The Animal Functional Genomics Resource
Lead Research Organisation:
University of Edinburgh
Department Name: The Roslin Institute
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The major goal of the proposed Animal Functional Genomics Resource (AFGR) is to maximize the usefulness of publicly archived functional genomic data for farmed and companion animal species in DNA databases.
The AFGR will index all the animal functional data available in the EMBL-EBI's European Nucleotide Archive (ENA). Experiments that meet our metadata standards will be processed through our standard analysis pipelines for RNA-Seq, ChIP-Seq and Methylation analysis. AFGR will use these pipelines to analyse and perform quality control (QC) on the data. Results that pass our QC metrics will then be distributed to the community and where appropriate passed to Ensembl to improve the gene and regulatory annotation of genomes.
We are involved in the FAANG metadata and data sharing committee (MDS), which is developing standards for sample, experimental and analysis metadata inside GitHub (records versions), to ensure the minimal metadata needed for data analysis are recorded in a well-structured manner. These standards use ontologies such as Uberon, the Cell Type Ontology and the Animal Trait Ontology for Livestock to provide specific descriptions for different sample and experimental attributes.
To ensure that the data being collected are useful to downstream analysis, we will establish stringent quality metrics to filter out anomalous datasets. These quality metrics will be generated as part of our standard analysis pipelines and presented to the community through both the FTP site and data portal, so that users can browse and filter data based on different QC criteria.
All the metadata stored will be fully indexed to allow for complete searching. We will also build views on the data, ensuring that users can easily browse the raw data and analysis files. This browser will also have a RESTful API, allowing programmatic access to the same metadata, enabling bulk queries and for other groups to build services on top of our data.
The AFGR will index all the animal functional data available in the EMBL-EBI's European Nucleotide Archive (ENA). Experiments that meet our metadata standards will be processed through our standard analysis pipelines for RNA-Seq, ChIP-Seq and Methylation analysis. AFGR will use these pipelines to analyse and perform quality control (QC) on the data. Results that pass our QC metrics will then be distributed to the community and where appropriate passed to Ensembl to improve the gene and regulatory annotation of genomes.
We are involved in the FAANG metadata and data sharing committee (MDS), which is developing standards for sample, experimental and analysis metadata inside GitHub (records versions), to ensure the minimal metadata needed for data analysis are recorded in a well-structured manner. These standards use ontologies such as Uberon, the Cell Type Ontology and the Animal Trait Ontology for Livestock to provide specific descriptions for different sample and experimental attributes.
To ensure that the data being collected are useful to downstream analysis, we will establish stringent quality metrics to filter out anomalous datasets. These quality metrics will be generated as part of our standard analysis pipelines and presented to the community through both the FTP site and data portal, so that users can browse and filter data based on different QC criteria.
All the metadata stored will be fully indexed to allow for complete searching. We will also build views on the data, ensuring that users can easily browse the raw data and analysis files. This browser will also have a RESTful API, allowing programmatic access to the same metadata, enabling bulk queries and for other groups to build services on top of our data.
Planned Impact
WHO WILL BENEFIT FROM THIS RESEARCH?
The immediate and direct beneficiaries will include scientists engaged in the international collaborative efforts to characterise the genomes of domesticated animals, in particular members of the Functional Annotation of Animal Genomes (FAANG), Genome10K and numerous target species (chicken, pig, sheep, cattle, etc.) genome consortia. The integrated, functional genome resources will also be useful to a wide range of scientists engaged in research on domesticated animals in agricultural, biomedical or animal health and welfare contexts. The resources will also benefit scientists engaged in characterising the human and other genomes by providing access to high quality functional genomics datasets for a number of vertebrates and associated software tools. The animal breeding and animal health sectors will also benefit from the project outputs through increased knowledge and access to new tools and resources. More generally, the research will benefit scientists concerned with understanding the regulation of gene expression and the genetic determinants of phenotypes.
These data will also be of value to other international consortia including the ENCODE, Epigenome Roadmap, FANTOM, International Human Epigenome and Blueprint Consortia for comparative analyses.
HOW WILL THEY BENEFIT FROM THIS RESEARCH?
The project will benefit the international FAANG and numerous target species (chicken, pig, sheep, cattle, etc.) genome consortia by developing a set of computational tools and resources to access functional genomics datasets. In particular, the project / resources will meet the FAANG project's need for a Data Coordination Centre. These new tools and resources will facilitate the detailed annotation of these genomes, such as defining transcripts, genes and regulatory regions. These annotations in turn will allow researchers and industry to annotate genome variation within specific populations of targets species to uncover causal relationships from sequence to molecular phenotype to macro-phenotype.
Computational solutions and resources will provide (i) access to available functional genomics datasets generated on farmed and companion animal species; (ii) together with high quality metadata facilitating further analysis of these data; (iii) quality metrics will be made available for these data to enable and encourage researchers to reuse these datasets to answer new biological questions; and (iv) finally, diverse functional genomics datasets will be assembled into a single resource for either direct download (raw data, metadata and QC metrics) from dedicated ftp sites or filtered from using a data portal to search for specific subsets of data.
This project will also provide training within and between collaborating labs to improve skills and foster new ways of working between biologists and computational scientists. Training and outreach will be core activities within the proposed project thus facilitating the delivery of impact. We will develop training materials and organise training workshops for postgraduate students, early stage and experienced researchers. Our outreach activities will encompass not only scientific conferences, but also events targeted at industry, e.g. through the Knowledge Transfer Network and directly with our industrial collaborators.
The immediate and direct beneficiaries will include scientists engaged in the international collaborative efforts to characterise the genomes of domesticated animals, in particular members of the Functional Annotation of Animal Genomes (FAANG), Genome10K and numerous target species (chicken, pig, sheep, cattle, etc.) genome consortia. The integrated, functional genome resources will also be useful to a wide range of scientists engaged in research on domesticated animals in agricultural, biomedical or animal health and welfare contexts. The resources will also benefit scientists engaged in characterising the human and other genomes by providing access to high quality functional genomics datasets for a number of vertebrates and associated software tools. The animal breeding and animal health sectors will also benefit from the project outputs through increased knowledge and access to new tools and resources. More generally, the research will benefit scientists concerned with understanding the regulation of gene expression and the genetic determinants of phenotypes.
These data will also be of value to other international consortia including the ENCODE, Epigenome Roadmap, FANTOM, International Human Epigenome and Blueprint Consortia for comparative analyses.
HOW WILL THEY BENEFIT FROM THIS RESEARCH?
The project will benefit the international FAANG and numerous target species (chicken, pig, sheep, cattle, etc.) genome consortia by developing a set of computational tools and resources to access functional genomics datasets. In particular, the project / resources will meet the FAANG project's need for a Data Coordination Centre. These new tools and resources will facilitate the detailed annotation of these genomes, such as defining transcripts, genes and regulatory regions. These annotations in turn will allow researchers and industry to annotate genome variation within specific populations of targets species to uncover causal relationships from sequence to molecular phenotype to macro-phenotype.
Computational solutions and resources will provide (i) access to available functional genomics datasets generated on farmed and companion animal species; (ii) together with high quality metadata facilitating further analysis of these data; (iii) quality metrics will be made available for these data to enable and encourage researchers to reuse these datasets to answer new biological questions; and (iv) finally, diverse functional genomics datasets will be assembled into a single resource for either direct download (raw data, metadata and QC metrics) from dedicated ftp sites or filtered from using a data portal to search for specific subsets of data.
This project will also provide training within and between collaborating labs to improve skills and foster new ways of working between biologists and computational scientists. Training and outreach will be core activities within the proposed project thus facilitating the delivery of impact. We will develop training materials and organise training workshops for postgraduate students, early stage and experienced researchers. Our outreach activities will encompass not only scientific conferences, but also events targeted at industry, e.g. through the Knowledge Transfer Network and directly with our industrial collaborators.
Organisations
- University of Edinburgh (Lead Research Organisation)
- Agrocampus Ouest (Collaboration)
- ETH Zurich (Collaboration)
- Polish Academy of Sciences (Collaboration)
- University of Liege (Collaboration)
- Aquicultura Balear SA (Collaboration)
- Arizona State University (Collaboration)
- Centre for Genomic Regulation (CRG) (Collaboration)
- Stolt-Nielsen (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- Oregon State University (Collaboration)
- UNIVERSITY OF BIRMINGHAM (Collaboration)
- Edinethics (Collaboration)
- AquaGen (Collaboration)
- Wageningen University & Research (Collaboration)
- Utrecht University (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- European Forum of Farm Animal Breeders (EFFAB) (Collaboration)
- Aarhus University (Collaboration)
- HARVARD UNIVERSITY (Collaboration)
- Norwegian University of Life Sciences (NMBU) (Collaboration)
- Panittica Italia Societa Agricola SRL (Collaboration)
- Faculdade de Medicina de Marília (Collaboration)
- University of East Anglia (Collaboration)
- European Federation of Animal Science (Collaboration)
- French Poultry and Aquaculture Breeders Association (Collaboration)
- Government of Catalonia (Collaboration)
- AgResearch (Collaboration)
- Valle Ca' Zuliani (S.R.L.) (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- Weizmann Institute of Science (Collaboration)
- Natural Resources Institute Finland (Collaboration)
- Swedish University of Agricultural Sciences (Collaboration)
- Diagenode (Collaboration)
- University of Padova (Collaboration)
- Iowa State University (Collaboration)
- Uppsala University (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- University of Limoges (Collaboration)
- UNIVERSITY OF ABERDEEN (Collaboration)
- U.S. Department of Agriculture USDA (Collaboration)
- University of Leipzig (Collaboration)
- University of Adelaide (Collaboration)
- University of Barcelona (Collaboration)
- University of Santiago de Compostela (Collaboration)
- University of Alberta (Collaboration)
- Kenya Agriculture & Livestock Research Organization (KALRO) (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- Martin Luther University of Halle-Wittenberg (Collaboration)
- OVAPISCIS SA (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- University of California, Davis (Collaboration)
- Geneaqua SL (Collaboration)
- University of Delaware (Collaboration)
- Hendrix Genetics (Collaboration)
- University of Missouri (Collaboration)
- National Institute of Allergy and Infectious Diseases (NIAID) (Collaboration)
- Leibniz Association (Collaboration)
- Hellenic Centre for Marine Research (HCMR) (Collaboration)
- University of Arkansas (Collaboration)
- Xelect Ltd (Collaboration)
Publications
Clark EL
(2017)
A high resolution atlas of gene expression in the domestic sheep (Ovis aries).
in PLoS genetics
Clark EL
(2020)
From FAANG to fork: application of highly annotated genomes to improve farmed animal production.
in Genome biology
Emily L. Clark A
(2020)
From FAANG to fork: application of highly annotated genomes to improve farmed animal production
Emily L. Clark A
(2020)
From FAANG to fork: application of highly annotated genomes to improve farmed animal production
Giuffra E
(2019)
Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap.
in Annual review of animal biosciences
Harrison PW
(2021)
The FAANG Data Portal: Global, Open-Access, "FAIR", and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes.
in Frontiers in genetics
Harrison PW
(2018)
FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community.
in Animal genetics
Harrison PW
(2019)
The FAANG Data Coordination Centre: Submitting and Retrieving Rich Datasets
Harrison PW
(2021)
The European Nucleotide Archive in 2020.
in Nucleic acids research
| Description | Established protocol for submission of long sequence reads (from PacBio iso-seq assay) associated with gene expression data to public database at EBI-EBI. The long read data from the Roslin Institute and now from other parts of the FAANG community that is submitted to the public archives at EMBL-EBI is being picked up by Ensembl for use in improving the assembly and annotations of key species of commercial importance for FAANG. The Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data) software has been updated and the paper describing the software and its use has been published. On-going support for the FAANG Data Coordination Centre and FAANG Data Portal has been secured through contributions from three EU Horizon 2020 projects. |
| Exploitation Route | Now others can submit long read data on gene expression data e.g. members of the international FAANG consortium. |
| Sectors | Agriculture Food and Drink Healthcare Pharmaceuticals and Medical Biotechnology |
| Description | Our development of a protocol for annotation of chicken transcriptome based on long sequencing reads (based on a PacBio Iso-seq assay we have developed together) can be used to annotate any species. So will have impact on other vertebrate genomes, such as those in the FAANG consortium. This work has been publicised in workshops, conferences and publications. The method is more robust and cost effective. The established protocol that is being promoted to FAANG consortia will allow the effective flow of long read data into the public archives for use in improving the assemblies and annotations available to the FAANG and wider animal communities. The establishment of the Functional Annotation of ANimal Genomes (FAANG) Data Coordination Centre and FAANG Data Portal with UKRI funding enables the research of FAANG research groups worldwide, but especially in Europe and North America. In Europe, the outputs and expertise from this UKRI funded project were valuable justifications for the three proposals that were funded as EU Horizon 2020 projects (AQUA-FAAG, BovReg and GENE-SWitCH) and the more recently awarded EuroFAANG infrastructure project. The outputs from these FAANG projects enabled by the FAANG Data Portal are contributing to improvements in models for genomic selection in farmed animal species. |
| First Year Of Impact | 2018 |
| Sector | Agriculture, Food and Drink,Healthcare,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Economic |
| Description | (BovReg) - BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Amount | € 6,033,458 (EUR) |
| Funding ID | 815668 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 08/2019 |
| End | 08/2023 |
| Description | AQUA-FAANG: Advancing European Aquaculture by Genome Functional Annotation |
| Amount | £668,211 (GBP) |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 04/2019 |
| End | 04/2023 |
| Description | Ensembl - adding value to animal genomes through high quality annotation |
| Amount | £368,856 (GBP) |
| Funding ID | BB/S02008X/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2019 |
| End | 07/2022 |
| Description | European Commission H2020-SFS30-2018-2020 Sustainable Food Security: The regulatory GENomE of SWine and CHicken: functional annotation during development |
| Amount | € 6,000,000 (EUR) |
| Funding ID | 817998 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 06/2019 |
| End | 06/2023 |
| Description | Impact Accelerator Award |
| Amount | £19,732 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2019 |
| End | 01/2020 |
| Description | Ovine FAANG Project |
| Amount | $500,000 (USD) |
| Organisation | U.S. Department of Agriculture USDA |
| Sector | Public |
| Country | United States |
| Start | 03/2017 |
| End | 04/2020 |
| Title | Animal Epigenomes data portal website |
| Description | Enabling the community to discover the samples and data we have indexed is vital to the success for the Animal Epigenome Resource project. In January we launched the data portal website, which allows users to explore the samples submitted for cow, sheep, goat, chicken, pig and horse. As more data is added to the Animal Epigenome database, the functionality of this website will be extended to allow users to explore the experiment and analysis data collected and view the data in Ensembl via TrackHub technology |
| Type Of Material | Data handling & control |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | We have noted any impacts yet. |
| URL | http://data.faang.org |
| Title | Pig transcriptome and gene expression atlas |
| Description | RNA sequencing of pig tissues for transcritpome annotation and expression analysis. Tissue specific RNA-seq data were generated to support annotation of coding and non-coding genes and to measure tissue specific expression. This study is part of the FAANG project, promoting rapid prepublication of data to support the research community. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | These data were used for annotation of the improved pig reference genome sequence |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB19386 |
| Title | The Animal Epigenome database |
| Description | The Animal Epigenome database imports samples and will import experiments and analyses from the EMBL-EBI data archives to provide query optimised representation of this data. This database currently includes all the samples submitted for the FAANG project and we are working to extend this to both add legacy sample records (the experimental data which has previously been submitted to the archive) as well as that which is now starting to be submitted by FAANG consortium members |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | This database will enable the community to discover what samples and experimental data exists; it will also support the FAANG data portal |
| Description | AQUA-FAANG |
| Organisation | AquaGen |
| Country | Norway |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Aquicultura Balear SA |
| Country | Spain |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | European Forum of Farm Animal Breeders (EFFAB) |
| Country | Netherlands |
| Sector | Learned Society |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Versailles |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | French Poultry and Aquaculture Breeders Association |
| Country | France |
| Sector | Charity/Non Profit |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Geneaqua SL |
| Country | Spain |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Hellenic Centre for Marine Research (HCMR) |
| Country | Greece |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Norwegian University of Life Sciences (NMBU) |
| Country | Norway |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | OVAPISCIS SA |
| Country | Spain |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Panittica Italia Societa Agricola SRL |
| Country | Italy |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Polish Academy of Sciences |
| Country | Poland |
| Sector | Public |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Stolt-Nielsen |
| Department | Stolt Sea Farm S.A. |
| Country | Spain |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | University of Aberdeen |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | University of Barcelona |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | University of Birmingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | University of Edinburgh |
| Department | The Roslin Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | University of Padova |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | University of Santiago de Compostela |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Valle Ca' Zuliani (S.R.L.) |
| Country | Italy |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Wageningen University & Research |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Xelect Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Aarhus University |
| Country | Denmark |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Centre for Genomic Regulation (CRG) |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Diagenode |
| Country | Belgium |
| Sector | Private |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | ETH Zurich |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Edinethics |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | European Federation of Animal Science |
| Country | Italy |
| Sector | Public |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Faculdade de Medicina de Marília |
| Country | Brazil |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Versailles |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Leibniz Association |
| Department | Leibniz Institute for Farm Animal Biology |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Martin Luther University of Halle-Wittenberg |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Natural Resources Institute Finland |
| Country | Finland |
| Sector | Public |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Polish Academy of Sciences |
| Department | Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences |
| Country | Poland |
| Sector | Public |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | University of Alberta |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | University of Edinburgh |
| Department | The Roslin Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | University of Liege |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | University of Limoges |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Utrecht University |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Wageningen University & Research |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | Collaboration with Wes Warren |
| Organisation | University of Missouri |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Analysis of genomic data and also single cell transcriptomic data |
| Collaborator Contribution | Access to chicken genome/transcriptomic data |
| Impact | Warren et al. Multiple chicken (Gallus gallus) genome references to advance genetic variation studies. In the 'Fourth Report on Chicken Genes and Chromosomes 2022'. Cytogenetic and Genome Research (2023) doi: 10.1159/000529376 Prof Warren will also visit Roslin for 3 months during June-Aug 2023 |
| Start Year | 2022 |
| Description | EBI FAANG Data Coordination Centre |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have made all the data and metadata information for the sheep gene expression atlas available to our collaborators at the FAANG data coordination centre at EBI in order for them to upload it to the FAANG data portal. |
| Collaborator Contribution | Our collaborators at EBI at the FAANG data coordination centre have created links to the metadata and data for the sheep gene expression atlas in the FAANG data portal in order to facilitate data and sample sharing within the FAANG consortium. |
| Impact | This collaboration has created an online database resource for the samples and dataset for the sheep gene expression atlas project, a large FAANG project. This facilitated data and sample sharing between research groups within the consortium and encouraging collaboration for grant applications and publications and reducing redundancy. |
| Start Year | 2016 |
| Description | Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | "The Animal Functional Genomics Resource" project is a collaboration between EMBL-EBI and The Roslin Institute and is supported through linked BBSRC grants to these two partners. The EMBL-EBI and Roslin Institute partners are also active members of the Functional Annotation of ANimal Genomes (FAANG) working group on Metadata and Data Sharing (M&DS). The Roslin partners bring knowledge of the target farmed animal species and exemplar datasets with which to test the draft data and metadata standards developed by the M&DS working group. The Roslin partners have also tested the systems for capturing metadata and for pre-publication data sharing. |
| Collaborator Contribution | The EMBL-EBI partners are developing and hosting the FAANG Data Portal (http://data.faang.org/home). The EMBL-EBI partners are also developing common data submission tools and QC tools. Scientists from EMBL-EBI and the University of Delaware co-chair the Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group. Scientists at Iowa State University provide links to the FAANG Bioinformatics and Data Analysis working group and to the USDA NRSP8 Bioinformatics Coordinator. Ninety-three of the 398 individuals who have joined as 'contributors' to the Functional Annotation of ANimal Genomes (FAANG) consortium have self-identified as members of the Metadata and Data Sharing (M&DS) Working group. For the sake of brevity only a few key partners are named here. |
| Impact | The FAANG Data Sharing Statement (https://www.faang.org/data-share-principle) and guidance on data submission (https://www.ebi.ac.uk/seqdb/confluence/display/FAANG/FAANG+Archive+Submission+guidelines) |
| Start Year | 2016 |
| Description | Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group |
| Organisation | Iowa State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | "The Animal Functional Genomics Resource" project is a collaboration between EMBL-EBI and The Roslin Institute and is supported through linked BBSRC grants to these two partners. The EMBL-EBI and Roslin Institute partners are also active members of the Functional Annotation of ANimal Genomes (FAANG) working group on Metadata and Data Sharing (M&DS). The Roslin partners bring knowledge of the target farmed animal species and exemplar datasets with which to test the draft data and metadata standards developed by the M&DS working group. The Roslin partners have also tested the systems for capturing metadata and for pre-publication data sharing. |
| Collaborator Contribution | The EMBL-EBI partners are developing and hosting the FAANG Data Portal (http://data.faang.org/home). The EMBL-EBI partners are also developing common data submission tools and QC tools. Scientists from EMBL-EBI and the University of Delaware co-chair the Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group. Scientists at Iowa State University provide links to the FAANG Bioinformatics and Data Analysis working group and to the USDA NRSP8 Bioinformatics Coordinator. Ninety-three of the 398 individuals who have joined as 'contributors' to the Functional Annotation of ANimal Genomes (FAANG) consortium have self-identified as members of the Metadata and Data Sharing (M&DS) Working group. For the sake of brevity only a few key partners are named here. |
| Impact | The FAANG Data Sharing Statement (https://www.faang.org/data-share-principle) and guidance on data submission (https://www.ebi.ac.uk/seqdb/confluence/display/FAANG/FAANG+Archive+Submission+guidelines) |
| Start Year | 2016 |
| Description | Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group |
| Organisation | University of Delaware |
| Department | Department of Animal and Food Sciences |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | "The Animal Functional Genomics Resource" project is a collaboration between EMBL-EBI and The Roslin Institute and is supported through linked BBSRC grants to these two partners. The EMBL-EBI and Roslin Institute partners are also active members of the Functional Annotation of ANimal Genomes (FAANG) working group on Metadata and Data Sharing (M&DS). The Roslin partners bring knowledge of the target farmed animal species and exemplar datasets with which to test the draft data and metadata standards developed by the M&DS working group. The Roslin partners have also tested the systems for capturing metadata and for pre-publication data sharing. |
| Collaborator Contribution | The EMBL-EBI partners are developing and hosting the FAANG Data Portal (http://data.faang.org/home). The EMBL-EBI partners are also developing common data submission tools and QC tools. Scientists from EMBL-EBI and the University of Delaware co-chair the Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group. Scientists at Iowa State University provide links to the FAANG Bioinformatics and Data Analysis working group and to the USDA NRSP8 Bioinformatics Coordinator. Ninety-three of the 398 individuals who have joined as 'contributors' to the Functional Annotation of ANimal Genomes (FAANG) consortium have self-identified as members of the Metadata and Data Sharing (M&DS) Working group. For the sake of brevity only a few key partners are named here. |
| Impact | The FAANG Data Sharing Statement (https://www.faang.org/data-share-principle) and guidance on data submission (https://www.ebi.ac.uk/seqdb/confluence/display/FAANG/FAANG+Archive+Submission+guidelines) |
| Start Year | 2016 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | AgResearch |
| Department | Invermay Agricultural Centre |
| Country | New Zealand |
| Sector | Private |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | Iowa State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | Swedish University of Agricultural Sciences |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | U.S. Department of Agriculture USDA |
| Department | Avian Disease and Oncology Laboratory (ADOL) |
| Country | United States |
| Sector | Public |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | U.S. Department of Agriculture USDA |
| Department | National Animal Disease Center |
| Country | United States |
| Sector | Public |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | University of Adelaide |
| Department | School of Animal and Veterinary Sciences |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | University of California, Davis |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | Uppsala University |
| Department | Department of Medical Biochemistry and Microbiology |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | Wageningen University & Research |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Agrocampus Ouest |
| Country | France |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Arizona State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Centre for Genomic Regulation (CRG) |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Rennes Centre |
| Country | France |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Toulouse |
| Country | France |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Harvard University |
| Department | Harvard Medical School |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Iowa State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Kenya Agriculture & Livestock Research Organization (KALRO) |
| Country | Kenya |
| Sector | Private |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Medical Research Council (MRC) |
| Department | Medical Research Council (MRC) Centre Cambridge |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | National Institute of Allergy and Infectious Diseases (NIAID) |
| Country | United States |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | National Institutes of Health (NIH) |
| Department | National Institute of Environmental Health Sciences |
| Country | United States |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Oregon State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Swedish University of Agricultural Sciences |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of Arkansas |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of California, Davis |
| Department | UC Davis Genome Cente |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of Delaware |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of Leipzig |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of Nottingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Weizmann Institute of Science |
| Country | Israel |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | Diagenode |
| Country | Belgium |
| Sector | Private |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | European Federation of Animal Science |
| Country | Italy |
| Sector | Public |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | European Forum of Farm Animal Breeders (EFFAB) |
| Country | Netherlands |
| Sector | Learned Society |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Toulouse |
| Country | France |
| Sector | Public |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | Government of Catalonia |
| Department | Institute for Research and Technology in Food and Agriculture |
| Country | Spain |
| Sector | Public |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | Hendrix Genetics |
| Country | Netherlands |
| Sector | Private |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | Uppsala University |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | Wageningen University & Research |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Title | TAMA update |
| Description | Transcriptome Annotation by Modular Algorithms (for isoseq data) |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | Enabled improved annotation of the chicken and duck transcriptomes |
| URL | https://github.com/GenomeRIK/tama |
| Title | Transcriptome Annotation by Modular Algorithms (TAMA) |
| Description | TAMA is a bioinformatics package intended to be used for constructing transcriptome/genome annotations. TAMA is ideal for working with Iso-Seq (long read RNA sequencing) data. However, due to its modular nature, it can be used for other data types as well. Most recent update 17 December 2020. See wiki for manual: https://github.com/GenomeRIK/tama/wiki |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | TAMA is currently being used to develop high quality transcriptomes for chicken and other farmed animal species for which current genome annotation provide an incomplete picture of transcriptome complexity. |
| URL | https://github.com/GenomeRIK/tama |
| Description | A talk on FAANG Data Coordination Centre at 1st FAANG-Europe Workshop on Functional Annotation of Animal Genomes (FAANG), Ljubljana, Slovenia, 5-7 March 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The 1st FAANG-Europe Workshop on Functional Annotation of Animal Genomes (FAANG) was organised by the COST Action CA15112 Functional Annotation of ANimal Genomes - European Network (FAANG-Europe) as an event to discuss progress and prospects for the global Functional Annotation of Animal Genomes (FAANG) initiative. This talk presented progress on the development of the FAANG Data Coordination Centre and FAANG Data Portal supported by this grant. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.faang-europe.org/news.html |
| Description | ARS 2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Jacqueline Smith presented a keynote talk at the Avian Researc Symposium 2023 (Edinburgh) - 'The avian genome: the current state of play' |
| Year(s) Of Engagement Activity | 2023 |
| Description | FAANG: Hands on metadata validation and data submission training |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This event was a four hour training session in the use of the tools developed for validation of metadata and data submission to the BioSamples (https://www.ebi.ac.uk/biosamples/), FAANG Data Portal (http://data.faang.org/home) and ENA (https://www.ebi.ac.uk/ena). |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://plan.core-apps.com/pag_2019/event/c3eb8177e7ac2f211aa9202c49285cf6 |
| Description | Presentation on "Functional Annotation of ANimal Genomes - European Network (FAANG-Europe) - opportunities from COST Action CA15112" at the 2018 Livestock Genomics workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The biennial Livestock Genomics workshop is a small international meeting held close to the large Genome Informatics conference that alternates between EMBL-EBI and Cold Spring Harbor Laboratory. This presentation introduced the work of an collaborative network concerned with promoting Functional Annotation of Animal Genomes (FAANG). |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation on data submission to BioSamples, FAANG Data Portal and ENA during the FAANG workshop during the 7th International Symposium on Animal Functional Genomics (ISAFG) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The purpose of the FAANG workshop during the 7th International Symposium on Animal Functional Genomics (ISAFG) and in particular the presentation on data submission was i) to train researchers in the systems for submitting data to support functional annotation and the aims of the Functional Annotation of Animal Genomes (FAANG) initiative; ii) to encourage participation in FAANG and iii) to encourage timely submission of data to the public data repositories and the FAANG Data Portal. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.isafg2018.com/program.html |