ENCODE2 Paper Collection
Papers in Nature
Analysis of variation at transcription factor binding sites in Drosophila and humans
Spivakov, M. et al.
Annotation of functional variation in personal genomes using RegulomeDB.
Boyle, A.P. et al.
Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3
Frietze, S. et al.
ChIP-seq guidelines and practices used by the ENCODE and modENCODE consortia.
Landt, S.G. et al.
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription related factors
Yip, K.Y. et al.
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
Howald, C. et al.
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
Tilgner, H. et al.
Discovery of hundreds of mirtrons in mouse and human small RNA data
Ladewig, E. et al.
Functional analysis of transcription factor binding sites in human promoters
Whitfield, T.W. et al.
GENCODE: The reference human genome annotation for the ENCODE project
Harrow, J. et al.
Linking disease associations with regulatory information in the human genome.
Schaub, M.A. et al.
Long noncoding RNAs are rarely translated in two human cell lines
Bánfai, B. et al.
Modeling gene expression using chromatin features in various cellular contexts
Dong, X. et al.
Personal and population genomics of human regulatory variation.
Vernot, B. et al.
Predicting cell-type–specific gene expression from regions of open chromatin.
Natarajan, A. et al.
RNA editing in the human ENCODE RNA-seq data
Park, E. et al.
Sequence and chromatin determinants of cell-type–specific transcription factor binding.
Arvey, A. et al.
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
Wang, J. et al.
Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data
Ni et al.
The GENCODE pseudogene resource
Pei, B. et al.
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression.
Derrien, T. et al.
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.
Kundaje, A. et al.
Understanding transcriptional regulation by integrative analysis of transcription factor binding data.
Cheng, C. et al.
Widespread plasticity in CTCF occupancy linked to DNA methylation
Wang, H. et al.
A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells.
Charos, A.E. et al.