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James Yurkovich
James Yurkovich
Translational Research Fellow at the Institute for Systems Biology
Verified email at systemsbiology.org - Homepage
Title
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Cited by
Year
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0
L Heirendt, S Arreckx, T Pfau, SN Mendoza, A Richelle, A Heinken, ...
Nature protocols 14 (3), 639-702, 2019
5542019
Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance
ES Kavvas, E Catoiu, N Mih, JT Yurkovich, Y Seif, N Dillon, D Heckmann, ...
Nature communications 9 (1), 1-9, 2018
1052018
Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics
A Bordbar, JT Yurkovich, G Paglia, O Rolfsson, ÓE Sigurjónsson, ...
Scientific reports 7 (1), 1-12, 2017
104*2017
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
CJ Norsigian, N Pusarla, JL McConn, JT Yurkovich, A Dräger, BO Palsson, ...
Nucleic acids research 48 (D1), D402-D406, 2020
872020
Gut microbiome pattern reflects healthy ageing and predicts survival in humans
T Wilmanski, C Diener, N Rappaport, S Patwardhan, J Wiedrick, ...
Nature metabolism 3 (2), 274-286, 2021
852021
Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities
X Fang, A Sastry, N Mih, D Kim, J Tan, JT Yurkovich, CJ Lloyd, Y Gao, ...
Proceedings of the National Academy of Sciences 114 (38), 10286-10291, 2017
752017
Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
Y Seif, E Kavvas, JC Lachance, JT Yurkovich, SP Nuccio, X Fang, ...
Nature communications 9 (1), 1-12, 2018
702018
Toward community standards and software for whole-cell modeling
D Waltemath, JR Karr, FT Bergmann, V Chelliah, M Hucka, M Krantz, ...
IEEE Transactions on Biomedical Engineering 63 (10), 2007-2014, 2016
582016
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655
Y Gao, JT Yurkovich, SW Seo, I Kabimoldayev, A Dräger, K Chen, ...
Nucleic Acids Research, gky752, 2018
542018
Cellular responses to reactive oxygen species are predicted from molecular mechanisms
L Yang, N Mih, A Anand, JH Park, J Tan, JT Yurkovich, JM Monk, CJ Lloyd, ...
Proceedings of the National Academy of Sciences 116 (28), 14368-14373, 2019
492019
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
ES Kavvas, Y Seif, JT Yurkovich, C Norsigian, S Poudel, WW Greenwald, ...
BMC systems biology 12 (1), 1-15, 2018
412018
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
L Yang, J Tan, EJ O’Brien, JM Monk, D Kim, HJ Li, P Charusanti, ...
Proceedings of the National Academy of Sciences 112 (34), 10810-10815, 2015
392015
Metabolic network analysis reveals altered bile acid synthesis and metabolism in Alzheimer’s disease
P Baloni, CC Funk, J Yan, JT Yurkovich, A Kueider-Paisley, K Nho, ...
Cell Reports Medicine 1 (8), 100138, 2020
37*2020
Modeling the multi-scale mechanisms of macromolecular resource allocation
L Yang, JT Yurkovich, ZA King, BO Palsson
Current opinion in microbiology 45, 8-15, 2018
372018
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
352017
Principles of proteome allocation are revealed using proteomic data and genome-scale models
L Yang, JT Yurkovich, CJ Lloyd, A Ebrahim, MA Saunders, BO Palsson
Scientific reports 6 (1), 1-8, 2016
342016
Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
E Brunk, RL Chang, J Xia, H Hefzi, JT Yurkovich, D Kim, E Buckmiller, ...
Proceedings of the National Academy of Sciences 115 (43), 11096-11101, 2018
312018
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
262018
A systems approach to clinical oncology uses deep phenotyping to deliver personalized care
JT Yurkovich, Q Tian, ND Price, L Hood
Nature Reviews Clinical Oncology 17 (3), 183-194, 2020
252020
Community standards to facilitate development and address challenges in metabolic modeling
MA Carey, A Dräger, ME Beber, JA Papin, JT Yurkovich
Molecular Systems Biology 16 (8), e9235, 2020
242020
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Articles 1–20