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Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

View ORCID ProfileMorteza Roodgar, View ORCID ProfileBenjamin H. Good, View ORCID ProfileNandita R. Garud, Stephen Martis, Mohan Avula, Wenyu Zhou, Samuel Lancaster, Hayan Lee, Afshin Babveyh, Sophia Nesamoney, Katherine S. Pollard, View ORCID ProfileMichael P. Snyder
doi: https://doi.org/10.1101/2019.12.21.886093
Morteza Roodgar
1Department of Genetics, Stanford University, Stanford, California, 94305
2Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305
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  • ORCID record for Morteza Roodgar
Benjamin H. Good
3Department of Applied Physics, Stanford University, Stanford, California 94305
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  • For correspondence: bhgood@stanford.edu katherine.pollard@gladstone.ucsf.edu mpsnyder@stanford.edu
Nandita R. Garud
4Department of Ecology and Evolutionary Biology, University of California Los Angeles
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Stephen Martis
5Department of Physics, University of California, Berkeley, CA 94720
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Mohan Avula
1Department of Genetics, Stanford University, Stanford, California, 94305
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Wenyu Zhou
1Department of Genetics, Stanford University, Stanford, California, 94305
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Samuel Lancaster
1Department of Genetics, Stanford University, Stanford, California, 94305
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Hayan Lee
1Department of Genetics, Stanford University, Stanford, California, 94305
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Afshin Babveyh
1Department of Genetics, Stanford University, Stanford, California, 94305
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Sophia Nesamoney
1Department of Genetics, Stanford University, Stanford, California, 94305
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Katherine S. Pollard
6Gladstone Institutes, San Francisco, CA 94158
7Department of Epidemiology & Biostatistics, University of California, San Francisco, Ca 94158
8Chan Zuckerberg Biohub, San Francisco, CA 94158
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  • For correspondence: bhgood@stanford.edu katherine.pollard@gladstone.ucsf.edu mpsnyder@stanford.edu
Michael P. Snyder
1Department of Genetics, Stanford University, Stanford, California, 94305
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  • ORCID record for Michael P. Snyder
  • For correspondence: bhgood@stanford.edu katherine.pollard@gladstone.ucsf.edu mpsnyder@stanford.edu
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Article Information

doi 
https://doi.org/10.1101/2019.12.21.886093
History 
  • December 23, 2019.

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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-NC 4.0 International license.

Author Information

  1. Morteza Roodgar1,2,*,
  2. Benjamin H. Good3,*,†,
  3. Nandita R. Garud4,
  4. Stephen Martis5,
  5. Mohan Avula1,
  6. Wenyu Zhou1,
  7. Samuel Lancaster1,
  8. Hayan Lee1,
  9. Afshin Babveyh1,
  10. Sophia Nesamoney1,
  11. Katherine S. Pollard6,7,8,† and
  12. Michael P. Snyder1,†
  1. 1Department of Genetics, Stanford University, Stanford, California, 94305
  2. 2Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305
  3. 3Department of Applied Physics, Stanford University, Stanford, California 94305
  4. 4Department of Ecology and Evolutionary Biology, University of California Los Angeles
  5. 5Department of Physics, University of California, Berkeley, CA 94720
  6. 6Gladstone Institutes, San Francisco, CA 94158
  7. 7Department of Epidemiology & Biostatistics, University of California, San Francisco, Ca 94158
  8. 8Chan Zuckerberg Biohub, San Francisco, CA 94158
  1. ↵†Correspondence should be addressed to: B.H.G. (bhgood{at}stanford.edu), K.S.P. (katherine.pollard{at}gladstone.ucsf.edu), or M.P.S. (mpsnyder{at}stanford.edu).
  1. ↵* These authors contributed equally to this work.

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Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment
Morteza Roodgar, Benjamin H. Good, Nandita R. Garud, Stephen Martis, Mohan Avula, Wenyu Zhou, Samuel Lancaster, Hayan Lee, Afshin Babveyh, Sophia Nesamoney, Katherine S. Pollard, Michael P. Snyder
bioRxiv 2019.12.21.886093; doi: https://doi.org/10.1101/2019.12.21.886093
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Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment
Morteza Roodgar, Benjamin H. Good, Nandita R. Garud, Stephen Martis, Mohan Avula, Wenyu Zhou, Samuel Lancaster, Hayan Lee, Afshin Babveyh, Sophia Nesamoney, Katherine S. Pollard, Michael P. Snyder
bioRxiv 2019.12.21.886093; doi: https://doi.org/10.1101/2019.12.21.886093

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