{"id":"W2613925306","doi":"10.1038/nprot.2017.029","title":"Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs","year":2017,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":139,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of British Columbia; BC Cancer Agency","funders":"","keywords":"Biology; Sequencing by hybridization; Genetics; DNA nanoball sequencing; DNA; Single molecule real time sequencing; Genome; Genomic library; DNA sequencing; Homologous recombination; Computational biology; Gene; DNA sequencer; Base sequence","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":[0.0002280403,0.0001368148,0.0001415679,0.00001717031,0.0002248557,0.0001556759,0.0004941635,0.0003398688,0.00001055686],"category_scores_gemma":[0.00009985194,0.00009459724,0.0000618955,0.00002487214,0.000118298,0.000008793951,0.0001165917,0.0002179416,9.90982e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001516495,"about_ca_system_score_gemma":0.0001229889,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000172423,"about_ca_topic_score_gemma":0.00002443488,"domain_scores_codex":[0.9992076,0.00003149077,0.0001955659,0.0002352458,0.000149904,0.0001802608],"domain_scores_gemma":[0.9990538,0.00001935286,0.0002963889,0.0004915174,0.00009591148,0.00004307421],"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":[0.00009373153,0.00005257195,0.001273328,0.00005557454,0.00002730323,0.000001594509,0.0000671123,0.000004663235,0.9947312,0.00003829988,0.0009695328,0.002685067],"study_design_scores_gemma":[0.0009189534,0.0002917339,0.002645365,0.00004371134,0.00001988883,0.000005531775,0.00001897115,0.000004807182,0.9398977,0.0001267499,0.05588967,0.0001369573],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9795173,0.0002014768,0.0003828612,0.0003186832,0.0001141521,0.01770228,0.0006847329,0.000008089878,0.001070399],"genre_scores_gemma":[0.9958814,0.00004039851,0.0001697015,0.0002260255,0.000198065,0.002914857,0.0002912419,0.00001969959,0.000258581],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.05492014,"threshold_uncertainty_score":0.3857564,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01889711629101098,"score_gpt":0.2809410640258254,"score_spread":0.2620439477348144,"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."}}