Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling. - Jan Schellenberger; Daniel C. Zielinski; Wing Choi; Sunthosh Madireddi; Vasiliy Portnoy; David A. Scott; Jennifer L. Reed; Andrei Osterman; Bernhard Ø. Palsson (BMC Syst. Biol., 2012)

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks. - Hojung Nam; Miguel Campodonico; Aarash Bordbar; Daniel R. Hyduke; Sangwoo Kim; Daniel C. Zielinski; Bernhard O. Palsson (PLoS Comput. Biol., 2014)

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. - Andreas Dräger; Daniel C. Zielinski; Roland Keller; Matthias Rall; Johannes Eichner; Bernhard O. Palsson; Andreas Zell (BMC Syst. Biol., 2015)

Using metabolic network reconstructions to analyze complex data sets. - Daniel C. Zielinski (2015)

Evaluation of rate law approximations in bottom-up kinetic models of metabolism. - Bin Du; Daniel C. Zielinski; Erol S. Kavvas; Andreas Dräger; Justin Tan; Zhen Zhang; Kayla E. Ruggiero; Garri A. Arzumanyan; Bernhard O. Palsson (BMC Syst. Biol., 2016)

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)

iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. - Anand V. Sastry; Yuan Yuan; Saugat Poudel; Kevin Rychel; Reo Yoo; Cameron R. Lamoureux; Gaoyuan Li; Joshua T. Burrows; Siddharth Chauhan; Zachary B. Haiman; Tahani Al Bulushi; Yara Seif; et al. (PLoS Comput. Biol., 2024)

Inferred regulons are consistent with regulator binding sequences in E. coli. - Sizhe Qiu; Xinlong Wan; Yueshan Liang; Cameron R. Lamoureux; Amir Akbari; Bernhard O. Palsson; Daniel C. Zielinski (PLoS Comput. Biol., 2024)