Solving Puzzles With Missing Pieces: The Power of Systems Biology [Point of View]. - James T. Yurkovich; Bernhard O. Palsson (Proc. IEEE, 2016)

Toward Community Standards and Software for Whole-Cell Modeling. - Dagmar Waltemath; Jonathan R. Karr; Frank T. Bergmann; Vijayalakshmi Chelliah; Michael Hucka; Marcus Krantz; Wolfram Liebermeister; Pedro Mendes 001; Chris J. Myers; Pinar Pir; Begum Alaybeyoglu; Naveen K. Aranganathan; et al. (IEEE Trans. Biomed. Eng., 2016)

Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells. - James T. Yurkovich; Laurence Yang 001; Bernhard O. Palsson (CCTA, 2017)

Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. - James T. Yurkovich; Laurence Yang 001; Bernhard O. Palsson (PLoS Comput. Biol., 2017)

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. - Erol S. Kavvas; Yara Seif; James T. Yurkovich; Charles J. Norsigian; Saugat Poudel; William W. Greenwald; Sankha Ghatak; Bernhard O. Palsson; Jonathan M. Monk (BMC Syst. Biol., 2018)

Systems biology as an emerging paradigm in transfusion medicine. - James T. Yurkovich; Aarash Bordbar; Ólafur E. Sigurjónsson; Bernhard O. Palsson (BMC Syst. Biol., 2018)

Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. - James T. Yurkovich; Miguel A. Alcantar; Zachary B. Haiman; Bernhard O. Palsson (PLoS Comput. Biol., 2018)

The Systems Biology of Red Cell Metabolism: Physiology under Storage Conditions - James T. Yurkovich (2018)

Visualizing metabolic network dynamics through time-series metabolomic data. - Lea Buchweitz; James T. Yurkovich; Christoph Blessing; Veronika Kohler; Fabian Schwarzkopf; Zachary A. King; Laurence Yang 001; Freyr Jóhannsson; Ólafur E. Sigurjónsson; Ottar Rolfsson; Julian Heinrich; Andreas Dräger (BMC Bioinform., 2020)

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. - Charles J. Norsigian; Neha Pusarla; John Luke McConn; James T. Yurkovich; Andreas Dräger; Bernhard O. Palsson; Zachary A. King (Nucleic Acids Res., 2020)

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. - Zachary B. Haiman; Daniel C. Zielinski; Yuko Koike; James T. Yurkovich; Bernhard O. Palsson (PLoS Comput. Biol., 2021)

A framework towards digital twins for type 2 diabetes. - Yue Zhang 024; Guangrong Qin; Boris Aguilar; Noa Rappaport; James T. Yurkovich; Lance Pflieger; Sui Huang; Leroy Hood; Ilya Shmulevich (Frontiers Digit. Health, 2024)