A5101575637- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- Machine Learning in Bioinformatics
- MicroRNA in disease regulation
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Circular RNAs in diseases
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Bacteriophages and microbial interactions
- Cancer, Hypoxia, and Metabolism
- interferon and immune responses
- Gene expression and cancer classification
- Radiomics and Machine Learning in Medical Imaging
- Antimicrobial Peptides and Activities
- Genomics and Chromatin Dynamics
- Evolution and Genetic Dynamics
- Wastewater Treatment and Nitrogen Removal
- Cancer-related gene regulation
- Aquaculture disease management and microbiota
- Bioinformatics and Genomic Networks
- Biochemical and Structural Characterization
- AI in cancer detection
- Advancements in Transdermal Drug Delivery
Nanjing Tech University
2024
State Key Laboratory of Pollution Control and Resource Reuse
2024
Tongji University
2024
Guilin University of Electronic Technology
2016-2024
Huaqiao University
2023-2024
Capital Medical University
2022
Beijing Children’s Hospital
2022
People's Hospital of Cangzhou
2021
Leiden University
2008-2020
Czech Academy of Sciences, Institute of Computer Science
2020
Abstract Periconceptional diet may persistently influence DNA methylation levels with phenotypic consequences. However, a comprehensive assessment of the characteristics prenatal malnutrition-associated differentially methylated regions (P-DMRs) is lacking in humans. Here we report on genome-scale analysis differential whole blood after periconceptional exposure to famine during Dutch Hunger Winter. We show that P-DMRs preferentially occur at regulatory regions, are characterized by...
Abstract Background DNA methylation has been recognized as a key mechanism in cell differentiation. Various studies have compared tissues to characterize epigenetically regulated genomic regions, but due differences study design and focus there still is no consensus the annotation of regions predominantly involved tissue-specific methylation. We used new algorithm identify annotate differentially methylated (tDMRs) from Illumina 450k chip data for four peripheral (blood, saliva, buccal swabs...
Abstract Motivation Many Gram-negative bacteria use type VI secretion systems (T6SS) to export effector proteins into adjacent target cells. These secreted effectors (T6SEs) play vital roles in the competitive survival bacterial populations, as well pathogenesis of bacteria. Although various computational analyses have been previously applied identify by certain species, there is no universal method available accurately predict T6SS from growing tide genome sequence data. Results We...
As a newly discovered post-translational modification (PTM), lysine malonylation (Kmal) regulates myriad of cellular processes from prokaryotes to eukaryotes and has important implications in human diseases. Despite its functional significance, computational methods accurately identify sites are still lacking urgently needed. In particular, there is currently no comprehensive analysis assessment different features machine learning (ML) that required for constructing the necessary prediction...
Abstract Motivation Type III secreted effectors (T3SEs) can be injected into host cell cytoplasm via type secretion systems (T3SSs) to modulate interactions between Gram-negative bacterial pathogens and their hosts. Due relevance in pathogen–host interactions, significant computational efforts have been put toward identification of T3SEs these turn stimulated new T3SE discoveries. However, as with characteristics are discovered, existing tools reveal important limitations: (i) most the...
Abstract Virulence factors (VFs) enable pathogens to infect their hosts. A wealth of individual, disease-focused studies has identified a wide variety VFs, and the growing mass bacterial genome sequence data provides an opportunity for computational methods aimed at predicting VFs. Despite attractive advantages performance improvements, existing have some limitations drawbacks. Firstly, as characteristics mechanisms VFs are continually evolving with emergence antibiotic resistance, it is...
Abstract Anti-CRISPRs are widespread amongst bacteriophage and promote infection by inactivating the bacterial host's CRISPR–Cas defence system. Identifying characterizing anti-CRISPR proteins opens an avenue to explore control machineries for development of new based biotechnological therapeutic tools. Past studies have identified anti-CRISPRs in several model phage genomes, but a challenge exists comprehensively screen accurately efficiently from genome metagenome sequence data. Here, we...
Abstract Gram-negative bacteria utilize secretion systems to export substrates into their surrounding environment or directly neighboring cells. These are proteins that function promote bacterial survival: by facilitating nutrient collection, disabling competitor species or, for pathogens, disable host defenses. Following a rapid development of computational techniques, growing number have been discovered and subsequently validated wet lab experiments. To date, several online databases...
Abstract Motivation Gram-positive bacteria have developed secretion systems to transport proteins across their cell wall, a process that plays an important role during host infection. These mechanisms also been harnessed for therapeutic purposes in many biotechnology applications. Accordingly, the identification of features select protein efficient from these microorganisms has become task. Among all secreted proteins, ‘non-classical’ are difficult identify as they lack discernable signal...
Ulcerative colitis (UC) is a disease with complex pathological mechanisms. We explored the potential molecular mechanisms behind therapeutic functions of Qingzi Zhitong decoction (QZZTD) in treatment UC by network pharmacology and docking. QZZTD formula Chinese traditional medicine consisting 10 herbs. The active ingredients their target genes were obtained from Traditional Medicine Systems Pharmacology Database Analysis Platform database, UC-related GeneCards OMIM databases. A total 138...
It has been postulated that aging is the consequence of an accelerated accumulation somatic DNA mutations and subsequent errors in primary structure proteins ultimately reach levels sufficient to affect organismal functions. The technical limitations detecting changes lack insight about minimum level erroneous cause error catastrophe hampered any firm conclusions on these theories. In this study, we sequenced whole genome blood two pairs monozygotic (MZ) twins, 40 100 years old, by...
Anti-CRISPR (Acr) proteins naturally inhibit CRISPR-Cas adaptive immune systems across bacterial and archaeal domains of life. This emerging field has caused a paradigm shift in the way we think about system, promises number useful applications from gene editing to phage therapy. As verified predicted Acrs rapidly expands, few online resources have been developed deal with this wealth information. To overcome shortcoming, AcrHub, an integrative database provide all-in-one solution for...
The proposed mechanism of the light-driven microbial desulphurization by CdS– H. neapolitanus biohybrid system.
Abstract Motivation: RNA-seq is a powerful technology for the study of transcriptome profiles that uses deep-sequencing technologies. Moreover, it may be used cellular phenotyping and help establishing etiology diseases characterized by abnormal splicing patterns. In RNA-Seq, exact nature events buried in reads span exon–exon boundaries. The accurate efficient mapping these to reference genome major challenge. Results: We developed PASSion, pattern growth algorithm-based pipeline splice site...
The common carp is a candidate model system for immunology research.Using nextgeneration sequencing technology, we have generated huge amount of sequence reads from the genome and transcriptome.Currently, our aim to identify genes involved in development innate immune response, particularly TIR domaincontaining genes, preliminary assembly.To achieve this, developed comprehensive gene identification pipeline.This analysis allowed us estimate that has 39 domain-containing transcript isoforms genes.
The common carp is a candidate model system for immunology research. Using next-generation sequencing technology, we have generated huge amount of sequence reads from the genome and transcriptome. Currently, our aim to identify genes involved in development innate immune response, particularly TIR domain-containing genes, preliminary assembly. To achieve this, developed comprehensive gene identification pipeline. This analysis allowed us estimate that has 39 transcript isoforms genes.
In response to the global problem of antimicrobial resistance, there are moves use bacteriophages (phages) as therapeutic agents. Selecting which phages will be effective therapeutics relies on interpreting features contributing shelf-life and applicability diagnosed infections.
Pancreatic ductal adenocarcinoma (PDAC) eludes early detection and is characterized by its aggressiveness resistance to current therapies. A number of gene expression screens have been carried out identify genes differentially expressed in cancerous tissue. To molecular markers suitable targets, these mapped protein interactions gain an understanding at systems level.Here, we take such a network-centric approach pancreas cancer re-constructing networks from known predicting novel structural...
Large variations in water quality and quantity are the main characteristics of rural wastewater China, biggest impact caused by this is lack carbon sources. In study, an anoxic–oxic (A/O) biological contact oxidation (BCO) reactor was used to explore feasibility using food waste fermentation liquid as supplementary source for enhanced nitrogen removal from wastewater. After supplements, performance A/O BCO system improved, with efficiencies COD, NH4+–N, TN at 92.4%, 97.8%, 67.6%,...
To explore the regulatory role of miR497-5p-CCNE1 axis in triple-negative breast cancer (TNBC) cells and its predictive value for early diagnosis.Cancer tissue adjacent samples were collected from 86 patients with TNBC.RT-PCR was used to detect expression miR497-5p CCNE1 (target gene) mRNA, determined by biological prediction TNBC cells. ROC analyze diagnostic TNBC. MTT, invasion, flow cytometry proliferation, cycle, apoptosis rate, related proteins overexpression or knockdown CCNE1.RT-qPCR...