There are many machine learning methods used in human genomics, taking deep learning as an example:

- DeepCpG. Based on Gated Recurrent Unit (GRU), is used for the prediction of methylation state from single-cell data. 
- DanQ. Based on Long Short-Term Memory networks (LSTMs), is used for the prediction of DNA function from sequence data.
- DeepBind. Based on Convolutional Neural Network (CNN), is used to characterise DNA- and RNA-binding protein specificity.
- Xpresso. Based on CNN, is used for the prediction of gene expression levels from genomic sequence.
- Entrez databases. Based on Natural Language Processing (NLP), is used to provide integrated access to nucleotide and protein sequence data, gene-centered and genomic mapping information, etc.
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