{"meta":{"page":1,"per_page":50,"max_per_page":100,"total":13,"total_is_capped":false,"direct_labels_cover":0,"predictions_cover":13,"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":"25dbb364e226","filters":{"venue":"Bioinformatics and Biology Insights"}},"results":[{"id":"W192939834","doi":"10.4137/bbi.s451","title":"Ontologies for Bioinformatics","year":2008,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"Biomedical Text Mining and Ontologies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":52,"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":"","keywords":"Interoperability; Computer science; Ontology; Data science; Context (archaeology); Semantic interoperability; Open Biomedical Ontologies; Semantics (computer science); Semantic Web; Meaning (existential); IDEF5; Semantic integration; World Wide Web; Knowledge management; Upper ontology; Semantic Web Stack; Ontology alignment; Biology","authors":[{"name":"Nadine Schuurman","is_ca":true},{"name":"Agnieszka Leszczynski","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.05290572275187795,"gpt":0.2885351413558813,"spread":0.2356294186040034,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001167598,0.0002000515,0.0002457934,0.00007865222,0.0002886803,0.00001646802,0.0001932656,0.0003822249,0.000003454302],"category_scores_gemma":[0.0002123787,0.0001388961,0.00008468071,0.00006791532,0.000626382,0.000007955406,0.0001322717,0.00007972591,0.00001029304],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00000649652,"about_ca_system_score_gemma":0.00006991281,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000005271214,"about_ca_topic_score_gemma":0.00001171077,"domain_scores_codex":[0.9990515,0.00001797237,0.0003869118,0.0001742844,0.00005534839,0.0003139847],"domain_scores_gemma":[0.9993705,0.00006152222,0.0001372892,0.0002435481,0.00008509852,0.0001020383],"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":[0.001438265,0.000604538,0.02624664,0.001144315,0.001282142,0.0000189312,0.01083393,0.00002327893,0.06317588,0.03116385,0.1640023,0.7000659],"study_design_scores_gemma":[0.002197662,0.002966756,0.003452272,0.00002847155,0.00003910933,0.0003007127,0.001079902,0.005512317,0.01068494,0.001983337,0.971037,0.0007174746],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.928537,0.003651698,0.06069596,0.0004934528,0.0006310917,0.0005696088,0.0001002222,0.0001316344,0.005189335],"genre_scores_gemma":[0.8294421,0.003332134,0.1641949,0.001512274,0.0003040773,0.00007934434,0.0004909388,0.00002028433,0.0006239114],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8070347,"threshold_uncertainty_score":0.5664017,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4401050272","doi":"10.1177/11779322241264145","title":"Antiviral Activity, Pharmacoinformatics, Molecular Docking, and Dynamics Studies of <i>Azadirachta indica</i> Against Nipah Virus by Targeting Envelope Glycoprotein: Emerging Strategies for Developing Antiviral Treatment","year":2024,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"Virology and Viral Diseases","field":"Medicine","cited_by":19,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Alberta","funders":"","keywords":"ADME; Docking (animal); Azadirachta; In silico; Pharmacology; Chemistry; Phytochemical; Drug; Biology; Computational biology; Biochemistry; Traditional medicine; Medicine; Veterinary medicine","authors":[{"name":"Otun Saha","is_ca":false},{"name":"Noimul Hasan Siddiquee","is_ca":false},{"name":"Rahima Akter","is_ca":false},{"name":"Nikkon Sarker","is_ca":false},{"name":"Uditi Paul Bristi","is_ca":false},{"name":"Khandokar Fahmida Sultana","is_ca":false},{"name":"SM Lutfor Rahman Remon","is_ca":false},{"name":"Afroza Sultana","is_ca":false},{"name":"Tushar Ahmed Shishir","is_ca":false},{"name":"Md. Mizanur Rahaman","is_ca":false},{"name":"Firoz Ahmed","is_ca":false},{"name":"Foysal Hossen","is_ca":false},{"name":"Mohammad Ruhul Amin","is_ca":false},{"name":"Mir Salma Akter","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.034576176879696,"gpt":0.343821857279817,"spread":0.309245680400121,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001795688,0.0003383708,0.0005890554,0.0002251718,0.0002379789,0.00006322762,0.00007331343,0.0001999782,0.00000112645],"category_scores_gemma":[0.00005386585,0.0002338192,0.0001015141,0.0001438856,0.0004596988,0.0004811798,0.0001184342,0.000155541,0.000002030733],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006729353,"about_ca_system_score_gemma":0.0001888296,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001707595,"about_ca_topic_score_gemma":0.00001161078,"domain_scores_codex":[0.998721,0.00004108034,0.0005773936,0.0002229137,0.00009302887,0.000344601],"domain_scores_gemma":[0.9993811,0.0001278125,0.0002265868,0.0001145529,0.0000784404,0.00007153222],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001830174,0.0006885904,0.01229107,0.01728209,0.008256917,0.0001803744,0.0296549,0.00002830494,0.3434982,0.05700233,0.002840176,0.5264468],"study_design_scores_gemma":[0.01270569,0.009111513,0.002164046,0.003197958,0.002777352,0.0001548854,0.02060867,0.4686964,0.4332204,0.01150918,0.0329235,0.002930345],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9826072,0.01147384,0.00383906,0.0003450621,0.0001973593,0.0006962641,0.0002591007,0.00007686247,0.000505206],"genre_scores_gemma":[0.9884112,0.007548548,0.003220719,0.0003760352,0.00004691515,0.00004276621,0.0003190428,0.00001760645,0.00001715476],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5235165,"threshold_uncertainty_score":0.9534871,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4225835073","doi":"10.1177/11779322221085077","title":"Molnupiravir Does Not Induce Mutagenesis in Host Lung Cells during SARS-CoV-2 Treatment","year":2022,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"Plant Virus Research Studies","field":"Agricultural and Biological Sciences","cited_by":19,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Alberta","funders":"","keywords":"Mutagenesis; Mutation; Host (biology); Biology; Virology; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Coronavirus disease 2019 (COVID-19); Genetics; Cell biology; Computational biology; Gene; Medicine; Pathology","authors":[{"name":"John Maringa Githaka","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.05590959123686111,"gpt":0.2752611054188153,"spread":0.2193515141819542,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001221391,0.0001713755,0.00024117,0.00005726972,0.0005477191,0.00003745392,0.0001833262,0.00007476491,0.0000289319],"category_scores_gemma":[0.00001108849,0.00005573997,0.00004837182,0.0002274662,0.00009630235,0.00009813666,0.0003309021,0.0001244821,0.00000990247],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008924681,"about_ca_system_score_gemma":0.00001124034,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005751847,"about_ca_topic_score_gemma":0.001068719,"domain_scores_codex":[0.9989971,0.00007456872,0.0002878557,0.0001916244,0.0001109214,0.0003379447],"domain_scores_gemma":[0.9996623,0.0001284822,0.00008948686,0.00005574052,0.00001840853,0.00004561773],"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":[0.00004431145,0.00006900533,0.002218754,0.00001198143,0.00002725724,0.00001443409,0.0007590202,0.000001254438,0.9936891,0.00006689126,0.00005872592,0.003039285],"study_design_scores_gemma":[0.0007099998,0.0008594574,0.07337108,0.00001480302,0.00001631877,0.00002385564,0.002008899,0.001117298,0.8893295,0.0001258229,0.03196883,0.000454129],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9980847,0.00029622,2.028509e-7,0.0003133793,0.0001115024,0.0002833153,0.0005499437,0.00002949303,0.0003312063],"genre_scores_gemma":[0.9984223,0.0009987098,0.00004761925,0.000222944,0.00004675645,0.00006975386,0.00008186276,7.95016e-7,0.0001092092],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1043596,"threshold_uncertainty_score":0.4212668,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1620090002","doi":"10.4137/bbi.s2578","title":"Predicting Consensus Structures for RNA Alignments via Pseudo-Energy Minimization","year":2009,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":16,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Western University","funders":"National Institute of Allergy and Infectious Diseases; American Heart Association; National Institutes of Health; Cancer Research Institute; National Science Foundation","keywords":"Multiple sequence alignment; Computer science; Sequence alignment; Sequence (biology); Energy minimization; Nucleic acid secondary structure; Heuristics; Protein secondary structure; Data mining; Set (abstract data type); Computational biology; Algorithm; Bioinformatics; RNA; Biology; Genetics","authors":[{"name":"Junilda Spirollari","is_ca":false},{"name":"Jason T.L. Wang","is_ca":false},{"name":"Kaizhong Zhang","is_ca":true},{"name":"Vivian Bellofatto","is_ca":false},{"name":"Yongkyu Park","is_ca":false},{"name":"Bruce A. Shapiro","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01487018981729811,"gpt":0.2437949654931788,"spread":0.2289247756758807,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00006948839,0.00016754,0.0001609158,0.00005312146,0.000171695,0.00002659795,0.0001032859,0.0002704664,0.000003810417],"category_scores_gemma":[0.00004926233,0.0001277977,0.00005320207,0.0000384153,0.00006174694,0.000005298108,0.00003393957,0.00002958053,8.022099e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005587005,"about_ca_system_score_gemma":0.00002472437,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000005616272,"about_ca_topic_score_gemma":0.000004591845,"domain_scores_codex":[0.9992262,0.00003142609,0.0003039838,0.0001817148,0.00004796937,0.0002087544],"domain_scores_gemma":[0.9995057,0.00002326125,0.0001646772,0.0001681109,0.00006525776,0.00007300703],"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":[0.0001770217,0.00003693229,0.0003087962,0.0000322987,0.0001007062,6.937768e-7,0.0001955962,0.00002237748,0.9045447,0.01513472,0.0009380133,0.07850818],"study_design_scores_gemma":[0.001612849,0.002237612,0.0007560779,0.000029848,0.00006673142,0.0000609055,0.0001587373,0.01617354,0.8940721,0.04241331,0.04183632,0.0005819796],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9135956,0.0009733468,0.08249307,0.0002742922,0.0004016387,0.0004866068,0.00006623059,0.00003735253,0.001671923],"genre_scores_gemma":[0.9793871,0.0002467774,0.0189733,0.0008385526,0.0001820319,0.00001665539,0.0002604435,0.000008582627,0.00008656711],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0779262,"threshold_uncertainty_score":0.521144,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3034782445","doi":"10.1177/1177932220921350","title":"Identifying Herbal Adverse Events From Spontaneous Reporting Systems Using Taxonomic Name Resolution Approach","year":2020,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"Complementary and Alternative Medicine Studies","field":"Medicine","cited_by":13,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":false,"ca_fund":false,"ca_venue":false,"about_ca":true},"ca_institutions":"","funders":"U.S. National Library of Medicine; National Institute of General Medical Sciences; National Institutes of Health","keywords":"Adverse Event Reporting System; Medicine; Pharmacovigilance; Traditional medicine; Adverse effect; Humulus lupulus; Hypericum perforatum; Milk Thistle; MedDRA; Pharmacology; Hop (telecommunications)","authors":[{"name":"Vivekanand Sharma","is_ca":false},{"name":"Luiz Fernando Fracassi Gelin","is_ca":false},{"name":"Indra Neil Sarkar","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.1840296287065401,"gpt":0.3327911922517634,"spread":0.1487615635452233,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000125429,0.0001580838,0.0004080331,0.00005710576,0.0001839484,0.000007864973,0.00005508216,0.0000378044,0.00001073284],"category_scores_gemma":[0.0001320963,0.0001125592,0.00005678173,0.0000692723,0.00008439532,0.00009679099,0.0001209352,0.0001400112,0.000006930918],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004470121,"about_ca_system_score_gemma":0.0000329392,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002229956,"about_ca_topic_score_gemma":0.000006903805,"domain_scores_codex":[0.9986229,0.00003504795,0.0008812535,0.000187232,0.00008930766,0.0001842428],"domain_scores_gemma":[0.9990299,0.000043754,0.0006537135,0.0001090163,0.00004664552,0.0001169224],"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":[0.002699476,0.000614067,0.8366972,0.004908389,0.005356743,0.002402543,0.06145618,0.000937247,0.05275532,0.008019024,0.001252954,0.02290082],"study_design_scores_gemma":[0.005431661,0.001523707,0.04290754,0.0008992045,0.0006977555,0.002265621,0.03217807,0.8931213,0.0004045613,0.0002704895,0.01955702,0.0007430861],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9851567,0.001115574,0.01176366,0.00008026768,0.0003491627,0.0003838333,0.00002514455,0.00003899798,0.001086694],"genre_scores_gemma":[0.9885395,0.0001163542,0.01048488,0.000214189,0.0004421355,0.000004902114,0.0001735389,0.000006468538,0.00001803792],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.892184,"threshold_uncertainty_score":0.4590033,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2001512779","doi":"10.4137/bbi.s13376","title":"Longitudinal Analysis of Whole Blood Transcriptomes to Explore Molecular Signatures Associated with Acute Renal Allograft Rejection","year":2014,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"Renal Transplantation Outcomes and Treatments","field":"Medicine","cited_by":10,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Prevention of Organ Failure; Ottawa Hospital; University of British Columbia; University of British Columbia Hospital","funders":"","keywords":"Transcriptome; Medicine; Gene expression; Immunology; Microarray analysis techniques; Transplantation; Gene expression profiling; Kidney transplantation; Phenotype; Gene signature; Bioinformatics; Gene; Biology; Internal medicine; Genetics","authors":[{"name":"Heesun Shin","is_ca":true},{"name":"Oliver P. Günther","is_ca":true},{"name":"Zsuzsanna Hollander","is_ca":true},{"name":"J. Wilson-McManus","is_ca":true},{"name":"Raymond T. Ng","is_ca":true},{"name":"Robert Balshaw","is_ca":true},{"name":"Paul Keown","is_ca":true},{"name":"Robert McMaster","is_ca":true},{"name":"Bruce M. McManus","is_ca":true},{"name":"Nicole M. Isbel","is_ca":false},{"name":"Greg Knoll","is_ca":true},{"name":"Scott J. Tebbutt","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.02648395705646558,"gpt":0.2839452773851155,"spread":0.2574613203286499,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00006132608,0.0001414227,0.0004078521,0.0003664992,0.00005491288,0.00001111418,0.00004058929,0.0001192035,0.000005526898],"category_scores_gemma":[0.00001157953,0.00008208777,0.0001081393,0.0004629379,0.00006709303,0.00005378736,0.000006933335,0.00007200937,0.000001094882],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008559625,"about_ca_system_score_gemma":0.00001608792,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001658683,"about_ca_topic_score_gemma":0.00003891576,"domain_scores_codex":[0.9993225,0.00002716725,0.0002804917,0.0001269759,0.0001060944,0.0001367821],"domain_scores_gemma":[0.9995286,0.00004338551,0.0001151914,0.000118829,0.00009664235,0.00009728994],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.002314162,0.001446301,0.5855103,0.0005038921,0.08588687,0.0002168861,0.01248322,0.0006824743,0.2974913,0.007791529,0.00009738405,0.005575688],"study_design_scores_gemma":[0.008080802,0.008217376,0.8987153,0.0005132409,0.02588171,0.00008776616,0.0003224376,0.008133115,0.04840352,0.0002444473,0.0008881532,0.0005121456],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9914164,0.00009892506,0.007738967,0.0001175683,0.00002650586,0.0001835918,0.00004036824,0.00002356204,0.0003541229],"genre_scores_gemma":[0.9963326,0.00008659443,0.002695606,0.0002364788,0.000007534739,0.00000953594,0.0005814008,0.000005503948,0.00004477654],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.313205,"threshold_uncertainty_score":0.3347442,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2168136021","doi":"10.4137/bbi.s11601","title":"Association between a Multi-Locus Genetic Risk Score and Inflammatory Bowel Disease","year":2013,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"Inflammatory Bowel Disease","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Amgen (Canada); Mount Sinai Hospital; SickKids Foundation; University of Toronto; Public Health Ontario; Hospital for Sick Children","funders":"National Institute of Diabetes and Digestive and Kidney Diseases","keywords":"Inflammatory bowel disease; Single-nucleotide polymorphism; Missing heritability problem; Genetic association; Locus (genetics); Genome-wide association study; Heritability; Disease; Genetic predisposition; Genetic variation; Genetics; Biology; Medicine; Genotype; Bioinformatics; Gene; Internal medicine","authors":[{"name":"Pingzhao Hu","is_ca":true},{"name":"Aleixo M. Muise","is_ca":true},{"name":"Xiang Xing","is_ca":true},{"name":"John H. Brumell","is_ca":true},{"name":"Mark S. Silverberg","is_ca":true},{"name":"Wei Xu","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01081222594618184,"gpt":0.2223677645512768,"spread":0.2115555386050949,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001340068,0.0002468173,0.0001715211,0.0000837765,0.0002172419,0.00007704789,0.0001292925,0.0003088882,0.00001366249],"category_scores_gemma":[0.0001784898,0.0001994388,0.00006304575,0.00003939464,0.0001713741,0.00002569583,0.0001894098,0.0001283961,0.00005778514],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002254771,"about_ca_system_score_gemma":0.00007552403,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002056217,"about_ca_topic_score_gemma":0.00004334997,"domain_scores_codex":[0.998824,0.00009330719,0.0004210793,0.0002589284,0.00008415132,0.0003185126],"domain_scores_gemma":[0.9989173,0.00003046147,0.0002975018,0.0002854582,0.0001297616,0.0003394598],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00002869384,0.00002303826,0.9936019,0.00008750032,0.0001592396,0.000004395126,0.0001609899,0.000004314474,0.00197352,0.0000687896,0.0007106577,0.003177029],"study_design_scores_gemma":[0.0008658454,0.0000872367,0.991956,0.00001694085,0.0001024008,0.000002503085,0.00004980265,0.002318632,0.0002723681,0.0004859347,0.003531102,0.0003112597],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9976168,0.0009069976,0.0005264126,0.00005601171,0.00009969884,0.0004943544,0.00009635085,0.00002862801,0.0001747417],"genre_scores_gemma":[0.9962469,0.001081801,0.001719516,0.0002553175,0.0002044529,0.00006312738,0.0002054865,0.00001835362,0.0002050006],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002865769,"threshold_uncertainty_score":0.813288,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2012083066","doi":"10.4137/bbi.s9197","title":"White Blood Cell Differentials Enrich Whole Blood Expression Data in the Context of Acute Cardiac Allograft Rejection","year":2012,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"Gene expression and cancer classification","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"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; Prevention of Organ Failure","funders":"Genome British Columbia; International Society for Heart and Lung Transplantation","keywords":"Context (archaeology); Heart transplantation; Transplantation; Microarray; Whole blood; Microarray analysis techniques; DNA microarray; Biomarker; Medicine; Gene chip analysis; Significance analysis of microarrays; Biology; Pathology; Internal medicine; Gene expression; Gene; Genetics","authors":[{"name":"Casey P. Shannon","is_ca":true},{"name":"Zsuzsanna Hollander","is_ca":true},{"name":"J. Wilson-McManus","is_ca":true},{"name":"Robert Balshaw","is_ca":true},{"name":"Raymond T. Ng","is_ca":true},{"name":"Robert McMaster","is_ca":true},{"name":"Bruce M. McManus","is_ca":true},{"name":"Paul Keown","is_ca":true},{"name":"Scott J. Tebbutt","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.02416367498633476,"gpt":0.2682835292168356,"spread":0.2441198542305009,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002784613,0.0001448562,0.0001879822,0.00007611747,0.00008222391,0.00001898029,0.0003117684,0.0002285124,0.00000442807],"category_scores_gemma":[0.00001636845,0.00008753048,0.00004674269,0.0001044862,0.00009580234,0.000024146,0.0002158506,0.00009322106,0.000002242449],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000002455356,"about_ca_system_score_gemma":0.00002538072,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009307934,"about_ca_topic_score_gemma":0.000007955195,"domain_scores_codex":[0.9990444,0.0001347808,0.0003565057,0.0001809196,0.00008226831,0.0002010796],"domain_scores_gemma":[0.999054,0.00001953695,0.0002192731,0.0006078852,0.00004487013,0.00005444957],"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":[0.00003197301,0.0001866321,0.0242306,0.00003296297,0.00006827633,1.2989e-7,0.001169883,1.624029e-7,0.971513,0.000103579,0.001656259,0.0010065],"study_design_scores_gemma":[0.001713965,0.0005322878,0.03902882,0.00004360322,0.0003197889,0.00001658844,0.00294894,0.0001118731,0.8635432,0.0000615453,0.09132015,0.0003592432],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9951096,0.002809309,0.0004562337,0.0000931455,0.0002787191,0.0002548097,0.0001212415,0.000006285375,0.0008706224],"genre_scores_gemma":[0.9957929,0.002079828,0.0005611753,0.0001743462,0.0001349293,0.00002292877,0.001138295,0.000006638426,0.00008898621],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1079699,"threshold_uncertainty_score":0.356939,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2059084454","doi":"10.4137/bbi.s11184","title":"Knowledge Discovery in Variant Databases Using Inductive Logic Programming","year":2013,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"","funders":"Institute of Genetics; Agence Nationale de la Recherche","keywords":"Inductive logic programming; Genetic programming; Computer science; Knowledge extraction; Missense mutation; Knowledge base; Computational biology; Database; Artificial intelligence; Mutation; Biology; Genetics; Gene","authors":[{"name":"Hoan Nguyen","is_ca":false},{"name":"Tien-Dao Luu","is_ca":false},{"name":"Olivier Poch","is_ca":false},{"name":"Julie Thompson","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.04595171220111181,"gpt":0.292339461767836,"spread":0.2463877495667242,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00006467622,0.000165894,0.0001658626,0.00009643003,0.00009259093,0.00005964292,0.0001085413,0.0001300764,0.000004573417],"category_scores_gemma":[0.00003722264,0.0001173238,0.00004104518,0.00009018704,0.000151837,0.00003229365,0.0002164976,0.00007270677,0.000009104058],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001249724,"about_ca_system_score_gemma":0.00008106536,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000157611,"about_ca_topic_score_gemma":0.00008801983,"domain_scores_codex":[0.9992085,0.00003521144,0.0002776984,0.0002051066,0.00002696195,0.0002465462],"domain_scores_gemma":[0.999566,0.00001476517,0.00009435947,0.0001919305,0.000056418,0.00007655479],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.000414228,0.002913563,0.07232564,0.001046109,0.00104999,0.000109489,0.007365654,0.0001771264,0.6401104,0.1169604,0.002249335,0.155278],"study_design_scores_gemma":[0.0185483,0.007870031,0.1863461,0.001183217,0.0006648285,0.002144855,0.02941486,0.1119657,0.06613628,0.04248382,0.5218142,0.01142782],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9934168,0.001682827,0.003786014,0.00002630494,0.0001457666,0.0003244667,0.00003167807,0.000007377939,0.0005787516],"genre_scores_gemma":[0.9911247,0.0003617199,0.007916109,0.0001594272,0.00009946132,0.00002543803,0.0002650762,0.000008777872,0.00003928081],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5739742,"threshold_uncertainty_score":0.4784327,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4403417479","doi":"10.1177/11779322241287485","title":"Intrinsically Disordered Compositional Bias in Proteins: Sequence Traits, Region Clustering, and Generation of Hypothetical Functional Associations","year":2024,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"McGill University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Intrinsically disordered proteins; Computational biology; Saccharomyces cerevisiae; Proteome; Chromatin; Biology; Genetics; Yeast; DNA; Biophysics","authors":[{"name":"Paul M. Harrison","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.08845480262163416,"gpt":0.2757028015146276,"spread":0.1872479988929935,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001312277,0.0001045274,0.0001294042,0.00008605366,0.00006175073,0.00003057497,0.00004351111,0.0001893935,0.000003876317],"category_scores_gemma":[0.00005277215,0.00008180211,0.00003192897,0.00006716089,0.0001238952,0.00001370447,0.00005081321,0.00006483194,0.000001311168],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000009963604,"about_ca_system_score_gemma":0.00005510187,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000007487476,"about_ca_topic_score_gemma":0.00005012351,"domain_scores_codex":[0.9993314,0.00005522142,0.0002944825,0.0001563893,0.00005682929,0.0001056932],"domain_scores_gemma":[0.9997542,0.00003327373,0.0000654433,0.00006764491,0.00004203265,0.00003742217],"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":[0.00005060369,0.00005840623,0.0005545146,0.00009772403,0.00005883004,0.000002069616,0.0003283732,0.00001920665,0.9354339,0.03795958,0.0001276972,0.02530913],"study_design_scores_gemma":[0.005168395,0.006108164,0.06003692,0.0009067347,0.0002073765,0.0008018404,0.0006685414,0.2274139,0.5943574,0.05487939,0.04701994,0.002431401],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9585591,0.001230978,0.03904771,0.0004098408,0.0001073749,0.0002904627,0.00005163941,0.0000122008,0.0002907016],"genre_scores_gemma":[0.9938493,0.0005258006,0.005135241,0.00009893859,0.00009125002,0.00002795958,0.0002355304,0.000005970192,0.00002996672],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3410764,"threshold_uncertainty_score":0.3335793,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2133353084","doi":"10.4137/bbi.s550","title":"Searching for Factors that Distinguish Disease-Prone and Disease-Resistant Prions via Sequence Analysis","year":2008,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"Prion Diseases and Protein Misfolding","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Alberta","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"In silico; Disease; Mutation; Biology; Genetics; Point mutation; Computational biology; Sequence (biology); Gene; Medicine","authors":[{"name":"Kanaka Durga Kedarisetti","is_ca":true},{"name":"Scott Dick","is_ca":true},{"name":"Lukasz Kurgan","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.05980582397224181,"gpt":0.2926126063113849,"spread":0.2328067823391431,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00009738404,0.000211465,0.0002287787,0.0001117738,0.0005397997,0.00004258701,0.0001357389,0.0001015351,0.000004498308],"category_scores_gemma":[0.0002220508,0.0001584939,0.0001454731,0.0001205337,0.000297339,0.00001532555,0.0001577052,0.00006533565,7.097279e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001079681,"about_ca_system_score_gemma":0.0001018387,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003076482,"about_ca_topic_score_gemma":0.00002353668,"domain_scores_codex":[0.9990344,0.00004133188,0.0002563855,0.0002989051,0.00008021288,0.0002887767],"domain_scores_gemma":[0.9989978,0.00005491446,0.0001318806,0.0002700179,0.00006694945,0.0004784446],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001959288,0.0003796211,0.8094954,0.001284427,0.003268632,0.00005119376,0.002741939,0.0001431023,0.1217672,0.01241529,0.0008151957,0.04567863],"study_design_scores_gemma":[0.003263667,0.001339737,0.8099234,0.0001816677,0.002244306,0.00003488222,0.0007636084,0.06285267,0.007435113,0.01269041,0.09654645,0.002724165],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9806437,0.006012335,0.01232849,0.0001317289,0.00005922483,0.0004087829,0.0003399446,0.00002296881,0.00005286817],"genre_scores_gemma":[0.9940229,0.002499083,0.002215226,0.0001849026,0.00006429766,0.00003633856,0.0009223009,0.00001145648,0.00004346316],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1143321,"threshold_uncertainty_score":0.6463193,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1633669323","doi":"10.4137/bbi.s706","title":"Methodology for Constructing Problem Definitions in Bioinformatics","year":2008,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"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":"Canadian Institutes of Health Research","keywords":"Computer science; Data science; Systems biology; Modelling biological systems; Computational model; Management science; Bioinformatics; Artificial intelligence; Biology","authors":[{"name":"Amy M. Hauth","is_ca":true},{"name":"Gertraud Burger","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.1268368712727283,"gpt":0.2927190043268492,"spread":0.1658821330541209,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002041606,0.0001846182,0.000273488,0.0001223359,0.0002176595,0.00001100407,0.0001162953,0.0002314275,0.000001606929],"category_scores_gemma":[0.0001117099,0.0001508228,0.0000661228,0.00008809582,0.0003400684,0.0000034011,0.0001263967,0.00007830255,0.000002813156],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008170728,"about_ca_system_score_gemma":0.00007602114,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001118941,"about_ca_topic_score_gemma":0.00005087966,"domain_scores_codex":[0.9989561,0.00004037257,0.0005020325,0.0001723927,0.00003200872,0.0002970869],"domain_scores_gemma":[0.9994091,0.0001113782,0.0001584677,0.000170256,0.00008774256,0.00006307997],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0006806646,0.0004922661,0.1637867,0.001150432,0.001215008,0.00001236671,0.02336471,0.0002554442,0.4837641,0.2501904,0.004492952,0.07059493],"study_design_scores_gemma":[0.0248639,0.0105569,0.04566967,0.000287234,0.0003891126,0.003707337,0.02200286,0.02365481,0.1356918,0.1502034,0.5765681,0.006404935],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9844249,0.001280475,0.009191968,0.0001017706,0.000188096,0.0004830709,0.00008033218,0.000008035782,0.004241352],"genre_scores_gemma":[0.6704975,0.002846929,0.3259231,0.0003955639,0.0000851133,0.00007218869,0.0001400428,0.00001140442,0.00002823165],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5720751,"threshold_uncertainty_score":0.6150374,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4408144000","doi":"10.1177/11779322251321071","title":"Gene Set Enrichment Analysis in Zebrafish Embryos Is Susceptible to False-Positive Results in the Absence of Differentially Expressed Genes","year":2025,"lang":"en","type":"article","venue":"Bioinformatics and Biology Insights","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Health Canada; University of Ottawa; Environment and Climate Change Canada; Carleton University","funders":"","keywords":"Biology; False positive paradox; Zebrafish; Gene; Computational biology; Sample size determination; False discovery rate; Gene expression; Gene expression profiling; Genetics; Bioinformatics; Statistics; Mathematics","authors":[{"name":"John D. H. Stead","is_ca":true},{"name":"Hyojin Lee","is_ca":true},{"name":"Andrew Williams","is_ca":true},{"name":"Sergio A. Cortés-Ramírez","is_ca":false},{"name":"Ella Atlas","is_ca":true},{"name":"Jan A. Mennigen","is_ca":true},{"name":"Jason M. O’Brien","is_ca":true},{"name":"Carole L. Yauk","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01212306264251705,"gpt":0.253986423598282,"spread":0.2418633609557649,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003331875,0.0001949548,0.0003352853,0.0003351339,0.00006559707,0.0000357945,0.0003253216,0.0002339735,0.00000274414],"category_scores_gemma":[0.00002721783,0.0001317484,0.00009169906,0.0005833067,0.0001064897,0.000008919744,0.000205516,0.0001047579,0.00000184006],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001354803,"about_ca_system_score_gemma":0.00005537091,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009822378,"about_ca_topic_score_gemma":0.000553345,"domain_scores_codex":[0.9986304,0.00007267542,0.0007304518,0.0002268703,0.00007814635,0.0002614308],"domain_scores_gemma":[0.9992387,0.00005756571,0.000183756,0.0003969502,0.0000755738,0.00004751363],"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":[0.001812517,0.0008463849,0.04546462,0.0005050099,0.002664842,0.0000119775,0.03608451,0.002386875,0.8518642,0.008676078,0.01142373,0.03825923],"study_design_scores_gemma":[0.01155257,0.003774837,0.2809247,0.000511987,0.000719983,0.00001897063,0.01015003,0.06307858,0.579653,0.006852405,0.04018006,0.002582949],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9921885,0.0007039199,0.004668205,0.0003824561,0.00009230128,0.0004275361,0.0001946528,0.000003970625,0.00133852],"genre_scores_gemma":[0.9958503,0.0007397557,0.001600708,0.001309776,0.00002743566,0.00002488456,0.0003723967,0.000003916829,0.00007080528],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2722113,"threshold_uncertainty_score":0.5372543,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null}]}