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Donovan Parks
PeerJ Editor, Author & Reviewer
1,135 Points

Contributions by role

Author 405
Preprint Author 210
Reviewer 120
Editor 400

Contributions by subject area

Genomics
Microbiology
Bioinformatics
Biodiversity
Biotechnology
Taxonomy
Molecular Biology
Biogeography
Marine Biology
Data Mining and Machine Learning
Computational Biology
Ecology
Plant Science

Donovan H Parks

PeerJ Editor, Author & Reviewer

Summary

Donovan Parks holds a PhD in computer science and has developed a number of bioinformatic programs used by the research community including CheckM, STAMP, and GenGIS. He has expertise in bioinformatics relating to microbial ecology, phylogenetics, and metagenome-assembled genomes. He is currently working as a bioinformatic consultant with the Australian Centre for Ecogenomics where he is working on an initiative to resolve long-standing issues within bacterial and archaeal nomenclature and developing new tools for reconstructing and validating genomes obtained directly from environmental samples.

Biodiversity Biogeochemistry Biogeography Bioinformatics Genomics Microbiology

Editing Journals

PeerJ - the Journal of Life & Environmental Sciences

Past or current institution affiliations

Dalhousie University
McGill University
University of Queensland

Work details

Bioinformatic Consultant

Sole Proprietor
January 2016
Sole Proprietor

Postdoctoral Research Fellow

University of Queensland
January 2013 - December 2015
Australian Centre for Ecogenomics

Master of Engineering

McGill University
September 2004 - August 2006
Electrical and Computer Engineering

PhD

Dalhousie University
September 2008 - August 2012
Computer Science

Websites

  • Google Scholar
  • GitHub
  • PubMed Search
  • LinkedIn
  • ORCID

PeerJ Contributions

  • Articles 3
  • Preprints 4
  • Edited 4
  • Reviewed 1
  • Feedback 1
May 21, 2015
Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus
Rochelle M. Soo, Ben J. Woodcroft, Donovan H. Parks, Gene W. Tyson, Philip Hugenholtz
https://doi.org/10.7717/peerj.968 PubMed 26038723
January 27, 2015
First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
Yuji Sekiguchi, Akiko Ohashi, Donovan H. Parks, Toshihiro Yamauchi, Gene W. Tyson, Philip Hugenholtz
https://doi.org/10.7717/peerj.740 PubMed 25650158
September 30, 2014
GroopM: an automated tool for the recovery of population genomes from related metagenomes
Michael Imelfort, Donovan Parks, Ben J. Woodcroft, Paul Dennis, Philip Hugenholtz, Gene W. Tyson
https://doi.org/10.7717/peerj.603 PubMed 25289188
May 20, 2015 - Version: 2
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Donovan H Parks, Michael Imelfort, Connor T Skennerton, Philip Hugenholtz, Gene W Tyson
https://doi.org/10.7287/peerj.preprints.554v2
June 10, 2014 - Version: 1
GroopM: An automated tool for the recovery of population genomes from related metagenomes
Michael Imelfort, Donovan Parks, Ben J Woodcroft, Paul Dennis, Philip Hugenholtz, Gene W Tyson
https://doi.org/10.7287/peerj.preprints.409v1
March 17, 2014 - Version: 2
Photosynthesis is not a universal feature of the phylum Cyanobacteria
Rochelle M Soo, Connor T Skennerton, Yuji Sekiguchi, Michael Imelfort, Samuel J Paech, Paul G Dennis, Jason A Steen, Donovan H Parks, Gene W Tyson, Philip Hugenholtz
https://doi.org/10.7287/peerj.preprints.204v2
May 3, 2013 - Version: 1
GenGIS 2: Geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework
Robert G Beiko, Donovan H Parks, Timothy Mankowski, Somayyeh Zangooei, Michael S Porter, David G Armanini, Donald J Baird, Morgan G I Langille
https://doi.org/10.7287/peerj.preprints.15

Academic Editor on

September 16, 2021
Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets
Nicholas D. Youngblut, Ruth E. Ley
https://doi.org/10.7717/peerj.12198 PubMed 34616633
April 6, 2020
Draft genome of Rosenbergiella nectarea strain 8N4T provides insights into the potential role of this species in its plant host
Sivan Laviad-Shitrit, Ido Izhaki, William B. Whitman, Nicole Shapiro, Tanja Woyke, Nikos C. Kyrpides, Malka Halpern
https://doi.org/10.7717/peerj.8822 PubMed 32292647
February 13, 2020
Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites
Vincent Hervé, Pengfei Liu, Carsten Dietrich, David Sillam-Dussès, Petr Stiblik, Jan Šobotník, Andreas Brune
https://doi.org/10.7717/peerj.8614 PubMed 32095380
April 18, 2018
Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences
Robert C. Edgar
https://doi.org/10.7717/peerj.4652 PubMed 29682424

Signed reviews submitted for articles published in PeerJ Note that some articles may not have the review itself made public unless authors have made them open as well.

July 10, 2017
290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology
Benjamin J. Tully, Rohan Sachdeva, Elaina D. Graham, John F. Heidelberg
https://doi.org/10.7717/peerj.3558 PubMed 28713657

Provided feedback on

07 Apr 2015

Photosynthesis is not a universal feature of the phylum Cyanobacteria

This manuscript has been published in Genome Biology and Evolution under the title "An Expanded Genomic Representation of the Phylum Cyanobacteria": http://gbe.oxfordjournals.org/...