{"id":"W3185964176","doi":"10.1186/s12915-021-01078-1","title":"Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri","year":2021,"lang":"en","type":"article","venue":"BMC Biology","topic":"Legionella and Acanthamoeba research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":36,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University; University of Alberta","funders":"College of Medicine, University of Cincinnati; Centro de Investigación Biomédica en Red Enfermedades Cardiovasculares; Faculty of Medicine and Dentistry, University of Alberta; Akademie Věd České Republiky; Alberta Heritage Foundation for Medical Research; Canada Research Chairs; Dalhousie University; Commonwealth Scientific and Industrial Research Organisation; University of Alberta; School of Medicine, Virginia Commonwealth University; Univerzita Karlova v Praze; Virginia Commonwealth University; University of Bern; Ostravská Univerzita v Ostravě; Grantová Agentura České Republiky; Biologické Centrum, Akademie Věd České Republiky; Inselspital, Universitätsspital Bern; Přírodovědecká Fakulta, Univerzita Karlova; University of Cincinnati; Cincinnati Children's Hospital Medical Center","keywords":"Biology; Naegleria fowleri; Pathogen; Transcriptome; Genomics; Naegleria; Computational biology; Protozoa; Genome; Microbiology; Genetics; Gene; Virology; 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":[0.0002223617,0.0001240673,0.0002539823,0.00001773864,0.00007495817,0.000004733441,0.0003757626,0.0003122577,0.00001058351],"category_scores_gemma":[0.0001008328,0.00007281535,0.0001632249,0.0001083399,0.0004491033,0.00000129283,0.0003417603,0.0001131093,9.62121e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001181765,"about_ca_system_score_gemma":0.0003420311,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005692034,"about_ca_topic_score_gemma":0.0001803062,"domain_scores_codex":[0.9987799,0.0003783656,0.0002881835,0.0002874478,0.0000456013,0.000220516],"domain_scores_gemma":[0.9991537,0.0000418557,0.0001232897,0.0005200296,0.000124502,0.00003662142],"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":[0.0000399481,0.00002805378,0.02039795,0.0001266501,0.00005293323,3.525394e-7,0.00005076851,0.00000239211,0.9733105,0.004765508,0.0000728292,0.00115208],"study_design_scores_gemma":[0.0007429513,0.0001786653,0.01517878,0.00004628221,0.00004078262,0.00008616564,0.0002798925,0.00005963763,0.9473765,0.0003489234,0.03550864,0.0001527121],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9895715,0.007763691,0.001025178,0.0002897014,0.0003863524,0.000221696,0.0002757262,0.000003243606,0.0004628749],"genre_scores_gemma":[0.9982121,0.0009374849,0.0003908732,0.0001359726,0.00009536613,0.00001316991,0.00003844221,0.00001233643,0.0001642403],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03543581,"threshold_uncertainty_score":0.2969324,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03470163474683405,"score_gpt":0.2689126058511946,"score_spread":0.2342109711043606,"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."}}