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

by James T Yurkovich, Laurence Yang, Bernhard O Palsson
Published 2017-03-01

The quantitative metabolome is shaped by abiotic constraints

by Amir Akbari, James T. Yurkovich, Daniel C. Zielinski, Bernhard O. Palsson
Published 2021-05-01

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

by James T Yurkovich, Miguel A Alcantar, Zachary B Haiman, Bernhard O Palsson
Published 2018-08-01

The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures

by Kumari S. Choudhary, Nathan Mih, Nathan Mih, Jonathan Monk, Erol Kavvas, James T. Yurkovich, James T. Yurkovich, George Sakoulas, Bernhard O. Palsson, Bernhard O. Palsson, Bernhard O. Palsson
Published 2018-05-01

Community standards to facilitate development and address challenges in metabolic modeling

by Maureen A Carey, Andreas Dräger, Moritz E Beber, Jason A Papin, James T Yurkovich
Published 2020-08-01

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

by Zachary B Haiman, Daniel C Zielinski, Yuko Koike, James T Yurkovich, Bernhard O Palsson
Published 2021-01-01

Analyzing Metabolic States of Adipogenic and Osteogenic Differentiation in Human Mesenchymal Stem Cells via Genome Scale Metabolic Model Reconstruction

by Thora Bjorg Sigmarsdottir, Sarah McGarrity, Sarah McGarrity, James T. Yurkovich, Óttar Rolfsson, Ólafur Eysteinn Sigurjónsson, Ólafur Eysteinn Sigurjónsson
Published 2021-06-01

Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine

by Þóra Sigmarsdóttir, Þóra Sigmarsdóttir, Sarah McGarrity, Sarah McGarrity, Óttar Rolfsson, James T. Yurkovich, Ólafur E. Sigurjónsson, Ólafur E. Sigurjónsson
Published 2020-03-01

Poliovirus Vaccination Induces a Humoral Immune Response That Cross Reacts With SARS-CoV-2

by Brittany A. Comunale, Lilly Engineer, Lilly Engineer, Yong Jiang, John C. Andrews, Qianna Liu, Lyuqing Ji, James T. Yurkovich, Roderick A. Comunale, Qiyi Xie
Published 2021-08-01

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

by Patrick V. Phaneuf, James T. Yurkovich, David Heckmann, Muyao Wu, Troy E. Sandberg, Zachary A. King, Justin Tan, Bernhard O. Palsson, Adam M. Feist
Published 2020-07-01

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

by Yara Seif, Erol Kavvas, Jean-Christophe Lachance, James T. Yurkovich, Sean-Paul Nuccio, Xin Fang, Edward Catoiu, Manuela Raffatellu, Bernhard O. Palsson, Jonathan M. Monk
Published 2018-09-01

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

by Eliza J.R. Peterson, Abrar A. Abidi, Mario L. Arrieta-Ortiz, Boris Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, Nitin S. Baliga
Published 2020-04-01

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

by Eliza J.R. Peterson, Abrar A. Abidi, Mario L. Arrieta-Ortiz, Boris Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, Nitin S. Baliga
Published 2021-06-01

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

by Erol S. Kavvas, Edward Catoiu, Nathan Mih, James T. Yurkovich, Yara Seif, Nicholas Dillon, David Heckmann, Amitesh Anand, Laurence Yang, Victor Nizet, Jonathan M. Monk, Bernhard O. Palsson
Published 2018-10-01

Visualizing metabolic network dynamics through time-series metabolomic data

by Lea F. Buchweitz, James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, Freyr Jóhannsson, Ólafur E. Sigurjónsson, Óttar Rolfsson, Julian Heinrich, Andreas Dräger
Published 2020-04-01