Visualizing multidimensional cancer genomics data

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations

(2012) Tobias Rausch et al.   CELL

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Representing genomic structural variation

(2012) Cydney Nielsen et al.   NATURE METHODS

Comparative analysis of algorithms for integration of copy number and expression data

(2012) Riku Louhimo et al.   NATURE METHODS

Functional impact bias reveals cancer drivers

(2012) Abel Gonzalez-Perez et al.   NUCLEIC ACIDS RESEARCH

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data

(2012) Shihua Zhang et al.   NUCLEIC ACIDS RESEARCH

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types

(2012) Gunes Gundem et al.   Genome Medicine

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

ggbio: an R package for extending the grammar of graphics for genomic data

(2012) Tengfei Yin et al.   GENOME BIOLOGY

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

Algorithms for Detecting Significantly Mutated Pathways in Cancer

(2011) Fabio Vandin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps

(2011) Christian Perez-Llamas et al.   PLoS One

Characterizing complex structural variation in germline and somatic genomes

(2011) Aaron R. Quinlan et al.   TRENDS IN GENETICS

Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer

(2011) Wigard P Kloosterman et al.   GENOME BIOLOGY

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

Cytoscape Web: an interactive web-based network browser

(2010) Christian T. Lopes et al.   BIOINFORMATICS

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

Genome remodelling in a basal-like breast cancer metastasis and xenograft

(2010) Li Ding et al.   NATURE

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

IntOGen: integration and data mining of multidimensional oncogenomic data

(2010) Gunes Gundem et al.   NATURE METHODS

Visualizing biological data—now and in the future

(2010) Seán I O'Donoghue et al.   NATURE METHODS

Visualizing genomes: techniques and challenges

(2010) Cydney B Nielsen et al.   NATURE METHODS

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

waviCGH: a web application for the analysis and visualization of genomic copy number alterations

(2010) Angel Carro et al.   NUCLEIC ACIDS RESEARCH

The UCSC cancer genomics browser: update 2011

(2010) J. Zachary Sanborn et al.   NUCLEIC ACIDS RESEARCH

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

A human functional protein interaction network and its application to cancer data analysis

(2010) Guanming Wu et al.   GENOME BIOLOGY

Caleydo: connecting pathways and gene expression

(2009) Marc Streit et al.   BIOINFORMATICS

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

(2009) Kevin R. Brown et al.   BIOINFORMATICS

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

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

Complex landscapes of somatic rearrangement in human breast cancer genomes

(2009) Philip J. Stephens et al.   NATURE

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

BioMart Central Portal—unified access to biological data

(2009) Syed Haider et al.   NUCLEIC ACIDS RESEARCH

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays

(2009) Tatiana Popova et al.   GENOME BIOLOGY

Enabling personalized cancer medicine through analysis of gene-expression patterns

(2008) Laura J. van 't Veer et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE