Francesco Beghini¹ Lauren J McIver² Aitor Blanco-Mìguez¹ Leonard Dubois¹ Francesco Asnicar¹ Sagun Maharjan^2,3 Ana Mailyan^2,3 Andrew Maltez Thomas¹ Paolo Manghi¹ Matthias Scholz^2,3 Mireia Valles-Colomer¹ George Weingart^2,3 Yancong Zhang^2,3 Moreno Zolfo¹ Curtis Huttenhower^2,3 Eric A Franzosa^2,3 Nicola Segata^1,5

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

eLife(2021) https://doi.org/10.7554/eLife.65088

¹ Department CIBIO, University of Trento, Italy

² Harvard T. H. Chan School of Public Health, Boston, MA, USA

³ The Broad Institute of MIT and Harvard, Cambridge, MA, USA

⁴ Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, Italy

⁵ IEO, European Institute of Oncology IRCCS, Milan, Italy

Lauren J McIver^1,2 Galeb Abu-Ali^1,2 Eric A Franzosa^1,2 Randall Schwager^1,2 Xochitl C Morgan^1,2,3 Levi Waldron⁴ Nicola Segata⁵ Curtis Huttenhower^1,2

bioBakery: a meta'omic analysis environment

Bioinformatics (2018) 10.1093/bioinformatics/btx754

¹ Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.

² The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

³ Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand.

⁴ Graduate School of Public Health and Health Policy, City University of New York, New York, NY 10027, USA.

⁵ Centre for Integrative Biology, University of Trento, Trento, Italy