Published in Bioinformatics on January 28, 2008
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 97.51
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (2010) 52.01
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics (2008) 24.32
CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics (2009) 20.45
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
Computation for ChIP-seq and RNA-seq studies. Nat Methods (2009) 16.11
SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. Bioinformatics (2009) 13.34
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol (2009) 11.24
Searching for SNPs with cloud computing. Genome Biol (2009) 10.12
Assembly algorithms for next-generation sequencing data. Genomics (2010) 8.56
AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res Notes (2012) 7.94
Annotating genomes with massive-scale RNA sequencing. Genome Biol (2008) 7.73
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol (2009) 7.59
BFAST: an alignment tool for large scale genome resequencing. PLoS One (2009) 7.48
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
RazerS--fast read mapping with sensitivity control. Genome Res (2009) 6.53
Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell (2012) 6.50
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics (2012) 6.16
From RNA-seq reads to differential expression results. Genome Biol (2010) 5.77
BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics (2009) 5.67
Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol (2009) 5.64
De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat Genet (2012) 5.61
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
The MaSuRCA genome assembler. Bioinformatics (2013) 5.07
High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet (2008) 4.86
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics (2010) 4.66
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res (2009) 4.47
Sense from sequence reads: methods for alignment and assembly. Nat Methods (2009) 4.44
The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol (2010) 4.25
Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol (2009) 4.24
High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism. PLoS Pathog (2011) 4.10
Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet (2010) 4.06
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics (2010) 4.02
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med (2013) 3.90
Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet (2010) 3.89
Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics (2009) 3.87
Structure and complexity of a bacterial transcriptome. J Bacteriol (2009) 3.55
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res (2008) 3.41
Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung. Proc Natl Acad Sci U S A (2009) 3.35
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res (2010) 3.34
De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics (2010) 3.32
Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol (2009) 3.30
Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature (2014) 3.24
Updates to the RMAP short-read mapping software. Bioinformatics (2009) 3.18
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods (2009) 3.16
Metagenomic analysis of fever, thrombocytopenia and leukopenia syndrome (FTLS) in Henan Province, China: discovery of a new bunyavirus. PLoS Pathog (2011) 2.95
Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nat Genet (2014) 2.84
Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development. Genome Biol (2009) 2.81
Identification of PRRT2 as the causative gene of paroxysmal kinesigenic dyskinesias. Brain (2011) 2.80
Simultaneous alignment of short reads against multiple genomes. Genome Biol (2009) 2.79
DNA methylome analysis using short bisulfite sequencing data. Nat Methods (2012) 2.77
RNA sequencing shows no dosage compensation of the active X-chromosome. Nat Genet (2010) 2.71
A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics (2009) 2.70
LookSeq: a browser-based viewer for deep sequencing data. Genome Res (2009) 2.70
Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (2009) 2.68
Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet (2010) 2.61
Cross-hybridization modeling on Affymetrix exon arrays. Bioinformatics (2008) 2.54
Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biol (2009) 2.54
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications. Bioinformatics (2008) 2.49
Genomic location analysis by ChIP-Seq. J Cell Biochem (2009) 2.44
Metagenomics - a guide from sampling to data analysis. Microb Inform Exp (2012) 2.42
The impact of next-generation sequencing on genomics. J Genet Genomics (2011) 2.41
Analysis of next-generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet (2010) 2.39
Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell (2009) 2.39
Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38
Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol (2010) 2.32
Population genetic inference from genomic sequence variation. Genome Res (2010) 2.29
SNP-o-matic. Bioinformatics (2009) 2.28
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res (2009) 2.27
Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet (2010) 2.25
Keeping up with the next generation: massively parallel sequencing in clinical diagnostics. J Mol Diagn (2008) 2.24
miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics (2009) 2.22
High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics (2008) 2.21
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics (2009) 2.20
Rho and NusG suppress pervasive antisense transcription in Escherichia coli. Genes Dev (2012) 2.13
A heterozygous moth genome provides insights into herbivory and detoxification. Nat Genet (2013) 2.13
MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One (2014) 2.12
De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics (2012) 2.11
Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics (2014) 2.07
Design of association studies with pooled or un-pooled next-generation sequencing data. Genet Epidemiol (2010) 2.06
inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics (2009) 2.06
Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol (2010) 2.03
A viral satellite RNA induces yellow symptoms on tobacco by targeting a gene involved in chlorophyll biosynthesis using the RNA silencing machinery. PLoS Pathog (2011) 1.98
Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA (2009) 1.97
Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.). BMC Genomics (2010) 1.96
Local alignment of two-base encoded DNA sequence. BMC Bioinformatics (2009) 1.94
Origins and functional evolution of Y chromosomes across mammals. Nature (2014) 1.89
SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Nucleic Acids Res (2009) 1.88
Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res (2010) 1.87
Classification of DNA sequences using Bloom filters. Bioinformatics (2010) 1.87
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47
Enterotypes of the human gut microbiome. Nature (2011) 24.36
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94
Genome sequence and analysis of the tuber crop potato. Nature (2011) 7.77
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition. Cancer Res (2008) 7.45
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med (2011) 7.11
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63
A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62
Aberrant excitatory neuronal activity and compensatory remodeling of inhibitory hippocampal circuits in mouse models of Alzheimer's disease. Neuron (2007) 6.60
Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet (2011) 5.73
Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 5.62
Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58
Building the sequence map of the human pan-genome. Nat Biotechnol (2009) 5.53
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet (2010) 5.20
Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Hippo pathway inhibits Wnt signaling to restrain cardiomyocyte proliferation and heart size. Science (2011) 4.76
Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ (2011) 4.50
Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A (2012) 4.26
The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol (2010) 4.25
Regression of castrate-recurrent prostate cancer by a small-molecule inhibitor of the amino-terminus domain of the androgen receptor. Cancer Cell (2010) 4.16
KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics (2006) 4.15
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Dynamic T cell migration program provides resident memory within intestinal epithelium. J Exp Med (2010) 4.09
Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet (2012) 4.07
Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet (2010) 4.06
Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell (2012) 4.03