{"id":"W2020558917","doi":"10.1021/pr050013h","title":"Robust Method for Proteome Analysis by MS/MS Using an Entire Translated Genome:  Demonstration on the Ciliome of<i>Tetrahymena</i><i>t</i><i>hermophila</i>","year":2005,"lang":"en","type":"article","venue":"Journal of Proteome Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":120,"is_retracted":false,"has_abstract":true,"ca_institutions":"York University; University of Toronto","funders":"","keywords":"Tetrahymena; Proteome; Genome; Computational biology; Biology; Proteomics; Genetics; Gene","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":[0.004227728,0.0002052516,0.0004151403,0.0004154858,0.000301675,0.00006630211,0.000516294,0.0001824668,0.00002962642],"category_scores_gemma":[0.0001523378,0.0001465501,0.0003803861,0.0008792857,0.0001720735,0.000007075283,0.00005642102,0.0003673785,7.053738e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005661422,"about_ca_system_score_gemma":0.0002376692,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004102489,"about_ca_topic_score_gemma":0.00004057974,"domain_scores_codex":[0.9973184,0.0005451975,0.0007044175,0.0003408898,0.0006352208,0.000455833],"domain_scores_gemma":[0.998054,0.0001111604,0.00038286,0.0003982043,0.0009055694,0.0001481904],"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":[0.0003865581,0.0002428814,0.0001758345,0.00003824578,0.0008123888,0.000001624708,0.0002134261,0.009315724,0.9869531,0.00001677651,0.0001470085,0.001696384],"study_design_scores_gemma":[0.001200739,0.002853419,0.00117515,0.00003466486,0.0003389412,0.0000366472,0.0001853617,0.006135995,0.9776462,0.0003094296,0.009808264,0.0002752254],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9607437,0.002044089,0.03443301,0.001229105,0.0000351912,0.001282284,0.0001480951,0.000001434709,0.00008308904],"genre_scores_gemma":[0.96637,0.0003010835,0.03261898,0.00005590309,0.0004084406,0.00007300115,0.00002717888,0.00003246104,0.000112934],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.009661254,"threshold_uncertainty_score":0.597614,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.09965045974532191,"score_gpt":0.3684659537830527,"score_spread":0.2688154940377309,"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."}}