Literature DB >> 26071446

Reply to Simmonds et al.: Codon pair and dinucleotide bias have not been functionally distinguished.

Bruce Futcher1, Oleksandr Gorbatsevych1, Sam H Shen1, Charles B Stauft1, Yutong Song1, Bingyin Wang1, Janet Leatherwood1, Justin Gardin1, Alisa Yurovsky1, Steffen Mueller1, Eckard Wimmer2.   

Abstract

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Year:  2015        PMID： 26071446      PMCID： PMC4507201          DOI： 10.1073/pnas.1507710112

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


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  4 in total

1.  Virus attenuation by genome-scale changes in codon pair bias.

Authors:  J Robert Coleman; Dimitris Papamichail; Steven Skiena; Bruce Futcher; Eckard Wimmer; Steffen Mueller
Journal:  Science       Date:  2008-06-27       Impact factor: 47.728

2.  Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference.

Authors:  Sam H Shen; Charles B Stauft; Oleksandr Gorbatsevych; Yutong Song; Charles B Ward; Alisa Yurovsky; Steffen Mueller; Bruce Futcher; Eckard Wimmer
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-30       Impact factor: 11.205

3.  Attenuation of dengue (and other RNA viruses) with codon pair recoding can be explained by increased CpG/UpA dinucleotide frequencies.

Authors:  Peter Simmonds; Fiona Tulloch; David J Evans; Martin D Ryan
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-12       Impact factor: 11.205

4.  RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies.

Authors:  Fiona Tulloch; Nicky J Atkinson; David J Evans; Martin D Ryan; Peter Simmonds
Journal:  Elife       Date:  2014-12-09       Impact factor: 8.140
  4 in total
  14 in total

1.  Zika Virus Attenuation by Codon Pair Deoptimization Induces Sterilizing Immunity in Mouse Models.

Authors:  Penghui Li; Xianliang Ke; Ting Wang; Zhongyuan Tan; Dan Luo; Yuanjiu Miao; Jianhong Sun; Yuan Zhang; Yan Liu; Qinxue Hu; Fuqiang Xu; Hanzhong Wang; Zhenhua Zheng
Journal:  J Virol       Date:  2018-08-16       Impact factor: 5.103

Review 2.  Synonymous Codons: Choose Wisely for Expression.

Authors:  Christina E Brule; Elizabeth J Grayhack
Journal:  Trends Genet       Date:  2017-03-12       Impact factor: 11.639

3.  CG dinucleotide suppression enables antiviral defence targeting non-self RNA.

Authors:  Matthew A Takata; Daniel Gonçalves-Carneiro; Trinity M Zang; Steven J Soll; Ashley York; Daniel Blanco-Melo; Paul D Bieniasz
Journal:  Nature       Date:  2017-09-27       Impact factor: 49.962

4.  Synonymous Deoptimization of Foot-and-Mouth Disease Virus Causes Attenuation In Vivo while Inducing a Strong Neutralizing Antibody Response.

Authors:  Fayna Diaz-San Segundo; Gisselle N Medina; Elizabeth Ramirez-Medina; Lauro Velazquez-Salinas; Marla Koster; Marvin J Grubman; Teresa de los Santos
Journal:  J Virol       Date:  2015-11-18       Impact factor: 5.103

5.  Extensive recoding of dengue virus type 2 specifically reduces replication in primate cells without gain-of-function in Aedes aegypti mosquitoes.

Authors:  Charles B Stauft; Sam H Shen; Yutong Song; Oleksandr Gorbatsevych; Emmanuel Asare; Bruce Futcher; Steffen Mueller; Anne Payne; Matthew Brecher; Laura Kramer; Eckard Wimmer
Journal:  PLoS One       Date:  2018-09-07       Impact factor: 3.240

6.  The role of ZAP and OAS3/RNAseL pathways in the attenuation of an RNA virus with elevated frequencies of CpG and UpA dinucleotides.

Authors:  Valerie Odon; Jelke J Fros; Niluka Goonawardane; Isabelle Dietrich; Ahmad Ibrahim; Kinda Alshaikhahmed; Dung Nguyen; Peter Simmonds
Journal:  Nucleic Acids Res       Date:  2019-09-05       Impact factor: 19.160

7.  CpG and UpA dinucleotides in both coding and non-coding regions of echovirus 7 inhibit replication initiation post-entry.

Authors:  Jelke Jan Fros; Isabelle Dietrich; Kinda Alshaikhahmed; Tim Casper Passchier; David John Evans; Peter Simmonds
Journal:  Elife       Date:  2017-09-29       Impact factor: 8.140

8.  mRNA structure regulates protein expression through changes in functional half-life.

Authors:  David M Mauger; B Joseph Cabral; Vladimir Presnyak; Stephen V Su; David W Reid; Brooke Goodman; Kristian Link; Nikhil Khatwani; John Reynders; Melissa J Moore; Iain J McFadyen
Journal:  Proc Natl Acad Sci U S A       Date:  2019-11-11       Impact factor: 11.205

Review 9.  Attenuation of Viruses by Large-Scale Recoding of their Genomes: the Selection Is Always Biased.

Authors:  Nikolaus Osterrieder; Dusan Kunec
Journal:  Curr Clin Microbiol Rep       Date:  2018-01-19

10.  Intra-genome variability in the dinucleotide composition of SARS-CoV-2.

Authors:  Paul Digard; Hui Min Lee; Colin Sharp; Finn Grey; Eleanor Gaunt
Journal:  Virus Evol       Date:  2020-08-13
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