A5052534041- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- Fungal and yeast genetics research
- Antifungal resistance and susceptibility
- Plant Pathogens and Fungal Diseases
- Fungal Infections and Studies
- Yeasts and Rust Fungi Studies
- Fermentation and Sensory Analysis
- Chromosomal and Genetic Variations
- Legume Nitrogen Fixing Symbiosis
- CRISPR and Genetic Engineering
- Geochemistry and Elemental Analysis
- Advances in Cucurbitaceae Research
- Bacterial Genetics and Biotechnology
- Plant nutrient uptake and metabolism
- Biofuel production and bioconversion
- interferon and immune responses
- Food Quality and Safety Studies
- RNA regulation and disease
- Photosynthetic Processes and Mechanisms
- Mitochondrial Function and Pathology
- Polyoxometalates: Synthesis and Applications
Centre for Genomic Regulation
2016-2025
International Institute of Molecular and Cell Biology
2015-2022
Universitat Pompeu Fabra
2010-2018
Institució Catalana de Recerca i Estudis Avançats
2013
Many genomes display high levels of heterozygosity (i.e. presence different alleles at the same loci in homologous chromosomes), being those hybrid organisms an extreme such case. The assembly highly heterozygous from short sequencing reads is a challenging task because it difficult to accurately recover haplotypes. When confronted with genomes, standard process tends collapse homozygous regions and reports alternative contigs. boundaries between result multiple paths that are hard resolve,...
Phylogenetic trees representing the evolutionary relationships of homologous genes are entry point for many analyses. For instance, use a phylogenetic tree can aid in inference orthology and paralogy relationships, detection relevant events such as gene family expansions contractions, horizontal transfer, recombination or incomplete lineage sorting. Similarly, given plurality histories among encoded genome, there is need combined analysis genome-wide collections (phylomes). Here, we...
Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true history of genes generally unknown orthologs are used very different applications across phyla, requiring precision–recall trade-offs. As a result, it difficult to assess performance methods. Here, we present community effort establish standards an automated web-based service facilitate benchmarking. Using this service, characterize 15 well-established...
Over the past two decades, several fungal outbreaks have occurred, including high-profile 'Vancouver Island' and 'Pacific Northwest' outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy humans animals. same time period, C. gattii was cause additional case clusters at localities outside tropical subtropical climate zones where species normally occurs. In every case, causative agent belongs to a previously rare genotype called AFLP6/VGII, but origin...
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult part because simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, nanopore-based approach sequence native tRNA populations that provides quantitative estimates of both abundances modification dynamics single experiment. We show default nanopore sequencing settings discard the vast majority reads, leading poor yields...
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...
Abstract RNA modifications influence function and fate, but detecting them in individual molecules remains challenging for most modifications. Here we present a novel methodology to generate training sets build modification-aware basecalling models. Using this approach, develop the m 6 ABasecaller , model that predicts A from raw nanopore signals. We validate its accuracy vitro vivo, revealing stable modification stoichiometry across isoforms, co-occurrence within molecules, A-dependent...
The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including reconstruction large collections phylogenetic trees. Here, we present third version PhylomeDB (http://phylomeDB.org), a public database for genome-wide gene phylogenies (phylomes). Currently, is largest repository and hosts 17 phylomes, comprising 416,093 trees 165,840 alignments. It also major source phylogeny-based orthology paralogy...
Candida metapsilosis is a rarely-isolated, opportunistic pathogen that belongs to clade of pathogenic yeasts known as the C. parapsilosis sensu lato species complex. To gain insight into recent evolution and genetic basis its virulence, we sequenced genome 11 clinical isolates from various locations, which compared each other available genomes two remaining members complex: orthopsilosis parapsilosis. Unexpectedly, found compelling genomic evidence highly heterozygous hybrid species, with...
The Candida parapsilosis species complex comprises a group of emerging human pathogens varying virulence. This was recently subdivided into three different species: C. sensu stricto, metapsilosis, and orthopsilosis. Within the latter, at least two clearly distinct subspecies seem to be present among clinical isolates (Type 1 Type 2). To gain insight genomic differences between these subspecies, we undertook sequencing isolate classified as compared it with available sequence 2 strain....
In recent years, nanopore direct RNA sequencing (DRS) became a valuable tool for studying the epitranscriptome, owing to its ability detect multiple modifications within same full-length native molecules. Although can be identified in form of systematic basecalling "errors" DRS data sets,
Reliable prediction of orthology is central to comparative genomics. Approaches based on phylogenetic analyses closely resemble the original definition and paralogy are known be highly accurate. However, large computational cost associated these a limiting factor that often prevents its use at genomic scales. Recently, several projects have addressed reconstruction collections high-quality trees from which relationships can inferred. This provides us with opportunity infer evolutionary genes...
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...
Invasive candidiasis is the most commonly reported invasive fungal infection worldwide. Although Candida albicans remains main cause, incidence of emerging species, such as C. parapsilosis increasing. It has been postulated that clinical isolates result from a recent global expansion virulent clone. However, availability single genome for this species so far prevented testing hypothesis at genomic scales. We present here sequence three additional strains and environmental samples. Our...
ABSTRACT In the earliest stages of animal development following fertilization, maternally deposited mRNAs direct biological processes to point zygotic genome activation (ZGA). These maternal undergo cytoplasmic polyadenylation (CPA), suggesting translational control their activation. To elucidate role CPA during embryogenesis, we performed genome-wide polysome profiling at several zebrafish development. Our analysis revealed a correlation between and polysome-association dynamics,...
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology-evolutionary relatedness-is many cases readily determined based on sequence similarity analysis. By contrast, whether or not two directly descended from common ancestor by speciation event (orthologs) duplication (paralogs) more challenging, yet provides critical information history gene. Since 2009, this task has been focus Quest for Orthologs (QFO) Consortium. The sixth...
ABSTRACT RNA modifications hold pivotal roles in shaping the fate and function of molecules. Although nanopore sequencing technologies have proven successful at transcriptome-wide detection modifications, current algorithms are limited to predicting a per-site level rather than within individual Herein, we introduce m 6 ABasecaller , an innovative method enabling direct basecalling A from raw signals This approach facilitates de novo prediction with precision down single nucleotide molecule...
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%...
Abstract Inferring homology relationships across genes in different species is a central task comparative genomics. Therefore, large number of resources and methods have been developed over the years. Some public databases include phylogenetic trees homologous gene families which can be used to further differentiate into orthology paralogy. MetaPhOrs web server that integrates information from sources provide paralogy based on common phylogeny-based predictive algorithm associated with...
Transcriptome data and qPCR analysis revealed new insight into genes regulatory mechanism related to cucumber sex determination. Cucumber (Cucumis sativus L.) is an economically important crop cultivated worldwide. Enhancing the genomic resources for may enable regulation of traits relevant productivity quality. Sequencing technologies bioinformatics tools provide opportunities development such resources. The aims this study were identify characterize involved in determination flower...
The field of epitranscriptomics is undergoing a technology-driven revolution. During past decades, RNA modifications like N6-methyladenosine (m6A), pseudouridine (ψ), and 5-methylcytosine (m5C) became acknowledged for playing critical roles in cellular processes. Direct sequencing by Oxford Nanopore Technologies (ONT) enabled the detection native RNA, detecting noncanonical nucleosides properties raw data. Consequently, field's cutting edge has heavy component computer science, opening new...
Boi1 and Boi2 (Boi1/2) are budding yeast plasma membrane proteins that function in polarized growth, cytokinesis inhibition response to chromosome bridges via the NoCut abscission checkpoint. How Boi1/2 act these two distinct processes is not understood. We demonstrate required for a late step fusion of secretory vesicles with growing bud. Cells lacking accumulate defective bud growth. In contrast, specifically cells chromatin bridges. The SH3 domain Boi2, which dispensable growth targets...
ABSTRACT Comparative genomics, metagenomics, and single-cell technologies have shown that populations of microbial species encompass assemblages closely related strains. This raises the question whether individual bacterial lineages respond to presence their close relatives by modifying gene expression or, instead, simply act as arithmetic addition components. Here, we took advantage transcriptome sequencing address this question. For this, analyzed transcriptomes two strains extremely...
RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining secondary is central understanding their function and evolution. In recent years several sequencing-based approaches have been developed allow probing structural features thousands present a sample. Here, we describe nextPARS, novel Illumina-based implementation vitro...