codonforge/CITATION.cff at main · Raghuboi/codonforge · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
cff-version: 1.2.0
message: "If you use CodonForge in research, please cite it as below."
type: software
title: "CodonForge"
version: "0.2.0"
authors:
  - family-names: "Prabhakar"
    given-names: "Raghunath"
repository-code: "https://github.com/raghuboi/codonforge"
license: "MIT"
date-released: "2026-06-10"
abstract: "CodonForge is a clean-room Rust CLI for mRNA codon optimization research. Version 0.2.0 adds deterministic beam-search optimization with CAI, GC%, U%, and repeat-penalty objectives, plus a public RP mini-benchmark and Kazusa-derived human codon usage provenance."
keywords:
  - bioinformatics
  - codon-optimization
  - mrna
  - codon-adaptation-index
  - rust
references:
  - type: article
    title: "The codon adaptation index--a measure of directional synonymous codon usage bias"
    authors:
      - family-names: "Sharp"
        given-names: "Paul M."
      - family-names: "Li"
        given-names: "Wen-Hsiung"
    year: 1987
    journal: "Nucleic Acids Research"
    volume: 15
    issue: 5
    start: 1281
    end: 1295
    doi: "10.1093/nar/15.5.1281"