Published in Nat Methods on January 17, 2010
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics (2012) 9.97
Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods (2010) 9.09
Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res (2010) 9.08
RNA sequencing: advances, challenges and opportunities. Nat Rev Genet (2010) 8.96
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol (2010) 6.07
Next-generation transcriptome assembly. Nat Rev Genet (2011) 5.89
Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res (2012) 4.81
Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell (2010) 3.42
The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA. BMC Biol (2010) 2.59
Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proc Natl Acad Sci U S A (2012) 2.59
The expanding scope of DNA sequencing. Nat Biotechnol (2012) 2.57
Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective. PLoS Genet (2012) 2.57
The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A (2012) 2.39
Amplification-free digital gene expression profiling from minute cell quantities. Nat Methods (2010) 2.07
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics (2013) 2.07
Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol (2010) 2.06
Whole-transcriptome RNAseq analysis from minute amount of total RNA. Nucleic Acids Res (2011) 1.97
Bias detection and correction in RNA-Sequencing data. BMC Bioinformatics (2011) 1.93
Strand-specific deep sequencing of the transcriptome. Genome Res (2010) 1.58
Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci U S A (2010) 1.47
A comparison of single molecule and amplification based sequencing of cancer transcriptomes. PLoS One (2011) 1.44
A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation. Genomics (2011) 1.37
Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. Silence (2011) 1.35
Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. BMC Genomics (2012) 1.26
Protocol dependence of sequencing-based gene expression measurements. PLoS One (2011) 1.19
A quality control system for profiles obtained by ChIP sequencing. Nucleic Acids Res (2013) 1.18
Dark Matter RNA: Existence, Function, and Controversy. Front Genet (2012) 1.18
The prevalence and regulation of antisense transcripts in Schizosaccharomyces pombe. PLoS One (2010) 1.13
Cleavage of rRNA ensures translational cessation in sperm at fertilization. Mol Hum Reprod (2011) 1.03
Effect of PCR extension temperature on high-throughput sequencing. Mol Biochem Parasitol (2010) 1.01
Functional transcriptomics in the post-ENCODE era. Genome Res (2013) 0.98
Transfection of shRNA-encoding Minivector DNA of a few hundred base pairs to regulate gene expression in lymphoma cells. Gene Ther (2010) 0.98
A new approach to bias correction in RNA-Seq. Bioinformatics (2012) 0.96
A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing. Mol Microbiol (2014) 0.95
Single-molecule direct RNA sequencing without cDNA synthesis. Wiley Interdiscip Rev RNA (2011) 0.95
Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics (2013) 0.94
A cost-effective RNA sequencing protocol for large-scale gene expression studies. Sci Rep (2015) 0.92
Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium. Genome Biol (2012) 0.91
High-throughput RNA sequencing of pseudomonas-infected Arabidopsis reveals hidden transcriptome complexity and novel splice variants. PLoS One (2013) 0.90
Single read and paired end mRNA-Seq Illumina libraries from 10 nanograms total RNA. J Vis Exp (2011) 0.88
Third-generation sequencing techniques and applications to drug discovery. Expert Opin Drug Discov (2012) 0.87
Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation. Mol Microbiol (2013) 0.86
Low-bias, strand-specific transcriptome Illumina sequencing by on-flowcell reverse transcription (FRT-seq). Nat Protoc (2011) 0.85
Pregnancy-specific glycoproteins bind integrin αIIbβ3 and inhibit the platelet-fibrinogen interaction. PLoS One (2013) 0.85
Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling. Curr Genomics (2013) 0.84
Methods, Challenges and Potentials of Single Cell RNA-seq. Biology (Basel) (2012) 0.83
Single-tube linear DNA amplification for genome-wide studies using a few thousand cells. Nat Protoc (2012) 0.83
The impact of amplification on differential expression analyses by RNA-seq. Sci Rep (2016) 0.81
Deep sequencing of coding and non-coding RNA in the CNS. Brain Res (2010) 0.79
Evaluation and application of the strand-specific protocol for next-generation sequencing. Biomed Res Int (2015) 0.79
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. Int Rev Neurobiol (2012) 0.77
RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri. BMC Genomics (2014) 0.76
An integrative method to normalize RNA-Seq data. BMC Bioinformatics (2014) 0.76
Current challenges in bacterial transcriptomics. Genomics Inform (2013) 0.76
The impact of RNA secondary structure on read start locations on the Illumina sequencing platform. PLoS One (2017) 0.75
Going small is the new big. Nat Methods (2010) 0.75
Local sequence and sequencing depth dependent accuracy of RNA-seq reads. BMC Bioinformatics (2017) 0.75
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol (2004) 101.91
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res (2008) 62.07
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res (2002) 40.03
The transcriptional landscape of the mammalian genome. Science (2005) 37.63
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell (2008) 32.65
Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods (2008) 31.04
Ensembl 2009. Nucleic Acids Res (2008) 25.38
Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics (2002) 20.59
Antisense transcription in the mammalian transcriptome. Science (2005) 15.69
A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A (2006) 11.81
BioMart--biological queries made easy. BMC Genomics (2009) 11.06
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods (2009) 10.41
Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res (2009) 9.40
The antisense transcriptomes of human cells. Science (2008) 6.29
Direct RNA sequencing. Nature (2009) 4.37
Quantification of the yeast transcriptome by single-molecule sequencing. Nat Biotechnol (2009) 3.86
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34
A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res (2009) 2.19
Reverse transcriptase adds nontemplated nucleotides to cDNAs during 5'-RACE and primer extension. Biotechniques (2001) 1.29
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72
A large genome center's improvements to the Illumina sequencing system. Nat Methods (2008) 15.56
Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature (2010) 12.27
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods (2009) 10.41
Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A (2004) 8.95
Target-enrichment strategies for next-generation sequencing. Nat Methods (2010) 8.78
The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) 8.52
The DNA sequence of the human X chromosome. Nature (2005) 6.97
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol (2010) 5.98
The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res (2007) 5.67
Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state. Mol Cell (2010) 5.43
CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature (2010) 4.86
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature (2012) 4.37
Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res (2009) 4.12
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
Replication timing of the human genome. Hum Mol Genet (2003) 4.10
High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res (2011) 4.09
A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood (2009) 3.63
Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat Genet (2010) 3.52
Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet (2010) 3.38
CEP152 is a genome maintenance protein disrupted in Seckel syndrome. Nat Genet (2010) 3.25
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet (2009) 2.87
Gene annotation: prediction and testing. Annu Rev Genomics Hum Genet (2003) 2.64
Genomic and epigenetic evidence for oxytocin receptor deficiency in autism. BMC Med (2009) 2.60
Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays. Hum Mol Genet (2005) 2.56
High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature (2012) 2.55
Gene expression profiles of CD34+ cells in myelodysplastic syndromes: involvement of interferon-stimulated genes and correlation to FAB subtype and karyotype. Blood (2006) 2.29
A transforming growth factorbeta1 signal peptide variant increases secretion in vitro and is associated with increased incidence of invasive breast cancer. Cancer Res (2003) 2.21
Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics (2012) 2.20
A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res (2009) 2.19
The GENCODE exome: sequencing the complete human exome. Eur J Hum Genet (2011) 1.88
iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J Vis Exp (2011) 1.80
Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome. Am J Hum Genet (2005) 1.78
P450 BM3: the very model of a modern flavocytochrome. Trends Biochem Sci (2002) 1.77
A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications. Hum Mol Genet (2002) 1.69
Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nat Protoc (2013) 1.54
Mobilization of giant piggyBac transposons in the mouse genome. Nucleic Acids Res (2011) 1.49
Convergent extension movements and ciliary function are mediated by ofd1, a zebrafish orthologue of the human oral-facial-digital type 1 syndrome gene. Hum Mol Genet (2008) 1.46
Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. PLoS One (2010) 1.44
Genetic basis of Y-linked hearing impairment. Am J Hum Genet (2013) 1.42
The transcriptional repressor Blimp1/Prdm1 regulates postnatal reprogramming of intestinal enterocytes. Proc Natl Acad Sci U S A (2011) 1.40
Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin Y. Hum Mol Genet (2006) 1.36
Improved protocols for the illumina genome analyzer sequencing system. Curr Protoc Hum Genet (2009) 1.36
Comprehensive assignment of roles for Salmonella typhimurium genes in intestinal colonization of food-producing animals. PLoS Genet (2013) 1.35
Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes. Genome Res (2007) 1.35
Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level. Genome Res (2009) 1.30
A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium. Nucleic Acids Res (2013) 1.26
Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and mammalian lung. PLoS One (2011) 1.25
EpiChIP: gene-by-gene quantification of epigenetic modification levels. Nucleic Acids Res (2010) 1.23
Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors. Genome Res (2005) 1.16
96-plex molecular barcoding for the Illumina Genome Analyzer. Methods Mol Biol (2011) 1.16
Histone methyltransferase MLL3 contributes to genome-scale circadian transcription. Proc Natl Acad Sci U S A (2013) 1.11
Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution. PLoS One (2010) 1.09
Germline transgenesis and insertional mutagenesis in Schistosoma mansoni mediated by murine leukemia virus. PLoS Pathog (2012) 1.05
Phe393 mutants of cytochrome P450 BM3 with modified heme redox potentials have altered heme vinyl and propionate conformations. Biochemistry (2004) 1.04
TSPY1 copy number variation influences spermatogenesis and shows differences among Y lineages. J Clin Endocrinol Metab (2009) 1.04
'Putting our heads together': insights into genomic conservation between human and canine intracranial tumors. J Neurooncol (2009) 1.01
Analysis of the domain properties of the novel cytochrome P450 RhF. FEBS Lett (2005) 1.00
CCR4-associated factor 1 coordinates the expression of Plasmodium falciparum egress and invasion proteins. Eukaryot Cell (2011) 1.00
Gene expression profiling in polycythemia vera using cDNA microarray technology. Cancer Res (2003) 1.00
Genomic and proteomic dissection of the ubiquitous plant pathogen, Armillaria mellea: toward a new infection model system. J Proteome Res (2013) 1.00
Retrospective application of transposon-directed insertion site sequencing to a library of signature-tagged mini-Tn5Km2 mutants of Escherichia coli O157:H7 screened in cattle. J Bacteriol (2011) 1.00
Genomic approaches uncover increasing complexities in the regulatory landscape at the human SCL (TAL1) locus. PLoS One (2010) 0.99
Interaction of nitric oxide with cytochrome P450 BM3. Biochemistry (2004) 0.98
A cytogenetically characterized, genome-anchored 10-Mb BAC set and CGH array for the domestic dog. J Hered (2007) 0.97
High altitude adaptation in Daghestani populations from the Caucasus. Hum Genet (2011) 0.96
Molecular analysis of tumor-promoting CD8+ T cells in two-stage cutaneous chemical carcinogenesis. J Invest Dermatol (2009) 0.95
Gene expression profiling in the myelodysplastic syndromes using cDNA microarray technology. Br J Haematol (2004) 0.95
A self-sufficient cytochrome p450 with a primary structural organization that includes a flavin domain and a [2Fe-2S] redox center. J Biol Chem (2003) 0.95
Amplification-free library preparation for paired-end Illumina sequencing. Methods Mol Biol (2011) 0.91
Comprehensive DNA copy number profiling of meningioma using a chromosome 1 tiling path microarray identifies novel candidate tumor suppressor loci. Cancer Res (2005) 0.91
A barcode screen for epigenetic regulators reveals a role for the NuB4/HAT-B histone acetyltransferase complex in histone turnover. PLoS Genet (2011) 0.89
Distinct patterns of 1p and 19q alterations identify subtypes of human gliomas that have different prognoses. Neuro Oncol (2010) 0.86
Behavior and target site selection of conjugative transposon Tn916 in two different strains of toxigenic Clostridium difficile. Appl Environ Microbiol (2012) 0.86
Selective modulation of the SM22alpha promoter by the binding of BTEB3 (basal transcription element-binding protein 3) to TGGG repeats. Biochem J (2003) 0.85
Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data. Hum Genet (2011) 0.85
Low-bias, strand-specific transcriptome Illumina sequencing by on-flowcell reverse transcription (FRT-seq). Nat Protoc (2011) 0.85
Redox properties of the isolated flavin mononucleotide- and flavin adenine dinucleotide-binding domains of neuronal nitric oxide synthase. Biochemistry (2004) 0.84
Identification of variation in the platelet transcriptome associated with glycoprotein 6 haplotype. Platelets (2008) 0.84