Ben Woodcroft

Modern studies of microbial ecology are often data-heavy since they involve the study of microbes in the context of their microbial community. Public databases hold ~1Pbp (1015 base pairs) of high quality shotgun metagenomic data, representing weird and wonderful communities from across the planet. Bioinformatics provides the statistical analysis, data science-based approaches and scalable computational toolsets necessary to study the structure and function of microbiomes.

The computational microbiology group at CMR, led by Dr Ben Woodcroft, aims to advance the science of microbial bioinformatics by developing widely applicable algorithms. Implementations of these are usually named after iconic Australian birds. Current specific areas of interest include strain-level resolution of microbial community dynamics, soil microbial ecology, genome recovery from metagenomes, symbiosis prediction, phylogenetics and the re-use of public shotgun metagenomic datasets. There are usually openings for perspective students at all levels, so if you are interested in our work then please feel free to reach out via email.

Ben has the happy knack of enjoying most things but gravitates towards the development and application of bioinformatic techniques to study the microbial communities that drive the health of our planet. He has attracted funding totalling AUD$15m, currently holds an ARC Future fellowship and has published >200 free software projects.

Contact

+61 7 3443 7334

b.woodcroft@qut.edu.au

Project themes

Selected publications

A full list of publications can be found at Google scholar. or through  ORCID. * indicates equal contribution.

  1. Ben J. Woodcroft*, Caitlin M. Singleton*, Joel A. Boyd, Paul N. Evans & Joanne B. Emerson et al. 2018, ‘Genome-centric view of carbon processing in thawing permafrost’, Nature, vol. 560, no. 7716, pp. 49–54, doi:10.1038/s41586-018-0338-1
  2. Rhiannon Mondav*, Ben J. Woodcroft*, Eun-Hae Kim, Carmody K. McCalley & Suzanne B. Hodgkins et al. 2014, ‘Discovery of a novel methanogen prevalent in thawing permafrost’, Nature Communications, vol. 5, no. 1, doi:10.1038/ncomms4212
  3. Carmody K. McCalley, Ben J. Woodcroft, Suzanne B. Hodgkins, Richard A. Wehr & Eun-Hae Kim et al. 2014, ‘Methane dynamics regulated by microbial community response to permafrost thaw’, Nature, vol. 514, no. 7523, pp. 478–481, doi:10.1038/nature13798
  4. Donovan H. Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil & Ben J. Woodcroft et al. 2017, ‘Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life’, Nature Microbiology, vol. 2, no. 11, pp. 1533–1542, doi:10.1038/s41564-017-0012-7
  5. Sophie C Oehring*, Ben J Woodcroft*, Suzette Moes, Johanna Wetzel & Olivier Dietz et al. 2012, ‘Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum’, Genome Biology, vol. 13, no. 11, pp. R108, doi:10.1186/gb-2012-13-11-r108
  6. Michael Imelfort, Donovan Parks, Ben J. Woodcroft, Paul Dennis & Philip Hugenholtz et al. 2014, ‘GroopM: an automated tool for the recovery of population genomes from related metagenomes’, PeerJ, vol. 2, pp. e603, doi:10.7717/peerj.603
  7. Caitlin M Singleton, Carmody K McCalley, Ben J Woodcroft, Joel A Boyd & Paul N Evans et al. 2018, ‘Methanotrophy across a natural permafrost thaw environment’, The ISME Journal, doi:10.1038/s41396-018-0065-5
  8. Inka Vanwonterghem, Paul N. Evans, Donovan H. Parks, Paul D. Jensen & Ben J. Woodcroft et al. 2016, ‘Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota’, Nature Microbiology, vol. 1, no. 12, doi:10.1038/nmicrobiol.2016.170
  9. Joel A Boyd*, Ben J Woodcroft* & Gene W Tyson 2018, ‘GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes’, Nucleic Acids Research, vol. 46, no. 10, pp. e59–e59, doi:10.1093/nar/gky174
  10. Joel A. Boyd, Sean P. Jungbluth, Andy O. Leu, Paul N. Evans & Ben J. Woodcroft et al. 2019, ‘Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi’, The ISME Journal, doi:10.1038/s41396-018-0343-2