Our Research

Dmitrijeva, Marija, Tackmann, Janko, Matias Rodrigues, Joao Frederico, Huerta-Cepas, Jaime, Coelho, Luis Pedro, von Mering, Christian (2024) A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer. Nature Ecology and Evolution, 8 (5), pp.986-998.

McGivern, Bridget B., Cronin, Dylan R., Ellenbogen, Jared B, Borton, Mikayla A, Knutson, Eleanor L, Freire-Zapata, Viviana, Bouranis, John A, Bernhardt, Lukas, Hernandez, Alma I, Flynn, Rory M, et al. (2024) Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nature Microbiology, 9 (6), pp.1454-1466.

Coelho, Luis Pedro, Santos-Junior, Celio Dias, de la Fuente-Nunez, Cesar (2024) Challenges in computational discovery of bioactive peptides in 'omics data. Proteomics, 24 (12-13), pp.Article number: 2300105.

Mahoney-Kurpe, Sam C., Palevich, Nikola, Gagic, Dragana, Biggs, Patrick J., Reid, Peter M., Altshuler, Ianina, Pope, Phil, Attwood, Graeme T., Moon, Christina D. (2024) Transcriptomic and proteomic changes associated with cobalamin-dependent propionate production by the rumen bacterium Xylanibacter ruminicola. mSystems, 9 (11), pp.e0086424.

Schmidt, Thomas S., Fullam, Anthony, Ferretti, Pamela, Orakov, Askarbek, Maistrenko, Oleksandr, Ruscheweyh, Hans, Letunic, Ivica, Duan, Yiqian, Rossum, Thea Van, Sunagawa, Shinichi, et al. (2024) SPIRE: a Searchable, Planetary-scale mIcrobiome REsource. Nucleic Acids Research, 52 (D1), pp.D777-D783.

Echeveste Medrano, Maider J., Leu, Andy O., Pabst, Martin, Lin, Yuemei, McIlroy, Simon J., Tyson, Gene W., van Ede, Jitske, Sanchez-Andrea, Irene, Jetten, Mike S.M., Jansen, Robert, et al. (2024) Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress. The ISME Journal, 18 (1), pp.Article number: wrae137.

Eisenhofer, Raphael, Alberdi, Antton, Woodcroft, Ben J. (2024) Quantifying microbial DNA in metagenomes improves microbial trait estimation. ISME Communications, 4 (1), pp.Article number: ycae111.

Gu, Yuqing, Zou, Yiwei, Huang, Yuxuan, Liang, Renjie, Wu, Yicong, Hu, Yifan, Hong, Yi, Zhang, Xianzhu, Toh, Yi Chin, Ouyang, Hongwei, et al. (2024) 3D-printed biomimetic scaffolds with precisely controlled and tunable structures guide cell migration and promote regeneration of osteochondral defect. Biofabrication, 16 (1), pp.Article number: 015003.

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., et al. (2024) Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost. mSystems, 9 (1), pp.Article number: e0069823.

Prabhu, Apoorva, Tule, Sanjana, Chuvochina, Maria, Boden, Mikael, McIlroy, Simon, Zaugg, Julian, Rinke, Christian (2024) Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary. ISME Communications, 4 (1), pp.Article number: ycae067.