Published in Bioinformatics on October 30, 2008
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform (2010) 18.05
Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res (2010) 2.84
Simultaneous alignment of short reads against multiple genomes. Genome Biol (2009) 2.79
Rapid genomic characterization of the genus vitis. PLoS One (2010) 2.04
Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. PLoS Comput Biol (2012) 1.93
Fast and accurate read alignment for resequencing. Bioinformatics (2012) 1.58
Benchmarking short sequence mapping tools. BMC Bioinformatics (2013) 1.48
Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. Sci Rep (2011) 1.25
Single-feature polymorphism discovery by computing probe affinity shape powers. BMC Genet (2009) 0.91
Bioinformatics for next generation sequencing data. Genes (Basel) (2010) 0.91
Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern. BMC Genomics (2010) 0.85
High Performance Multiple Sequence Alignment System for Pyrosequencing Reads from Multiple Reference Genomes. J Parallel Distrib Comput (2011) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45
Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics (2008) 39.08
Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics (2005) 24.54
Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res (2002) 17.31
Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res (2008) 10.49
The new paradigm of flow cell sequencing. Genome Res (2008) 5.81
High-throughput sequence alignment using Graphics Processing Units. BMC Bioinformatics (2007) 5.56
MPBLAST : improved BLAST performance with multiplexed queries. Bioinformatics (2000) 3.18
ABySS: a parallel assembler for short read sequence data. Genome Res (2009) 43.20
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
Assembling millions of short DNA sequences using SSAKE. Bioinformatics (2006) 18.71
The Genome sequence of the SARS-associated coronavirus. Science (2003) 16.68
ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med (2010) 13.07
Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature (2010) 9.81
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature (2011) 9.71
De novo assembly and analysis of RNA-seq data. Nat Methods (2010) 9.69
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
De novo transcriptome assembly with ABySS. Bioinformatics (2009) 8.38
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med (2011) 7.35
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics (2010) 6.57
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics (2008) 6.53
The new paradigm of flow cell sequencing. Genome Res (2008) 5.81
Alternative expression analysis by RNA sequencing. Nat Methods (2010) 5.02
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science (2005) 4.74
The genetic landscape of high-risk neuroblastoma. Nat Genet (2013) 4.71
PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res (2003) 4.25
The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A (2006) 4.18
Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature (2012) 4.13
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res (2008) 4.11
Sequence biases in large scale gene expression profiling data. Nucleic Acids Res (2006) 3.83
ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res (2007) 3.80
Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Hum Genet (2006) 3.29
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics (2006) 2.98
High quality SNP calling using Illumina data at shallow coverage. Bioinformatics (2010) 2.82
Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res (2006) 2.82
Systematic sequencing of cDNA clones using the transposon Tn5. Nucleic Acids Res (2002) 2.78
Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res (2004) 2.72
Hive plots--rational approach to visualizing networks. Brief Bioinform (2011) 2.46
A SAGE approach to discovery of genes involved in autophagic cell death. Curr Biol (2003) 2.40
A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci U S A (2005) 2.35
An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones. Nucleic Acids Res (2002) 2.27
Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses. Genomics (2005) 2.27
Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers. J Pathol (2011) 2.27
Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers. N Engl J Med (2011) 2.25
The completion of the Mammalian Gene Collection (MGC). Genome Res (2009) 2.21
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics (2013) 2.18
Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers. J Clin Oncol (2006) 2.11
Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol (2010) 2.06
A physical map of the genome of Atlantic salmon, Salmo salar. Genomics (2005) 2.03
The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol (2006) 2.00
Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Res (2005) 1.93
Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. Genome Res (2010) 1.90
A regulatory toolbox of MiniPromoters to drive selective expression in the brain. Proc Natl Acad Sci U S A (2010) 1.85
Sockeye: a 3D environment for comparative genomics. Genome Res (2004) 1.80
Bromodomain-containing protein 4 (BRD4) regulates RNA polymerase II serine 2 phosphorylation in human CD4+ T cells. J Biol Chem (2012) 1.76
Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. Genome Res (2002) 1.72
Meta-analysis of colorectal cancer gene expression profiling studies identifies consistently reported candidate biomarkers. Cancer Epidemiol Biomarkers Prev (2008) 1.72
Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Res (2005) 1.71
ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult. Dev Biol (2008) 1.55
A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics (2008) 1.55
Assessment of SAGE in transcript identification. Genome Res (2003) 1.52
14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma. Proc Natl Acad Sci U S A (2012) 1.51
An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans. PLoS Genet (2009) 1.50
Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc Natl Acad Sci U S A (2011) 1.50
AcePrimer: automation of PCR primer design based on gene structure. Bioinformatics (2002) 1.48
Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genome Biol (2013) 1.46
Mutations in EZH2 cause Weaver syndrome. Am J Hum Genet (2011) 1.46
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res (2010) 1.45
Iron-regulated transcription and capsule formation in the fungal pathogen Cryptococcus neoformans. Mol Microbiol (2005) 1.40
Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags. BMC Biol (2008) 1.39
Aberrant patterns of H3K4 and H3K27 histone lysine methylation occur across subgroups in medulloblastoma. Acta Neuropathol (2012) 1.33
Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res (2006) 1.31
Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome. BMC Genomics (2010) 1.30
Systematic recovery and analysis of full-ORF human cDNA clones. Genome Res (2004) 1.28
Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res (2002) 1.27
Text-mining assisted regulatory annotation. Genome Biol (2008) 1.26
Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries. BMC Genomics (2009) 1.24
ALEXA: a microarray design platform for alternative expression analysis. Nat Methods (2008) 1.23
Identification and analysis of internal promoters in Caenorhabditis elegans operons. Genome Res (2007) 1.21
A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant J (2007) 1.20
SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour (2011) 1.18
Software for automated analysis of DNA fingerprinting gels. Genome Res (2003) 1.18
Optimally discriminative subnetwork markers predict response to chemotherapy. Bioinformatics (2011) 1.17
A computational approach to finding novel targets for existing drugs. PLoS Comput Biol (2011) 1.17
Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans. Genome Res (2002) 1.16
Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics (2008) 1.14
A survey of genomic properties for the detection of regulatory polymorphisms. PLoS Comput Biol (2007) 1.14
Diagnostic utility of galectin-3 in thyroid cancer. Am J Pathol (2010) 1.14
Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests. Insect Biochem Mol Biol (2012) 1.13
Inferring cancer subnetwork markers using density-constrained biclustering. Bioinformatics (2010) 1.13
Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing. J Endocrinol (2009) 1.13
Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1. J Bacteriol (2004) 1.12
Recurrent targets of aberrant somatic hypermutation in lymphoma. Oncotarget (2012) 1.11
Physical map-assisted whole-genome shotgun sequence assemblies. Genome Res (2006) 1.10
Spark: a navigational paradigm for genomic data exploration. Genome Res (2012) 1.10