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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectGetting started in gene orthology and functional analysisGenomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoidesAn integrative genomic approach to uncover molecular mechanisms of prokaryotic traitsComparative analysis of processed ribosomal protein pseudogenes in four mammalian genomesThe GENCODE pseudogene resourceClassification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factorsThe CRIT framework for identifying cross patterns in systems biology and application to chemogenomicsIdentification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primatesPublishing perishing? Towards tomorrow's information architectureUsing 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structuresOpen access: taking full advantage of the contentClosure of the NCBI SRA and implications for the long-term future of genomics data storageIntegrative annotation of variants from 1092 humans: application to cancer genomicsWhat is a gene, post-ENCODE? History and updated definitionPseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolutionMolecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22Personal genome sequencing: current approaches and challengesDefining functional DNA elements in the human genomeThe morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays.A database of macromolecular motionsIdentification of pseudogenes in the Drosophila melanogaster genomeSpectral biclustering of microarray data: coclustering genes and conditionsRNA-Seq: a revolutionary tool for transcriptomicsGENCODE: the reference human genome annotation for The ENCODE ProjectMapping copy number variation by population-scale genome sequencingThe genomic complexity of primary human prostate cancerDynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencingThe transcriptional landscape of the yeast genome defined by RNA sequencingNucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint libraryNormal modes for predicting protein motions: a comprehensive database assessment and associated Web toolN-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancerPaired-end mapping reveals extensive structural variation in the human genomeZebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organizationA myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA clusterThe transcriptional activity of human Chromosome 22Structured RNAs in the ENCODE selected regions of the human genomeThe DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel lociPseudogene.org: a comprehensive database and comparison platform for pseudogene annotation
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