James A Eddy
James A Eddy
Director of Informatics & Biocomputing, Sage Bionetworks
Verified email at sagebase.org - Homepage
Title
Cited by
Cited by
Year
The immune landscape of cancer
V Thorsson, DL Gibbs, SD Brown, D Wolf, DS Bortone, THO Yang, ...
Immunity 48 (4), 812-830. e14, 2018
12962018
IL-10 alters immunoproteostasis in APP mice, increasing plaque burden and worsening cognitive behavior
P Chakrabarty, A Li, C Ceballos-Diaz, JA Eddy, CC Funk, B Moore, ...
Neuron 85 (3), 519-533, 2015
2742015
Dynamic analysis of integrated signaling, metabolic, and regulatory networks
JM Lee, EP Gianchandani, JA Eddy, JA Papin
PLoS computational biology 4 (5), e1000086, 2008
2542008
Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
Y Wang, JA Eddy, ND Price
BMC systems biology 6 (1), 153, 2012
2292012
Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major
AK Chavali, JD Whittemore, JA Eddy, KT Williams, JA Papin
Molecular systems biology 4 (1), 177, 2008
1672008
Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases
M Allen, MM Carrasquillo, C Funk, BD Heavner, F Zou, CS Younkin, ...
Scientific data 3, 160089, 2016
1622016
Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states
S Chandrasekaran, SA Ament, JA Eddy, SL Rodriguez-Zas, BR Schatz, ...
Proceedings of the National Academy of Sciences 108 (44), 18020-18025, 2011
1552011
In silico models of cancer
LB Edelman, JA Eddy, ND Price
Wiley Interdisciplinary Reviews: Systems Biology and Medicine 2 (4), 438-459, 2010
1292010
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052
C Milne, J Eddy, R Raju, S Ardekani, PJ Kim, R Senger, YS Jin, ...
BMC systems biology 5 (1), 130, 2011
1112011
Relative expression analysis for molecular cancer diagnosis and prognosis
JA Eddy, J Sung, D Geman, ND Price
Technology in cancer research & treatment 9 (2), 149-159, 2010
1002010
Accomplishments in genome‐scale in silico modeling for industrial and medical biotechnology
CB Milne, PJ Kim, JA Eddy, ND Price
Biotechnology journal 4 (12), 1653-1670, 2009
972009
Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC)
JA Eddy, L Hood, ND Price, D Geman
PLoS computational biology 6 (5), e1000792, 2010
902010
Partial exhaustion of CD8 T cells and clinical response to teplizumab in new-onset type 1 diabetes
SA Long, J Thorpe, HA DeBerg, V Gersuk, J Eddy, KM Harris, M Ehlers, ...
Science immunology 1 (5), 2016
752016
Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain
Y Ko, SA Ament, JA Eddy, J Caballero, JC Earls, L Hood, ND Price
Proceedings of the National Academy of Sciences 110 (8), 3095-3100, 2013
702013
Integrated proteomics and genomics analysis reveals a novel mesenchymal to epithelial reverting transition in leiomyosarcoma through regulation of slug
J Yang, JA Eddy, Y Pan, A Hategan, I Tabus, Y Wang, D Cogdell, ...
Molecular & Cellular Proteomics 9 (11), 2405-2413, 2010
692010
A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily
A Korkut, S Zaidi, RS Kanchi, S Rao, NR Gough, A Schultz, X Li, ...
Cell systems, 2018
622018
Single-cell RNA sequencing reveals expanded clones of islet antigen-reactive CD4+ T cells in peripheral blood of subjects with type 1 diabetes
K Cerosaletti, F Barahmand-pour-Whitman, J Yang, HA DeBerg, ...
The Journal of Immunology 199 (1), 323-335, 2017
262017
Mechanistic modeling of aberrant energy metabolism in human disease
V Sangar, JA Eddy, E Simeonidis, ND Price
Frontiers in physiology 3, 2012
252012
Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa
A Samal, JP Craig, ST Coradetti, JP Benz, JA Eddy, ND Price, NL Glass
Biotechnology for biofuels 10 (1), 225, 2017
242017
Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup
AT Magis, JC Earls, YH Ko, JA Eddy, ND Price
Bioinformatics 27 (6), 872-873, 2011
132011
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Articles 1–20