Published in Mol Cell on September 01, 2003
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Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
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A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
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Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
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The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
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Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
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Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol (2009) 5.13
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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