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The validation and clinical implementation of BRCAplus: a comprehensive high-risk breast cancer diagnostic assay. PLoS One (2014) 1.21

Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC. PLoS One (2015) 0.84

Current status of comprehensive chromosome screening for elective single-embryo transfer. Obstet Gynecol Int (2014) 0.83

Allele-specific copy-number discovery from whole-genome and whole-exome sequencing. Nucleic Acids Res (2015) 0.82

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Assessing the reproducibility of exome copy number variations predictions. Genome Med (2016) 0.77

Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma. Hum Genomics (2015) 0.77

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Evolutionary and Functional Features of Copy Number Variation in the Cattle Genome. Front Genet (2016) 0.75

Gene-based comparative analysis of tools for estimating copy number alterations using whole-exome sequencing data. Oncotarget (2017) 0.75

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The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39

Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 97.51

Exome sequencing identifies the cause of a mendelian disorder. Nat Genet (2009) 32.06

High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res (2009) 12.09

Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature (2009) 9.47

Gene copy number for epidermal growth factor receptor (EGFR) and clinical response to antiEGFR treatment in colorectal cancer: a cohort study. Lancet Oncol (2005) 7.43

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics (2011) 5.45

Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer (2006) 5.39

Copy number variation detection and genotyping from exome sequence data. Genome Res (2012) 4.44

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics (2012) 3.10

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics (2011) 2.86

Detecting copy number variation with mated short reads. Genome Res (2010) 2.75

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ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One (2011) 2.34

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. Bioinformatics (2011) 1.69

Modeling read counts for CNV detection in exome sequencing data. Stat Appl Genet Mol Biol (2011) 1.55

Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity. PLoS Comput Biol (2010) 1.51

Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm. Nucleic Acids Res (2011) 1.40

EGFR and HER2 gene copy number and response to first-line chemotherapy in patients with advanced non-small cell lung cancer (NSCLC). J Thorac Oncol (2007) 1.25

Analysis of DNA copy number aberrations in hepatitis C virus-associated hepatocellular carcinomas by conventional CGH and array CGH. Mod Pathol (2004) 1.15

A comparison of different metaphase CGH methods for the detection of cryptic chromosome aberrations of defined size. Eur J Hum Genet (2004) 0.90

Custom oligonucleotide array-based CGH: a reliable diagnostic tool for detection of exonic copy-number changes in multiple targeted genes. Eur J Hum Genet (2013) 0.89

Array-CGH fine mapping of minor and cryptic HR-CGH detected genomic imbalances in 80 out of 590 patients with abnormal development. Eur J Hum Genet (2008) 0.87

Copy number variation on chromosome 10q26.3 for obesity identified by a genome-wide study. J Clin Endocrinol Metab (2012) 0.86

Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Invest (2011) 14.22

Survival in BRAF V600-mutant advanced melanoma treated with vemurafenib. N Engl J Med (2012) 13.17

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Roles of the Raf/MEK/ERK pathway in cell growth, malignant transformation and drug resistance. Biochim Biophys Acta (2006) 7.33

EGFR, p16, HPV Titer, Bcl-xL and p53, sex, and smoking as indicators of response to therapy and survival in oropharyngeal cancer. J Clin Oncol (2008) 5.46

Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. Gastroenterology (2009) 4.08

Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet (2003) 4.01

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Pathogenic mitochondrial DNA mutations are common in the general population. Am J Hum Genet (2008) 3.56

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A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes. Nat Genet (2008) 2.82

Significance of p63 amplification and overexpression in lung cancer development and prognosis. Cancer Res (2003) 2.70

What causes mitochondrial DNA deletions in human cells? Nat Genet (2008) 2.70

The relationship between dose of vitamin E and suppression of oxidative stress in humans. Free Radic Biol Med (2007) 2.62

Plasma cytokine levels predict mortality in patients with acute renal failure. Kidney Int (2004) 2.52

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A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Med (2006) 2.16

Short preoperative treatment with erlotinib inhibits tumor cell proliferation in hormone receptor-positive breast cancers. J Clin Oncol (2008) 2.10

Evaluating markers for the early detection of cancer: overview of study designs and methods. Clin Trials (2006) 2.10

Proteomic-based prognosis of brain tumor patients using direct-tissue matrix-assisted laser desorption ionization mass spectrometry. Cancer Res (2005) 2.06

Gene expression differences associated with human papillomavirus status in head and neck squamous cell carcinoma. Clin Cancer Res (2006) 2.05

Variation in germline mtDNA heteroplasmy is determined prenatally but modified during subsequent transmission. Nat Genet (2012) 1.94

Mitochondrial aging is accelerated by anti-retroviral therapy through the clonal expansion of mtDNA mutations. Nat Genet (2011) 1.92

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The receptor tyrosine kinase inhibitor SU11248 impedes endothelial cell migration, tubule formation, and blood vessel formation in vivo, but has little effect on existing tumor vessels. Angiogenesis (2004) 1.87

A novel BH3 mimetic reveals a mitogen-activated protein kinase-dependent mechanism of melanoma cell death controlled by p53 and reactive oxygen species. Cancer Res (2006) 1.85

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Regulation of heparin-binding EGF-like growth factor by miR-212 and acquired cetuximab-resistance in head and neck squamous cell carcinoma. PLoS One (2010) 1.77

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TNBCtype: A Subtyping Tool for Triple-Negative Breast Cancer. Cancer Inform (2012) 1.72

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Influence of initiation of maintenance hemodialysis on biomarkers of inflammation and oxidative stress. Kidney Int (2004) 1.66

Accumulation of mitochondrial DNA mutations in ageing, cancer, and mitochondrial disease: is there a common mechanism? Lancet (2002) 1.65

Genetic disease in the children of Danish survivors of childhood and adolescent cancer. J Clin Oncol (2011) 1.63

Effects of intercellular adhesion molecule 1 (ICAM-1) null mutation on radiation-induced pulmonary fibrosis and respiratory insufficiency in mice. J Natl Cancer Inst (2002) 1.63

Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PLoS One (2013) 1.61

Bone morphogenetic protein 4 promotes pulmonary vascular remodeling in hypoxic pulmonary hypertension. Circ Res (2005) 1.61

Impaired tumor microenvironment in EphA2-deficient mice inhibits tumor angiogenesis and metastatic progression. FASEB J (2005) 1.61

DC isoketal-modified proteins activate T cells and promote hypertension. J Clin Invest (2014) 1.59

In vitro effects of the BH3 mimetic, (-)-gossypol, on head and neck squamous cell carcinoma cells. Clin Cancer Res (2004) 1.55

Evidence Combination From an Evolutionary Game Theory Perspective. IEEE Trans Cybern (2015) 1.54

Molecular profiling of the residual disease of triple-negative breast cancers after neoadjuvant chemotherapy identifies actionable therapeutic targets. Cancer Discov (2013) 1.54

A kinome-wide screen identifies the insulin/IGF-I receptor pathway as a mechanism of escape from hormone dependence in breast cancer. Cancer Res (2011) 1.53

Genetic and clinical predictors for breast cancer risk assessment and stratification among Chinese women. J Natl Cancer Inst (2010) 1.51

Monster cells in malignant melanoma. Am J Dermatopathol (2005) 1.49

Alcohol drinking, cigarette smoking, and risk of colorectal adenomatous and hyperplastic polyps. Am J Epidemiol (2008) 1.47

Transgenic mice expressing a dominant-negative mutant type II transforming growth factor-beta receptor exhibit impaired mammary development and enhanced mammary tumor formation. Am J Pathol (2003) 1.46

Adult-onset spinocerebellar ataxia syndromes due to MTATP6 mutations. J Neurol Neurosurg Psychiatry (2012) 1.46

Proteomic patterns and prediction of glomerulosclerosis and its mechanisms. J Am Soc Nephrol (2005) 1.44

Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data. BMC Genomics (2012) 1.44

Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling. J Proteome Res (2010) 1.43

Quantitative metrics in clinical radiology reporting: a snapshot perspective from a single mixed academic-community practice. Magn Reson Imaging (2012) 1.42

Cancer-associated immunodeficiency and dendritic cell abnormalities mediated by the prostaglandin EP2 receptor. J Clin Invest (2003) 1.42

Diagnostic accuracy of MALDI mass spectrometric analysis of unfractionated serum in lung cancer. J Thorac Oncol (2007) 1.40

Early involvement of the phosphatidylinositol 3-kinase/Akt pathway in lung cancer progression. Am J Respir Crit Care Med (2004) 1.40

Predictive and pharmacodynamic biomarker studies in tumor and skin tissue samples of patients with recurrent or metastatic squamous cell carcinoma of the head and neck treated with erlotinib. J Clin Oncol (2007) 1.40

Functional genomic screens identify CINP as a genome maintenance protein. Proc Natl Acad Sci U S A (2009) 1.38

Finding the lost treasures in exome sequencing data. Trends Genet (2013) 1.36

A training-testing approach to the molecular classification of resected non-small cell lung cancer. Clin Cancer Res (2003) 1.36

Cyclin-dependent kinase 9-cyclin K functions in the replication stress response. EMBO Rep (2010) 1.36

Epigenetics, epidemiology and mitochondrial DNA diseases. Int J Epidemiol (2012) 1.36

Depletion of mitochondrial DNA in leucocytes harbouring the 3243A->G mtDNA mutation. J Med Genet (2006) 1.34

The effect of strand bias in Illumina short-read sequencing data. BMC Genomics (2012) 1.34

A multicenter application and evaluation of the oxford classification of IgA nephropathy in adult chinese patients. Am J Kidney Dis (2012) 1.32

Selection against pathogenic mtDNA mutations in a stem cell population leads to the loss of the 3243A-->G mutation in blood. Am J Hum Genet (2008) 1.32

Proteomic patterns of preinvasive bronchial lesions. Am J Respir Crit Care Med (2005) 1.32

Transforming growth factor beta-regulated gene expression in a mouse mammary gland epithelial cell line. Breast Cancer Res (2003) 1.32

Fish, shellfish, and long-chain n-3 fatty acid consumption and risk of incident type 2 diabetes in middle-aged Chinese men and women. Am J Clin Nutr (2011) 1.32

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis. Bioinformatics (2013) 1.31

Three-stage quality control strategies for DNA re-sequencing data. Brief Bioinform (2013) 1.30

The relation of magnesium and calcium intakes and a genetic polymorphism in the magnesium transporter to colorectal neoplasia risk. Am J Clin Nutr (2007) 1.30

A phase II study of celecoxib in combination with paclitaxel, carboplatin, and radiotherapy for patients with inoperable stage IIIA/B non-small cell lung cancer. Clin Cancer Res (2009) 1.27

Enhanced hepatocyte growth factor signaling by type II transforming growth factor-beta receptor knockout fibroblasts promotes mammary tumorigenesis. Cancer Res (2007) 1.27

Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity. Am J Hum Genet (2011) 1.26

Improvement in nutritional parameters after initiation of chronic hemodialysis. Am J Kidney Dis (2002) 1.26

Differential gene expression in anaplastic lymphoma kinase-positive and anaplastic lymphoma kinase-negative anaplastic large cell lymphomas. Hum Pathol (2005) 1.26

TGF-β receptor II loss promotes mammary carcinoma progression by Th17 dependent mechanisms. Cancer Discov (2011) 1.26

RNA interference (RNAi) screening approach identifies agents that enhance paclitaxel activity in breast cancer cells. Breast Cancer Res (2010) 1.25

Induction of frameshift and base pair substitution mutations by the major DNA adduct of the endogenous carcinogen malondialdehyde. Proc Natl Acad Sci U S A (2003) 1.25

Uremic malnutrition is a predictor of death independent of inflammatory status. Kidney Int (2004) 1.25

Therapeutic effects of oral nutritional supplementation during hemodialysis. Kidney Int (2002) 1.25

Disparate outcomes in patients with colorectal cancer: effect of race on long-term survival. Arch Surg (2002) 1.24

Targeting cyclooxygenase-2 in recurrent non-small cell lung cancer: a phase II trial of celecoxib and docetaxel. Clin Cancer Res (2005) 1.23

Eph/ephrin profiling in human breast cancer reveals significant associations between expression level and clinical outcome. PLoS One (2011) 1.22

Reactivation of p53 by a specific MDM2 antagonist (MI-43) leads to p21-mediated cell cycle arrest and selective cell death in colon cancer. Mol Cancer Ther (2008) 1.22

Urea space and total body water measurements by stable isotopes in patients with acute renal failure. Kidney Int (2004) 1.22

OPA1 mutations cause cytochrome c oxidase deficiency due to loss of wild-type mtDNA molecules. Hum Mol Genet (2010) 1.22

The distribution of mitochondrial DNA heteroplasmy due to random genetic drift. Am J Hum Genet (2008) 1.22

Lymphovascular invasion in colorectal cancer: an interobserver variability study. Am J Surg Pathol (2008) 1.21

Improved prediction of lysine acetylation by support vector machines. Protein Pept Lett (2009) 1.20

The loss of TGF-beta signaling promotes prostate cancer metastasis. Neoplasia (2003) 1.20

A novel comprehensive wave-form MS data processing method. Bioinformatics (2009) 1.20