A5073934272- Inflammatory Bowel Disease
- Autophagy in Disease and Therapy
- Gut microbiota and health
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Bioinformatics and Genomic Networks
- Helicobacter pylori-related gastroenterology studies
- Single-cell and spatial transcriptomics
- Microscopic Colitis
- Digestive system and related health
- Pancreatic and Hepatic Oncology Research
- Oral microbiology and periodontitis research
- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
- Bacterial Infections and Vaccines
- Clostridium difficile and Clostridium perfringens research
- RNA Research and Splicing
- MicroRNA in disease regulation
- IL-33, ST2, and ILC Pathways
- Cell Image Analysis Techniques
- Computational Drug Discovery Methods
- Microbial Metabolic Engineering and Bioproduction
- Vibrio bacteria research studies
- Ferroptosis and cancer prognosis
- Gastrointestinal motility and disorders
KU Leuven
2019-2024
Indian Institute of Rice Research
2024
Acharya Nagarjuna University
2024
Norwich Research Park
2018-2022
Quadram Institute
2017-2022
Earlham Institute
2018-2022
Norwich University
2019-2020
Biotechnology and Biological Sciences Research Council
2017
YR Gaitonde Centre for AIDS Research and Education
2016
Universität Hamburg
2012-2014
Abstract The gastrointestinal (GI) tract harbours a complex microbial community, which contributes to its homeostasis. A disrupted microbiome can cause GI‐related diseases, including inflammatory bowel disease (IBD), therefore identifying host‐microbe interactions is crucial for better understanding gut health. Bacterial extracellular vesicles (BEVs), released into the lumen, cross mucus layer and access underlying immune cells. To study BEV‐host interactions, we examined influence of BEVs...
Crohn's disease (CD), a form of inflammatory bowel (IBD), is characterized by heterogeneity along multiple clinical axes, which in turn impacts progression and treatment modalities. Using advanced data integration approaches systems biology tools, we studied the contribution CD susceptibility variants gene expression distinct peripheral immune cell subsets (CD14+ monocytes CD4+ T cells) to relevant traits. Our analyses revealed that most traits capturing could be associated with CD14+ rather...
Microbiome–host interactions play significant roles in health and various diseases including autoimmune disorders. Uncovering these inter-kingdom cross-talks propels our understanding of disease pathogenesis provides useful leads on potential therapeutic targets. Despite the biological significance microbe–host interactions, there is a big gap downstream effects host processes. Computational methods are expected to fill this by generating, integrating, prioritizing predictions—as...
Signaling networks represent the molecular mechanisms controlling a cell's response to various internal or external stimuli. Most currently available signaling databases contain only part of complex network intertwining pathways, leaving out key interactions processes. Hence, we have developed SignaLink3 (http://signalink.org/), value-added knowledge-base that provides manually curated data on pathways and integrated from several types (interaction, regulation, localisation, disease, etc.)...
The gastrointestinal tract (GIT) harbors a complex community of microbes termed the microbiota that plays role in maintaining host’s health and wellbeing. How this comes about nature microbe-host cell interactions GIT is still unclear.
Inflammatory bowel disease [IBD] has a multifactorial origin and originates from complex interplay of environmental factors with the innate immune system at intestinal epithelial interface in genetically susceptible individual. All these make its aetiology intricate largely unknown. Multi-omic datasets obtained IBD patients are required to gain further insights into biology. We here review landscape multi-omic data availability identify barriers gaps for future research. also outline various...
Inflammatory Bowel Disease (IBD), which includes Ulcerative Colitis (UC) and Crohn’s (CD), is marked by dysbiosis of the gut microbiome. Despite therapeutic interventions with biological agents like Vedolizumab, Ustekinumab, anti-TNF agents, variability in clinical, histological, molecular responses remains significant due to inter-individual inter-population differences. This study introduces a novel approach using Individual Specific Networks (ISNs) derived from faecal microbial...
4 different actinomycetes strains (A1, A2, A3 and A4) were isolated from the laterite soil samples of Guntur region. Growth pattern antifungal profiles evaluated against test fungi such as Aspergillus flavus, Aspergillus niger,Candida albicans and Fusarium oxysporum. Based on cultural, morphological physiological characteristics, A1, A2 A4 identified as species of Streptomyces while strain was assigned to Nocardia. Among tested strains, Streptomyces sp. A1 showed strong activity which may...
The epithelial lining of the small intestine consists multiple cell types, including Paneth cells and goblet cells, that work in cohort to maintain gut health. 3D vitro cultures human primary called organoids, have become a key model study functions normal diseased conditions. Advances these models include ability skew differentiation particular lineages, providing useful tool type specific function/dysfunction context epithelium. Here, we use comprehensive profiling mRNA, microRNA long...
Salmonella enterica is a prominent bacterial pathogen with implications on human and animal health. serovars could be classified as gastro-intestinal or extra-intestinal. Genome-wide comparisons revealed that extra-intestinal strains are closer relatives of than to each other indicating parallel evolution this trait. Given the complexity differences, systems-level comparison reveal key mechanisms enabling cause systemic infections. Accordingly, in work, we introduce unique resource,...
Pancreatic ductal adenocarcinoma (PDAC) is driven by metabolic changes in pancreatic cells caused oncogenic mutations and dysregulation of p53. PDAC cell lines PDAC-derived xenografts grow as a result altered pathways, stroma, autophagy. Selective targeting inhibition one these may open avenues for the development new therapeutic strategies. In this study, we performed genome-wide siRNA screen line using endogenous autophagy readout identified several regulators that were required...
We describe a precision medicine workflow, the integrated single nucleotide polymorphism network platform (iSNP), designed to determine mechanisms by which SNPs affect cellular regulatory networks, and how SNP co-occurrences contribute disease pathogenesis in ulcerative colitis (UC). Using profiles of 378 UC patients we map effects human signalling containing protein-protein, miRNA-mRNA transcription factor binding interactions. With unsupervised clustering algorithms group these...
Abstract Background Mutans streptococci are a group of gram-positive bacteria including the primary cariogenic dental pathogen Streptococcus mutans and closely related species. Two component systems (TCSs) composed signal sensing histidine kinase (HK) response regulator (RR) play key roles in pathogenicity, but have not been comparatively studied for these oral bacterial pathogens. Results HKs RRs 8 newly sequenced strains, S. sobrinus DSM20742, ratti DSM20564 six were identified compared to...
Microbial dysbiosis is an established finding in patients with inflammatory bowel disease (IBD), but host-microbial interactions are poorly understood. We aimed to unravel the effect of microbiota exposure on intestinal epithelial cells. Confluent Transwell® organoid monolayers eight UC and non-IBD controls were co-cultured for six hours (3x108 cells) or a healthy volunteer (HV), presence absence cytokine mix. Transepithelial electrical resistance (TEER), fluorescein isothiocyanate (FITC)...
Inflammatory responses of the intestinal epithelial barrier in patients with Crohn's disease (CD), a chronic inflammatory bowel (IBD), are associated gut microbial alterations. At community level, there is scarce mechanistic evidence on effects alterations host mucosal responses. We used computational microbe-host interaction prediction framework based network diffusion and systems biology to integrate publicly available paired gene expression datasets. The ileal signaling potentially...
Paneth cells are key epithelial providing an antimicrobial barrier and maintaining integrity of the small intestinal stem cell niche. abnormalities unfortunately detrimental to gut health often associated with digestive pathologies such as Crohn's disease or infections. Similar alterations observed in individuals impaired autophagy, a process which recycles cellular components. The direct effect autophagy-impairment on has not been analysed. To investigate this, we generated mouse model...
Abstract Background Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about network (GRN) associated with phenotypic effect across ecologically diverse species. Here we use a novel approach for comparative GRN analysis in species to study representative the most striking examples adaptive radiations, East African cichlids. We previously demonstrated how explosive diversification cichlids be...
Carolacton is a newly identified secondary metabolite causing altered cell morphology and death of Streptococcus mutans biofilm cells. To unravel key regulators mediating these effects, the transcriptional regulatory response network S. biofilms upon carolacton treatment was constructed analyzed. A systems biological approach integrating time-resolved transcriptomic data, reverse engineering, transcription factor binding sites, experimental validation carried out.The co-expression from data...
The SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects coronavirus virus and its infection. For fruitful rapid investigation viral pathomechanisms, a collaborative interdisciplinary approach is required. Therefore, we have developed ViralLink: systems biology workflow which reconstructs analyses networks representing effect viruses on intracellular signalling. These trace flow signal from proteins through their human binding downstream signalling...