@article{wilson2026methanotrophic,title={Methanotrophic potential of a northern fen},author={Wilson, Rachel M. and Ellenbogen, Jared B. and Yang, Shuai and Li, Zhen and McIlroy, Simon J. and Cory, Alex B. and Bosman, Samantha and Perry, Apryl L. and Jones, Cheristy P. and McGivern, Bridget B. and Bechtold, Emily K. and Li, Yueh-Fen and Hodgkins, Suzanne B. and Kuhn, McKenzie A. and Morales, Lyreshka Castro and Becker, Kitty and Williams, Kenneth H. and Beutler, Curtis and Rich, Virginia I. and Aroney, Samuel T. N. and Woodcroft, Ben J. and Saleska, Scott and Tyson, Gene and Tang, Jinyun and Wrighton, Kelly C. and Chanton, Jeff P. and Varner, Ruth K.},journal={Frontiers in Environmental Science},volume={14},year={2026},publisher={Frontiers Media SA},doi={10.3389/fenvs.2026.1858695}}
@article{guo2026mobile,title={Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils},author={Guo, Jiarong and Aroney, Samuel T. N. and Domínguez-Huerta, Guillermo and Smith, Derek and Vik, Dean and Owusu-Ansah, Carlos and Pratama, Akbar Adjie and Solonenko, Sergei and Tian, Funing and Howard-Varona, Cristina and Zhong, Zhi-Ping and Fofana, Aminata and Smith, Garrett J. and Hodgkins, Suzanne B. and Cronin, Dylan and Anderson, Darya and Bennett, Kathryn and Dominguez, Sky and Fahnestock, Maria Florencia and Hough, Moira and Jansen, Joachim and Mondav, Rhiannon and Perry, Apryl and Trubl, Gareth and Varner, Ruth K. and Crill, Patrick and Gilman Ernakovich, Jessica and Ferriere, Regis and Ibba, Mike and Tfaily, Malak M. and Varner, Ruth K. and Zayed, Ahmed A. and Woodcroft, Ben J. and Tyson, Gene W. and Rich, Virginia I. and Sullivan, Matthew B. and Roux, Simon and Bagby, Sarah C.},journal={Nature Microbiology},volume={11},number={7},pages={1800–1814},year={2026},publisher={Springer Science and Business Media LLC},doi={10.1038/s41564-026-02391-7}}
@article{aroney2025bin,title={Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes},author={Aroney, Samuel T. N. and Newell, Rhys J. P. and Tyson, Gene W. and Woodcroft, Ben J.},journal={Nature Methods},volume={22},number={12},pages={2516–2524},year={2025},publisher={Springer Science and Business Media LLC},doi={10.1038/s41592-025-02901-1}}
@article{woodcroft2025comprehensive,title={Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper},author={Woodcroft, Ben J. and Aroney, Samuel T. N. and Zhao, Rossen and Cunningham, Mitchell and Mitchell, Joshua A. M. and Nurdiansyah, Rizky and Blackall, Linda and Tyson, Gene W.},journal={Nature Biotechnology},volume={44},number={6},pages={948–953},year={2025},publisher={Springer Science and Business Media LLC},doi={10.1038/s41587-025-02738-1}}
@article{aroney2025coverm,title={CoverM: read alignment statistics for metagenomics},author={Aroney, Samuel T N and Newell, Rhys J P and Nissen, Jakob N and Camargo, Antonio Pedro and Tyson, Gene W and Woodcroft, Ben J},journal={Bioinformatics},volume={41},number={4},year={2025},publisher={Oxford University Press (OUP)},doi={10.1093/bioinformatics/btaf147}}
@article{singleton2025microflora,title={The Microflora Danica atlas of Danish environmental microbiomes},author={Singleton, C. M. and Jensen, T. B. N. and Delogu, F. and Knudsen, K. S. and Sørensen, E. A. and Jørgensen, V. R. and Karst, S. M. and Yang, Y. and Sereika, M. and Petriglieri, F. and Knutsson, S. and Dall, S. M. and Kirkegaard, R. H. and Kristensen, J. M. and Overgaard, C. K. and Woodcroft, B. J. and Speth, D. R. and Aroney, S. T. N. and Thomsen, Henning C. and Christensen, Bent T. and de Jonge, Lis W. and Danielsen, Anne-Cathrine S. and Hermansen, Cecilie and Greve, Mogens H. and Ejrnæs, Rasmus and Davidson, Thomas A. and Normand, Signe and Treier, Urs A. and Madsen, Bjarke and Schramm, Andreas and Marshall, Ian P. G. and Dam, Ann-Sofie and Kjeldsen, Kasper U. and Finster, Kai and Thomsen, Philip F. and Sigsgaard, Eva E. and Klepke, Martin J. and Vestergård, Marie and Aude, Erik and Thomsen, Lene and Lemming, Camilla and Hørfarter, Rita and Jensen, Marlene M. and Frøslev, Tobias G. and Gram, Lone and Svendsen, Peter B. and Schostag, Morten Dencker and Kjellerup, Sanne and Skovhus, Torben L. and Søborg, Ditte A. and Reitzel, Kasper and Pedersen, Jørgen F. and Giguere, Andrew and Pedersen, Inge S. and Sønderkær, Mads and Vollertsen, Jes and Liu, Fan and Roslev, Peter and Iversen, Niels and Nielsen, Kåre L. and de Jonge, Nadieh and Bruhn, Dan and Nielsen, Jeppe L. and Kristensen, Torsten N. and Jiang, Chenjing and Nierychlo, Marta A. and Dottorini, Giulia and Wagner, M. and Dueholm, M. K. D. and Nielsen, P. H. and Albertsen, M.},journal={Nature},volume={649},number={8098},pages={971–981},year={2025},publisher={Springer Science and Business Media LLC},doi={10.1038/s41586-025-09794-2}}
@article{cronin2025stable,title={Stable states in an unstable landscape: microbial resistance at the front line of climate change},author={Cronin, Dylan R. and Holland-Moritz, Hannah and Smith, Derek A. and Aroney, Samuel T. N. and Hodgkins, Suzanne B. and Borton, Mikayla and Li, Yueh-Fen and Zayed, Ahmed and Healy, Kieran and Persson, Andreas and Tfaily, Malak M. and Crill, Patrick and McCalley, Carmody K. and Wrighton, Kelly and Varner, Ruth K. and Tyson, Gene W. and Woodcroft, Ben J. and Bagby, Sarah C. and Ernakovich, Jessica and Rich, Virginia I.},year={2025},publisher={openRxiv},doi={10.1101/2025.02.07.636677},}
@article{speth2024globdb,title={GlobDB: a comprehensive species-dereplicated microbial genome resource},author={Speth, Daan R and Pullen, Nick and Aroney, Samuel T N and Coltman, Benjamin L and Osvatic, Jay and Woodcroft, Ben J and Rattei, Thomas and Wagner, Michael},journal={Bioinformatics Advances},volume={5},number={1},year={2024},publisher={Oxford University Press (OUP)},doi={10.1093/bioadv/vbaf280}}
@article{freirezapata2024microbiome,title={Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient},author={Freire-Zapata, Viviana and Holland-Moritz, Hannah and Cronin, Dylan R. and Aroney, Sam and Smith, Derek A. and Wilson, Rachel M. and Ernakovich, Jessica G. and Woodcroft, Ben J. and Bagby, Sarah C. and Hodgkins, Suzanne B. and Mondav, Rhiannon and E. Cross, Jennifer and Fahnestock, Maria Florencia and Ferriere, Regis and Ibba, Michael and Saleska, Scott R. and Varner, Ruth K. and Zayed, Ahmed A. and Rich, Virginia I. and Sullivan, Matthew B. and Stegen, James C. and Tfaily, Malak M.},journal={Nature Microbiology},volume={9},number={11},pages={2892–2908},year={2024},publisher={Springer Science and Business Media LLC},doi={10.1038/s41564-024-01800-z}}
@article{aroney2024motility,title={The motility and chemosensory systems of Rhizobium leguminosarum, their role in symbiosis, and link to PTSNtr regulation},author={Aroney, Samuel T. N. and Pini, Francesco and Kessler, Celia and Poole, Philip S. and Sánchez‐Cañizares, Carmen},journal={Environmental Microbiology},volume={26},number={2},year={2024},publisher={Wiley},doi={10.1111/1462-2920.16570}}
@article{knights2024rhizobium,title={<i>Rhizobium</i> determinants of rhizosphere persistence and root colonization},author={Knights, Hayley E and Ramachandran, Vinoy K and Jorrin, Beatriz and Ledermann, Raphael and Parsons, Jack D and Aroney, Samuel T N and Poole, Philip S},journal={The ISME Journal},volume={18},number={1},year={2024},publisher={Oxford University Press (OUP)},doi={10.1093/ismejo/wrae072}}
@misc{newell2024aviary,title={Aviary: hybrid assembly and genome recovery from metagenomes with Aviary},author={Newell, Rhys J. P. and Aroney, Samuel T. N. and Zaugg, Julian and Sternes, Peter and Tyson, Gene W. and Woodcroft, Ben J.},howpublished={Software},year={2024},url={https://github.com/rhysnewell/aviary},}
@misc{aroney2024galah,title={Galah: more scalable dereplication for metagenome assembled genomes},author={Aroney, Samuel T. N. and Camargo, Antonio Pedro and Tyson, Gene W. and Woodcroft, Ben J.},howpublished={Software},year={2024},url={https://github.com/wwood/galah},}
Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials
Jiarui Sun, Apoorva Prabhu, Samuel T. N. Aroney, and Christian Rinke
@article{sun2022insights,title={Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials},author={Sun, Jiarui and Prabhu, Apoorva and Aroney, Samuel T. N. and Rinke, Christian},journal={Microbial Genomics},volume={8},number={6},year={2022},publisher={Microbiology Society},doi={10.1099/mgen.0.000842}}
@article{aroney2021rhizobial,title={Rhizobial Chemotaxis and Motility Systems at Work in the Soil},author={Aroney, Samuel T. N. and Poole, Philip S. and Sánchez-Cañizares, Carmen},journal={Frontiers in Plant Science},volume={12},year={2021},publisher={Frontiers Media SA},doi={10.3389/fpls.2021.725338}}
@article{wheatley2020lifestyle,title={Lifestyle adaptations of <i>Rhizobium</i> from rhizosphere to symbiosis},author={Wheatley, Rachel M. and Ford, Brandon L. and Li, Li and Aroney, Samuel T. N. and Knights, Hayley E. and Ledermann, Raphael and East, Alison K. and Ramachandran, Vinoy K. and Poole, Philip S.},journal={Proceedings of the National Academy of Sciences},volume={117},number={38},pages={23823–23834},year={2020},publisher={National Academy of Sciences},doi={10.1073/pnas.2009094117}}
@article{sullivan2015rapid,title={A rapid extraction method for glycogen from formalin-fixed liver},author={Sullivan, Mitchell A. and Li, Shihan and Aroney, Samuel T.N. and Deng, Bin and Li, Cheng and Roura, Eugeni and Schulz, Benjamin L. and Harcourt, Brooke E. and Forbes, Josephine M. and Gilbert, Robert G.},journal={Carbohydrate Polymers},volume={118},pages={9–15},year={2015},publisher={Elsevier BV},doi={10.1016/j.carbpol.2014.11.005}}
@article{sullivan2014changes,title={Changes in Glycogen Structure over Feeding Cycle Sheds New Light on Blood-Glucose Control},author={Sullivan, Mitchell A. and Aroney, Samuel T. N. and Li, Shihan and Warren, Frederick J. and Joo, Jin Suk and Mak, Ka Sin and Stapleton, David I. and Bell-Anderson, Kim S. and Gilbert, Robert G.},journal={Biomacromolecules},volume={15},number={2},pages={660–665},year={2014},publisher={American Chemical Society (ACS)},doi={10.1021/bm401714v}}