{"engine_version":"IndoVarClassifier-v1.0","citation_count":10,"citations":[{"id":"hopf2017","title":"Mutation effects predicted from sequence co-variation","authors":"Hopf et al.","journal":"Nature Biotechnology","year":2017,"volume":"35:128-135","doi":"10.1038/nbt.3769","used_for":"EVmutation methodology — precedent for zero-shot variant effect scoring from sequence signal"},{"id":"meier2021","title":"Language models enable zero-shot prediction of the effects of mutations on protein function","authors":"Meier et al.","journal":"NeurIPS 2021","year":2021,"doi":"10.1101/2021.07.09.450648","used_for":"ESM zero-shot baseline that our BLOSUM62 + conservation scorer emulates behind the same delta-log-likelihood interface"},{"id":"lin2023","title":"Evolutionary-scale prediction of atomic-level protein structure","authors":"Lin et al.","journal":"Science","year":2023,"volume":"379:1123-1130","doi":"10.1126/science.ade2574","used_for":"ESM-2 architecture — target of the swap-in path (model_version='esm2_t33_650M_UR50D' when GPU allocated)"},{"id":"sivasubbu2020","title":"The IndiGen initiative: population-scale genome sequencing to catalyse precision medicine in India","authors":"Sivasubbu et al.","journal":"Journal of Biosciences","year":2020,"doi":"10.1007/s12038-020-9976-1","used_for":"IndiGen Indian-cohort allele frequencies for the 16 pharmacogenomic variants in the curated proxy table"},{"id":"cpic","title":"Clinical Pharmacogenetics Implementation Consortium (CPIC) Guidelines","authors":"CPIC","journal":"cpicpgx.org","year":2024,"used_for":"Gene-drug edge weights, evidence levels (A/B/C/D), and clinical action strings"},{"id":"pharmgkb","title":"PharmGKB Knowledge Base","authors":"PharmGKB","journal":"pharmgkb.org","year":2024,"used_for":"Variant annotation, drug-gene edge evidence when CPIC is Level C or below"},{"id":"imppat","title":"IMPPAT 2.0: an enhanced and expanded phytochemical atlas of Indian medicinal plants","authors":"Vivek-Ananth et al.","journal":"Scientific Reports","year":2023,"used_for":"Herb-CYP inhibition edges (curcumin, piperine, ashwagandha, quercetin, brahmi, tulsi, neem, giloy)"},{"id":"gnomad_v4","title":"gnomAD v4 (Genome Aggregation Database)","authors":"Broad Institute","journal":"gnomad.broadinstitute.org","year":2024,"used_for":"Global + South Asian allele frequencies via live GraphQL API"},{"id":"clinvar","title":"ClinVar (NCBI)","authors":"NCBI","journal":"ncbi.nlm.nih.gov/clinvar","year":2024,"used_for":"Clinical significance annotations via NCBI eUtils esearch + esummary"},{"id":"ensembl_vep","title":"The Ensembl Variant Effect Predictor (VEP)","authors":"McLaren et al.","journal":"Genome Biology","year":2016,"doi":"10.1186/s13059-016-0974-4","used_for":"Variant annotation and canonical protein sequence retrieval via Ensembl REST API"}],"usage_note":"Every score, edge weight, or annotation produced by this pipeline traces back to at least one citation above. This citation list is the reference bibliography for any grant application, publication, or regulatory-facing document derived from IndoVarClassifier output."}