A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.

ICML 2026 · AI × Biomedical Papers — 315 curated papers on protein design, genomics, drug discovery, clinical AI, and more

3,722 AI × Biology papers from ICLR / ICML / NeurIPS (2010–2026) — browsable by venue & year

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Structure-Based Virtual Screening Pipeline for AI Agents

ESM-2 style protein language model (9.6M params) trained on Swiss-Prot with MLU370

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A curated, auditable directory of AI-first biology labs worldwide — lab/team-centric, provenance-tagged. Live: biotender.online/labs

Biomni 平台技能目录 - 覆盖单细胞、多组学、药物发现、遗传学等生物医学研究全流程

One command to install bio agent skills into your AI coding agent — npx bioskill install

Convert academic PDF papers to engaging videos using AI

Comprehensive molecular visualization and analysis skill powered by PyMOL. One description → publication-quality figure + analysis.

A curated list of AI tools, models, and resources for biology and life sciences

BioTender · AI×Biology Corpus: 3,722 papers at the intersection of ML and biology (ICLR/ICML/NeurIPS 2010-2026)

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AbDev: Antibody Developability Assessment Pipeline — in-silico developability profiling for therapeutic antibodies and nanobodies

Shotgun Metagenomics & 16S rRNA Analysis Engine

ESM-2 Zero-Shot Mutation Fitness Prediction with ProteinGym Benchmark Validation

Independent benchmark of 4 open-source protein structure prediction models (Chai-1, Boltz-2, ESMCFold2, ESMCFold2-Fast) on 50 new CAMEO targets — accuracy, speed, failure rate, confidence calibration.

GitHub Profile README

Phylogenetic analysis: NJ/UPGMA trees, bootstrap support, ancestral sequence reconstruction

47 curated computational biology & bioinformatics skills for AI agents

LigandAI end-to-end peptide & protein binder design skills — discovery, generation, folding, scoring, bivalent design

Pure NumPy/SciPy Hi-C chromatin 3D genome analysis engine — ICE normalization, TAD detection, A/B compartments, loop calling

End-to-end training kit for compact protein language models — ESM-2 architecture, Swiss-Prot data pipeline, MLM training, zero-shot fitness evaluation, and model upload.

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BioTender 中文长文公开档案库 — AI×生物学深度分析文章

AI agent for peptide design: multi-agent pipeline with PDB, UniProt, conservation, Boltz structure prediction, and literature tools.

A curated list of awesome AI tools, libraries, papers, datasets, and frameworks that accelerate scientific discovery — from physics and chemistry to biology, materials, and beyond.

😎 Awesome lists about all kinds of interesting topics

A curated collection of 1000+ agent skills from official dev teams and the community, compatible with Claude Code, Codex, Gemini CLI, Cursor, and more.

A curated list of awesome Claude Skills, resources, and tools for customizing Claude AI workflows

Expert SKILL.md packages for 52 landmark computational biologists — distilled from primary sources, interviews, and landmark papers. Each package includes reasoning frameworks, heuristics, mental models, anti-patterns, quotes, and an AI-generated avatar.

Scientific writing skill for AI × Biology researchers — full pipeline from results to submission

📖 深度学习蛋白质复合物预测与设计 | PhD Thesis Notes (Ziwei Xie, TTIC 2026)

Max-Biomni: StemCellGenomicsEngine — AI×Bio computational engine

Max-Biomni: GeneTherapyEngine — AI×Bio computational engine

Max-Biomni: AlternativePolyadenylationEngine — AI×Bio computational engine

Max-Biomni: DNAEncodedLibraryEngine — AI×Bio computational engine

Max-Biomni: VariantInterpretationEngine — AI×Bio computational engine

Max-Biomni: LongReadGenomicsEngine — AI×Bio computational engine

Max-Biomni: NetworkPharmacologyEngine — AI×Bio computational engine

Max-Biomni: PharmacogenomicsEngine — AI×Bio computational engine

Max-Biomni: DrugResistanceEngine — AI×Bio computational engine

Max-Biomni: CancerDriverEngine — AI×Bio computational engine

Max-Biomni: StructureBasedDrugEngine — AI×Bio computational engine

Max-Biomni: BrainAgeEngine — AI×Bio computational engine

Max-Biomni: NeuroimagingGenomicsEngine — AI×Bio computational engine

Max-Biomni: GlialSignalingEngine — AI×Bio computational engine

Max-Biomni: PangenomeEngine — AI×Bio computational engine

Max-Biomni: SpatialNeurogenomicsEngine — AI×Bio computational engine

Max-Biomni: NeuralCircuitEngine — AI×Bio computational engine

Max-Biomni: MolecularEvolutionEngine — AI×Bio computational engine

Max-Biomni: AncientDNAEngine — AI×Bio computational engine

Max-Biomni: AutoimmuneGenomicsEngine — AI×Bio computational engine

Max-Biomni: SelectionScanEngine — AI×Bio computational engine

Max-Biomni: VaccineResponseEngine — AI×Bio computational engine

Max-Biomni: PopulationStructureEngine — AI×Bio computational engine

Max-Biomni: ImmunePhenotypeEngine — AI×Bio computational engine

Max-Biomni: BCRRepertoireEngine — AI×Bio computational engine

Max-Biomni: MultiomeIntegrationEngine — AI×Bio computational engine

Max-Biomni: SpatialTranscriptomicsEngine2 — AI×Bio computational engine

Max-Biomni: TCRRepertoireEngine — AI×Bio computational engine

Max-Biomni: PerturbSeqEngine — AI×Bio computational engine

Max-Biomni: CellCommunicationEngine — AI×Bio computational engine

Max-Biomni: TrajectoryInferenceEngine — AI×Bio computational engine

Max-Biomni: CancerImmunogenomicsEngine — AI×Bio computational engine

Max-Biomni: SyntheticLethalityEngine — AI×Bio computational engine

Max-Biomni: MutationalSignatureEngine — AI×Bio computational engine

Max-Biomni: TumorMutationalBurdenEngine — AI×Bio computational engine

Max-Biomni: IntrinsicallyDisorderedEngine — AI×Bio computational engine

Max-Biomni: DeepMutationalScanningEngine — AI×Bio computational engine

Max-Biomni: ProteinProteinInteractionEngine — AI×Bio computational engine

Max-Biomni: ProteinDynamicsEngine — AI×Bio computational engine

Max-Biomni: AlphaFoldAnalysisEngine — AI×Bio computational engine

Ubiquitin-proteasome system: site prediction, E3 ligase network, chain type scoring, degradation ODE

Brain transcriptomics: cell-type deconvolution, synaptic scoring, neurodegeneration risk, region analysis

Two-sample MR: IVW, MR-Egger, weighted median, MR-PRESSO, Steiger filtering

Flux balance analysis: FBA, FVA, gene essentiality, GIMME expression integration

Boolean GRN inference: mutual information, attractor analysis, perturbation, motif detection

CAR-T cell therapy: antigen scoring, exhaustion analysis, killing kinetics ODE, response prediction

NF-kB/JAK-STAT ODE models: cytokine dose-response, signaling crosstalk, inflammatory signatures

Kinase activity inference: KSEA, phosphosite differential analysis, signaling network

ATAC-seq analysis: peak calling, NFR classification, TF footprinting, differential accessibility

Somatic CNA analysis: CBS segmentation, ploidy/purity estimation, aneuploidy score, NMF signatures

Genome-wide CRISPR knockout screen: MAGeCK-style RRA, essential gene identification, pathway enrichment

Tumor clonal evolution: CCF estimation, subclone detection, phylogenetic tree, fitness

RNA secondary structure: Nussinov MFE folding, SHAPE integration, structure-function correlation

miRNA target prediction: seed sequence matching, anti-correlation network, regulatory hubs

Ribo-seq translational efficiency: TE computation, uORF detection, codon usage bias

lncRNA regulatory analysis: co-expression network, RBP motif enrichment, ceRNA network

circRNA detection: back-splice junction scoring, miRNA sponge activity, regulatory network

Activity-by-Contact (ABC) model for enhancer-gene linking and differential enhancer activity

ChIP-seq histone mark analysis: peak calling, bivalent domains, 5-state chromatin segmentation

WGBS analysis: CpG island detection, DMR calling, epigenetic clock, methylation entropy

16S rRNA & metagenomics: OTU clustering, alpha/beta diversity, differential abundance, PICRUSt pathway inference, dysbiosis index

Iron-dependent cell death: GPX4/ACSL4 scoring, lipid peroxidation ODE, iron metabolism network, RSL3/Erastin response, cell death classifier

3D genome Hi-C analysis: ICE normalization, TAD boundary detection, loop calling, A/B compartments, loop extrusion simulation

ctDNA/cfDNA analysis: fragment length profiling, tumor fraction estimation, low-VAF variant calling, methylation deconvolution

m6A RNA modification analysis: MeRIP-seq peak calling, DRACH motif scanning, stoichiometry estimation, YTHDF reader affinity scoring

SV detection: read-pair signatures, breakpoint refinement, genotyping, cancer driver analysis

scRNA+scATAC integration: WNN, gene activity scores, CRE linking, TF activity inference

Computational molecular docking: pocket detection, ligand scoring, virtual screening, ADMET filtering

Tumor immune evasion: checkpoint scoring, MHC-I loss, T cell exclusion, TMB, ICI response prediction

Cellular senescence analysis: ssGSEA scoring, telomere length, SASP factors, cell cycle arrest, pseudotime

Drug combination synergy: Bliss independence, Loewe additivity, HSA, Hill equation fitting

Fusion gene detection: split-read scoring, in-frame prediction, oncogenic scoring, COSMIC lookup

Polygenic risk scores: C+T method, LD clumping, population stratification PCA

Alternative splicing: PSI calculation, differential splicing, RBP motif enrichment

DDA proteomics: peptide scoring, MaxLFQ quantification, differential abundance, GO enrichment

Disease module identification, DIAMOnD expansion, drug-target network proximity in PPI networks

Plasma metabolomics: differential analysis, PCA, PLS-DA, KEGG pathway enrichment

Spatial transcriptomics: Moran's I, SVG detection, neighborhood enrichment, spatial co-expression

Cell-cell communication via ligand-receptor analysis from scRNA-seq

Multi-method transcription factor activity inference from bulk and single-cell RNA-seq using decoupler

Disease signature mining from CZ CELLxGENE Census: lung adenocarcinoma vs normal

Pure NumPy molecular dynamics trajectory analysis: RMSD, RMSF, contact maps, PCA, H-bond occupancy

Pure Python Neoantigen Prediction Pipeline — MHC-I PSSM scoring, immunogenicity filtering, prioritization

Pure Python Bulk RNA-seq Cell Type Deconvolution Engine — NNLS, 22 immune cell types, bootstrap CIs

Pure Python TCR/BCR Immune Repertoire Analysis Engine — no external bioinformatics dependencies

scGPT fine-tuning on PBMC3k · 7-method benchmark · Nature Methods 2024 framework

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David Baker knowledge base — structured Q&A for 2024 Nobel Laureate in Chemistry

Pure Python GWAS Analysis Engine — NumPy/SciPy/sklearn only, no PLINK

Curated collection of claw4s executable AI-agent skills and research papers from clawRxiv q-bio category — quantitative biology. 190 papers, 55 skills.

Tumor Genomic Analysis Engine — pure NumPy/SciPy/sklearn. CNV, TMB, COSMIC signatures, neoantigen prediction, clonal architecture.

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Protein Thermodynamic Stability Prediction Engine — ΔΔG scan, Tm prediction, thermal denaturation curves

RNA Secondary Structure Prediction & Design Engine in Pure NumPy

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Joint NMF factorization for spatial proteomics and transcriptomics integration

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Protein thermal shift analysis pipeline

Variation graph construction and allele-specific k-mer GWAS for bacterial pan-genomes

Drug-microbiome interaction analysis from metagenomic data

Agent-executable spatial transcriptomics analysis tool for Visium/MERFISH data

Benchmark for gene set enrichment stability under background universe perturbations

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PPI Interface Analysis & Hotspot Prediction — BSA, alanine scanning, ColabFold, FreeBindCraft

Protein-protein interface hotspot prediction via computational alanine scanning

Protenix v2 trial report - Installation, problems and solutions

Single-cell multimodal integration pipeline for scRNA-seq + scATAC-seq with scGLUE and MOFA+

Ligand-Conditioned Protein Design Pipeline for AI Agents

Research agent for paper search, analysis and idea generation

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