Published in Bioinformatics on August 06, 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
Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (2010) 52.01
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
SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol (2009) 11.24
Assembly algorithms for next-generation sequencing data. Genomics (2010) 8.56
Annotating genomes with massive-scale RNA sequencing. Genome Biol (2008) 7.73
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
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Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol (2009) 4.24
Updates to the RMAP short-read mapping software. Bioinformatics (2009) 3.18
RNA-seq: from technology to biology. Cell Mol Life Sci (2009) 3.03
Simultaneous alignment of short reads against multiple genomes. Genome Biol (2009) 2.79
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Genomic location analysis by ChIP-Seq. J Cell Biochem (2009) 2.44
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
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MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One (2014) 2.12
Expression of distinct RNAs from 3' untranslated regions. Nucleic Acids Res (2010) 2.08
Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat Struct Mol Biol (2010) 1.69
ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. PLoS Biol (2009) 1.61
Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics. J Pathol Inform (2012) 1.58
Benchmarking short sequence mapping tools. BMC Bioinformatics (2013) 1.48
Hobbes: optimized gram-based methods for efficient read alignment. Nucleic Acids Res (2011) 1.44
Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host. PLoS One (2011) 1.34
Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Res (2010) 1.32
Data structures and compression algorithms for high-throughput sequencing technologies. BMC Bioinformatics (2010) 1.31
Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. Sci Rep (2011) 1.25
SEED: efficient clustering of next-generation sequences. Bioinformatics (2011) 1.14
Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins. RNA (2011) 1.13
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. Nucleic Acids Res (2014) 1.06
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Next generation sequence analysis and computational genomics using graphical pipeline workflows. Genes (Basel) (2012) 0.97
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Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects. Sci Rep (2013) 0.95
A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells. RNA (2010) 0.92
ZOOM Lite: next-generation sequencing data mapping and visualization software. Nucleic Acids Res (2010) 0.92
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VARiD: a variation detection framework for color-space and letter-space platforms. Bioinformatics (2010) 0.86
Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data. Genes (Basel) (2010) 0.83
An empirical study of choosing efficient discriminative seeds for oligonucleotide design. BMC Genomics (2009) 0.82
A hybrid short read mapping accelerator. BMC Bioinformatics (2013) 0.81
Evaluation and comparison of multiple aligners for next-generation sequencing data analysis. Biomed Res Int (2014) 0.80
Correlating measurements across samples improves accuracy of large-scale expression profile experiments. Genome Biol (2009) 0.80
Deep sequencing of target linkage assay-identified regions in familial breast cancer: methods, analysis pipeline and troubleshooting. PLoS One (2010) 0.80
A coverage criterion for spaced seeds and its applications to support vector machine string kernels and k-mer distances. J Comput Biol (2014) 0.79
Designing Efficient Spaced Seeds for SOLiD Read Mapping. Adv Bioinformatics (2010) 0.79
BatAlign: an incremental method for accurate alignment of sequencing reads. Nucleic Acids Res (2015) 0.78
Detecting and comparing non-coding RNAs in the high-throughput era. Int J Mol Sci (2013) 0.78
High throughput sequencing approaches to mutation discovery in the mouse. Mamm Genome (2012) 0.76
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Plant noncoding RNA gene discovery by "single-genome comparative genomics". RNA (2011) 0.76
CHOPER filters enable rare mutation detection in complex mutagenesis populations by next-generation sequencing. PLoS One (2015) 0.75
High Performance Multiple Sequence Alignment System for Pyrosequencing Reads from Multiple Reference Genomes. J Parallel Distrib Comput (2011) 0.75
SAP--a sequence mapping and analyzing program for long sequence reads alignment and accurate variants discovery. PLoS One (2012) 0.75
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Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species. BMC Genomics (2016) 0.75
Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. J Immunol (2017) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Rapid and sensitive protein similarity searches. Science (1985) 76.83
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics (2008) 39.08
PatternHunter: faster and more sensitive homology search. Bioinformatics (2002) 35.65
Whole-genome re-sequencing. Curr Opin Genet Dev (2006) 35.24
Accurate multiplex polony sequencing of an evolved bacterial genome. Science (2005) 20.91
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
Genome-wide in situ exon capture for selective resequencing. Nat Genet (2007) 19.97
Complete MHC haplotype sequencing for common disease gene mapping. Genome Res (2004) 12.09
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods (2005) 7.87
Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods (2008) 6.22
Finding motifs using random projections. J Comput Biol (2002) 4.61
Patternhunter II: highly sensitive and fast homology search. J Bioinform Comput Biol (2004) 4.24
Multiseed lossless filtration. IEEE/ACM Trans Comput Biol Bioinform (2006) 3.01
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics (2008) 39.08
PatternHunter: faster and more sensitive homology search. Bioinformatics (2002) 35.65
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66
ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res (2003) 12.81
Epidermal electronics. Science (2011) 8.65
Effect of PCI on quality of life in patients with stable coronary disease. N Engl J Med (2008) 7.75
The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev (2002) 7.61
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc Natl Acad Sci U S A (2003) 7.30
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. Dev Cell (2003) 6.86
Regulating gene expression through RNA nuclear retention. Cell (2005) 5.58
Histone hypercitrullination mediates chromatin decondensation and neutrophil extracellular trap formation. J Cell Biol (2009) 5.27
Trends in cardiovascular health metrics and associations with all-cause and CVD mortality among US adults. JAMA (2012) 5.17
Network-based global inference of human disease genes. Mol Syst Biol (2008) 5.01
PAD4 is essential for antibacterial innate immunity mediated by neutrophil extracellular traps. J Exp Med (2010) 4.74
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom (2003) 4.56
An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet (2006) 4.56
An immunosurveillance mechanism controls cancer cell ploidy. Science (2012) 4.35
Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev (2008) 4.24
Patternhunter II: highly sensitive and fast homology search. J Bioinform Comput Biol (2004) 4.24
Critical roles for Dicer in the female germline. Genes Dev (2007) 4.23
Large-scale structure of genomic methylation patterns. Genome Res (2005) 4.11
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol (2013) 4.04
Human infection with avian influenza A H7N9 virus: an assessment of clinical severity. Lancet (2013) 3.90
Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell (2013) 3.81
APOBEC3 proteins mediate the clearance of foreign DNA from human cells. Nat Struct Mol Biol (2010) 3.61
Paternally inherited inactivating mutations of the GNAS1 gene in progressive osseous heteroplasia. N Engl J Med (2002) 3.31
Mental health system in China: history, recent service reform and future challenges. World Psychiatry (2011) 3.23
The dominant role of CD8+ dendritic cells in cross-presentation is not dictated by antigen capture. Proc Natl Acad Sci U S A (2006) 3.19
Updates to the RMAP short-read mapping software. Bioinformatics (2009) 3.18
A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J (2010) 3.18
High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res (2009) 3.08
Direct coupling of the cell cycle and cell death machinery by E2F. Nat Cell Biol (2002) 3.00
Cost-effectiveness of eplerenone compared with placebo in patients with myocardial infarction complicated by left ventricular dysfunction and heart failure. Circulation (2005) 2.85
DNACompress: fast and effective DNA sequence compression. Bioinformatics (2002) 2.82
Novel Foxo1-dependent transcriptional programs control T(reg) cell function. Nature (2012) 2.77
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res (2005) 2.73
Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection. Nature (2011) 2.71
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Res (2009) 2.69
Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics (2004) 2.51
Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res (2003) 2.50
A glimpse of streptococcal toxic shock syndrome from comparative genomics of S. suis 2 Chinese isolates. PLoS One (2007) 2.47
Open mesh techniques for inguinal hernia repair: a meta-analysis of randomized controlled trials. Ann Surg (2009) 2.44
Th17 and natural Treg cell population dynamics in systemic lupus erythematosus. Arthritis Rheum (2009) 2.43
Discovering patterns to extract protein-protein interactions from full texts. Bioinformatics (2004) 2.42
Molecular censusing doubles giant panda population estimate in a key nature reserve. Curr Biol (2006) 2.39
DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A (2006) 2.38
NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res (2013) 2.37
PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification. Mol Cell Proteomics (2011) 2.37
Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci U S A (2005) 2.36
Sodium and potassium intakes among US adults: NHANES 2003-2008. Am J Clin Nutr (2012) 2.32
Host immunity contributes to the anti-melanoma activity of BRAF inhibitors. J Clin Invest (2013) 2.30
RAPTOR: optimal protein threading by linear programming. J Bioinform Comput Biol (2003) 2.27
Regulation of p53 target gene expression by peptidylarginine deiminase 4. Mol Cell Biol (2008) 2.27
PatternHunter II: highly sensitive and fast homology search. Genome Inform (2003) 2.26
Waterproof AlInGaP optoelectronics on stretchable substrates with applications in biomedicine and robotics. Nat Mater (2010) 2.20
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res (2007) 2.16
Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol (2004) 2.12
Interacting models of cooperative gene regulation. Proc Natl Acad Sci U S A (2004) 2.09
"Nerve combing" for trigeminal neuralgia without vascular compression: report of 10 cases. Clin J Pain (2009) 2.01
From dopamine to salience to psychosis--linking biology, pharmacology and phenomenology of psychosis. Schizophr Res (2005) 2.00
Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res (2006) 2.00
Global impact of oncogenic Src on a phosphotyrosine proteome. J Proteome Res (2008) 1.94
High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res (2008) 1.88
Human IgG2 antibodies display disulfide-mediated structural isoforms. J Biol Chem (2008) 1.88
Cell-type-based analysis of microRNA profiles in the mouse brain. Neuron (2012) 1.85
Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A (2006) 1.83
Patient health status and costs in heart failure: insights from the eplerenone post-acute myocardial infarction heart failure efficacy and survival study (EPHESUS). Circulation (2009) 1.82
Pro12Ala polymorphism in the PPARG gene contributes to the development of diabetic nephropathy in Chinese type 2 diabetic patients. Diabetes Care (2009) 1.82
SPIDER: software for protein identification from sequence tags with de novo sequencing error. J Bioinform Comput Biol (2005) 1.81
Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics (2005) 1.81
Adaptively inferring human transcriptional subnetworks. Mol Syst Biol (2006) 1.81
Increasing fluoroquinolone resistance in Campylobacter jejuni, Pennsylvania, USA,1982-2001. Emerg Infect Dis (2002) 1.81
Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics (2009) 1.80
L-4F treatment reduces adiposity, increases adiponectin levels, and improves insulin sensitivity in obese mice. J Lipid Res (2008) 1.80
A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy. Nat Genet (2011) 1.77
Dynamically tunable hemispherical electronic eye camera system with adjustable zoom capability. Proc Natl Acad Sci U S A (2011) 1.74
Sodium intake and blood pressure among US children and adolescents. Pediatrics (2012) 1.72
Increased frequency of circulating follicular helper T cells in patients with rheumatoid arthritis. Clin Dev Immunol (2012) 1.70
Extracorporeal high intensity focused ultrasound ablation in the treatment of 1038 patients with solid carcinomas in China: an overview. Ultrason Sonochem (2004) 1.70
Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res (2005) 1.70
Conformation of the AcrB multidrug efflux pump in mutants of the putative proton relay pathway. J Bacteriol (2006) 1.66
Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol Cell Proteomics (2009) 1.66
Cav3.1 (alpha1G) T-type Ca2+ channels mediate vaso-occlusion of sickled erythrocytes in lung microcirculation. Circ Res (2003) 1.66
Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces. Structure (2010) 1.65
Hospitalization costs associated with hypertension as a secondary diagnosis among insured patients aged 18-64 years. Am J Hypertens (2009) 1.64
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics (2013) 1.64
Liquid chromatography-tandem mass spectrometric method for the analysis of fluconazole and evaluation of the impact of phenolic compounds on the concentration of fluconazole in Candida albicans. J Pharm Biomed Anal (2004) 1.64
RN181 suppresses hepatocellular carcinoma growth by inhibition of the ERK/MAPK pathway. Hepatology (2011) 1.64
Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biol (2005) 1.64
Surgery for patients with Marfan syndrome with type A dissection involving the aortic arch using total arch replacement combined with stented elephant trunk implantation: the acute versus the chronic. J Thorac Cardiovasc Surg (2011) 1.62