A5030568610- Single-cell and spatial transcriptomics
- Advanced Proteomics Techniques and Applications
- Molecular Biology Techniques and Applications
- Neurobiology and Insect Physiology Research
- Gene expression and cancer classification
- Biomedical Text Mining and Ontologies
- Circadian rhythm and melatonin
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Cell Image Analysis Techniques
- Biotin and Related Studies
- Insect and Arachnid Ecology and Behavior
- Developmental Biology and Gene Regulation
- Research Data Management Practices
- Scientific Computing and Data Management
- Metabolomics and Mass Spectrometry Studies
- Insect Pheromone Research and Control
- RNA Research and Splicing
- Machine Learning in Bioinformatics
- Congenital Ear and Nasal Anomalies
- Viral Infectious Diseases and Gene Expression in Insects
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Kawasaki Disease and Coronary Complications
- Diabetes and associated disorders
European Bioinformatics Institute
2019-2025
Wellcome Trust
2020
Institute of Entomology
2012-2019
Czech Academy of Sciences, Biology Centre
2012-2019
University of Cambridge
2012-2017
Czech Academy of Sciences
2012-2013
University of South Bohemia in České Budějovice
2013
Abstract Expression Atlas is EMBL-EBI’s resource for gene and protein expression. It sources compiles data on the abundance localisation of RNA proteins in various biological systems contexts provides open access to this research community. With increased availability single cell RNA-Seq datasets public archives, we have now extended with a new added-value service display expression cells. Single Cell was launched 2018 currently includes 123 studies from 12 species. The website can be...
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources vertebrate genomics developed in context of project (http://www.ensembl.org). Together, two provide a consistent set interfaces to genomic across tree life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform...
The EMBL-EBI Expression Atlas is an added value knowledge base that enables researchers to answer the question of where (tissue, organism part, developmental stage, cell type) and under which conditions (disease, treatment, gender, etc) a gene or protein interest expressed. brings together data from >4500 expression studies >65 different species, across tissues. It makes these freely available in easy visualise form, after expert curation accurately represent intended experimental design,...
Abstract ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data at EMBL-EBI, established in 2002, initially as for publication-related microarray and was later extended to accept sequencing-based data. Over the last decade increasing share biological experiments involve multiple technologies assaying different modalities, such epigenetics, RNA protein expression, thus BioStudies database (https://www.ebi.ac.uk/biostudies) deal with multimodal Its central...
Expression Atlas (www.ebi.ac.uk/gxa) and its newest counterpart the Single Cell (www.ebi.ac.uk/gxa/sc) are EMBL-EBI's knowledgebases for gene protein expression localisation in bulk at single cell level. These resources aim to allow users investigate their normal tissue (baseline) or response perturbations such as disease changes genotype (differential) across multiple species. Users invited search genes metadata terms species biological conditions a standardised consistent interface....
The PRIDE database is the largest public data repository of mass spectrometry-based proteomics and currently stores more than 40,000 sets covering a wide range organisms, experimental techniques, biological conditions. During past few years, has seen significant increase in amount submitted data-independent acquisition (DIA) sets. This provides an excellent opportunity for large-scale reanalysis reuse. We have reanalyzed 15 label-free DIA across various healthy human tissues to provide...
The increasingly large amount of proteomics data in the public domain enables, among other applications, combined analyses datasets to create comparative protein expression maps covering different organisms and biological conditions. Here we have reanalysed from mouse rat tissues (14 9 datasets, respectively), assess baseline abundance. Overall, aggregated dataset contained 23 individual including a total 211 samples coming 34 across 14 organs, comprising 3 strains, respectively. In all...
The availability of an increasingly large amount public proteomics data sets presents opportunity for performing combined analyses to generate comprehensive organism-wide protein expression maps across different organisms and biological conditions. Sus scrofa, a domestic pig, is model organism relevant food production human biomedical research. Here, we reanalyzed 14 from the PRIDE database coming pig tissues assess baseline (without any perturbation) abundance in organs, encompassing total...
Repressors are frequently deployed to limit the transcriptional response signalling pathways. For example, several co-repressors interact directly with DNA-binding protein CSL and proposed keep target genes silenced in absence of Notch activity. However, scope their contributions remains unclear. To investigate co-repressor activity context this well defined pathway, we have analysed genome-wide binding profile best-characterized Drosophila, Hairless, a second interacting repressor, SMRTER....
Drosophila melanogaster has served as an excellent genetic model to decipher the molecular basis of circadian clock. Two key proteins, PERIOD (PER) and TIMELESS (TIM), are particularly well explored a number various arrhythmic, slow, fast clock mutants have been identified in classical screens. Interestingly, free running period (tau, τ) is influenced by temperature some these mutants, whereas τ temperature-independent other mutant lines wild-type flies. This, so-called "temperature...
Females of the Indian meal moth, Plodia interpunctella, and females Mediterranean flour month, Ephestia kuehniella (both Lepidoptera: Pyralidae), exhibit daily rhythms in calling behavior. The peak P. interpunctella occurs at dusk, whereas E. calls preferentially dawn. This behavior turned arrhythmic constant darkness (DD) remained light (LL), showed a persistent rhythm DD suppression LL, indicating regulation by circadian clock mechanism. male locomotor activity corresponded well with...
Abstract The PRIDE database is the largest public repository of mass spectrometry-based proteomics data and currently stores more than 40,000 datasets covering a wide range organisms, experimental techniques biological conditions. During past few years, has seen an increase in amount submitted Data-Independent Acquisition (DIA) datasets, parallel with trends field. This provides excellent opportunity for large scale reanalysis reuse. We have systematically reanalysed 15 label-free DIA across...
Abstract The amount of public proteomics data is increasing at an extraordinary rate. Hundreds datasets are submitted each month to ProteomeXchange repositories, representing many types studies, focusing on different aspects such as quantitative experiments, post-translational modifications, protein-protein interactions, or subcellular localization, among others. For every dataset, two levels captured: the dataset description, and files (encoded in file formats). Whereas description formats...
Abstract The increasingly large amount of proteomics data in the public domain enables, among other applications, combined analyses datasets to create comparative protein expression maps covering different organisms and biological conditions. Here we have reanalysed from mouse rat tissues (14 9 datasets, respectively), assess baseline abundance. Overall, aggregated dataset contained 23 individual including a total 211 samples coming 34 across 14 organs, comprising 3 strains, respectively. In...
Abstract One of the most powerful ways to develop hypotheses regarding biological functions conserved genes in a given species, such as humans, is first look at what known about function another species. Model organism databases (MODs) and other resources are rich with functional information but difficult mine. Gene2Function (G2F) addresses broad need by integrating single online resource.
Abstract The availability of an increasingly large amount public proteomics datasets presents opportunity for performing combined analyses to generate comprehensive organism-wide protein expression maps across different organisms and biological conditions. Sus scrofa , the domestic pig, is a model organism relevant food production human biomedical research. Here we reanalyzed 14 from PRIDE database coming pig tissues assess baseline (without any perturbation) abundance in organs,...