| OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains J Kim, JL Reed BMC systems biology 4, 1-19, 2010 | 290 | 2010 |
| Machine learning for metabolic engineering: A review CE Lawson, JM Martí, T Radivojevic, SVR Jonnalagadda, R Gentz, ... Metabolic Engineering 63, 34-60, 2021 | 190 | 2021 |
| Large-scale bi-level strain design approaches and mixed-integer programming solution techniques J Kim, JL Reed, CT Maravelias PloS one 6 (9), e24162, 2011 | 128 | 2011 |
| RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations J Kim, JL Reed Genome biology 13, 1-12, 2012 | 126 | 2012 |
| Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli KW George, MG Thompson, J Kim, EEK Baidoo, G Wang, VT Benites, ... Metabolic Engineering 47, 60-72, 2018 | 122 | 2018 |
| An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models D Barua, J Kim, JL Reed PLoS computational biology 6 (10), e1000970, 2010 | 64 | 2010 |
| Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and … DH Keating, Y Zhang, IM Ong, S McIlwain, EH Morales, JA Grass, ... Frontiers in microbiology 5, 402, 2014 | 53 | 2014 |
| A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides LC Nora, M Wehrs, J Kim, JF Cheng, A Tarver, BA Simmons, J Magnuson, ... Microbial cell factories 18, 1-11, 2019 | 44 | 2019 |
| Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass J Kirby, GM Geiselman, J Yaegashi, J Kim, X Zhuang, MB Tran-Gyamfi, ... Biotechnology for biofuels 14, 1-16, 2021 | 37 | 2021 |
| Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides J Kim, ST Coradetti, YM Kim, Y Gao, J Yaegashi, JD Zucker, N Munoz, ... Frontiers in Bioengineering and Biotechnology 8, 612832, 2021 | 33 | 2021 |
| Refining metabolic models and accounting for regulatory effects J Kim, JL Reed Current opinion in biotechnology 29, 34-38, 2014 | 29 | 2014 |
| Transcriptomic analysis of the oleaginous yeast Lipomyces starkeyi during lipid accumulation on enzymatically treated corn stover hydrolysate KR Pomraning, JR Collett, J Kim, EA Panisko, DE Culley, Z Dai, S Deng, ... Biotechnology for Biofuels 12, 1-15, 2019 | 23 | 2019 |
| Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger MC Reilly, J Kim, J Lynn, BA Simmons, JM Gladden, JK Magnuson, ... Applied microbiology and biotechnology 102, 1797-1807, 2018 | 20 | 2018 |
| Effect of initial glucose concentrations on carbon and energy balances in hydrogen-producing Clostridium tyrobutyricum JM1 JH Jo, DS Lee, J Kim, JM Park J. Microbiol. Biotechnol 19 (3), 291-298, 2009 | 19 | 2009 |
| PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements A Bilbao, N Munoz, J Kim, DJ Orton, Y Gao, K Poorey, KR Pomraning, ... Nature communications 14 (1), 2461, 2023 | 16 | 2023 |
| Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus KR Pomraning, Z Dai, N Munoz, YM Kim, Y Gao, S Deng, J Kim, ... Frontiers in Bioengineering and Biotechnology 9, 603832, 2021 | 16 | 2021 |
| High-Throughput Large-Scale Targeted Proteomics Assays for Quantifying Pathway Proteins in Pseudomonas putida KT2440 Y Gao, TL Fillmore, N Munoz, GJ Bentley, CW Johnson, J Kim, ... Frontiers in Bioengineering and Biotechnology 8, 603488, 2020 | 14 | 2020 |
| Multiomics data collection, visualization, and utilization for guiding metabolic engineering S Roy, T Radivojevic, M Forrer, JM Marti, V Jonnalagadda, T Backman, ... Frontiers in bioengineering and biotechnology 9, 612893, 2021 | 13 | 2021 |
| Systems Metabolic Engineering of Escherichia coli Improves Coconversion of Lignocellulose‐Derived Sugars J Kim, M Tremaine, JA Grass, HM Purdy, R Landick, PJ Kiley, JL Reed Biotechnology journal 14 (9), 1800441, 2019 | 13 | 2019 |
| Engineering Rhodosporidium toruloides for production of 3-hydroxypropionic acid from lignocellulosic hydrolysate D Liu, HJ Hwang, PB Otoupal, GM Geiselman, J Kim, KR Pomraning, ... Metabolic Engineering 78, 72-83, 2023 | 10 | 2023 |
John M GladdenSandia National Laboratories在 lbl.gov 的电子邮件经过验证
