Search Results - James A. Eddy

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  1. 1
    Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

    Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE by Yuliang Wang, James A. Eddy, Nathan D. Price

    Published 2012
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  2. 2
    <i>In silico</i> models of cancer

    <i>In silico</i> models of cancer by Lucas B. Edelman, James A. Eddy, Nathan D. Price

    Published 2009
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  3. 3
    Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)

    Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC) by James A. Eddy, Leroy Hood, Nathan D. Price, Donald Geman

    Published 2010
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  4. 4
    Relative Expression Analysis for Molecular Cancer Diagnosis and Prognosis

    Relative Expression Analysis for Molecular Cancer Diagnosis and Prognosis by James A. Eddy, Jaeyun Sung, Donald Geman, Nathan D. Price

    Published 2010
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  5. 5
    Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

    Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks by Jong Min Lee, Erwin P. Gianchandani, James A. Eddy, Jason A. Papin

    Published 2008
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  6. 6
    Correction: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

    Correction: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks by Jong Min Lee, Erwin P. Gianchandani, James A. Eddy, Jason A. Papin

    Published 2008
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  7. 7
    Accomplishments in genome‐scale <i>in silico</i> modeling for industrial and medical biotechnology

    Accomplishments in genome‐scale <i>in silico</i> modeling for industrial and medical biotechnology by Caroline B. Milne, Pan‐Jun Kim, James A. Eddy, Nathan D. Price

    Published 2009
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  8. 8
    Systems analysis of metabolism in the pathogenic trypanosomatid <i>Leishmania major</i>

    Systems analysis of metabolism in the pathogenic trypanosomatid <i>Leishmania major</i> by Arvind K. Chavali, Jeffrey D Whittemore, James A. Eddy, Kyle T Williams, Jason A. Papin

    Published 2008
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  9. 9
    Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain

    Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain by Younhee Ko, Seth A. Ament, James A. Eddy, Juan Caballero-Pérez, John C. Earls, Leroy Hood, Nathan D. Price

    Published 2013
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  10. 10
    Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states

    Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states by Sriram Chandrasekaran, Seth A. Ament, James A. Eddy, Sandra L. Rodriguez‐Zas, Bruce R. Schatz, Nathan D. Price, Gene E. Robinson

    Published 2011
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  11. 11
    Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

    Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052 by Caroline B. Milne, James A. Eddy, Ravali Raju, Soroush Ardekani, Pan‐Jun Kim, Ryan S. Senger, Yong‐Su Jin, Hans P. Blaschek, Nathan D. Price

    Published 2011
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  12. 12
    Partial exhaustion of CD8 T cells and clinical response to teplizumab in new-onset type 1 diabetes

    Partial exhaustion of CD8 T cells and clinical response to teplizumab in new-onset type 1 diabetes by S. Alice Long, Jerill Thorpe, Hannah A. DeBerg, Vivian H. Gersuk, James A. Eddy, Kristina M. Harris, Mario R. Ehlers, Kevan C. Herold, Gerald T. Nepom, Peter S. Linsley

    Published 2016
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  13. 13
    CRI iAtlas: an interactive portal for immuno-oncology research

    CRI iAtlas: an interactive portal for immuno-oncology research by James A. Eddy, Vésteinn Thórsson, Andrew Lamb, David L. Gibbs, Carolina Heimann, Jia Xin Yu, Verena Chung, Yooree Chae, Kristen K. Dang, Benjamin G. Vincent, Ilya Shmulevich, Justin Guinney

    Published 2020
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  14. 14
    Integrated Proteomics and Genomics Analysis Reveals a Novel Mesenchymal to Epithelial Reverting Transition in Leiomyosarcoma through Regulation of Slug

    Integrated Proteomics and Genomics Analysis Reveals a Novel Mesenchymal to Epithelial Reverting Transition in Leiomyosarcoma through Regulation of Slug by Jilong Yang, James A. Eddy, Yuan Pan, Andrea Hategan, Ioan Tăbuş, Yingmei Wang, David Cogdell, Nathan D. Price, Raphael E. Pollock, Alexander J. Lazar, Kelly K. Hunt, Jonathan C. Trent, Wei Zhang

    Published 2010
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  15. 15
    IL-10 Alters Immunoproteostasis in APP Mice, Increasing Plaque Burden and Worsening Cognitive Behavior

    IL-10 Alters Immunoproteostasis in APP Mice, Increasing Plaque Burden and Worsening Cognitive Behavior by Paramita Chakrabarty, Andrew Li, Carolina Ceballos‐Diaz, James A. Eddy, Cory C. Funk, Brenda D. Moore, Nadia DiNunno, Awilda M. Rosario, Pedro E. Cruz, Christophe Verbeeck, Amanda N. Sacino, Sarah Nix, Christopher Janus, Nathan D. Price, Pritam Das, Todd E. Golde

    Published 2015
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  16. 16
    Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes

    Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes by Karen Cerosaletti, Fariba Barahmand-pour-Whitman, Junbao Yang, Hannah A. DeBerg, Matthew J. Dufort, Sara A. Murray, Elisabeth Israelsson, Cate Speake, Vivian H. Gersuk, James A. Eddy, Helena Reijonen, Carla J. Greenbaum, William W. Kwok, Erik Wambre, Martin Prlic, Raphaël Gottardo, Gerald T. Nepom, Peter S. Linsley

    Published 2017
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  17. 17
    Sharing data from the Human Tumor Atlas Network through standards, infrastructure and community engagement

    Sharing data from the Human Tumor Atlas Network through standards, infrastructure and community engagement by Ino de Bruijn, Milen Nikolov, Clarisse Lau, Ashley Clayton, David L. Gibbs, Elvira Mitraka, Dar’ya Pozhidayeva, Alex E. Lash, S. Onur Sumer, Jennifer Altreuter, Kristen Anton, Mialy DeFelice, Xiang Li, Aaron Lisman, William J.R. Longabaugh, Jeremy L. Muhlich, Sandro Santagata, Subhiksha Nandakumar, Peter K. Sorger, Christine Suver, Xengie Doan, Justin Guinney, Nikolaus Schultz, Adam Taylor, Vésteinn Thórsson, Ethan Cerami, James A. Eddy

    Published 2025
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  18. 18
    Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases

    Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases by Mariet Allen, Minerva M. Carrasquillo, Cory C. Funk, Ben Heavner, Fanggeng Zou, Curtis Younkin, Jeremy D. Burgess, High-Seng Chai, Julia E. Crook, James A. Eddy, Hong‐Dong Li, Ben Logsdon, Mette A. Peters, Kristen K. Dang, Xue Wang, Daniel Serie, Chen Wang, Thuy Nguyen, Sarah Lincoln, Kimberly G. Malphrus, Gina Bisceglio, Li Ma, Todd E. Golde, Lara M. Mangravite, Yan W. Asmann, Nathan D. Price, Ronald Petersen, Neill R. Graff‐Radford, Dennis W. Dickson, Steven G. Younkin, Nilüfer Ertekin‐Taner

    Published 2016
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  19. 19
    AI-readiness for Biomedical Data: Bridge2AI Recommendations

    AI-readiness for Biomedical Data: Bridge2AI Recommendations by Tim W. Clark, J. Harry Caufield, Jillian A. Parker, Mohammad Sadnan Al Manir, Edilberto Amorim, James A. Eddy, Nayoon Gim, Brian Gow, Wesley Goar, Melissa Haendel, Jan N. Hansen, Nomi L. Harris, Henning Hermjakob, Marcin P. Joachimiak, G. K. S. Jordan, In‐Hee Lee, Shannon K. McWeeney, Camille Nebeker, Milen Nikolov, Jamie Shaffer, Nathan C. Sheffield, Gloria Sheynkman, James Stevenson, Jake Y. Chen, Chris Mungall, Alex H. Wagner, Sek Won Kong, Satrajit Ghosh, Bhavesh Patel, Andrew E. Williams, Monica Muñoz‐Torres

    Published 2024
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  20. 20
    Meta-analysis of the human brain transcriptome identifies heterogeneity across human AD coexpression modules robust to sample collection and methodological approach

    Meta-analysis of the human brain transcriptome identifies heterogeneity across human AD coexpression modules robust to sample collection and methodological approach by Benjamin A. Logsdon, Thanneer M. Perumal, Vivek Swarup, Minghui Wang, Cory C. Funk, Chris Gaiteri, Mariet Allen, Xue Wang, Eric B. Dammer, Gyan Srivastava, Sumit Mukherjee, Solveig K. Sieberts, Larsson Omberg, Kristen D. Dang, James A. Eddy, Phil Snyder, Yooree Chae, Sandeep Amberkar, Wenbin Wei, Yoshihide Hayashizaki, Christoph Preuß, Ayla Ergün, Phillip J. Ebert, David Airey, Gregory W. Carter, Sara Mostafavi, Lei Yu, Hans‐Ulrich Klein, David Collier, Todd E. Golde, Allan I. Levey, David A. Bennett, Karol Estrada, Michael Decker, Zhandong Liu, Joshua M. Shulman, Bin Zhang, Eric E. Schadt, Phillip L. De Jager, Nathan D. Price, Nilüfer Ertekin‐Taner, Lara M. Mangravite

    Published 2019
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