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The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
A quantitative sequencing-based method is developed for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome, and it is demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed.
Architecture of the human regulatory network derived from ENCODE data
The combinatorial, co-association of transcription factors is found to be highly context specific: distinct combinations of factors bind at specific genomic locations.
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
An integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium identified highly enriched sequence motifs in most data sets, revealing new motifs and validating known ones.
MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays.
The predicted MKK-MPK phosphorylation network constitutes a valuable resource to understand the function and specificity of MPK signaling systems.
Performance comparison of exome DNA sequencing technologies
The results suggest that the Nimblegen platform, which is the only one to use high-density overlapping baits, covers fewer genomic regions than the other platforms but requires the least amount of sequencing to sensitively detect small variants.
Linking disease associations with regulatory information in the human genome.
The results show that the experimental data sets generated by the ENCODE Consortium can be successfully used to suggest functional hypotheses for variants associated with diseases and other phenotypes.
Variation in Transcription Factor Binding Among Humans
Like Father, Like Mother, Like Child Transcriptional regulation is mediated by chromatin structure, which may affect the binding of transcription factors, but the extent of how
Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays
It is suggested that calcium functions through distinct CaM/CML proteins to regulate a wide range of targets and cellular activities.
A single-molecule long-read survey of the human transcriptome
The results show the feasibility of deep sequencing full-length RNA from complex eukaryotic transcriptomes on a single-molecule level and high-confidence mappings are consistent with GENCODE annotations.