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Advancing ALS Research: Collaborative Efforts with Precision ALS

Recently we had the pleasure to start collaborating with Precision ALS, a research programme for Amyotrophic Lateral Sclerosis (ALS) research across Europe, which brings together ALS clinicians, data scientists, and industries to provide new insights into the understanding of this rare disease. 

This month, we attended a Precision ALS meeting in Basel, where clinical, scientific, and industry experts gathered to discuss the latest frontiers in the development and utilisation of predictive models for ALS. Together with our partners from the University of Torino, we presented our research work in the field and the new models and tools developed within the H2020 BRAINTEASER Project.

Building upon our collective knowledge of AI applied to ALS research, we aspire to bring our expertise and insights into the collaborative initiatives of Precision ALS, advancing the understanding and treatment of this multifaceted, complex disease.

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Charting the Course: Insights from AI Methodological Review for ALS Progression in the BRAINTEASER Project

In the context of the H2020 BRAINTEASER project, our group is in charge of developing predictive models for the progression of Amyotrophic Lateral Sclerosis (ALS) and Multiple Sclerosis (MS). In order to identify the most promising approaches to be implemented, we coordinated a systematic review of the artificial intelligence (AI) methodological landscape in ALS, focusing on patient stratification and disease progression prediction, which we performed together with the other project partners.

Out of 1604 reports, we identified 15 studies on patient stratification, 28 on ALS progression prediction, and 6 on both. We highlighted a general agreement in terms of input variable selection for both stratification and prediction of ALS progression, and in terms of prediction targets. A striking lack of validated models emerged, as well as a general difficulty in reproducing many published studies, mainly due to the absence of the corresponding parameter lists. While deep learning seems promising for prediction applications, its superiority with respect to traditional methods has not been established; there is, instead, ample room for its application in the subfield of patient stratification. Finally, an open question remains on the role of new environmental and behavioural variables collected via novel, real-time sensors.

The full article is available here.

These findings laid the groundwork for the development of our models within the project, providing valuable insights into the most effective AI methodologies for patient stratification and disease progression prediction in ALS. They are also guiding our direction in identifying key areas for further development and refinement.

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✨ CIBB2023 Success: Advancing Computational Intelligence

The General Chairs and Local Committee want to express their heartfelt gratitude to all of you who contributed to this unforgettable and remarkable conference 🙏 From inspiring keynote lecture to innovative talk and networking opportunities, CIBB2023 has bring together brilliant researchers from Bioinformatics, Biostatistics, Systems and Synthetic Biology, and Medical Informatics 🖥️

We are proud to have contributed to the event with

  • “Leveraging on somatic sample simulators for realistic data-driven generation of tumoral genomes“, Francesca Longhin, Enidia Hazizaj, Giacomo Baruzzo and Barbara Di Camillo
  • “N2BPC: an algorithmic approach from Networks to Bacteria’s metabolite Production and Consumption“, Matteo Baldan, Giacomo Baruzzo and Barbara Di Camillo
  • “Bactlife: A Dash GUI to simulate bacterial communities evolution“, Massimo Bellato, Marco Cappellato, Sara Rebecca, Andrea Calzavara, Alessandro Lucchiari, Niccolò Venturini Degli Esposti and Barbara Di Camillo
  • “Differential cellular communication analysis from large-scale single-cell RNA sequencing data“, Giulia Cesaro, Giacomo Baruzzo and Barbara Di Camillo
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Exciting moments at ISMB/ECCB2023 conference in Lyon

Our group has attended the 31st Annual Intelligent Systems For Molecular Biology (ISMB) and the 22nd Annual European Conference on Computational Biology (ECCB) conference. It was an incredibly successful event!

🚀 Our Tutorial was a triumph!

We are elated by the overwhelming response to our tutorial “How to make reproducible, portable and reusable bioinformatics software using software containerization“. The high demand showcased the significance of this topic in the software development landscape.

🎤 Sysbiobig on the Stage!

It was a privilege and an honor to present our work among esteemed professionals and researchers through 4 oral presentations and 8 poster contributions

  • Oral communication & Poster contribution “Modeling the tumor microenvironment with a hybrid Multi-Agent Spatio-Temporal model fed with sequencing data” (Mikele Milia, Giulia Cesaro, Giacomo Baruzzo, Piegiorgio Alotto, Noel Filipe da Cunha Carvalho de Miranda, Zlatko Trajanoski, Francesca Finotello, Barbara Di Camillo)
  • Oral communication “CClens: a cellular communication workflow for large-scale single-cell RNA sequencing data” (Giulia Cesaro, Giacomo Baruzzo, Barbara Di Camillo)
  • Oral communication & Poster contribution “scSeqComm: a statistical and network-based framework to infer inter- and intra-cellular communication from single-cell RNA sequencing data” (Giacomo Baruzzo, Giulia Cesaro, Barbara Di Camillo)
  • Oral communication & Poster contribution “Comprehensive benchmarking of differential abundance methods in microbiome data” (Marco Cappellato, Giacomo Baruzzo, Barbara Di Camillo)
  • Oral communication “Interactive and effective visualization framework for interpreting and exploring cellular communication data” (Giulia Cesaro, Giacomo Baruzzo, Barbara Di Camillo)
  • Poster contribution: “Bactlife – A Dash GUI to simulate bacterial communities’ evolution via agent-based modeling” (Massimo Bellato, Marco Cappellato, Sara Rebecca, Andrea Calzavara, Alessandro Lucchiari, Niccolò Venturini Degli Espositi, Barbara Di Camillo)
  • Poster contribution “Towards automatic ACMG evidence identification for variant interpretation” (Francesca Longhin, Alessandro Guazzo, Enrico Longato, Diego Boscarino, Dino Paladin, Nicola Ferro, Barbara Di Camillo)
  • Poster contribution “Comprehensive review of tumoral sample simulators: building a realistic gold standard for somatic variant calling validation” (Francesca Longhin, Enidia Hazizaj, Giacomo Baruzzo, Barbara Di Camillo)
  • Poster contribution “mopo16Sweb: A webapp for multi-objective optimization of 16S rRNA primers sequences on the cloud” (Mikele Milia, Nicola Ferro, Barbara Di Camillo, Giacomo Baruzzo)
  • Poster contribution: “Shedding light on cellular communication analysis: the present and the future” (Giulia Cesaro, James S. Nagai, Alice Chiodi, Vanessa Klöker, Nicolò Gnoato, Ettore Mosca, Ivan Costa, Enrica Calura, Barbara Di Camillo, Giacomo Baruzzo)

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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

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SysBioBig is now on LinkedIn!

We’re excited to inform you that our newest LinkedIn account has been officially opened.

Be sure to follow us on LinkedIn too, to stay updated on our latest projects and keep in touch with us even further.

Let’s connect and innovate together!

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Invited talk @ the Italian Internal Medicine Society Congress 2023

Today our post-doc Enrico Longato gave a talk at the Italian Internal Medicine Society Congress 2023 on the use of Big Data in the management of non-transmissible chronic diseases. This was a great opportunity to showcase the work performed by our team and open the discussion on how to best cooperate with internal medicine specialists.

Thank you for the invitation to the SIMI society and the congress organisers!

Systems Biology and Bioinformatics Group
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