Weekly Brief, 27 November 2023

This week's highlights

Announcement of co-leads for the new Science Priority Areas

As ELIXIR prepares for the start of the 2024-2028 ELIXIR Scientific Programme, we are pleased to announce the selection of the co-leads for the new Science Priority Areas.

Cellular and Molecular Research will be led by:
Fotis Psomopoulos, ELIXIR Greece | Silvio Tosatto, ELIXIR Italy |
Patrick Aloy, ELIXIR Spain
With the support of Fabio Liberante (Coordinator) and Clare Garrard from ELIXIR Hub
Biodiversity, Food Security & Pathogens will be led by:
Robert Waterhouse, ELIXIR Switzerland | Cyril Pommier, ELIXIR France |
Tereza Manousaki, ELIXIR Greece
With the support of Katharina Heil (Coordinator) and Physilia Chua from ELIXIR Hub

Please join us in welcoming them to their new roles. More information about the Priority Areas and how ELIXIR Members can participate will be published throughout 2024.

ELIXIR Communications Group meeting - Sharing experiences of generative AI

4 December 2023 | 13:30-14:30 CET

The next ELIXIR Communications Group meeting will focus on experiences of generative AI. Everyone with an interest in generative AI are welcome to join.

Agenda and Zoom link to the meeting

New vacancy: International Relations Officer

ELIXIR is currently seeking an enthusiastic International Relations Officer to join the External Relations team. The role will include working on EU-funded projects - notably the new ELIXIR-STEERS (starting February 2024) - with an expectation of working on other external grants awarded to ELIXIR in future.

Find out more

Recommended reads

Predictive biomarkers of immunotherapy response with pharmacological applications in solid tumors

An ELIXIR-HU paper

Immune-checkpoint inhibitors show promising effects in the treatment of multiple tumor types. Biomarkers are biological indicators used to select patients for a systemic anticancer treatment, but there are only a few clinically useful biomarkers such as PD-L1 expression and tumor mutational burden, which can be used to predict immunotherapy response. In this study, the authors established a database consisting of both gene expression and clinical data to identify biomarkers of response to anti-PD-1, anti-PD-L1, and anti-CTLA-4 immunotherapies. A database and a web platform were established to investigate biomarkers of immunotherapy response in a large cohort of solid tumor samples. The results could help to identify new patient cohorts eligible for immunotherapy.

Read more

Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data

An OpenEBench paper

The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. There is an increasing need for benchmarks and for the provision of infrastructure for continuous method evaluation. The authors reviewed 17 tools and benchmarked eight on their ability to perform APA identification and quantification, using a comprehensive set of RNA-seq experiments comprising real, synthetic, and matched 3-end sequencing data. To support continuous benchmarking, the authors have incorporated the results into the OpenEBench online platform, which allows for continuous extension of the set of methods, metrics, and challenges.

Read more

Updates from Nodes

New method for measuring gut microbiota

Gut microbiota have an effect on human health, but how they work is not known well enough. The behaviour of microbiota at protein level is studied at the University of Turku by means of metaproteomics.

Find out more

Updates from Focus Groups

First Research Infrastructure Career Paths Focus Group meeting

1 December 2023 | 11:00-13:00 CET | Online

The new Focus Group aims to promote interest in research infrastructure roles to support the career development of researchers beyond the traditional academic paths. More information about the Focus Group on ELIXIR website

Join the mailing list and email for more information on the first meeting

Updates from other initiatives

RDA end-of-year Cross-Community Carousel webinar

30 November 2023 | 6:00-7:30 UTC & 16:00-17:30 UTC

The Community Cross-Fertilisation Carousel will bring together the RDA's 10th anniversary celebrations, reflecting on the outcomes of the Community Cross-Fertilisation workshop series held this year. Join the carousel for a tour of the workshop series, exploring the content, and learning about the main challenges and future actions for the RDA community to focus on.

EUCAIM Stakeholder Survey about the Cancer Image Europe platform

The purpose of this survey is to gather insights that can significantly contribute to understanding the expectations of potential end-users and stakeholders, and identifying crucial aspects for future engagement and collaboration with the platform.

Fill out the survey

Help shape the future of pandemic prep, schema consensus, sequencing metadata, and categorical variants in four new GA4GH groups

The Global Alliance for Genomics and Health (GA4GH), a Strategic Partner of ELIXIR, welcomes any interested ELIXIR community members to join four new groups. These international teams are just getting started and are eager for new voices. Learn more and sign up:

GA4GH fireside chat with Wellcome Sanger Institute Director Matthew Hurles

12 December 2023 | 15:00 CET | Online

The next GA4GH virtual fireside chat invites Matthew Hurles, Director of the Wellcome Sanger Institute, to sit down with GA4GH Chair Ewan Birney to discuss the latest in responsible genomic data use. Beyond directing the Institute, Hurles leads a research group on genomic mutation and severe developmental disorders.

Register today

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

8th de.NBI Genomics training course
11-12 December 2023 | Giessen, Germany

BioSB course: Integrated modeling and optimization
11-15 December 2023 | Wageningen, the Netherlands

PerMedCoE course: From transcriptomics to mechanistic models of signalling
12 December 2023 | 12:00-16:30 CET | Online

SIB course: First Steps with UNIX in Life Sciences
16 January 2024 | Basel, Switzerland

EMBL-EBI course: Livestock genomics
18 - 22 March 2024 | Online

ELIXIR Events and Conferences

ELIXIR hCNV Community F2F/hybrid meeting
30 November-1 December 2023 | Hybrid - Hinxton, UK

RDM Community & Implementation Study Kick-off Meeting
4-6 December 2023 | Hybrid - Bergen, Norway

ELIXIR Compute Platform 2024 Face-to-Face Meeting
24 January 2024 | Brno, Czech Republic

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

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