Donovan H Parks

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 20

Top Venues

University of Queensland

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Queensland Jan 01 2013

Australia

Postdoctoral research fellow; Consultant :: Australian Centre for Ecogenomics

Publications

Alex Chklovski, Donovan H Parks, Benjamin J Woodcroft, Gene W Tyson
Author Correction: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature methods (2024)
Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio Gonzalez, James T Morton, Giorgia Nicolaou, Donovan H Parks, Søren M Karst, Mads Albertsen, Philip Hugenholtz, Todd DeSantis, Se Jin Song, Andrew Bartko, Aki Samuli Havulinna, Pekka Jousilahti, Susan Cheng, Michael Inouye, Teemu Niiranen, Mohit Jain, Veikko V Salomaa, Leo Lahti, Siavash Mirarab, Rob Knight
Author Correction: Greengenes2 unifies microbial data in a single reference tree. Nature biotechnology (2023)
Alex Chklovski, Donovan H Parks, Benjamin J Woodcroft, Gene W Tyson
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature methods (2023)
Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio Gonzalez, James T Morton, Giorgia Nicolaou, Donovan H Parks, Søren M Karst, Mads Albertsen, Philip Hugenholtz, Todd DeSantis, Se Jin Song, Andrew Bartko, Aki Samuli Havulinna, Pekka Jousilahti, Susan Cheng, Michael Inouye, Teemu Niiranen, Mohit Jain, Veikko V Salomaa, Leo Lahti, Siavash Mirarab, Rob Knight
Greengenes2 unifies microbial data in a single reference tree. Nature biotechnology (2023)
Jean-Baptiste Raina, Bennett S Lambert, Donovan H Parks, Christian Rinke, Nachshon Siboni, Anna R Bramucci, Martin Ostrowski, Brandon Signal, Adrian Lutz, Himasha Mendis, Francesco Rubino, Vicente I Fernandez, Roman Stocker, Philip Hugenholtz, Gene W Tyson, Justin R Seymour
Chemotaxis shapes the microscale organization of the ocean's microbiome. Nature 605 (7908) (2022)
Brian P Hedlund, Maria Chuvochina, Philip Hugenholtz, Konstantinos T Konstantinidis, Alison E Murray, Marike Palmer, Donovan H Parks, Alexander J Probst, Anna-Louise Reysenbach, Luis M Rodriguez-R, Ramon Rosselló-Móra, Iain C Sutcliffe, Stephanus N Venter, William B Whitman
SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nature microbiology 7 (10) (2022)
Pierre-Alain Chaumeil, Aaron J Mussig, Philip Hugenholtz, Donovan H Parks
GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics (Oxford, England) 38 (23) (2022)
Søren Hallstrøm, Jean-Baptiste Raina, Martin Ostrowski, Donovan H Parks, Gene W Tyson, Philip Hugenholtz, Roman Stocker, Justin R Seymour, Lasse Riemann
Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N<sub>2</sub> fixation in the pelagic ocean. The ISME journal 16 (11) (2022)
Philip Hugenholtz, Maria Chuvochina, Aharon Oren, Donovan H Parks, Rochelle M Soo
Prokaryotic taxonomy and nomenclature in the age of big sequence data. The ISME journal 15 (7) (2021)
Donovan H Parks, Maria Chuvochina, Christian Rinke, Aaron J Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic acids research (2021)
Joanne B Emerson, Ruth K Varner, Martin Wik, Donovan H Parks, Rebecca B Neumann, Joel E Johnson, Caitlin Margaret Singleton, Benjamin J Woodcroft, Rodney Tollerson, Akosua Owusu-Dommey, Morgan Binder, Nancy L Freitas, Patrick M Crill, Scott R Saleska, Gene W Tyson, Virginia I Rich
Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes. Nature communications 12 (1) (2021)
Christian Rinke, Maria Chuvochina, Aaron J Mussig, Pierre-Alain Chaumeil, Adrián A Davín, David W Waite, William B Whitman, Donovan H Parks, Philip Hugenholtz
A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature microbiology 6 (7) (2021)
Alison E Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T Konstantinidis, Christopher E Lane, R Thane Papke, Donovan H Parks, Ramon Rossello-Mora, Matthew B Stott, Iain C Sutcliffe, J Cameron Thrash, Stephanus N Venter, William B Whitman, Silvia G Acinas, Rudolf I Amann, Karthik Anantharaman, Jean Armengaud, Brett J Baker, Roman A Barco, Helge B Bode, Eric S Boyd, Carrie L Brady, Paul Carini, Patrick S G Chain, Daniel R Colman, Kristen M DeAngelis, Maria Asuncion de Los Rios, Paulina Estrada-de Los Santos, Christopher A Dunlap, Jonathan A Eisen, David Emerson, Thijs J G Ettema, Damien Eveillard, Peter R Girguis, Ute Hentschel, James T Hollibaugh, Laura A Hug, William P Inskeep, Elena P Ivanova, Hans-Peter Klenk, Wen-Jun Li, Karen G Lloyd, Frank E Löffler, Thulani Peter Makhalanyane, Duane P Moser, Takuro Nunoura, Marike Palmer, Victor Parro, Carlos Pedrós-Alió, Alexander J Probst, Theo H M Smits, Andrew D Steen, Emma T Steenkamp, Anja Spang, Frank J Stewart, James M Tiedje, Peter Vandamme, Michael Wagner, Feng-Ping Wang, Pablo Yarza, Brian P Hedlund, Anna-Louise Reysenbach
Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature microbiology (2020)
Alexandre Almeida, Stephen Nayfach, Miguel Boland, Francesco Strozzi, Martin Beracochea, Zhou Jason Shi, Katherine S Pollard, Ekaterina Sakharova, Donovan H Parks, Philip Hugenholtz, Nicola Segata, Nikos C Kyrpides, Robert D Finn
A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature biotechnology 39 (1) (2020)
Alison E Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T Konstantinidis, Christopher E Lane, R Thane Papke, Donovan H Parks, Ramon Rossello-Mora, Matthew B Stott, Iain C Sutcliffe, J Cameron Thrash, Stephanus N Venter, William B Whitman, Silvia G Acinas, Rudolf I Amann, Karthik Anantharaman, Jean Armengaud, Brett J Baker, Roman A Barco, Helge B Bode, Eric S Boyd, Carrie L Brady, Paul Carini, Patrick S G Chain, Daniel R Colman, Kristen M DeAngelis, Maria Asuncion de Los Rios, Paulina Estrada-de Los Santos, Christopher A Dunlap, Jonathan A Eisen, David Emerson, Thijs J G Ettema, Damien Eveillard, Peter R Girguis, Ute Hentschel, James T Hollibaugh, Laura A Hug, William P Inskeep, Elena P Ivanova, Hans-Peter Klenk, Wen-Jun Li, Karen G Lloyd, Frank E Löffler, Thulani Peter Makhalanyane, Duane P Moser, Takuro Nunoura, Marike Palmer, Victor Parro, Carlos Pedrós-Alió, Alexander J Probst, Theo H M Smits, Andrew D Steen, Emma T Steenkamp, Anja Spang, Frank J Stewart, James M Tiedje, Peter Vandamme, Michael Wagner, Feng-Ping Wang, Pablo Yarza, Brian P Hedlund, Anna-Louise Reysenbach
Roadmap for naming uncultivated Archaea and Bacteria. Nature microbiology 5 (8) (2020)
Donovan H Parks, Maria Chuvochina, Pierre-Alain Chaumeil, Christian Rinke, Aaron J Mussig, Philip Hugenholtz
A complete domain-to-species taxonomy for Bacteria and Archaea. Nature biotechnology 38 (9) (2020)
Soo Jen Low, Mária Džunková, Pierre-Alain Chaumeil, Donovan H Parks, Philip Hugenholtz
Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales. Nature microbiology 4 (8) (2019)
Paul N Evans, Joel A Boyd, Andy O Leu, Ben J Woodcroft, Donovan H Parks, Philip Hugenholtz, Gene W Tyson
An evolving view of methane metabolism in the Archaea. Nature reviews. Microbiology 17 (4) (2019)
Donovan H Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J Woodcroft, Paul N Evans, Philip Hugenholtz, Gene W Tyson
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature microbiology 2 (11) (2017)
Robert M Bowers, Nikos C Kyrpides, Ramunas Stepanauskas, Miranda Harmon-Smith, Devin Doud, T B K Reddy, Frederik Schulz, Jessica Jarett, Adam R Rivers, Emiley A Eloe-Fadrosh, Susannah G Tringe, Natalia N Ivanova, Alex Copeland, Alicia Clum, Eric D Becraft, Rex R Malmstrom, Bruce Birren, Mircea Podar, Peer Bork, George M Weinstock, George M Garrity, Jeremy A Dodsworth, Shibu Yooseph, Granger G Sutton, Frank O Glöckner, Jack A Gilbert, William C Nelson, Steven J Hallam, Sean P Jungbluth, Thijs J G Ettema, Scott Tighe, Konstantinos T Konstantinidis, Wen-Tso Liu, Brett J Baker, Thomas Rattei, Jonathan A Eisen, Brian Hedlund, Katherine D McMahon, Noah Fierer, Rob Knight, Rob Finn, Guy Cochrane, Ilene Karsch-Mizrachi, Gene W Tyson, Christian Rinke, null null, Alla L Lapidus, Folker Meyer, Pelin Yilmaz, Donovan H Parks, A Murat Eren, Lynn Schriml, Jillian F Banfield, Philip Hugenholtz, Tanja Woyke
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature biotechnology 35 (8) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Donovan H Parks