{"id":"W2165759219","doi":"10.1101/gr.112169.110","title":"Comparative genomics of citric-acid-producing<i>Aspergillus niger</i>ATCC 1015 versus enzyme-producing CBS 513.88","year":2011,"lang":"en","type":"article","venue":"Genome Research","topic":"Enzyme Production and Characterization","field":"Biochemistry, Genetics and Molecular Biology","cited_by":367,"is_retracted":false,"has_abstract":true,"ca_institutions":"Concordia University","funders":"Lawrence Berkeley National Laboratory; Biomass Program; Los Alamos National Laboratory; Biological and Environmental Research; Office of Science; Lawrence Livermore National Laboratory; U.S. Department of Energy","keywords":"Biology; Genetics; Aspergillus niger; Genome; Gene; Transcriptome; Reference genome; Whole genome sequencing; Single-nucleotide polymorphism; Genotype; Biochemistry; Gene expression","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001311857,0.0002234828,0.0003158416,0.0002566735,0.0002390993,0.00003394965,0.000466783,0.0001812027,0.0002712663],"category_scores_gemma":[0.0002761549,0.0002298347,0.0001027994,0.0005904482,0.0002808567,0.00001680407,0.0003527796,0.0003261207,0.0001266302],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009473341,"about_ca_system_score_gemma":0.0002738907,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000953139,"about_ca_topic_score_gemma":0.00003187939,"domain_scores_codex":[0.997368,0.0002956138,0.0004301686,0.000879221,0.0004369826,0.0005899877],"domain_scores_gemma":[0.9978448,0.00002137581,0.0001575962,0.000983808,0.0008226647,0.0001697576],"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":[0.0007398148,0.0001476049,0.0004621128,0.00005390327,0.0001082911,0.000003175568,0.003104286,0.00003826789,0.9940287,0.00006940807,0.0007242946,0.0005200878],"study_design_scores_gemma":[0.000701608,0.0006211366,0.004936676,0.000009501099,0.00001408635,0.000009258455,0.0008247859,0.00002214453,0.9682785,0.00004585459,0.02428484,0.0002516611],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9911814,0.002051134,0.0005687326,0.0001356252,0.0004592035,0.0004674453,0.0000441611,0.00002550996,0.005066748],"genre_scores_gemma":[0.9946818,0.0007388888,0.001377514,0.00003617061,0.0007742501,0.00004156155,0.0002812568,0.00004338536,0.002025137],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02575031,"threshold_uncertainty_score":0.9372388,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1493636227696736,"score_gpt":0.3502610496640595,"score_spread":0.2008974268943859,"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."}}