Published in Nat Biotechnol on January 01, 2002
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A (2006) 5.24
Complex Loci in human and mouse genomes. PLoS Genet (2006) 3.74
Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species. PLoS Genet (2008) 3.69
Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Res (2006) 2.81
Why are there still over 1000 uncharacterized yeast genes? Genetics (2007) 2.71
A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res (2002) 2.07
Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic Acids Res (2003) 1.90
Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res (2002) 1.89
Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast (2006) 1.85
A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization. BMC Genomics (2003) 1.51
Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PLoS Comput Biol (2005) 1.46
Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res (2003) 1.43
Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq. Elife (2014) 1.40
The uses of genome-wide yeast mutant collections. Genome Biol (2004) 1.36
Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae. Genome Biol (2004) 1.33
A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA. Genes Dev (2002) 1.16
Dictyostelium finds new roles to model. Genetics (2010) 1.13
Extensive transcript diversity and novel upstream open reading frame regulation in yeast. G3 (Bethesda) (2013) 1.05
An overview of nested genes in eukaryotic genomes. Eukaryot Cell (2009) 0.99
Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22. Genome Res (2005) 0.94
Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes. Nucleic Acids Res (2005) 0.91
Mitochondria of the yeasts Saccharomyces cerevisiae and Kluyveromyces lactis contain nuclear rDNA-encoded proteins. PLoS One (2011) 0.91
GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucleic Acids Res (2002) 0.88
Unconventional genomic architecture in the budding yeast saccharomyces cerevisiae masks the nested antisense gene NAG1. Eukaryot Cell (2008) 0.87
Expression of the rDNA-encoded mitochondrial protein Tar1p is stringently controlled and responds differentially to mitochondrial respiratory demand and dysfunction. Curr Genet (2008) 0.84
An integrated approach for finding overlooked genes in Shigella. PLoS One (2011) 0.79
Small proteins: untapped area of potential biological importance. Front Genet (2013) 0.78
Converging evidence of mitochondrial dysfunction in a yeast model of homocysteine metabolism imbalance. J Biol Chem (2011) 0.77
Small toxic protein encoded on chromosome VII of Saccharomyces cerevisiae. PLoS One (2015) 0.75
Microbial diversity in various types of paper mill sludge: identification of enzyme activities with potential industrial applications. Springerplus (2016) 0.75
'To-day, we have naming of parts...'. Nat Biotechnol (2002) 0.75
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr (2010) 108.52
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
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
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 systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
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
Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr (2012) 11.31
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
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
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
Relating three-dimensional structures to protein networks provides evolutionary insights. Science (2006) 5.50
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
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
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics (2006) 4.55
Advancing translational research with the Semantic Web. BMC Bioinformatics (2007) 4.38
The GENCODE pseudogene resource. Genome Biol (2012) 4.18
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
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
The Phenix software for automated determination of macromolecular structures. Methods (2011) 3.81
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
Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science (2013) 3.60
Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48
Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets. Cancer Discov (2011) 3.43
The reality of pervasive transcription. PLoS Biol (2011) 3.41
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
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23
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
Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell (2008) 3.18
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