PeerJ Author & Reviewer

1,725 Points

Contributions by role

Contributions by subject area

Matthew B Sullivan

PeerJ Author & Reviewer

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

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

1 Question

Why are these authors misrepresenting our work -- again?

about Ribovirus classification by a polymerase barcode sequence