{"id":"W4401517399","doi":"10.1080/19490976.2024.2379440","title":"Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the <i>Helicobacter pylori</i> Genome Project","year":2024,"lang":"en","type":"article","venue":"Gut Microbes","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias; Fondo Nacional de Desarrollo Científico y Tecnológico; National Institute on Minority Health and Health Disparities; U.S. National Library of Medicine; National Institute of Environmental Health Sciences; National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; National Cancer Institute; Horizon 2020; Comisión Nacional de Investigación Científica y Tecnológica; Ministry of Education; Universiti Malaya; Agencia Nacional de Investigación y Desarrollo; National Medical Research Council; Alberta Innovates; Fundação de Amparo à Pesquisa do Estado de São Paulo; Ministry of Science and Technology; Institut National Du Cancer; Ministry of Health, British Columbia; Conselho Nacional de Desenvolvimento Científico e Tecnológico; Ministero della Salute; ArcticNet; Fundação para a Ciência e a Tecnologia; Ministry of Higher Education; Bundesministerium für Bildung und Forschung; National Research Foundation; European Commission; Universidad de Costa Rica; National Cancer Center; National Institutes of Health; Health Research; U.S. Department of Veterans Affairs","keywords":"Prophage; Biology; Genome; Genetics; Helicobacter pylori; Gene; Genomics; Comparative genomics; Whole genome sequencing; Bacteriophage; Escherichia coli","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":[],"consensus_categories":[],"category_scores_codex":[0.0002232296,0.0002213125,0.0001587904,0.00006967477,0.0001705959,0.0002903238,0.0002039573,0.00008923215,0.0001388732],"category_scores_gemma":[0.000008752972,0.0001609505,0.00006139017,0.0002569929,0.0001342351,0.0007472116,0.0001355401,0.0002373609,0.00009907902],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002936812,"about_ca_system_score_gemma":0.0000252298,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006106874,"about_ca_topic_score_gemma":0.0001794069,"domain_scores_codex":[0.9987333,0.00007482903,0.0003057175,0.0004684709,0.0001181127,0.0002995926],"domain_scores_gemma":[0.9996021,0.00003073597,0.00007408627,0.0002461503,0.000009579964,0.00003728055],"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":[0.00002590163,0.00009720115,0.00009966546,0.00003065894,0.00001310391,0.000008820017,0.002232865,0.0001976319,0.9935471,0.00002236481,0.001341707,0.002382952],"study_design_scores_gemma":[0.002022828,0.0003273852,0.1906448,0.0001843457,0.0001829523,0.0003700461,0.001231162,0.03160473,0.6885127,0.0007163322,0.08270969,0.001493062],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9958983,0.000435375,0.0009786515,0.0005504973,0.0001174579,0.001002628,0.0001699484,0.00006095486,0.0007861891],"genre_scores_gemma":[0.9961556,0.000159382,0.0008181402,0.0003953713,0.00006762316,0.00009767404,0.0001521086,0.00003555465,0.00211859],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3050345,"threshold_uncertainty_score":0.6563371,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01814735249301469,"score_gpt":0.233516123395285,"score_spread":0.2153687709022704,"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."}}