Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

StrainHub: A phylogenetic tool to construct pathogen transmission networks

View ORCID ProfileAdriano de Bernardi Schneider, View ORCID ProfileColby T. Ford, Reilly Hostager, John Williams, Michael Cioce, Ümit V. Çatalyürek, Joel O. Wertheim, Daniel Janies
doi: https://doi.org/10.1101/650283
Adriano de Bernardi Schneider
Department of Medicine, University of California San Diego, San Diego, 92103, United States of AmericaDepartment of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, 28223, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Adriano de Bernardi Schneider
  • For correspondence: adeberna@ucsd.edu djanies@uncc.edu
Colby T. Ford
Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, 28223, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Colby T. Ford
Reilly Hostager
Department of Medicine, University of California San Diego, San Diego, 92103, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John Williams
Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, 28223, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michael Cioce
Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, 28223, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ümit V. Çatalyürek
School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, 30332, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Joel O. Wertheim
Department of Medicine, University of California San Diego, San Diego, 92103, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Daniel Janies
Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, 28223, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: adeberna@ucsd.edu djanies@uncc.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

Summary

In epidemiology of infectious diseases, networks have been used to reconstruct contacts among patients. Summarizing networks using pathogen metadata (e.g., host species and place of isolation) and a phylogenetic tree is a nascent approach. In this paper, we introduce a tool for reconstructing transmission networks in arbitrary space from phylogenetic information and metadata. Our goals are to provide a means of deriving new insights and infection control strategies based on the dynamics of the pathogen derived from networks and metrics. We created a web-based application, called StrainHub, in which a user can input a phylogenetic tree along with characters derived from metadata using their preferred tree search method. StrainHub generates a transmission network for the user metadata based on character state changes mapped on the phylogenetic tree. The user has the option to calculate centrality metrics on the nodes including betweenness, closeness, degree, and a new metric, source/hub ratio. The outputs include the network with values for metrics on its nodes and the tree with characters reconstructed. All of these results can be exported for further analysis.

Availability https://github.com/abschneider/StrainHub and strainhub.io

Footnotes

  • http://strainhub.io

  • https://github.com/abschneider/StrainHub

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-ND 4.0 International license.
Back to top
PreviousNext
Posted May 31, 2019.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
StrainHub: A phylogenetic tool to construct pathogen transmission networks
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
Share
StrainHub: A phylogenetic tool to construct pathogen transmission networks
Adriano de Bernardi Schneider, Colby T. Ford, Reilly Hostager, John Williams, Michael Cioce, Ümit V. Çatalyürek, Joel O. Wertheim, Daniel Janies
bioRxiv 650283; doi: https://doi.org/10.1101/650283
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
StrainHub: A phylogenetic tool to construct pathogen transmission networks
Adriano de Bernardi Schneider, Colby T. Ford, Reilly Hostager, John Williams, Michael Cioce, Ümit V. Çatalyürek, Joel O. Wertheim, Daniel Janies
bioRxiv 650283; doi: https://doi.org/10.1101/650283

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (1544)
  • Biochemistry (2500)
  • Bioengineering (1757)
  • Bioinformatics (9727)
  • Biophysics (3928)
  • Cancer Biology (2990)
  • Cell Biology (4235)
  • Clinical Trials (135)
  • Developmental Biology (2653)
  • Ecology (4129)
  • Epidemiology (2033)
  • Evolutionary Biology (6931)
  • Genetics (5243)
  • Genomics (6531)
  • Immunology (2207)
  • Microbiology (7012)
  • Molecular Biology (2782)
  • Neuroscience (17410)
  • Paleontology (127)
  • Pathology (432)
  • Pharmacology and Toxicology (712)
  • Physiology (1068)
  • Plant Biology (2515)
  • Scientific Communication and Education (647)
  • Synthetic Biology (835)
  • Systems Biology (2698)
  • Zoology (439)