Our Focus
We take S protein as the research focus and take coronavirus recombination as the exploration direction.
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Group 1:
1. Identification of 2019-nCoV related coronaviruses 1 in Malayan pangolins in southern China (管轶）
2. MAFFT-DASH: integrated protein sequence and structural alignment
3. PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference
4. A new coronavirus associated with human respiratory disease in China 中文版 Yongzheng Zhang | Chines2
5. A pneumonia outbreak associated with a new coronavirus of probable bat origin Zhengli Shi Newnature
6. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. 中文版
8. Median-Joining Networks for Inferring Intraspecific Phylogenies
9. On the use of median-joining networks in evolutionary biology
10.RDP4: Detection and analysis of recombination patterns in virus genomes.
11. Evidence of recombination in coronaviruses implicating pangolin origins of nCoV- 2019
12. Structure, Function, and Evolution of Coronavirus Spike Proteins
15. Discovery of a rich gene pool of bat SARS-related coronaviruses (Zhengli Shi PLOS Pathogens，2017）
16. Origin and evolution of pathogenic coronaviruses （(Zhengli ShiNATURE REVIEWS MICROBIOLOGY，2019）
17. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor （Zhengli Shi，nature，2013）
18. SARS-like cluster of circulating bat coronaviruses shows potential for human emergence （Baric，Nat Med. 2015 who make new virus）
19. Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China （Science，2004） supp
20. Cross-host evolution of severe acute respiratorysyndrome coronavirus in palm civet and human(PNAS,2005,zhao guoping)
21.Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2. （2.27Published）
22. Early Phylogenetic Estimate of the Effective Reproduction Number Of Sars-CoV-2 （2020-Feb-25）
23. Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed with Receptor
24. Mechanisms of host receptor adaptation by severe acute respiratory syndrome coronavirus
25. Mutations, Recombination and Insertion in the Evolution of 2019-nCoV || 中文版
26. Bat Coronaviruses in China
27. A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19
28. Cross‐species transmission of the newly identified coronavirus 2019‐nCoV
29. Cross-species virus transmission and the emergence of new epidemic diseases （Review）
30.Recombination, Reservoirs, and the Modular Spike: Mechanisms of Coronavirus Cross-Species Transmission （Review）
31. Prediction of cross-species infection propensities of viruses with receptor similarity
32. Molecular Evolution of Human Coronavirus Genomes （Review）
33. Jumping species - a mechanism for coronavirus persistence and survival
35. Geographical structure of bat SARS-related coronaviruses （Zhengli Shi）（Review）
36. Global Epidemiology of Bat Coronaviruses （Review）
37. Bat-to-human: spike features determining 'host jump' of coronaviruses SARS-CoV, MERS-CoV, and beyond. （Review）
38. Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS. （Review）
39. Viral Quasispecies Evolution.（Review）
41. Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins
42. COVID‐2019:The role of the nsp2 and nsp3 in its pathogenesis
43. Detecting Natural Selection in Genomic Data （ANNUAL REVIEW OF GENETICS，2013）
44. SWISS-MODEL: homology modelling of protein structures and complexes
45. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core
46. The HHpred interactive server for protein homology detection and structure prediction
The following three articles are the three most important articles in the structure of cov-2 (all can be downloaded directly):
48. Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein
49. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation
50. Structure and dynamics of molecular networks: A novel paradigm of drug discovery A comprehensive review
51. Phylogenetic network analysis of SARS-CoV-2 genomes (PNAS, 2020.3.30)