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Genedata Phylosopher selected for ERA-NET sncRNA Project
BASEL, Switzerland—Genedata has been selected to participate in an ERA-NET-funded applied pathogenomics project using systems biology to identify the role of small non-coding RNA (sncRNA) in infectious diseases.
Genedata is a provider of advanced software solutions for drug discovery and life science research. The sncRNAomics European Research Consortium—which is a project formed in part under the grant framework of the second multinational ERA-NET PathoGenoMics call—is identifying novel targets for diagnostics and therapy of five major high-risk gram-positive human microbial pathogens.
The Genedata Phylosopher biological data management solution was chosen as the central management and infrastructure platform for sharing and interpreting the experimental data, in particular the next- generation sequencing and tiling array data generated within the consortium.
According to Dr. Hans Peter Fischer, head of the Genedata Phylosopher business unit, Genedata contributes two major components to the ERA-NET sncRNA Project: First, Genedata technology—the Genedata Phylosopher system will be used as a technology platform by all project partners to support concrete, day-to-day research activities. Second, research and development activities—including both data analysis activities to analyze and interpret experimental data that is produced by the working groups of the consortium (e.g. next-generation sequencing data), and software development to extend Genedata's software to support new experimental technologies and to accommodate new data formats and novel research processes.
"The Genedata Phylosopher biological data management solution is key for the project since it integrates data and research results from pathogens and host organisms and is the central management and infrastructure platform for sharing and interpreting all data, in particular the next-generation sequencing and tiling array data generated within the consortium," Fischer says. "Phylosopher also bridges the gap between experimental evidence and computer models by supporting the reconstruction of disease pathways, in particular the refinement of functional assignment of genes, transcripts, proteins, regulatory motifs, RNAs and their molecular interactions, to regulatory networks during host-pathogen interactions."
Dr. Torsten Hain of the University of Giessen (Germany) and sncRNAomics project coordinator, says Genedata was selected because it has a successful track record in transcriptome-based biomarker identification and also because it has the strongest product portfolio for centralized data management for target validation.
"In healthcare, and especially in a clinical environment, microbial resistance increases exponentially," he says. "Antibiotics have become a blunt sword and we need new approaches in diagnostics and therapy,"
Hain continues by noting that "small non-coding RNAs in bacteria are an emerging class of new gene expression regulators, but their role in colonization and pathogenicity is largely unknown. Within this interdisciplinary project we are applying for the first time a systems biology approach on major human pathogens to elucidate the role of sncRNAs, and to identify and validate new sncRNA-based diagnostic biomarkers and drug targets."
Moreover, Genedata Phylosopher supports the reconstruction of disease pathways, in particular the refinement of functional assignment of genes, transcripts, proteins, regulatory motifs, RNAs and their molecular interactions, to regulatory networks during host-pathogen interactions.
Fischer points out that Phylosopher is a biological data management and analysis solution established in pharmaceutical and biotechnology organizations across the globe.
"Phylosopher is enterprise software that has been developed in close collaboration with major commercial research and development organizations (mostly big pharma and biotech) and renowned public research institutions," he says. "So far, Genedata has invested more than 160 person-years of development into the Phylosopher technology."
From a technical perspective, Phylosopher consists of four different layers:
This includes, for example, the database for storing and integrating all experimental data (e.g. genomes, pathways, sequences, annotations, etc) and the tools and visualizers for analyzing the experimental data and for drawing conclusions (e.g. biological mechanisms regarding host- pathogen interactions).
"Generally speaking, the Phylosopher system employs a systems biology approach to provide a holistic view of the processes under study in order to create new insights from data and iteratively generate the next series of testable hypotheses," he notes.
Dr. Othmar Pfannes, CEO of Genedata, says his company is pleased to have the international and interdisciplinary consortium choose Genedata as their central data management and analysis infrastructure.
"This partnership further demonstrates Genedata's leadership in delivering scalable and flexible research IT infrastructure solutions for target validation, drug development, and biomarker discovery, even for novel target classes such as sncRNAs," he says.
Novel anti-infectives are of high priority for global healthcare and sncRNAs in bacteria are an emerging class of new gene expression regulators, but their role in colonization and pathogenicity in largely unknown. The sncRNAomics European Research Consortium brings together seven research groups from three countries to combine novel high-throughput sncRNA screening methods, whole-genome transcriptomics and proteomics and bioinformatics.
According to Fischer, the success of the project will be quantified on two levels.
"First is biological research results," he says. "The direct biological and scientific results of the project. For instance, the discovery of specific sncRNAs as a basis for novel diagnostic tools or as targets for novel therapeutics will represent a major success."
The second gauge for success will be technology development results.
"Genedata will use knowledge gained from this collaboration to extend our technology platform," Fischer says, "specifically the Genedata Phylosopher platform, by adding new functionalities to handle data coming from new technologies and to support new processes." Among those new functionalities, he notes, would be systematic, fully automated next-generation sequencing-based biomarker discovery and validation.