Congratulations to our post-doc researcher Giulia Cesaro who has been awarded the PhD Thesis Award 🏆 by the Istituto di BioRobotica – Scuola Superiore Sant’Anna during the XLIV Annual School 2025 of the Gruppo Nazionale di Bioingegneria (GNB).
✨ Her doctoral dissertation was recognized by the committee “for the originality of the content and the ability to apply engineering approaches to the analysis of cell-to-cell communication from transcriptomic data, in a complex biological system, tackled with methods that reveal and model its complexity.” 💻
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.
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“
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”.
🚀 We’re excited to share that our latest paper is now published in NAR Genomics and Bioinformatics: Differential cellular communication inference framework for large-scale single-cell RNA-sequencing data, https://doi.org/10.1093/nargab/lqaf084
We introduce a novel computational framework tailored for analyzing and interpreting differential cell–cell communication in complex, large-scale scRNA-seq datasets. The framework incorporates two tools: scSeqCommDiff, which identifies and characterizes alterations in cell–cell communication in a fast and memory-efficient manner, and CClens, which facilitates interpretation and exploration through an interactive R/Shiny interface.ì
What’s new? 👥 Works across diverse experimental designs 🔍 Captures both intercellular and intracellular signaling 📊 Designed for big data: fast and memory-efficient 🖥️ Comes with an interactive Shiny app for easy and insightful exploration
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.
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.
Last week, we had an incredible time at the BITS 2025 – Bioinformatics Italian Society Conference in Naples: three days full of exciting events, inspiring talks, and cutting-edge research! 🎉🎤✨
First and foremost, we were excited to show the community what we’ve been working on! 🔹 Giacomo Baruzzo held an oral presentation: “Sustainable computation on large, sparse omics matrices with quickSparseM.” 💻🌿 Learn more about how quickSparseM is advancing efficient omics data analysis ➡️ https://doi.org/10.1109/PDP66500.2025.00045 🔹 Giulia Cesaro presented a poster on her latest project, developed in collaboration with RWTH Aachen University, “Intracellular signaling pathway reconstruction at single-cell resolution.” 🧬🔬
But that’s not all! Members of our group also contributed to organizing two exciting events at BITS 2025: 🧠 The First International BioHackathon of the Bioinformatics Italian Society 👥 The Young Symposium session The goal was to provide early-career scientists with opportunities to develop critical research skills, engage in interdisciplinary teamwork, and build a supportive scientific network. 🧬📘
In collaboration with CostaLab of RWTH University of Aachen, we are hosting a tutorial titled “Computational approaches for deciphering cell-cell communication from single-cell transcriptomics and spatial transcriptomics data” at the ISMB/ECCB 2025.
This tutorial will provide a comprehensive introduction to computational approaches for inferring cell-cell communication using single-cell and spatial transcriptomics data. We will cover the fundamental concepts of cellular communication, the assumptions underlying the analysis, and focus on the main computational methods currently used in the field.
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.
