Published in Bioinformatics on August 12, 2008
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (2010) 52.01
A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform (2010) 18.05
Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics (2010) 17.53
An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol (2008) 13.96
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. Bioinformatics (2009) 13.34
Statistical inferences for isoform expression in RNA-Seq. Bioinformatics (2009) 12.50
Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res (2010) 6.95
Most "dark matter" transcripts are associated with known genes. PLoS Biol (2010) 6.60
RazerS--fast read mapping with sensitivity control. Genome Res (2009) 6.53
Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol (2010) 6.10
Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol (2009) 3.30
Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol (2013) 2.84
Simultaneous alignment of short reads against multiple genomes. Genome Biol (2009) 2.79
Cross-hybridization modeling on Affymetrix exon arrays. Bioinformatics (2008) 2.54
Structure and activity of putative intronic miRNA promoters. RNA (2010) 2.50
Genomic location analysis by ChIP-Seq. J Cell Biochem (2009) 2.44
The impact of next-generation sequencing on genomics. J Genet Genomics (2011) 2.41
Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol (2010) 2.32
miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics (2009) 2.22
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics (2009) 2.20
A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res (2010) 2.07
CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat Protoc (2013) 2.05
MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline. Dev Cell (2011) 1.94
GASSST: global alignment short sequence search tool. Bioinformatics (2010) 1.81
Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature (2010) 1.63
Human transcriptome array for high-throughput clinical studies. Proc Natl Acad Sci U S A (2011) 1.62
Fast and accurate read alignment for resequencing. Bioinformatics (2012) 1.58
sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites. PLoS One (2014) 1.54
Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods (2015) 1.53
Statistical Modeling of RNA-Seq Data. Stat Sci (2011) 1.49
SAMMate: a GUI tool for processing short read alignments in SAM/BAM format. Source Code Biol Med (2011) 1.47
Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res (2010) 1.41
Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq. RNA (2010) 1.39
Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila. Front Genet (2011) 1.38
Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol (2010) 1.38
RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. Genome Res (2012) 1.36
A flexible approach for highly multiplexed candidate gene targeted resequencing. PLoS One (2011) 1.35
SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data. Front Genet (2011) 1.31
An innovative approach for testing bioinformatics programs using metamorphic testing. BMC Bioinformatics (2009) 1.30
Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. Eukaryot Cell (2011) 1.28
Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. Sci Rep (2011) 1.25
Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of hepatic nuclear factor 4 alpha. BMC Genomics (2010) 1.25
De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments. BMC Genomics (2012) 1.19
Somatic CRISPR/Cas9-mediated tumour suppressor disruption enables versatile brain tumour modelling. Nat Commun (2015) 1.17
Identification and validation of potential prognostic lncRNA biomarkers for predicting survival in patients with multiple myeloma. J Exp Clin Cancer Res (2015) 1.17
NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors. Genome Res (2013) 1.15
Mapping accuracy of short reads from massively parallel sequencing and the implications for quantitative expression profiling. PLoS One (2009) 1.15
SEED: efficient clustering of next-generation sequences. Bioinformatics (2011) 1.14
proTRAC--a software for probabilistic piRNA cluster detection, visualization and analysis. BMC Bioinformatics (2012) 1.10
Biogenesis pathways of piRNAs loaded onto AGO3 in the Drosophila testis. RNA (2010) 1.08
Altered antisense-to-sense transcript ratios in breast cancer. Proc Natl Acad Sci U S A (2010) 1.08
Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline. Genome Res (2014) 1.07
Efficient generation of gene-modified pigs via injection of zygote with Cas9/sgRNA. Sci Rep (2015) 1.07
Relapse-related long non-coding RNA signature to improve prognosis prediction of lung adenocarcinoma. Oncotarget (2016) 1.06
Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data. PLoS One (2011) 1.06
A potential prognostic long non-coding RNA signature to predict metastasis-free survival of breast cancer patients. Sci Rep (2015) 1.04
Next generation sequencing in cardiovascular diseases. World J Cardiol (2012) 1.04
Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis. Genome Biol (2013) 1.04
DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation. Nat Struct Mol Biol (2012) 1.03
Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. J Comput Biol (2012) 1.02
Molecular basis for the action of a dietary flavonoid revealed by the comprehensive identification of apigenin human targets. Proc Natl Acad Sci U S A (2013) 1.01
Gain-of-function p53 mutants have widespread genomic locations partially overlapping with p63. Oncotarget (2012) 1.00
Identification of a binding motif specific to HNF4 by comparative analysis of multiple nuclear receptors. Nucleic Acids Res (2012) 1.00
De Novo transcriptome sequencing reveals important molecular networks and metabolic pathways of the plant, Chlorophytum borivilianum. PLoS One (2013) 0.98
3D chromatin conformation correlates with replication timing and is conserved in resting cells. Nucleic Acids Res (2012) 0.98
Using high-density exon arrays to profile gene expression in closely related species. Nucleic Acids Res (2009) 0.98
Generation of gene-modified goats targeting MSTN and FGF5 via zygote injection of CRISPR/Cas9 system. Sci Rep (2015) 0.98
How do alignment programs perform on sequencing data with varying qualities and from repetitive regions? BioData Min (2012) 0.96
Addressing the role of microRNAs in reprogramming leaf growth during drought stress in Brachypodium distachyon. Mol Plant (2012) 0.94
High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis. Genome Biol Evol (2009) 0.94
A potential panel of six-long non-coding RNA signature to improve survival prediction of diffuse large-B-cell lymphoma. Sci Rep (2016) 0.94
UMARS: Un-MAppable Reads Solution. BMC Bioinformatics (2011) 0.93
Low Dose Iron Treatments Induce a DNA Damage Response in Human Endothelial Cells within Minutes. PLoS One (2016) 0.91
STELLAR: fast and exact local alignments. BMC Bioinformatics (2011) 0.91
Optimization of extraction of circulating RNAs from plasma--enabling small RNA sequencing. PLoS One (2014) 0.91
Prediction of piRNAs using transposon interaction and a support vector machine. BMC Bioinformatics (2014) 0.91
Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR. RNA (2011) 0.91
Effects of Alu elements on global nucleosome positioning in the human genome. BMC Genomics (2010) 0.91
Discovery of potential prognostic long non-coding RNA biomarkers for predicting the risk of tumor recurrence of breast cancer patients. Sci Rep (2016) 0.91
The oscillating miRNA 959-964 cluster impacts Drosophila feeding time and other circadian outputs. Cell Metab (2012) 0.90
Comprehensive transcriptomic study on horse gram (Macrotyloma uniflorum): De novo assembly, functional characterization and comparative analysis in relation to drought stress. BMC Genomics (2013) 0.89
Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed development and grain filling via a mechanism distinct from Arabidopsis. PLoS Genet (2013) 0.89
BOAT: Basic Oligonucleotide Alignment Tool. BMC Genomics (2009) 0.89
SlideSort: all pairs similarity search for short reads. Bioinformatics (2010) 0.88
Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus. Genome Res (2012) 0.88
Discovery and validation of immune-associated long non-coding RNA biomarkers associated with clinically molecular subtype and prognosis in diffuse large B cell lymphoma. Mol Cancer (2017) 0.88
Protein-coding cis-natural antisense transcripts have high and broad expression in Arabidopsis. Plant Physiol (2013) 0.87
MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads. BMC Genomics (2009) 0.87
Global profiling of stimulus-induced polyadenylation in cells using a poly(A) trap. Nat Chem Biol (2013) 0.87
Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes. BMC Vet Res (2012) 0.86
HSP90α plays an important role in piRNA biogenesis and retrotransposon repression in mouse. Nucleic Acids Res (2014) 0.85
Pyrophosphate-dependent fructose-6-phosphate 1-phosphotransferase induction and attenuation of Hsp gene expression during endosperm modification in quality protein maize. Plant Physiol (2011) 0.85
piRNAs from Pig Testis Provide Evidence for a Conserved Role of the Piwi Pathway in Post-Transcriptional Gene Regulation in Mammals. PLoS One (2015) 0.84
Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome. BMC Genomics (2010) 0.84
Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data. Genes (Basel) (2010) 0.83
Nuclear receptor HNF4α binding sequences are widespread in Alu repeats. BMC Genomics (2011) 0.82
Piwi proteins and piRNAs in mammalian oocytes and early embryos: From sample to sequence. Genom Data (2015) 0.82
Tupaia small RNAs provide insights into function and evolution of RNAi-based transposon defense in mammals. RNA (2015) 0.82
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes. BMC Bioinformatics (2009) 0.82
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics (2008) 39.08
MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA (2008) 5.78
Statistical inferences for isoform expression in RNA-Seq. Bioinformatics (2009) 12.50
Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res (2010) 6.95
dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics (2004) 6.78
Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol (2010) 6.10
MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA (2008) 5.78
TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics (2005) 5.68
Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics (2009) 4.32
Transitive functional annotation by shortest-path analysis of gene expression data. Proc Natl Acad Sci U S A (2002) 3.93
Novel mechanisms of T-cell and dendritic cell activation revealed by profiling of psoriasis on the 63,100-element oligonucleotide array. Physiol Genomics (2003) 3.39
Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol (2006) 3.39
ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res (2003) 3.31
Functional annotation and network reconstruction through cross-platform integration of microarray data. Nat Biotechnol (2005) 3.30
Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS One (2006) 3.03
ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci U S A (2009) 2.96
A gene regulatory network in mouse embryonic stem cells. Proc Natl Acad Sci U S A (2007) 2.94
Exon arrays provide accurate assessments of gene expression. Genome Biol (2007) 2.86
Cross-hybridization modeling on Affymetrix exon arrays. Bioinformatics (2008) 2.54
Improving PacBio long read accuracy by short read alignment. PLoS One (2012) 2.06
Completely phased genome sequencing through chromosome sorting. Proc Natl Acad Sci U S A (2010) 1.96
Assessing the conservation of mammalian gene expression using high-density exon arrays. Mol Biol Evol (2007) 1.81
Six2 and Wnt regulate self-renewal and commitment of nephron progenitors through shared gene regulatory networks. Dev Cell (2012) 1.75
Human transcriptome array for high-throughput clinical studies. Proc Natl Acad Sci U S A (2011) 1.62
Statistical Modeling of RNA-Seq Data. Stat Sci (2011) 1.49
Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci U S A (2013) 1.48
Expression of heat shock proteins and heat shock protein messenger ribonucleic acid in human prostate carcinoma in vitro and in tumors in vivo. Cell Stress Chaperones (2005) 1.41
RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. Genome Res (2012) 1.36
Analysis of factorial time-course microarrays with application to a clinical study of burn injury. Proc Natl Acad Sci U S A (2010) 1.33
Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes. Proc Natl Acad Sci U S A (2002) 1.28
A small-molecule inhibitor of Mps1 blocks the spindle-checkpoint response to a lack of tension on mitotic chromosomes. Curr Biol (2005) 1.26
Computational biology: toward deciphering gene regulatory information in mammalian genomes. Biometrics (2006) 1.16
Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data. BMC Genet (2005) 1.14
Array comparative genome hybridization for tumor classification and gene discovery in mouse models of malignant melanoma. Cancer Res (2003) 1.12
Using CisGenome to analyze ChIP-chip and ChIP-seq data. Curr Protoc Bioinformatics (2011) 1.11
CisGenome Browser: a flexible tool for genomic data visualization. Bioinformatics (2010) 1.10
The analysis of ChIP-Seq data. Methods Enzymol (2011) 1.00
Using high-density exon arrays to profile gene expression in closely related species. Nucleic Acids Res (2009) 0.98
IN02, a positive regulator of lipid biosynthesis, is essential for the formation of inducible membranes in yeast. Mol Biol Cell (2002) 0.96
A study of density of states and ground states in hydrophobic-hydrophilic protein folding models by equi-energy sampling. J Chem Phys (2006) 0.95
A new FACS approach isolates hESC derived endoderm using transcription factors. PLoS One (2011) 0.94
Energy landscape of a spin-glass model: exploration and characterization. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.89
Simultaneous isoform discovery and quantification from RNA-seq. Stat Biosci (2013) 0.86
Integrated analysis of microarray data and gene function information. OMICS (2004) 0.81
A sparse transmission disequilibrium test for haplotypes based on Bradley-Terry graphs. Hum Hered (2012) 0.77
HumanUpstream and MouseUpstream: databases of promoter sequences in the human and mouse genomes. OMICS (2005) 0.75