A5081314775- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Oral microbiology and periodontitis research
- Salivary Gland Disorders and Functions
- Dental Research and COVID-19
- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Protein Structure and Dynamics
- Advanced Proteomics Techniques and Applications
- CRISPR and Genetic Engineering
- Enzyme Structure and Function
- Plant Disease Resistance and Genetics
- Microbial Metabolic Engineering and Bioproduction
- Single-cell and spatial transcriptomics
- Species Distribution and Climate Change
- Machine Learning in Bioinformatics
- Genomics and Chromatin Dynamics
- Plant-Microbe Interactions and Immunity
- Wikis in Education and Collaboration
- Peptidase Inhibition and Analysis
- Language and cultural evolution
- Insect Resistance and Genetics
- Scientific Computing and Data Management
Institute for Research in Biomedicine
2024
Universitat Politècnica de Catalunya
2024
Barcelona Supercomputing Center
2024
Institució Catalana de Recerca i Estudis Avançats
2024
Instituto de Salud Carlos III
2024
Centre for Genomic Regulation
2014-2023
Barcelona Institute for Science and Technology
2017-2021
Institute of Science and Technology
2020
Universitat Pompeu Fabra
2014-2017
Centro Nacional de Análisis Genómico
2016
Alternative splicing (AS) generates remarkable regulatory and proteomic complexity in metazoans. However, the functions of most AS events are not known, programs regulated remain to be identified. To address these challenges, we describe Vertebrate Splicing Transcription Database (VastDB), largest resource genome-wide, quantitative profiles assembled date. VastDB provides readily accessible information on inclusion levels functional associations detected RNA-seq data from diverse vertebrate...
The subcellular localization of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring newly discovered lncRNAs involves time-consuming and costly experimental methods. We have created “lncATLAS,” a comprehensive resource lncRNA in human cells based on RNA-sequencing data sets. Altogether, 6768 GENCODE-annotated are represented across various compartments 15 cell lines. introduce relative concentration index (RCI) as useful measure derived from...
Long non-coding RNAs (lncRNAs) are functional non-translated molecules greater than 200 nt. Their roles diverse and they usually involved in transcriptional regulation. LncRNAs still remain largely uninvestigated plants with few exceptions. Experimentally validated plant lncRNAs have been shown to regulate important agronomic traits such as phosphate starvation response, flowering time interaction symbiotic organisms, making them of great interest biology breeding. There is a lack most...
The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of genome, represents milestone for both boosting breeding programmes ascertaining origin diversification flatfish. We compare genome model fish genomes to investigate teleost chromosome evolution. observe conserved macrosyntenic pattern within Percomorpha identify large syntenic blocks related...
The oral cavity comprises a rich and diverse microbiome, which plays important roles in health disease. Previous studies have mostly focused on adult populations or very young children, whereas the adolescent microbiome remains poorly studied. Here, we used citizen science approach 16S profiling to assess of 1500 adolescents around Spain its relationships with lifestyle, diet, hygiene, socioeconomic environmental parameters.Our results provide detailed snapshot how it varies lifestyle other...
The Plant Resistance Genes database (PRGdb; http://prgdb.org) is a comprehensive resource on resistance genes (R-genes), major class of in plant genomes that convey disease against pathogens. Initiated 2009, the has grown more than 6-fold to recently include annotation derived from recent genome sequencing projects. Release 2.0 currently hosts useful biological information set 112 known and 104 310 putative R-genes present 233 species conferring 122 different Moreover, website been...
Abstract The Catalan Initiative for the Earth BioGenome Project (CBP) is an EBP-affiliated project network aimed at sequencing genome of >40 000 eukaryotic species estimated to live in Catalan-speaking territories (Catalan Linguistic Area, CLA). These represent a biodiversity hotspot. While covering less than 1% Europe, they are home about one fourth all known European species. include high proportion endemisms, many which threatened. This trend likely get worse as effects global...
Nna1 is a recently described gene product that has sequence similarity with metallocarboxypeptidases. In the present study, five additional Nna1-like genes were identified in mouse genome and named cytosolic carboxypeptidase (CCP) 2 through 6. Modeling suggests domain folds into structure resembles metallocarboxypeptidases of M14 family, all necessary residues for catalytic activity broad substrate specificity. All CCPs are abundant testis also expressed brain, pituitary, eye, other tissues....
CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling individual loci, parallelized loss-of-function screens thousands regulatory elements. However, no solution presented the unique bioinformatic design requirements CRISPR deletion. We here present CRISPETa, a pipeline flexible and scalable paired sgRNA based on an empirical scoring model....
The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for measurement of molecules without the need conversion to complementary DNA, fragmentation or amplification. As such, it is virtually capable detecting any given modification present in molecule that being sequenced, as well provide polyA tail length estimations at level individual molecules. Although this technology has been publicly available since 2017, complexity raw data, together with lack systematic...
QCloud is a cloud-based system to support proteomics laboratories in daily quality assessment using user-friendly interface, easy setup, and automated data processing. Since its release, has facilitated control for experiments many laboratories. provides quick effortless evaluation of instrument performance that helps overcome analytical challenges derived from clinical translational research. Here we present an improved version the system, QCloud2. This new includes enhancements scalability...
Nna1 has some sequence similarity to metallocarboxypeptidases, but the biochemical characterization of not previously been reported. In this work we performed a detailed genomic scan and found >100 homologues in bacteria, Protista, Animalia, including several paralogs most eukaryotic species. Phylogenetic analysis Nna1-like sequences demonstrates major divergence between peptidases known metallocarboxypeptidases subfamilies: M14A, M14B, M14C. Conformational modeling representative proteins...
Insects are capable of extraordinary feats long-distance movement that have profound impacts on the function terrestrial ecosystems. The ability to undertake these movements arose multiple times through evolution a suite traits make up migratory syndrome, however underlying genetic pathways involved remain poorly understood. Migratory hoverflies (Diptera: Syrphidae) an emerging model group for studies migration. They seasonal in huge numbers across large parts globe and important...
MyMpn (http://mympn.crg.eu) is an online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections. Due its small size, ability grow in vitro, and amount of data produced over past decades, M. pneumoniae interesting model organisms for development systems biology approaches unicellular organisms. Our database hosts wealth omics-scale datasets generated by hundreds experimental computational analyses. These include...
Multitasking or moonlighting is the capability of some proteins to execute two more biochemical functions. Usually, are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict multifunctionality, especially because large amounts sequences from genome projects. In present work, we analyze and describe several approaches use sequences, structures, interactomics, current bioinformatics algorithms programs try overcome problem. Among these...
We present SuperFly (http://superfly.crg.eu), a relational database for quantified spatio-temporal expression data of segmentation genes during early development in different species dipteran insects (flies, midges and mosquitoes). has special focus on emerging non-drosophilid model systems. The currently includes high resolution three species: the vinegar fly Drosophila melanogaster, scuttle Megaselia abdita moth midge Clogmia albipunctata. At this point, covers up to 9 16 time points per...
Abstract Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection exon homology relationships. Here, we present ExOrthist , a fully reproducible Nextflow -based software enabling inference homologs orthogroups, visualization evolution exon-intron structures, assessment conservation alternative splicing patterns. evaluates sequence considers surrounding context to derive...
Hi-Cpipe is a bioinformatics pipeline for the automated analysis of data generated by high-throughput chromatin conformation capture (HiC). The workflow comprises steps formatting, genome alignment, quality control and filtering, identification genome-wide interactions, visualization statistics. An interactive browser enables visual inspection interaction results.
A structural classification of loops has been obtained from a set 141 protein structures classified as kinases. total 1813 was into 133 subclasses (9 betabeta(links), 15 betabeta(hairpins), 31 alpha-alpha, 46 alpha-beta and 32 beta-alpha). Functional information specific features relating function were included in the classification. such P-loop (shared by different folds) or Gly-rich-loop, among others, motifs. As result, common mechanism catalysis substrate binding proved for most...
TrSDB-TranScout Database-(http://ibb.uab.es/trsdb) is a proteome database of eukaryotic transcription factors based upon predicted motifs by TranScout and data sources such as InterPro Gene Ontology Annotation. Nine proteomes are included in the current version. Extensive diverse information for each entry, different analyses considering classification similarity relationships offered research on or gene expression.