{"id":"W4411705236","doi":"10.1093/bioinformatics/btaf375","title":"Benchmarking peak calling methods for CUT&amp;RUN","year":2025,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Princess Margaret Cancer Centre","funders":"Canadian Institutes of Health Research","keywords":"Benchmarking; Computer science; Chromatin; Chromatin immunoprecipitation; Histone; Micrococcal nuclease; Identification (biology); Bottleneck; Data mining; Benchmark (surveying); Computational biology; Biology; Nucleosome; DNA; Genetics; Gene; Gene expression","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003871588,0.0001457029,0.0001510036,0.00005906913,0.0001411774,0.00005749757,0.0002267269,0.0001568721,0.000006416251],"category_scores_gemma":[0.0001291318,0.000142335,0.0001234985,0.00008727171,0.000035184,0.000004181632,0.0001431932,0.00006302824,0.000005108931],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002436166,"about_ca_system_score_gemma":0.0001029921,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004512475,"about_ca_topic_score_gemma":0.00002061936,"domain_scores_codex":[0.9991788,0.00001874023,0.0003617139,0.0001399253,0.00005180089,0.0002490075],"domain_scores_gemma":[0.9993572,0.00004040141,0.0001150098,0.0003449642,0.0000935714,0.00004881102],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001916719,0.0002094582,0.001199744,0.002038033,0.0007650665,6.66648e-7,0.001637636,0.005035582,0.3408968,0.02026268,0.03082508,0.5969375],"study_design_scores_gemma":[0.0008554925,0.000145249,0.0002427219,0.00006763015,0.00007881875,0.000008094782,0.0003849455,0.2445582,0.02630254,0.001706324,0.7252131,0.0004369619],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.05534918,0.0003439976,0.9351112,0.00008991906,0.0004685351,0.0003028775,0.00002980931,0.00001902748,0.008285444],"genre_scores_gemma":[0.03789405,0.0002089314,0.9590743,0.0006518235,0.0001614609,0.00003925613,0.0004393616,0.00001892642,0.001511881],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.694388,"threshold_uncertainty_score":0.5804253,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0150960926637293,"score_gpt":0.319743551025407,"score_spread":0.3046474583616777,"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."}}