A5041882822- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
- Chromosomal and Genetic Variations
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- CRISPR and Genetic Engineering
- Pluripotent Stem Cells Research
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- Renal and related cancers
- Cancer-related gene regulation
- Machine Learning in Bioinformatics
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Gene Regulatory Network Analysis
- Angiogenesis and VEGF in Cancer
- Fungal and yeast genetics research
- Insect Resistance and Genetics
- Kruppel-like factors research
- Acute Myeloid Leukemia Research
- Single-cell and spatial transcriptomics
- T-cell and B-cell Immunology
MRC London Institute of Medical Sciences
2020-2024
Imperial College London
2020-2024
Max Planck Institute for Molecular Biomedicine
2013-2024
Hammersmith Hospital
2021-2022
University of Münster
2016-2022
Medical Research Council
2021
Max Planck Society
2015
European Bioinformatics Institute
2008-2013
Wellcome Trust
2008-2013
Centro de Investigacion Principe Felipe
2005-2007
The genetic code—the binding specificity of all transfer-RNAs—defines how protein primary structure is determined by DNA sequence. also dictates when and where proteins are expressed, this information encoded in a pattern specific sequence motifs that recognized transcription factors. However, the DNA-binding only known for small fraction ∼1400 human factors (TFs). We describe here high-throughput method analyzing factor based on systematic evolution ligands exponential enrichment (SELEX)...
Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools often single-purpose, or limited in compatibility a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we present FAN-C, an easy-to-use command-line tool powerful Python API with broad feature set covering matrix generation, analysis, visualisation for C-like (...
Abstract The relationship between chromatin organization and gene regulation remains unclear. While disruption of domains domain boundaries can lead to misexpression developmental genes, acute depletion regulators genome has a relatively small effect on expression. It is therefore uncertain whether expression state drive or changes in facilitate cell-type-specific activation Here, using the dorsoventral patterning Drosophila melanogaster embryo as model system, we provide evidence for...
We have developed a web tool, PupasView, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupasView constitutes an interactive environment in which functional information and population frequency data can be used as sequential filters over linkage disequilibrium parameters to obtain final list SNPs optimal genotyping purposes. is first resource that integrates effects caused by at both translational transcriptional level. retrieves could affect...
We present a new version of Babelomics, complete suite web tools for functional analysis genome-scale experiments, with and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An indexing has considerably speeded up several the modules. FatiScan method studying coordinate behaviour groups related genes is presented, along similar tool, Gene Set Enrichment Analysis. Babelomics now more oriented to test...
We present Babelomics, a complete suite of web tools for the functional analysis groups genes in high-throughput experiments, which includes use information on Gene Ontology terms, interpro motifs, KEGG pathways, Swiss-Prot keywords, predicted transcription factor binding sites, chromosomal positions and presence tissues with determined histological characteristics, through five integrated modules: FatiGO (fast assignment transference information), FatiWise, association test, GenomeGO mining...
Transcriptional regulation is one of the most important processes for modulating gene expression. Though much this control attributed to transcription factors, histones, and associated enzymes, it increasingly apparent that spatial organization chromosomes within nucleus has a profound effect on transcriptional activity. Studies in yeast indicate nuclear pore complex might promote by recruiting chromatin periphery. In higher eukaryotes, however, not known whether such global significance....
We have developed a web tool, PupaSuite, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect, specifically oriented to help in design large-scale genotyping projects. PupaSuite uses collection data on SNPs from heterogeneous sources and large number pre-calculated predictions offer flexible intuitive interface selecting an optimal set SNPs. It improves functionality PupaSNP PupasView programs implements new facilities such as analysis user's derive...
Chromatin conformation constitutes a fundamental level of eukaryotic genome regulation. However, our ability to examine its biological function and role in disease is limited by the large amounts starting material required perform current experimental approaches. Here, we present Low-C, Hi-C method for low input material. By systematically comparing libraries made with decreasing show that Low-C highly reproducible robust noise. To demonstrate suitability analyse rare cell populations,...
Abstract Mediating the expansion of vascular beds in many physiological and pathological settings, angiogenesis requires dynamic changes endothelial cell behavior. However, molecular mechanisms governing activity during different phases growth, remodeling, maturation, quiescence remain elusive. Here, we characterize gene expression postnatal development identify critical angiogenic factors mouse retinal cells. Using actively translating transcriptome analysis silico computational analyses,...
Chromatin architecture mapping in 3D formats has increased our understanding of how regulatory sequences and gene expression are connected regulated a genome. The chromatin genome shows extensive remodeling during embryonic development, although the cleavage-stage embryos most species lack structure before zygotic activation (pre-ZGA), zebrafish been reported to have structure. Here, we aimed determine chromosomal paternal/sperm gamete cells discern whether it either resembles or informs...
There is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies humans and mice are limited by difficulty working with mammalian embryos relative scarcity active TEs these organisms. The zebrafish an outstanding model for study vertebrate development, over half its genome consists diverse TEs. However, remain poorly characterized. Here we describe demography genomic distribution their expression throughout embryogenesis using bulk...
Zebrafish, a popular organism for studying embryonic development and modeling human diseases, has so far lacked systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium created central repository store process zebrafish developmental genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines total of 1,802 sets unpublished re-analyzed published data, which used improve existing...
Sperm production and function require the correct establishment of DNA methylation patterns in germline. Here, we examined genome-wide changes during human spermatogenesis its alterations disturbed spermatogenesis. We found that is associated with remodeling methylome, comprising a global decline primary spermatocytes followed by selective remethylation, resulting spermatids/sperm-specific methylome. Hypomethylated regions spermatids/sperm were enriched specific transcription factor binding...