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ArticlesPeer ReviewedFull Text
Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance
Author / Creator:Kavvas, Erol S ; Catoiu, Edward ; Mih, Nathan ; Yurkovich, James T ; Seif, Yara ; Dillon, Nicholas ; Heckmann, David ; Anand, Amitesh ; Yang, Laurence ; Nizet, Victor ; Monk, Jonathan M ; Palsson, Bernhard O
Publisher:London: Nature Publishing Group
Journal title:Nature communications, 2018-10, Vol.9, p.1-9
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Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
Author / Creator:Seif, Yara ; Kavvas, Erol ; Lachance, Jean-Christophe ; Yurkovich, James T ; Sean-Paul Nuccio ; Fang, Xin ; Catoiu, Edward ; Raffatellu, Manuela ; Palsson, Bernhard O ; Monk, Jonathan M
Publisher:London: Nature Publishing Group
Journal title:Nature communications, 2018-09, Vol.9, p.1-12
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MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics
Author / Creator:Haiman, Zachary B. ; Zielinski, Daniel C. ; Koike, Yuko ; Yurkovich, James T. ; Palsson, Bernhard O.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2021-01, Vol.17 (1), p.e1008208
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Is the kinetome conserved?
Author / Creator:Palsson, Bernhard O ; Yurkovich, James T
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2022-02, Vol.18 (2), p.e10782-n/a
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Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics
Author / Creator:Bordbar, Aarash ; Yurkovich, James T. ; Paglia, Giuseppe ; Rolfsson, Ottar ; Sigurjónsson, Ólafur E. ; Palsson, Bernhard O.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2017-04, Vol.7 (1), p.46249, Article 46249
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The quantitative metabolome is shaped by abiotic constraints
Author / Creator:Akbari, Amir ; Yurkovich, James T. ; Zielinski, Daniel C. ; Palsson, Bernhard O.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-05, Vol.12 (1), p.3178-19, Article 3178
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Community standards to facilitate development and address challenges in metabolic modeling
Author / Creator:Carey, Maureen A ; Dräger, Andreas ; Beber, Moritz E ; Papin, Jason A ; Yurkovich, James T
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2020-08, Vol.16 (8), p.e9235-n/a
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Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity
Author / Creator:Phaneuf, Patrick V. ; Yurkovich, James T. ; Heckmann, David ; Wu, Muyao ; Sandberg, Troy E. ; King, Zachary A. ; Tan, Justin ; Palsson, Bernhard O. ; Feist, Adam M.
Publisher:England: BioMed Central Ltd
Journal title:BMC genomics, 2020-07, Vol.21 (1), p.514-16, Article 514
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Visualizing metabolic network dynamics through time-series metabolomic data
Author / Creator: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
Publisher:England: BioMed Central
Journal title:BMC bioinformatics, 2020-04, Vol.21 (1), p.130-10, Article 130
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Genome-scale metabolic model of the rat liver predicts effects of diet restriction
Author / Creator:Baloni, Priyanka ; Sangar, Vineet ; Yurkovich, James T. ; Robinson, Max ; Taylor, Scott ; Karbowski, Christine M. ; Hamadeh, Hisham K. ; He, Yudong D. ; Price, Nathan D.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2019-07, Vol.9 (1), p.9807-12, Article 9807
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Temperature Dependence of Platelet Metabolism
Author / Creator:Jóhannsson, Freyr ; Yurkovich, James T. ; Guðmundsson, Steinn ; Sigurjónsson, Ólafur E. ; Rolfsson, Óttar
Publisher:Switzerland: MDPI AG
Journal title:Metabolites, 2024-01, Vol.14 (2), p.91
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Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells
Author / Creator:Yurkovich, James T. ; Yang, Laurence ; Palsson, Bernhard O.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2017-03, Vol.13 (3), p.e1005424
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Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
Author / Creator: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.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2015-08, Vol.112 (34), p.10810-10815
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Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials
Author / Creator:Yurkovich, James T. ; Alcantar, Miguel A. ; Haiman, Zachary B. ; Palsson, Bernhard O.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2018-08, Vol.14 (8), p.e1006356
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Metabolic and Transcriptional Changes across Osteogenic Differentiation of Mesenchymal Stromal Cells
Author / Creator:Sigmarsdottir, Thora Bjorg ; McGarrity, Sarah ; de Lomana, Adrián López García ; Kotronoulas, Aristotelis ; Sigurdsson, Snaevar ; Yurkovich, James T. ; Rolfsson, Ottar ; Sigurjonsson, Olafur Eysteinn
Publisher:Switzerland: MDPI AG
Journal title:Bioengineering (Basel), 2021-12, Vol.8 (12), p.208
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Blood Is a Window into Health and Disease
Author / Creator:Yurkovich, James T ; Hood, Leroy
Publisher:England: Oxford University Press
Journal title:Clinical chemistry (Baltimore, Md.), 2019-10, Vol.65 (10), p.1204-1206
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A systems approach to clinical oncology uses deep phenotyping to deliver personalized care
Author / Creator:Yurkovich, James T. ; Tian, Qiang ; Price, Nathan D. ; Hood, Leroy
Publisher:London: Nature Publishing Group UK
Journal title:Nature reviews. Clinical oncology, 2020-03, Vol.17 (3), p.183-194
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The transition from genomics to phenomics in personalized population health
Author / Creator:Yurkovich, James T. ; Evans, Simon J. ; Rappaport, Noa ; Boore, Jeffrey L. ; Lovejoy, Jennifer C. ; Price, Nathan D. ; Hood, Leroy E.
Publisher:London: Nature Publishing Group UK
Journal title:Nature reviews. Genetics, 2024-04, Vol.25 (4), p.286-302
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Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities
Author / Creator:Fang, Xin ; Sastry, Anand ; Mih, Nathan ; Kim, Donghyuk ; Tan, Justin ; Yurkovich, James T. ; Lloyd, Colton J. ; Gao, Ye ; Yang, Laurence ; Palsson, Bernhard O.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2017-09, Vol.114 (38), p.10286-10291
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Gut microbiome pattern reflects healthy ageing and predicts survival in humans
Author / Creator:Wilmanski, Tomasz ; Diener, Christian ; Rappaport, Noa ; Patwardhan, Sushmita ; Wiedrick, Jack ; Lapidus, Jodi ; Earls, John C. ; Zimmer, Anat ; Glusman, Gustavo ; Robinson, Max ; Yurkovich, James T. ; Kado, Deborah M. ; Cauley, Jane A. ; Zmuda, Joseph ; Lane, Nancy E. ; Magis, Andrew T. ; Lovejoy, Jennifer C. ; Hood, Leroy ; Gibbons, Sean M. ; Orwoll, Eric S. ; Price, Nathan D.
Publisher:London: Nature Publishing Group UK
Journal title:Nature metabolism, 2021-02, Vol.3 (2), p.274-286
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Showing 1 to 20 of 46 results

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Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

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Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

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

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Is the kinetome conserved?

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Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

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The quantitative metabolome is shaped by abiotic constraints

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Community standards to facilitate development and address challenges in metabolic modeling

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

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Visualizing metabolic network dynamics through time-series metabolomic data

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Genome-scale metabolic model of the rat liver predicts effects of diet restriction

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Temperature Dependence of Platelet Metabolism

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

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

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

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Metabolic and Transcriptional Changes across Osteogenic Differentiation of Mesenchymal Stromal Cells

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Blood Is a Window into Health and Disease

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A systems approach to clinical oncology uses deep phenotyping to deliver personalized care

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The transition from genomics to phenomics in personalized population health

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

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Gut microbiome pattern reflects healthy ageing and predicts survival in humans

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