A5006214397- Genomics and Chromatin Dynamics
- Plant pathogens and resistance mechanisms
- Soybean genetics and cultivation
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- RNA modifications and cancer
- Agronomic Practices and Intercropping Systems
- Legume Nitrogen Fixing Symbiosis
- RNA and protein synthesis mechanisms
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- Protein Structure and Dynamics
- Chromosomal and Genetic Variations
- Plant Disease Resistance and Genetics
- Marine Bivalve and Aquaculture Studies
- Plant Molecular Biology Research
- Bioinformatics and Genomic Networks
- Single-cell and spatial transcriptomics
- Genetic and Environmental Crop Studies
- Fish Ecology and Management Studies
- Gene expression and cancer classification
- Plant-Microbe Interactions and Immunity
- Software Engineering Research
- Software System Performance and Reliability
- Aquaculture disease management and microbiota
Research Institute of Molecular Pathology
2018-2024
Vienna Biocenter
2019-2024
Centre for Genomic Regulation
2016-2023
Universitat Politècnica de Catalunya
2021-2023
Institute for Research in Biomedicine
2021-2023
Barcelona Supercomputing Center
2021-2023
Universitat Pompeu Fabra
2015-2022
Lomonosov Moscow State University
2020
University of Vienna
2020
Barcelona Institute for Science and Technology
2018
Significance In eusocial insect societies, such as ants and some bees wasps, phenotypes are highly plastic, generating alternative (queens workers) from the same genome. The greatest plasticity is found in simple which individuals can switch between adults. genomic, transcriptional, epigenetic underpinnings of largely unknown. contrast to complex societies honeybee, we find that lack distinct transcriptional differentiation coherently patterned DNA methylomes. Instead, defined by subtle...
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.
Abstract Background The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive resilient to biotic abiotic stressors causing recurrent massive mortalities in other bivalves. Although these traits have been recently linked with the maintenance of a high genetic variation within natural populations, factors underlying evolutionary success this species remain unclear. Results Here, after assembly 1.28-Gb reference...
Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on single haploid reference genome. Here, we present the EN-TEx resource 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating catalog >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes less conserved...
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...
Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding origins and concurrent shaping genome this crop limited. We sequenced genomes 29 accessions representing 12 Phaseolus species. Single nucleotide...
Summary We sequenced the genome of highly heterozygous almond Prunus dulcis cv. Texas combining short‐ and long‐read sequencing. obtained a assembly totaling 227.6 Mb estimated size 238 Mb, which 91% is anchored to eight pseudomolecules corresponding its haploid chromosome complement, annotated 27 969 protein‐coding genes 6747 non‐coding transcripts. By phylogenomic comparison with genomes 16 additional close distant species we that peach ( persica ) diverged around 5.88 million years ago....
As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started genome assembly and annotation. The guidelines given are broadly applicable, intended be stable over time, cover all aspects from start finish general annotation project. Intrinsic properties genomes discussed, as is importance using high quality DNA. Different sequencing technologies generally applicable workflows for also detailed. We structural functional...
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...
Even though transcription factors (TFs) are central players of gene regulation and have been extensively studied, their regulatory trans-activation domains (tADs) often remain unknown a systematic functional characterization tADs is lacking. Here, we present novel high-throughput approach tAD-seq to functionally test thousands candidate from different TFs in parallel. The identify by pooled screening validate individual luciferase assays, whereas neutral regions do not. Interestingly, the...
The C-terminal domain (CTD) of the largest subunit RNA polymerase II (Pol II) is a regulatory hub for transcription and processing. Here, we identify PHD-finger protein 3 (PHF3) as regulator mRNA stability that docks onto Pol CTD through its SPOC domain. We characterize reader preferentially binds two phosphorylated Serine-2 marks in adjacent repeats. PHF3 drives liquid-liquid phase separation II, colocalizes with clusters tracks across length genes. knock-out or deletion human cells results...
Abstract Recruitment of RNA polymerase II (Pol II) to promoters is essential for transcription. Despite conflicting evidence, the Pol preinitiation complex (PIC) often thought have a uniform composition and assemble at all via an identical mechanism. Here, using Drosophila melanogaster S2 cells as model, we demonstrate that different promoter classes function distinct PICs. Promoter DNA developmentally regulated genes readily associates with canonical PIC, whereas housekeeping do not,...
Abstract Background To identify as many different transcripts/genes in the Atlantic salmon genome possible, it is crucial to acquire good cDNA libraries from tissues and developmental stages, their relevant sequences (ESTs or full length sequences) attempt predict function. Such allow identification of a large number transcripts can provide valuable information on genes expressed particular tissue at specific stage. This data important constructing microarray chip, identifying SNPs coding...
We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these reveals that most body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural, and blood cells. These act as basic components many tissues organs. Based on gene expression, types redefine histological by been traditionally classified. identified genes whose expression is specific to types, genes, we...
The molecular complexity of human breast cancer (BC) renders the clinical management disease challenging. Long non-coding RNAs (lncRNAs) are promising biomarkers for BC patient stratification, early detection, and monitoring. Here, we identified involvement long intergenic RNA 01087 (LINC01087) in oncogenesis. LINC01087 appeared significantly downregulated triple-negative BCs (TNBCs) upregulated luminal subtypes comparison to mammary samples from cancer-free women matched normal pairs....
Abstract Aquaporin-mediated oocyte hydration is considered important for the evolution of pelagic eggs and radiative success marine teleosts. However, molecular regulatory mechanisms controlling this vital process are not fully understood. Here, we analyzed >400 piscine genomes to uncover a previously unknown teleost-specific aquaporin-1 cluster (TSA1C) comprised tandemly arranged aqp1aa-aqp1ab2-aqp1ab1 genes. Functional evolutionary analysis TSA1C reveals ∼300-million-year history...
Abstract Mussels are ecologically and economically relevant edible marine bivalves, highly invasive resilient to biotic abiotic stressors causing recurrent massive mortalities in other species. Here we show that the Mediterranean mussel Mytilus galloprovincialis has a complex pan-genomic architecture, which includes core set of 45,000 genes shared by all individuals plus surprisingly high number dispensable (∼15,000). The latter subject presence/absence variation (PAV), i.e., they may be...
Abstract All multicellular life relies on differential gene expression, determined by regulatory DNA elements and DNA‐binding transcription factors that mediate activation repression via cofactor recruitment. While activators have been extensively characterized, repressors are less well studied: the identities properties of their repressive domains (RDs) typically unknown specific co‐repressors (CoRs) they recruit not determined. Here, we develop a high‐throughput, next‐generation...
Differential gene transcription enables development and homeostasis in all animals is regulated by two major classes of distal cis-regulatory DNA elements (CREs): enhancers silencers. Although have been thoroughly characterized, the properties mechanisms silencers remain largely unknown. By an unbiased genome-wide functional screen Drosophila melanogaster S2 cells, we discover a class that bind one three factors (TFs) are generally not included chromatin-defined CRE catalogs as they mostly...
DATA REPORT article Front. Aging Neurosci., 20 March 2017Sec. Alzheimer's Disease and Related Dementias Volume 9 - 2017 | https://doi.org/10.3389/fnagi.2017.00064
Abstract Background Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment sequencers. Each file contains information which can be interpreted specialised software to reveal the sequence (base calling). This is done sequencer proprietary publicly available programs. Depending on size of a project number trace vary from just few thousands files. Sequencing quality assessment various criteria important at stage preceding clustering and contig...