Published in BMC Bioinformatics on March 15, 2010
De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat Genet (2012) 5.61
ConDeTri--a content dependent read trimmer for Illumina data. PLoS One (2011) 2.78
Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proc Natl Acad Sci U S A (2011) 1.99
Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics (2011) 1.88
Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers. Nat Biotechnol (2013) 1.43
Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data. PLoS One (2013) 1.19
Co-phylog: an assembly-free phylogenomic approach for closely related organisms. Nucleic Acids Res (2013) 0.97
Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate. BMC Genomics (2010) 0.96
SNP discovery using Next Generation Transcriptomic Sequencing in Atlantic herring (Clupea harengus). PLoS One (2012) 0.95
Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar. Proc Natl Acad Sci U S A (2013) 0.85
Brain transcriptome of the violet-eared waxbill Uraeginthus granatina and recent evolution in the songbird genome. Open Biol (2013) 0.81
Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms. BMC Genomics (2012) 0.81
Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum). BMC Plant Biol (2011) 0.81
Next generation quantitative genetics in plants. Front Plant Sci (2011) 0.79
Reference-free comparative genomics of 174 chloroplasts. PLoS One (2012) 0.78
Reliable in silico identification of sequence polymorphisms and their application for extending the genetic map of sugar beet (Beta vulgaris). PLoS One (2014) 0.77
4Pipe4 - A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information. BMC Bioinformatics (2016) 0.75
SNP Mining in Functional Genes from Nonmodel Species by Next-Generation Sequencing: A Case of Flowering, Pre-Harvest Sprouting, and Dehydration Resistant Genes in Wheat. Biomed Res Int (2016) 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
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Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
Human-mouse alignments with BLASTZ. Genome Res (2003) 35.49
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature (2000) 19.19
Direct selection of human genomic loci by microarray hybridization. Nat Methods (2007) 17.73
SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol (2009) 11.24
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods (2008) 8.26
The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res (2009) 7.87
WindowMasker: window-based masker for sequenced genomes. Bioinformatics (2005) 5.91
Gene-boosted assembly of a novel bacterial genome from very short reads. PLoS Comput Biol (2008) 2.04
SNP discovery in swine by reduced representation and high throughput pyrosequencing. BMC Genet (2008) 1.92
Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey. BMC Genomics (2009) 1.31
Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome. BMC Genomics (2009) 1.29
Selection for heterozygosity gives hope to a wild population of inbred wolves. PLoS One (2006) 1.29
Reduced heterozygosity impairs sperm quality in endangered mammals. Biol Lett (2009) 1.02
Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species. Pac Symp Biocomput (2010) 0.93
Wildlife biology. A devil of a disease. Science (2005) 0.82
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
Galaxy: a platform for interactive large-scale genome analysis. Genome Res (2005) 35.75
Human-mouse alignments with BLASTZ. Genome Res (2003) 35.49
MEGAN analysis of metagenomic data. Genome Res (2007) 25.29
Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res (2004) 24.52
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A (2003) 16.58
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Fever with thrombocytopenia associated with a novel bunyavirus in China. N Engl J Med (2011) 13.18
Prepublication data sharing. Nature (2009) 12.24
The developmental transcriptome of Drosophila melanogaster. Nature (2010) 11.85
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res (2003) 11.12
Diverse somatic mutation patterns and pathway alterations in human cancers. Nature (2010) 10.83
Complete Khoisan and Bantu genomes from southern Africa. Nature (2010) 9.06
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature (2007) 8.68
Nucleosome organization in the Drosophila genome. Nature (2008) 8.65
Integrative analysis of environmental sequences using MEGAN4. Genome Res (2011) 8.60
The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) 8.52
Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science (2005) 8.14
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res (2008) 7.89
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res (2005) 7.09
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Ancestral polyploidy in seed plants and angiosperms. Nature (2011) 7.00
Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol (2006) 6.73
Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A (2008) 6.50
A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res (2007) 5.97
Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74
Distinguishing regulatory DNA from neutral sites. Genome Res (2003) 5.63
Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol (2005) 5.32
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res (2003) 4.97
Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res (2006) 4.70
Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PLoS Genet (2006) 4.65
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One (2008) 4.54
Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res (2007) 4.52
Sequence and analysis of rice chromosome 4. Nature (2002) 4.39
An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. Proc Natl Acad Sci U S A (2005) 4.38
Sequencing the nuclear genome of the extinct woolly mammoth. Nature (2008) 4.31
zPicture: dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res (2004) 4.26
Abnormal spine morphology and enhanced LTP in LIMK-1 knockout mice. Neuron (2002) 4.18
OSLay: optimal syntenic layout of unfinished assemblies. Bioinformatics (2007) 4.10
iPS cells can support full-term development of tetraploid blastocyst-complemented embryos. Cell Stem Cell (2009) 4.04
A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science (2004) 3.87
Comparative and demographic analysis of orang-utan genomes. Nature (2011) 3.83
Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell (2011) 3.81
Reconstructing contiguous regions of an ancestral genome. Genome Res (2006) 3.68
HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server. Hum Mutat (2002) 3.65
Synthetic spike-in standards for RNA-seq experiments. Genome Res (2011) 3.58
Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Res (2004) 3.53
Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet (2003) 3.52
The genome of Theobroma cacao. Nat Genet (2010) 3.47
LSD1 is a subunit of the NuRD complex and targets the metastasis programs in breast cancer. Cell (2009) 3.34
Phase I and correlative biology study of cilengitide in patients with recurrent malignant glioma. J Clin Oncol (2007) 3.29
Label-free oxygen-metabolic photoacoustic microscopy in vivo. J Biomed Opt (2011) 3.16
Mammalian target of rapamycin up-regulation of pyruvate kinase isoenzyme type M2 is critical for aerobic glycolysis and tumor growth. Proc Natl Acad Sci U S A (2011) 3.14
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol (2005) 3.12
Mutations in cadherin 23 affect tip links in zebrafish sensory hair cells. Nature (2004) 3.02
The molecular mechanism governing the oncogenic potential of SOX2 in breast cancer. J Biol Chem (2008) 3.01
Evolution and functional classification of vertebrate gene deserts. Genome Res (2004) 2.92
Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Res (2004) 2.91
Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science (2007) 2.85
Demasculinization of X chromosomes in the Drosophila genus. Nature (2007) 2.85
The structure and evolution of centromeric transition regions within the human genome. Nature (2004) 2.78
A comparative study of platelet-rich fibrin (PRF) and platelet-rich plasma (PRP) on the effect of proliferation and differentiation of rat osteoblasts in vitro. Oral Surg Oral Med Oral Pathol Oral Radiol Endod (2009) 2.67
ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Res (2006) 2.65
Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol Microbiol (2003) 2.65
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res (2009) 2.64
Intrinsic peroxidase-like activity of ferromagnetic nanoparticles. Nat Nanotechnol (2007) 2.61
Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics (2009) 2.60
CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics (2008) 2.58
Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc Natl Acad Sci U S A (2010) 2.57
GALA, a database for genomic sequence alignments and annotations. Genome Res (2003) 2.56
Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci U S A (2008) 2.56
HDAC6 controls major cell response pathways to cytotoxic accumulation of protein aggregates. Genes Dev (2007) 2.56
Ecology. Importing timber, exporting ecological impact. Science (2005) 2.54
HDAC6-p97/VCP controlled polyubiquitin chain turnover. EMBO J (2006) 2.52
Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach. Nat Genet (2011) 2.51
The deacetylase HDAC6 is a novel critical component of stress granules involved in the stress response. Genes Dev (2007) 2.43
Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol (2007) 2.43
Rapid induction and long-term self-renewal of primitive neural precursors from human embryonic stem cells by small molecule inhibitors. Proc Natl Acad Sci U S A (2011) 2.39
Evolution of protein-coding genes in Drosophila. Trends Genet (2008) 2.36
The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. Plant Cell (2002) 2.36
COP1 and ELF3 control circadian function and photoperiodic flowering by regulating GI stability. Mol Cell (2008) 2.34
Mechanisms of programmed DNA lesions and genomic instability in the immune system. Cell (2013) 2.32
The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Res (2009) 2.30
Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature (2005) 2.27
Whole-genome prokaryotic phylogeny. Bioinformatics (2004) 2.26
Molecular and genomic data identify the closest living relative of primates. Science (2007) 2.26
Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies. Nucleic Acids Res (2004) 2.24
HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update. Hum Mutat (2007) 2.22