Ensembl and enabling genetics and genomics research in farmed animal species
Lead Research Organisation:
University of Edinburgh
Department Name: The Roslin Institute
Abstract
The sequence of almost all genes (a draft genome sequence) has been determined for several farmed and companions animals including cattle, pigs, chickens, turkeys, dogs and horses. Draft genome sequences for several other species such as sheep, ducks and salmon will be completed soon. 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 the coding and regulatory parts of genes, and 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 an 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 the so-called next generation sequencing technology, 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. Recently developed features within the Ensembl system enable the analysis and visualisation of genetic variation (i.e. sequence differences) between individuals of the same species. This genetic variation explains the differences in traits such as growth, milk yield and susceptibility to disease. We will populate the Ensembl-animal Variation databases with sequence and genotype data acquired from the animal genetics research community. Visualising these variation data and making them accessible to the scientific community and the animal breeding industry will facilitate research to understand the genetic control of complex traits in animals and genetic improvement of farmed animals. A high quality annotated reference genome sequence is a critical bioinformatics resource for the effective prosecution of contempary research in the biological sciences. 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
A high quality annotated reference genome sequence is critical to contempary research in the biological sciences. The Ensembl browser and associated annotation tools and database have been shown to be robust and effective means for making genomic information useful to a wide range of users. Draft reference genome sequences have been established for several farmed animal species (chicken, cattle, pig, horse, turkey) and sequencing is well advanced for several others (including sheep, duck, salmon). Annotated assemblies have already been made available through the Ensembl (chicken, cattle, pig, horse) and Pre-Ensembl (duck, turkey, sheep) genome browsers. However, the utility of a bioinformatics resource are critically dependent upon the currency of the resource. Genome sequence assemblies, including the 'finished' human and mouse sequences are subject to continual revision as new data are acquired and errors corrected. This proposal is concerned with maintaining the currency of Ensembl in respect of farmed and companion animal species, including poultry and farmed fish. Whilst first draft genome sequences have been established for several of the species of interest, improved genome assemblies and increased volumes of ancillary data, including RNAseq and ChIPseq data are also being generated for these species. Thus, we will use these growing and improving data to develop up-to-date and enhanced annotation for these species. Not only are the genomes of more farmed animal species but also the genomes of multiple individuals within a species are being sequenced. The recently developed Ensembl variation resources allow these additional data to be captured and visualised for the benefit of scientists engaged in genetics and genomics, and other lines of, research on the target species. We will work with the animal sciences research community to acquire re-sequence data, SNP and CNV genotypes with which to populate the Ensembl-animal variation databases.
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. 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. 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. In the past 40+ years, there have been major productivity gains in dairy cattle, pigs and poultry and there have also been significant reductions in the greenhouse gas emissions and global warming potential per tonne of animal product. These gains have been achieved through genetic improvement alone or in combination with better husbandry, nutrition and disease control. 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 Illumina chips can be linked to annotated genes and genome locations respectively, thus enabling more effective use of these products. 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)
- Agrocampus Ouest (Collaboration)
- University of Minnesota (Collaboration)
- Jeju National University (Collaboration)
- Arizona State University (Collaboration)
- GLASGOW CALEDONIAN UNIVERSITY (Collaboration)
- Centre for Genomic Regulation (CRG) (Collaboration)
- The Wellcome Trust Sanger Institute (Collaboration)
- University of California, Berkeley (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- DURHAM UNIVERSITY (Collaboration)
- Oregon State University (Collaboration)
- Science for Life Laboratory (Collaboration)
- Seoul National University (Collaboration)
- Huazhong Agricultural University (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- Wageningen University & Research (Collaboration)
- HARVARD UNIVERSITY (Collaboration)
- University of Illinois at Urbana-Champaign (Collaboration)
- University of Copenhagen (Collaboration)
- Korea Research Institute of Bioscience and Biotechnology (KRIBB) (Collaboration)
- National Institute of Animal Science, Korea (Collaboration)
- University of East Anglia (Collaboration)
- Parco Tecnologico Padano (Collaboration)
- Konkuk University (Collaboration)
- AgResearch (Collaboration)
- National Institute of Agrobiological Science, Japan (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- Weizmann Institute of Science (Collaboration)
- EARLHAM INSTITUTE (Collaboration)
- Swedish University of Agricultural Sciences (Collaboration)
- Catalan Institution for Research and Advanced Studies (ICREA) (Collaboration)
- ABERYSTWYTH UNIVERSITY (Collaboration)
- Iowa State University (Collaboration)
- Uppsala University (Collaboration)
- Penn State University (Collaboration)
- Aarhus University Hospital (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- U.S. Department of Agriculture USDA (Collaboration)
- University of Leipzig (Collaboration)
- University of Adelaide (Collaboration)
- Kenya Agriculture & Livestock Research Organization (KALRO) (Collaboration)
- Eversole Associates (Collaboration)
- University College London (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- JSR Genetics (Collaboration)
- Beijing Genomics Institute (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- University of California, Davis (Collaboration)
- University of Delaware (Collaboration)
- Genetic Information Research Institute (Collaboration)
- National Institute of Allergy and Infectious Diseases (NIAID) (Collaboration)
- University of Illinois Urbana-Champaign (Collaboration)
- Kansas State University (Collaboration)
- Cytocell Ltd (Collaboration)
- University of Arkansas (Collaboration)
- UNIVERSITY OF KENT (Collaboration)
- National Health and Medical Research Council (Collaboration)
Publications
Andersson L
(2015)
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.
in Genome biology
Archibald AL
(2013)
Adding value to the pig genome sequence
Clarke L
(2013)
Using Ensembl to understand variation data
Cunningham F
(2015)
Ensembl 2015.
in Nucleic acids research
Dawson HD
(2013)
Structural and functional annotation of the porcine immunome.
in BMC genomics
Eöry L
(2015)
Avianbase: a community resource for bird genomics.
in Genome biology
Flicek P
(2013)
Ensembl 2013.
in Nucleic acids research
| Description | This grant has been used to support the annotation of the reference genome sequences of farmed animal species. The genome of an animal comprises the totality of the genetic information for the animal. The initial step in characterising the genome of an animal involves sequencing the DNA molecules in which the genetic information is encoded. The latest sequencing technologies allow the sequence of the four bases (or letters) in DNA to be determined. However, the raw DNA sequence information is not immediately useful to most scientists. The utility of the sequence is greatly enhanced if the genome sequence is annotated. The annotation process typically involves using other sequence data, for example, from other individuals or sequences representing the expressed parts of the genome (i.e. genes) in order to identify genetic variants and gene structures. This grant was used to analyse and annotate the following genome sequences using the Ensembl piplelines: pig (Sus scrofa; assembly Sscrofa10.2); chicken (Gallus gallus; assembly Galgal4), duck (Anas platyrhynchos; BGI_duck_1.0) and sheep (Ovis aries; assembly Oar_v3.1). These analyses have contributed to genome papers for pig (Groenen et al. 2012), duck (Huang et al. 2013) and sheep (Jiang et al. 2014). |
| Exploitation Route | This grant has enabled the annotation of genome sequences for several farmed animal species and updating of the annotation as new data have been generated by the research community. The value of these annotated reference genome sequences to the research community is demonstrated by the access statistics for the Ensembl genome browser for these species, e.g. >50,000 pages views for each of Ensembl-chicken, Ensembl-cow and Ensembl-pig per quarter. |
| Sectors | Agriculture Food and Drink |
| 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 | 2012 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Economic |
| Description | Bioinformatics and Biological Resources Fund |
| Amount | £884,274 (GBP) |
| Funding ID | BB/M011461/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2015 |
| End | 07/2019 |
| 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 | Brazil Partnering Award |
| Amount | £60,174 (GBP) |
| Funding ID | BB/K021125/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2013 |
| End | 11/2015 |
| 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 | Sheep mini tissue gene expression atlas |
| Description | Sheep total RNA was extracted from embryonic and adult tissues. Sequencing libraries were prepared from the RNA using the Illumina TruSeq stranded total RNA with the Ribo Zero gold option for the rRNA removal. The fragmentation in the standard protocol was modified to increase the average insert size in the library. Sequencing with 151 base paired end reads was performed on an Illumina HiSeq 2500 in rapid mode. These RNA-seq data were generated from 83 different adult and embryonic tissue / cell samples. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2014 |
| Provided To Others? | Yes |
| Impact | These RNA-seq data were a key resource for the annotation of the draft sheep reference genome sequence (Oar_v3.1) and the associated genome paper (Jiang et al. 2014. Science 344:1168-73) and a subsequent paper by Xiang et al. 2016. PeerJ 4:e1762. |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJEB6169 |
| Title | Sheep reference genome sequence Oar_v3.1 |
| Description | A single Texel ewe and a single Texel ram were sequenced and the 75-fold coverage by Illumina reads of the Texel ewe were assembled de novo into contigs and scaffolds with SOAPdenovo. Then 120-fold coverage Illumina sequences from both the ewe and the ram were used for a round of gap-filling. At this point, the N50 length of contigs was 18 kb, and the N50 length of the assembled scaffolds was 1.1Mb, achieving a total length of 2.64 Gb and leaving 6.9% gaps. This assembly was the previous Oar v2.0. The current assembly, Oar_v3.1, was created with another round of gap-filling by adding 21-fold coverage of GC content unbiased Illumina sequencing data from the male and 3 Gb MeDIP-seq for high GC content sequence from the female to the original datasets. Approximately 200,000 gaps were filled, including about 5000 that were filled using CHORI-243 BAC library sequences and 454 reads generated for the Oar v1.0 assembly (ACIV000000000, BioProject PRJNA33937). Segmental duplicates were identified by Whole Genome Assembly Comparison (WAGC), and their read coverage checked by GC content adjustment. Probable artificial tandem duplicates were identified using the larger insert 454 and BAC libraries and comparison to the UMD3 bovine genome assembly, and one copy of the tandem pairs was removed. The assembly of 775 overlapping scaffold ends were revised and these adjacent scaffold pairs were linked together. Artificial duplicated copies that had been generated by multiple gap-filling steps using gapcloser were removed, and erroneously assembled scaffolds identified during the error checking were manually split. A high-density RH map with 39,042 SNP markers and Ovine SNP50 genotyping linkage data were used to check scaffold integrity and to anchor scaffolds and super-scaffolds to chromosomes, leaving roughly 5700 unplaced scaffolds. Of the data cited above, the Illumina sequence data generated from the Texel ram were produced by the ARK-Genomics Centre for Comparative and Functional Genomics, The Roslin Institute, University of Edinburgh (now part of Edinburgh Genomics). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2012 |
| Provided To Others? | Yes |
| Impact | The generation, analysis and annotation of this draft sheep reference genome sequence was described in the sheep genome paper (Jiang et al. 2014. Science 344:1168-1173. As at 13 March 2017, this sheep genome paper has been cited 74 times. |
| URL | https://www.ncbi.nlm.nih.gov/assembly/GCF_000298735.1/ |
| Title | Whole genome sequence data from Texel ram 20118011 |
| Description | The DNA of a male Texel sheep (20118011) was sequenced to great depth using a combination of different insert size libraries. Insert sizes of approximately 400 bp, and 700 bp were used for the bulk of the sequencing. An additional library of Illumina Mate paired inserts with an average insert size of 3.2kbp is included in the data set. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2014 |
| Provided To Others? | Yes |
| Impact | These data contributed to the draft reference sheep genome sequence Oar_v3.1 (Jiang et al. 2014. Science 344:1168-73) and the sheep genome paper describing the analysis and annotation of the draft genome sequence. |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJEB6251 |
| 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 | Ensembl - farm animal |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner(s) in this three-centre collaboration concerned with maintaining the currency of the annotation of farmed animal genome bring extensive links to the farm animal research community, and especially to research groups engaged in genetics and genomics research on farmed animal species. The Roslin Institute partner(s) are also major generators of genomics data for these farmed animal species. |
| Collaborator Contribution | The Ensembl genome database and associated tools were developed by a cross-institute team (EMBL-EBI and Sanger). This EBI-Sanger Ensembl team have developed the database and software tools which allow the effective semi-automated annotation of reference genome sequences. |
| Impact | This collaboration has annotated the reference genome sequences for chicken, cow, pig, sheep, dog, horse, turkey, duck |
| Description | Ensembl - farm animal |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | The Roslin Institute partner(s) in this three-centre collaboration concerned with maintaining the currency of the annotation of farmed animal genome bring extensive links to the farm animal research community, and especially to research groups engaged in genetics and genomics research on farmed animal species. The Roslin Institute partner(s) are also major generators of genomics data for these farmed animal species. |
| Collaborator Contribution | The Ensembl genome database and associated tools were developed by a cross-institute team (EMBL-EBI and Sanger). This EBI-Sanger Ensembl team have developed the database and software tools which allow the effective semi-automated annotation of reference genome sequences. |
| Impact | This collaboration has annotated the reference genome sequences for chicken, cow, pig, sheep, dog, horse, turkey, duck |
| 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 | International Swine Genome Sequencing Consortium |
| Organisation | Aarhus University Hospital |
| Country | Denmark |
| Sector | Hospitals |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Aberystwyth University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Beijing Genomics Institute |
| Country | China |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Catalan Institution for Research and Advanced Studies (ICREA) |
| Department | ICREA Centre for Research in Agricultural Genomics (CRAG) |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Durham University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Eversole Associates |
| Country | United States |
| Sector | Private |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | French National Institute of Agricultural Research |
| Department | GABI: Animal Genetics and Integrative Biology unit |
| Country | France |
| Sector | Private |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | French National Institute of Agricultural Research |
| Department | Physiology of Reproduction and Behavior |
| Country | France |
| Sector | Private |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Genetic Information Research Institute |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Glasgow Caledonian University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Huazhong Agricultural University |
| Country | China |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Iowa State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Jeju National University |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Kansas State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Konkuk University |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Konkuk University |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Korea Research Institute of Bioscience and Biotechnology (KRIBB) |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | National Health and Medical Research Council |
| Country | Australia |
| Sector | Public |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | National Institute of Agrobiological Science, Japan |
| Country | Japan |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | National Institute of Animal Science, Korea |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | National Institute of Animal Science, Korea |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Parco Tecnologico Padano |
| Country | Italy |
| Sector | Private |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Penn State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Science for Life Laboratory |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Seoul National University |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | U.S. Department of Agriculture USDA |
| Department | Beltsville Agricultural Research Center |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | U.S. Department of Agriculture USDA |
| Department | U.S. Meat Animal Research Center |
| Country | United States |
| Sector | Public |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | U.S. Department of Agriculture USDA |
| Country | United States |
| Sector | Public |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University College London |
| Department | Division of Infection and Immunity |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of California, Berkeley |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of California, Davis |
| Department | UC Davis Genome Cente |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Copenhagen |
| Department | Department of Basic Animal and Veterinary Sciences (IBHV) |
| Country | Denmark |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Illinois |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Illinois at Urbana-Champaign |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Illinois at Urbana-Champaign |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Illinois at Urbana-Champaign |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Illinois at Urbana-Champaign |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Illinois at Urbana-Champaign |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Kent |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Leipzig |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Minnesota |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Uppsala University |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Uppsala University |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Wageningen University & Research |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | Avian Genomics: current status and future opportunities. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk: Avian Genomics: current status and future opportunities. International Ornithological Congress (ioc26) 18-24th August 2014, Tokyo, Japan |
| Year(s) Of Engagement Activity | 2014 |
| 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 | Avian genomics: current status and future opportunities |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Talk at 16th ADNAT Convention on Animal Genetics and Genomics. Talk: Avian genomics: current status and future opportunities. Hyderabad, Dec 17-19, 2012. |
| Year(s) Of Engagement Activity | 2012 |
| 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 | Chicken Genome: Current Status and Future Trends from Next Generation Sequencing |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk at the 3rd Annual NGS Asia Congress. Talk: Chicken Genome: Current Status and Future Trends from Next Generation Sequencing. 8 - 9 Oct 2013, Singapore. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Chicken genome update, consortia for RNAseq, SNPs and more ... |
| 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 Avian Model Systems 7. Talk: Chicken genome update, consortia for RNAseq, SNPs and more " 14-19 Nov, Nagoya, Japan 2012. |
| Year(s) Of Engagement Activity | 2012 |
| 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 | Development of New Tools for Genetic Selection for a Sustainable Poultry Industry |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk: Development of New Tools for Genetic Selection for a Sustainable Poultry Industry (2014), Veterinary Advances in Animal Health and Welfare Research - Impact and Opportunities, Feb 20-24, 2014, NIANP Auditorium, Adugodi, Bangalore, India |
| Year(s) Of Engagement Activity | 2014 |
| Description | Ensembl Genome Browser workshop, 2013, 2014, 2015 |
| 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 | The workshops were organised and hosted by The Roslin Institute partner and the training course content delivered by staff from the Ensembl team. The workshop content included introduction to: - Ensembl project - Features and customisation of the Ensembl Genome Browser - BioMart, the data mining utility, which gives easy access to data stored in Ensembl and two of the following four modules: - Genebuild: how are Ensembl gene and transcript predictions made? - Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions - Variation: SNPs and other polymorphisms, haplotypes, linkage disquilibrium, structual variants like CNVs - Regulation: Sequences that may be involved in gene regulation, and integration of the ENCODE data The participants who include a mix of postgraduate students, post-doctoral research scientists and research group leader, were not expect to be familiar with computer programming, so the workshop was managed to suit anyone who would like to know more about the Ensembl Genome Browser and the data stored in Ensembl. The workshop was run on five occasions (22, 23 August 2013; 20, 21 August 2014; 7 July 2015) with ca. 20-30 participants on each occasion. |
| Year(s) Of Engagement Activity | 2013,2014 |
| 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 | ISAG Conference 2012. Talk: NGS of multiple chicken lines and development of a high-density 600K SNP genotyping array, 16-20 July, Cairns, Australia 2012. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk at ISAG Conference 2012. Talk: NGS of multiple chicken lines and development of a high-density 600K SNP genotyping array, 16-20 July, Cairns, Australia 2012. |
| Year(s) Of Engagement Activity | 2012 |
| Description | Livestock Genomics meeting 2014 |
| 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 EBI organises the 'Livestock Genomics' meeting every other year. This is a workshop / conference focusing on Livestock Genomics. During the meeting in 2014, Anja Thorman, Ian Streeter and Daniel Zerbino gave the following talks respectively: Ensembl-Variation - Ready for variation data from the livestock community The Ensembl Epigenomics Pipeline What services does the livestock genomics community need? The workshop enabled members of the community to meet and share ideas for their work. There was a lot of discussion on the future for livestock genomics, including funding opportunities. |
| Year(s) Of Engagement Activity | 2014 |
| Description | NODAI International Symposium "Genome Research: Current Challenges and Future Directions" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | presented a talk at •the NODAI International Symposium "Genome Research: Current Challenges and Future Directions", Kokuyo Hall in Shinagawa, Tokyo, Japan, on 21st January, 2012 |
| Year(s) Of Engagement Activity | 2012 |
| 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 | Next Generation Sequencing of multiple chicken lines reveals a rich source of Single nucleotide polymorphisms for high resolution genetic studies |
| 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 The 1st International Conference on Genomics in the Americas. Talk: Next Generation Sequencing of multiple chicken lines reveals a rich source of Single nucleotide polymorphisms for high resolution genetic studies, 27-28 Sept, Philadelphia, USA. |
| Year(s) Of Engagement Activity | 2012 |
| 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 PAGXXIII, San Diego, California, 2015 |
| 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 on 'The Ensembl farm: all you need is livestock' at PAGXXIII. This enabled him to interact with many researchers in the Life Sciences, and disseminate the resources available in Ensembl for researchers working on farm animals. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Talk at Animal Genomics Research Group "The global genomic approaches to climate change impact on livestock production". Talk: Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing. 10-15 July, Seoul, Korea, 2013. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk at the 8th International Conference on Genomics (ICG-8). Talk: Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing. 29 Oct - 1 Nov 2013, Shenzhen, China. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Press release by EMBL-EBI on sheep genome |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Press release detailed the availability of the sheep genome and the importance of this to a wide audience. Impact of the press release has not been evaluated yet. |
| Year(s) Of Engagement Activity | 2014 |
| URL | http://www.ebi.ac.uk/about/news/press-releases/sheep-genome |
| 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 | Structural aspects of genomes across species |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk at The 8th European Poultry Genetics Symposium. Talk: Structural aspects of genomes across species. 25-27 Sept, Venice Italy, 2013. |
| Year(s) Of Engagement Activity | 2013 |
| 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 | The chicken genome 10 years on. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Keynote lecture: chicken genome - 10 years on. Avian Model Systems - the 8th International Meeting, Cold Spring Harbour, USA, 4-8th March, 2014. CSHL Leading Strand - Keynote Lecture Series (http://theleadingstrand.cshl.edu/Course/Keynote/2014/AVIAN/150 The chicken genome 10 years on - BBSRC (http://www.bbsrc.ac.uk/news/events/1403-chicken-genome.aspx) |
| Year(s) Of Engagement Activity | 2014 |
| Description | Training workshops in 2013 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. Several training workshops with an emphasis on using the Ensembl Genome Browser for farmed animal genomes have been held: 13th May 2013 at the University of North Carolina, Chapel Hill, North Carolina, USA 6th June 2013 at The Genome Analysis Centre, Norwich 1st July 2013 at Maastricht University, Maastricht, The Netherlands 22nd and 23rd August 2013 at The Roslin Institute, University of Edinburgh. Overduin B, 2013. Genome resources at EBI - Ensembl and Ensembl Genomes. In: Plant and Animal Genome XXI Conference, 12-16 January, 2013, Town & Country Convention Center San Diego, California. Abstract W343. Overduin B, 2013. Genome Annotation Resources at the EBI - Ensembl and Ensembl Genomes. In: Plant and Animal Genome Asia 2013, 17-19 March, 2013, Grand Copthorne Waterfront Hotel, Singapore. Abstract W040. Clarke L, Cunningham F, McLaren W, Ritchie G, Gil L, Thorman A, Hunt S, 2013. Using Ensembl to understand variation data. In: Plant and Animal Genome XXI Conference, 12-16 January, 2013, Town & Country Convention Center San Diego, California. Abstract W345. Additionally, all of the Ensembl's general, multi-species workshops include mention of the farm animal resources. In total, there were exactly 100 Ensembl workshops in 2013 and details of the locations and dates of these training events can be provided on request. Impacts include increased use of the data by individual users due to improved understanding of Ensembl by workshop participants (this is evidenced by feedback gathered from participants), and incremental improvements to Ensembl and Ensembl courses from participant feedback. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Training workshops in 2014 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. 29 Sept - 2nd October 2014: Animal Genome Informatics, EBI. Workshop on working with NGS data specific to farmed animals. Demonstrations of the Ensembl Genome Browser were provided at both the Plant and Animal Genome Conference, San Diego, USA, and at the Plant and Animal Genomes Conference Asia, Singapore. Ensembl gave an Ensembl browser demonstration at the Avian Genomics Meeting at Cold Spring Harbour Laboratory (USA), March 2014; 18 people attended. Ensembl also gave presentations on the browser, RNA-Seq analysis and regulation analysis at the Animal Genome Informatics, held at EBI in September 2014. Ensembl gave a two-day workshop at the Chinese Agricultural University in China in November 2014, as part of the collaboration with a visiting worker. All of these training workshops and presentations are a valuable way for Ensembl to disseminate its resources for farm animal species to intersted researchers, and to help ensure that researchers are trained to use the data. |
| Year(s) Of Engagement Activity | 2014 |
| 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 |