A5069309421- Advanced Proteomics Techniques and Applications
- Machine Learning in Bioinformatics
- Power Systems and Technologies
- Herpesvirus Infections and Treatments
- RNA and protein synthesis mechanisms
- Smart Grid and Power Systems
- Genomics and Phylogenetic Studies
- Immunotherapy and Immune Responses
- Peptidase Inhibition and Analysis
- Mass Spectrometry Techniques and Applications
- Electric Motor Design and Analysis
- Mitochondrial Function and Pathology
- Power Systems and Renewable Energy
- RNA Interference and Gene Delivery
- Toxin Mechanisms and Immunotoxins
- Hemoglobinopathies and Related Disorders
- Iron Metabolism and Disorders
- Power Systems Fault Detection
- Genomics and Chromatin Dynamics
- Educational Technology and Pedagogy
- Power System Optimization and Stability
- Heat transfer and supercritical fluids
- ATP Synthase and ATPases Research
- vaccines and immunoinformatics approaches
- Virus-based gene therapy research
BGI Group (China)
2012-2024
Hospital of Hebei Province
2024
Shanghai Jiao Tong University
2022-2024
BGI Genomics
2022-2024
Fujian Agriculture and Forestry University
2022-2024
Hebei Medical University
2024
Changchun University of Science and Technology
2023
Changzhou Institute of Technology
2023
Soochow University
2022
Shandong University
2022
The accuracy of peptide retention time (RT) prediction model in liquid chromatography (LC) is still not sufficient for wider implementation proteomics practice. Herein, we propose deep learning as an ideal tool to considerably improve this prediction. A new RT tool, DeepRT, was designed using a capsule network model, and the public data sets containing peptides separated by reverse-phase were used evaluate DeepRT performance. Compared with other prevailing predictors, attained overall...
Compared to classical antibodies, camel heavy chain antibodies (HCAbs) are smaller in size due lack of the light and first constant domain (CH1 region). The variable regions HCAbs (VHHs) more soluble stable than that conventional (VHs). Even with such simple structure, they still functional antigen binding. Although have been extensively investigated over past two decades, most efforts based upon low throughput sequence analysis, there only limited reports trying analyze describe complete...
Oxidative stress is one of the main causes myocardial injury, which associated with cardiomyocyte death. Mitochondria play a key role in triggering necrosis and apoptosis pathway cardiomyocytes under oxidative stress. Although prohibitin (PHB) has been acknowledged as mitochondrial chaperone, its functions are poorly characterized. The present research was designed to investigate cardioprotective PHB mitochondria. can increase content mitochondria time-dependent manner. Overexpression...
Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present open source software tool, termed IPeak, a peptide identification pipeline that designed to combine the Percolator post-processing algorithm and multi-search strategy enhance sensitivity of identifications without compromising accuracy. IPeak provides graphical user interface (GUI) as well command-line interface, which implemented JAVA can...
Identification of α-thalassemia silent carriers is challenging with conventional phenotype-based screening methods. A liquid chromatography tandem mass spectrometry (LC–MS/MS)-based approach may offer novel biomarkers to address this conundrum. In study, we collected dried blood spot samples from individuals three subtypes for biomarker discovery and validation. We observed differential expression patterns hemoglobin subunits among various normal controls through proteomic profiling 51 in...
Rice (Oryza sativa) is one of the most important worldwide crops. The genome has been available for over 10 years and undergone several rounds annotation. We created a comprehensive database transcripts from 29 public RNA sequencing data sets, officially predicted genes Ensembl plants, common contaminants in which to search protein-level evidence. re-analyzed nine publicly accessible rice proteomics sets. In total, we identified 420K peptide spectrum matches 47K peptides 8,187 protein...
Phosphorylation is one of the most prevalent post-translational modifications and plays a key role in regulating cellular processes. We carried out bioinformatics analysis pre-existing phosphoproteomics data, to profile two model species representing largest subclasses flowering plants dicot Arabidopsis thaliana monocot Oryza sativa, understand extent which phosphorylation signaling function conserved across evolutionary divergent plants. identified 6537 phosphopeptides from 3189...
Under the guidance of Chromosome-centric Human Proteome Project (C-HPP),(1, 2) we conducted a systematic survey expression status genes located at human chromosome 20 (Chr.20) in three cancer tissues, gastric, colon, and liver carcinoma, their representative cell lines. We have globally profiled proteomes these samples with combined technology LC–MS/MS acquired corresponding mRNA information upon RNA-seq RNAchip. In total, 323 unique proteins were identified, covering 60% coding (323/547)...
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...
Herpes simplex virus type 1 (HSV-1) is an important human pathogenic virus. It urgent to develop novel antiviral targets because of the limited treatment options and emergence drug resistant strains. In this study, we tested activity lupeol, a triterpenoid compound, against HSV-1 acyclovir (ACV) Lupeol significantly inhibited (F strain) ACV-resistant strains including HSV-1/106, HSV-1/153, HSV-1/Blue. HSV-1α0 α4 promoters, therefore down regulating expression α0, α4, α27 genes. Collectively,...
β-Defensins (DEFBs) have a variety of functions. The majority these proteins were not identified in recent proteome survey. Neither protein detection nor the analysis transcriptomic data based on RNA-seq for three liver cancer cell lines any expression products. Extensive investigation into DEFB transcripts over 70 offered similar results. This fact naturally begs question—Why are genes scarcely expressed? After examining gene annotation and physicochemical properties its products, we...
In this paper, an improved magnetic equivalent circuit (MEC) is applied to calculate the nonlinear field in interior-type permanent-magnet (IPM) brushless DC (BLDC) motor. Compared with finite element method, MEC method much more time efficient, whereas compared conventional accurate since it takes complicate topological structure of motor into account. A rough design IPM BLDC was firstly conducted by method. The particle swarm optimization (PSO) algorithm then employed refine for optimal...
Abstract Background Accurate prediction of epitopes presented by human leukocyte antigen (HLA) is crucial for personalized cancer immunotherapies targeting T cell epitopes. Mass spectrometry (MS) profiling eluted HLA ligands, which provides high-throughput measurements associated peptides in vivo , can be used to faithfully model the presentation on surface. In addition, gene expression profiles measured RNA-seq data a specific cell/tissue type significantly improve performance epitope...
Database searches of MS/MS spectra are the main approach to peptide/protein identification in proteomics. Since most database search engines only utilize a small portion original signals for peptide detection, how improve quality is primary concern enhancement rate. A fundamental issue that some noise MS signals, informative or uninformative, have be filtered out prior searching. Herein, an integrative preprocessing algorithm was designed, termed pClean, which incorporates three modules...
Abstract In the process of teaching English in colleges and universities, variability students’ performance factors affecting this have been considered by teachers students. paper, data mining is applied to systematic design framework system universities constructed improving decision tree algorithm. The encompasses seven modules, from login module personalized analysis based on tree, which includes entire learning universities. For model total error rate training samples 2.14, while overall...
Abstract To investigate the relationship between maternal nutritional status of multiple amino acids and vitamins during early pregnancy risk preterm birth, plasma samples 7952 pregnant women 12~24 gestational weeks were enrolled, levels 20 10 measured. The abundance differences representative nutrients among stratified groups potential birth analyzed evaluated. aspartate, methionine, retinol significantly higher, that 4-pyridoxic acid was lower in group compared to full-term pregnancy. odds...
Abstract Background To explore a method for screening and diagnosing neonatal congenital heart disease (CHD) applicable to grassroots level, evaluate the prevalence of CHD, establish hierarchical management system CHD treatment at level. Methods A total 24,253 newborns born in Tang County between January 2016 December 2020 were consecutively enrolled screened by trained primary physicians via “twelve-section ultrasonic diagnosis method” (referred as method”). Specialized staff from Screening...