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Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies.
Alexaki A, Hettiarachchi GK, Athey JC, Katneni UK, Simhadri V, Hamasaki-Katagiri N, Nanavaty P, Lin B, Takeda K, Freedberg D, Monroe D, McGill JR, Peters R, Kames JM, Holcomb DD, Hunt RC, Sauna ZE, Gelinas A, Janjic N, DiCuccio M, Bar H, Komar AA, Kimchi-Sarfaty C. Alexaki A, et al. Among authors: athey jc. Sci Rep. 2019 Oct 29;9(1):15449. doi: 10.1038/s41598-019-51984-2. Sci Rep. 2019. PMID: 31664102 Free PMC article.
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.
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.
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.
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.