{"id":"W4410361128","doi":"10.1101/2025.05.13.653884","title":"Identification of genes that differentiate <i>Mannheimia haemolytica</i> genotypes 1 and 2 using a pangenome approach","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Plant Pathogenic Bacteria Studies","field":"Agricultural and Biological Sciences","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan","funders":"","keywords":"Biology; Genotype; Genetics; Microbiology; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002299604,0.000395684,0.0004445274,0.001046143,0.0002680613,0.0005818579,0.0002377797,0.0003837627,0.001036139],"category_scores_gemma":[0.00034868,0.0001733179,0.0004563848,0.00104106,0.0001255654,0.0002922531,0.0004462016,0.0004151117,0.0003828641],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000294251,"about_ca_system_score_gemma":0.0002463888,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001430309,"about_ca_topic_score_gemma":0.002919337,"domain_scores_codex":[0.9997848,0.0000223273,0.00001451936,0.000102371,0.00003484069,0.00004117721],"domain_scores_gemma":[0.9997897,0.00004182921,0.00009081448,0.00001974049,0.00002733945,0.00003073598],"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":[0.00026108,0.00004451771,0.01237724,0.0002468791,0.00005709333,0.00009375354,0.0001088556,0.0001915988,0.976853,0.0001027503,0.0003638631,0.009299428],"study_design_scores_gemma":[0.00006347823,0.000621756,0.7620164,0.0001234744,0.0003957315,0.002016277,0.0005595986,0.005730797,0.2047556,0.0005227252,0.02313967,0.0000545015],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9692783,0.00279721,0.009354656,0.0002264839,0.00004053482,0.0000834814,0.01632501,0.0002790037,0.001615368],"genre_scores_gemma":[0.9264301,0.001506847,0.03363114,0.0004124204,0.00003619367,0.0001506905,0.03560273,0.0001209271,0.002108861],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001430309,"threshold_uncertainty_score":0.003466249,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03157886413970787,"score_gpt":0.2085264655368168,"score_spread":0.1769476013971089,"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."}}