IRTA seeks post-doc researcher
IRTA (the Animal Breeding and Genetics Program) is currently seeking a postdoctoral researcher to participate in studies within the framework of the GENE-SWitCH project regarding:
• The identification of expression QTL (eQTLs) in relevant metabolic porcine tissues using high-throughput genomic sequence data;
• Validation of new predictive models (Bayesian and machine learning models) using functional genome annotations (including eQTLs) to increase the accuracy of genomic predictions.
Please check here for more information.
Post-doc position at Roslin Institute
A postdoc position developing reproducible pipelines and software infrastructure to analyse functional genomics data is available at the Roslin Institute. This position is available as a part of the GENE-SWitCH project. The deadline for the application is 21 September. For more information, please check here.
First Annual Meeting of GENE-SWitCH
On July 8-9, GENE-SWitCH held its first Annual Meeting by videoconference, with mornings dedicated to general presentations on project progress by Work Package (WP) and Pillar leaders. The afternoons were dedicated to workshops on specific topics.
Stakeholder Advisory Board recommendations
One most interesting aspect of this Annual Meeting was to meet for the first time “in person” (albeit virtually) with some of our Stakeholder Advisory Board members. We received from them very interesting suggestions and useful remarks. Among them, it was recognized that the strong interconnections between Pillars and WPs is a strength of this project, with the recommendation to not underestimate the time and skills required to exploit it at its full potential.
They also recommended to disseminate our findings as efficiently as possible, as these are inherently relevant to sustainable development and global changes regarding climate and environment. Moreover, the planned actions to contribute to the education of the younger generation of scientists in the public and livestock industry sectors are of particular relevance.
Strength in numbers
The clustering with the other EU and international FAANG projects, with the recent establishment of the EUROFAANG node, offers an important change of scale for dissemination and outreach, and as such, a strong opportunity to inspire the public at large about the genomics of FAANG.
In conclusion, we had a nice and productive meeting. The project has been advanced well in its initial year, and we expect the first consolidated results about a year from now. Despite the recent activities being coordinated remotely, our Consortium appears to be well connected, and, until now, we encountered only limited delays caused by the COVID-19 pandemic.
GENE-SWitCH's brochure online
We are pleased to announce the first GENE-SWitCH brochure is now available on our website! The introductory brochure of the GENE-SWitCH project provides compact information on the project aim, structure, partners, expected outputs and impact.
First Annual Meeting will be held online
Due to Covid-19 pandemic, GENE-SWitCH project's first annual meeting will be done remotely on 8th and 9th July 2020. More information will be available soon!
GENE-SWitCH's 1st Newsletter is published!
We are delighted to announce that the first newsletter of the GENE-SWitCH project is now available!
This very first issue includes news and developments about the project, scientific articles and a closer look at the coordination team of the GENE-SWitCH project.
Please click on the image below to enjoy reading our newsletter! Don't forget to subscribe to our mailing list if you wish to receive the newsletters of the GENE-SWitCH project!
FAANG Shared Workshop: "Foundation for the Future Agenda"
FAANG shared workshop was held at the Rosalind Franklin Pavilion, Wellcome Genome Campus Conference Centre, Hinxton, UK on the 25th-27th February 2020.
The aim of the workshop was to establish coordination of plans for cross project (species) comparative analysis, standardised metadata, standardised FAANG analysis workflows/pipelines, planning for future shared dissemination, training and management meetings. An overview of GENE-SWitCH and the core annotation workplan ("GENE-SWitCH project overview, approach to bioinformatics and comparative analysis") was given by Sarah Djebali (INSERM, France).
This meeting was an excellent opportunity for cross project networking, with concrete actions such as the establishment of common working groups for bioinformatic pipelines validation and comparative genomics.
FAANG Europe Workshop
The 2nd FAANG-Europe COST Action Conference on Functional Annotation of Animal Genomes (FAANG) took place in Prague, Czech Republic between 11 – 13 February 2020.
Peter Harrison from EMBL-EBI gave a talk about “The FAANG Data Coordination Centre: New European perspectives for our continued global effort” at the conference, representing EMBL-EBI's Data Coordination Centre work on GENE-SWitCH, AQUA-FAANG and BovReg projects.
International Plant & Animal Genome Conference XXVIII
The International Plant and Animal Genome Conference (PAG XXVIII) took place in San Diago, CA, USA between 11-15 January 2020. It is designed to provide a forum on recent developments and future plans for plant and animal genome projects. Consisting of technical presentations, poster sessions, exhibits and workshops, the conference is an excellent opportunity to exchange ideas and applications on this internationally important project.
GENE-SWitCH project coordinator Elisabetta Giuffra made a poster presentation (click image on the left) at the conference providing information about the aims, first achievements and perspectives of the GENE-SWitCH project.
At the conference, Peter Harrison (EMBL-EBI) presented "The FAANG Data Coordination Centre: New European Perspectives for Our Continued Global Effort", explaining the development of FAANG DCC and FAANG Data Portal. Mick Watson (Roslin Institute) also gave a presentation about "A Vision for Bioinformatics within the Global FAANG Project". Watson presented the development of bioinformatics pipelines across the entire set of FAANG projects, based on the principles of open science, open source code and reproducible workflows and environments. Both presentations are available by clicking on the images below.
GENE-SWitCH at ISAG 2019
The 37th International Society for Animal Genetics (ISAG) Conference was held in Lleida, Spain in July 2019. The Conference brought together outstanding scientists, policy makers, professionals and students from interdisciplinary animal genetics fields to share the latest developments, meet old friends and form new partnerships.
At the ISAG conference, Elisabetta Giuffra from INRA presented "Introduction to FAANG (Functional Annotation of Animal Genomes"-Goals and Opportunities". Giuffra mentioned about the Data Coordination Centre and FAANG Data Portal. She presented 3 projects of the FAANG consortium, BovReg, AQUA-FAANG and GENE-SWitCH. Her presentation covered the overall objective, concept and the consortium of GENE-SWitCH, which can be found here.
GENE-SWitCH project has started!
"The regulatory GENomE of SWine and CHicken: functional annotation during development - GENE-SWitCH" project's fruitful kick-off meeting took place on September 10-11, 2019 in beautiful Paris.
Director of the INRA Animal Genetic Division Edwige Quillet started the opening session of the meeting with the presentation of INRA. Jean-Charles Cavitte from the European Commission took the floor to present GENE-SWitCH and related EU funded research landscape. GENE-SWitCH project coordinator Elisabetta Giuffra talked about the overall project’s aims, concept, ambition, structure and highlighted the connections with the global FAANG initiative.
First day of the meeting continued with the presentations on the project's 3 pillars namely "Identification and characterization of functional genomic elements" (Pillar 1), "Implementing FAANG innovation for animal breeding" (Pillar 2) and "Standardization of data and processes, dissemination and outreach" (Pillar 3) and ended with the parallel session discussions on the work packages of the project.
Second day of the meeting started with the clustering activities session with the presentations of BovReg and AQUA-FAANG, followed by round table discussions. During the plenary session, work packages of the project were further discussed and the meeting concluded with action points to be completed for the upcoming months.
GENE-SWitCH project has started!
The Kick-off Meeting of GENE-SWitCH will take place on September 10-11, 2019 in Paris, France!
The GENE-SWitCH project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No 817998. This publication reflects the views only of the author, and the European Union cannot be held responsible for any use which may be made of the information contained therein.