Trimming of mammalian transcriptional networks using network component analysis

por Tran, Linh M, Hyduke, Daniel R, Liao, James C
Publicado 2010

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

por Ebrahim, Ali, Lerman, Joshua A, Palsson, Bernhard O, Hyduke, Daniel R
Publicado 2013

Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland

por Datta, Kamal, Hyduke, Daniel R, Suman, Shubhankar, Moon, Bo-Hyun, Johnson, Michael D, Fornace, Albert J
Publicado 2012

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

por O’Brien, Edward J, Lerman, Joshua A, Chang, Roger L, Hyduke, Daniel R, Palsson, Bernhard Ø
Publicado 2013

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks

por Nam, Hojung, Campodonico, Miguel, Bordbar, Aarash, Hyduke, Daniel R., Kim, Sangwoo, Zielinski, Daniel C., Palsson, Bernhard O.
Publicado 2014

Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella

por McDermott, Jason E., Yoon, Hyunjin, Nakayasu, Ernesto S., Metz, Thomas O., Hyduke, Daniel R., Kidwai, Afshan S., Palsson, Bernhard O., Adkins, Joshua N., Heffron, Fred
Publicado 2011

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92

por Charusanti, Pep, Chauhan, Sadhana, McAteer, Kathleen, Lerman, Joshua A, Hyduke, Daniel R, Motin, Vladimir L, Ansong, Charles, Adkins, Joshua N, Palsson, Bernhard O
Publicado 2011

TGx-DDI, a Transcriptomic Biomarker for Genotoxicity Hazard Assessment of Pharmaceuticals and Environmental Chemicals

por 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.
Publicado 2019

Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells

por Buick, Julie K., Moffat, Ivy, Williams, Andrew, Swartz, Carol D., Recio, Leslie, Hyduke, Daniel R., Li, Heng‐Hong, Fornace, Albert J., Aubrecht, Jiri, Yauk, Carole L.
Publicado 2015

A predictive toxicogenomics signature to classify genotoxic versus non-genotoxic chemicals in human TK6 cells

por Williams, Andrew, Buick, Julie K., Moffat, Ivy, Swartz, Carol D., Recio, Leslie, Hyduke, Daniel R., Li, Heng-Hong, Fornace, Albert J., Aubrecht, Jiri, Yauk, Carole L.
Publicado 2015

Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs

por Li, Heng-Hong, Chen, Renxiang, Hyduke, Daniel R., Williams, Andrew, Frötschl, Roland, Ellinger-Ziegelbauer, Heidrun, O’Lone, Raegan, Yauk, Carole L., Aubrecht, Jiri, Fornace, Albert J.
Publicado 2017

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

por Bordbar, Aarash, Mo, Monica L, Nakayasu, Ernesto S, Schrimpe-Rutledge, Alexandra C, Kim, Young-Mo, Metz, Thomas O, Jones, Marcus B, Frank, Bryan C, Smith, Richard D, Peterson, Scott N, Hyduke, Daniel R, Adkins, Joshua N, Palsson, Bernhard O
Publicado 2012

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

por Thiele, Ines, Hyduke, Daniel R, Steeb, Benjamin, Fankam, Guy, Allen, Douglas K, Bazzani, Susanna, Charusanti, Pep, Chen, Feng-Chi, Fleming, Ronan MT, Hsiung, Chao A, De Keersmaecker, Sigrid CJ, Liao, Yu-Chieh, Marchal, Kathleen, Mo, Monica L, Özdemir, Emre, Raghunathan, Anu, Reed, Jennifer L, Shin, Sook-Il, Sigurbjörnsdóttir, Sara, Steinmann, Jonas, Sudarsan, Suresh, Swainston, Neil, Thijs, Inge M, Zengler, Karsten, Palsson, Bernhard O, Adkins, Joshua N, Bumann, Dirk
Publicado 2011

Do genome-scale models need exact solvers or clearer standards?

por Ebrahim, Ali, Almaas, Eivind, Bauer, Eugen, Bordbar, Aarash, Burgard, Anthony P, Chang, Roger L, Dräger, Andreas, Famili, Iman, Feist, Adam M, Fleming, Ronan MT, Fong, Stephen S, Hatzimanikatis, Vassily, Herrgård, Markus J, Holder, Allen, Hucka, Michael, Hyduke, Daniel, Jamshidi, Neema, Lee, Sang Yup, Le Novère, Nicolas, Lerman, Joshua A, Lewis, Nathan E, Ma, Ding, Mahadevan, Radhakrishnan, Maranas, Costas, Nagarajan, Harish, Navid, Ali, Nielsen, Jens, Nielsen, Lars K, Nogales, Juan, Noronha, Alberto, Pal, Csaba, Palsson, Bernhard O, Papin, Jason A, Patil, Kiran R, Price, Nathan D, Reed, Jennifer L, Saunders, Michael, Senger, Ryan S, Sonnenschein, Nikolaus, Sun, Yuekai, Thiele, Ines
Publicado 2015