Codon-Optimization

Spring 2019 CS287 Final Project. We take a neural based approach to the task of genetic codon optimization.

References

Codon optimization literature

Tian, Jian, et al. "Predicting synonymous codon usage and optimizing the heterologous gene for expression in E. coli." Scientific reports 7.1 (2017): 9926.

Tian, Jian, et al. "Presyncodon, a Web Server for Gene Design with the Evolutionary Information of the Expression Hosts." International journal of molecular sciences 19.12 (2018): 3872.

Goodman, Daniel B., George M. Church, and Sriram Kosuri. "Causes and effects of N-terminal codon bias in bacterial genes." Science 342.6157 (2013): 475-479.

Possible benchmark tasks

Becq, Jennifer, Cécile Churlaud, and Patrick Deschavanne. "A benchmark of parametric methods for horizontal transfers detection." PLoS One 5.4 (2010): e9989.

NLP References

Mueller, Jonas, David Gifford, and Tommi Jaakkola. "Sequence to better sequence: continuous revision of combinatorial structures." Proceedings of the 34th International Conference on Machine Learning-Volume 70. JMLR. org, 2017.

Zhao, Yanpeng, et al. "Language Style Transfer from Non-Parallel Text with Arbitrary Styles." (2018).

Shen, Tianxiao, et al. "Style transfer from non-parallel text by cross-alignment." Advances in neural information processing systems. 2017.

Prabhumoye, Shrimai, et al. "Style transfer through back-translation." arXiv preprint arXiv:1804.09000 (2018).

TODO

Misc. Notes

Data Sources

Orthologous genes

Ensembl download cDNA genomes

Ensembl genome download ftp link for e.coli

NCBI E.coli search