A5062632432- Genomics and Phylogenetic Studies
- Plant nutrient uptake and metabolism
- SARS-CoV-2 detection and testing
- Cell Image Analysis Techniques
- SARS-CoV-2 and COVID-19 Research
- Plant Taxonomy and Phylogenetics
- Legume Nitrogen Fixing Symbiosis
- Bioenergy crop production and management
- Animal testing and alternatives
- Gut microbiota and health
- CRISPR and Genetic Engineering
- Bacterial Identification and Susceptibility Testing
- Bacteriophages and microbial interactions
- Soil and Water Nutrient Dynamics
- Bacterial biofilms and quorum sensing
- Plant Virus Research Studies
- Vector-borne infectious diseases
- Advanced biosensing and bioanalysis techniques
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- Machine Learning in Bioinformatics
- Biosensors and Analytical Detection
- Environmental Science and Technology
- Plant Pathogenic Bacteria Studies
- Viral Infections and Vectors
Rice University
2020-2024
Huaqiao University
2024
University of South China
2024
University of Chinese Academy of Sciences
2022
Jiangsu University
2022
Women's Hospital, School of Medicine, Zhejiang University
2022
Institute of Geographic Sciences and Natural Resources Research
2022
University of Wisconsin–Madison
2021
Hainan University
2019-2020
Tropical Crops Genetic Resources Institute
2020
The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number single nucleotide polymorphisms (SNPs) that differentiate main SARS-CoV-2 lineages have spread throughout world. In study, we investigated 129 RNA-seq data sets and 6928 consensus genomes contrast intra-host inter-host diversity SARS-CoV-2. Our analyses yielded three major observations....
Phosphorus (P) deficiency is one of the major constraints limiting plant growth, especially in acid soils. Stylosanthes (stylo) a pioneer tropical legume with excellent adaptability to low P stress, but its underlying mechanisms remain largely unknown.
Abstract As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection based quasi-unique mutations. The benefits QuaID are three-fold: (i) provides up to 3-week earlier detection, (ii) accurate (>95% precision simulated benchmarks), and (iii) leverages all mutational signatures (including insertions & deletions).
Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost. Tracking frequency intra-host variants provides important insights with respect to elucidating within-host viral population dynamics transmission. However, given the higher error rate of ONT, accurate identification allele frequencies remains an open challenge no viable computational solutions available. In response this need, we present Variabel, a novel approach first...
The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number single nucleotide polymorphisms (SNPs) that differentiate main SARS-CoV-2 clades have spread throughout world. In study, we investigated over 7,000 datasets unveil both intrahost and interhost diversity. Our diversity analyses yielded three major observations. First, mutational profile...
Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant human health and disease. However, contaminant sequences in metagenomic samples can potentially impact interpretation findings reported microbiome studies, especially low-biomass environments. Contamination from DNA extraction kits or sampling lab environments leaves taxonomic "bread crumbs" across multiple distinct sample types. Here we describe Squeegee, a de novo contamination...
Wastewater surveillance for SARS-CoV-2 provides early warnings of emerging variants concerns and can be used to screen novel cryptic linked-read mutations, which are co-occurring single nucleotide mutations that rare, or entirely missing, in existing databases. While previous approaches have focused on specific regions the genome, there is a need computational tools capable efficiently tracking across entire genome investigating their potential origin. We present Crykey, tool rapidly...
Hypertension may result in atrial fibrillation (AF) and lipid metabolism disorders. The Sirtuins3 (SIRT3)/AMP-activated protein kinase (AMPK) signaling pathway has the capacity to regulate disorders onset of AF. We hypothesize that SIRT3/AMPK suppresses disorders, thereby mitigating salt-sensitive hypertension (SSHT)-induced susceptibility
The purpose of this study is to prove the lipid-regulating effects neohesperidin (NHP) and explore potential mechanisms related fibroblast growth factor 21 (FGF21) AMP-activated protein kinase (AMPK). Free fatty acids (FFAs)-induced lipid-accumulated HepG<sub>2</sub> cells, acutely egg yolk-induced dyslipidemia chronically diet-induced obese (DIO) model mice were treated with NHP. Biochemical analyses carried out determine lipid profiles. Western blotting real-time PCR employed...
The coronavirus disease 2019 (COVID-19) pandemic caused by frequently mutating severe acute respiratory syndrome 2 (SARS-CoV-2) has had a worldwide impact. However, detailed data on the potential aerosol transmission of SARS-CoV-2 in real-world and controlled laboratory settings remain sparse. During COVID-19 Shanghai, China 2022, samples were collected Fangcang shelter hospital, large-scale temporary hospital rapidly built converting existing National Exhibition Convention Center (Shanghai)...
ABSTRACT Genomic surveillance and epidemiology have shed light on the viral diversity driving coronavirus disease 2019 (COVID-19) outbreaks are important during waves of highly transmissible immune-escaping variants interest or concern (VOCs). We analyzed epidemiological data understudied country Malta related patterns observed with genetic sequences obtained through system headed by Mater Dei Hospital University Malta. reconstructed evolutionary history spatiotemporal dynamics Maltese...
With recent advances in sequencing technology it has become affordable and practical to sequence genomes very high depth-of-coverage, allowing researchers discover low-frequency variants the genome. However, due errors is an active area of research develop algorithms that can separate noise from true variants. LoFreq a state art algorithm for variant detection but relatively long runtime compared other tools. In addition this, interface running parallel could be simplified, multithreading as...
Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost, exemplified by well over a half of million ONT SARS-COV-2 datasets. Tracking frequency intra-host variants has provided important insights with respect to elucidating within host viral population dynamics transmission. However, given the higher error rate ONT, accurate identification allele frequencies remains an open challenge no viable solutions available. In response...
ABSTRACT The COVID-19 pandemic forever underscored the need for biosurveillance platforms capable of rapid detection previously unseen pathogens. Oxford Nanopore Technology (ONT) couples long-read sequencing with in-field capability, opening door to real-time, biosurveillance. Though a promising technology, streaming assignment accurate functional and taxonomic labels nanopore reads remains challenging given: (i) individual can span multiple genes, (ii) may contain truncated pseudogenes,...
The COVID-19 pandemic forever underscored the need for bio-surveillance platforms capable of rapidly detecting emerging pathogens. Oxford Nanopore Technology (ONT) couples long-read sequencing with in-field capability, opening door to real-time, biosurveillance. Though a promising technology, streaming assignment accurate functional and taxonomic labels nanopore reads remains challenging given: (i) individual can span multiple genes, (ii) may contain truncated genes pseudogenes, (iii) error...
Schizophrenia is a chronic, serious and disabling mental disorder. Most patients can effectively control their condition through drug treatment, but there are still some who difficult to gain benefits from treatment. Among them, the failure respond clozapine full-scale treatment ultra-treatment-resistant schizophrenia. We generated induced pluripotent stem cells (iPSCs) an schizophrenia patient by electroporation of peripheral blood mononuclear (PBMCs) with episomal plasmids encoding OCT 4,...
Abstract Hibernation is a mammalian strategy that uses metabolic plasticity to reduce energy demands and enable long-term fasting. Fasting mitigates winter food scarcity but eliminates dietary nitrogen, jeopardizing body protein balance. Here, we reveal gut microbiome-mediated urea nitrogen recycling in hibernating 13-lined ground squirrels (TLGS). Ureolytic microbes incorporate into organic compounds are absorbed by the host, with reincorporated TLGS pool. Urea greatest after prolonged...
Abstract As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variants concern (VoC) in communities. Multiple recent studies support that wastewater-based detection circulating VoC precede cases by up to two weeks. Furthermore, based epidemiology enables wide population-based screening and study viral evolutionary dynamics. However, highly sensitive emerging remains a complex task due pooled nature environmental samples genetic...