{"doi":"10.1016/j.xgen.2025.100879","title":"Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex","abstract":"Identifying cell-type-specific enhancers is critical for developing genetic tools to study the mammalian brain. We organized the \"Brain Initiative Cell Census Network (BICCN) Challenge: Predicting Functional Cell Type-Specific Enhancers from Cross-Species Multi-Omics\" to evaluate machine learning and feature-based methods for nominating enhancer sequences targeting mouse cortical cell types. Methods were assessed using in vivo data from hundreds of adeno-associated virus (AAV)-packaged, retro-orbitally delivered enhancers. Open chromatin was the strongest predictor of functional enhancers, while sequence models improved prediction of non-functional enhancers and identified cell-type-specific transcription factor codes to inform in silico enhancer design. This challenge establishes a benchmark for enhancer prioritization and highlights computational and molecular features critical for identifying functional cortical enhancers, advancing efforts to map and manipulate gene regulation in the mammalian cortex.","journal":"Cell Genomics","year":2025,"id":511287,"datarank":0.42498200160843247,"base_score":2.833213344056216,"endowment":2.833213344056216,"self_citation_contribution":0.42498200160843247,"citation_network_contribution":0.0,"self_endowment_contribution":0.42498200160843247,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":16,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8338,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1329708,"name":"Niklas Kempynck","orcid":"0000-0002-0104-4844","position":1,"is_corresponding":false},{"id":995499,"name":"Nathan R. 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