Table 2. Overview of studies developing deep learning methodologies in genomics.

Annotation	Usage	Preprocessing	Data	Species	Architecture	Reference
epigenetic mark	Bio. mechanism	one-hot-encoding	DNA + chromatin accessibility	human	CNN	Yin et al. (2019)
			DNA + CpG neighborhood of cells	human	CNN + RNN	Angermueller et al. (2017)
			DNA sequence	human	CNN	Zeng & Gifford (2017)
			RNA sequence	human + mouse + zebrafish	CNN + RNN	Zhang & Hamada (2018)
polyadenylation	Bio. mechanism	one-hot-encoding	DNA sequence	Arabidopsis thaliana	CNN	Gao et al. (2018)
				human	CNN	Leung, Delong & Frey (2018)
	Syn. genomics	one-hot-encoding	DNA sequence	human	CNN	Bogard et al. (2019)
polyadenylation + translation initiation site	transfer	one-hot-encoding	DNA sequence	human + mouse + bovine + drosophilia	CNN	Kalkatawi et al. (2019)
splicing	Bio. mechanism	one-hot-encoding	DNA sequence	human	CNN	Cheng et al. (2019)
						Cheng et al. (2021)
						Du et al. (2018)
			RNA sequence	human	CNN	Jaganathan et al. (2019)
					CNN	Wang & Wang (2019)
D architecture	Bio. mechanism	one-hot-encoding	DNA sequence	human	CNN	Zhou (2021)
					CNN	Fudenberg, Kelley & Pollard, 2020
					CNN + RNN	Singh et al. (2019)
				human + mouse	CNN	Schwessinger et al. (2020)
nucleosome	Bio. mechanism	one-hot-encoding	DNA sequence	yeast	CNN	Routhier et al. (2021)
nucleosome + TFBS	Bio. mechanism	one-hot-encoding	DNA sequence	yeast + human	CNN	Cakiroglu et al. (2021)
enhancer	transfer	embedding	DNA sequence	6 species	CNN	Chen, Fish & Capra (2018)
	Bio. mechanism + Syn. genomics	one-hot-encoding	DNA sequence	6 pecies	CNN + RNN	Minnoye et al. (2020)
	Bio. mechanism	one-hot-encoding	DNA sequence	human	CNN	Min et al. (2017b))
promoter	transfer	one-hot-encoding	DNA sequence	5 species	CNN	Khodabandelou, Routhier & Mozziconacci (2020)
promoter + enhancer + TFBS + chromatin accessibility	Bio. mechanism	one-hot-encoding	DNA sequence	human	CNN	Wesolowska-Andersen et al. (2020)
translation initiation site	Bio. mechanism	one-hot-encoding	DNA sequence	human	CNN + RNN	Zhang et al. (2017)
sgRNA	Syn. genomics	one-hot-encoding	DNA + TFBS + epigenetic + accessibility	human	CNN	Chuai et al. (2018)
binding site			DNA sequence	human + mouse	CNN	Xue et al. (2018)
Virus integration	Bio. mechanism	one-hot-encoding	DNA sequence	human	CNN + Attention	Tian et al. (2021)
Overview of studies applying deep learning in genomics, segmented by their usage.