彭司实验室

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Coronavirus

HIV

Influnenza

hepatitis B

hepatitis C

EBV

HPV

HTLV-1

Virus Database

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Coronavirus papers

phylogenetic dynamics

Antiviral drug design

Computer-aided vaccine design

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============= Mutation papers =============

============= Recombination =============

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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 复旦张永正 参考基因组 | 中文2

5. A pneumonia outbreak associated with a new coronavirus of probable bat origin 石正丽最新nature

6. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. 中文版

7. Receptor recognition by novel coronavirus from Wuhan: 3 An analysis based on decade-long structural studies of SARS

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

13. Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination

14. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event

15. Discovery of a rich gene pool of bat SARS-related coronaviruses (石正丽 PLOS Pathogens，2017）

16. Origin and evolution of pathogenic coronaviruses （(石正丽NATURE REVIEWS MICROBIOLOGY，2019）

17. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor （石正丽，nature，2013）

18. SARS-like cluster of circulating bat coronaviruses shows potential for human emergence （Baric，Nat Med. 2015造新病毒）

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月27日出版）

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 （综述）

30.Recombination, Reservoirs, and the Modular Spike: Mechanisms of Coronavirus Cross-Species Transmission （综述）

31. Prediction of cross-species infection propensities of viruses with receptor similarity

32. Molecular Evolution of Human Coronavirus Genomes （综述）

33. Jumping species - a mechanism for coronavirus persistence and survival

34. The recent ancestry of Middle East respiratory syndrome coronavirus in Korea has been shaped by recombination

35. Geographical structure of bat SARS-related coronaviruses （石正丽）（综述）

36. Global Epidemiology of Bat Coronaviruses （综述）

37. Bat-to-human: spike features determining 'host jump' of coronaviruses SARS-CoV, MERS-CoV, and beyond. （综述）

38. Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS. （综述）

39. Viral Quasispecies Evolution.（综述）

40. 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

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

以下三篇文章是cov-2的结构方面最重要的三篇文章（都可以直接下载原文）：

47. Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus

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, 3月30日)