Published in Funct Integr Genomics on September 01, 2002
Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (1995) 88.48
Exploring the metabolic and genetic control of gene expression on a genomic scale. Science (1997) 60.15
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature (2000) 47.15
Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
Life with 6000 genes. Science (1996) 41.51
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science (1999) 36.25
Genome-wide location and function of DNA binding proteins. Science (2000) 31.25
Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol (2001) 28.01
Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science (2001) 24.48
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol (1999) 21.92
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature (2001) 21.55
A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell (1998) 19.67
YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res (2001) 16.22
Global analysis of protein activities using proteome chips. Science (2001) 13.74
Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science (2000) 13.20
Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol (1999) 12.42
MIPS: a database for genomes and protein sequences. Nucleic Acids Res (2002) 11.98
Characterization of the yeast transcriptome. Cell (1997) 11.33
Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci U S A (2000) 10.98
Printing proteins as microarrays for high-throughput function determination. Science (2000) 10.77
Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature (1999) 9.87
Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A (1994) 9.59
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev (1994) 6.12
Overview of the yeast genome. Nature (1997) 5.86
A sampling of the yeast proteome. Mol Cell Biol (1999) 5.12
A biochemical genomics approach for identifying genes by the activity of their products. Science (1999) 3.98
Analysis of yeast protein kinases using protein chips. Nat Genet (2000) 3.94
Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res (2001) 2.71
The TRIPLES database: a community resource for yeast molecular biology. Nucleic Acids Res (2002) 1.29
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Unlocking the secrets of the genome. Nature (2009) 11.80
Annotation of functional variation in personal genomes using RegulomeDB. Genome Res (2012) 11.47
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Variation in transcription factor binding among humans. Science (2010) 9.33
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
HTRA1 promoter polymorphism in wet age-related macular degeneration. Science (2006) 7.12
Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79
Linking disease associations with regulatory information in the human genome. Genome Res (2012) 5.47
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol (2009) 5.13
What is a gene, post-ENCODE? History and updated definition. Genome Res (2007) 4.96
High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A (2006) 4.84
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol (2009) 4.64
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59
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
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res (2008) 4.11
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89
An integrated approach for finding overlooked genes in yeast. Nat Biotechnol (2002) 3.88
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res (2012) 3.83
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res (2012) 3.61
Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48
GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A (2002) 3.41
Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc Natl Acad Sci U S A (2007) 3.35
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34
ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol (2002) 3.32
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A (2010) 3.28
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22
Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet (2011) 3.20
Protein analysis on a proteomic scale. Nature (2003) 3.12
Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer (2009) 3.03
Getting connected: analysis and principles of biological networks. Genes Dev (2007) 3.03
Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res (2007) 2.96
Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal (2010) 2.95
Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A (2010) 2.90
Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A (2009) 2.89
Extensive variation in chromatin states across humans. Science (2013) 2.83
Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A (2009) 2.83
Protein chip technology. Curr Opin Chem Biol (2003) 2.80
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
Genetic analysis of variation in transcription factor binding in yeast. Nature (2010) 2.69
MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev (2008) 2.66
DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A (2004) 2.66
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66
Major molecular differences between mammalian sexes are involved in drug metabolism and renal function. Dev Cell (2004) 2.65
Impact of chromatin structures on DNA processing for genomic analyses. PLoS One (2009) 2.63
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics (2010) 2.62
Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol (2007) 2.48
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet (2010) 2.46
TOS9 regulates white-opaque switching in Candida albicans. Eukaryot Cell (2006) 2.42
Target hub proteins serve as master regulators of development in yeast. Genes Dev (2006) 2.39
Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet (2011) 2.38
Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38
The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proc Natl Acad Sci U S A (2009) 2.36
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet (2005) 2.36
Bud-site selection and cell polarity in budding yeast. Curr Opin Microbiol (2002) 2.35
The human proteome project: current state and future direction. Mol Cell Proteomics (2011) 2.34
Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLoS Genet (2008) 2.34
Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. Genome Res (2010) 2.34
Variation and genetic control of protein abundance in humans. Nature (2013) 2.32
Sexual dimorphism in mammalian gene expression. Trends Genet (2005) 2.31
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res (2010) 2.30
CREB binds to multiple loci on human chromosome 22. Mol Cell Biol (2004) 2.28
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics (2010) 2.26
A single-molecule long-read survey of the human transcriptome. Nat Biotechnol (2013) 2.24
Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays. Proc Natl Acad Sci U S A (2007) 2.22
A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood (2009) 2.18
Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res (2008) 2.17
Regulation of gene expression by a metabolic enzyme. Science (2004) 2.15
Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc Natl Acad Sci U S A (2007) 2.15
Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol (2010) 2.15
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol (2012) 2.14