{"meta":{"page":1,"per_page":50,"max_per_page":100,"total":19,"total_is_capped":false,"direct_labels_cover":0,"predictions_cover":19,"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":"a3aab9766ab5","filters":{"venue":"Molecular Omics"}},"results":[{"id":"W2889710563","doi":"10.1039/c8mo00136g","title":"Single-platform ‘multi-omic’ profiling: unified mass spectrometry and computational workflows for integrative proteomics–metabolomics analysis","year":2018,"lang":"en","type":"review","venue":"Molecular Omics","topic":"Metabolomics and Mass Spectrometry Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":53,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Toronto; Toronto Public Health","funders":"Canadian Institutes of Health Research; University of Toronto; Boston University","keywords":"Workflow; Proteomics; Profiling (computer programming); Computer science; Metabolomics; Computational biology; Systems biology; Instrumentation (computer programming); Data science; Bioinformatics; Chemistry; Biology; Database","authors":[{"name":"Benjamin C. Blum","is_ca":false},{"name":"Fatemeh Mousavi","is_ca":true},{"name":"Andrew Emili","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.04032942762022122,"gpt":0.3120568441569527,"spread":0.2717274165367314,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.009243068,0.002249655,0.003141145,0.004716591,0.0007663936,0.005510615,0.004096463,0.001781095,0.001269166],"category_scores_gemma":[0.005053353,0.001448052,0.002233574,0.005323765,0.001691638,0.005651194,0.005634645,0.003620041,0.002344871],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001676749,"about_ca_system_score_gemma":0.003208209,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001807127,"about_ca_topic_score_gemma":0.001588496,"domain_scores_codex":[0.9957242,0.0009869704,0.0004785135,0.0008064219,0.001765936,0.0002380349],"domain_scores_gemma":[0.9973229,0.0006544761,0.0002966902,0.0006867464,0.0008139813,0.0002254089],"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":[0.0005728346,0.00023904,0.002869227,0.00725367,0.0009483689,0.000583473,0.0007977922,0.03451918,0.2008608,0.07181744,0.02071332,0.6588249],"study_design_scores_gemma":[0.000135284,0.000519191,0.005414872,0.002034441,0.000558544,0.001457666,0.0004910626,0.375767,0.142465,0.1257012,0.3445486,0.0009070989],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"review","genre_scores_codex":[0.003753306,0.02019957,0.9665994,0.001130993,0.0002251201,0.0002594724,0.0009787414,0.00494188,0.001911477],"genre_scores_gemma":[0.02197457,0.02391956,0.9478184,0.0005160716,0.0002886656,0.000454342,0.003572118,0.0008302912,0.0006259476],"genre_candidate":"review","genre_consensus":null,"teacher_disagreement_score":0.009243068,"threshold_uncertainty_score":0.0488826,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3112689085","doi":"10.1039/d0mo90019b","title":"Glycomics &amp; Glycoproteomics: From Analytics to Function","year":2020,"lang":"en","type":"editorial","venue":"Molecular Omics","topic":"Glycosylation and Glycoproteins Research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":28,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Discovery Centre","funders":"","keywords":"Glycoproteomics; Glycomics; Function (biology); Computer science; Analytics; Data science; Chemistry; Proteomics; Biology","authors":[{"name":"Morten Thaysen‐Andersen","is_ca":true},{"name":"Daniel Kolarich","is_ca":false},{"name":"Nicolle H. Packer","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01218982742853409,"gpt":0.2756124404677996,"spread":0.2634226130392656,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.009016209,0.003192049,0.002696785,0.003388594,0.00256664,0.008849965,0.002874364,0.01140369,0.02303776],"category_scores_gemma":[0.0197212,0.00118776,0.002139049,0.001603971,0.002627012,0.006440396,0.002135725,0.02090787,0.02388832],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.002857859,"about_ca_system_score_gemma":0.003262493,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001498286,"about_ca_topic_score_gemma":0.004750957,"domain_scores_codex":[0.9947742,0.0008508383,0.0004441704,0.000530074,0.003100935,0.0002998259],"domain_scores_gemma":[0.9800676,0.007458491,0.0009848449,0.0004620651,0.006833278,0.004193891],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00002785617,0.000006417107,0.00001189144,0.0001254921,0.000008573692,0.00003204792,0.000006137435,0.00001557557,0.00007324678,0.0004887992,0.9930537,0.0061503],"study_design_scores_gemma":[0.00003541265,0.00002905612,0.0001086533,0.0002312236,0.00001850389,0.0001177793,0.00001777551,0.0001108252,0.0001028457,0.001667827,0.9975457,0.00001444639],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"editorial","genre_gemma":"editorial","genre_scores_codex":[0.00001932962,0.008439602,0.0002461566,0.03056885,0.9585906,0.00001879809,0.00005353524,0.0000861639,0.001976885],"genre_scores_gemma":[0.0003141962,0.009862082,0.0002529127,0.0318459,0.937596,0.00002497549,0.00006043433,0.00009623471,0.01994724],"genre_candidate":"editorial","genre_consensus":"editorial","teacher_disagreement_score":0.02303776,"threshold_uncertainty_score":0.07706898,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3033815479","doi":"10.1039/d0mo00030b","title":"MetaboKit: a comprehensive data extraction tool for untargeted metabolomics","year":2020,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Metabolomics and Mass Spectrometry Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":25,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Sciex (Canada); Spinal Cord Injury BC","funders":"National Medical Research Council; Ministry of Education, India; Medical Research Council; SCIEX; Ministry of Education - Singapore; Agency for Science, Technology and Research","keywords":"Metabolomics; Identification (biology); Mass spectrometry; Computational biology; Data extraction; Chromatography; Extraction (chemistry); Chemistry; Computer science; Biology; MEDLINE; Biochemistry","authors":[{"name":"Pradeep Narayanaswamy","is_ca":false},{"name":"Guoshou Teo","is_ca":false},{"name":"Jin Rong Ow","is_ca":false},{"name":"Adam Lau","is_ca":true},{"name":"Philipp Kaldis","is_ca":false},{"name":"Stephen Tate","is_ca":true},{"name":"Hyungwon Choi","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.04457005209719302,"gpt":0.3026611938410162,"spread":0.2580911417438232,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.004810102,0.003211726,0.002049291,0.004436106,0.0006380037,0.002206966,0.002675107,0.0009301313,0.01700309],"category_scores_gemma":[0.006261651,0.001857558,0.002260724,0.002615078,0.0005739921,0.002555935,0.003572856,0.00241382,0.008881914],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006591936,"about_ca_system_score_gemma":0.001856765,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001213338,"about_ca_topic_score_gemma":0.001711795,"domain_scores_codex":[0.9979776,0.0002892053,0.000332369,0.0004648616,0.0007891945,0.0001467507],"domain_scores_gemma":[0.9973917,0.00108491,0.0004426605,0.0004347245,0.0004807257,0.0001652758],"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":[0.003842178,0.0004585476,0.01098569,0.00659404,0.002206879,0.001847277,0.001153874,0.01322133,0.2122124,0.01306544,0.1931009,0.5413114],"study_design_scores_gemma":[0.001098822,0.0009208092,0.01667544,0.0008267603,0.0006633573,0.002535471,0.0002580141,0.1883875,0.3376316,0.02741196,0.4226749,0.0009154776],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.004428864,0.0005745518,0.6768045,0.0001727501,0.0001198756,0.0004700611,0.02927161,0.2865077,0.001649986],"genre_scores_gemma":[0.03000518,0.0009461824,0.8508001,0.0006535408,0.0001015429,0.003257259,0.05971825,0.05073154,0.003786374],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.01700309,"threshold_uncertainty_score":0.05688101,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3026925244","doi":"10.1039/d0mo00015a","title":"Pan-transcriptomic analysis identified common differentially expressed genes of <i>Acinetobacter baumannii</i> in response to polymyxin treatments","year":2020,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":17,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Institute of Infection and Immunity","funders":"National Institute of Allergy and Infectious Diseases; National Health and Medical Research Council; Medical Research Council; National Institutes of Health","keywords":"Acinetobacter baumannii; Polymyxin; Transcriptome; Polymyxin B; Efflux; Microbiology; Biology; Gene; Colistin; Bacterial outer membrane; Antibiotics; Genetics; Bacteria; Gene expression; Pseudomonas aeruginosa","authors":[{"name":"Mengyao Li","is_ca":true},{"name":"Su Mon Aye","is_ca":true},{"name":"Maizbha Uddin Ahmed","is_ca":false},{"name":"Mei‐Ling Han","is_ca":true},{"name":"Chen Li","is_ca":false},{"name":"Jiangning Song","is_ca":false},{"name":"John D. Boyce","is_ca":true},{"name":"David Powell","is_ca":false},{"name":"Mohammad Abul Kalam Azad","is_ca":true},{"name":"Tony Velkov","is_ca":false},{"name":"Yan Zhu","is_ca":true},{"name":"Jian Li","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01029755843115755,"gpt":0.2474613728710941,"spread":0.2371638144399365,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001201763,0.0004831762,0.0007484982,0.0006521828,0.0003580096,0.0005461172,0.0001585963,0.0003892026,0.001450079],"category_scores_gemma":[0.0002193881,0.0001498844,0.0005767942,0.001156297,0.0002089008,0.0003074088,0.0003779835,0.0004797335,0.0004556631],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003055875,"about_ca_system_score_gemma":0.0003149126,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001739676,"about_ca_topic_score_gemma":0.001828031,"domain_scores_codex":[0.9997568,0.00001403471,0.00001463576,0.00009751993,0.00005438122,0.00006269457],"domain_scores_gemma":[0.9998509,0.00002614881,0.00004416248,0.000009981914,0.00004600162,0.00002278827],"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":[0.0003825688,0.00002747071,0.005457457,0.0002981322,0.00002460355,0.00008241178,0.00006803476,0.0001468238,0.9883834,0.00004319442,0.0003519185,0.004733971],"study_design_scores_gemma":[0.00003411527,0.001056256,0.6125653,0.0001292893,0.0002899362,0.001034157,0.001228457,0.004808772,0.361033,0.0004072833,0.01732598,0.00008739649],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9580839,0.003646442,0.002481526,0.0002550693,0.00009036814,0.00006916169,0.03327167,0.0002934598,0.001808396],"genre_scores_gemma":[0.9498751,0.002665966,0.006422678,0.0004791786,0.00005324495,0.0002414842,0.03705801,0.0001086239,0.003095655],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001739676,"threshold_uncertainty_score":0.004851043,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2793688464","doi":"10.1039/c7mo00142h","title":"Systems analysis of the genetic interaction network of yeast molecular chaperones","year":2018,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Regina; University of Toronto; Toronto Public Health","funders":"National Safety Academic Fund; Canadian Institutes of Health Research; University of Toronto","keywords":"Yeast; Computational biology; Biology; Genetics","authors":[{"name":"Kamran Rizzolo","is_ca":true},{"name":"Ashwani Kumar","is_ca":true},{"name":"Yoshito Kakihara","is_ca":true},{"name":"Sadhna Phanse","is_ca":true},{"name":"Zoran Minić","is_ca":true},{"name":"Jamie Snider","is_ca":true},{"name":"Igor Štagljar","is_ca":true},{"name":"Sandra Zilles","is_ca":true},{"name":"Mohan Babu","is_ca":true},{"name":"Walid A. Houry","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.005204173780401849,"gpt":0.2153310235194896,"spread":0.2101268497390877,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002685171,0.0003684786,0.000298363,0.001070781,0.0002806893,0.0004940329,0.0002882102,0.0002110599,0.0008191992],"category_scores_gemma":[0.0008980091,0.0001204154,0.000618256,0.0006256206,0.0002406461,0.0003152466,0.0003517733,0.0002456818,0.00009342864],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007998309,"about_ca_system_score_gemma":0.0005904017,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006001388,"about_ca_topic_score_gemma":0.004176368,"domain_scores_codex":[0.9998299,0.00006196224,0.000008156088,0.00004714221,0.00002955215,0.00002333148],"domain_scores_gemma":[0.9996464,0.0001935687,0.00005670377,0.00002616297,0.00005010852,0.00002702088],"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":[0.0001984004,0.0001446876,0.02447139,0.0002153789,0.000307857,0.0004136546,0.0001581349,0.8860384,0.03866959,0.02507725,0.0008293517,0.02347589],"study_design_scores_gemma":[0.000004647605,0.00002993038,0.00565846,0.000003374105,0.00003400191,0.00003236805,0.00003595796,0.9866462,0.001853188,0.005188892,0.0005068814,0.000006101453],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8799234,0.0004012111,0.1143082,0.0001952776,0.00001534,0.00006555331,0.001907397,0.0003945487,0.002789166],"genre_scores_gemma":[0.9819829,0.000189593,0.01620657,0.00001200365,0.000005140454,0.00005145926,0.001127693,0.00001761072,0.0004070267],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006001388,"threshold_uncertainty_score":0.01193291,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3216144308","doi":"10.1039/d1mo00354b","title":"Investigation of cattle plasma proteome in response to pain and inflammation using next generation proteomics technique, SWATH-MS","year":2021,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Meat and Animal Product Quality","field":"Agricultural and Biological Sciences","cited_by":13,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Saskatchewan","funders":"Meat and Livestock Australia","keywords":"Medicine; Pain assessment; Inflammation; Acute-phase protein; Bioinformatics; Proteomics; Internal medicine; Anesthesia; Pain management; Biology","authors":[{"name":"Priya D. Ghodasara","is_ca":true},{"name":"Nana Satake","is_ca":false},{"name":"Paweł Sadowski","is_ca":false},{"name":"Steven Kopp","is_ca":false},{"name":"Paul C. Mills","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.06256018597785265,"gpt":0.250036121860055,"spread":0.1874759358822024,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003685204,0.0003819757,0.0003378761,0.0005457951,0.000345877,0.0005019904,0.000196971,0.0004487002,0.0006464503],"category_scores_gemma":[0.0002543867,0.000148115,0.0002700872,0.0005831314,0.0002179426,0.0003343232,0.0001939909,0.0004421732,0.0002280766],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002376058,"about_ca_system_score_gemma":0.0002349502,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001131557,"about_ca_topic_score_gemma":0.00170949,"domain_scores_codex":[0.9998349,0.00002024704,0.000007339176,0.0000620406,0.00004753317,0.00002787541],"domain_scores_gemma":[0.9998825,0.00002190446,0.000037879,0.000006602225,0.00003441878,0.00001668665],"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":[0.000242059,0.00002493072,0.003985691,0.0001098128,0.00002778034,0.00006155419,0.00006491307,0.00007221646,0.9915845,0.00004402857,0.0000756744,0.003706814],"study_design_scores_gemma":[0.00005169251,0.001326074,0.3494246,0.00007424488,0.0003280567,0.001678163,0.000657764,0.00763349,0.6300721,0.0006497661,0.008036771,0.00006729789],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9792964,0.003823223,0.01352351,0.0001301004,0.00005343136,0.00004564063,0.002147801,0.00009305824,0.0008867988],"genre_scores_gemma":[0.9549013,0.005243609,0.03205331,0.0004627713,0.0000729028,0.0001661579,0.004531057,0.00004749036,0.002521528],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001131557,"threshold_uncertainty_score":0.002249897,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4407771499","doi":"10.1039/d4mo00222a","title":"Revealing the dynamics of fungal disease with proteomics","year":2025,"lang":"en","type":"review","venue":"Molecular Omics","topic":"Antifungal resistance and susceptibility","field":"Medicine","cited_by":12,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Guelph","funders":"Institute of Infection and Immunity; Canadian Institutes of Health Research; Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs","keywords":"Dynamics (music); Proteomics; Computational biology; Biology; Computer science; Psychology; Genetics","authors":[{"name":"Mariana Cavalcante e. Almeida Sá","is_ca":true},{"name":"Brianna Ball","is_ca":true},{"name":"Jennifer Geddes‐McAlister","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01578474683241027,"gpt":0.3098466002429805,"spread":0.2940618534105702,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007144528,0.0008295469,0.00114279,0.002701497,0.0002297018,0.001169782,0.0006174483,0.00111309,0.002151542],"category_scores_gemma":[0.0007666959,0.0002803232,0.0005389528,0.001863633,0.0004444126,0.001271197,0.0007546598,0.001613547,0.001503445],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006434467,"about_ca_system_score_gemma":0.0007378327,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000707841,"about_ca_topic_score_gemma":0.0008155836,"domain_scores_codex":[0.9997205,0.00004769951,0.00002737601,0.00004796344,0.0001298018,0.00002656144],"domain_scores_gemma":[0.9996122,0.0001548167,0.00004988609,0.0000165461,0.0001335997,0.00003296138],"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":[0.00007344724,0.00007091647,0.0005032475,0.01467576,0.0002164209,0.0002422385,0.00006298305,0.0004879331,0.007124823,0.006967636,0.03369126,0.9358833],"study_design_scores_gemma":[0.00001277735,0.0001150708,0.001662113,0.002612202,0.0001562168,0.001697267,0.00007968494,0.0004133423,0.002884109,0.004832076,0.9854956,0.00003969326],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.0002172125,0.9976549,0.0003892223,0.0003460724,0.0002741221,0.000004882381,0.00002530639,0.00001452954,0.001073699],"genre_scores_gemma":[0.001845303,0.9965985,0.000408458,0.0002545996,0.0002521268,0.00000656412,0.00004765779,0.000002265891,0.0005845007],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.002701497,"threshold_uncertainty_score":0.007197618,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4309158979","doi":"10.1039/d2mo00251e","title":"Early-stage responses to <i>Plasmodiophora brassicae</i> at the transcriptome and metabolome levels in clubroot resistant and susceptible oilseed <i>Brassica napus</i>","year":2022,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Plant Disease Resistance and Genetics","field":"Agricultural and Biological Sciences","cited_by":11,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Trent University; University of Alberta","funders":"","keywords":"Clubroot; Biology; Metabolome; Brassicaceae; Transcriptome; Brassica; Phenylpropanoid; Inoculation; Metabolomics; Silique; Obligate; Canola; Botany; Microbiology; Gene; Horticulture; Gene expression; Biochemistry; Arabidopsis thaliana; Biosynthesis","authors":[{"name":"Dinesh Adhikary","is_ca":true},{"name":"Anna Kisiała","is_ca":true},{"name":"Ananya Sarkar","is_ca":true},{"name":"Urmila Basu","is_ca":true},{"name":"Habibur Rahman","is_ca":true},{"name":"R. J. Neil Emery","is_ca":true},{"name":"Nat N. V. Kav","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.0137637355681481,"gpt":0.2137465535994468,"spread":0.1999828180312987,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00007380787,0.0003483068,0.0003230448,0.0003883292,0.000221512,0.0003149654,0.0001102299,0.0002428216,0.0007969869],"category_scores_gemma":[0.00008399364,0.0001553529,0.0003246308,0.0003363967,0.0001663227,0.0002609929,0.0001791395,0.0003691021,0.0002234504],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002644549,"about_ca_system_score_gemma":0.0001335333,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002919579,"about_ca_topic_score_gemma":0.003413379,"domain_scores_codex":[0.9999088,0.000006943806,0.000004561709,0.00003873794,0.00001947002,0.00002154891],"domain_scores_gemma":[0.9998962,0.00001506898,0.00003612305,0.000006970443,0.00001760314,0.00002799878],"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":[0.0000855242,0.000006127374,0.0009420749,0.00002905691,0.000005868736,0.00003416669,0.00002727081,0.00002094504,0.9984073,0.000009992258,0.00001905693,0.0004125859],"study_design_scores_gemma":[0.00002421433,0.0004631023,0.6244963,0.00002781713,0.00009612147,0.0005467815,0.0006649611,0.001835859,0.3683819,0.0001242135,0.003304986,0.00003363684],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9949162,0.0009997817,0.0007682625,0.00006823184,0.0000088613,0.00001433086,0.002634575,0.00005980633,0.0005299692],"genre_scores_gemma":[0.9901704,0.0006431769,0.001141086,0.0001117495,0.000007541554,0.00004027822,0.004794817,0.00003107592,0.003059856],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002919579,"threshold_uncertainty_score":0.005805135,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2913386002","doi":"10.1039/c8mo00234g","title":"Network-based approach to identify principal isoforms among four cancer types","year":2019,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Princess Margaret Cancer Centre; University Health Network","funders":"Natural Science Foundation of Shaanxi Province; China Scholarship Council","keywords":"Gene isoform; Biology; Cancer; Alternative splicing; Carcinogenesis; Gene; Computational biology; Cancer cell; Genetics; Bioinformatics; Cancer research","authors":[{"name":"Jun Ma","is_ca":true},{"name":"Jenny Wang","is_ca":true},{"name":"Laleh Soltan Ghoraie","is_ca":true},{"name":"Xin Men","is_ca":false},{"name":"Benjamin Haibe‐Kains","is_ca":true},{"name":"Penggao Dai","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.009741757063842331,"gpt":0.2408841110213312,"spread":0.2311423539574889,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001499474,0.0009563699,0.000739679,0.006825138,0.0006106566,0.001082467,0.0007936561,0.0005557601,0.001768714],"category_scores_gemma":[0.003105712,0.000367844,0.002385421,0.003779268,0.0002726689,0.0006663548,0.000835581,0.0006935357,0.0002819534],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00119575,"about_ca_system_score_gemma":0.001045476,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.007640348,"about_ca_topic_score_gemma":0.01045359,"domain_scores_codex":[0.9992099,0.000252887,0.00005881382,0.000288917,0.0001230007,0.00006641498],"domain_scores_gemma":[0.9987128,0.0007630157,0.0002137305,0.00008412667,0.0001551407,0.00007124433],"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":[0.001453119,0.0006891498,0.2522136,0.001510642,0.008665885,0.00119253,0.0006090586,0.44526,0.02709914,0.01597989,0.008739114,0.2365879],"study_design_scores_gemma":[0.00004164521,0.0001395976,0.03570348,0.00006704529,0.001109496,0.0003404545,0.0001638819,0.9322328,0.001942657,0.02259662,0.005627245,0.00003520516],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.2759127,0.004652898,0.6872179,0.001289144,0.0001517344,0.0006861827,0.02479774,0.002152947,0.003138652],"genre_scores_gemma":[0.7553152,0.00129646,0.219764,0.0002413701,0.00009858685,0.0007354785,0.02060909,0.0001297298,0.001810179],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.007640348,"threshold_uncertainty_score":0.01519179,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4391115192","doi":"10.1039/d3mo00210a","title":"Proteome- and metabolome-level changes during early stages of clubroot infection in <i>Brassica napus</i> canola","year":2024,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Plant Disease Resistance and Genetics","field":"Agricultural and Biological Sciences","cited_by":7,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Trent University; University of Alberta","funders":"Canada Foundation for Innovation","keywords":"Clubroot; Metabolome; Canola; Brassica; Proteome; Biology; Metabolite; Sphingolipid; Rapeseed; Biochemistry; Botany","authors":[{"name":"Dinesh Adhikary","is_ca":true},{"name":"Devang Mehta","is_ca":true},{"name":"Anna Kisiała","is_ca":true},{"name":"Urmila Basu","is_ca":true},{"name":"R. Glen Uhrig","is_ca":true},{"name":"R. J. Neil Emery","is_ca":true},{"name":"Habibur Rahman","is_ca":true},{"name":"Nat N. V. Kav","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01178679419843304,"gpt":0.2074484675023878,"spread":0.1956616733039548,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0000955227,0.0004178283,0.0003446415,0.0005148894,0.0002367269,0.0002895968,0.0001751293,0.0002338547,0.0007631323],"category_scores_gemma":[0.0001008732,0.0001455233,0.0002553422,0.0003283785,0.0001452245,0.0002524827,0.0001893121,0.0003812345,0.0002196692],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002996678,"about_ca_system_score_gemma":0.0001310184,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003798401,"about_ca_topic_score_gemma":0.00451347,"domain_scores_codex":[0.9999272,0.000006100536,0.000003526425,0.00002578263,0.00001859912,0.00001876463],"domain_scores_gemma":[0.9998735,0.00001791121,0.00003766962,0.000008732722,0.00002390049,0.00003819279],"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":[0.00008619903,0.000006145905,0.0003905486,0.00002009049,0.000004328397,0.00002513612,0.00001529174,0.000009232697,0.9991782,0.000004123023,0.00001175577,0.0002488962],"study_design_scores_gemma":[0.00002150617,0.0004541193,0.4311803,0.00001645222,0.00007870711,0.0004700538,0.0003862249,0.001107343,0.5634985,0.00006672986,0.002687075,0.00003301462],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9961669,0.001063068,0.0005178333,0.00005065901,0.000008947229,0.00001383779,0.001659013,0.00005614495,0.00046364],"genre_scores_gemma":[0.9906527,0.0007509156,0.001343022,0.00009685441,0.000009453849,0.0000380883,0.00462166,0.0000350653,0.002452328],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003798401,"threshold_uncertainty_score":0.007552564,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4391974076","doi":"10.1039/d3mo00152k","title":"Genome-scale metabolic models in translational medicine: the current status and potential of machine learning in improving the effectiveness of the models","year":2024,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Microbial Metabolic Engineering and Bioproduction","field":"Biochemistry, Genetics and Molecular Biology","cited_by":7,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Concordia University","funders":"Marmara Üniversitesi; Yükseköğretim Kurulu; Türkiye Bilimsel ve Teknolojik Araştırma Kurumu","keywords":"Translational medicine; Computational biology; Scale (ratio); Current (fluid); Biology; Artificial intelligence; Machine learning; Computer science; Data science; Bioinformatics; Engineering; Genetics; Geography; Cartography","authors":[{"name":"Beste Turanlı","is_ca":false},{"name":"Gizem Gülfidan","is_ca":false},{"name":"Ozge Onluturk Aydogan","is_ca":false},{"name":"Ceyda Kula","is_ca":false},{"name":"Gurudeeban Selvaraj","is_ca":true},{"name":"Kazım Yalçın Arğa","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.004541521177219274,"gpt":0.210376656495652,"spread":0.2058351353184327,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.008111308,0.001550236,0.002615049,0.001737064,0.0004247548,0.003997485,0.002903123,0.001990155,0.00248871],"category_scores_gemma":[0.01634625,0.0009143889,0.002036939,0.001597772,0.002269614,0.004361026,0.002309882,0.004218732,0.001050974],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00192787,"about_ca_system_score_gemma":0.00256339,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002921123,"about_ca_topic_score_gemma":0.002458575,"domain_scores_codex":[0.9977703,0.001463133,0.0001315085,0.0003076559,0.0002742755,0.00005312253],"domain_scores_gemma":[0.9877243,0.01005705,0.0005351995,0.000906215,0.0005119154,0.0002653131],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.0003562549,0.0001194037,0.004112408,0.003029967,0.0006493038,0.0002376157,0.0002105395,0.6408222,0.004284952,0.1178861,0.005091326,0.2231999],"study_design_scores_gemma":[0.00004406516,0.0001162878,0.000570111,0.0004248607,0.0001198161,0.0001235473,0.00006075816,0.7326053,0.001485406,0.2413409,0.02303173,0.00007723697],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"review","genre_scores_codex":[0.009723475,0.04538212,0.9312287,0.009393114,0.0003634801,0.00005513338,0.0005748165,0.0009943758,0.002284772],"genre_scores_gemma":[0.2514709,0.09221756,0.6485862,0.002109496,0.001550094,0.0004012459,0.001798467,0.0007147417,0.001151269],"genre_candidate":"review","genre_consensus":null,"teacher_disagreement_score":0.008111308,"threshold_uncertainty_score":0.04289722,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4401715405","doi":"10.1039/d4mo00108g","title":"Sequencing, assembly, and genomic annotation of <i>Leucoagaricus gongylophorus</i> LEU18496, a dikarya mutualistic species","year":2024,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Mycorrhizal Fungi and Plant Interactions","field":"Agricultural and Biological Sciences","cited_by":4,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of New Brunswick","funders":"Consejo Nacional de Ciencia y Tecnología","keywords":"Annotation; Fungus; Biology; Computational biology; Evolutionary biology; Genetics; Botany","authors":[{"name":"Freddy Castillo-Alfonso","is_ca":false},{"name":"Cecilio Valadez‐Cano","is_ca":true},{"name":"Gabriela Cejas-Añón","is_ca":false},{"name":"José Utrilla","is_ca":false},{"name":"Juan‐Carlos Sigala","is_ca":false},{"name":"Sylvie Le Borgne","is_ca":false},{"name":"Alfonso Mauricio Sales-Cruz","is_ca":false},{"name":"Gabriel Vigueras-Ramírez","is_ca":false},{"name":"Roberto Olivares‐Hernández","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01240696215031706,"gpt":0.2037101894131449,"spread":0.1913032272628279,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001625874,0.0005214971,0.0003650603,0.0006427042,0.0003161317,0.0005478938,0.000252938,0.0002857783,0.0008187423],"category_scores_gemma":[0.000357653,0.0001735471,0.0004949496,0.0009236095,0.0001644644,0.0001571793,0.0003864692,0.000372948,0.0005798609],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002440613,"about_ca_system_score_gemma":0.0004395933,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002152932,"about_ca_topic_score_gemma":0.003154794,"domain_scores_codex":[0.9998204,0.00001812689,0.00001378784,0.00008133769,0.00004228284,0.00002395638],"domain_scores_gemma":[0.999791,0.00003458752,0.00007235863,0.00002793977,0.00003175388,0.00004249191],"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":[0.0003276849,0.00003368138,0.005205197,0.0002059268,0.00002966209,0.0002613761,0.0001717582,0.0003973704,0.9851892,0.00006058718,0.000262034,0.007855582],"study_design_scores_gemma":[0.0001520948,0.0007653276,0.6116578,0.0002179617,0.0003933633,0.002671824,0.001098214,0.0082601,0.3232249,0.0004616548,0.05101075,0.00008593273],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9595947,0.0007102801,0.005826189,0.00008811228,0.0000252251,0.0001106351,0.03187454,0.0003708056,0.001399531],"genre_scores_gemma":[0.8627966,0.0007350925,0.02898105,0.0001363012,0.0000304894,0.0001765978,0.1036314,0.0003038165,0.003208833],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002152932,"threshold_uncertainty_score":0.004280806,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3010631477","doi":"10.1039/c9mo00168a","title":"Mass spectrometric analysis of core fucosylation and sequence variation in a human–camelid monoclonal antibody","year":2020,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Glycosylation and Glycoproteins Research","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":"University of Winnipeg; University of Manitoba","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Fucosylation; Monoclonal antibody; Fucose; Chemistry; Glycan; Molecular biology; Antibody; Biochemistry; Biology; Immunology; Glycoprotein","authors":[{"name":"Lynda J. Donald","is_ca":true},{"name":"Maureen Spearman","is_ca":true},{"name":"Neha Mishra","is_ca":true},{"name":"Emy Komatsu","is_ca":true},{"name":"Michael Butler","is_ca":true},{"name":"Hélène Perreault","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.02958217308922314,"gpt":0.3211590984025713,"spread":0.2915769253133482,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003277027,0.0002892554,0.000239728,0.0004925141,0.0001821351,0.0002522428,0.0002294229,0.0004063027,0.0005187209],"category_scores_gemma":[0.0003700017,0.00009262758,0.0002633591,0.0002680843,0.0001512463,0.0001592924,0.0001698619,0.0003181833,0.0002184078],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003480331,"about_ca_system_score_gemma":0.00009907797,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002772305,"about_ca_topic_score_gemma":0.0002870878,"domain_scores_codex":[0.9998114,0.00002262992,0.00001527032,0.0000540358,0.00006963079,0.00002710576],"domain_scores_gemma":[0.9998129,0.00002644656,0.00005214795,0.00001608363,0.00005398448,0.00003841762],"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":[0.00005232796,0.00000804206,0.0004944458,0.0000115918,0.000007201414,0.00004675356,0.00001301288,0.00001511336,0.9984126,0.0000187739,0.0000273535,0.0008926674],"study_design_scores_gemma":[0.00001345986,0.0002966038,0.02283115,0.000006088034,0.0000455799,0.001249099,0.0000282497,0.001200836,0.9719051,0.00005071739,0.002364331,0.00000892318],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9893593,0.001159415,0.00759781,0.0001005218,0.00003939904,0.00003321139,0.0006716358,0.00009599052,0.0009428352],"genre_scores_gemma":[0.9853374,0.000587028,0.01057741,0.0002673471,0.00002962884,0.0000485425,0.001759431,0.00003795312,0.001355219],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0005187209,"threshold_uncertainty_score":0.002525151,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3124757045","doi":"10.1039/d0mo00138d","title":"Genome scale metabolic model driven strategy to delineate host response to <i>Mycobacterium tuberculosis</i> infection","year":2021,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Microbial Metabolic Engineering and Bioproduction","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Toronto Metropolitan University","funders":"Department of Biotechnology, Ministry of Science and Technology, India; Jadavpur University","keywords":"Flux balance analysis; Mycobacterium tuberculosis; Virulence; Context (archaeology); Tuberculosis; Biology; Proteomics; Computational biology; Host (biology); Flux (metallurgy); Genome; Gene; Genetics; Medicine; Chemistry","authors":[{"name":"Ankur Gupta","is_ca":false},{"name":"Ajay Kumar","is_ca":false},{"name":"Rajat Anand","is_ca":false},{"name":"Nandadulal Bairagi","is_ca":true},{"name":"Samrat Chatterjee","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.006049289782309707,"gpt":0.2239876307454565,"spread":0.2179383409631468,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001874686,0.0005673622,0.0003914551,0.0003287184,0.0001388824,0.0004327997,0.0003085672,0.0003684133,0.0006632003],"category_scores_gemma":[0.0003229487,0.0001728149,0.0006569141,0.0002470642,0.0001495101,0.0002347358,0.0002752267,0.0003081376,0.0001381551],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004110005,"about_ca_system_score_gemma":0.0003587271,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002063747,"about_ca_topic_score_gemma":0.00151124,"domain_scores_codex":[0.9999444,0.00001581046,0.000002440984,0.00001892646,0.00001116719,0.000007169375],"domain_scores_gemma":[0.9999278,0.00002672786,0.00001656125,0.00001054624,0.00001136337,0.000007110412],"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":[0.0001678009,0.00008974698,0.002858236,0.0001327575,0.00008895919,0.00009690248,0.00003953281,0.8241313,0.1532555,0.003592422,0.0001795946,0.01536719],"study_design_scores_gemma":[0.000003793977,0.00005688809,0.0008290504,0.000002255381,0.0000145352,0.00001496009,0.000007577733,0.9895154,0.008255592,0.0009395787,0.0003539644,0.000006504577],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.4844033,0.0002560681,0.5108244,0.0001403213,0.00003229056,0.00007418662,0.0008860709,0.001010988,0.002372407],"genre_scores_gemma":[0.8649974,0.0002748691,0.1323524,0.0000298829,0.000009692475,0.0002252083,0.0009992037,0.0001000764,0.001011294],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.002063747,"threshold_uncertainty_score":0.004103482,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4410244304","doi":"10.1039/d4mo00245h","title":"A multi-omics machine learning classifier for outgrowth of cow's milk allergy in children","year":2025,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Microbial Inactivation Methods","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"","funders":"Wageningen University and Research; Danone Nutricia Research; Radboud Universitair Medisch Centrum; Prince of Songkla University; Newcastle upon Tyne Hospitals NHS Foundation Trust; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; Universiteit Utrecht; Precursory Research for Embryonic Science and Technology; York University; Mahidol University; Danone; Chulalongkorn University; Texas Children's Hospital","keywords":"Omics; Classifier (UML); Cow's milk allergy; Allergy; Machine learning; Artificial intelligence; Computer science; Food allergy; Medicine; Biology; Bioinformatics; Immunology","authors":[{"name":"Diana M. Hendrickx","is_ca":false},{"name":"Mariyana V. Savova","is_ca":false},{"name":"Pingping Zhu","is_ca":false},{"name":"Sjef Boeren","is_ca":false},{"name":"Kelly Klomp","is_ca":false},{"name":"Sumanth Mutte","is_ca":false},{"name":"Presto Study Team","is_ca":false},{"name":"Harm Wopereis","is_ca":false},{"name":"Renate G. van der Molen","is_ca":false},{"name":"Amy C. Harms","is_ca":false},{"name":"Clara Belzer","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.0120414734768786,"gpt":0.2893750955830766,"spread":0.277333622106198,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001906356,0.0008964972,0.0008911339,0.001965694,0.0005194727,0.001158601,0.000596089,0.001219318,0.001107224],"category_scores_gemma":[0.003402711,0.0001611515,0.001127564,0.0009230258,0.0002098723,0.0004986699,0.0008006907,0.00122231,0.0006415252],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006149389,"about_ca_system_score_gemma":0.0009384804,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004741004,"about_ca_topic_score_gemma":0.003629556,"domain_scores_codex":[0.9993105,0.0001525034,0.00007451684,0.0001801194,0.0001499618,0.0001323547],"domain_scores_gemma":[0.9988517,0.000543451,0.0001874751,0.00006910704,0.000235957,0.0001123292],"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":[0.001316739,0.0006527313,0.6678712,0.0001802813,0.0005164829,0.0005890151,0.0001773973,0.02385012,0.01493268,0.0004498598,0.005152483,0.2843111],"study_design_scores_gemma":[0.00006185148,0.0007655296,0.2075427,0.0001471997,0.0003972754,0.0007734323,0.0004956478,0.7707253,0.0144275,0.001605701,0.002989217,0.00006874821],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9158907,0.002153601,0.07340462,0.001007463,0.0001740722,0.0001799133,0.00486791,0.0007929393,0.00152892],"genre_scores_gemma":[0.9496077,0.0003588432,0.04376866,0.0001904919,0.00006656786,0.0001533236,0.004836025,0.00003427577,0.0009841499],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004741004,"threshold_uncertainty_score":0.01008189,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4415659242","doi":"10.1039/d5mo00152h","title":"Global spinal cord peptidome profiling in response to osteoarthritis in rats","year":2025,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Osteoarthritis Treatment and Mechanisms","field":"Medicine","cited_by":2,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true},"ca_institutions":"Cegep de Saint Hyacinthe; Université de Montréal","funders":"National Institute of Diabetes and Digestive and Kidney Diseases; National Institute on Drug Abuse; National Institute on Aging; Natural Sciences and Engineering Research Council of Canada; National Center for Research Resources; Office of the Vice Chancellor for Research and Graduate Education, University of Wisconsin-Madison; Canada Foundation for Innovation; University of Wisconsin-Madison; Wisconsin Alumni Research Foundation; National Institutes of Health; National Science Foundation","keywords":"Osteoarthritis; Spinal cord; Neuropeptide; Disease; Central nervous system; Prohormone; Rheumatoid arthritis; Pathological; Chronic pain","authors":[{"name":"Gaoyuan Lu","is_ca":false},{"name":"Marilyn Frézier","is_ca":true},{"name":"Colombe Otis","is_ca":true},{"name":"Vu Ngoc Huong Tran","is_ca":false},{"name":"Bertrand Lussier","is_ca":true},{"name":"Guillaume St‐Jean","is_ca":true},{"name":"Hélène Beaudry","is_ca":true},{"name":"Éric Troncy","is_ca":true},{"name":"Lingjun Li","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.00974603304619575,"gpt":0.2948839225949606,"spread":0.2851378895487648,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001913284,0.0004209697,0.0003668285,0.000838525,0.000188337,0.0003291235,0.0001308232,0.0002894408,0.0009061805],"category_scores_gemma":[0.0001618809,0.0001258609,0.0003406977,0.0004070132,0.0003045677,0.0002369909,0.0002136187,0.0005643239,0.000286259],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002325872,"about_ca_system_score_gemma":0.0002872805,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009851082,"about_ca_topic_score_gemma":0.001954849,"domain_scores_codex":[0.9998524,0.00001130468,0.000007206622,0.00004170724,0.00004749993,0.0000398795],"domain_scores_gemma":[0.9997751,0.00001779156,0.00007628689,0.00001270727,0.00004996398,0.00006821899],"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":[0.0005287129,0.00002901563,0.000830103,0.00004469049,0.0000152392,0.00003396016,0.0000147584,0.00003521546,0.9967115,0.00001665398,0.00003983989,0.001700267],"study_design_scores_gemma":[0.00004144014,0.00250499,0.094859,0.00002855812,0.0001180532,0.0004518063,0.0002307509,0.001453624,0.8982087,0.0001460796,0.001920719,0.00003632643],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9869617,0.002540676,0.006083568,0.0001485977,0.00007303533,0.00008071971,0.002925771,0.0001639271,0.001021915],"genre_scores_gemma":[0.9789932,0.003295924,0.008107402,0.0003986529,0.00003444004,0.000252942,0.003492074,0.00006800515,0.005357427],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0009851082,"threshold_uncertainty_score":0.003031433,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4403033594","doi":"10.1039/d4mo00052h","title":"Comprehensive untargeted lipidomic profiling of third generation lentiviral vectors and packaging cells","year":2024,"lang":"en","type":"article","venue":"Molecular Omics","topic":"RNA Interference and Gene Delivery","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Ottawa; Ottawa Hospital; Carleton University","funders":"Natural Sciences and Engineering Research Council of Canada; Terry Fox Foundation; Government of Ontario; Canada Foundation for Innovation; Ontario Research Foundation; Carleton University","keywords":"Viral vector; Profiling (computer programming); Computational biology; Computer science; Biology; Recombinant DNA; Biochemistry; Gene","authors":[{"name":"Joshua Roberts","is_ca":true},{"name":"Elena Godbout","is_ca":true},{"name":"J. Ménard","is_ca":true},{"name":"Christopher N. Boddy","is_ca":true},{"name":"Jean‐Simon Diallo","is_ca":true},{"name":"Jeffrey C. Smith","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01227132995029583,"gpt":0.241541166947215,"spread":0.2292698369969191,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004698336,0.0004107524,0.0003187009,0.0005020291,0.000204512,0.0007681882,0.0002540101,0.0002922411,0.0004965215],"category_scores_gemma":[0.0003187468,0.0001547312,0.0003443047,0.0003994794,0.0002136849,0.0002791971,0.0004252931,0.0005531913,0.0004543062],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004105477,"about_ca_system_score_gemma":0.000275304,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007760234,"about_ca_topic_score_gemma":0.0008571252,"domain_scores_codex":[0.9996986,0.00002817537,0.00002630289,0.00006033977,0.0001453908,0.00004116778],"domain_scores_gemma":[0.9998438,0.00003015279,0.00003675915,0.00002406169,0.00004920762,0.00001594213],"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":[0.0000304853,0.000006768238,0.0002978009,0.00001681647,0.000003630531,0.00001489365,0.00001113535,0.00005876291,0.9978651,0.00003433643,0.0000244975,0.001635767],"study_design_scores_gemma":[0.000002191497,0.00006499519,0.003915717,0.000005280457,0.00001507426,0.00006846443,0.00001639593,0.001223509,0.9932129,0.00004806854,0.001421248,0.000006144815],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9205134,0.001802886,0.0688299,0.0001083443,0.0000683354,0.0002460716,0.005737847,0.000549766,0.002143583],"genre_scores_gemma":[0.9222552,0.002345296,0.05824787,0.000256925,0.00002054006,0.0004117784,0.01175095,0.0003371542,0.004374392],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0007760234,"threshold_uncertainty_score":0.002978683,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4414730605","doi":"10.1039/d5mo00151j","title":"Multi-omics data integration for topology-based pathway activation assessment and personalized drug ranking","year":2025,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Cancer-related molecular mechanisms research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Lethbridge","funders":"","keywords":"Data integration; DNA methylation; Gene; Ranking (information retrieval); Gene expression; Coding (social sciences); DNA; RNA; Genomics","authors":[{"name":"Nicolas Borisov","is_ca":false},{"name":"Yaroslav Ilnytsky","is_ca":true},{"name":"Boseon Byeon","is_ca":false},{"name":"Olga Kovalchuk","is_ca":true},{"name":"Igor Kovalchuk","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.02741876399503397,"gpt":0.3514515337609794,"spread":0.3240327697659455,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002258748,0.00166157,0.001493979,0.006235592,0.0005871839,0.00243439,0.0007505886,0.0005946616,0.003969597],"category_scores_gemma":[0.004167034,0.0003995468,0.002250599,0.00430616,0.0002890865,0.001339786,0.001735938,0.0009719247,0.0009846231],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009653005,"about_ca_system_score_gemma":0.002139636,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002750638,"about_ca_topic_score_gemma":0.003681345,"domain_scores_codex":[0.9990069,0.0003002202,0.0001078605,0.0002278314,0.0002874971,0.00006966625],"domain_scores_gemma":[0.9986287,0.000521555,0.0001931182,0.0002317534,0.0003238174,0.0001011235],"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":[0.002103934,0.0007388314,0.05785714,0.004369034,0.002798151,0.0009152675,0.0006107902,0.3437912,0.1048933,0.02900062,0.01981997,0.4331018],"study_design_scores_gemma":[0.00008457906,0.0003016955,0.01595751,0.0001553598,0.0005435068,0.0002765998,0.0002852524,0.8852635,0.03298825,0.03927545,0.02473952,0.0001288363],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.08339357,0.002180545,0.846075,0.0008617807,0.0001671572,0.0007000985,0.04637067,0.01610447,0.004146633],"genre_scores_gemma":[0.4666128,0.00158163,0.4883666,0.0002793506,0.0000883141,0.001007841,0.04037439,0.0006874503,0.001001565],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.006235592,"threshold_uncertainty_score":0.01327968,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4380683663","doi":"10.1039/d2mo00325b","title":"Protein network analysis links the NSL complex to Parkinson’s disease <i>via</i> mitochondrial and nuclear biology","year":2023,"lang":"en","type":"article","venue":"Molecular Omics","topic":"Parkinson's Disease Mechanisms and Treatments","field":"Medicine","cited_by":0,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"","funders":"Alzheimer’s Research UK; Alzheimer's Association; Aligning Science Across Parkinson’s; Masonic Charitable Foundation; Weston Brain Institute; Michael J. Fox Foundation for Parkinson's Research","keywords":"Interactome; Biology; Mitophagy; Computational biology; Genetics; Exposome; PINK1; Bioinformatics; Gene","authors":[{"name":"Katie Kelly","is_ca":false},{"name":"Patrick A. Lewis","is_ca":false},{"name":"Hélène Plun‐Favreau","is_ca":false},{"name":"Claudia Manzoni","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01509187336122223,"gpt":0.2606351952447123,"spread":0.2455433218834901,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002513497,0.000384457,0.0002523919,0.003051098,0.0005269789,0.0006244887,0.0002339053,0.0002866389,0.005251891],"category_scores_gemma":[0.000810214,0.0001205827,0.000737057,0.002232817,0.0001854466,0.0004370437,0.0006373388,0.0002724324,0.0007834701],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005620533,"about_ca_system_score_gemma":0.0004521518,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005598413,"about_ca_topic_score_gemma":0.009112043,"domain_scores_codex":[0.9997866,0.00003628453,0.00001722809,0.00007810708,0.00005133645,0.00003045218],"domain_scores_gemma":[0.9996151,0.0001335823,0.0001254775,0.00002146156,0.00005502527,0.00004929339],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001794619,0.0002583186,0.6527303,0.004329566,0.002862356,0.003409157,0.0008380302,0.03389906,0.1696189,0.007670275,0.02916313,0.09342626],"study_design_scores_gemma":[0.00005121293,0.0002176937,0.7716297,0.0001973965,0.0009790224,0.003032803,0.0004900832,0.1596742,0.0180398,0.008706124,0.03691407,0.00006785601],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9372656,0.00465017,0.0151491,0.0009729938,0.00006094019,0.00006620567,0.03456529,0.001313873,0.005955815],"genre_scores_gemma":[0.9528298,0.002027896,0.01062206,0.000112663,0.00003263146,0.00005183593,0.03212045,0.00008115973,0.0021216],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005598413,"threshold_uncertainty_score":0.0175693,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null}]}