Aitor Blanco-Miguez¹ Francesco Beghini¹ Fabio Cumbo¹ Lauren J McIver^2,3 Kelsey N Thompson^2,3 Moreno Zolfo¹ Paolo Manghi¹ Leonard Dubois¹ Kun D Huang¹ Andrew Maltez Thomas¹ Gianmarco Piccinno¹ Elisa Piperni^1,4 Michal Punčochář¹ Mireia Valles-Colomer¹ Adrian Tett^1,5 Francesca Giordano⁶ Richard Davies⁶ Jonathan Wolf⁶ Sarah E. Berry⁷ Tim D Spector⁸ Eric A Franzosa^2,3 Edoardo Pasolli⁹ Francesco Asnicar¹ Curtis Huttenhower^2,3 Nicola Segata^1,4

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Nature Biotechnology(2023) https://doi.org/10.1038/s41587-023-01688-w

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

⁵ Centre for Microbiology and Environmental Systems Science, University of Vienna, Austria

⁶ Zoe Global, London, UK

⁷ Department of Nutritional Sciences, King’s College London, London, UK

⁸ Department of Twin Research, King’s College London, London, UK

⁹ Department of Agricultural Sciences, University of Naples, Naples, Italy

Moreno Zolfo^1,2 Andrea Silverj^1,3,4 Aitor Blanco-Miguez¹ Paolo Manghi¹ Omar Rota-Stabelli^1,3,4 Vitor Heidrich¹ Jordan Jensen⁵ Sagun Maharjan⁵ Eric Franzosa⁵ Cristina Menni⁶ Alessia Visconti⁷ Federica Pinto¹ Matteo Ciciani¹ Curtis Huttenhower⁵ Anna Cereseto¹ Francesco Asnicar¹ Hiroaki Kitano^2,8,9 Takuji Yamada^{2,10,11,12,13} Nicola Segata^1,14

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples

bioRxiv(2024) https://doi.org/10.1101/2024.02.19.580813

¹ Department CIBIO, University of Trento, Italy

² Integrated Open Systems Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan

³ Center Agriculture Food Environment (C3A), University of Trento, Italy

⁴ Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy

⁵ Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA

⁶ Department of Twin Research & Genetic Epidemiology, King’s College London, London, UK

⁷ Center of Biostatistics, Epidemiology and Public Health, Department of Clinical and Biological Sciences, University of Turin, Turin, Italy

⁸ The Systems Biology Institute (SBI), Tokyo, Japan

⁹ IOM Bioworks Pvt. Ltd., Centre for Cellular and Molecular Platforms (C-CAMP), GKVK Post, Bellary Rd, Bengaluru, Karnataka-560065, India

¹⁰ School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan

¹¹ Metagen, Inc., Yamagata, Japan

¹² Metagen Therapeutics, Inc., Yamagata, Japan

¹³ Digzyme, Inc., Tokyo, Japan

¹⁴ Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy

Francesco Beghini¹ Lauren J McIver² Aitor Blanco-Miguez¹ 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