A5023727941- Gut microbiota and health
- Bayesian Methods and Mixture Models
- Metabolomics and Mass Spectrometry Studies
- Gene expression and cancer classification
- Thermal properties of materials
- Clostridium difficile and Clostridium perfringens research
- Oral microbiology and periodontitis research
- Nasal Surgery and Airway Studies
- Statistical Methods and Inference
- GaN-based semiconductor devices and materials
- Nutritional Studies and Diet
- Bioinformatics and Genomic Networks
- Surface and Thin Film Phenomena
- Graphene research and applications
- Cleft Lip and Palate Research
- Semiconductor materials and interfaces
- Genetic and phenotypic traits in livestock
- Forensic Anthropology and Bioarchaeology Studies
- Salivary Gland Disorders and Functions
- Advanced Thermoelectric Materials and Devices
- Colorectal Cancer Screening and Detection
- Genomics and Phylogenetic Studies
- Metallic Glasses and Amorphous Alloys
- vaccines and immunoinformatics approaches
- Machine Learning in Materials Science
Shanghai Jiao Tong University
2011-2024
Shanghai Mental Health Center
2023
Peking University
2021
Nanjing Jiangning Hospital
2021
Nanjing Medical University
2021
Ruhr University Bochum
2017-2020
Shanghai Center for Brain Science and Brain-Inspired Technology
2019
Shanghai Institute for Science of Science
2019
Fudan University
2019
The University of Texas Southwestern Medical Center
2019
Abstract Metaproteomics can provide valuable insights into the functions of human gut microbiota (GM), but is challenging due to extreme complexity and heterogeneity GM. Data-independent acquisition (DIA) mass spectrometry (MS) has been an emerging quantitative technique in conventional proteomics, still at early stage development field metaproteomics. Herein, we applied library-free DIA (directDIA)-based metaproteomics compared directDIA with other MS-based quantification techniques for on...
Abstract Tetraploid Artemisia annua plants were successfully inducted by using colchicine, and their ploidy was confirmed flow cytometry. Higher stomatal length but lower frequency in tetraploids revealed could be considered as indicators of polyploidy. The average level artemisinin increased from 39% to 56% than that the diploids during vegetation period, detected high‐performance liquid chromatography–evaporative light scattering detector. Gene expressions 10 key enzymes related...
Heat management in thermoelectric and power devices as well random access memories poses a grand challenge can make the difference between working an abandoned device design. Despite prevalence of dislocations all these technologies, modeling their thermal resistance is based on 50-year-old analytical approximations, whose simplicity was driven by practical limitations rather than physical insight. We introduce efficient ab initio approach Green's functions computed two-dimensional...
Summary Understanding the factors that alter composition of human microbiota may help personalized healthcare strategies and therapeutic drug targets. In many sequencing studies, microbial communities are characterized by a list taxa, their counts, evolutionary relationships represented phylogenetic tree. this article, we consider an extension Dirichlet multinomial distribution, called Dirichlet-tree for multivariate, over-dispersed, tree-structured count data. To address between these...
Schizophrenia is a debilitating mental disorder and often has prodromal period, referred to as clinical high risk (CHR) for psychosis, prior the first episode. The etiology pathogenesis of schizophrenia remain unclear. Despite human gut microbiome being associated with schizophrenia, role oral microbiome, which vital player in mouth-body connection, not well understood. To address this, we performed 16S rRNA gene sequencing investigate salivary 85 patients drug-naïve first-episode (FES), 43...
Abstract The analysis of microbiome data has several technical challenges. In particular, count matrices contain a large proportion zeros, some which are biological, whereas others technical. Furthermore, the measurements suffer from unequal sequencing depth, overdispersion, and redundancy. These nuisance factors introduce substantial noise. We propose an accurate robust method, mbDenoise, for denoising data. Assuming zero-inflated probabilistic PCA (ZIPPCA) model, mbDenoise uses variational...
The development of a neoantigen-based personalized vaccine has promise in the hunt for cancer immunotherapy. challenge neoantigen design is need to rapidly and accurately identify, patients, those neoantigens with potential. Evidence shows that can be derived from noncoding sequences, but there are few specific tools identifying regions. In this work, we describe proteogenomics-based pipeline, namely PGNneo, use discovering region human genome reliability. four modules included: (1) somatic...
Crystal imperfections such as dislocations strongly influence the performance and thermal transport behavior of GaN-based devices. We show that experimental data used to parametrize effect on conductivity can be explained using only reported film thickness point defect concentrations. The analysis highlights boundary-scattering-governed reduction in GaN, which had been underestimated earlier models. To quantify we adopt a Green's function approach based accurate ab initio interatomic force...
Analysis of compositions microbiomes (ANCOM) compares the absolute abundances microbes between two or more ecosystems using relative in specimens derived from these ecosystems. Despite its impressive performance, there are drawbacks to ANCOM. First, with K it requires fitting K(K-1)/2 models for log-ratios counts, and so can be computationally intensive. Second, does not output P-values detected as differentially abundant. We propose a fast implementation ANCOM, fastANCOM, that fits only...
Abstract Background Advances in DNA sequencing have offered researchers an unprecedented opportunity to better study the variety of species living and on human body. However, analysis microbiome data is complicated by several challenges. First, depth may vary orders magnitude across samples. Second, are rare often contain many zeros. Third, specimen a fraction microbial ecosystem, so compositional carrying only relative information. Other characteristics include pronounced over-dispersion...
Bone morphogenetic protein 6 (BMP6) has neuroprotective effects against various neuronal injuries, but its effect on amyloid-β (Aβ)-induced neurotoxicity remains unclear. We exposed rat hippocampal neurons to different concentrations of Aβ25-35 in
The coevolution between human and bacteria colonizing the body has profound implications for heath development, with a growing of evidence linking altered microbiome composition wide array disease states. Yet dimension reduction visualization analysis data are still in their infancy many challenges exist. In this article, we introduce general framework, zero-inflated probabilistic principal component (ZIPPCA), ordination multivariate abundance data, propose an efficient variational...
Microbiome data have proven extremely useful for understanding microbial communities and their impacts in health disease. Although microbiome analysis methods standards are evolving rapidly, obtaining meaningful interpretable results from studies still requires careful statistical treatment. In particular, many existing emerging differential abundance (DA) fail to account the fact that high-dimensional sparse, compositional, negatively positively correlated phylogenetically structured. To...
Abstract One goal of human microbiome studies is to relate host traits with compositions. The analysis microbial community sequencing data presents great statistical challenges, especially when the samples have different library sizes and are overdispersed many zeros. To address these we introduce a new framework, called predictive in metagenomics via inverse regression (PAMIR), analyze data. Within this an model developed for microbiota counts given trait, then prediction rule constructed...
Abstract Advances in sequencing technologies and bioinformatics tools have vastly improved our ability to collect analyze data from complex microbial communities. A major goal of microbiome studies is correlate the overall composition with clinical or environmental variables. La Rosa et al . recently proposed a parametric test for comparing populations between two more groups subjects. However, this method not applicable testing association community continuous variable. Although...
Abstract As our understanding of the microbiome has expanded, so recognition its critical role in human health and disease, thereby emphasizing importance testing whether microbes are associated with environmental factors or clinical outcomes. However, many fundamental challenges that concern surveys arise from statistical experimental design issues, such as sparse overdispersed nature count data complex correlation structure among samples. For example, project (HMP) dataset, repeated...
Setup computational fluid dynamics (CFD) model of the nasal cavity in patients with Crouzon syndrome analyze inspiratory airflow hydrokinetics its cavity. After changing morphosis structure by operation, compare preoperative and postoperative alteration field evaluate effect operation on physiological function ventilation.Eleven were underwent spiral computed tomographic laminar scanning to obtain DICOM data establish CFD model. The features static state phase simulated analyzed Fluent...