ReviewPeerJ2022
Genomics enters the deep learning era.
Review in PeerJ, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Application of artificial intelligence in the diagnosis of malignant digestive tract tumors: focusing on opportunities and challenges in endoscopy and pathology.Journal of translational medicine · 2025Pooled it
- seqLens: Optimizing Language Models for Genomic Predictions.Molecular biology and evolution · 2026Article
- Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models.Briefings in bioinformatics · 2026Review
- Discriminating models of trait evolution.Evolution; international journal of organic evolution · 2026Article
- A Systematic Review: Deep Learning for Analyzing Genomic Data to Discover Evolutionary Patterns.Scientifica · 2026Review
- Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs.bioRxiv : the preprint server for biology · 2025Article
- Increasing pathogenic germline variant diagnosis rates in precision medicine: current best practices and future opportunities.Human genomics · 2025Review
- DNA promoter task-oriented dictionary mining and prediction model based on natural language technology.Scientific reports · 2025Article
- Multi-omics approaches for biomarker discovery and precision diagnosis of prediabetes.Frontiers in endocrinology · 2025Review
- Image-based deep learning model using DNA methylation data predicts the origin of cancer of unknown primary.Neoplasia (New York, N.Y.) · 2024Article
- In silico design of DNA sequences for in vivo nucleosome positioning.Nucleic acids research · 2024Article
- An Explainable Deep Learning Classifier of Bovine Mastitis Based on Whole-Genome Sequence Data-Circumventing the p >> n Problem.International journal of molecular sciences · 2024Article
- DeepReg: a deep learning hybrid model for predicting transcription factors in eukaryotic and prokaryotic genomes.Scientific reports · 2024Article
- Advancing Regulatory Genomics With Machine Learning.Bioinformatics and biology insights · 2024Review
- Multiple-instance learning of somatic mutations for the classification of tumour type and the prediction of microsatellite status.Nature biomedical engineering · 2024Article
- Deep learning-derived 12-lead electrocardiogram-based genotype prediction for hypertrophic cardiomyopathy: a pilot study.Annals of medicine · 2023Article
- Toward a comprehensive catalog of regulatory elements.Human genetics · 2023Review
- OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes.Nucleic acids research · 2023Article
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Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The tremendous amount of biological sequence data available, combined with the recent methodological breakthrough in deep learning in domains such as computer vision or natural language processing, is leading today to the transformation of bioinformatics through the emergence of deep genomics, the application of deep learning to genomic sequences. We review here the new applications that the use of deep learning enables in the field, focusing on three aspects: the functional annotation of genomes, the sequence determinants of the genome functions and the possibility to write synthetic genomic sequences.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.