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Computational Pan-Genomics: Status, Promises and Challenges
The Computational Pan-Genomics Consortium, 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, Raoul J. P. Bonnal, 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 D. 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
1Center for Bioinformatics, Saarland University, Saarbrücken, Germany
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
9Computational Science Lab, University of Amsterdam, Amsterdam, 1098XG, The Netherlands
10Department of High Performance Computing, ITMO University, Saint Petersburg, 197101, Russia
Bas E. Dutilh
11Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, Netherlands
12Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
13Department 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
14EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
Wigard P. Kloosterman
15Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
Veli Mäkinen
16HIIT and Department of Computer Science, University of Helsinki, Finland
Adam M. Novak
17Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Benedict Paten
17Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
David Porubsky
18European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, AV Groningen 9713, The Netherlands
Eric Rivals
19LIRMM, CNRS and Université de Montpellier, Montpellier, France
20Institut de Biologie Computationnelle, CNRS and Université de Montpellier, Montpellier, France
Can Alkan
21Department of Computer Engineering, Bilkent University, Bilkent, Ankara, 06800, Turkey
Jasmijn Baaijens
22Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands
Paul I. W. De Bakker
15Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
Valentina Boeva
23Institut Curie, Centre de Recherche, Inserm U900, F-75005 Paris, France
24Mines ParisTech, F-77305 cedex Fontainebleau, France
25PSL Research University, F-75005 Paris, France
26Institut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, F-75014 Paris, France
Raoul J. P. Bonnal
8Istituto Nazionale Genetica Molecolare INGM, ‘Romeo ed Enrica Invernizzi’, Milan 20122, Italy.
Francesca Chiaromonte
27Departments of Statistics, The Pennsylvania State University, University Park, PA, 16802
Rayan Chikhi
28CNRS, Univ. Lille, UMR 9189 CRIStAL, F-59000 Lille, France
Francesca D. Ciccarelli
29Division of Cancer Studies, King’s College London, London SE11UL, UK
Robin Cijvat
30MonetDB Solutions, Amsterdam, The Netherlands
Erwin Datema
31KeyGene N.V, Agro Business Park 90, 6708 PW Wageningen, The Netherlands
Cornelia M. Van Duijn
32Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
Evan E. Eichler
33Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
34Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
Corinna Ernst
35Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Eleazar Eskin
36Department of Computer Science, University of California, Los Angeles, USA
37Department of Human Genetics, University of California, Los Angeles, USA
Erik Garrison
38Wellcome Trust Sanger Institute, Cambridge, UK
Mohammed El-Kebir
22Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands
39Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands
40Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA
Gunnar W. Klau
22Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands
Jan O. Korbel
14EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
41European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Eric-Wubbo Lameijer
42Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, The Netherlands
Benjamin Langmead
43Department of Computer Science and Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland
Marcel Martin
44Science for Life Laboratory, Dept. of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-17121 Solna, Sweden
Paul Medvedev
45Department of Computer Science and Engineering, The Pennsylvania State University, USA
46Department of Biochemistry and Molecular Biology, The Pennsylvania State University, USA
47Genomic Sciences Institute of the Huck, The Pennsylvania State University, USA
John C. Mu
48Bina Technologies, Roche Sequencing, Redwood City, CA 94065, USA
Pieter Neerincx
42Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, The Netherlands
Klaasjan Ouwens
49Biological Psychology, Vrije Universiteit Amsterdam, The Netherlands
50Genalice BV, Harderwijk, The Netherlands
Pierre Peterlongo
51INRIA Campus de Beaulieu-Rennes, Rennes Cedex 35042, France
Nadia Pisanti
52Dipartimento di Informatica, University degli Studi di Pisa, Pisa, Italy
53Erable Team, INRIA
Sven Rahmann
35Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Ben Raphael
40Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA
Knut Reinert
54Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
Dick de Ridder
55Bioinformatics 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
56Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
Ole Schulz-Trieglaff
57Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK
Ashley D. Sanders
58Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
Siavash Sheikhizadeh
55Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
Carl Shneider
59Leiden Observatory, Leiden University, P.O. Box 9513, 2300 RA Leiden, The Netherlands
Sandra Smit
55Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
Daniel Valenzuela
16HIIT and Department of Computer Science, University of Helsinki, Finland
Jiayin Wang
60School of Management, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, China
61Institute of Data Science and Information Quality, Xi’an Jiaotong University
62Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University
Lodewyk Wessels
63Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
Ying Zhang
30MonetDB Solutions, Amsterdam, The Netherlands
22Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands
Victor Guryev
18European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, AV Groningen 9713, The Netherlands
15Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
Fabio Vandin
64Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
40Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA
Kai Ye
65School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, China
66Kai Ye Young Scientist Studio, Xi’an Jiaotong University
62Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University
Alexander Schönhuth
22Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands
Article usage
Posted August 25, 2016.
Computational Pan-Genomics: Status, Promises and Challenges
The Computational Pan-Genomics Consortium, 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, Raoul J. P. Bonnal, 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 D. 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
The Computational Pan-Genomics Consortium, 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, Raoul J. P. Bonnal, 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 D. 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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