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Computational Pan-Genomics: Status, Promises and Challenges
Tobias Marschall, Manja Marz, Thomas Abeel, Louis Dijkstra, Bas E. Dutilh, Ali Ghaffaari, Paul Kersey, Wigard P. Kloosterman, Veli Mäkinen, Adam M. Novak, Benedict Paten, David Porubsky, Eric Rivals, Can Alkan, Jasmijn Baaijens, Paul I. W. De Bakker, Valentina Boeva, Francesca Chiaromonte, Rayan Chikhi, Francesca D. Ciccarelli, Robin Cijvat, Erwin Datema, Cornelia M. Van Duijn, Evan E. Eichler, Corinna Ernst, Eleazar Eskin, Erik Garrison, Mohammed El-Kebir, Gunnar W. Klau, Jan O. Korbel, Eric-Wubbo Lameijer, Benjamin Langmead, Marcel Martin, Paul Medvedev, John C. Mu, Pieter Neerincx, Klaasjan Ouwens, Pierre Peterlongo, Nadia Pisanti, Sven Rahmann, Ben Raphael, Knut Reinert, Dick de Ridder, Jeroen de Ridder, Matthias Schlesner, Ole Schulz-Trieglaff, Ashley Sanders, Siavash Sheikhizadeh, Carl Shneider, Sandra Smit, Daniel Valenzuela, Jiayin Wang, Lodewyk Wessels, Ying Zhang, Victor Guryev, Fabio Vandin, Kai Ye, Alexander Schönhuth
doi: https://doi.org/10.1101/043430
Tobias Marschall
1Center for Bioinformatics, Saarland University, Saarbrücken, Germany;
2Max Planck Institute for Informatics, Saarbrücken, Germany;
Manja Marz
3Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany;
4FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745 Jena, Germany;
5Michael Stifel Center Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany;
6German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig;
Thomas Abeel
7The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Mekelweg 4, 2628 CD, Delft, The Netherlands;
Louis Dijkstra
8Computational Science Lab, University of Amsterdam, Amsterdam, 1098XG, The Netherlands;
9Department of High Performance Computing, ITMO University, Saint Petersburg, 197101, Russia;
Bas E. Dutilh
10Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, Netherlands;
11Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands;
12Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil;
Ali Ghaffaari
1Center for Bioinformatics, Saarland University, Saarbrücken, Germany;
2Max Planck Institute for Informatics, Saarbrücken, Germany;
Paul Kersey
13EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK;
Wigard P. Kloosterman
14Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands;
Veli Mäkinen
15HIIT and Department of Computer Science, University of Helsinki, Finland;
Adam M. Novak
16Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
Benedict Paten
16Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
David Porubsky
17European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, AV Groningen 9713, The Netherlands;
Eric Rivals
18LIRMM, CNRS and Université de Montpellier, Montpellier, France;
19Institut de Biologie Computationnelle, CNRS and Université de Montpellier, Montpellier, France;
Can Alkan
20Department of Computer Engineering, Bilkent University, Bilkent, Ankara, 06800, Turkey;
Jasmijn Baaijens
21Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands;
Paul I. W. De Bakker
14Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands;
Valentina Boeva
22Institut Curie, Centre de Recherche, Inserm U900, F-75005 Paris, France;
23Mines ParisTech, F-77305 cedex Fontainebleau, France;
24PSL Research University, F-75005 Paris, France;
25Institut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, F-75014 Paris, France;
Francesca Chiaromonte
26Departments of Statistics, The Pennsylvania State University, University Park, PA, 16802;
Rayan Chikhi
27CNRS, Univ. Lille, UMR 9189 CRIStAL, F-59000 Lille, France;
Francesca D. Ciccarelli
28Division of Cancer Studies, King’s College London, London SE11UL, UK;
Robin Cijvat
29MonetDB Solutions, Amsterdam, The Netherlands;
Erwin Datema
30KeyGene N.V, Agro Business Park 90, 6708 PW Wageningen, The Netherlands;
Cornelia M. Van Duijn
31Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands;
Evan E. Eichler
32Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA;
33Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA;
Corinna Ernst
34Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany;
Eleazar Eskin
35Department of Computer Science, University of California, Los Angeles, USA;
36Department of Human Genetics, University of California, Los Angeles, USA;
Erik Garrison
37Wellcome Trust Sanger Institute, Cambridge, UK;
Mohammed El-Kebir
21Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands;
38Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands;
39Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA;
Gunnar W. Klau
21Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands;
Jan O. Korbel
13EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK;
40European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany;
Eric-Wubbo Lameijer
41Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, The Netherlands;
Benjamin Langmead
42Department of Computer Science and Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland;
Marcel Martin
43Science for Life Laboratory, Dept. of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-17121 Solna, Sweden;
Paul Medvedev
44Department of Computer Science and Engineering, The Pennsylvania State University, USA;
45Department of Biochemistry and Molecular Biology, The Pennsylvania State University, USA;
46Genomic Sciences Institute of the Huck, The Pennsylvania State University, USA;
John C. Mu
47Bina Technologies, Roche Sequencing, Redwood City, CA 94065, USA;
Pieter Neerincx
41Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, The Netherlands;
Klaasjan Ouwens
48Biological Psychology, Vrije Universiteit Amsterdam, The Netherlands;
49Genalice BV, Harderwijk, The Netherlands;
Pierre Peterlongo
50INRIA Campus de Beaulieu-Rennes, Rennes Cedex 35042, France;
Nadia Pisanti
51Dipartimento di Informatica, University degli Studi di Pisa, Pisa, Italy;
52Erable Team, INRIA;
Sven Rahmann
34Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany;
Ben Raphael
39Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA;
Knut Reinert
53Department of Mathematics and Computer Science, Freie Universitüt Berlin, Berlin, Germany;
Dick de Ridder
54Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands;
Jeroen de Ridder
7The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Mekelweg 4, 2628 CD, Delft, The Netherlands;
Matthias Schlesner
55Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;
Ole Schulz-Trieglaff
56Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK;
Ashley Sanders
57Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada;
Siavash Sheikhizadeh
54Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands;
Carl Shneider
58Leiden Observatory, Leiden University, P.O. Box 9513, 2300 RA Leiden, The Netherlands;
Sandra Smit
54Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands;
Daniel Valenzuela
15HIIT and Department of Computer Science, University of Helsinki, Finland;
Jiayin Wang
59School of Management, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, China;
60Institute of Data Science and Information Quality, Xi’an Jiaotong University;
61Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University;
Lodewyk Wessels
62Netherlands Cancer Institute (NKI), Amsterdam, the Netherlands;
Ying Zhang
29MonetDB Solutions, Amsterdam, The Netherlands;
21Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands;
Victor Guryev
17European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, AV Groningen 9713, The Netherlands;
14Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands;
Fabio Vandin
63Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark;
39Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA;
Kai Ye
64School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, China;
65Kai Ye Young Scientist Studio, Xi’an Jiaotong University
61Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University;
Alexander Schönhuth
21Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands;
Article usage
Posted March 29, 2016.
Computational Pan-Genomics: Status, Promises and Challenges
Tobias Marschall, Manja Marz, Thomas Abeel, Louis Dijkstra, Bas E. Dutilh, Ali Ghaffaari, Paul Kersey, Wigard P. Kloosterman, Veli Mäkinen, Adam M. Novak, Benedict Paten, David Porubsky, Eric Rivals, Can Alkan, Jasmijn Baaijens, Paul I. W. De Bakker, Valentina Boeva, Francesca Chiaromonte, Rayan Chikhi, Francesca D. Ciccarelli, Robin Cijvat, Erwin Datema, Cornelia M. Van Duijn, Evan E. Eichler, Corinna Ernst, Eleazar Eskin, Erik Garrison, Mohammed El-Kebir, Gunnar W. Klau, Jan O. Korbel, Eric-Wubbo Lameijer, Benjamin Langmead, Marcel Martin, Paul Medvedev, John C. Mu, Pieter Neerincx, Klaasjan Ouwens, Pierre Peterlongo, Nadia Pisanti, Sven Rahmann, Ben Raphael, Knut Reinert, Dick de Ridder, Jeroen de Ridder, Matthias Schlesner, Ole Schulz-Trieglaff, Ashley Sanders, Siavash Sheikhizadeh, Carl Shneider, Sandra Smit, Daniel Valenzuela, Jiayin Wang, Lodewyk Wessels, Ying Zhang, Victor Guryev, Fabio Vandin, Kai Ye, Alexander Schönhuth
bioRxiv 043430; doi: https://doi.org/10.1101/043430
Computational Pan-Genomics: Status, Promises and Challenges
Tobias Marschall, Manja Marz, Thomas Abeel, Louis Dijkstra, Bas E. Dutilh, Ali Ghaffaari, Paul Kersey, Wigard P. Kloosterman, Veli Mäkinen, Adam M. Novak, Benedict Paten, David Porubsky, Eric Rivals, Can Alkan, Jasmijn Baaijens, Paul I. W. De Bakker, Valentina Boeva, Francesca Chiaromonte, Rayan Chikhi, Francesca D. Ciccarelli, Robin Cijvat, Erwin Datema, Cornelia M. Van Duijn, Evan E. Eichler, Corinna Ernst, Eleazar Eskin, Erik Garrison, Mohammed El-Kebir, Gunnar W. Klau, Jan O. Korbel, Eric-Wubbo Lameijer, Benjamin Langmead, Marcel Martin, Paul Medvedev, John C. Mu, Pieter Neerincx, Klaasjan Ouwens, Pierre Peterlongo, Nadia Pisanti, Sven Rahmann, Ben Raphael, Knut Reinert, Dick de Ridder, Jeroen de Ridder, Matthias Schlesner, Ole Schulz-Trieglaff, Ashley Sanders, Siavash Sheikhizadeh, Carl Shneider, Sandra Smit, Daniel Valenzuela, Jiayin Wang, Lodewyk Wessels, Ying Zhang, Victor Guryev, Fabio Vandin, Kai Ye, Alexander Schönhuth
bioRxiv 043430; doi: https://doi.org/10.1101/043430
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