Our Research

Our world-renowned researchers and use novel culture-independent molecular approaches and bioinformatics tools to answer important questions about the role of microbial communities in human and environmental health.

Research Programs


Recent Publications

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

Schoelmerich, Marie C., Ly, Lynn, West-Roberts, Jacob, Shi, Ling Dong, Shen, Cong, Malvankar, Nikhil S., Taib, Najwa, Gribaldo, Simonetta, Woodcroft, Ben J., Schadt, Christopher W., et al. (2024) Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires. Nature Communications, 15, pp.Article number: 5414.
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Whole genome CRISPRi screening identifies druggable vulnerabilities in an isoniazid resistant strain of Mycobacterium tuberculosis

Wang, Xin Yue, Jowsey, William J., Cheung, Chen Yi, Smart, Caitlan J., Klaus, Hannah R., Seeto, Noon E.J., Waller, Natalie J.E., Chrisp, Michael T., Peterson, Amanda L., Ofori-Anyinam, Boatema, et al. (2024) Whole genome CRISPRi screening identifies druggable vulnerabilities in an isoniazid resistant strain of Mycobacterium tuberculosis. Nature Communications, 15 (1), pp.Article number: 9791.
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Altered immunophenotypic expression in the peripheral bladder cancer immune landscape

Mackenzie, Nathan J, Zimmermann, Kate, Nicholls, Clarissa, Perera, Mahasha PJ, Ngoo, Alexander, Jeffery, Penny L, Vela, Ian, Kenna, Tony J, Williams, Elizabeth D., Thomas, Patrick B (2024) Altered immunophenotypic expression in the peripheral bladder cancer immune landscape. Immunology and Cell Biology, 102 (10), pp.949-962.
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Multiple serum biomarkers associate with mortality and interstitial lung disease progression in systemic sclerosis

Parker, Matthew James Sinclair, Jee, Adelle S., Hansen, Dylan, Proudman, Susanna, Youssef, Peter, Kenna, Tony J., Stevens, Wendy, Nikpour, Mandana, Sahhar, Joanne, Corte, Tamera J. (2024) Multiple serum biomarkers associate with mortality and interstitial lung disease progression in systemic sclerosis. Rheumatology, 63 (11), pp.2981-2988.
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Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient

Freire-Zapata, Viviana, Holland-Moritz, Hannah, Cronin, Dylan R., Aroney, Sam, Smith, Derek A., Wilson, Rachel M., Ernakovich, Jessica G., Woodcroft, Ben J., Bagby, Sarah C., Mondav, Rhiannon, et al. (2024) Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient. Nature Microbiology, 9 (11), pp.2892-2908.
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Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health

Vera Ponce de Leon, Arturo, Hensen, Tim, Hoetzinger, Matthias, Gupta, Shashank, Weston, Bronson, Johnsen, Sander M., Rasmussen, Jacob A., Gronlund Clausen, Cecilie, Pless, Louisa, Andrade Verissimo, Ana Raquel, et al. (2024) Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health. Nature Microbiology, 9 (11), pp.3059-3074.
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Quest for Orthologs in the Era of Biodiversity Genomics

Langschied, Felix, Bordin, Nicola, Cosentino, Salvatore, Fuentes-Palacios, Diego, Glover, Natasha, Hiller, Michael, Hu, Yanhui, Huerta-Cepas, Jaime, Coelho, Luis Pedro, Iwasaki, Wataru, et al. (2024) Quest for Orthologs in the Era of Biodiversity Genomics. Genome Biology and Evolution, 16 (10), pp.Article number: evae224.
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The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production

Gupta, Shashank, Vera Ponce de Leon, Arturo, Kodama, Miyako, Hoetzinger, Matthias, Gronlund Clausen, Cecilie, Pless, Louisa, Andrade Verissimo, Ana Raquel, Stengel, Bruno, Calabuig, Virginia, Kvingedal, Renate, et al. (2024) The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production. Communications Biology, 7 (1), pp.Article number: 1391.
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Soft robotic artificial left ventricle simulator capable of reproducing myocardial biomechanics

Davies, James, Thai, Mai Thanh, Sharma, Bibhu, Hoang, Trung Thien, Nguyen, Chi Cong, Phan, Phuoc Thien, Vuong, Thao Nhu Anne Marie, Ji, Adrienne, Zhu, Kefan, Nicotra, Emanuele, et al. (2024) Soft robotic artificial left ventricle simulator capable of reproducing myocardial biomechanics. Science Robotics, 9 (94), pp.Article number: eado4553.
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Liver click dECM hydrogels for engineering hepatic microenvironments

Milton, Laura A., Davern, Jordan W., Hipwood, Luke, Chaves, Juliana D.S., McGovern, Jacqui, Broszczak, Daniel, Hutmacher, Dietmar W., Meinert, Christoph, Toh, Yi Chin (2024) Liver click dECM hydrogels for engineering hepatic microenvironments. Acta Biomaterialia, 185, pp.144-160.
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Other Publications

A full list of CMR research publications can be found on the CMR Google Scholar listing.