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Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies.
Sci Rep. 2019 Oct 29;9(1):15449. doi: 10.1038/s41598-019-51984-2.
Sci Rep. 2019.
PMID: 31664102
Free PMC article.
TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression.
Kames J, Alexaki A, Holcomb DD, Santana-Quintero LV, Athey JC, Hamasaki-Katagiri N, Katneni U, Golikov A, Ibla JC, Bar H, Kimchi-Sarfaty C.
Kames J, et al. Among authors: athey jc.
J Mol Biol. 2020 May 15;432(11):3369-3378. doi: 10.1016/j.jmb.2020.01.011. Epub 2020 Jan 23.
J Mol Biol. 2020.
PMID: 31982380
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Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX.
Alexaki A, Kames J, Hettiarachchi GK, Athey JC, Katneni UK, Hunt RC, Hamasaki-Katagiri N, Holcomb DD, DiCuccio M, Bar H, Komar AA, Kimchi-Sarfaty C.
Alexaki A, et al. Among authors: athey jc.
F1000Res. 2020 Mar 10;9:174. doi: 10.12688/f1000research.22400.2. eCollection 2020.
F1000Res. 2020.
PMID: 33014344
Free PMC article.
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Structural, functional, and immunogenicity implications of F9 gene recoding.
Katneni UK, Alexaki A, Hunt RC, Hamasaki-Katagiri N, Hettiarachchi GK, Kames JM, McGill JR, Holcomb DD, Athey JC, Lin B, Parunov LA, Kafri T, Lu Q, Peters R, Ovanesov MV, Freedberg DI, Bar H, Komar AA, Sauna ZE, Kimchi-Sarfaty C.
Katneni UK, et al. Among authors: athey jc.
Blood Adv. 2022 Jul 12;6(13):3932-3944. doi: 10.1182/bloodadvances.2022007094.
Blood Adv. 2022.
PMID: 35413099
Free PMC article.
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Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design.
Alexaki A, Kames J, Holcomb DD, Athey J, Santana-Quintero LV, Lam PVN, Hamasaki-Katagiri N, Osipova E, Simonyan V, Bar H, Komar AA, Kimchi-Sarfaty C.
Alexaki A, et al.
J Mol Biol. 2019 Jun 14;431(13):2434-2441. doi: 10.1016/j.jmb.2019.04.021. Epub 2019 Apr 26.
J Mol Biol. 2019.
PMID: 31029701
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Translational and transcriptional responses in human primary hepatocytes under hypoxia.
Hettiarachchi GK, Katneni UK, Hunt RC, Kames JM, Athey JC, Bar H, Sauna ZE, McGill JR, Ibla JC, Kimchi-Sarfaty C.
Hettiarachchi GK, et al. Among authors: athey jc.
Am J Physiol Gastrointest Liver Physiol. 2019 Jun 1;316(6):G720-G734. doi: 10.1152/ajpgi.00331.2018. Epub 2019 Mar 28.
Am J Physiol Gastrointest Liver Physiol. 2019.
PMID: 30920299
Free PMC article.
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A new and updated resource for codon usage tables.
Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-Quintero LV, Katneni U, Simonyan V, Kimchi-Sarfaty C.
Athey J, et al.
BMC Bioinformatics. 2017 Sep 2;18(1):391. doi: 10.1186/s12859-017-1793-7.
BMC Bioinformatics. 2017.
PMID: 28865429
Free PMC article.
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Complete Genome Sequence of Spiroplasma kunkelii Strain CR2-3x, Causal Agent of Corn Stunt Disease in Zea mays L.
Davis RE, Shao J, Dally EL, Zhao Y, Gasparich GE, Gaynor BJ, Athey JC, Harrison NA, Donofrio N.
Davis RE, et al. Among authors: athey jc.
Genome Announc. 2015 Oct 22;3(5):e01216-15. doi: 10.1128/genomeA.01216-15.
Genome Announc. 2015.
PMID: 26494665
Free PMC article.
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