Published in Proc Natl Acad Sci U S A on January 30, 2009
RNA sequencing: advances, challenges and opportunities. Nat Rev Genet (2010) 8.96
Integrative analysis of the melanoma transcriptome. Genome Res (2010) 8.46
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol (2011) 6.23
Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics (2012) 4.95
Understanding the language of Lys36 methylation at histone H3. Nat Rev Mol Cell Biol (2012) 3.52
RNA-seq: from technology to biology. Cell Mol Life Sci (2009) 3.03
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol (2010) 2.79
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Genome Biol (2009) 2.65
RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings. Cell Res (2012) 2.41
A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics (2009) 2.27
Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1. Nat Struct Mol Biol (2010) 2.15
A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Res (2011) 1.77
N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer. Neoplasia (2009) 1.68
Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Res (2012) 1.47
ChimerDB 2.0--a knowledgebase for fusion genes updated. Nucleic Acids Res (2009) 1.36
Epigenetic inactivation of the Sotos overgrowth syndrome gene histone methyltransferase NSD1 in human neuroblastoma and glioma. Proc Natl Acad Sci U S A (2009) 1.27
Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. Brief Bioinform (2012) 1.23
Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer. Nucleic Acids Res (2010) 1.17
Our changing view of the genomic landscape of cancer. J Pathol (2010) 1.13
nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing. Genome Res (2012) 1.12
FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data. PLoS One (2012) 1.11
Role for the nuclear receptor-binding SET domain protein 1 (NSD1) methyltransferase in coordinating lysine 36 methylation at histone 3 with RNA polymerase II function. Proc Natl Acad Sci U S A (2010) 1.09
Recurrent read-through fusion transcripts in breast cancer. Breast Cancer Res Treat (2014) 1.05
Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms. PLoS One (2012) 1.04
Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing. Genome Biol (2010) 1.01
The breast cancer somatic 'muta-ome': tackling the complexity. Breast Cancer Res (2009) 0.98
Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines. Cancer Genet (2011) 0.98
Next-generation sequencing. Breast Cancer Res (2009) 0.94
Genetic pathways leading to therapy-related myeloid neoplasms. Mediterr J Hematol Infect Dis (2011) 0.93
Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing. BMC Genomics (2010) 0.93
Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro? Nucleic Acids Res (2014) 0.92
Clinical applications of next-generation sequencing in colorectal cancers. World J Gastroenterol (2013) 0.89
Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Res (2011) 0.88
JAFFA: High sensitivity transcriptome-focused fusion gene detection. Genome Med (2015) 0.85
Are breast cancers driven by fusion genes? Breast Cancer Res (2012) 0.84
Detection of a common chimeric transcript between human chromosomes 7 and 16. Biol Direct (2012) 0.83
Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes. BMC Genomics (2012) 0.83
NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision. Nucleic Acids Res (2015) 0.82
Whole-genome cancer analysis as an approach to deeper understanding of tumour biology. Br J Cancer (2009) 0.82
Histone methyltransferases: novel targets for tumor and developmental defects. Am J Transl Res (2015) 0.82
Prediction and prognosis: impact of gene expression profiling in personalized treatment of breast cancer patients. EPMA J (2010) 0.81
The DNA damage response: the omics era and its impact. DNA Repair (Amst) (2014) 0.80
A novel gammaretroviral shuttle vector insertional mutagenesis screen identifies SHARPIN as a breast cancer metastasis gene and prognostic biomarker. Oncotarget (2015) 0.78
NSD1 mitigates caspase-1 activation by listeriolysin O in macrophages. PLoS One (2013) 0.78
Transcriptome Analysis in Domesticated Species: Challenges and Strategies. Bioinform Biol Insights (2016) 0.75
Steric Clash in the SET Domain of Histone Methyltransferase NSD1 as a Cause of Sotos Syndrome and Its Genetic Heterogeneity in a Brazilian Cohort. Genes (Basel) (2016) 0.75
An integrated genomic analysis of Tudor domain-containing proteins identifies PHD finger protein 20-like 1 (PHF20L1) as a candidate oncogene in breast cancer. Mol Oncol (2015) 0.75
MicroRNAs in the pathobiology of sarcomas. Lab Invest (2015) 0.75
Computational characterisation of cancer molecular profiles derived using next generation sequencing. Contemp Oncol (Pozn) (2015) 0.75
Serial analysis of gene expression. Science (1995) 60.15
The consensus coding sequences of human breast and colorectal cancers. Science (2006) 60.02
Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science (2005) 39.06
The genomic landscapes of human breast and colorectal cancers. Science (2007) 38.12
Complementary DNA sequencing: expressed sequence tags and human genome project. Science (1991) 19.42
Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol (2000) 15.79
Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature (1973) 15.28
Paradoxical roles of the immune system during cancer development. Nat Rev Cancer (2006) 10.57
A common sequence motif associated with recombination hot spots and genome instability in humans. Nat Genet (2008) 8.64
Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res (2007) 6.91
Tumor stroma and regulation of cancer development. Annu Rev Pathol (2006) 6.66
Recurrent gene fusions in prostate cancer. Nat Rev Cancer (2008) 6.08
Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques (2001) 5.92
Multiple loci with different cancer specificities within the 8q24 gene desert. J Natl Cancer Inst (2008) 5.82
CAGE: cap analysis of gene expression. Nat Methods (2006) 5.04
Transcriptome sequencing of malignant pleural mesothelioma tumors. Proc Natl Acad Sci U S A (2008) 4.75
Chromatid cohesion defects may underlie chromosome instability in human colorectal cancers. Proc Natl Acad Sci U S A (2008) 3.52
A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells. Science (2008) 3.52
Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer. Mod Pathol (2007) 3.37
The cancer genome anatomy project: building an annotated gene index. Trends Genet (2000) 3.02
Chromosome translocations: dangerous liaisons revisited. Nat Rev Cancer (2001) 3.01
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics (2006) 2.98
NUP98-NSD1 links H3K36 methylation to Hox-A gene activation and leukaemogenesis. Nat Cell Biol (2007) 2.85
DNA strand break repair and human genetic disease. Annu Rev Genomics Hum Genet (2007) 2.80
The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome. Proc Natl Acad Sci U S A (2001) 2.71
Expression of the TMPRSS2:ERG fusion gene predicts cancer recurrence after surgery for localised prostate cancer. Br J Cancer (2007) 2.62
Three classes of genes mutated in colorectal cancers with chromosomal instability. Cancer Res (2004) 2.51
Mammalian meiotic recombination hot spots. Annu Rev Genet (2007) 1.90
Human MRE11 is inactivated in mismatch repair-deficient cancers. EMBO Rep (2002) 1.80
Breast cancer risk is associated with the genes encoding the DNA double-strand break repair Mre11/Rad50/Nbs1 complex. Cancer Epidemiol Biomarkers Prev (2007) 1.34
Paired-end diTagging for transcriptome and genome analysis. Curr Protoc Mol Biol (2007) 1.30
Exon repetition in mRNA. Proc Natl Acad Sci U S A (1999) 1.21
Mutation screening of Mre11 complex genes: indication of RAD50 involvement in breast and ovarian cancer susceptibility. J Med Genet (2003) 1.15
MRE11 expression is impaired in gastric cancer with microsatellite instability. Carcinogenesis (2004) 1.06
Alterations of the double-strand break repair gene MRE11 in cancer. Cancer Res (2001) 1.06
Association of chromosomal locus 8q24 and risk of prostate cancer: a hospital-based study of German patients treated with brachytherapy. Urol Oncol (2008) 0.89
A Rad50-dependent pathway of DNA repair is deficient in Fanconi anemia fibroblasts. Nucleic Acids Res (2004) 0.86
An integrated genomic analysis of human glioblastoma multiforme. Science (2008) 51.36
Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58
Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods (2009) 22.47
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
Creation of a bacterial cell controlled by a chemically synthesized genome. Science (2010) 13.45
Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science (2008) 10.90
Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol (2009) 9.59
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
Cancer/testis antigens, gametogenesis and cancer. Nat Rev Cancer (2005) 9.46
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci U S A (2006) 7.17
Mobile elements create structural variation: analysis of a complete human genome. Genome Res (2009) 7.06
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol (2002) 6.96
Genetic variation in an individual human exome. PLoS Genet (2008) 6.68
Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A (2006) 6.31
Glioblastoma stem-like cells give rise to tumour endothelium. Nature (2010) 6.18
Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
Acquired resistance to imatinib in gastrointestinal stromal tumor occurs through secondary gene mutation. Clin Cancer Res (2005) 5.44
Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature (2002) 5.38
Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci U S A (2003) 5.10
Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics (2008) 5.00
The cancer/testis genes: review, standardization, and commentary. Cancer Immun (2004) 4.78
An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A (2002) 4.45
An agenda for personalized medicine. Nature (2009) 4.14
The dynamic genome of Hydra. Nature (2010) 4.00
Genome transplantation in bacteria: changing one species to another. Science (2007) 3.95
Mutation of GATA3 in human breast tumors. Oncogene (2004) 3.92
Long-range heterogeneity at the 3' ends of human mRNAs. Genome Res (2002) 3.91
Structural and functional diversity of the microbial kinome. PLoS Biol (2007) 3.74
PIK3CA gene mutations in pediatric and adult glioblastoma multiforme. Mol Cancer Res (2006) 3.72
Cell-free cloning using phi29 DNA polymerase. Proc Natl Acad Sci U S A (2005) 3.54
Circulating tumor cell analysis in patients with progressive castration-resistant prostate cancer. Clin Cancer Res (2007) 3.53
Plasmodium, human and Anopheles genomics and malaria. Nature (2002) 3.42
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res (2011) 3.36
Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet (2008) 3.23
The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A (2002) 3.19
Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science (2010) 3.18
Intratumoral heterogeneity of receptor tyrosine kinases EGFR and PDGFRA amplification in glioblastoma defines subpopulations with distinct growth factor response. Proc Natl Acad Sci U S A (2012) 3.12
Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma. Nat Genet (2011) 3.10
High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol (2002) 3.04
Human chromosome 7: DNA sequence and biology. Science (2003) 3.02
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J (2011) 2.97
Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature (2010) 2.93
The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS One (2008) 2.91
Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol (2007) 2.90
One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc Natl Acad Sci U S A (2008) 2.82
Towards a comprehensive structural variation map of an individual human genome. Genome Biol (2010) 2.79
Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proc Natl Acad Sci U S A (2010) 2.76
Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science (2009) 2.74
Cancer-testis genes are coordinately expressed and are markers of poor outcome in non-small cell lung cancer. Clin Cancer Res (2005) 2.73
Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science (2005) 2.71
Genome-wide analysis of cancer/testis gene expression. Proc Natl Acad Sci U S A (2008) 2.66
Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc Natl Acad Sci U S A (2003) 2.64