A5103079512- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Plant and Fungal Interactions Research
- SARS-CoV-2 and COVID-19 Research
- Chromosomal and Genetic Variations
- Single-cell and spatial transcriptomics
- Molecular Biology Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Vasculitis and related conditions
- Neonatal Respiratory Health Research
- Coronary Artery Anomalies
- Mesenchymal stem cell research
- Gene expression and cancer classification
- Kawasaki Disease and Coronary Complications
- Epigenetics and DNA Methylation
- Genetics and Neurodevelopmental Disorders
- Dengue and Mosquito Control Research
- Machine Learning in Bioinformatics
- Organ Transplantation Techniques and Outcomes
- Network Packet Processing and Optimization
- Dietary Effects on Health
Sun Yat-sen University
2020-2025
Southern Medical University Shenzhen Hospital
2025
State Grid Corporation of China (China)
2023-2024
Kunming Institute of Zoology
2022
Chinese Academy of Sciences
2022
Southern University of Science and Technology
2022
Clemson University
2022
University of Chinese Academy of Sciences
2022
BGI Group (China)
2022
BGI Genomics
2022
Translational systems can respond promptly to sudden environmental changes provide rapid adaptations stress. Unlike the well-studied translational responses oxidative stress in eukaryotic systems, little is known regarding how prokaryotes rapidly terms of translation. In this study, we measured protein synthesis from entire Escherichia coli proteome and found that was severely slowed down under With unchanged translation initiation, slowdown caused by decreased elongation speed. We further...
Although long-read single-cell RNA isoform sequencing (scISO-Seq) can reveal alternative splicing in individual cells, it suffers from a low read throughput. Here, we introduce HIT-scISOseq, method that removes most artifact cDNAs and concatenates multiple for PacBio circular consensus (CCS) to achieve high-throughput high-accuracy sequencing. HIT-scISOseq yield >10 million long-reads single Sequel II SMRT Cell 8M. We also report the development of scISA-Tools demultiplex concatenated reads...
Abstract Canonical three-dimensional (3D) genome structures represent the ensemble average of pairwise chromatin interactions but not single-allele topologies in populations cells. Recently developed Pore-C can capture multiway contacts that reflect regional single chromosomes. By carrying out high-throughput Pore-C, we reveal extensive regionally restricted clusters aggregate into canonical 3D two human cell types. We show fragments multi-contact reads generally coexist same TAD. In...
DNA methylation changes within the genome can be used to predict human age.However, existing biological age prediction models based on are predominantly adult-oriented.We established a methylation-based model for children (9-212 months old) using data from 716 blood samples in 11 datasets.Our elastic net includes 111 CpG sites, mostly genes associated with development and aging.The performed well exhibited high precision, yielding 98% correlation between chronological age, an error of only...
Abstract Background Smoking leads to the aging of organs. However, no studies have been conducted quantify effect smoking on respiratory organs and aging-reversing ability cessation. Results We collected genome-wide methylation datasets buccal cells, airway esophagus tissue, lung tissue from non-smokers, smokers, ex-smokers. used “epigenetic clock” method epigenetic age acceleration in four The statistical analyses showed following: (1) increased cells by an average 4.9 years 4.3 years. (2)...
In the process of translation, ribosomes first assemble on mRNAs (translation initiation) and then translate along mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant co-translational folding nascent peptides functionality protein products, which positioned evaluation elongation speed as one central questions in field translational control. By integrating three types RNA-seq methods, we experimentally computationally resolved speed, with our proposed...
Abstract Immunotherapy has revolutionized cancer treatment by leveraging the patient's immune system, yet its efficacy is often hampered immunosuppressive tumor microenvironment (TME). Adenosine, a key player in this milieu, suppresses cell activity via cAMP signaling. Here, an innovative strategy to remodel TME using genetically engineered strain of Escherichia coli Nissle 1917 that expresses adenosine deaminase on surface under hypoxic conditions presented. This probiotic targets tumors,...
Abstract The scientific observation of gamma-ray bursts (GRBs) paves the way towards unveiling a novel perspective dynamic universe. In past few years, several nano-satellite (NanoSat) GRB missions were deployed, especially Gamma-Ray Integrated Detectors (GRID) Mission which is currently constructing constellation NanoSats with more than ten compact detectors. Owing to unpredictability time and location GRBs, angular response such detector one most important aspects for not only localization...
Correct and bias-free interpretation of the deep sequencing data is inevitably dependent on complete mapping all mappable reads to reference sequence, especially for quantitative RNA-seq applications. Seed-based algorithms are generally slow but robust, while Burrows-Wheeler Transform (BWT) based fast less robust. To have both advantages, we developed an algorithm FANSe2 with iterative strategy statistics real-world error distribution substantially accelerate without compromising accuracy....
Abstract Coronavirus disease 2019 (COVID-19), driven by SARS-CoV-2, is a severe infectious that has become global health threat. Vaccines are among the most effective public tools for combating COVID-19. Immune status critical evaluating safety and response to vaccine, however, evolution of immune during immunization remains poorly understood. Single-cell RNA sequencing (scRNA-seq) represents powerful tool dissecting multicellular behavior discovering therapeutic antibodies. Herein,...
Chromosome-centric human proteome project (C-HPP) aims at differentiating chromosome-based and tissue-specific protein compositions in terms of expression, quantification, modification. We previously found that the analysis translating mRNA (mRNA attached to ribosome-nascent chain complex, RNC-mRNA) can explain over 94% mRNA-protein abundance. Therefore, we propose here use full-length RNC-mRNA information illustrate expression both qualitatively quantitatively. performed RNA-seq on...
We previously found that shorter mRNAs are preferably translated in various eukaryotic cells. However, the theoretical basis of this phenomenon is unclear. hypothesize mRNA length correlates to decreased translational error rate reduce energy consumption on defective protein degradation. In study, we established a computational model explain length-dependent translation initiation efficiency. provided mathematical evidence preference, rather than degradation, major factor shape genome-wide...
Finding protein evidence (PE) for coding genes is a primary task of the Phase I Chromosome-Centric Human Proteome Project (C-HPP). Currently, there are 2948 PE level 2–4 per neXtProt, which deemed missing proteins in human proteome. As most samples prepared and analyzed C-HPP framework were focusing on detergent soluble proteins, we posit that as natural composition cytoplasmic detergent-insoluble (DIPs) represent source finding proteins. We optimized workflow separated DIPs from three lung...
ABSTRACT Kawasaki disease (KD) is a systemic vasculitis syndrome that leads to coronary artery aneurysm (CAA). While echocardiography the most important imaging modality for assessment, specific diagnostic biomarker complementary CAA has not been reported. We aimed analyze profiles of exosomal miRNAs extracted from serum KD patients and controls identify candidate biomarkers CAA. Serum samples 39 healthy children, 42 patients, 38 dilatation (CAD) 45 virus‐infected including 24 EBV 21 ADV...
Respiratory syncytial virus (RSV) infection is the main cause of lower respiratory tract in children. However, there no effective treatment for RSV infection. Here, we aimed to identify potential biomarkers aid Children acute and convalescence phases were recruited proteomic analysis was performed differentially expressed proteins (DEPs). Subsequently, promising candidate determined by functional enrichment protein-protein interaction network analysis, underwent further validation western...
Abstract Single-cell isoform sequencing can reveal transcriptomic dynamics in individual cells invisible to bulk- and single-cell RNA analysis based on short-read sequencing. However, current long-read technologies have been limited by low throughput high error rate. Here we introduce HIT-scISOseq for high-throughput This method was made possible full-length cDNA capture using biotinylated PCR primers, our novel library preparation procedure that combines head-to-tail concatemeric cDNAs into...
Abstract Cultivation and environmental changes can induce development of novel phenotypes in plants. For example, the root morphology cultivated purple Eichhornia crassipes differs remarkably from normal also shows an enhanced ability to absorb heavy metal groundwater. However, gene expression associated with these processes are unknown because lack information on its large unsequenced genome complex plant-rhizosphere symbiotic system. To investigate changes, we applied a new strategy,...
Multiple search engines based on various models have been developed to MS/MS spectra against a reference database, providing different results for the same data set. How integrate these efficiently with minimal compromise false discoveries is an open question due lack of independent, reliable, and highly sensitive standard. We took advantage translating mRNA sequencing (RNC-seq) result as standard evaluate integration strategies protein identifications from engines. used seven mainstream...
Cancer genomics unveils many cancer-related mutations, including some chromosome 20 (Chr.20) genes. The mutated messages have been found in the corresponding mRNAs; however, whether they could be translated to proteins still requires more evidence. Herein, we proposed a transomics strategy profile expression status of human Chr.20 genes (555 Ensembl v72). data transcriptome and translatome (the mRNAs bound with ribosome, translating mRNAs) revealed that ∼80% coding on were detected mRNA...
We upgraded the preliminary CCPD 1.0 to 2.0 using latest deep-profiling proteome (CCPD 2013) of three hepatocellular carcinoma (HCC) cell lines, namely, Hep3B, MHCC97H, and HCCLM3 (ProteomeXchange identifiers: PXD000529, PXD000533, PXD000535). totally covered 63.6% (438/689) Chr. 8-coded proteins 62.6% (439/701) protein-coding genes. Interestingly, we found that missing exhibited a tendency form cluster region in chromosomes, such as two β-defensins clusters 8, caused perhaps by their...
Decompression has been considered a valuable tool for odontogenic cystic lesions to minimize cyst size with low morbidity and recurrence. However, whether decompression role in regulating stem cell properties of orofacial bone marrow stromal cells (BMSCs) around the cysts not fully investigated. The present study compared marker profile osteogenic differentiation potential BMSCs prior following marsupialization (pre‑BMSCs vs. post‑BMSCs) same individuals. results demonstrated that post‑BMSCs...
Asthma is one of the most common childhood chronic diseases worldwide. Subcutaneous immunotherapy (SCIT) commonly used in treatment house dust mite (HDM)‑related asthma children. However, therapeutic mechanism SCIT remains unclear. The present study aimed to investigate molecular biomarkers associated with HDM‑related asthmatic children prior and subsequent compared those healthy via proteomic analysis. included a control group (30 children), ‑Treatment allergic asthma) +Treatment treated...