Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)

<tt>BLAT</tt>—The <tt>BLAST</tt>-Like Alignment Tool

2002 • 8,153 citations

Genome sequencing in microfabricated high-density picolitre reactors

2005 • 7,594 citations

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

2007 • 5,117 citations

Serial Analysis of Gene Expression

1995 • 3,659 citations

The ENCODE (ENCyclopedia Of DNA Elements) Project

2004 • 2,327 citations

Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome

2005 • 1,373 citations

Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays

2000 • 1,356 citations

Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution

2005 • 1,152 citations

A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome

2006 • 1,137 citations

Global Identification of Human Transcribed Sequences with Genome Tiling Arrays

2004 • 1,020 citations

A high-resolution map of active promoters in the human genome

2005 • 922 citations

Human LINE retrotransposons generate processed pseudogenes

2000 • 807 citations

Chromosome aberrations in solid tumors

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Sequence identification of 2,375 human brain genes

1992 • 764 citations

Detection and mapping of amplified DNA sequences in breast cancer by comparative genomic hybridization.

1994 • 748 citations

A breakpoint map of recurrent chromosomal rearrangements in human neoplasia

1997 • 718 citations

GENCODE: producing a reference annotation for ENCODE

2006 • 616 citations

The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)

2004 • 554 citations

Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes

2005 • 484 citations

Pseudogenes: Are They “Junk” or Functional DNA?

2003 • 453 citations

Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome

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An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene

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Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer

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Recent duplication, domain accretion and the dynamic mutation of the human genome

2001 • 332 citations

Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays

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Transcription-mediated gene fusion in the human genome

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Neuronal Expression of Neural Nitric Oxide Synthase (nNOS) Protein Is Suppressed by an Antisense RNA Transcribed from an NOS Pseudogene

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Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation

2005 • 243 citations

Digital karyotyping

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STI571: A Paradigm of New Agents for Cancer Therapeutics

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Studying Genomes Through the Aeons: Protein Families, Pseudogenes and Proteome Evolution

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Tandem chimerism as a means to increase protein complexity in the human genome

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Molecular Fossils in the Human Genome: Identification and Analysis of the Pseudogenes in Chromosomes 21 and 22

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Role of the TEL-AML1 fusion gene in the molecular pathogenesis of childhood acute lymphoblastic leukaemia

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Intron gain and loss in segmentally duplicated genes in rice

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Chromosome instability in human lung cancers: possible underlying mechanisms and potential consequences in the pathogenesis

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Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes

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Detection of DNA amplification in 17 primary breast carcinomas with homogeneously staining regions by a modified comparative genomic hybridization technique

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Chromosomal alterations in 15 breast cancer cell lines by comparative genomic hybridization and spectral karyotyping

2000 • 121 citations

Single nucleotide polymorphism array analysis of cancer

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Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing

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Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer†

2002 • 112 citations

Alternative trans‐splicing: a novel mode of pre‐mRNA processing

2006 • 102 citations

The interactive online SKY/M‐FISH &amp; CGH Database and the Entrez Cancer Chromosomes search database: Linkage of chromosomal aberrations with the genome sequence

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High Efficiency Selection of Full-length cDNA by Improved Biotinylated Cap Trapper

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Finding fusion genes resulting from chromosome rearrangement by analyzing the expressed sequence databases

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Overexpression of P70 S6 kinase protein is associated with increased risk of locoregional recurrence in node-negative premenopausal early breast cancer patients

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Jumping translocations are common in solid tumor cell lines and result in recurrent fusions of whole chromosome arms

2001 • 89 citations

Transcriptional analysis of the PTEN/MMAC1 pseudogene, ΨPTEN

1999 • 87 citations

Spectral karyotyping and multicolor fluorescence in situ hybridization reveal new tumor-specific chromosomal aberrations

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Prevalence estimates of recurrent balanced cytogenetic aberrations and gene fusions in unselected patients with neoplastic disorders

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STI571: A Paradigm of New Agents for Cancer Therapeutics

2002 • 80 citations

Integrated Pseudogene Annotation for Human Chromosome 22: Evidence for Transcription

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Pre-mRNA trans-splicing: from kinetoplastids to mammals, an easy language for life diversity

2005 • 61 citations

Molecular Biology of Chronic Myeloid Leukemia

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Decoding the fine-scale structure of a breast cancer genome and transcriptome

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Cloning, mRNA localization and evolutionary conservation of a human 5-HT7 receptor pseudogene

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Delay in Synthesis of the 3′ Splice Site Promotes trans-Splicing of the Preceding 5′ Splice Site

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Transcription of a human dopamine D5 pseudogene

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PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data

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Specificity of interphase fluorescence in situ hybridization for detection of chromosome aberrations in tumor pathology

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The human serotonin 5-hydroxytryptamine1D receptor pseudogene is transcribed

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Identification of novel proteins induced by estradiol, 4-hydroxytamoxifen and acolbifene in T47D breast cancer cells

2006 • 25 citations

Oncogenic protein tyrosine kinases

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Chromosomal translocations in cancer and their relevance for therapy

2005 • 23 citations

Cloning of a kallikrein pseudogene

2004 • 21 citations

Expression patterns of the LPP–HMGA2 fusion transcript in pulmonary chondroid hamartomas with t(3;12)(q27∼28;q14∼15)

2005 • 19 citations

Identification of a transcriptionally active hVH-5 pseudogene on 10q22.2

2005 • 8 citations

The Application of Molecular Analyses for Primary Granulocytic Sarcoma with a Specific Chromosomal Translocation

2005 • 7 citations