Encode Information

From PubInfo

Table of 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 (http://papers.gersteinlab.org/papers/tilinghmm) 2.1.1.2 Tilescope: online analysis pipeline for high-density tiling microarray data (http://papers.gersteinlab.org/papers/tilescope) 2.1.1.3 Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. (http://papers.gersteinlab.org/papers/Tiling-analysis/) 2.1.1.4 Design optimization methods for genomic DNA tiling arrays. (http://papers.gersteinlab.org/papers/tilingtools) 2.1.1.5 Extrapolating Traditional DNA Microarray Statistics to the Tiling and Protein Microarray Technologies (http://papers.gersteinlab.org/papers/mie.microarray.analysis.review/) 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 (http://papers.gersteinlab.org/papers/chipchipcmp) 2.1.2.2 Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome (http://papers.gersteinlab.org/papers/platformcmp) 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. (http://papers.gersteinlab.org/papers/encoderaceseq) 2.2.2 A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray. (http://papers.gersteinlab.org/papers/pilot-rice-tiling) 2.2.1 Pseudogene Annotation 2.2.1.1 Pseudogene.org: A comprehensive database and comparison platform for pseudogene annotation (http://papers.gersteinlab.org/papers/pgenedb) 2.2.1.2 A computational approach for identifying pseudogenes in the ENCODE regions (http://papers.gersteinlab.org/papers/pseudopiped) 2.2.1.3 Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis of Transcription and Evolution (http://papers.gersteinlab.org/papers/encodepgenes/) 2.2.1.4 Integrated pseudogene annotation for human chromosome 22: evidence for transcription. (http://papers.gersteinlab.org/papers/chr22-pgene-exp) 2.2.1.5 Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. (http://papers.gersteinlab.org/papers/est-pgene-exp) 2.2.2 Relating TARs to ncRNAs 2.2.2.1 Structured RNAs in the ENCODE Selected Regions of the Human Genome (http://papers.gersteinlab.org/papers/encoderna/) 2.2.3 Categorization and Clustering of TARs, the DART database 2.2.3.1 Analysis and Classification of Unannotated Transcription within the ENCODE Regions: Associating Transcription with Known and Novel Loci (http://papers.gersteinlab.org/papers/dart/) 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 (http://papers.gersteinlab.org/papers/tredist/) 2.3.2 Integrated analysis of experimental datasets reveals many novel promoters in 1% of the human genome (http://papers.gersteinlab.org/papers/encodepromoters) 2.3.3 BoCaTFBS: a Boosted-cascade Learner to Refine the Binding Sites Suggested by ChIP-chip experiments (http://papers.gersteinlab.org/papers/bocatfbs/)

Encode Resources

• Yale ENCODE site (http://encode.gersteinlab.org)
• Lab ENCODE information (http://wiki.gersteinlab.org/encode/index.php/Main_Page)
• National Human Genome Research Institute (NHGRI) ENCODE site (http://www.genome.gov/10005107)
• ENCODE Project Wiki (http://genomewiki.ucsc.edu/EncodeDCC/index.php/Main_Page) (encode/human)
• Media:Expressed_HumanTFs_Summary.xls - Listing of expressed human transcription factors (from RS, 22-Mar-07)
• Private spreadsheet of encode progress (http://spreadsheets.google.com/a/gersteinlab.org/ccc?key=pmo9zgFG74Q-h2gE4ggeQEg&hl=en)
• 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 (http://papers.gersteinlab.org/papers/tilinghmm)

Tilescope: online analysis pipeline for high-density tiling microarray data (http://papers.gersteinlab.org/papers/tilescope)

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. (http://papers.gersteinlab.org/papers/Tiling-analysis/)

Design optimization methods for genomic DNA tiling arrays. (http://papers.gersteinlab.org/papers/tilingtools)

Extrapolating Traditional DNA Microarray Statistics to the Tiling and Protein Microarray Technologies (http://papers.gersteinlab.org/papers/mie.microarray.analysis.review/)

Platform Comparison and Scoring

Platform comparison of ChIP-chip and ChIP-PET for optimal detection of transcription factor binding regions in mammalian cells (http://papers.gersteinlab.org/papers/chipchipcmp)

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome (http://papers.gersteinlab.org/papers/platformcmp)

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. (http://papers.gersteinlab.org/papers/encoderaceseq)

A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray. (http://papers.gersteinlab.org/papers/pilot-rice-tiling)

Pseudogene Annotation

Pseudogene.org: A comprehensive database and comparison platform for pseudogene annotation (http://papers.gersteinlab.org/papers/pgenedb)

A computational approach for identifying pseudogenes in the ENCODE regions (http://papers.gersteinlab.org/papers/pseudopiped)

Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis of Transcription and Evolution (http://papers.gersteinlab.org/papers/encodepgenes/)

Integrated pseudogene annotation for human chromosome 22: evidence for transcription. (http://papers.gersteinlab.org/papers/chr22-pgene-exp)

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. (http://papers.gersteinlab.org/papers/est-pgene-exp)

Relating TARs to ncRNAs

Structured RNAs in the ENCODE Selected Regions of the Human Genome (http://papers.gersteinlab.org/papers/encoderna/)

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 (http://papers.gersteinlab.org/papers/dart/)

Global Analysis of Regulatory Elements

Global Analysis of the Genomic Distribution and Correlation of Regulatory Elements in the ENCODE Regions (http://papers.gersteinlab.org/papers/tredist/)

Integrated analysis of experimental datasets reveals many novel promoters in 1% of the human genome (http://papers.gersteinlab.org/papers/encodepromoters)

BoCaTFBS: a Boosted-cascade Learner to Refine the Binding Sites Suggested by ChIP-chip experiments (http://papers.gersteinlab.org/papers/bocatfbs/)