{"meta":{"page":1,"per_page":50,"max_per_page":100,"total":6,"total_is_capped":false,"direct_labels_cover":0,"predictions_cover":6,"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":"d381c7fc5ff3","filters":{"venue":"Gene Regulation and Systems Biology"}},"results":[{"id":"W2153763768","doi":"10.4137/grsb.s361","title":"MicroRNA Expression in Alzheimer Blood Mononuclear Cells","year":2007,"lang":"en","type":"article","venue":"Gene Regulation and Systems Biology","topic":"MicroRNA in disease regulation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":245,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"McGill University; Jewish General Hospital","funders":"McGill University; Jewish General Hospital; University of Louisville","keywords":"microRNA; Gene; Microarray; Peripheral blood mononuclear cell; Gene expression; Disease; Biology; Microarray analysis techniques; Medicine; Downregulation and upregulation; Bioinformatics; Allele; Messenger RNA; Genetics; Pathology","authors":[{"name":"Hyman M. Schipper","is_ca":true},{"name":"Olivier Maës","is_ca":true},{"name":"Howard Chertkow","is_ca":true},{"name":"Eugenia Wang","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01397153377907953,"gpt":0.2508936016890427,"spread":0.2369220679099631,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004254787,0.0001390172,0.0001564217,0.0001082946,0.00005446829,0.00001583521,0.00007643169,0.0002951737,0.00001570839],"category_scores_gemma":[0.00001324455,0.0001313274,0.00004143222,0.00008066292,0.00006406011,0.00000462314,0.00006102415,0.00004822137,0.00001178463],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001095452,"about_ca_system_score_gemma":0.00002106277,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000026227,"about_ca_topic_score_gemma":0.00001805566,"domain_scores_codex":[0.9988834,0.0001173848,0.0003435956,0.0003598417,0.000056328,0.0002394278],"domain_scores_gemma":[0.9994786,0.00001351292,0.0001286206,0.0002428688,0.00005170196,0.00008474187],"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":[0.00006720047,0.00003079334,0.004155226,0.00001071198,0.0000301276,0.000001800773,0.00003343477,0.0001579581,0.9941666,0.0001039959,0.0002425911,0.0009995475],"study_design_scores_gemma":[0.0007330569,0.00008229816,0.03535699,0.00001871051,0.00002226332,0.00003635411,0.00004632373,0.0002555894,0.94704,0.00005341947,0.016169,0.0001860011],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9902514,0.005033752,0.003846097,0.0000217585,0.0002179887,0.0002920906,0.00001079472,0.00001445297,0.0003116861],"genre_scores_gemma":[0.9985553,0.0001104724,0.0007074039,0.00003963696,0.0002482178,0.000008575533,0.0001666934,0.00001861015,0.0001451155],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04712662,"threshold_uncertainty_score":0.5355376,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4242505789","doi":"10.1177/117762500700100010","title":"Computational Systems Biology in Cancer: Modeling Methods and Applications","year":2007,"lang":"en","type":"article","venue":"Gene Regulation and Systems Biology","topic":"Gene Regulatory Network Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":31,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Alberta; National Institute for Nanotechnology","funders":"","keywords":"Rotation formalisms in three dimensions; Systems biology; Computer science; Petri net; Cellular automaton; Modelling biological systems; Process (computing); Computational biology; Data science; Bioinformatics; Biology; Artificial intelligence; Distributed computing; Mathematics; Programming language","authors":[{"name":"Wayne Materi","is_ca":true},{"name":"David S. Wishart","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.02554654658986862,"gpt":0.3442053910913375,"spread":0.3186588445014689,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001144049,0.0001641591,0.000301735,0.0001894063,0.0001092852,0.00002180247,0.00008027277,0.0003199192,0.000003014834],"category_scores_gemma":[0.00001476662,0.0001570396,0.00004118569,0.0001906367,0.0001062526,0.000004096087,0.00006804258,0.00006380797,0.000001345066],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003314476,"about_ca_system_score_gemma":0.00004541119,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002735616,"about_ca_topic_score_gemma":0.00009969318,"domain_scores_codex":[0.9983827,0.0003121523,0.0004965721,0.0004893252,0.00005016692,0.0002690151],"domain_scores_gemma":[0.9993742,0.00004836835,0.0001521908,0.0002092182,0.0001206799,0.00009530868],"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":[0.00005215078,0.0000334073,0.07731047,0.000078109,0.0001836187,5.541879e-7,0.00006586649,0.5443655,0.3367242,0.01451602,0.00004429634,0.02662575],"study_design_scores_gemma":[0.0008993844,0.0001216631,0.01436835,0.00002545177,0.00005871839,0.00009487693,0.0002514613,0.952967,0.001961404,0.001642543,0.02715995,0.0004492149],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.4486726,0.01638659,0.5343549,0.00003299595,0.0001428648,0.0003036525,0.00001363342,0.00001217635,0.0000806004],"genre_scores_gemma":[0.9946766,0.0005809333,0.003731239,0.00003358136,0.0004219284,0.0001016127,0.0003304105,0.00001555619,0.000108131],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.5460041,"threshold_uncertainty_score":0.640389,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2042159401","doi":"10.4137/grsb.s4525","title":"Transcriptional Response of <i>E. coli</i> Upon FimH-mediated Fimbrial Adhesion","year":2010,"lang":"en","type":"article","venue":"Gene Regulation and Systems Biology","topic":"Bacterial Genetics and Biotechnology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":30,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"National Institute for Nanotechnology; University of Alberta","funders":"Genome Alberta; Genome Canada","keywords":"Biofilm; Adhesion; Escherichia coli; Gene; Cell biology; Cell adhesion; Biology; Bacteria; Microbiology; Chemistry; Genetics","authors":[{"name":"Prasanna Bhomkar","is_ca":true},{"name":"Wayne Materi","is_ca":true},{"name":"Valentyna Semenchenko","is_ca":true},{"name":"David S. Wishart","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.009676734189361753,"gpt":0.2278152033053702,"spread":0.2181384691160085,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004452487,0.0001283888,0.0001999812,0.00008007957,0.00006282587,0.00001101436,0.00009971907,0.0006444728,0.00003183711],"category_scores_gemma":[0.00008395068,0.0001133034,0.00005548965,0.00007184736,0.0001610474,0.000002350162,0.00004238991,0.00008921899,0.000005275851],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000004134099,"about_ca_system_score_gemma":0.00006654852,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002412245,"about_ca_topic_score_gemma":0.00003402011,"domain_scores_codex":[0.9989522,0.0001870775,0.0003347635,0.0002952993,0.00006378893,0.0001669016],"domain_scores_gemma":[0.9994182,0.00002936831,0.0001396781,0.0002368538,0.0001132569,0.00006266521],"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":[0.0008644364,0.0000248457,0.0006999692,0.00001238373,0.00002171502,2.948733e-7,0.00001298112,0.000006447326,0.9964729,0.00113626,0.0001649484,0.0005828007],"study_design_scores_gemma":[0.001020005,0.0006718151,0.03181366,0.000007165256,0.00001327529,0.00005205053,0.00001677874,0.0003359247,0.8242469,0.00007170715,0.1415793,0.0001713879],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9974679,0.0003745303,0.0004593089,0.0002337467,0.00105271,0.0002266369,0.0001195463,0.00001497096,0.00005062441],"genre_scores_gemma":[0.9983361,0.0001533936,0.0003973312,0.00004959197,0.000375752,0.00001534031,0.0004674674,0.000011704,0.0001933364],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.172226,"threshold_uncertainty_score":0.4970764,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2011256652","doi":"10.4137/grsb.s13946","title":"Tetracycline Derivative Minocycline Inhibits Autophagy and Inflammation in Concanavalin-A-Activated Human Hepatoma Cells","year":2014,"lang":"en","type":"article","venue":"Gene Regulation and Systems Biology","topic":"Autophagy in Disease and Therapy","field":"Medicine","cited_by":17,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Université du Québec à Montréal","funders":"","keywords":"Minocycline; Autophagy; Vacuole; Gene silencing; Concanavalin A; Signal transduction; Cell biology; Inflammation; STAT3; Biology; Chemistry; Cancer research; Molecular biology; Biochemistry; Immunology; Gene; Apoptosis; In vitro","authors":[{"name":"Michel Desjarlais","is_ca":true},{"name":"Jonathan Pratt","is_ca":true},{"name":"Mohamed Amine Lounis","is_ca":true},{"name":"Cathérine Mounier","is_ca":true},{"name":"Khadidja Haïdara","is_ca":true},{"name":"Borhane Annabi","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01849701418208709,"gpt":0.2900405716986565,"spread":0.2715435575165694,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003087392,0.0001543093,0.0003912323,0.0001783445,0.00007377141,0.00001447437,0.00002736701,0.0002083775,0.00003559417],"category_scores_gemma":[0.00004183485,0.0001304557,0.00002788314,0.0001276151,0.0001087886,0.000060171,0.00001946628,0.00008764651,0.000005907197],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003794353,"about_ca_system_score_gemma":0.00002556262,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001165074,"about_ca_topic_score_gemma":0.00002897944,"domain_scores_codex":[0.9987636,0.0002367759,0.0004676902,0.0002843815,0.000075884,0.0001716641],"domain_scores_gemma":[0.9993821,0.00008625902,0.0001877057,0.0001560969,0.00007907379,0.0001087695],"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":[0.00009319338,0.00003128244,0.02461091,0.00006939693,0.00004126054,0.000003791967,0.0002130683,0.00001972248,0.9671696,0.002962332,0.00002148785,0.004763947],"study_design_scores_gemma":[0.003107782,0.0003027918,0.3585476,0.00007048692,0.00002792598,0.00003434777,0.00005681049,0.00983376,0.6242676,0.0006019586,0.002986151,0.0001627939],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9979302,0.0004816224,0.0005576912,0.0002049236,0.0001311401,0.0004680608,0.00001028367,0.00004363998,0.0001724187],"genre_scores_gemma":[0.9989375,0.0000638431,0.000115032,0.0001166654,0.0002421646,0.00002408662,0.0002289557,0.00001401715,0.0002577032],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.342902,"threshold_uncertainty_score":0.5319831,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1581686517","doi":"10.4137/grsb.s882","title":"The MAPK Signaling Cascade is a Central Hub in the Regulation of Cell Cycle, Apoptosis and Cytoskeleton Remodeling by Tripeptidyl-Peptidase II","year":2008,"lang":"en","type":"article","venue":"Gene Regulation and Systems Biology","topic":"Peptidase Inhibition and Analysis","field":"Medicine","cited_by":16,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Université de Montréal; Institute for Research in Immunology and Cancer","funders":"","keywords":"Biology; Cell biology; Cell cycle; Signal transduction; Gene knockdown; Mitosis; Actin cytoskeleton; Centrosome; Apoptosis; Genetics; Cytoskeleton; Cell","authors":[{"name":"Ramakrishna Sompallae","is_ca":false},{"name":"Vaia Stavropoulou","is_ca":false},{"name":"Mathieu Houde","is_ca":true},{"name":"Maria G. Masucci","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01847118655714859,"gpt":0.2471503477347679,"spread":0.2286791611776193,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005704477,0.0001478136,0.0003273582,0.0001357882,0.000370318,0.00001738522,0.00005607789,0.0001721946,0.00001523747],"category_scores_gemma":[0.00003298847,0.00009186661,0.00008653197,0.0002529274,0.0001638409,0.00005293726,0.00002403955,0.0001195674,0.000001445566],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003776366,"about_ca_system_score_gemma":0.00003385427,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002293719,"about_ca_topic_score_gemma":0.0000113095,"domain_scores_codex":[0.9984397,0.0002946334,0.0005778451,0.0002717167,0.0001741433,0.0002419726],"domain_scores_gemma":[0.9992533,0.00012059,0.0002448441,0.0002193384,0.00008637068,0.00007560875],"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":[0.00008556511,0.00004586293,0.002585039,0.00006232463,0.00002840144,8.846928e-7,0.001629898,0.0003117235,0.9933519,0.0002316337,0.00077266,0.000894131],"study_design_scores_gemma":[0.007371685,0.0007725395,0.05605557,0.0008203329,0.0002834579,0.0005797161,0.005497517,0.2611771,0.6588889,0.0007549749,0.007090133,0.0007080173],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9961824,0.001080688,0.001100881,0.0009894347,0.00003062755,0.0003592075,0.00002045353,0.00001661018,0.0002197123],"genre_scores_gemma":[0.9983587,0.0004103499,0.0001319354,0.0002051971,0.000116261,0.0000161664,0.0001240386,0.000009885841,0.0006275277],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3344629,"threshold_uncertainty_score":0.3746212,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2621688785","doi":"10.1177/1177625017713996","title":"A Transcriptional Regulatory Role for the Membrane Type-1 Matrix Metalloproteinase in Carcinogen-Induced Inflammasome Gene Expression","year":2017,"lang":"en","type":"article","venue":"Gene Regulation and Systems Biology","topic":"Inflammasome and immune disorders","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":"Université du Québec à Montréal","funders":"","keywords":"Inflammasome; Gene expression; Matrix metalloproteinase; Carcinogen; Regulation of gene expression; Computational biology; Cancer research; Cell biology; Gene; Medicine; Bioinformatics; Biology; Genetics; Inflammation; Immunology","authors":[{"name":"Samuel Sheehy","is_ca":true},{"name":"Borhane Annabi","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.0194507736865096,"gpt":0.2679983846700278,"spread":0.2485476109835182,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004932924,0.0001696384,0.000219412,0.00006413441,0.0003900637,0.00005156987,0.0002232042,0.0002797263,0.00001062521],"category_scores_gemma":[0.00007440216,0.0001270502,0.00008973198,0.00003359152,0.0001175624,0.00001399521,0.00006208794,0.00006536371,0.000003583832],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001466014,"about_ca_system_score_gemma":0.00006577602,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001046631,"about_ca_topic_score_gemma":0.00006967733,"domain_scores_codex":[0.9988919,0.0001169002,0.0003240877,0.000345394,0.00007859361,0.0002431522],"domain_scores_gemma":[0.9990766,0.00001863565,0.0001922493,0.0005593253,0.0001097954,0.00004340342],"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":[0.0002456117,0.00001322169,0.003120565,0.00002681766,0.00004710668,4.912547e-7,0.0000735945,0.0001890529,0.994381,0.000983689,0.00002659337,0.0008922939],"study_design_scores_gemma":[0.001694873,0.0001996957,0.05626071,0.00001820154,0.00002750947,0.00002472503,0.0001695052,0.001273623,0.9180536,0.0001947757,0.02184778,0.0002350052],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9917912,0.006131291,0.0005617453,0.0001790073,0.0004287294,0.0007869755,0.00002236753,0.000008779727,0.00008993794],"genre_scores_gemma":[0.9980263,0.0002665878,0.0001667255,0.00002943334,0.0003179678,0.0001742802,0.000257882,0.00001932181,0.0007415681],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.07632738,"threshold_uncertainty_score":0.5180956,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null}]}