Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

(2012) Andrey Alexeyenko et al.   BMC BIOINFORMATICS

A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes

(2012) B Dutta et al.   BRITISH JOURNAL OF CANCER

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

(2012) Jordi Barretina et al.   NATURE

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Context-dependent robustness to 5′ splice site polymorphisms in human populations

(2011) Zhi-xiang Lu et al.   HUMAN MOLECULAR GENETICS

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma

(2011) Ignacio Varela et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Scalable Transcriptome Preparation for Massive Parallel Sequencing

(2011) Henrik Stranneheim et al.   PLoS One

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

(2010) Valentina Boeva et al.   BIOINFORMATICS

Fes Tyrosine Kinase Expression in the Tumor Niche Correlates with Enhanced Tumor Growth, Angiogenesis, Circulating Tumor Cells, Metastasis, and Infiltrating Macrophages

(2010) Shengnan Zhang et al.   CANCER RESEARCH

Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk

(2010) Chandra A. Reynolds et al.   HUMAN MOLECULAR GENETICS

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity

(2010) Andrey Alexeyenko et al.   PLoS One

An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

(2010) Rod K. Nibbe et al.   PLoS Computational Biology

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Global networks of functional coupling in eukaryotes from comprehensive data integration

(2009) A. Alexeyenko et al.   GENOME RESEARCH

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome

(2009) Elaine R. Mardis et al.   NEW ENGLAND JOURNAL OF MEDICINE

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks

(2008) Antonio Reverter et al.   BIOINFORMATICS

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

Loss of ATRX leads to chromosome cohesion and congression defects

(2008) Kieran Ritchie et al.   JOURNAL OF CELL BIOLOGY

Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype

(2008) Helene R. McMurray et al.   NATURE

Somatic mutations affect key pathways in lung adenocarcinoma

(2008) Li Ding et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE