Peter Pak‐Hang Cheung
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View article: Author Correction: ARF4-mediated intracellular transport as a broad-spectrum antiviral target
Author Correction: ARF4-mediated intracellular transport as a broad-spectrum antiviral target Open
View article: Multiplexed detection of respiratory virus RNA using optical pH sensors and injection-molded centrifugal microfluidics
Multiplexed detection of respiratory virus RNA using optical pH sensors and injection-molded centrifugal microfluidics Open
The application is demonstrated of injection-molded centrifugal microfluidic chips with integrated optical pH sensors for multiplexed detection of respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, and influenza B RNA. The optic…
View article: Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations
Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations Open
The concentration of circulating cell-free DNA (cfDNA) in plasma is an important determinant of the robustness of liquid biopsies. However, biological mechanisms that lead to inter-individual differences in cfDNA concentrations remain unex…
View article: The effect of pre-COVID and post-COVID vaccination on long COVID: A systematic review and meta-analysis
The effect of pre-COVID and post-COVID vaccination on long COVID: A systematic review and meta-analysis Open
Our study suggests that 2-dose pre-COVID vaccination and 1-dose post-COVID vaccination are associated with a lower risk of long COVID. Since long COVID reduces quality of life substantially, vaccination could be a possible measure to maint…
View article: Multiplexed Detection of Respiratory Virus RNA Using Optical pH Sensors and Injection Molded Centrifugal Microfluidics
Multiplexed Detection of Respiratory Virus RNA Using Optical pH Sensors and Injection Molded Centrifugal Microfluidics Open
Infectious pathogens, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are a threat to global health and prosperity, with the coronavirus disease 2019 (COVID-19) pandemic causing deaths and negative economic impact…
View article: Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations
Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations Open
Influenza virus continuously evolves to escape human adaptive immunity and generates seasonal epidemics. Therefore, influenza vaccine strains need to be updated annually for the upcoming flu season to ensure vaccine effectiveness. We devel…
View article: Targeting ARF4-mediated intracellular transport as broad-spectrum antivirals
Targeting ARF4-mediated intracellular transport as broad-spectrum antivirals Open
Host factors that regulate cellular vesicular trafficking also contribute to progeny virions’ destination, thus representing as potential antiviral drug targets. Here we demonstrate that genetic deletion of ARF4, a regulator in vesicle tra…
View article: A jingmenvirus RNA-dependent RNA polymerase structurally resembles the flavivirus counterpart but with different features at the initiation phase
A jingmenvirus RNA-dependent RNA polymerase structurally resembles the flavivirus counterpart but with different features at the initiation phase Open
Jingmenviruses are a category of emerging segmented viruses that have garnered global attention in recent years, and are close relatives of the flaviviruses in the Flaviviridae family. One of their genome segments encodes NSP1 homologous t…
View article: Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations
Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations Open
A predictive evolutionary model was developed to forecast representative influenza viral strains and select vaccine strains for upcoming epidemic seasons. Influenza virus continuously evolves to escape human adaptive immunity and generates…
View article: Predicting the antigenic evolution of SARS-COV-2 with deep learning
Predicting the antigenic evolution of SARS-COV-2 with deep learning Open
The relentless evolution of SARS-CoV-2 poses a significant threat to public health, as it adapts to immune pressure from vaccines and natural infections. Gaining insights into potential antigenic changes is critical but challenging due to …
View article: Fragmentation landscape of cell-free DNA revealed by deconvolutional analysis of end motifs
Fragmentation landscape of cell-free DNA revealed by deconvolutional analysis of end motifs Open
Cell-free DNA (cfDNA) fragmentation is nonrandom, at least partially mediated by various DNA nucleases, forming characteristic cfDNA end motifs. However, there is a paucity of tools for deciphering the relative contributions of cfDNA cleav…
View article: Improving in silico prediction of influenza vaccine effectiveness by genome analysis incorporating epitope information
Improving in silico prediction of influenza vaccine effectiveness by genome analysis incorporating epitope information Open
Fast evaluation of vaccine effectiveness (VE) is valuable for facilitating vaccine development and making vaccination strategy. In previous studies, we developed the computational model linking molecular variations and VE for the influenza…
View article: Infection rate in Guangzhou after easing the zero-COVID policy: seroprevalence results to ORF8 antigen
Infection rate in Guangzhou after easing the zero-COVID policy: seroprevalence results to ORF8 antigen Open
View article: Minimum number of vaccine doses required to protect against long COVID symptoms: a systematic review and meta-analysis of observational studies
Minimum number of vaccine doses required to protect against long COVID symptoms: a systematic review and meta-analysis of observational studies Open
Review question / Objective: Following the COVID-19 global outbreak, Long Covid is currently the most urgent global health problem. Primary clinical research have produced widely varying findings demonstrating the protective and even count…
View article: Fragmentomics of urinary cell-free DNA in nuclease knockout mouse models
Fragmentomics of urinary cell-free DNA in nuclease knockout mouse models Open
Urinary cell-free DNA (ucfDNA) is a potential biomarker for bladder cancer detection. However, the biological characteristics of ucfDNA are not well understood. We explored the roles of deoxyribonuclease 1 (DNASE1) and deoxyribonuclease 1-…
View article: Predicting the antigenic evolution of SARS-COV-2 with deep learning
Predicting the antigenic evolution of SARS-COV-2 with deep learning Open
The severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) antigenic profile evolves in response to the vaccine and natural infection-derived immune pressure, resulting in immune escape and threatening public health. Exploring the po…
View article: Effectiveness of heterologous and homologous covid-19 vaccine regimens: living systematic review with network meta-analysis
Effectiveness of heterologous and homologous covid-19 vaccine regimens: living systematic review with network meta-analysis Open
Objective To evaluate the effectiveness of heterologous and homologous covid-19 vaccine regimens with and without boosting in preventing covid-19 related infection, hospital admission, and death. Design Living systematic review and network…
View article: Systematic comparison between BNT162b2 and CoronaVac in the seroprotection against SARS-CoV-2 Alpha, Beta, Gamma, and Delta variants
Systematic comparison between BNT162b2 and CoronaVac in the seroprotection against SARS-CoV-2 Alpha, Beta, Gamma, and Delta variants Open
View article: The importance of external quality assessment data in evaluating SARS-CoV-2 virus genome detection assays – Authors‘ reply
The importance of external quality assessment data in evaluating SARS-CoV-2 virus genome detection assays – Authors‘ reply Open
View article: A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase
A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase Open
During RNA elongation, the influenza A viral (IAV) RNA-dependent RNA polymerase (RdRp) residues in the active site interact with the triphosphate moiety of nucleoside triphosphate (NTP) for catalysis. The molecular mechanisms by which they…
View article: An Efficient Method to Quantify Structural Distributions in Heterogeneous cryo-EM Datasets
An Efficient Method to Quantify Structural Distributions in Heterogeneous cryo-EM Datasets Open
Cryogenic Electron Microscopy (cryo-EM) preserves the ensemble of protein conformations in solution and thus provide a promising way to characterize conformational changes underlying protein functions. However, it remains challenging for e…
View article: Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model
Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model Open
Significance The initiation of bacterial transcription requires DNA loading via flexible loading gate of the RNA polymerase complex, consisting of the clamp and β-lobe domain. While the clamp is important in transcription initiation, the r…
View article: EmPC-seq: Accurate RNA-sequencing and Bioinformatics Platform to Map RNA Polymerases and Remove Background Error
EmPC-seq: Accurate RNA-sequencing and Bioinformatics Platform to Map RNA Polymerases and Remove Background Error Open
Transcription errors can substantially affect metabolic processes in organisms by altering the epigenome and causing misincorporations in mRNA, which is translated into aberrant mutant proteins. Moreover, within eukaryotic genomes there ar…
View article: Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain
Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain Open
The significant improvement in the binding affinity of the stapled peptide to the PSD-95 GK domain is mostly contributed by the reduction in the entropy penalty of the stapled peptide due to the restriction in the α-helical structure by st…
View article: Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome
Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome Open
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is responsible for the recent COVID-19 pandemic and polymerase chain reaction (PCR) is the current standard method for its diagnosis from patient sa…
View article: Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro
Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro Open
View article: Geographical distribution of removed data from Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome
Geographical distribution of removed data from Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome Open
Geographical analysis of removed data for 3 primers/probe with the highest frequency
View article: Geographical distribution of included sequence dataset and mismatches from Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome
Geographical distribution of included sequence dataset and mismatches from Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome Open
Geographical data used to draw graphs in figure 4
View article: Supplementary material from "Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome"
Supplementary material from "Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome" Open
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is responsible for the recent COVID-19 pandemic and polymerase chain reaction (PCR) is the current standard method for its diagnosis from patient sa…
View article: Acknowledgement table from Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome
Acknowledgement table from Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome Open
List of accession numbers and authors of the sequences