A5034809841- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Oral microbiology and periodontitis research
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Dental Research and COVID-19
- Salivary Gland Disorders and Functions
- Soybean genetics and cultivation
- Plant pathogens and resistance mechanisms
- Legume Nitrogen Fixing Symbiosis
- Pluripotent Stem Cells Research
- Gut microbiota and health
- Genomics and Chromatin Dynamics
- MicroRNA in disease regulation
- Acute Myeloid Leukemia Research
- Histone Deacetylase Inhibitors Research
- Genital Health and Disease
- Female Genital Mutilation/Cutting Issues
- RNA Interference and Gene Delivery
- Molecular Biology Techniques and Applications
- Immune Cell Function and Interaction
- Protein Degradation and Inhibitors
- Cancer, Hypoxia, and Metabolism
Centre for Genomic Regulation
2016-2025
Universitat Pompeu Fabra
2012-2021
Barcelona Institute for Science and Technology
2017-2020
Ceinge Biotecnologie Avanzate (Italy)
2008-2016
Stanford Medicine
2012
European School of Molecular Medicine
2008
University of Naples Federico II
2005
We report the genome sequence of melon, an important horticultural crop worldwide. assembled 375 Mb double-haploid line DHL92, representing 83.3% estimated melon genome. predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping orthology and paralogy relationships sequenced plant genomes. observed absence recent whole-genome duplications in lineage since ancient eudicot triplication, our data suggest that transposon amplification...
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...
Legumes are the third largest family of angiosperms and second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared legumes.
Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns genomic erosion that might limit viability, offer tools for effective conservation. The Iberian lynx (Lynx pardinus) is the most felid a unique example on brink extinction.
Nanopore direct RNA sequencing (DRS) enables measurement of molecules, including their native modifications, without prior conversion to cDNA. However, commercial methods for molecular barcoding multiple DRS samples are lacking, and community-driven efforts, such as DeePlexiCon, not compatible with newer chemistry flowcells the latest-generation GPU cards. To overcome these limitations, we introduce SeqTagger, a rapid robust method that can demultiplex datasets 99% precision 95% recall. We...
The Polycomb repressive complex 1 (PRC1) is required for decisions of stem cell fate. In mouse embryonic cells (ESCs), two major variations PRC1 complex, defined by the mutually exclusive presence Cbx7 or RYBP, have been identified. Here, we show that although genomic localization Cbx7- and RYBP-containing complexes overlaps in certain genes, it can also be exclusive. At molecular level, necessary recruitment Ring1B to chromatin, whereas RYBP enhances enzymatic activity. Genes occupied lower...
Altered stem cell homeostasis is linked to organismal aging. However, the mechanisms involved remain poorly understood. Here we report novel alterations in hair follicle cells during skin aging, including increased numbers, decreased function, and an inability tolerate stress. Performing high-throughput RNA sequencing on aging cells, cytokine arrays, functional assays, identify age-associated imbalance epidermal Jak–Stat signaling that inhibits function. Collectively, this study reveals a...
MicroRNAs (miRNAs) play an important role in proper function and differentiation of mouse embryonic stem cells (ESCs). We performed a systematic comparison miRNA expression undifferentiated vs. differentiating ESCs. report that 138 miRNAs are increased on the induction differentiation. compared entire list candidate mRNA targets up-regulated with down-regulated ESCs Among emerging from this analysis, we found three genes, Smarca5, Jarid1b, Sirt1, previously demonstrated to be involved...
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 relevance of the human oral microbiome to our understanding health has grown in recent years as studies continue develop. Given links cavity with digestive, respiratory and circulatory systems, composition is relevant beyond just health, impacting systemic processes across body. However, we still have a very limited about intrinsic extrinsic factors that shape healthy microbiome. Here, followed citizen-science approach assess relative impact on selected biological, social, lifestyle 1648...
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...
The human respiratory tract pathogen M. pneumoniae is one of the best characterized minimal bacterium. Until now, two main groups clinical isolates this bacterium have been described (types 1 and 2), differing in sequence P1 adhesin gene. Here, we sequenced genomes 23 pneumoniae. Studying SNPs, non-synonymous mutations, indels genome rearrangements these strains 4 previously ones, has revealed new subclasses groups, some them being associated with country isolation. Integrative analysis...
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...
The biological relevance and dynamics of mRNA modifications have been extensively studied; however, whether rRNA are dynamically regulated, under which conditions, remains unclear. Here, we systematically characterize bacterial upon exposure to diverse antibiotics using native RNA nanopore sequencing. To identify significant modification changes, develop NanoConsensus, a novel pipeline that is robust across types, stoichiometries coverage, with very low false positive rates, outperforming...
Novosphingobium sp. strain PP1Y is a marine α-proteobacterium adapted to grow at the water/fuel oil interface. It exploits aromatic fraction of fuel oils as carbon and energy source. able on wide range mono-, poly- heterocyclic hydrocarbons. Here, we report complete functional annotation whole genome.PP1Y genome analysis its comparison with other Sphingomonadal genomes has yielded novel insights into molecular basis PP1Y's phenotypic traits, such peculiar ability encapsulate degrade oils. In...
Abstract Background To date, the microbiota of human penis has been studied mostly in connection with circumcision, HIV risk and female partner bacterial vaginosis (BV). These studies have shown that male circumcision reduces penile anaerobic bacteria, greater abundance bacteria is correlated increased cytokine levels infection, an important harbour for BV-associated bacteria. While to significantly reduce acquiring papillomavirus (HPV) relationship HPV still unknown. In this study, we...
ABSTRACT Nanopore direct RNA sequencing (DRS) enables measurement of molecules, including their native modifications, without prior conversion to cDNA. However, commercial methods for molecular barcoding multiple DRS samples are lacking, and community-driven efforts, such as DeePlexiCon, not compatible with newer chemistry flowcells the latest-generation GPU cards. To overcome these limitations, we introduce SeqTagger, a rapid robust method that can demultiplex datasets 99% precision 95%...
Subcellular compartmentalization of metabolic enzymes establishes a unique environment that elicits specific cellular functions. Indeed, the nuclear translocation certain is required for epigenetic regulation and gene expression control. Here, we show localization mitochondrial enzyme methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) ensures mitosis progression. Nuclear MTHFD2 interacts with proteins involved in centromere stability, including methyltransferases KMT5A DNMT3B. Loss induces...
A growing body of evidence has shown that Krüppel-like transcription factors play a crucial role in maintaining embryonic stem cell (ESC) pluripotency and governing ESC fate decisions. factor 5 (Klf5) appears to critical these processes, but detailed knowledge the molecular mechanisms this function is still not completely addressed.By combining genome-wide chromatin immunoprecipitation microarray analysis, we have identified 161 putative primary targets Klf5 ESCs. We address three main...