SysBioBiG partecipate at BITS 2026

🧬 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.

New Article on N2SIMBA: a microbial community simulator published in Frontiers in Bioinformatics!

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.

The paper is available at: https://doi.org/10.3389/fbinf.2026.1783447

SysBioBiG at DEILeaks 2026

🚀 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 Health Informatics 🧬 💻

Two Research Contributions from Our Group Presented at ATTD 2026

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.

Celebrating a top PhD graduate

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.

Participation in the UNIPD Annual Event of the DARE Initiative

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.

Bioinformatics seminars @ University of Parma

🎙️ ✨ Last week, Giacomo and Giulia were invited to give a seminar at the Department of Mathematical Physical and Computer Science of University of Parma, where they presented the current bioinformatics research of our group.

The talks showcased our efforts to advance computational modelling of cell-cell communication, ranging from our 📔 work providing a comprehensive overview of the field (Briefings in Bioinformatics, 2025) to the presentation of our tools:
– 🧬scSeqComm (Bioinformatics, 2022) and scSeqCommDiff (NAR Genomics & Bioinformatics, 2025) for inferring cellular interactions
– 💻 quickSparseM (IEEE Proceedings of PDP 2025) for time- and memory-efficient computation on large, sparse omics matrices,
– 📊 CClens (NAR Genomics & Bioinformatics, 2025) for intuitive visualization and interpretation of multidimensional cell-cell communication results
– 📈 MAST (Bioinformatics Advances, 2022) for modeling tumor–immune dynamics across time and space using an hybrid multi-agent model

It was a great opportunity to share our recent progress, exchange ideas, and engage in stimulating discussions.
We warmly thank Professor Vincenzo Bonnici for the invitation and for organizing this seminar series at the Università degli studi di Parma.

Our Research Group at AI@DEI 2025 – From Research to Industry

Last week our research group took part in AI@DEI 2025 – From Research to Industry, the annual event organised by the Department of Information Engineering (DEI) of the University of Padova and the Regional Innovation Network IMPROVENET, with the support of UniSMART.
The initiative aims to strengthen the dialogue between academia and industry, showcasing concrete applications of Artificial Intelligence across a wide range of sectors, from computer vision to predictive maintenance, industrial decision-making, robotics, automation, and conversational technologies.

As part of the programme, our researcher Erica Tavazzi delivered the presentation: “Fondo Italiano per le Scienze Applicate: AI e diagnostica avanzata nella partnership DEI–AB Analitica contro l’antibiotico resistenza”.

The talk, prepared together with Dino Paladin (AB Analitica), introduced READY – Responsive Early Antibiotic resistance Detection and therapY, the project funded by the Italian Applied Sciences Fund (FISA) and launched this year. READY focuses on integrating AI, automation, and advanced diagnostics to support the early detection of antimicrobial resistance.

We warmly thank DEI, IMPROVENET, and UniSMART for organising the event, as well as all participating companies and colleagues for the productive exchange of perspectives.
A special acknowledgement goes to Sara Brugnerotto, whose photos beautifully captured the atmosphere of the day.

New article on biologically informed feature summarization in spatial transcriptomics now published!

procedure scheme

🚀 We’re excited to share that our latest paper is out: Biologically Informed Procedure for Feature Summarization in Spatial Transcriptomics — a new framework designed to uncover the spatial organization of rare yet biologically crucial features, such as transcription factors, in imaging-based single-cell RNA sequencing data (e.g., MERFISH).

📊 In this work, we introduce a comprehensive procedure that integrates:
TANGRAM, to align and integrate MERFISH with scRNA-seq data.
Decoupler with COLLECTRI prior knowledge, to derive biologically grounded activity scores for transcription factors.
Spatial statistics, to detect spatially informative features and highlight their organizational patterns across tissue sections.

🔍 By combining these elements, our workflow enables the discovery of subtle yet functionally relevant spatial signatures that would otherwise remain hidden — providing a powerful tool for interrogating tissue architecture in single-cell spatial genomics.

👥 This achievement was made possible thanks to the collaborative work of all authors and the support of the IJCNN organizers. Special thanks to the members of SysBioBiG – Systems Biology and Bioinformatics Group at UNIPD, who shared this journey with us.

🔗 The paper is available at: https://doi.org/10.1109/IJCNN64981.2025.11227921

New article on realistic tumoral sample simulation published in BMC Bioinformatics!

🚀 We’re excited to share that our latest paper is now published in BMC Bioinformatics: MOV&RSim: computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation, https://doi.org/10.1186/s12859-025-06292-0

📊 We developed MOV&RSIM, a novel simulator that leverages data-driven information to set variants and reads characteristics, producing realistic tumoral samples, and providing full control on biological and technical parameters. Additionally, we leveraged well-annotated variant databases to create cancer-specific presets that inform the simulator’s parameters for 21 cancer types.

🔍 The proposed simulator and presets represent the most adaptable and comprehensive computational framework currently available for generating tumor samples, enabling comprehensive benchmarking and, ultimately, the optimization of somatic variant callers across diverse cancer types.

👥 This research is the result of a collaboration between our group and AB ANALITICA srl. Congratulations to the first author, Dr. Francesca Longhin, who developed MOV&RSim during her doctoral studies in our research group!

🔗 The tool is freely available on gitlab at: https://gitlab.com/sysbiobig/movarsim

Systems Biology and Bioinformatics Group
Privacy Overview

This website uses cookies so that we can provide you with the best user experience possible. Cookie information is stored in your browser and performs functions such as recognising you when you return to our website and helping our team to understand which sections of the website you find most interesting and useful.