BH12.12/op.ENcode/paper catalog

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1. An integrated encyclopedia of DNA elements in the human genome http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html

2. Landscape of transcription in human cells http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html

3. The accessible chromatin landscape of the human genome http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html


4. An expansive human regulatory lexicon encoded in transcription factor footprints http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html


5. Architecture of the human regulatory network derived from ENCODE data http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html

6. The long-range interaction landscape of gene promoters http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html

7. Annotation of functional variation in personal genomes using RegulomeDB http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431494/


8. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia http://genome.cshlp.org/content/22/9/1813


9. Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431487/


10. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431479/

11. Discovery of hundreds of mirtrons in mouse and human small RNA data http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431481/

12. GENCODE: The reference human genome annotation for The ENCODE Project http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431492/

13. Linking disease associations with regulatory information in the human genome http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431491/

14. Long noncoding RNAs are rarely translated in two human cell lines http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431482/

15. Personal and population genomics of human regulatory variation http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431486/

16. Predicting cell-type–specific gene expression from regions of open chromatin http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431488/

17. RNA editing in the human ENCODE RNA-seq data http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431480/


18. Sequence and chromatin determinants of cell-type–specific transcription factor binding 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 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431493/

20. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431490/

21. Understanding transcriptional regulation by integrative analysis of transcription factor binding data http://genome.cshlp.org/content/22/9/1658.abstract

22. Widespread plasticity in CTCF occupancy linked to DNA methylation http://genome.cshlp.org/content/22/9/1680.abstract

23. A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells http://genome.cshlp.org/content/22/9/1668.abstract

24. Analysis of variation at transcription factor binding sites in Drosophila and humans http://genomebiology.com/2012/13/9/R49

25. Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3 http://genomebiology.com/2012/13/9/R52

26. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription related factors http://genomebiology.com/2012/13/9/R48

27. Functional analysis of transcription factor binding sites in human promoters http://genomebiology.com/2012/13/9/R50

28. Modeling gene expression using chromatin features in various cellular contexts http://genomebiology.com/2012/13/9/R53

29. The GENCODE pseudogene resource http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491395/

30. Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data http://www.biomedcentral.com/1471-2156/13/46

31. Circuitry and dynamics of human transcription factor regulatory networks http://www.cell.com/abstract/S0092-8674(12)00639-3?script=true


32. Evidence of abundant purifying selection in humans for recently acquired regulatory functions. http://www.sciencemag.org/content/337/6102/1675.long

33. Systematic localization of common disease-associated variation in regulatory DNA. http://www.sciencemag.org/content/early/2012/09/04/science.1222794.full?explicitversion=true

34. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431495/

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