Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Reuse of public genome-wide gene expression data

(2012) Johan Rung et al.   NATURE REVIEWS GENETICS

ArrayExpress update—trends in database growth and links to data analysis tools

(2012) Gabriella Rustici et al.   NUCLEIC ACIDS RESEARCH

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

(2012) Aaron K. Wong et al.   NUCLEIC ACIDS RESEARCH

Making sense out of massive data by going beyond differential expression

(2012) P. R. Schmid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression

(2011) Jesse M. Engreitz et al.   BIOINFORMATICS

PILGRM: an interactive data-driven discovery platform for expert biologists

(2011) C. S. Greene et al.   NUCLEIC ACIDS RESEARCH

Subtype and pathway specific responses to anticancer compounds in breast cancer

(2011) L. M. Heiser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Frozen robust multiarray analysis (fRMA)

(2010) M. N. McCall et al.   BIOSTATISTICS

A global map of human gene expression

(2010) Margus Lukk et al.   NATURE BIOTECHNOLOGY

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources

(2010) M. Gremse et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes

(2010) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH

Bayesian approach to transforming public gene expression repositories into disease diagnosis databases

(2010) H. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components

(2010) Christopher Y. Park et al.   PLoS Computational Biology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Predicting gene function in a hierarchical context with an ensemble of classifiers

(2008) Yuanfang Guan et al.   GENOME BIOLOGY