Ensembl genome portal for farm and companion animals
Lead Research Organisation:
University of Edinburgh
Department Name: The Roslin Institute
Abstract
Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in the animal sector of agriculture, contributing to medical research by providing animal models, improving animal health and welfare and informing understanding of natural and wild animal populations. Knowledge of the genes that shape farm and companion animals is essential for such research.
The sequence of almost all genes (a draft genome sequence) has been determined for major farmed and companion animal species such as cattle, goats, sheep, pigs, chickens, ducks, turkeys, dogs and horses. Draft genome sequences are also available, or soon will be, for several important fish species, including cod, rainbow trout, salmon and tilapia. However, the strings of billions of bases (symbolised as four letters A, C, G, T) that constitute these genome sequences are not immediately useful to biological research scientists.
Annotating these draft genome sequences with features such as where the coding and regulatory parts of genes are located, and the bases which differ between individuals within a species (genetic variants) greatly enhances the value and utility of the genome sequence. Visualising the genome sequences complete with annotations in a freely accessible manner further improves the value of the information.
The web-mounted Ensembl genome browser, databases and associated annotation tools have been shown to be powerful and effective means of annotating the complex genomes of animal species including humans, mice and more recently farmed and companion animals.
This project is concerned with improving the quality of genome annotation for farmed and companion animal genomes. International consortia of scientists are using so-called next generation sequencing technologies, not only to sequence the genomes of more economically important species, but also the genomes of multiple individuals for each species of interest and to improve or finish the reference genome sequences for key species. These new sequencing technologies are also being used increasingly in assays, for example, of the extent of gene expression in different cells or under different conditions (transcriptomics) or of the state of the genome (epigenomics). Mapping the sequence read-outs from these assays back to the relevant genome sequence not only provides a genome-wide framework for analysis but also provides further information with which to annotate the genome sequence itself. Thus, there is a recurring need to refresh the genome sequence annotation for important animal species.
We will use the Ensembl system to annotate the genome sequences of key farmed and companion animal species. The resulting annotated genome sequences will be made freely available as resources mounted on the World Wide Web.
A high quality annotated reference genome sequence is a key source of information and critical bioinformatics resource for the effective prosecution of contemporary research in the biological sciences. This key information is valuable not only to academic researchers, but also to scientists working in industry, including those in the animal breeding, animal health and pharmaceutical sectors. However, the value and utility of such bioinformatics resources are critically dependent upon the currency of the resource. Thus, this project is concerned with delivering high quality up-to-date annotated reference genomes for key farmed and companion animal species to enable research on these economically or socially important animal species.
The sequence of almost all genes (a draft genome sequence) has been determined for major farmed and companion animal species such as cattle, goats, sheep, pigs, chickens, ducks, turkeys, dogs and horses. Draft genome sequences are also available, or soon will be, for several important fish species, including cod, rainbow trout, salmon and tilapia. However, the strings of billions of bases (symbolised as four letters A, C, G, T) that constitute these genome sequences are not immediately useful to biological research scientists.
Annotating these draft genome sequences with features such as where the coding and regulatory parts of genes are located, and the bases which differ between individuals within a species (genetic variants) greatly enhances the value and utility of the genome sequence. Visualising the genome sequences complete with annotations in a freely accessible manner further improves the value of the information.
The web-mounted Ensembl genome browser, databases and associated annotation tools have been shown to be powerful and effective means of annotating the complex genomes of animal species including humans, mice and more recently farmed and companion animals.
This project is concerned with improving the quality of genome annotation for farmed and companion animal genomes. International consortia of scientists are using so-called next generation sequencing technologies, not only to sequence the genomes of more economically important species, but also the genomes of multiple individuals for each species of interest and to improve or finish the reference genome sequences for key species. These new sequencing technologies are also being used increasingly in assays, for example, of the extent of gene expression in different cells or under different conditions (transcriptomics) or of the state of the genome (epigenomics). Mapping the sequence read-outs from these assays back to the relevant genome sequence not only provides a genome-wide framework for analysis but also provides further information with which to annotate the genome sequence itself. Thus, there is a recurring need to refresh the genome sequence annotation for important animal species.
We will use the Ensembl system to annotate the genome sequences of key farmed and companion animal species. The resulting annotated genome sequences will be made freely available as resources mounted on the World Wide Web.
A high quality annotated reference genome sequence is a key source of information and critical bioinformatics resource for the effective prosecution of contemporary research in the biological sciences. This key information is valuable not only to academic researchers, but also to scientists working in industry, including those in the animal breeding, animal health and pharmaceutical sectors. However, the value and utility of such bioinformatics resources are critically dependent upon the currency of the resource. Thus, this project is concerned with delivering high quality up-to-date annotated reference genomes for key farmed and companion animal species to enable research on these economically or socially important animal species.
Technical Summary
High quality annotated reference genome sequences are essential bioinformatics resources for 21st century biological research.
Draft reference genome sequences have been established for several farmed and companion animal species - chicken, cattle, sheep, goat, pig, turkey, duck, dog, horse, and most recently rainbow trout. In addition draft genome sequences for Atlantic salmon, Indicine cattle and water buffalo will be released in the near future.
However, unannotated genome sequences are not immediately useful to biologists. Similarly, genome assemblies which are incomplete or for which the annotation is dated hinder progress in biological research.
This proposal is concerned with using the Ensembl system to establish high quality annotation of the genomes of farm and companion animal species, including poultry and farmed fish, and maintain its currency. We will annotate new or improved genome assemblies for farm and companion animals prioritising the genomes of cattle, sheep, pigs, chickens, salmon and dogs.
We will acquire sequence data being generated by the research community in experiments to characterise the extent of gene expression in different cells or under different conditions (transcriptomics, RNA-seq) or of the state of the genome (epigenomics, histone marks, methylation states) or to identify transcription start sites (CAGE) or transcription factor binding sites (ChIP-seq). We will use these data to enhance the functional annotation of the target species genomes and to make the resulting annotated genomes freely available to the research community via Ensembl. Similarly, we will acquire data that provide evidence for genetic variation within species - SNPs, indels and structural variants - and display the variation in its genomic context. We will generate comparative genomics resources including pairwise genome alignments and gene trees.
We will provide training in the use of the Ensembl genome browser and associated tools.
Draft reference genome sequences have been established for several farmed and companion animal species - chicken, cattle, sheep, goat, pig, turkey, duck, dog, horse, and most recently rainbow trout. In addition draft genome sequences for Atlantic salmon, Indicine cattle and water buffalo will be released in the near future.
However, unannotated genome sequences are not immediately useful to biologists. Similarly, genome assemblies which are incomplete or for which the annotation is dated hinder progress in biological research.
This proposal is concerned with using the Ensembl system to establish high quality annotation of the genomes of farm and companion animal species, including poultry and farmed fish, and maintain its currency. We will annotate new or improved genome assemblies for farm and companion animals prioritising the genomes of cattle, sheep, pigs, chickens, salmon and dogs.
We will acquire sequence data being generated by the research community in experiments to characterise the extent of gene expression in different cells or under different conditions (transcriptomics, RNA-seq) or of the state of the genome (epigenomics, histone marks, methylation states) or to identify transcription start sites (CAGE) or transcription factor binding sites (ChIP-seq). We will use these data to enhance the functional annotation of the target species genomes and to make the resulting annotated genomes freely available to the research community via Ensembl. Similarly, we will acquire data that provide evidence for genetic variation within species - SNPs, indels and structural variants - and display the variation in its genomic context. We will generate comparative genomics resources including pairwise genome alignments and gene trees.
We will provide training in the use of the Ensembl genome browser and associated tools.
Planned Impact
Who will benefit?
The primary beneficiaries from this proposed development and maintenance of Ensembl resources for farmed and companion animals will be researchers in academia and industry in the UK and beyond. The access statistics and citations of Ensembl papers provide evidence of the demand for Ensembl resources from the research community.
Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in the animal sector of agriculture, contributing to medical research by providing animal models, improving animal health and welfare and informing understanding of natural and wild animal populations.
The world's leading animal breeding and aquaculture breeding companies, of which some of the largest are UK companies, have in-house genetics expertise. Thus, these companies have the expertise to exploit the information captured and disseminated through Ensembl resources.
Evidence of the value of animal genome sequences to the pharmaceutical sector is provided by their recent investments in sequencing pig and dog genomes.
Suppliers of species specific 'omics tools such as expression arrays, SNP chips and proteomics system will benefit from access to annotated genomes sequences which include links to features (e.g. probes) on their products.
There are potential indirect benefits to the wider public through the addressing of the food security agenda as discussed below.
How will they benefit?
The proposed enhanced Ensembl resources, especially the genetic variation resources, will enable research to dissect the genetic control of economically important (and complex) traits in farmed animals including feed efficiency and susceptibility to infectious diseases. In companion animals such as dogs these resources will enable the identification of the determinants of inherited diseases.
This enabling of genetics research in farmed animals and fish will facilitate advanced genetic improvement for these species. Genetic improvement of farmed animal species is a key means of addressing the food security agenda for the animal agriculture and aquaculture sectors.
In companion animals the benefits will be improved tools for selective breeding to minimise inherited diseases and inbreeding and to improve animal welfare.
The utility of 'omics technology products such as expression microarrays and SNP chips is greatly enhanced when the features on these products can be linked to a well-annotated genome sequence and other information sources. For example, probe sets for Affymetrix arrays and SNPs on Affymetrix and Illumina chips can be linked to annotated genes and genome locations respectively, thus enabling more effective use of these products. Well-annotated genomes facilitate the design of capture probes for exome sequencing; current developers of such products include Agilent and Roche Nimblegen.
Academic and other researchers will benefit from the ability to link the read-out from assay by sequence assays to an annotated genome sequence. Without such a frame of reference such assays are of limited value.
The impacts on research will be delivered within the timeframe of the proposed project to enhance Ensembl resources for farmed and companion animals and continue thereafter. Maintaining the currency of the genome assemblies and the associated annotation is critical to ensuring that these impacts continue to be effective. The indirect impacts, for example, on the food security agenda and hence the benefits to the agriculture and aquaculture sectors and the wider public will take longer to be felt. However, the time to impact for genetic tests for susceptibility to inherited or infectious diseases in animals with their positive impacts on animal welfare can be short - 1 to 3 years.
The primary beneficiaries from this proposed development and maintenance of Ensembl resources for farmed and companion animals will be researchers in academia and industry in the UK and beyond. The access statistics and citations of Ensembl papers provide evidence of the demand for Ensembl resources from the research community.
Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in the animal sector of agriculture, contributing to medical research by providing animal models, improving animal health and welfare and informing understanding of natural and wild animal populations.
The world's leading animal breeding and aquaculture breeding companies, of which some of the largest are UK companies, have in-house genetics expertise. Thus, these companies have the expertise to exploit the information captured and disseminated through Ensembl resources.
Evidence of the value of animal genome sequences to the pharmaceutical sector is provided by their recent investments in sequencing pig and dog genomes.
Suppliers of species specific 'omics tools such as expression arrays, SNP chips and proteomics system will benefit from access to annotated genomes sequences which include links to features (e.g. probes) on their products.
There are potential indirect benefits to the wider public through the addressing of the food security agenda as discussed below.
How will they benefit?
The proposed enhanced Ensembl resources, especially the genetic variation resources, will enable research to dissect the genetic control of economically important (and complex) traits in farmed animals including feed efficiency and susceptibility to infectious diseases. In companion animals such as dogs these resources will enable the identification of the determinants of inherited diseases.
This enabling of genetics research in farmed animals and fish will facilitate advanced genetic improvement for these species. Genetic improvement of farmed animal species is a key means of addressing the food security agenda for the animal agriculture and aquaculture sectors.
In companion animals the benefits will be improved tools for selective breeding to minimise inherited diseases and inbreeding and to improve animal welfare.
The utility of 'omics technology products such as expression microarrays and SNP chips is greatly enhanced when the features on these products can be linked to a well-annotated genome sequence and other information sources. For example, probe sets for Affymetrix arrays and SNPs on Affymetrix and Illumina chips can be linked to annotated genes and genome locations respectively, thus enabling more effective use of these products. Well-annotated genomes facilitate the design of capture probes for exome sequencing; current developers of such products include Agilent and Roche Nimblegen.
Academic and other researchers will benefit from the ability to link the read-out from assay by sequence assays to an annotated genome sequence. Without such a frame of reference such assays are of limited value.
The impacts on research will be delivered within the timeframe of the proposed project to enhance Ensembl resources for farmed and companion animals and continue thereafter. Maintaining the currency of the genome assemblies and the associated annotation is critical to ensuring that these impacts continue to be effective. The indirect impacts, for example, on the food security agenda and hence the benefits to the agriculture and aquaculture sectors and the wider public will take longer to be felt. However, the time to impact for genetic tests for susceptibility to inherited or infectious diseases in animals with their positive impacts on animal welfare can be short - 1 to 3 years.
Organisations
- University of Edinburgh (Lead Research Organisation)
- Medical Research Council (MRC) (Collaboration)
- Agrocampus Ouest (Collaboration)
- Natural Resources Institute Finland (Collaboration)
- Aquicultura Balear SA (Collaboration)
- Polish Academy of Sciences (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)
- Swedish University of Agricultural Sciences (Collaboration)
- Edinethics (Collaboration)
- University of Delaware (Collaboration)
- UNIVERSITY OF EAST ANGLIA (Collaboration)
- Utrecht University (Collaboration)
- Wageningen University & Research (Collaboration)
- European Forum of Farm Animal Breeders (EFFAB) (Collaboration)
- HARVARD UNIVERSITY (Collaboration)
- Panittica Italia Societa Agricola SRL (Collaboration)
- Norwegian University of Life Sciences (NMBU) (Collaboration)
- Faculdade de Medicina de Marília (Collaboration)
- European Federation of Animal Science (Collaboration)
- French Poultry and Aquaculture Breeders Association (Collaboration)
- Government of Catalonia (Collaboration)
- ETH Zurich (Collaboration)
- AgResearch (Collaboration)
- Valle Ca' Zuliani (S.R.L.) (Collaboration)
- University of Liege (Collaboration)
- Weizmann Institute of Science (Collaboration)
- Functional Annotation of ANimal Genomes (FAANG) (Collaboration)
- Diagenode (Collaboration)
- Iowa State University (Collaboration)
- Uppsala University (Collaboration)
- University of Padova (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- AquaGen (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 Santiago de Compostela (Collaboration)
- University of Barcelona (Collaboration)
- University of Alberta (Collaboration)
- Kenya Agriculture & Livestock Research Organization (KALRO) (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- Aarhus University (Collaboration)
- JSR Genetics (Collaboration)
- Martin Luther University of Halle-Wittenberg (Collaboration)
- University of Arkansas (Collaboration)
- OVAPISCIS SA (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- University of California, Davis (Collaboration)
- Geneaqua SL (Collaboration)
- Hendrix Genetics (Collaboration)
- National Institute of Allergy and Infectious Diseases (NIAID) (Collaboration)
- Leibniz Association (Collaboration)
- Cytocell Ltd (Collaboration)
- Hellenic Centre for Marine Research (HCMR) (Collaboration)
- UNIVERSITY OF KENT (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- Xelect Ltd (Collaboration)
Publications
Aken BL
(2016)
The Ensembl gene annotation system.
in Database : the journal of biological databases and curation
Archibald A
(2020)
An improved pig reference genome sequence to enable pig genetics and genomics research
in GigaScience
Eory L
(2019)
Suina genomes and phylogenomics
Farré M
(2016)
Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles.
in Genome biology and evolution
Giuffra E
(2019)
Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap.
in Annual review of animal biosciences
Hourlier T
(2017)
Updated pig genome resources in Ensembl
| Description | Since the start of the current round of funding in summer 2015, there have been 17 releases of Ensembl annotation from Ensembl Release 81 in July 2015 to Ensembl release 97 in July 2019. The key deliverables and milestones with respect to the farmed and companion animal species of interest are: Chicken October 2016, Release 86 - Annotation of the improved chicken genome assembly (Gallus_gallus-5.0) released December 2016, Release 87 - Patched and updated gene set for Gallus_gallus-5.0 assembly December 2017, Release 91 - Details of current annotation available here: http://www.ensembl.org/Gallus_gallus/Info/Annotation Long (Iso-Seq) and short read RNA-seq data generated on the Pacific Biosciences and Illumina next generation sequencing platforms by the Roslin Institute partner was used to improve the annotation of alternative transcripts and gene models. January 2019, Release 95 - updated annotation and gene build for improved reference genome assembly GRCg6a and available here: https://www.ensembl.org/Gallus_gallus/Info/Index Cattle December 2017 Release 91 - Details of the current annotation of cow reference genome assembly UMD3.1 is available here: http://www.ensembl.org/Bos_taurus/Info/Index January 2019 Release 95 - new much improved cattle reference genome assembly (ARS-UCD1.2) annotated and available here: https://www.ensembl.org/Bos_taurus/Info/Index Release 97 - Haplotype resolved assemblies of a Bos taurus x Bos indicus F1 hybrid individual were annotated as i) Bos taurus assembly (UOA_Angus_1) and ii) Bos indicus assembly (UOA_Braham_1) and are available here: and http://www.ensembl.org/Bos_taurus_hybrid/Info/Index http://www.ensembl.org/Bos_indicus_hybrid/Info/Index Pig August 2017, release 90 - Annotation of the improved pig reference genome assembly (Sscrofa11.1) released. Available here: https://www.ensembl.org/Sus_scrofa/Info/Index Generation of the Sscrofa11.1 assembly was led by The Roslin Institute partner. Illumina short read RNA-seq data generated by The Roslin Institute partner and Pacific Biosciences long read Iso-seq data were used to develop improved gene models and a better representation of transcript complexity and alternative transcripts. A second highly contiguous pig genome assembly (USMARCv1.0) was annotated and released in July 2019 (Release 97) and the annotation is available here: http://www.ensembl.org/Sus_scrofa_usmarc/Location/Genome?db=core Sheep July 2015, release 81 - a patched and improved gene set for sheep reference genome assembly Oar_v3.1 was released The Roslin Institute has generated and released a very extensive RNA-seq dataset that will be used to annotate the new improved sheep genome assembly which will be released within the next few months. Goat April 2018 Release 92 - new and greatly improved goat reference genome sequence (ARS1) annotated and released. Available here: https://www.ensembl.org/Capra_hircus/Info/Index Cat December 2017, Release 91 - a full Gene Build for the new cat reference genome sequence (Felis_catus_8.0) was released. July 2018, Release 93 - a full Gene Build for improved cat reference genome sequence (Felis_catus_9.0) was released. Available here: https://www.ensembl.org/Felis_catus/Info/Index Dog July 2016, Release 85 - the Genebuild for the dog CanFam3.1 genome assembly was updated and a patched version released. Available here: https://www.ensembl.org/Canis_familiaris/Info/Index |
| Exploitation Route | Annotated reference genome sequences are a key resource for biological research. Thus, the annotated genomes generated in this project are a key reference to which researchers studying the target species can and will refer. Moreover, scientists with interests in comparative genomics and evolution will use these resources. The annotated reference genome sequences provide an essential framework for the work of the international Functional Annotation of Animal Genomes consortium that currently comprises over 300 scientists from around the world. In Q3, 2019 there were a total of 27,814 independent Ensembl sessions launched for (pig, chicken, cow, cat, dog, sheep, horse, tilapia, goat, rabbit, cod, duck and turkey) with a total of 322,056 page views. Pig (6,512 sessions, 67,116 page views), cow (5,394 sessions, 58,101 page views), chicken (5,072 sessions, 54,077 page views) and dog (3,924 sessions, 49,224) are the 5th, 6th, 7th and 8th most accessed genomes in Ensembl in this period (human, mouse, zebrafish and rat are 1st - 4th). |
| Sectors | Agriculture Food and Drink Healthcare |
| URL | http://www.ensembl.org |
| Description | Annotated reference genome sequences are a key resource not only for biological research but also for the exploitation of genomic information by the private sector. For example, genomic selection, in which genome-wide genetic marker data are used to estimate genomic breeding values (GEBVs) of individuals by means of a genomic prediction equation, has facilitated significant acceleration in the genetic improvement of farmed animals, especially dairy cattle, pigs and poultry. This genomic prediction equation is calculated using a 'training' or 'reference' population where animals have both genotypes and phenotypes, and is then applied to selection candidates, which often have marker genotype information only. The annotated reference genome sequences are a key resource and framework for the identification of genetic variation such as Single Nucleotide Polymorphisms (SNPs) and subsequent development of SNP chips. The genotypic information required for implementation of genomic selection are acquired through the use of these SNP chips. |
| First Year Of Impact | 2015 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Economic |
| Description | Bioinformatics and Biological Resources Fund |
| Amount | £791,463 (GBP) |
| Funding ID | BB/N019202/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2016 |
| End | 10/2020 |
| Description | Ensembl - adding value to animal genomes through high quality annotation |
| Amount | £378,425 (GBP) |
| Funding ID | BB/S020152/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2019 |
| End | 07/2022 |
| 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 | General Scheme - Jeff Schoenebeck - Fit for Purpose: A Reference Genome to Empower Canine Health Research |
| Amount | £199,937 (GBP) |
| Funding ID | 5126826 |
| Organisation | Dogs Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2021 |
| Description | National Institute of Food and Agriculture Default Scheme - Alan Archibald - Consortium funding - Emily Clark - Ovine FAANG Project |
| Amount | £46,415 (GBP) |
| Funding ID | 2017-67016-26301 |
| Organisation | U.S. Department of Agriculture USDA |
| Department | National Institute for Food and Agriculture |
| Sector | Public |
| Country | United States |
| Start | 03/2017 |
| End | 03/2020 |
| Title | lncRNA analysis pipeline |
| Description | We are developing a new pipeline to analyse long non-coding RNAs (lncRNAs). We have used this pipeline for for all recent annotations including cow, horse, chicken and pig. The data are available through Ensembl. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | The data is fairly new, so we have not detected any notable impacts yet. |
| URL | http://www.ensembl.org/ |
| Title | Pig reference genome sequence Sscrofa11 |
| Description | This pig genome sequence (Sscrofa11) has been released by the International Swine Genome Sequencing Consortium under the terms of the Toronto Statement (Nature 2009, 461: 168). The Consortium is coordinating genome-wide analysis, annotation and publication. The sequence data from which this assembly was constructed largely comprise 65x genome coverage in whole genome shotgun (WGS) Pacific Biosciences long reads (Pacific Biosciences RSII, with P6/C4 chemistry). Illumina HiSeq2500 WGS paired-end and mate pair reads were used for final error correction using PILON. Sanger and Oxford Nanopore sequence data from a few CHORI-242 BAC clones were used to fill gaps. All the WGS data were generated from a single Duroc female (TJ Tabasco, also known as Duroc 2-14) which was also the source of DNA for the CHORI-BAC library. Sscrofa11 replaces the previous assembly, Sscrofa10.2, which was largely established from the same Duroc 2-14 DNA source. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | The Sscrofa11 assembly has been updated recently to Sscrofa11.1 by the addition of the SSCY sequence data from Skinner et al. 2016 (Genome Res 26:130-9). The BAC and fosmid clone resource from Duroc 2-14 will facilitate further targeted sequence closure. These improved genome assemblies will be a key resource for research in pigs and will enable applications in agriculture and biomedicine. The SScrofa11.1 assembly is currently being analysed and annotated. |
| URL | https://www.ncbi.nlm.nih.gov/assembly/GCA_000003025.5/ |
| 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 | Supporting data for "An improved pig reference genome sequence to enable pig genetics and genomics research" |
| Description | The domestic pig ( Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited its utility. We present two annotated highly contiguous chromosome-level genome assemblies created with more recent long read technologies and a whole genome shotgun strategy, one for the same Duroc female (Sscrofa11.1) and one for an outbred, composite breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. These highly contiguous assemblies plus annotation of a further 11 short read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | http://gigadb.org/dataset/100732 |
| 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 | Development of tools to detect chromosomal translocations in pigs |
| Organisation | Cytocell Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | I provided my detailed knowledge of the Swine Genome Sequencing Consortium's project that produced the draft pig reference genome sequence (Sscrofa10.2) as described by Groenen et al. 2012. Pig genomes provide insight into porcine demography and evolution. Nature 491: 393-398 and the pig physical mapping project as described by Humphray et al. 2007. A high utility integrated map of the pig genome. Genome Biology 8:R139. My research team had also established the bacterial artificial chromosome (BAC) library resource described by Anderson et al. 2000. A large fragment porcine genomic library resource in a BAC vector. Mammalian Genome 11, 811-814. BAC clones from this library were used as probes for fluorescent in situ hybridisation (FISH) experiments in this collaborative project. My knowledge of the pig physical mapping and pig genome sequencing projects was critical in interpreting the anomalous and unexpected results from the initial FISH experiments. |
| Collaborator Contribution | This collaboration was initiated and led by Prof Darren Griffin and colleagues at the University of Kent. In addition to leading the collaboration the Kent team delivered the expertise in cytogenetics analysis. JSR Genetics provided animal materials and phenotypes. Cytocell Ltd provided technical expertise and the Chromoprobe Multiprobe System. The work was funded by an Innovate UK Knowledge Transfer Partnership to Prof Darren Griffin and Cytocell Ltd. |
| Impact | The project has demonstrated that FISH-based translocation screening is a powerful and reliable approach to screening for chromosomal translocation that can have adverse effects on fertility. The device described by O'Connor et al. (see below) is now a commercial product marketed by Cytocell Ltd. The project results have been useful if anchoring the new improved pig reference genome sequence to chromosomes and confirming the order and orientation for each chromosomal sequence. The results of the study have been published by O'Connor et al. Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly. Animal Genetics (in press). The research undertaken by Rebecca O'Connor is a major component of her PhD research studies. |
| Start Year | 2014 |
| Description | Development of tools to detect chromosomal translocations in pigs |
| Organisation | JSR Genetics |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | I provided my detailed knowledge of the Swine Genome Sequencing Consortium's project that produced the draft pig reference genome sequence (Sscrofa10.2) as described by Groenen et al. 2012. Pig genomes provide insight into porcine demography and evolution. Nature 491: 393-398 and the pig physical mapping project as described by Humphray et al. 2007. A high utility integrated map of the pig genome. Genome Biology 8:R139. My research team had also established the bacterial artificial chromosome (BAC) library resource described by Anderson et al. 2000. A large fragment porcine genomic library resource in a BAC vector. Mammalian Genome 11, 811-814. BAC clones from this library were used as probes for fluorescent in situ hybridisation (FISH) experiments in this collaborative project. My knowledge of the pig physical mapping and pig genome sequencing projects was critical in interpreting the anomalous and unexpected results from the initial FISH experiments. |
| Collaborator Contribution | This collaboration was initiated and led by Prof Darren Griffin and colleagues at the University of Kent. In addition to leading the collaboration the Kent team delivered the expertise in cytogenetics analysis. JSR Genetics provided animal materials and phenotypes. Cytocell Ltd provided technical expertise and the Chromoprobe Multiprobe System. The work was funded by an Innovate UK Knowledge Transfer Partnership to Prof Darren Griffin and Cytocell Ltd. |
| Impact | The project has demonstrated that FISH-based translocation screening is a powerful and reliable approach to screening for chromosomal translocation that can have adverse effects on fertility. The device described by O'Connor et al. (see below) is now a commercial product marketed by Cytocell Ltd. The project results have been useful if anchoring the new improved pig reference genome sequence to chromosomes and confirming the order and orientation for each chromosomal sequence. The results of the study have been published by O'Connor et al. Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly. Animal Genetics (in press). The research undertaken by Rebecca O'Connor is a major component of her PhD research studies. |
| Start Year | 2014 |
| Description | Development of tools to detect chromosomal translocations in pigs |
| Organisation | University of Kent |
| Department | Medway School of Pharmacy |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | I provided my detailed knowledge of the Swine Genome Sequencing Consortium's project that produced the draft pig reference genome sequence (Sscrofa10.2) as described by Groenen et al. 2012. Pig genomes provide insight into porcine demography and evolution. Nature 491: 393-398 and the pig physical mapping project as described by Humphray et al. 2007. A high utility integrated map of the pig genome. Genome Biology 8:R139. My research team had also established the bacterial artificial chromosome (BAC) library resource described by Anderson et al. 2000. A large fragment porcine genomic library resource in a BAC vector. Mammalian Genome 11, 811-814. BAC clones from this library were used as probes for fluorescent in situ hybridisation (FISH) experiments in this collaborative project. My knowledge of the pig physical mapping and pig genome sequencing projects was critical in interpreting the anomalous and unexpected results from the initial FISH experiments. |
| Collaborator Contribution | This collaboration was initiated and led by Prof Darren Griffin and colleagues at the University of Kent. In addition to leading the collaboration the Kent team delivered the expertise in cytogenetics analysis. JSR Genetics provided animal materials and phenotypes. Cytocell Ltd provided technical expertise and the Chromoprobe Multiprobe System. The work was funded by an Innovate UK Knowledge Transfer Partnership to Prof Darren Griffin and Cytocell Ltd. |
| Impact | The project has demonstrated that FISH-based translocation screening is a powerful and reliable approach to screening for chromosomal translocation that can have adverse effects on fertility. The device described by O'Connor et al. (see below) is now a commercial product marketed by Cytocell Ltd. The project results have been useful if anchoring the new improved pig reference genome sequence to chromosomes and confirming the order and orientation for each chromosomal sequence. The results of the study have been published by O'Connor et al. Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly. Animal Genetics (in press). The research undertaken by Rebecca O'Connor is a major component of her PhD research studies. |
| Start Year | 2014 |
| Description | EMBL-EBI collaboration with the Functional Analysis of ANimal Genomes (FAANG) Consortium |
| Organisation | Functional Annotation of ANimal Genomes (FAANG) |
| Country | Global |
| Sector | Charity/Non Profit |
| PI Contribution | We participate in conference calls on the analysis of data. Peter Harrison co-chairs the Metadata and Data Sharing Committee and is a member of the FAANG steering committee. The objective of the Metadata and Data Sharing committee is to recommend standard methods to record information for all samples, experiments and analyses carried out by FAANG consortium members; recommend best practice for data archiving; and define data sharing methodologies that encourage sharing within the FAANG consortium and rapid public release of raw data and analysis results. |
| Collaborator Contribution | There are numerous partners that are part of this collaboration. They contribute data, tools, and other expertise. |
| Impact | The collaboration is still in the early stages, and we are aiming to get funding for this work. FAANG aims to: Standardize core assays and experimental protocols Coordinate and facilitate data sharing Establish an infrastructure for analysis of these data Provide high quality functional annotation of animal genomes |
| Start Year | 2014 |
| Description | Ensembl - farmed and companion animals 2014 |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This partnership continues a 10 year collaborative effort to annotate the reference genome sequences of the major farmed animal species. The Roslin Institute partner contributes reference genome sequences for some of these farmed animal species through its leadership and participation in international farm animal genome sequencing projects / consortia. The Roslin Institute partner also provides ancillary sequence data which are used for annotation, such as extensive RNA-seq data from multiple sheep tissues. Finally, the Roslin Institute partner also provides key links to the farm animal genetics and genomics research community and the user communities in academia and industry. |
| Collaborator Contribution | The Ensembl team at EMBL-EBI provide the expertise semi-automated genome sequence annotation, including gene builds, comparative genome analyses, functional annotation and evaluation of sequence variants. The EMBL-EBI also provide the compute infrastructure for the annotation processing and for access to the annotated genomes via the Ensembl Genome Browser. Finally, the EMBL-EBI team lead the training activities. |
| Impact | The primary output from this collaboration are annotated reference genome sequences for farmed and companion animal species, including chickens, duck, turkey, pig, sheep, cattle, dog and horse. |
| 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 |
| Description | A presentation on "Phylogenomics of Suina Species" 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 larger Genome Informatics conference that alternates between EMBL-EBI and Cold Spring Harbor Laboratory. This talk was an opportunity to present progress on characterising the genomes of three African Suina species - common warthog, red river hog and bushpig. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Avian genome evolution and the origins of species diversity. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited lecture: Avian genome evolution and the origins of species diversity. In "Molecular evolution of avian species", SMBE2016, Queensland's Gold Coast, Australia, 3-7 July, 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Boden Conference: avian comparative genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk at Boden Conference: Comparative Genomics Conference, July 2015, Adelaide, Australia |
| Year(s) Of Engagement Activity | 2015 |
| Description | Creation of multiple genome alignments and clade-based tools to facilitate the study of speciation and adaptation in birds |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk at EOU215: Badajoz, Spain, August 2105. Roundtable 7 (Genetics): Creation of multiple genome alignments and clade-based tools to facilitate the study of speciation and adaptation in birds |
| Year(s) Of Engagement Activity | 2015 |
| Description | Ensembl dissemination at PAG XXV 'Chicken annotation in Ensembl' |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Thibaut Hourlier presented a poster on 'Chicken annotation in Ensembl', disseminating the work to improve the annotation for chicken, and to raise awareness of the resource. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.intlpag.org/2017a/ |
| Description | Ensembl eHive workshop for programmers |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This course/workshop was part of the outreach and training effort associated with this award. The workshop was organised and hosted by The Roslin Institute partner and the course content was delivered by staff from the Ensembl team. Briefly, eHive is a general pipeline manager framework which underpins most of the genome analysis pipelines run by the Ensembl team. It is scalable and flexible and can manage millions of jobs on different computer platforms. eHive is a Perl-based framework for configuring, managing and scheduling computational pipelines running across one or more compute clusters. One of the most exciting features of eHive is that it is self-regulating and is designed to concurrently handle data of many formats and complexity, from single jobs that run for two weeks, to hundreds of thousands of jobs, without overloading the database server or compute cluster. While the framework has been developed with bioinformatics applications in mind, it is applicable to all calculations and data types. This course aimed to teach the skills needed to effectively manage and run computational pipelines using eHive. The course provided an overview of eHive concepts and architecture, instruction on running preexisting eHive pipelines, and instruction on creating new eHive pipelines. The target audience was researchers who are interested in running pipelines created with the eHive framework. Prerequisites: Persons taking this module should have some experience working in a command line environment, and should be comfortable with writing small shell scripts and programs in a scripting language (e.g. Perl, Python). |
| Year(s) Of Engagement Activity | 2017 |
| Description | Flash talk on "Ensembl Farmed and Domesticated Animals" at ELIXIR UK All Hands meeting, Birmingham 28-29 November 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | "Ensembl farmed and domesticated animals" is recognised as an ELIXIR UK Node Resource. The flash talk and associated poster was an opportunity to disseminate information about the resource to other researchers engaged with ELIXIR UK Node. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://elixiruknode.org/uncategorized/elixir-uk-all-hands-2018-28th-29th-november/ |
| Description | From Sequences to Consequences |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | talk and meet industry at "21st Century Genomics for Animal Breeding and Animal Health. In "From Sequences to Consequences: What The Roslin Institute can do for you in the livestock sector", Industry Day. The Roslin Institute Building, Edinburgh, 18th March 2016." |
| Year(s) Of Engagement Activity | 2016 |
| Description | Gene annotation of the chicken genome. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited lecture: Gene annotation of the chicken genome. Next Generation Sequencing Conference (NGS) 2016, Barcelona, Spain, 4-6 April, 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Improved pig reference genome in GENE-SWitCH newsletter |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Alan Archibald wrote a article on the development and publication of an improved pig reference genome sequence for the second H2020 GENE-SWitCH newsletter published in February 2021. The newsletter was written for a general audience, widely advertised on Twitter and the social media and will be read by academic researchers and policy makers in the European Commission. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.gene-switch.eu/uploads/1/2/6/6/126678735/gene_switch_newsletter2_final.pdf |
| Description | New tools and prospects for chicken genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk at Genetics Society of Australia (GSA), July 2015, University of Adelaide, Australia |
| Year(s) Of Engagement Activity | 2015 |
| Description | Non-Model Avian Genomics Fit for Purpose - the End of the Model Organism? |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk: Non-Model Avian Genomics Fit for Purpose - the End of the Model Organism? Avian Genomes: Plant & Animal Genomes, San Diego, Jan 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Past, Present and Future of Genomics in Poultry Breeding. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk: Past, Present and Future of Genomics in Poultry Breeding. 25th World's Poultry Congress, Beijing, 5-9 September, 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Poster at PAGXXIV, San Diego, California, 2016 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Thibaut Hourlier gave a poster presentation at the Plant and Animal Genomes conference on 'Ensembl: Non coding RNA gene annotation'. This helped to raise awareness of the resources for livestock animals in Ensembl, as well as raising awareness of new ncRNA data for cow in Ensembl. |
| Year(s) Of Engagement Activity | 2016 |
| 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 | Production Animal Health and Welfare Research: Impacts and Opportunities. |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk at Production Animal Health and Welfare Research: Impacts and Opportunities. 19-20 Feb, 2015, Indian Council for Agricultural Research (ICAR), New Delhi, India |
| Year(s) Of Engagement Activity | 2015 |
| Description | So many avian genomes - problems of annotation and data access |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk at Genome10K Conference: So many avian genomes - problems of annotation and data access, 1-5 March, 2015, California, USA |
| Year(s) Of Engagement Activity | 2015 |
| Description | The Chicken and other Avian Genomes: new insights and opportunities for all from high throughput sequencing and bioinformatics. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk: the Chicken and other Avian Genomes: new insights and opportunities for all from high throughput sequencing and bioinformatics. In "Avian Model Systems 9: a new integrative platform", Taipei, Taiwan, 38 March to 3 April, 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Training workshops in 2015 for researchers to use the data generated |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | The Ensembl Outreach team regularly give workshops to Ensembl's users. Here we have captured all workshops in one entry per year, since materials from previous workshops are reused in later workshops. Ensembl gave a talk, computer demonstration and poster about the resources for vertebrate genomics at PAG 2015, with approximately 120 participants. Ensembl gave an Ensembl browser workshop at the Royal Veterinary College in February 2015, focusing mainly on cat and dog genome resources, with approximately 16 participants. Ensembl gave a talk and demonstration on the Ensembl browser at the canine and feline genetics conference in Cambridge in June 2015, with approximately 70 participants. Ensembl gave an Ensembl browser workshop at the Roslin Institute in July 2015, this was a general browser workshop but the chicken genome was given during examples, there were approximately 16 participants. Ensembl gave a talk and presentation on the Ensembl browser at the canine and feline genetics conference in Cambridge in June 2015, with approximately 70 participants. Ensembl gave an Ensembl browser workshop at PAGAsia (Singapore) in July 2015, there were approximately 16 participants. Ensembl gave an Ensembl browser workshop on salmon and salmon louse at the Sea Lice Centre, Bergen (Norway) in November 2015, there were approximately 27 participants. Zebrafish and mosquito were used as a proxy for the species of interest. Ensembl gave an Ensembl browser workshop at the Univeristy of Cambridge in November 2015, this was a general browser workshop but the chicken genome was given during examples, there were approximately 33 participants. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Transcriptional and Epigenetic Regulation of Seasonal Timing. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited lecture: Transcriptional and Epigenetic Regulation of Seasonal Timing. In "Evolution of seasonal timers". The 64th NIBB Conference, Okazaki Conference Centre, Okazaki, Japan. 22-24 April, 2016. |
| Year(s) Of Engagement Activity | 2016 |