Mouse Epigenetics and Gene Expression
- Dynamics of microRNA expression during mouse prenatal development https://genome.cshlp.org/content/early/2019/10/23/gr.248997.119
- An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis https://genome.cshlp.org/content/early/2020/03/04/gr.255760.119
Human Transcripts and RNA Regulation
- A limited set of transcriptional programs define major cell types http://www.genome.org/cgi/doi/10.1101/gr.263186.120
- Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01982-9
- Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function https://genome.cshlp.org/content/29/9/1402.full
Computational Analysis and Tools
- RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01979-4
- Epigenome-based splicing prediction using a recurrent neural network https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008006
- TopicNet: a framework for measuring transcriptional regulatory network change https://doi.org/10.1093/bioinformatics/btaa403
- DiNeR: a Differential Graphical Model of Network Rewiring to Infer Transcription Factor Co-binding Alterations https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03605-3
- A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1924-8
- Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01977-6
- Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01978-5
- Measuring the reproducibility and quality of Hi-C data https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1658-7
- IDR2D identifies reproducible genomic interactions https://academic.oup.com/nar/article/48/6/e31/5721212
An exhaustive list of all ENCODE and community publications can be found on the ENCODE portal: https://www.encodeproject.org/publications/