Journal Articles
Chklovski, Alex, Parks, Donovan H., Woodcroft, Ben J. and Tyson, Gene W. (2024). Author Correction: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 21 (4), 735-735. doi: 10.1038/s41592-024-02248-z
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., Chanton, Jeffrey P., Woodcroft, Ben J., Tfaily, Malak M., Tyson, Gene W., Rich, Virginia I. and Wrighton, Kelly C. (2023). Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost. Msystems, 9 (1), e0069823. doi: 10.1128/msystems.00698-23
Chklovski, Alex, Parks, Donovan H., Woodcroft, Ben J. and Tyson, Gene W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20 (8), 1203-1212. doi: 10.1038/s41592-023-01940-w
Volmer, James G., Soo, Rochelle M., Evans, Paul N., Hoedt, Emily C., Astorga Alsina, Ana L., Woodcroft, Benjamin J., Tyson, Gene W., Hugenholtz, Philip and Morrison, Mark (2023). Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated. BMC Biology, 21 (1) 59, 1-17. doi: 10.1186/s12915-023-01524-2
McIlroy, Simon J., Leu, Andy O., Zhang, Xueqin, Newell, Rhys, Woodcroft, Ben J., Yuan, Zhiguo, Hu, Shihu and Tyson, Gene W. (2023). Anaerobic methanotroph ‘Candidatus Methanoperedens nitroreducens’ has a pleomorphic life cycle. Nature Microbiology, 8 (2), 321-331. doi: 10.1038/s41564-022-01292-9
Wang, Yu, Ni, Gaofeng, Tian, Wei, Yang, Lin, Hosegood, Ian, Newell, Rhys, Woodcroft, Ben J., Yang, Bicheng, Hu, Shihu and Guo, Jianhua (2022). Detection of SARS-CoV-2 variants of concern with tiling amplicon sequencing from wastewater. ACS ES and T Water, 2 (11), 2185-2193. doi: 10.1021/acsestwater.2c00083
Wilson, Rachel M., Hough, Moira A., Verbeke, Brittany A., Hodgkins, Suzanne B., Tyson, Gene, Sullivan, Matthew B., Brodie, Eoin, Riley, William J., Woodcroft, Ben, McCalley, Carmody, Dominguez, Sky C., Crill, Patrick M., Varner, Ruth K., Frolking, Steve, Cooper, William T., Chanton, Jeff P., Saleska, Scott D., Rich, Virginia I. and Tfaily, Malak M. (2022). Plant organic matter inputs exert a strong control on soil organic matter decomposition in a thawing permafrost peatland. Science of the Total Environment, 820 152757, 152757. doi: 10.1016/j.scitotenv.2021.152757
Sun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2022). Correction: Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota. ISME Communications, 2 (1) 6, 6. doi: 10.1038/s43705-021-00048-6
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. and Zhang, Tong (2021). Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years. Microbiome, 9 (1) 199, 199. doi: 10.1186/s40168-021-01151-5
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, Owusu-Dommey, Akosua, Binder, Morgan, Freitas, Nancy L., Crill, Patrick M., Saleska, Scott R., Tyson, Gene W. and Rich, Virginia I. (2021). Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes. Nature Communications, 12 (1) 5815. doi: 10.1038/s41467-021-25983-9
Sun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2021). Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME Communications, 1 (1) 30, 1-14. doi: 10.1038/s43705-021-00032-0
Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric ... Eloe-Fadrosh, Emiley A. (2021). Author Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6). Nature Biotechnology, 39 (4), 521-521. doi: 10.1038/s41587-021-00898-4
Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric ... Eloe-Fadrosh, Emiley A. (2021). A genomic catalog of Earth’s microbiomes. Nature Biotechnology, 39 (4), 499-509. doi: 10.1038/s41587-020-0718-6
Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric ... Eloe-Fadrosh, Emiley A. (2021). Publisher Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6). Nature Biotechnology, 39 (4), 520-520. doi: 10.1038/s41587-020-00769-4
Wilson, R. M., Zayed, A. A., Crossen, K. B., Woodcroft, B., Tfaily, M. M., Emerson, J., Raab, N., Hodgkins, S. B., Verbeke, B., Tyson, G., Crill, P., Saleska, S., Chanton, J. P., Rich, V. I., IsoGenie Project Coordinators and IsoGenie Project Field Team (2021). Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation. PLoS One, 16 (2) e0245857, 1-33. doi: 10.1371/journal.pone.0245857
Dombrowski, Nina, Williams, Tom A., Sun, Jiarui, Woodcroft, Benjamin J., Lee, Jun-Hoe, Minh, Bui Quang, Rinke, Christian and Spang, Anja (2020). Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nature Communications, 11 (1) 3939, 3939. doi: 10.1038/s41467-020-17408-w
Priyam, Anurag, Woodcroft, Ben J., Rai, Vivek, Moghul, Ismail, Munagala, Alekhya, Ter, Filip, Chowdhary, Hiten, Pieniak, Iwo, Maynard, Lawrence J., Gibbins, Mark Anthony, Moon, HongKee, Davis-Richardson, Austin, Uludag, Mahmut, Watson-Haigh, Nathan S., Challis, Richard, Nakamura, Hiroyuki, Favreau, Emeline, Gómez, Esteban A., Pluskal, Tomás, Leonard, Guy, Rumpf, Wolfgang and Wurm, Yannick (2019). Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases. Molecular biology and evolution, 36 (12), 2922-2924. doi: 10.1093/molbev/msz185
Wilson, Rachel M., Neumann, Rebecca B., Crossen, Kelsey B., Raab, Nicole M., Hodgkins, Suzanne B., Saleska, Scott R., Bolduc, Ben, Woodcroft, Ben J., Tyson, Gene W., Chanton, Jeffrey P. and Rich, Virginia (2019). Microbial community analyses inform geochemical reaction network models for predicting pathways of greenhouse gas production. Frontiers in Earth Science, 7 59. doi: 10.3389/feart.2019.00059
Evans, Paul N., Boyd, Joel A., Leu, Andy O., Woodcroft, Ben J., Parks, Donovan H., Hugenholtz, Philip and Tyson, Gene W. (2019). An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology, 17 (4), 219-232. doi: 10.1038/s41579-018-0136-7
Boyd, Joel A., Jungbluth, Sean P., Leu, Andy O., Evans, Paul N., Woodcroft, Ben J., Chadwick, Grayson L., Orphan, Victoria J., Amend, Jan P., Rappé, Michael S. and Tyson, Gene W. (2019). Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. The ISME Journal, 13 (5), 1269-1279. doi: 10.1038/s41396-018-0343-2
Martinez, Miguel A., Woodcroft, Ben J., Ignacio Espinoza, Julio C., Zayed, Ahmed A., Singleton, Caitlin M., Boyd, Joel A., Li, Yueh-Fen, Purvine, Samuel, Maughan, Heather, Hodgkins, Suzanne B., Anderson, Darya, Sederholm, Maya, Temperton, Ben, Bolduc, Benjamin, Saleska, Scott R., Tyson, Gene W. and Rich, Virginia I. (2019). 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, 42 (1), 54-66. doi: 10.1016/j.syapm.2018.12.003
Trubl, Gareth, Jang, Ho Bin, Roux, Simon, Emerson, Joanne B., Solonenko, Natalie, Vik, Dean R., Solden, Lindsey, Ellenbogen, Jared, Runyon, Alexander T., Bolduc, Benjamin, Woodcroft, Ben J., Saleska, Scott R., Tyson, Gene W., Wrighton, Kelly C., Sullivan, Matthew B. and Rich, Virginia I. (2018). Soil viruses are underexplored players in ecosystem carbon processing. mSystems, 3 (5) e0007618. doi: 10.1128/mSystems.00076-18
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, 3 (8), 870-880. doi: 10.1038/s41564-018-0190-y
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, 560 (7716), 49-54. doi: 10.1038/s41586-018-0338-1
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, 12 (10), 2544-2558. 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, 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) e2486, 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) e0159128, e0159128. doi: 10.1371/journal.pone.0159128
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 (1) 18165. 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) e968, 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) e603, 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, 3212.1-3212.7. doi: 10.1038/ncomms4212
Woodcroft, Ben J., McMillan, Paul J., Dekiwadia, Chaitali, Tilley, Leann and Ralph, Stuart A. (2012). Determination of protein subcellular localization in apicomplexan parasites. Trends in Parasitology, 28 (12), 546-554. doi: 10.1016/j.pt.2012.08.008
Ludin, Philipp, Woodcroft, Ben, Ralph, Stuart A. and Mäser, Pascal (2012). In silico prediction of antimalarial drug target candidates. International Journal for Parasitology: Drugs and Drug Resistance, 2, 191-199. doi: 10.1016/j.ijpddr.2012.07.002
Oehring, Sophie C., Woodcroft, Ben J., Moes, Suzette, Wetzel, Johanna, Dietz, Olivier, Pulfer, Andreas, Dekiwadia, Chaitali, Maeser, Pascal, Flueck, Christian, Witmer, Kathrin, Brancucci, Nicolas M. B., Niederwieser, Igor, Jenoe, Paul, Ralph, Stuart A. and Voss, Till S. (2012). Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum. Genome Biology, 13 (11), R108. doi: 10.1186/gb-2012-13-11-r108
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, 9.1-9.16. doi: 10.1186/1742-9994-9-9
Bonnal, R. J. P., Aerts, J., Githinji, G., Goto, N., MacLean, D., Miller, C. A., Mishima, H., Pagani, M., Ramirez-Gonzalez, R., Smant, G., Strozzi, F., Syme, R., Vos, R., Wennblom, T. J., Woodcroft, B. J., Katayama, T. and Prins, P. (2012). Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. Bioinformatics, 28 (7), 1035-1037. doi: 10.1093/bioinformatics/bts080
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 ... Rokhsar, Daniel S. (2010). The Amphimedon queenslandica genome and the evolution of animal complexity. Nature, 466 (7307), 720-726. doi: 10.1038/nature09201
Koay, Ann, Woodcroft, Ben, Petrie, Emma J., Yue, Helen, Emanuelle, Shane, Bieri, Michael, Bailey, Michael F., Hargreaves, Mark, Park, Jong-Tae, Park, Kwan-Hwa, Ralph, Stuart, Neumann, Dietbert, Stapleton, David and Gooley, Paul R. (2010). AMPK β subunits display isoform specific affinities for carbohydrates. FEBS Letters, 584 (15), 3499-3503. doi: 10.1016/j.febslet.2010.07.015
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
Gardiner, Donald L., Woodcroft, Ben J., Dixon, Matthew W. A., Ralph, Stuart A. and Trenholme, Katharine R. (2009). REX1 and Pf62: are they one and the same?. Parasitology Research, 104 (5), 967-968. doi: 10.1007/s00436-009-1382-4
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 Papers
Woodcroft, Ben J., Boyd, Joel A. and Tyson, Gene W. (2016). OrfM: a fast open reading frame predictor for metagenomic data. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/bioinformatics/btw241
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. 7th International Symposium on Abalone Biology, Fisheries and Culture, Pattaya, Thailand, 19-24 July 2009. Hanover, PA, United States: National Shellfisheries Association. doi: 10.2983/035.029.0328