The impact of host genetic variation on susceptibility and pathology

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

In this theme, we aim to pursue genetic variation underlying disease prevalence. By combining resistance data with genome mapping techniques we are able to define loci associated with resistance to a very wide range of infections in production animals. Genetic variation can impact upon every stage of infection from initial entry to the nature and resolution of pathology and subsequent memory responses. Each pathogen-host combination offers new challenges. Targets for study are prioritised on the basis of economic importance/impact and clear evidence of heritable resistance. The aim in each study is to link genotype to phenotype (e.g. variation in an innate immune response; difference in resistance to a pathogen) in a predictive manner. We will focus on (1) poultry infection by Salmonella and Campylobacter as sources of human infection. Some S. enterica serovars as well as avian pathogenic E. coli (APEC) also threaten poultry welfare and exert a substantial economic and welfare burden owing to their ability to migrate to systemic sites, causing fowl typhoid or colibacillosis respectively. (2) Mycobacterial infections of cattle and sheep.

Organisations

Publications

10 25 50
 
Description In this theme, our main aim was to pursue host genetic variation underlying disease prevalence in farm animals, focusing on identification of loci and genes responsible for variation in innate responses to endemic pathogens of livestock species and poultry, and the gene variants that lead to disease resistance. The work brought together scientists across several disciplines including molecular and quantitative genetics, bioinformatics, genomics, transcriptomics, immunology, pathology and pathogen biology.
By combining phenotyptic infectious disease resistance data with genome mapping techniques we are able to define loci associated with resistance to a very wide range of infections in production animals including cattle, sheep, and chickens. Genetic variation can impact upon every stage of infection from initial entry to the nature and resolution of pathology and subsequent memory responses. Each pathogen-host combination offers new challenges. Targets for study were prioritised on the basis of economic importance/impact and clear evidence of heritable resistance. The aim in each study within this theme was to link genotype to phenotype (e.g. variation in an innate immune response; difference in resistance or tolerance to a pathogen) in a predictive manner. In general, the studies involved the identification of quantitative trait loci (QTL) by linking genotypes to phenotypes. Genotypes were determined through an integrated post-genomics approach investigating various types of genomic variation including SNPs and copy number variants (CNV) across the genome as well as SNPs in candidate genes. Many of these were resources developed at Edinburgh Genomics and in ISP1). The phenotypes involved careful selection of appropriate data that was related to an appropriate immune response, correlate of protection, pathology or mortality identified through experimental challenge and/or ISPs 1 and 4. Data were also collected from the field (for example statutory skin test data and abattoir for bovine tuberculosis, or industry data). Identification of candidate genes and causal variants was aided by knowledge of gene function, pathway data and annotation generated in theme 1. Knowledge gained by determining the way in which variation alters disease outcome can be translated into a strategy for disease mitigation, most often through selective breeding. We focused on (1) poultry infection by Salmonella and Campylobacter as sources of human infection. Some S. enterica serovars as well as avian pathogenic E. coli (APEC) also threaten poultry welfare and exert a substantial economic and welfare burden owing to their ability to migrate to systemic sites, causing fowl typhoid or colibacillosis respectively. (2) Mycobacterial infections of cattle and sheep, some of which have a zoonotic potential.
Highlights:
• Copy number variants (CNVs) are being identified as underpinning variation in disease resistance in many species and a survey among chicken breeds has found many CNVs, some of which are associated with chicken lines selected for resistance. A 600K SNP chip has also been developed as a further resource for chicken disease resistance traits
• Campylobacter intestinal colonisation in chickens has been defined as a complex trait in broiler bird lines and several QTLs investigated using expression and pathway analysis to identify potential candidate genes. Campylobacter resistance has been associated with the avian MHC, and innate and acquired immune responses.
• Variation in antibody response was associated to genotypic variation (SNPs) in indigenous Ethiopian chickens to various pathogens causing major production losses. These included bacteria (Salmonella gallinarum and Pasteurella multocida causal agents of fowl typhoid and fowl cholera respectively) and viruses (Infectious Bursal Disease Virus and Marek's Disease Virus). Genetic variation in resistance to the avian apicomplexan parasite Eimeria and to cestode parasitism was also observed. These results indicate that selective breeding for disease resistance could provide a safe and sustainable strategy for chickens in countries such as Ethiopia.
• The sheep nematode Teladorsagia circumcincta is a common pathogen of sheep and represents with important economic impact in many countries of the world, including the UK. Control is by anthelmintics but there are issues with resistance. No vaccine is available. Several immune-associated candidate genes have been associated with resistance and susceptibility to this nematode using transcriptomics of the mucosal tissue of infected sheep. These include the T Cell Transcription Factor and IL-23. GATA3 and IL17RB are associated with enhanced resistance to this nematode.
• Mycobacterium avium subspecies paratuberculosis is a widespread gastrointestinal pathogen of sheep in the UK and elsewhere, and causes two distinct forms of disease, multibacillary and paucibacillary. Transcript variants of various cytokine transcription factors, cytokines and cytokine receptors were associated independently with the two forms of disease. The results suggested that the pathology associated with multibacillary paratuberculosis is induced by a Th2 biased response whereas the pathology associated with the paucibacillary is determined by Th1 and Th17 biased responses. These studies have identified various candidate genes associated with these types of T cell response and suggest that the two forms of disease may be under distinct genetic control.
• Bovine tuberculosis (bTB) is caused by the pathogen Mycobacterium bovis and despite statutory control measures remains an important issue in the UK and many other countries. Spill over into wildlife means there is no simple solution. Vaccination is not currently a viable option. Genetic control through selective breeding could provide an alternative strategy. Previously we have shown that there is heritable variation in the major dairy breed, the Holstein. With previous BBSRC funding and in collaboration with AFBI, Northern Ireland, we conducted a case-control study of cattle in high prevalence areas. We were able to locate novel regions of the bovine genome using the high density bovine SNP chip with 700,000 SNP markers that were associated with infection with M. bovis. This work demonstrated that resistance to bTB is polygenic and likely controlled by many loci of small effect.
• We have now shown that there are two pathological outcomes following infection that are distinguished by detectable and non-detectable lesions. We have provided evidence that these traits appear to be under separate genetic control, suggesting that the outcome of infection is dependent on distinct pathways. Nonetheless, these two traits share some genetic regions and therefore selective breeding for infection with either outcome is achievable.
• Using our case-control data we also demonstrated that SNP based genomic prediction for bTB resistance is feasible.
• In collaboration with SRUC, we have demonstrated that the genetic architecture that underpins variation in bTB resistance in the population of UK dairy cattle is also polygenic with many loci of small effect.
• In collaboration with SRUC the earlier pedigree based research has led to national evaluations for bTB resistance in the Holstein dairy breed, and the information in the form of an index (TB advantage) is offered through the auspices of AHDB. We have used this phenotype to sequence high and low risk sires for bTB. Altogether, the information gained will help progress to genomic evaluations based on SNP data in the future. Such an approach will result in faster and more accurate genetic gain and the pathway to impact is likely to be similar to the pedigree-based approach.
Exploitation Route We continue to work with the livestock industry to advance genetic approaches to improve disease resistance in farmed species
Sectors Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology

 
Description The research brought together scientists across several disciplines including molecular and quantitative genetics, bioinformatics, genomics, transcriptomics, immunology, pathology and pathogen biology to improve our understanding of genetic variation in disease resistance and susceptibility as it relates to endemic diseases of livestock species. We aimed to explore the impact of genetic variation on the host immune response across the whole genome as well as focusing on candidate genes. Our research links to both ISP1 (ISP1 Analysis and Prediction in Complex Animal Systems) [BB/J004235/1] and to other themes in ISP3 in particular Theme 1. Our focus has been on production animals including cattle, sheep, pigs and chickens and we prioritised major endemic diseases that are of economic importance in the UK and that are not currently well controlled. We have advanced our understanding of the impact of host genetic variation on Salmonella, Campylobacter and E. coli in poultry, Mycobacterium avium subspecies paratuberculosis in sheep and M. bovis in cattle. We have identified loci and candidate genes, many of which are related to innate and acquired immunity. However others loci contain novel genetic variation with no clear candidates as of yet. We have also been able to catalogue distinct types of genetic variation across the genome including SNPs and CNVs. Significant progress has been made towards translating this research into new breeding strategies for the UK livestock industry that would provide a safe and sustainable means of controlling disease. In particular our research is contributing towards genomic evaluations for bTB in Holsteins being made available to UK farmers in high prevalence areas. In the future it is anticipated that this research can be expanded to other breeds of cattle, and also will provide a proof-of-principle approach to combat other infectious pathogens of livestock. BBSRC strategic investment at Roslin via this and other Institute Strategic Programmes has sustained expertise and facilities that have attracted substantial inward investment at Easter Bush. This has recently included £15M Gates Foundation funding to establish the Centre for Tropical Livestock Genetics & Health to implement genetic gain and treatments in support of farmers in low- and middle-income farmers, including to control endemic and zoonotic diseases. It has also driven dozens of productive collaborations with industry via contracts and leveraging schemes, leading to £10M private equity investment to form Roslin Technologies to commercialise our research and construction of a new £32M Innovation Centre adjacent to the Institute to engage and grow businesses. Moreover, the expertise supported by this funding has attracted major investment in Agri-Tech Centres at Easter Bush funded by InnovateUK (Centre for Innovation Excellence in Livestock & Agri-EPI). These Centres will increase national capacity for infectious challenge in farmed animals, gene editing and collection of novel phenotypes and be linked to stakeholders throughout the food supply chain.
First Year Of Impact 2013
Sector Agriculture, Food and Drink
Impact Types Societal,Economic

 
Description Animal Health Research Club (ARC)
Amount £723,120 (GBP)
Funding ID BB/L004054/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 04/2014 
End 09/2017
 
Description Animal health and disease and veterinary immune reagents collaboration with USDA
Amount £21,877 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 08/2015 
End 08/2018
 
Description BBSRC Industrial Partnering Award
Amount £631,000 (GBP)
Funding ID BB/P022049/1 (with Cobb Vantress as industry partner) 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 08/2017 
End 09/2020
 
Description BBSRC Industrial Partnering Award Scheme
Amount £516,308 (GBP)
Funding ID BB/J015296/1 (Role of AKT1 & SIVA1 in resistance to avian salmonellosis) 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 10/2012 
End 09/2015
 
Description BBSRC-NIFA scheme for UK-US collaboration on animal diseases
Amount £417,191 (GBP)
Funding ID BB/M028208/1 (Host resistance to avian pathogenic E. coli) 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 10/2015 
End 09/2018
 
Description European Commission H2020-INFRAIA-2016-1
Amount € 367,000 (EUR)
Funding ID EU project 731014 
Organisation European Commission H2020 
Sector Public
Country Belgium, Kingdom of
Start 04/2017 
End 03/2022
 
Description Funding for genotyping from Hy-Line International
Amount £30,000 (GBP)
Organisation HyLine 
Sector Private
Country United States of America
Start  
 
Description Scottish Government RESAS initiative
Amount £450,000 (GBP)
Organisation Scottish Government 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 10/2016 
End 09/2019
 
Description The Houghton Trust, Small Project Grant Scheme
Amount £10,000 (GBP)
Organisation The Houghton Trust 
Sector Charity/Non Profit
Country Unknown
Start  
 
Description open call
Amount
Funding ID BB/L00478X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 06/2014 
End 06/2017
 
Description open call
Amount £379,303 (GBP)
Funding ID BB/L004003/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 04/2014 
End 04/2017
 
Description BBSRC-FAPESP tick resistance in cattle consortium 
Organisation Rothamsted Research
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution The Roslin Institute, University of Edinburgh partner contributes expertise in quantitative genetics, genome-wide association studies, including the genetics of disease resistance in farm animal species. The team also provides access to the expertise and capabilities of the University of Edinburgh's genomics facility (Edinburgh Genomics).
Collaborator Contribution The Rothamsted partner contributes expertise in biochemistry and analysis of semio-chemical involved in the attraction of insects. The Sao Paulo partner provides essential expertise and access to biological samples (sebum, DNA) and phenotypic data.
Impact Joint BBSRC-FAPESP grant funding to study the genetics of resistance to ticks in cattle. The partnership combines expertise in genetics, and biochemistry.
Start Year 2010
 
Description BBSRC-FAPESP tick resistance in cattle consortium 
Organisation University of Sao Paulo
Country Brazil, Federative Republic of 
Sector Academic/University 
PI Contribution The Roslin Institute, University of Edinburgh partner contributes expertise in quantitative genetics, genome-wide association studies, including the genetics of disease resistance in farm animal species. The team also provides access to the expertise and capabilities of the University of Edinburgh's genomics facility (Edinburgh Genomics).
Collaborator Contribution The Rothamsted partner contributes expertise in biochemistry and analysis of semio-chemical involved in the attraction of insects. The Sao Paulo partner provides essential expertise and access to biological samples (sebum, DNA) and phenotypic data.
Impact Joint BBSRC-FAPESP grant funding to study the genetics of resistance to ticks in cattle. The partnership combines expertise in genetics, and biochemistry.
Start Year 2010
 
Description Bovine Tuberculosis sequencing and modelling collaboration 
Organisation University of Glasgow
Department MRC - University of Glasgow Centre for Virus Research
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Help with analysis of bovine tuberculois sequences with Phylodynamics computational techniques
Collaborator Contribution Lead of Tb project, collection of bovine Tb sequences and other modelling expertise
Impact Papers resulting: Trewby et al (2016) "Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis" Epidemics, Vol 14 March 2016, Pages 26-35 Crispbell (2017) "Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand" BMC Genomics 2017 Feb 16;18(1):180 Successful grant application due to start April 2017: Bilateral BBSRC-SFI: Tackling a multi-host pathogen problem - phylodynamic analyses of the epidemiology of M. bovis in Britain and Ireland PI: Professor Rowland Kao:University of Glasgow BB/P010598/1
Start Year 2014
 
Description Collaboration relating to genetics of bovine tuberculosis 
Organisation Agri-Food and Biosciences Institute (AFBI)
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Public 
PI Contribution Secured two rounds of grant funding from BBSRC. Expertise in genome wide association studies.
Collaborator Contribution Epidemiology of bovine TB and data and samples from cases and controls to genotype and analyse.
Impact Multi-disciplinary: AFBI: epidemiology; bovine TB expertise; data analysis; surveillance Roslin: genetics; GWAS; genotyping; immunogenetics; innate immunity; host-pathogen interactions Outputs: See BB/E018335/1 and BB/E018335/2; BB/L004054/1; BB/L004119/1 Publications: Bermingham ML, Handel IG, Glass EJ, Woolliams JA, de Clare Bronsvoort BM, McBride SH..Bishop SC. (2015). Hui and Walter's latent-class model extended to estimate diagnostic test properties from surveillance data: a latent model for latent data. Scientific reports, pp. 11861 Bermingham ML, Bishop SC, Woolliams JA, Pong-Wong R, Allen AR, McBride SH..Glass EJ. (2014). Genome-wide association study identifies novel loci associated with resistance to bovine tuberculosis. Heredity, 112 (5), pp. 543-51 Tsairidou, S. Woolliams, J.A., Allen, A.R., Skuce, R.A., McBride, S.H., Wright, D.M., Bermingham, M.L., Pong-Wong, R., Matika, O., McDowell, S.W., Glass, E.J., Bishop, S.C. Genomic prediction for tuberculosis resistance in dairy cattle (2014) PLoS ONE, 9, e96728. doi:10.1371 Tsairidou S, Woolliams JA, Allen AR, Skuce RA, McBride SH, Wright DM..Bishop SC. (2014). Genomic prediction for tuberculosis resistance in dairy cattle. PloS one, 9 (5), pp. e96728
Start Year 2006
 
Description Collaboration relating to genomic selection for resistance to bovine tuberculosis 
Organisation Scottish Rural University College
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Genotyping and analysing additional animals and phenotypes related to bovine TB. Combining data sets from different sources to conduct a meta-analysis. Sequencing high and low risk sires. Novel SNP discovery.
Collaborator Contribution R and D to underpin development of sustainable systems of livestock production. Responsible for UK implementation of genomic breeding values in dairy cattle. Statistics, genetic and genomic evaluations for bovine TB. Implementation of pedigree based evaluations and genomic evaluations for bovine TB into the routine systems of evaluation and dissemination to industry. Publication: Banos G, Winters M, Mrode R, Mitchell A, Bishop S, Woolliams J..Coffey M. (2017). Genetic evaluation for bovine tuberculosis resistance in dairy cattle. Journal of Dairy Science, 100 (2), pp. 1272-1281
Impact Outputs: See BB/L004119/1 and BB/L004054/1.
Start Year 2014
 
Description Collaboration with Aviagen Ltd 
Organisation Aviagen Group
Country United States of America 
Sector Private 
PI Contribution The project was funded via the BBSRC LINK scheme and involved a close collaboration with Aviagen Ltd, part or the Erich Wesjohann Group and a major global breeder of poultry. In broad terms, the project sought to define the genetic basis of avian resistance to Campylobacter colonisation. This involved genome-wide association studies using the progeny of crosses of inbred lines that differ in heritable resistance to Campylobacter (specifically backcross and advanced inter-cross populations derived from lines 6 and N), and identified quantitative trait loci (QTL) associated with resistance (Psifidi et al. 2016). The project also involved a genome-wide association study using over 3000 Aviagen broilers in a simulated field context. High quality genotypes and Campylobacter colonisation phenotypes were identified for 2750 broilers and QTL associated with resistance were identified, two of which were shared with the study using inbred lines (manuscript in preparation). Studies to validate QTL and understand how they exert their effect are ongoing with core funding from the BBSRC and a grant from the Scottish Government.
Collaborator Contribution As above. Aviagen provided access to its flocks and expertise, as well as costs for genotyping and validation of QTL.
Impact See publications & additional funding sections of this return. By defining the genomic architecture of avian resistance to Campylobacter our studies will inform the scope to breed selectively for birds with improved control of an important zoonotic pathogen. Our studies show that a relatively modest proportion of the variation in the trait (caecal C. jejuni numbers) can be explained by bird genetics and that resistance-associated QTL are already prevalent in the commercial broiler line studied. Work is ongoing to validate the associations between QTL and Campylobacter levels, and understand how they exert their effect. There is scope for long-term societal gain from the research as chicken continues to be the primary reservoir of human campylobacteriosis.
Start Year 2011
 
Description Identifying and exploiting the molecular basis of resistance to gastrointestinal parasites 
Organisation Sheep Improved Genetics Ltd
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution Teladorsagia circumcincta is a common parasitic nematode of the sheep abomasum, causing reduced growth in young lambs. The widespread development of anthelmintic resistant parasites has driven the need for alternative control strategies. Resistant immunity is acquired through repeated exposure to the parasite. The immune response and clinical outcome vary greatly between animals, but resistance is heritable. The aims of this project were: 1) understand how sheep respond to nematode infection; 2) understand and identify genes associated with the response; 3) identify variation within those genes which may contribute to resistance. Using an artificially infected animal model, transcriptomic analysis in resistant and susceptible lambs identified genes involved in T helper cell polarization as integral to disease outcome. T helper cell (Th)1 and Th17 activation was associated with susceptibility (low antibody, high worm numbers) while a Th2 response was associated with resistance (high antibody levels and clearance of infection). The Th cell transcription factors (GATA3, TBX21, RORC2 and RORA) were sequenced with splice variants and SNPs identified. Analysis of gene expression in the abomasal lymph node identified RORAv2 as associated with susceptibility and RORAv5 as associated with resistance. In the abomasal mucosa, GATA3 expression was linked to resistance. Expression analysis of cytokine receptors expressed by Th cells identified IL17RB and IL17RBv2 as associated with resistance in the abomasal mucosa. Analysis of the SNPs within these genes in 3 naturally infected populations identified a significant association between SNPs in IL23R with weight and FEC. This project has provided an in-depth analysis of the ovine transcriptome and identified several genes associated with the development of resistance to nematodes.
Collaborator Contribution The support/sponsorship of SIG Ltd was initially essential to obtain funding for a BBSRC Industrial CASE Award. In addition, SIG Ltd were highly supportive of the work and acted as advisors on the impact of the research. They also supplied a large number of biological samples from sheep with known phenotypic characteristics in relation to gastrointestinal nematode parasite infection.
Impact 1. Wilkie, H.E. (2016) Identifying and Exploiting the Molecular Basis of Resistance to Gastro-intestinal Nematodes in Sheep. PhD Thesis, University of Edinburgh. 2. Wilkie, H., S. Xu, A. G. Gossner and J. Hopkins. (2015). Variable exon usage of differentially-expressed genes associated with resistance of sheep to Teladorsagia circumcincta. Vet. Parasitol 212, 206-213. PMID: 26330386, doi:10.1016/j.vetpar.2015.08.023. 3. Wilkie, H., A. G. Gossner, S. Bishop and J. Hopkins. (2016). Variations in T cell transcription factor sequence and expression associated with resistance to the sheep nematode Teladorsagia circumcincta. PLoS ONE 11(2): e0149644. PMID: 26890074, doi:10.1371/journal.pone.0149644. 4. Wilkie. H., L. Nicol, A. G. Gossner and J. Hopkins. (2016). Mucosal expression of T cell gene variants is associated with differential resistance to Teladorsagia circumcincta. PLoS ONE 11(12): e0168194. PMID: 27973603. doi:10.1371/journal.pone.0168194. 5. Wilkie, H., V. Riggio, O. Matika, K. Watt, R. Sinclair, A. Sparks, D. Nussey, J. Pemberton, R. D. Houston and J. Hopkins. (2017). Identification of single nucleotide polymorphisms associated with growth in parasitized lambs. Vet. Parasitol. (revised, resubmitted).
Start Year 2013
 
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 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 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
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
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 French National Institute of Agricultural Research
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 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
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)
Department 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 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 Institute of Environmental Health Sciences
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 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 Molecular immunology of sheep paratuberculosis 
Organisation Moredun Research Institute
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Charity/Non Profit 
PI Contribution Collaborative work has investigated the host response to Mycobacterium avium subspecies paratuberculosis, the causative agent of Johne's disease, to explain the molecular basis for the development of the different pathological forms of the disease. Previous collaborative work with the Moredun Research Institute led to the hypothesis that differential T cell activation was critical for the development of paucibacillary and multibacillary paratuberculosis. Analysis of similar diseases in humans (tuberculosis and leprosy) supported this hypothesis. Consequently, initial studies focussed on the identification of cytokine receptor and transcription factor genes of sheep that, in humans and mice, are known to influence T cell polarization and tuberculosis/leprosy pathology. This was extended to identify the transcript variants of these genes. Assays were developed to allow accurate quantification of these genes in the ileo-caecal lymph node (the primary immune inductive site of paratuberculosis lesions) of pathologically-defined animals. These experiments measured the expression of specific transcript variants; linking IL23 and IL25 receptors, and the GATA3, RORC2 and RORA transcription factors, with paucibacillary and multibacillary disease. These data showed that the two disease forms were not just a result of a simple switch from Th1 to Th2 but that sheep with multibacillary disease had a broad immune dysfunction. To examine this immune dysfunction, we performed Illumina Truseq analysis on these same samples. This showed that paucibacillary and multibacillary disease are different stages of the same process. The inflammatory response of both diseases is an acute phase response (chronic inflammation) and not an acute inflammatory response. Animals with both forms of pathology also show a large increase in the expression of immunoglobulin genes. The major difference between paucibacillary and multibacillary animals is that there is a significant reduction in the expression of most genes associated with T cell function and activation. Perhaps the most surprising result was that all diseased animals showed a large reduction in the expression of transcripts associated with mast cells, and this was supported by subsequent histochemistry.
Collaborator Contribution The Moredun Research Institute provided biological material from diseased sheep. These sheep were clinical cases with naturally-acquired paratuberculosis. They had been culled for clinical reasons and subjected to post-mortem examination, including a full pathological/bacteriological examination. This had been done for more than 100 animals and 18 animals were chosen for the molecular immunology studies. These included animals with defined paucibacillary (tuberculoid) and multibacillary (lepromatous) pathologies. Coolleagues were also fully involved in discussions of the data and also in editing manuscripts.
Impact 1. Nicol, L., A. G. Gossner, C. Watkins, F. Chianini, R. G. Dalziel and J. Hopkins. (2016). Variations in IL-23 and IL-25 receptor gene structure, sequence and expression associated with the two disease forms of sheep paratuberculosis. Veterinary Research 47; 27. PMID: 26861902, doi: 10.1186/s13567-016-0314-4. 2 Nicol, L., H. Wilkie, A. G. Gossner, C. Watkins, R. G. Dalziel and J. Hopkins. (2016). Variations in T cell transcription factor gene structure and expression associated with the two disease forms of sheep paratuberculosis. Veterinary Research 47:83. PMID: 27530627.doi: 10.1186/s13567-016-0368-3. 3. Gossner, A. C. Watkins, F. Chianini and J Hopkins. (2017). Pathways and genes associated with immune dysfunction in sheep paratuberculosis. Scientific Reports (revision under review).
Start Year 2013
 
Description The Evolution of Mycobacterium bovis evolution in Africa 
Organisation U.S. Department of Agriculture USDA
Country United States of America 
Sector Public 
PI Contribution We have made available a collection of Mycobacterium isolates from cattle from across Africa that the BBSRC funded plus one has coordinated.
Collaborator Contribution The USDA have sequenced these isolates using their WGS pipeline.
Impact work is still in progress
Start Year 2016
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Animal Health Research Institute
Country Taiwan 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Animal Health Service
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Animal and Plant Health Agency
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Animal and Plant Quarantine Agency
Country Korea, Republic of 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Centers for Disease Control and Prevention (CDC)
Country United States of America 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Chinese Academy of Agricultural Sciences
Department Harbin Veterinary Research Institute (HVRI)
Country China, People's Republic of 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Erasmus University Medical Center
Department Department of Viroscience
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Fonds de la Recherche Scientifique
Country Belgium, Kingdom of 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Friedrich Loeffler Institute
Country Germany, Federal Republic of 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Government of Canada
Department Canadian Food Inspection Agency (CFIA)
Country Canada 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Government of Canada
Department Canadian Food Inspection Agency (CFIA)
Country Canada 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Hokkaido University
Department Graduate School of Veterinary Medicine
Country Japan 
Sector Academic/University 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Hokkaido University
Department Research Center for Zoonosis Control
Country Japan 
Sector Academic/University 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Hungarian Academy of Sciences (MTA)
Country Hungary, Republic of 
Sector Academic/University 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation International Livestock Research Institute (ILRI)
Country Kenya, Republic of 
Sector Charity/Non Profit 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Istituto Zooprofilattico Sperimentale Delle Venezie (IZSVe)
Country Italy, Italian Republic 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Konkuk University
Country Korea, Republic of 
Sector Academic/University 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation National Food Chain Safety Office
Department Veterinary Diagnostic Directorate
Country Hungary, Republic of 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation National Veterinary Institute
Country Sweden, Kingdom of 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation U.S. Department of Agriculture USDA
Department National Wildlife Research Center
Country United States of America 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation U.S. Department of Agriculture USDA
Department Southeast Poultry Research Laboratory
Country Georgia 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation U.S. Department of Agriculture USDA
Country United States of America 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation US Geological Survey
Country United States of America 
Sector Public 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation University Libre Bruxelles (Université Libre de Bruxelles ULB)
Department Spatial Epidemiology Laboratory
Country Belgium, Kingdom of 
Sector Academic/University 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation University of Oxford
Department Centre for Tropical Medicine and Global Health
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Hospitals 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation University of Oxford
Department Department of Zoology
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation University of Wageningen
Country Netherlands, Kingdom of the 
Sector Academic/University 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Utrecht University
Department Department of Farm Animal Health
Country Netherlands, Kingdom of the 
Sector Academic/University 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 2014
 
Description The Global Consortium for H5N8 and Related Influenza Viruses 
Organisation Wellcome Trust
Department Wellcome Trust Major Overseas Programme in Ho Chi Minh City Vietnam
Country Vietnam, Socialist Republic of 
Sector Charity/Non Profit 
PI Contribution I performed phylogeographic analysis on avian influenza sequence data from the 2014/2015 highly pathogenic bird flu outbreaks supplied by the collaborators, resulting in a paper in Science. Since then I have also been performing analysis on the recent 2016/2017 outbreaks.
Collaborator Contribution The partners contributed sequence data from avian influenza cases, other avian influenza case data and expertise relating to bird migration. This collaboration was mediated through GISAID http://platform.gisaid.org/epi3/frontend The main collaborators are Erasmus Medical Centre, University of Utrecht and Friedrich Loeffler Institute.
Impact Paper: "Role for migratory wild birds in the global spread of avian influenza H5N8" The Global Consortium for H5N8 and Related Influenza Viruses: S Lycett, R Bodewes, (many others), .. M Woolhouse, T Kuiken Science 14 Oct 2016: Vol. 354, Issue 6309, pp. 213-217 DOI: 10.1126/science.aaf8852
Start Year 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 Bovine TB Resistance & Genetics Workshop; Belfast November 2016 
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 Following the success of the Workshop that the team ran in November 2015 in Cardiff, this was the second 2 day workshop on genetic improvement for bovine tuberculosis (bTB)resistance. The aim of the workshop was to discuss the genetics of bTB and breeding for bTB resistance between academic researchers, industry and government officials. attendees came from England, Northern Ireland and the Republic of Ireland and included representatitives from DEFRA, DAERA, AFBI, BBSRC and the Knowledge Transfer Network. The first day of the workshop discussed the current situation in England, Wales and Northern Ireland as well as Ireland; scientific advances in the genetics of bTB in dairy cattle as well as genetic evaluations for bTB resistance in UK and Ireland. The plan to sequence high and low risk sires for bTB resistance was presented. A new topic was discussed that of infectivity and the potential to combine selection for infectivity and susceptibility. The uptake of bTB resistance EBVs through AHDB as "TB Advantage" index was discussed. Future research priorities, including the potential impact of selection on economics and health and welfare of cattle in the dairy industry, potential for EBVs for bTB for beef breeds, interaction with other traits including Johne's disease and sharing of data were also discussed. The workshop further fostered dialogue between government officials, academics and industry on tackling bTB and was found to be useful and informative by all.
Year(s) Of Engagement Activity 2016
 
Description Bovine TB Resistance & Genetics Workshop; Cardiff November 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact The project team organised a 2 day workshop on bTB resistance held in 18-19 November 2015, Cardiff, UK. The aim of the workshop was to discuss the genetics of bTB and breeding for bTB resistance between not just academic researchers, but also importantly industry and government officials. Attendees included academics from United Kingdom, Northern Ireland and the Republic of Ireland and DEFRA, AFBI and representatives from the Welsh Government, BBSRC. The first day of the workshop involved a series of presentations from academics detailing the latest research results on the genetics of bTB resistance and officials describing the current situation on bTB prevalence across parts of the UK and ROI. The second day of the workshop started with presentations on the publications of EBVs for bTB resistance followed by a round-table discussion on bTB issues. Overall, it was shown that a genetic strategy to reduce bTB prevalence is a feasible option and this message was well received and supported. Concerns on the impact of breeding for bTB resistance on response to the tuberculin skin test were discussed. In addition, there were discussions on future directions of research on bTB genetics. The workshop fostered dialogue between government officials, academics and industry on tackling bTB and was found to be useful and informative by all.
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 Edinburgh India Institute, Inaugural conference on 15-16 May 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Gave a short talk about avian influenza BBSRC-DBT project and how it came about, joint talk with our India collaborators. Edinburgh India Institute, Inaugural conference on 15-16 May 2014. John McIntyre Conference Centre, Edinburgh. Conference theme: Innovative Engagement for Sustainable Development: the Edinburgh-India Story.
Year(s) Of Engagement Activity 2014
 
Description Feature for BBC2 Food Detectives programme 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Professor Stevens took part in a BBC2 Food Detectives programme which featured Campylobacter in chickens. He helped to design a survey of Campylobacter contamination in a sample of fresh chicken obtained from Scottish retailers and interpret the findings. This were close to Food Standards Agency findings, which were broadcast as part of an interview with Prof. Alice Roberts. The interview took place at The Roslin Institute and included a lay description of Campylobacter, the importance of chickens as a reservoir of infection and strategies by which consumers can protect themselves. It also highlighted BBSRC-funded work at Roslin to mitigate the problem based on genetic selection (this project) and vaccines (other BBSRC projects held by Prof. Stevens).
Year(s) Of Engagement Activity 2016
 
Description H5N8 bird flu press release 
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 Media (as a channel to the public)
Results and Impact Press release about H5N8 bird flu study; also covered by BBC news http://www.bbc.co.uk/news/science-environment-37643894
Year(s) Of Engagement Activity 2016
URL http://www.roslin.ed.ac.uk/news/2016/10/14/migration-routes-hold-key-to-bird-flu-spread-global-study...
 
Description Immunology conference (Germany) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Oral presentation at the avian immunology research group meeting in Germany, Sept 2016.
Audience included industry members post graduate students, junior and senior scientists.
UK was voted to be the organisers of the next meeting in 2018 in Oxford and I will be part of the organising team. This will lead to great publicity for the funded avian immunology research funded by the RCUK.
Year(s) Of Engagement Activity 2016
URL http://www.airg2016.vetmed.uni-muenchen.de/airg_2018/index.html
 
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 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 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 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 Public lecture on Campylobacter in chickens 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Public talk on 'Chickens and the enemy within' at The Roslin Institute Open Doors Day in 2012. This highlighted the problem of Campylobacter infections in people, the role of poultry as a reservoir, and research at Roslin to control the problem via genetic selection and vaccination in poultry and to understand the molecular basis of virulence of the organism.
Year(s) Of Engagement Activity 2012
 
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 Wellcome Trust Board of Governors and Executive Board 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact The Wellcome Trust's Board of Governors and Executive Board visited Edinburgh University including the Roslin Institute on 19/20 September. The Post-doc on this grant, Samantha Wilkinson, Smaragda Tsairidou and Adrian Mwonge presented a joint poster on their work on various aspects of bovine TB host genetics, epidemiology and the detection test characteristics.
Year(s) Of Engagement Activity 2016