{"id":"W2096482937","doi":"10.1093/bioinformatics/btv321","title":"ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments","year":2015,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":25,"is_retracted":false,"has_abstract":true,"ca_institutions":"Princess Margaret Cancer Centre; University Health Network; University of Toronto; Ontario Institute for Cancer Research","funders":"National Cancer Institute; Canadian Institutes of Health Research","keywords":"Perl; Computational biology; Computer science; Biology; SNP; False positive paradox; Chromatin; Genetics; Transcription factor; Single-nucleotide polymorphism; Gene; Artificial intelligence; Programming language","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003878289,0.002864481,0.002528374,0.003792874,0.001494933,0.002231675,0.003713161,0.002055724,0.06055212],"category_scores_gemma":[0.0147273,0.001724692,0.002157281,0.002301753,0.000823201,0.001347308,0.002762221,0.002032726,0.02090928],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009971097,"about_ca_system_score_gemma":0.002275451,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003813809,"about_ca_topic_score_gemma":0.007824335,"domain_scores_codex":[0.9982284,0.0004228893,0.000201243,0.0005049094,0.0005011245,0.0001415379],"domain_scores_gemma":[0.9920958,0.006049869,0.0004581654,0.0005808347,0.0006073423,0.0002081356],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.002080378,0.0003773807,0.02205574,0.005287975,0.001640267,0.001483665,0.0005742857,0.01903336,0.03860926,0.009948601,0.7248269,0.1740822],"study_design_scores_gemma":[0.002315281,0.0004165568,0.02164195,0.0006852277,0.0009611594,0.002898832,0.0002961262,0.5496525,0.06910203,0.03790439,0.3134528,0.0006731275],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01751034,0.0009273255,0.514573,0.0006878196,0.0005182551,0.0007860613,0.07363368,0.3849043,0.006459138],"genre_scores_gemma":[0.07846132,0.0005874793,0.7621419,0.001687267,0.000168465,0.005065973,0.08568411,0.05967208,0.006531318],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.06055212,"threshold_uncertainty_score":0.202567,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03939331742921866,"score_gpt":0.2816686085563228,"score_spread":0.2422752911271041,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}