A5023911818- Celiac Disease Research and Management
- Microbial Metabolites in Food Biotechnology
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Helicobacter pylori-related gastroenterology studies
- Microbial Metabolic Engineering and Bioproduction
- Digestive system and related health
- RNA Research and Splicing
- Gut microbiota and health
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Gene expression and cancer classification
- Nutrition, Genetics, and Disease
- Epigenetics and DNA Methylation
- Pharmaceutical and Antibiotic Environmental Impacts
- Genetics, Bioinformatics, and Biomedical Research
- Probiotics and Fermented Foods
- RNA and protein synthesis mechanisms
- Cancer Immunotherapy and Biomarkers
- Gene Regulatory Network Analysis
- Antibiotic Resistance in Bacteria
- Cancer, Hypoxia, and Metabolism
- CRISPR and Genetic Engineering
- Listeria monocytogenes in Food Safety
- Advanced Proteomics Techniques and Applications
Greenwood Genetic Center
2024
Frederick National Laboratory for Cancer Research
2024
Cosmos Corporation (United States)
2019-2023
University of Maryland, College Park
2015-2022
National Cancer Institute
2019-2021
National Institutes of Health
2020-2021
Center for Cancer Research
2019
Universitat de Lleida
2011-2014
Biomedical Research Institute of Lleida
2011-2014
Significance The incidence of chronic inflammatory autoimmune conditions, such as celiac disease (CD), is increasing at an alarming rate. CD the only condition for which trigger, gluten, known. However, its etiology and pathogenesis remain incompletely defined recent studies suggest other environmental stimuli may play a key role in pathogenesis. Here, we prospectively examine trajectory gut microbiota starting 18 mo before onset 10 infants who developed did not. We identified alterations...
Background Model organisms are used for research because they provide a framework on which to develop and optimize methods that facilitate standardize analysis. Such should be representative of the living beings serve as proxy. However, in practice, model organism is often selected ad hoc, without considering its representativeness, systematic rational method include this consideration selection process still lacking. Methodology/Principal Findings In work we propose such apply it pilot...
Abstract Background Celiac disease (CD) is an autoimmune digestive disorder that occurs in genetically susceptible individuals response to ingesting gluten, a protein found wheat, rye, and barley. Research shows genetic predisposition exposure gluten are necessary but not sufficient trigger the development of CD. This suggests other environmental stimuli early life, e.g., cesarean section delivery antibiotics or formula feeding, may also play key role CD pathogenesis through yet unknown...
Abstract Diets rich in minimally processed foods are associated with numerous health benefits, part, due to their diverse, natural microbiota. However, antimicrobials, such as chlorine and peracetic acid (PAA), that used address food safety concerns may damage the microflora of fresh produce. One promising approach for targeting pathogenic bacteria without impacting normal microbiota bacteriophages. In this study, we observed combinational treatment conventional antimicrobials (PAA chlorine)...
Introduction. Prosthetic joint infections (PJIs) are challenging to treat therapeutically because the infectious agents often resistant antibiotics and capable of abundant growth in surface-attached biofilms. Though infection rates low, ca. 1-2 %, overall increase sheer number replacement surgeries results an patients at risk.Aims. This study investigates consensus microbial species comprising PJI ecology, which is currently lacking.Methodology. In this study, populations from seven were...
Abstract Background Reconstruction of genes and/or protein networks from automated analysis the literature is one current targets text mining in biomedical research. Some user-friendly tools already perform this on precompiled databases abstracts scientific papers. Other allow expert users to elaborate and analyze full content a corpus documents. However, our knowledge, no user friendly tool that simultaneously analyzes latest set documents available line reconstructs referenced those...
Signal transduction systems mediate the response and adaptation of organisms to environmental changes. In prokaryotes, this signal is often done through Two Component Systems (TCS). These TCS are phosphotransfer protein cascades, in their prototypical form they composed by a kinase that senses signals (SK) regulator (RR) regulates cellular response. This basic motif can be modified addition third interacts either with SK or RR way could change dynamic module. work we aim at understanding...
Genes conferring carbapenem resistance have disseminated worldwide among Gram-negative bacteria. Here we present longitudinal changes in clinically obtained Escherichia coli isolates from 1 immunocompromised pediatric patient. This report demonstrates potential for antibiotic genes and plasmids to emerge over time clinical patients receiving intensive anticancer chemotherapy broad-spectrum antibiotics.Thirty-three 7 months patient were included. Clinical data abstracted the medical record....
Antimicrobial resistance associated with the spread of plasmid-encoded extended-spectrum β-lactamase (ESBL) genes conferring to third generation cephalosporins is increasing worldwide. However, data on population ESBL producing E. coli in different animal sources and their antimicrobial characteristics are limited. The purpose this study was investigate potential reservoirs ESBL-encoded isolated from swine, beef, dairy, poultry collected regions United States using whole-genome sequencing...
Abstract To predict in vivo occupancy of a transcription factor (TF), current models consider only the immediate genomic context putative binding site (BS) – impact site’s spatial chromatin is not known. Using clusters spatially proximal enhancers, or archipelagos, and DNase footprints to quantify TF occupancy, we report for first time an emergent group-level effect on whereby BS within archipelago experience greater than comparable outside i.e. proximity with other homotypic BS. This boost...
Abstract In various contexts, spatially proximal genes have been shown to be functionally related. However, the extent which spatial proximity of in a pathway contributes pathway’s context-specific activity is not known. Leveraging Hi-C data six human cell-lines, we show that highly correlated with expression and function. Furthermore, correlates interactions their protein products, specific are one another tend occupy higher levels regulatory hierarchy. addition intra-pathway proximity,...
Modifier genes are believed to account for the clinical variability observed in many Mendelian disorders, but their identification remains challenging due limited availability of genomics data from large patient cohorts. Here, we present GENDULF (GENetic moDULators identiFication), one first methods facilitate prediction disease modifiers using healthy and diseased tissue gene expression data. is designed monogenic diseases which mechanism loss function leading reduced mutated gene. When...
One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such a topic active research, and those are typically included bioinformaticians in pipelines used mine curate large literature datasets. Nevertheless, experimental biologists have limited number available user-friendly tools that use network require no programming skills use. these Biblio-MetReS. Originally, this tool permitted an on-the-fly...
Abstract Background: Celiac disease (CD) is an autoimmune digestive disorder that occurs in genetically susceptible individuals response to ingesting gluten, a protein found wheat, rye, and barley. Research shows genetic predisposition exposure gluten are necessary but not sufficient trigger the development of CD. This suggests other environmental stimuli early life, e.g., cesarean section delivery, antibiotics or formula feeding, may also play key role CD pathogenesis through yet unknown...
Abstract Background : Celiac disease (CD) is an autoimmune digestive disorder that occurs in genetically susceptible individuals response to ingesting gluten, a protein found wheat, rye, and barley. Research shows genetic predisposition exposure gluten are necessary but not sufficient trigger the development of CD. This suggests other environmental stimuli early life, e.g., cesarean section delivery, antibiotics or formula feeding, may also play key role CD pathogenesis through yet unknown...
Our group developed two biological applications, Biblio-MetReS and Homol-MetReS , accessing the same database of organisms with annotated genes. is a data-mining application that facilitates reconstruction molecular networks based on automated text-mining analysis published scientific literature. allows functional (re)annotation proteomes, to properly identify both individual proteins involved in process(es) interest their function. It also enables sets different be compared directly. The...
Abstract Spatial organization of the genome is critical for condition-specific gene expression. Previous studies have shown that functionally related genes tend to be spatially proximal. However, these not been extended multiple human cell types, and extent which context-specific spatial proximity a pathway its activity known. We report first pathway-centric analyses in six lines. find tends context-specific, manner consistent with pathway’s expression function; housekeeping are ubiquitously...