{"meta":{"page":1,"per_page":50,"max_per_page":100,"total":366,"total_is_capped":false,"direct_labels_cover":0,"predictions_cover":366,"direct_label_status":"direct model label, unvalidated","prediction_status":"machine_predicted_unvalidated (Codex and Gemma teacher distillation)","score_status":"score_only:v0-immature-baseline (scores rank; they never assert a category)","snapshot":{"source":"OpenAlex, pinned release, all 482 partitions","release":"2026-06-24","frame_built":"2026-07-12","author_layer_release":"2026-06-26"},"query_hash":"51ec71e6003a","filters":{"venue":"Genome Biology and Evolution"}},"results":[{"id":"W2095854550","doi":"10.1093/gbe/evu050","title":"A Phylogenomic View of Ecological Specialization in the Lachnospiraceae, a Family of Digestive Tract-Associated Bacteria","year":2014,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":749,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Dalhousie University","funders":"Canadian Institutes of Health Research; Genome Atlantic; Canada Research Chairs","keywords":"Lachnospiraceae; Biology; Microbiome; Ecology; Firmicutes; Adaptation (eye); Gene; Animal ecology; Genetics; Evolutionary biology; Zoology","authors":[{"name":"Conor J. Meehan","is_ca":true},{"name":"Robert G. Beiko","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.0101374870117947,"gpt":0.2452735232511712,"spread":0.2351360362393765,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003338057,0.0003978346,0.0003430728,0.002117272,0.0005682901,0.0008922678,0.000230689,0.0003647258,0.001241393],"category_scores_gemma":[0.0004617529,0.0001357937,0.0003905622,0.001968646,0.0004896711,0.0005560688,0.0005995735,0.0005801509,0.000346886],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003447276,"about_ca_system_score_gemma":0.0005281996,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002426214,"about_ca_topic_score_gemma":0.002803089,"domain_scores_codex":[0.9998078,0.00003804799,0.000007831419,0.00008002573,0.00002747376,0.0000387355],"domain_scores_gemma":[0.999655,0.00004901568,0.0001109848,0.00003307186,0.00006310309,0.00008880335],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0006985394,0.0001364105,0.2335802,0.0005352969,0.0002965291,0.0006999575,0.001648491,0.002289319,0.6973534,0.004078967,0.001012493,0.05767038],"study_design_scores_gemma":[0.00001326003,0.0002218527,0.9739034,0.00007041418,0.0001272469,0.0008438415,0.001234004,0.004983156,0.004823638,0.003490438,0.01025804,0.00003065288],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9709086,0.008945989,0.0107081,0.000997911,0.0000212086,0.00003301252,0.002415071,0.0001330216,0.005837112],"genre_scores_gemma":[0.984703,0.002953134,0.008098651,0.0003096642,0.00002416471,0.00002537795,0.002719456,0.00002637679,0.001140143],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002426214,"threshold_uncertainty_score":0.004824162,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2332689805","doi":"10.1093/gbe/evv069","title":"Mutation Rates in Plastid Genomes: They Are Lower than You Might Think","year":2015,"lang":"en","type":"letter","venue":"Genome Biology and Evolution","topic":"Photosynthetic Processes and Mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":320,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Western University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Plastid; Biology; Genome; Mitochondrial DNA; Mitochondrion; Mutation rate; Genetics; Evolutionary biology; Mutation; Chloroplast; Gene","authors":[{"name":"David Roy Smith","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01012588516719947,"gpt":0.234586681994613,"spread":0.2244607968274135,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.004290267,0.0005645431,0.0008361588,0.0003998223,0.00142703,0.002347389,0.001194032,0.01542317,0.003980668],"category_scores_gemma":[0.02227857,0.0003851782,0.0005208858,0.0004223265,0.00488634,0.004363505,0.001136481,0.01810353,0.006580034],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001952788,"about_ca_system_score_gemma":0.0005787236,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009054599,"about_ca_topic_score_gemma":0.0007023886,"domain_scores_codex":[0.9968204,0.0007727792,0.0003347706,0.001022325,0.0007901384,0.0002596343],"domain_scores_gemma":[0.9895607,0.006275601,0.001042506,0.001038241,0.001239048,0.0008439214],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.0007846263,0.0001188051,0.01419841,0.0006710631,0.0001468074,0.008782845,0.0009893132,0.0006632552,0.01498515,0.02706971,0.7120181,0.2195718],"study_design_scores_gemma":[0.0002575425,0.0003715894,0.01126141,0.000359182,0.00007770663,0.01937646,0.0008184172,0.001182756,0.007053401,0.07563356,0.8834268,0.0001812259],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":null,"genre_codex":"commentary","genre_gemma":"commentary","genre_scores_codex":[0.004966273,0.01051935,0.001690938,0.9659778,0.01206237,0.00001021639,0.00009567871,0.0001896358,0.00448781],"genre_scores_gemma":[0.08241934,0.009492014,0.002638334,0.8543136,0.04349451,0.00005763289,0.0001317505,0.0001037056,0.007349269],"genre_candidate":"commentary","genre_consensus":"commentary","teacher_disagreement_score":0.01542317,"threshold_uncertainty_score":0.0226894,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2155993242","doi":"10.1093/gbe/evt008","title":"Strikingly Bacteria-Like and Gene-Rich Mitochondrial Genomes throughout Jakobid Protists","year":2013,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":260,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Dalhousie University; Université de Montréal","funders":"Canadian Institutes of Health Research; Dalhousie University; Medical Research Council Canada; Canada Research Chairs; Medical Research Council; Canadian Institute for Advanced Research","keywords":"Biology; Genetics; Gene; Genome; Mitochondrial DNA; Horizontal gene transfer; Transfer RNA; RNA","authors":[{"name":"Gertraud Burger","is_ca":true},{"name":"Michael W. Gray","is_ca":true},{"name":"Lise Forget","is_ca":true},{"name":"B. Franz Lang","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.007580588548539115,"gpt":0.2267582726713856,"spread":0.2191776841228465,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00002941919,0.000140313,0.0001135609,0.0006448517,0.0003730029,0.0004375656,0.00009468844,0.0001372018,0.001516059],"category_scores_gemma":[0.0001576251,0.00009805151,0.000131953,0.0006952596,0.0002269958,0.0001766023,0.0003631756,0.0002113644,0.0005191163],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002017122,"about_ca_system_score_gemma":0.0002020682,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001036932,"about_ca_topic_score_gemma":0.002204824,"domain_scores_codex":[0.9999151,0.000005237965,0.000006320844,0.00003301699,0.00002214243,0.0000181654],"domain_scores_gemma":[0.9998558,0.00001534478,0.00005635876,0.0000135447,0.00001943432,0.00003957389],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001830179,0.000006968515,0.01369307,0.0001068707,0.00001767977,0.0002213083,0.0003091325,0.00004831009,0.9792723,0.0003048238,0.00006792865,0.005768638],"study_design_scores_gemma":[0.00001561872,0.0001121243,0.8573653,0.00005879678,0.00007054606,0.003717555,0.001074239,0.0004112257,0.1028931,0.0004978494,0.03376175,0.00002200657],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9942346,0.001176199,0.0007891681,0.00004385452,0.00001120157,0.000007262478,0.00120429,0.0000461856,0.002487145],"genre_scores_gemma":[0.9924494,0.0006009497,0.001953693,0.00004659543,0.000006767531,0.00001289768,0.00253989,0.00002574771,0.002364099],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001516059,"threshold_uncertainty_score":0.005071759,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2589006132","doi":"10.1093/gbe/evx030","title":"The Complete Genome Sequence of the Phytopathogenic Fungus Sclerotinia sclerotiorum Reveals Insights into the Genome Architecture of Broad Host Range Pathogens","year":2017,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Plant pathogens and resistance mechanisms","field":"Agricultural and Biological Sciences","cited_by":257,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Agriculture and Agri-Food Canada","funders":"Biotechnology and Biological Sciences Research Council; National Institute of Food and Agriculture; Directorate for Biological Sciences; Agence Nationale de la Recherche; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; Curtin University of Technology; Australian Government; Grains Research and Development Corporation; Government of Western Australia; Government of Canada; Koninklijke Nederlandse Akademie van Wetenschappen; Saskatchewan Canola Development Commission; U.S. Department of Agriculture","keywords":"Sclerotinia sclerotiorum; Biology; Genome; Effector; Genetics; Gene; Virulence; Genome evolution; Botany; Cell biology","authors":[{"name":"Mark C. Derbyshire","is_ca":false},{"name":"Matthew Denton‐Giles","is_ca":false},{"name":"Dwayne D. Hegedus","is_ca":true},{"name":"Shirin Seifbarghy","is_ca":true},{"name":"Jeffrey A. Rollins","is_ca":false},{"name":"J.A.L. van Kan","is_ca":false},{"name":"Michael Seidl","is_ca":false},{"name":"Luigi Faino","is_ca":false},{"name":"Malick Mbengué","is_ca":false},{"name":"Olivier Navaud","is_ca":false},{"name":"Sylvain Raffaele","is_ca":false},{"name":"Stephanie C. Heard","is_ca":false},{"name":"Richard P. Oliver","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.02289879212057392,"gpt":0.2169107662010039,"spread":0.19401197408043,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001659327,0.0007209108,0.0005679579,0.0008485335,0.0003868428,0.0005461476,0.000266669,0.0005857552,0.001544328],"category_scores_gemma":[0.0004222675,0.0002454153,0.000593516,0.001431532,0.0001853445,0.0003659776,0.0002680189,0.0007802768,0.001344613],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000328999,"about_ca_system_score_gemma":0.0006900405,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002099209,"about_ca_topic_score_gemma":0.003352308,"domain_scores_codex":[0.9998259,0.00001895953,0.0000156707,0.00005776832,0.00005683036,0.00002493262],"domain_scores_gemma":[0.9996603,0.00006957566,0.00008231233,0.00002734248,0.00008074359,0.00007970243],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0003803922,0.00004063546,0.0021444,0.0004620469,0.00003348653,0.0003083328,0.0001155047,0.0004349934,0.9855005,0.0001722614,0.0006435714,0.009763885],"study_design_scores_gemma":[0.0001753662,0.001158333,0.5024557,0.0004064233,0.0007878601,0.003985412,0.0007996095,0.008465263,0.3397287,0.00147015,0.1403685,0.0001986562],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8259382,0.008063388,0.03146476,0.0005189255,0.0002079563,0.0001896283,0.1283444,0.0009118013,0.004360868],"genre_scores_gemma":[0.5435816,0.007449951,0.06607857,0.0004247298,0.0001337614,0.0002309139,0.375188,0.0004911765,0.006421322],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002099209,"threshold_uncertainty_score":0.005166292,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2099000855","doi":"10.1093/gbe/evp040","title":"Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales","year":2009,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":256,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"National Institutes of Health","keywords":"Brassicaceae; Biology; Arabidopsis; Carica; Genome; Gene duplication; Genetics; Botany; Gene","authors":[{"name":"Michael S. Barker","is_ca":true},{"name":"Heiko Vogel","is_ca":false},{"name":"M. Eric Schranz","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.03175599109768618,"gpt":0.2556595418175582,"spread":0.223903550719872,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00009865532,0.0001093157,0.0001661002,0.0005251429,0.0002489601,0.000374188,0.00009964,0.0002652333,0.0005367817],"category_scores_gemma":[0.0002266108,0.0000900522,0.0001863421,0.0003763787,0.0001919277,0.0002800208,0.0002466012,0.000359915,0.0002151961],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002561568,"about_ca_system_score_gemma":0.0001441191,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001372075,"about_ca_topic_score_gemma":0.00355598,"domain_scores_codex":[0.99994,0.000005089807,0.000003573339,0.00002644361,0.00001348824,0.00001142863],"domain_scores_gemma":[0.9998586,0.00003448189,0.00004143253,0.0000161528,0.00001867802,0.00003059399],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001229409,0.000006564575,0.0115578,0.00003597658,0.000009575268,0.00009402652,0.0001919129,0.00009255191,0.9849068,0.0001133221,0.00001606491,0.002852426],"study_design_scores_gemma":[0.000009780165,0.00007977319,0.9426026,0.00001649621,0.00002709439,0.0006043369,0.0003736519,0.000634193,0.05171802,0.0002840046,0.003636851,0.00001326352],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.998163,0.0004393364,0.0004260081,0.00003231127,0.000001387597,0.000003903328,0.0003852941,0.00001029049,0.0005384816],"genre_scores_gemma":[0.9951763,0.0005201451,0.001223796,0.00009296377,0.000007308241,0.00001355204,0.001826788,0.00001688805,0.001122219],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001372075,"threshold_uncertainty_score":0.002728224,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3016662794","doi":"10.1093/gbe/evaa081","title":"Sex Chromosome Evolution: So Many Exceptions to the Rules","year":2020,"lang":"en","type":"review","venue":"Genome Biology and Evolution","topic":"Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities","field":"Biochemistry, Genetics and Molecular Biology","cited_by":235,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"H2020 European Research Council; Biotechnology and Biological Sciences Research Council; Natural Environment Research Council; Sight Research UK","keywords":"Biology; Evolutionary biology; Chromosome; Genetics; Computational biology; Gene","authors":[{"name":"Benjamin L. S. Furman","is_ca":true},{"name":"David C. H. Metzger","is_ca":true},{"name":"Iulia Darolti","is_ca":true},{"name":"Alison E. Wright","is_ca":false},{"name":"Benjamin A. Sandkam","is_ca":true},{"name":"Pedro Almeida","is_ca":false},{"name":"Jacelyn J. Shu","is_ca":true},{"name":"Judith E. Mank","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.02082244159786993,"gpt":0.2972904199618903,"spread":0.2764679783640203,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.009656239,0.0007848787,0.001922478,0.001114575,0.001847527,0.004508755,0.002635978,0.004908281,0.001675469],"category_scores_gemma":[0.02404122,0.0005388403,0.0007214679,0.0009926396,0.01701045,0.008131921,0.003119489,0.00813658,0.0007920517],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006526725,"about_ca_system_score_gemma":0.0007769417,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001551784,"about_ca_topic_score_gemma":0.001715648,"domain_scores_codex":[0.9930147,0.001372791,0.0006477534,0.003112119,0.001509647,0.0003430091],"domain_scores_gemma":[0.9804301,0.01260583,0.001445849,0.003441242,0.001488853,0.000588118],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0003844551,0.0001408191,0.0304304,0.001825341,0.0009187565,0.00246622,0.004810229,0.005105754,0.003565854,0.589164,0.03574407,0.3254441],"study_design_scores_gemma":[0.00005224905,0.00005648888,0.007373075,0.0004509338,0.00009436643,0.001403486,0.001307186,0.001616419,0.0008232557,0.9020617,0.08463109,0.0001297486],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"commentary","genre_gemma":"review","genre_scores_codex":[0.2186718,0.2786251,0.1294582,0.2878579,0.01172658,0.0001075927,0.001026892,0.001564758,0.07096113],"genre_scores_gemma":[0.7825875,0.09393369,0.04270127,0.0572678,0.01323276,0.0001727665,0.0005936967,0.000414471,0.009096111],"genre_candidate":"review","genre_consensus":null,"teacher_disagreement_score":0.009656239,"threshold_uncertainty_score":0.05106765,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2164849432","doi":"10.1093/gbe/evv090","title":"Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants","year":2015,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Plant Pathogens and Fungal Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":191,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"Agricultural Research Service; U.S. Department of Agriculture; Office of Science; Joint Genome Institute; Broad Institute; U.S. Department of Energy","keywords":"Biology; Chytridiomycota; Lineage (genetic); Ascomycota; Fungus; Phylogenetics; Botany; Genome; Gene; Genetics","authors":[{"name":"Ying Chang","is_ca":true},{"name":"Sishuo Wang","is_ca":true},{"name":"Satoshi Sekimoto","is_ca":true},{"name":"Andrea Aerts","is_ca":false},{"name":"Cindy Choi","is_ca":false},{"name":"Alicia Clum","is_ca":false},{"name":"Kurt LaButti","is_ca":false},{"name":"Erika Lindquist","is_ca":false},{"name":"Chew Yee Ngan","is_ca":false},{"name":"Robin A. Ohm","is_ca":false},{"name":"Asaf Salamov","is_ca":false},{"name":"Igor V. Grigoriev","is_ca":false},{"name":"Joseph W. Spatafora","is_ca":false},{"name":"Mary L. Berbee","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.04361082017396127,"gpt":0.2706214408695644,"spread":0.2270106206956031,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002119423,0.0003208719,0.0002947665,0.0009999975,0.0004739849,0.0004850439,0.0001323372,0.0002817991,0.001241022],"category_scores_gemma":[0.0003204095,0.0001533178,0.000415123,0.001054187,0.0002407735,0.0003389303,0.0003581893,0.0004041456,0.0003787804],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002267528,"about_ca_system_score_gemma":0.0002024336,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009776782,"about_ca_topic_score_gemma":0.002139635,"domain_scores_codex":[0.999886,0.00001010588,0.000005992401,0.00005880285,0.00001806729,0.00002093885],"domain_scores_gemma":[0.9996346,0.00009207781,0.0001153686,0.00003361281,0.00004422047,0.00008006064],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0004539161,0.00005633128,0.2868555,0.0004057886,0.0003018956,0.0006735779,0.0006264209,0.000688833,0.6689098,0.001113539,0.0002827286,0.03963167],"study_design_scores_gemma":[0.00001006158,0.00009372889,0.9822536,0.00003813958,0.0001075369,0.0007423208,0.0003595364,0.001222122,0.009049617,0.0006140182,0.005493855,0.00001533565],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9908137,0.00158009,0.003775587,0.00006689343,0.000009627763,0.00001855993,0.001936779,0.0000666475,0.0017321],"genre_scores_gemma":[0.9872326,0.001567295,0.005890642,0.000113083,0.00001070064,0.00002272773,0.003944308,0.00003195281,0.001186727],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001241022,"threshold_uncertainty_score":0.004151642,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2953086962","doi":"10.1093/gbe/evy014","title":"Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group","year":2018,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Protist diversity and phylogeny","field":"Biochemistry, Genetics and Molecular Biology","cited_by":177,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada; University of Tsukuba; Dalhousie University; Division of Environmental Biology; Japan Society for the Promotion of Science; Canada Research Chairs; University of Oxford; Mississippi State University; National Science Foundation","keywords":"Phylogenomics; Biology; Evolutionary biology; Phylogenetics; Group (periodic table); Ecology; Zoology; Computational biology; Genetics; Gene; Clade","authors":[{"name":"Matthew W. Brown","is_ca":false},{"name":"Aaron A. Heiss","is_ca":true},{"name":"Ryoma Kamikawa","is_ca":false},{"name":"Yuji Inagaki","is_ca":false},{"name":"Akinori Yabuki","is_ca":false},{"name":"Alexander K. Tice","is_ca":false},{"name":"Takashi Shiratori","is_ca":false},{"name":"Ken‐ichiro Ishida","is_ca":false},{"name":"Tetsuo Hashimoto","is_ca":false},{"name":"Alastair G. B. Simpson","is_ca":true},{"name":"Andrew J. Roger","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.009392115342265611,"gpt":0.2307647112660558,"spread":0.2213725959237902,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002720566,0.0002578706,0.0003270363,0.000752256,0.0007600692,0.00067279,0.0002423869,0.0003609128,0.001478405],"category_scores_gemma":[0.0005818634,0.0001842768,0.0002580485,0.0007145836,0.000397797,0.0006555507,0.0009258267,0.0004934869,0.0003790292],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000235095,"about_ca_system_score_gemma":0.0003492866,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006927919,"about_ca_topic_score_gemma":0.002277591,"domain_scores_codex":[0.9998077,0.00002107521,0.00001255671,0.00009301872,0.00003508115,0.00003075774],"domain_scores_gemma":[0.9995529,0.0001057622,0.0001481736,0.00008792365,0.00004086674,0.00006422788],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0006168263,0.00006221003,0.3806897,0.0002404966,0.0002614775,0.000466738,0.002027252,0.001123645,0.5792534,0.002718271,0.0002599224,0.03227999],"study_design_scores_gemma":[0.00002193726,0.000266312,0.9636715,0.00005534327,0.0001647105,0.001064162,0.001477018,0.008954719,0.01397737,0.004242328,0.006073861,0.00003068413],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9956878,0.0002520708,0.003128718,0.0000620806,0.000002644,0.000006133033,0.0002529151,0.00004361796,0.0005640457],"genre_scores_gemma":[0.9946003,0.0001917237,0.004061795,0.00006269341,0.00000613562,0.000008704346,0.0008145071,0.00001724523,0.000236912],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001478405,"threshold_uncertainty_score":0.004945755,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1988865197","doi":"10.1093/gbe/evt072","title":"RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations","year":2013,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genetic diversity and population structure","field":"Biochemistry, Genetics and Molecular Biology","cited_by":168,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Genetics; Hybrid; Allele; Gene; Gene expression; Heterosis; Botany","authors":[{"name":"Graeme Douglas Milton Bell","is_ca":true},{"name":"Nolan C. Kane","is_ca":true},{"name":"Loren H. Rieseberg","is_ca":true},{"name":"Keith L. Adams","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.00909352225104106,"gpt":0.2092477139375544,"spread":0.2001541916865133,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002337747,0.0002227663,0.0004333174,0.0005051551,0.0004161169,0.0004593904,0.0002372122,0.0003380405,0.0008358561],"category_scores_gemma":[0.0003842692,0.0001911579,0.0004472372,0.0004627877,0.0002503793,0.0001795266,0.0002986216,0.0006497227,0.0002733368],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003092814,"about_ca_system_score_gemma":0.0001691962,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001481804,"about_ca_topic_score_gemma":0.00337968,"domain_scores_codex":[0.9997408,0.00001304093,0.00001299485,0.0001418762,0.00006150395,0.00002982746],"domain_scores_gemma":[0.9997433,0.00009679895,0.00005179051,0.0000141373,0.00005919949,0.00003470819],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001090693,0.00001270783,0.004478976,0.00008658149,0.00003775157,0.0001172072,0.0002410794,0.0001574409,0.9924906,0.0001209202,0.00009250966,0.002055122],"study_design_scores_gemma":[0.00005532765,0.0003914985,0.6186385,0.00005337906,0.000467402,0.001356158,0.001137935,0.009011141,0.3455208,0.0007062744,0.0225375,0.0001241332],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9847147,0.0006339942,0.006130086,0.00003592144,0.00003547827,0.00003489503,0.006707652,0.0001634729,0.00154382],"genre_scores_gemma":[0.9671497,0.0003875208,0.01194004,0.0002823528,0.00002436858,0.0002105982,0.01640191,0.0003072651,0.003296284],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001481804,"threshold_uncertainty_score":0.002946436,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2149144579","doi":"10.1093/gbe/evr089","title":"Conserved Meiotic Machinery in Glomus spp., a Putatively Ancient Asexual Fungal Lineage","year":2011,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Mycorrhizal Fungi and Plant Interactions","field":"Agricultural and Biological Sciences","cited_by":164,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Ottawa; Dalhousie University; Canadian Institute for Advanced Research; Université de Montréal","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institute for Advanced Research","keywords":"Biology; Meiosis; Homologous recombination; Genetics; Ploidy; Phylogenetic tree; Phylogenetics; Genome; Genetic recombination; Lineage (genetic); Asexual reproduction; Evolutionary biology; Homologous chromosome; Gene; Recombination","authors":[{"name":"Sébastien Halary","is_ca":true},{"name":"Shehre-Banoo Malik","is_ca":true},{"name":"Levannia Lildhar","is_ca":true},{"name":"Claudio H. Slamovits","is_ca":true},{"name":"Mohamed Hijri","is_ca":true},{"name":"Nicolas Corradi","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.02690130181267518,"gpt":0.222132475371436,"spread":0.1952311735587608,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00007042209,0.0001837579,0.0001638389,0.0004351541,0.0002291116,0.0002579184,0.0001705433,0.0002330296,0.0003567359],"category_scores_gemma":[0.0001844856,0.0001116887,0.0002156116,0.0002608909,0.0001996073,0.0002370655,0.0002245602,0.0002139022,0.0002418355],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000187061,"about_ca_system_score_gemma":0.0002364754,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005204014,"about_ca_topic_score_gemma":0.001016551,"domain_scores_codex":[0.9999274,0.000005308484,0.000006296988,0.00003569658,0.0000134511,0.0000117508],"domain_scores_gemma":[0.9998522,0.00001580207,0.00006154777,0.0000228381,0.00001398449,0.00003366595],"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":[0.000100048,0.000009140107,0.01131558,0.0001106908,0.000009142068,0.0001402986,0.00009817258,0.00006485477,0.981448,0.0001753611,0.00003254311,0.006496087],"study_design_scores_gemma":[0.00002375201,0.0004929857,0.7512831,0.00005165063,0.0000894029,0.00354178,0.0002957086,0.001719962,0.22978,0.0005639141,0.01213086,0.00002681248],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9955677,0.001089783,0.001871309,0.00003432344,0.000003760885,0.00002055418,0.0005710874,0.00005965973,0.0007816886],"genre_scores_gemma":[0.9904401,0.0006239603,0.005010928,0.00005268918,0.000005174905,0.00003287223,0.002745337,0.00001623468,0.001072666],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0005204014,"threshold_uncertainty_score":0.001357198,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3024872414","doi":"10.1093/gbe/evaa096","title":"Genomic Insights into Plastid Evolution","year":2020,"lang":"en","type":"review","venue":"Genome Biology and Evolution","topic":"Protist diversity and phylogeny","field":"Biochemistry, Genetics and Molecular Biology","cited_by":163,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada; Gordon and Betty Moore Foundation","keywords":"Plastid; Biology; Eukaryote; Endosymbiosis; Evolutionary biology; Tree of life (biology); Monophyly; Phylogenetics; Chloroplast; Genome; Genetics; Gene; Clade","authors":[{"name":"Shannon J. Sibbald","is_ca":true},{"name":"John M. Archibald","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01431738633490309,"gpt":0.2512263141165595,"spread":0.2369089277816564,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005194148,0.000736291,0.0008921751,0.00190034,0.0002284019,0.000962943,0.0006980468,0.001105434,0.002853933],"category_scores_gemma":[0.0007593163,0.0002922542,0.0003671927,0.00208248,0.0006017017,0.00166821,0.0007515555,0.001633065,0.001862255],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008608186,"about_ca_system_score_gemma":0.00114553,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001156919,"about_ca_topic_score_gemma":0.001145766,"domain_scores_codex":[0.9998724,0.00001593876,0.00001464049,0.00004358406,0.00003880708,0.00001448147],"domain_scores_gemma":[0.999749,0.0001276814,0.00002699501,0.00001050059,0.00006092964,0.00002488595],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00007727386,0.0000315542,0.0002879955,0.01528901,0.00006094716,0.0003575163,0.0000992128,0.0006021548,0.004568791,0.01161031,0.01789818,0.9491172],"study_design_scores_gemma":[0.000007573666,0.00003890253,0.0009218123,0.00216468,0.00006412408,0.0009826875,0.00004699859,0.00008276499,0.0008871736,0.003884424,0.9909019,0.0000169149],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.0001307848,0.998302,0.0001849709,0.0003088688,0.0001291752,0.000001598545,0.00002395113,0.000008593494,0.0009100405],"genre_scores_gemma":[0.0008944172,0.9982195,0.0001669,0.0001884299,0.0001113186,0.000002379023,0.00004868293,0.000001788486,0.0003664112],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.002853933,"threshold_uncertainty_score":0.009547353,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3027390390","doi":"10.1093/gbe/evaa108","title":"Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure","year":2020,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":160,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia; Canada's Michael Smith Genome Sciences Centre; Université Laval; Genome British Columbia","funders":"Genome Alberta; Genome British Columbia; Genome Canada","keywords":"Biology; Genome; Mitochondrial DNA; Gymnosperm; Genetics; Genome size; Evolutionary biology; Gene; Botany","authors":[{"name":"Shaun D. Jackman","is_ca":true},{"name":"Lauren Coombe","is_ca":true},{"name":"René L. Warren","is_ca":true},{"name":"Heather Kirk","is_ca":true},{"name":"Eva Trinh","is_ca":true},{"name":"Tina MacLeod","is_ca":true},{"name":"Stephen Pleasance","is_ca":true},{"name":"Pawan Pandoh","is_ca":true},{"name":"Yongjun Zhao","is_ca":true},{"name":"Robin Coope","is_ca":true},{"name":"Jean Bousquet","is_ca":true},{"name":"Jöerg Bohlmann","is_ca":true},{"name":"Steven J.M. Jones","is_ca":true},{"name":"İnanç Birol","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01578817432420364,"gpt":0.2328093170309573,"spread":0.2170211427067537,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00008410978,0.0003142123,0.0002146037,0.0006200339,0.0003788502,0.000256046,0.000140839,0.0001891043,0.001347968],"category_scores_gemma":[0.0002137976,0.0001825089,0.0002852276,0.0006417839,0.0002155138,0.0002751078,0.0002497061,0.0002985434,0.0006243575],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002152486,"about_ca_system_score_gemma":0.0003254476,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002386698,"about_ca_topic_score_gemma":0.006979542,"domain_scores_codex":[0.9999399,0.000004206837,0.000003950748,0.00003141721,0.00001433568,0.000006244857],"domain_scores_gemma":[0.9998129,0.00003425358,0.00004566514,0.0000274204,0.00003972704,0.0000400873],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0002243863,0.00002737727,0.00910743,0.0002869922,0.00006435631,0.0002728288,0.0002625083,0.0005268318,0.9773811,0.0003571335,0.0003267482,0.01116238],"study_design_scores_gemma":[0.00003599546,0.0005563446,0.7839379,0.0001209325,0.0003870478,0.002967314,0.0006245286,0.003086622,0.1679788,0.00108284,0.03915825,0.0000633918],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9724494,0.00173306,0.009872187,0.0001074131,0.00002159444,0.00003083711,0.01269142,0.0003720735,0.002722064],"genre_scores_gemma":[0.9252476,0.0008328982,0.01899491,0.00008420578,0.00001076996,0.00003628418,0.05204933,0.0001313112,0.002612705],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002386698,"threshold_uncertainty_score":0.004745603,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2068623154","doi":"10.1093/gbe/evp022","title":"Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates","year":2009,"lang":"en","type":"letter","venue":"Genome Biology and Evolution","topic":"Protist diversity and phylogeny","field":"Biochemistry, Genetics and Molecular Biology","cited_by":158,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia; Dalhousie University","funders":"Norges Forskningsråd; Joint Genome Institute; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; Universitetet i Oslo; Tula Foundation; National Science Foundation","keywords":"Protist; Biology; Evolutionary biology; Phylogenomics; Scale (ratio); Phylogenetics; Genetics; Gene; Clade","authors":[{"name":"Fabien Burki","is_ca":false},{"name":"Yuji Inagaki","is_ca":false},{"name":"Jon Bråte","is_ca":false},{"name":"John M. Archibald","is_ca":true},{"name":"Patrick J. Keeling","is_ca":true},{"name":"Thomas Cavalier‐Smith","is_ca":false},{"name":"Miako Sakaguchi","is_ca":false},{"name":"Tetsuo Hashimoto","is_ca":false},{"name":"Aleš Horák","is_ca":true},{"name":"Surendra Kumar","is_ca":false},{"name":"Dag Klaveness","is_ca":false},{"name":"Kjetill S. Jakobsen","is_ca":false},{"name":"Jan Pawłowski","is_ca":false},{"name":"Kamran Shalchian‐Tabrizi","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01230591327282595,"gpt":0.2602443671085793,"spread":0.2479384538357533,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00009311405,0.0002596811,0.0001800017,0.0006032406,0.0003597378,0.0002468529,0.0001228334,0.0001997846,0.0007976313],"category_scores_gemma":[0.0002071836,0.0001007089,0.0001908405,0.0004641812,0.0002466405,0.0003310141,0.0002930681,0.00026464,0.0003551361],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001144267,"about_ca_system_score_gemma":0.0001526473,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005120172,"about_ca_topic_score_gemma":0.001096302,"domain_scores_codex":[0.9999355,0.000004353968,0.000004010696,0.00002866989,0.00001805913,0.00000932593],"domain_scores_gemma":[0.9997544,0.00006832481,0.00008634668,0.00002529827,0.0000247372,0.00004085911],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001319388,0.00002761512,0.06038128,0.0001836038,0.00005390853,0.0001560182,0.0003719731,0.0001882452,0.9171499,0.0001776939,0.00008212156,0.0210957],"study_design_scores_gemma":[0.000008940317,0.0001887826,0.9391322,0.00002990309,0.0001096205,0.0009584519,0.0006578068,0.001419847,0.04932238,0.0005780361,0.007577761,0.00001626429],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9941342,0.00135754,0.002938949,0.00003828213,0.000003665705,0.000009935914,0.000851052,0.00004720716,0.0006192501],"genre_scores_gemma":[0.9886137,0.001407931,0.005489651,0.00008209693,0.00001061552,0.00002079623,0.003459956,0.00001763298,0.0008976757],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0007976313,"threshold_uncertainty_score":0.002668321,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3167015799","doi":"10.1093/gbe/evab141","title":"Effects of Synonymous Mutations beyond Codon Bias: The Evidence for Adaptive Synonymous Substitutions from Microbial Evolution Experiments","year":2021,"lang":"en","type":"review","venue":"Genome Biology and Evolution","topic":"Evolution and Genetic Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":150,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Ottawa","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Synonymous substitution; Biology; Nonsynonymous substitution; Genetics; Neutral mutation; Silent mutation; Neutral theory of molecular evolution; Genetic Fitness; Experimental evolution; Fitness landscape; Gene; Molecular evolution; Directed evolution; Mutation; Mutation rate; Codon usage bias; Adaptation (eye); Evolutionary biology; Mutant; Phylogenetics; Missense mutation; Population; Genome","authors":[{"name":"Susan F. Bailey","is_ca":false},{"name":"Luz Angela Alonso Morales","is_ca":true},{"name":"Rees Kassen","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.04709467167788768,"gpt":0.336831654909981,"spread":0.2897369832320933,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001387037,0.0008869658,0.001573436,0.002069493,0.0002668005,0.001169709,0.001102875,0.00184316,0.001869997],"category_scores_gemma":[0.002172478,0.0004071207,0.0006026157,0.001816074,0.001346832,0.002198793,0.0007949951,0.003566859,0.001646689],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00104415,"about_ca_system_score_gemma":0.001175742,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009518656,"about_ca_topic_score_gemma":0.00115277,"domain_scores_codex":[0.9995421,0.0001062934,0.00006234874,0.0001009561,0.0001571338,0.00003115322],"domain_scores_gemma":[0.9983743,0.001162379,0.0001024875,0.00004908912,0.0002400612,0.00007158326],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001155043,0.00004593452,0.0003092199,0.02324794,0.0001793653,0.0003758948,0.0001124902,0.0006442235,0.00438862,0.01921099,0.03071749,0.9206523],"study_design_scores_gemma":[0.00001622739,0.00008184042,0.0008533435,0.003821961,0.0001356507,0.001194551,0.00004760989,0.0001079286,0.001582582,0.01032187,0.9818006,0.00003596628],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.00006903781,0.9985593,0.0001755415,0.0003876197,0.0001873736,0.000001149259,0.000009014413,0.000004796169,0.0006061204],"genre_scores_gemma":[0.0007198399,0.9979554,0.0002243849,0.000581344,0.000197425,0.000003868625,0.00001674278,0.000002824107,0.0002981612],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.002069493,"threshold_uncertainty_score":0.007575929,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2517999713","doi":"10.1093/gbe/evx150","title":"Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis)","year":2017,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genetic diversity and population structure","field":"Biochemistry, Genetics and Molecular Biology","cited_by":145,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Université Laval","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Gene flow; Evolutionary biology; Sympatric speciation; Reproductive isolation; Ecological speciation; Allopatric speciation; Disruptive selection; Genetic divergence; Introgression; Coregonus clupeaformis; Population; Ecology; Natural selection; Genetics; Genetic variation; Gene; Genetic diversity","authors":[{"name":"Clément Rougeux","is_ca":true},{"name":"Louis Bernatchez","is_ca":true},{"name":"Pierre‐Alexandre Gagnaire","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.02947590690487799,"gpt":0.2160402505633524,"spread":0.1865643436584744,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0009279943,0.0003864944,0.0004227623,0.0005573558,0.0005258123,0.0007094503,0.0007990607,0.0007981992,0.0009815656],"category_scores_gemma":[0.00212374,0.000397264,0.001012202,0.0004649714,0.000545193,0.0007266406,0.0009082305,0.0006293194,0.0001136207],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006813678,"about_ca_system_score_gemma":0.0006214005,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01117927,"about_ca_topic_score_gemma":0.01523944,"domain_scores_codex":[0.9997663,0.0001025665,0.00001152702,0.0000790078,0.00001490279,0.00002568474],"domain_scores_gemma":[0.9995995,0.0002236012,0.00007861719,0.00003458155,0.00001968305,0.00004400609],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00007392428,0.00004881499,0.0787592,0.00004913933,0.0002360387,0.0001981267,0.0003683311,0.8999919,0.006755576,0.007282301,0.0001288466,0.00610779],"study_design_scores_gemma":[0.00000974181,0.00002540504,0.01283376,0.000004739409,0.00003190748,0.00005604902,0.00008448689,0.9818634,0.0002203784,0.004579718,0.0002785966,0.00001180058],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.953464,0.00008973773,0.04574244,0.0001378571,0.000005246047,0.00001139639,0.0001155729,0.0000388958,0.0003949153],"genre_scores_gemma":[0.9903671,0.00006359314,0.008846541,0.00002850282,0.000006368427,0.0000221387,0.0001293483,0.00001277532,0.000523654],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01117927,"threshold_uncertainty_score":0.02222842,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2166638314","doi":"10.1093/gbe/evr001","title":"Correlation between Nuclear Plastid DNA Abundance and Plastid Number Supports the Limited Transfer Window Hypothesis","year":2011,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":135,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Dalhousie University","funders":"Nanjing University of Posts and Telecommunications","keywords":"Plastid; Biology; Genome; Nuclear DNA; Mitochondrial DNA; Evolutionary biology; Nuclear gene; DNA; DNA sequencing; Genetics; Gene","authors":[{"name":"David Roy Smith","is_ca":true},{"name":"Kate Crosby","is_ca":true},{"name":"W. Robert Lee","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01476398154950196,"gpt":0.197565140250176,"spread":0.1828011587006741,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000554061,0.0001715825,0.0002510822,0.0004970974,0.0002486664,0.0002938392,0.0002379495,0.0002158076,0.002848478],"category_scores_gemma":[0.002329086,0.0001420548,0.0001480657,0.0004384176,0.0005866248,0.0006213893,0.0003779785,0.0003843022,0.000492054],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001311758,"about_ca_system_score_gemma":0.0001106487,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000465825,"about_ca_topic_score_gemma":0.0005048888,"domain_scores_codex":[0.9997097,0.00004010228,0.00001988665,0.0001585841,0.0000514007,0.00002035295],"domain_scores_gemma":[0.9956955,0.002302977,0.001184985,0.0002437764,0.0003143427,0.0002584714],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.000728958,0.00008481255,0.7894009,0.0002086029,0.0002395146,0.0005280788,0.0003499305,0.0009925085,0.1876103,0.001084894,0.0003273631,0.01844398],"study_design_scores_gemma":[0.000008202504,0.0002032566,0.9823506,0.00001138175,0.00003660337,0.001429352,0.0001665571,0.00228977,0.0110363,0.001546247,0.000905066,0.0000166265],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.991461,0.001080603,0.005419906,0.0001428081,0.00001302462,0.000007880614,0.0003095661,0.00005376094,0.001511446],"genre_scores_gemma":[0.9984215,0.0001739684,0.0008442457,0.00003298271,0.00001579208,0.000004744093,0.0002547026,0.000004992192,0.000246938],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002848478,"threshold_uncertainty_score":0.009529114,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2293946955","doi":"10.1093/gbe/evw048","title":"Genome Sequencing of the Phytoseiid Predatory Mite<i>Metaseiulus occidentalis</i>Reveals Completely Atomized<i>Hox</i>Genes and Superdynamic Intron Evolution","year":2016,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Insect-Plant Interactions and Control","field":"Agricultural and Biological Sciences","cited_by":134,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"PricewaterhouseCoopers (Canada)","funders":"Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung","keywords":"Biology; Genome; Evolutionary biology; Genetics; Tetranychus urticae; Hox gene; Gene; Mite; Ecology","authors":[{"name":"Marjorie A. Hoy","is_ca":true},{"name":"Robert M. Waterhouse","is_ca":false},{"name":"Ke Wu","is_ca":false},{"name":"Alden S. Estep","is_ca":false},{"name":"Panagiotis Ioannidis","is_ca":false},{"name":"William J. Palmer","is_ca":false},{"name":"Aaron Pomerantz","is_ca":false},{"name":"Felipe A. Simão","is_ca":false},{"name":"Jainy Thomas","is_ca":false},{"name":"Francis M. Jiggins","is_ca":false},{"name":"Terence D. Murphy","is_ca":false},{"name":"Ellen J. Pritham","is_ca":false},{"name":"Hugh M. Robertson","is_ca":false},{"name":"Evgeny M. Zdobnov","is_ca":false},{"name":"Richard A. Gibbs","is_ca":false},{"name":"Stephen Richards","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01054165120111583,"gpt":0.2009501880279532,"spread":0.1904085368268373,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00005937647,0.0003472015,0.0001919802,0.0003278148,0.0002900179,0.0003964811,0.0001502724,0.0002427241,0.000952669],"category_scores_gemma":[0.0001615718,0.0001444187,0.0003664456,0.0003724214,0.0001214408,0.0001627111,0.0002118801,0.0003541211,0.0005925735],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002757025,"about_ca_system_score_gemma":0.0002931651,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002698327,"about_ca_topic_score_gemma":0.008049851,"domain_scores_codex":[0.9999534,0.000002443214,0.000002075323,0.00002246047,0.00001174791,0.00000785387],"domain_scores_gemma":[0.9999158,0.00001560271,0.00002588808,0.000009945219,0.00001380234,0.00001886884],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0003016508,0.00002603965,0.01623869,0.0002495634,0.00007040703,0.0004227537,0.0002430571,0.0004524487,0.9640313,0.000252258,0.0008046179,0.01690714],"study_design_scores_gemma":[0.00003727851,0.000397763,0.7402231,0.0001338292,0.0004065914,0.002146326,0.0005702151,0.005446851,0.202501,0.0007413721,0.04733327,0.00006250255],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9791672,0.001135435,0.004239711,0.000121814,0.00002555628,0.000020582,0.01322968,0.0004071471,0.001652896],"genre_scores_gemma":[0.9227843,0.001388247,0.0189178,0.0001485007,0.000028128,0.00004541052,0.05344119,0.0002599276,0.002986468],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002698327,"threshold_uncertainty_score":0.005365193,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2158957550","doi":"10.1093/gbe/evq022","title":"The Reduced Genome of the Parasitic Microsporidian Enterocytozoon bieneusi Lacks Genes for Core Carbon Metabolism","year":2010,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Parasitic Infections and Diagnostics","field":"Immunology and Microbiology","cited_by":132,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia; Canadian Institute for Advanced Research","funders":"National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research; Canadian Institute for Advanced Research; National Science Foundation; National Institutes of Health; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; Michael Smith Health Research BC","keywords":"Biology; Enterocytozoon bieneusi; Gene; Genome; Genetics; Metabolic pathway; Microsporidia; Pentose phosphate pathway; Glycolysis; Biochemistry; Metabolism; Microbiology","authors":[{"name":"Patrick J. Keeling","is_ca":true},{"name":"Nicolas Corradi","is_ca":true},{"name":"Hilary G. Morrison","is_ca":false},{"name":"Karen Luisa Haag","is_ca":false},{"name":"Dieter Ebert","is_ca":false},{"name":"Louis M. Weiss","is_ca":false},{"name":"Donna E. Akiyoshi","is_ca":false},{"name":"Saul Tzipori","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01010905236203954,"gpt":0.2512489081449494,"spread":0.2411398557829098,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0000702875,0.000270003,0.000188439,0.0002905024,0.000158553,0.0002453912,0.0001301019,0.0002581078,0.0006527046],"category_scores_gemma":[0.0002465723,0.0001115003,0.0001796218,0.0002987689,0.0001132547,0.0001627954,0.0001995439,0.0003034814,0.0002995424],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001113648,"about_ca_system_score_gemma":0.0001575316,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001005344,"about_ca_topic_score_gemma":0.001551656,"domain_scores_codex":[0.9999306,0.000006793699,0.000005647137,0.00002242127,0.00002284773,0.00001164139],"domain_scores_gemma":[0.9998435,0.00004512599,0.00003688813,0.00002505071,0.00002032626,0.00002906007],"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":[0.0000956479,0.000006476754,0.001091016,0.00003574623,0.000007868251,0.00005205124,0.00002966463,0.00003212575,0.9967127,0.0000482798,0.00002768642,0.00186079],"study_design_scores_gemma":[0.00003837012,0.0007174378,0.427448,0.0000358317,0.0001999969,0.004184726,0.000341154,0.001979187,0.5479535,0.0003410573,0.01672535,0.00003534882],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.99458,0.0004549649,0.002072103,0.00004034293,0.000009410886,0.00001176191,0.002217091,0.00008178975,0.0005325375],"genre_scores_gemma":[0.9797685,0.0004282808,0.005131595,0.00008297124,0.000005584385,0.0000297769,0.01278858,0.00003617862,0.00172866],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001005344,"threshold_uncertainty_score":0.002183497,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2155124413","doi":"10.1093/gbe/evt200","title":"Shared Subgenome Dominance Following Polyploidization Explains Grass Genome Evolutionary Plasticity from a Seven Protochromosome Ancestor with 16K Protogenes","year":2013,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":129,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"","funders":"Centre National de la Recherche Scientifique; Simon Fraser University; Agence Nationale de la Recherche; Institut national de recherche en informatique et en automatique (INRIA)","keywords":"Biology; Genome; Synteny; Genetics; Evolutionary biology; Gene; Chromosomal rearrangement; Genomics; Chromosome; Karyotype","authors":[{"name":"Florent Murat","is_ca":false},{"name":"Rongzhi Zhang","is_ca":false},{"name":"Sébastien Guizard","is_ca":false},{"name":"Raphaël Flores","is_ca":false},{"name":"Alix Armero","is_ca":false},{"name":"Caroline Pont","is_ca":false},{"name":"Delphine Steinbach","is_ca":false},{"name":"Hadi Quesneville","is_ca":false},{"name":"Richard Cooke","is_ca":false},{"name":"Jérôme Salse","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01266968733412227,"gpt":0.2057092111908929,"spread":0.1930395238567706,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00008591934,0.0001534948,0.0001611182,0.000340465,0.000198732,0.0002883625,0.0001627819,0.0001645156,0.002216218],"category_scores_gemma":[0.000149139,0.0001371735,0.000220693,0.0002507721,0.0001713285,0.000347726,0.0004724775,0.0002202226,0.000390473],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003390231,"about_ca_system_score_gemma":0.0001160286,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007778287,"about_ca_topic_score_gemma":0.001595849,"domain_scores_codex":[0.9999632,0.000002868757,0.000002119362,0.00001665864,0.000008218864,0.000006910491],"domain_scores_gemma":[0.9999481,0.000009146695,0.00001286164,0.0000103068,0.000005035888,0.00001446236],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001412861,0.000005415031,0.01166273,0.00008627433,0.00001418622,0.0003629099,0.0002579043,0.0005866312,0.973273,0.001187076,0.0001128772,0.01230971],"study_design_scores_gemma":[0.0000580537,0.0003888092,0.5489479,0.00007149475,0.0002270573,0.005425917,0.0008191768,0.02160618,0.3637856,0.00862957,0.04992673,0.000113476],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9905523,0.0004598228,0.006031322,0.00003865689,0.000005007267,0.000009599547,0.0005750998,0.0002443223,0.002083928],"genre_scores_gemma":[0.9890108,0.0003812075,0.007533233,0.00003057647,0.000004757484,0.0000126565,0.001415849,0.0001318123,0.001479261],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002216218,"threshold_uncertainty_score":0.007413983,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2119177774","doi":"10.1093/gbe/evu043","title":"Chromera velia, Endosymbioses and the Rhodoplex Hypothesis—Plastid Evolution in Cryptophytes, Alveolates, Stramenopiles, and Haptophytes (CASH Lineages)","year":2014,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Protist diversity and phylogeny","field":"Biochemistry, Genetics and Molecular Biology","cited_by":124,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Université de Montréal","funders":"Deutsche Forschungsgemeinschaft","keywords":"Biology; Plastid; Endosymbiosis; Eukaryote; Haptophyte; Evolutionary biology; Phylogenomics; Peridinin; Genetics; Genome; Phylogenetics; Botany; Gene; Algae; Clade; Ecology; Chloroplast","authors":[{"name":"Jörn Petersen","is_ca":false},{"name":"Ann-Kathrin Ludewig","is_ca":false},{"name":"Victoria Michael","is_ca":false},{"name":"Boyke Bunk","is_ca":false},{"name":"Michael Jarek","is_ca":false},{"name":"Denis Baurain","is_ca":false},{"name":"Henner Brinkmann","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.005987607017957291,"gpt":0.1969924049239343,"spread":0.191004797905977,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002940965,0.0002680907,0.0002159068,0.0007776068,0.0005167469,0.001014237,0.0004423806,0.0004327268,0.0004715417],"category_scores_gemma":[0.0002378581,0.0001474867,0.0002696313,0.000381885,0.0006180215,0.000642872,0.0009074956,0.0004950141,0.0001250531],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003837289,"about_ca_system_score_gemma":0.000365506,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001480172,"about_ca_topic_score_gemma":0.001404865,"domain_scores_codex":[0.9998899,0.000009457735,0.000006016114,0.00005080878,0.00001447443,0.00002943611],"domain_scores_gemma":[0.999827,0.00002960693,0.00005498352,0.00002089357,0.00002118684,0.00004643848],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0004489641,0.0000370001,0.09821735,0.0001937534,0.00006965802,0.000647256,0.001114669,0.0007439321,0.8672307,0.004114608,0.0001015076,0.02708058],"study_design_scores_gemma":[0.00002496665,0.0003808611,0.9074448,0.0001057125,0.0001168632,0.001448469,0.002458405,0.00393493,0.07203534,0.003253906,0.008747654,0.0000479946],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.995604,0.00144351,0.001728232,0.00009502691,0.000005337432,0.00000713537,0.0000897627,0.00002920882,0.0009977478],"genre_scores_gemma":[0.9978372,0.0004686437,0.00109731,0.00003658158,0.000004284134,0.000005767159,0.0001606498,0.000007996872,0.0003816268],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001480172,"threshold_uncertainty_score":0.002943099,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2187655481","doi":"10.1093/gbe/evt019","title":"A Broad Phylogenetic Survey Unveils the Diversity and Evolution of Telomeres in Eukaryotes","year":2013,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Protist diversity and phylogeny","field":"Biochemistry, Genetics and Molecular Biology","cited_by":124,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Université de Montréal","funders":"Advanced Scientific Computing Research; European Regional Development Fund; Central European Institute of Technology; Grantová Agentura České Republiky","keywords":"Biology; Phylogenetic tree; Genome; Evolutionary biology; Phylogenetics; Telomere; Minisatellite; Genome evolution; Genetics; Gene; Microsatellite","authors":[{"name":"Jana Fulnečková","is_ca":false},{"name":"Tereza Ševčíková","is_ca":false},{"name":"Jiřı́ Fajkus","is_ca":false},{"name":"Alena Lukešová","is_ca":false},{"name":"Martin Lukeš","is_ca":false},{"name":"Čestmı́r Vlček","is_ca":false},{"name":"B. Franz Lang","is_ca":true},{"name":"Eunsoo Kim","is_ca":false},{"name":"Marek Eliáš","is_ca":false},{"name":"Eva Sýkorová","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01171827351635895,"gpt":0.2114527692816841,"spread":0.1997344957653251,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004341545,0.0003520803,0.0004299548,0.001892276,0.0004955411,0.0005969944,0.0001886853,0.0003684308,0.00102874],"category_scores_gemma":[0.0005381913,0.0001582475,0.0003906026,0.002456982,0.0002314992,0.000595675,0.0007240004,0.0004152481,0.0006245057],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009827918,"about_ca_system_score_gemma":0.0002097843,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004046298,"about_ca_topic_score_gemma":0.000708962,"domain_scores_codex":[0.9997447,0.00003478266,0.00003025234,0.0001075727,0.00004463244,0.00003811169],"domain_scores_gemma":[0.9995418,0.0001267096,0.0001017694,0.00006623927,0.00006616869,0.00009740193],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.001008435,0.00007390854,0.2556172,0.00112658,0.000308114,0.0007473537,0.001550446,0.001176897,0.6186319,0.0009447547,0.0004965871,0.1183178],"study_design_scores_gemma":[0.00001198728,0.0003644497,0.9469841,0.0002403938,0.0002701952,0.002405776,0.0007451568,0.001042112,0.01419469,0.0006613582,0.03304133,0.0000384432],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9691752,0.0163244,0.006715505,0.0001085519,0.00001661165,0.00001730445,0.005138118,0.0001178939,0.002386417],"genre_scores_gemma":[0.9570767,0.01415438,0.01093745,0.0001678476,0.00004901535,0.00002331339,0.01676319,0.00005358186,0.0007744908],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001892276,"threshold_uncertainty_score":0.003441513,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2162730802","doi":"10.1093/gbe/evu279","title":"Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus","year":2014,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Cancer-related molecular mechanisms research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":120,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Toronto","funders":"Major Research Plan; National Natural Science Foundation of China","keywords":"Biology; Zebrafish; Adaptation (eye); Evolutionary biology; Transcriptome; Gene; Genome; Local adaptation; Lineage (genetic); Genetics; Gene expression","authors":[{"name":"Liandong Yang","is_ca":false},{"name":"Ying Wang","is_ca":false},{"name":"Zhaolei Zhang","is_ca":true},{"name":"Shunping He","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01406816269923471,"gpt":0.275327112157694,"spread":0.2612589494584593,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00007538439,0.0002279724,0.0001960697,0.000679678,0.0003246057,0.0001777726,0.00008914033,0.0001602321,0.0007553452],"category_scores_gemma":[0.00009769602,0.0001369573,0.0002982822,0.0006877079,0.0002012583,0.0001701052,0.0002962572,0.0002214445,0.0001794657],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001979259,"about_ca_system_score_gemma":0.0002905063,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003180752,"about_ca_topic_score_gemma":0.006879854,"domain_scores_codex":[0.9999489,0.000002869253,0.000003058477,0.00002096722,0.00001244368,0.00001185479],"domain_scores_gemma":[0.9999421,0.000008617773,0.00001604477,0.000005434581,0.00001163425,0.00001605316],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001538236,0.00001123926,0.0194755,0.00009300468,0.00002644681,0.0001633116,0.0002504079,0.0001646867,0.9743212,0.00006483664,0.00008914724,0.005186371],"study_design_scores_gemma":[0.000009515276,0.0001308667,0.9835454,0.000009551005,0.0000536635,0.0002423619,0.0002040228,0.0006894566,0.01357911,0.00008347781,0.001441486,0.00001112795],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9967475,0.0003140641,0.0007160115,0.00002385755,0.000003551909,0.000007289101,0.001692295,0.00002556521,0.0004699737],"genre_scores_gemma":[0.9855155,0.0005214064,0.002322775,0.0000733974,0.000008671719,0.00004031154,0.009378307,0.00002790541,0.002111713],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003180752,"threshold_uncertainty_score":0.00632447,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1987240370","doi":"10.1093/gbe/evq014","title":"The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae","year":2010,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":119,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Université Laval","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Genome; Chloroplast DNA; Group II intron; Genetics; Inverted repeat; Lineage (genetic); Chlorophyceae; Group I catalytic intron; Phylogenetic tree; Gene; Intron; Evolutionary biology; Botany; RNA splicing; Algae; Chlorophyta; RNA","authors":[{"name":"Jean Sébastien Brouard","is_ca":true},{"name":"Christian Otis","is_ca":true},{"name":"Claude Lemieux","is_ca":true},{"name":"Monique Turmel","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.00471694963921484,"gpt":0.1894076661578661,"spread":0.1846907165186513,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00007652368,0.0002586133,0.0002143424,0.0004568114,0.0003453141,0.0003563523,0.0001937456,0.0002893147,0.0007283301],"category_scores_gemma":[0.0002273386,0.000107633,0.0001954399,0.0003615423,0.0001777221,0.0003169118,0.0003619216,0.0002820505,0.0003062206],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001542352,"about_ca_system_score_gemma":0.0002422125,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001005445,"about_ca_topic_score_gemma":0.001441876,"domain_scores_codex":[0.9999391,0.000003237001,0.000004453768,0.00002722847,0.0000172298,0.000008696186],"domain_scores_gemma":[0.9998432,0.00002694945,0.00004178576,0.0000190192,0.00002435042,0.0000445982],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00008957858,0.00002591937,0.01932349,0.0002377974,0.00003645901,0.0005747506,0.0002407006,0.0001862571,0.958276,0.0002545736,0.000220238,0.02053431],"study_design_scores_gemma":[0.00003713429,0.0004506684,0.7717695,0.0001344139,0.000200951,0.007480897,0.001101684,0.001448211,0.178694,0.001256607,0.03737017,0.00005576016],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9937543,0.00170642,0.001523531,0.0001099698,0.00001582256,0.000006753082,0.001968169,0.00009193256,0.0008230333],"genre_scores_gemma":[0.9818092,0.001431397,0.005728832,0.00008076449,0.00003316376,0.00001834902,0.009835639,0.00002678067,0.001035927],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001005445,"threshold_uncertainty_score":0.002436519,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2122340226","doi":"10.1093/gbe/evr085","title":"Reduced Efficacy of Natural Selection on Codon Usage Bias in Selfing Arabidopsis and Capsella Species","year":2011,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Photosynthetic Processes and Mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":116,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Genome Canada; University of Toronto","funders":"Biotechnology and Biological Sciences Research Council","keywords":"Biology; Outcrossing; Selfing; Genetics; Inbreeding; Codon usage bias; Population; Natural selection; Evolutionary biology; Gene; Ecology; Genome","authors":[{"name":"Suo Qiu","is_ca":false},{"name":"Kai Zeng","is_ca":false},{"name":"Tanja Slotte","is_ca":true},{"name":"Stephen Wright","is_ca":true},{"name":"Deborah Charlesworth","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.02448706768400186,"gpt":0.2401777868589555,"spread":0.2156907191749537,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006247212,0.0002219442,0.0003111523,0.0007680093,0.0001738832,0.0003782602,0.000352724,0.0002538,0.0003834975],"category_scores_gemma":[0.0009818003,0.0001921875,0.0002564459,0.0003023527,0.000400975,0.000243682,0.0003540595,0.0002206712,0.00009697585],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003071097,"about_ca_system_score_gemma":0.0001591422,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00066613,"about_ca_topic_score_gemma":0.001108511,"domain_scores_codex":[0.9996806,0.00007027127,0.00003170959,0.0001176224,0.00006921936,0.00003059992],"domain_scores_gemma":[0.9989458,0.0002877022,0.0003553451,0.0001889806,0.0001190443,0.0001031796],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0003084103,0.0000346276,0.07841345,0.00008334073,0.0001784059,0.0001517356,0.0002218523,0.0009299988,0.9106679,0.0004067021,0.00002500277,0.008578575],"study_design_scores_gemma":[0.00002896033,0.0002643643,0.9436042,0.000008883579,0.0001444099,0.0006455599,0.0001580519,0.004538334,0.04928562,0.0007734671,0.0005162686,0.00003179451],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9994004,0.000129321,0.0002984511,0.000005071449,6.997307e-7,9.739149e-7,0.00002163019,0.00001010112,0.00013329],"genre_scores_gemma":[0.9995453,0.00005251653,0.000242563,0.000009882198,0.000001497357,0.000002267785,0.00008543742,0.000004672296,0.00005575878],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0007680093,"threshold_uncertainty_score":0.003303826,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2139454502","doi":"10.1093/gbe/evr068","title":"Extending the Limited Transfer Window Hypothesis to Inter-organelle DNA Migration","year":2011,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"DNA and Nucleic Acid Chemistry","field":"Biochemistry, Genetics and Molecular Biology","cited_by":116,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia; Canadian Institute for Advanced Research","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Plastid; Biology; Genome; Mitochondrial DNA; Organelle; Mitochondrion; DNA; Genetics; Evolutionary biology; Chloroplast; Gene","authors":[{"name":"David Roy Smith","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01605125892824511,"gpt":0.2077552973860154,"spread":0.1917040384577703,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0009570308,0.0004323724,0.0005413438,0.0007503204,0.0005180659,0.0008594544,0.001258307,0.001038706,0.004049696],"category_scores_gemma":[0.003196891,0.0003130847,0.0007011347,0.0006761298,0.001492292,0.004570093,0.001687086,0.001072317,0.0009139607],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000450444,"about_ca_system_score_gemma":0.0003251077,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002711045,"about_ca_topic_score_gemma":0.0002511631,"domain_scores_codex":[0.9996001,0.00006196254,0.00001420009,0.0002321295,0.00004670986,0.0000448825],"domain_scores_gemma":[0.998321,0.0009679117,0.0002897224,0.000219077,0.00007825969,0.0001240262],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.0008867641,0.0003000146,0.0437372,0.001744939,0.0003335631,0.005258884,0.002367956,0.03753012,0.4885872,0.2686213,0.001316363,0.1493157],"study_design_scores_gemma":[0.0002004894,0.001536122,0.07227086,0.0003056445,0.00029007,0.006889533,0.001538058,0.1505648,0.1246053,0.6145678,0.02701481,0.0002166373],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5757591,0.007427877,0.4003813,0.00186271,0.0003261638,0.0001208181,0.0002704922,0.0004000659,0.01345146],"genre_scores_gemma":[0.9657331,0.002570512,0.0282763,0.000402497,0.0001568796,0.0001604856,0.0001605808,0.00006584344,0.00247374],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004049696,"threshold_uncertainty_score":0.01354754,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2782887715","doi":"10.1093/gbe/evy004","title":"Elevated Proportions of Deleterious Genetic Variation in Domestic Animals and Plants","year":2018,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genetic and phenotypic traits in livestock","field":"Biochemistry, Genetics and Molecular Biology","cited_by":115,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"","funders":"European Social Fund; Institute of Genetics; Japan Society for the Promotion of Science; Fundação para a Ciência e a Tecnologia; Ministério da Ciência, Tecnologia e Ensino Superior","keywords":"Biology; Domestication; Nonsynonymous substitution; Population; Population bottleneck; Genetic variation; Effective population size; Wild boar; Allele; Genetics; Zoology; Genome; Gene; Ecology; Microsatellite","authors":[{"name":"Takashi Makino","is_ca":false},{"name":"Carl‐Johan Rubin","is_ca":false},{"name":"Miguel Carneiro","is_ca":false},{"name":"Erik Axelsson","is_ca":false},{"name":"Leif Andersson","is_ca":false},{"name":"Matthew T. Webster","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.007498218153115438,"gpt":0.2428841631209608,"spread":0.2353859449678453,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002858342,0.0001736117,0.0002899247,0.0007962852,0.0002287713,0.0003309099,0.0001494818,0.0003039861,0.001141588],"category_scores_gemma":[0.0005050653,0.0001224428,0.0001814646,0.0005845398,0.0004479388,0.0001922995,0.0003008133,0.0002001968,0.0001922715],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008330874,"about_ca_system_score_gemma":0.00005602569,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000302087,"about_ca_topic_score_gemma":0.0005697463,"domain_scores_codex":[0.99966,0.00007033499,0.00002739447,0.000145381,0.00006462653,0.00003221559],"domain_scores_gemma":[0.9993504,0.000144709,0.0003231783,0.00007703887,0.00003270656,0.00007187937],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0002633436,0.0000332837,0.1608255,0.0001080336,0.0002320473,0.0002523856,0.000282957,0.0001206653,0.8306588,0.0001606998,0.00007968773,0.00698273],"study_design_scores_gemma":[0.000003881505,0.00009210708,0.9866094,0.000005735704,0.00004661398,0.0008740844,0.0001085053,0.0002057269,0.01122817,0.0001268053,0.0006937807,0.000005138129],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9985434,0.0003603113,0.0004971184,0.00001727128,0.000002117616,0.000001614919,0.0001981784,0.00001221803,0.0003678739],"genre_scores_gemma":[0.9988329,0.0001160709,0.000463985,0.00003404066,0.000004000394,0.000003619656,0.0003960794,0.000006112211,0.0001432157],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001141588,"threshold_uncertainty_score":0.003818929,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2145230470","doi":"10.1093/gbe/evr094","title":"Genomic Determinants of Protein Evolution and Polymorphism in Arabidopsis","year":2011,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Photosynthetic Processes and Mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":111,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Toronto","funders":"Danmarks Frie Forskningsfond","keywords":"Biology; Arabidopsis; Genetics; Evolutionary biology; Polymorphism (computer science); Computational biology; Gene; Allele","authors":[{"name":"Tanja Slotte","is_ca":true},{"name":"Thomas Bataillon","is_ca":false},{"name":"Troels T. Hansen","is_ca":false},{"name":"Kate St. Onge","is_ca":false},{"name":"Stephen Wright","is_ca":true},{"name":"Mikkel Heide Schierup","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01113869440713498,"gpt":0.2197153288751617,"spread":0.2085766344680267,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001925212,0.0001968197,0.0001855082,0.0008887444,0.0001525227,0.0002445259,0.0001457186,0.0002151278,0.0004216408],"category_scores_gemma":[0.0004702521,0.0001469534,0.0001756785,0.0004870581,0.0002907654,0.0001816584,0.0001690369,0.0002552302,0.0001443812],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003785675,"about_ca_system_score_gemma":0.0001003011,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00078175,"about_ca_topic_score_gemma":0.001306814,"domain_scores_codex":[0.9998859,0.00002274907,0.000007420516,0.00004882613,0.00002265286,0.00001250087],"domain_scores_gemma":[0.9996012,0.0001493328,0.0001340809,0.00002814593,0.00002153921,0.00006577699],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0003619356,0.00002817039,0.04845462,0.00008193021,0.000065726,0.000213361,0.0001282961,0.001733827,0.9411603,0.0004272969,0.00005897532,0.007285478],"study_design_scores_gemma":[0.00002728116,0.0001145073,0.9718103,0.000007518656,0.00003924506,0.0005995368,0.00006276824,0.004553594,0.02101839,0.001206635,0.0005383723,0.00002185454],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9989518,0.0002391543,0.0004556277,0.00001769814,0.00000102118,0.00000154067,0.0001751604,0.00002091091,0.0001370393],"genre_scores_gemma":[0.9990313,0.0000653396,0.0005051165,0.00001080358,0.000002404341,0.000002627848,0.0003105111,0.000009000511,0.00006293004],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0008887444,"threshold_uncertainty_score":0.002746701,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2169153007","doi":"10.1093/gbe/evr131","title":"Mitochondrial Genome Sequences of Nematocera (Lower Diptera): Evidence of Rearrangement following a Complete Genome Duplication in a Winter Crane Fly","year":2011,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Insect behavior and control techniques","field":"Agricultural and Biological Sciences","cited_by":108,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Simon Fraser University","funders":"Natural Sciences and Engineering Research Council of Canada; National Science Foundation","keywords":"Biology; Mitochondrial DNA; Gene duplication; Genome; Gene rearrangement; Tandem exon duplication; Genetics; Gene; Evolutionary biology; Tandem repeat","authors":[{"name":"Andrew T. Beckenbach","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.04523839111043453,"gpt":0.257600789347085,"spread":0.2123623982366504,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00004779213,0.000190231,0.0001588589,0.0006618567,0.0002631653,0.0002112886,0.000120717,0.0001799527,0.001274976],"category_scores_gemma":[0.000316833,0.0001021119,0.0001404922,0.0005624287,0.0001198161,0.0001058851,0.0001244916,0.0002308683,0.0003188559],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002516691,"about_ca_system_score_gemma":0.000202895,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003445028,"about_ca_topic_score_gemma":0.0101726,"domain_scores_codex":[0.9999535,0.000004105293,0.000005065552,0.00001433842,0.00001305157,0.00001004952],"domain_scores_gemma":[0.999716,0.00003774707,0.00009088022,0.00001951461,0.00005140308,0.00008448563],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0006458739,0.00004024918,0.04194027,0.0003349737,0.0000616191,0.0005341255,0.0005072154,0.0002818451,0.9331676,0.0001350467,0.0001597623,0.02219137],"study_design_scores_gemma":[0.00002682324,0.0003948385,0.9583503,0.00006587888,0.0001282201,0.002093654,0.0003752345,0.0005193743,0.03023324,0.0000605561,0.007735995,0.0000158207],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9972371,0.000530951,0.0003647588,0.00001983616,0.00000271021,0.00001040516,0.001397903,0.00001198132,0.0004244243],"genre_scores_gemma":[0.9817849,0.001004016,0.003029047,0.00004159002,0.000008340404,0.00002249889,0.01312258,0.00001165947,0.0009754217],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003445028,"threshold_uncertainty_score":0.006849945,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2153031843","doi":"10.1093/gbe/evp032","title":"Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus","year":2009,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Protist diversity and phylogeny","field":"Biochemistry, Genetics and Molecular Biology","cited_by":108,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Dalhousie University","funders":"Canadian Institutes of Health Research","keywords":"Prochlorococcus; Biology; Synechococcus; Ecology; Cyanobacteria; Bacteria; Paleontology","authors":[{"name":"Olga Zhaxybayeva","is_ca":true},{"name":"W. Ford Doolittle","is_ca":true},{"name":"R. Thane Papke","is_ca":false},{"name":"J. Peter Gogarten","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.004747432171117655,"gpt":0.2077673969787239,"spread":0.2030199648076063,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003320951,0.0001528384,0.0001992912,0.001499187,0.0004882098,0.0004812163,0.000215175,0.0002957938,0.0004100206],"category_scores_gemma":[0.001003297,0.0001604353,0.0001836427,0.001054089,0.00051784,0.0004542672,0.0006446043,0.0002919985,0.0001397394],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002606346,"about_ca_system_score_gemma":0.0002347214,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001476203,"about_ca_topic_score_gemma":0.002580871,"domain_scores_codex":[0.9997404,0.00004685263,0.00001577591,0.0001126023,0.00004202227,0.00004232214],"domain_scores_gemma":[0.9993211,0.0001677877,0.000167289,0.00006556369,0.0001584947,0.000119825],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0004438896,0.00005327085,0.756443,0.0001075009,0.000143352,0.0003691388,0.004573829,0.0007628787,0.2127057,0.001096918,0.00008035508,0.02322009],"study_design_scores_gemma":[0.000003486388,0.0000541776,0.995604,0.000009392927,0.00002639195,0.0002918572,0.0006581183,0.0008123739,0.001571613,0.0002069373,0.000752455,0.000009147835],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9993795,0.0001807085,0.0001234853,0.00001056789,9.583304e-7,0.000001476233,0.00003449908,0.000002567205,0.0002662753],"genre_scores_gemma":[0.9991891,0.0001230359,0.0003218664,0.00001072788,0.000002725077,0.00000378681,0.0002216753,0.000004162751,0.0001229344],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001499187,"threshold_uncertainty_score":0.00293529,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1899220380","doi":"10.1093/gbe/evv130","title":"Dynamic Evolution of the Chloroplast Genome in the Green Algal Classes Pedinophyceae and Trebouxiophyceae","year":2015,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Protist diversity and phylogeny","field":"Biochemistry, Genetics and Molecular Biology","cited_by":107,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Université Laval","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Genome; Genetics; Gene; Evolutionary biology; GC-content; Chloroplast DNA; Horizontal gene transfer; Operon; Genome evolution","authors":[{"name":"Monique Turmel","is_ca":true},{"name":"Christian Otis","is_ca":true},{"name":"Claude Lemieux","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.009098498404826454,"gpt":0.2181931318963658,"spread":0.2090946334915394,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001650873,0.0001529877,0.0002580822,0.000834144,0.0004066146,0.0005179341,0.0001933389,0.0003057127,0.0005074157],"category_scores_gemma":[0.0005692759,0.0001478662,0.0001878275,0.000946208,0.0002246189,0.0004261191,0.0003810982,0.0003220565,0.0001414428],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004480902,"about_ca_system_score_gemma":0.0002411509,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002208756,"about_ca_topic_score_gemma":0.00239459,"domain_scores_codex":[0.9998585,0.00001569227,0.000006991578,0.00005894749,0.00003302709,0.00002682938],"domain_scores_gemma":[0.9997129,0.00006464357,0.00009282832,0.00002361871,0.00005515454,0.00005083576],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0005467265,0.00004228038,0.193224,0.0001462728,0.00007720671,0.0003802867,0.001362784,0.0009974041,0.77211,0.0004943294,0.0001112458,0.03050749],"study_design_scores_gemma":[0.000008186804,0.00007226134,0.9888776,0.00001070505,0.00002529775,0.0004429314,0.0003929459,0.001125092,0.006844057,0.0002122913,0.00197521,0.00001343617],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9989636,0.0003901838,0.0001502407,0.00001914888,8.538183e-7,0.000001983584,0.0001365713,0.000006279708,0.0003312139],"genre_scores_gemma":[0.9980698,0.0003228282,0.0005519825,0.00002269645,0.000003488056,0.000007010503,0.0007534573,0.000007980236,0.0002607732],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002208756,"threshold_uncertainty_score":0.004391849,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2156488982","doi":"10.1093/gbe/evt101","title":"A Comparative Analysis of Mitochondrial ORFans: New Clues on Their Origin and Role in Species with Doubly Uniparental Inheritance of Mitochondria","year":2013,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Aquatic Invertebrate Ecology and Behavior","field":"Environmental Science","cited_by":104,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Université de Montréal","funders":"","keywords":"ORFS; Biology; Mitochondrial DNA; Genetics; Mitochondrion; Genome; Gene; Non-Mendelian inheritance; Nuclear gene; Evolutionary biology; Open reading frame; Peptide sequence","authors":[{"name":"Liliana Milani","is_ca":false},{"name":"Fabrizio Ghiselli","is_ca":false},{"name":"Davide Guerra","is_ca":false},{"name":"Sophie Breton","is_ca":true},{"name":"Marco Passamonti","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01741514721814694,"gpt":0.2398911646956171,"spread":0.2224760174774701,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001625863,0.0001912833,0.0002065818,0.0009541061,0.0003098108,0.000230915,0.0001567979,0.0002840323,0.0005403764],"category_scores_gemma":[0.0002685811,0.0001126401,0.0002993577,0.0003881941,0.000245066,0.0004892249,0.0003243155,0.0001737657,0.0001815574],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001040425,"about_ca_system_score_gemma":0.000107446,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002209623,"about_ca_topic_score_gemma":0.0003681033,"domain_scores_codex":[0.9999157,0.00000773695,0.00001064512,0.00003611128,0.00001119466,0.00001862684],"domain_scores_gemma":[0.9995678,0.00008530486,0.000140583,0.00004483036,0.00006800745,0.00009335316],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001708023,0.00002458187,0.04023291,0.0001377655,0.00003047571,0.0006106436,0.0003445816,0.00005840796,0.9492203,0.0001668727,0.00001977617,0.008982931],"study_design_scores_gemma":[0.000008248603,0.0004688226,0.9109452,0.00005782902,0.0001796452,0.005572727,0.0006333528,0.0009878662,0.07437012,0.0004828757,0.006263043,0.00003042067],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9971622,0.001055685,0.001260762,0.00001100391,0.000002805039,0.000004401451,0.0001299788,0.00000858989,0.0003644032],"genre_scores_gemma":[0.9955213,0.0004669967,0.00309962,0.00001928888,0.0000070396,0.00000696291,0.0005602931,0.000008371476,0.0003101502],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0009541061,"threshold_uncertainty_score":0.001807749,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2885671209","doi":"10.1093/gbe/evy157","title":"Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome","year":2018,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Amphibian and Reptile Biology","field":"Environmental Science","cited_by":103,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Alberta Children's Hospital; University of Calgary; Carleton University; University of Toronto","funders":"National Human Genome Research Institute; National Institute of General Medical Sciences; Natural Sciences and Engineering Research Council of Canada; National Institutes of Health; National Science Foundation","keywords":"Biology; Colubridae; Amniote; Genome; Evolutionary biology; Genome evolution; W chromosome; Lineage (genetic); Comparative genomics; Genetics; Gene; Genomics; Chromosome; Zoology; Vertebrate","authors":[{"name":"Blair W. Perry","is_ca":false},{"name":"Daren C. Card","is_ca":false},{"name":"Joel W. McGlothlin","is_ca":false},{"name":"Giulia Irene Maria Pasquesi","is_ca":false},{"name":"Richard H. Adams","is_ca":false},{"name":"Drew R. Schield","is_ca":false},{"name":"Nicole R. Hales","is_ca":false},{"name":"Andrew B. Corbin","is_ca":false},{"name":"Jeffery P. Demuth","is_ca":false},{"name":"Federico G. Hoffmann","is_ca":false},{"name":"Michael W. Vandewege","is_ca":false},{"name":"Ryan K. Schott","is_ca":true},{"name":"Nihar Bhattacharyya","is_ca":true},{"name":"Belinda S. W. Chang","is_ca":true},{"name":"Nicholas R. Casewell","is_ca":false},{"name":"Gareth Whiteley","is_ca":false},{"name":"Jacobo Reyes‐Velasco","is_ca":false},{"name":"Stephen P. Mackessy","is_ca":false},{"name":"Tony Gamble","is_ca":false},{"name":"Kenneth B. Storey","is_ca":true},{"name":"Kyle K. Biggar","is_ca":true},{"name":"Courtney N. Passow","is_ca":false},{"name":"Chih‐Horng Kuo","is_ca":false},{"name":"Suzanne E. McGaugh","is_ca":false},{"name":"Anne M. Bronikowski","is_ca":false},{"name":"A. P. Jason de Koning","is_ca":true},{"name":"Scott V. Edwards","is_ca":false},{"name":"Michael E. Pfrender","is_ca":false},{"name":"Patrick Minx","is_ca":false},{"name":"Edmund D. Brodie","is_ca":false},{"name":"Wesley C. Warren","is_ca":false},{"name":"Todd A. Castoe","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01016625394931876,"gpt":0.2058264283864978,"spread":0.1956601744371791,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001400039,0.0002745067,0.0002086715,0.0009065403,0.0002874728,0.0004190595,0.0001591923,0.0003900269,0.0009718386],"category_scores_gemma":[0.0003149174,0.0001769276,0.000429812,0.0008979774,0.0002003037,0.0003792366,0.0004697668,0.0005325703,0.0002740912],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001411923,"about_ca_system_score_gemma":0.0001829754,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005387035,"about_ca_topic_score_gemma":0.001431929,"domain_scores_codex":[0.9999318,0.000006836629,0.00000545259,0.00002844776,0.00001725431,0.0000101837],"domain_scores_gemma":[0.9998317,0.00005343415,0.00004856723,0.00002127526,0.00001832736,0.00002675393],"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":[0.0001679502,0.0000223352,0.02573206,0.0003183821,0.00005230755,0.0004580585,0.0006815499,0.0003936038,0.9531844,0.000532103,0.0002818678,0.01817537],"study_design_scores_gemma":[0.00002154349,0.0001982248,0.8872453,0.0001675379,0.0002580338,0.002555473,0.0009316836,0.00204264,0.06666827,0.001697773,0.03816839,0.00004508551],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9876743,0.002961261,0.003650344,0.0002979996,0.00001952484,0.00001035311,0.003459383,0.0001761808,0.001750636],"genre_scores_gemma":[0.9583206,0.003916359,0.01838251,0.0003953206,0.00003888439,0.0000370956,0.01723221,0.0001309294,0.001546138],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0009718386,"threshold_uncertainty_score":0.003251076,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2010139559","doi":"10.1093/gbe/evu098","title":"Distinguishing between \"Function\" and \"Effect\" in Genome Biology","year":2014,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Philosophy and History of Science","field":"Arts and Humanities","cited_by":100,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Guelph; Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research","keywords":"Conflation; Biology; Confusion; Function (biology); Genome; Parsing; Evolutionary biology; Computational biology; Genetics; Epistemology; Gene; Computer science; Artificial intelligence; Psychology; Philosophy","authors":[{"name":"W. Ford Doolittle","is_ca":true},{"name":"T. D. P. Brunet","is_ca":true},{"name":"Stefan Linquist","is_ca":true},{"name":"T. Ryan Gregory","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.02265698489364312,"gpt":0.2210261321664553,"spread":0.1983691472728121,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":["sts"],"consensus_categories":[],"category_scores_codex":[0.01735941,0.0009314327,0.001460834,0.002808045,0.003552631,0.008413169,0.002290429,0.005916706,0.002908293],"category_scores_gemma":[0.0181613,0.0006853258,0.0009891862,0.002113429,0.06616022,0.02332556,0.0040625,0.01176335,0.0009428172],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.002525555,"about_ca_system_score_gemma":0.001835824,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001747246,"about_ca_topic_score_gemma":0.001309505,"domain_scores_codex":[0.9916117,0.005012348,0.0004881902,0.001251826,0.00129043,0.0003456387],"domain_scores_gemma":[0.9852844,0.01159592,0.0005536909,0.001483047,0.0007326907,0.0003502209],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.0000317993,0.000006181272,0.0003235919,0.00008773826,0.00001023564,0.00004294788,0.001910095,0.0001335518,0.000282278,0.9876766,0.001970957,0.007524057],"study_design_scores_gemma":[0.000008191874,0.00001249865,0.0003643658,0.00007422529,0.00001273236,0.00009683259,0.0006283605,0.0002518251,0.0002646291,0.9791315,0.01913618,0.00001863476],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":"theoretical_or_conceptual","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.03977618,0.0622959,0.5335618,0.2466892,0.01831482,0.00008960481,0.0004384129,0.0009568721,0.09787721],"genre_scores_gemma":[0.750748,0.01990587,0.1454477,0.06656481,0.008451587,0.0003514588,0.0003138216,0.000712359,0.007504319],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.9964474,"threshold_uncertainty_score":0.09180641,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2174770506","doi":"10.1093/gbe/evv237","title":"The<i>Physarum polycephalum</i>Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling","year":2015,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Slime Mold and Myxomycetes Research","field":"Engineering","cited_by":100,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Carleton University; Western University","funders":"National Institute of General Medical Sciences; Biotechnology and Biological Sciences Research Council; National Human Genome Research Institute; Bundesministerium für Bildung und Forschung; Austrian Science Fund; International Max Planck Research School for Environmental, Cellular and Molecular Microbiology; Wellcome Trust; National Institutes of Health; National Science Foundation","keywords":"Biology; Physarum polycephalum; Eukaryote; Genetics; Genome; Most recent common ancestor; Evolutionary biology; Horizontal gene transfer; Histidine kinase; Gene; Cell biology","authors":[{"name":"Pauline Schaap","is_ca":false},{"name":"Israel Barrantes","is_ca":false},{"name":"Pat Minx","is_ca":false},{"name":"Narie Sasaki","is_ca":false},{"name":"Roger W. Anderson","is_ca":false},{"name":"Marianne Bénard","is_ca":false},{"name":"Kyle K. Biggar","is_ca":true},{"name":"Nicolas E. Buchler","is_ca":false},{"name":"Ralf Bundschuh","is_ca":false},{"name":"Xiao Chen","is_ca":false},{"name":"Catrina C. Fronick","is_ca":false},{"name":"Lucinda A. Fulton","is_ca":false},{"name":"Georg Golderer","is_ca":false},{"name":"Niels Jahn","is_ca":false},{"name":"Volker Knoop","is_ca":false},{"name":"Laura F. Landweber","is_ca":false},{"name":"Chrystelle Maric","is_ca":false},{"name":"Dennis L. Miller","is_ca":false},{"name":"Angelika A. Noegel","is_ca":false},{"name":"Rob Peace","is_ca":true},{"name":"Gérard Pierron","is_ca":false},{"name":"Taeko Sasaki","is_ca":false},{"name":"Mareike Schallenberg‐Rüdinger","is_ca":false},{"name":"Michael Schleicher","is_ca":false},{"name":"Reema Singh","is_ca":false},{"name":"Thomas Spaller","is_ca":false},{"name":"Kenneth B. Storey","is_ca":true},{"name":"Takamasa Suzuki","is_ca":false},{"name":"Chad Tomlinson","is_ca":false},{"name":"John J. Tyson","is_ca":false},{"name":"Wesley C. Warren","is_ca":false},{"name":"Ernst R. Werner","is_ca":false},{"name":"Gabriele Werner‐Felmayer","is_ca":false},{"name":"Richard K. Wilson","is_ca":false},{"name":"Thomas Winckler","is_ca":false},{"name":"Jonatha M. Gott","is_ca":false},{"name":"Gernot Glöckner","is_ca":false},{"name":"Wolfgang Marwan","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.03658960306102423,"gpt":0.2622127568553192,"spread":0.225623153794295,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00004684581,0.0002992852,0.0002028599,0.0005424049,0.0003081723,0.0003764431,0.0001366113,0.0001966105,0.0007573987],"category_scores_gemma":[0.0001337508,0.0000839416,0.0003152319,0.0009949072,0.0001561091,0.000166194,0.000301796,0.0003283206,0.0003228145],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002300858,"about_ca_system_score_gemma":0.0003982661,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002337399,"about_ca_topic_score_gemma":0.003086094,"domain_scores_codex":[0.9999113,0.000005862317,0.000004473233,0.0000409337,0.00002143643,0.00001589971],"domain_scores_gemma":[0.9999043,0.00001571702,0.00004086337,0.00001226153,0.000009204325,0.00001764885],"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":[0.0001514923,0.00002317973,0.01735714,0.0002364069,0.00004934886,0.000573352,0.0001991925,0.0003067352,0.9681372,0.0003550743,0.0004094929,0.01220133],"study_design_scores_gemma":[0.00001383247,0.0001549657,0.8194245,0.00006102164,0.0002022291,0.003489262,0.0005853769,0.001079328,0.1303371,0.0006199799,0.04399329,0.00003916444],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9674709,0.001826179,0.005353845,0.0001573808,0.00002629791,0.00004478441,0.02125277,0.000404279,0.003463638],"genre_scores_gemma":[0.9394049,0.001604613,0.01006321,0.0001740544,0.00002387034,0.00007082571,0.04630606,0.00009584254,0.002256669],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002337399,"threshold_uncertainty_score":0.004647553,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2119649249","doi":"10.1093/gbe/evu113","title":"Genome-Wide Identification of Long Intergenic Noncoding RNA Genes and Their Potential Association with Domestication in Pigs","year":2014,"lang":"en","type":"letter","venue":"Genome Biology and Evolution","topic":"Cancer-related molecular mechanisms research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":96,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Diabetes Canada; University of Toronto","funders":"National Key Research and Development Program of China; National High-tech Research and Development Program; Yunnan Provincial Science and Technology Department; National Natural Science Foundation of China","keywords":"Biology; Domestication; Synteny; Intergenic region; Gene; Genome; Genetics; Evolutionary biology","authors":[{"name":"Zhongyin Zhou","is_ca":false},{"name":"Aimin Li","is_ca":false},{"name":"Adeniyi C. Adeola","is_ca":false},{"name":"Liu Yan-hu","is_ca":false},{"name":"David M. Irwin","is_ca":true},{"name":"Hai‐Bing Xie","is_ca":false},{"name":"Ya‐Ping Zhang","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.006391867305368824,"gpt":0.2353625864073522,"spread":0.2289707191019834,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003800597,0.0001484606,0.0001980905,0.0003488127,0.0003448348,0.0004310904,0.0002223943,0.001840451,0.001343318],"category_scores_gemma":[0.001366186,0.0001064246,0.0001613878,0.0004160659,0.0003906053,0.0002436351,0.0002431132,0.00101481,0.0006070078],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003426198,"about_ca_system_score_gemma":0.0001278416,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006730796,"about_ca_topic_score_gemma":0.0008626731,"domain_scores_codex":[0.9997457,0.00005949485,0.00002179971,0.00007242094,0.00005960151,0.00004096988],"domain_scores_gemma":[0.9992895,0.0003340139,0.0001079728,0.00006527215,0.0001320648,0.00007109158],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.002148903,0.0001856498,0.4533588,0.0005193862,0.000209899,0.0527379,0.0008043777,0.0006160292,0.09887243,0.002627353,0.1521506,0.2357687],"study_design_scores_gemma":[0.0001651478,0.0005960756,0.5669581,0.0002986566,0.0002777358,0.1164283,0.001104829,0.005115126,0.0221035,0.007339704,0.2795011,0.0001118475],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7609585,0.01821112,0.006525476,0.1906515,0.003696548,0.00007220098,0.002612292,0.0003858694,0.01688658],"genre_scores_gemma":[0.9250515,0.00729256,0.003346769,0.05100646,0.004835193,0.00006378025,0.001349967,0.00006589755,0.00698787],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001840451,"threshold_uncertainty_score":0.004493833,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2758163810","doi":"10.1093/gbe/evx204","title":"The Role of Alternative Splicing and Differential Gene Expression in Cichlid Adaptive Radiation","year":2017,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":93,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Simon Fraser University","funders":"Karl-Franzens-Universität Graz; Austrian Science Fund; TU Graz, Internationale Beziehungen und Mobilitätsprogramme","keywords":"Biology; Cichlid; Adaptive radiation; Evolutionary biology; Alternative splicing; Gene; Trophic level; Adaptation (eye); Gene expression; RNA splicing; Genetics; Ecology; Phylogenetics; Exon; RNA; Neuroscience; Fish <Actinopterygii>","authors":[{"name":"Pooja Singh","is_ca":false},{"name":"Christine Borger","is_ca":false},{"name":"Heather L. More","is_ca":true},{"name":"Christian Sturmbauer","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.007662472114977925,"gpt":0.233136142945308,"spread":0.2254736708303301,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002375496,0.0001438321,0.0001966587,0.0005089852,0.0003359869,0.0003440334,0.0001734111,0.0002732,0.0004856794],"category_scores_gemma":[0.000334533,0.0001325409,0.0001957072,0.0003804006,0.0004673917,0.0002409838,0.0003947493,0.0002571006,0.000108757],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002371753,"about_ca_system_score_gemma":0.0002434581,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001791155,"about_ca_topic_score_gemma":0.003411605,"domain_scores_codex":[0.9997607,0.00001767727,0.00001593592,0.00013621,0.00003825402,0.00003115549],"domain_scores_gemma":[0.9997444,0.00006301184,0.00008592219,0.00002630968,0.00005132856,0.00002899306],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001666547,0.00001729333,0.08127274,0.0001460692,0.00005908987,0.0003406878,0.001289291,0.0002141981,0.905242,0.0004092478,0.0001049428,0.0107378],"study_design_scores_gemma":[0.000004528524,0.00006952,0.9836934,0.00001654242,0.00003532849,0.0002336992,0.0004170086,0.000567211,0.01330744,0.0003203839,0.001321262,0.00001376084],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9975998,0.0006503535,0.0007754919,0.00003575655,0.000006498463,0.00000462581,0.0002484696,0.000009486097,0.000669551],"genre_scores_gemma":[0.9970349,0.0003197743,0.00105958,0.0001015589,0.00001022379,0.0000222114,0.0005229412,0.000009423998,0.0009194062],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001791155,"threshold_uncertainty_score":0.003561497,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2171477019","doi":"10.1093/gbe/evp011","title":"Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes","year":2009,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Protist diversity and phylogeny","field":"Biochemistry, Genetics and Molecular Biology","cited_by":91,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Université de Montréal","funders":"Johnson and Johnson","keywords":"Biology; Phylogenetics; Symbiosis; Evolutionary biology; Computational biology; Genetics; Gene; Bacteria","authors":[{"name":"Igor B. Rogozin","is_ca":false},{"name":"Malay Kumar Basu","is_ca":false},{"name":"Miklós Csürös","is_ca":true},{"name":"Eugene V. Koonin","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.00585114761222988,"gpt":0.2084927546175484,"spread":0.2026416070053185,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000326797,0.0002229731,0.000290754,0.0009036878,0.0003580128,0.0004247323,0.0002708446,0.0003342964,0.001406468],"category_scores_gemma":[0.0009618839,0.00007606272,0.0003684252,0.001013922,0.0004482066,0.0002821804,0.0003822141,0.0003933685,0.0002676239],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002194477,"about_ca_system_score_gemma":0.0003255305,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001898145,"about_ca_topic_score_gemma":0.006036932,"domain_scores_codex":[0.9996666,0.0000286548,0.00003250186,0.0001349188,0.00009238264,0.00004496688],"domain_scores_gemma":[0.9988046,0.0003391965,0.0003397012,0.0002103078,0.0001146773,0.0001916003],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0008165091,0.000067455,0.4148545,0.0003033566,0.0004470489,0.001530722,0.0004542099,0.0004824671,0.5488914,0.001012528,0.0002103022,0.03092953],"study_design_scores_gemma":[0.00001907733,0.0001495491,0.9801012,0.00002074869,0.0001645234,0.0017303,0.0003513631,0.001234234,0.01327311,0.0005211943,0.002420001,0.00001461477],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9967281,0.0003335398,0.001382394,0.0000435155,0.000009577173,0.00001012356,0.000511014,0.00004327729,0.0009384633],"genre_scores_gemma":[0.9977909,0.000105784,0.00118416,0.00006605505,0.000005608306,0.000005770385,0.0006285924,0.000006725757,0.0002063521],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001898145,"threshold_uncertainty_score":0.004705071,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2154297799","doi":"10.1093/gbe/evt112","title":"Structure, Transcription, and Variability of Metazoan Mitochondrial Genome: Perspectives from an Unusual Mitochondrial Inheritance System","year":2013,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Aquatic Invertebrate Ecology and Behavior","field":"Environmental Science","cited_by":90,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Université de Montréal","funders":"National Institute of General Medical Sciences; National Institutes of Health; Ministero dell'Università e della Ricerca; Ministero dell’Istruzione, dell’Università e della Ricerca","keywords":"Biology; Mitochondrial DNA; Genetics; Intergenic region; Evolutionary biology; mtDNA control region; Population; Non-Mendelian inheritance; Genome; Gene; Haplotype; Allele","authors":[{"name":"Fabrizio Ghiselli","is_ca":false},{"name":"Liliana Milani","is_ca":false},{"name":"Davide Guerra","is_ca":false},{"name":"Peter L. Chang","is_ca":false},{"name":"Sophie Breton","is_ca":true},{"name":"Sergey V. Nuzhdin","is_ca":false},{"name":"Marco Passamonti","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.007058639857708256,"gpt":0.2153243111581842,"spread":0.2082656713004759,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000181613,0.0001838138,0.0002352663,0.0005128598,0.0002507537,0.0004592637,0.0003039183,0.0003461844,0.0003715372],"category_scores_gemma":[0.0002207246,0.000165755,0.0001602442,0.0004220307,0.0006833429,0.0007421562,0.0003556589,0.0003958853,0.0001065299],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003542663,"about_ca_system_score_gemma":0.0001669612,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008163467,"about_ca_topic_score_gemma":0.001221697,"domain_scores_codex":[0.9998978,0.00001553505,0.000005636809,0.0000516493,0.00001631261,0.00001306487],"domain_scores_gemma":[0.9997795,0.00004242438,0.00007784597,0.00002464246,0.00002944062,0.00004615978],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0002220816,0.00003125126,0.05547661,0.0002449122,0.00002979532,0.0005596573,0.0009827383,0.0007576176,0.9209836,0.002454882,0.00007438554,0.01818252],"study_design_scores_gemma":[0.00002718508,0.0003561281,0.897508,0.00005437242,0.00009097204,0.002067357,0.001286922,0.00531097,0.0811018,0.007200095,0.004914152,0.00008207172],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9862302,0.008248886,0.003932914,0.000262854,0.00001150807,0.000005270028,0.0001875742,0.00002698958,0.001093741],"genre_scores_gemma":[0.9956573,0.001752093,0.002062765,0.00005589926,0.00004087884,0.000008749395,0.0001520672,0.00001051745,0.0002597821],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0008163467,"threshold_uncertainty_score":0.002570331,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2113657329","doi":"10.1093/gbe/evv035","title":"Insights on the Emergence of Mycobacterium tuberculosis from the Analysis of Mycobacterium kansasii","year":2015,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":90,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Institut National de la Recherche Scientifique; McGill University and Génome Québec Innovation Centre; Armand Frappier Museum; McGill University Health Centre; McGill University","funders":"Fonds de Recherche du Québec - Santé; Canadian Institutes of Health Research; Agence Nationale de la Recherche","keywords":"Mycobacterium kansasii; Biology; Mycobacterium tuberculosis; Pathogen; Virulence; Microbiology; Tuberculosis; Genetics; Mycobacterium; Plasmid; Genome; Human pathogen; Virology; Gene; Bacteria; Medicine","authors":[{"name":"Joyce Wang","is_ca":true},{"name":"Fiona McIntosh","is_ca":true},{"name":"Nicolas Radomski","is_ca":true},{"name":"Ken Dewar","is_ca":true},{"name":"Roxane Siméone","is_ca":false},{"name":"Jost Enninga","is_ca":false},{"name":"Roland Brosch","is_ca":false},{"name":"Eduardo P. C. Rocha","is_ca":false},{"name":"Frédéric J. Veyrier","is_ca":true},{"name":"Marcel A. Behr","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.03235777735659175,"gpt":0.2845780220117202,"spread":0.2522202446551285,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002702897,0.0002166733,0.000232695,0.0005770859,0.0003199284,0.0005857697,0.0002369549,0.0005248451,0.0004042415],"category_scores_gemma":[0.0005633337,0.0002617413,0.0001590614,0.0004303191,0.0002562873,0.000425299,0.000343446,0.0007326021,0.0003096868],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005135657,"about_ca_system_score_gemma":0.0002255793,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00300747,"about_ca_topic_score_gemma":0.004541405,"domain_scores_codex":[0.9998519,0.00002747954,0.00001245283,0.00003558518,0.00003241676,0.00004012061],"domain_scores_gemma":[0.9997296,0.00005587378,0.00006834669,0.00002601928,0.00005967903,0.00006049145],"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":[0.0002766456,0.00006625181,0.08470552,0.0003958868,0.0000242659,0.001347795,0.001226542,0.0002725159,0.8857548,0.001038608,0.0004576189,0.02443359],"study_design_scores_gemma":[0.00001899381,0.0003976406,0.8505222,0.0002190215,0.000111615,0.002959013,0.002329453,0.002171087,0.102389,0.001369507,0.03746452,0.00004802128],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9847565,0.007303729,0.003799644,0.0007217309,0.00003129936,0.0000187269,0.0005768596,0.0000799835,0.002711564],"genre_scores_gemma":[0.9900655,0.003429002,0.004498449,0.0002626617,0.00003066553,0.000007705251,0.0005997775,0.00001881748,0.001087531],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00300747,"threshold_uncertainty_score":0.005979955,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2789422248","doi":"10.1093/gbe/evy030","title":"Fitness Tradeoffs of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli","year":2018,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Evolution and Genetic Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":90,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Carleton University","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; University of Manitoba","keywords":"Biology; Antibiotic resistance; Experimental evolution; Trade-off; Genetics; Antibiotics; Trait; Drug resistance; Escherichia coli; Evolutionary dynamics; Gene; Evolutionary biology; Ecology; Population; Demography","authors":[{"name":"Prabh Basra","is_ca":true},{"name":"Ahlam Alsaadi","is_ca":true},{"name":"Gabriela Bernal-Astrain","is_ca":true},{"name":"Michael Liam O’Sullivan","is_ca":true},{"name":"Bryn Hazlett","is_ca":true},{"name":"Leah Clarke","is_ca":true},{"name":"Andrew Schoenrock","is_ca":true},{"name":"Sylvain Pitre","is_ca":true},{"name":"Alex Wong","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.007909289906783672,"gpt":0.2423967496017124,"spread":0.2344874596949287,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00038901,0.0002696318,0.0002640437,0.0005159773,0.0002030716,0.0005216368,0.0002791417,0.0003607083,0.00030769],"category_scores_gemma":[0.001533891,0.0001548472,0.0001845456,0.0004534815,0.000375975,0.0003067875,0.0004567733,0.0003490173,0.00006845302],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004963964,"about_ca_system_score_gemma":0.0001474907,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009241452,"about_ca_topic_score_gemma":0.001449501,"domain_scores_codex":[0.9995406,0.0001908558,0.00003267073,0.0001038209,0.00008580691,0.00004634259],"domain_scores_gemma":[0.9991751,0.0003655862,0.0002572019,0.00008391716,0.0000622409,0.00005590034],"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":[0.0004039309,0.0001968366,0.1694182,0.00007573874,0.0001231164,0.0003051776,0.000215775,0.005516839,0.8027256,0.0004157342,0.00007662144,0.02052645],"study_design_scores_gemma":[0.0000194434,0.0004735664,0.9019912,0.000008566989,0.00004686399,0.001124046,0.0003514367,0.01985661,0.07422572,0.001274046,0.0005762879,0.00005230011],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9992042,0.0000793707,0.0005209933,0.00001335492,7.190746e-7,0.000002274374,0.00003369104,0.000004780688,0.0001405101],"genre_scores_gemma":[0.9991351,0.00007633598,0.0006386309,0.00001323949,0.000001351613,0.000004613071,0.00006564858,0.000004174364,0.00006096096],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0009241452,"threshold_uncertainty_score":0.00360167,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2199155364","doi":"10.1093/gbe/evv120","title":"How did arthropod sesquiterpenoids and ecdysteroids arise? Comparison of hormonal pathway genes in non-insect arthropod genomes","year":2015,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Neurobiology and Insect Physiology Research","field":"Neuroscience","cited_by":89,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Toronto; Queen's University","funders":"Chinese University of Hong Kong; Lee Hysan Foundation","keywords":"Biology; Arthropod; Juvenile hormone; Ecdysteroid; Insect; Moulting; Ecdysone; Evolutionary biology; Metamorphosis; Genome; Gene; Zoology; Ecology; Genetics; Larva","authors":[{"name":"Zhe Qu","is_ca":false},{"name":"Nathan J. Kenny","is_ca":false},{"name":"Hon‐Ming Lam","is_ca":false},{"name":"Ting‐Fung Chan","is_ca":false},{"name":"Ka Hou Chu","is_ca":false},{"name":"William G. Bendena","is_ca":true},{"name":"Stephen S. Tobe","is_ca":true},{"name":"Jerome H. L. Hui","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.0516180071074574,"gpt":0.3025244606273456,"spread":0.2509064535198882,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000166276,0.0001234334,0.0001721344,0.0005843925,0.0002512979,0.0004897857,0.0001656916,0.0003307787,0.001072467],"category_scores_gemma":[0.000298171,0.0001117435,0.0002713225,0.0006014531,0.0001655033,0.0005395768,0.0002715647,0.0003397211,0.0003106434],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002900336,"about_ca_system_score_gemma":0.000186918,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001115705,"about_ca_topic_score_gemma":0.00181898,"domain_scores_codex":[0.9998749,0.00001030622,0.000006970814,0.00005958557,0.00001807412,0.00003006489],"domain_scores_gemma":[0.9998792,0.00002798181,0.00002833844,0.00001189216,0.00002320229,0.00002930338],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0003323584,0.00002498469,0.06088987,0.0002179789,0.0000531066,0.0006585305,0.0007179254,0.0002233866,0.9065498,0.001405024,0.0002211159,0.02870609],"study_design_scores_gemma":[0.00001810407,0.0001654748,0.9341658,0.00005908826,0.0001208086,0.001827001,0.001226198,0.001359523,0.03751266,0.001095033,0.02242071,0.00002960317],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9947678,0.001687956,0.0008960421,0.0001006559,0.00001195806,0.00000713056,0.0008013214,0.00001746823,0.001709818],"genre_scores_gemma":[0.991507,0.001661925,0.002049597,0.0001997834,0.00001309383,0.00001213782,0.002772575,0.00002479748,0.001759079],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001115705,"threshold_uncertainty_score":0.003587782,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2404399045","doi":"10.1093/gbe/evw262","title":"Salmonid chromosome evolution as revealed by a novel method for comparing RADseq linkage maps","year":2016,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":89,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Université du Québec à Rimouski; Centre Intégré de Santé et de Services Sociaux des Laurentides; Université Laval","funders":"","keywords":"Biology; Synteny; Evolutionary biology; Genome; Genetics; Chromosome; Phylogenetic tree; Salvelinus; Genetic linkage; Sister group; Gene; Clade; Trout","authors":[{"name":"Ben Sutherland","is_ca":true},{"name":"Thierry Gosselin","is_ca":true},{"name":"Éric Normandeau","is_ca":true},{"name":"Manuel Lamothe","is_ca":true},{"name":"Nathalie Isabel","is_ca":true},{"name":"Céline Audet","is_ca":true},{"name":"Louis Bernatchez","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01309109849183986,"gpt":0.2660961664218487,"spread":0.2530050679300088,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001033941,0.0004746411,0.0003916895,0.002635583,0.0004520896,0.0006964407,0.000621657,0.0003812685,0.002454059],"category_scores_gemma":[0.001658484,0.0004016219,0.0005089479,0.001699482,0.0002415387,0.0003889654,0.0008365905,0.0006651087,0.0008045626],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003752611,"about_ca_system_score_gemma":0.0004112053,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001141391,"about_ca_topic_score_gemma":0.003418426,"domain_scores_codex":[0.999055,0.0001167356,0.00008426744,0.0004098854,0.0002864581,0.00004771442],"domain_scores_gemma":[0.9991797,0.0002546399,0.0001709858,0.0001724327,0.00015868,0.00006354182],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0002876623,0.0001122454,0.0238196,0.0003358974,0.0003454816,0.0003881699,0.0004898527,0.001892822,0.8364835,0.004603312,0.001713723,0.1295276],"study_design_scores_gemma":[0.0001614958,0.0004699421,0.3028329,0.00007914822,0.0004820435,0.002423376,0.0002462822,0.08276024,0.5403214,0.004134623,0.06586863,0.0002199021],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.4738442,0.0005444098,0.502459,0.0001090426,0.0001048465,0.0003391001,0.007451528,0.005252772,0.009895092],"genre_scores_gemma":[0.297976,0.0001999248,0.6891726,0.00009245173,0.00002855607,0.0005967963,0.008210603,0.0004602208,0.003262908],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.002635583,"threshold_uncertainty_score":0.008209705,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2791346574","doi":"10.1093/gbe/evy034","title":"The DNA Methylation Landscape of Stickleback Reveals Patterns of Sex Chromosome Evolution and Effects of Environmental Salinity","year":2018,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":86,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Stickleback; DNA methylation; Epigenetics; Gasterosteus; Evolutionary biology; Dosage compensation; Context (archaeology); Genetics; Genome; Chromosome; Gene; Fishery","authors":[{"name":"David C. H. Metzger","is_ca":true},{"name":"Patricia M. Schulte","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.005166263829043121,"gpt":0.2291302797431008,"spread":0.2239640159140577,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00005757139,0.00009475365,0.0001364502,0.0003477759,0.0001452965,0.0001857803,0.00008108647,0.0001841656,0.0006556979],"category_scores_gemma":[0.0001275554,0.0001046359,0.0001145144,0.0002014633,0.0001606221,0.0001018924,0.0001778686,0.0001910351,0.0001169081],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001698308,"about_ca_system_score_gemma":0.00009624263,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004754656,"about_ca_topic_score_gemma":0.008652567,"domain_scores_codex":[0.9999609,0.000003221838,0.00000248645,0.00001757651,0.000007721848,0.00000806593],"domain_scores_gemma":[0.9999208,0.000009591446,0.00003166335,0.000006297625,0.00001277752,0.00001880143],"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":[0.0001981236,0.00000819525,0.06154656,0.00002556669,0.00003267292,0.00003542011,0.0002145842,0.0001070197,0.9335351,0.00005789578,0.00003381655,0.004205146],"study_design_scores_gemma":[0.000002223541,0.00007229964,0.9809085,0.000003044268,0.00001683537,0.00007591808,0.0001247654,0.0003616889,0.0181087,0.00006357723,0.0002574198,0.000005096342],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9992062,0.0001974688,0.0002204086,0.00001169358,0.000001458284,0.00000152119,0.000160389,0.000006498303,0.0001943788],"genre_scores_gemma":[0.9989161,0.0001037711,0.0002571411,0.00001971339,0.000001182507,0.000003776285,0.0002483599,0.000003704622,0.0004461453],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004754656,"threshold_uncertainty_score":0.009453952,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2112081361","doi":"10.1093/gbe/evv134","title":"The Highly Reduced Plastome of Mycoheterotrophic<i>Sciaphila</i>(Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection","year":2015,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":84,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"","keywords":"Biology; Plastid; Phylogenetic tree; Genome; Chloroplast DNA; Evolutionary biology; Negative selection; Genetics; Context (archaeology); Phylogenomics; Phylogenetics; Gene; Chloroplast","authors":[{"name":"Vivienne K. Y. Lam","is_ca":true},{"name":"Marybel Soto Gomez","is_ca":true},{"name":"Sean W. Graham","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01770630257098191,"gpt":0.2417182828050463,"spread":0.2240119802340644,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001108244,0.0002715875,0.0002858009,0.0007216147,0.0005180746,0.0004728499,0.0001709929,0.0002172636,0.001420835],"category_scores_gemma":[0.0003172029,0.000145272,0.0003796709,0.0008605554,0.0002477539,0.0002900143,0.000453343,0.000428885,0.0004730544],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001659432,"about_ca_system_score_gemma":0.0001812727,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001255526,"about_ca_topic_score_gemma":0.002971528,"domain_scores_codex":[0.9999027,0.000007196517,0.000009026523,0.00004639206,0.00002012889,0.00001443712],"domain_scores_gemma":[0.9997439,0.00005423954,0.00008142785,0.00005554719,0.00002926417,0.0000355924],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001005418,0.0000134491,0.03864367,0.0001166056,0.00004479656,0.0002187147,0.0003244066,0.00008819194,0.9466021,0.0001036482,0.00009193033,0.01365195],"study_design_scores_gemma":[0.000007233396,0.00013365,0.9069829,0.00003225845,0.0001055024,0.003121422,0.0004721789,0.0006987557,0.0717271,0.0002016144,0.01649831,0.00001904251],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9942635,0.0006385062,0.002235701,0.00004025878,0.000008412622,0.000009050103,0.001759782,0.00009252461,0.000952217],"genre_scores_gemma":[0.9875173,0.0004114119,0.003317043,0.00005002212,0.00000722814,0.00001292569,0.007795162,0.00004497676,0.0008438932],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001420835,"threshold_uncertainty_score":0.004753113,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2265097017","doi":"10.1093/gbe/evv263","title":"Evidence of Natural Hybridization in Brazilian Wild Lineages of<i>Saccharomyces cerevisiae</i>","year":2016,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Fermentation and Sensory Analysis","field":"Agricultural and Biological Sciences","cited_by":83,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Université de Montréal; Cégep Marie-Victorin; Université Laval","funders":"Natural Sciences and Engineering Research Council of Canada; Fundação de Amparo à Pesquisa do Estado de Minas Gerais; Universidade Federal de Minas Gerais; Conselho Nacional de Desenvolvimento Científico e Tecnológico","keywords":"Biology; Population; Population genomics; Domestication; Phylogeography; Natural population growth; Ecology; Evolutionary biology; Phylogenetics; Genetics; Genome; Genomics; Gene","authors":[{"name":"Raquel Barbosa","is_ca":false},{"name":"Pedro Almeida","is_ca":false},{"name":"Silvana V. B. Safar","is_ca":false},{"name":"Renata Santos","is_ca":false},{"name":"Paula B. Morais","is_ca":false},{"name":"Lou Nielly‐Thibault","is_ca":true},{"name":"Jean‐Baptiste Leducq","is_ca":true},{"name":"Christian R. Landry","is_ca":true},{"name":"Paula Gonçalves","is_ca":false},{"name":"Carlos A. Rosa","is_ca":false},{"name":"José Paulo Sampaio","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.0186492227449454,"gpt":0.2461101217749686,"spread":0.2274608990300232,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003114904,0.0002294439,0.0002628932,0.0007545674,0.000635128,0.0004089721,0.0002819021,0.0002230852,0.0009928605],"category_scores_gemma":[0.0008040342,0.0001640854,0.0002447274,0.0006306589,0.0004647822,0.0001667125,0.0006609386,0.0002764519,0.0001307061],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003269681,"about_ca_system_score_gemma":0.0003019233,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006797661,"about_ca_topic_score_gemma":0.01408948,"domain_scores_codex":[0.9997012,0.00005484684,0.00002602601,0.0001190421,0.00005013713,0.00004867305],"domain_scores_gemma":[0.999481,0.000115867,0.0001775386,0.0000656494,0.00009226328,0.00006777883],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0003918893,0.00009584967,0.3651222,0.0001452867,0.0001139057,0.000535864,0.00266654,0.00009483694,0.613843,0.0005181498,0.00008952484,0.01638303],"study_design_scores_gemma":[0.00001816354,0.0002369959,0.9728121,0.00002961617,0.0000835264,0.001654756,0.002117024,0.0004190247,0.01988779,0.0003253256,0.002392786,0.00002302716],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9986903,0.0001546877,0.0003589715,0.00001930063,0.000001771832,0.000006737909,0.00009183893,0.000005529581,0.0006708963],"genre_scores_gemma":[0.9987245,0.0001463447,0.0006926587,0.00002901452,0.000001818988,0.000007942953,0.0002864933,0.000004258869,0.0001069858],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006797661,"threshold_uncertainty_score":0.01351619,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2674191287","doi":"10.1093/gbe/evx110","title":"Genetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalis","year":2017,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Reproductive tract infections research","field":"Immunology and Microbiology","cited_by":83,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"","funders":"National Institute of Allergy and Infectious Diseases; Centers for Disease Control and Prevention; Chang Gung Medical Foundation; Tulane University; York University; Grundy Educational Trust; National Institutes of Health","keywords":"Biology; Trichomonas vaginalis; Genetics; Single-nucleotide polymorphism; Drug resistance; Gene; Trichomoniasis; Genotype","authors":[{"name":"Martina Bradić","is_ca":false},{"name":"Sally D. Warring","is_ca":false},{"name":"Grace E. Tooley","is_ca":false},{"name":"Paul Scheid","is_ca":false},{"name":"W. Evan Secor","is_ca":false},{"name":"Kirkwood M. Land","is_ca":false},{"name":"Po-Jung Huang","is_ca":false},{"name":"Ting-Wen Chen","is_ca":false},{"name":"Chi‐Ching Lee","is_ca":false},{"name":"Petrus Tang","is_ca":false},{"name":"Steven A. Sullivan","is_ca":false},{"name":"Jane M. Carlton","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01109567029163368,"gpt":0.2755823247348304,"spread":0.2644866544431967,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001549351,0.0002113958,0.0002114644,0.0008435445,0.000204519,0.0002791864,0.0001619738,0.000324762,0.001015186],"category_scores_gemma":[0.0007250824,0.0001247178,0.000241723,0.0006929764,0.0002022846,0.00009028452,0.0002295152,0.0003695567,0.000182878],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001991282,"about_ca_system_score_gemma":0.0001188875,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001720257,"about_ca_topic_score_gemma":0.002392688,"domain_scores_codex":[0.9997486,0.00004603737,0.00002082069,0.00008041391,0.000063236,0.00004081265],"domain_scores_gemma":[0.9995623,0.0001119006,0.0001814141,0.00003790835,0.00005378484,0.00005277076],"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":[0.0002855973,0.00005467104,0.05194368,0.00005772816,0.00006213287,0.000231644,0.0001833154,0.0001310472,0.9407563,0.00007700975,0.00005347629,0.00616336],"study_design_scores_gemma":[0.00001462793,0.0003008112,0.9589872,0.00001631543,0.00007804603,0.001365081,0.0001964955,0.0009154275,0.03677373,0.00009509136,0.001243571,0.00001352882],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.998122,0.0001956445,0.0007009947,0.00001905516,0.000003153703,0.00001119887,0.0005863365,0.0000216109,0.0003399436],"genre_scores_gemma":[0.9973416,0.00009362724,0.001226675,0.00002987285,0.000003103616,0.00001250574,0.0009625834,0.000009929429,0.0003202334],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001720257,"threshold_uncertainty_score":0.003420472,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2970153829","doi":"10.1093/gbe/evz184","title":"Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes","year":2019,"lang":"en","type":"review","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":81,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Metagenomics; Biology; Horizontal gene transfer; Computational biology; Genome; Gene; Context (archaeology); Contig; Gene duplication; Genetics; Shotgun sequencing","authors":[{"name":"Gavin M. Douglas","is_ca":true},{"name":"Morgan G. I. Langille","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.1047116907146183,"gpt":0.3239519014606665,"spread":0.2192402107460482,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.004291762,0.001685003,0.001741415,0.004200271,0.0007471623,0.003920855,0.002307445,0.00218305,0.002085541],"category_scores_gemma":[0.004251243,0.0008994996,0.001495249,0.003339041,0.001851431,0.005207345,0.002038938,0.003712995,0.001899056],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001399546,"about_ca_system_score_gemma":0.001572256,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001110094,"about_ca_topic_score_gemma":0.001831478,"domain_scores_codex":[0.997821,0.0006249025,0.000130511,0.0005950123,0.0007137271,0.0001148916],"domain_scores_gemma":[0.9975298,0.001117943,0.0003534051,0.0002905961,0.0005464033,0.0001618551],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0002636451,0.0001853115,0.006680821,0.01911978,0.0005305029,0.0005041474,0.0008962895,0.002983332,0.1854521,0.03862643,0.007919776,0.7368379],"study_design_scores_gemma":[0.0001065574,0.0006562163,0.01914784,0.007733357,0.0008023432,0.003318992,0.002065499,0.01841322,0.1572871,0.1681341,0.6218875,0.0004474159],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.01150849,0.6879966,0.2799606,0.008708267,0.001323586,0.0002410294,0.001122512,0.0009605091,0.008178513],"genre_scores_gemma":[0.06240987,0.5242914,0.4024334,0.003482641,0.000867894,0.0004908523,0.002078928,0.0002370562,0.003707864],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.004291762,"threshold_uncertainty_score":0.02269727,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2729843280","doi":"10.1093/gbe/evx115","title":"Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance","year":2017,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":80,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":false,"ca_fund":false,"ca_venue":false,"about_ca":true},"ca_institutions":"","funders":"Institut National Du Cancer; University of Technology Sydney; Universidad El Bosque; Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS)","keywords":"Plasmid; Klebsiella pneumoniae; Acinetobacter baumannii; Biology; Microbiology; Antibiotic resistance; Molecular epidemiology; Enterobacteriaceae; Multiple drug resistance; Acinetobacter; Escherichia coli; Antibiotics; Genetics; Gene; Bacteria; Genotype; Pseudomonas aeruginosa","authors":[{"name":"Ricaurte Alejandro Marquez-Ortíz","is_ca":false},{"name":"Leanne Haggerty","is_ca":false},{"name":"Narda Olarte","is_ca":false},{"name":"Carolina Duarte","is_ca":false},{"name":"Ulises Garza–Ramos","is_ca":false},{"name":"Jesús Silva-Sánchez","is_ca":false},{"name":"Betsy E. Castro","is_ca":false},{"name":"Eby Sim","is_ca":false},{"name":"Mauricio Beltrán","is_ca":false},{"name":"Maria Victoria Moncada","is_ca":false},{"name":"Alberto Valderrama","is_ca":false},{"name":"Jaime E. Castellanos","is_ca":false},{"name":"Ian G. Charles","is_ca":false},{"name":"Natasha Vanegas","is_ca":false},{"name":"Javier Escobar-Pérez","is_ca":false},{"name":"Nicola K. Petty","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.0235061111204774,"gpt":0.3223262243502231,"spread":0.2988201132297457,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001140427,0.0002417029,0.0001801309,0.000706751,0.0002590419,0.0004126476,0.0001457072,0.0002244202,0.000759995],"category_scores_gemma":[0.000532329,0.0001008014,0.0001655699,0.0006364099,0.0002091701,0.00009685442,0.0002489207,0.0002422589,0.0001039356],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005294209,"about_ca_system_score_gemma":0.0003143456,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.02272485,"about_ca_topic_score_gemma":0.02100792,"domain_scores_codex":[0.999859,0.00001695585,0.00001282889,0.00005617387,0.00002316171,0.00003184952],"domain_scores_gemma":[0.9997624,0.00003498601,0.0001150129,0.00001941187,0.00003957552,0.00002871037],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0007377408,0.00006123332,0.8650755,0.0001666449,0.00007000437,0.0008776392,0.001159073,0.0001936584,0.1136437,0.0001201244,0.0002544992,0.01764025],"study_design_scores_gemma":[0.000007927692,0.00005262628,0.9927443,0.00002287123,0.00004522591,0.001136443,0.0006109022,0.0001636505,0.003618301,0.00001904065,0.001573077,0.000005796036],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9979615,0.0004854789,0.0001979751,0.00005322232,0.000002665729,0.00001660609,0.0006538427,0.000008557676,0.0006201247],"genre_scores_gemma":[0.9980705,0.0003595677,0.000534157,0.00003585273,0.000003003051,0.00001118489,0.0007652522,0.000003584594,0.0002168433],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02272485,"threshold_uncertainty_score":0.04518515,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2137633181","doi":"10.1093/gbe/evt083","title":"Reconstructing the Phylogenetic History of Long-Term Effective Population Size and Life-History Traits Using Patterns of Amino Acid Replacement in Mitochondrial Genomes of Mammals and Birds","year":2013,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genetic diversity and population structure","field":"Biochemistry, Genetics and Molecular Biology","cited_by":77,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Université de Montréal","funders":"Compute Canada","keywords":"Biology; Effective population size; Evolutionary biology; Nonsynonymous substitution; Phylogenetic tree; Population; Phylogenetics; Mitochondrial DNA; Genetics; Genome; Zoology; Genetic variation; Gene; Demography","authors":[{"name":"Benoît Nabholz","is_ca":false},{"name":"Nicole Uwimana","is_ca":true},{"name":"Nicolas Lartillot","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01174940932785595,"gpt":0.2160052960971697,"spread":0.2042558867693137,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001680339,0.0002129316,0.0002573809,0.001136263,0.0004016104,0.0006167911,0.0004656117,0.0003657498,0.000430787],"category_scores_gemma":[0.005810889,0.0002159371,0.0006392139,0.0009718446,0.0005228519,0.0007847733,0.000731133,0.0005497652,0.0001072106],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003697491,"about_ca_system_score_gemma":0.0002674542,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002247078,"about_ca_topic_score_gemma":0.003586529,"domain_scores_codex":[0.9996299,0.0001252165,0.00002567477,0.0001580285,0.00003290693,0.0000284197],"domain_scores_gemma":[0.9978901,0.001067784,0.0006126513,0.0001753243,0.0001242077,0.0001300427],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0001736483,0.00004932667,0.8192948,0.000121252,0.0005768475,0.0002180801,0.0008250785,0.0600994,0.06766018,0.008373858,0.0001525976,0.042455],"study_design_scores_gemma":[0.00001271929,0.00006001868,0.7188019,0.00001786395,0.0001014671,0.0003767668,0.0002827786,0.2653695,0.003705269,0.01078284,0.0004276074,0.0000612782],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9629479,0.0001119752,0.03657044,0.0000394021,0.000002210408,0.000003872394,0.00008976978,0.00003237372,0.0002021639],"genre_scores_gemma":[0.9938388,0.00003335377,0.00593558,0.000009798026,0.000003200031,0.000004704867,0.000131936,0.000009940182,0.00003254536],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002247078,"threshold_uncertainty_score":0.008886635,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1997520854","doi":"10.1093/gbe/evp047","title":"The Complete Plastid Genome Sequence of the Secondarily Nonphotosynthetic Alga Cryptomonas paramecium: Reduction, Compaction, and Accelerated Evolutionary Rate","year":2009,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Protist diversity and phylogeny","field":"Biochemistry, Genetics and Molecular Biology","cited_by":77,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Dalhousie University; Canadian Institute for Advanced Research","funders":"Canadian Institutes of Health Research; Nova Scotia Health Research Foundation; Canadian Institute for Advanced Research","keywords":"Biology; Plastid; Genome; Paramecium; Genetics; Pseudogene; Endosymbiosis; Gene; Botany; Chloroplast; Cell biology","authors":[{"name":"Natalie Donaher","is_ca":true},{"name":"Goro Tanifuji","is_ca":true},{"name":"Naoko T. Onodera","is_ca":true},{"name":"Stephanie Malfatti","is_ca":false},{"name":"Patrick Chain","is_ca":false},{"name":"Yoshiaki Hara","is_ca":false},{"name":"John M. Archibald","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01703300121636314,"gpt":0.2374325273979152,"spread":0.2203995261815521,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00008695915,0.0007339343,0.0004495952,0.0005636928,0.000370807,0.0003401552,0.0003675463,0.0004227172,0.003906925],"category_scores_gemma":[0.0003155747,0.000252351,0.0005661845,0.0009409434,0.0001351563,0.0003241715,0.0002871373,0.0008840658,0.002972506],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004439701,"about_ca_system_score_gemma":0.0007363836,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002835667,"about_ca_topic_score_gemma":0.002161685,"domain_scores_codex":[0.999897,0.000006337775,0.000007680052,0.00004135843,0.00003258093,0.00001513868],"domain_scores_gemma":[0.999742,0.00004855333,0.00005307867,0.00003642152,0.00006755372,0.00005246619],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.000540489,0.00004905974,0.002516624,0.000633652,0.00004109354,0.0003442003,0.0001519443,0.0003463348,0.9712636,0.0002179956,0.001309028,0.02258586],"study_design_scores_gemma":[0.0002784382,0.0007514713,0.3339108,0.0003297362,0.0006781151,0.004510617,0.0004545143,0.003977824,0.4624644,0.001021774,0.1914842,0.0001381508],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7580023,0.009985235,0.03138715,0.0007809703,0.0003149019,0.000217294,0.1925345,0.001181715,0.00559607],"genre_scores_gemma":[0.4317409,0.005946206,0.03705225,0.0002857495,0.0001301541,0.0002322481,0.5148046,0.0006529914,0.009154868],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003906925,"threshold_uncertainty_score":0.01306999,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null}]}