Author: Giacomo Baruzzo

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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.

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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”.
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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!

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University meets Industry: AI @ DEI

On November 20 and 21, 2024, the Department of Information Engineering of the University of Padova, in collaboration with Fondazione UniSMART, organized two events on Artificial Intelligence: “AI@DEI for Industry” and “AI@DEI for Biomeds and Health”.

The events focused on innovative topics such as Generative AI, Data Analytics, AI in biomedical research and healthcare, Bioinformatics, and Health Informatics, showcasing practical applications and future perspectives for collaboration between University and Industry.

During the event, our researcher Giacomo Baruzzo presented the AI activities in Bioinformatics and Health Informatics carried out by the computer engineering group, including some research projects conducted by our research group.

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Great moments at BITS 2024 conference in Trento

Our group has attended the 20th Annual Meeting of the Bioinformatics Italian Society (BITS 2024) in Trento. It was an incredibly successful event!
We are proud to have contributed to the event with 2 oral presentations from Gaia and Piero:

  • “Limitations of the co-occurrence-based approach in the inference of microbiota interaction networks” Piero Mariotto, Matteo Baldan, Barbara Di Camillo, Giacomo Baruzzo
  • “Interactive exploration of cell-cell communication results from single-cell RNA sequencing data through a webapp” Gaia Tussardi, Giulia Cesaro, Barbara Di Camillo, Giacomo Baruzzo

Also, Gaia co-chaired the “YOUNG BITS, RSG-Italy & CINI Young-InfoLife” Symposium, a supporting and stimulating forum for undergraduate, master, PhD students and early stage researchers to present their research and to connect with the wider Italian Bioinformatics Community.

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In two weeks we will attend the 19th Annual Meeting of the Bioinformatics Italian Society (BITS 2023) with 1 oral communication & 3 poster contributions

  • Oral communication: “CClens: effective and efficient differential cellular communication analysis of large-scale single-cell RNA sequencing data” (G. Cesaro, G. Baruzzo, B. Di Camillo)
  • Poster contribution: “Data-driven meta-simulation of realistic tumoral samples” (F. Longhin, E. Hazizaj, G. Baruzzo, B. Di Camillo)
  • Poster contribution: “mopo16Sweb: a cloud-based app for multi-objective optimization of bacterial 16S PCR primers” (M. Milia, N. Ferro, B. Di Camillo, G. Baruzzo)
  • Poster contribution: “From microbial ground truth network simulation to inference method benchmark” (M. Baldan, A. Rossato, M. Bellato, G. Baruzzo, B. Di Camillo)

For more details, check the conference website: https://bioinformatics.it/bits2023

Systems Biology and Bioinformatics Group
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