{"id":"W2149770991","doi":"10.1371/journal.pone.0006864","title":"Whole Genome Amplification and De novo Assembly of Single Bacterial Cells","year":2009,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Bacterial Genetics and Biotechnology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":265,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"University of California, San Diego; National Institute of Allergy and Infectious Diseases; Natural Sciences and Engineering Research Council of Canada; Broad Institute; U.S. Department of Energy; Gordon and Betty Moore Foundation; National Institutes of Health; U.S. Department of Health and Human Services; National Science Foundation","keywords":"Genome; Sequence assembly; Multiple displacement amplification; Contig; Biology; Computational biology; DNA sequencing; Deep sequencing; Whole genome sequencing; Genomics; Genetics; Reference genome; Bacterial genome size; DNA; Gene; Polymerase chain reaction; Transcriptome","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":[],"consensus_categories":[],"category_scores_codex":[0.00006208287,0.0000757221,0.000116944,0.00002629986,0.00001822317,0.00001458319,0.00009412187,0.0001878561,0.000005774337],"category_scores_gemma":[0.00001897333,0.00007821521,0.00002035449,0.00003936505,0.00004586665,0.000001571489,0.00003806651,0.00003683873,0.000002453769],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000006459342,"about_ca_system_score_gemma":0.00002073172,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00000242674,"about_ca_topic_score_gemma":0.000003679854,"domain_scores_codex":[0.9994814,0.00001714644,0.0001321293,0.0001784556,0.00005263144,0.000138273],"domain_scores_gemma":[0.9996448,0.00000263908,0.00006528615,0.0001982125,0.00004978104,0.00003927483],"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":[0.00005006585,0.000425624,0.00005484124,0.00001240372,0.00003180383,3.65854e-7,0.00001215126,5.136559e-7,0.9985638,0.00002588964,0.00001269123,0.000809903],"study_design_scores_gemma":[0.0002475422,0.0007089687,0.005004607,0.000008946586,0.00003132635,0.000002408489,0.000004794916,0.000004575218,0.9912027,0.00006496876,0.002630003,0.00008919093],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9990616,0.0001732703,0.0001613356,0.0003197129,0.00002352934,0.0001006348,0.00003006473,0.00001364518,0.0001161702],"genre_scores_gemma":[0.9952683,0.0001670864,0.004128369,0.00008648978,0.0001697206,0.000002671254,0.00008426564,0.0000106737,0.00008240911],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.007361079,"threshold_uncertainty_score":0.3189524,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01984193161847208,"score_gpt":0.2065213218140294,"score_spread":0.1866793901955573,"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."}}