A5100727472- Computational Drug Discovery Methods
- vaccines and immunoinformatics approaches
- Monoclonal and Polyclonal Antibodies Research
- Single-cell and spatial transcriptomics
- Listeria monocytogenes in Food Safety
- Vibrio bacteria research studies
- Genomics and Chromatin Dynamics
- Protein Structure and Dynamics
- Machine Learning in Materials Science
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Genomics, phytochemicals, and oxidative stress
- Immunotherapy and Immune Responses
- Topic Modeling
- RNA Research and Splicing
- Antibiotic Resistance in Bacteria
- Ferroptosis and cancer prognosis
- Biomedical Text Mining and Ontologies
- Antibiotics Pharmacokinetics and Efficacy
- Vehicle Routing Optimization Methods
- Epigenetics and DNA Methylation
- Gut microbiota and health
- Gene expression and cancer classification
- Aluminum Alloy Microstructure Properties
City University of Hong Kong
2021-2025
Guangxi University of Science and Technology
2025
Hainan Normal University
2024
Inner Mongolia University
2021-2024
Guizhou University
2024
Beihai People's Hospital
2024
Wenzhou Medical University
2021-2024
City University of Hong Kong, Shenzhen Research Institute
2024
Hong Kong Polytechnic University
2024
Guangxi Medical University
2024
Abstract Listeria monocytogenes ( Lm ) is a major human and animal foodborne pathogen. Here we show that hypervirulent clones, particularly CC1, are strongly associated with dairy products, whereas hypovirulent CC9 CC121, meat products. Clone adaptation to distinct ecological niches and/or different food products contamination routes may account for this uneven distribution. Indeed, clones colonize better the intestinal lumen invade more tissues than ones, reflecting their adaption host...
Abstract Structure-based generative chemistry is essential in computer-aided drug discovery by exploring a vast chemical space to design ligands with high binding affinity for targets. However, traditional silico methods are limited computational inefficiency, while machine learning approaches face bottlenecks due auto-regressive sampling. To address these concerns, we have developed conditional deep model, PMDM, 3D molecule generation fitting specified PMDM consists of equivariant diffusion...
The viable bacterial strains in conventional yogurt are intolerant to bile acid, which consequently cannot survive the conditions and their beneficial bioactivities thus lost. We have previously shown that Lactobacillus casei Q14 ( Lac-Q14), a probiotic, has potential alleviate diabetes rats. Herein, we used Lac-Q14 as starter culture ferment explore mechanisms of bioactivity diabetic results showed improved blood glucose insulin level, lowered gene expression critical enzymes involved liver...
The identification of drug-target interactions (DTIs) plays a vital role for in silico drug discovery, which the is chemical molecule, and target protein residues binding pocket. Manual DTI annotation approaches remain reliable; however, it notoriously laborious time-consuming to test each pair exhaustively. Recently, rapid growth labelled data has catalysed interests high-throughput prediction. Unfortunately, those methods highly rely on manual features denoted by human, leading...
Molecule generation, especially generating 3D molecular geometries from scratch (i.e., de novo generation), has become a fundamental task in drug design. Existing diffusion based molecule generation methods could suffer unsatisfactory performances, when large molecules. At the same time, generated molecules lack enough diversity. This paper proposes novel model to address those two challenges. First, interatomic relations are not included molecules' point cloud representations. Thus, it is...
Scope Gut microbiota imbalance, inflammation, and gut barrier deficiency play an important role in carcinogenesis. Sulforaphane (SFN), isothiocyanate found cruciferous vegetables, has been proven to be highly effective inhibiting cancer. The objective of this study is investigate the potential roles inhibition BBN-induced bladder cancer by SFN. Methods Results N-butyl-N-(4-hydroxybutyl)-nitrosamine used induce male C57BL/6 mice, with or without SFN for 23 weeks. ameliorates histological...
Listeria innocua is considered a nonpathogenic species. Natural atypical hemolytic L. isolates have been reported but not characterized in detail. Here, we report the genomic and functional characterization of representative from two known natural clades. Whole-genome sequencing confirmed presence pathogenicity islands (LIPI) characteristic monocytogenes Functional assays showed that LIPI-1 inlA genes are transcribed, corresponding gene products expressed functional. Using vitro vivo assays,...
Capsule networks (CapsNets), a new class of deep neural network architectures proposed recently by Hinton et al., have shown great performance in many fields, particularly image recognition and natural language processing. However, CapsNets not yet been applied to drug discovery-related studies. As the first attempt, we this investigation adopted develop classification models hERG blockers/nonblockers; drugs with blockade activity are thought potential risk cardiotoxicity. Two capsule were...
Abstract The single‐cell RNA sequencing (scRNA‐seq) quantifies the gene expression of individual cells, while bulk (bulk RNA‐seq) characterizes mixed transcriptome cells. inference drug sensitivities for cells can provide new insights to understand mechanism anti‐cancer response heterogeneity and resistance at cellular resolution. However, pharmacogenomic information related their corresponding scRNA‐Seq is often limited. Therefore, a transfer learning model proposed infer level. This...
Gene regulatory networks (GRNs) involve complex and multi-layer interactions between regulators their target genes. Precise knowledge of GRNs is important in understanding cellular processes molecular functions. Recent breakthroughs single-cell sequencing technology made it possible to infer at level. Existing methods, however, are limited by expensive computations, sometimes simplistic assumptions. To overcome these obstacles, we propose scGREAT, a framework GRN using gene embeddings...
Lysine acetylation is a well-studied post-translational modification on both histone and nonhistone proteins. More than 2000 acetylated proteins 4000 lysine sites have been identified by large scale mass spectrometry or traditional experimental methods. Although over 20 (K)-acetyl-transferases (KATs) characterized, which KAT responsible for given protein site mostly unknown. In this work, we collected KAT-specific manually analyzed sequence features surrounding the of substrates from three...
Listeriosis, caused by Listeria monocytogenes , is a severe food-borne infection. The nationwide surveillance in China concerning listeriosis urgently needed. In the present study, 144 L. isolates were collected from samples of blood, cerebrospinal fluid (CSF), and fetal membrane/placenta for 12 years 2008 to 2019. We summarized these patients’ demographical clinical features outcomes. susceptibility profile antibiotics was also determined broth microdilution method. Multilocus sequence...
Abstract The significant load disparity between the two decks of a cable-stayed bridge with separated unequal-width results in complex asymmetric static effects jointed dual-pylon. To investigate structural behaviour and reliability dual-pylon under loads, 1:30 scaled model test numerical simulation were conducted based on world's first road-railway same-level pylons. indicate when unbalanced horizontal force structure reaches its maximum during service phase, stress at connectivity node...
Abstract Single‐cell Hi‐C (scHi‐C) has provided unprecedented insights into the heterogeneity of 3D genome organization. However, its sparse and noisy nature poses challenges for computational analyses, such as chromatin architectural feature identification. Here, scCAFE is introduced, which a deep learning model multi‐scale detection features at single‐cell level. provides unified framework annotating loops, TAD‐like domains (TLDs), compartments across individual cells. This outperforms...
Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomic methods have been widely used to identify lysine acylation proteins. However, these experimental approaches often fail detect proteins that are in low abundance or absent specific biological samples. To circumvent problems, we developed a computational method predict acylation, including acetylation, malonylation, succinylation, and glutarylation. The prediction algorithm integrated flanking primary sequence...