{"id":"W2904850278","doi":"10.1186/s13059-018-1598-7","title":"Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate","year":2018,"lang":"en","type":"article","venue":"Genome biology","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":62,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of General Medical Sciences; National Cancer Institute; National Institutes of Health; School of Medicine, New York University; York University","keywords":"Biology; Transposable element; Human genetics; Genetics; Gene; Computational biology; Host (biology); DNA Transposable Elements; Genome Biology; Genome; Functional genomics; Evolutionary biology; Genomics; Computational genomics","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0001261859,0.0001181832,0.0002593801,0.00006457519,0.0002274653,0.00002690232,0.0002518506,0.00007161426,0.003774544],"category_scores_gemma":[0.000006233043,0.00005383082,0.0001489047,0.0005161404,0.0001455753,0.00005424209,0.00006823982,0.00004122683,0.00006715502],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002087728,"about_ca_system_score_gemma":0.00001166589,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007503269,"about_ca_topic_score_gemma":0.01469628,"domain_scores_codex":[0.9989995,0.00007065266,0.0003102526,0.0002979707,0.00006862592,0.0002529406],"domain_scores_gemma":[0.9995301,0.00004229329,0.0001637537,0.00009878538,0.0001081773,0.000056921],"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":[0.00002147088,0.00003928864,0.0721206,0.000001760014,0.0004717597,4.923691e-7,0.0001226943,0.00001567343,0.9216342,0.00005770729,0.000008785643,0.005505564],"study_design_scores_gemma":[0.0001281059,0.0002320827,0.9495471,0.00000308506,0.0004896871,0.000003132742,0.0001032379,0.000213941,0.01455374,0.0002627616,0.03429346,0.0001697323],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9979177,0.0002435775,0.00006306782,0.0003371052,0.0002867215,0.0001204349,0.0005925027,0.00002368139,0.0004151939],"genre_scores_gemma":[0.9979004,0.0001481488,0.0002670416,0.000072748,0.0002195921,0.00001046012,0.0006491833,9.978661e-7,0.0007313856],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9070805,"threshold_uncertainty_score":0.9971361,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01878543730555607,"score_gpt":0.2418978370868538,"score_spread":0.2231123997812977,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}