Category: news

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

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.

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

Data science and artificial intelligence for supporting the care and cure of amyotrophic lateral sclerosis and multiple sclerosis patients

BRAINTEASER is a data science project that seeks to exploit the value of large clinical datasets integrated with personal and environmental data collected through low-cost sensors, to develop AI-based clinical software and mobile apps to support patients with amyotrophic lateral sclerosis and multiple sclerosis and their clinicians.

The meeting is an important opportunity to share with a wider audience the first results achieved by the project through a multidisciplinary approach implemented during the last 2 years, to discuss the most relevant issues of the models and technology put in place, highlighting future opportunities and challenges.

The workshop will also serve as a place for reflection on the importance of transformative research, with a view to identifying the opportunities that arise from the National Plan for Recovery and Resilience and the related strategic lines of use of the funds envisaged by the Next Generation EU Programme.

When?

BRAINTEASER has planned the mid-term workshop on the 28th February 2023 from 09:30 to 12:00 CET.

How to attend?

Do not miss the opportunity to attend this mid-term workshop.

The event, which can be also attended online, will be held at the prestigious venue of the Botanical Garden of the University of Padua. You can use the following links:

• to join the event online
• to join the event in presence

Full programme

The BRAINTEASER mid-term workshop full programme can be accessed here.

The last years have seen an impressive revolution in the theory and application of bioinformatics since new technologies and the abundance of different types of data to be integrated in a personalized medicine perspective are posing various methodological challenges in different fields such as, for example, single cell analysis, individual genome analysis and pan-genomes, Multi-omics data analysis and integration with clinical data.
In this special issue, we invite researchers to submit primary research focusing on translational bioinformatics methods that, starting from population-based molecular profiling, clinical data, epidemiological data, and other types of data make healthcare decisions tailored to groups of patients or individual patients.

📢 SPECIAL ISSUE on Journal of Biomedical Informatics
🗓️SUBMISSION DEADLINE: January 31, 2023
ℹ️MORE INFO: https://doi.org/10.1016/j.jbi.2022.104170
➡️GUEST EDITORS: Prof. Barbara Di Camillo (SysBioBig, Unipd) and Prof. Rosalba Giugno (InfOmics, Univr)

• Oral communication: “Differential cellular communication analysis across multi-condition and multi-patient scRNA-seq data” (G. Cesaro, G. Baruzzo, B. Di Camillo)
• Oral communication: “An agent-based simulator for microbial communities’ evolution” (M. Bellato, M. Cappellato, A. Calzavara, S. Rebecca, A. Lucchiari, B. Di Camillo)

• Poster contribution: “Somatic read simulators: how to build a realistic gold standard using data from well-annotated cancer databases” (E. Hazizaj, F. Longhin, G. Baruzzo, B. Di Camillo)
• Poster contribution: “Simulation of ground truth interaction networks from microbial community model” (A. Rossato, M. Cappellato, G. Baruzzo, B. Di Camillo)
• Poster contribution: “Simulate tumor microenvironment evolution from sequencing data through a hybrid Multi-Agent Spatio-Temporal model” (G. Cesaro, M. Milia, G. Baruzzo, P. Alotto, N.F. da Cunha Carvalho de Miranda, Z. Trajanoski, F. Finotello, B. Di Camillo)

For more details, check the conference website: https://www.bbcc-meetings.it/

Just come back from ECCB2022 in Sitges, Barcellona. We had the opportunity to participate (finally in presence) in this great conference. Lots of talks, new opportunities for collaboration and exchange of ideas. This is research and science!
A list of our contributions:
– Workshop: “Spatial transcriptomics and cell-cell communication modeling: new opportunities to study the cellular dynamics of biological systems” (Baruzzo G, Calura E, Risso D, Romualdi C, Sales G, García-Alonso L, Vento-Tormo R, Saez-Rodriguez J, Saeys Y)
– Tutorial: “Software containerization in bioinformatics: how to make reproducible, portable and reusable bioinformatics software&pipelines” (Baruzzo G, Di Camillo B, Cappellato M, Cesaro G, Milia M)
– Poster contribution: “Differential Abundance analysis of microbiome data: which tool and how to choose it?” (Cappellato M, Baruzzo G, Di Camillo B)
– Poster contribution: “Analysis of differential cellular communication from single cell RNA-seq data with scSeqComm” (Cesaro G, Baruzzo G, Di Camillo B)
– Poster contribution: “Temporal changes in microbiome composition after FMT in subject with Clostridioides difficile infection: a network perspective” (Cappellato M, Bellato M, Baruzzo G, Facchin S, Barzon L, Besutti V, Brun P, Del Favero S, Schenato L, Savarino EV, Castagliuolo I, Di Camillo B)
– Poster contribution: “Tumor microenvironment evolution simulated through a hybrid Multi-Agent Spatio-Temporal model informed using sequencing data” (Milia M, Cesaro G, Baruzzo G, Finco G, Morandini F, Lazzarini A, Alotto P, de Miranda NF, Trajanoski Z, Finotello F, Di Camillo B)
– Poster contribution: “Simulation of ground truth interaction networks from microbial community model” (Rossato A, Cappellato M, Nikoloska N, Baruzzo G, Di Camillo B)