All Competitors
Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 1–15 of 15 filtered models
HoloCell
———860M-parameter generative single-cell foundation model that jointly represents and generates epigenomic, transcriptomic, and proteomic modalities.
Single-cellDNA & Gene21OpennessTransformer that infers whole-genome DNA methylation from gene expression, generalizing zero-shot to unmeasured CpG sites and unseen samples.
DNA & Gene10OpennessGenoME
—1—Mixture-of-Experts generative model turning DNA sequence plus cell-type ATAC-seq into unified epigenomic, transcriptomic, and 3D chromatin profiles.
DNA & GeneSingle-cell8OpennessMelody
———Deep learning framework that predicts DNA methylation from genomic sequence across 39 human tissues, with an scRNA-seq variant for unseen cell types.
DNA & Gene8OpennessChromatin-state language model pretrained on ROADMAP annotations from 127 human cell types to find chromatin-state motifs and predict gene expression.
DNA & Gene86OpennessMuLan-Methyl
7105Multi-language transformer framework using five pre-trained language models to predict DNA methylation (6mA, 4mC, 5hmC) across species.
DNA & Gene89OpennessmEthAE
34—Chromosome-wise explainable autoencoder that compresses DNA methylation array data up to 400-fold while keeping CpG groupings interpretable.
DNA & Gene47OpennessEpiGePT
3311—Transformer model predicting context-specific epigenomic signals across cell types using DNA sequence and transcription factor activity profiles.
DNA & Gene65OpennessTransferChrome
—20—Gene expression prediction from histone modifications, combining self-attention with dense convolutions and transfer learning across cell types.
DNA & Gene22OpennessChromoformer
3944—Transformer predicting gene expression from histone modifications, using promoter-enhancer Hi-C interactions to capture distal regulatory effects.
DNA & Gene71OpennessiDNA-ABF
15141—DNA language model for interpretable prediction of 4mC, 5hmC, and 6mA methylation sites across species, using multi-scale k-mer BERT encoders.
DNA & Gene53OpennessINTERACT
1125—Lieber Institute for Brain DevelopmentAugust 16, 2022deep_learningdna_methylationepigenomic_prediction+4Deep learning model predicting DNA methylation regulatory variants at CpG sites in the human brain, fine-mapping psychiatric disorder risk loci.
DNA & Gene9OpennessBERT6mA
516—BERT-based predictor of DNA N6-methyladenine (6mA) modification sites, using word2vec encoding and cross-species transfer learning.
DNA & Gene45OpennessCpG Transformer
3921—Transformer that imputes missing CpG methylation states from sparse single-cell bisulfite sequencing, modeling genomic and cell-level structure.
DNA & Gene79OpennessAttentiveChrome
27101—Attention-based model predicting gene expression from histone modification signals across 56 cell types, with interpretable attention scores.
DNA & Gene80Openness