Coronavirus HIV Influnenza hepatitis B hepatitis C EBV HPV HTLV-1 Virus Database
     
========
software
========		 ======
Data
======		 ======
paper
======

======
VIP
======

  

=====
Paper
=====

  
   
Epitope prediction Mutation prediction
viral disease outbreak forecasting Evolution Dynamics
Transmission Dynamics Infectious disease intelligence

Evolution Dynamics

1 Global circulation patterns of seasonal influenza viruses vary with antigenic drift .2015 Nature
2 Univ-flu: A structure-based model of influenza A virus hemagglutinin for universal antigenic prediction 2022
3 Development of PREDAC-H1pdm to model the antigenic evolution of influenza A/(H1N1) pdm09 viruses . 2023
4 Prediction of Antigenic Distance in Influenza A Using Attribute Network Embedding .2023
5 Integrating influenza antigenic dynamics with molecular evolution . 2014
6 Antigenic cartography of H1N1 influenza viruses using sequence-based antigenic distance calculation .2018
7 Ecological and evolutionary dynamics of multi-strain RNA viruses . 2022 NATURE ECOLOGY & EVOLUTION
8 Computation of Antigenicity Predicts SARS-CoV-2 Vaccine Breakthrough Variants .2022
9 A human coronavirus evolves antigenically to escape antibody immunity .2021
10 Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold . 2023
11 Predicting Antigenic Distance from Genetic Data for PRRSV-Type 1: Applications of Machine Learning .2023
12 Antigenic evolution of dengue viruses over 20 years .2021 Science
13 Global and local evolutionary dynamics of Dengue virus serotypes 1, 3, and 4 . 2023
14 Antigenic evolution of dengue viruses over 20 years .2021 Science
15 Evolutionary dynamics of dengue virus in India . 2023
16 Global Evolutionary History and Dynamics of Dengue Viruses Inferred from Whole Genome Sequences . 2022
17 A Deep Learning Approach for Predicting Antigenic Variation of Influenza A H3N2 .2021
18 Machine Learning Prediction and Experimental Validation of Antigenic Drift in H3 Influenza A Viruses in Swine . 2021
19 Convolutional Neural Network Based Approach to In Silico Non-Anticipating Prediction of Antigenic Distance for Influenza Virus 2020
20 Antigenicity prediction and vaccine recommendation of human influenza virus A (H3N2) using convolutional neural networks . 2020
21 Predicting evolution . 2017 NATURE ECOLOGY & EVOLUTION
22 Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses . 2016. PNAS
23 The impact of COVID-19 nonpharmaceutical interventions on the future dynamics of endemic infections . 2020 PNAS
24

A predictive fitness model for influenza .Nature 2014

季节性人类 A/H3N2 流感病毒经历快速进化，导致流行毒株群体逐年发生显着的序列更替。 适应性突变响应人类免疫挑战，主要发生在抗原表位，即病毒表面蛋白血凝素的抗体结合域。 在这里，我们开发了一个血凝素适应度模型，可以预测病毒种群从一年到下一年的演变。 有两个因素可以确定菌株的适应性：适应性表位变化和表位外的有害突变。 我们使用所有先前菌株的种群遗传数据来推断给定年份中传播的菌株的两个适应度组成部分。 根据每个菌株的适应度和频率，我们预测其后代菌株在下一年的频率。 该适应性模型绘制了甲型流感的适应历史，并提出了疫苗选择的原则方法。 我们的结果要求对流感和其他快速进化的病原体进行更全面的流行病学研究，将抗原表型与通过遗传连锁耦合的其他病毒功能整合起来。
25 Population immunity predicts evolutionary trajectories of SARS-CoV-2 。 Cell 2023
26 Praemonitus praemunitus: can we forecast and prepare for future viral disease outbreaks? FEMS MICROBIOLOGY REVIEWS. 2023
27 Predicting Dominant Genotypes in Norovirus Seasons in Japan . Life. 2023
28 Prediction of Antigenic Distance in Influenza A Using Attribute Network Embedding . VIRUSES-BASEL . 2023
29 MutaGAN: A sequence-to-sequence GAN framework to predict mutations of evolving protein populations . VIRUS EVOLUTION . 2023
30 Incorporating variant frequencies data into short-term forecasting for COVID-19 cases and deaths in the USA: a deep learning approach . EBIOMEDICINE . 2023
31 Oriented transformer for infectious disease case prediction . APPLIED INTELLIGENCE . 2023
32 Predicting the mutational drivers of future SARS-CoV-2 variants of concern. SCIENCE TRANSLATIONAL MEDICINE . 2022
33 GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics . 2023.11 INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS
34 Fitness evaluation of SARS-CoV-2 variants: A retrospective study .2023. JMV
35 UniBind: a novel artificial intelligence-based prediction model for SARS-CoV-2 infectivity and variant evolution . SIGNAL TRANSDUCTION AND TARGETED THERAPY . 2023.12
36

Deep-learning-enabled protein-protein interaction analysis for prediction of SARS-CoV-2 infectivity and variant evolution . 2023 . NATURE MEDICINE .

UniBind/UniBind (GitHub)
37 Deep mutational learning predicts ACE2 binding and antibody escape to combinatorial mutations in the SARS-CoV-2 receptor-binding domain .2022 CELL
38

GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics.2023.11 pdf2 || GitHub: genslm VIP

39 TEMPO: A transformer-based mutation prediction framework for SARS-CoV-2 evolution . 2023. COMPUTERS IN BIOLOGY AND MEDICINE

40 Fitness, growth and transmissibility of SARS-CoV-2 genetic variants .2023. NATURE REVIEWS GENETICS
41 Early computational detection of potential high-risk SARS-CoV-2 variants . 2023. COMPUTERS IN BIOLOGY AND MEDICINE
42  
43  
44  
45  
46  
47  

 

 

 

 

Group paper

1 Influenza, Nature Reviews, 2018
2 Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States. . 2023 Oct 3:2023medRxiv
3 The evolutionary potential of influenza A virus hemagglutinin is highly constrained by epistatic interactions with neuraminidase . cells host & microbe. 2022
4 Co-evolution of immunity and seasonal influenza viruses. Nature. 2023
5 Comparing the transmission potential from sequence and surveillance data of 2009 North American influenza pandemic waves . Infectious Disease Modelling. 2023
6 The human antibody response to influenza A virus infection and vaccination. Nature Reviews Immunology .2019
7 Epistasis reduces fitness costs of influenza A virus escape from stem-binding antibodies. PNAS. 2023
8  
9  
10  
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   

 

 

 

 

 

Influenza virus

Influenza is divided into three types: A, B, and C. The influenza virus discovered in recent years will be classi