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RNA-Seq: a revolutionary tool for transcriptomics
RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity ofExpand
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Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.
The functions of many open reading frames (ORFs) identified in genome-sequencing projects are unknown. New, whole-genome approaches are required to systematically determine their function. A total ofExpand
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The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
The identification of untranslated regions, introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq for mappingExpand
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These dataExpand
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PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
Chromatin immunoprecipitation (ChIP) followed by tag sequencing (ChIP-seq) using high-throughput next-generation instrumentation is fast, replacing chromatin immunoprecipitation followed by genomeExpand
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A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data
We have developed an approach using Bayesian networks to predict protein-protein interactions genome-wide in yeast. Our method naturally weights and combines into reliable predictions genomicExpand
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Architecture of the human regulatory network derived from ENCODE data
Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; the ensemble of these binding events forms a regulatory network, constituting the wiring diagram for aExpand
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Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
Proteins interact with genomic DNA to bring the genome to life; and these interactions also define many functional features of the genome. SBF and MBF are sequence-specific transcription factors thatExpand
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Nim1-related kinases coordinate cell cycle progression with the organization of the peripheral cytoskeleton in yeast.
The mechanisms that couple cell cycle progression with the organization of the peripheral cytoskeleton are poorly understood. In Saccharomyces cerevisiae, the Swe1 protein has been shown previouslyExpand
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HTRA1 promoter polymorphism in wet age-related macular degeneration.
Age-related macular degeneration (AMD), the most common cause of irreversible vision loss in individuals aged older than 50 years, is classified as either wet (neovascular) or dry (nonneovascular).Expand
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