{"id":"W2972200133","doi":"10.1038/s41467-019-12046-3","title":"Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration","year":2019,"lang":"en","type":"article","venue":"Nature Communications","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":123,"is_retracted":false,"has_abstract":true,"ca_institutions":"The Scarborough Hospital","funders":"Generalitat de Catalunya; Ministerio de Economía y Competitividad; Deutsche Forschungsgemeinschaft; Centres de Recerca de Catalunya; Hrvatska Zaklada za Znanost; Deutsches Zentrum für Infektionsforschung","keywords":"Human immunodeficiency virus (HIV); Enhancer; Computational biology; Biology; Genetics; Gene; Virology; Transcription factor","routes":{"ca_aff":true,"ca_fund":false,"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":[0.00009992853,0.0001121345,0.000186598,0.00008343773,0.0001309496,0.000007879527,0.0005378069,0.0002471407,0.0002682217],"category_scores_gemma":[0.00008949646,0.00008189309,0.00005368972,0.0001365213,0.0001824307,0.00007189484,0.000134257,0.0006649765,0.0007026327],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000821405,"about_ca_system_score_gemma":0.00009603434,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001450191,"about_ca_topic_score_gemma":0.004072626,"domain_scores_codex":[0.9992463,0.0001949607,0.0001757671,0.0001559122,0.00005155773,0.0001754862],"domain_scores_gemma":[0.9982134,0.0002260694,0.0001483638,0.00116376,0.0002272304,0.00002120217],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001035743,0.001871227,0.385705,0.00007914688,0.001381401,0.000004302761,0.003007248,0.0001215351,0.5668268,0.005797844,0.02214028,0.01202955],"study_design_scores_gemma":[0.01136727,0.001476362,0.3516455,0.0004513644,0.0001910107,0.00003881264,0.002580873,0.0003957246,0.3725296,0.0001660189,0.2584409,0.0007166029],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9219946,0.04186434,0.002621655,0.01062639,0.0004799228,0.00288688,0.001427729,0.0001903891,0.01790812],"genre_scores_gemma":[0.9934341,0.0003116648,0.00248534,0.00007499581,0.000005217849,0.00006090503,0.002470311,0.00001084494,0.001146677],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2363006,"threshold_uncertainty_score":0.9031156,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01318681955537082,"score_gpt":0.2746636192340094,"score_spread":0.2614767996786386,"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."}}