO cell lines elucidates metabolic reprogramming and nutrient uptake bottlenecks S Gopalakrishnan, W Johnson, MA Valderrama-Gomez, E Icten, J Tat, ... Metabolic Engineering 85, 94-104, 2024 | 4 | 2024 |
| Phenotype-centric modeling for rational metabolic engineering MÁ Valderrama-Gómez, MA Savageau Metabolic Engineering 72, 365-375, 2022 | 1 | 2022 |
| Molecular Systems Predict Equilibrium Distributions of Phenotype Diversity Available for Selection MA Valderrama-Gómez, MA Savageau bioRxiv, 2021.05. 27.446045, 2021 | 1 | 2021 |
| Computer-guided metabolic engineering MA Valderrama-Gomez, SG Wagner, A Kremling Hydrocarbon and Lipid Microbiology Protocols: Synthetic and Systems Biology …, 2016 | 1 | 2016 |
| End to End Cell Culture Modeling: Improving Process Development Agility. Starting and Ending With Data M Demers, MA Valderrama-Gomez, T Kim, W Heymann, J Glaser, S Xu, ... 2024 AIChE Annual Meeting, 2024 | | 2024 |
| Optimizing Bioreactor Performance through in silico Models SJ Kang, S Golshan, M Ahmadi, T El Geitani, I Mirzaee, J Fisher, ... 2024 AIChE Annual Meeting, 2024 | | 2024 |
| Improving Numerical Methods for Bioreactor Process Simulation and Parameter Estimation T Kim, MA Valderrama-Gomez, W Heymann, J Glaser, M Demers, S Xu, ... 2024 AIChE Annual Meeting, 2024 | | 2024 |
| Integrated Omic Analysis Elucidates Phenotypic Plurality and Metabolic Bottlenecks in Industrial Antibody-Producing Chinese Hamster Ovary (CHO) Cell Lines S Gopalakrishnan, MA Valderrama-Gomez, W Johnson, J Tat, EI Gencer, ... 2024 AIChE Annual Meeting, 2024 | | 2024 |
| COSMIC-dFBA: A Novel Dynamic Flux Balance Analysis Framework to Interface Reactor Conditions with Metabolism Using Machine Learning Methods S Gopalakrishnan, W Johnson, MA Valderrama-Gomez, E Icten, ... 2023 AIChE Annual Meeting, 2023 | | 2023 |
| Multi-Omic Characterization of CHO Cells Reveals Fluxomic Diversity and Amino Acid Utilization Bottlenecks in High-producer Clones S Gopalakrishnan, W Johnson, MA Valderrama-Gomez, E Icten, ... 2023 AIChE Annual Meeting, 2023 | | 2023 |
| An Industrial in silico Modeling Platform for Reliable, Efficient, and Agile Process & Product Development F Schlegel, PA Rolandi, I Mirzaee, M Maritato, S Seifi, ... 2022 AIChE Annual Meeting, 2022 | | 2022 |
| Multi-Scale Modeling of a CHO Production Process Using Integrated Machine Learning Models and Genome-Scale Metabolic Models S Gopalakrishnan, J Tat, MA Valderrama-Gomez, F Schlegel, PA Rolandi, ... 2022 AIChE Annual Meeting, 2022 | | 2022 |
| Predicting Antibody Titer Using Multi-Scale Dynamic Flux Balance Analysis Bioreactor Models S Gopalakrishnan, J Tat, MA Valderrama-Gomez, F Schlegel, W Johnson, ... 2022 AIChE Annual Meeting, 2022 | | 2022 |