Published in Biotechniques on July 01, 2008
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Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science (2008) 36.02
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics (2011) 25.76
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature (2009) 18.08
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Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics (2011) 2.84
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A comparison of single molecule and amplification based sequencing of cancer transcriptomes. PLoS One (2011) 1.44
Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PLoS Comput Biol (2010) 1.33
A novel SND1-BRAF fusion confers resistance to c-Met inhibitor PF-04217903 in GTL16 cells through [corrected] MAPK activation. PLoS One (2012) 1.30
Characterization of the Conus bullatus genome and its venom-duct transcriptome. BMC Genomics (2011) 1.29
RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics (2011) 1.27
BCL6 repression of EP300 in human diffuse large B cell lymphoma cells provides a basis for rational combinatorial therapy. J Clin Invest (2010) 1.26
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
Dark Matter RNA: Existence, Function, and Controversy. Front Genet (2012) 1.18
Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors. Cancer Cell (2015) 1.18
Single-molecule mRNA detection and counting in mammalian tissue. Nat Protoc (2013) 1.18
Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct. BMC Genomics (2012) 1.16
Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21. PLoS One (2011) 1.15
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Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies. Nucleic Acids Res (2010) 1.13
Our changing view of the genomic landscape of cancer. J Pathol (2010) 1.13
A comparative study of techniques for differential expression analysis on RNA-Seq data. PLoS One (2014) 1.12
Targeted assembly of short sequence reads. PLoS One (2011) 1.12
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The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44. PLoS One (2011) 1.08
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Whole transcriptome profiling of successful immune response to Vibrio infections in the oyster Crassostrea gigas by digital gene expression analysis. PLoS One (2011) 1.04
Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. Genome Res (2010) 1.01
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RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications. BMC Plant Biol (2014) 0.92
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STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma. G3 (Bethesda) (2013) 0.91
Pharmacogene regulatory elements: from discovery to applications. Genome Med (2012) 0.91
The transcriptome profile of the mosquito Culex quinquefasciatus following permethrin selection. PLoS One (2012) 0.90
Epigenetic and transcriptional determinants of the human breast. Nat Commun (2015) 0.89
iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data. Nucleic Acids Res (2015) 0.88
Deep SAGE analysis of the Caenorhabditis elegans transcriptome. Nucleic Acids Res (2010) 0.88
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A fast and accurate SNP detection algorithm for next-generation sequencing data. Nat Commun (2012) 0.86
GLI2 inhibition abrogates human leukemia stem cell dormancy. J Transl Med (2015) 0.86
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Mutation spectrum in human colorectal cancers and potential functional relevance. BMC Med Genet (2013) 0.85
Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis. Viruses (2013) 0.85
Comprehensive genomic studies: emerging regulatory, strategic, and quality assurance challenges for biorepositories. Am J Clin Pathol (2012) 0.84
Transcriptome profiling of fruit development and maturation in Chinese white pear (Pyrus bretschneideri Rehd). BMC Genomics (2013) 0.84
Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches. BMC Bioinformatics (2016) 0.84
Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity. Nucleic Acids Res (2009) 0.84
Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling. Curr Genomics (2013) 0.84
Integrative systems biology for data-driven knowledge discovery. Semin Nephrol (2010) 0.84
Next generation DNA sequencing and the future of genomic medicine. Genes (Basel) (2010) 0.84
Comprehensive molecular screening: from the RT-PCR to the RNA-seq. Transl Lung Cancer Res (2013) 0.83
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
International network of cancer genome projects. Nature (2010) 20.35
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Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature (2009) 18.08
The Genome sequence of the SARS-associated coronavirus. Science (2003) 16.68
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med (2010) 13.57
ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med (2010) 13.07
The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature (2012) 11.91
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet (2010) 10.97
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res (2008) 10.18
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 genome of the kinetoplastid parasite, Leishmania major. Science (2005) 8.64
De novo transcriptome assembly with ABySS. Bioinformatics (2009) 8.38
Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med (2011) 7.35
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics (2008) 6.53
Next-generation tag sequencing for cancer gene expression profiling. Genome Res (2009) 6.50
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Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
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The genetic landscape of high-risk neuroblastoma. Nat Genet (2013) 4.71
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol (2011) 4.66
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Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell (2012) 4.41
ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner. Cell (2010) 4.34
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Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res (2008) 4.11
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Identification of miR-145 and miR-146a as mediators of the 5q- syndrome phenotype. Nat Med (2009) 4.03
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics (2010) 4.02
Transcriptome analysis of the normal human mammary cell commitment and differentiation process. Cell Stem Cell (2008) 3.87
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res (2009) 3.83
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In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res (2008) 3.55
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JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics (2012) 3.21
SKPs derive from hair follicle precursors and exhibit properties of adult dermal stem cells. Cell Stem Cell (2009) 3.20
DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell (2011) 3.10
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