Myrto Kostadima
A5029443733- Platelet Disorders and Treatments
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
- Blood groups and transfusion
- Epigenetics and DNA Methylation
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- MicroRNA in disease regulation
- Eosinophilic Disorders and Syndromes
- Antiplatelet Therapy and Cardiovascular Diseases
- Erythrocyte Function and Pathophysiology
- Immune responses and vaccinations
- Genomics and Rare Diseases
- RNA and protein synthesis mechanisms
- Immune cells in cancer
- Blood Coagulation and Thrombosis Mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Immune Response and Inflammation
- Genomic variations and chromosomal abnormalities
- Blood disorders and treatments
- Immunodeficiency and Autoimmune Disorders
- Cell Adhesion Molecules Research
University of Cambridge
2014-2022
Cambridge School
2020
European Bioinformatics Institute
2011-2019
National Health Service
2014-2019
NHS Blood and Transplant
2014-2018
Wellcome Trust
2011-2018
National Institute for Health Research
2016
The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of draft human genome, with aim accelerating genomics research through rapid open distribution public data. Large amounts raw data are thus transformed into knowledge, which is made available via a multitude channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded multiple directions. First, resources describe fields genomics, gene...
Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank INTERVAL studies, testing 29.5 million genetic for 36 red cell, white platelet properties 173,480 European-ancestry participants. This effort yielded hundreds low frequency (<5%) rare (<1%) strong impact on blood cell phenotypes. Our data highlight general allelic architecture complex...
The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation comparative genomics across the vertebrate subphylum key model organisms. pipeline capable of integrating experimental reference data from multiple providers into single integrated resource. Here, we present 94 newly annotated re-annotated genomes, bringing total number genomes offered by to 227. This represents largest expansion resource since its...
Highlights•High-resolution maps of promoter interactions in 17 human primary blood cell types•Interaction patterns are type specific and segregate with the hematopoietic tree•Promoter-interacting regions enriched for regulatory chromatin features eQTLs•Promoter link non-coding GWAS variants putative target genesSummaryLong-range between elements gene promoters play key roles transcriptional regulation. The vast majority uncharted, constituting a major missing understanding genome control....
The Ensembl project (https://www.ensembl.org) makes key genomic data sets available to the entire scientific community without restrictions. seeks be a fundamental resource driving progress by creating, maintaining and updating reference genome annotation comparative genomics resources. This year we describe our new expanded gene, variant capabilities, which led 50% increase in number of vertebrate genomes support. We have also doubled human variants added regulatory regions for many mouse...
Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate integrate diverse collection of large-scale reference data to create more comprehensive view biology than would be possible from any individual dataset. Our extensive resources include evidence-based gene regulatory region annotation, variation trees. An accompanying suite tools, infrastructure programmatic access methods ensure uniform analysis distribution all...
Inflammation drives atherosclerotic plaque rupture. Although inflammation can be measured using fluorine-18-labeled fluorodeoxyglucose positron emission tomography ([18F]FDG PET), [18F]FDG lacks cell specificity, and coronary imaging is unreliable because of myocardial spillover. This study tested the efficacy gallium-68-labeled DOTATATE (68Ga-DOTATATE), a somatostatin receptor subtype-2 (SST2)-binding PET tracer, for inflammation. We confirmed 68Ga-DOTATATE binding in macrophages excised...
A BLUEPRINT of immune cell development To determine the epigenetic mechanisms that direct blood cells to develop into many components our system, consortium examined regulation DNA and RNA transcription dissect molecular traits govern differentiation. By inducing responses, Saeed et al. document changes in genome underlie Cheng demonstrate trained monocytes are highly dependent on breakdown sugars presence oxygen, which allows produce energy needed mount an response. Chen examine transcripts...
E527K hyperactive SRC results in megakaryocytes with increased podosome formation, thrombocytopenia, myelofibrosis, bleeding, and bone pathologies.
Neutrophils are short-lived blood cells that play a critical role in host defense against infections. To better comprehend neutrophil functions and their regulation, we provide complete epigenetic overview, assessing important functional features of differentiation stages from bone marrow-residing progenitors to mature circulating cells. Integration chromatin modifications, methylation, transcriptome dynamics reveals an enforced regulation differentiation, for cellular such as release...
Abstract Linking non-coding genetic variants associated with the risk of diseases or disease-relevant traits to target genes is a crucial step realize GWAS potential in introduction precision medicine. Here we set out determine mechanisms underpinning variant association platelet quantitative using cell type-matched epigenomic data and promoter long-range interactions. We identify regulatory functions for 423 565 (75%) demonstrate, through ex vivo proof principle genome editing validation,...
Abstract Gray platelet syndrome (GPS) is an autosomal recessive bleeding disorder characterized by a lack of α-granules in platelets and progressive myelofibrosis. Rare loss-of-function variants neurobeachin-like 2 (NBEAL2), member the family beige Chédiak-Higashi (BEACH) genes, are causal GPS. It suggested that BEACH domain containing proteins involved fusion, fission, trafficking vesicles granules. Studies knockout mice suggest NBEAL2 may control formation retention granules neutrophils....
Genome-wide association studies have identified a genetic variant at 3p14.3 (SNP rs1354034) that strongly associates with platelet number and mean volume in humans. While originally proposed to be intronic, analysis of mRNA expression primary human hematopoietic subpopulations reveals this SNP is located directly upstream the predominantly expressed ARHGEF3 isoform megakaryocytes (MK). We found ARHGEF3, which encodes Rho guanine exchange factor, dramatically upregulated during both murine MK...
Bioinformatics and high-throughput technologies such as microarray studies allow the measure of expression levels large numbers genes simultaneously, thus helping us to understand molecular mechanisms various biological processes in a cell.We calculate Pearson Correlation Coefficient (r-value) between probe set signal values from Affymetrix Human Genome Microarray samples cluster human according r-value correlation matrix using Neighbour Joining (NJ) clustering method. A hyper-geometric...
The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There currently a shortage cutting-edge bioinformatics training courses Australia as consequence scarcity skilled trainers with time funding develop deliver courses. To address this, consortium organizations, including Bioplatforms...
Transcriptional profiling of hematopoietic cell subpopulations has helped to characterize the developmental stages system and molecular bases malignant non-malignant blood diseases. Previously, only genes targeted by expression microarrays could be profiled genome-wide. High-throughput RNA sequencing, however, encompasses a broader repertoire molecules, without restriction previously annotated genes. We analyzed BLUEPRINT consortium RNA-sequencing data for mature types. The comprised 90...
Abstract Transcriptional profiling of hematopoietic cell subpopulations has helped characterize the developmental stages system and molecular basis malignant non-malignant blood diseases for past three decades. The introduction high-throughput RNA sequencing increased knowledge full repertoire molecules in cells different types, without relying on prior gene annotation. Here, we introduce analysis BLUEPRINT consortium expression data mature cells, comprising 90 total 32 small experiments,...
The advancement of high-throughput sequencing (HTS) technologies and the rapid development numerous analysis algorithms pipelines in this field has resulted an unprecedentedly high demand for training scientists HTS data analysis. Embarking on developing new materials is challenging many reasons. Trainers often do not have prior experience preparing or delivering such struggle to keep them up date. A repository curated would support trainers preparation, reduce duplication effort by...