Please use this identifier to cite or link to this item: doi:10.22028/D291-28723
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Title: Computational pan-genomics: status, promises and challenges
Author(s): Marschall, Tobias
Marz, M.
Abeel, T.
Dijkstra, L.
Dutilh, B. E.
Ghaffaari, P.
Kersey, P.
Kloosterman, W. P.
Mäkinen, V.
Novak, A. M.
Paten, B.
Porubsky, D.
Rivals, E.
Alkan, C.
Baaijens, J.
de Bakker, P. I. W.
Boeva, V.
Bonnal, R. J. P.
Chiaromonte, F.
Chikhi, R.
Ciccarelli, F. D.
Cijvat, R.
Datema, E.
Duijn, C. M. V.
Eichler, E. E.
Ernst, C.
Eskin, E.
Garrison, E.
El-Kebir, M.
Klau, G. W.
Korbel, J. O.
Lameijer, E.
Langmead, B.
Martin, M.
Medvedev, P.
Mu, J. C.
Neerincx, P.
Ouwens, K.
Peterlongo, P.
Pisanti, N.
Rahmann, S.
Raphael, B.
Reinert, K.
de Ridder, D.
de Ridder, J.
Schlesner, M.
Schulz-Trieglaff, O.
Sanders, A.
Sheikhizadeh, S.
Shneider, C.
Smit, S.
Valenzuela, V.
Wang, J.
Wessels, L.
Zhang, Y.
Guryev, V.
Vandin, F.
Ye, K.
Schönhuth, A.
Language: English
Title: Briefings in bioinformatics
Volume: 19
Issue: 1
Startpage: 118
Endpage: 135
Publisher/Platform: Oxford University Press
Year of Publication: 2018
Publikation type: Journal Article
Abstract: Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.
DOI of the first publication: 10.1093/bib/bbw089
Link to this record: hdl:20.500.11880/27716
ISSN: 1467-5463
Date of registration: 7-Sep-2019
Faculty: MI - Fakultät für Mathematik und Informatik
Department: MI - Informatik
Professorship: MI - Prof. Dr. Tobias Marschall
Collections:SciDok - Der Wissenschaftsserver der Universität des Saarlandes

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