1st Call of ELIXIRxNextGenIT for National Open Access (TNA/NOA)
ELIXIRxNextGenIT offers free remote access to Italian research facilities for Genomics and Metabolomics. Services include analysis, consumables, and data repository.
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"ELIXIR-IT: A Bridge Between Research and Biotechnological Industry": Key Takeaways
Researchers, academics and entrepreneurs discussed how ELIXIR-IT can play a key role in connecting the world of public research with that of biotechnology companies.
"ELIXIR-IT: A Bridge Between Research and Biotechnological Industry": Key Outcomes and Report
The event in Bari brought together academia and biotech industry. It highlighted ELIXIR-IT's role in fostering collaboration and innovation in the life sciences.
ELIXIR-IT & Researchalize Partnership: Empowering Collaboration in Biomedical Research
ELIXIR-IT is collaborating with Researchalize, a platform connecting biomedical researchers in Italy. It facilitates networking, knowledge sharing, and access to resources, funding and the latest research topics.
Agreement signed between the Italian nodes of the Research Infrastructures BBMRI and ELIXIR (BBMRI.IT and ELIXIR.IT) to promote synergies for Biomedical Research in Italy
BBMRI.it and ELIXIR-IT are collaborating to advance biomedical research and precision medicine in Italy by integrating bioinformatics and biobanking.
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Recent publications
Ab initio detection of multiple epitranscriptomic modifications from ONT direct RNA sequencing data
Non-canonical nucleotides are widespread chemical modifications in eukaryotic genomes and transcriptomes, especially within the epitranscriptome. Traditional enrichment-based sequencing methods cannot detect them at single-molecule resolution, a limitation overcome by nanopore sequencing. Researchers from the University of Bari (Italy) present a transformer-based model for the ab initio detection of multiple RNA modifications, along with two tools, NanoListener and NanoSpeech, to create training datasets and develop modification-aware basecallers. Their approach enables the simultaneous identification of up to nine ribonucleotide variants.
Embedding-Based Alignments Capture Structural and Sequence Domains of Distantly Related Multifunctional Human Proteins
Protein embeddings encode sequence information using protein language models. The Embedding-Based Alignment (EBA) method enables pairwise embedding comparison and remote homolog detection. In this paper we show that, when applied to a set of multifunctional human proteins, EBA identifies remote homologs sharing structural and functional features, validated on the Swiss-Prot database.
CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications
CREDO, a Customizable, REproducible, DOcker file generator for bioinformatics applications, has been developed as a tool to moderate reproducibility issues by building and distributing docker containers with embedded bioinformatics tools. CREDO simplifies the process of generating Docker images, facilitating reproducibility and efficient research in bioinformatics.
An automated pipeline integrating AlphaFold 2 and MODELLER for protein structure prediction
In this work, it is evaluated the possibility of improving AlphaFold2’s three-dimensional predictions by developing a new pipeline (AlphaMod) that integrates AlphaFold2 with MODELLER, a traditional homology modeling program. For this study, MARCONI100 at HPC@CINECA was used, which was made available through an ELIXIR project.