Alexandros Kanterakis
A5014724586- Scientific Computing and Data Management
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
- Distributed and Parallel Computing Systems
- Genomics and Rare Diseases
- Genetics, Bioinformatics, and Biomedical Research
- Pharmacogenetics and Drug Metabolism
- Spam and Phishing Detection
- Computational Drug Discovery Methods
- Research Data Management Practices
- Semantic Web and Ontologies
- Genetic Mapping and Diversity in Plants and Animals
- T-cell and B-cell Immunology
- Genomic variations and chromosomal abnormalities
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Cholesterol and Lipid Metabolism
- Misinformation and Its Impacts
- Celiac Disease Research and Management
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
Foundation for Research and Technology Hellas
2010-2023
FORTH Institute of Computer Science
2007-2023
FORTH Institute of Electronic Structure and Laser
2022
University of Patras
2018-2020
Hella (Germany)
2020
University Medical Center Groningen
2010-2019
University of Groningen
2010-2019
Czech Academy of Sciences, Institute of Computer Science
2018
University of Crete
2008
FORTH Institute of Molecular Biology and Biotechnology
2008
Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as node European BBMRI. One aims BBMRI-NL is to enrich with different types molecular phenotype data. Here, we describe Genome (GoNL), one projects within BBMRI-NL. GoNL whole-genome-sequencing project in representative sample consisting 250 trio-families from all provinces Netherlands, which characterize DNA sequence variation Dutch...
There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures capture, exchange, exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, generic, open source, toolkit quickly produce bespoke MOLecular GENetics Information Systems needed. The MOLGENIS provides simple language model biological data structures interfaces. At push button, MOLGENIS' generator suite automatically translates these models into...
Negative selection against deleterious alleles produced by mutation influences within-population variation as the most pervasive form of natural selection. However, it is not known whether affect fitness independently, so that cumulative loss depends exponentially on number alleles, or synergistically, each additional allele results in a larger decrease relative fitness. with synergistic epistasis should produce negative linkage disequilibrium between and, therefore, an underdispersed...
Abstract Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority studies provide neither global view full spectrum these variants nor integrate them into reference panels genetic variation. Here, we analyse whole genome sequencing data 769 individuals from 250 Dutch families, haplotype-resolved map 1.9 million across 9 different variant classes, including novel forms complex indels,...
Although genome-wide association studies (GWAS) have identified many common variants associated with complex traits, low-frequency and rare not been interrogated in a comprehensive manner. Imputation from dense reference panels, such as the 1000 Genomes Project (1000G), enables testing of ungenotyped for association. Here we present results imputation using large, new population-specific panel: Genome The Netherlands (GoNL). We benchmarked performance 1000G GoNL sets by comparing genotypes...
Holoprosencephaly is a pathology of forebrain development characterized by high phenotypic heterogeneity. The disease presents with various clinical manifestations at the cerebral or facial levels. Several genes have been implicated in holoprosencephaly but its genetic basis remains unclear: different transmission patterns described including autosomal dominant, recessive and digenic inheritance. Conventional molecular testing approaches result very low diagnostic yield most cases remain...
With the completion of human genome and entrance into post-genomic era, translational research rises as a major need. In this paper, we present knowledge discovery workflow (KDw) its utilization in context clinico-genomic trials. KDw aims towards 'evidential' correlations between patients' genomic clinical profiles. Application on real-world (breast cancer) study demonstrates reliability, efficacy, efficiency approach.
Racial and ethnic differences in drug responses are now well studied documented. Pharmacogenomics research seeks to unravel the genetic underpinnings of inter-individual variability with aim tailored-made theranostics therapeutics. Taking into account differential expression pharmacogenes coding for key metabolic enzymes transporters that affect pharmacokinetics pharmacodynamics, we advise data interpretation analysis need occur light geographical ancestry, if implications development global...
Pathway analysis methodologies couple traditional gene expression with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early methodologies, named as set (GSA), view pathways just plain lists genes without taking into account either underlying network topology or involved regulatory relations. These approaches, even if they achieve computational efficiency and simplicity,...
Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe proximity-biotinylation approach for capturing the RNAs of known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this RNA detection, silico, and high-resolution imaging approaches, studied PBs under normal conditions heat stress. showed...
One of the challenges that arise from advent personal genomics services is to efficiently couple individual data with state art Pharmacogenomics (PGx) knowledge. Existing are limited either providing static views PGx variants or applying a simplistic match between genotypes and existing variants. Moreover, there considerable amount haplotype variation associated drug metabolism currently insufficiently addressed. Here, we present web-based electronic Assistant (ePGA; http://www.epga.gr/)...
Gilthead seabream (\textit{Sparus aurata}) is a teleost of considerable economic importance in Southern European aquaculture. The aquaculture industry shows growing interest the application genetic methods that can locate phenotype-genotype associations with high impact. Through selective breeding, exploit this information to maximize financial yield. Here, we present Genome Wide Association Study (GWAS) 112 samples belonging seven different families collected from Greek commercial company....
Celiac disease is a multifactorial disorder caused by an unknown number of genetic factors interacting with environmental factor. Hence, most patients are singletons and large families segregating celiac rare. We report on three-generation family six in which the inheritance pattern consistent autosomal dominant model. To date, 27 loci explain up to 40% heritable risk. hypothesized that part missing heritability because low frequency or rare variants. Such causal variants could be more...
Abstract Telomere length (TL) regulation is an important factor in ageing, reproduction and cancer development. Genetic, hereditary environmental factors regulating TL are currently widely investigated, however, their relative contribution to variability still understudied. We have used whole genome sequencing data of 250 family trios from the Genome Netherlands project perform computational measurement a series regression genome-wide association analyses reveal inheritance patterns...
Introduction The two-stage molecular profile of the progression SARS-CoV-2 (SCOV2) infection is explored in terms five key biological/clinical questions: (a) does SCOV2 exhibits a profile? (b) SARS-CoV-1 (SCOV1) vs. SCOV2: do they differ? (c) and how differs from Influenza/INFL infection? (d) low viral-load (e) COVID-19 early host response relate to We provide positive answers above questions by analyzing time-series gene-expression profiles preserved cell-lines infected with SCOV1/2 or,...
The highly competitive environment of post-genomics biomedical research is pushing towards the production qualified results and their utilization in clinical practice. Due to this pressure, an important factor scientific progress has been underestimated namely, reproducibility results. To end, it critical design implement computational platforms that enable seamless unhindered access distributed bio-data, software infrastructures. Furthermore, need support collaboration form synergistic...
Genotype imputation is an important procedure in current genomic analysis such as genome-wide association studies, meta-analyses and fine mapping. Although high quality tools are available that perform the steps of this process, considerable effort expertise required to set up run a best practice pipeline, particularly for larger genotype datasets, where has scale out parallel on computer clusters. Here we present MOLGENIS-impute, 'imputation box' solution seamlessly transparently automates...