{"id":"W4409344968","doi":"10.1101/2025.04.08.647885","title":"Single-cell phylogenomics identifies major groups of marine eugregarine parasites (Apicomplexa)","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Aquaculture disease management and microbiota","field":"Immunology and Microbiology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; Hakai Institute; Tula Foundation; Gordon and Betty Moore Foundation","keywords":"Phylogenomics; Apicomplexa; Biology; Evolutionary biology; Phylogenetics; Genetics; Protozoal disease; Gene; Clade; Immunology","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001222278,0.0002063267,0.0002596155,0.0005438202,0.0004316093,0.0005726844,0.0001607705,0.0002965712,0.000750093],"category_scores_gemma":[0.0002076234,0.0001480108,0.0001957322,0.0005327112,0.0002548788,0.0003352175,0.0003604802,0.0002840301,0.0002689732],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003800477,"about_ca_system_score_gemma":0.0002893354,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006963304,"about_ca_topic_score_gemma":0.02390943,"domain_scores_codex":[0.9999195,0.00000373188,0.000004988452,0.00003651744,0.00001696681,0.00001831515],"domain_scores_gemma":[0.9998765,0.00001784897,0.00002912321,0.00001560177,0.00003480961,0.0000261647],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00008082011,0.00001111109,0.04268614,0.0001081868,0.00003656118,0.00006534441,0.0002092457,0.0002705951,0.9508301,0.0001029584,0.0002366967,0.005362165],"study_design_scores_gemma":[0.000007865421,0.00007052377,0.9566122,0.00003094471,0.00006540652,0.0002151889,0.0007569709,0.003776587,0.0325073,0.0002544905,0.00568677,0.00001568483],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9931638,0.0007241084,0.002046188,0.00006682981,0.000007840953,0.00001211147,0.003121018,0.00004584664,0.0008122765],"genre_scores_gemma":[0.985503,0.0006870005,0.004263682,0.0001161626,0.000007414937,0.00003109278,0.008147592,0.00002559609,0.001218551],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006963304,"threshold_uncertainty_score":0.01384556,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01158589141409071,"score_gpt":0.2051025718142383,"score_spread":0.1935166804001476,"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."}}