Our paper is out in NAR Genomics and Bioinformatics

🚀 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

Explore the tools:
🔗 https://gitlab.com/sysbiobig/scseqcomm
🔗 https://gitlab.com/sysbiobig/cclens

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.

Sysbiobig @BITS2025

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. 🧬📘

JOIN OUR TUTORIAL ON CELL-CELL COMMUNICATION AT ISMB/ECCB 2025

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.

📅 Date: July 15, 2025

💻 Where: Online (Virtual)

🔗 Register at ISMB/ECCB25: https://www.iscb.org/ismbeccb2025/register

👉 Learn more: https://www.iscb.org/ismbeccb2025/programme-agenda/tutorials#vt3

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!

First International BioHackathon of BITS-2025 

CINI Young-InfoLife, RSG-Italy, and Young BITS invite you to the “First International Biohackathon of BITS”, an exciting team-based bioinformatics challenge in collaboration with the BITS 2025 conference in Naples and the HPC4AI computing center of the University of Turin.

The BioHackathon event
📅 When? June 10, 2025 – Live Hackathon, on the eve of BITS 2025 (June 11-13)
📍Where? Faculty of Biotechnology, Via Tommaso De Amicis, 95, 80131 Naples, Italy
🔍The Challenge: Get ready to dive into single-cell RNA-seq data analysis! The exact theme will be revealed live during the event.

Get ready through webinars
Before the competition, there will be preparation live-streamed webinars, with recordings available to the Young-Infolife YouTube channel
🔗 https://www.youtube.com/@younginfolife
📅 Webinar Schedule:
April 1 – Reproducibility, containerization, and HPC usage
April 15 – Single-cell RNA-seq: wet lab protocol and quality control
April 29 – Single-cell RNA-seq: computational methods (part 1)
May 13 – Single-cell RNA-seq: computational methods (part 2)
May 27 – Q&A + spoiler session

✍️ Pre-registration: fill this form (https://forms.gle/ZSA11FSSkVMqNKye9) by May 1, 2025

📩 Stay updated! Please fill the form below to be added into the dedicated mailing list and be updated about the webinars, the in-person event and all the latest news!

https://younginfolife.github.io/events/2025-biohackathon

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.

Systems Biology and Bioinformatics Group
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