Published in Genome Biol on March 17, 2010
De novo assembly and analysis of RNA-seq data. Nat Methods (2010) 9.69
RNA sequencing: advances, challenges and opportunities. Nat Rev Genet (2010) 8.96
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol (2011) 6.23
From RNA-seq reads to differential expression results. Genome Biol (2010) 5.77
Alternative expression analysis by RNA sequencing. Nat Methods (2010) 5.02
Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet (2010) 3.19
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol (2010) 2.79
Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat Struct Mol Biol (2011) 2.73
Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med Genomics (2011) 1.84
High-throughput sequencing for biology and medicine. Mol Syst Biol (2013) 1.75
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biol (2014) 1.60
Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins. PLoS Genet (2011) 1.60
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics (2011) 1.58
HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data. PLoS One (2010) 1.36
Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing. Genome Biol (2010) 1.13
QUANTIFYING ALTERNATIVE SPLICING FROM PAIRED-END RNA-SEQUENCING DATA. Ann Appl Stat (2014) 1.00
Detecting structural variations in the human genome using next generation sequencing. Brief Funct Genomics (2011) 0.98
IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data. BMC Bioinformatics (2011) 0.98
Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data. BMC Genomics (2012) 0.96
Exome RNA sequencing reveals rare and novel alternative transcripts. Nucleic Acids Res (2012) 0.96
RNA-Seq mapping and detection of gene fusions with a suffix array algorithm. PLoS Comput Biol (2012) 0.95
eQTL Mapping Using RNA-seq Data. Stat Biosci (2013) 0.93
A comprehensive survey of non-canonical splice sites in the human transcriptome. Nucleic Acids Res (2014) 0.90
Advanced Applications of RNA Sequencing and Challenges. Bioinform Biol Insights (2015) 0.88
Highly sensitive and ultrafast read mapping for RNA-seq analysis. DNA Res (2016) 0.87
Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases. Mol Genet Genomic Med (2013) 0.83
Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits. Eur J Hum Genet (2011) 0.82
ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping. Bioinformatics (2010) 0.81
Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput. Wiley Interdiscip Rev RNA (2014) 0.81
No more non-model species: the promise of next generation sequencing for comparative immunology. Dev Comp Immunol (2014) 0.80
Application of the whole-transcriptome shotgun sequencing approach to the study of Philadelphia-positive acute lymphoblastic leukemia. Blood Cancer J (2012) 0.80
Next generation quantitative genetics in plants. Front Plant Sci (2011) 0.79
LEMONS - A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes. PLoS One (2015) 0.76
Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing Data In Silico. Biomed Res Int (2015) 0.76
Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA. Biomed Res Int (2014) 0.75
Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length. BMC Bioinformatics (2011) 0.75
GFusion: an Effective Algorithm to Identify Fusion Genes from Cancer RNA-Seq Data. Sci Rep (2017) 0.75
The human genome browser at UCSC. Genome Res (2002) 168.23
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res (2002) 76.95
BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods (2008) 31.04
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet (2008) 24.51
mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods (2009) 11.71
Transcriptome sequencing to detect gene fusions in cancer. Nature (2009) 11.63
Annotating genomes with massive-scale RNA sequencing. Genome Biol (2008) 7.73
Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30
RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data. Bioinformatics (2009) 1.81
Meta-analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat (2003) 1.73
Global variation in copy number in the human genome. Nature (2006) 57.50
Detection of large-scale variation in the human genome. Nat Genet (2004) 49.18
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
Biological, clinical and population relevance of 95 loci for blood lipids. Nature (2010) 28.21
Origins and functional impact of copy number variation in the human genome. Nature (2009) 23.63
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet (2010) 23.08
Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature (2010) 20.01
New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat Genet (2010) 17.89
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet (2010) 16.96
Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet (2008) 15.51
Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nat Genet (2007) 14.05
Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet (2010) 13.70
Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nat Genet (2008) 12.32
Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature (2010) 12.27
Prepublication data sharing. Nature (2009) 12.24
Copy number variation: new insights in genome diversity. Genome Res (2006) 8.66
Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat Genet (2010) 7.94
Genome assembly comparison identifies structural variants in the human genome. Nat Genet (2006) 6.93
Challenges and standards in integrating surveys of structural variation. Nat Genet (2007) 6.05
New loci associated with kidney function and chronic kidney disease. Nat Genet (2010) 5.58
Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res (2006) 5.50
Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations. PLoS Genet (2009) 4.97
The Norway spruce genome sequence and conifer genome evolution. Nature (2013) 4.74
Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma. Nat Genet (2009) 4.52
The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res (2013) 4.42
Genome-wide association study identifies five loci associated with lung function. Nat Genet (2009) 4.10
Public data archives for genomic structural variation. Nat Genet (2010) 3.92
Copy-number variation in control population cohorts. Hum Mol Genet (2007) 3.88
Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol (2011) 3.25
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nat Genet (2013) 3.25
mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences. Nucleic Acids Res (2006) 3.23
Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. PLoS Genet (2012) 3.21
NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE Consortium. PLoS Genet (2009) 3.18
Genome-wide association analyses identify 18 new loci associated with serum urate concentrations. Nat Genet (2012) 3.04
Common variants associated with plasma triglycerides and risk for coronary artery disease. Nat Genet (2013) 2.92
Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits. PLoS Genet (2013) 2.83
Towards a comprehensive structural variation map of an individual human genome. Genome Biol (2010) 2.79
Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat Struct Mol Biol (2011) 2.73
Common variants in the JAZF1 gene associated with height identified by linkage and genome-wide association analysis. Hum Mol Genet (2008) 2.66
Excessive genomic DNA copy number variation in the Li-Fraumeni cancer predisposition syndrome. Proc Natl Acad Sci U S A (2008) 2.22
Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. Genome Res (2003) 2.12
Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. PLoS Genet (2012) 1.79
Genetic determinants of circulating sphingolipid concentrations in European populations. PLoS Genet (2009) 1.77
Continuous Aging of the Human DNA Methylome Throughout the Human Lifespan. PLoS One (2013) 1.74
Linkage disequilibrium patterns vary substantially among populations. Eur J Hum Genet (2005) 1.73
Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders. Nat Genet (2013) 1.72
A genome-wide association search for type 2 diabetes genes in African Americans. PLoS One (2012) 1.72
Speech and language impairment and oromotor dyspraxia due to deletion of 7q31 that involves FOXP2. Am J Med Genet A (2006) 1.70
Genome-wide association and functional follow-up reveals new loci for kidney function. PLoS Genet (2012) 1.68
Genes predict village of origin in rural Europe. Eur J Hum Genet (2010) 1.61
Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins. PLoS Genet (2011) 1.60
Major gender difference in association of FTO gene variant among severely obese children with obesity and obesity related phenotypes. Biochem Biophys Res Commun (2008) 1.55
Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing. PLoS One (2012) 1.54
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. PLoS Genet (2013) 1.52
Real-time PCR-based system for simultaneous quantification of human papillomavirus types associated with high risk of cervical cancer. J Clin Microbiol (2003) 1.52
SNP frequency estimation using massively parallel sequencing of pooled DNA. Eur J Hum Genet (2008) 1.51
Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring. Proc Natl Acad Sci U S A (2012) 1.49
Genome-wide linkage analysis of serum creatinine in three isolated European populations. Kidney Int (2009) 1.48
Genomics meets glycomics-the first GWAS study of human N-Glycome identifies HNF1α as a master regulator of plasma protein fucosylation. PLoS Genet (2010) 1.43
Use of FTA card for dry collection, transportation and storage of cervical cell specimen to detect high-risk HPV. J Clin Virol (2009) 1.41
A genome-wide association scan of RR and QT interval duration in 3 European genetically isolated populations: the EUROSPAN project. Circ Cardiovasc Genet (2009) 1.35
Type-specific associations of human papillomavirus load with risk of developing cervical carcinoma in situ. Int J Cancer (2004) 1.33
Strategies for the detection of copy number and other structural variants in the human genome. Hum Genomics (2006) 1.32
TP53 codon 72 polymorphism and cervical cancer: a pooled analysis of individual data from 49 studies. Lancet Oncol (2009) 1.26
Welander distal myopathy caused by an ancient founder mutation in TIA1 associated with perturbed splicing. Hum Mutat (2013) 1.26
Genome-wide association study of susceptibility loci for cervical cancer. J Natl Cancer Inst (2013) 1.22
Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors. Proc Natl Acad Sci U S A (2012) 1.17
Evidence of inbreeding depression on human height. PLoS Genet (2012) 1.16
Diagnostic interpretation of array data using public databases and internet sources. Hum Mutat (2012) 1.16
Frequent appearance of novel protein-coding sequences by frameshift translation. Genomics (2006) 1.14
Genetic variation in a haplotype block spanning IDE influences Alzheimer disease. Hum Mutat (2003) 1.14
Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function. Hum Mol Genet (2012) 1.14
Genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the biosynthesis of long-chain omega-3 and omega-6 fatty acids. Am J Hum Genet (2012) 1.13
Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing. Genome Biol (2010) 1.13
Elevated amyloid beta protein (Abeta42) and late onset Alzheimer's disease are associated with single nucleotide polymorphisms in the urokinase-type plasminogen activator gene. Hum Mol Genet (2004) 1.13
A comprehensive evaluation of potential lung function associated genes in the SpiroMeta general population sample. PLoS One (2011) 1.13
Rate variation between mitochondrial domains and adaptive evolution in humans. Hum Mol Genet (2007) 1.12
Haplotypes extending across ACE are associated with Alzheimer's disease. Hum Mol Genet (2003) 1.11
Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing. Development (2012) 1.11
Modeling of environmental effects in genome-wide association studies identifies SLC2A2 and HP as novel loci influencing serum cholesterol levels. PLoS Genet (2010) 1.10
Comparison of participant information and informed consent forms of five European studies in genetic isolated populations. Eur J Hum Genet (2009) 1.05
Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data. BMC Genomics (2010) 1.02
Genetic determinants of heel bone properties: genome-wide association meta-analysis and replication in the GEFOS/GENOMOS consortium. Hum Mol Genet (2014) 1.02
HPV test shows low sensitivity of Pap screen in older women. Lancet Oncol (2010) 1.01
A meta-analysis of genome-wide data from five European isolates reveals an association of COL22A1, SYT1, and GABRR2 with serum creatinine level. BMC Med Genet (2010) 1.00
Abolished InsP3R2 function inhibits sweat secretion in both humans and mice. J Clin Invest (2014) 1.00
Identification of genetic variants influencing the human plasma proteome. Proc Natl Acad Sci U S A (2013) 1.00
Towards compendia of negative genetic association studies: an example for Alzheimer disease. Hum Genet (2005) 1.00
Polymorphisms in B3GAT1, SLC9A9 and MGAT5 are associated with variation within the human plasma N-glycome of 3533 European adults. Hum Mol Genet (2011) 0.99
Sequence variants of IDE are associated with the extent of beta-amyloid deposition in the Alzheimer's disease brain. Neurobiol Aging (2005) 0.99
High-risk human papilloma virus (HPV) and survival in patients with esophageal carcinoma: a pilot study. BMC Cancer (2006) 0.98
Full-length sequence analysis of the HLA-DRB1 locus suggests a recent origin of alleles. Immunogenetics (2007) 0.98
Affected sib-pair analysis of the contribution of HLA class I and class II loci to development of cervical cancer. Hum Mol Genet (2004) 0.98
Type-specific detection of high-risk human papillomavirus (HPV) in self-sampled cervicovaginal cells applied to FTA elute cartridge. J Clin Virol (2011) 0.97
A genome-wide screen for interactions reveals a new locus on 4p15 modifying the effect of waist-to-hip ratio on total cholesterol. PLoS Genet (2011) 0.97