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High-resolution sweep metagenomics using fast probabilistic inference

View ORCID ProfileTommi Mäklin, View ORCID ProfileTeemu Kallonen, Sophia David, Christine J. Boinett, View ORCID ProfileBen Pascoe, View ORCID ProfileGuillaume Méric, David M. Aanensen, Edward J. Feil, Stephen Baker, View ORCID ProfileJulian Parkhill, View ORCID ProfileSamuel K. Sheppard, View ORCID ProfileJukka Corander, View ORCID ProfileAntti Honkela
doi: https://doi.org/10.1101/332544
Tommi Mäklin
Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Finland
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  • ORCID record for Tommi Mäklin
Teemu Kallonen
Department of Biostatistics, University of Oslo, NorwayWellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
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  • ORCID record for Teemu Kallonen
Sophia David
Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Christine J. Boinett
Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, VietnamCentre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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Ben Pascoe
The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath University, Bath, United Kingdom
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  • ORCID record for Ben Pascoe
Guillaume Méric
The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath University, Bath, United Kingdom
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  • ORCID record for Guillaume Méric
David M. Aanensen
Wellcome Sanger Institute, Hinxton, Cambridge, United KingdomDepartment of Infectious Disease Epidemiology, Imperial College London, London, United KingdomBig Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Edward J. Feil
The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath University, Bath, United Kingdom
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Stephen Baker
Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, VietnamCentre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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Julian Parkhill
Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
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  • ORCID record for Julian Parkhill
Samuel K. Sheppard
The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath University, Bath, United Kingdom
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  • ORCID record for Samuel K. Sheppard
Jukka Corander
Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, FinlandDepartment of Biostatistics, University of Oslo, NorwayWellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
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Antti Honkela
Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, FinlandDepartment of Public Health, University of Helsinki, FinlandHelsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Finland
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  • ORCID record for Antti Honkela
  • For correspondence: antti.honkela@helsinki.fi
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Article Information

doi 
https://doi.org/10.1101/332544
History 
  • July 10, 2019.

Article Versions

  • Version 1 (June 5, 2018 - 08:47).
  • You are viewing Version 2, the most recent version of this article.
Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.

Author Information

  1. Tommi Mäklin1,
  2. Teemu Kallonen2,3,
  3. Sophia David4,
  4. Christine J. Boinett5,6,
  5. Ben Pascoe7,
  6. Guillaume Méric7,
  7. David M. Aanensen3,8,9,
  8. Edward J. Feil7,
  9. Stephen Baker5,6,
  10. Julian Parkhill3,
  11. Samuel K. Sheppard7,
  12. Jukka Corander1,2,3 and
  13. Antti Honkela1,10,11,*
  1. 1Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Finland
  2. 2Department of Biostatistics, University of Oslo, Norway
  3. 3Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
  4. 4Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
  5. 5Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
  6. 6Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
  7. 7The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath University, Bath, United Kingdom
  8. 8Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
  9. 9Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
  10. 10Department of Public Health, University of Helsinki, Finland
  11. 11Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Finland
  1. ↵*Corresponding author email: antti.honkela{at}helsinki.fi
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High-resolution sweep metagenomics using fast probabilistic inference
Tommi Mäklin, Teemu Kallonen, Sophia David, Christine J. Boinett, Ben Pascoe, Guillaume Méric, David M. Aanensen, Edward J. Feil, Stephen Baker, Julian Parkhill, Samuel K. Sheppard, Jukka Corander, Antti Honkela
bioRxiv 332544; doi: https://doi.org/10.1101/332544
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High-resolution sweep metagenomics using fast probabilistic inference
Tommi Mäklin, Teemu Kallonen, Sophia David, Christine J. Boinett, Ben Pascoe, Guillaume Méric, David M. Aanensen, Edward J. Feil, Stephen Baker, Julian Parkhill, Samuel K. Sheppard, Jukka Corander, Antti Honkela
bioRxiv 332544; doi: https://doi.org/10.1101/332544

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