BH12.12/op.ENcode/ENCODE論文一覧

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  1. An integrated encyclopedia of DNA elements in the human genome
    1. http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955616
  2. Landscape of transcription in human cells
    1. http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955620
  3. The accessible chromatin landscape of the human genome
    1. http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955617
  4. An expansive human regulatory lexicon encoded in transcription factor footprints
    1. http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955618
  5. Architecture of the human regulatory network derived from ENCODE data
    1. http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955619
  6. The long-range interaction landscape of gene promoters
    1. http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955621
  7. Annotation of functional variation in personal genomes using RegulomeDB
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431494/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955989
  8. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    1. http://genome.cshlp.org/content/22/9/1813
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955991
  9. Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431487/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955982
  10. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431479/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955974
  11. Discovery of hundreds of mirtrons in mouse and human small RNA data
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431481/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955976
  12. GENCODE: The reference human genome annotation for The ENCODE Project
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431492/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955987
  13. Linking disease associations with regulatory information in the human genome
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431491/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955986
  14. Long noncoding RNAs are rarely translated in two human cell lines
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431482/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955977
  15. Personal and population genomics of human regulatory variation
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431486/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955981
  16. Predicting cell-type–specific gene expression from regions of open chromatin
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431488/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955983
  17. RNA editing in the human ENCODE RNA-seq data
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431480/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955975
  18. Sequence and chromatin determinants of cell-type–specific transcription factor binding
    1. http://genome.cshlp.org/content/22/9/1723.full
  19. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431493/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955988
  20. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431490/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955985
  21. Understanding transcriptional regulation by integrative analysis of transcription factor binding data
    1. http://genome.cshlp.org/content/22/9/1658.abstract
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955978
  22. Widespread plasticity in CTCF occupancy linked to DNA methylation
    1. http://genome.cshlp.org/content/22/9/1680.abstract
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955980
  23. A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells
    1. http://genome.cshlp.org/content/22/9/1668.abstract
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955979
  24. Analysis of variation at transcription factor binding sites in Drosophila and humans
    1. http://genomebiology.com/2012/13/9/R49
    2. http://www.ncbi.nlm.nih.gov/pubmed/22950968
  25. Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3
    1. http://genomebiology.com/2012/13/9/R52
    2. http://www.ncbi.nlm.nih.gov/pubmed/22951069
  26. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription related factors
    1. http://genomebiology.com/2012/13/9/R48
    2. http://www.ncbi.nlm.nih.gov/pubmed/22950945
  27. Functional analysis of transcription factor binding sites in human promoters
    1. http://genomebiology.com/2012/13/9/R50
    2. http://www.ncbi.nlm.nih.gov/pubmed/22951020
  28. Modeling gene expression using chromatin features in various cellular contexts
    1. http://genomebiology.com/2012/13/9/R53
    2. http://www.ncbi.nlm.nih.gov/pubmed/22950368
  29. The GENCODE pseudogene resource
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491395/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22951037
  30. Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data
    1. http://www.biomedcentral.com/1471-2156/13/46
    2. http://www.ncbi.nlm.nih.gov/pubmed/22963177
  31. Circuitry and dynamics of human transcription factor regulatory networks
    1. http://www.cell.com/abstract/S0092-8674(12)00639-3?script=true
    2. http://www.ncbi.nlm.nih.gov/pubmed/22959076
  32. Evidence of abundant purifying selection in humans for recently acquired regulatory functions.
    1. http://www.sciencemag.org/content/337/6102/1675.long
    2. http://www.ncbi.nlm.nih.gov/pubmed/22956687
  33. Systematic localization of common disease-associated variation in regulatory DNA.
    1. http://www.sciencemag.org/content/early/2012/09/04/science.1222794.full?explicitversion=true
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955828
  34. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
    1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431495/
    2. http://www.ncbi.nlm.nih.gov/pubmed/22955990
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