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Research Article | Host-Microbe Biology

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease

Robert H. Mills, Yoshiki Vázquez-Baeza, Qiyun Zhu, Lingjing Jiang, James Gaffney, Greg Humphrey, Larry Smarr, Rob Knight, David J. Gonzalez
Marcus J. Claesson, Editor
Robert H. Mills
aDepartment of Pharmacology, University of California, San Diego, San Diego, California, USA
bSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, California, USA
cDepartment of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, San Diego, California, USA
gCenter for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
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Yoshiki Vázquez-Baeza
cDepartment of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, San Diego, California, USA
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Qiyun Zhu
cDepartment of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, San Diego, California, USA
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Lingjing Jiang
cDepartment of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, San Diego, California, USA
dDepartment of Family Medicine and Public Health, University of California, San Diego, San Diego, California, USA
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James Gaffney
cDepartment of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, San Diego, California, USA
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Greg Humphrey
cDepartment of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, San Diego, California, USA
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Larry Smarr
eDepartment of Computer Science and Engineering, University of California, San Diego, San Diego, California, USA
fCalifornia Institute for Telecommunications and Information Technology, University of California, San Diego, San Diego, California, USA
gCenter for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
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Rob Knight
cDepartment of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, San Diego, California, USA
gCenter for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
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David J. Gonzalez
aDepartment of Pharmacology, University of California, San Diego, San Diego, California, USA
bSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, California, USA
gCenter for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
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Marcus J. Claesson
University College Cork
Roles: Editor
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DOI: 10.1128/mSystems.00337-18
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Article Information

DOI 
https://doi.org/10.1128/mSystems.00337-18

Published By 
American Society for Microbiology Journals
History 
  • Received December 19, 2018
  • Accepted January 17, 2019
  • Published online February 12, 2019.

Copyright & Usage 
Copyright © 2019 Mills et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Editors and / or Reviewers 
  • Marcus J. Claesson, Editor, University College Cork

Author Information

  1. Robert H. Millsa,b,c,g,
  2. Yoshiki Vázquez-Baezac,
  3. Qiyun Zhuc,
  4. Lingjing Jiangc,d,
  5. James Gaffneyc,
  6. Greg Humphreyc,
  7. Larry Smarre,f,g,
  8. Rob Knightc,g and
  9. David J. Gonzaleza,b,g
  1. aDepartment of Pharmacology, University of California, San Diego, San Diego, California, USA
  2. bSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, California, USA
  3. cDepartment of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, San Diego, California, USA
  4. dDepartment of Family Medicine and Public Health, University of California, San Diego, San Diego, California, USA
  5. eDepartment of Computer Science and Engineering, University of California, San Diego, San Diego, California, USA
  6. fCalifornia Institute for Telecommunications and Information Technology, University of California, San Diego, San Diego, California, USA
  7. gCenter for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
  • Address correspondence to Rob Knight, robknight{at}ucsd.edu, or David J. Gonzalez, djgonzalez{at}ucsd.edu.
  • Citation Mills RH, Vázquez-Baeza Y, Zhu Q, Jiang L, Gaffney J, Humphrey G, Smarr L, Knight R, Gonzalez DJ. 2019. Evaluating metagenomic prediction of the metaproteome in a 4.5-year study of a patient with Crohn's disease. mSystems 4:e00337-18. https://doi.org/10.1128/mSystems.00337-18.

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Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease
Robert H. Mills, Yoshiki Vázquez-Baeza, Qiyun Zhu, Lingjing Jiang, James Gaffney, Greg Humphrey, Larry Smarr, Rob Knight, David J. Gonzalez
mSystems Feb 2019, 4 (1) e00337-18; DOI: 10.1128/mSystems.00337-18

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Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease
Robert H. Mills, Yoshiki Vázquez-Baeza, Qiyun Zhu, Lingjing Jiang, James Gaffney, Greg Humphrey, Larry Smarr, Rob Knight, David J. Gonzalez
mSystems Feb 2019, 4 (1) e00337-18; DOI: 10.1128/mSystems.00337-18
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KEYWORDS

colonic Crohn's disease
inflammatory bowel disease
metagenomics
metaproteomics
microbiome
multiomics
tandem mass tags
time series
gut inflammation
proteomics

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