Computational Biology
371 items from inoue0426/awesome-computational-biology ★159
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ClawBio github.com
Bioinformatics-native AI agent skill library with local-first pharmacogenomics, ancestry PCA, semantic similarity, nutrigenomics, and metagenomics skills.
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PrimeKG github.com
Multi-modal precision medicine knowledge graph integrating clinical, genetic, and drug data.
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HyenaDNA github.com
Long-range genomic foundation model handling sequences up to 1M tokens with sub-quadratic attention.
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CellChat github.com
Inference and analysis of cell-cell communication ligand-receptor networks from single-cell transcriptomics data.
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UNI github.com
General-purpose self-supervised pathology foundation model trained on 100K+ whole-slide images for diverse computational pathology tasks.
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TAPE (Tasks Assessing Protein Embeddings) github.com
Benchmark suite of five biologically meaningful semi-supervised learning tasks for evaluating protein representations.
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Virtual Lab github.com
Human–AI collaborative research environment in which an LLM principal investigator coordinates specialized scientist agents for scientific discovery.
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State github.com
Transition model for predicting cellular perturbation responses across diverse contexts and sets of cells.
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CHIEF github.com
Clinical Histopathology Imaging Evaluation Foundation model integrating histology images and clinical context for pan-cancer analysis.
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ProGen2 github.com
Protein language model trained on diverse protein families for sequence generation and fitness prediction.
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EvoDiff github.com
Discrete diffusion framework for protein sequence generation trained on evolutionary-scale data, supporting unconditional generation, disordered region design, and functional motif scaffolding. [ paper-2023 ]
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Harmony github.com
Fast and scalable integration of single-cell data across datasets, conditions, technologies, and species.
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TxAgent github.com
Therapeutic reasoning agent using multi-step reasoning and a large scientific tool universe for drug interactions, contraindications, and personalized treatment analysis.
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GigaPath github.com
Slide-level digital pathology foundation model pretrained on 1.3 billion pathology image tokens from whole-slide images.
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DoubletFinder github.com
Machine learning approach for detecting multiplet (doublet) artifacts in single-cell RNA-seq data.
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JTVAE github.com
Junction tree variational autoencoder for molecular graph generation that guarantees chemical validity via a hierarchical tree decomposition.
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CONCH github.com
Vision-language foundation model for computational pathology trained with contrastive captioning on pathology image–text pairs.
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DiffSBDD github.com
Equivariant diffusion model for structure-based drug design that generates molecules and binding conformations for protein targets.
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scVelo github.com
RNA velocity estimation for single-cell transcriptomics, inferring the direction and speed of cell differentiation.
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ChemBERTa-2 github.com
RoBERTa-based molecular language model pretrained on SMILES for small-molecule representation learning.
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SCENIC github.com
Single-cell regulatory network inference and clustering linking transcription factors to co-expressed gene modules.
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Genomi github.com
Local-first genomics agent runtime that indexes personal variants, queries evidence, and generates evidence-grounded reports while keeping raw genome data on-device.
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GLUE github.com
Graph-Linked Unified Embedding framework for unpaired single-cell multi-omics data integration across RNA, ATAC, methylation, and protein modalities.
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ProteinGym github.com
Large-scale benchmark of deep mutational scanning assays for evaluating protein fitness landscape models.
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scFoundation github.com
Large-scale foundation model for single-cell gene expression, enabling multiple downstream tasks.
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scIB (Single-cell Integration Benchmarks) github.com
Comprehensive benchmarking framework for single-cell data integration methods.
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MOFA+ github.com
Multi-Omics Factor Analysis framework identifying shared axes of variation across bulk and single-cell datasets including RNA, ATAC, proteomics, methylation, and copy number.
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MolFormer github.com
Linear attention transformer pretrained on millions of SMILES strings for efficient molecular embeddings.
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GEARS github.com
Graph-based model for predicting transcriptional responses to single and combinatorial genetic perturbations using biological priors.
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scArches github.com
Transfer learning framework for mapping new single-cell datasets onto pre-trained reference atlases across batches, conditions, and modalities.
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GROVER github.com
Self-supervised graph transformer for large-scale molecular representation learning from unlabeled compounds.
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RNA-FM github.com
General-purpose RNA foundation model pretrained on large-scale RNA sequences for structural and functional representation learning.
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GPN (Genomic Pre-trained Network) github.com
Masked language model for DNA sequences enabling zero-shot variant effect prediction without requiring functional annotations.
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PLIP github.com
Vision-language foundation model for pathology trained with contrastive learning on pathology image–text pairs for image classification and text-to-image retrieval.
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ReLeaSE github.com
Deep reinforcement learning framework for de novo drug design combining a generative and predictive model.
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TITAN github.com
Multimodal whole-slide pathology foundation model that combines image and language supervision for slide-level representation and zero-shot analysis.
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scBERT github.com
BERT-based foundation model pretrained on large-scale scRNA-seq data for cell type annotation.
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