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The regulatory GENomE of SWine and CHicken: functional annotation during development


Fully functional data coordination platform for production use

Production release of the data coordination platform for the validation enrichment and submission of GENESWitCH sample experiment and analysis data to FAANG through the European public archives The preliminary system will already have been heavily tested optimised and utilised from sample and raw data will be submitted steadily from the start of the project This final version will contain the full configuration of the submission process for the requirements of work packages 1 2 4 and 5

Reproducible, scale-able workflows for FAANG data analysis

We will release on GitHub workflows that are 100% reproducible and scale-able from laptop to HPC to cloud, using a workflow language such as Snakemake or NextFlow, integrating best-in-class bioinformatics open-source software

Raw sequences of WGBS and RRBS delivered to ENA and FAANG

fastq files and metadata available at FAANG and ENA.

Raw sequences of RNA-seq delivered to ENA and FAANG

fastq files and metadata available at FAANG and ENA.

Bio-repository of 3120 samples

A list of 3120 samples corresponding to 10 aliquots * 13 tissues * 4 replicates * 3 developmental stages * 2 species

Project Management Guidelines

Report compiling the guidelines and rules in place for the coordination, reporting and quality control of the project.

Report on coordinated data production, recording and archiving within the European node of FAANG DCC

Report on the establishment of the European node of the FAANG Data Coordination Centre through agreement of scope, remit, objectives and priorities between the SFS-30 funded projects. The report will outline the interoperability development work, a basis for sharing of data and analysis methodologies and framework that will lead to cross project comparative analyses.

Outreach, dissemination, and training plan

D61 will be used to implement and evaluate the progress of the activities targeted to relevant stakeholders

Validation of developed models with simulated or publicly available data

Results of the validation of the developed models and benchmarking against other models will be described in a scientific publication

Operational analysis workflows in Embassy Cloud

Full analysis containerised workflows archived in GitHub and actively processing incoming project data Evidenced by analysis data flowing into FAANG through the European public archives managed by the data coordination platform D32 WP2 will be implementing initial workflows as soon as raw data becomes available By month 24 the operational infrastructure will be in place for analysis results from WP2 WP4 and WP5 to be delivered in the later half of the project

GENE-SWitCH Data Management Plan

Report on the data management plan for GENE-SWitCH in accordance with the latest FAANG data standards, SOPs and FAANG Data Sharing Principles.


Microbial Regulation of Host Physiology by Short-chain Fatty Acids

Autoren: Bart van der Hee; Jerry M. Wells
Veröffentlicht in: Trends in Microbiology, Issue Aug;29(8): 2021, 2021, Page(s) 700-712, ISSN 0966-842X
Herausgeber: Elsevier BV
DOI: 10.1016/j.tim.2021.02.001

From FAANG to fork: application of highly annotated genomes to improve farmed animal production

Autoren: Emily L. Clark, Alan L. Archibald, Hans D. Daetwyler, Martien A. M. Groenen, Peter W. Harrison, Ross D. Houston, Christa Kühn, Sigbjørn Lien, Daniel J. Macqueen, James M. Reecy, Diego Robledo, Mick Watson, Christopher K. Tuggle, Elisabetta Giuffra
Veröffentlicht in: Genome Biology, Issue 21/1, 2020, ISSN 1474-760X
Herausgeber: Springer
DOI: 10.1186/s13059-020-02197-8

The European Nucleotide Archive in 2019

Autoren: Clara Amid, Blaise T F Alako, Vishnukumar Balavenkataraman Kadhirvelu, Tony Burdett, Josephine Burgin, Jun Fan, Peter W Harrison, Sam Holt, Abdulrahman Hussein, Eugene Ivanov, Suran Jayathilaka, Simon Kay, Thomas Keane, Rasko Leinonen, Xin Liu, Josue Martinez-Villacorta, Annalisa Milano, Amir Pakseresht, Nadim Rahman, Jeena Rajan, Kethi Reddy, Edward Richards, Dmitriy Smirnov, Alexey Sokolov, Sen
Veröffentlicht in: Nucleic Acids Research, 2019, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkz1063

Accounting for overlapping annotations in genomic prediction models of complex traits

Autoren: Mollandin, F., Gilbert, H., Croiseau, P., and Rau, A.
Veröffentlicht in: BMC Bioinformatics, 2022, ISSN 1471-2105
Herausgeber: BioMed Central
DOI: 10.1186/s12859-022-04914-5

Ensembl 2022

Autoren: Fiona Cunningham, James E Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Ruth Bennett, Andrew Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis, Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tama
Veröffentlicht in: Nucleic Acids Research, 2022, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkab1049

The FAANG Data Portal: Global, Open-Access,“FAIR”, and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes

Autoren: Peter W Harrison, Alexey Sokolov, Akshatha Nayak, Jun Fan, Daniel Zerbino, Guy Cochrane, Paul Flicek
Veröffentlicht in: Frontiers in Genetics, Issue 12 2021/6/17, 2021, Page(s) 873, ISSN 1664-8021
Herausgeber: Frontiers Media
DOI: 10.3389/fgene.2021.639238

Ensembl 2021

Autoren: Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos Garcia Giron, Tiago Grego, Cristina Guijarro-Clarke, Lea
Veröffentlicht in: Nucleic Acids Research, Issue 49/D1, 2020, Page(s) D884-D891, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkaa942

The European Nucleotide Archive in 2020

Autoren: Peter W Harrison, Alisha Ahamed, Raheela Aslam, Blaise T F Alako, Josephine Burgin, Nicola Buso, Mélanie Courtot, Jun Fan, Dipayan Gupta, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Rodrigo Lopez, Simon Kay, Rasko Leinonen, Xin Liu, Colman O’Cathail, Amir Pakseresht, Youngmi Park, Stephane Pesant, Nadim Rahm
Veröffentlicht in: Nucleic Acids Research, Issue 49/D1, 2020, Page(s) D82-D85, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkaa1028

An evaluation of the predictive performance and mapping power of the BayesR model for genomic prediction

Autoren: Mollandin, F., Rau, A., and Croiseau, P.
Veröffentlicht in: G3 Genes|Genomes|Genetics, 2022, ISSN 2160-1836
Herausgeber: Genetics Society of America
DOI: 10.1093/g3journal/jkab225

Prediction performance of linear models and gradient boosting machine on complex phenotypes in outbred mice

Autoren: B. C. Perez, M. C. A. M. Bink, K. L. Svenson, G. A. Churchill and M. P. L. Calus
Veröffentlicht in: G3 Genes|Genomes|Genetics, Issue 12; 4; 2022, 2022, Page(s) jkac039, ISSN 2160-1836
Herausgeber: Genetics Society of America
DOI: 10.1093/g3journal/jkac039

Identifying muscle transcriptional regulatory elements in the pig genome

Autoren: D. Crespo-Piazuelo , O. González-Rodríguez, M. Mongellaz, H. Acloque, M.-J. Mercat, M. C. A. M. Bink, A. E. Huisman, Y. Ramayo-Caldas, J. P. Sánchez, and M. Ballester
Veröffentlicht in: ISAG 2021 Book of abstracts, 2021, Page(s) 19; 113
Herausgeber: -

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