{"id":"W4388812701","doi":"10.1101/2023.11.18.567690","title":"Genomically integrated orthogonal translation in <i>Escherichia coli</i> , a new synthetic auxotrophic chassis with altered genetic code, genetic firewall, and enhanced protein expression","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba","funders":"Canada Research Chairs","keywords":"Synthetic biology; Chassis; Genetic code; CRISPR; Biology; Computational biology; Cas9; Computer science; Genetics; Gene; Engineering","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001751146,0.0003901606,0.0002099782,0.0001754941,0.0001495961,0.0004907084,0.0002658212,0.0003052823,0.0004543064],"category_scores_gemma":[0.0001310544,0.0001484937,0.0002322234,0.0001548068,0.0002905972,0.00018803,0.000348337,0.0006503292,0.0003556029],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002946923,"about_ca_system_score_gemma":0.000247438,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005817525,"about_ca_topic_score_gemma":0.0007410184,"domain_scores_codex":[0.9997696,0.00003628218,0.00002425643,0.00004963,0.00008001298,0.00004021583],"domain_scores_gemma":[0.9998682,0.0000133249,0.00005350009,0.00002045542,0.00001675458,0.00002770782],"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":[0.00001320826,0.00001018458,0.00008444067,0.00001634976,0.000002243109,0.00003530955,0.000005462227,0.0000583347,0.9986362,0.0002671401,0.000033341,0.000837794],"study_design_scores_gemma":[0.000002905267,0.00007241354,0.0004140673,0.000003723996,0.000005534869,0.0001252022,0.000009516433,0.001070136,0.9949261,0.00004331555,0.00332112,0.000005957118],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9482747,0.0007730876,0.04565212,0.0002838105,0.0001380782,0.00008489989,0.0004872339,0.0006758563,0.003630292],"genre_scores_gemma":[0.9660906,0.0004984053,0.02891847,0.00009981966,0.00001197932,0.00005059579,0.0005425502,0.0001117011,0.003675927],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0005817525,"threshold_uncertainty_score":0.002138078,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01461619621593316,"score_gpt":0.2082029831847214,"score_spread":0.1935867869687883,"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."}}