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Author Details

James A Eddy
Benaroya Research Institute at Virginia Mason, Institute for Systems Biology, Sage Bionetworks, University of Illinois at Urbana-Champaign
0000-0001-9758-0176
2008
29
20
PMIDPaper TitleJournal TitlePublished Year
37608937The ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge 2023: Intracranial Meningioma.ArXiv2023
35735230Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database.Database (Oxford)2022
35072136GA4GH: International policies and standards for data sharing across genomic research and healthcare.Cell Genom2021
32668255Meta-Analysis of the Alzheimer's Disease Human Brain Transcriptome and Functional Dissection in Mouse Models.Cell Rep2020
33214875CRI iAtlas: an interactive portal for immuno-oncology research.F1000Res2020
33046718Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions.Sci Data2020
31433971The Immune Landscape of Cancer.Immunity2019
28566371Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4<sup>+</sup> T Cells in Peripheral Blood of Subjects with Type 1 Diabetes.J Immunol2017
28947916Network reconstruction and systems analysis of plant cell wall deconstruction by <i>Neurospora crassa</i>.Biotechnol Biofuels2017
27727239Human whole genome genotype and transcriptome data for Alzheimer's and other neurodegenerative diseases.Sci Data2016
28664195Partial exhaustion of CD8 T cells and clinical response to teplizumab in new-onset type 1 diabetes.Sci Immunol2016
25619653IL-10 alters immunoproteostasis in APP mice, increasing plaque burden and worsening cognitive behavior.Neuron2015
26013981Fostering synergy between cell biology and systems biology.Trends Cell Biol2015
23496976AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures.BMC Bioinformatics2013
24146911Transcriptional analysis of aggressiveness and heterogeneity across grades of astrocytomas.PLoS One2013
23386717Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain.Proc Natl Acad Sci U S A2013
23112774Mechanistic modeling of aberrant energy metabolism in human disease.Front Physiol2012
23234303Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE.BMC Syst Biol2012
22967466[Expression of PRUNE2 mRNA and its positive correlation with non-coding RNA PCA3 in leiomyosarcoma].Zhonghua Zhong Liu Za Zhi2012
21257608Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup.Bioinformatics2011
21846360Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052.BMC Syst Biol2011
21960440Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states.Proc Natl Acad Sci U S A2011
20218737Relative expression analysis for molecular cancer diagnosis and prognosis.Technol Cancer Res Treat2010
20836040In silico models of cancer.Wiley Interdiscip Rev Syst Biol Med2010
20523739Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC).PLoS Comput Biol2010
20651304Integrated proteomics and genomics analysis reveals a novel mesenchymal to epithelial reverting transition in leiomyosarcoma through regulation of slug.Mol Cell Proteomics2010
19964680Relative expression analysis for identifying perturbed pathways.Annu Int Conf IEEE Eng Med Biol Soc2009
19946878Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology.Biotechnol J2009
18364711Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major.Mol Syst Biol2008
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Collaborators

Nathan D Price
Institute for Systems Biology
Co-authored papers 20
Cory C Funk
Institute for Systems Biology
Co-authored papers 6
Kristen K Dang
Benaroya Research Institute at Virginia Mason
Co-authored papers 4
Nil??fer Ertekin-Taner
Mayo Clinic
Co-authored papers 3
John C Earls
Institute for Systems Biology
Co-authored papers 3
Younhee Ko
Hankuk University of Foreign Studies
Co-authored papers 3
Xue Wang
Mayo Clinic
Co-authored papers 3
Donald Geman
Johns Hopkins University
Co-authored papers 3
Benjamin A Logsdon
Fred Hutchinson Cancer Research Center
Co-authored papers 3
Mariet Allen
Mayo Clinic
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Lara M Mangravite
Children's Hospital Oakland Research Institute
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Emory Center for Neurodegenerative Disease
Co-authored papers 3
David Cogdell
The University of Texas MD Anderson Cancer Center
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Philip L De Jager
Columbia University Medical Center
Co-authored papers 2
Caroline B Milne
University of Illinois
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Tianjin Medical University Cancer Institute and Hospital
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Andrew T Magis
Institute for Systems Biology
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Minerva M Carrasquillo
Mayo Clinic
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Ilya Shmulevich
Institute for Systems Biology
Co-authored papers 2
Seth A Ament
Institute for Genome Sciences, University of Maryland School of Medicine
Co-authored papers 2
Benjamin G Vincent
UNC School of Medicine, The University of North Carolina at Chapel Hill
Co-authored papers 2
Pan-Jun Kim
Hong Kong Baptist University
Co-authored papers 2
David L Gibbs
Institute for Systems Biology
Co-authored papers 2
Vesteinn Thorsson
Institute for Systems Biology
Co-authored papers 2
Thanneer M Perumal
F. Hoffmann-La Roche Ltd
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Jonathan C Trent
Sylvester Comprehensive Cancer Center, University of Miami
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Sara Mostafavi
University of British Columbia and BC Children's Hospital
Co-authored papers 2
Verena Chung
Blavatnik Institute, Harvard Medical School
Co-authored papers 2
Paramita Chakrabarty
Center for Translational Research in Neurodegenerative Disease, University of Florida
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