| 1 |
Nielsen_2020 |
Synonymous mutations and the molecular evolution of SARS-Cov-2 origins |
Rasmus Nielsen; Hongru Wang; Lenore Pipes |
2020 |
2020-04-21 |
BioRxiv |
Y |
|
|
10.1101/2020.04.20.052019 |
z11exbyu |
0.787629 |
Gu_W_2004, Zhang_2014 |
|
| 2 |
Padhi_2008 |
Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein |
Padhi, Abinash; Verghese, Bindhu |
2008 |
2008-02-29 |
PMC |
N |
PMC7114232 |
17931731.0 |
10.1016/j.virusres.2007.08.014 |
rws11uel |
0.774953 |
Gu_W_2004, Liu_Y_2010 |
|
| 3 |
Tang_2020 |
On the origin and continuing evolution of SARS-CoV-2 |
Tang, Xiaolu; Wu, Changcheng; Li, Xiang; Song, Yuhe; Yao, Xinmin; Wu, Xinkai; Duan, Yuange; Zhang, Hong; Wang, Yirong; Qian, Zhaohui; Cui, Jie; Lu, Jian |
2020 |
2020-03-03 |
COMM-USE |
Y |
PMC7107875 |
|
10.1093/nsr/nwaa036 |
j99cgsjt |
0.740472 |
|
|
| 4 |
Ren_L_2015 |
Genetic drift of human coronavirus OC43 spike gene during adaptive evolution |
Ren, Lili; Zhang, Yue; Li, Jianguo; Xiao, Yan; Zhang, Jing; Wang, Ying; Chen, Lan; Paranhos-Baccalà, Gláucia; Wang, Jianwei |
2015 |
2015-06-22 |
COMM-USE |
N |
PMC4476415 |
26099036.0 |
10.1038/srep11451 |
zk44e4qy |
0.737631 |
Gu_W_2004 |
|
| 5 |
Lv_L_2020 |
Comparative genomic analysis revealed specific mutation pattern between human coronavirus SARS-CoV-2 and Bat-SARSr-CoV RaTG13 |
Longxian Lv; Gaolei Li; Jinhui Chen; Xinle Liang; Yudong Li |
2020 |
2020-03-02 |
BioRxiv |
Y |
|
|
10.1101/2020.02.27.969006 |
3h1o0oz3 |
0.699588 |
Gu_W_2004, Zhang_2014, Liu_Y_2010 |
|
| 6 |
Yang_2000 |
Statistical methods for detecting molecular adaptation |
Yang, Ziheng; Bielawski, Joseph P. |
2000 |
2000-12-01 |
PMC |
N |
PMC7134603 |
11114436.0 |
10.1016/s0169-5347(00)01994-7 |
jf2mj16z |
0.673630 |
Gu_W_2004 |
van_Hemert_2007 |
| 7 |
SHANG_2006 |
Polymorphism of SARS-CoV Genomes |
SHANG, Lei; QI, Yan; BAO, Qi-Yu; TIAN, Wei; XU, Jian-Cheng; FENG, Ming-Guang; YANG, Huan-Ming |
2006 |
2006-04-30 |
PMC |
N |
PMC7131822 |
16625834.0 |
10.1016/s0379-4172(06)60061-9 |
6vw88jib |
0.617701 |
|
|
| 8 |
Zhang_2006 |
Using maximum likelihood method to detect adaptive evolution of HCV envelope protein-coding genes |
Zhang, Wenjuan; Zhang, Yuan; Zhong, Yang |
2006 |
2006-01-01 |
PMC |
N |
PMC7089483 |
|
10.1007/s11434-006-2118-9 |
rowoylge |
0.603933 |
Gu_W_2004, Zhang_2014 |
Sheikh_2020 |
| 9 |
Lara_2014 |
Genetic host specificity of hepatitis E virus |
Lara, James; Purdy, Michael A.; Khudyakov, Yury E. |
2014 |
2014-06-30 |
None |
N |
PMC5745802 |
24667049.0 |
10.1016/j.meegid.2014.03.011 |
is4yyblp |
0.597485 |
|
|
| 10 |
Chaw_2020 |
The origin and underlying driving forces of the SARS-CoV-2 outbreak |
Shu-Miaw Chaw; Jui-Hung Tai; Shi-Lun Chen; Chia-Hung Hsieh; Sui-Yuan Chang; Shiou-Hwei Yeh; Wei-Shiung Yang; Pei-Jer Chen; Hurng-Yi Wang |
2020 |
2020-04-14 |
BioRxiv |
Y |
|
|
10.1101/2020.04.12.038554 |
bawgldfi |
0.554915 |
Zhang_2014 |
|
| 11 |
Gu_H_2020 |
Multivariate Analyses of Codon Usage of SARS-CoV-2 and other betacoronaviruses |
Haogao Gu; Daniel Chu; Malik Peiris; Leo L.M. Poon |
2020 |
2020-02-20 |
BioRxiv |
Y |
|
|
10.1101/2020.02.15.950568 |
9aegg5sd |
0.548580 |
Gu_W_2004 |
|
| 12 |
Leary_2020 |
Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence |
Shay Leary; Silvana Gaudieri; Abha Chopra; Suman Pakala; Eric Alves; Mina John; Suman Das; Simon Mallal; Phillips Jane Phillips |
2020 |
2020-04-11 |
BioRxiv |
Y |
|
|
10.1101/2020.04.10.029454 |
9xueqdri |
0.546454 |
Gu_W_2004 |
|
| 13 |
Pavlović-Lažetić_2016 |
SARS-CoV Genome Polymorphism: A Bioinformatics Study |
Pavlović-Lažetić, Gordana M.; Mitić, Nenad S.; Tomović, Andrija M.; Pavlović, Mirjana D.; Beljanski, Miloš V. |
2016 |
2016-11-28 |
None |
N |
PMC5172477 |
16144519.0 |
10.1016/s1672-0229(05)03004-4 |
9ot6khmh |
0.531473 |
Liu_Y_2010, Gu_W_2004 |
|
| 14 |
dos_Passos_Cunha_2018 |
Codon adaptation biases among sylvatic and urban genotypes of Dengue virus type 2 |
dos Passos Cunha, Marielton; Ortiz-Baez, Ayda Susana; de Melo Freire, Caio César; de Andrade Zanotto, Paolo Marinho |
2018 |
2018-10-31 |
None |
N |
PMC7106335 |
29792991.0 |
10.1016/j.meegid.2018.05.017 |
kllrqoxi |
0.515120 |
Butt_2014 |
Butt_2016 |
| 15 |
Faria_2009 |
Rooting human parechovirus evolution in time |
Faria, Nuno R; de Vries, Michel; van Hemert, Formijn J; Benschop, Kimberley; van der Hoek, Lia |
2009 |
2009-07-15 |
COMM-USE |
N |
PMC2723090 |
19604368.0 |
10.1186/1471-2148-9-164 |
1xgjdhkx |
0.514505 |
Gu_W_2004, Zhang_2014 |
|
| 16 |
Li_X_2020 |
Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection |
Xiaojun Li; Elena E. Giorgi; Manukumar Honnayakanahalli Marichann; Brian Foley; Chuan Xiao; Xiang-peng Kong; Yue Chen; Bette Korber; Feng Gao |
2020 |
2020-03-22 |
BioRxiv |
Y |
|
|
10.1101/2020.03.20.000885 |
7v5aln90 |
0.495138 |
|
|
| 17 |
van_Hemert_2007 |
Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function |
van Hemert, Formijn J; Lukashov, Vladimir V; Berkhout, Ben |
2007 |
2007-03-07 |
COMM-USE |
N |
PMC1828050 |
17343744.0 |
10.1186/1743-422x-4-25 |
o76qvk49 |
0.488781 |
Gu_W_2004, Liu_Y_2010 |
Sheikh_2020 |
| 18 |
Chen_2017 |
Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus |
Chen, Ye; Xu, Quanming; Yuan, Xiaomin; Li, Xinxin; Zhu, Ting; Ma, Yanmei; Chen, Ji-Long |
2017 |
2017-11-27 |
COMM-USE |
N |
PMC5746386 |
29299151.0 |
10.18632/oncotarget.22738 |
4r3vy2k4 |
0.470546 |
Gu_W_2004, Zhang_2014 |
|
| 19 |
Dilucca_2020 |
Codon usage and evolutionary rates of the 2019-nCoV genes |
Maddalena Dilucca; Athanasia Pavlopoulou; Sergio Forcelloni; ANDREA GIANSANTI; Alexandros G Georgakilas |
2020 |
2020-03-27 |
BioRxiv |
Y |
|
|
10.1101/2020.03.25.006569 |
l9vtsj3e |
0.466981 |
Gu_W_2004 |
Sheikh_2020, Gu_W_2004 |
| 20 |
Hünemeier_2012 |
Evolutionary Responses to a Constructed Niche: Ancient Mesoamericans as a Model of Gene-Culture Coevolution |
Hünemeier, Tábita; Amorim, Carlos Eduardo Guerra; Azevedo, Soledad; Contini, Veronica; Acuña-Alonzo, Víctor; Rothhammer, Francisco; Dugoujon, Jean-Michel; Mazières, Stephane; Barrantes, Ramiro; Villarreal-Molina, María Teresa; Paixão-Côrtes, Vanessa Rodrigues; Salzano, Francisco M.; Canizales-Quinteros, Samuel; Ruiz-Linares, Andres; Bortolini, Maria Cátira |
2012 |
2012-06-21 |
COMM-USE |
N |
PMC3380856 |
22768049.0 |
10.1371/journal.pone.0038862 |
05y53vbg |
0.455564 |
|
Tibayrenc_2015, Harper_2013 |
| 21 |
Wu_G_2003 |
Prediction of amino acid pairs sensitive to mutations in the spike protein from SARS related coronavirus |
Wu, Guang; Yan, Shaomin |
2003 |
2003-12-31 |
PMC |
N |
PMC7124255 |
15127935.0 |
10.1016/j.peptides.2003.10.008 |
zmqaigqf |
0.445679 |
Gu_W_2004, Zhang_2014, Yan_S_2009 |
|
| 22 |
Brandão_2013 |
The evolution of codon usage in structural and non-structural viral genes: The case of Avian coronavirus and its natural host Gallus gallus |
Brandão, Paulo Eduardo |
2013 |
2013-12-26 |
PMC |
N |
PMC7114390 |
24091362.0 |
10.1016/j.virusres.2013.09.033 |
dtfw8o4g |
0.445032 |
Gu_W_2004, Liu_Y_2010, Liu_Y_2011 |
Sheikh_2020, Ahn_I_2009 |
| 23 |
Tort_2020 |
A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES |
Tort, Fernando L.; Castells, Matías; Cristina, Juan |
2020 |
2020-04-12 |
PMC |
Y |
|
|
10.1016/j.virusres.2020.197976 |
hidirfkv |
0.419475 |
Gu_W_2004, Zhang_2014, Liu_Y_2010, Xu_X_2019, Zhang_2012 |
Gu_W_2004, Sheikh_2020, Chen_2017 |
| 24 |
Zhang_2010 |
Complex positive selection pressures drive the evolution of HIV-1 with different co-receptor tropisms |
Zhang, ChiYu; Ding, Na; Chen, KePing; Yang, RongGe |
2010 |
2010-10-17 |
PMC |
N |
PMC7089306 |
20953943.0 |
10.1007/s11427-010-4066-5 |
vqhyyp88 |
0.416287 |
|
|
| 25 |
Brandão_2018 |
Could human coronavirus OC43 have co-evolved with early humans? |
Brandão, Paulo Eduardo |
2018 |
2018-06-28 |
COMM-USE |
N |
PMC6136381 |
30004106.0 |
10.1590/1678-4685-gmb-2017-0192 |
yu1fqq0q |
0.402623 |
Gu_W_2004 |
|
| 26 |
Ahn_I_2009 |
Comparative study of synonymous codon usage variations between the nucleocapsid and spike genes of coronavirus, and C-type lectin domain genes of human and mouse |
Ahn, Insung; Jeong, Byeong-Jin; Son, Hyeon Seok |
2009 |
2009-01-01 |
None |
N |
PMC2772977 |
19561398.0 |
10.3858/emm.2009.41.10.081 |
afvhp7z6 |
0.391773 |
Gu_W_2004, Liu_Y_2010 |
|
| 27 |
Vijgen_2004 |
Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13) |
Vijgen, Leen; Keyaerts, Els; Zlateva, Kalina; Van Ranst, Marc |
2004 |
2004-07-31 |
PMC |
N |
PMC7129141 |
15234325.0 |
10.1016/j.ijid.2004.03.004 |
01q775up |
0.363727 |
|
|
| 28 |
Ahn_I_2011 |
Comparative study of codon substitution patterns in foot-and-mouth disease virus (serotype O) |
Ahn, Insung; Bae, Se-Eun; Son, Hyeon Seok |
2011 |
2011-01-01 |
PMC |
N |
PMC3222820 |
21825834.0 |
10.3858/emm.2011.43.10.066 |
pnk26rg7 |
0.356314 |
Gu_W_2004, Liu_Y_2010, Zhang_2014 |
Liu_Y_2010, Gu_W_2004 |
| 29 |
Sheikh_2020 |
Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design |
Sheikh, Abdullah; Al-Taher, Abdulla; Al-Nazawi, Mohammed; Al-Mubarak, Abdullah I.; Kandeel, Mahmoud |
2020 |
2020-03-31 |
PMC |
N |
PMC7119019 |
31911390.0 |
10.1016/j.jviromet.2019.113806 |
z9p1ylsr |
0.350858 |
Gu_W_2004, Liu_Y_2010, Zhang_2014, Liu_Y_2011 |
Gu_W_2004 |
| 30 |
He_W_2019 |
Comprehensive codon usage analysis of porcine deltacoronavirus |
He, Wei; Wang, Ningning; Tan, Jimin; Wang, Ruyi; Yang, Yichen; Li, Gairu; Guan, Haifei; Zheng, Yuna; Shi, Xinze; Ye, Rui; Su, Shuo; Zhou, Jiyong |
2019 |
2019-12-31 |
PMC |
N |
PMC7111727 |
31536759.0 |
10.1016/j.ympev.2019.106618 |
oununr9g |
0.304465 |
Gu_W_2004, Zhang_2014, Xu_X_2019, Liu_Y_2011 |
|