A Nextflow pipeline model zoo for RNA deep learning — 22 models across translation, structure, splicing, modification, and more.
| Model | Track | Task | Paper | License |
|---|---|---|---|---|
| RiboNN | Translation | TE prediction (82 cell types) | Nature Biotech 2025 | Apache 2.0 |
| Riboformer | Translation | Codon-level ribosome density | Nature Comms 2024 | MIT |
| RiboTIE | Translation | ORF detection from ribo-seq | Nature Comms 2025 | MIT |
| TranslationAI | Translation | TIS / TTS / ORF prediction | NAR 2025 | AGPL-3.0 + CC BY-NC 4.0 |
| Saluki | Translation | mRNA half-life | Genome Biology 2022 | Apache 2.0 |
| CodonTransformer | Translation | Codon optimization (164 organisms) | Nature Comms 2025 | Apache 2.0 |
| RNA-FM | Foundation | RNA embeddings (640-d) | arXiv 2022 | MIT |
| RiNALMo | Foundation | RNA embeddings (1280-d) | Nat. Commun. 2025 | Apache 2.0 |
| ERNIE-RNA | Foundation | Structure-aware embeddings (768-d) | Nature Comms 2025 | MIT |
| Orthrus | Foundation | Mamba mRNA embeddings (4-track, 512-d, GPU) | Nature Methods 2026 | MIT |
| RNAErnie | Foundation | Motif-aware RNA embeddings (768-d) | Nature Mach Intell 2024 | Apache-2.0 |
| PlantRNA-FM | Foundation | Plant-only RNA embeddings (480-d) | Nature Mach Intell 2024 | MIT |
| CaLM | Foundation | Codon-level RNA embeddings (768-d) | Nature Mach Intell 2024 | BSD-3-Clause |
| mRNABERT | Foundation | Hybrid UTR/CDS mRNA embeddings (768-d) | Nature Comms 2025 | Apache-2.0 |
| RhoFold | Structure | 3D structure (PDB output) | Nature Methods 2024 | Apache 2.0 |
| SPOT-RNA | Structure | 2D structure + pseudoknots | Nature Comms 2019 | MPL-2.0 |
| DRfold2 | Structure | Single-seq ab initio 3D (GPU) | PLOS Biology 2026 | MIT |
| Pangolin | Splicing | Tissue-specific variant-effect splice scores | Genome Biology 2022 | GPL-3.0 |
| SpliceAI | Splicing | Variant-effect splicing scores (4-class delta) | Cell 2019 | PolyForm Strict + CC BY-NC 4.0 |
| SpliceBERT | Splicing | Vertebrate primary-RNA embeddings (512-d) | Brief. Bioinform. 2024 | BSD-3-Clause |
| MultiRM | Modification | 12 RNA modification types | Nat. Commun. 2021 | MIT |
| UTR-LM | mRNA Design | 5'UTR MRL / TE / expression | Nature Mach Intell 2024 | GPL-3.0 |