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


Publications


10 25 50
 
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
 
Title Cattle Ensembl database and releases 
Description The annotated reference genome sequences have been delivered through a series of Ensembl releases. The initial annotation work was funded through the BBSRC (grant BB/I025506/1), with future developments and updates funded by further grants from the BBSRC (BB/I025360/2 and BB/M011615/1) within the relevant periods). The following updates for cattle have occurred: - initial genebuild in July 2005, on assembly Btau_1.0 (release 32) - new assembly Btau_2.0 with new genebuild in December 2005 (release 36) - new assembly Btau_3.1 with new genebuild in September 2006 (release 44) - new assembly Btau_4.0 with new genebuild in January 2008 (release 50) - genebuild update in May 2010 (release 58) - new assembly UMD3.1 with new genebuild in September 2011 (release 64) Ensembl Release 74 (December 2013) Cattle: new dbSNP (build 138) have been imported. More details about new features for cow in release 74 can be found at: http://www.ensembl.org/Bos_taurus/Info/WhatsNew?db=core Ensembl Release 80 (May 2015) Cow: variation database updated to dbSNP142 OMIA phenotype data update AnimalQTL update Cow: variation database updated to dbSNP143 OMIA phenotype data update AnimalQTL update Ensembl Release 82 (September 2015) Xrefs update OMIA data import AnimalQTL update Updated ProteinTrees, ncRNATrees and homologies Ensembl Release 83 (December 2015) Other GOA data for Cow OMIA data for Cow AnimalQTL for Cow Updated ProteinTrees, ncRNATrees and homologies Ensembl Release 84 (March 2016) Update for dbSNP 146 Ensembl Release 85 (July 2016) Phenotype data updated Ensembl Release 86 (October 2016) Update for dbSNP 148 Phenotype data updated Structural variants updated from DGVa 
Type Of Material Database/Collection of data 
Year Produced 2006 
Provided To Others? Yes  
Impact The data are highly accessed by researchers- there were 42464 site visits (and over 250,000 page views) in 2016 alone. 
URL http://www.ensembl.org/Bos_taurus/Info/Index
 
Title Chicken Ensembl database and releases 
Description Ensembl website for chicken Gallus_gallus-4.0 (GCA_000002315.2) released in April 2013 (Ensembl 71). This website comprises full annotation of the chicken reference genome assembly using the Ensembl automatic annotation system. Protein-coding models were generated by aligning vertebrate protein sequences from UniProt to the repeat-masked genome and by using RNA-Seq data for a selection of adult and embryo tissues provided by the Chicken Genome Consortium. The final gene set includes models from both the UniProt alignments and the RNAseq data. It comprises 15508 protein-coding models, 1558 small noncoding RNAs and 42 pseudogenes. 5,139 of the genes were exclusively annotated using the RNA-seq data. The Ensembl website for chicken includes pairwise genome alignments with human, mouse, zebrafish, anole lizard, Chinese soft-shell turtle, Xenopus tropicalis, duck, flycatcher, turkey, and zebra finch. Users can view the indexed BAM files, tissue-specific gene models and the full set of splice junctions (introns) identified by the RNA-Seq pipeline alongside the chicken gene set, chicken cDNAs and chicken ESTs on the Ensembl genome browser http://www.ensembl.org/Gallus_gallus. We also provide gene orthologues, cross-references to external databases, and variations from dbSNP and the Affymetrix Chicken600K genotyping chip. Data can be downloaded from our FTP site or queried using our VEP, REST API, Perl API or BioMart query system. The annotated reference genome sequences have been delivered through a series of Ensembl releases. The initial annotation work was funded through the BBSRC (grant BB/I025506/1), with future developments and updates funded by further grants from the BBSRC (BB/I025360/2 and BB/M011615/1) within the relevant periods). The following updates for chicken have occurred: Ensembl Release 71 (April 2013) The annotation of the latest chicken genome assembly (Galgal4) was from Pre-Ensembl to the full Ensembl site, including a revised Gene Build. For more details see: http://apr2013.archive.ensembl.org/Gallus_gallus/Info/WhatsNew?db=core Ensembl Release 74 (December 2013) Updates to chromosome z and new alignments to saurian reptiles have been implemented. More details about new features for chicken in release 74 can be found at: http://www.ensembl.org/Gallus_gallus/Info/WhatsNew?db=core Ensembl Release 75 (February 2014) Cross-references to external databases updated Ensembl Release 76 (August 2014) Updated whole-genome (LASTZ) alignments to the new human assembly New dbSNP build 140 was imported Added 'QTL chromosome name' and 'QTL region' filters in BioMart Ensembl Release 77 (October 2014) RefSeq's GFF3 annotation added in order to facilitate comparison of gene sets New synteny data for Chicken vs Zebrafinch, Chicken vs Opossum Updated data from the Animal Quantitative Trait Loci (QTL) Database Ensembl Release 79 (March 2015) Cross-references to external databases updated Ensembl Release 80 (May 2015) OMIA phenotype data update AnimalQTL update Ensembl Release 81 (July 2015) AnimalQTL update Ensembl Release 82 (September 2015) dbSNP 144 import for Chicken AnimalQTL update for Chicken Recompute TBlat pairwise comparisons with LastZ for {M.mus, G.gal, T.nig} vs X.tro and for G.gal vs C.sav Updated ProteinTrees, ncRNATrees and homologies Ensembl Release 83 (December 2015) Chicken dbSNP 145 update Other GOA data update for Chicken AnimalQTL import for Chicken Updated ProteinTrees, ncRNATrees and homologies Ensembl Release 84 (March 2016) Phenotype data update Ensembl Release 85 (July 2016) External database references update Phenotype data update Ensembl Release 86 (October 2016) A new genebuild on the new chicken assembly, Gallus_gallus-5.0 Chicken-specific cDNAs and ESTs were aligned to the chicken genome and are made available through the Ensembl website and the chicken otherfeatures database. In addition to the gene annotation for Galgal_5.0, an RNA-Seq database was released where users can view BAM files and transcript models for different tissues. A recompute of all LASTZ alignements for chicken Updated to dbSNP version 147. Phenotype data update Syntenies recomputed for the new assembly 
Type Of Material Database/Collection of data 
Provided To Others? Yes  
Impact There were 49902 site visits in 2016, and 225823 unique page views. 
URL http://www.ensembl.org/Gallus_gallus/Info/Index
 
Title Duck Ensembl database and releases 
Description The annotated reference genome sequences have been delivered through a series of Ensembl releases. The initial annotation work was funded through the BBSRC (grant BB/I025506/1), with future developments and updates funded by further grants from the BBSRC (BB/I025360/2 and BB/M011615/1) within the relevant periods). The following updates for duck have occurred: Ensembl Release 73 (September 2013) Duck: Annotation of the duck reference genome sequence was migrated from Pre-Ensembl to the full Ensembl site, including a revised Gene Build. For more details see: http://sep2013.archive.ensembl.org/Anas_platyrhynchos/Info/WhatsNew?db=core Ensembl Release 74 (December 2013) Created a new 'saurian reptile' multi-species whole-genome alignment that includes duck. Ensembl Release 76 (August 2014) Duck: Cross-references to external databases updated 
Type Of Material Database/Collection of data 
Year Produced 2012 
Provided To Others? Yes  
Impact The data are highly accessed by researchers- there were 5211 site visits in 2016 alone. 
URL http://www.ensembl.org/Anas_platyrhynchos/Info/Index
 
Title Pig Ensembl database and releases 
Description The annotated reference genome sequences have been delivered through a series of Ensembl releases. The initial annotation work was funded through the BBSRC (grant BB/I025506/1), with future developments and updates funded by further grants from the BBSRC (BB/I025360/2 and BB/M011615/1) within the relevant periods). The following updates for pig have occurred: Initial genebuild was in September 2009, on assembly Sscrofa9 Ensembl Release 67 (May 2012) Pig: The annotation of the pig genome assembly (Sscrofa10.2) on which the pig genome sequence paper was based was migrated from Pre-Ensembl to the full Ensembl site. The annotated reference genome sequences have been delivered through a series of Ensembl releases. The following updates for pig have occurred: Ensembl Release 69 (October 2012) Pig: An Ensembl-Havana gene set was added to the annotation. The VEGA manual annotation which had been generated through a community effort was added. For more details see: http://oct2012.archive.ensembl.org/Sus_scrofa/Info/Index Ensembl Release 74 (December 2013) Pig: secondary structure of non-coding RNAs are now shown on the gene summary page, using the R2R package. More details about new features for pig in release 74 can be found at: http://www.ensembl.org/Sus_scrofa/Info/WhatsNew?db=core Ensembl Release 75 (February 2014) DGVa data was updated and new studies imported. Transcript ENSSSCT00000011005 was deleted. There remains an overlapping transcript within the same gene that has been manually annotated by Havana. Merged genes and transcripts can be fetched using 'source' column Ensembl Release 76 (August 2014) Updated whole-genome (LASTZ) alignments to the new human assembly New dbSNP build 140 was imported SIFT analysis was updated to version 5.1.0 Ensembl Release 77 (October 2014) RefSeq's GFF3 annotation added in order to facilitate comparison of gene sets Cross-references to external databases updated Ensembl Release 78 (December 2014) Updated data from the Animal Quantitative Trait Loci (QTL) Database Ensembl Release 80 (May 2015) variation database updated to dbSNP143 AnimalQTL update Ensembl Release 81 (July 2015) AnimalQTL update Ensembl Release 82 (September 2015) AnimalQTL update for Pig Updated ProteinTrees, ncRNATrees and homologies Ensembl Release 83 (December 2015) Pig dbSNP 145 update External cross-references updated Updated ProteinTrees, ncRNATrees and homologies Updated ProteinTrees, ncRNATrees and homologies AnimalQTL update Ensembl Release 84 (March 2016) New chips for pig: • GeneSeek Genomic Profiler Porcine - HD (Illumina) • GeneSeek Genomic Profiler Porcine - LD BeadChip (Illumina) • Axiom Porcine Genotyping Array (Affymetrix) Ensembl Release 85 (July 2016) Phenotype update Ensembl Release 86 (October 2016) Phenotype update 
Type Of Material Database/Collection of data 
Year Produced 2009 
Provided To Others? Yes  
Impact The data are highly accessed by researchers- there were 44041 site visits (over 240,000 page views) in 2016 alone. 
URL http://www.ensembl.org/Sus_scrofa/Info/Index
 
Title Sheep Ensembl database and releases 
Description Ensembl website for sheep Oar_v3.1 (GCA_000298735.1) released in December 2013 (Ensembl 74). This website comprises full annotation of the sheep reference genome assembly using the Ensembl automatic annotation system. Protein-coding models were generated by aligning vertebrate protein sequences from UniProt to the repeat-masked genome and by using RNA-Seq data provided by the ISGC. The final gene set includes models from both the UniProt alignments and the RNAseq data. It comprises 20921 protein-coding models, 3985 small noncoding RNAs and 291 pseudogenes. The ISGC RNA-Seq data set includes a range of tissue samples shared between a trio: ram, ewe and their lamb. In total, we aligned 800 GB data from 89 tissue samples to the sheep genome assembly. This RNA-Seq data set is larger than for any other species in Ensembl. The Ensembl website for sheep also includes pairwise genome alignments with human, cow and pig. Users can view the indexed BAM files, tissue-specific gene models and the full set of splice junctions (introns) identified by the RNA-Seq pipeline alongside the sheep gene set on the Ensembl genome browser http://www.ensembl.org/Ovis_aries. We also provide gene orthologues, cross-references to external databases, and variations from dbSNP and selected genotyping chips. Data can be downloaded from our FTP site or queried using our Perl API or BioMart query system. The annotated reference genome sequences have been delivered through a series of Ensembl releases. The initial annotation work was funded through the BBSRC (grant BB/I025506/1), with future developments and updates funded by further grants from the BBSRC (BB/I025360/2 and BB/M011615/1) within the relevant periods). The following updates for sheep have occurred: Ensembl Release 74 (December 2013) Sheep: Annotation of the sheep reference genome sequence was made available through the full Ensembl site. Given the large volumes of RNAseq data it was necessary to use a matrix configuration / menu for displaying these data. More details about the sheep annotation in release 74 can be found at http://www.ensembl.org/Ovis_aries/Info/WhatsNew?db=core#cat-genebuild. Ensembl Release 76 (August 2014) Updated whole-genome (LASTZ) alignments to the new human assembly New dbSNP build 140 was imported Added "QTL chromosome name" and "QTL region" filters in BioMart Imported markers from SheepMap4.7 and CAB Ovine Linkage Map Ensembl Release 77 (October 2014) BAC clone track added Cross-references to external databases updated Ensembl Release 78 (December 2014) Updated data from the Animal Quantitative Trait Loci (QTL) Database. Ensembl Release 79 (March 2015) New genotype data from the NextGen Project for Sheep, from 3 populations: Iranian Ovis aries, Iranian Ovis orientalis, Moroccan Ovis aries. Full details about new data and features for Ensembl release 80 can be found at: http://www.ensembl.org/info/website/news.html?id=80 Cow: variation database updated to dbSNP142 Pig: variation database updated to dbSNP143 Cow, dog, horse, chicken, turkey, sheep: OMIA phenotype data update Cow, horse, chicken, pig: AnimalQTL update Ensembl Release 81 (July 2015) OMIA phenotype data update AnimalQTL update DGVa update Ensembl Release 82 (September 2015) OMIA data import AnimalQTL update Ensembl Release 83 (December 2015) Other GOA data update OMIA data import AnimalQTL update Ensembl Release 84 (March 2016) Phenotype update Ensembl Release 85 (July 2016) Phenotype update Ensembl Release 86 (October 2016) External database references update 
Type Of Material Database/Collection of data 
Year Produced 2013 
Provided To Others? Yes  
Impact The data are highly accessed by researchers- there were 16724 site visits (and over 100,000 page views) in 2016 alone. 
URL http://www.ensembl.org/Ovis_aries/Info/Index
 
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/
 
Description Development of tools to detect chromosomal translocations in pigs 
Organisation Cytocell Ltd
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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 of Great Britain & Northern Ireland (UK) 
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 of Great Britain & Northern Ireland (UK) 
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 European Molecular Biology Laboratory (EMBL)
Department European Bioinformatics Institute (EBI)
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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 of Great Britain & Northern Ireland (UK) 
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 European Molecular Biology Laboratory (EMBL)
Department European Bioinformatics Institute (EBI)
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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 of Great Britain & Northern Ireland (UK) 
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 (INRA)
Country France, French Republic 
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 Iowa State University
Country United States of America 
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, Kingdom of 
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 of America 
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 USDA Agricultural Research Service, National Animal Diseases Center
Country United States of America 
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, Commonwealth of 
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 of America 
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 Wageningen
Country Netherlands, Kingdom of the 
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, Kingdom of 
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, French Republic 
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 of America 
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 of Great Britain & Northern Ireland (UK) 
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 (INRA)
Department INRA Rennes Centre
Country France, French Republic 
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 (INRA)
Department INRA Toulouse
Country France, French Republic 
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 Government of Catalonia
Department Centre for Genomic Regulation (CRG)
Country Spain, Kingdom of 
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 of America 
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 (ICL)
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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 of America 
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, Republic of 
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) Centre Cambridge
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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 Allergy and Infectious Diseases (NIAID)
Country United States of America 
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 (NIEHS)
Country United States of America 
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 of America 
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, Kingdom of 
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 of America 
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 of America 
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 of America 
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 of Great Britain & Northern Ireland (UK) 
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, Federal Republic of 
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 of Great Britain & Northern Ireland (UK) 
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, State of 
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, Kingdom 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 Aberystwyth University
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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 Australian Government
Department National Health and Medical Research Council (Australia)
Country Australia, Commonwealth of 
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 Beijing Genomics Institute (BGI)
Country China, People's 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 Biotechnology and Biological Sciences Research Council (BBSRC)
Department Earlham Institute
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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, Kingdom 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 Department of Medical Biochemistry
Department Science for Life Laboratory
Country Sweden, Kingdom 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 Durham University
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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 European Molecular Biology Laboratory (EMBL)
Department European Bioinformatics Institute (EBI)
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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 of America 
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 (INRA)
Department GABI: Animal Genetics and Integrative Biology unit
Country France, French Republic 
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 (INRA)
Department Physiology of Reproduction and Behavior
Country France, French Republic 
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 (INRA)
Country France, French Republic 
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 Genetic Information Research Institute
Country United States of America 
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 (GCU)
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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, People's 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 Iowa State University
Country United States of America 
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 of America 
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 Institute of Agrobiological Science, Japan
Country Japan 
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 Animal Science, Korea
Country Korea, Republic of 
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 Animal Science, Korea
Country Korea, Republic of 
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 Parco Tecnologico Padano
Country Italy, Italian Republic 
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 of America 
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 of Great Britain & Northern Ireland (UK) 
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
Country United States of America 
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 USDA ARS BARC
Country United States of America 
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 USDA, ARS, US Meat Animal Research Center
Country United States of America 
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 (UCL)
Department UCL Division of Infection & Immunity
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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
Department University of California, Berkeley
Country United States of America 
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 of America 
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 (Københavns Universitet UCPH)
Department Department of Basic Animal and Veterinary Sciences (IBHV)
Country Denmark, Kingdom 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 University of Illinois
Department University of Illinois (Urbana-Champaign)
Country United States of America 
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
Department University of Illinois (Urbana-Champaign)
Country United States of America 
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
Department University of Illinois (Urbana-Champaign)
Country United States of America 
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
Department University of Illinois (Urbana-Champaign)
Country United States of America 
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
Department University of Illinois (Urbana-Champaign)
Country United States of America 
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 of America 
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 of Great Britain & Northern Ireland (UK) 
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, Federal 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 University of Minnesota
Country United States of America 
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 Uppsala
Country Sweden, Kingdom 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 University of Uppsala
Country Sweden, Kingdom 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 University of Wageningen
Country Netherlands, Kingdom of the 
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 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 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 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 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 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 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 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 6th International chick meeting, Edinburgh (2011) Avian Genome Evolution 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Organised conference and presented a talk "Avian Genome Evolution" at the 6th International chick meeting, Edinburgh (2011). Aim was to inform, build network, seek collaborations, etc. in the avian research community. Further consortia (e.g. the chicken RNAseq consortium) and projects were created.
Year(s) Of Engagement Activity 2011
 
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