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Matthew Sullivan
PeerJ Author
1,690 Points

Contributions by role

Author 1,585
Preprint Author 105

Contributions by subject area

Bioinformatics
Genomics
Microbiology
Virology
Ecology
Taxonomy
Environmental Sciences
Soil Science
Ecosystem Science
Data Science
Computational Biology
Marine Biology

Matthew B Sullivan

PeerJ Author

Summary

We leverage virus-host model systems in the laboratory to test hypotheses about viral ecology and evolution and virus-host interactions that are derived from data-driven, quantitative inquiry of natural communities.

Bioinformatics Ecology Genomics Microbiology

Past or current institution affiliations

Ohio State University
University of Arizona

Work details

Professor

Ohio State University
June 2015
Microbiology and Civil, Environmental and Geodetic Engineering

Websites

  • Google Scholar

PeerJ Contributions

  • Articles 12
  • Preprints 3
June 14, 2021
Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation
Akbar Adjie Pratama, Benjamin Bolduc, Ahmed A. Zayed, Zhi-Ping Zhong, Jiarong Guo, Dean R. Vik, Maria Consuelo Gazitúa, James M. Wainaina, Simon Roux, Matthew B. Sullivan
https://doi.org/10.7717/peerj.11447 PubMed 34178438
March 30, 2021
VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature
Olivier Zablocki, Michelle Michelsen, Marie Burris, Natalie Solonenko, Joanna Warwick-Dugdale, Romik Ghosh, Jennifer Pett-Ridge, Matthew B. Sullivan, Ben Temperton
https://doi.org/10.7717/peerj.11088 PubMed 33850654
August 13, 2020
The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research
Benjamin Bolduc, Suzanne B. Hodgkins, Ruth K. Varner, Patrick M. Crill, Carmody K. McCalley, Jeffrey P. Chanton, Gene W. Tyson, William J. Riley, Michael Palace, Melissa B. Duhaime, Moira A. Hough, Scott R. Saleska, Matthew B. Sullivan, Virginia I. Rich
https://doi.org/10.7717/peerj.9467
July 4, 2019
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
Gareth Trubl, Simon Roux, Natalie Solonenko, Yueh-Fen Li, Benjamin Bolduc, Josué Rodríguez-Ramos, Emiley A. Eloe-Fadrosh, Virginia I. Rich, Matthew B. Sullivan
https://doi.org/10.7717/peerj.7265 PubMed 31309007
May 9, 2019
Optimizing de novo genome assembly from PCR-amplified metagenomes
Simon Roux, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A. Ahlgren, Yuanchao Zhan, David Marsan, Feng Chen, Jed A. Fuhrman, Trent R. Northen, Matthew B. Sullivan, Virginia I. Rich, Rex R. Malmstrom, Emiley A. Eloe-Fadrosh
https://doi.org/10.7717/peerj.6902 PubMed 31119088
April 25, 2019
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
Joanna Warwick-Dugdale, Natalie Solonenko, Karen Moore, Lauren Chittick, Ann C. Gregory, Michael J. Allen, Matthew B. Sullivan, Ben Temperton
https://doi.org/10.7717/peerj.6800 PubMed 31086738
September 21, 2017
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
Simon Roux, Joanne B. Emerson, Emiley A. Eloe-Fadrosh, Matthew B. Sullivan
https://doi.org/10.7717/peerj.3817 PubMed 28948103
June 15, 2017
Putative archaeal viruses from the mesopelagic ocean
Dean R. Vik, Simon Roux, Jennifer R. Brum, Ben Bolduc, Joanne B. Emerson, Cory C. Padilla, Frank J. Stewart, Matthew B. Sullivan
https://doi.org/10.7717/peerj.3428 PubMed 28630803
May 3, 2017
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria
Benjamin Bolduc, Ho Bin Jang, Guilhem Doulcier, Zhi-Qiang You, Simon Roux, Matthew B. Sullivan
https://doi.org/10.7717/peerj.3243 PubMed 28480138
December 8, 2016
Towards quantitative viromics for both double-stranded and single-stranded DNA viruses
Simon Roux, Natalie E. Solonenko, Vinh T. Dang, Bonnie T. Poulos, Sarah M. Schwenck, Dawn B. Goldsmith, Maureen L. Coleman, Mya Breitbart, Matthew B. Sullivan
https://doi.org/10.7717/peerj.2777 PubMed 28003936
May 17, 2016
Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient
Gareth Trubl, Natalie Solonenko, Lauren Chittick, Sergei A. Solonenko, Virginia I. Rich, Matthew B. Sullivan
https://doi.org/10.7717/peerj.1999 PubMed 27231649
May 28, 2015
VirSorter: mining viral signal from microbial genomic data
Simon Roux, Francois Enault, Bonnie L. Hurwitz, Matthew B. Sullivan
https://doi.org/10.7717/peerj.985 PubMed 26038737
April 6, 2019 - Version: 1
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
Gareth Trubl, Simon Roux, Natalie Solonenko, Yueh-Fen Li, Benjamin Bolduc, Josué Rodríguez-Ramos, Emiley A. Eloe-Fadrosh, Virginia I. Rich, Matthew B. Sullivan
https://doi.org/10.7287/peerj.preprints.27640v1
December 28, 2018 - Version: 1
Optimizing de novo genome assembly from PCR-amplified metagenomes
Simon Roux, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A Ahlgren, Yuanchao Zhan, David Marsan, Feng Chen, Jed A Fuhrman, Trent R Northen, Matthew B Sullivan, Virginia I Rich, Rex R Malmstrom, Emiley A Eloe-Fadrosh
https://doi.org/10.7287/peerj.preprints.27453v1
June 26, 2017 - Version: 1
Benchmarking viromics: An in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
Simon Roux, Joanne B Emerson, Emiley A Eloe-Fadrosh, Matthew B Sullivan
https://doi.org/10.7287/peerj.preprints.3053v1