C-BIG - Bioinformatics Tools

About CING-CYI Collaboration

The Bioinformatics Department (C-BIG) at the Cyprus Institute of Neurology & Genetics (CING) and the High Performance Computing Facility (HPCF) of the Cyprus Institute (CyI) are collaborating to develop this web-based HPC-powered Bioinformatics Suite of Tools and Resources, available to the Public.

The Department of Bioinformatics

The Department of Bioinformatics at CING has been established on 2016 as a Group under the support of the EU H2020 ERA Chair grant, BIORISE (Grant Number 669026) with an EU contribution of EUR 2 273 546 for the period 2015-2020 and then was upgraded to a permanent new Department within CING. The mission of the Department is to function as a hub of excellence in the areas of applied bioinformatics to early diagnosis, effective prognosis and drug discovery contributing to the concepts of Preventive, Personalized and Precise Medicine. This is accomplished through state-of-the-art bioinformatics research, advanced education in postgraduate level and a bundle of bioinformatics pipelines that are offered either as services or as resources for collaboration.

The High Performance Computing Facility (HPCF)

The mission of the CyI High Performance Computing Facility (HPCF) is to provide Advanced computing ICT services and support the activities of CyI and its Research Centres. The HPCF is the national supercomputing facility for Cyprus and provides compute and data resources to the research community of Cyprus and the Eastern Mediterranean region. It is also the mission of the HPCF to assist CyI in collaborating and providing ICT services to the national and regional/international academic research communities, as well as the public and private sectors. The ICT Services provided by the facility include access to HPC resources with multi-level user support, Cloud and Data Storage. The Facility also provides services related to software and systems integration.

The two partners have already a good collaboration history that includes participation in collaboration proposals, some of them successful, and many synergies in the development of bioinformatics pipelines set up by C-BIG within the HPCF. The current synergy includes optimization and hosting of bioinformatics web-based tools (designed and developed by CING Bioinformatics and optimized and powered/hosted by CyI HPCF).

complex dynamics is the key for perfection

we use Systems Bioinformatics approaches to develop next generation tools

Bioinformatics Services

We provide a diverse set of computational pipelines in the context of Systems Bioinformatics approach: a relatively new approach, which lies in the intersection of systems biology and classical Bioinformatics.

Drug Repurposing Tools

We develop drug repurposing tools against known or unknown pathogens, especially in periods where the emergence for repurposed drugs plays significant role in handling viral outbreaks, until reaching a vaccine.

We also provide pipelines that involve: the selection of proper gene expression datasets, data preprocessing and statistical analysis, selection of the most important genes related to the disease, analysis of biological pathways, investigation of related molecular mechanisms, identification of fibrosis-related microRNAs, drug repurposing, structural and literature-based analysis of the repurposed drugs.

Pathway Network Analysis

We develop tools that facilitate the construction of complementary pathway-to-pathway networks and subnetworks of them, based on the rich information available in KEGG or Reactome and Wiki Pathways repositories. We further extend the results of differential expression analysis of proteins and genes, to the construction of protein-to-protein and gene-to-gene co-expression networks and to identification of significant pathways related to a specific experiment under study.

These tools are simple yet informative tools towards identifying connected groups of pathways that are significantly related to specific diseases.

Protein-Gene Expression Statistics

We develop post-processing workflows for the analysis of protein and gene expression datasets, using network-based bioinformatics approaches, that facilitate differential expression analysis and co-expression network analysis as well as pathway and post-pathway analysis.

These tools are useful towards the understanding and exploitation of protein and gene expression datasets, especially for those that do not have the expertise and local resources to replicate specific analyses in the context of collaborative and scientific data exchanging.

Next Generation Sequencing (NGS)

We perform state of the art Next Generation Sequencing (NGS) analysis using cutting edge tools and methods, even at a single-cell level and cell–cell interactions.Our NGS pipelines support: read quality assessment, mapping reads, preprocessing duplicate reads, variant calling for SNP and indel variants using the GATK Haplotype Caller. Annotation is performed by: (1) Variant Effect Predictor (VEP) from the Ensemble tools and (2) GEMINI (GEnome MINIng).

We further develop tools for selecting variants of unknown significance through network-based gene-association significantly, improving risk prediction for disease-control cohorts.

Multilevel Omics Networks

The advancement of scientific and medical research over the past years has generated a wealth of experimental data from multiple technologies, including genomics, transcriptomics, proteomics, and other forms of -omics data, which are available for a number of diseases.

In the CING Bioinformatics Department we have developed methodologies for the integration of such multisource data. The capability to integrate multisource molecular data, concluding to something more than the sum of the existing information, empowers precision and personalized medicine approaches.

Bioinformatics Tools

we use state of the art approaches for developing