TGx-DDI, a Transcriptomic Biomarker for Genotoxicity Hazard Assessment of Pharmaceuticals and Environmental Chemicals. - Li, Heng-Hong; Yauk, Carole L.; Chen, Renxiang; Hyduke, Daniel R.; Williams, Andrew; Frötschl, Roland; Ellinger-Ziegelbauer, Heidrun; Pettit, Syril; Aubrecht, Jiri; Fornace, Albert J., Jr. (Frontiers Big Data, 2019)

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

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. - Schmidt, Brian J.; Ebrahim, Ali; Metz, Thomas O.; Adkins, Joshua N.; Palsson, Bernhard Ø.; Hyduke, Daniel R. (Bioinform., 2013)

COBRApy: COnstraints-Based Reconstruction and Analysis for Python. - Ebrahim, Ali; Lerman, Joshua A.; Palsson, Bernhard Ø.; Hyduke, Daniel R. (BMC Syst. Biol., 2013)

Identifying radiation exposure biomarkers from mouse blood transcriptome. - Hyduke, Daniel R.; Laiakis, Evagelia C.; Li, Heng-Hong; Fornace, Albert J., Jr. (Int. J. Bioinform. Res. Appl., 2013)

Session introduction. - McDermott, Jason E.; Braun, Pascal; Bonneau, Richard; Hyduke, Daniel R. (2012)

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. - Thiele, Ines; Hyduke, Daniel R.; Steeb, Benjamin; Fankam, Guy; Allen, Douglas K.; Bazzani, Susanna; Charusanti, Pep; Chen, Feng-Chi; Fleming, Ronan M. T.; Hsiung, Chao A.; Keersmaecker, Sigrid C. J. De; Liao, Yu-Chieh; et al. (BMC Syst. Biol., 2011)

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. - Charusanti, Pep; Chauhan, Sadhana; McAteer, Kathleen; Lerman, Joshua A.; Hyduke, Daniel R.; Motin, Vladimir L.; Ansong, Charles; Adkins, Joshua N.; Palsson, Bernhard O. (BMC Syst. Biol., 2011)

Trimming of mammalian transcriptional networks using network component analysis. - Tran, Linh M.; Hyduke, Daniel R.; Liao, James C. (BMC Bioinform., 2010)