Encode Information

From GersteinInfo

Contents 1 Encode Resources 2 Published Papers 2.1 Scoring Tiling Arrays 2.1.1 Scoring TARs and ChIP-hits, Using them to Pick Subsets for Further Validation 2.1.1.1 A Supervised Hidden Markov Model Framework for Efficiently Segmenting Tiling Array Data in Transcriptional and ChIP-chip Experiments: Systematically Incorporating Validated Biological Knowledge 2.1.1.2 Tilescope: online analysis pipeline for high-density tiling microarray data 2.1.1.3 Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. 2.1.1.4 Design optimization methods for genomic DNA tiling arrays. 2.1.1.5 Extrapolating Traditional DNA Microarray Statistics to the Tiling and Protein Microarray Technologies 2.1.2 Platform Comparison and Scoring 2.1.2.1 Platform comparison of ChIP-chip and ChIP-PET for optimal detection of transcription factor binding regions in mammalian cells 2.1.2.2 Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome 2.2 TAR characterization and inter-relation with annotation 2.2.1 Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. 2.2.2 A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray. 2.2.3 Pseudogene Annotation 2.2.3.1 Pseudogene.org: A comprehensive database and comparison platform for pseudogene annotation 2.2.3.2 A computational approach for identifying pseudogenes in the ENCODE regions 2.2.3.3 Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis of Transcription and Evolution 2.2.3.4 Integrated pseudogene annotation for human chromosome 22: evidence for transcription. 2.2.3.5 Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. 2.2.4 Relating TARs to ncRNAs 2.2.4.1 Structured RNAs in the ENCODE Selected Regions of the Human Genome 2.2.5 Categorization and Clustering of TARs, the DART database 2.2.5.1 Analysis and Classification of Unannotated Transcription within the ENCODE Regions: Associating Transcription with Known and Novel Loci 2.3 Global Analysis of Regulatory Elements 2.3.1 Global Analysis of the Genomic Distribution and Correlation of Regulatory Elements in the ENCODE Regions 2.3.2 Integrated analysis of experimental datasets reveals many novel promoters in 1% of the human genome 2.3.3 BoCaTFBS: a Boosted-cascade Learner to Refine the Binding Sites Suggested by ChIP-chip experiments

Encode Resources

• Yale ENCODE site
• Lab ENCODE information
• National Human Genome Research Institute (NHGRI) ENCODE site
• ENCODE Project Wiki (encode/human)
• Media:Expressed_HumanTFs_Summary.xls - Listing of expressed human transcription factors (from RS, 22-Mar-07)
• Private spreadsheet of encode progress
• DeadLines

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