{"id":"W3004582548","doi":"10.1101/2020.02.03.932665","title":"High contiguity long read assembly of <i>Brassica nigra</i> allows localization of active centromeres and provides insights into the ancestral <i>Brassica</i> genome","year":2020,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"National Research Council Canada; Plant Biotechnology Institute; Thompson Rivers University; University of Ottawa; Global Institute for Water Security; Saskatchewan Research Council (Canada); University of Saskatchewan; Agriculture and Agri-Food Canada","funders":"Canada First Research Excellence Fund; Agriculture and Agri-Food Canada; Mitacs","keywords":"Centromere; Genome; Contiguity; Contig; Biology; Genetics; Sequence assembly; Computational biology; Brassica; Ploidy; Chromosome; Transposition (logic); Evolutionary biology; Computer science; Gene; Botany; Artificial intelligence","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0002783811,0.0005016874,0.0004068835,0.0004258235,0.0005239971,0.000795025,0.0004117321,0.0003730733,0.001410725],"category_scores_gemma":[0.0007218255,0.0002791348,0.0005582559,0.0004851597,0.0002152238,0.0002901155,0.0003732683,0.000562407,0.0007547505],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004440835,"about_ca_system_score_gemma":0.0003962731,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.007141578,"about_ca_topic_score_gemma":0.01435341,"domain_scores_codex":[0.9997904,0.00001701147,0.00001396012,0.0001056755,0.00005198605,0.00002099527],"domain_scores_gemma":[0.9997237,0.00007716796,0.00003988213,0.00006289616,0.00006679082,0.00002950739],"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":[0.0001539338,0.00002230455,0.003751366,0.0001035774,0.00004055885,0.0002052587,0.0001441102,0.005174474,0.9810662,0.0003967502,0.0004082783,0.008533174],"study_design_scores_gemma":[0.00003691246,0.000174942,0.06627435,0.00003354795,0.0001143953,0.0004890761,0.0002956478,0.1192945,0.7964922,0.001904617,0.01483158,0.0000583154],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8574889,0.0003204346,0.1268287,0.0001157097,0.00003233591,0.00005015984,0.009710496,0.002884534,0.002568832],"genre_scores_gemma":[0.8077666,0.0001797701,0.1566832,0.00005131949,0.000007174081,0.00007670898,0.03129018,0.0008499696,0.003095046],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.007141578,"threshold_uncertainty_score":0.01420003,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01079542755470723,"score_gpt":0.2116640847801105,"score_spread":0.2008686572254033,"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."}}