BH12.12/op.ENcode/paper catalog


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1. An integrated encyclopedia of DNA elements in the human genome

2. Landscape of transcription in human cells

3. The accessible chromatin landscape of the human genome

4. An expansive human regulatory lexicon encoded in transcription factor footprints

5. Architecture of the human regulatory network derived from ENCODE data

6. The long-range interaction landscape of gene promoters

7. Annotation of functional variation in personal genomes using RegulomeDB

8. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

9. Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

10. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

11. Discovery of hundreds of mirtrons in mouse and human small RNA data

12. GENCODE: The reference human genome annotation for The ENCODE Project

13. Linking disease associations with regulatory information in the human genome

14. Long noncoding RNAs are rarely translated in two human cell lines

15. Personal and population genomics of human regulatory variation

16. Predicting cell-type–specific gene expression from regions of open chromatin

17. RNA editing in the human ENCODE RNA-seq data

18. Sequence and chromatin determinants of cell-type–specific transcription factor binding

19. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

20. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

21. Understanding transcriptional regulation by integrative analysis of transcription factor binding data

22. Widespread plasticity in CTCF occupancy linked to DNA methylation

23. A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells

24. Analysis of variation at transcription factor binding sites in Drosophila and humans

25. Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3

26. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription related factors

27. Functional analysis of transcription factor binding sites in human promoters

28. Modeling gene expression using chromatin features in various cellular contexts

29. The GENCODE pseudogene resource

30. Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data

31. Circuitry and dynamics of human transcription factor regulatory networks

32. Evidence of abundant purifying selection in humans for recently acquired regulatory functions.

33. Systematic localization of common disease-associated variation in regulatory DNA.

34. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors