Browsing by Subject "bioinformatics"

3D protein-protein docking using shape complementarity and fast alignment

Axenopoulos, A.; Daras, P.; Papadopoulos, G.; Houstis, E. (2011)

In this paper, a novel approach for fast protein-protein docking based on geometric complementarity is introduced. Complementarity matching is achieved using a rotation-invariant 3D shape descriptor, the Shape Impact ...

Acinetobacter baumannii antibiotic resistance mechanisms

Kyriakidis I., Vasileiou E., Pana Z.D., Tragiannidis A. (2021)

Acinetobacter baumannii is a Gram-negative ESKAPE microorganism that poses a threat to public health by causing severe and invasive (mostly nosocomial) infections linked with high mortality rates. During the last years, ...

Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN

Beam J.P., Becraft E.D., Brown J.M., Schulz F., Jarett J.K., Bezuidt O., Poulton N.J., Clark K., Dunfield P.F., Ravin N.V., Spear J.R., Hedlund B.P., Kormas K.A., Sievert S.M., Elshahed M.S., Barton H.A., Stott M.B., Eisen J.A., Moser D.P., Onstott T.C., Woyke T., Stepanauskas R. (2020)

Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have ...

Are computational applications the “crystal ball” in the IVF laboratory? The evolution from mathematics to artificial intelligence

Simopoulou M., Sfakianoudis K., Maziotis E., Antoniou N., Rapani A., Anifandis G., Bakas P., Bolaris S., Pantou A., Pantos K., Koutsilieris M. (2018)

Mathematics rules the world of science. Innovative technologies based on mathematics have paved the way for implementation of novel strategies in assisted reproduction. Ascertaining efficient embryo selection in order to ...

An automated blastomere identification method for the evaluation of day 2 embryos during IVF/ICSI treatments

Strouthopoulos C., Anifandis G. (2018)

Purpose Evaluation of human embryos is one of the most important challenges in vitro fertilization (IVF) programs. The morphology and the morphokinetic parameters of the early cleaving embryo are of critical clinical ...

A bioinformatics analysis reveals novel pathogens as molecular mimicry triggers of systemic sclerosis

Gkoutzourelas A., Barmakoudi M., Bogdanos D.P. (2020)

A recent bioinformatic analysis revealing dominant B cell epitopes of systemic sclerosis-specific autoantibodies, including anti-centromere B, anti-topoisomerase I and anti-fibrillarin, has demonstrated the existence of ...

Bridging plant and human radiation response and DNA repair through an in silico approach

Nikitaki Z., Pavlopoulou A., Holá M., Donà M., Michalopoulos I., Balestrazzi A., Angelis K.J., Georgakilas A.G. (2017)

The mechanisms of response to radiation exposure are conserved in plants and animals. The DNA damage response (DDR) pathways are the predominant molecular pathways activated upon exposure to radiation, both in plants and ...

Cadherin and Wnt signaling pathways as key regulators in diabetic nephropathy

Tziastoudi M., Tsezou A., Stefanidis I. (2021)

Aim A recent meta-analysis of genome-wide linkage studies (GWLS) has identified multiple genetic regions suggestive of linkage with DN harboring hundreds of genes. Moving this number of genetic loci forward into biological ...

Characterization and Quantitative Determination of a Diverse Group of Bacillus subtilis subsp. subtilis NCIB 3610 Antibacterial Peptides

Karagiota A., Tsitsopoulou H., Tasakis R.N., Zoumpourtikoudi V., Touraki M. (2021)

Five antibacterial peptides produced by Bacillus subtilis NCIB 3610 were purified, quantified, characterized, and identified in the present study. Cell-free extracts were subjected to three purification protocols employing ...

Comparative Analysis of SARS-CoV-2 Variants of Concern, Including Omicron, Highlights Their Common and Distinctive Amino Acid Substitution Patterns, Especially at the Spike ORF

Nikolaidis M., Papakyriakou A., Chlichlia K., Markoulatos P., Oliver S.G., Amoutzias G.D. (2022)

In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant of concern (VoC), a study of amino acid substitution (AAS) patterns was performed and compared with those of the other ...

Diana-map: Analyzing mirna from raw ngs data to quantification

Alexiou A., Zisis D., Kavakiotis I., Miliotis M., Koussounadis A., Karagkouni D., Hatzigeorgiou A.G. (2021)

microRNAs (miRNAs) are small non-coding RNAs (~22 nts) that are considered central post-transcriptional regulators of gene expression and key components in many pathological conditions. Next-Generation Sequencing (NGS) ...

DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data

Vlachos I.S., Vergoulis T., Paraskevopoulou M.D., Lykokanellos F., Georgakilas G., Georgiou P., Chatzopoulos S., Karagkouni D., Christodoulou F., Dalamagas T., Hatzigeorgiou A.G. (2016)

Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 (http://www.microrna. gr/mirextrav2) ...

DIANA-miTED: A microRNA tissue expression database

Kavakiotis I., Alexiou A., Tastsoglou S., Vlachos I.S., Hatzigeorgiou A.G. (2022)

microRNAs (miRNAs) are short (∼23nt) single-stranded non-coding RNAs that act as potent post-transcriptional gene expression regulators. Information about miRNA expression and distribution across cell types and tissues is ...

Discovery Strategies of bioactive compounds synthesized by nonribosomal peptide synthetases and type-I polyketide synthases derived from marine microbiomes

Amoutzias G.D., Chaliotis A., Mossialos D. (2016)

Considering that 70% of our planet's surface is covered by oceans, it is likely that undiscovered biodiversity is still enormous. A large portion of marine biodiversity consists of microbiomes. They are very attractive ...

Evolution and taxonomic distribution of nonribosomal peptide and polyketide synthases

Amoutzias, G. D.; Van De Peer, Y.; Mossialos, D. (2008)

The majority of nonribosomal peptide synthases and type I polyketide synthases are multimodular megasynthases of oligopeptide and polyketide secondary metabolites, respectively. Owing to their multimodular architecture, ...

Fasting-mediated metabolic and toxicity reprogramming impacts circulating microRNA levels in humans

Ravanidis S., Grundler F., de Toledo F.W., Dimitriou E., Tekos F., Skaperda Z., Kouretas D., Doxakis E. (2021)

It is well-established that long-term fasting improves metabolic health, enhances the total antioxidant capacity and increases well-being. MicroRNAs oversee energy homeostasis and metabolic processes and are widely used ...

Functional analysis of miRNAs using the DIANA tools online suite

Vlachos I.S., Hatzigeorgiou A.G. (2017)

microRNAs (miRNAs) are central regulators of gene expression. They are actively studied for their involvement in numerous physiological and pathological conditions but also as diagnostic biomarkers or promising therapeutic ...

Genome-wide association study identifies candidate markers related to lincRNAs associated with male infertility in the Greek population

Kyrgiafini M.-A., Markantoni M., Sarafidou T., Chatziparasidou A., Christoforidis N., Mamuris Z. (2020)

Background: Male infertility is currently one of the most common problems faced by couples worldwide. We performed a GWAS on Greek population and gathered statistically significant SNPs in order to investigate whether they ...

Guidelines on the use of external ventricular drain and its associated complications: do we “AGREE II”?

Brotis A.G., Karvouniaris M., Tzerefos C., Gatos C., Fountas K.N. (2021)

Insertion of an external ventricular drain is a common procedure used in everyday practice by neurosurgeons all around the world. It consists of the placement of an external ventricular drain (EVD) into the ventricular ...

HDAC7 is a major contributor in the pathogenesis of infant t(4;11) proB acute lymphoblastic leukemia

de Barrios O., Galaras A., Trincado J.L., Azagra A., Collazo O., Meler A., Agraz-Doblas A., Bueno C., Ballerini P., Cazzaniga G., Stam R.W., Varela I., De Lorenzo P., Valsecchi M.G., Hatzis P., Menéndez P., Parra M. (2021)

[No abstract available]