Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria

Autor: Li, Chenhao, Stražar, Martin, Mohamed, Ahmed M.T., Pacheco, Julian A., Walker, Rebecca L., Lebar, Tina, Zhao, Shijie, Lockart, Julia, Dame, Andrea, Thurimella, Kumar, Jeanfavre, Sarah, Brown, Eric M., Ang, Qi Yan, Berdy, Brittany, Sergio, Dallis, Invernizzi, Rachele, Tinoco, Antonio, Pishchany, Gleb, Vasan, Ramachandran S., Balskus, Emily, Huttenhower, Curtis, Vlamakis, Hera, Clish, Clary, Shaw, Stanley Y., Plichta, Damian R., Xavier, Ramnik J.

Publikováno v: In Cell 11 April 2024 187(8):1834-1852

SCNIC: Sparse correlation network investigation for compositional data.

Autor: Shaffer, Michael, Thurimella, Kumar, Sterrett, John D., Lozupone, Catherine A.

Publikováno v: Molecular Ecology Resources; Jan2023, Vol. 23 Issue 1, p312-325, 14p

Protein Language Models Uncover Carbohydrate-Active Enzyme Function in Metagenomics.

Autor: Thurimella K; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.; Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK.; School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Mohamed AMT; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Graham DB; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Owens RM; Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK., La Rosa SL; Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway., Plichta DR; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Bacallado S; Department of Pure Mathematics and Mathematical Statistics, University of Cambridge, Cambridge, UK., Xavier RJ; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2023 Oct 25. Date of Electronic Publication: 2023 Oct 25.