The lab as of March 2019.

Nicola Segata

Nicola Segata

Principal Investigator

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Nicola Segata is a Full Professor and Principal Investigator. His background is in metagenomics, machine learning, microbiome research, and microbial genomics. He started and he is leading the Laboratory of Computational Metagenomics at the Department CIBIO (University of Trento).

Postdoctoral Fellows

Francesco Asnicar

Francesco Asnicar

Postdoctoral fellow

CV

Francesco joined the lab in March 2014 and his major research interests are the developing of computational tools for metagenomic and phylogenetic analyses.

Aitor Blanco-Míguez

Aitor Blanco-Míguez

Postdoctoral fellow

 

Aitor joined the Lab in July 2019 as a postdoctoral fellow. He is currently developing methods for metagenomic data analysis. His research interests include interaction of commensal bacteria with epithelial/immune cells and how the environmental microbiomes (i.e. food microbiome) interact with that of the host (H2020 project MASTER).

Serena Manara

Serena Manara

Postdoctoral fellow

 

Serena has joined the lab in November 2014, where she pursued her PhD. Her major research interests are host-microbiome interactions (including both human and non-human hosts) and the vertical transmission of microbiome members from mothers to infants.

Liviana Ricci

Liviana Ricci

Postdoctoral fellow

 

Liviana joined the lab in January 2021, after obtaining a PhD in Gut Microbiology, to isolate and study uncharacterised bacterial species associated to humans. She is interested in bacterial metabolic functions and their participation to host health and defence from infections.

Marta Selma-Royo

Marta Selma-Royo

Postdoctoral fellow

 

Marta joined the lab in July 2021 after obtaining her PhD in Biotechnology from the Polytechnic University of Valencia. Her scientific interests are the interaction of uncharacterized bacteria with the host, especially in the context of pregnancy and infant growth.

sabry

Mohamed S. Sarhan

Postdoctoral fellow

 

Sabry joined the lab in November 2022 as a postdoctoral fellow. He is working with Christian Fuchsberger from Eurac Research to analyze the microbiome and metabolomics data of the Cooperative Health Research In South Tyrol (CHRIS) study in relation to type 2 diabetes and non-alcoholic fatty liver disease (NAFLD).

Mireia Valles-Colomer

Mireia Valles-Colomer

Postdoctoral fellow

 

Mireia is a postdoctoral fellow studying human microbiome transmission by large scale strain-level metagenomic profiling. With a background in Computational Biology and Biotechnology, she pursued her PhD on the role of the gut microbiome in mental health at the Raes Lab (VIB-KU Leuven, Belgium). She is interested in human-associated microbial communities and their interaction with the host.

Paolo Manghi

Paolo Manghi

Postdoctoral fellow

 

Paolo has joined the lab in January 2017. His main research interests are bounded to the History & Geography of human being and to the machine-learning approach in Bioinformatics.

Research Scientists

Sabrina Tamburini

Sabrina Tamburini

Group Scientist

@ IEO, Milan

Sabrina is a Group Scientist in the Department of Experimental Oncology at IEO, Istituto Europeo di Oncologia in Milan, Italy). Here, she is leading a project about gut microbiome in healthy aging and she is interested in understanding the role of gut microbiome in: modulating cancer risk, preventing cancer development and responding to cancer treatment especially for immunotherapy approaches. She performed her postdoctoral training at Icanh School of Medicine at Mount Sinai (New York, USA) studying the viable gut microbiome during fecal microbial transplantation in Clostridium difficile patients.

Research Assistants

Federica Armanini

Federica Armanini

Research Assistant

 

Federica is a biologist working as a wet lab technician, she has joined the lab in March 2015. Currently she is processing the samples from different projects, preparing them for sequencing.

Federica Pinto

Federica Pinto

Scientific Projects Manager

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Federica joined the Lab in November 2016 as a postdoctoral fellow. She is interested in microbial biodiversity, focusing mainly in viruses, in aquatic ecosystems. Her project (MetaVirAlp-Marie Skłodowska-Curie IF) focuses on the characterisation of viral and bacterial communities in Alpine Lakes.

Katarina Mladenovic

Katarina Mladenovic

Katarina Mladenovic

Katarina joined the lab in March 2022. She obtained her Master's degree in Electrical and Computer Engineering at the University of Novi Sad. She is working on developing software tools and managing of computational pipelines.

PhD Students

Giacomo Antonello

Giacomo Antonello

3rd year PhD Student

 

Giacomo joined the lab in November 2019. He is a PhD student jointly supervised by Nicola Segata and Christian Fuchsberger from Eurac Research. His project involves studying the interaction of the salivary microbiome with genetic, lifestyle, and physiological parameters in the context of the Cooperative Health Research In South Tyrol (CHRIS) study.

Joint with: Christian Fuchsberger (EURAC Research)

Niccolò Carlino

Niccolò Carlino

3rd year PhD Student

 

Niccolò research aims at developing and applying strain-level metagenomics computational tools on human, as well as environmental, microbiomes for the H2020 MASTER project.

Joint with: Edoardo Pasolli (UniNA)

Léonard Dubiois

Léonard Dubiois

3rd year PhD Student

 

Léonard is a PhD student in Biomolecular Sciences who joined the lab in September 2019. Coming from a computational biology background and data analysis in various fields of biology, he now focuses on both analyzing metagenomic data and developing tools for it.

Davide Golzato

Davide Golzato

2nd year PhD Student

 

Davide joined the lab in September 2019. He is a master student in Quantitative and Computational Biology at the University of Trento. His interests span molecular biology, metagenomics and bioinformatics.

Amir NabiNejad

Amir NabiNejad

SEMM PhD Student

@ IEO, Milan

Amir joined the lab in October 2021. He focused on the metabolic interplay between the gut microbiome and immune system in colorectal cancer patients during his Master’s degree in Molecular Biology of the Cell (UniMi-IEO) and his following fellowship. As a PhD student, he tries to unravel links between the human microbiome and healthy aging as well as cancer.

Gianmarco Piccinno

Gianmarco Piccinno

3rd year PhD Student

 

Gianmarco obtained his Master's degree in Quantitative and Computational Biology at University of Trento. His main research interests are Bioinformatics and its implications in Genetic Engineering and Data Analysis.

Elisa Piperni

Elisa Piperni

SEMM PhD Student

@ IEO, Milan

Elisa joined the lab in 2021 after obtaining her Master's degree in Quantitative and Computational Biology. She is currently studying relations between healthy aging, cancer, and the human microbiome.

Michal Punčochář

Michal Punčochář

2nd year PhD Student

 

Michal has joined the lab in September 2020. He is interested in the application of statistics and machine learning to metagenomics. Currently he is working on a project aiming to understand the mechanics of engraftment after fecal microbiota transplantation.

Matteo Ciciani

Matteo Ciciani

1st year PhD Student

 

Matteo joined the lab in April 2021. He obtained his Master's degree in Quantitative and Computational Biology at University of Trento. His main research interest is the bioinformatic analysis of CRISPR/Cas systems in the human microbiome.

Joint with: Laboratory of Molecular Virology - University of Trento (PI: Annna Cereseto)

Andrea Silverj

Andrea Silverj

3rd year PhD Student

CV

Andrea has joined the lab in November 2019. He obtained his Master's degree in Evolutionary Biology at the University of Padova with a thesis on the molecular evolution of Zika virus. He is currently a PhD student in Agrifood and Environmental Sciences, co-supervised by Dr. Omar Rota-Stabelli from Edmund Mach Foundation. His research interests include virus evolution, phylogenomics and metagenomics.

Joint with: Omar Rota-Stabelli (Fond. Edmund Mach)

Pre-doctoral fellows

Charlotte Servais

Charlotte Servais

Predoctoral fellow

Charlotte joined the lab in July 2022 after obtaining her Master's degree in Biomedical Sciences. She is interested in the isolation of microbial strains from species previously identified by metagenomic analysis as relevant but not yet cultured and characterized in vitro.

Master Students

Former visitors

Nicole Treichel

Visiting PostDoc

Uniklinik RWTH Aachen (Germany)

Maria Camila Alvarez Silva

Visiting PhD student

Arumugam lab, University of Copenhagen (Denmark)

Thomas Yssing Michaelsen

Visiting PhD student

Albertsen lab, Aalborg University (Denmark)

Malo Le Boulch

Visiting PhD student

GenPhySE, INRA (France)

Marisa Metzger

Visiting student

University Heidelberg (Germany)

Galo Adrián Serrano

Visiting PhD student

Iñaki Comas Lab (Spain)

Tom van Wijk

Visiting Scientist

Eelco Franz Lab, RIVM (Utrecht)

Kristen Meyer

Visiting Student

Aagaard Lab, BCM (US)

Bruno Fosso

Visiting PostDoc

IBIOM - CNR Bari (Italy)

Vedrana Vidulin

Visiting Researcher

Jozef Stefan Institute (Slovenia)

Atara Uzan

Visiting PhD Student

Koren Lab, Bar Ilan University (Israel)

Lucas Schiffer

Visiting PhD Student

Waldron Lab, CUNY (US)

Daniela Dolce

Visiting Scientist

Meyer Hospital (Italy)

Yadira Galeano

Visiting PhD Student

Universidad de Antioquia (Colombia)

Urša Bole

Visiting Bachelor Student

Sander Wuyts

Visiting PhD Student

University of Antwerp (Belgium)

Valerio Iebba

Postdoctoral research visit

Sapienza University of Rome (Italy)

Sokhna Gueye

Postdoctoral research visit

 

Former Group Members

Alberto Arrè

QCB Master Student

Vittoria Ossanna

QCB Master Student

Andrew Thomas

Postdoctoral fellow

Now at Microbiotica, UK

Nikolai Karcher

PhD Student

Now at EMBL Heidelberg

Kun D. Huang

PhD Student

Now at Helmholtz Centre for Infection Research

Francesco Beghini

PhD Student

Now at Human Nature Lab at Yale University

Fabio Cumbo

Postdoctoral Fellow

Now at Genomic Medicine Institute, Cleveland

Giulia Masetti

Postdoctoral Fellow

Moreno Zolfo

Postdoctoral Fellow

Now at Tokyo Institute of Technology

Davide Bazzani

QCB Master Student

Now at PreBiomics

Adrian Tett

Postdoctoral Fellow

Now at University of Vienna

Eleonora Nigro

Predoctoral Fellow

Now at University of Copenhagen

Germana Baldi

QCB Master Student

 

Chiara Mazzoni

QCB Master Student

 

Claudia Mengoni

DISI Bachelor Student

 

Paolo Ghensi

PhD Student

Now at PreBiomics

Edoardo Pasolli

Postdoctoral Fellow

Now at University of Naples

Mattia Bolzan

Research Assistant

Now at PreBiomics

Pamela Ferretti

Master Student

Now PhD Student at EMBL

Tin Duy Truong

Postdoctoral Fellow

Now in Industry

Matthias Scholz

Postdoctoral Fellow

Now at Edmund Mach Foundation

Giulia Corsi

DISI Master Student

 

Federico Taverna

DISI Master Student

 

Luca Erculiani

DISI Master Student

 

Thomas Tolio

DISI Master Student

 

Roman Stolyarov

Bachelor Student

Now at MIT

Manuel Micheloni

High School Student

Now at University of Trento

Temesgen Dadi

Master Student

Now at the Max Planck Institute