https://info.gersteinlab.org/index.php?action=history&feed=atom&title=Encode_Information 2026-05-14T06:28:23Z Revision history for this page on the wiki MediaWiki 1.42.6 https://info.gersteinlab.org/index.php?title=Encode_Information&diff=98&oldid=prev 2010-06-10T14:00:50Z

<p>Created page with &#039;==Encode Resources== * [http://encode.gersteinlab.org Yale ENCODE site] * [http://wiki.gersteinlab.org/encode/index.php/Main_Page Lab ENCODE information] * [http://www.genome.gov…&#039;</p> <p><b>New page</b></p><div>==Encode Resources==<br /> * [http://encode.gersteinlab.org Yale ENCODE site]<br /> * [http://wiki.gersteinlab.org/encode/index.php/Main_Page Lab ENCODE information]<br /> * [http://www.genome.gov/10005107 National Human Genome Research Institute (NHGRI) ENCODE site]<br /> * [http://genomewiki.ucsc.edu/EncodeDCC/index.php/Main_Page ENCODE Project Wiki] (encode/human)<br /> * [[Media:Expressed_HumanTFs_Summary.xls]] - Listing of expressed human transcription factors (from RS, 22-Mar-07)<br /> * [http://spreadsheets.google.com/a/gersteinlab.org/ccc?key=pmo9zgFG74Q-h2gE4ggeQEg&amp;hl=en Private spreadsheet of encode progress]<br /> * [[DeadLines]]<br /> <br /> <br /> <br /> ==Published Papers==<br /> &#039;&#039;(Taken from google docs version at http://docs.google.com/View?docid=ddpspxzw_30g8b7xg)&#039;&#039;<br /> <br /> <br /> <br /> ===Scoring Tiling Arrays===<br /> ====Scoring TARs and ChIP-hits, Using them to Pick Subsets for Further Validation====<br /> =====[http://papers.gersteinlab.org/papers/tilinghmm A Supervised Hidden Markov Model Framework for Efficiently Segmenting Tiling Array Data in Transcriptional and ChIP-chip Experiments: Systematically Incorporating Validated Biological Knowledge]=====<br /> =====[http://papers.gersteinlab.org/papers/tilescope Tilescope: online analysis pipeline for high-density tiling microarray data]=====<br /> =====[http://papers.gersteinlab.org/papers/Tiling-analysis/ Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.]=====<br /> =====[http://papers.gersteinlab.org/papers/tilingtools Design optimization methods for genomic DNA tiling arrays.]=====<br /> =====[http://papers.gersteinlab.org/papers/mie.microarray.analysis.review/ Extrapolating Traditional DNA Microarray Statistics to the Tiling and Protein Microarray Technologies]=====<br /> <br /> ====Platform Comparison and Scoring====<br /> =====[http://papers.gersteinlab.org/papers/chipchipcmp Platform comparison of ChIP-chip and ChIP-PET for optimal detection of transcription factor binding regions in mammalian cells]=====<br /> =====[http://papers.gersteinlab.org/papers/platformcmp Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome]=====<br /> <br /> <br /> <br /> ===TAR characterization and inter-relation with annotation===<br /> =====[http://papers.gersteinlab.org/papers/encoderaceseq Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.]=====<br /> =====[http://papers.gersteinlab.org/papers/pilot-rice-tiling A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.]=====<br /> ====Pseudogene Annotation====<br /> =====[http://papers.gersteinlab.org/papers/pgenedb Pseudogene.org: A comprehensive database and comparison platform for pseudogene annotation]=====<br /> =====[http://papers.gersteinlab.org/papers/pseudopiped A computational approach for identifying pseudogenes in the ENCODE regions]=====<br /> =====[http://papers.gersteinlab.org/papers/encodepgenes/ Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis of Transcription and Evolution]=====<br /> =====[http://papers.gersteinlab.org/papers/chr22-pgene-exp Integrated pseudogene annotation for human chromosome 22: evidence for transcription.]=====<br /> =====[http://papers.gersteinlab.org/papers/est-pgene-exp Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.]=====<br /> <br /> ====Relating TARs to ncRNAs====<br /> =====[http://papers.gersteinlab.org/papers/encoderna/ Structured RNAs in the ENCODE Selected Regions of the Human Genome]=====<br /> ====Categorization and Clustering of TARs, the DART database====<br /> =====[http://papers.gersteinlab.org/papers/dart/ Analysis and Classification of Unannotated Transcription within the ENCODE Regions: Associating Transcription with Known and Novel Loci]=====<br /> <br /> <br /> ===Global Analysis of Regulatory Elements===<br /> =====[http://papers.gersteinlab.org/papers/tredist/ Global Analysis of the Genomic Distribution and Correlation of Regulatory Elements in the ENCODE Regions]=====<br /> =====[http://papers.gersteinlab.org/papers/encodepromoters Integrated analysis of experimental datasets reveals many novel promoters in 1% of the human genome]=====<br /> <br /> =====[http://papers.gersteinlab.org/papers/bocatfbs/ BoCaTFBS: a Boosted-cascade Learner to Refine the Binding Sites Suggested by ChIP-chip experiments]=====</div>

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