A5090023284- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Mass Spectrometry Techniques and Applications
- Long-Term Effects of COVID-19
- COVID-19 Clinical Research Studies
- Genetic Associations and Epidemiology
- SARS-CoV-2 and COVID-19 Research
- RNA modifications and cancer
- Gut microbiota and health
- Receptor Mechanisms and Signaling
- Plant Gene Expression Analysis
- Cancer-related molecular mechanisms research
- SARS-CoV-2 detection and testing
- Thermal Regulation in Medicine
- Plant Molecular Biology Research
- Plant Stress Responses and Tolerance
- Mitochondrial Function and Pathology
- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Molecular Biology Techniques and Applications
- Bioinformatics and Genomic Networks
- Infectious Encephalopathies and Encephalitis
- Diabetes and associated disorders
Westlake University
2022-2025
Hangzhou First People's Hospital
2025
Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences
2022-2024
South China Normal University
2024
Hangzhou Center for Disease Control and Prevention
2023
Identification of protein quantitative trait loci (pQTL) helps understand the underlying mechanisms diseases and discover promising targets for pharmacological intervention. For most important class drug targets, genetic evidence needs to be generalizable diverse populations. Given that majority previous studies were conducted in European ancestry populations, little is known about protein-associated variants East Asians. Based on data-independent acquisition mass spectrometry technique, we...
The blood proteome contains biomarkers of ageing and age-associated diseases, but such markers are rarely validated longitudinally. Here we map the longitudinal in 7,565 serum samples from a cohort 3,796 middle-aged elderly adults across three time points over 9-year follow-up period. We pinpoint 86 ageing-related proteins that exhibit signatures associated with 32 clinical traits incidence 14 major chronic diseases. Leveraging machine-learning model, pick 22 these to generate proteomic...
Metabolic syndrome (MetS) is a complex metabolic disorder with global prevalence of 20%–25%. Early identification and intervention would help minimize the burden on healthcare systems. Here, we measured over 400 proteins from ∼20,000 proteomes using data-independent acquisition mass spectrometry for 7,890 serum samples longitudinal cohort 3,840 participants two follow-up time points 10 years. We then built machine-learning model predicting risk developing MetS within Our model, composed 11...
ABSTRACT In eukaryotes, RNA N 6 ‐methyladenosine (m A) modification and microRNA (miRNA)‐mediated silencing represent two critical epigenetic regulatory mechanisms. The m A methyltransferase complex (MTC) the microprocessor both undergo liquid–liquid phase separation to form nuclear membraneless organelles. Although has been shown positively regulate miRNA biogenesis, a mechanism of reciprocal regulation between MTC remained elusive. Here, we demonstrate that associate with each other...
Abstract Abscisic acid (ABA) signaling is crucial for plant responses to various abiotic stresses. The Arabidopsis (Arabidopsis thaliana) transcription factor ABA INSENSITIVE 5 (ABI5) a central regulator of signaling. ABI5 BINDING PROTEIN 1 (AFP1) interacts with and facilitates its 26S-proteasome-mediated degradation, although the detailed mechanism has remained unclear. Here, we report that an ABA-responsive U-box E3 ubiquitin ligase, PLANT U-BOX 35 (PUB35), physically AFP1 ABI5. PUB35...
The mouse is a valuable model organism for biomedical research. Here, we established comprehensive spectral library and the data-independent acquisition-based quantitative proteome maps 41 organs, including some rarely reported organs such as cornea, retina, nine paired organs. contained 178,304 peptides from 12,320 proteins, 1678 proteins not in previous libraries. Our data suggested that nervous system immune expressed most distinct compared with other We also found characteristic protein...
Analysis of large-scale data-independent acquisition mass spectrometry (DIA-MS) metaproteomics data remains a computational challenge. Here, we present pipeline called metaExpertPro for analysis. This encompasses spectral library generation using data-dependent MS (DDA-MS), protein identification and quantification DIA-MS, functional taxonomic annotation, as well quantitative matrix both microbiota hosts. By integrating FragPipe DIA-NN, offers compatibility with Orbitrap timsTOF instruments....
Quality control (QC) in mass spectrometry (MS)-based proteomics is mainly based on data-dependent acquisition (DDA) analysis of standard samples. Here, we collect 2754 files acquired by data independent (DIA) and paired 2638 DDA from mouse liver digests using 21 spectrometers across nine laboratories over 31 months. Our demonstrate that DIA-based LC-MS/MS-related consensus QC metrics exhibit higher sensitivity compared to DDA-based detecting changes LC-MS status. We then prioritize 15 invite...
USP7, a ubiquitin-specific peptidase (USP), plays an important role in many cellular processes through its catalytic deubiquitination of various substrates. However, nuclear function that shapes the transcriptional network mouse embryonic stem cells (mESCs) remains poorly understood. We report USP7 maintains mESC identity both activity-dependent and -independent repression lineage differentiation genes. Usp7 depletion attenuates SOX2 levels derepresses genes thereby compromising...
Serum antibodies IgM and IgG are elevated during Coronavirus Disease 2019 (COVID-19) to defend against viral attacks. Atypical results such as negative abnormally high antibody expression were frequently observed whereas the underlying molecular mechanisms elusive. In our cohort of 144 COVID-19 patients, 3.5% both negative, 29.2% remained only negative. The remaining patients exhibited positive expression, with 9.3% them exhibiting over 20-fold higher titers than others at their plateau. in...
Abstract Background Analysis of mass spectrometry-based metaproteomic data, in particular large-scale data-independent acquisition MS (DIA-MS) remains a computational challenge. Here, we aim to develop software tool for efficiently constructing spectral libraries and analyzing extensive datasets DIA-based metaproteomics. Results We present pipeline called metaExpertPro metaproteomics data analysis. This encompasses library generation using data-dependent (DDA-MS), protein identification...
<title>Abstract</title> Quality control (QC) in mass spectrometry (MS)-based proteomics is mainly based on data-dependent acquisition (DDA) analysis of standard samples. Here, we collected 2638 files acquired by data independent (DIA) and paired DDA from mouse liver digests using 21 spectrometers across nine laboratories over 31 months. Our demonstrated that DIA-based LC-MS/MS-related consensus QC metrics exhibit higher sensitivity compared to DDA-based detecting changes LC-MS status. We...
This study investigated host responses to long COVID by following up with 89 of the original 144 cohorts for 1-year (
ABSTRACT Metabolic syndrome (MetS) is a complex metabolic disorder with global prevalence of 20-25%. Early identification and intervention would help minimize the burden on healthcare systems. Here, we measured over 400 proteins from ∼20,000 proteomes using data-independent acquisition mass spectrometry for 7890 serum samples longitudinal cohort 3840 participants two follow-up time points ten years. We then built machine learning model predicting risk developing MetS within Our model,...
Abstract Background Analysis of mass spectrometry-based metaproteomic data, in particular large-scale data-independent acquisition MS (DIA-MS) remains a computational challenge. Here, we aim to develop software tool for efficiently constructing spectral libraries and analyzing extensive datasets DIA-based metaproteomics. Results We present pipeline called metaExpertPro metaproteomics data analysis. This encompasses library generation using data-dependent (DDA-MS), protein identification...
Abstract More than 450 million individuals have recovered from COVID-19, but little is known about the host responses to long COVID. We performed proteomic and metabolomic analyses of 991 blood urine specimens 144 COVID-19 patients with comprehensive clinical data up 763 days follow up. Our showed that lungs kidneys are most vulnerable organs in COVID patients. Pulmonary renal one-year revisit can be predicted by a machine learning model based on multi-omics collected during first month...
Abstract Serum antibodies IgM and IgG are elevated during COVID-19 to defend against viral attack. Atypical results such as negative abnormally high antibody expression were frequently observed whereas the underlying molecular mechanisms elusive. In our cohort of 144 patients, 3.5% both 29.2% remained only negative. The remaining patients exhibited positive expression, with 9.3% them exhibiting over 20-fold higher titers than others at their plateau. in all significantly boosted after...