A5101602357- Advanced Proteomics Techniques and Applications
- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
- Marine Sponges and Natural Products
- Bioinformatics and Genomic Networks
- Algorithms and Data Compression
- Oxidative Organic Chemistry Reactions
- Biomedical Text Mining and Ontologies
- Glycosylation and Glycoproteins Research
- Distributed systems and fault tolerance
- Nanoplatforms for cancer theranostics
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Peptidase Inhibition and Analysis
- Luminescence and Fluorescent Materials
- Microbial Natural Products and Biosynthesis
- Logic, programming, and type systems
- Mass Spectrometry Techniques and Applications
- vaccines and immunoinformatics approaches
- Chronic Lymphocytic Leukemia Research
- Magnolia and Illicium research
- Plant-derived Lignans Synthesis and Bioactivity
- Parallel Computing and Optimization Techniques
- Bioactive Natural Diterpenoids Research
- Rheumatoid Arthritis Research and Therapies
South China University of Technology
2025
Bioinformatics Solutions (Canada)
2023-2025
Solutions Inc. (Japan)
2023-2025
Nanchang University
2025
Naval University of Engineering
2024
Hangzhou Normal University
2024
Xiamen University
2021-2023
Collaborative Innovation Center of Chemistry for Energy Materials
2021-2022
Western University
2007-2008
Abstract Here we present GlycanFinder, a database search and de novo sequencing tool for the analysis of intact glycopeptides from mass spectrometry data. GlycanFinder integrates peptide-based glycan-based strategies to address challenge complex fragmentation glycopeptides. A deep learning model is designed capture glycan tree structures their fragment ions glycans that do not exist in database. We performed extensive analyses validate false discovery rates (FDRs) at both peptide levels...
We disclose unified, protecting-group-free, bioinspired divergent total syntheses of eight allo-cedrane and seco-prezizaane Illicium sesquiterpenes formal five anislactone sesquiterpenes. The efficiency our approach derives from rapid access to the 15-carbon tricyclic carboxylic acid through cationic epoxide-ene cyclization HAT oxygenation, transformation this intermediate into three distinct precursors via Lewis acid-mediated skeletal reorganizations, subsequent programmed oxidation level...
A concise and divergent synthesis of the polychlorinated marine steroids clionastatin B from inexpensive testosterone has been achieved through a unique two-stage chlorination–oxidation strategy. Key features include (1) conformationally controlled, highly stereoselective dichlorination at C1 C2 C4–OH-directed C19 oxygenation followed by challenging neopentyl chlorination to install three chlorine atoms; (2) desaturation one-pot photochemical dibromination–reductive debromination...
<title>Abstract</title> In this paper, we propose a new search algorithm for proteoform identification that computes the largest size error correction alignments between protein mass graph (PMG) and spectrum (SMG). We also design filtering algorithm. The combined method uses to get some candidates then apply report final results. Our exact searching is 3.9 9.0 times faster than popular methods such as TopMG TopPIC. can further speed up running time of our sTopMG by 6.2 without affecting...
The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. While modern pre-trained models have achieved great success in analyzing these macromolecules individually, their interconnected nature remains under-explored. In this paper, we follow guidance redesign both data model pipeline offer a comprehensive framework, Life-Code, that spans different functions. As for flow, propose unified integrate...
Abstract Background Rheumatoid arthritis (RA) increases the risk of stroke. However, relationship between RA and stroke remains unclear. This study aimed to explore shared genetics architecture (i.e., common genetic basis different traits, diseases, or phenotypes) stroke, aiming improve intervention management patients with Methods Pooled statistics from publicly available genome-wide association studies for (8,255 cases 409,001 controls) (43,132 43,132 were used. A positive was conducted...
Multiplexed CRISPR design, which allows for the concurrent and efficient editing of multiple genomic sites, is a powerful tool complex genetic modifications. However, designing effective multiplexed guide RNA (gRNA) arrays remains challenging due to exponential increase in potential gRNA array candidates significant impact different target site selections on efficiency specificity. Recognizing that more stable gRNAs, characterized by lower minimum free energy (MFE), have prolonged activity...
Abstract De novo peptide sequencing is a fundamental research area in mass spectrometry (MS) based proteomics. However, those methods have often been evaluated using couple of simple metrics that do not fully reflect their overall performance. Moreover, there has an established method to estimate the false discovery rate (FDR) and significance de peptide-spectrum matches (PSMs). Here we propose NovoBoard, comprehensive framework evaluate performance methods. The consists diverse benchmark...
Open AccessCCS ChemistryRESEARCH ARTICLE1 Mar 2022Total Synthesis of Stemarene and Betaerene Diterpenoids: Divergent Ring-Formation Strategy Late-Stage C–H Functionalization Renzhi Chen†, Feng Zhang†, Yuhui Hua†, Dong Shi, Xin Lei, Hongxiu Xiao, Yinong Wang, Shihao Ding, Yang Shen Yandong Zhang Chen† Department Chemistry, Chemical Biology, Key Laboratory Biology Fujian Province, iChEM, College Chemistry Engineering, Xiamen University, Xiamen, 361005 , Zhang† Hua† Shi Lei Xiao Wang Ding...
Abstract Here we proposed DeepImmu, a complete pipeline for neoantigen identification and validation that was based solely on mass spectrometry (MS) immunopeptidomics. In particular, new enrichment kit developed HLA peptide purification from small amount of biopsied tissue as low 18mg. To identify candidate neoantigens such sample, built DeepNovo Peptidome, highly sensitive de novo sequencing-based workflow identification. Furthermore, DeepSelf, personalized model immunogenicity prediction...
Omphalane diterpenoids usually contain a cyclohexane-fused bicyclo[3.2.1]octane scaffold embedded with two continuous quaternary carbon centers, which pose considerable challenges to synthetic chemists. Herein, we reported the first total synthesis of omphalic acid high stereochemical control, featuring an intermolecular Diels–Alder cycloaddition, ring reorganization through Criegee oxidative cleavage and programmed aldol condensations, conformationally controlled hydrogenation, Pd-catalyzed...
Comprehensive Summary A full account of semisyntheses polychlorinated marine steroids clionastatins and B is described. We have developed a unique two‐stage chlorination‐oxidation strategy that enabled concise divergent in 16 steps from inexpensive testosterone. Key transformations chlorination stage include (a) conformationally controlled, stereospecific dichlorination through an unusual β‐chloronium intermediate to install the diequatorial C1,C2‐dichloride; (b) C4‐OH directed C19–H...
A photo-controlled optical molecular switch has been achieved. Apparent and emissive color changes under visible light irradiation temperature stimulation have achieved used to develop anti-counterfeiting materials.
The integration of deep learning approaches in biomedical research has been transformative, enabling breakthroughs various applications. Despite these strides, its application protein inference is impeded by the scarcity extensively labeled data sets, a challenge compounded high costs and complexities accurate annotation. In this study, we introduce GraphPI, novel framework that treats as node classification problem. We treat proteins interconnected nodes within protein–peptide–PSM graph,...
This paper introduces two advancements in the field of Large Language Model Annotation with a focus on punctuation restoration tasks. Our first contribution is application LLaMA for restoration, which demonstrates superior performance compared to established benchmark. Despite its impressive quality, faces challenges regarding inference speed and hallucinations. To address this, our second presents Forward Pass Only Decoding (FPOD), novel decoding approach annotation innovative method...