Category: important_news

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Key Takeaways from Our Team’s Participation at the World Health Forum Veneto 2024

On 21-22 March 2024, our team had the pleasure of attending the Artificial Intelligence for Medicine conference, hosted within the World Health Forum Veneto in Padova.

Our PI Prof. Barbara Di Camillo delivered an insightful talk titled “Bringing AI into clinical practice: A deep dive into the BRAINTEASER project”, where she presented our work to bring responsible AI into clinical practice. On this occasion, Professor Di Camillo was also interviewed by the prestigious Corriere della Sera, as featured in the article below.

This event was also an opportunity to present some of our group’s latest work. Our senior researchers Erica Tavazzi and Enrico Longato presented a poster titled “Improving Discrimination Performance in Artificial Intelligence Models for Rare Diseases: Strategies for Dealing with Data Scarcity”, sharing insights into strategies for enhancing predictive model performance with limited data.

This event, designed to examine the current state and explore the future of medical sciences and technologies aimed at enhancing care and life quality, was a great opportunity to network and foster new collaborations.

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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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✨ 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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📢 Call for contribution for CIBB 2023 📢

The 18th Computational Intelligence Methods for Bioinformatics and Biostatistics Conference CIBB 2023 will take place in 📍 Padova (Italy) on 📆 6-8 September 2023.

👉 Call for papers

Submit your short paper (4-6 pages) describing your original contributions in the fields of bioinformatics, biostatistics, systems and synthetic biology, and medical informatics.

🗓️ Deadline: 30 April 2023

ℹ️ For submission guidelines and further information have a look at the Conference website: https://cibb2023.dei.unipd.it/call-for-paper.html

👉 Check the special sessions

In addition to the main track, the conference will provide for a number of special sessions focused on specific, cutting-edge topics: you can find all the details at https://cibb2023.dei.unipd.it/call-for-special.html.

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Join our workshop “Introduction to Software Containerization in Bioinformatics” on February 21st with RSG Italy & ISCB

making reproducible, portable and reusable bioinformatics software&pipelines 🧬💻

Reproducibility is a major principle underpinning the scientific method, and it is of pivotal importance for bioinformatics studies. Bioinformatics analyses are typically the results of pipelines of software packages, each one having multiple running options and frequent updates that often changes their default behaviors. Moreover, bioinformatics softwares extensively rely on external libraries/packages, thus limiting the portability and reusability of the software, requiring to properly install and configur a large amount of dependencies, and building/compiling of the application on different target systems. Containers are the solutions to most of the above issues.

🤝The workshop is organized in collaboration with RSG Italy (italian regional student group of ISCB).

📖 PREREQUISITES: Basic knowledge of Linux-based operating systems (e.g. Ubuntu) and Linux terminals is required.

🗓 WHEN: the 21th February 2023 from 2:30 to 6:00 PM
📍WHERE: online ZOOM
📢 REGISTRATION: register now on Eventbrite