On September 25–26, our group is taking part in the international conference “Skeletal Muscle in ALS – Mechanisms, Biomarkers, and Therapeutic Perspectives”, held in Padova and organised by ASLA APS, with Gianni Sorarù, Maria Pennuto, Manuela Basso and Matteo Zanovello as members of the organising committee. The conference brings together researchers and clinicians to discuss the role of skeletal muscle in ALS, from disease mechanisms and biomarkers to emerging therapeutic strategies.
As part of the session “Muscle Biomarkers in ALS”, our group leader Barbara Di Camillo will present the talk “Toward reliable and responsible ALS progression prediction: development and external validation of clinical models”, focusing on the development of computational approaches for reliable prediction of ALS progression.
The conference highlights the increasingly interdisciplinary nature of ALS research, connecting neurology, molecular biology, biomarker research and data-driven approaches to better understand disease progression and support more personalised strategies.
We warmly thank the organisers for the invitation and for creating this opportunity for exchange across different areas of ALS research.
Last week, Barbara Di Camillo, Davide Dei Cas, and Sergio Gaiotti from our research group attended the XLV GNB Annual School – “Generative Artificial Intelligence for Bioengineering” in Brixen.
The school explored the methodological and practical applications of Generative AI in bioengineering, including data analysis, biological modelling, experimental design, and scientific communication.
🎤During the school, Barbara delivered a lecture on Responsible AI, focusing on data quality, model validation and generalisation, interpretability, and human oversight.
💻🏆Davide and Sergio participated in the school and in the hands-on challenge. The week ended with a great result: Davide’s team won the challenge with a project on generating dermatoscopic images from conventional clinical images of skin lesions.
The school was a valuable opportunity to deepen our knowledge of Generative AI, reflect on its responsible use, and exchange ideas with researchers from different areas of bioengineering.
We are happy to share the latest milestones reached by our PhD students, who recently presented the progress of their research activities.
Admission to the Third Year of the PhD Programme
Elena, Matteo, and Piero successfully presented the progress of their research and were admitted to the third year of the PhD programme.
Elena presented the latest developments in her research on phenotype- and patient-specific network representations of multi-omics data for interpretable network medicine (in collaboration with FBK). Her work combines recent advances in network science and machine learning to develop computational approaches for the analysis and interpretation of complex biomedical data.
Matteo presented his research on scalable and interpretable computational methods for large biomedical datasets. His work combines High-Performance Computing (HPC) and Large Language Models (LLMs) to extract knowledge from heterogeneous sources of biomedical data.
Piero presented his project on the inference of bacterial interaction networks from metagenomic data (in collaboration with Eubiome srl). His current work includes the simulation of large-scale complex interaction networks, the benchmarking of state-of-the-art network inference methods, and the development of robust computational pipelines for network reconstruction.
Admission to the Thesis External Evaluation Phase
Gaia and Matteo successfully presented the results of their PhD research and were admitted to the external thesis evaluation phase.
Gaia presented her PhD project on interactive visual analytics for interpretable biomedical network modelling. Her research focuses on designing and developing effective visualization approaches and network models for investigating cell–cell communication from single-cell transcriptomics data, as well as on leveraging interactive visualization to enhance explainable artificial intelligence in the biomedical domain.
Matteo presented the results of his three years of research on complex networks for the analysis of biological systems. His work spans several areas, from the simulation of microbial interaction networks to the development of scalable software libraries for large-scale multilayer networks, and from graph-based machine learning to multilayer network approaches for studying cellular communication in spatial transcriptomics.
Congratulations to Elena, Matteo, Piero, Gaia, and Matteo on reaching these important milestones, and best wishes for the next stages of their PhD journey!
Our research group participated in the 21st Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2026), held in Rome from September 2 to 4, 2026.
During the conference, our PhD student Sergio Gaiotti presented the contribution “Treatment persistence drives estimator performance in longitudinal causal inference based on observational data: A simulation study”, authored by Sergio Gaiotti, Sara Poletto, Enrico Longato, Erica Tavazzi, and Martina Vettoretti.
The work, developed within the European REDDIE – Real-World Evidence for Decisions in Diabetes project, investigates how treatment dynamics influence the performance of causal inference methods for longitudinal observational data. In particular, the study highlights the role of treatment persistence in determining the behaviour of baseline and longitudinal estimators, showing that treatment dynamics can have a greater impact than functional complexity on estimator performance.
We thank the session chairs and the CIBB 2026 organisers for the stimulating discussion and for another great edition of a conference that has long been a regular appointment for our group.
🧬 Our group had a great time participating in BITS2026, the 22nd Annual Conference of the Bioinformatics Italian Society, held in Padua from May 27–29, 2026.
The conference provided an excellent opportunity to share our latest research, exchange ideas with colleagues, and connect with the vibrant Italian and international bioinformatics community.
A special highlight was the 2nd International BioHackathon, organized by our group members Giulia Cesaro and Giacomo Bruzzo in collaboration with Young BITS, CINI Young InfoLife, and ISCB RSG Italy. Bringing together talented young scientists from across Italy and Europe, the BioHackathon challenged participants to decode biological networks from omics data through collaboration, creativity, and innovation. The event showcased the enthusiasm and scientific excellence of the next generation of computational biologists.
🎤 We were also proud to see our PhD student Matteo Andriolo present our work on ArchetypalC, a scalable and high-performance C++ implementation of Archetypal Analysis for large-scale bioinformatics applications. ArchetypalC supports sparse matrices, parallel computation, and interactive visualization, enabling efficient exploration of complex biological datasets.
Our group also contributed with two additional posters:
🎤 Elena Marinello presented GRAPHIA, a pipeline for deriving patient-specific network features by weighting a shared biological interaction graph according to individual gene expression profiles.
🎤 Mikele Milia presented scTransformer, a novel framework for SingleCellTranscriptomics that incorporates prior biological knowledge into the self-attention mechanism of Transformer models.
We’re excited to share that our latest paper is now published in Frontiers in Bioinformatics: “N2SIMBA: from Network topology to SIMulation of interactions and BActerial abundance, using microbial consumer resource model.”
In this work, we introduce N2SIMBA, a modular simulation framework designed to generate realistic 16S rDNA-seq count tables starting from known microbial interaction networks. Since experimentally validated ground-truth interaction networks are rarely available, especially for complex bacterial communities, N2SIMBA provides a flexible in silico tool to systematically benchmark network inference methods.
The framework leverages the Microbial Consumer Resource Model to simulate microbial community dynamics through metabolite-mediated interactions, accounting for both competitive and promotional effects between taxa. By combining ecological modelling with sequencing count simulation, N2SIMBA enables users to study how community composition changes under different network topologies, environmental conditions, and perturbations.
We hope this framework will be useful for researchers interested in microbial ecology, systems biology, and the design of robust bacterial communities. New features and extensions are already under active development!.
Congratulations to Matteo Baldan, Giacomo Baruzzo, Piero Mariotto, Ada Rossato, Marco Cappellato, and Barbara Di Camillo for this work.
🚀 We are excited to take part in DEILeaks – ResearchBeyondExams, an initiative giving Bachelor’s and Master’s students the opportunity to discover ongoing research activities and meet research groups working across different scientific fields.
During the event, our team have presented the activities of the SysBioBiG Research Group at the Department of Information Engineering, focusing on research in Bioinformatics and HealthInformatics 🧬 💻
Last week, our research group had the opportunity to take part in the 19th International Conference on Advanced Technologies and Treatments for Diabetes (ATTD 2026), held in the fascinating city of Barcelona, Spain.
During the conference, our PhD student Sara Poletto presented two research contributions developed within the framework of the European project REDDIE, which we are proud to be part of.
Advancing research in diabetes is essential to improve prevention, management, and quality of life for millions of people worldwide, and we are excited to contribute to this collective effort.
On February 12, 2026, Mikele Milia successfully defended his PhD thesis in Information Engineering at the University of Padua. His outstanding research and dedication culminated in a PhD awarded with honors. 🏅🏆
🖥️ His PhD thesis focused on the integration of omics data with prior biological knowledge as input to advanced models to generate meaningful insights. His outstanding work addressed significant methodological and computational challenges posed by large-scale biological data.
On 16 January 2026, the “Guido Petter” Conference Hall at the School of Psychology hosted the annual meeting dedicated to the UNIPD’s activities within the DARE (DigitAl lifelong pRevEntion) initiative. The event featured an overview of the ongoing DARE projects led by UNIPD researchers, a seminar delivered by the Arsenal.IT consortium on the secondary use of healthcare data, and two roundtable discussions designed to encourage multidisciplinary exchange.
During the meeting, Professor Barbara Di Camillo took part in an insightful roundtable discussion entitled “From Research to Healthcare Practice: Working Together for New Perspectives in Prevention.” In addition, our researcher Enrico Longato presented the current progress of Work Package 3, Task 3.3a, entitled “Digitally-Empowered Management of Type 2 Diabetes: From Diagnosis to the Prediction of Complications.”
Overall, the meeting provided an important opportunity to exchange ideas, strengthen collaborations, and gain a comprehensive view of the diverse and innovative contributions of UNIPD within the DARE initiative.
