Bioinformatic analysis
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
We aim to deliver, for research and industry community use, novel and statistically-sound software to capture, integrate, interpret and visualise large multidimensional data sets produced by highly parallel, high throughput ‘omics technologies. The availability of relevant software with genomic verisimilitude is an essential aspect of our research in the genomics of farmed and companion animals, since bioinformatic interpretation of data obtained from ‘omic technology provides the foundation for all subsequent interpretation, from gene networks to generating genomic breeding values. This project addresses the BBSRC overarching priority of ‘Technology Development for Bioscience’, and specific priorities such as new approaches to data analysis, interpretation and sharing, and the development of software tools and algorithms for this purpose. We are committed to data sharing in the field of genome sequences of livestock and their annotation and supporting the use of community resources such as Ensembl. The bioinformatic analysis of ‘omics data is a cornerstone for enabling the systems biology and genetic mapping of all other ISP, since it provides support for (i) managing the volume of data arising from ‘omic technology, (ii) biological annotation and interpretation, and (iii) presentation in a tractable form fit for purpose. The programme will underpin systems biology approaches relevant to all strategic programmes of The Roslin Institute.
Planned Impact
unavailable
Organisations
- University of Edinburgh (Lead Research Organisation)
- Agrocampus Ouest (Collaboration)
- International Livestock Research Institute (ILRI) (Collaboration)
- UNIVERSITY OF ABERDEEN (Collaboration)
- Swedish University of Agricultural Sciences (Collaboration)
- Arizona State University (Collaboration)
- Aviagen Group (Collaboration)
- Centre for Genomic Regulation (CRG) (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- UNIVERSITY OF EAST ANGLIA (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- Oregon State University (Collaboration)
- University of Leipzig (Collaboration)
- University of Delaware (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- Kenya Agriculture & Livestock Research Organization (KALRO) (Collaboration)
- Harvard University (Collaboration)
- Ingenza Ltd (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- Iowa State University (Collaboration)
- Scotland's Rural College (Collaboration)
- University of California, Davis (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- University of Missouri (Collaboration)
- THE PIRBRIGHT INSTITUTE (Collaboration)
- Weizmann Institute of Science (Collaboration)
- University of Arkansas (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- Federal University of Agriculture, Abeokuta (Collaboration)
People |
ORCID iD |
| John Woolliams (Principal Investigator) |
Publications
Alibhai J
(2016)
Distribution of Misfolded Prion Protein Seeding Activity Alone Does Not Predict Regions of Neurodegeneration.
in PLoS biology
Andersson L
(2015)
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.
in Genome biology
Arner E
(2015)
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.
in Science (New York, N.Y.)
Auffret M
(2018)
Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using Diverse Bos Taurus Breeds and Basal Diets
in Frontiers in Microbiology
Baillie J
(2018)
Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease
in PLOS Computational Biology
Banks CJ
(2016)
Functional transcription factor target discovery via compendia of binding and expression profiles.
in Scientific reports
Bonnet E
(2015)
Integrative Multi-omics Module Network Inference with Lemon-Tree
in PLOS Computational Biology
Brown BL
(2017)
MinIONâ„¢ nanopore sequencing of environmental metagenomes: a synthetic approach.
in GigaScience
| Description | A core activity in the bioinformatic theme is to generate tools for managing, querying, collating, joining, visualising, analysing massive datasets from collections of 'omic analyses, generated locally and/or internationally, and so enable scientific discovery. 1. We have developed tools and methods that enable researchers to access, use and manipulate large sequencing datasets. Specifically: PORE, one of the first tools to enable researchers to use MinION nanopore sequencing data, this is an R package that enables users to QC sequencing runs and extract information from them; VIROME, insects are important vectors of viral diseases of both humans and animals; and the insect immune response to viruses often includes both a small RNA (viRNA) and PIWI-interacting RNA (piRNA) response; META4, a simple web-tool that enables the sharing and searching of large and complex meta-genomic sequence data consisting of assemblies, gene predictions and annotations. (see for example [https://github.com/mw55309/poRe_docs]). In collaboration with Pacific Biosciences we have developed refinements and additions to their software for processing Iso-Seq data (i.e. full length transcript sequences generated on Pacific Biosciences long read next generation sequencing platforms) [github.com/rkizen/ice_cycle]. The latest software development for Iso-Seq data is TAMA (Transcriptome Annotation by Modular Algorithms) [https://github.com/GenomeRIK/tama]. 2. We have provided a suite of software, JEnsembl, to simultaneously retrieve and map data from all versions of the Ensembl and Ensembl Genomes, which is one of the most widely used bioinformatics resources on the Internet providing genome assembly data for vertebrates and other taxonomic groups. JEnsembl allows all versions of the databases to be queried and so underpins the robustness of variant discovery and comparative mapping. Its modular design greatly simplifies the maintenance and upgrading of the code with each Ensembl release. [http://jensembl.sourceforge.net/]. 3. We have developed novel analytical methods and software to model the complex variations of traits and diseases between cell types, tissues and individuals using large-scale multi-omics data. Specifically LEMON-TREE to infer module network from integrated genomic data measured in a large number of individuals or experimental conditions. KRUX for simultaneously performing millions of non-parametric ANOVA tests using matrix-multiplication methods which are required for example for seeking eQTL associations in multi-tissue transcriptome datasets. FINDR is a fast and scalable software for causal inference and gene network reconstruction from genome-transcriptome variation data which outperforms existing causal inference methods on real and simulated data. We have developed a visualisation tool for transcriptome analysis, BioLayout Express3D , which has been made available as a community resource and has also been commercialised (known as Miru in this context). [http://www.biolayout.org/] 4. We developed new tools for genomic analysis and evaluation in populations: (i) VIPER to check for genotype inheritance checking of large scale genotyping projects and visualise the pedigree and associated errors allowing the inheritance pattern of reported errors to be explored, and the likely underlying bad datapoint resolved. (ii) DISSECT, an easy to use and freely available software tool to exploit the parallel computer architectures of supercomputers to perform a wide range of genomic and epidemiologic analyses which can currently only be performed on reduced sample sizes or in restricted conditions. With DISSECT we can make genomic predictions based for traits from half a million individuals genotyped for 590,004 SNPs using the combined computational power of 8,400 processor cores. We found that prediction accuracies in excess of 80% of the theoretical maximum could be achieved with this sample size. These findings build on previous software work in this project in producing ACTA and REACTA which had produced orders of magnitude improvements in computational efficiency for genomic prediction and regional heritability analysis. [http://www.dissect.ed.ac.uk/]. (iii) We have made fundamental enhancements to our suite of software for providing low-cost genomic data for breeders using imputation, which underpins Genomic Selection 2.0, and the AlphaGenes resource. - AlphaImpute: Genotype and sequence imputation software. AlphaImpute is part of the regular evaluation pipelines for PIC, Aviagen, Geno. On-going developments to increase the speed of imputation whilst maintaining high accuracies. - AlphaPhase: Genotype phasing software. AlphaPhase is integrated as part of AlphaImpute's family-based imputation algorithm and is regularly used by commercial partners listed above. - AlphaFamSeq: Family based sequence phasing algorithm. Uses raw sequence data as input and aims to phase sequenced haplotypes, which is necessary for imputation. - AlphaSeqOpt: Optimal distribution of sequencing resources within a population. Has two main methods: 1 - Identify individuals in the population that have the largest genetic footprint and optimise the way in which these individuals and their family members are sequenced. The aim is to maximise the use of this data for sequence imputation. 2 - Identify regions of the genome that are not well-represented in existing sequence data and select individuals to sequence that carry these regions. Work towards integrating the two methods is complete and they are now a single software tool Developments for speed to decrease run time have been finalised but not fully tested. - AlphaSimR - software for simulating plant and animal breeding programs. New and improved R version of the original AlphaSim Fortran Software. Main features: faster, easier to use, outputs only information required so have very small computational storage requirements. Being used across all projects to simulate breeding programs similar in design to their current programs. This will form the basis for future simulations to test new breeding strategies prior to implementation. Simulating the effect and value of genomic technologies vs. standard pedigree-based selection methods in developing countries. [http://www.alphagenes.roslin.ed.ac.uk/alphasuite-softwares/]. |
| Exploitation Route | The Alpha suite of software is used by leading players in the animal breeding sector as it provides key tools to integrate their rapidly expanding genomic data with their key decision making among selection candidates and on objectives. The DISSECT family of software is targeted towards all sectors using all genomic analyses and its application goes beyond the breeding sector into medical genetics. Biolayout Express (now Miru) is widely used by academic researchers and has application in industrial biotechnology and pharmaceutical industries where complex pathway visualisation is needed. The sequence dataset tools can (and are) taken on by both academic and commercial generators and users of 'omics data. JEnsembl is directly targeted at the large Ensembl user community. |
| Sectors | Agriculture Food and Drink Digital/Communication/Information Technologies (including Software) Leisure Activities including Sports Recreation and Tourism Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology Other |
| Description | 1. The code base of BioLayout has been licensed and a spin-out company Kajeka Ltd has been formed. Kajeka aim to supply big data solutions to analysts and enterprises from many different commercial sectors based on the technology and approach behind BioLayout. The website receives 40-100 hits a day and in the first six months of 2015 the tool was opened 11,529 times from 2060 unique addresses. 2. The AlphaSuite of software is used by leading players in the animal breeding sector to support selective animal breeding using the latest genomic tools and information, and the imputation tools developed in this project are key to the cost-effectiveness of their genomic programmes. 3. The R packages such as PORE and META4 are used by industrial biotechnology companies e.g. Ingenza to process the massive data sets arising from the 'omic technologies. |
| First Year Of Impact | 2014 |
| Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology,Other |
| Impact Types | Economic |
| Description | Training in genomics |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Our genomics training activity is open to all, including academia, industry, professionals and the public. We train people in software development and data analysis as pertains to the analysis of genomic data. Our training programme has so far consisted of 37 workshops in the last 2 years (each consisting of between 1 and 5 days hands-on training), and has provided advanced training in bioinformatics to 483 unique individuals, 47% of whom come from outside of the University of Edinburgh, spanning 15 countries including The Netherlands, India, Denmark, Belgium, Germany, Ireland, Luxembourg, Finland, Northern Ireland, Spain, Sweden, France, South Africa and Norway. Whilst the majority of our trainees are academics, we have also trained individuals from private companies and the NHS. At present we do not collect detailed statistics about training level, though we are certain that the vast majority of our trainees are post-docs and PhD students in need of vital expertise to complete their training/projects. The data underlying this report are available upon request, but should not be shared widely as they contain sensitive information. |
| URL | http://genomics.ed.ac.uk/services/training |
| Description | A global shared data biological sample resource to support productivity improvement for tropical livestock |
| Amount | £5,000,000 (GBP) |
| Organisation | Bill and Melinda Gates Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 09/2015 |
| End | 09/2020 |
| Description | BBSRC Responsive Mode |
| Amount | £1,640,000 (GBP) |
| Funding ID | BB/V009818/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2021 |
| End | 08/2025 |
| Description | Bioinformatics and Biological Resources Fund |
| Amount | £884,274 (GBP) |
| Funding ID | BB/M011461/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2015 |
| End | 07/2019 |
| Description | Bioinformatics and Biological Resources Fund |
| Amount | £791,463 (GBP) |
| Funding ID | BB/N019202/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2016 |
| End | 10/2020 |
| Description | Comparison between maize-based and wheat-based diets on intestinal microbiome and intestinal gene expression after anticoccidial vaccine administration in broiler chickens |
| Amount | £302,278 (GBP) |
| Organisation | Industry Partners |
| Sector | Private |
| Country | United States |
| Start | 08/2016 |
| End | 09/2019 |
| Description | Comprehensive training in computational biology techniques for analyzing second and third generation sequencing data |
| Amount | £28,000 (GBP) |
| Funding ID | BB/N019636/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2015 |
| End | 05/2018 |
| Description | GCRF Data and Resources round 1 |
| Amount | £946,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2016 |
| End | 07/2017 |
| Description | Microbiome and metagenomic study of the rumen microbial population and their microbial enzyme genes |
| Amount | £90,000 (GBP) |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2016 |
| End | 09/2019 |
| Description | Solutions-Based Approach to Genetic Diseases in Dogs |
| Amount | £200,000 (GBP) |
| Organisation | Dogs Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 08/2014 |
| End | 08/2016 |
| Title | Network analysis of short read sequencing data |
| Description | The method developed under this grant supports the visualisation and analysis of short read sequencing data. Paper describing this work submitted. |
| Type Of Material | Improvements to research infrastructure |
| Provided To Others? | No |
| Impact | None as yet |
| URL | http://seq-graph.roslin.ed.ac.uk/ |
| Title | Pathway modelling app |
| Description | There is a need for formalised diagrams that both summarise current biological pathway knowledge and support modelling approaches that explain and predict their behaviour. Here, we present a new, freely available modelling framework that includes a biologist friendly pathway modelling language (mEPN), a simple but sophisticated method to support model parameterisation using available biological information; a stochastic flow algorithm that simulates the dynamics of pathway activity; and a 3-D visualisation engine that aids understanding of the complexities of a system's dynamics. We present example pathway models that illustrate of the power of approach to depict a diverse range of systems. |
| Type Of Material | Model of mechanisms or symptoms - in vitro |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | This approach has been used to model a range of biological systems and we are slowly seeing in an increasing number of people adopting the method. |
| URL | https://www.virtuallyimmune.org/ |
| Title | Analysis of RNA-seq data deriving from different studies and platforms |
| Description | This describes an analysis technique that permits merging of RNA sequencing data that derive from different approaches (poly A selected and rRNA depleted). This means that data sets from different laboratories or collected for different purposes can be merged to extract further information and maximise the ability to mine the data. |
| Type Of Material | Data analysis technique |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | The method has been used in our continuing analysis of a large set of samples from different sheep tissues, to make the sheep transcriptomic atlas. |
| Title | BioLayout Express3D |
| Description | BioLayout Express3D is a powerful tool for the visualization and analysis of network graphs. Network-based approaches are becoming increasingly popular for the analysis of complex systems of interaction and high dimensional data. Networks can be produced from a wide variety of relationships between entities. In biology this includes the interactions between individuals, disease transmission, sequence similarity, metabolic pathways, protein interactions, pathways, regulatory cascades, gene expression, clinical data. This tool represents the product of over 15 years research and development and uses a combination of high end 3D graphics, algorithms and user-friendly graphical interfaces to allow the user to explore and better analyse their data. |
| Type Of Material | Data analysis technique |
| Year Produced | 2007 |
| Provided To Others? | Yes |
| Impact | The website currently receives hits from approx. 700 users a month from around the globe and is used 1500-2000 times a month. This tool has been used in analyses that have contributed to over 40 publications. The technology and know how developed is currently en route to being commercialised and developed further by a new spin out company called Kajeka. |
| URL | http://www.biolayout.org/ |
| Title | Data from: Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis) |
| Description | The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In Western Europe one such threat is large-scale introductions of commercial strains (C-lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M-lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C-lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (FST=1) is introduced when the sample size is small (N=10) and when sampling only captures a small fraction of a population's genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training dataset to design four independent SNP assays selected from pairwise FST between the Iberian and C-lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid datasets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A. m. iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia, and South America, in a time- and cost-effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | None recorded as yet. |
| URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.v8cp134 |
| Title | Dogslife, a longitudinal study of Labrador Retrievers |
| Description | This database collects life information for Labrador Retrievers from early life onwards. The information is based on owner recording rather than veterinary or insurance records and therefore captures minor illnesses and issues that would not present to the veterinary practice. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2010 |
| Provided To Others? | Yes |
| Impact | There have been a number of research publications about the data, the design of the collection method and more generally about the utility of cohort studies particularly in the dog, and the dog as a model for human and other animal conditions. |
| URL | http://www.dogslife.ac.uk |
| Title | PRJEB10338 |
| Description | This collection of data represents whole metagenome sequence data for 8 cattle chosen for low and high methane emissions after matching for breed and diet |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | This is a critically important dataset for linking genotype to phenotype (methane) in the cattle rumen microbiome. Since its release, the papers based on these data have been cited over 100 times |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB10338 |
| Title | Pig reference genome sequence Sscrofa11 |
| Description | This pig genome sequence (Sscrofa11) has been released by the International Swine Genome Sequencing Consortium under the terms of the Toronto Statement (Nature 2009, 461: 168). The Consortium is coordinating genome-wide analysis, annotation and publication. The sequence data from which this assembly was constructed largely comprise 65x genome coverage in whole genome shotgun (WGS) Pacific Biosciences long reads (Pacific Biosciences RSII, with P6/C4 chemistry). Illumina HiSeq2500 WGS paired-end and mate pair reads were used for final error correction using PILON. Sanger and Oxford Nanopore sequence data from a few CHORI-242 BAC clones were used to fill gaps. All the WGS data were generated from a single Duroc female (TJ Tabasco, also known as Duroc 2-14) which was also the source of DNA for the CHORI-BAC library. Sscrofa11 replaces the previous assembly, Sscrofa10.2, which was largely established from the same Duroc 2-14 DNA source. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | The Sscrofa11 assembly has been updated recently to Sscrofa11.1 by the addition of the SSCY sequence data from Skinner et al. 2016 (Genome Res 26:130-9). The BAC and fosmid clone resource from Duroc 2-14 will facilitate further targeted sequence closure. These improved genome assemblies will be a key resource for research in pigs and will enable applications in agriculture and biomedicine. The SScrofa11.1 assembly is currently being analysed and annotated. |
| URL | https://www.ncbi.nlm.nih.gov/assembly/GCA_000003025.5/ |
| Title | WGS - Hyline flu -2 |
| Description | Whole genome sequences (30x) of ~197 chickens (survivors of highly pathogenic avian flu and controls) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | These data have allowed for GWAS analysis that has identified significant genomic regions for avian flu survival. Candidate genes/SNPs have subsequently been identified. Understanding the genetic basis of resistance to avian flu has huge potential implications for both the poultry industry and human health |
| Title | WGS of Sasso birds |
| Description | WGS of 45 Sasso birds (Hendrix Genetics) - 30x coverage |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Data being used for selective sweep analysis, ERV analysis, SNP analysis, CNV analysis etc. by various researchers |
| Title | eChickAtlas |
| Description | The e-Chick Atlas of Gene Expression |
| Type Of Material | Database/Collection of data |
| Year Produced | 2012 |
| Provided To Others? | Yes |
| Impact | Six associated publications to date. |
| URL | http://www.echickatlas.org/ecap/home.html |
| Description | Aviagen |
| Organisation | Aviagen Group |
| Country | United States |
| Sector | Private |
| PI Contribution | We are working with Aviagen to explore the role of the chicken gut microbiome in performance of their chickens in diverse environments. So far this includes the placement of one of their staff members in my group for a short period of time for training and development |
| Collaborator Contribution | Aviagen provide access to large commercial flocks of chickens under both controlled and natural environments |
| Impact | No outputs so far |
| Start Year | 2017 |
| Description | BioLayout Express3D project |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Together we have worked as a team in developing the BioLayout tool with almost all of the coding has been performed in Edinburgh. |
| Collaborator Contribution | Advice, shared publications, ideas. |
| Impact | Outcomes from this work include the tool itself, numerous publications by ourselves and others. The original paper published in PLoS Comp Biol (2007) has been cited 243 times and the Nature Protocols paper (2009) has been cited 239 times (Google Scholar, Feb 2019). This was a multidisciplinary collaboration involving biologists, computer scientists, software engineers and mathematicians.The codebase for this software was licensed from the University of Edinburgh by Kajeka Ltd a UoE spinout company (www.kajeka.com). |
| Start Year | 2006 |
| Description | Centre for Tropical Livestock Genetics and Health |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | This project formed part of the establishment of a joint centre with ILRI to develop new approaches to improving the productivity of African Livestock |
| Collaborator Contribution | There is a formal joint venture |
| Impact | The Centre attracted funding from the Bill and Melinda Gates Foundation. It is too early to identify outcomes, but the centre is fully functional and pursuing multiple collaborative projects |
| Start Year | 2015 |
| Description | Centre for tropical livestock genetics and health (CTLGH) |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | Mick Watson is co-leading programme 5 (informatics and bioresources) programme of CTLGH which aims to collect data on genotype and phenotype into a central database which can subsequently be mined for useful associations. So far we have ensured that scientists have access to the latest high performance computing environment for research, we have analysed and continue to analyse hundreds of farm animal genomes from LMIC countries, and we have built the data portal (http://data.ctlgh.org) |
| Collaborator Contribution | The partners are involved in all programmes, which include:Program 1: Harnessing genetic variability among indigenous and exotic breeds of cattle (as well as their crosses) to develop genetic and genomic tools that will be used to improve productivity under harsh tropical conditions and to mitigate the impact of cattle on climate change. Program 2: Harnessing genetic variability in tropical productivity and adaptation among various breeds of Chickens. Program 3: Development and application of precision breeding (through novel reproductive and germplasm technologies) to achieve step changes in livestock genetic improvement. Program 4: Understanding the genetic and molecular mechanisms underlying the tolerance of certain cattle and poultry breeds to tropical diseases and pests. Program 5: A shared global data and biological sample resource to support continued research and development on tropical livestock genetics and health. |
| Impact | The data portal so far: http://data.ctlgh.org The collaboration is multi-disciplinary, bringing together geneticists, parasitologists, virologists, epidemiologists and data scientists together. |
| Start Year | 2016 |
| Description | Centre for tropical livestock genetics and health (CTLGH) |
| Organisation | Scotland's Rural College |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Mick Watson is co-leading programme 5 (informatics and bioresources) programme of CTLGH which aims to collect data on genotype and phenotype into a central database which can subsequently be mined for useful associations. So far we have ensured that scientists have access to the latest high performance computing environment for research, we have analysed and continue to analyse hundreds of farm animal genomes from LMIC countries, and we have built the data portal (http://data.ctlgh.org) |
| Collaborator Contribution | The partners are involved in all programmes, which include:Program 1: Harnessing genetic variability among indigenous and exotic breeds of cattle (as well as their crosses) to develop genetic and genomic tools that will be used to improve productivity under harsh tropical conditions and to mitigate the impact of cattle on climate change. Program 2: Harnessing genetic variability in tropical productivity and adaptation among various breeds of Chickens. Program 3: Development and application of precision breeding (through novel reproductive and germplasm technologies) to achieve step changes in livestock genetic improvement. Program 4: Understanding the genetic and molecular mechanisms underlying the tolerance of certain cattle and poultry breeds to tropical diseases and pests. Program 5: A shared global data and biological sample resource to support continued research and development on tropical livestock genetics and health. |
| Impact | The data portal so far: http://data.ctlgh.org The collaboration is multi-disciplinary, bringing together geneticists, parasitologists, virologists, epidemiologists and data scientists together. |
| Start Year | 2016 |
| Description | Collaboration with FUNAAB, Nigeria |
| Organisation | Federal University of Agriculture, Abeokuta |
| Country | Nigeria |
| Sector | Academic/University |
| PI Contribution | Prof Tumi Adebambo and Damilola Adebambo visited for 1 month in 2022< when we provided training in RNASeq analysis |
| Collaborator Contribution | Provision of samples for transcriptomic sequencing and analysis of laying in guinea fowl |
| Impact | Multidisciplinary collaboration: genomics/bioinformatics/animal breeding/genetics |
| Start Year | 2022 |
| Description | Collaboration with Wes Warren |
| Organisation | University of Missouri |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Analysis of genomic data and also single cell transcriptomic data |
| Collaborator Contribution | Access to chicken genome/transcriptomic data |
| Impact | Warren et al. Multiple chicken (Gallus gallus) genome references to advance genetic variation studies. In the 'Fourth Report on Chicken Genes and Chromosomes 2022'. Cytogenetic and Genome Research (2023) doi: 10.1159/000529376 Prof Warren will also visit Roslin for 3 months during June-Aug 2023 |
| Start Year | 2022 |
| Description | ILRI |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | We work with ILRI on all aspects of genomics and data science, including whole genome sequencing of multiple African animals, data recording and database design, web and web content development, and bioinformatics training. |
| Collaborator Contribution | We work with ILRI on all aspects of genomics and data science, including whole genome sequencing of multiple African animals, data recording and database design, web and web content development, and bioinformatics training. |
| Impact | So far we have sequenced the genomes of approx 800 African farm animals from diverse breeds and ecotypes |
| Start Year | 2016 |
| Description | Ingenza |
| Organisation | Ingenza Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Ingenza are a local biofuels and biotechnology company who are interested in novel enzymes of industrial value from metagenomic sequence data. |
| Collaborator Contribution | My group can provide 1000s of potential leads from metagenomic sequencing data - proteins of potential industrial value that are novel and of interest. Ingenza can then test the functionality of those proteins in E coli and yeast expression systems |
| Impact | We have provided 1000s of leads to Ingenza that we hope will eventually be used in their core biofuels business. In addition, one of our students, Deppie Roumpeka, has spent 6 months in the lab at Ingenza purifying some of the proteins that we identified using metagenomics. These proteins show potential activity related to the degradation of cellulose, specifically they are novel beta-glucosidases that break down comples carbohydrates into sugar that can be subsequently used by yeast in ethanol production. |
| Start Year | 2011 |
| 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 | SRUC - Rainer Roehe |
| Organisation | Scotland's Rural College |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have collaborated with Rainer Roehe at SRUC since 2011, and we provide expertise in genomics, DNA sequencing, metagenomics and bioinformatics. We use this to investigate the role of the microbiome in methane emissions and feed conversion ratio. |
| Collaborator Contribution | The SRUC partners provide expertise in rumen biology and function, alongside samples collected and measured for methane emissions and feed conversion ratio |
| Impact | • Rumen metagenomics: we have sequenced the rumen metagenome of 8 cattle selected for high- and low- methane emissions, matched for breed and diet; and we have demonstrated that high methane emitters are enriched for (i) methanogenic Archaea and (ii) enzymes involved in the methane production pathway. Of the latter, we show that there exists over 5000 novel versions of known enzymes involved in methane production. We have made available a database of over 1.9 million proteins, the majority of them novel, as part of this study (10.1186/s12864-015-2032-0) • Host control of the microbiome: using the same dataset, we demonstrate that largely speaking the rumen microbiome structure and function if under genetic control; and can be significantly associated with both methane emissions and feed-conversion-ratio (FCR) (journal.pgen.1005846) • We have subsequently sequenced over 300 Scottish cattle rumens as part of a project funded by BBSRC. These ruminant metagenomes have resulted in the assembly and publication of several hundred novel rumen microbial genomes (10.1101/162578), publication of a novel pipeline for annotating such genomes (10.1101/233544), publication of robust methane markers in across multiple breeds (10.3389/fmicb.2017.02642) and associations between diet, rumen microbes and anti-microbial resistance (10.1186/s40168-017-0378-z) |
| Start Year | 2011 |
| Description | The University of Aberdeen |
| Organisation | University of Aberdeen |
| Department | Institute of Medical Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have been working with Alan Walker and Tim Snelling in the field of rumen metagenomic profiling |
| Collaborator Contribution | Alan and Tim are experts in rumen microbiology and 16S sequencing, whereas my group is expert in whole-genome-shotgun metagenomics and bioinformatics |
| Impact | As part of a Scottish government project, we have sequenced 90 rumen metagenomes using whole genome sequencing, and almost 300 using 16S profiling. Data analysis is ongoing, but my team have assembled hundreds of microbial genomes from the rumen (10.1101/162578) and written a pipeline for analysiing such data(10.1101/233544) |
| Start Year | 2016 |
| Description | Venu Nair, The Pirbright Institute |
| Organisation | The Pirbright Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have been working with Venu Nair at The Pirbright Institute for over 10 years, broadly in the area of avian oncogenic viruses such as Marek's disease and ALV. |
| Collaborator Contribution | Venu's group are expert in virology and virus research whereas my group is expert in genomics and bioinformatics. Together we use genomics to explore virus-host interactions. |
| Impact | 28113043 24155381 23967013 22492913 19403687 19297609 18256158 |
| Start Year | 2006 |
| Title | Discovery of biomass degrading enzymes |
| Description | We work with a local biofuels company to discover novel enzymes involved in the degradation of complex carbohydrates into glucose, which may then be used by yeast for conversion to bioethanol. We have discovered several thousand of these, and the local company have assayed the activity of 5 of them |
| IP Reference | |
| Protection | Protection not required |
| Year Protection Granted | 2016 |
| Licensed | No |
| Impact | Our collaborators have assayed the activity of 5 enzymes of potential interest and have demonstrated that 3 of them have activity as good as or better than commercially available alternatives |
| Title | Pig exome sequencing |
| Description | We have exome sequenced 96 pigs for a large pig breeding company and have provided these data to said company |
| IP Reference | |
| Protection | Protection not required |
| Year Protection Granted | 2014 |
| Licensed | No |
| Impact | The exome variants are being used by the company internally for R&D and breeding decisions |
| Title | AlphaPhase |
| Description | The use of phased sequencing data has been shown to significantly increase the accuracy of imputation. AlphaPhase has been used as part of an imputation pipeline. Existing programs for phasing, have generally scaled poorly to large datasets with long and expensive burden in the computational resources available. Additionally, the increasing production of large sequencing data bundles and its heterogeneity complicate the phasing process. The current version of AlhaPhase implements methods to determine phase using an extended Long Range Phasing and Haplotype Library Imputation. |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Impact | The AlphaPhase package is freely available in AlphSuite and includes supporting manual, and access to technical support with the aim of benefiting the academic research community in animal breeding. Since its recent publication in the AlphaSuite, AlphaPhase have been downloaded 5 times. The AlphaPhase program is closely related to AlphaImpute, and is playing a key role in the Innovate UK funded project in collaboration with PIC, Innovate UK, Aviangen Innovate UK and ICBF. |
| URL | http://www.alphagenes.roslin.ed.ac.uk/alphasuite-softwares/ |
| Title | AlphaPlantImpute |
| Description | AlphaPlantImpute is a software package designed for phasing and imputing genotype data in plant breeding populations. AlphaPlantImpute can be implemented within and across bi-parental populations to phase and impute focal individuals genotyped at low-density to high-density. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Impact | This package was found to be extremely useful by our project partner global breeder KWS Saat SE. |
| URL | https://alphagenes.roslin.ed.ac.uk/wp/software/alphaplantimpute/ |
| Title | Findr - Fast Inference of Networks of Directed Regulations |
| Description | Findr is a fast and scalable software for causal inference and gene network reconstruction from genome-transcriptome variation data |
| Type Of Technology | Software |
| Year Produced | 2015 |
| Open Source License? | Yes |
| Impact | Findr is an ultra-fast software for the statistical inference of causal gene regulatory interactions between ten-thousands of genes from large-scale omics data. In comparison to existing state-of-the-art solutions, Findr predicts real biological interactions more accurately, while being nearly a million times faster. A paper describing Findr has been published in PLOS Computational Biology. |
| URL | https://github.com/lingfeiwang/findr |
| Title | Glmnat - Natural coordinate descent algorithm for L1-penalised regression in generalized linear models. |
| Description | Glmnat is Matlab toolbox for L1-penalised regression in generalised linear models, using the natural coordinate descent algorithm, a novel algorithm hat is entirely described in terms of the natural formulation of the model and is guaranteed to converge to the true optimum. Currently Glmnat is available for penalised logistic regression, more models will be added in the future. |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Open Source License? | Yes |
| Impact | Glmnat was published in: Michoel T. "Natural coordinate descent algorithm for L1-penalised regression in generalised linear models." Computational Statistics & Data Analysis 97 (2016): 60-70. |
| URL | http://tmichoel.github.io/glmnat/ |
| Title | Graphia Professional |
| Description | This is a network analysis tool designed for the analysis of biological data. It is a commercial product produced by Kajeka Ltd a company founded on the IP and know how behind BioLayout Express3D. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2015 |
| Open Source License? | Yes |
| Impact | This is the first product of Kajeka Ltd and sales of it will help support the company as it grows. |
| URL | https://kajeka.com/graphia-professional/ |
| Title | Hapbin |
| Description | hapbin is an ultra-efficient program for performing haplotype-based scans for positive selection in very large genomic datasets. |
| Type Of Technology | Software |
| Year Produced | 2015 |
| Open Source License? | Yes |
| Impact | The github page is getting approximately 40-50 unique visitors per month. Recent publications using this software include: Sams et al. Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans. Genome Biol. 2016 Nov 29;17(1):246. Barber et al. Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans. PLoS Genet. 2016 May 20;12(5):e1006063. |
| URL | https://github.com/evotools/hapbin |
| Title | JEnsembl |
| Description | JEnsembl is an API (application programmable interface) which provides access to all versions of databases at Ensembl and EnsemblGenomes. It implements a varied selection of data access functions to demonstrate data retrieval from 'Core', 'Variation' and 'Compara' databases; mapping between CoordinateSystems and mapping transparently between database versions where there has been a change in schema requiring alternate data access methods. 27-08-2014 Release version 1.76. Updated to handle up to Ensembl Schema 76 (Ensembl Genomes 23). Handles changes to homology records in Compara databases. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2012 |
| Impact | JEnsembl is an API (application programmable interface) which provides access to all versions of databases at Ensembl and EnsemblGenomes. |
| URL | http://jensembl.sourceforge.net/ |
| Title | JEnsembl Java API to Ensembl data systems |
| Description | This is an implementation of a modular Java-based API to the Ensemble data systems. The demonstration architecture addresses a number of objectives: specifically, it provides access to all versions of databases at Ensembl and EnsemblGenomes. It implements a varied selection of data access functions to demonstrate data retrieval from 'Core', 'Variation' and 'Compara' databases; mapping between CoordinateSystems and mapping transparently between database versions where there has been a change in schema requiring alternate data access methods. |
| Type Of Technology | Software |
| Year Produced | 2012 |
| Open Source License? | Yes |
| Impact | The modular architecture allows us to update access as the Ensemble schema evolves whilst maintaining backwards compatibility with previous releases. This allows across-release comparisons to be conducted within a single code base, something that is not possible with other available APIs. |
| URL | http://jensembl.sourceforge.net |
| Title | Lemon-Tree - Learning Module Networks |
| Description | Lemon-Tree is a "one-stop shop" software suite for module network inference that aims to make module network methods available to a broader community of users while simultaneously facilitating and encouraging collaborations between developers. Module networks are probabilistic graphical models which consist of modules of coregulated genes and their regulatory programs, and they can be inferred from integrated genomic data compendia (including gene expression, microRNA expression, copy number variation, and more) measured in a large number of individuals or experimental conditions. |
| Type Of Technology | Software |
| Year Produced | 2015 |
| Open Source License? | Yes |
| Impact | Lemon-Tree is an open-source, platform-independent, modular, extensible software package implementing state-of-the-art ensemble methods for module network inference. We benchmarked Lemon-Tree using large-scale tumor datasets and showed that Lemon-Tree algorithms compare favorably with state-of-the-art module network inference software. We also analyzed a large dataset of somatic copy-number alterations and gene expression levels measured in glioblastoma samples from The Cancer Genome Atlas and found that Lemon-Tree correctly identifies known glioblastoma oncogenes and tumor suppressors as master regulators in the inferred module network. Novel candidate driver genes predicted by Lemon-Tree were validated using tumor pathway and survival analyses. Lemon-Tree was published as a PLOS Computational Biology Software article (Bonnet E, Calzone L, Michoel T (2015) Integrative Multi-omics Module Network Inference with Lemon-Tree. PLoS Comput Biol 11(2): e1003983. doi:10.1371/journal.pcbi.1003983). PLOS Computational Biology Software articles "describe outstanding open source software of exceptional importance that has been shown to provide new biological insights." Thanks to its open-source nature, Lemon-Tree is being used by researchers in a wide range of application domains, including those within BBSRC remit (e.g. Alexandre et al. "Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle." BMC Genomics 2015; Bai et al. "Uncovering co-expression gene network modules regulating fruit acidity in diverse apples." BMC Genomics 2015; Arhondakis et al. "In silico Transcriptional Regulatory Networks Involved in Tomato Fruit Ripening." Frontiers in Plant Science 2016). |
| URL | https://github.com/eb00/lemon-tree |
| Title | LocaTR |
| Description | LocaTR identification pipeline for annotating LTR retrotransposons in any assembled genome |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Open Source License? | Yes |
| Impact | No impact yet |
| URL | https://github.com/andrewstephenmason |
| Title | Meta4: a web application for sharing and annotating metagenomic gene predictions using web services |
| Description | Whole-genome shotgun metagenomics experiments produce DNA sequence data from entire ecosystems, and provide a huge amount of novel information. Gene discovery projects require up-to-date information about sequence homology and domain structure for millions of predicted proteins to be presented in a simple, easy-to-use system. There is a lack of simple, open, flexible tools that allow the rapid sharing of metagenomics datasets with collaborators in a format they can easily interrogate. We present Meta4, a flexible and extensible web application that can be used to share and annotate metagenomic gene predictions. Proteins and predicted domains are stored in a simple relational database, with a dynamic front-end which displays the results in an internet browser. Web services are used to provide up-to-date information about the proteins from homology searches against public databases. Information about Meta4 can be found on the project website1, code is available on Github2, a cloud image is available, and an example implementation can be seen at http://www.ark-genomics.org/tools/meta4 |
| Type Of Technology | Software |
| Year Produced | 2013 |
| Open Source License? | Yes |
| Impact | NA |
| URL | http://www.ark-genomics.org/tools/meta4 |
| Title | TAMA update |
| Description | Transcriptome Annotation by Modular Algorithms (for isoseq data) |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | Enabled improved annotation of the chicken and duck transcriptomes |
| URL | https://github.com/GenomeRIK/tama |
| Title | Transcriptome Annotation by Modular Algorithms (TAMA) |
| Description | TAMA is a bioinformatics package intended to be used for constructing transcriptome/genome annotations. TAMA is ideal for working with Iso-Seq (long read RNA sequencing) data. However, due to its modular nature, it can be used for other data types as well. Most recent update 17 December 2020. See wiki for manual: https://github.com/GenomeRIK/tama/wiki |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | TAMA is currently being used to develop high quality transcriptomes for chicken and other farmed animal species for which current genome annotation provide an incomplete picture of transcriptome complexity. |
| URL | https://github.com/GenomeRIK/tama |
| Title | kruX - A Matlab/R/Python tool for simultaneously performing millions of non-parametric ANOVA tests using matrix-multiplication methods. |
| Description | kruX is an algorithm implemented in Matlab, Python and R that uses matrix multiplications to simultaneously calculate the Kruskal-Wallis test statistic for several millions of marker-trait combinations at once. KruX is more than ten thousand times faster than computing associations one-by-one on a typical human dataset. |
| Type Of Technology | Software |
| Year Produced | 2014 |
| Open Source License? | Yes |
| Impact | We used kruX and a dataset of more than 500k SNPs and 20k expression traits measured in 102 human blood samples to compare eQTLs detected by the Kruskal-Wallis test to eQTLs detected by the parametric ANOVA and linear model methods. We found that the Kruskal-Wallis test is more robust against data outliers and heterogeneous genotype group sizes and detects a higher proportion of non-linear associations, but is more conservative for calling additive linear associations. kruX has been published in BMC Bioinformatics (J Qi, HF Asl, J Björkegren, T Michoel. kruX: matrix-based non-parametric eQTL discovery. BMC Bioinformatics 15:11, 2014). kruX has been used to study eQTL associations in a multi-tissue datasets, by our group and others (e.g Pasterkamp et al. "Human validation of genes associated with a murine atherosclerotic phenotype." ATVB 2016; Van Der Laan et al. "Variants in ALOX5, ALOX5AP and LTA4H are not associated with atherosclerotic plaque phenotypes: The Athero-Express Genomics Study." Atherosclerosis 2015; Foroughi Asl et al. "Expression quantitative trait Loci acting across multiple tissues are enriched in inherited risk for coronary artery disease." Circulation: Cardiovascular Genetics 2015). |
| URL | https://github.com/tmichoel/krux |
| Title | nf-core/isoseq |
| Description | nf-core/isoseq is a bioinformatics best-practice analysis pipeline for Isoseq gene annotation with uLTRA and TAMA. Starting from raw isoseq subreads, the pipeline: Generates the Circular Consensus Sequences (CSS) Cleans and polishes CCS to create Full Length Non Chimeric (FLNC) reads Maps FLNCs on the genome Defines and cleans gene models |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | Paper under review: Simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing. Users report increased ease of analysis of data. |
| URL | https://nf-co.re/isoseq |
| Title | obsERVer |
| Description | Identification of novel ERV integration in WGS data |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Open Source License? | Yes |
| Impact | No impact yet |
| URL | https://github.com/andrewstephenmason |
| Title | resSpecies |
| Description | Database and associated web interface to handle pedigree populations, genotypes and phenotypes for genetic linkage mapping and quantitative trait linkage mapping studies. System checks inheritance of markers and formats/reformats data in readiness for import into common analysis programs. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2008 |
| Impact | Non computer-literate scientists can manipulate data - error free - within minutes rather than days |
| URL | http://www.resspecies.org/ |
| Company Name | Graphia |
| Description | Graphia develops software that is capable of efficiently analysing and plotting large amounts of data from a variety of sources. The company claims that its software can be used by both experienced data analysts and non-specialist. |
| Year Established | 2014 |
| Impact | The company is still at an early stage in its development but is beginning to gain commercial traction and clients for the software. We have won one Scottish Enterprise grant and have submitted a second for the development of our next generation software. We also secured seed investment of £230k last year. We are collaborating with academic scientists who develop network analysis algorithms or who use network analysis in their work. We have a number of ongoing discussions with major pharmaceutical and platform providers. |
| Website | http://kajeka.com |
| Description | ARS 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Sebastien Guizard presented a talk at the Avian Research Symposium 2022 (Edinburgh) - 'Exploring Chicken early transcripts landscape with Isoseq' |
| Year(s) Of Engagement Activity | 2022 |
| Description | Aviagen / CP workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | I presented our work on functional microbiome analysis during a one-day workshop which I set up and organised at The Roslin Institute. In attendance were employees of CP (a large Asian conglomerate) and Aviagen (one of the world's largest chicken breeding companies). The focus of the workshop was animal genetics and microbiome. |
| Year(s) Of Engagement Activity | 2010,2017 |
| Description | Avian Genomics: current status and future opportunities. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk: Avian Genomics: current status and future opportunities. International Ornithological Congress (ioc26) 18-24th August 2014, Tokyo, Japan |
| Year(s) Of Engagement Activity | 2014 |
| Description | Avian genome evolution and the origins of species diversity. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited lecture: Avian genome evolution and the origins of species diversity. In "Molecular evolution of avian species", SMBE2016, Queensland's Gold Coast, Australia, 3-7 July, 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Big Data in Agriculture, Part of the DuPont Pioneer Plant Sciences Symposia Series, at Roslin Institute, 14-15 May 2018 |
| 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 | Symposium held at the Roslin institute, organised by members of my group, sponsored by third parties from the breeding industry |
| Year(s) Of Engagement Activity | 2018 |
| Description | Biology Teachers CPD Event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk and discussions with 20 Higher Biology teachers about science, specifically about next generation sequence analysis technology and how that is being applied to address many different scientific questions |
| Year(s) Of Engagement Activity | 2018 |
| Description | Boden Conference: avian comparative genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk at Boden Conference: Comparative Genomics Conference, July 2015, Adelaide, Australia |
| Year(s) Of Engagement Activity | 2015 |
| Description | DDI interview |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Women in Data interview - Jacqueline Smith |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://ddi.ac.uk/women-in-data/ |
| Description | Easter Bush Campus Open Day 2018 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | The group ran two stands at this event, one on our work with honey bees including general interest items about beekeeping and bees, another was a display of the network analysis tools we have developed initially through BBSRC funding and more laterally as part of the spinout company Kajeka Ltd. Presenters Dr Mark Barnett and Prof Tom Freeman |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.ed.ac.uk/roslin/community-engagement/public-events/campus-open-day-2018 |
| Description | FARM-GTEX workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation to the farm animal genomics community re the FARM-GTEX initiative. Talk entitled 'Chicken genomes, annotation and transcriptomes' |
| Year(s) Of Engagement Activity | 2021 |
| Description | Fetival of Genomics 2016 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Mick Watson presented at a workshop, hosted by Edinburgh Genomics, on software for the handling and analysis of MinION sequencing data |
| Year(s) Of Engagement Activity | 2016 |
| Description | Gene annotation of the chicken genome. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited lecture: Gene annotation of the chicken genome. Next Generation Sequencing Conference (NGS) 2016, Barcelona, Spain, 4-6 April, 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Highland Show |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Institute stand at the Royal Highland Show. Demonstrating focussed activity and discussing the work of the University and the institute in relation to food safety, farm animal welfare, production efficiency, disease resistance etc. |
| Year(s) Of Engagement Activity | 2018 |
| Description | IPA workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Around 25 researchers attended a training workshop organized by Kasia Miedzinska and hosted by Qiagen. This workshop detailed use of the Ingenuity Pathway Analysis software and taught existing users new methods of analysis and attracted potential new users. |
| Year(s) Of Engagement Activity | 2019 |
| Description | ISAG 2021 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Sebastien Guizard presented a talk at ISAG 2021 - 'Nextflow IsoSeq (nf-isoseq) pipeline provides a first insight into the chicken transcript landscape'. |
| Year(s) Of Engagement Activity | 2021 |
| 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 | Interactive presentations at the Royal Highland Show |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | I supported the Roslin Institute's interactive presentation at the Royal Highland Show. Topics we covered were widely varied, including genetics and genomics, infection and immunity, farm animal health, and companion animal welfare. |
| Year(s) Of Engagement Activity | 2014,2015 |
| URL | http://royalhighlandshow.org |
| Description | MIck Watson comments on Genia |
| 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 | Mick Watson published a blog post on the patent dispute between Genia and the Unioversity of California, which was subsequently picked up by GenomeWeb, a website and news outlet followed by genomics investors, scientists and industry professionals |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://www.genomeweb.com/sequencing/university-california-files-suit-against-genia-cofounder |
| Description | Meet The Scientists |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Visit to a local primary school to engage with a questions and answers session about science and science careers |
| Year(s) Of Engagement Activity | 2018 |
| Description | Mick Watson comments on MinION |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Mick Watson was interviewed by the local press in Texas and this was then covered by multiple international news outlets. The focus was the MinION, a handheld sequencer capable of producing large amounts of DNA sequence data quickly and cheaply, and on which Mick Watson is considered an expert. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.research.ed.ac.uk/portal/en/clippings/mick-watson-helps-to-develop-minion-a-handheld-dev... |
| Description | Mick Watson comments on MinION sequencing of human genome |
| 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 | Mick Watson provided quotes and comments to a STAT news article on the recent MinION sequencing of a whole human genome |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.statnews.com/2018/01/29/hand-held-dna-sequencer-minion/ |
| Description | Mick Watson comments on NGS market |
| 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 | Mick Watson comments on the NGS market and the future of technologies such as the PacBio Sequel, Illumina and the Oxford Nanopore MinION |
| Year(s) Of Engagement Activity | 2015 |
| URL | https://www.genomeweb.com/sequencing-technology/technology-improvements-long-reads-lead-ngs-market-a... |
| Description | Mick Watson comments on PacBio Sequel |
| 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 | MIck Watson provided comments to an article on the PacBio Sequel, a (at the time) new sequencer from Pacific Biosciences |
| Year(s) Of Engagement Activity | 2015 |
| URL | https://www.genomeweb.com/business-news/pacbio-launches-higher-throughput-lower-cost-single-molecule... |
| Description | Modern plant and animal applied genomics driven by genotype and sequence data, University of Zagreb, Croatia, 17-19 July 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Workshop organised and given by me and two other members of my group. |
| Year(s) Of Engagement Activity | 2018 |
| 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 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Sebastien Guizard presented a talk at PAG 2022 - 'Exploring Chicken Early Transcripts and Isoforms Landscape with IsoSeq' |
| Year(s) Of Engagement Activity | 2022 |
| Description | PAG 2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Sebastien Guizard presented a talk at PAG 2023 - 'Exploring Chicken Early Transcript Landscape with IsoSeq' |
| Year(s) Of Engagement Activity | 2023 |
| Description | PAG 2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | SEbastien Guizard presented a talk at PAG 2023 - 'Exploring Pig Early Transcript Landscape with IsoSeq' |
| Year(s) Of Engagement Activity | 2023 |
| Description | PacBio Day 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Sebastien Guizard presented a talk at Edinburgh Genomics/PacBio Day 2022 (Edinburgh) - 'Exploring pig and chicken early transcripts landscape with Iso-Seq' |
| Year(s) Of Engagement Activity | 2022 |
| 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 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 | Presentation to Gates Foundation and DfID |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Mick Watson presented work on African farm animal genomics and data science to attendees from the Bill and Melinda Gates Foundation (BMGF) and the department for international development (DfID) |
| Year(s) Of Engagement Activity | 2017 |
| Description | Primary School "Big Science" visit |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Visit to local primary school as part of their Big Science activity. Discussing science and scientific careers with the pupils and presenting awards to them based on a science project they had recently completed. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Production Animal Health and Welfare Research: Impacts and Opportunities. |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk at Production Animal Health and Welfare Research: Impacts and Opportunities. 19-20 Feb, 2015, Indian Council for Agricultural Research (ICAR), New Delhi, India |
| Year(s) Of Engagement Activity | 2015 |
| Description | Question of Taste PCR Masterclass |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Practical workshop run by the Roslin Institute public engagement outreach team to allow High School pupils to run PCRs and investigate the genetics of a specific taste receptor. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Short course in Evolutionary Quantitative Genetics |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Evolutionary Quantitative Genetics course was a comprehensive review of modern concepts in Evolutionary Quantitative Genetics. The contents of the course are basic statistics, population genetics, quantitative genetics, evolutionary response in quantitative traits, estimating the fitness of traits and mixed models and their extensions. the instructor was Dr Bruce Walsh, Department of Ecology Evolutionary Biology, University of Arizona, and co-author of Genetics and Analysis of Quantitative Traits. The Course was hosted by Professor John Hickey at the Roslin Institute. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.alphagenes.roslin.ed.ac.uk/bruce-walsh-visit/ |
| Description | So many avian genomes - problems of annotation and data access |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk at Genome10K Conference: So many avian genomes - problems of annotation and data access, 1-5 March, 2015, California, USA |
| Year(s) Of Engagement Activity | 2015 |
| Description | Talk at the Eden Project |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | This was a meeting of individuals interested in honey bees and the conservation of native black bees. Our recently published work on honey bees was presented by Dr Mark Barnett. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.edenproject.com/media/2018/02/event-at-eden-to-look-at-future-of-honey-bees |
| Description | The chicken genome 10 years on. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Keynote lecture: chicken genome - 10 years on. Avian Model Systems - the 8th International Meeting, Cold Spring Harbour, USA, 4-8th March, 2014. CSHL Leading Strand - Keynote Lecture Series (http://theleadingstrand.cshl.edu/Course/Keynote/2014/AVIAN/150 The chicken genome 10 years on - BBSRC (http://www.bbsrc.ac.uk/news/events/1403-chicken-genome.aspx) |
| Year(s) Of Engagement Activity | 2014 |
| Description | Training Videos published on YouTube |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | A series of Training Videos based on recoded lectures delivered by members of Roslin Institute staff on a variety of different tools, statistical methodologies and other aspects of computer analysis. Lecture series include: An Introduction to Biolayout Express Graphical and Computational Modelling of Biological Pathways Molecular Epidemiology Phylogenetics and Phylogeography A brief introduction to R |
| Year(s) Of Engagement Activity | 2015,2016,2017,2018 |
| URL | https://www.youtube.com/channel/UCiwUjefHbg36OnW2Uh_5eUw/ |
| Description | Transcriptional and Epigenetic Regulation of Seasonal Timing. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited lecture: Transcriptional and Epigenetic Regulation of Seasonal Timing. In "Evolution of seasonal timers". The 64th NIBB Conference, Okazaki Conference Centre, Okazaki, Japan. 22-24 April, 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Visit of Bill Gates |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Bill Gates and Penny Mordaunt visited the Easter Bush campus to open the new Global Academy for Food Security. At that event, I presented our work on african farm animal genomes and programme 5 of the CTLGH. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.gov.uk/government/speeches/penny-mordaunt-speech-at-edinburgh-university-with-bill-gates |
| Description | Visit to University of Perugia |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I was invited to University of Perugia to lecture to a group of International MSc students. I spoke about ongoing work at the Roslin Institute (avian genomics), involvement with BBSRC research and study/research opportunities. Several students indicated an interest in visiting Roslin/Edinburgh to study. The visit also allowed development of a collaboration with Prof Emiliano Lasagna and his group. |
| Year(s) Of Engagement Activity | 2022 |