Weekly Brief, 17 June 2024

This week's highlights

Thank you for joining us in Uppsala!

Thank you to all who attended, spoke at and engaged with the ELIXIR All Hands 2024. It was great to see everyone having lively discussions in person. We look forward to meeting with you all again next year in Greece!

Recommended reads

Prioritisation of oligogenic variant combinations in whole exomes

An ELIXIR-BE paper

This paper presents the High-throughput oligogenic prioritizer, a novel prioritization method that uses direct oligogenic information at the variant, gene and gene pair level to detect digenic variant combinations in WES data. This method leverages information from a knowledge graph, together with specialized pathogenicity predictions in order to effectively rank variant combinations based on how likely they are to explain the patients phenotype. The results provide a significant improvement over alternative approaches that depend simply on a monogenic assessment of pathogenicity, including early attempts for digenic ranking using monogenic pathogenicity scores.

Read more

Detection of ribonucleotides embedded in DNA by Nanopore sequencing

An ELIXIR-IT paper

Ribonucleotides represent the most common non-canonical nucleotides found in eukaryotic genomes. The sources of chromosome-embedded ribonucleotides and the mechanisms by which unrepaired rNMPs trigger genome instability and human pathologies are not fully understood. The authors synthesised two types of DNA molecules containing rNMPs at known or random positions and developed data analysis pipelines for DNA-embedded ribonucleotides detection by ONT. This paper proposes that ONT may be successfully employed to directly map rNMPs in genomic DNA and suggests a strategy to build an ad hoc basecaller to analyse native genomes.

Read more

Updates from Nodes

 

How FAIRsharing helps you enable FAIR: focus on standards, repositories and policies

27 June, 12 -1.30 pm BST | Online

With Allyson Lister, University of Oxford, this workshop introduces FAIRsharing, a widely-adopted, curated, informative and educational resource on standards inter-related to repositories and policies across all disciplines.

Register now

Updates from Platforms

Compute Platform face-to-face report

The ELIXIR Compute Platform is pleased to share the report on this year's successful face-to-face event which took place 24-25 January 2024 in Brno, Czech Republic. The report with full information can be found on Zenodo.

Check the report

Interoperability Survey on data practices and challenges

As part of the Interoperability project plan, ELIXIR Interoperability Platform wants to collect challenges and best practices within ELIXIR communities. Please fill out the short survey to help the Platform members understand your data practices and challenges related to interoperability within life sciences.

Fill out the survey

Upcoming ELIXIR events & webinars

ELIXIR Training Courses & Webinars

The ELIXIR TeSS portal has a variety of interesting events and courses organised by the ELIXIR Nodes. For more, visit TeSS portal

3D-BioInfo Webinar: High Throughput Structural Bioinformatics
18 June 2024 | 17:00 - 18:00 CEST

ELIXIR Events and Conferences

ECCB 2024
16-20 September 2024 | Turku, Finland

ELIXIR Data Platform F2F 2024
1 - 2 October 2024 | Padova, Italy

ELIXIR STEERS WP2 & WP3 Workshop
2 - 3 October 2024 | Padova,. Italy

BioHackathon Europe 2024
4 - 8 November 2024 | Barcelona, Spain

Job vacancies

All vacancies are also published on the ELIXIR website (also including those from industry). If you need our help communicating your new open positions, you can submit a job advertisement and it will automatically appear on our newsletters. Go to our vacancy page to submit a job
 

Data Science Internship

WhiteLab Genomics

Research Software Engineer

RECETOX

Scientific Database Curator

EMBL EBI

Junior Professorship in AI and Multiscale Modeling in Biology and Bio-medicine

University of Montpellier / CNRS / INSERM

FutureData4EU PhD Program

Universities of Bologna - Parma - Modena and Reggio Emilia - Ferrara