{"id":"W2915269011","doi":"10.1101/558130","title":"Pooled CRISPR Inverse PCR sequencing (PCIP-seq): simultaneous sequencing of retroviral insertion points and the associated provirus in thousands of cells with long reads","year":2019,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"T-cell and Retrovirus Studies","field":"Immunology and Microbiology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan","funders":"Vlaamse regering; Amis de l'Institut Bordet; Université de Liège; Fonds Wetenschappelijk Onderzoek","keywords":"Minion; Provirus; CRISPR; Nanopore sequencing; Inverse polymerase chain reaction; Endogenous retrovirus; DNA sequencing; Deep sequencing; Genome; Identification (biology)","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.001407533,0.0006306795,0.001424328,0.0003761743,0.000184145,0.0000391705,0.0004629285,0.0009733567,0.00001496237],"category_scores_gemma":[0.0006342007,0.0004568758,0.000170623,0.0005114946,0.000956253,0.0001310139,0.0005673613,0.001361242,0.00001659248],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005935896,"about_ca_system_score_gemma":0.0008626414,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002261329,"about_ca_topic_score_gemma":0.0002884179,"domain_scores_codex":[0.9965479,0.0007598656,0.001009891,0.0008464931,0.0001887001,0.000647088],"domain_scores_gemma":[0.9966964,0.0005030393,0.001332392,0.0008687166,0.0005508821,0.00004862902],"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":[0.001072452,0.0001029959,0.04944267,0.0006539605,0.0007860192,0.00005694134,0.0004399767,0.0007868246,0.9465312,0.00009121953,0.0000320783,0.000003635311],"study_design_scores_gemma":[0.005745761,0.0004576886,0.02621541,0.001797845,0.0006374365,3.144174e-7,0.0002184611,0.0006087975,0.9634942,0.000005780562,0.00004133282,0.000777011],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9947842,0.002787058,0.0001120302,0.00005882179,0.0007140844,0.001218334,0.0001865388,0.0001110961,0.00002787859],"genre_scores_gemma":[0.9987634,0.0006557354,0.0002541949,0.00009431431,0.00004000118,0.00005601521,0.000001894602,0.00008546559,0.00004894485],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02322726,"threshold_uncertainty_score":0.9997883,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01079683934733902,"score_gpt":0.200142631234738,"score_spread":0.189345791887399,"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."}}