Single sample scoring of molecular phenotypes

PerPAS: Topology-Based Single Sample Pathway Analysis Method

(2018) Chengyu Liu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Combinatorial Targeting by MicroRNAs Co-ordinates Post-transcriptional Control of EMT

(2018) Joseph Cursons et al.   Cell Systems

A Transcriptional Program for Detecting TGFβ-Induced EMT in Cancer

(2017) Momeneh Foroutan et al.   MOLECULAR CANCER RESEARCH

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients

(2014) T. Z. Tan et al.   EMBO Molecular Medicine

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Modeling precision treatment of breast cancer

(2013) Anneleen Daemen et al.   GENOME BIOLOGY

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Bias detection and correction in RNA-Sequencing data

(2011) Wei Zheng et al.   BMC BIOINFORMATICS

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology