Tag: news

🚀 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

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”.

Last week, our group attended the 23^rd 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:

• Davide Dei Cas held a short oral presentation entitled “Exploring the Use of Projecting Conflicting Gradients in Multi-Task Neural Networks with an Application to Amyotrophic Lateral Sclerosis.”

• Erica Tavazzi co-authored the poster “Towards Distributed Process Discovery in Healthcare: Testing and Proving the Feasibility of the Federated Alpha+ Algorithm.”

• At the 2^nd 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.

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.

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!