Dr Benjamin Woodcroft

ARC DECRA

School of Chemistry and Molecular Biosciences
Faculty of Science
b.woodcroft@uq.edu.au
+61 7 336 54957

Overview

Qualifications

  • Doctor of Philosophy, University of Melbourne

Publications

  • Woodcroft, Ben J., Singleton, Caitlin M., Boyd, Joel A., Evans, Paul N., Emerson, Joanne B., Zayed, Ahmed A. F., Hoelzle, Robert D., Lamberton, Timothy O., McCalley, Carmody K., Hodgkins, Suzanne B., Wilson, Rachel M., Purvine, Samuel O., Nicora, Carrie D., Li, Changsheng, Frolking, Steve, Chanton, Jeffrey P., Crill, Patrick M., Saleska, Scott R., Rich, Virginia I. and Tyson, Gene W. (2018) Genome-centric view of carbon processing in thawing permafrost. Nature, . doi:10.1038/s41586-018-0338-1

  • Emerson, Joanne B., Roux, Simon, Brum, Jennifer R., Bolduc, Benjamin, Woodcroft, Ben J., Jang, Ho Bin, Singleton, Caitlin M., Solden, Lindsey M., Naas, Adrian E., Boyd, Joel A., Hodgkins, Suzanne B., Wilson, Rachel M., Trubl, Gareth, Li, Changsheng, Frolking, Steve, Pope, Phillip B., Wrighton, Kelly C., Crill, Patrick M., Chanton, Jeffrey P., Saleska, Scott R., Tyson, Gene W., Rich, Virginia I. and Sullivan, Matthew B. (2018) Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology, . doi:10.1038/s41564-018-0190-y

  • Singleton, Caitlin M., McCalley, Carmody K., Woodcroft, Ben J., Boyd, Joel A., Evans, Paul N., Hodgkins, Suzanne B., Chanton, Jeffrey P., Frolking, Steve, Crill, Patrick M., Saleska, Scott R., Rich, Virginia I. and Tyson, Gene W. (2018) Methanotrophy across a natural permafrost thaw environment. The ISME journal, . doi:10.1038/s41396-018-0065-5

View all Publications

Grants

View all Grants

Supervision

  • Doctor Philosophy

  • Doctor Philosophy

  • Doctor Philosophy

View all Supervision

Publications

Journal Article

  • Woodcroft, Ben J., Singleton, Caitlin M., Boyd, Joel A., Evans, Paul N., Emerson, Joanne B., Zayed, Ahmed A. F., Hoelzle, Robert D., Lamberton, Timothy O., McCalley, Carmody K., Hodgkins, Suzanne B., Wilson, Rachel M., Purvine, Samuel O., Nicora, Carrie D., Li, Changsheng, Frolking, Steve, Chanton, Jeffrey P., Crill, Patrick M., Saleska, Scott R., Rich, Virginia I. and Tyson, Gene W. (2018) Genome-centric view of carbon processing in thawing permafrost. Nature, . doi:10.1038/s41586-018-0338-1

  • Emerson, Joanne B., Roux, Simon, Brum, Jennifer R., Bolduc, Benjamin, Woodcroft, Ben J., Jang, Ho Bin, Singleton, Caitlin M., Solden, Lindsey M., Naas, Adrian E., Boyd, Joel A., Hodgkins, Suzanne B., Wilson, Rachel M., Trubl, Gareth, Li, Changsheng, Frolking, Steve, Pope, Phillip B., Wrighton, Kelly C., Crill, Patrick M., Chanton, Jeffrey P., Saleska, Scott R., Tyson, Gene W., Rich, Virginia I. and Sullivan, Matthew B. (2018) Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology, . doi:10.1038/s41564-018-0190-y

  • Singleton, Caitlin M., McCalley, Carmody K., Woodcroft, Ben J., Boyd, Joel A., Evans, Paul N., Hodgkins, Suzanne B., Chanton, Jeffrey P., Frolking, Steve, Crill, Patrick M., Saleska, Scott R., Rich, Virginia I. and Tyson, Gene W. (2018) Methanotrophy across a natural permafrost thaw environment. The ISME journal, . doi:10.1038/s41396-018-0065-5

  • Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip and Tyson, Gene W. (2017) Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 2 11: 1533-1542. doi:10.1038/s41564-017-0012-7

  • Vanwonterghem, Inka, Evans, Paul N., Parks, Donovan H., Jensen, Paul D., Woodcroft, Ben J., Hugenholtz, Philip and Tyson, Gene W. (2016) Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology, 1 16170: 16170. doi:10.1038/nmicrobiol.2016.170

  • Rinke, Christian, Low, Serene, Woodcroft, Ben J., Raina, Jean-Baptista, Skarshewski, Adam, Le, Xuyen H., Butler, Margaret K., Stocker, Roman, Seymour, Justin, Tyson, Gene W. and Hugenholtz, Philip (2016) Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ, 4 9: 1-28. doi:10.7717/peerj.2486

  • McDougall, Carmel, Woodcroft, Ben J. and Degnan, Bernard M. (2016) The widespread prevalence and functional significance of silk-like structural proteins in metazoan biological materials. PLoS ONE, 11 7: . doi:10.1371/journal.pone.0159128

  • Woodcroft, Ben J., Boyd, Joel A. and Tyson, Gene W. (2016) OrfM: a fast open reading frame predictor for metagenomic data. Bioinformatics, 32 17: 2702-2703. doi:10.1093/bioinformatics/btw241

  • Kao-Kniffin, J., Woodcroft, B.J., Carver, S.M., Bockheim J.G., Handelsman, J., Tyson, G.W., Hinkel, K.M. and Mueller, C.W. (2015) Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic Alaska. Scientific Reports, 5 . doi:10.1038/srep18165

  • Soo, Rochelle M., Woodcroft, Ben J., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2015) Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.. PeerJ, 2015 5: Art. No.: e968-Art. No.: e968. doi:10.7717/peerj.968

  • McCalley, Carmody K., Woodcroft, Ben J., Hodgkins, Suzanne B., Wehr, Richard A., Kim, Eun-Hae, Mondav, Rhiannon, Crill, Patrick M., Chanton, Jeffrey P., Rich, Virginia I., Tyson, Gene W. and Saleska, Scott R. (2014) Methane dynamics regulated by microbial community response to permafrost thaw. Nature, 514 7523: 478-481. doi:10.1038/nature13798

  • Imelfort, Michael, Parks, Donovan, Woodcroft, Ben J., Dennis, Paul, Hugenholtz, Philip and Tyson, Gene W. (2014) GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ, 2014 1: 1-16. doi:10.7717/peerj.603

  • Mondav, Rhiannon, Woodcroft, Ben J., Kim, Eun-Hae, McCalley, Carmody K., Hodgkins, Suzanne B., Crill, Patrick M., Chanton, Jeffrey, Hurst, Gregory B., VerBerkmoes, Nathan C., Saleska, Scott R., Hugenholtz, Philip, Rich, Virginia I. and Tyson, Gene W. (2014) Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications, 5 1: 3212.1-3212.7. doi:10.1038/ncomms4212

  • York, Patrick S., Cummins, Scott F., Degnan, Sandie M., Woodcroft, Ben J. and Degnan, Bernard M. (2012) Marked changes in neuropeptide expression accompany broadcast spawnings in the gastropod Haliotis asinina. Frontiers in Zoology, 9 1: 9.1-9.16. doi:10.1186/1742-9994-9-9

  • Erpenbeck, D., Voigt, O., Adamski, M., Woodcroft, B. J., Hooper, J. N. A., Worheide, G. and Degnan, B. M. (2011) NUMTs in the sponge genome reveal conserved transposition mechanisms in metazoans. Molecular Biology and Evolution, 28 1: 1-5. doi:10.1093/molbev/msq217

  • Srivastava, Mansi, Simakov, Oleg, Chapman, Jarrod, Fahey, Bryony, Gauthier, Marie E. A., Mitros, Therese, Richards, Gemma S., Conaco, Cecilia, Dacre, Michael, Hellsten, Uffe, Larroux, Claire, Putnam, Nicholas H., Stanke, Mario, Adamska, Maja, Darling, Aaron, Degnan, Sandie M., Oakley, Todd H., Plachetzki, David C., Zhai, Yufeng F., Adamski, Marcin, Calcino, Andrew, Cummins, Scott F., Goodstein, David M., Harris, Christina, Jackson, Daniel J., Leys, Sally P., Shu, Shengqiang Q., Woodcroft, Ben J., Vervoort, Michel, Kosik, Kenneth S., Manning, Gerard, Degnan, Bernard M. and Rokhsar, Daniel S. (2010) The Amphimedon queenslandica genome and the evolution of animal complexity. Nature, 466 7307: 720-726. doi:10.1038/nature09201

  • Jackson, Daniel J., McDougall, Carmel, Woodcroft, Ben, Moase, Patrick, Rose, Robert A., Kube, Michael, Reinhardt, Richard, Rokhsar, Daniel S., Montagnani, Caroline, Joubert, Caroline, Piquemal, David and Degnan, Bernard M. (2010) Parallel evolution of nacre building gene sets in molluscs. Molecular Biology and Evolution, 27 3: 591-608. doi:10.1093/molbev/msp278

  • Woodcroft, B. J., Hammond, L, Stow, J. L. and Hamilton, N. A. (2009) Automated organelle-based colocalization in whole-cell imaging. Cytometry Part A, 75A 11: 941-950. doi:10.1002/cyto.a.20786

  • Williams, Elizabeth A., Degnan, Bernard M., Gunter, Helen, Jackson, Daniel J., Woodcroft, Ben J. and Degnan, Sandie M. (2009) Widespread transcriptional changes pre-empt the critical pelagic–benthic transition in the vetigastropod Haliotis asinina. Molecular Ecology, 18 5: 1006-1025. doi:10.1111/j.1365-294X.2008.04078.x

  • Grimson, A., Srivastava, M., Fahey, B., Woodcroft, B., Chiang, H.R., King, N., Degnan, B.M., Rokhsar, D.S. and Bartel, D.P. (2008) Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature, 455 7217: 1193-1197. doi:10.1038/nature07415

  • Fahey, B., Larroux, C., Woodcroft, B. and Degnan, B.M. (2008) Does the high gene density in the Sponge NK Homeobox gene cluster reflect limited regulatory capacity?. Biological Bulletin, 214 3: 205-217. doi:10.2307/25470664

Conference Publication

  • York, Patrick S., Cummins, Scott F., Degnan, Sandie M., Woodcroft, Ben J. and Degnan, Bernard M. (2010). Identification of genes differentially expressed in the ganglia of growing haliotis asinina. In: Peter A. Cook, Journal of Shellfish Research. 7th International Symposium on Abalone Biology, Fisheries and Culture, Pattaya, Thailand, (741-752). 19-24 July 2009. doi:10.2983/035.029.0328

Grants (Administered at UQ)

PhD and MPhil Supervision

Current Supervision

  • Doctor Philosophy — Principal Advisor

  • Doctor Philosophy — Associate Advisor

    Other advisors:

  • Doctor Philosophy — Associate Advisor

    Other advisors: