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Found 105 Skills
Search and analyze cryo-EM maps, single particle structures, tomography datasets, and raw micrograph data from EMDB, EMPIAR, and CryoET Data Portal. Cross-reference with PDB structures and AlphaFold predictions. Use for cryo-EM map discovery, structure fitting analysis, raw data access, and tomography exploration.
Population genetics research using the 1000 Genomes Project (IGSR) -- search populations by superpopulation ancestry (AFR, AMR, EAS, EUR, SAS), retrieve samples by population code, list available data collections, and integrate with GWAS tools for population stratification analysis. Use when users ask about 1000 Genomes populations, sample ancestry, allele frequency variation across continental groups, population-specific GWAS interpretation, or IGSR data collections like the 30x high-coverage resequencing or HGSVC.
Find and evaluate research datasets for any scientific question. Teaches how to reason about data needs, search across public repositories, evaluate dataset fitness, and identify access requirements. Use whenever users ask to find data, search for datasets, identify cohort studies, or need data for analysis. Also use when users ask about a specific survey or cohort (NHANES, HRS, UK Biobank, TCGA, etc.), when they want to know what data exists for a research question, or when they need to compare available data sources. If the user mentions "where can I get data" or "is there a dataset for X", this is the right skill.
Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxonomy, essential proteins, predicts structures, and screens existing drugs via docking. Use when facing novel pathogens, emerging infections, or needing rapid therapeutic options during outbreaks.
Comprehensive analysis of CRISPR knockout/activation screens with gene essentiality scoring, pathway enrichment, functional annotation, and therapeutic target identification. Identifies essential genes, synthetic lethal interactions, and actionable drug targets from pooled or arrayed CRISPR screens. Use when analyzing CRISPR screen data, identifying gene dependencies, or prioritizing hits for validation.
Comprehensive antibody engineering and optimization for therapeutic development. Covers humanization, affinity maturation, developability assessment, and immunogenicity prediction. Use when asked to optimize antibodies, humanize sequences, or engineer therapeutic antibodies from lead to clinical candidate.
Comprehensive epigenomics and gene regulation analysis integrating ENCODE functional genomics data, JASPAR transcription factor binding motifs, SCREEN cis-regulatory elements, ReMap TF binding sites, RegulomeDB variant regulatory scoring, 4D Nucleome chromatin conformation, and Ensembl regulatory features. Performs regulatory element cataloging, transcription factor analysis, variant regulatory impact scoring, chromatin conformation mapping, and gene-centric regulatory landscape profiling. Use when asked about gene regulation, enhancers, promoters, transcription factor binding, epigenetic modifications, chromatin structure, regulatory variants, or non-coding genome function.
Systematic clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Aggregates evidence from ClinVar, gnomAD, CIViC, UniProt, and PDB across ACMG criteria. Produces pathogenicity scores (0-100), clinical recommendations, and treatment implications. Use when interpreting genetic variants, classifying variants of uncertain significance (VUS), performing ACMG variant classification, or translating variant calls to clinical actionability.
Discover genes associated with diseases and traits using GWAS data from the GWAS Catalog (500,000+ associations) and Open Targets Genetics (L2G predictions). Identifies genetic risk factors, prioritizes causal genes via locus-to-gene scoring, and assesses druggability. Use when asked to find genes associated with a disease or trait, discover genetic risk factors, translate GWAS signals to gene targets, or answer questions like "What genes are associated with type 2 diabetes?"
Analyze spatial transcriptomics data to map gene expression in tissue architecture. Supports 10x Visium, MERFISH, seqFISH, Slide-seq, and imaging-based platforms. Performs spatial clustering, domain identification, cell-cell proximity analysis, spatial gene expression patterns, tissue architecture mapping, and integration with single-cell data. Use when analyzing spatial transcriptomics datasets, studying tissue organization, identifying spatial expression patterns, mapping cell-cell interactions in tissue context, characterizing tumor microenvironment spatial structure, or integrating spatial and single-cell RNA-seq data for comprehensive tissue analysis.
Find, characterize, and source small molecules for chemical biology and drug discovery. Covers compound identification (PubChem, ChEMBL), structure search, binding affinity data, ADMET/drug-likeness prediction, and commercial availability (eMolecules, Enamine). Use when asked to find compounds, assess drug-likeness, search by structure, retrieve binding affinities, or source chemicals.
Drug regulatory and approval research -- FDA substance registry lookup, drug classification by ATC/EPC/MoA via RxClass, Orange Book generic availability and patent status, DailyMed label parsing (adverse reactions, dosing, contraindications), and clinical trial search. Use when users ask about FDA-approved drugs, drug regulatory status, generic availability, patent expiration, drug class membership, drug labeling, or substance identification.