Published in Bioinformatics on July 01, 2007
Functional copy-number alterations in cancer. PLoS One (2008) 4.27
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation. BMC Genomics (2012) 1.74
CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. Bioinformatics (2009) 1.73
Detecting simultaneous changepoints in multiple sequences. Biometrika (2010) 1.34
Targeting cadherin-17 inactivates Wnt signaling and inhibits tumor growth in liver carcinoma. Hepatology (2009) 1.32
Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. Bioinformatics (2009) 1.23
Getting started in probabilistic graphical models. PLoS Comput Biol (2007) 1.09
Genome-wide identification of significant aberrations in cancer genome. BMC Genomics (2012) 1.03
A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control. Nucleic Acids Res (2013) 0.89
Comparative analysis of methods for identifying recurrent copy number alterations in cancer. PLoS One (2012) 0.88
Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously. BMC Bioinformatics (2009) 0.85
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Model-based clustering of array CGH data. Bioinformatics (2009) 0.79
Multisample aCGH data analysis via total variation and spectral regularization. IEEE/ACM Trans Comput Biol Bioinform (2013) 0.79
Fast MCMC sampling for hidden Markov Models to determine copy number variations. BMC Bioinformatics (2011) 0.79
Identification of cancer-driver genes in focal genomic alterations from whole genome sequencing data. Sci Rep (2016) 0.77
Improved Statistical Analysis for Array CGH-Based DNA Copy Number Aberrations. Cancer Inform (2011) 0.75
Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. PLoS Comput Biol (2016) 0.75
Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields. Bioinformatics (2008) 0.75
A Novel Graph-based Algorithm to Infer Recurrent Copy Number Variations in Cancer. Cancer Inform (2016) 0.75
Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes. Cancer Inform (2009) 0.75
Penalized weighted low-rank approximation for robust recovery of recurrent copy number variations. BMC Bioinformatics (2015) 0.75
PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities. BMC Bioinformatics (2016) 0.75
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet (2005) 15.37
A comprehensive analysis of common copy-number variations in the human genome. Am J Hum Genet (2006) 8.61
A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet (2004) 7.68
The functional role of long non-coding RNA in human carcinomas. Mol Cancer (2011) 6.37
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics (2010) 4.02
Resolving the resolution of array CGH. Genomics (2007) 3.66
PIK3CA mutations and copy number gains in human lung cancers. Cancer Res (2008) 3.42
Alterations in genes of the EGFR signaling pathway and their relationship to EGFR tyrosine kinase inhibitor sensitivity in lung cancer cell lines. PLoS One (2009) 2.79
Integrating copy number polymorphisms into array CGH analysis using a robust HMM. Bioinformatics (2006) 2.50
Multiple microalterations detected at high frequency in oral cancer. Cancer Res (2005) 2.47
Human cancer long non-coding RNA transcriptomes. PLoS One (2011) 2.38
Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics (2007) 2.36
Characterisation of retinoblastomas without RB1 mutations: genomic, gene expression, and clinical studies. Lancet Oncol (2013) 2.32
High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH. Int J Cancer (2006) 2.16
Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression. Genome Res (2012) 2.10
A stepwise framework for the normalization of array CGH data. BMC Bioinformatics (2005) 2.08
SeeGH--a software tool for visualization of whole genome array comparative genomic hybridization data. BMC Bioinformatics (2004) 2.04
Comprehensive copy number profiles of breast cancer cell model genomes. Breast Cancer Res (2006) 2.02
Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells. PLoS One (2009) 1.94
Lung cancer cell lines as tools for biomedical discovery and research. J Natl Cancer Inst (2010) 1.92
Patient-derived first generation xenografts of non-small cell lung cancers: promising tools for predicting drug responses for personalized chemotherapy. Clin Cancer Res (2010) 1.77
3p14 and 9p21 loss is a simple tool for predicting second oral malignancy at previously treated oral cancer sites. Cancer Res (2002) 1.75
EZH2 promotes E2F-driven SCLC tumorigenesis through modulation of apoptosis and cell-cycle regulation. J Thorac Oncol (2013) 1.72
Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet (2006) 1.61
MDQC: a new quality assessment method for microarrays based on quality control reports. Bioinformatics (2007) 1.61
Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation. Hum Genet (2011) 1.60
Acquired resistance to EGFR inhibitors is associated with a manifestation of stem cell-like properties in cancer cells. Cancer Res (2013) 1.54
Genome-wide profiling of follicular lymphoma by array comparative genomic hybridization reveals prognostically significant DNA copy number imbalances. Blood (2008) 1.52
Effect of active smoking on the human bronchial epithelium transcriptome. BMC Genomics (2007) 1.50
Genetic alteration and gene expression modulation during cancer progression. Mol Cancer (2004) 1.50
MET gene amplification or EGFR mutation activate MET in lung cancers untreated with EGFR tyrosine kinase inhibitors. Int J Cancer (2009) 1.48
Toluidine blue staining identifies high-risk primary oral premalignant lesions with poor outcome. Cancer Res (2005) 1.44
TRAF6 is an amplified oncogene bridging the RAS and NF-κB pathways in human lung cancer. J Clin Invest (2011) 1.42
Epigenomics: mapping the methylome. Cell Cycle (2006) 1.42
Sharing visual features for multiclass and multiview object detection. IEEE Trans Pattern Anal Mach Intell (2007) 1.40
Integrative genomic analyses identify BRF2 as a novel lineage-specific oncogene in lung squamous cell carcinoma. PLoS Med (2010) 1.38
Identification of a long non-coding RNA as a novel biomarker and potential therapeutic target for metastatic prostate cancer. Oncotarget (2014) 1.38
Genome-wide identification of human microRNAs located in leukemia-associated genomic alterations. Blood (2010) 1.36
High-resolution array CGH increases heterogeneity tolerance in the analysis of clinical samples. Genomics (2005) 1.35
Array CGH technologies and their applications to cancer genomes. Chromosome Res (2005) 1.33
Computational approaches for RNA energy parameter estimation. RNA (2010) 1.33
Multiple aberrations of chromosome 3p detected in oral premalignant lesions. Cancer Prev Res (Phila) (2008) 1.30
DNA extraction from paraffin embedded material for genetic and epigenetic analyses. J Vis Exp (2011) 1.27
Comprehensive whole genome array CGH profiling of mantle cell lymphoma model genomes. Hum Mol Genet (2004) 1.27
Whole-genome analysis and HLA genotyping of enteropathy-type T-cell lymphoma reveals 2 distinct lymphoma subtypes. Gastroenterology (2007) 1.25
Copy number alterations of c-MYC and PTEN are prognostic factors for relapse after prostate cancer radiotherapy. Cancer (2012) 1.23
Cytogenetically balanced translocations are associated with focal copy number alterations. Hum Genet (2006) 1.23
Methods for high throughput validation of amplified fragment pools of BAC DNA for constructing high resolution CGH arrays. BMC Genomics (2004) 1.19
Epigenetics of cancer progression. Pharmacogenomics (2008) 1.18
Arsenic exposure and the induction of human cancers. J Toxicol (2011) 1.16
Correlation of Short Form-36 and disability status with outcomes of arthroscopic acetabular labral debridement. Am J Sports Med (2005) 1.15
Genomic markers for malignant progression in pulmonary adenocarcinoma with bronchioloalveolar features. Proc Natl Acad Sci U S A (2008) 1.14
Whole genome tiling path array CGH analysis of segmental copy number alterations in cervical cancer cell lines. Int J Cancer (2007) 1.14
Proteomic signatures in plasma during early acute renal allograft rejection. Mol Cell Proteomics (2010) 1.14
MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data. BMC Bioinformatics (2008) 1.13
Identification of novel lung genes in bronchial epithelium by serial analysis of gene expression. Am J Respir Cell Mol Biol (2006) 1.13
Activation of GATA binding protein 6 (GATA6) sustains oncogenic lineage-survival in esophageal adenocarcinoma. Proc Natl Acad Sci U S A (2012) 1.12
miR-101 DNA copy loss is a prominent subtype specific event in lung cancer. J Thorac Oncol (2011) 1.12
An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer. BMC Syst Biol (2010) 1.10
Chromosome 5p aberrations are early events in lung cancer: implication of glial cell line-derived neurotrophic factor in disease progression. Oncogene (2005) 1.10
An integrated mBAND and submegabase resolution tiling set (SMRT) CGH array analysis of focal amplification, microdeletions, and ladder structures consistent with breakage-fusion-bridge cycle events in osteosarcoma. Genes Chromosomes Cancer (2005) 1.10
Genetic alterations defining NSCLC subtypes and their therapeutic implications. Lung Cancer (2013) 1.10
Reliability and diagnostic accuracy of 5 physical examination tests and combination of tests for subacromial impingement. Arch Phys Med Rehabil (2009) 1.10
High-resolution array CGH identifies novel regions of genomic alteration in intermediate-risk prostate cancer. Prostate (2009) 1.08
Genomic alterations in lobular neoplasia: a microarray comparative genomic hybridization signature for early neoplastic proliferationin the breast. Genes Chromosomes Cancer (2006) 1.07
Gain of a region on 7p22.3, containing MAD1L1, is the most frequent event in small-cell lung cancer cell lines. Genes Chromosomes Cancer (2006) 1.07
SIGMA: a system for integrative genomic microarray analysis of cancer genomes. BMC Genomics (2006) 1.07
Translating cancer 'omics' to improved outcomes. Genome Res (2012) 1.07
A sequence-based approach to identify reference genes for gene expression analysis. BMC Med Genomics (2010) 1.07
Genetic disruption of KEAP1/CUL3 E3 ubiquitin ligase complex components is a key mechanism of NF-kappaB pathway activation in lung cancer. J Thorac Oncol (2011) 1.06
Divergent genomic and epigenomic landscapes of lung cancer subtypes underscore the selection of different oncogenic pathways during tumor development. PLoS One (2012) 1.06
Microarray-based CGH of sporadic and syndrome-related pheochromocytomas using a 0.1-0.2 Mb bacterial artificial chromosome array spanning chromosome arm 1p. Genes Chromosomes Cancer (2006) 1.05
Methylated DNA immunoprecipitation. J Vis Exp (2009) 1.04
Overexpression of LRP12, a gene contained within an 8q22 amplicon identified by high-resolution array CGH analysis of oral squamous cell carcinomas. Oncogene (2004) 1.04
Use of complete coverage array comparative genomic hybridization to define copy number alterations on chromosome 3p in oral squamous cell carcinomas. Cancer Res (2003) 1.04
Functional genomic analysis of peripheral blood during early acute renal allograft rejection. Transplantation (2009) 1.03
Whole blood genomic biomarkers of acute cardiac allograft rejection. J Heart Lung Transplant (2009) 1.03
Mechanistic Roles of Noncoding RNAs in Lung Cancer Biology and Their Clinical Implications. Genet Res Int (2012) 1.03
Genomic deregulation of the E2F/Rb pathway leads to activation of the oncogene EZH2 in small cell lung cancer. PLoS One (2013) 1.03
Multiple pathways in the FGF signaling network are frequently deregulated by gene amplification in oral dysplasias. Int J Cancer (2009) 1.02
Diagnosis of superior labral lesions: comparison of noncontrast MRI with indirect MR arthrography in unexercised shoulders. Skeletal Radiol (2006) 1.01
An efficient method for the assessment of DNA quality of archival microdissected specimens. Mod Pathol (2002) 1.01
SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes. BMC Bioinformatics (2008) 1.00
Characterization of the recurrent translocation t(1;1)(p36.3;q21.1-2) in non-Hodgkin lymphoma by multicolor banding and fluorescence in situ hybridization analysis. Genes Chromosomes Cancer (2003) 1.00
Novel regions of amplification on 8q distinct from the MYC locus and frequently altered in oral dysplasia and cancer. Genes Chromosomes Cancer (2004) 1.00
Lung adenocarcinoma of never smokers and smokers harbor differential regions of genetic alteration and exhibit different levels of genomic instability. PLoS One (2012) 0.99
Contrasting transcriptional responses of a virulent and an attenuated strain of Mycobacterium tuberculosis infecting macrophages. PLoS One (2010) 0.98
Transcriptome profiles of carcinoma-in-situ and invasive non-small cell lung cancer as revealed by SAGE. PLoS One (2010) 0.97