Synbionics is an interdisciplinary research laboratory based at the University of Parma (Italy), operating at the intersection of computer science, artificial intelligence, and the life sciences. Our mission is to develop and adapt advanced AI algorithms tailored to the needs of bioinformatics, medical informatics, and biomedical research, with a strong focus on real-world impact in medicine and biology.

What sets Synbionics apart is its emphasis on the symbiosis between computer science and the life sciences. Our work not only applies AI to solve complex problems in biology and healthcare, but also draws deep inspiration from biological systems to design novel computational models. By exploring this bidirectional relationship, we aim to create AI solutions that are both biologically inspired and biomedically driven — advancing innovation within life sciences while also contributing to the broader field of computer science.

At Synbionics, we believe that the future of artificial intelligence lies in collaboration — between disciplines, methodologies, and scientific communities.

People

Prof. Vincenzo Bonnici

Head of the laboratory

Prof. Alessandro Dal Palù

Co-head of the laboratory

Dr. Flavio Bertini

Assistant professor

Current members

Dr. Emiliano Maresi, Ph.D. - Post-doc

Fiorenzo Tittaferrante - Grant holder

Simone Colli - Master student

Matteo Boroni Grazioli - Master student

Francesco Minei - Bachelor student

Mattia Pasquali - Bachelor student

Michelle Shuaipi - Bachelor student

Hamdi Ben Abdallah - Bachelor student

Hiba El Kaouak - Bachelor student

Davide Perazzoli - Bachelor student

Dorin Nicorean - Bachelor student

Ramandeep Singh - Bachelor student

Pietro Pontremoli - Bachelor student

Former members

Mattia Numeroso - Bachelor student

Costantin ALlincai - Bachelor student

Leopoldo Antozzi - Bachelor student

Simone Lo Castro - Bachelor student

Mirko Uni - Bachelor student

Samuele Rota - Bachelor student

Research areas

Computational pangenomics

Computational microbiology and metagenomics

Omics and multiomics data analysis

Projects

B4WEB - A Biomolecular taxonomy, Biosources and Bioactivities to liberate the potential of Biodiversity through a web-based platform

The "B4Web" project focuses on developing the 3-NBFC platform, a web-based system designed to integrate and systematize information about biodiversity. This platform aims to facilitate the understanding and utilization of biodiversity by bringing together data on biomolecular taxonomy, biosources, and bioactivities. The project is part of the PNRR-M4C2-I1.4-BAC initiative, with the specific reference NBFC- CN00000033, focusing on unlocking the potential of biodiversity.

BIOCHAIN-AI - A platform for securely sharing and analysing microbiological data

BIOCHAIN-AI aims at developing a platform for managing the data of biological collections of a consortium. The platform registers the requests and their responses to the digital information. In particular, what has been requested, who requested the information, when, and for what purpose.

In addition, it will allow consortium members to perform computational analyses for exploiting public and private information in a federated learning manner. In this way, members owning specific rights to a given dataset are motivated to share their data because they are rewarded by the possibility of combining it with data owned by other members to perform holistic analyses, without explicitly revealing the data itself.

The platform will be composed of two layers. A layer will implement the security aspects of the platform and ensure fairness among consortium members. In fact, through a distributed ledger system (a blockchain), data sharing transactions will be registered, so that every member actively stores and verifies them. The data itself will be stored off-chain and identified by a unique identifier, primarily the hash code of the information it contains. Access to the data will be guaranteed by smart contracts that run on the blockchain. The smart contracts will interact with the second layer of the platform, which will be responsible for defining the protocol for exposing data, requesting it, and managing federated learning jobs.

It is expected that the prototype, as well as future developments of it, will have a significant impact on the national and European networks of institutions related to microbiology. Microbial resources are of great interest for many research fields such as agri-food (biofertilizers and biopesticides for sustainable agriculture, starter, protective or aromatic strains to produce fermented foods), human health (nutraceuticals, probiotics, human microbiomes for personalized medicine), environment (bioremediation strategies and development of bioprocesses aimed at obtaining compounds of technological interest, like nanomaterials).

Bonnici, V., Arceri, V., Diana, A., Bertini, F., Iotti, E., Levante, A., ... & Dal Palù, A. (2023, May). Biochain: towards a platform for securely sharing microbiological data. In Proceedings of the 27th International Database Engineered Applications Symposium (pp. 59-63).

News

CIBB 2025 - Special Session on "Computational Methods for Microbiological Research"

Dear Colleagues,

We are pleased to invite you to submit your latest research to the Special Session on "Computational Methods for Microbiological Research" to be held within the 20th Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2025).

The conference will take place in Milan, Italy, from September 10th to 12th, 2025. Conference Website: https://www.bioinformatics.polimi.it/CIBB2025/

This special session explores computational approaches driving advancements in our understanding of the microbial world. Microbes play crucial roles in diverse ecosystems, from human health and disease to biogeochemical cycles and industrial processes. Unlocking their secrets requires sophisticated computational tools capable of analyzing the massive datasets generated by modern sequencing technologies.

This session aims to showcase the latest computational intelligence methods applied to microbial genomics, pangenomics, and metagenomics. We invite submissions that address novel algorithms, machine learning approaches, network analysis, and statistical methods for microbial data. We particularly encourage contributions that tackle the challenges of data integration, visualization, and interpretation in the context of complex microbial datasets.

The scope encompasses diverse applications, including: understanding the role of the microbiome in health and disease, discovering novel antimicrobials, engineering microbial communities for biotechnology, and assessing the impact of environmental changes on microbial ecosystems.

This special session aims to foster a better understanding of microbial life, serve as a forum for information sharing, spark new collaborations, and inspire future research in this rapidly evolving field.

Topics include, but are not limited to:

Sequence Assembly and Annotation
Comparative Genomics
Metagenomic Analysis
Pangenomics
Machine Learning in Microbiology
Network Analysis
Microbiome Research
Antimicrobial Resistance
Microbial Ecology
Data Visualization and Integration

Submission Deadline: April 30, 2025 - Please note this upcoming deadline!

Submission System: Papers should be submitted electronically through the CIBB 2025 EasyChair submission page (link available on the main conference website: https://www.bioinformatics.polimi.it/CIBB2025/).

Formatting: Please follow the paper submission guidelines available on the CIBB 2025 website. Ensure you select the "Special Session on Computational Methods for Microbiological Research" during the submission process.

Special Session Organizers:

Vincenzo Bonnici, Department of Mathematical, Physical and Computer Sciences, University of Parma, Italy.
Alessia Levante, Department of Food and Drug, University of Parma, Italy.
Gabriele Andrea Lugli, Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Italy.
Christian Milani, Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Italy.

Partners

CINI Infolife Laboratory

Synbionics is active partner of the CINI (Consorzioni Iteruniversitario Nazionale per l'Informatica) bioinformatics laboratory Infolife.

If you are a young bioinformatician and you would like to become part of the Infolife community, enrol in the young-Infolife group https://younginfolife.github.io/

InfOmics

Bioinformatics reseach laboratory of the University of Verona, Italy.
https://infomics.github.io/InfOmics/

iOR - Bioinformatics Core Unit

Institute of Oncology Research - Università della Svizzera Italia - Bellinzona, Switzerland
https://ior.usi.ch/facilities/bioinformatics-core-unit

SYNBIONICS - Bioinformatics Research Lab - University of Parma, Italy