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Publications

CODA

Gutman G.A. and Hatfield G.W. "Nonrandom Utilization of Codon Pairs in Escherichia coli." The Proceedings of the National Academy of Sciences USA, 86:3699-3703. (1989). We analyzed protein-coding sequences of Escherichia coli and found that codon-pair utilization is highly biased, reflecting over-representation or under-representation of many pairs compared with their random expectations. (view/download PDF)

Hatfield G. W. and Gutman G. A. "Codon Pair Utilization Bias in Bacteria, Yeast and Mammals." In Transfer RNA in Protein Synthesis. (Edited by D. L. Hatfield, B. J. Lee, and R. M. Pirtle). Published by CRC Press, Boca Raton, FL, 1993. A comprehensive review of codon pair bias and its relationship to codon context effects on translation. (view/download PDF)

Irwin B., Heck J.D., and Hatfield G.W. "Codon Pair Utilization Biases Influence Translational Elongation Step Times." The Journal of Biological Chemistry, 270:22801-22806 (1995). Two independent assays capable of measuring the relative in vivo translational step times across a selected codon pair in a growing polypeptide in Escherichia coli were developed and then employed to demonstrate that codon pairs observed in protein coding sequences occur more frequently than predicted (over-represented codon pairs) and are translated more slowly (translational pausing) than pairs observed less frequently than expected (under-represented codon pairs). (view/download PDF)

Roth,D.A., Larsen,L.S.Z, and G.W. Hatfield. "Translation Engineering and Synthetic Biology" In Cell-Free Expression. (Edited by W. Antoni Kudlicki). Published by Landes Bioscience, Georgetown, Texas, 2007. Translation Engineering TM combined with synthetic biology (gene synthesis) techniques makes it possible to deliberately alter the presumed translation kinetics of genes without altering the amino acid sequence. CODA Genomics, Inc. has developed proprietary technologies that design and assemble synthetic genes for high expression and enhanced protein production, and offers new insights and methodologies for affecting protein structure and function in a variety of heterologous host and cell-free expression systems. (view/download PDF)

Hatfield, G.W. and Roth, D.A. "Optimizing Scaleup yield for protein production: Computationally Optimized DNA Assembly (CODA) and Translational Engineering." Biotechnol. Annu. Rev., 13:27-42 (2007). A discussion of coupling synthetic biology algorithms and translational engineering principles for the production of commercially valuable proteins.

Larsen, LS., Wassman, C.D., Hatfield, G.W., and Lathrop, R.H. "Computationally Optimized DNA Assembly of synthetic genes." Intl. J. Bionform. Res. Appl.., 4:324-36 (2008). A methods paper. This paper describes the computational and biological methods for the design and synthesis of CODA synthetic genes.

Chan SW, Hung SP, Raman SK, Hatfield GW, Lathrop RH, Da Silva NA, Wang SW. "Recombinant human collagen and biomimetic variants using a de novo gene optimized for modular assembly." Biomacromolecules ;11(6):1460-92010. This paper describes a modular synthesis strategy of the complete human collagen III gene and specifically defined variants for clinical applications.

Baronio R, Danziger SA, Hall LV, Salmon K, Hatfield GW, Lathrop RH, Kaiser P. "All-codon scanning identifies p53 cancer rescue mutations." Nucleic Acids Res. 2010 Jun 25. This paper describes the use of CODA technology to create a fast and simple All-Codon Scanning strategy to make a defined gene library of p53 in order to identify single amino-acid substitutions that can restore activity to inactive p53 found in human cancers.

Danziger SA, Baronio R, Ho L, Hall L, Salmon K, Hatfield GW, Kaiser P, Lathrop RH. "Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning." PLoS Comput Biol. 5(9) 2009. This paper describes computational methods for the prediction of protein structural changes induced by mutation of the human p53 gene that results in restoration of function.

Baronio R, Danziger SA, Hall LV, Salmon K, Hatfield GW, Lathrop RH, Kaiser P. "All-codon scanning identifies p53 cancer rescue mutations." Nucleic Acids Res. 38(20):7079-88. 2010. This paper describes the use of CODA to produce wholly defined gene libraries with each of all 64 codons at each of one and only one codon position for each molecule across an entire gene.

Fang F, Salmon K, Shen MW, Aeling KA, Ito E, Irwin B, Tran UP, Hatfield GW, Da Silva NA, Sandmeyer S. "A vector set for systematic metabolic engineering in Saccharomyces cerevisiae." Yeast. 28(2):123-36. 2011.

Demir O, Baronio R, Salehi F, Wassman CD, Hall L, Hatfield GW, Chamberlin R, Kaiser P, Lathrop RH, Amaro RE. "Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants." PLoS Comput Biol. 2011 7(10):e1002238. Epub 2011.

Wassman CD, Baronio R, Demir O, Wallentine BD, Chen CK, Hall LV, Salehi F, Lin DW, Chung BP, Hatfield GW, Chamberlin RA, Luecke H, Lathrop RH, Kaiser P, Amaro RE. "Computational identification of a transiently open L1/S3 pocket for reactivation or mutant p53." Nature Commun. 2013:4, 1407.

Lathrop, R.H. and Hatfield, G.W. "Method for producing a synthetic gene or other DNA." U.S. Patent no. 7,262,031. Issued August 28, 2007. This patent fully describes the CODA technology.