{"id":"W2407523666","doi":"10.1186/s12864-016-2709-z","title":"Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database","year":2016,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":395,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institutes of Health; Institut National de la Recherche Agronomique; Agence Nationale de la Recherche; Agentschap voor Natuur en Bos; Centre National de la Recherche Scientifique; Université de Pau et des Pays de l'Adour; Université Laval","keywords":"Biology; Gene duplication; Gene; Evolutionary biology; Lineage (genetic); Genome; Transcriptome; Vertebrate; Gene expression; Phylogenetics; Concerted evolution; DNA microarray; Database; Genetics","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":{"n_in":0,"stratum":"fund_new","weight":1678.9,"opus":{"tier":"OUT","genre":"empirical","about_ca":false,"confidence":"medium","reason":"Transcriptome analyses plus release of the PhyloFish database; a domain genomics resource, not infrastructure of the research ecosystem in the metaresearch sense."},"gpt":{"tier":"T3","genre":"infrastructure/announcement","about_ca":false,"confidence":"high","reason":"This describes a genomics database resource and is an infrastructure announcement rather than an analytic study."},"grok":{"tier":"OUT","genre":"empirical","about_ca":false,"confidence":"high","reason":"Domain genomics resource (PhyloFish) for fish gene evolution; uses a database tool rather than studying research infrastructure."}},"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001321926,0.001525202,0.002186114,0.007403498,0.0009044218,0.00163168,0.001496675,0.001363742,0.009752586],"category_scores_gemma":[0.002270235,0.0008421692,0.001599844,0.007923772,0.0005152733,0.0009821646,0.002394219,0.001051011,0.008407955],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008192987,"about_ca_system_score_gemma":0.001808644,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002700414,"about_ca_topic_score_gemma":0.004861986,"domain_scores_codex":[0.9991711,0.0000639376,0.0001258303,0.000326095,0.0001931997,0.0001198975],"domain_scores_gemma":[0.9991891,0.0002440113,0.0001869727,0.0001567557,0.00009599287,0.0001270877],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.005643252,0.0002402323,0.1117904,0.03017073,0.002750227,0.006008185,0.003426996,0.009362453,0.2453281,0.008130653,0.4315397,0.1456092],"study_design_scores_gemma":[0.0005254417,0.0003669488,0.1570705,0.001324305,0.001306821,0.004091328,0.0004978693,0.006192787,0.01537168,0.005214678,0.8077661,0.0002716199],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"dataset","genre_gemma":"empirical","genre_scores_codex":[0.03875693,0.004509601,0.006331119,0.0001283985,0.00007234971,0.00007559702,0.9384223,0.008233305,0.003470361],"genre_scores_gemma":[0.02959245,0.00196792,0.01514839,0.0001313423,0.0000195722,0.0003535062,0.9510278,0.001073824,0.0006852206],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.009752586,"threshold_uncertainty_score":0,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01235442107017771,"score_gpt":0.2190058728731684,"score_spread":0.2066514518029907,"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."}}