Donovan H. Parks - Publications, H-index & Citations

Donovan H. Parks

University of Queensland

57H指数

147论文数

7.1W被引数

收录论文 45

发表时间

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes GTDB release 10：一套完整的系统分类系统，用于715 230个细菌基因组及17 245个古菌基因组

NUCLEIC ACIDS RESEARCH

IF13.1

2025-10-01

PREAI

Parks, Donovan H.; Chaumeil, Pierre-Alain; Mussig, Aaron J.; Rinke, Christian; Chuvochina, Maria; Hugenholtz, Philip

GenomeFISH: genome-based fluorescence in situ hybridization for strain-level visualization of microbial communities GenomeFISH：基于基因组的荧光原位杂交技术，用于菌株水平微生物群落的可视化

The ISME Journal

IF0

2025-07-07

OAAI

J Pamela Engelberts; Jun Ye; Donovan H Parks; Eilish S McMaster; Allison S McInnes; Ben J Woodcroft; James G Volmer; Simon J McIlroy; Gene W Tyson

Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens 宏基因组学: 胃肠道病原体常规病理学检测的新领域

GUT PATHOGENS

IF4

2025-01-18

OAAI

Angel, Nicola Z.; Sullivan, Mitchell J.; Alsheikh-Hussain, Areej; Fang, Liang; Macdonald, Samantha; Pribyl, Alena; Wills, Blake; Tyson, Gene W.; Hugenholtz, Philip; Parks, Donovan H.; Griffin, Paul; Wood, David L. A.

Putative genome contamination has minimal impact on the GTDB taxonomy 推定的基因组污染对GTDB分类学的影响最小

MICROBIAL GENOMICS

IF4

2024-05-29

OAAI

Mussig, Aaron J.; Chaumeil, Pierre - Alain; Chuvochina, Maria; Rinke, Christian; Parks, Donovan H.; Hugenholtz, Philip

AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods

BRIEFINGS IN BIOINFORMATICS

IF7.7

2024-05-14

OAAI

Wei, Xin; Tan, Huagang; Lobb, Briallen; Zhen, William; Wu, Zijing; Parks, Donovan H.; Neufeld, Josh D.; Moreno-Hagelsieb, Gabriel; Doxey, Andrew C.

CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning (vol 20, pg 1203, 2023)

NATURE METHODS

IF32.1

2024-03-21

OAAI

Chklovski, Alex; Parks, Donovan H.; Woodcroft, Ben J.; Tyson, Gene W.

Greengenes2 unifies microbial data in a single reference tree (Jul, 10.1038/s41587-023-01845-1, 2023)Greengenes2将微生物数据统一在一个参考树中 (7月，10.1038/s41587-023-01845-1，2023)

NATURE BIOTECHNOLOGY

IF41.7

2023-10-18

OAAI

McDonald, Daniel; Jiang, Yueyu; Balaban, Metin; Cantrell, Kalen; Zhu, Qiyun; Gonzalez, Antonio; Morton, James T.; Nicolaou, Giorgia; Parks, Donovan H.; Karst, Soren M.; Albertsen, Mads; Hugenholtz, Philip; DeSantis, Todd; Song, Se Jin; Bartko, Andrew; Havulinna, Aki S.; Jousilahti, Pekka; Cheng, Susan; Inouye, Michael; Niiranen, Teemu; Jain, Mohit; Salomaa, Veikko; Lahti, Leo; Mirarab, Siavash; Knight, Rob

Greengenes2 unifies microbial data in a single reference tree Greengenes2将微生物数据统一在一个参考树中

NATURE BIOTECHNOLOGY

IF41.7

2023-07-27

OAAI

McDonald, Daniel; Jiang, Yueyu; Balaban, Metin; Cantrell, Kalen; Zhu, Qiyun; Gonzalez, Antonio; Morton, James T. T.; Nicolaou, Giorgia; Parks, Donovan H. H.; Karst, Soren M.; Albertsen, Mads; Hugenholtz, Philip; DeSantis, Todd; Song, Se Jin; Bartko, Andrew; Havulinna, Aki S. S.; Jousilahti, Pekka; Cheng, Susan; Inouye, Michael; Niiranen, Teemu; Jain, Mohit; Salomaa, Veikko; Lahti, Leo; Mirarab, Siavash; Knight, Rob

CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning CheckM2: 使用机器学习评估微生物基因组质量的快速，可扩展和准确的工具

NATURE METHODS

IF32.1

2023-07-27

202

OAAI

Chklovski, Alex; Parks, Donovan H.; Woodcroft, Ben J. J.; Tyson, Gene W.

Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type SeqCode的开发: 以DNA序列为类型的未培养原核生物的拟议命名代码

SYSTEMATIC AND APPLIED MICROBIOLOGY

IF4.2

2022-09-01

OAAI

Whitman, William B.; Chuvochina, Maria; Hedlund, Brian P.; Hugenholtz, Philip; Konstantinidis, Konstantinos T.; Murray, Alison E.; Palmer, Marike; Parks, Donovan H.; Probst, Alexander J.; Reysenbach, Anna-Louise; Rodriguez-R, Luis M.; Rossello-Mora, Ramon; Sutcliffe, Iain; Venter, Stephanus N.

Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean

ISME JOURNAL

IF10

2022-08-01

OAAI

Hallstrom, Soren; Raina, Jean-Baptiste; Ostrowski, Martin; Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip; Stocker, Roman; Seymour, Justin R.; Riemann, Lasse

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years 盐活性污泥微生物群落超过9年的演替动力学和替代稳定状态

MICROBIOME

IF12.7

2021-10-06

OAAI

Wang, Yulin; Ye, Jun; Ju, Feng; Liu, Lei; Boyd, Joel A.; Deng, Yu; Parks, Donovan H.; Jiang, Xiaotao; Yin, Xiaole; Woodcroft, Ben J.; Tyson, Gene W.; Hugenholtz, Philip; Polz, Martin F.; Zhang, Tong

Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes 北极湖泊中不同的沉积物微生物群形状的甲烷排放温度敏感性

NATURE COMMUNICATIONS

IF15.7

2021-10-05

OAAI

Emerson, Joanne B.; Varner, Ruth K.; Wik, Martin; Parks, Donovan H.; Neumann, Rebecca B.; Johnson, Joel E.; Singleton, Caitlin M.; Woodcroft, Ben J.; Tollerson, Rodney, II; Owusu-Dommey, Akosua; Binder, Morgan; Freitas, Nancy L.; Crill, Patrick M.; Saleska, Scott R.; Tyson, Gene W.; Rich, Virginia I.

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy GTDB: 通过系统发育一致，等级标准化和基于完整基因组的分类学对细菌和古细菌多样性进行的普查

NUCLEIC ACIDS RESEARCH

IF13.1

2021-09-14

783

OAAI

Parks, Donovan H.; Chuvochina, Maria; Rinke, Christian; Mussig, Aaron J.; Chaumeil, Pierre-Alain; Hugenholtz, Philip

Critical evaluation of faecal microbiome preservation using metagenomic analysis

ISME COMMUNICATIONS

IF6.1

2021-05-05

OAAI

Pribyl, Alena L.; Parks, Donovan H.; Angel, Nicola Z.; Boyd, Joel A.; Hasson, Alexander G.; Fang, Liang; MacDonald, Samantha L.; Wills, Blake A.; Wood, David L. A.; Krause, Lutz; Tyson, Gene W.; Hugenholtz, Philip

Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome 对来自人类肠道微生物组的宏基因组数据集进行分类分析的Microba社区分析器的评估

FRONTIERS IN MICROBIOLOGY

IF4.5

2021-04-20

OAAI

Parks, Donovan H.; Rigato, Fabio; Vera-Wolf, Patricia; Krause, Lutz; Hugenholtz, Philip; Tyson, Gene W.; Wood, David L. A.

Prokaryotic taxonomy and nomenclature in the age of big sequence data

ISME JOURNAL

IF10

2021-04-06

106

OAAI

Hugenholtz, Philip; Chuvochina, Maria; Oren, Aharon; Parks, Donovan H.; Soo, Rochelle M.

A unified catalog of 204,938 reference genomes from the human gut microbiome 来自人类肠道微生物组的204,938参考基因组的统一目录

NATURE BIOTECHNOLOGY

IF41.7

2020-07-20

637

OAAI

Almeida, Alexandre; Nayfach, Stephen; Boland, Miguel; Strozzi, Francesco; Beracochea, Martin; Shi, Zhou Jason; Pollard, Katherine S.; Sakharova, Ekaterina; Parks, Donovan H.; Hugenholtz, Philip; Segata, Nicola; Kyrpides, Nikos C.; Finn, Robert D.

Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae

MBIO

IF4.7

2020-06-30

OAAI

Leu, Andy O.; McIlroy, Simon J.; Ye, Jun; Parks, Donovan H.; Orphan, Victoria J.; Tyson, Gene W.

A complete domain-to-species taxonomy for Bacteria and Archaea (vol 58, pg 561, 2020)

NATURE BIOTECHNOLOGY

IF41.7

2020-05-04

OAAI

Parks, Donovan H.; Chuvochina, Maria; Chaumeil, Pierre-Alain; Rinke, Christian; Mussig, Aaron J.; Hugenholtz, Philip

研究方向