{"id":"W3170360714","doi":"10.1101/2021.06.08.447172","title":"Shotgun Immunoproteomic Approach for the Discovery of Linear B Cell Epitopes in Biothreat Agents <i>Francisella tularensis</i> and <i>Burkholderia pseudomallei</i>","year":2021,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Lawrence Livermore National Laboratory; National Nuclear Security Administration; National Institute of Allergy and Infectious Diseases; National Research Council Canada; National Institutes of Health; Sandia National Laboratories; Laboratory Directed Research and Development; U.S. Department of Energy","keywords":"Epitope; Francisella tularensis; Proteome; Biology; Computational biology; Antigen; Epitope mapping; Immune system; Burkholderia pseudomallei; Francisella; Reverse vaccinology; Microbiology; Virology; Immunology; Bacteria; Gene; Bioinformatics; Genetics; Virulence","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0005371663,0.000552593,0.0006638143,0.0001008702,0.0001414413,0.0002132911,0.0006285349,0.0005786553,0.000004239363],"category_scores_gemma":[0.0001044214,0.000467226,0.0002795452,0.0002061857,0.0001202583,0.00002644319,0.0009041455,0.0003827511,7.750874e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003476744,"about_ca_system_score_gemma":0.0003275436,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008153439,"about_ca_topic_score_gemma":0.000003488229,"domain_scores_codex":[0.9977396,0.00008365791,0.0007504491,0.0007722562,0.0001981861,0.0004558604],"domain_scores_gemma":[0.9977757,0.00004065687,0.0004685458,0.001383813,0.000254402,0.00007685465],"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":[0.0001186587,0.0001930148,0.001346593,0.001222523,0.0002077821,0.000002296769,0.00003176995,0.0006335974,0.9960334,0.00001632555,0.0001894479,0.000004636441],"study_design_scores_gemma":[0.001355913,0.0001008456,0.00940441,0.0002127984,0.000134602,1.057115e-7,0.00006979764,0.003749779,0.9834987,5.60783e-7,0.0008746049,0.0005978942],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9732896,0.01611554,0.008154174,0.00004782767,0.0003149892,0.001551719,0.0004969932,0.00001862285,0.00001054529],"genre_scores_gemma":[0.9785588,0.004476521,0.01603315,0.0001350982,0.000214398,0.0004364739,0.00002608808,0.0001090695,0.00001039031],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01253467,"threshold_uncertainty_score":0.999778,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01237912843704474,"score_gpt":0.2083255692858349,"score_spread":0.1959464408487901,"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."}}