{"paper":{"title":"MOSAIC: Codon Harmonization of Monte Carlo-Based Simulated Annealing for Linked Codons in Heterologous Protein Expression","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"A Monte Carlo-based algorithm for harmonizing linked codon sets improves heterologous expression of rate-sensitive proteins like ribosomal S18.","cross_cats":[],"primary_cat":"q-bio.QM","authors_text":"Chengcheng Yang, Eok Kyun Lee, Insung S. Choi, Jihoo Kim, Ryan Fernandez Medina Hariri, Seung Seo Lee, Won June Kim, Yoonho Jeong, Younghoon Lee","submitted_at":"2025-11-13T07:07:32Z","abstract_excerpt":"Codon usage bias has a crucial impact on the translation efficiency and co-translational folding of proteins, necessitating the algorithmic development of codon optimization/harmonization methods, particularly for heterologous recombinant protein expression. Codon harmonization is especially valuable for proteins sensitive to translation rates, because it can potentially replicate native translation speeds, preserving proper folding and maintaining protein activity. This work proposes a Monte Carlo-based codon harmonization algorithm, MOSAIC (Monte Carlo-based Simulated Annealing for Linked Co"},"claims":{"count":4,"items":[{"kind":"strongest_claim","text":"The harmonized gene of RP S18 was expressed and compared with the expression of the wild-type gene. The harmonized gene clearly yielded a larger quantity of the protein, from which the amount of the soluble protein was also significant.","source":"verdict.strongest_claim","status":"machine_extracted","claim_id":"C1","attestation":"unclaimed"},{"kind":"weakest_assumption","text":"That harmonizing linked codon sets will replicate native translation speeds and thereby preserve proper co-translational folding for proteins sensitive to translation rates, without introducing new folding problems.","source":"verdict.weakest_assumption","status":"machine_extracted","claim_id":"C2","attestation":"unclaimed"},{"kind":"one_line_summary","text":"MOSAIC applies simulated annealing to harmonize linked codon sets, yielding higher total and soluble protein levels for ribosomal protein S18 versus wild-type in heterologous expression.","source":"verdict.one_line_summary","status":"machine_extracted","claim_id":"C3","attestation":"unclaimed"},{"kind":"headline","text":"A Monte Carlo-based algorithm for harmonizing linked codon sets improves heterologous expression of rate-sensitive proteins like ribosomal S18.","source":"verdict.pith_extraction.headline","status":"machine_extracted","claim_id":"C4","attestation":"unclaimed"}],"snapshot_sha256":"7f9b623b8b65cd182a1d44ec5cd5662ba53aa4212f85d27921a7b27de8261511"},"source":{"id":"2511.10708","kind":"arxiv","version":4},"verdict":{"id":"a66bfe20-abb7-49e9-b544-83f17001b99e","model_set":{"reader":"grok-4.3"},"created_at":"2026-05-17T22:44:16.328340Z","strongest_claim":"The harmonized gene of RP S18 was expressed and compared with the expression of the wild-type gene. The harmonized gene clearly yielded a larger quantity of the protein, from which the amount of the soluble protein was also significant.","one_line_summary":"MOSAIC applies simulated annealing to harmonize linked codon sets, yielding higher total and soluble protein levels for ribosomal protein S18 versus wild-type in heterologous expression.","pipeline_version":"pith-pipeline@v0.9.0","weakest_assumption":"That harmonizing linked codon sets will replicate native translation speeds and thereby preserve proper co-translational folding for proteins sensitive to translation rates, without introducing new folding problems.","pith_extraction_headline":"A Monte Carlo-based algorithm for harmonizing linked codon sets improves heterologous expression of rate-sensitive proteins like ribosomal S18."},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2511.10708/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":2,"snapshot_sha256":"9571ae747dff4611bf5215b90e11004622432b581972094a581beb12104e273f"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}