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A directory of tools, AI models, datasets, and research resources for biotech, bioinformatics, and other scientific fields. Aggregated from curated GitHub awesome-lists, HuggingFace, bio.tools, Bioconductor, and more.
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10 of 5,940 resources
Gene expression prediction
Transformer encoder-decoder for de novo peptide sequencing from tandem mass spectrometry, translating MS/MS spectra directly to peptide sequences without reference databases, enabling identification of novel peptides for immunopeptidomics, antibody repertoires, and metaproteomes (Noble Lab UW, Nature Communications 2024)
Google DeepMind's unified DNA sequence foundation model predicting molecular consequences of genetic variants from single-base resolution up to 1 megabase context, jointly outputting thousands of regulatory tracks (RNA expression, splicing, chromatin accessibility, TF binding, contact maps) for human and mouse genomes via a Python client and non-commercial API (2025)
General-purpose RNA language model with 650M parameters pretrained on 36M non-coding RNA sequences, achieving strong generalization on structure prediction tasks including secondary structure prediction, splice-site prediction, mean ribosome loading, and ncRNA classification (lbcb-sci, 165+ stars, Apache-2.0)
First architecture deeply integrating a DNA foundation model with an LLM for multimodal biological reasoning, achieving 98% accuracy on KEGG disease pathway prediction and 15%+ average gains on variant effect prediction with interpretable step-by-step reasoning traces (bowang-lab, 390+ stars)
Apache 2.0 single-cell foundation model family scaling to 3B parameters, pretrained on 266M cell profiles including perturbation data and released with training, embedding, and downstream benchmarking workflows for disease-relevant single-cell tasks (2025)
Efficient foundation model and benchmark for multi-species genome understanding with context-aware nucleotide representations, improving upon DNABERT for diverse genomic task transfer learning (UIUC MAGICS Lab, 484+ stars)
Teaching Large Language Models the Language of Biology through single-cell transcriptomics (ICML 2024)
End-to-end RNA 3D structure prediction using RNA language model pretrained on 23.7M sequences, outperforming existing methods and human expert groups on RNA-Puzzles and CASP15 (Nature Methods 2024)
Google DeepMind's AlphaFold-derived classifier for proteome-wide missense variant effect prediction, providing pathogenicity scores for all ~71M possible human missense variants and classifying 89% with 90% precision; pre-computed predictions are integrated into Ensembl VEP and UCSC Genome Browser to support clinical variant interpretation (Science 2023)