Published in Bioinformatics on July 15, 2006
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet (2010) 10.97
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PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics (2009) 4.31
MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature (2011) 3.22
Sparse representation and Bayesian detection of genome copy number alterations from microarray data. Bioinformatics (2008) 2.65
Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol (2010) 2.60
Bayesian Nonparametric Hidden Markov Models with application to the analysis of copy-number-variation in mammalian genomes. J R Stat Soc Series B Stat Methodol (2011) 2.20
Divergent clonal selection dominates medulloblastoma at recurrence. Nature (2016) 1.81
Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays. Ann Appl Stat (2008) 1.75
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Major copy proportion analysis of tumor samples using SNP arrays. BMC Bioinformatics (2008) 1.62
Flexible and accurate detection of genomic copy-number changes from aCGH. PLoS Comput Biol (2007) 1.54
Multiple aberrations of chromosome 3p detected in oral premalignant lesions. Cancer Prev Res (Phila) (2008) 1.30
A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array. BMC Bioinformatics (2007) 1.21
MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data. BMC Bioinformatics (2008) 1.13
An improved method for detecting and delineating genomic regions with altered gene expression in cancer. Genome Biol (2008) 1.07
Statistical issues in the analysis of DNA Copy Number Variations. Int J Comput Biol Drug Des (2008) 1.02
Computational analysis of whole-genome differential allelic expression data in human. PLoS Comput Biol (2010) 0.99
Bayesian hierarchical mixture modeling to assign copy number from a targeted CNV array. Genet Epidemiol (2011) 0.93
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization. Bioinformatics (2008) 0.93
Detecting copy number variations from array CGH data based on a conditional random field model. J Bioinform Comput Biol (2010) 0.93
Learning smoothing models of copy number profiles using breakpoint annotations. BMC Bioinformatics (2013) 0.93
Fast detection of de novo copy number variants from SNP arrays for case-parent trios. BMC Bioinformatics (2012) 0.86
Interpreting genomic data via entropic dissection. Nucleic Acids Res (2012) 0.85
Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model. BMC Bioinformatics (2010) 0.83
Parsimonious higher-order hidden Markov models for improved array-CGH analysis with applications to Arabidopsis thaliana. PLoS Comput Biol (2012) 0.83
Epigenetic regulation of WNT signaling in chronic lymphocytic leukemia. Epigenomics (2010) 0.82
Cancer gene discovery in mouse and man. Biochim Biophys Acta (2009) 0.81
Fast MCMC sampling for hidden Markov Models to determine copy number variations. BMC Bioinformatics (2011) 0.79
Model-integrated estimation of normal tissue contamination for cancer SNP allelic copy number data. Cancer Inform (2011) 0.79
Genome destabilizing mutator alleles drive specific mutational trajectories in Saccharomyces cerevisiae. Genetics (2013) 0.79
Model-based clustering of array CGH data. Bioinformatics (2009) 0.79
A bayesian integrative model for genetical genomics with spatially informed variable selection. Cancer Inform (2014) 0.77
NBN gain is predictive for adverse outcome following image-guided radiotherapy for localized prostate cancer. Oncotarget (2014) 0.76
A bayesian analysis for identifying DNA copy number variations using a compound poisson process. EURASIP J Bioinform Syst Biol (2010) 0.75
Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median Method. Cancer Inform (2010) 0.75
Assessing Population Level Genetic Instability via Moving Average. Stat Biosci (2010) 0.75
A novel approach to DNA copy number data segmentation. J Bioinform Comput Biol (2011) 0.75
Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. PLoS Comput Biol (2016) 0.75
T cells of patients with myelodysplastic syndrome are frequently derived from the malignant clone. Br J Haematol (2012) 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
Fate tracing of mature hepatocytes in mouse liver homeostasis and regeneration. J Clin Invest (2011) 2.83
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
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
Economic analysis: randomized placebo-controlled clinical trial of erlotinib in advanced non-small cell lung cancer. J Natl Cancer Inst (2010) 1.83
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
MicroRNAs control hepatocyte proliferation during liver regeneration. Hepatology (2010) 1.64
Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet (2006) 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
Modeling recurrent DNA copy number alterations in array CGH data. Bioinformatics (2007) 1.52
Genome-wide profiling of follicular lymphoma by array comparative genomic hybridization reveals prognostically significant DNA copy number imbalances. Blood (2008) 1.52
Genetic alteration and gene expression modulation during cancer progression. Mol Cancer (2004) 1.50
Effect of active smoking on the human bronchial epithelium transcriptome. BMC Genomics (2007) 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
Significance of Plk1 regulation by miR-100 in human nasopharyngeal cancer. Int J Cancer (2010) 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
Development of a next-generation sequencing method for BRCA mutation screening: a comparison between a high-throughput and a benchtop platform. J Mol Diagn (2012) 1.21
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
Whole genome tiling path array CGH analysis of segmental copy number alterations in cervical cancer cell lines. Int J Cancer (2007) 1.14
Genomic markers for malignant progression in pulmonary adenocarcinoma with bronchioloalveolar features. Proc Natl Acad Sci U S A (2008) 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
SIGMA: a system for integrative genomic microarray analysis of cancer genomes. BMC Genomics (2006) 1.07
Genomic alterations in lobular neoplasia: a microarray comparative genomic hybridization signature for early neoplastic proliferationin the breast. Genes Chromosomes Cancer (2006) 1.07
MicroRNA-494 within an oncogenic microRNA megacluster regulates G1/S transition in liver tumorigenesis through suppression of mutated in colorectal cancer. Hepatology (2013) 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
Translating cancer 'omics' to improved outcomes. Genome Res (2012) 1.07
Impact of colony-stimulating factors to reduce febrile neutropenic events in breast cancer patients receiving docetaxel plus cyclophosphamide chemotherapy. Support Care Cancer (2010) 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
Multiple dysregulated pathways in nasopharyngeal carcinoma revealed by gene expression profiling. Int J Cancer (2006) 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
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
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
Nucleophosmin interacts with HEXIM1 and regulates RNA polymerase II transcription. J Mol Biol (2008) 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
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
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
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
Core promoter recognition complex changes accompany liver development. Proc Natl Acad Sci U S A (2011) 0.97
Inference of transcriptional regulation relationships from gene expression data. Bioinformatics (2003) 0.97
Technical demonstration of whole genome array comparative genomic hybridization. J Vis Exp (2008) 0.97