Published in Genome Res on June 01, 2007
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63
Ensembl 2008. Nucleic Acids Res (2007) 20.67
Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature (2009) 13.45
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
Recurrent gene fusions in prostate cancer. Nat Rev Cancer (2008) 6.08
Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res (2009) 4.47
Expressed pseudogenes in the transcriptional landscape of human cancers. Cell (2012) 4.22
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol (2009) 4.18
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
Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76
ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics (2011) 2.74
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66
Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol (2008) 2.40
A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics (2009) 2.27
Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. PLoS One (2010) 2.13
Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med Genomics (2011) 1.84
RCP is a human breast cancer-promoting gene with Ras-activating function. J Clin Invest (2009) 1.71
Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res (2011) 1.67
Cancer genome-sequencing study design. Nat Rev Genet (2013) 1.55
Sequence features that drive human promoter function and tissue specificity. Genome Res (2010) 1.40
ChimerDB 2.0--a knowledgebase for fusion genes updated. Nucleic Acids Res (2009) 1.36
Transcriptional consequences of genomic structural aberrations in breast cancer. Genome Res (2011) 1.30
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. Genome Res (2011) 1.20
Deep sequencing analysis of the developing mouse brain reveals a novel microRNA. BMC Genomics (2011) 1.19
Scanning the human genome at kilobase resolution. Genome Res (2008) 1.13
Second generation sequencing of the mesothelioma tumor genome. PLoS One (2010) 1.12
TFG, a target of chromosome translocations in lymphoma and soft tissue tumors, fuses to GPR128 in healthy individuals. Haematologica (2009) 1.01
A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. Mol Cancer (2009) 1.01
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
The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome. BMC Med Genomics (2011) 0.95
Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis. Plant Physiol (2012) 0.88
Functional genomics using RIKEN Arabidopsis thaliana full-length cDNAs. J Plant Res (2009) 0.88
Genomic interaction profiles in breast cancer reveal altered chromatin architecture. PLoS One (2013) 0.88
Detection of novel 3' untranslated region extensions with 3' expression microarrays. BMC Genomics (2010) 0.86
Brief overview of bioinformatics activities in Singapore. PLoS Comput Biol (2009) 0.84
Detection of a common chimeric transcript between human chromosomes 7 and 16. Biol Direct (2012) 0.83
Functional annotation of HOT regions in the human genome: implications for human disease and cancer. Sci Rep (2015) 0.80
Optimizing PCR assays for DNA-based cancer diagnostics. J Comput Biol (2010) 0.80
Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis. PLoS One (2015) 0.78
Kleat: cleavage site analysis of transcriptomes. Pac Symp Biocomput (2015) 0.77
Construction of mate pair full-length cDNAs libraries and characterization of transcriptional start sites and termination sites. Nucleic Acids Res (2014) 0.76
The use of multiple displacement amplification to amplify complex DNA libraries. Nucleic Acids Res (2008) 0.75
Using chimaeric expression sequence tag as the reference to identify three-dimensional chromosome contacts. DNA Res (2012) 0.75
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Serial analysis of gene expression. Science (1995) 60.15
The ENCODE (ENCyclopedia Of DNA Elements) Project. Science (2004) 38.24
A high-resolution map of active promoters in the human genome. Nature (2005) 24.35
Accurate multiplex polony sequencing of an evolved bacterial genome. Science (2005) 20.91
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82
Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol (2000) 15.79
GENCODE: producing a reference annotation for ENCODE. Genome Biol (2006) 15.08
A breakpoint map of recurrent chromosomal rearrangements in human neoplasia. Nat Genet (1997) 12.94
Sequence identification of 2,375 human brain genes. Nature (1992) 9.53
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods (2005) 7.87
Chromosome aberrations in solid tumors. Nat Genet (2003) 7.01
Human LINE retrotransposons generate processed pseudogenes. Nat Genet (2000) 6.64
Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res (2005) 6.08
Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nat Genet (2004) 5.75
Detection and mapping of amplified DNA sequences in breast cancer by comparative genomic hybridization. Proc Natl Acad Sci U S A (1994) 5.74
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res (2005) 5.22
Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res (2006) 4.51
Digital karyotyping. Proc Natl Acad Sci U S A (2002) 3.96
Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet (2001) 3.94
An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature (2003) 3.90
Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res (2005) 3.89
Pseudogenes: are they "junk" or functional DNA? Annu Rev Genet (2003) 3.47
Transcription-mediated gene fusion in the human genome. Genome Res (2005) 3.19
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res (2002) 2.89
Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc Natl Acad Sci U S A (2003) 2.64
Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene. J Neurosci (1999) 2.49
Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol (2005) 2.32
Chromosomal alterations in 15 breast cancer cell lines by comparative genomic hybridization and spectral karyotyping. Genes Chromosomes Cancer (2000) 2.24
High efficiency selection of full-length cDNA by improved biotinylated cap trapper. DNA Res (1997) 2.11
Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res (2006) 2.09
Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. J Mol Biol (2002) 2.07
Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer. Genes Chromosomes Cancer (2002) 2.04
Alternative trans-splicing: a novel mode of pre-mRNA processing. Biol Cell (2006) 1.92
Delay in synthesis of the 3' splice site promotes trans-splicing of the preceding 5' splice site. Mol Cell (2005) 1.72
Transcriptional analysis of the PTEN/MMAC1 pseudogene, psiPTEN. Oncogene (1999) 1.72
The interactive online SKY/M-FISH & CGH database and the Entrez cancer chromosomes search database: linkage of chromosomal aberrations with the genome sequence. Genes Chromosomes Cancer (2005) 1.70
Single nucleotide polymorphism array analysis of cancer. Curr Opin Oncol (2007) 1.66
Finding fusion genes resulting from chromosome rearrangement by analyzing the expressed sequence databases. Proc Natl Acad Sci U S A (2004) 1.59
Prevalence estimates of recurrent balanced cytogenetic aberrations and gene fusions in unselected patients with neoplastic disorders. Genes Chromosomes Cancer (2005) 1.57
STI571: a paradigm of new agents for cancer therapeutics. J Clin Oncol (2002) 1.38
Jumping translocations are common in solid tumor cell lines and result in recurrent fusions of whole chromosome arms. Genes Chromosomes Cancer (2001) 1.38
PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data. BMC Bioinformatics (2006) 1.38
Detection of DNA amplification in 17 primary breast carcinomas with homogeneously staining regions by a modified comparative genomic hybridization technique. Genes Chromosomes Cancer (1994) 1.30
Chromosome instability in human lung cancers: possible underlying mechanisms and potential consequences in the pathogenesis. Oncogene (2002) 1.29
Role of the TEL-AML1 fusion gene in the molecular pathogenesis of childhood acute lymphoblastic leukaemia. Oncogene (2004) 1.23
Overexpression of P70 S6 kinase protein is associated with increased risk of locoregional recurrence in node-negative premenopausal early breast cancer patients. Br J Cancer (2004) 1.14
Pre-mRNA trans-splicing: from kinetoplastids to mammals, an easy language for life diversity. Mem Inst Oswaldo Cruz (2005) 1.06
Chromosomal translocations in cancer and their relevance for therapy. Curr Opin Oncol (2006) 1.05
Cloning, mRNA localization and evolutionary conservation of a human 5-HT7 receptor pseudogene. Gene (1999) 1.02
The multitasking genome. Nat Genet (2006) 0.94
Spectral karyotyping and multicolor fluorescence in situ hybridization reveal new tumor-specific chromosomal aberrations. Semin Hematol (2000) 0.94
Identification of novel proteins induced by estradiol, 4-hydroxytamoxifen and acolbifene in T47D breast cancer cells. Steroids (2006) 0.91
Molecular biology of chronic myeloid leukemia. Int J Hematol (2001) 0.90
Expression patterns of the LPP-HMGA2 fusion transcript in pulmonary chondroid hamartomas with t(3;12)(q27 approximately 28;q14 approximately 15). Cancer Genet Cytogenet (2005) 0.87
Specificity of interphase fluorescence in situ hybridization for detection of chromosome aberrations in tumor pathology. Cancer Genet Cytogenet (2004) 0.87
Transcription of a human dopamine D5 pseudogene. Biochem Biophys Res Commun (1991) 0.86
Identification of a transcriptionally active hVH-5 pseudogene on 10q22.2. Cancer Genet Cytogenet (2005) 0.85
Abl: the prototype of oncogenic fusion proteins. Cell Mol Life Sci (2004) 0.85
Cloning of a kallikrein pseudogene. Clin Biochem (2004) 0.83
The human serotonin 5-hydroxytryptamine1D receptor pseudogene is transcribed. Gene (1995) 0.82
The application of molecular analyses for primary granulocytic sarcoma with a specific chromosomal translocation. Int J Hematol (2005) 0.81
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet (2006) 20.76
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
Landscape of transcription in human cells. Nature (2012) 20.18
An oestrogen-receptor-alpha-bound human chromatin interactome. Nature (2009) 12.16
The mutational landscape of lethal castration-resistant prostate cancer. Nature (2012) 11.82
Transcriptome sequencing to detect gene fusions in cancer. Nature (2009) 11.63
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res (2006) 8.08
Dynamic changes in the human methylome during differentiation. Genome Res (2010) 7.96
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods (2005) 7.87
Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer. Science (2008) 7.59
Urinary-cell mRNA profile and acute cellular rejection in kidney allografts. N Engl J Med (2013) 7.40
Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell (2007) 7.05
Distribution and three-dimensional structure of AIDS virus envelope spikes. Nature (2006) 6.78
CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet (2011) 6.55
Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol (2011) 6.54
Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity (2010) 6.48
Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet (2009) 6.39
A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol (2010) 6.01
Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection. Lancet (2003) 5.99
Methylation protects miRNAs and siRNAs from a 3'-end uridylation activity in Arabidopsis. Curr Biol (2005) 5.99
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci U S A (2009) 5.86
Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet (2007) 5.85
Nuclear receptor-dependent bile acid signaling is required for normal liver regeneration. Science (2006) 5.52
Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science (2005) 5.47
Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A (2006) 5.27
Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet (2010) 5.26
Predialysis nephrology care of older patients approaching end-stage renal disease. Arch Intern Med (2011) 5.11
A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. Nat Med (2012) 4.90
Initial sequence and comparative analysis of the cat genome. Genome Res (2007) 4.67
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59
Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res (2006) 4.51
Electrochemical energy storage for green grid. Chem Rev (2011) 4.48
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res (2009) 4.47
Towards a transgenic model of Huntington's disease in a non-human primate. Nature (2008) 4.47
Expressed pseudogenes in the transcriptional landscape of human cancers. Cell (2012) 4.22
ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell (2012) 4.18
K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas. Acta Neuropathol (2012) 4.00
Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics (2006) 3.94
Body mass index and risk, age of onset, and survival in patients with pancreatic cancer. JAMA (2009) 3.86
Anticonvulsant medications and the risk of suicide, attempted suicide, or violent death. JAMA (2010) 3.85
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82