Gruppo Ramazzotti
ComBiRama
Computational and Molecular Biology Lab
Coordinator: Matteo Ramazzotti, Ph.D.
Position: Associate Professor of Molecular Biology
e-mail: matteo.ramazzotti@unifi.it
Phone: +39 055 2751238
Member of Ph.D. program in Biochemistry and Molecular Biology - Bibim 2.0, Siena, IT
Italian Society of Biochemistry (SIB)
Italian Society of Biochemistry and Molecular Biology (SIBBM)
Brief Biographical sketch of the Coordinator
Matteo Ramazzotti earned a Master degree in Biology (2002) and a Ph.D. in Biochemistry and Applied Biology from the University of Florence (2005). He started his career at the Department of Biochemistry of Florence with cloning and purifying acylphosphatase proteins for deciphering the determinants of amyloid formation. In 2010 he collaborated with Ronald Melki group at the CNRS Biochemistry lab at Gif-sur-Yvette (Paris, France) in implementing algorithms and methods for detecting amyloid aggregation propensity in proteins with polyQ expansions. In 2011 he was enrolled in the in the group of Duccio Cavalieri (UniFi, Italy) where he started to approach the analysis of microbial communities. In 2012 he worked on recombinant antibody selection and production at the Department of Biomedical, Experimental and Clinical Sciences (DSBSC) at the University of Florence. In 2014 he was enrolled as a researcher (RTD) in biochemistry and in 2020 he earned the role of Associate Professor of Molecular Biology, teaching in Biotechnology and Medicine courses topics such as Molecular Biology and Computational biology . Since 2021 he is a member of the BiBIM 2.0 Ph.D. program in Siena.
Keywords
OMICS, COMPUTATIONAL BIOLOGY, BIOINFORMATICS, DATA ANALYSIS, DATA SCIENCE, MOLECULAR BIOLOGY, MICROBIAL COMMUNITY ANALYSIS, MOLECULAR BIOLOGY, DNA/RNA PURIFICATION, CLONING
Research Team
The ComBiRama Lab currently hosts 2 post-doc researchers:
Dr. Leandro di Gloria, Ph.D., Post-doctoral fellow
Microbial communities
Molecular analyses
Omics data analysis
Dr. Lorenzo Casbarra, Ph.D., Post-doctoral fellow
Computational biology
Software development
Omics data analysis
ComBiRama lab hosts most of the equipments to support the exploration of molecular aspects of samples (PCR, ddPCR, blotting, sequencing) and a large computational equipment to face complex, computationally intensive tasks. Additional resources are furthermore available using the new IT infrastructure at SBSC.
Current projects
Characterization of microbial communities through NGS and bioinformatic analysis.
The work starts from wet lab procedures to extract genomic DNA and amplify specific, highly taxonomically relevant regions from the total genomes, sequencing them with Illumina, optimizing the resulting reads and, eventually, applying specific computational pipelines to obtain a comprehensive view on the identity and abundance of members of the microbial community. Graphical approaches will allow to define appropriate experimental questions and set an analysis strategy that results in the identification of differentially abundant taxa and the prediction of their behavior in the environment of interest.
Meta exploration of human disease using multi-omics data
Meta-based projects allow to focus on project with an ample spectrum of of criteria. Nowadays a lot of datasets have been produced to explore the different molecular aspects of biology (trascriptomics, mirnomics, proteomics, metabolomics, chromain accessibility, methylation status of the promoters). Finding programs in cells and organisms is all about deciphering their intricate dynamics, so the more the perspective we can observe, the better our understanding is. Biological data banks can be explored to distill and collect appropriate datasets for the samples of interest to integrate, thanks to an appropriate biological reasoning and computational strategy, the emerging properties of the system under analysis.
Development of software tools for computational biology
As a bioinfomatics Lab, we frequently face the necessity to approach analyses with novel strategies and therefore to abandon the “easy way” and design novel programs, routines or pieces of software. Sometimes we develop optimized strategies that adapt the input/output of known programs to collectively produce biologically sounding results. Some other times, simply the program has to be invented de-novo because no appropriate existing tools or solutions are feasible for the specific task. Accordingly, we develop, in the most appropriate languages (R, Python, Perl, Ruby, RAST etc.) solutions for specific applications or improvement for existing ones. During the year many of them have been published and freely available, Please visit https://github.com/matteoramazzotti for discovering the entire collection of our tools developed during the years.
Publication performances
Prof. Matteo Ramazzotti at 2025 counts 115 scientific papers, among which 11 as first author and 4 as last author. Elsevier JCR and Google Scholar report, respectively, H-index of 28 and 34 and Total citations of 7.695 and 11.377
Current/recent sources of funding
Intesa San Paolo, Ingegnerie Toscane, Regione Toscana, PNRR Tuscany Health Ecosystem (THE), PRIN N4EN
Ten best publications in the last 5 years
Di Gloria L. Lotti T. van Loosdrecht M.C. Ramazzotti M. Who calls granules “home”? Domain-spanning meta-analysis charting microbial ecosystems underlying aerobic granular sludge reactors, Bioresource Technology 2026
Di Gloria L. Casbarra L. Lotti T. Ramazzotti M. Testing the limits of short-reads metagenomic classifications programs in wastewater treating microbial communities. Scientific Reports 2025
Russo E. Bellando-Randone S. Carboni D. Fioretto B.S. Romano E. Baldi S. El Aoufy K. Ramazzotti M.,[…], Amedei A. The differential crosstalk of the skin-gut microbiome axis as a new emerging actor in systemic sclerosis. Rheumatology (United Kingdom) 2024
Russo E. Gloria L.D. Nannini G. Meoni G. Niccolai E. Ringressi M.N. Baldi S. Fani R. Tenori L. Taddei A. Ramazzotti M. Amedei A. From adenoma to CRC stages: the oral-gut microbiome axis as a source of potential microbial and metabolic biomarkers of malignancy.Neoplasia (United States) 2023
Niccolai E. Baldi S. Nannini G. Gensini F. Papi L. Vezzosi V. Bianchi S. Orzalesi L. Ramazzotti M. Amedei A. Breast cancer: the first comparative evaluation of oncobiome composition between males and females. Biology of Sex Differences 2023
Correnti M. Cappon A. Pastore M. […] Ramazzotti M. Parri M. Recalcati S. di Tommaso L. Campani C. Invernizzi P. Torzilli G. Marra F. Pontisso P. Raggi C. The protease-inhibitor SerpinB3 as a critical modulator of the stem-like subset in human cholangiocarcinoma. Liver International 2022
La Rosa G. Iaconelli M. [...] Ramazzotti M. [...] Suffredini E. The rapid spread of SARS-COV-2 Omicron variant in Italy reflected early through wastewater surveillance. Science of the Total Environment 2022
Raggi C. Taddei M.L. [...] Ramazzotti M. Orlandi I. Arcangeli A. Chiarugi P. Marra F. Mitochondrial oxidative metabolism contributes to a cancer stem cell phenotype in cholangiocarcinoma. Journal of Hepatology 2021
Niccolai E. Russo E. [...] Ramazzotti M. Amedei A. Significant and Conflicting Correlation of IL-9 With Prevotella and Bacteroides in Human Colorectal Cancer. Frontiers in Immunology 2021
Emmi G. Bettiol A. Niccolai E. Ramazzotti M. […] Becatti M. Butyrate-Rich Diets Improve Redox Status and Fibrin Lysis in Behçet's Syndrome Circulation Research 2021
Collaborations
Tommaso Lotti (DICEA UniFi)for metagenomics of industrial bioreactors
Giulio Munz (DICEA UniFi) for metagenomics of industrial bioreactors
Amedeo Amedei (DMSC UniFi) for microbiota in pathology
Guidi Marchi (DAGRI UniFi) for bacteria genomics
Duccio Cavalieri (DBAG UniFi) for Saccharomyces genomics
Ultimo aggiornamento
25.03.2026