Mingda Hu
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A VLP-based mRNA vaccine elicits potent humoral and cellular immunity against Oropouche virus Open
Oropouche virus (OROV) is reemerging in the Americas, along with a growing threat to global public health. Recent outbreaks have witnessed the first reported fatalities, vertical transmissions, and intercontinental importations of OROV, un…
A highly potent, stable, and safe dePEGylated lipopeptide against Nipah virus and related henipaviruses Open
Nipah virus (NiV) poses a significant threat owing to its high mortality and the lack of approved therapeutics. Targeting the conserved heptad repeat 1 (HR1) domain of the viral fusion (F) protein constitutes a promising antiviral strategy…
Predicting antibiotic resistance genes and bacterial phenotypes based on protein language models Open
Introduction Antibiotic resistance is emerging as a critical global public health threat. The precise prediction of bacterial antibiotic resistance genes (ARGs) and phenotypes is essential to understand resistance mechanisms and guide clin…
Genetic characteristics of rotavirus a in Shenzhen and Zhuhai, China, 2020–2023 Open
we observed significant variability and complexity in the evolutionary characteristics of RVA in Shenzhen and Zhuhai. These insights enhance our understanding of global evolution and transmission of RVA and provide guidance for future rese…
Genetic diversity of norovirus in Shenzhen Based on continuous surveillance from 2016 to 2022 Open
Introduction Norovirus is a key pathogen of acute gastroenteritis and poses a significant burden on both the economy and public health. This study focuses on continuous monitoring of norovirus in Shenzhen, China, from 2016 to 2022, aiming …
Coinfection of human adenovirus and recombinant human astrovirus in a case of acute gastroenteritis: A report from China Open
Diarrhea is one of the major public health issues worldwide. Although the infections of individual enteric virus have been extensively studied, elucidation of the coinfection involving multiple viruses is still limited. In this study, we i…
Detecting genetic gain and loss events in terms of protein domain: Method and implementation Open
Continuous gain and loss of genes are the primary driving forces of bacterial evolution and environmental adaptation. Studying bacterial evolution in terms of protein domain, which is the fundamental function and evolutionary unit of prote…
Predicting the transmission trend of respiratory viruses in new regions via geospatial similarity learning Open
The outbreak and spread of COVID-19 remind us again of the devastating attack that human-to-human transmitted respiratory infectious diseases (H-HRIDs) bring to global economics and public health. Predicting the trend of H-HRIDs yields imp…
Flu-CNN: predicting host tropism of influenza A viruses via character-level convolutional networks Open
Throughout history, Influenza A viruses (IAVs) have caused significant harm and catastrophic pandemics. The presence of host barriers results in viral host tropism, where infected hosts are subject to strict restrictions due to the hindere…
View article: Genetic characteristics of classical astroviruses in Shenzhen, China, 2016–2019
Genetic characteristics of classical astroviruses in Shenzhen, China, 2016–2019 Open
Human astrovirus (HAstV) is a single‐stranded, positive‐sense RNA virus and is the leading cause of viral gastroenteritis. However, despite its prevalence, astroviruses still remain one of the least studied enteroviruses. In this study, we…
Characterization and Diversity of Klebsiella pneumoniae Prophages Open
Klebsiella pneumoniae is a common human commensal and opportunistic pathogen. In recent years, the clinical isolation and resistance rates of K. pneumoniae have shown a yearly increase, leading to a special interest in mobile genetic eleme…
View article: Evaluating the effect of SARS-CoV-2 spike mutations with a linear doubly robust learner
Evaluating the effect of SARS-CoV-2 spike mutations with a linear doubly robust learner Open
Driven by various mutations on the viral Spike protein, diverse variants of SARS-CoV-2 have emerged and prevailed repeatedly, significantly prolonging the pandemic. This phenomenon necessitates the identification of key Spike mutations for…
Comparative genomics reveals new insights into the evolution of the IncA and IncC family of plasmids Open
Incompatibility groups IncA and IncC plasmids are of great concern due to their ability to disseminate antibiotic resistance in bacteria via conjugative transfer. A deep understanding of their genomic structures and evolutionary characteri…
View article: Evaluating the Effect of SARS-CoV-2 Spike Mutations by Causal Inference
Evaluating the Effect of SARS-CoV-2 Spike Mutations by Causal Inference Open
Driven by various mutations on the viral Spike protein, diverse variants of SARS-CoV-2 have emerged and prevailed repeatedly, which necessitates the identification of key Spike mutations for fitness enhancement. To address the need, this m…
Comparative Genomics Reveals New Insights into the Evolution of the IncA and IncC Family of Plasmids Open
Incompatibility groups IncA and IncC plasmids are of great concern due to their ability to disseminate antibiotic resistance in bacteria via conjugative transfer. A deep understanding of their genomic structures and evolutionary characteri…
View article: A Standardized Framework for Better Understanding of Phenotypic Differences within Bacterial Phyla Based on Protein Domain
A Standardized Framework for Better Understanding of Phenotypic Differences within Bacterial Phyla Based on Protein Domain Open
A 3-step framework was designed which can be applied to clustering species based on their protein domains, and different candidate models are proposed in each step for better adaptation of various scenarios. We show its implementation for …
View article: A Standardized Framework for Taxonomy Analysis in Bacterial Kingdom based on Protein Domain
A Standardized Framework for Taxonomy Analysis in Bacterial Kingdom based on Protein Domain Open
The taxonomy research on the bacterial kingdom is important and can be usually conducted by the analysis on conserved genes, 16s rRNA, protein domain, and so on. Comparatively, the protein domains maintain a most direct relationship with p…
Global Mutational Sweep of SARS-CoV-2: From Chaos to Order Open
OPINION article Front. Microbiol., 08 February 2022 | https://doi.org/10.3389/fmicb.2022.820919
View article: Inactivated Rabies Virus Vectored MERS-Coronavirus Vaccine Induces Protective Immunity in Mice, Camels, and Alpacas
Inactivated Rabies Virus Vectored MERS-Coronavirus Vaccine Induces Protective Immunity in Mice, Camels, and Alpacas Open
Middle East respiratory syndrome coronavirus (MERS-CoV) is an emergent coronavirus that has caused frequent zoonotic events through camel-to-human spillover. An effective camelid vaccination strategy is probably the best way to reduce huma…
Reassortment Network of Influenza A Virus Open
Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments. Genetic exchange through reassortment of the segmented genomes often endows IAVs with new genetic characteristics, which may affect transmissibility and pa…
Characterizing the Core Internal Gene Pool of H9N2 Responsible for Continuous Reassortment With Other Influenza A Viruses Open
Reassortment among avian influenza viruses is the main source of novel avian influenza virus subtypes. Studies have shown that the H9N2 virus often donates internal segments to generate novel reassortant avian influenza viruses, acting as …
A Non-phylogeny-dependent Reassortment Detection Method for Influenza A Viruses Open
Influenza A virus is a segmented RNA virus whose genome consists of 8 single-stranded negative-sense RNA segments. This unique genetic structure allows viruses to exchange their segments through reassortment when they infect the same host …
Global Mutational Sweep of SARS-CoV-2: from Chaos to Order Open
Analysis of large-scale genome sequences demonstrates the mutation of SARS-CoV-2 has been undergoing significant sweeps. Driven by emerging variants, global sweeps are accelerated and purified over time. This may prolong the pandemic with …
Reassortment Network of Influenza A Virus Open
Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments. Genetic exchange through reassortment of the segmented genomes often endows IAVs with new genetic characteristics, which may affect transmissibility and pa…
View article: Characterization of Burkholderia cepacia Complex Core Genome and the Underlying Recombination and Positive Selection
Characterization of Burkholderia cepacia Complex Core Genome and the Underlying Recombination and Positive Selection Open
Recombination and positive selection are two key factors that play a vital role in pathogenic microorganisms' population adaptation and diversification. The Burkholderia cepacia complex (Bcc) represents bacterial species with high similari…