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Encode Resources

Published Papers

(Taken from google docs version at http://docs.google.com/View?docid=ddpspxzw_30g8b7xg)

Scoring Tiling Arrays

Scoring TARs and ChIP-hits, Using them to Pick Subsets for Further Validation

A Supervised Hidden Markov Model Framework for Efficiently Segmenting Tiling Array Data in Transcriptional and ChIP-chip Experiments: Systematically Incorporating Validated Biological Knowledge
Tilescope: online analysis pipeline for high-density tiling microarray data
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.
Design optimization methods for genomic DNA tiling arrays.
Extrapolating Traditional DNA Microarray Statistics to the Tiling and Protein Microarray Technologies

Platform Comparison and Scoring

Platform comparison of ChIP-chip and ChIP-PET for optimal detection of transcription factor binding regions in mammalian cells
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

TAR characterization and inter-relation with annotation

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.
A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.

Pseudogene Annotation

Pseudogene.org: A comprehensive database and comparison platform for pseudogene annotation
A computational approach for identifying pseudogenes in the ENCODE regions
Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis of Transcription and Evolution
Integrated pseudogene annotation for human chromosome 22: evidence for transcription.
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.

Relating TARs to ncRNAs

Structured RNAs in the ENCODE Selected Regions of the Human Genome

Categorization and Clustering of TARs, the DART database

Analysis and Classification of Unannotated Transcription within the ENCODE Regions: Associating Transcription with Known and Novel Loci

Global Analysis of Regulatory Elements

Global Analysis of the Genomic Distribution and Correlation of Regulatory Elements in the ENCODE Regions
Integrated analysis of experimental datasets reveals many novel promoters in 1% of the human genome
BoCaTFBS: a Boosted-cascade Learner to Refine the Binding Sites Suggested by ChIP-chip experiments
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