CONVECS @ HPCSIM2025

Last week, Giacomo attended HPCSIM25 – Frontiers of High-Performance & Cloud Computing in Modeling and Simulation, held in Padova, Italy, on September 11–12, 2025.

The event focused on the latest methodologies and technologies in the field of High-Performance Computing (HPC), offering researchers and practitioners an overview of the current landscape and future directions of HPC in both real-world applications and scientific research.

Giacomo delivered an oral presentation titled “High-Performance Scientific Computing in Veneto: The CONVECS Initiative”, introducing the CONVECS project (COmuNità VEneta per il Calcolo Scientifico) where he is responsible for leading multiple core tasks. This initiative, recognized as an Operation of Strategic Importance by the Veneto Regional Government, aims to enhance, consolidate, and interconnect the HPC infrastructures currently available across universities and research laboratories in the Veneto region. Its goal is to create a unified, scalable computing environment accessible to both academic researchers and technology-driven enterprises, driving measurable impact in science, industry, and society.

Sysbiobig @ CIBB2025

Last week we attended the 20th Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB2025) in Milano from September 10th to 12th, 2025.

We’re proud to share that our group contributed to the scientific program with three oral presentations showcasing our recent research efforts:

🧠 Piero Mariotto, Ilaria Patuzzi, Giada Innocente, Barbara Simionati, Barbara Di Camillo, Giacomo Baruzzo “A network science-based approach to unveil the effects of faecal microbiota transplantation in enteropathic dogs” (great collaboration with EuBiome srl)

📊 Federico De Mori Bajolin, Anna Maria Bianchi, Erica Tavazzi “A multivariate deep-learning approach for stratifying Amyotrophic Lateral Sclerosis patients based on temporal dynamics


💉 Davide Dei Cas, Barbara Di Camillo, Gian Paolo Fadini, Giovanni Sparacino, Enrico Longato “The impact of clinical history on the predictive performance of machine learning and deep learning models for renal complications of diabetes

Sysbiobig @ISMB/ECCB 2025

Last week, Barbara, Giacomo, Giulia, Gaia, and Matteo attended the 33rd Conference on Intelligent Systems for Molecular Biology & 24th European Conference on Computational Biology (ISMB/ECCB 2025), held in Liverpool, UK, from July 20–24, 2025.

The conference was a valuable opportunity to attend cutting-edge presentations, engage in discussions on the latest advances in bioinformatics, and foster new collaborations.

We’re proud to share that our group contributed to the scientific program with several presentations:

  • Giulia Cesaro delivered an oral presentation in the NetBio session titled “Cell-specific Graph Operation Strategy on Signaling Intracellular Pathways” showcasing work done in collaboration with the CostaLab at RWTH Aachen University.
  • Giacomo Baruzzo presented the poster “Realistic Simulation of NGS Reads from Tumoral Samples with MOV&RSim”, a project led by Francesca Longhin (former PhD student of our group), in collaboration with AB Analitica.
  • Matteo Baldan presented the poster “Integrating Biological Knowledge for Feature Summarization in Spatial Transcriptomics”.
  • Gaia Tussardi presented the poster “Multilevel Network Visualization for Deciphering Dysregulated Cellular Signalling”.
  • In collaboration with the CostaLab at RWTH Aachen University, we also co-organized the tutorial “Computational Approaches for Deciphering Cell-Cell Communication from Single-Cell and Spatial Transcriptomics Data”.

Our contribution to AIME 2025 in Pavia

Last week, our group attended the 23rd International Conference on Artificial Intelligence in Medicine (AIME 2025) in Pavia, Italy.

It was a fantastic opportunity to follow high-quality presentations and engage with leading researchers and professionals from across the AI and healthcare communities.

We are proud to share that we contributed to the scientific program with four research papers:

  • Erica Tavazzi co-authored the poster “Towards Distributed Process Discovery in Healthcare: Testing and Proving the Feasibility of the Federated Alpha+ Algorithm.”
  • At the 2nd International Workshop on Process Mining Applications for Healthcare (PM4H 2025), our group was also involved in two contributions: “Predicting Next Clinical Event in Amyotrophic Lateral Sclerosis using Process-Oriented Machine Learning Models: a Case Study” and “Federated I-PALIA: Privacy-By-Design Distributed Process Discovery for Duplicated Activities in Healthcare” (🏆Best Paper Award – PM4H 2025).

We sincerely thank the conference organizers for hosting this event and for giving us the opportunity to share our research.

New Review on Cell–Cell Communication Published in Briefings in Bioinformatics!

We are excited to share our latest review article, “Advances and challenges in cell–cell communication inference: a comprehensive review of tools, resources, and future directions”, now published in Briefings in Bioinformatics:
📖 https://doi.org/10.1093/bib/bbaf280

This review offers a detailed overview of the current landscape of computational methods and databases used to infer cell–cell communication.

Key highlights include:
🔍 Analysis of 26 ligand-receptor resources, highlighting differences in coverage, species, signaling types, etc-
🔍 Classification of 58 bioinformatics tools for CCC inference, evaluated by input data requirements, computational strategies (intercellular, intracellular, differential communication), and output characteristics, as well as implementation choices
🔍 It also features a curated online catalog of CCC resouces and tools, designed to support researchers in identifying the most appropriate methods based on their data and analysis goals: https://sysbiobig.gitlab.io/ccc-catalog

This work is a collaboration between groups from the Departments of Information Engineering and Biology at the University of Padova, the Institute of Biomedical Technologies at the National Research Council (CNR), and the RWTH Aachen Medical Faculty’s Institute for Computational Genomics.

Three New PhD Graduates in Our Research Group!

On March 20th, 2025, we proudly celebrated the achievements of Isotta Trescato, Giulia Cesaro, and Francesca Longhin, who successfully defended their Ph.D. theses in Information Engineering at the University of Padua. 🎉

Each of them conducted outstanding research on cutting-edge topics in computational medicine and bioinformatics, contributing valuable knowledge and tools to their respective fields.

🔬 Giulia Cesaro focused her PhD research on the development of computational methods to infer cell-cell communication using single-cell RNA sequencing data. Her work allows for a deeper understanding of how cells interact with each other in complex tissues—knowledge that is critical for interpreting biological processes such as development, immune response, and disease progression.

🧬 Francesca Longhin worked on enhancing variant calling and interpretation pipelines through data-driven in-silico simulations and artificial intelligence techniques. Her project improves the accuracy and reliability of genetic variant analysis, a fundamental aspect of personalized medicine and genomic diagnostics.

📊 Isotta Trescato dedicated her thesis to transparent artificial intelligence approaches for modeling disease progression using real-world clinical registry data. Her goal was to build predictive models that are not only accurate but also interpretable by clinicians—an essential requirement for integrating AI into real-world healthcare settings.

Sharing Our Research in High Performance Computing applied to Bioinformatics at PDP 2025 & Best Paper Award!

Last week, Giacomo attended the 33rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (March 10-12, 2025 – Turin, Italy).

It was a great opportunity to attend insightful talks and engage in discussions about the present and future of high-performance computing!

We are also proud to share that our work, “quickSparseM: a library for memory- and time-efficient computation on large, sparse matrices with application to omics data” by Giacomo Baruzzo, Giulia Cesaro, and Barbara Di Camillo, received the Best Paper Award in the “High Performance Computing in Modelling and Simulation” session. The article will soon be available in the conference proceedings on the IEEE website (https://www.computer.org/csdl/proceedings/1000543).

We extend our sincere thanks to the conference and session organizers for hosting this event and giving us the opportunity to present our research!

2nd progress meeting of the REDDIE project @UNIPD

In the past few days, we had the pleasure of hosting the second progress meeting of the Horizon Europe REDDIE project at our Department of Information Engineering. Over two days of discussions, we reviewed progress across work packages, shared insights on emerging results, and conducted workshops on key challenges within each WP.
It was a fantastic opportunity to welcome our international partners, exchange ideas in person, and strengthen collaborations—while also enjoying good food and the first signs of spring in Padua! 😊

2nd Annual Meeting of the DARE Initiative

On 20-21 February 2025, the Istituto Ortopedico Rizzoli in Bologna hosted the 2nd Annual Meeting of the DARE – Digital lifelong prevention initiative – Spoke 3 on Digitally Enabled Secondary and Tertiary Prevention. The event gathered researchers, clinicians, and experts working on innovative digital health solutions to enhance disease prevention and early diagnosis.
Our researcher Enrico Longato presented our latest work within Work Package 3 (WP3), focusing on the development of AI-driven digital tools for kidney disease prediction in diabetes. These tools leverage data and computational models to support personalised and data-driven healthcare approaches, aligning with the broader goals of the DARE Initiative.
We are proud to contribute to this important initiative and to collaborate with a multidisciplinary network of researchers committed to advancing digital health. The meeting provided a valuable opportunity for discussions, knowledge exchange, and new perspectives on integrating AI into clinical workflows.
We look forward to further developments and continued collaboration within the DARE Initiative.

Building Bridges Between Engineering and Medicine Through AI

On Tuesday, 21 January 2025, the Aula Morgagni at the Policlinico Universitario of Padua hosted the event “Introduction to Artificial Intelligence in Medicine.” Organised by the Departments of Information Engineering (DEI) and Medicine (DIMED), the meeting brought together experts and researchers to discuss the transformative role of AI in healthcare.

The session was opened by Professors Gaudenzio Meneghesso, Director of the DEI, and Paolo Simioni, Director of the DIMED, who welcomed attendees and highlighted the interdisciplinary collaboration driving AI innovation.

The scientific programme included a series of engaging presentations:

  • Introduction to Machine Learning by Prof. Barbara Di Camillo (DEI) provided a comprehensive overview of the fundamentals of machine learning and its applications in medical research.
  • Applications to Clinical Records by Dr. Erica Tavazzi (DEI), a researcher from our group, explored AI-driven approaches to extracting insights from patient data.
  • Applications to Imaging Data by Dr. Marco Castellaro (DEI) demonstrated how AI enhances diagnostic imaging techniques.
  • Large Language Models and Generative AI and Chatbots were expertly discussed by Prof. Giorgio Satta (DEI), who highlighted their potential to revolutionise communication and support activities.
  • Data Representation and Knowledge in Generative AI by Prof. Nicola Ferro (DEI) delved into the technical challenges and opportunities in knowledge-based systems.

The event concluded with a dynamic Q&A session, fostering lively discussions among attendees and speakers.

Systems Biology and Bioinformatics Group
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