All Competitors

CRISPR/Cas9 off-target prediction that fine-tunes a DNA language model and gates in chromatin signal, reaching 0.550 PR-AUC on GUIDE-seq data.

Whole-genome bacterial pathogenicity prediction from ProtT5 embeddings, alignment-free and taxonomy-agnostic, with per-protein attention scores.

Multi-modal single-cell foundation model that projects Enformer DNA embeddings into a transcriptome model token space to predict gene regulation.

Multimodal 3D genome foundation model pairing Hi-C contact maps with epigenomic tracks, pretrained on over one million paired samples.

C/D box snoRNA gene predictor for any eukaryote genome, built on DNABERT and able to separate expressed snoRNAs from their pseudogenes.

Bacterial genome language model tokenizing whole genomes as ordered conserved elements; frozen embeddings beat Pfam baselines on 23 of 25 phenotypes.

DNA and RNA language model with a data-driven 4,096-token unigram vocabulary, matching larger genomic foundation models at 89.2M parameters.

Enhancer models predicting cell-type-specific chromatin accessibility from DNA sequence, with a pretrained zoo and synthetic enhancer design tools.

Hi-C resolution enhancement model combining a U²-Net with self-attention to recover TAD boundaries and chromatin loops from sparse contact maps.

Regulatory genomics foundation model pretrained on 6,391 human ChIP-seq cistromes, representing how ~1,000 transcription regulators cooperate.

Protein function prediction fusing five Gene Ontology pipelines, two of them deep models over protein and DNA language model embeddings.

DNA language model for SELEX aptamer libraries that embeds single-stranded oligonucleotides so enrichment and target specificity become measurable.

265M-parameter genomic foundation model whose BioToken scheme folds variants and region annotations into the tokens for variant effect prediction.

Splice-site and variant-impact prediction from DNA sequence, with pretrained models for human, mouse, zebrafish, honey bee, and Arabidopsis.

Long-context genomic foundation model reading up to 192,000 base pairs at single-nucleotide resolution with dense LLaMA-style self-attention.

Bacterial genome encoder that renders draft assemblies as Chaos Game Representation images and embeds them for nearest-neighbour species search.

Enhancer prediction from DNA sequence alone, reaching 88.05% accuracy and 76.22% MCC on held-out ENCODE cCRE regions and annotating the whole genome.

Natural product chemistry prediction from biosynthetic gene clusters, assigning ChemOnt ontology classes from the cluster's Pfam domain composition.

Phylogenetic tree inference from unaligned nucleotide sequences, using a 2D genomic-footprint encoding and CNN classification of triplet topologies.

Genomic language models with disentangled attention, pretrained on prokaryotic and eukaryotic genomes for sequence classification and variant effects.

Genomic language model for variant effect prediction that scores deleterious mutations from a single DNA sequence, with no alignment at inference.

Secondary metabolite structure prediction from microbial biosynthetic gene clusters, generating SMILES strings from Pfam functional-domain tokens.

Structure-aware adapter that injects chromatin-derived gene regulatory networks into single-cell RNA foundation models like scGPT and scFoundation.