Published in BMC Genomics on June 17, 2010
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
lincRNAs: genomics, evolution, and mechanisms. Cell (2013) 6.50
A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics (2013) 4.36
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol (2014) 3.99
Synthetic spike-in standards for RNA-seq experiments. Genome Res (2011) 3.58
The reality of pervasive transcription. PLoS Biol (2011) 3.41
Long noncoding RNAs: past, present, and future. Genetics (2013) 3.16
Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol (2011) 3.12
Transcribed dark matter: meaning or myth? Hum Mol Genet (2010) 2.87
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol (2010) 2.79
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotechnol (2013) 2.53
The transcriptional diversity of 25 Drosophila cell lines. Genome Res (2010) 2.47
A comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in C. elegans. PLoS One (2011) 1.46
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Res (2010) 1.35
Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. Silence (2011) 1.35
RNA-Seq vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering. PLoS One (2012) 1.20
Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using Deep RNA sequencing. PLoS One (2012) 1.19
The role of the 5'-3' exoribonuclease XRNA in transcriptome-wide mRNA degradation. RNA (2011) 1.13
The transcriptome of Leishmania major in the axenic promastigote stage: transcript annotation and relative expression levels by RNA-seq. BMC Genomics (2013) 1.11
pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns. Nucleic Acids Res (2011) 1.02
Developmental transcriptome analysis of human erythropoiesis. Hum Mol Genet (2014) 0.99
Transcriptome sequencing of mung bean (Vigna radiate L.) genes and the identification of EST-SSR markers. PLoS One (2015) 0.98
De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing. Plant Cell Rep (2012) 0.98
A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums. BMC Plant Biol (2014) 0.90
Functional genomic and proteomic analysis reveals disruption of myelin-related genes and translation in a mouse model of early life neglect. Front Psychiatry (2011) 0.90
Transcriptome analysis of the parasite Encephalitozoon cuniculi: an in-depth examination of pre-mRNA splicing in a reduced eukaryote. BMC Genomics (2013) 0.90
Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies. Appl Environ Microbiol (2012) 0.89
Transcriptomic complexity in young maize primary roots in response to low water potentials. BMC Genomics (2014) 0.88
Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis. Plant Physiol (2012) 0.88
The human transcriptome: an unfinished story. Genes (Basel) (2012) 0.86
The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression. Nucleic Acids Res (2011) 0.85
An integrative functional genomics approach for discovering biomarkers in schizophrenia. Brief Funct Genomics (2011) 0.83
A differential sequencing-based analysis of the C. elegans noncoding transcriptome. RNA (2012) 0.82
A preliminary study of the mechanism of nitrate-stimulated remarkable increase of rifamycin production in Amycolatopsis mediterranei U32 by RNA-seq. Microb Cell Fact (2015) 0.81
Deep profiling of the novel intermediate-size noncoding RNAs in intraerythrocytic Plasmodium falciparum. PLoS One (2014) 0.80
The noncoding universe. BMC Biol (2011) 0.79
Cross-species Transcriptomic Comparison of In Vitro and In Vivo Mammalian Neural Cells. Bioinform Biol Insights (2015) 0.78
A method for detecting long non-coding RNAs with tiled RNA expression microarrays. PLoS One (2014) 0.78
Comprehensive evaluation of AmpliSeq transcriptome, a novel targeted whole transcriptome RNA sequencing methodology for global gene expression analysis. BMC Genomics (2015) 0.77
Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments. Microb Biotechnol (2011) 0.77
A Computational Pipeline for Cross-Species Analysis of RNA-seq Data Using R and Bioconductor. Bioinform Biol Insights (2015) 0.77
Understanding Host-Pathogen Interactions with Expression Profiling of NILs Carrying Rice-Blast Resistance Pi9 Gene. Front Plant Sci (2017) 0.75
Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence. BMC Genomics (2017) 0.75
Flexible and efficient genome tiling design with penalized uniqueness score. BMC Bioinformatics (2012) 0.75
New technologies accelerate the exploration of non-coding RNAs in horticultural plants. Hortic Res (2017) 0.75
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Identification of common molecular subsequences. J Mol Biol (1981) 130.53
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (2003) 82.89
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
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
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
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) 18.84
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01
Statistical inferences for isoform expression in RNA-Seq. Bioinformatics (2009) 12.50
A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A (2006) 11.81
mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods (2009) 11.71
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res (2008) 10.10
Bidirectional promoters generate pervasive transcription in yeast. Nature (2009) 9.29
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol (2008) 9.09
Transcript length bias in RNA-seq data confounds systems biology. Biol Direct (2009) 8.53
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics (2009) 6.41
Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat Genet (2006) 6.20
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A (2009) 6.01
The beginning of the end for microarrays? Nat Methods (2008) 4.19
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res (2009) 3.83
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82
Digital transcriptome profiling using selective hexamer priming for cDNA synthesis. Nat Methods (2009) 3.73
Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics (2002) 3.65
Structure and complexity of a bacterial transcriptome. J Bacteriol (2009) 3.55
Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A (2009) 3.16
PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (2006) 2.85
Big data: How do your data grow? Nature (2008) 2.80
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. Nucleic Acids Res (2007) 2.39
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet (2005) 2.36
Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol (2005) 2.32
Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics (2007) 2.08
Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics (2007) 1.77
Profound influence of microarray scanner characteristics on gene expression ratios: analysis and procedure for correction. BMC Genomics (2004) 1.60
A multivariate prediction model for microarray cross-hybridization. BMC Bioinformatics (2006) 1.07
The real life of pseudogenes. Sci Am (2006) 0.90
An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping. BMC Res Notes (2009) 0.84
Empirical comparison of tests for differential expression on simulated time series microarray experiments. AMIA Annu Symp Proc (2006) 0.79
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature (2008) 38.13
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol (2003) 13.32
The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature (2003) 12.44
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Unlocking the secrets of the genome. Nature (2009) 11.80
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Variation in transcription factor binding among humans. Science (2010) 9.33
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res (2011) 8.18
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
Punctuated evolution of prostate cancer genomes. Cell (2013) 7.23
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
The DNA sequence of the human X chromosome. Nature (2005) 6.97
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Automated cell lineage tracing in Caenorhabditis elegans. Proc Natl Acad Sci U S A (2006) 6.22
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol (2007) 6.18
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
The genome of a songbird. Nature (2010) 5.90
Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79
Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol (2009) 5.45
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
A physical map of the mouse genome. Nature (2002) 4.97
Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nat Methods (2008) 4.81
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
p38 MAPK regulates expression of immune response genes and contributes to longevity in C. elegans. PLoS Genet (2006) 4.47
Completing the map of human genetic variation. Nature (2007) 4.38
Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature (2003) 4.31
The GENCODE pseudogene resource. Genome Biol (2012) 4.18
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res (2009) 3.83
X-chromosome silencing in the germline of C. elegans. Development (2002) 3.69
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res (2006) 3.62
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer. J Natl Cancer Inst (2008) 3.55
Genomic analysis of essentiality within protein networks. Trends Genet (2004) 3.52
Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51
Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48
Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets. Cancer Discov (2011) 3.43
GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A (2002) 3.41
Structured digital abstract makes text mining easy. Nature (2007) 3.38
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34
Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr Biol (2002) 3.30
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A (2010) 3.28
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22
The DNA sequence of human chromosome 7. Nature (2003) 3.18
The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am J Med Genet A (2012) 3.12
Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature (2012) 3.09
Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer (2009) 3.03