Published in Nat Protoc on January 21, 2010
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res (2012) 2.53
Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol (2010) 2.32
High-throughput sequencing for biology and medicine. Mol Syst Biol (2013) 1.75
Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. Genome Biol Evol (2012) 1.69
Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PLoS One (2013) 1.61
A High-Throughput Method for Illumina RNA-Seq Library Preparation. Front Plant Sci (2012) 1.20
What can whole genome expression data tell us about the ecology and evolution of personality? Philos Trans R Soc Lond B Biol Sci (2010) 1.10
The centrality of RNA for engineering gene expression. Biotechnol J (2013) 0.94
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program. Nucleic Acids Res (2011) 0.94
Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani. PLoS Pathog (2014) 0.91
mRNA-seq analysis of the Gossypium arboreum transcriptome reveals tissue selective signaling in response to water stress during seedling stage. PLoS One (2013) 0.91
Transcriptome analysis of the parasite Encephalitozoon cuniculi: an in-depth examination of pre-mRNA splicing in a reduced eukaryote. BMC Genomics (2013) 0.90
Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications. Nat Protoc (2013) 0.89
PPARG: Gene Expression Regulation and Next-Generation Sequencing for Unsolved Issues. PPAR Res (2010) 0.88
New approaches to Prunus transcriptome analysis. Genetica (2011) 0.88
Large scale in-silico identification and characterization of simple sequence repeats (SSRs) from de novo assembled transcriptome of Catharanthus roseus (L.) G. Don. Plant Cell Rep (2014) 0.88
Genomic mRNA profiling reveals compensatory mechanisms for the requirement of the essential splicing factor U2AF. Mol Cell Biol (2010) 0.87
Quantitative analysis of 5HT(2C) receptor RNA editing patterns in psychiatric disorders. Neurobiol Dis (2011) 0.85
Towards an improved apple reference transcriptome using RNA-seq. Mol Genet Genomics (2014) 0.84
High-throughput sequencing and De Novo assembly of the Isatis indigotica transcriptome. PLoS One (2014) 0.81
Deep Sequencing Insights in Therapeutic shRNA Processing and siRNA Target Cleavage Precision. Mol Ther Nucleic Acids (2014) 0.81
TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. BMC Bioinformatics (2016) 0.79
The conservation and signatures of lincRNAs in Marek's disease of chicken. Sci Rep (2015) 0.78
Sequencing, De novo Assembly, Functional Annotation and Analysis of Phyllanthus amarus Leaf Transcriptome Using the Illumina Platform. Front Plant Sci (2016) 0.77
De Novo RNA Sequencing and Transcriptome Analysis of Monascus purpureus and Analysis of Key Genes Involved in Monacolin K Biosynthesis. PLoS One (2017) 0.75
sizzled function and secreted factor network dynamics. Biol Open (2012) 0.75
Sequencing-based expression profiling in zebrafish. Methods Cell Biol (2011) 0.75
Prosaposin activates the androgen receptor and potentiates resistance to endocrine treatment in breast cancer. Breast Cancer Res (2015) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res (1998) 106.16
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet (2008) 68.81
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
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
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
Origins and Mechanisms of miRNAs and siRNAs. Cell (2009) 20.77
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science (2009) 20.75
Long non-coding RNAs: insights into functions. Nat Rev Genet (2009) 19.61
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) 18.84
A large genome center's improvements to the Illumina sequencing system. Nat Methods (2008) 15.56
Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci U S A (2008) 11.86
SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol (2009) 11.24
Genome-wide transcription and the implications for genomic organization. Nat Rev Genet (2007) 9.45
Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res (2009) 9.40
Annotating genomes with massive-scale RNA sequencing. Genome Biol (2008) 7.73
Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods (2008) 7.14
How to map billions of short reads onto genomes. Nat Biotechnol (2009) 6.59
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A (2009) 6.01
Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics (2008) 5.00
RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods (2009) 4.02
Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data. BMC Genomics (2003) 3.30
Wasp gene expression supports an evolutionary link between maternal behavior and eusociality. Science (2007) 2.60
Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis. BMC Genomics (2009) 2.21
A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res (2009) 2.19
Swift: primary data analysis for the Illumina Solexa sequencing platform. Bioinformatics (2009) 2.03
Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet (2006) 1.95
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet (2008) 19.97
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) 18.84
The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83
Population genomics of domestic and wild yeasts. Nature (2009) 11.79
The genome of the African trypanosome Trypanosoma brucei. Science (2005) 11.48
Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing. Proc Natl Acad Sci U S A (2008) 7.22
Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell (2003) 6.04
Periodic gene expression program of the fission yeast cell cycle. Nat Genet (2004) 5.60
Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage. Cell (2004) 4.99
The transcriptional program of meiosis and sporulation in fission yeast. Nat Genet (2002) 4.80
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat Rev Genet (2008) 3.84
Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature (2007) 3.32
Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data. BMC Genomics (2003) 3.30
Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell (2012) 3.26
Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res (2008) 3.26
RNA-seq: from technology to biology. Cell Mol Life Sci (2009) 3.03
PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res (2011) 2.84
The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. J Bacteriol (2008) 2.71
Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes. Genome Res (2007) 2.67
Genome-wide characterization of fission yeast DNA replication origins. EMBO J (2006) 2.53
Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis. PLoS One (2009) 2.38
Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem Sci (2005) 2.33
A network of multiple regulatory layers shapes gene expression in fission yeast. Mol Cell (2007) 2.29
Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates. Genome Res (2007) 2.29
Telomeric expression sites are highly conserved in Trypanosoma brucei. PLoS One (2008) 2.22
The nuclear poly(A)-binding protein interacts with the exosome to promote synthesis of noncoding small nucleolar RNAs. Mol Cell (2010) 2.22
A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res (2009) 2.19
Global effects on gene expression in fission yeast by silencing and RNA interference machineries. Mol Cell Biol (2005) 1.98
Analysis of Campylobacter jejuni capsular loci reveals multiple mechanisms for the generation of structural diversity and the ability to form complex heptoses. Mol Microbiol (2005) 1.79
YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. Nucleic Acids Res (2006) 1.73
A coordinated global control over cellular transcription. Curr Biol (2010) 1.72
Multiple pathways differentially regulate global oxidative stress responses in fission yeast. Mol Biol Cell (2007) 1.72
Transcriptional regulatory network for sexual differentiation in fission yeast. Genome Biol (2007) 1.67
Global roles of Ste11p, cell type, and pheromone in the control of gene expression during early sexual differentiation in fission yeast. Proc Natl Acad Sci U S A (2006) 1.59
Rapidly regulated genes are intron poor. Trends Genet (2008) 1.47
Next-generation sequencing: applications beyond genomes. Biochem Soc Trans (2008) 1.45
Global role for polyadenylation-assisted nuclear RNA degradation in posttranscriptional gene silencing. Mol Cell Biol (2007) 1.43
Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast. Genome Biol (2012) 1.40
Negative regulation of meiotic gene expression by the nuclear poly(a)-binding protein in fission yeast. J Biol Chem (2010) 1.37
RNA-binding protein Csx1 mediates global control of gene expression in response to oxidative stress. EMBO J (2003) 1.35
Key function for the CCAAT-binding factor Php4 to regulate gene expression in response to iron deficiency in fission yeast. Eukaryot Cell (2008) 1.32
Global gene expression responses of fission yeast to ionizing radiation. Mol Biol Cell (2003) 1.30
Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast. Nat Struct Mol Biol (2008) 1.28
An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe. Nat Struct Mol Biol (2009) 1.27
The fission yeast HIRA histone chaperone is required for promoter silencing and the suppression of cryptic antisense transcripts. Mol Cell Biol (2009) 1.25
The S. pombe SAGA complex controls the switch from proliferation to sexual differentiation through the opposing roles of its subunits Gcn5 and Spt8. Genes Dev (2008) 1.24
A Pre-mRNA degradation pathway that selectively targets intron-containing genes requires the nuclear poly(A)-binding protein. Mol Cell (2011) 1.24
Impairment of the TFIIH-associated CDK-activating kinase selectively affects cell cycle-regulated gene expression in fission yeast. Mol Biol Cell (2005) 1.21
Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries. Mol Cell Biol (2007) 1.18
Upf1, an RNA helicase required for nonsense-mediated mRNA decay, modulates the transcriptional response to oxidative stress in fission yeast. Mol Cell Biol (2006) 1.18
Translational control of gene expression from transcripts to transcriptomes. Int Rev Cell Mol Biol (2008) 1.17
FYPO: the fission yeast phenotype ontology. Bioinformatics (2013) 1.17
CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR. Nature (2010) 1.17
Coordinating genome expression with cell size. Trends Genet (2012) 1.14
A novel linear plasmid mediates flagellar variation in Salmonella Typhi. PLoS Pathog (2007) 1.12
urg1: a uracil-regulatable promoter system for fission yeast with short induction and repression times. PLoS One (2008) 1.12
Autoregulation of ribosome biosynthesis by a translational response in fission yeast. Mol Cell Biol (2006) 1.12
Mfc1 is a novel forespore membrane copper transporter in meiotic and sporulating cells. J Biol Chem (2011) 1.10
Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study. Genome Biol (2007) 1.09
SCF(Pof1)-ubiquitin and its target Zip1 transcription factor mediate cadmium response in fission yeast. EMBO J (2005) 1.09
TORC1 signaling inhibition by rapamycin and caffeine affect lifespan, global gene expression, and cell proliferation of fission yeast. Aging Cell (2013) 1.08
Simplified primer design for PCR-based gene targeting and microarray primer database: two web tools for fission yeast. Yeast (2006) 1.06
Exploring long non-coding RNAs through sequencing. Semin Cell Dev Biol (2011) 1.06
The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback. PLoS Genet (2009) 1.05
Elimination of a specific histone H3K14 acetyltransferase complex bypasses the RNAi pathway to regulate pericentric heterochromatin functions. Genes Dev (2011) 1.00
TOR complex 2 controls gene silencing, telomere length maintenance, and survival under DNA-damaging conditions. Mol Cell Biol (2009) 1.00
Cip1 and Cip2 are novel RNA-recognition-motif proteins that counteract Csx1 function during oxidative stress. Mol Biol Cell (2006) 0.98
Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast. Mol Cell Biol (2013) 0.98
Int6/eIF3e promotes general translation and Atf1 abundance to modulate Sty1 MAPK-dependent stress response in fission yeast. J Biol Chem (2008) 0.97
Meta-analysis of genome regulation and expression variability across hundreds of environmental and genetic perturbations in fission yeast. Mol Biosyst (2009) 0.97
Response of Schizosaccharomyces pombe to zinc deficiency. Eukaryot Cell (2008) 0.97
Role of septins in the orientation of forespore membrane extension during sporulation in fission yeast. Mol Cell Biol (2010) 0.96
Global expression changes resulting from loss of telomeric DNA in fission yeast. Genome Biol (2004) 0.95
Website review: how to get the best from fission yeast genome data. Comp Funct Genomics (2002) 0.95
A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi. Mol Microbiol (2007) 0.95
Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast. Genome Biol (2011) 0.94
Expression of a RecQ helicase homolog affects progression through crisis in fission yeast lacking telomerase. J Biol Chem (2004) 0.94
Failed gene conversion leads to extensive end processing and chromosomal rearrangements in fission yeast. EMBO J (2009) 0.94
Sites of strong Rec12/Spo11 binding in the fission yeast genome are associated with meiotic recombination and with centromeres. Chromosoma (2008) 0.94
Individual letters of the RNA polymerase II CTD code govern distinct gene expression programs in fission yeast. Proc Natl Acad Sci U S A (2014) 0.93
In silico characterization and prediction of global protein-mRNA interactions in yeast. Nucleic Acids Res (2011) 0.93
Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe. Mol Cell Biol (2011) 0.93