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Queensland University of Technology: Brisbane, Queensland, AU

Employment
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Queensland University of Technology PURE

Education and qualifications (1)

University of Melbourne: VIC, VIC, AU

2008 to 2014 | PhD (Biochemistry)
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Ben J. Woodcroft

Works (50 of 79)

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Page 1 of 2

Aerobic hydrocarbon oxidation in a novel archaeal lineage

2025-01-22 | Preprint
Contributors: Andy Leu; Ben Woodcroft; Simon McIlroy; Gene Tyson
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Crossref

A functional microbiome catalogue crowdsourced from North American rivers

Nature
2025-01-02 | Journal article
Contributors: Mikayla A. Borton; Bridget B. McGivern; Kathryn R. Willi; Ben J. Woodcroft; Annika C. Mosier; Derick M. Singleton; Ted Bambakidis; Aaron Pelly; Rebecca A. Daly; Filipe Liu et al.
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Crossref
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Impact of storage and extraction methods on peat soil microbiomes

PeerJ
2024-12-23 | Journal article
Contributors: Dylan Cronin; Yueh-Fen Li; Paul Evans; Gene W. Tyson; Ben J. Woodcroft; Virginia I. Rich
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Crossref
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GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities

2024-12-17 | Preprint
Contributors: Pam Engelberts; Jun Ye; Donovan Parks; Eilish McMaster; Allison McInnes; Ben Woodcroft; James Volmer; Simon McIlroy; Gene Tyson
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Crossref

Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes

2024-11-25 | Preprint
Contributors: Samuel T. N. Aroney; Rhys J. P. Newell; Gene W. Tyson; Ben J. Woodcroft
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Crossref

Recovering novel genomes from the rare biosphere using Bin Chicken

2024-10-30 | Report
Contributors: Sam Aroney; Rhys Newell; Gene Tyson; Ben Woodcroft
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Crossref

Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient

Nature Microbiology
2024-10-01 | Journal article
Contributors: Viviana Freire-Zapata; Hannah Holland-Moritz; Dylan R. Cronin; Sam Aroney; Derek A. Smith; Rachel M. Wilson; Jessica G. Ernakovich; Ben J. Woodcroft; Sarah C. Bagby; Suzanne B. Hodgkins et al.
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CompareM2 is a genomes-to-report pipeline for comparing microbial genomes

2024-07-16 | Preprint
Contributors: Carl M. Kobel; Velma T. E. Aho; Ove Øyås; Niels Nørskov-Lauritsen; Ben J. Woodcroft; Phillip B. Pope
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Crossref
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Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution

The ISME Journal
2024-07-13 | Journal article | Author
SOURCE-WORK-ID:

a7b44f28-2abe-48ab-ae7e-81acc74b45e2

EID:

2-s2.0-85200342382

Contributors: Tom A. Williams; Adrian A. Davin; Lenard l. Szantho; Alexandros Stamatakis; Noah A. Wahl; Ben J. Woodcroft; Rochelle M. Soo; Laura Eme; Paul O. Sheridan; Cecile Gubry-Rangin et al.
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Queensland University of Technology PURE

Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle

Nature Microbiology
2024-06 | Journal article | Author
SOURCE-WORK-ID:

85968604-12c3-4d82-993a-7f745e82e40c

EID:

2-s2.0-85194537813

Contributors: Bridget B. McGivern; Dylan R. Cronin; Jared B Ellenbogen; Mikayla A Borton; Eleanor L Knutson; Viviana Freire-Zapata; John A Bouranis; Lukas Bernhardt; Alma I Hernandez; Rory M Flynn et al.
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Queensland University of Technology PURE

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Nature Communications
2024-06-26 | Journal article
Contributors: Marie C. Schoelmerich; Lynn Ly; Jacob West-Roberts; Ling-Dong Shi; Cong Shen; Nikhil S. Malvankar; Najwa Taib; Simonetta Gribaldo; Ben J. Woodcroft; Christopher W. Schadt et al.
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Crossref
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Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns

2024-05-17 | Preprint
Contributors: Raphael Eisenhofer; Antton Alberdi; Ben J. Woodcroft
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Crossref

Author Correction: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

Nature Methods
2024-04 | Journal article
Contributors: Alex Chklovski; Donovan H. Parks; Ben J. Woodcroft; Gene W. Tyson
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Crossref
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Methylotrophy in the Mire

mSystems
2024-01 | Journal article | Author
SOURCE-WORK-ID:

63aa3c67-aff5-4673-9a6b-1c60932d5e23

EID:

2-s2.0-85183459073

Contributors: Jared B Ellenbogen; Mikayla A. Borton; Bridget B McGivern; Dylan R. Cronin; David W Hoyt; Viviana Freire-Zapata; Carmody K. McCalley; Ruth K. Varner; Patrick M. Crill; Richard A. Wehr et al.
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Queensland University of Technology PURE
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SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data

2024-01-31 | Preprint
Contributors: Ben J. Woodcroft; Samuel T. N. Aroney; Rossen Zhao; Mitchell Cunningham; Joshua A. M. Mitchell; Linda Blackall; Gene W. Tyson
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Crossref

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

BioRxiv
2023 | Journal article
Contributors: Schoelmerich, Marie C.; Ly, Lynn; West-Roberts, Jacob; Shi, Ling-Dong; Shen, Cong; Malvankar, Nikhil S.; Taib, Najwa; Gribaldo, Simonetta; Woodcroft, Ben J.; Al-Shayeb, Christopher W. et al.
Source: check_circle
Web of Science Researcher Profile Sync

Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost

BioRxiv
2023 | Journal article
Contributors: Ellenbogen, Jared B.; Borton, Mikayla A.; McGivern, Bridget B.; Cronin, Dylan R.; Hoyt, David W.; Freire-Zapata, Viviana; McCalley, Carmody K.; Varner, Ruth K.; Crill, Patrick M.; Wehr, Richard A. et al.
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Web of Science Researcher Profile Sync

Population ecology and potential biogeochemical impacts of ssDNA and dsDNA soil viruses along a permafrost thaw gradient

BioRxiv
2023 | Journal article
Contributors: Trubl, Gareth; Roux, Simon; Borton, Mikayla A.; Varsani, Arvind; Li, Yueh-Fen; Sun, Christine; Jang, Ho Bin; Woodcroft, Ben J.; Tyson, Gene W.; Wrighton, Kelly C. et al.
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Web of Science Researcher Profile Sync

CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

Nature Methods
2023-08 | Journal article
Contributors: Alex Chklovski; Donovan H. Parks; Ben J. Woodcroft; Gene W. Tyson
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Crossref
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An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event

2023-08-11 | Preprint
Contributors: Adrián A. Davín; Ben J. Woodcroft; Rochelle M. Soo; Benoit Morel; Ranjani Murali; Dominik Schrempf; James Clark; Bastien Boussau; Edmund R. R. Moody; Lénárd L. Szánthó et al.
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Crossref
grade
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A functional microbiome catalog crowdsourced from North American rivers

2023-07-22 | Preprint
Contributors: Mikayla A. Borton; Bridget B. McGivern; Kathryn R. Willi; Ben J. Woodcroft; Annika C. Mosier; Derick M. Singleton; Ted Bambakidis; Aaron Pelly; Filipe Liu; Janaka N. Edirisinghe et al.
Source: check_circle
Crossref

Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment

Science Advances
2023-07-05 | Journal article | Author
SOURCE-WORK-ID:

c1f03620-1bed-4c6b-9b99-4e488d5e721d

EID:

2-s2.0-85163932605

Contributors: Jialin Hou; Yinzhao Wang; Pengfei Zhu; Na Yang; Lewen Liang; Tiantian Yu; Mingyang Niu; Kurt Konhauser; Ben J. Woodcroft; Fengping Wang
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Queensland University of Technology PURE
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Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated

BMC Biology
2023-03-22 | Journal article | Author
SOURCE-WORK-ID:

88d9ecc1-9b88-4399-a3a1-b23ac0e359c3

EID:

2-s2.0-85150796188

Contributors: James G Volmer; Rochelle M. Soo; Paul N. Evans; Emily C. Hoedt; Ana L Astorga Alsina; Ben J. Woodcroft; GW Tyson; Philip Hugenholtz; Mark Morrison
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Queensland University of Technology PURE
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Anaerobic methanotroph ‘Candidatus Methanoperedens nitroreducens’ has a pleomorphic life cycle

Nature Microbiology
2023-01-12 | Journal article
Contributors: Simon J. McIlroy; Andy O. Leu; Xueqin Zhang; Rhys Newell; Ben J. Woodcroft; Zhiguo Yuan; Shihu Hu; Gene W. Tyson
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Crossref
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Correction: Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota

ISME Communications
2022-12-01 | Journal article
Contributors: Jiarui Sun; Paul N Evans; Emma J Gagen; Ben J Woodcroft; Brian P Hedlund; Tanja Woyke; Philip Hugenholtz; Christian Rinke
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Crossref
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Detection of SARS-CoV-2 Variants of Concern with Tiling Amplicon Sequencing from Wastewater

ACS ES and T Water
2022-11-11 | Journal article | Author
SOURCE-WORK-ID:

bdb12f75-ba9f-4048-8a3f-457dbef2885d

EID:

2-s2.0-85135941087

Contributors: Yu Wang; Gaofeng Ni; Wei Tian; Lin Yang; Ian Hosegood; Rhys Newell; Ben J. Woodcroft; Bicheng Yang; Shihu Hu; Jianhua Guo
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Queensland University of Technology PURE
grade
Preferred source (of 2)‎

CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

2022-07-11 | Preprint
Contributors: Alex Chklovski; Donovan H. Parks; Ben J. Woodcroft; Gene W. Tyson
Source: check_circle
Crossref
grade
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Plant organic matter inputs exert a strong control on soil organic matter decomposition in a thawing permafrost peatland

Science of the Total Environment
2022-05-10 | Journal article | Author
SOURCE-WORK-ID:

bbc5e622-b0cd-45d2-9655-61c14b3d7d22

EID:

2-s2.0-85123711364

Contributors: Rachel M. Wilson; Moira A. Hough; Brittany A. Verbeke; Suzanne B. Hodgkins; GW Tyson; Matthew B. Sullivan; Eoin Brodie; William J. Riley; Ben J. Woodcroft; Carmody McCalley et al.
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Queensland University of Technology PURE
grade
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Coupling plant litter quantity to a novel metric for litter quality explains C storage changes in a thawing permafrost peatland

Global Change Biology
2022-02 | Journal article | Author
SOURCE-WORK-ID:

db23f7bf-1ff2-44ee-bc5d-5fd1e45982d1

EID:

2-s2.0-85123389539

Contributors: Moira Hough; Samantha McCabe; S. Rose Vining; Emily Pickering Pedersen; Rachel M. Wilson; Ryan Lawrence; Kuang Yu Chang; Gil Bohrer; William J. Riley; Patrick M. Crill et al.
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Queensland University of Technology PURE

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years

Microbiome
2021-12 | Journal article | Author
SOURCE-WORK-ID:

18da223b-fb32-4501-8bc1-8d2e63847a8a

EID:

2-s2.0-85116467756

Contributors: Yulin Wang; Jun Ye; Feng Ju; Lei Liu; Joel A Boyd; Yu Deng; Donovan H Parks; Xiaotao Jiang; Xiaole Yin; Ben J. Woodcroft et al.
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Queensland University of Technology PURE
grade
Preferred source (of 2)‎

Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes

Nature Communications
2021-12-01 | Journal article | Author
SOURCE-WORK-ID:

8fc16c05-40e9-433e-b67b-e94745c019a8

EID:

2-s2.0-85116373672

Contributors: Joanne B. Emerson; Ruth K Varner; Martin Wik; Donovan H Parks; Rebecca B Neumann; Joel E Johnson; Caitlin M Singleton; Ben J. Woodcroft; Rodney Tollerson; Akosua Owusu-Dommey et al.
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Queensland University of Technology PURE
grade
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Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages

ISME Communications
2021-06-28 | Journal article | Author
SOURCE-WORK-ID:

6162cd53-1453-4cec-8dde-2aa12af0a791

Contributors: Jiarui Sun; Paul N. Evans; Emma J. Gagen; Ben J. Woodcroft; Brian P. Hedlund; Tanja Woyke; Philip HugenHoltz; Christian Rinke
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Queensland University of Technology PURE
grade
Preferred source (of 2)‎

A genomic catalog of Earth's microbiomes

Nature Biotechnology
2021-04 | Journal article
SOURCE-WORK-ID:

f62139ae-3a58-465b-a2de-eb2fe260efc6

EID:

2-s2.0-85095709328

Contributors: Stephen Nayfach; Simon Roux; Rekha Seshadri; Daniel Udwary; Neha Varghese; Frederik Schulz; Dongying Wu; David Paez-Espino; I. Min Chen; Marcel Huntemann et al.
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Queensland University of Technology PURE

Author Correction

Nature Biotechnology
2021-04 | Journal article
SOURCE-WORK-ID:

a3174fb8-ebb1-451a-a980-8a83b4fff5a1

EID:

2-s2.0-85103599785

Contributors: Stephen Nayfach; Simon Roux; Rekha Seshadri; Daniel Udwary; Neha Varghese; Frederik Schulz; Dongying Wu; David Paez-Espino; I. Min Chen; Marcel Huntemann et al.
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Queensland University of Technology PURE

Publisher Correction

Nature Biotechnology
2021-04 | Other
SOURCE-WORK-ID:

3b89fb50-ceca-43f3-813b-83c507844d5a

EID:

2-s2.0-85104275811

Contributors: Stephen Nayfach; Simon Roux; Rekha Seshadri; Daniel Udwary; Neha Varghese; Frederik Schulz; Dongying Wu; David Paez-Espino; I. Min Chen; Marcel Huntemann et al.
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Queensland University of Technology PURE

Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation

PLoS ONE
2021-02 | Journal article | Author
SOURCE-WORK-ID:

d7608b1d-23ea-466c-bf22-093f2c9816fb

EID:

2-s2.0-85102095774

Contributors: R. M. Wilson; A. A. Zayed; K. B. Crossen; Ben J. Woodcroft; M. M. Tfaily; J. Emerson; N. Raab; S. B. Hodgkins; B. Verbeke; GW Tyson et al.
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Queensland University of Technology PURE
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Recoding enhances the metabolic capabilities of two novel methylotrophic Asgardarchaeota lineages

2021-02-19 | Preprint
Contributors: Jiarui Sun; Paul N. Evans; Emma J. Gagen; Ben J. Woodcroft; Brian P. Hedlund; Tanja Woyke; Philip Hugenholtz; Christian Rinke
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Crossref
grade
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The IsoGenie database

PeerJ
2020 | Journal article | Author
SOURCE-WORK-ID:

e2097986-eeed-4ad1-b19c-6a128a676a40

EID:

2-s2.0-85090471114

Contributors: Benjamin Bolduc; Suzanne B. Hodgkins; Ruth K. Varner; Patrick M. Crill; Carmody K. McCalley; Jeffrey P. Chanton; GW Tyson; William J. Riley; Michael Palace; Melissa B. Duhaime et al.
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Queensland University of Technology PURE

Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution

Nature Communications
2020-08-07 | Journal article
Contributors: Nina Dombrowski; Tom A. Williams; Jiarui Sun; Benjamin J. Woodcroft; Jun-Hoe Lee; Bui Quang Minh; Christian Rinke; Anja Spang
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Crossref
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Undinarchaeota illuminate the evolution of DPANN archaea

2020-03-05 | Preprint
Contributors: Nina Dombrowski; Tom A. Williams; Jiarui Sun; Benjamin J. Woodcroft; Jun-Hoe Lee; Bui Quang Minh; Christian Rinke; Anja Spang
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Crossref

Diverse Arctic lake sediment microbiota shape methane emission temperature sensitivity.

2020-02-10 | Preprint | Author
SOURCE-WORK-ID:

89b0260c-e2f5-4067-88f2-e9aaf3e9c5ce

Contributors: Ben J. Woodcroft; Joanne B. Emerson; Ruth K. Varner; Martin Wik; Donovan H. Parks; Rebecca B. Neumann; Joel E. Johnson; Caitlin M. Singleton; Rodney Tollerson; Akosua Owusu-Dommey et al.
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Queensland University of Technology PURE

Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases

Molecular Biology and Evolution
2019-08 | Journal article
Part of ISSN: 0737-4038
Contributors: Anurag Priyam; Ben J Woodcroft; Vivek Rai; Ismail Moghul; Alekhya Munagala; Filip Ter; Hiten Chowdhary; Iwo Pieniak; Lawrence J Maynard; Mark Anthony Gibbins et al.
Source: Self-asserted source
Ben J. Woodcroft via Crossref Metadata Search
grade
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Microbial Community Analyses Inform Geochemical Reaction Network Models for Predicting Pathways of Greenhouse Gas Production

Frontiers in Earth Science
2019-03 | Journal article
Part of ISSN: 2296-6463
Contributors: Rachel M. Wilson; Rebecca B. Neumann; Kelsey B. Crossen; Nicole M. Raab; Suzanne B. Hodgkins; Scott R. Saleska; Ben Bolduc; Ben J. Woodcroft; Gene W. Tyson; Jeffrey P. Chanton et al.
Source: Self-asserted source
Ben J. Woodcroft via Crossref Metadata Search
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An evolving view of methane metabolism in the Archaea

Nature Reviews Microbiology
2019-01 | Journal article
Part of ISSN: 1740-1526
Contributors: Paul N. Evans; Joel A. Boyd; Andy O. Leu; Ben J. Woodcroft; Donovan H. Parks; Philip Hugenholtz; Gene W. Tyson
Source: Self-asserted source
Ben J. Woodcroft via Crossref Metadata Search
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Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

The ISME Journal
2019-01 | Journal article
Part of ISSN: 1751-7362
Contributors: Joel A. Boyd; Sean P. Jungbluth; Andy O. Leu; Paul N. Evans; Ben J. Woodcroft; Grayson L. Chadwick; Victoria J. Orphan; Jan P. Amend; Michael S. Rappé; Gene W. Tyson
Source: Self-asserted source
Ben J. Woodcroft via Crossref Metadata Search
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Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Nature Microbiology
2018 | Journal article | Author
SOURCE-WORK-ID:

36d74099-09bb-44dc-aadb-cc257e0f8c0a

WOSUID:

000422987500019

EID:

2-s2.0-85040978777

Contributors: Donovan H. Parks; Christian Rinke; Maria Chuvochina; Pierre-Alain Chaumeil; Ben J. Woodcroft; Paul N. Evans; Philip Hugenholtz; GW Tyson
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Queensland University of Technology PURE
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Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov.

Systematic and Applied Microbiology
2018 | Journal article
Part of ISSN: 0723-2020
Contributors: Miguel A. Martinez; Ben J. Woodcroft; Julio C. Ignacio Espinoza; Ahmed A. Zayed; Caitlin M. Singleton; Joel A. Boyd; Yueh-Fen Li; Samuel Purvine; Heather Maughan; Suzanne B. Hodgkins et al.
Source: Self-asserted source
Ben J. Woodcroft via Crossref Metadata Search
grade
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Methanotrophy across a natural permafrost thaw environment

The ISME Journal
2018-10 | Journal article
Contributors: Caitlin M Singleton; Carmody K McCalley; Ben J Woodcroft; Joel A Boyd; Paul N Evans; Suzanne B Hodgkins; Jeffrey P Chanton; Steve Frolking; Patrick M Crill; Scott R Saleska et al.
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Crossref
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Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

mSystems
2018-10-02 | Journal article
Part of ISSN: 2379-5077
Contributors: Gareth Trubl; Ho Bin Jang; Simon Roux; Joanne B. Emerson; Natalie Solonenko; Dean R. Vik; Lindsey Solden; Jared Ellenbogen; Alexander T. Runyon; Benjamin Bolduc et al.
Source: Self-asserted source
Ben J. Woodcroft via Crossref Metadata Search
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Genome-centric view of carbon processing in thawing permafrost

Nature
2018-07 | Journal article
Part of ISSN: 0028-0836
Contributors: Ben J. Woodcroft; Caitlin M. Singleton; Joel A. Boyd; Paul N. Evans; Joanne B. Emerson; Ahmed A. F. Zayed; Robert D. Hoelzle; Timothy O. Lamberton; Carmody K. McCalley; Suzanne B. Hodgkins et al.
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Ben J. Woodcroft via Crossref Metadata Search
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Peer review (11 reviews for 6 publications/grants)

Review activity for Cell reports. (2)
Review activity for Chemosphere. (1)
Review activity for Nature (1)
Review activity for Nature biotechnology. (2)
Review activity for Nature communications (4)
Review activity for PloS one. (1)