How to cite

Webserver

Guillen-Ramirez, H.A., Hermoso, T., Ponomarenko, J., R., Johnson (2021). ElementaLdb: a user-friendly webserver for exploring and retrieving lncRNA elements. Noncoding RNA World: From Mechanism to Therapy Conference.

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
BROADHISTONE	Please refer to the experiment table
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.
CHROMREMODELER	Please refer to the experiment table
COFACTOR	Please refer to the experiment table
COHESIN	Please refer to the experiment table
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.
DNAREPAIR	Please refer to the experiment table
DNAREPLICATION	Please refer to the experiment table
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.
NARROWHISTONE	Please refer to the experiment table
phastCons	Siepel, A. (2005). Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research, 15(8), 1034–1050.
RBP-DNA	Please refer to the experiment table
RBP-RNA	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.
RNAPOLCOMPLEX	Please refer to the experiment table
TF	Please refer to the experiment table
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.