New Results
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 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
60FLI Leibniz Institute for Age Research, Beutenbergstraβe 11, 07745 Jena, Germany
61Michael Stifel Center Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
62German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig;
Thomas Abeel
49The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Mekelweg 4, 2628 CD, Delft, The Netherlands;
Louis Dijkstra
6Computational Science Lab, University of Amsterdam, Amsterdam, 1098XG, The Netherlands;
7Department of High Performance Computing, ITMO University, Saint Petersburg, 197101, Russia
Bas E. Dutilh
8Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, Netherlands
9Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
10Department 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
11EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
Wigard P. Kloosterman
12Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands;
Veli Mäkinen
13HIIT and Department of Computer Science, University of Helsinki, Finland
Adam Novak
15Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Benedict Paten
15Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
David Porubsky
16European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, AV Groningen 9713, The Netherlands;
Eric Rivals
17LIRMM, CNRS and Université de Montpellier, Montpellier, France
63Institut de Biologie Computationnelle, CNRS and Universitée de Montpellier, Montpellier, France
Can Alkan
18Department of Computer Engineering, Bilkent University, Bilkent, Ankara, 06800, Turkey
Jasmijn Baaijens
5Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands;
Paul I. W. De Bakker
12Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands;
Valentina Boeva
19Institut Curie, Centre de Recherche, Inserm U900, F-75005 Paris, France
64Mines ParisTech, F-77305 cedex Fontainebleau, France
65PSL Research University, F-75005 Paris, France
66Institut Cochin, Inserm U1016, CNRS UMR 8104, Universite Paris Descartes UMR-S1016, F-75014 Paris, France
Francesca Chiaromonte
20Departments of Statistics, The Pennsylvania State University, University Park, PA, 16802;
Rayan Chikhi
21CNRS, Univ. Lille, UMR 9189 CRIStAL, F-59000 Lille, France
Francesca D. Ciccarelli
22Division of Cancer Studies, King’s College London, London SE11UL, UK
Robin Cijvat
23MonetDB Solutions, Amsterdam, The Netherlands;
Erwin Datema
24Plant Research International, Business Unit of Bioscience, cluster Applied Bioinformatics, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands;
25Wageningen University Centre for Biosystems Genomics, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands;
26KeyGene N.V, Agro Business Park 90, 6708 PW Wageningen, The Netherlands;
Cornelia M. Van Duijn
27Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands;
Evan E. Eichler
28Department of Genome Sciences, University of Washington, Seattle, 98105, USA
Corinna Ernst
29Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Eleazar Eskin
30Department of Computer Science, University of California, Los Angeles, USA
31Department of Human Genetics, University of California, Los Angeles, USA
Erik Garrison
32Wellcome Trust Sanger Institute, Cambridge, UK
Mohammed El-Kebir
5Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands;
33Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands;
34Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA
Gunnar W. Klau
5Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands;
Jan O. Korbel
11EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
35European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Eric-Wubbo Lameijer
36Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, The Netherlands;
Benjamin Langmead
37Department of Computer Science and Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland
Marcel Martin
59Science for Life Laboratory, Dept. of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-17121 Solna, Sweden
Paul Medvedev
38Department of Computer Science and Engineering, The Pennsylvania State University, USA
39Department of Biochemistry and Molecular Biology, The Pennsylvania State University, USA
40Genomic Sciences Institute of the Huck, The Pennsylvania State University, USA
John C. Mu
41Bina Technologies, Roche Sequencing, Redwood City, CA 94065, USA
Pieter Neerincx
36Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, The Netherlands;
Klaasjan Ouwens
42Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands;
67Genalice BV, Harderwijk, The Netherlands;
Pierre Peterlongo
43INRIA Campus de Beaulieu-Rennes, Rennes Cedex 35042, France
Nadia Pisanti
44Dipartimento di Informatica, University degli Studi di Pisa, Pisa, Italy
45Erable Team, INRIA
Sven Rahmann
29Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
Ben Raphael
46Department of Computer Science, Brown University, Providence, Rhode Island 02912, USA
47Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
Knut Reinert
48Department of Mathematics and Computer Science, Freie Universitat Berlin, Berlin, Germany
Dick de Ridder
50Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands;
Jeroen de Ridder
49The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Mekelweg 4, 2628 CD, Delft, The Netherlands;
Matthias Schlesner
51Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
Ole Schulz-Trieglaff
52Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK
Ashley Sanders
53Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
Siavash Sheikhizadeh
50Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands;
Carl Shneider
54Leiden Observatory, Leiden University, P.O. Box 9513, 2300 RA Leiden, The Netherlands;
Sandra Smit
50Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands;
Daniel Valenzuela
13HIIT and Department of Computer Science, University of Helsinki, Finland
Jiayin Wang
70School of Management, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, China
71Institute of Data Science and Information Quality, Xi’an Jiaotong University;
72Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University
Lodewyk Wessels
56Netherlands Cancer Institute (NKI), Amsterdam, the Netherlands;
Ying Zhang
23MonetDB Solutions, Amsterdam, The Netherlands;
5Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands;
Victor Guryev
16European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, AV Groningen 9713, The Netherlands;
12Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands;
Fabio Vandin
57Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
34Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA
Kai Ye
68School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, China
69Kai Ye Young Scientist Studio, Xi’an Jiaotong University;
72Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University
Alexander Schönhuth
5Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, 1098XG, The Netherlands;
Article usage
Posted March 12, 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 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 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
Subject Area
Subject Areas
- Biochemistry (11745)
- Bioengineering (8751)
- Bioinformatics (29195)
- Biophysics (14971)
- Cancer Biology (12095)
- Cell Biology (17411)
- Clinical Trials (138)
- Developmental Biology (9421)
- Ecology (14178)
- Epidemiology (2067)
- Evolutionary Biology (18306)
- Genetics (12245)
- Genomics (16801)
- Immunology (11867)
- Microbiology (28083)
- Molecular Biology (11592)
- Neuroscience (60965)
- Paleontology (451)
- Pathology (1870)
- Pharmacology and Toxicology (3238)
- Physiology (4959)
- Plant Biology (10427)
- Synthetic Biology (2885)
- Systems Biology (7339)
- Zoology (1651)