Εξειδίκευση τύπου :	Άρθρο σε επιστημονικό περιοδικό
Τίτλος:	A computational pipeline for the extraction of actionable biological information from NGS-phage display experiments
Δημιουργός/Συγγραφέας:	Vekris A. Pilalis E. [EL] Χατζηιωάννου, Αριστοτέλης[EN] Chatziioannou, Aristotelis Petry K.G.
Εκδότης:	Frontiers Media S.A.
Ημερομηνία:	2019
Γλώσσα:	Αγγλικά
ISSN:	1664-042X
DOI:	10.3389/fphys.2019.01160
Περίληψη:	Phage Display is a powerful method for the identification of peptide binding to targets of variable complexities and tissues, from unique molecules to the internal surfaces of vessels of living organisms. Particularly for in vivo screenings, the resulting repertoires can be very complex and difficult to study with traditional approaches. Next Generation Sequencing (NGS) opened the possibility to acquire high resolution overviews of such repertoires and thus facilitates the identification of binders of interest. Additionally, the ever-increasing amount of available genome/proteome information became satisfactory regarding the identification of putative mimicked proteins, due to the large scale on which partial sequence homology is assessed. However, the subsequent production of massive data stresses the need for high-performance computational approaches in order to perform standardized and insightful molecular network analysis. Systems-level analysis is essential for efficient resolution of the underlying molecular complexity and the extraction of actionable interpretation, in terms of systemic biological processes and pathways that are systematically perturbed. In this work we introduce PepSimili, an integrated workflow tool, which performs mapping of massive peptide repertoires on whole proteomes and delivers a streamlined, systems-level biological interpretation. The tool employs modules for modeling and filtering of background noise due to random mappings and amplifies the biologically meaningful signal through coupling with BioInfoMiner, a systems interpretation tool that employs graph-theoretic methods for prioritization of systemic processes and corresponding driver genes. The current implementation exploits the Galaxy environment and is available online. A case study using public data is presented, with and without a control selection.
Τίτλος πηγής δημοσίευσης:	Frontiers in Physiology
Τόμος/Κεφάλαιο:	10
Τεύχος:	SEP
Θεματική Κατηγορία:	[EL] Βιολογία (Γενικά)[EN] Biology (General)
Λέξεις-Κλειδιά:	Biological interpretation Enrichment analysis Galaxy platform Gene Ontology Network analysis Phage display Reactome
Αξιολόγηση από ομότιμους (peer reviewed):	Ναι
Κάτοχος πνευματικών δικαιωμάτων:	© 2019 Vekris, Pilalis, Chatziioannou and Petry.
Όροι και προϋποθέσεις δικαιωμάτων:	All Open Access, Gold, Green
Σημειώσεις:	MIS-5001552; European Commission, EC; Agence Nationale de la Recherche, ANR; Institut National de la Santé et de la Recherche Médicale, Inserm; Ministry of Education, Lifelong Learning and Religious Affairs: MIS 5017608; European Regional Development Fund, FEDER. This research is co-financed by Greece and the European Union (European Social Fund-ESF) through the Operational Programme ?Human Resources Development, Education and Lifelong Learning? in the context of the project ?Reinforcement of Postdoctoral Researchers? (MIS-5001552), implemented by the State Scholarships Foundation (IKY). This work was funded by the Operational Program ?Competitiveness, Entrepreneurship and Innovation 2014?2020? (co-funded by the European Regional Development Fund) and managed by the General Secretariat of Research and Technology, Ministry of Education, Research and Religious Affairs, under the project ?Innovative Nanopharmaceuticals: Targeting Breast Cancer Stem Cells by. a Novel Combination of Epigenetic and Anticancer Drugs with Gene Therapy (INNOCENT) (MIS 5017608)? (7th Joint Translational Call ? 2016, European Innovative Research and Technological Development Projects in Nanomedicine) of the ERA-NET EuroNanoMed II. This work was also supported by INSERM and the French National Research Agency (ANR 2006?2015).
Εμφανίζεται στις συλλογές:	Ινστιτούτο Χημικής Βιολογίας - Επιστημονικό έργο