A5060533782- Genomics and Phylogenetic Studies
- Gut microbiota and health
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Bacteriophages and microbial interactions
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Microbial Community Ecology and Physiology
- Gastrointestinal motility and disorders
- Probiotics and Fermented Foods
- Diet and metabolism studies
- Genomics and Chromatin Dynamics
- SARS-CoV-2 and COVID-19 Research
- EEG and Brain-Computer Interfaces
- Plant Virus Research Studies
- Genomic variations and chromosomal abnormalities
- Clostridium difficile and Clostridium perfringens research
- Microbial infections and disease research
- Functional Brain Connectivity Studies
- COVID-19 diagnosis using AI
- Cancer-related molecular mechanisms research
- Nutritional Studies and Diet
- Neurological disorders and treatments
- Metabolomics and Mass Spectrometry Studies
- RNA modifications and cancer
Peking University
2016-2025
Center for Life Sciences
2025
Georgia Institute of Technology
2020-2024
Emory University
2020-2024
King University
2023
State Key Laboratory of Turbulence and Complex Systems
2009-2022
Tsinghua University
2019-2022
National Institute of Biological Sciences, Beijing
2018-2022
Beijing Academy of Agricultural and Forestry Sciences
2022
The Wallace H. Coulter Department of Biomedical Engineering
2020
<b>Introduction:</b> Medullary cystic kidney disease 2 (MCKD2) and familial juvenile hyperuricaemic nephropathy (FJHN) are both autosomal dominant renal diseases characterised by onset of hyperuricaemia, gout, progressive failure. Clinical features conditions vary in presence severity. Often definitive diagnosis is possible only after significant pathology has occurred. Genetic linkage studies have localised genes for to overlapping regions chromosome 16p11-p13. These clinical genetic...
Ethylene has been regarded as a stress hormone to regulate myriad responses. Salinity is one of the most serious abiotic stresses limiting plant growth and development. But how ethylene signaling involved in response salt poorly understood. Here we showed that Arabidopsis plants pretreated with exhibited enhanced tolerance stress. Gain- loss-of-function studies demonstrated EIN3 (ETHYLENE INSENSITIVE 3) EIL1 (EIN3-LIKE 1), two ethylene-activated transcription factors, are necessary...
Abstract Background Human gut microbiota are important for human health and have been regarded as a “forgotten organ”, whose variation is closely linked with various factors, such host genetics, diet, pathological conditions external environment. The diversity of has correlated aging, which was characterized by different abundance bacteria in age groups. In the literature, most previous studies age-related changes focused on individual species community supervised methods. Here, we aimed to...
Phages and plasmids are the major components of mobile genetic elements, fragments from such elements generally co-exist with chromosome-derived in sequenced metagenomic data. However, there is a lack efficient methods that can simultaneously identify phages data, existing tools identifying either or have not yet presented satisfactory performance.
Abstract The recent outbreak of pneumonia in Wuhan, China caused by the 2019 Novel Coronavirus (2019-nCoV) emphasizes importance detecting novel viruses and predicting their risks infecting people. In this report, we introduced VHP (Virus Host Prediction) to predict potential hosts using deep learning algorithm. Our prediction suggests that 2019-nCoV has close infectivity with other human coronaviruses, especially severe acute respiratory syndrome coronavirus (SARS-CoV), Bat SARS-like...
Abstract Motivation To characterize long non-coding RNAs (lncRNAs), both identifying and functionally annotating them are essential to be addressed. Moreover, a comprehensive construction for lncRNA annotation is desired facilitate the research in field. Results We present LncADeep, novel identification functional tool. For identification, LncADeep integrates intrinsic homology features into deep belief network constructs models targeting full- partial-length transcripts. annotation,...
Abstract Background Shine-Dalgarno (SD) signal has long been viewed as the dominant translation initiation in prokaryotes. Recently, leaderless genes, which lack 5'-untranslated regions (5'-UTR) on their mRNAs, have shown abundant archaea. However, current large-scale silico analyses mechanisms bacteria are mainly based SD-led way, other than one. The study of genes remains open, causes uncertain understanding for Results Here, we signals all over 953 bacterial and 72 archaeal genomes, then...
Prokaryotic viruses referred to as phages can be divided into virulent and temperate phages. Distinguishing phage-derived sequences in metavirome data is important for elucidating their different roles interactions with bacterial hosts regulation of microbial communities. However, there no experimental or computational approach effectively classify culture-independent metavirome. We present a new method, DeePhage, which directly rapidly judge each read contig fragment.
Abstract Background Metagenomic sequencing is becoming a powerful technology for exploring micro-ogranisms from various environments, such as human body, without isolation and cultivation. Accurately identifying genes metagenomic fragments one of the most fundamental issues. Results In this article, we present novel gene prediction method named MetaGUN based on machine learning approach SVM. It implements in three-stage strategy to predict genes. Firstly, it classifies input into...
Epistatic gene–gene interactions could contribute to the heritability of complex multigenic disorders, but few examples have been reported. Here, we focus on role aberrant dopaminergic signaling, involving dopamine transporter DAT, a cocaine target, and D2 receptor, which physically interacts with DAT. Splicing polymorphism rs2283265 DRD2, encoding receptors, were shown confer risk overdose/death (odds ratio ∼3) in subjects controls from Miami Dade County Brain Bank.1 Risk cocaine-related...
Piezoelectric effects of two-dimensional (2D) group III-V compounds have received considered attention in recent years because their wide applications semiconductor devices. However, they face a problem that only metastable or unstable structures are noncentrosymmetric with piezoelectricity, thus leading to the difficulty experimental observation. Motivated by advances synthesis 2D III nitrides, this paper, for first time, we study piezoelectric properties nitrides (XN, X = Al, Ga, and In)...
Acute ischemic stroke (AIS) is a major cause of acquired adult disability and death. Our previous studies proved the efficacy effectiveness Tanhuo decoction (THD) on AIS. However, therapeutic mechanism remains unclear. We recruited 49 AIS patients 30 healthy people to explore effects THD+basic treatment poststroke gut microbiota using 16S rRNA sequencing, in which 23 received basic (control group) 26 (THD group). By comparing data before after treatments, we found THD group better outcome...
Abstract Background Protein secondary structure prediction method based on probabilistic models such as hidden Markov model (HMM) appeals to many because it provides meaningful information relevant sequence-structure relationship. However, at present, the accuracy of pure HMM-type methods is much lower than that machine learning-based neural networks (NN) or support vector machines (SVM). Results In this paper, we report a new nature for protein prediction, dynamic Bayesian (DBN). The...
Abstract Motivation: A high-quality assembly of reads generated from shotgun sequencing is a substantial step in metagenome projects. Although traditional assemblers have been employed initial analysis metagenomes, they cannot surmount the challenges created by features metagenomic data. Result: We present de novo approach and its implementation named MAP (metagenomic program). Based on an improved overlap/layout/consensus (OLC) strategy incorporated with several special algorithms, uses...
Background: Irritable bowel syndrome (IBS) is reported associated with the alteration of gut microbial composition termed as dysbiosis. However, pathogenic mechanism IBS remains unclear, while studies Chinese individuals are scarce. This study aimed to understand concept dysbiosis among patients diarrhea-predominant (IBS-D), a degree variance between microbiomes IBS-D population and that healthy population. Methods: The were recruited (assessed according Rome III criteria, by symptom...
Enterobacter cloacae complex (ECC) is composed of multiple species and the taxonomic status consecutively updated. In last decades ECC frequently associated with multidrug resistance become an important nosocomial pathogen. Currently, rapid accurate identification to level remains a technical challenge, thus impedes our understanding population at level. Here, we aimed develop simple, reliable, economical method distinguish four epidemiologically prevalent clinical significance, i.e., E. ,...
As a life-threatening disease, stroke is the leading cause of death and also induces adult disability worldwide. To investigate efficacy integrated traditional Chinese medicine (ITCM) on therapeutic effects acute ischemic (AIS) patients, we enrolled 26 patients in ITCM [Tanhuo decoction (THD) + Western (WM)] group 23 WM group. Thirty healthy people were included control (HC) achieved better functional outcomes than WM, including significant reduction phlegm-heat syndrome neurological...
As one of human pathogens, the genome Uropathogenic Escherichia coli strain CFT073 was sequenced and published in 2002, which significant pathogenetic bacterial genomics research. However, current RefSeq annotation this pathogen is now outdated to some degree, due missing or misannotation essential genes associated with its virulence. We carried out a systematic reannotation by combining automated tools manual efforts provide comprehensive understanding virulence for genome.The excluded 608...
During the past decade, development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled characterization microbial communities through metagenomics, metatranscriptomics, metaproteomics metabolomics data. To reveal diversity interactions between living conditions microbes, it is necessary to introduce comparative based upon integration all four types data mentioned above. Comparative meta-omics, especially metageomics, has been established as a routine...
Emerging human infectious viruses originating from animals continue to pose a persistent threat global public health. Understanding the host range of animal is crucial for identifying potential spillover pathways and mitigating risk future pandemics. Here, we present VirHRanger, prediction method that integrates foundation models trained on viral genome protein sequences, alongside genomic compositional traits, phylogeny, protein-protein interactions. To systematically predict range,...
In recent decades, Acinetobacter baumannii has become a major global nosocomial pathogen, with bloodstream infections (BSIs) exhibiting mortality rates exceeding 60% and imposing substantial economic burdens. However, limited large-scale genomic epidemiology hindered understanding of its population dynamics. Here, we analyzed 1506 non-repetitive BSI-causing A. isolates from 76 Chinese hospitals over decade (2011-2021). We identified 149 sequence types (STs) 101 K-locus (KLs), revealing...
Abstract Motivation: At present the computational gene identification methods in microbial genomes have a high prediction accuracy of verified translation termination site (3′ end), but much lower initiation (TIS, 5′ end). The latter is important to analysis and understanding putative protein regulatory machinery translation. Improving TIS one remaining open problems. Results: In this paper, we develop four-component statistical model describe prokaryotic genes. incorporates several features...
Abstract Background Despite a remarkable success in the computational prediction of genes Bacteria and Archaea, lack comprehensive understanding prokaryotic gene structures prevents from further elucidation differences among genomes. It continues to be interesting develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative studies Results This paper describes genefinding algorithm based on statistical model protein coding Open Reading Frames...