Published in Bioinformatics on February 10, 2010
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CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res (2010) 1.88
Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med Genomics (2011) 1.84
T cell fate and clonality inference from single-cell transcriptomes. Nat Methods (2016) 1.81
Compression of next-generation sequencing reads aided by highly efficient de novo assembly. Nucleic Acids Res (2012) 1.76
The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification. Nat Cell Biol (2014) 1.76
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An integrative analysis of colon cancer identifies an essential function for PRPF6 in tumor growth. Genes Dev (2014) 1.73
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BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics (2013) 1.64
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Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. Mol Plant Microbe Interact (2012) 1.59
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Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell (2011) 1.53
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The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet (2016) 1.52
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Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol (2013) 1.49
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Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability. Genome Res (2013) 1.47
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Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proc Natl Acad Sci U S A (2011) 1.46
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SMIM1 underlies the Vel blood group and influences red blood cell traits. Nat Genet (2013) 1.41
DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton. PLoS Genet (2016) 1.39
Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. BMC Biol (2017) 1.39
Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia. Genome Res (2014) 1.38
Hybrid Dysgenesis in Drosophila simulans Associated with a Rapid Invasion of the P-Element. PLoS Genet (2016) 1.38
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Loss-of-function mutations in IGSF1 cause an X-linked syndrome of central hypothyroidism and testicular enlargement. Nat Genet (2012) 1.34
PolyCat: a resource for genome categorization of sequencing reads from allopolyploid organisms. G3 (Bethesda) (2013) 1.34
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
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
dbSNP: the NCBI database of genetic variation. Nucleic Acids Res (2001) 76.97
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
SSAHA: a fast search method for large DNA databases. Genome Res (2001) 48.64
SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47
Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics (2008) 39.08
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GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics (2005) 21.04
Eukaryotic cytosine methyltransferases. Annu Rev Biochem (2005) 15.45
SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol (2009) 11.24
Optimal spliced alignments of short sequence reads. Bioinformatics (2008) 9.45
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol (2004) 9.00
Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol (2006) 8.87
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol (2009) 7.59
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Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci U S A (2002) 5.49
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Efficient q-gram filters for finding all epsilon-matches over a given length. J Comput Biol (2006) 4.24
Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res (2009) 4.16
A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res (2008) 4.06
Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet (2004) 3.73
SNP-o-matic. Bioinformatics (2009) 2.28
A conserved non-homeodomain Hoxa9 isoform interacting with CBP is co-expressed with the 'typical' Hoxa9 protein during embryogenesis. Gene Expr Patterns (2004) 1.52
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