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1.

The transition from genomics to phenomics in personalized population health.

Yurkovich, James T; Evans, Simon J; Rappaport, Noa; Boore, Jeffrey L; Lovejoy, Jennifer C; Price, Nathan D; Hood, Leroy E.

Nat Rev Genet; 25(4): 286-302, 2024 Apr.

Artículo en Inglés | MEDLINE | ID: mdl-38093095

2.

Is the kinetome conserved?

Palsson, Bernhard O; Yurkovich, James T.

Mol Syst Biol; 18(2): e10782, 2022 02.

Artículo en Inglés | MEDLINE | ID: mdl-35188334

3.

Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo.

Gao, Ye; Lim, Hyun Gyu; Verkler, Hans; Szubin, Richard; Quach, Daniel; Rodionova, Irina; Chen, Ke; Yurkovich, James T; Cho, Byung-Kwan; Palsson, Bernhard O.

Nucleic Acids Res; 49(17): 9696-9710, 2021 09 27.

Artículo en Inglés | MEDLINE | ID: mdl-34428301

4.

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics.

Haiman, Zachary B; Zielinski, Daniel C; Koike, Yuko; Yurkovich, James T; Palsson, Bernhard O.

PLoS Comput Biol; 17(1): e1008208, 2021 01.

Artículo en Inglés | MEDLINE | ID: mdl-33507922

5.

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.

Norsigian, Charles J; Pusarla, Neha; McConn, John Luke; Yurkovich, James T; Dräger, Andreas; Palsson, Bernhard O; King, Zachary.

Nucleic Acids Res; 48(D1): D402-D406, 2020 01 08.

Artículo en Inglés | MEDLINE | ID: mdl-31696234

6.

Cellular responses to reactive oxygen species are predicted from molecular mechanisms.

Yang, Laurence; Mih, Nathan; Anand, Amitesh; Park, Joon Ho; Tan, Justin; Yurkovich, James T; Monk, Jonathan M; Lloyd, Colton J; Sandberg, Troy E; Seo, Sang Woo; Kim, Donghyuk; Sastry, Anand V; Phaneuf, Patrick; Gao, Ye; Broddrick, Jared T; Chen, Ke; Heckmann, David; Szubin, Richard; Hefner, Ying; Feist, Adam M; Palsson, Bernhard O.

Proc Natl Acad Sci U S A; 116(28): 14368-14373, 2019 07 09.

Artículo en Inglés | MEDLINE | ID: mdl-31270234

7.

Community standards to facilitate development and address challenges in metabolic modeling.

Carey, Maureen A; Dräger, Andreas; Beber, Moritz E; Papin, Jason A; Yurkovich, James T.

Mol Syst Biol; 16(8): e9235, 2020 08.

Artículo en Inglés | MEDLINE | ID: mdl-32845080

8.

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow.

Brunk, Elizabeth; Chang, Roger L; Xia, Jing; Hefzi, Hooman; Yurkovich, James T; Kim, Donghyuk; Buckmiller, Evan; Wang, Harris H; Cho, Byung-Kwan; Yang, Chen; Palsson, Bernhard O; Church, George M; Lewis, Nathan E.

Proc Natl Acad Sci U S A; 115(43): 11096-11101, 2018 10 23.

Artículo en Inglés | MEDLINE | ID: mdl-30301795

9.

Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models.

Dahal, Sanjeev; Yurkovich, James T; Xu, Hao; Palsson, Bernhard O; Yang, Laurence.

Proteomics; 20(17-18): e1900282, 2020 09.

Artículo en Inglés | MEDLINE | ID: mdl-32579720

10.

Visualizing metabolic network dynamics through time-series metabolomic data.

Buchweitz, Lea F; Yurkovich, James T; Blessing, Christoph; Kohler, Veronika; Schwarzkopf, Fabian; King, Zachary A; Yang, Laurence; Jóhannsson, Freyr; Sigurjónsson, Ólafur E; Rolfsson, Óttar; Heinrich, Julian; Dräger, Andreas.

BMC Bioinformatics; 21(1): 130, 2020 Apr 03.

Artículo en Inglés | MEDLINE | ID: mdl-32245365

11.

Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity.

Phaneuf, Patrick V; Yurkovich, James T; Heckmann, David; Wu, Muyao; Sandberg, Troy E; King, Zachary A; Tan, Justin; Palsson, Bernhard O; Feist, Adam M.

BMC Genomics; 21(1): 514, 2020 Jul 25.

Artículo en Inglés | MEDLINE | ID: mdl-32711472

12.

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.

Gao, Ye; Yurkovich, James T; Seo, Sang Woo; Kabimoldayev, Ilyas; Dräger, Andreas; Chen, Ke; Sastry, Anand V; Fang, Xin; Mih, Nathan; Yang, Laurence; Eichner, Johannes; Cho, Byung-Kwan; Kim, Donghyuk; Palsson, Bernhard O.

Nucleic Acids Res; 46(20): 10682-10696, 2018 11 16.

Artículo en Inglés | MEDLINE | ID: mdl-30137486

13.

Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities.

Fang, Xin; Sastry, Anand; Mih, Nathan; Kim, Donghyuk; Tan, Justin; Yurkovich, James T; Lloyd, Colton J; Gao, Ye; Yang, Laurence; Palsson, Bernhard O.

Proc Natl Acad Sci U S A; 114(38): 10286-10291, 2017 09 19.

Artículo en Inglés | MEDLINE | ID: mdl-28874552

14.

Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.

Yurkovich, James T; Alcantar, Miguel A; Haiman, Zachary B; Palsson, Bernhard O.

PLoS Comput Biol; 14(8): e1006356, 2018 08.

Artículo en Inglés | MEDLINE | ID: mdl-30086174

15.

Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.

Du, Bin; Zhang, Zhen; Grubner, Sharon; Yurkovich, James T; Palsson, Bernhard O; Zielinski, Daniel C.

Biophys J; 114(11): 2691-2702, 2018 06 05.

Artículo en Inglés | MEDLINE | ID: mdl-29874618

16.

Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks.

Yurkovich, James T; Zielinski, Daniel C; Yang, Laurence; Paglia, Giuseppe; Rolfsson, Ottar; Sigurjónsson, Ólafur E; Broddrick, Jared T; Bordbar, Aarash; Wichuk, Kristine; Brynjólfsson, Sigurður; Palsson, Sirus; Gudmundsson, Sveinn; Palsson, Bernhard O.

J Biol Chem; 292(48): 19556-19564, 2017 12 01.

Artículo en Inglés | MEDLINE | ID: mdl-29030425

17.

Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells.

Yurkovich, James T; Yang, Laurence; Palsson, Bernhard O.

PLoS Comput Biol; 13(3): e1005424, 2017 03.

Artículo en Inglés | MEDLINE | ID: mdl-28264007

18.

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

Yang, Laurence; Tan, Justin; O'Brien, Edward J; Monk, Jonathan M; Kim, Donghyuk; Li, Howard J; Charusanti, Pep; Ebrahim, Ali; Lloyd, Colton J; Yurkovich, James T; Du, Bin; Dräger, Andreas; Thomas, Alex; Sun, Yuekai; Saunders, Michael A; Palsson, Bernhard O.

Proc Natl Acad Sci U S A; 112(34): 10810-5, 2015 Aug 25.

Artículo en Inglés | MEDLINE | ID: mdl-26261351

19.

Blood Is a Window into Health and Disease.

Yurkovich, James T; Hood, Leroy.

Clin Chem; 65(10): 1204-1206, 2019 10.

Artículo en Inglés | MEDLINE | ID: mdl-31171530

20.

Temperature Dependence of Platelet Metabolism.

Jóhannsson, Freyr; Yurkovich, James T; Guðmundsson, Steinn; Sigurjónsson, Ólafur E; Rolfsson, Óttar.

Metabolites; 14(2)2024 Jan 26.

Artículo en Inglés | MEDLINE | ID: mdl-38392983

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