A5036165777- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Microbial Community Ecology and Physiology
- Machine Learning in Bioinformatics
- Viral gastroenteritis research and epidemiology
- Gut microbiota and health
- Plant Virus Research Studies
- Viral Infections and Immunology Research
- Protein Structure and Dynamics
- Pharmacogenetics and Drug Metabolism
- RNA Research and Splicing
- Environmental DNA in Biodiversity Studies
- Metabolomics and Mass Spectrometry Studies
- MicroRNA in disease regulation
- Helicobacter pylori-related gastroenterology studies
- Advanced biosensing and bioanalysis techniques
- Bioinformatics and Genomic Networks
- Antimicrobial Peptides and Activities
- RNA Interference and Gene Delivery
- Chromium effects and bioremediation
- Microbial infections and disease research
- Curcumin's Biomedical Applications
Helmholtz Zentrum München
2019-2025
Technical University of Munich
2018-2025
Northwest A&F University
2014-2025
Institute of Virology of the Slovak Academy of Sciences
2024
Hong Kong Baptist University
2015
Beijing University of Chinese Medicine
2015
Dalian University of Technology
2015
Modern medicine often clashes with traditional such as Chinese herbal because of the little understanding underlying mechanisms action herbs. In an effort to promote integration both sides and accelerate drug discovery from medicines, efficient systems pharmacology platform that represents ideal information convergence pharmacochemistry, ADME properties, drug-likeness, targets, associated diseases interaction networks, are urgently needed.The database analysis (TCMSP) was built based on...
The world is facing a hard battle against soil pollution such as heavy metals. Metagenome sequencing, 16S rRNA and quantitative polymerase chain reaction (qPCR) were used to examine microbial adaptation mechanism contaminated sediments under natural conditions. Results showed that sediment from tributary of the Yellow River, which was named Dongdagou River (DDG) supported less bacterial biomass owned lower richness than Maqu (MQ), an uncontaminated site in upper reaches River. Additionally,...
Abstract Motivation: Drug combinations are a promising strategy for combating complex diseases by improving the efficacy and reducing corresponding side effects. Currently, widely studied problem in pharmacology is to predict effective drug combinations, either through empirically screening clinic or pure experimental trials. However, large-scale prediction of combination systems method rarely considered. Results: We report framework (PreDCs) on computational model, termed probability...
Stunting, a severe and multigenerational growth impairment, globally affects 22% of children under the age 5 years. Stunted have altered gut bacterial communities with higher proportions Proteobacteria, phylum several known human pathogens. Despite links between an microbiota stunting, role bacteriophages, highly abundant viruses, is unknown. Here, we describe bacteriophage Bangladeshi stunted younger than 38 months. We show that these harbor distinct bacteriophages relative to their...
The treatment outcomes of oral medications against ulcerative colitis (UC) have long been restricted by low drug accumulation in the mucosa and subsequent unsatisfactory therapeutic efficacy. Here, high-performance pluronic F127 (P127)-modified gold shell (AuS)-polymeric core nanotherapeutics loading with curcumin (CUR) is constructed. Under near-infrared irradiation, resultant P127-AuS@CURs generate transient mild photothermia (TMP; ≈42 °C, 10 min), which facilitates their penetration...
A system-level identification of drug-target direct interactions is vital to drug repositioning and discovery. However, the biological means on a large scale remains challenging expensive even nowadays. The available computational models mainly focus predicting indirect or small scale. To address these problems, in this work, novel algorithm termed weighted ensemble similarity (WES) has been developed identify targets based large-scale 98,327 relationships. WES includes: (1) identifying key...
Bacteriophages play central roles in the maintenance and function of most ecosystems by regulating bacterial communities. Yet, our understanding their diversity remains limited due to lack robust bioinformatics standards. Here we present ViroProfiler, an in-silico workflow for analyzing shotgun viral metagenomic data. ViroProfiler can be executed on a local Linux computer or cloud computing environments. It uses containerization technique ensure computational reproducibility facilitate...
DHAV-3 is one of the main causative agents duck viral hepatitis (DVH), an acute and highly lethal infectious disease in industry. However, understanding pathogenesis this virus ducklings limited. To dissect molecular characteristics associated with pathobiology to DHAV-3, we applied single-cell RNA-sequencing approach profile transcriptome 1.4 million cells from 14 livers susceptible (S) resistant (R) during infection 4 uninfected healthy controls. We found that infected S ducks exhibited...
Abstract Background The volume of protein sequence data has grown exponentially in recent years, driven by advancements metagenomics. Despite this, a substantial proportion these sequences remain poorly annotated, underscoring the need for robust bioinformatics tools to facilitate efficient characterisation and annotation functional studies. Results We present PyPropel, Python-based computational tool developed streamline large-scale analysis data, with particular focus on applications...
Structural variations (SVs) are diverse forms of genetic alterations and drive a wide range human diseases. Accurately genotyping SVs, particularly occurring at repetitive genomic regions, from short-read sequencing data remains challenging. Here, we introduce SVLearn, machine-learning approach for bi-allelic SVs. It exploits dual-reference strategy to engineer curated set genomic, alignment, features based on reference genome in concert with an allele-based alternative genome. Using 38,613...
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. While a close correlation between chronic Helicobacter pylori infection and CRC has been reported, role virome overlooked. Here, we infected Apc-mutant mouse models C57BL/6 mice with H. conducted comprehensive metagenomics analysis pylori-induced changes in lower gastrointestinal tract bacterial viral communities. We observed an expansion temperate phages Apc+/1638N at early stage carcinogenesis. Some were...
Given the complex nature of cardiovascular disease (CVD), information derived from a systems-level will allow us to fully interrogate features CVD better understand pathogenesis and identify new drug targets. Here, we describe systematic assessment multi-layer interactions underlying drugs, targets, genes disorders reveal comprehensive insights into systems biology pharmacology. We have identified 206 effect-mediating which are modulated by 254 unique which, 43% display activities across...
Aberrant miRNA expression has been associated with a large number of human diseases. Therefore, targeting miRNAs to regulate their levels become an important therapy against diseases that stem from the dysfunction pathways regulated by miRNAs. In recent years, small molecules have demonstrated enormous potential as drugs (i.e., SM-miR). A clear understanding mechanism action on upregulation and downregulation allows precise diagnosis treatment oncogenic pathways. However, outside slow costly...
The relationship between viruses (dominated by bacteriophages or phages) and lower gastrointestinal (GI) tract diseases has been investigated, whereas the gut upper GI diseases, such as esophageal which mainly include Barrett’s esophagus (BE) adenocarcinoma (EAC), remains poorly described. This study aimed to reveal bacteriophage community their behavior in progression of diseases. In total, we analyzed phage sixteen samples from patients with (six BE four EAC patients) well six healthy...
Hydrocarbon pollution poses substantial environmental risks to water and soil. Bioremediation, which utilizes microorganisms manage pollutants, offers a cost-effective solution. However, the role of viruses, particularly bacteriophages (phages), in bioremediation remains unexplored. This study examines diversity activity hydrocarbon-degradation genes encoded by focusing on phages, within public databases. We identified 57 high-quality phage-encoded auxiliary metabolic (AMGs) related...
Increasing antibiotic resistance has led to renewed attention being paid bacteriophage therapy. Commercial phage cocktails are available but often their contents of the phages not well defined. Some metagenomic studies have been done retrospectively characterise these cocktails, little is known about replication cycle included phages, or possible bacterial DNA contamination. In this study, published sequences were reanalysed using recent advances in viromics tools. Signs temperate contigs...
Alpine lakes are considered pristine freshwater ecosystems and sensitive to direct indirect changes in water temperature as induced by climate change. The bacterial plankton constitutes a key component the column metabolic activity has consequences for quality. In order understand response global rise five alpine located Austrian Alps (1700-2188 m a.S.L.) was compared within decadal period. Depth-integrated samples were characterized community composition 16S rDNA deep-amplicon sequencing...
It has been generally hypothesized that mobile elements can induce genomic rearrangements and influence the distribution functionality of toxic/bioactive peptide synthesis pathways in microbes. In this study, we performed depth analysis by completing genomes 13 phylogenetically diverse strains bloom-forming freshwater cyanobacteria
Abstract Motivation Viruses are the most abundant biological entities on earth. The majority of these bacterial viruses or phages which specifically infect bacteria. Phages can use different replication strategies to invade their hosts including lytic, lysogenic, chronic cycle and pseudolysogeny. While determination strategy used by is important explore phage-bacteria relationships in ecosystems there not many tools that predict this metagenomic data. In addition, available only lytic...