Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review

Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer

(2011) Y. Yuan et al.   BIOINFORMATICS

PREDA: an R-package to identify regional variations in genomic data

(2011) Francesco Ferrari et al.   BIOINFORMATICS

CNAmet: an R package for integrating copy number, methylation and expression data

(2011) Riku Louhimo et al.   BIOINFORMATICS

Linear and non-linear dependencies between copy number aberrations and mRNA expression reveal distinct molecular pathways in breast cancer

(2011) Hiroko K Solvang et al.   BMC BIOINFORMATICS

Integrated Analysis of Gene Expression and Copy Number Data on Gene Shaving Using Independent Component Analysis

(2011) Jinhua Sheng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Prioritization and Evaluation of Depression Candidate Genes by Combining Multidimensional Data Resources

(2011) Chung-Feng Kao et al.   PLoS One

Regularized multivariate regression for identifying master predictors with application to integrative genomics study of breast cancer

(2010) Jie Peng et al.   Annals of Applied Statistics

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

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Identification of novel cluster groups in pediatric high-risk B-precursor acute lymphoblastic leukemia with gene expression profiling: correlation with genome-wide DNA copy number alterations, clinical characteristics, and outcome

(2010) R. C. Harvey et al.   BLOOD

Integrative analysis of gene expression and copy number alterations using canonical correlation analysis

(2010) Charlotte Soneson et al.   BMC BIOINFORMATICS

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

Segmentation of genomic and transcriptomic microarrays data reveals major correlation between DNA copy number aberrations and gene–loci expression

(2010) M. Ortiz-Estevez et al.   GENOMICS

Multi-Platform Whole-Genome Microarray Analyses Refine the Epigenetic Signature of Breast Cancer Metastasis with Gene Expression and Copy Number

(2010) Joseph Andrews et al.   PLoS One

Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalities

(2009) Martin Schäfer et al.   BIOINFORMATICS

MIRAGAA—a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer

(2009) Raj K. Gaire et al.   BIOINFORMATICS

DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data

(2009) Keyan Salari et al.   BIOINFORMATICS

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6

(2009) Henrik Bengtsson et al.   BIOINFORMATICS

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis

(2009) Ronglai Shen et al.   BIOINFORMATICS

integrOmics: an R package to unravel relationships between two omics datasets

(2009) Kim-Anh Lê Cao et al.   BIOINFORMATICS

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis

(2009) D. M. Witten et al.   BIOSTATISTICS

Integrated analysis of DNA copy number and gene expression microarray data using gene sets

(2009) Renée X Menezes et al.   BMC BIOINFORMATICS

Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays

(2009) Leo Lahti et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Deletion ofIKZF1and Prognosis in Acute Lymphoblastic Leukemia

(2009) Charles G. Mullighan et al.   NEW ENGLAND JOURNAL OF MEDICINE

A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets †

(2009) Silvio Bicciato et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes

(2008) Hyunju Lee et al.   BIOINFORMATICS

Estimation and assessment of raw copy numbers at the single locus level

(2008) H. Bengtsson et al.   BIOINFORMATICS

Nonparametric Testing for DNA Copy Number Induced Differential mRNA Gene Expression

(2008) Wessel N. van Wieringen et al.   BIOMETRICS

High-resolution genomic and expression analyses of copy number alterations in breast tumors

(2008) Peter M. Haverty et al.   GENES CHROMOSOMES & CANCER

Integrated gene copy number and expression microarray analysis of gastric cancer highlights potential target genes

(2008) Samuel Myllykangas et al.   INTERNATIONAL JOURNAL OF CANCER

Translating insights from the cancer genome into clinical practice

(2008) Lynda Chin et al.   NATURE

BCR–ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros

(2008) Charles G. Mullighan et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE