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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
45652018
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
3822015
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 (1), 1-10, 2016
3612016
Dynamic analysis of integrated signaling, metabolic, and regulatory networks
JM Lee, EP Gianchandani, JA Eddy, JA Papin
PLoS Comput Biol 4 (5), e1000086, 2008
3012008
Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
Y Wang, JA Eddy, ND Price
BMC systems biology 6 (1), 1-16, 2012
2982012
Meta-analysis of the Alzheimer’s disease human brain transcriptome and functional dissection in mouse models
YW Wan, R Al-Ouran, CG Mangleburg, TM Perumal, TV Lee, K Allison, ...
Cell reports 32 (2), 107908, 2020
2152020
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
2012016
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
1972008
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
1932011
In silico models of cancer
LB Edelman, JA Eddy, ND Price
Wiley Interdisciplinary Reviews: Systems Biology and Medicine 2 (4), 438-459, 2010
1642010
GA4GH: international policies and standards for data sharing across genomic research and healthcare
HL Rehm, AJH Page, L Smith, JB Adams, G Alterovitz, LJ Babb, ...
Cell Genomics 1 (2), 100029, 2021
1492021
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052
CB Milne, JA Eddy, R Raju, S Ardekani, PJ Kim, RS Senger, YS Jin, ...
BMC systems biology 5 (1), 1-15, 2011
1312011
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
1212010
Accomplishments in genome‐scale in silico modeling for industrial and medical biotechnology
CB Milne, PJ Kim, JA Eddy, ND Price
Biotechnology Journal: Healthcare Nutrition Technology 4 (12), 1653-1670, 2009
1042009
Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC)
JA Eddy, L Hood, ND Price, D Geman
PLoS Comput Biol 6 (5), e1000792, 2010
972010
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
902013
Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions
SK Sieberts, TM Perumal, MM Carrasquillo, M Allen, JS Reddy, ...
Scientific data 7 (1), 1-11, 2020
872020
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
802010
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
642017
CRI iAtlas: an interactive portal for immuno-oncology research
JA Eddy, V Thorsson, AE Lamb, DL Gibbs, C Heimann, JX Yu, V Chung, ...
F1000Research 9, 2020
432020
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