A5068938981- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Genomics and Rare Diseases
- RNA and protein synthesis mechanisms
- Algorithms and Data Compression
- Genetic Associations and Epidemiology
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- Epigenetics and DNA Methylation
- Cell Image Analysis Techniques
- Chromosomal and Genetic Variations
- Gene Regulatory Network Analysis
- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Metabolic Engineering and Bioproduction
- Genetic and phenotypic traits in livestock
- Cancer-related molecular mechanisms research
- Genomics and Chromatin Dynamics
- Sports Performance and Training
- Computational Drug Discovery Methods
- CRISPR and Genetic Engineering
- Genetic diversity and population structure
- MicroRNA in disease regulation
University of Cambridge
2015-2024
Chinese University of Hong Kong, Shenzhen
2024
University of Glasgow
2020
British Heart Foundation
2020
Public Health Agency of Canada
2017
Centro de Investigacion Principe Felipe
2006-2015
European Bioinformatics Institute
2015
Wellcome Trust
2015
Instituto de Instrumentación para Imagen Molecular
2014
Universitat Politècnica de València
2012-2014
We report for the first time genomics of a nuclear compartment eukaryotic cell. 454 sequencing and microarray analysis revealed pattern nucleolus-associated chromatin domains (NADs) in linear human genome identified different gene families certain satellite repeats as major building blocks NADs, which constitute about 4% genome. Bioinformatic evaluation showed that NAD-localized genes take part specific biological processes, like response to other organisms, odor perception, tissue...
Paul Flicek and colleagues provide an update on the European Genome-phenome Archive (EGA), a service of Bioinformatics Institute (EMBL-EBI) Center for Genome Regulation (CRG). The authors describe EGA policies infrastructure, how access decisions are made, methods data submission future plans expansion this database. (EGA) is permanent archive that promotes distribution sharing genetic phenotypic consented specific approved uses but not fully open, public distribution. follows strict...
Babelomics is a response to the growing necessity of integrating and analyzing different types genomic data in an environment that allows easy functional interpretation results. includes complete suite methods for analysis gene expression include normalization (covering most commercial platforms), pre-processing, differential (case-controls, multiclass, survival or continuous values), predictors, clustering; large-scale genotyping assays (case controls TDTs, population stratification...
Abstract MicroRNAs (miRNAs) are small non-coding RNAs (18–26 nucleotides) that regulate gene expression by interacting with target mRNAs, affecting various physiological and pathological processes. miRTarBase, a database of experimentally validated miRNA–target interactions (MTIs), now features over 3 817 550 MTIs from 13 690 articles, significantly expanding its previous version. The updated includes miRNA therapeutic agents, revealing roles in drug resistance strategies. It also highlights...
The ultimate goal of any genome-scale experiment is to provide a functional interpretation the data, relating available information with hypotheses that originated experiment. Thus, profiling methods have become essential in diverse scenarios such as microarray experiments, proteomics, etc. We present FatiGO+, web-based tool for specially oriented experiments. In addition different annotations (gene ontology, KEGG pathways, Interpro motifs, Swissprot keywords and text-mining based...
Phylemon 2.0 is a new release of the suite web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as response to increasing demand sequence analyses experts non-expert users. several unique features that differentiates it from other similar resources: (i) offers an integrated environment enables evolutionary analyses, format conversion, file storage edition results; (ii) suggests further thereby guiding users through server; (iii) allows...
A curated Web-based user-friendly sequence typing tool based on antimicrobial resistance determinants in Neisseria gonorrhoeae was developed and is publicly accessible (https://ngstar.canada.ca). The N. Sequence Typing for Antimicrobial Resistance (NG-STAR) molecular scheme uses the DNA sequences of 7 genes (penA, mtrR, porB, ponA, gyrA, parC, 23S rRNA) associated with to β-lactam antimicrobials, macrolides, or fluoroquinolones. NG-STAR entire penA sequence, combining historical nomenclature...
Babelomics has been running for more than one decade offering a user-friendly interface the functional analysis of gene expression and genomic data. Here we present its fifth release, which includes support Next Generation Sequencing data including (RNA-seq), exome or genome resequencing. simplified interface, being now intuitive. Improved visualization options, such as viewer well an interactive network viewer, have implemented. New technical enhancements at both, client server sides, makes...
We present a new version of Babelomics, complete suite web tools for the functional profiling genome scale experiments, with and improved methods as well more types definitions.Babelomics includes different flavours conventional enrichment advanced gene set analysis that makes it unique tool among similar resources available.In addition to well-known definitions (GO, KEGG), Babelomics ones such Biocarta pathways or text mining-derived terms.Regulatory modules implemented include...
The immunodeficiency, centromere instability and facial anomalies (ICF) syndrome is associated to mutations of the DNA methyl-transferase DNMT3B, resulting in a reduction enzyme activity. Aberrant expression immune system genes hypomethylation pericentromeric regions accompanied by chromosomal were determined as alterations driving disease phenotype. However, so far only technologies capable analyze single loci applied determine epigenetic ICF patients. In current study, we performed...
B16 melanoma (B16M) cells with high glutathione (GSH) content show rapid proliferation in vitro and metastatic activity the liver vivo . γ-Glutamyl transpeptidase (GGT)-mediated extracellular GSH cleavage intracellular synthesis were studied B16M (F10) low (F1) potential. GGT was modified by transfection human gene (B16MF1/Tet-GGT cells) or acivicin-induced inhibition. B16MF1/Tet-GGT B16MF10 exhibited higher (35 ± 6 40 5 nmol/10 cells, respectively) (89 9 37 7 mU/10 as compared ( P < .05)...
Gene Expression Profile Analysis Suite (GEPAS) is one of the most complete and extensively used web-based packages for microarray data analysis. During its more than 5 years activity it has continuously been updated to keep pace with state-of-the-art in changing analysis arena. GEPAS offers diverse options that include well established as novel algorithms normalization, gene selection, class prediction, clustering functional profiling experiment. New time-course (or dose-response)...
Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in human genome. SNPs are associated altered response to drug treatment, susceptibility disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutations groups patients control individuals, distinction between causing mutation polymorphism is often unclear. Annotation functional structural implications single changes thus provides...
Genome-wide association studies have become a popular strategy to find associations of genes traits interest. Despite the high-resolution available today carry out genotyping studies, success its application in real has been limited by testing used. As an alternative brute force solutions involving use very large cohorts, we propose Gene Set Analysis (GSA), different analysis based on modules functionally related genes. We show here how Set-based Polymorphisms (GeSBAP), which is simple...
Whole-exome sequencing has become a fundamental tool for the discovery of disease-related genes familial diseases and identification somatic driver variants in cancer. However, finding causal mutation among enormous background individual variability small number samples is still big challenge. Here we describe web-based tool, BiERapp, which efficiently helps causative family sporadic genetic diseases. The program reads lists predicted (nucleotide substitutions indels) affected individuals or...
The massive use of Next-Generation Sequencing (NGS) technologies is uncovering an unexpected amount variability. functional characterization such variability, particularly in the most common form variation found, Single Nucleotide Variants (SNVs), has become a priority that needs to be addressed systematic way. VARIANT (VARIant ANalyis Tool) reports information on variants found include consequence type and annotations taken from different databases repositories (SNPs dbSNP 1000 genomes,...
During the past years, advances in high-throughput technologies have produced an unprecedented growth number and size of repositories databases storing relevant biological data. Today, there is more information than ever but, unfortunately, current status many these far from being optimal. Some most common problems are that spread out small databases; frequently different standards among some no longer supported or they contain too specific unconnected information. In addition, data...
The discovery of actionable targets is crucial for targeted therapies and also a constituent part the drug process. success an intervention over target depends critically on its contribution, within complex network gene interactions, to cellular processes responsible disease progression or therapeutic response. Here we present PathAct, web server that predicts effect interventions genes (inhibitions activations simulate knock-outs, treatments over-expressions) can have signal transmission...
Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. It has been developed as a web server that integrates suite different tools selected among the most popular stand-alone programs in analysis. conceived natural response to increasing demand data analysis many experimental scientists wishing add evolution phylogenetics insight into their research. Tools included cover wide yet range programs: from basic multiple alignment elaborate...
MicroRNAs (miRNAs) are key components of the gene regulatory network in many species. During past few years, these elements have been shown to be involved an increasing number and range diseases. Consequently, compilation a comprehensive map natural variability healthy population seems obvious requirement for future research on miRNA-related pathologies. Data 14 populations from 1000 Genomes Project were analyzed, along with new data extracted 60 exomes individuals southern Spain, sequenced...
Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of brought about by new generation sequencing technologies is, at same time, causing a subtle but continuous decrease in efficiency conventional genome browsers. Here, we present Maps, browser that implements an innovative model data transfer management. The program uses highly efficient from HTML5 standard, such scalable vector graphics, optimize workloads both...
As sequencing technologies progress, the amount of data produced grows exponentially, shifting bottleneck discovery towards analysis phase. In particular, currently available mapping solutions for RNA-seq leave room improvement in terms sensitivity and performance, hindering an efficient transcriptomes by massive sequencing. Here, we present innovative approach that combines re-engineering, optimization parallelization. This solution results a significant increase over wide range read...
Abstract Sample classification and class prediction is the aim of many gene expression studies. We present a web-based application, Prophet, which builds rules allows using them for further sample classification. Prophet automatically chooses best classifier, along with optimal selection genes, strategy that renders unbiased cross-validated errors. linked to different microarray data analysis modules, includes unique feature: possibility performing functional interpretation molecular...