J
James A. Eddy
Researcher at Sage Bionetworks
Publications - 42
Citations - 6342
James A. Eddy is an academic researcher from Sage Bionetworks. The author has contributed to research in topics: Systems biology & Gene. The author has an hindex of 21, co-authored 38 publications receiving 4146 citations. Previous affiliations of James A. Eddy include University of Illinois at Urbana–Champaign & Institute for Systems Biology.
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Journal ArticleDOI
The Immune Landscape of Cancer
Vesteinn Thorsson,David L Gibbs,Scott D. Brown,Denise M. Wolf,Dante S. Bortone,Tai-Hsien Ou Yang,Eduard Porta-Pardo,Galen F. Gao,Christopher L. Plaisier,James A. Eddy,Elad Ziv,Aedín C. Culhane,Evan O. Paull,I K Ashok Sivakumar,Andrew J. Gentles,Raunaq Malhotra,Farshad Farshidfar,Antonio Colaprico,Joel S. Parker,Lisle E. Mose,Nam S Vo,Jianfang Liu,Yuexin Liu,Janet S. Rader,Varsha Dhankani,Sheila Reynolds,Reanne Bowlby,Andrea Califano,Andrew D. Cherniack,Dimitris Anastassiou,Davide Bedognetti,Arvind Rao,Ken Chen,Alexander Krasnitz,Hai Hu,Tathiane M. Malta,Houtan Noushmehr,Houtan Noushmehr,Chandra Sekhar Pedamallu,Susan Bullman,Akinyemi I. Ojesina,Andrew Lamb,Wanding Zhou,Hui Shen,Toni K. Choueiri,John N. Weinstein,Justin Guinney,Joel H. Saltz,Robert A. Holt,Charles E Rabkin,Alexander J. Lazar +50 more
TL;DR: An extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA identifies six immune subtypes that encompass multiple cancer types and are hypothesized to define immune response patterns impacting prognosis.
Journal ArticleDOI
IL-10 Alters Immunoproteostasis in APP Mice, Increasing Plaque Burden and Worsening Cognitive Behavior
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 +15 more
TL;DR: The observations that IL-10 has an unexpected negative effect on Aβ proteostasis and cognition in APP mouse models demonstrate the complex interplay between innate immunity and protestasis in neurodegenerative diseases, an interaction the authors call immunoproteostasis.
Journal ArticleDOI
Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases
Mariet Allen,Minerva M. Carrasquillo,Cory C. Funk,Benjamin D. Heavner,Fanggeng Zou,Curtis S. 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 J. Serie,Chen Wang,Thuy Nguyen,Sarah Lincoln,Kimberly G. Malphrus,Gina Bisceglio,Ma Li,Todd E. Golde,Lara M. Mangravite,Yan W. Asmann,Nathan D. Price,Ronald C. Petersen,Neill R. Graff-Radford,Dennis W. Dickson,Steven G. Younkin,Nilufer Ertekin-Taner +30 more
TL;DR: This work has analyzed gene expression levels in the brain tissue of subjects with AD and related diseases and expects that these datasets will enable investigators to explore and identify transcriptional mechanisms contributing to neurodegenerative diseases.
Journal ArticleDOI
Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions.
Solveig K. Sieberts,Thanneer M. Perumal,Minerva M. Carrasquillo,Mariet Allen,Joseph S. Reddy,Gabriel E. Hoffman,Kristen K. Dang,John N. Calley,Phillip J. Ebert,James A. Eddy,Xue Wang,Anna K. Greenwood,Sara Mostafavi,Sara Mostafavi,S Akbarian,J Bendl,M S Breen,K Brennand,L Brown,A Browne,J D Buxbaum,A Charney,Andrew Chess,Couto L,Gregory E. Crawford,Devillers O,Bernie Devlin,Amanda Dobbyn,E Domenici,M Filosi,E Flatow,Nancy Francoeur,John F. Fullard,S E Gil,Kiran Girdhar,A Gulyás-Kovács,R.E. Gur,C G Hahn,Vahram Haroutunian,Mads E. Hauberg,Laura M. Huckins,Rivka Jacobov,Y Jiang,Jessica S. Johnson,Bibi Kassim,Y Kim,Lambertus Klei,Robin Kramer,Mario Lauria,Thomas Lehner,David A. Lewis,Barbara K. Lipska,Kelsey S. Montgomery,R Park,C Rosenbluh,Panagiotis Roussos,Douglas M. Ruderfer,G Senthil,Hardik Shah,Laura G. Sloofman,L Song,E Stahl,P.F. Sullivan,R Visintainer,J Wang,Y C Wang,Jennifer Wiseman,E Xia,W Zhang,Elizabeth Zharovsky,L Addis,S N Addo,David C. Airey,Matthias Arnold,David A. Bennett,Y Bi,K Biber,Colette Blach,E Bradhsaw,Paul Brennan,R Canet-Aviles,S Cao,A Cavalla,Yooree Chae,W W Chen,J Cheng,David A. Collier,J L Dage,Eric B. Dammer,J W Davis,John B. Davis,Derek Drake,D Duong,Brian J. Eastwood,Michelle E. Ehrlich,B Ellingson,B W Engelmann,S Esmaeelinieh,Daniel Felsky,Cory C. Funk,Chris Gaiteri +100 more
TL;DR: A colocalization analysis is applied to identify genes underlying the GWAS association peaks for schizophrenia and identify a potentially novel gene colocalized with lncRNA RP11-677M14.
Journal ArticleDOI
Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE.
TL;DR: The eicosanoid metabolic pathway is identified, especially reactions catalyzing the production of leukotrienes from arachidnoic acid, as potential drug targets that selectively affect tumor tissues.