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James Yurkovich - Publications

Affiliations: 
2013-2018 University of California, San Diego, La Jolla, CA 
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35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Yurkovich JT, Evans SJ, Rappaport N, Boore JL, Lovejoy JC, Price ND, Hood LE. The transition from genomics to phenomics in personalized population health. Nature Reviews. Genetics. PMID 38093095 DOI: 10.1038/s41576-023-00674-x  0.442
2022 Palsson BO, Yurkovich JT. Is the kinetome conserved? Molecular Systems Biology. 18: e10782. PMID 35188334 DOI: 10.15252/msb.202110782  0.407
2021 Phaneuf PV, Zielinski DC, Yurkovich JT, Johnsen J, Szubin R, Yang L, Kim SH, Schulz S, Wu M, Dalldorf C, Ozdemir E, Lennen RM, Palsson BO, Feist AM. Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data. Acs Synthetic Biology. PMID 34762392 DOI: 10.1021/acssynbio.1c00337  0.762
2021 Gao Y, Lim HG, Verkler H, Szubin R, Quach D, Rodionova I, Chen K, Yurkovich JT, Cho BK, Palsson BO. Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo. Nucleic Acids Research. PMID 34428301 DOI: 10.1093/nar/gkab735  0.769
2021 Akbari A, Yurkovich JT, Zielinski DC, Palsson BO. The quantitative metabolome is shaped by abiotic constraints. Nature Communications. 12: 3178. PMID 34039963 DOI: 10.1038/s41467-021-23214-9  0.645
2021 Wilmanski T, Diener C, Rappaport N, Patwardhan S, Wiedrick J, Lapidus J, Earls JC, Zimmer A, Glusman G, Robinson M, Yurkovich JT, Kado DM, Cauley JA, Zmuda J, Lane NE, et al. Author Correction: Gut microbiome pattern reflects healthy ageing and predicts survival in humans. Nature Metabolism. PMID 33731896 DOI: 10.1038/s42255-021-00377-9  0.413
2021 Wilmanski T, Diener C, Rappaport N, Patwardhan S, Wiedrick J, Lapidus J, Earls JC, Zimmer A, Glusman G, Robinson M, Yurkovich JT, Kado DM, Cauley JA, Zmuda J, Lane NE, et al. Gut microbiome pattern reflects healthy ageing and predicts survival in humans. Nature Metabolism. 3: 274-286. PMID 33619379 DOI: 10.1038/s42255-021-00348-0  0.442
2021 Haiman ZB, Zielinski DC, Koike Y, Yurkovich JT, Palsson BO. MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. Plos Computational Biology. 17: e1008208. PMID 33507922 DOI: 10.1371/journal.pcbi.1008208  0.64
2020 Baloni P, Funk CC, Yan J, Yurkovich JT, Kueider-Paisley A, Nho K, Heinken A, Jia W, Mahmoudiandehkordi S, Louie G, Saykin AJ, Arnold M, Kastenmüller G, Griffiths WJ, Thiele I, et al. Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease. Cell Reports. Medicine. 1: 100138. PMID 33294859 DOI: 10.1016/j.xcrm.2020.100138  0.632
2020 Carey MA, Dräger A, Beber ME, Papin JA, Yurkovich JT. Community standards to facilitate development and address challenges in metabolic modeling. Molecular Systems Biology. 16: e9235. PMID 32845080 DOI: 10.15252/Msb.20199235  0.523
2020 Phaneuf PV, Yurkovich JT, Heckmann D, Wu M, Sandberg TE, King ZA, Tan J, Palsson BO, Feist AM. Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. Bmc Genomics. 21: 514. PMID 32711472 DOI: 10.1186/S12864-020-06920-4  0.739
2020 Dahal S, Yurkovich JT, Xu H, Palsson BO, Yang L. Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models. Proteomics. e1900282. PMID 32579720 DOI: 10.1002/Pmic.201900282  0.488
2019 Norsigian CJ, Pusarla N, McConn JL, Yurkovich JT, Dräger A, Palsson BO, King Z. BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic Acids Research. PMID 31696234 DOI: 10.1093/Nar/Gkz1054  0.783
2019 Yurkovich JT, Tian Q, Price ND, Hood L. A systems approach to clinical oncology uses deep phenotyping to deliver personalized care. Nature Reviews. Clinical Oncology. PMID 31619755 DOI: 10.1038/S41571-019-0273-6  0.466
2019 Baloni P, Sangar V, Yurkovich JT, Robinson M, Taylor S, Karbowski CM, Hamadeh HK, He YD, Price ND. Genome-scale metabolic model of the rat liver predicts effects of diet restriction. Scientific Reports. 9: 9807. PMID 31285465 DOI: 10.1038/S41598-019-46245-1  0.523
2019 Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, et al. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proceedings of the National Academy of Sciences of the United States of America. PMID 31270234 DOI: 10.1073/Pnas.1905039116  0.647
2019 Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, ... ... Yurkovich JT, et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nature Protocols. PMID 30787451 DOI: 10.1038/S41596-018-0098-2  0.768
2018 Kavvas ES, Catoiu E, Mih N, Yurkovich JT, Seif Y, Dillon N, Heckmann D, Anand A, Yang L, Nizet V, Monk JM, Palsson BO. Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. Nature Communications. 9: 4306. PMID 30333483 DOI: 10.1038/S41467-018-06634-Y  0.738
2018 Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D, Buckmiller E, Wang HH, Cho BK, Yang C, Palsson BO, Church GM, Lewis NE. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proceedings of the National Academy of Sciences of the United States of America. PMID 30301795 DOI: 10.1073/Pnas.1811971115  0.788
2018 Seif Y, Kavvas E, Lachance JC, Yurkovich JT, Nuccio SP, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM. Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nature Communications. 9: 3771. PMID 30218022 DOI: 10.1038/S41467-018-06112-5  0.786
2018 Gao Y, Yurkovich JT, Seo SW, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L, Eichner J, Cho BK, Kim D, Palsson BO. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. Nucleic Acids Research. PMID 30137486 DOI: 10.1093/Nar/Gky752  0.769
2018 Yurkovich JT, Alcantar MA, Haiman ZB, Palsson BO. Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. Plos Computational Biology. 14: e1006356. PMID 30086174 DOI: 10.1371/Journal.Pcbi.1006356  0.384
2018 Choudhary KS, Mih N, Monk J, Kavvas E, Yurkovich JT, Sakoulas G, Palsson BO. The Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Frontiers in Microbiology. 9: 1082. PMID 29887846 DOI: 10.3389/Fmicb.2018.01082  0.783
2018 Du B, Zhang Z, Grubner S, Yurkovich JT, Palsson BO, Zielinski DC. Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method. Biophysical Journal. 114: 2691-2702. PMID 29874618 DOI: 10.1016/J.Bpj.2018.04.030  0.653
2018 Yurkovich JT, Bordbar A, Sigurjónsson ÓE, Palsson BO. Systems biology as an emerging paradigm in transfusion medicine. Bmc Systems Biology. 12: 31. PMID 29514691 DOI: 10.1186/S12918-018-0558-X  0.607
2018 Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson BO, Monk JM. Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. Bmc Systems Biology. 12: 25. PMID 29499714 DOI: 10.1186/S12918-018-0557-Y  0.73
2018 Yurkovich JT, Palsson BO. Quantitative -omic data empowers bottom-up systems biology. Current Opinion in Biotechnology. 51: 130-136. PMID 29414439 DOI: 10.1016/J.Copbio.2018.01.009  0.416
2018 Yang L, Yurkovich JT, King ZA, Palsson BO. Modeling the multi-scale mechanisms of macromolecular resource allocation. Current Opinion in Microbiology. 45: 8-15. PMID 29367175 DOI: 10.1016/J.Mib.2018.01.002  0.424
2017 Yurkovich JT, Zielinski DC, Yang L, Paglia G, Rolfsson O, Sigurjónsson ÓE, Broddrick JT, Bordbar A, Wichuk K, Brynjólfsson S, Palsson S, Gudmundsson S, Palsson BO. Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks. The Journal of Biological Chemistry. PMID 29030425 DOI: 10.1074/Jbc.M117.804914  0.765
2017 Yurkovich JT, Yurkovich BJ, Dräger A, Palsson BO, King ZA. A Padawan Programmer's Guide to Developing Software Libraries. Cell Systems. PMID 28988801 DOI: 10.1016/J.Cels.2017.08.003  0.333
2017 Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson BO. Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. Proceedings of the National Academy of Sciences of the United States of America. PMID 28874552 DOI: 10.1073/Pnas.1702581114  0.747
2017 Bordbar A, Yurkovich JT, Paglia G, Rolfsson O, Sigurjónsson ÓE, Palsson BO. Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics. Scientific Reports. 7: 46249. PMID 28387366 DOI: 10.1038/Srep46249  0.637
2017 Yurkovich JT, Yang L, Palsson BO. Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. Plos Computational Biology. 13: e1005424. PMID 28264007 DOI: 10.1371/Journal.Pcbi.1005424  0.396
2016 Yang L, Yurkovich JT, Lloyd CJ, Ebrahim A, Saunders MA, Palsson BO. Principles of proteome allocation are revealed using proteomic data and genome-scale models. Scientific Reports. 6: 36734. PMID 27857205 DOI: 10.1038/Srep36734  0.793
2015 Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, et al. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proceedings of the National Academy of Sciences of the United States of America. PMID 26261351 DOI: 10.1073/Pnas.1501384112  0.766
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