Systems Biology of innate immunity in livestock
Lead Research Organisation:
University of Edinburgh
Department Name: The Roslin Institute
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
Although genome sequences for livestock and poultry have recently become available, gene annotation, particularly with respect to immune-related genes, is partial at best. We aim to enhance the current base by undertaking a systems based analysis to identify, annotate and determine the function of key molecules, specifically major sets of pattern recognition receptors (PRR) and the defense pathways they regulate. The research will utilise data from wide-scale transcriptomic studies on early host-pathogen interactions between innate immune cells and economically important bacterial pathogens that breach or manipulate the innate defenses of the host. The functional relevance of PRR to vaccine design will be further explored through molecular studies of their interactions with ligands and modifiers. The outputs will focus on the most important genes and pathways and should translate into interventions, including vaccines and immuno-modulators, that are effective in the appropriate species.
Planned Impact
unavailable
Organisations
- University of Edinburgh (Lead Research Organisation)
- Agrocampus Ouest (Collaboration)
- Swedish University of Agricultural Sciences (Collaboration)
- INDIAN COUNCIL OF AGRICULTURAL RESEARCH (Collaboration)
- Iowa State University (Collaboration)
- Centre for Genomic Regulation (CRG) (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- UNIVERSITY OF EAST ANGLIA (Collaboration)
- University of Arkansas (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- Oregon State University (Collaboration)
- University of California, Davis (Collaboration)
- Harvard University (Collaboration)
- Arizona State University (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- Kenya Agriculture & Livestock Research Organization (KALRO) (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- RIKEN (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- AGRI-FOOD AND BIOSCIENCES INSTITUTE (Collaboration)
- Moredun Research Institute (Collaboration)
- University of Massachusetts (Collaboration)
- University of Delaware (Collaboration)
- Weizmann Institute of Science (Collaboration)
- THE PIRBRIGHT INSTITUTE (Collaboration)
- University of Leipzig (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
People |
ORCID iD |
| David Gally (Principal Investigator) |
Publications
Athanasiadou S
(2015)
Genome wide transcriptomic analysis identifies pathways affected by the infusion of Clostridium perfringens culture supernatant in the duodenum of broilers in situ.
in Journal of animal science
Borowska D
(2019)
Highly multiplexed quantitative PCR-based platform for evaluation of chicken immune responses.
in PloS one
Cheng Y
(2015)
Evolution of the avian ß-defensin and cathelicidin genes.
in BMC evolutionary biology
Chrzastek K
(2014)
Class B CpG ODN stimulation upregulates expression of TLR21 and IFN-? in chicken Harderian gland cells.
in Veterinary immunology and immunopathology
Connelley TK
(2014)
Genomic analysis offers insights into the evolution of the bovine TRA/TRD locus.
in BMC genomics
Crooijmans RP
(2013)
Large scale variation in DNA copy number in chicken breeds.
in BMC genomics
Dawson HD
(2013)
Structural and functional annotation of the porcine immunome.
in BMC genomics
Egan SA
(2012)
Vru (Sub0144) controls expression of proven and putative virulence determinants and alters the ability of Streptococcus uberis to cause disease in dairy cattle.
in Microbiology (Reading, England)
FANTOM Consortium And The RIKEN PMI And CLST (DGT)
(2014)
A promoter-level mammalian expression atlas.
in Nature
| Description | Key findings: The main aims were to identify the major players in the early interactions between host and pathogen, which ultimately determine the outcome of infection in order to develop and refine intervention strategies such as more efficacious vaccines and enhance genetic disease resistance traits. This work brings together scientists across several disciplines including bioinformatics, genomics, transcriptomics, evolution and functional studies in cell lines and host derived immune cells. An appropriate innate immune response depends upon the ability of the host to distinguish self from non-self, and commensal from pathogen. The aim is to focus on the early stages of host-pathogen interactions as the genes and pathways involved are under powerful evolutionary selection. The variation in homologues and orthologues across species will be investigated in terms of their copy number, protein sequence and regulation. Critically, understanding the similarities and differences between species in these fundamental events will provide essential insights into how the innate immune response links to and directs the adaptive immune system in key production animals (theme 4). Although genome sequences for livestock and poultry have recently become available, gene annotation, particularly with respect to immune-related genes, is partial at best. Within this theme, we aim to enhance the current base by undertaking a systems based analysis to identify, annotate and determine the function of key molecules, specifically major sets of pattern recognition receptors (PRR) and the defense pathways they regulate. The research will utilise data from wide-scale transcriptomic studies on early host-pathogen interactions between innate immune cells and economically important bacterial pathogens that breach or manipulate the innate defenses of the host. The functional relevance of PRR to vaccine design will be further explored through molecular studies of their interactions with ligands and modifiers. The outputs will complement and interact directly with the other three themes within this programme, in order to focus on the most important genes and pathways and should translate into interventions, including vaccines and immuno-modulators that are effective in the appropriate species. Highlight findings: • Improved annotation of the cattle, chicken, and pig immune related data has been conducted. Outputs include gene-expression atlases, transcriptomes of immune-related cells such as macrophages, dendritic cells and B cells as well as immune-tissue related transcriptomes. In addition, analysis has been undertaken to investigate global changes in gene expression in these cell types following in vitro stimulation with toll-receptor agonists and several pathogens of endemic and/or zoonotic potential. We have shown that within two hours of infection of bovine macrophages and dendritic cells with S. Typhimurium, their transcriptomic profiles show distinct changes which may impact on later outcomes of infection. Improved understanding of these pathways may lead to more efficacious vaccines. • A novel process of necrotic cell death in response to cytosolic DNA has been discovered in avian macrophages, underscoring the importance of early recognition of foreign DNA. • New antibodies to important immune related molecules across farm animal species have been developed including ones to cell surface markers such as the definitive blood monocyte marker CSF1 receptor, CD115 and the IL-1 Receptor Antagonist and cytokines such as IL-10 and IL-13. These have enabled species specific functional studies to investigate their roles in immune responses. • Comparative genomics between and within different species can shed light on the evolutionary pressure that pathogens impact on farm animal species. For example the diversity of some members of the avian beta-defensins, which are important in the early innate immune response, show conservation whereas others are highly divergent at specific sites, possibly because of varying life-histories. Understanding their molecular evolution may lead to improved vaccine design by optimising ways of targeting their regulation and tissue expression. • Even closely related species can show marked differences in their response to endemic pathogens. Understanding the underlying pathways may lead to new control strategies. We have investigated the innate immune response of sheep and cattle to Chlamydia abortus, which causes abortion in sheep but not cattle. We have shown that barrier epithelial cells derived from the oro-nasal mucosa in both species have very similar responses producing the cytokine CXCL8. This suggests that the host-pathogen interactions that differ are more likely to be discovered in innate immune cells and this forms part of ongoing research. • We have demonstrated that TLR5 is functional in ruminants (cattle) despite previous published work indicating that the variant should not signal due to an altered putative phosphorylation site. The TLR5-dependent recognition of flagellin in calves is associated with the level of the IgA response and ongoing work is examining the consequence of this response for stimulating mucosal responses to heterologous antigens attached to H7 flagellin as well as the importance of the flagella as part of a subunit EHEC vaccine to limit EHEC shedding from cattle. • M cell biology: large quantities of calcium and phosphate ions are actively secreted into the distal small intestine. These secretions have now been shown to form micrometer-sized amorphous calcium phosphate nanoparticles that can trap soluble antigens in the gut lumen and are acquired by M cells and play an important role in the immunosurveillance of the gut lumenal contents. We have shown that ageing dramatically impairs the maturation and function of M cells and were awarded a BBSRC grant to identify the aging-related factors which cause this impairment and determine the effects this has on mucosal immunity. While progress has been made in our understanding of the role M cells play in antigen uptake in the mammalian intestine, almost nothing is known of the methods of antigen uptake in the avian intestine. We have been awarded a grant and are now actively studying this. • We are now using bovine intestinal organoids (with Moredun Research Institute) as a platform for analysing enteric pathogens and their interaction with the host in a much more meaningful manner than current in vitro systems allow. Organoids are self-propagating 'mini-guts' that derive from intestinal stem cells and are representative of the range of cell types present in intestinal tissue. As well as providing a compelling experimental system, organoids also represent a potential route for reduction of future experimental animal use. |
| Exploitation Route | The main application will be development of improved vaccines and antigen delivery systems for livestock as well as work to guide to breeding or genetic modification to improve resistance and/or resilience to infectious diseases. There is now an expanding area of research at the Roslin around growth of organoid cultures for tissues of different livestock animal species and we know that such systems are generating a broad interest at both academic and commercial levels as they allow testing of reagents and compounds in vitro but under conditions and with cells much closer to those found in animals. The work in this theme overlaps with host genetic variation being investigated in theme 2 with findings that help predict susceptibility of animals to specific infections and functionality of vaccines. |
| Sectors | Agriculture Food and Drink Pharmaceuticals and Medical Biotechnology |
| Description | The research brought together scientists with expertise in the innate immunity of diverse farm animal species at the genomic, transcriptomic, molecular and functional levels to improve the functional annotation of important immune-related genes through investigating their variation, expression and involvement in immunity and pathogenesis. Our focus has been on early host-pathogen interactions encompassing endemic pathogens affecting chickens, pigs, sheep and cattle. We have advanced the genomic annotation of key genes and their encoded products that play a role in immunity. We have described cellular pathways that are key to early induction of host defences against important endemic pathogens of livestock. Mucosal epithelial cells and innate immune cells are crucial to prevent or reduce pathogen invasion and undertake continuous surveillance and are equipped for immediate defence responses. Our focus has been on their transcriptomes in their surveillance mode and following infection. Significant progress has been made on identification of key host defence pathways and enabled insights into the species' specific adaption of hosts to pathogen exposure. Thus, the research in this theme has had an impact on the other themes in this ISP. In particular, innate immune pathways are likely to play key roles in genetic resistance to infection and disease and our improved understanding and annotation of livestock innate immunity is helping to identify key candidate genes underpinning these traits (theme 2). The evolution of resistance mechanisms in livestock by gene duplication, substitutions and polymorphisms relates to the evolution of virulence in key endemic pathogens (theme 3). Understanding this interplay is essential to develop new strategies for control of infectious disease. The identification of more effective species' specific adjuvants (theme 4) requires knowledge of the appropriate host innate immune responses. The initiation of an acquired immune response absolutely requires an innate immune response. The outcome of an infection is determined by the early host-pathogen dynamic and the way in which it directs and drives the acquired immune response. 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. The science of this ISP research theme overlaps significantly with the 2nd theme on 'Genetics of Host Resistance' and so specific examples of impact have been listed in that report. |
| First Year Of Impact | 2013 |
| Sector | Agriculture, Food and Drink,Healthcare |
| Impact Types | Societal Economic |
| Description | Expert group member on coronavirus for for DISCONTOOLS |
| Geographic Reach | Europe |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Impact | The policy is currently in work. |
| Description | Animal Research Club |
| Amount | £868,556 (GBP) |
| Funding ID | BB/M012808/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2015 |
| End | 07/2018 |
| Description | BBSRC Animal Health Research Club - Macrophage Biology and Disease Susceptibility in Poultry |
| Amount | £915,216 (GBP) |
| Funding ID | BB/M011925/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | |
| Description | BBSRC Responsive Mode |
| Amount | £644,177 (GBP) |
| Funding ID | BB/R008272/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2021 |
| Description | BBSRC Vaccinology Highlight |
| Amount | £696,488 (GBP) |
| Funding ID | BB/P003958/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2017 |
| End | 01/2020 |
| Description | BBSRC-NIFA Collaboration US-UK: Reassembly of cattle immune gene clusters for quantitative analysis |
| Amount | £428,690 (GBP) |
| Funding ID | BB/M027155/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2015 |
| End | 08/2018 |
| Description | EU H2020 |
| Amount | € 5,500,000 (EUR) |
| Organisation | European Commission |
| Department | Horizon 2020 |
| Sector | Public |
| Country | European Union (EU) |
| Start | |
| Description | European Commission H2020-INFRAIA-2016-1 |
| Amount | € 10,000,000 (EUR) |
| Funding ID | EU project 731014 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 03/2017 |
| End | 03/2022 |
| Description | MRC - CSF1R in homeostasis and immunity |
| Amount | £819,116 (GBP) |
| Funding ID | MR/M019969/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2015 |
| End | 04/2018 |
| Description | MRC Confidence in Concept Scheme |
| Amount | £89,205 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2016 |
| End | 09/2017 |
| Description | Study of effects of ageing on M cells |
| Amount | £450,000 (GBP) |
| Funding ID | BB/M024288/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2015 |
| End | 10/2018 |
| Description | Study of the immunobiology of M cells (Sehgal) |
| Amount | £75,000 (GBP) |
| Funding ID | EASTBIO DTP |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2012 |
| End | 08/2016 |
| Description | open call |
| Amount | £761,556 (GBP) |
| Funding ID | BB/M011925/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2015 |
| End | 06/2018 |
| Title | ELispot for PCV2 |
| Description | The assay is able to detect a cellular immune response to PCV2. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2017 |
| Provided To Others? | No |
| Impact | Improvement of vaccine efficacy assessment. |
| Title | India flu - chicken transcriptome |
| Description | Transcriptomes from brain, lung and ileum tissue from chicken in response to high and low path avian flu |
| Type Of Material | Database/Collection of data |
| Provided To Others? | No |
| Impact | Identification of genes involved in resistance/susceptibility to avian flu |
| Title | India flu - crow transcriptome |
| Description | Transcriptomes from brain, lung and ileum tissue from crow in response to high and low path avian flu |
| Type Of Material | Database/Collection of data |
| Provided To Others? | No |
| Impact | Identification of genes involved in resistance/susceptibility to avian flu |
| Title | India flu - duck transcriptome |
| Description | Transcriptomes from brain, lung and ileum tissue from duck in response to high and low path avian flu |
| Type Of Material | Database/Collection of data |
| Provided To Others? | No |
| Impact | Identification of genes involved in resistance/susceptibility to avian flu |
| Title | India flu - goose transcriptome |
| Description | Transcriptomes from brain, lung and ileum tissue from goose in response to high and low path avian flu |
| Type Of Material | Database/Collection of data |
| Provided To Others? | No |
| Impact | Identification of genes involved in resistance/susceptibility to avian flu |
| Title | India flu - pigeon transcriptome |
| Description | Transcriptomes from brain, lung and ileum tissue from pigeon in response to high and low path avian flu |
| Type Of Material | Database/Collection of data |
| Provided To Others? | No |
| Impact | Identification of genes involved in resistance/susceptibility to avian flu |
| Title | India flu - turkey transcriptome |
| Description | Transcriptomes from brain, lung and ileum tissue from turkey in response to high and low path avian flu |
| Type Of Material | Database/Collection of data |
| Provided To Others? | No |
| Impact | Identification of genes involved in resistance/susceptibility to avian flu |
| Title | PRJEB14552 |
| Description | The MHC region contains many genes that are key regulators of both innate and adaptive immunity including the polymorphic MHCI and MHCII genes. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation that determines the nature of immune responses. Currently our knowledge of the bovine MHCI repertoire is limited with only the Holstein-Friesian breed having been studied in any depth. Traditional methods of MHCI genotyping are of low resolution and laborious and this has been a major impediment to a more comprehensive analysis of the MHCI repertoire of other cattle breeds. Next-generation sequencing (NGS) technologies have been used to enable high throughput and much higher resolution MHCI typing in a number of species. In this study we have developed a MiSeq platform approach and requisite bioinformatics pipeline to facilitate typing of bovine MHCI repertoires. The method was validated initially on a cohort of Holstein-Friesian animals and then demonstrated to enable characterisation of MHCI repertoires in African cattle breeds, for which there was limited or no available data. During the course of these studies we identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire. Construction protocol: Total RNAs were extracted from white blood cell pellets prepared form blood obtained by venepuncture using Tri-reagent (Sigma-Aldrich, Dorset) and cDNA prepared using the Reverse Transcription Kit (Promega, WI); both according to the manufacturer's protocols. PCR amplification was performed with the Phusion HF PCR kit (NEB, Herts.) using bovine MHCI primers that included Illumina sequencing primer annealing sites, multiple sample identifier tags (D501-508 and D701-712) and Illumina ligation adaptors. PCR products from ~96 animals were pooled to form a library which was then sequenced on the Illumina Miseq platform. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | These data represent a reference dataset of novel MHC alleles in cattle and may underpin research into cattle immunogenetic diversity for many years in the future |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB14552 |
| Description | Bovine gamma delta T cells |
| Organisation | University of Massachusetts |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | This builds upon a long term partnership between J Hope and C Baldwin group who have common interests in bovine gamma delta T cells. This resulted in a grant award to Baldwin, Telfer (both U Mass), Connelley and Hope (both Roslin). J Hope contributed scientific knowledge and background to the development of a grant proposal to USDA-NIFA to assess expression of T cell receptors. Dr Connelley will provide scientific input and be directly involved in sequencing the T cell receptor genes. |
| Collaborator Contribution | The Baldwin and Telfer groups at UMass have worked on bovine gamma delta T cells for a significant period of time and provide expertise on the biology of gamma delta T cells in leptospira and Mycobacterial infections and extensive knowledge of WC1 receptor family expressed by these cells. |
| Impact | USDA-NIFA AFRI animal health award (#2016-09379; Role of the T cell receptor in interacting with WC1 for bovine gamma delta T cell activation). |
| Start Year | 2012 |
| Description | Bovine mycobacteria in vivo studies |
| Organisation | Agri-Food and Biosciences Institute |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | We have studied immune cell populations in cattle infected with M bovis and M. avium paratuberculosis to define correlates of protective immunity. |
| Collaborator Contribution | Provided blood and tissue samples from infected cattle as part of their ongoing studies. Provided laboratory space and assistance for a PhD student visiting to collect samples. |
| Impact | This collaboration contributed to PhD theses from C Hamilton and H Mathie. |
| Start Year | 2012 |
| Description | IAH - Pete Kaiser- MDV/IBDV/IBV |
| Organisation | The Pirbright Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Microarray analysis of samples from infected and control chickens after infection with different viruses (MDV, IBDV and IBV) |
| Collaborator Contribution | Infection studies of resistant and susceptible lines of birds with MDV, IBDV and IBV. Collection of samples and preparation of RNA |
| Impact | Profile of host responses to avian viral infections and identification of candidate genes for resistance/susceptibility |
| Start Year | 2006 |
| Description | Immune correlates and immune resources for ruminants |
| Organisation | Moredun Research Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Myeloid cell biology of ruminants Transcriptome analysis of ruminant myeloid cells |
| Collaborator Contribution | Development of resources for sheep and cattle immunity Host-pathogen interactions involving ruminant innate cells Ruminant innate cell interactions with acquired immune cell populations Vaccines |
| Impact | Outputs See: BB/I020519/1; BB/I019863/1; BB/J500513/1 Publications: Corripio-Miyar Y, Hope J, McInnes CJ, Wattegedera SR, Jensen K, Pang Y, Entrican G.. Glass EJ. (2015). Phenotypic and functional analysis of monocyte populations in cattle peripheral blood identifies a subset with high endocytic and allogeneic T-cell stimulatory capacity. Veterinary research, 46:112. Doull L, Wattegedera S, Longbottom D, Mwangi D, Nath M, Glass E, Entrican G. (2015). Late production of CXCL8 in ruminant oro-nasal turbinate cells in response to Chlamydia abortus infection. Veterinary Immunology and Immunopathology, 168 (1-2), pp. 97-102. |
| Description | India DBT collaboration |
| Organisation | Indian Council of Agricultural Research |
| Department | National Institute of High Security Animal Diseases |
| Country | India |
| Sector | Public |
| PI Contribution | Using the tissues collected in Bhopal, we have sequenced and analysed the avian transcriptomic response to avian influenza challenge in 6 bird species (chicken, turkey, crow, goose, pigeon, duck). |
| Collaborator Contribution | All influenza challenge experiments were carried out by the team in Bhopal, tissues collected and sent over to the UK for processing and analysis |
| Impact | Identification of candidate genes for resistance to avian flu. |
| Start Year | 2014 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Agrocampus Ouest |
| Country | France |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Arizona State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Centre for Genomic Regulation (CRG) |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Rennes Centre |
| Country | France |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Toulouse |
| Country | France |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Harvard University |
| Department | Harvard Medical School |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Iowa State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Kenya Agriculture & Livestock Research Organization (KALRO) |
| Country | Kenya |
| Sector | Private |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Medical Research Council (MRC) |
| Department | Medical Research Council (MRC) Centre Cambridge |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | National Institutes of Health (NIH) |
| Department | National Institute of Allergy and Infectious Diseases (NIAID) |
| Country | United States |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | National Institutes of Health (NIH) |
| Department | National Institute of Environmental Health Sciences |
| Country | United States |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Oregon State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Swedish University of Agricultural Sciences |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of Arkansas |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of California, Davis |
| Department | UC Davis Genome Cente |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of Delaware |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of Leipzig |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of Nottingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Weizmann Institute of Science |
| Country | Israel |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | Jim Kaufman - MHC |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have collected hundreds of DNA samples from various African chicken populations which have been sent to Prof Jim Kaufman for MHC haplotyping |
| Collaborator Contribution | Prof Kaufman is MHC haplotyping the African birds for which we have collected samples. This will allow us to associate particular MHC haplotypes with disease traits in the bird populations ie. level of robustness |
| Impact | MHC haplotypes have been determined for >20 bird populations from Ethiopia. Work is underway to analyse birds from Nigeria, Oman, Iraq.... |
| Start Year | 2017 |
| Description | Study of M cell immunobiology and their role in mucosally-acquired infections (RIKEN) |
| Organisation | RIKEN |
| Department | RIKEN Center for Integrative Medical Sciences (IMS) |
| Country | Japan |
| Sector | Private |
| PI Contribution | We provided the ageing and prion disease pathogenesis mouse models. |
| Collaborator Contribution | Prof. Hiroshi Ohno and his colleagues provided expertise in M cell immunobiology. |
| Impact | Several publications: DNA RESEARCH 19, 407-422, (2012); doi:10.1093/dnares/dss022 Mucosal Immunology 5, 216-225; doi: 10.1038/mi.2011.68 Mucosal Immunology 6, 1027-1037; doi:10.1038/mi.2012.141 Mucosal Immunology 6, 666-677; doi:10.1038/mi.2013.30 Prof. Ohno is also a named collaborator on the following BBSRC grants: BB/J014672/1 BB/M024288/1 and BBSRC Japan Partnering Award |
| Start Year | 2007 |
| Description | Avian genome evolution and the origins of species diversity. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited lecture: Avian genome evolution and the origins of species diversity. In "Molecular evolution of avian species", SMBE2016, Queensland's Gold Coast, Australia, 3-7 July, 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Avian genomics: current status and future opportunities |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Talk at 16th ADNAT Convention on Animal Genetics and Genomics. Talk: Avian genomics: current status and future opportunities. Hyderabad, Dec 17-19, 2012. |
| Year(s) Of Engagement Activity | 2012 |
| Description | Brain infection study reveals how disease spreads from gut |
| 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 describing our study published in the Journal of Virology: http://jvi.asm.org/content/89/18/9532.long |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://www.ed.ac.uk/news/2015/prions-040815 |
| Description | Comparative genome responses of chicken and ducks to avian influenza infections |
| 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 "Comparative genome responses of chicken and ducks to avian influenza infections" at the 4th International Influenza Conference, Oxford (2011). Aim was to report findings from microarray experiments and seek further collaborations. Led to other contacts and finally a BBSRC-DBT research grant. |
| Year(s) Of Engagement Activity | 2011 |
| 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 | Flu talk - journalists |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Presentation of our work on avian flu to a selection of Indian and Japanese journalists. Government representatives were also present. Interest in future Scottish/Indian proposals was shown. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Gut cells are gatekeepers of infectious brain diseases, study finds |
| 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 via the media describing our recent research published in PLoS Pathogens |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.bbsrc.ac.uk/news/health/2016/161214-pr-gut-cells-gatekeepers-of-infectious-brain-diseases... |
| Description | ISAG Conference 2012. Talk: NGS of multiple chicken lines and development of a high-density 600K SNP genotyping array, 16-20 July, Cairns, Australia 2012. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk at ISAG Conference 2012. Talk: NGS of multiple chicken lines and development of a high-density 600K SNP genotyping array, 16-20 July, Cairns, Australia 2012. |
| Year(s) Of Engagement Activity | 2012 |
| Description | Invited lecture at MSD-Animal Health |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Invited lecture at MSD-Animal Health in Boxmeer the Netherlands, with WebEx connection to all other location o MSD -AH around the world. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited speaker at the fifth Edinburgh Infectious Diseases Annual Symposium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Talk at the fifth Edinburgh Infectious Diseases Annual Symposium, sparked vivid discussions and awareness of the use of livestock animals for fundamental research. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.eid.ed.ac.uk/symposium2016 |
| Description | Keeping bugs at Bay: a Public Engagement Activity at the Roslin Institute 2014 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | This activity aims to teach people how the immune system fights bugs. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Keeping bugs at Bay: a Public Engagement Activity at the Royal Highland Show 2015 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | This activity aims to teach people how the immune system fights bugs. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Mercks Digital Journal |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Online publication: De Castro AMMG, Opriessnig T. PCV2 genotypes and cross protection. Mercks digital magazine. 2019 |
| Year(s) Of Engagement Activity | 2019 |
| 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 | PAG 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited speaker at Plant and Animal Genome conference 2018 (San Diego, USA) 'Avian flu: the winners and the losers' - Jan 2018 |
| Year(s) Of Engagement Activity | 2018 |
| 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 Breeders Roundtable |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | • Invited speaker at National poultry breeders roundtable meeting (St Louis, USA) - JS May 2017 |
| Year(s) Of Engagement Activity | 2017 |
| Description | Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Talk at Animal Genomics Research Group "The global genomic approaches to climate change impact on livestock production". Talk: Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing. 10-15 July, Seoul, Korea, 2013. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk at the 8th International Conference on Genomics (ICG-8). Talk: Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing. 29 Oct - 1 Nov 2013, Shenzhen, China. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Presenation on PCR and sequencing. International Pig Digestive Disease Symposium (PDDS) Session 3, Diagnostics, Nanyang, 10 April 2024. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk on PCR and sequencing at the International Pig Digestive Disease Symposium (PDDS) Session 3, Diagnostics, Nanyang, 10 April 2024. |
| Year(s) Of Engagement Activity | 2024 |
| 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 | Roslin flu meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | 'Avian flu: the winners and the losers' at Annual influenza meeting, Roslin Nov 2017 |
| Year(s) Of Engagement Activity | 2017 |
| Description | Swine Practitioner workshop - France |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Practitioners discussed the pro and cons of control of swine diseases in France. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Swine Practitioner workshop - Germany |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | 3--40 veterinarians/industry representatives discussed other approached to diagnose and treat infectious disease in pigs. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Swine Practitioner workshop - Italy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | 50-60 practitioners discussed other approached to diagnose and treat infectious disease in pigs. |
| Year(s) Of Engagement Activity | 2019 |
| 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 avian genome revealed, Avian Immunology Research Group, Budapest, Hungary |
| 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 research talk: "The avian genome revealed" to the Avian Immunology Research Group, Budapest, Hungary (2010). Purpose was to inform and initiate collaborations. |
| Year(s) Of Engagement Activity | 2010 |
| 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 |