Search Results - "Hyduke, Daniel R."

COBRApy: COnstraints-Based Reconstruction and Analysis for Python by Ebrahim, Ali, Lerman, Joshua A, Palsson, Bernhard O, Hyduke, Daniel R

“…COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and…”
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Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction by O'Brien, Edward J, Lerman, Joshua A, Chang, Roger L, Hyduke, Daniel R, Palsson, Bernhard Ø

“…Growth is a fundamental process of life. Growth requirements are well‐characterized experimentally for many microbes; however, we lack a unified model for…”
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Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs by 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.

“…Interpretation of positive genotoxicity findings using the current in vitro testing battery is a major challenge to industry and regulatory agencies. These…”
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Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water by Moffat, Ivy, Chepelev, Nikolai L., Labib, Sarah, Bourdon-Lacombe, Julie, Kuo, Byron, Buick, Julie K., Lemieux, France, Williams, Andrew, Halappanavar, Sabina, Malik, Amal I, Luijten, Mirjam, Aubrecht, Jiri, Hyduke, Daniel R., Fornace, Albert J., Swartz, Carol D., Recio, Leslie, Yauk, Carole L.

“…Abstract Toxicogenomics is proposed to be a useful tool in human health risk assessment. However, a systematic comparison of traditional risk assessment…”
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Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells by Li, Heng-Hong, Hyduke, Daniel R., Chen, Renxiang, Heard, Pamela, Yauk, Carole L., Aubrecht, Jiri, Fornace Jr, Albert J.

“…The development of in vitro molecular biomarkers to accurately predict toxicological effects has become a priority to advance testing strategies for human…”
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A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks by Nam, Hojung, Campodonico, Miguel, Bordbar, Aarash, Hyduke, Daniel R, Kim, Sangwoo, Zielinski, Daniel C, Palsson, Bernhard O

“…Altered metabolism in cancer cells has been viewed as a passive response required for a malignant transformation. However, this view has changed through the…”
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Model‐driven multi‐omic data analysis elucidates metabolic immunomodulators of macrophage activation by 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

“…Macrophages are central players in immune response, manifesting divergent phenotypes to control inflammation and innate immunity through release of cytokines…”
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AMP-activated protein kinase promotes human prostate cancer cell growth and survival by Park, Hyeon Ung, Suy, Simeng, Danner, Malika, Dailey, Vernon, Zhang, Ying, Li, Henghong, Hyduke, Daniel R, Collins, Brian T, Gagnon, Gregory, Kallakury, Bhaskar, Kumar, Deepak, Brown, Milton L, Fornace, Albert, Dritschilo, Anatoly, Collins, Sean P

“…The molecular mechanisms underlying the development and progression of prostate cancer are poorly understood. AMP-activated protein kinase (AMPK) is a…”
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Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli by Hyduke, Daniel R, Jarboe, Laura R, Tran, Linh M, Chou, Katherine J.Y, Liao, James C

“…Nitric oxide (NO) is used by mammalian immune systems to counter microbial invasions and is produced by bacteria during denitrification. As a defense,…”
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Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland by Datta, Kamal, Hyduke, Daniel R, Suman, Shubhankar, Moon, Bo-Hyun, Johnson, Michael D, Fornace, Jr, Albert J

“…Breast tissue is among the most sensitive tissues to the carcinogenic actions of ionizing radiation and epidemiological studies have linked radiation exposure…”
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Nitric Oxide is Consumed, Rather Than Conserved, by Reaction with Oxyhemoglobin under Physiological Conditions by Joshi, Mahesh S., Ferguson, T. Bruce, Han, Tae H., Hyduke, Daniel R., Liao, James C., Rassaf, Tienush, Bryan, Nathan, Feelisch, Martin, Lancaster, Jack R.

“…Although irreversible reaction of NO with the oxyheme of hemoglobin (producing nitrate and methemoglobin) is extremely rapid, it has been proposed that, under…”
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Trimming of mammalian transcriptional networks using network component analysis by Tran, Linh M, Hyduke, Daniel R, Liao, James C

“…Network Component Analysis (NCA) has been used to deduce the activities of transcription factors (TFs) from gene expression data and the TF-gene binding…”
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GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data by Schmidt, Brian J, Ebrahim, Ali, Metz, Thomas O, Adkins, Joshua N, Palsson, Bernhard Ø, Hyduke, Daniel R

“…Genome-scale metabolic models have been used extensively to investigate alterations in cellular metabolism. The accuracy of these models to represent cellular…”
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Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 by Schellenberger, Jan, Que, Richard, Fleming, Ronan M T, Thiele, Ines, Orth, Jeffrey D, Feist, Adam M, Zielinski, Daniel C, Bordbar, Aarash, Lewis, Nathan E, Rahmanian, Sorena, Kang, Joseph, Hyduke, Daniel R, Palsson, Bernhard Ø

“…Over the past decade, a growing community of researchers has emerged around the use of constraint-based reconstruction and analysis (COBRA) methods to…”
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Determination of the Escherichia coli S-Nitrosoglutathione Response Network Using Integrated Biochemical and Systems Analysis by Jarboe, Laura R., Hyduke, Daniel R., Tran, Linh M., Chou, Katherine J.Y., Liao, James C.

“…During infection or denitrification, bacteria encounter reactive nitrogen species. Although the molecular targets of and defensive response against nitric…”
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Modulation of Nitric Oxide Bioavailability by Erythrocytes by Huang, Kuang-Tse, Han, Tae H., Hyduke, Daniel R., Vaughn, Mark W., Van Herle, Helga, Hein, Travis W., Zhang, Cuihua, Kuo, Lih, Liao, James C.

“…Nitric oxide (NO) activates soluble guanylyl cyclase in smooth muscle cells to induce vasodilation in the vasculature. However, as hemoglobin (Hb) is an…”
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A predictive toxicogenomics signature to classify genotoxic versus non-genotoxic chemicals in human TK6 cells by 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.

“…Genotoxicity testing is a critical component of chemical assessment. The use of integrated approaches in genetic toxicology, including the incorporation of…”
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Analysis of omics data with genome-scale models of metabolism by Hyduke, Daniel R, Lewis, Nathan E, Palsson, Bernhard Ø

“…Over the past decade a massive amount of research has been dedicated to generating omics data to gain insight into a variety of biological phenomena, including…”
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Nitric Oxide Reaction with Red Blood Cells and Hemoglobin under Heterogeneous Conditions by Han, Tae H., Hyduke, Daniel R., Vaughn, Mark W., Fukuto, Jon M., Liao, James C.

“…Understanding the interaction of nitric oxide (NO) with red blood cells (RBCs) is vital to elucidating the metabolic fate of NO in the vasculature. Because…”
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In silico method for modelling metabolism and gene product expression at genome scale by Lerman, Joshua A., Hyduke, Daniel R., Latif, Haythem, Portnoy, Vasiliy A., Lewis, Nathan E., Orth, Jeffrey D., Schrimpe-Rutledge, Alexandra C., Smith, Richard D., Adkins, Joshua N., Zengler, Karsten, Palsson, Bernhard O.

“…Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular…”
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