Applications of DNA tiling arrays for whole-genome analysis

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

2003 • 10,537 citations

Gene Silencing in Cancer in Association with Promoter Hypermethylation

2003 • 3,332 citations

A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.

1992 • 3,099 citations

Transcriptional Regulatory Networks in Saccharomyces cerevisiae

2002 • 2,967 citations

Light-Directed, Spatially Addressable Parallel Chemical Synthesis

1991 • 2,692 citations

Mechanisms of Alternative Pre-Messenger RNA Splicing

2003 • 2,547 citations

High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays

1998 • 2,266 citations

The Role of DNA Methylation in Mammalian Epigenetics

2001 • 1,956 citations

Cytosine methylation and the ecology of intragenomic parasites

1997 • 1,906 citations

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

2003 • 1,841 citations

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

2002 • 1,612 citations

Genome-wide analysis of DNA copy-number changes using cDNA microarrays

1999 • 1,445 citations

Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays

2003 • 1,406 citations

Messenger-RNA-binding proteins and the messages they carry

2002 • 1,398 citations

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

2000 • 1,356 citations

Light-generated oligonucleotide arrays for rapid DNA sequence analysis.

1994 • 1,353 citations

A genomic view of alternative splicing

2002 • 1,307 citations

Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer

2001 • 1,297 citations

Discovery of Gene Function by Expression Profiling of the Malaria Parasite Life Cycle

2003 • 1,244 citations

Alternative splicing: increasing diversity in the proteomic world

2001 • 1,218 citations

Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21

2001 • 1,168 citations

Microarray Identification of FMRP-Associated Brain mRNAs and Altered mRNA Translational Profiles in Fragile X Syndrome

2001 • 1,113 citations

E2F integrates cell cycle progression with DNA repair, replication, and G₂/M checkpoints

2002 • 1,102 citations

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

2001 • 1,101 citations

Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs

2004 • 1,079 citations

CLIP Identifies Nova-Regulated RNA Networks in the Brain

2003 • 1,064 citations

Heterochromatin and Epigenetic Control of Gene Expression

2003 • 1,039 citations

Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome

2003 • 906 citations

Complete sequencing and characterization of 21,243 full-length human cDNAs

2003 • 888 citations

Large-Scale Transcriptional Activity in Chromosomes 21 and 22

2002 • 839 citations

RNA regulation: a new genetics?

2004 • 744 citations

Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array

1999 • 725 citations

Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle

2001 • 664 citations

Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast

2004 • 661 citations

Widespread occurrence of antisense transcription in the human genome

2003 • 655 citations

A tiling resolution DNA microarray with complete coverage of the human genome

2004 • 644 citations

Functional Annotation of a Full-Length Arabidopsis cDNA Collection

2002 • 636 citations

ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments

2004 • 609 citations

Thermodynamics and NMR of Internal G·T Mismatches in DNA

1997 • 588 citations

Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene

2004 • 585 citations

Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2

1993 • 584 citations

Challenging the dogma: the hidden layer of non‐protein‐coding RNAs in complex organisms

2003 • 567 citations

Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22

2004 • 529 citations

Comparative genomics and evolution of proteins involved in RNA metabolism

2002 • 524 citations

Resequencing and mutational analysis using oligonucleotide microarrays

1999 • 517 citations

DNA Methylation and Epigenetic Inheritance in Plants and Filamentous Fungi

2001 • 501 citations

THE ROLE OF DNA METHYLATION IN CANCER GENETICS AND EPIGENETICS

1996 • 480 citations

Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes

1996 • 458 citations

Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis

2002 • 449 citations

Purification of CpG islands using a methylated DNA binding column

1994 • 449 citations

Experimental annotation of the human genome using microarray technology

2001 • 446 citations

A Small Modulatory dsRNA Specifies the Fate of Adult Neural Stem Cells

2004 • 440 citations

Genomewide Analysis of mRNA Processing in Yeast Using Splicing-Specific Microarrays

2002 • 406 citations

High-Resolution Analysis of DNA Copy Number Using Oligonucleotide Microarrays

2004 • 398 citations

Large-Scale Identification of Single-Feature Polymorphisms in Complex Genomes

2003 • 385 citations

Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: Evaluation using experimental models

1992 • 381 citations

Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography

2002 • 356 citations

Thermodynamic parameters for DNA sequences with dangling ends

2000 • 352 citations

Over 20% of human transcripts might form sense-antisense pairs

2004 • 326 citations

A model of molecular interactions on short oligonucleotide microarrays

2003 • 325 citations

How prevalent is functional alternative splicing in the human genome?

2003 • 310 citations

Distribution of NF-κB-binding sites across human chromosome 22

2003 • 302 citations

Loss of methylation activates Xist in somatic but not in embryonic cells.

1995 • 300 citations

In search of antisense

2004 • 293 citations

The transcriptional activity of human Chromosome 22

2003 • 293 citations

Widespread cytoplasmic mRNA transport in yeast: Identification of 22 bud-localized transcripts using DNA microarray analysis

2003 • 288 citations

Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays

2002 • 278 citations

Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex

2002 • 275 citations

Do natural antisense transcripts make sense in eukaryotes?

1998 • 275 citations

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae

2002 • 265 citations

Antisense Transcripts With FANTOM2 Clone Set and Their Implications for Gene Regulation

2003 • 254 citations

Nearest-Neighbor Thermodynamics of Internal A·C Mismatches in DNA: Sequence Dependence and pH Effects

1998 • 251 citations

Antisense transcripts in the human genome

2002 • 242 citations

Nearest Neighbor Thermodynamic Parameters for Internal G·A Mismatches in DNA

1998 • 239 citations

Thermodynamics of internal C.T mismatches in DNA

1998 • 236 citations

The methylated component of the Neurospora crassa genome

2003 • 234 citations

Program-Specific Distribution of a Transcription Factor Dependent on Partner Transcription Factor and MAPK Signaling

2003 • 228 citations

A Dnmt2-like protein mediates DNA methylation inDrosophila

2003 • 226 citations

Analysing uncharted transcriptomes with SAGE

2000 • 217 citations

Finding signals that regulate alternative splicing in the post-genomic era.

2002 • 214 citations

Methylation and gene control

1982 • 210 citations

Genome-wide analysis of RNA–protein interactions illustrates specificity of the mRNA export machinery

2003 • 198 citations

Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing

2004 • 193 citations

The Use of MPSS for Whole-Genome Transcriptional Analysis in Arabidopsis

2004 • 190 citations

Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the mRNA Transcripts Encoded by the Mouse Transcriptome

2003 • 189 citations

Genetic Diversity in Yeast Assessed With Whole-Genome Oligonucleotide Arrays

2003 • 187 citations

Analysis of Myc Bound Loci Identified by CpG Island Arrays Shows that Max Is Essential for Myc-Dependent Repression

2003 • 185 citations

Computational discovery of sense-antisense transcription in the human and mouse genomes

2002 • 185 citations

Full-length messenger RNA sequences greatly improve genome annotation

2002 • 177 citations

CREB Binds to Multiple Loci on Human Chromosome 22

2004 • 172 citations

Genome-Wide Profiling of DNA Methylation Reveals Transposon Targets of CHROMOMETHYLASE3

2002 • 165 citations

Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays

2003 • 162 citations

Analyzing mRNA–protein complexes using a yeast three-hybrid system

2002 • 145 citations

Antisense transcripts with rice full-length cDNAs

2003 • 129 citations

Probe selection for high-density oligonucleotide arrays

2003 • 128 citations

DNA hybridization to mismatched templates: A chip study

2002 • 122 citations

Arabidopsis MPSS. An Online Resource for Quantitative Expression Analysis

2004 • 120 citations

Regulation of gene expression by natural antisense RNA transcripts

1997 • 120 citations

Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays

2004 • 116 citations

Genome wide identification and classification of alternative splicing based on EST data

2004 • 93 citations

NMR solution structure of a DNA dodecamer containing single G*T mismatches

1998 • 93 citations

Evolutionarily Conserved Sequences on Human Chromosome 21

2001 • 92 citations

Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays

2002 • 89 citations

Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing

2003 • 85 citations

Regulation of Elongating RNA Polymerase II by Forkhead Transcription Factors in Yeast

2003 • 75 citations

Computational Discovery of Internal Micro-Exons

2003 • 74 citations

Identification of mRNAs Associated with αCP2-Containing RNP Complexes

2003 • 68 citations

Regulation of Alternative Splicing

1990 • 61 citations

Stochastic models inspired by hybridization theory for short oligonucleotide arrays

2004 • 54 citations

Scp160p associates with specific mRNAs in yeast

2003 • 52 citations

Strand-biased DNA methylation associated with centromeric regions in Arabidopsis

2003 • 47 citations

The new role of SAGE in gene discovery

2003 • 44 citations

Identifying transcriptional targets.

2004 • 37 citations

Piecing together the significance of splicing

2001 • 30 citations

Sex, AGility, and the Regulation of Alternative Splicing

2002 • 30 citations

Digital Optical Chemistry: A Novel System for the Rapid Fabrication of Custom Oligonucleotide Arrays

2002 • 17 citations

Microfabricated Sensors

2002 • 6 citations