Orchestrating high-throughput genomic analysis with Bioconductor

W Huber, VJ Carey, R Gentleman, S Anders… - Nature …, 2015 - nature.com
Bioconductor is an open-source, open-development software project for the analysis and
comprehension of high-throughput data in genomics and molecular biology. The project …

[HTML][HTML] Machine learning and its applications to biology

AL Tarca, VJ Carey, X Chen, R Romero… - PLoS computational …, 2007 - journals.plos.org
The term machine learning refers to a set of topics dealing with the creation and evaluation
of algorithms that facilitate pattern recognition, classification, and prediction, based on …

[8] Bioconductor: an open source framework for bioinformatics and computational biology

M Reimers, VJ Carey - Methods in enzymology, 2006 - Elsevier
This chapter describes the Bioconductor project and details of its open source facilities for
analysis of microarray and other high‐throughput biological experiments. Particular attention …

[HTML][HTML] Bioconductor: open software development for computational biology and bioinformatics

RC Gentleman, VJ Carey, DM Bates, B Bolstad… - Genome biology, 2004 - Springer
The Bioconductor project is an initiative for the collaborative creation of extensible software
for computational biology and bioinformatics. The goals of the project include: fostering …

[HTML][HTML] Comparison of weight-loss diets with different compositions of fat, protein, and carbohydrates

FM Sacks, GA Bray, VJ Carey, SR Smith… - … England Journal of …, 2009 - Mass Medical Soc
Background The possible advantage for weight loss of a diet that emphasizes protein, fat, or
carbohydrates has not been established, and there are few studies that extend beyond 1 …

[HTML][HTML] Stromal fibroblasts present in invasive human breast carcinomas promote tumor growth and angiogenesis through elevated SDF-1/CXCL12 secretion

A Orimo, PB Gupta, DC Sgroi, F Arenzana-Seisdedos… - Cell, 2005 - cell.com
Fibroblasts often constitute the majority of the stromal cells within a breast carcinoma, yet the
functional contributions of these cells to tumorigenesis are poorly understood. Using a …

[HTML][HTML] Software for computing and annotating genomic ranges

M Lawrence, W Huber, H Pagès… - PLoS computational …, 2013 - journals.plos.org
We describe Bioconductor infrastructure for representing and computing on annotated
genomic ranges and integrating genomic data with the statistical computing features of R …

Abdominal adiposity and coronary heart disease in women

KM Rexrode, VJ Carey, CH Hennekens, EE Walters… - Jama, 1998 - jamanetwork.com
Context.—Obesity is a well-established risk factor for coronary heart disease (CHD), but
whether regional fat distribution contributes independently to risk remains unclear …

Effects of protein, monounsaturated fat, and carbohydrate intake on blood pressure and serum lipids: results of the OmniHeart randomized trial

LJ Appel, FM Sacks, VJ Carey, E Obarzanek, JF Swain… - Jama, 2005 - jamanetwork.com
ContextReduced intake of saturated fat is widely recommended for prevention of
cardiovascular disease. The type of macronutrient that should replace saturated fat remains …

An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors

I Ben-Porath, MW Thomson, VJ Carey, R Ge, GW Bell… - Nature …, 2008 - nature.com
Cancer cells possess traits reminiscent of those ascribed to normal stem cells. It is unclear,
however, whether these phenotypic similarities reflect the activity of common molecular …