Emmanouil Athanasiadis

University of West Attica | TEIATH

Innate lymphoid cells (ILCs) are important mediators of the immune response and homeostasis in barrier tissues of mammals. However, the existence and function of ILCs in other vertebrates are poorly understood. Here, we use single-cell RNA sequencing to generate a comprehensive atlas of zebrafish lymphocytes during tissue homeostasis and after immu...

The success of marker-based approaches for dissecting haematopoiesis in mouse and human is reliant on the presence of well-defined cell surface markers specific for diverse progenitor populations. An inherent problem with this approach is that the presence of specific cell surface markers does not directly reflect the transcriptional state of a cel...

ChemBioServer is a publicly available web application for effectively mining and filtering chemical compounds used in drug discovery. It provides researchers with the ability to (i) browse and visualize compounds along with their properties, (ii) filter chemical compounds for a variety of properties such as steric clashes and toxicity, (iii) apply...

Systemic approaches are essential in the discovery of disease-specific genes, offering a different perspective and new tools on the analysis of several types of molecular relationships, such as gene co-expression or protein-protein interactions. However, due to lack of experimental information, this analysis is not fully applicable. The aim of this...

CD4$^+$ T cells are at the nexus of the innate and adaptive arms of the immune system. However, little is known about the evolutionary history of CD4$^+$ T cells, and it is unclear whether their differentiation into specialized subsets is conserved in early vertebrates. In this study, we have created transgenic zebrafish with vibrantly labeled CD4$...

Liver disease is on the rise, which has created the urgent need for new treatments. An attractive therapeutic approach is the understanding and manipulation of the regenerative pathways of the liver. The regenerative capability of the liver is dependent on the nature of the injury. It is known that mild injury and hepatectomy induce hepatocyte prol...

Deep sequencing of human tumours has uncovered a previously unappreciated role for epigenetic regulators in tumorigenesis. H3K4 methyltransferase KMT2C/MLL3 is mutated in several solid malignancies, including more than 10% of breast tumours. To study the tumour suppressor role of KMT2C in breast cancer, we generated mouse models of Erbb2/Neu, Myc o...

The strain that dominated in Greece during the first pandemic wave was primarily imported from a group of returning travelers in February 2020, while molecular and clinical data suggest that the origin of the transmission was Egypt. The observed molecular transmission clusters reflect the transmission dynamics of this particular strain bearing the...

Objectives Patients with lupus nephritis (LN) are in urgent need for early diagnosis and therapeutic interventions targeting aberrant molecular pathways enriched in affected kidneys. Methods We used mRNA-sequencing in effector (spleen) and target (kidneys, brain) tissues from lupus and control mice at sequential time points, and in the blood from...

Lung cancer is the leading cause of cancer-related deaths worldwide, and elucidation of its complicated pathobiology has been traditionally targeted by studies incorporating genomic as well other high-throughput approaches. Recently, a collection of methods used for cancer imaging, supplemented by quantitative aspects leading towards imaging biomar...

Signaling through adhesion-related molecules is important for cancer growth and metastasis and cancer cells are resistant to anoikis, a form of cell death ensued by cell detachment from the extracellular matrix. Herein, we report that detached carcinoma cells and immortalized fibroblasts display defects in TNF and CD40 ligand (CD40L)-induced MEK-ER...

Protein tyrosine phosphatase receptor zeta 1 (PTPRZ1) is a transmembrane tyrosine phosphatase receptor highly expressed in embryonic stem cells. In the present work, gene expression analyses of Ptprz1 -/- and Ptprz1 +/+ mice endothelial cells and hearts pointed to an unidentified role of PTPRZ1 in heart development through regulation of heart-speci...

Recent advances in sequencing technologies have allowed the in-depth molecular study of tumors, even at the single cell level. Sequencing efforts have uncovered a previously unappreciated heterogeneity among tumor cells, which has been postulated to be the driving force of tumor evolution and to facilitate recurrence, metastasis, and drug resistanc...

Haematopoietic stem cells (HSCs) first arise during development in the aorta-gonad-mesonephros (AGM) region of the embryo from a population of haemogenic endothelial cells which undergo endothelial-to-haematopoietic transition (EHT). Despite the progress achieved in recent years, the molecular mechanisms driving EHT are still poorly understood, esp...

Haematopoietic stem cells (HSC) first arise during development in the aorta-gonad-mesonephros (AGM) region of the embryo from a population of haemogenic endothelial cells which undergo endothelial-to-haematopoietic transition (EHT). Despite the progress achieved in recent years, the molecular mechanisms driving EHT are still poorly understood, espe...

ChemBioServer 2.0 is the advanced sequel of a web-server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse and visualize compounds along with their physicochemical and toxicity properties, (ii) perform property-based filtering o...

p>ChemBioServer 2.0 is the advanced sequel of a web-server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse and visualize compounds along with their physicochemical and toxicity properties, (ii) perform property-based filtering...

Innate lymphoid cells (ILCs) are important mediators of the immune response and homeostasis in barrier tissues of mammals. However, the existence and function of ILCs in other vertebrates is poorly understood. Here, we use single-cell RNA sequencing to generate a comprehensive atlas of zebrafish lymphocytes during tissue homeostasis and following i...

The success of marker-­based approaches for dissecting haematopoiesis in mouse and human is reliant on the presence of well-­defined cell-­surface markers specific for diverse progenitor populations. An inherent problem with this approach is that the presence of specific cell surface markers does not directly reflect the transcriptional state of a...

Background Familial dyslipidemias of either heterozygous (heFH) or combined (FCH) type lead to accelerated atherogenesis and increased cardiovascular risk. Objective The aim of this study was to investigate in statin-naïve adult patients with familial dyslipidemias whether inflammatory activation and liver, spleen and bone marrow metabolic activit...

The success of marker-based approaches for dissecting haematopoiesis in mouse and human is reliant on the presence of well-defined cell-surface markers specific for diverse progenitor populations. An inherent problem with this approach is that the presence of specific cell surface markers does not directly reflect the transcriptional state of a cel...

Introduction: 18F-FDG-PET scan is regarded the gold standard for quantification of carotid inflammation. Microwave radiometry (MWR) allows in vivo evaluation of arterial inflammation in atherosclerotic plaques by measuring temperatures.Hypothesis: We investigated the hypothesis whether a) there is a correlation between temperature measurements by M...

Herein, miRNA candidates relevant to mycosis fungoides were investigated to provide data on the molecular mechanisms underlying the pathogenesis of the disease. The miRNA expression profile of skin biopsies from patients with tumor stage MF (tMF) and normal donors was compared using miRNA microarrays. Overall, 154 miRNAs were found differentially e...

The aim of the present work was to design and develop a database of simulated solitary pulmonary nodules (SPN) in pairs of computed tomography (CT) and positron emission tomography (PET) images, using Monte Carlo (MC) simulation methods. We have developed an SPN image modeling pipeline to feed the database entitled SPNsim. The database is web-acces...

CD4+ T cells are at the nexus of the innate and adaptive arms of the immune system. However, little is known about the evolutionary history of CD4+ T cells, and it is unclear whether their differentiation into specialized subsets is conserved in early vertebrates. In this study, we have created transgenic zebrafish with vibrantly labeled CD4+ cells...

Differential rewiring of cellular interaction networks between disease and healthy state is of great importance. Through a systems level approach, malfunctioned mechanisms that are absent in the normal cases, may enlighten the key-players in terms of genes and their interaction chains related to disease. We have developed D-Map, a publicly availabl...

Aims To explore the relationship between temperature measurements derived by microwave radiometry (MWR) and carotid flurodeoxyglucose (FDG) uptake and assess their association with histological and immunohistochemistry findings in patients with high-grade carotid stenosis.Methods and results In 21 patients undergoing carotid endarterectomy, carotid...

We have developed ZoomOut web server in order to provide the research community with a tool for analysis, visualization and clustering of networks as a super network, based on their calculated feature properties. Networks can be analysed and be further treated as single nodes in a super network that describe their relations. Specifically, the user...

Alarming epidemiological features of Alzheimer's disease impose curative treatment rather than symptomatic relief. Drug repurposing, that is reappraisal of a substance's indications against other diseases, offers time, cost and efficiency benefits in drug development, especially when in silico techniques are used. In this study, we have used gene s...

In the last few years, mobile devices such as smartphones and tablets have become an integral part of everyday life, due to their software/hardware rapid development, as well as the increased portability they offer. Nevertheless, up to now, only few Apps have been developed in the field of bioinformatics, capable to perform fast and robust access t...

Gene expression analysis, using high throughput genomic technologies,has become an indispensable step for the meaningful interpretation of the underlying molecular complexity, which shapes the phenotypic manifestation of the investigated biological mechanism. The modularity of the cellular response to different experimental conditions can be compre...

Results of KEGG pathway enrichment analysis of the Type I Diabetes Mellitus gene list, using KENeV, DAVID, Webgestalt and GeneTrail.

We updated a field synopsis of cutaneous melanoma (CM) genetics by systematically retrieving and combining data from genetic association studies published as of August 31, 2013. Data were available from 197 studies, which included 83,343 CM cases and 187,809 controls and reported on 1,126 polymorphisms in 289 different genes. Random-effects meta-an...

The publicly available online database MelGene provides a comprehensive, regularly updated, collection of data from genetic association studies in cutaneous melanoma (CM), including random-effects meta-analysis results of all eligible polymorphisms. The updated database version includes data from 192 publications with information on 1114 significan...

Antimicrobial peptides are a promising alternative to conventional antibiotics. Plants are an important source of such peptides; their pharmacological properties are known since antiquity. Access to relevant information, however, is not straightforward, as there are practically no major repositories of experimentally validated and/or predicted plan...

To design a pattern recognition (PR) system for discriminating between low- and high-grade laryngeal cancer cases, employing immunohistochemically stained, for p63 expression, histopathology images. The PR system was designed to assist in the physician's diagnosis for improving patient survival. The material comprised 55 verified cases of laryngeal...

The aim of this study was to employ state-of-art graphics processing unit (GPU) technology and CUDA parallel programming to design and implement a stand-alone pattern recognition (PR) system to discriminate between patients with micro-ischaemic (mIS) and multiple sclerosis (MS) lesions. The dataset comprised MRI image series of 32 patients with mIS...

BiDaS is a web-application that can generate massive Monte Carlo simulated sequence or numerical feature data sets (e.g. dinucleotide content, composition, transition, distribution properties) based on small user-provided data sets. BiDaS server enables users to analyze their data and generate large amounts of: (i) Simulated DNA/RNA and aminoacid (...

Purpose: To improve the computer-aided diagnosis of breast lesions, by designing a pattern recognition system (PR-system) on commercial graphics processing unit (GPU) cards using parallel programming and textural information from multimodality imaging. Material and methods: Patients with histologically verified breast lesions underwent both ultr...

The aim was to design a pattern-recognition (PR) system for discriminating between normal and pathological knee articular cartilage of the medial femoral (MFC) and tibial condyles (MTC). The data set comprised segmented regions of interest (ROIs) from coronal and sagittal 3-T magnetic resonance images of the MFC and MTC cartilage of young patients,...

The application of an in-house developed web server called ChemBioServer to the filtering and selection of drug candidates for the inhibition of the PI3Kα protein is presented. 1000 candidate molecules were initially selected from a virtual screening experiment. Those molecules were then filtered for steric clashes, physicochemical and toxicity pro...

Breast cancer diagnosis requires specific expertise from the Medical Doctors. Furthermore, prognosis, monitoring and early detection of malignant findings can be successfully realized through synergies between physicians, researchers and general population in concert with the health policy program of each country. Information technology and computa...

ChemBioServer is a publicly available web application for effectively mining and filtering chemical compounds used in drug discovery. It provides researchers with the ability to (i) browse and visualize compounds along with their properties, (ii) filter chemical compounds for a variety of properties such as steric clashes and toxicity, (iii) apply...

In the present study, an adaptation of the Markov Random Field (MRF) segmentation model, by means of the stationary wavelet transform (SWT), applied to complementary DNA (cDNA) microarray images is proposed (WMRF). A 3-level decomposition scheme of the initial microarray image was performed, followed by a soft thresholding filtering technique. With...

A wavelet-based modification of the Markov random field (WMRF) model is proposed for segmenting complementary DNA (cDNA) microarray images. For evaluation purposes, five simulated and a set of five real microarray images were used. The one-level stationary wavelet transform (SWT) of each microarray image was used to form two images, a denoised imag...

The objective of this paper was to investigate the segmentation ability of the fuzzy Gaussian mixture model (FGMM) clustering algorithm, applied on complementary DNA (cDNA) images. Following a standard established procedure, a simulated microarray image of 1600 cells, each containing one spot, was produced. For further evaluation of the algorithm,...

Three-dimensional (3D) texture analysis of volumetric brain magnetic resonance (MR) images has been identified as an important indicator for discriminating among different brain pathologies. The purpose of this study was to evaluate the efficiency of 3D textural features using a pattern recognition system in the task of discriminating benign, malig...

The objective of this work was to investigate the segmentation ability of the Fuzzy Gaussian Mixture Model (FGMM) clustering algorithm, applied on complementary DNA (cDNA) images. Following a standard established procedure, a simulated microarray image of 1600 cells, each containing one spot, was produced. For further evaluation of the algorithm, t...

Grading of astrocytomas is an important task for treatment planning; however, it suffers from significantly great inter-observer variability. Computer-assisted diagnosis systems have been propose to assist towards minimizing subjectivity, however, these systems present either moderate accuracy or utilize specialized staining protocols and grading s...