{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T13:14:47Z","timestamp":1770815687894,"version":"3.50.1"},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Computer-assisted studies of structure, function and evolution of viruses remains a neglected area of research. The attention of bioinformaticians to this interesting and challenging field is far from commensurate with its medical and biotechnological importance. It is telling that out of &amp;gt;200 talks held at ISMB 2013, the largest international bioinformatics conference, only one presentation explicitly dealt with viruses. In contrast to many broad, established and well-organized bioinformatics communities (e.g. structural genomics, ontologies, next-generation sequencing, expression analysis), research groups focusing on viruses can probably be counted on the fingers of two hands.<\/jats:p>\n               <jats:p>Results: The purpose of this review is to increase awareness among bioinformatics researchers about the pressing needs and unsolved problems of computational virology. We focus primarily on RNA viruses that pose problems to many standard bioinformatics analyses owing to their compact genome organization, fast mutation rate and low evolutionary conservation. We provide an overview of tools and algorithms for handling viral sequencing data, detecting functionally important RNA structures, classifying viral proteins into families and investigating the origin and evolution of viruses.<\/jats:p>\n               <jats:p>Contact: \u00a0manja@uni-jena.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online. The references for this article can be found in the Supplementary Material.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu105","type":"journal-article","created":{"date-parts":[[2014,3,4]],"date-time":"2014-03-04T05:09:20Z","timestamp":1393909760000},"page":"1793-1799","source":"Crossref","is-referenced-by-count":51,"title":["Challenges in RNA virus bioinformatics"],"prefix":"10.1093","volume":"30","author":[{"given":"Manja","family":"Marz","sequence":"first","affiliation":[{"name":"1 Friedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, 2 Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 3 SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, 4 Universit\u00e4tsklinikum Bonn, Institut f\u00fcr Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, 5 Technische Universit\u00e4t Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, 6 Helmholtz Center Munich\u2013German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolst\u00e4dter Landstra\u00dfe 1, D-85764 Neuherberg, Germany, 7 Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny 141700, Russia, 8 Institut f\u00fcr theoretische Chemie, Universit\u00e4t Wien, W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria, 9 Institute of Virology, Technical University of Munich, Trogerstr. 30, 81675 M\u00fcnchen, Germany, 10 University of Leipzig, Faculty of Mathematics and Computer Science, Insti"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niko","family":"Beerenwinkel","sequence":"additional","affiliation":[{"name":"1 Friedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, 2 Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 3 SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, 4 Universit\u00e4tsklinikum Bonn, Institut f\u00fcr Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, 5 Technische Universit\u00e4t Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, 6 Helmholtz Center Munich\u2013German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolst\u00e4dter Landstra\u00dfe 1, D-85764 Neuherberg, Germany, 7 Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny 141700, Russia, 8 Institut f\u00fcr theoretische Chemie, Universit\u00e4t Wien, W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria, 9 Institute of Virology, Technical University of Munich, Trogerstr. 30, 81675 M\u00fcnchen, Germany, 10 University of Leipzig, Faculty of Mathematics and Computer Science, Insti"},{"name":"1 Friedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, 2 Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 3 SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, 4 Universit\u00e4tsklinikum Bonn, Institut f\u00fcr Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, 5 Technische Universit\u00e4t Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, 6 Helmholtz Center Munich\u2013German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolst\u00e4dter Landstra\u00dfe 1, D-85764 Neuherberg, Germany, 7 Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny 141700, Russia, 8 Institut f\u00fcr theoretische Chemie, Universit\u00e4t Wien, W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria, 9 Institute of Virology, Technical University of Munich, Trogerstr. 30, 81675 M\u00fcnchen, Germany, 10 University of Leipzig, Faculty of Mathematics and Computer Science, Insti"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Drosten","sequence":"additional","affiliation":[{"name":"1 Friedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, 2 Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 3 SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, 4 Universit\u00e4tsklinikum Bonn, Institut f\u00fcr Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, 5 Technische Universit\u00e4t Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, 6 Helmholtz Center Munich\u2013German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolst\u00e4dter Landstra\u00dfe 1, D-85764 Neuherberg, Germany, 7 Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny 141700, Russia, 8 Institut f\u00fcr theoretische Chemie, Universit\u00e4t Wien, W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria, 9 Institute of Virology, Technical University of Munich, Trogerstr. 30, 81675 M\u00fcnchen, Germany, 10 University of Leipzig, Faculty of Mathematics and Computer Science, Insti"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Markus","family":"Fricke","sequence":"additional","affiliation":[{"name":"1 Friedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, 2 Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 3 SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, 4 Universit\u00e4tsklinikum Bonn, Institut f\u00fcr Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, 5 Technische Universit\u00e4t Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, 6 Helmholtz Center Munich\u2013German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolst\u00e4dter Landstra\u00dfe 1, D-85764 Neuherberg, Germany, 7 Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny 141700, Russia, 8 Institut f\u00fcr theoretische Chemie, Universit\u00e4t Wien, W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria, 9 Institute of Virology, Technical University of Munich, Trogerstr. 30, 81675 M\u00fcnchen, Germany, 10 University of Leipzig, Faculty of Mathematics and Computer Science, Insti"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dmitrij","family":"Frishman","sequence":"additional","affiliation":[{"name":"1 Friedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, 2 Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 3 SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, 4 Universit\u00e4tsklinikum Bonn, Institut f\u00fcr Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, 5 Technische Universit\u00e4t 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L.","family":"Hofacker","sequence":"additional","affiliation":[{"name":"1 Friedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, 2 Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 3 SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, 4 Universit\u00e4tsklinikum Bonn, Institut f\u00fcr Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, 5 Technische Universit\u00e4t Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, 6 Helmholtz Center Munich\u2013German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolst\u00e4dter Landstra\u00dfe 1, D-85764 Neuherberg, Germany, 7 Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny 141700, Russia, 8 Institut f\u00fcr theoretische Chemie, Universit\u00e4t Wien, W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria, 9 Institute of Virology, 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