J
James W. MacDonald
Researcher at University of Washington
Publications - 92
Citations - 6899
James W. MacDonald is an academic researcher from University of Washington. The author has contributed to research in topics: Gene & DNA methylation. The author has an hindex of 32, co-authored 80 publications receiving 5616 citations. Previous affiliations of James W. MacDonald include University of Michigan.
Papers
More filters
Journal ArticleDOI
Orchestrating high-throughput genomic analysis with Bioconductor
Wolfgang Huber,Vincent J. Carey,Robert Gentleman,Simon Anders,Marc R. J. Carlson,Benilton S. Carvalho,Héctor Corrada Bravo,Sean Davis,Laurent Gatto,Thomas Girke,Raphael Gottardo,Florian Hahne,Kasper D. Hansen,Rafael A. Irizarry,Michael S. Lawrence,Michael I. Love,James W. MacDonald,Valerie Obenchain,Andrzej K. Oleś,Hervé Pagès,Alejandro Reyes,Paul Shannon,Gordon K. Smyth,Dan Tenenbaum,Levi Waldron,Martin Morgan +25 more
TL;DR: An overview of Bioconductor, an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology, which comprises 934 interoperable packages contributed by a large, diverse community of scientists.
Journal ArticleDOI
Gene Expression Signatures for Predicting Prognosis of Squamous Cell and Adenocarcinomas of the Lung
Mitch Raponi,Yi Zhang,Jack X. Yu,Guoan Chen,Grace J. Lee,Jeremy M. G. Taylor,James W. MacDonald,Dafydd G. Thomas,Christopher A. Moskaluk,Yixin Wang,David G. Beer +10 more
TL;DR: The SCC classifier was combined with the previously identified adenocarcinoma prognostic signature and showed that the combined classifier had a predictive accuracy of 71% in 72 NSCLC samples also showing significant differences in overall survival.
Journal ArticleDOI
Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy
Edgar A. Otto,Toby W. Hurd,Rannar Airik,Moumita Chaki,Weibin Zhou,Corinne Stoetzel,Suresh B. Patil,Shawn Levy,Amiya K. Ghosh,Carlos Murga-Zamalloa,Jeroen van Reeuwijk,Stef J.F. Letteboer,Liyun Sang,Rachel H. Giles,Qin Liu,Karlien L.M. Coene,Alejandro Estrada-Cuzcano,Rob W.J. Collin,Heather M. McLaughlin,Susanne Held,Jennifer M. Kasanuki,Gokul Ramaswami,Jinny Conte,Irma Lopez,Joseph Washburn,James W. MacDonald,Jinghua Hu,Yukiko M. Yamashita,Eamonn R. Maher,Lisa M. Guay-Woodford,Hartmut P. H. Neumann,Nicholas Obermüller,Robert K. Koenekoop,Carsten Bergmann,Xiaoshu Bei,Richard A. Lewis,Nicholas Katsanis,Vanda S. Lopes,David S. Williams,Robert H. Lyons,Chi V. Dang,Daniela A Brito,Mónica Bettencourt Dias,Xinmin Zhang,James D. Cavalcoli,Gudrun Nürnberg,Peter Nürnberg,Eric A. Pierce,Peter K. Jackson,Corinne Antignac,Sophie Saunier,Ronald Roepman,Hélène Dollfus,Hemant Khanna,Friedhelm Hildebrandt +54 more
TL;DR: This work identifies loss of SDCCAG8 function as a cause of a retinal-renal ciliopathy and validates exome capture analysis for broadly heterogeneous single-gene disorders.
Journal ArticleDOI
Identification and characterization of Hoxa9 binding sites in hematopoietic cells
Yongsheng Huang,Kajal V. Sitwala,Joel Bronstein,Daniel S. Sanders,Monisha Dandekar,Cailin Collins,Gordon Robertson,James W. MacDonald,Timothee Cezard,Misha Bilenky,Nina Thiessen,Yongjun Zhao,Thomas Zeng,Martin Hirst,Alfred O. Hero,Steven J.M. Jones,Jay L. Hess +16 more
TL;DR: The binding sites for Hoxa9 and the Hox cofactor Meis1 are identified on a genome-wide level and their associated epigenetic modifications and transcriptional targets are profiled to suggest that HoxA9 regulates transcription by interacting with enhancers of genes important for hematopoiesis and leukemia.
Journal ArticleDOI
Human Organ-Specific Endothelial Cell Heterogeneity.
Raluca Marcu,Yoon Jung Choi,Jun Xue,Chelsea L. Fortin,Yuliang Wang,Ryan J. Nagao,Jin Xu,James W. MacDonald,Theo K. Bammler,Charles E. Murry,Kimberly A. Muczynski,Kelly R. Stevens,Jonathan Himmelfarb,Stephen M. Schwartz,Ying Zheng +14 more
TL;DR: The link between human EC heterogeneity and organ development is shown and can be exploited therapeutically to contribute in organ regeneration, disease modeling, as well as guiding differentiation of tissue-specific ECs from human pluripotent stem cells.