| Title | Citation |
|---|---|
| GENCODE | Frankish, Adam, et al. "GENCODE 2021." Nucleic acids research 49.D1 (2021): D916-D923. |
| ezTracks | Guillen-Ramirez, H.A., Johnson, R. (2021). ezTracks (Version v0.1.0). Zenodo. http://doi.org/10.5281/zenodo.4749431 |
| cCRE (Candidate cis-Regulatory Elements by ENCODE) | Moore, Jill E., et al. "Expanded encyclopaedias of DNA elements in the human and mouse genomes." Nature 583.7818 (2020): 699-710. |
| CpG Islands | Kent, W. James, et al. "The human genome browser at UCSC." Genome research 12.6 (2002): 996-1006. |
| CRS | Seemann, Stefan E., et al. "The identification and functional annotation of RNA structures conserved in vertebrates." Genome research 27.8 (2017): 1371-1383. |
| MREs/encori | Zhou KR, Liu S, Cai L, Bin L, et al. ENCORI: The Encyclopedia of RNA Interactomes. |
| MREs/mircode.highcons | Jeggari, Ashwini, Debora S. Marks, and Erik Larsson. "miRcode: a map of putative microRNA target sites in the long non-coding transcriptome." Bioinformatics 28.15 (2012): 2062-2063. |
| MREs/mircode.mediumcons | Jeggari, Ashwini, Debora S. Marks, and Erik Larsson. "miRcode: a map of putative microRNA target sites in the long non-coding transcriptome." Bioinformatics 28.15 (2012): 2062-2063. |
| phastCons | Siepel, A. (2005). Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research, 15(8), 1034–1050. |
| RBP | Please refer to the experiment table |
| repeats | Smit, A., Hubley, R., & Green, P. (2013, 2015). RepeatMasker Open-4.0. http://www.repeatmasker.org |
| RIDLS | Carlevaro-Fita, Joana, et al. "Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs." Genome research 29.2 (2019): 208-222. |
| RNA:DNA/R-Loop | Sanz, Lionel A., et al. "Prevalent, dynamic, and conserved R-loop structures associate with specific epigenomic signatures in mammals." Molecular cell 63.1 (2016): 167-178. |
| RNA:DNA/TriplexRNA | Sentürk Cetin, Nevcin, et al. "Isolation and genome-wide characterization of cellular DNA: RNA triplex structures." Nucleic acids research 47.5 (2019): 2306-2321. |
| TFBS | Pachkov, Mikhail, et al. "SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates." Nucleic acids research 41.D1 (2012): D214-D220. |
| UCSC literature | Haeussler, Maximilian, Martin Gerner, and Casey M. Bergman. "Annotating genes and genomes with DNA sequences extracted from biomedical articles." Bioinformatics 27.7 (2011): 980-986. |
| RNA modifications | Sun, Wen-Ju, et al. "RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data." Nucleic acids research 44.D1 (2016): D259-D265. |
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska Curie grant agreement No 884178 (RNADOMAIN)