Bioinformatic analysis

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

Abstract

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.

Organisations

Publications

10 25 50
 
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 10/2015 
End 09/2020
 
Description Adapted yeast for superior carbon conversion
Amount £573,511 (GBP)
Funding ID 100962 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 08/2011 
End 07/2014
 
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 09/2016 
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 05/2015 
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 10/2016 
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 09/2016 
End 09/2019
 
Description Mining new enzymes in the rumen for biomass processing and chiral synthesis
Amount £356,941 (GBP)
Funding ID 100970 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 08/2011 
End 01/2014
 
Description Solutions-Based Approach to Genetic Diseases in Dogs
Amount £200,000 (GBP)
Organisation Dogs Trust 
Sector Charity/Non Profit
Country Unknown
Start 09/2014 
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 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 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 Dog Biomedical Variant Database Consortium 
Organisation Animal Health Trust
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database.
Collaborator Contribution To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company.
Impact Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation Mars Nutrition Research Council, Mars Incorporated
Country United States 
Sector Private 
PI Contribution I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database.
Collaborator Contribution To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company.
Impact Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation North Carolina State University
Country United States 
Sector Academic/University 
PI Contribution I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database.
Collaborator Contribution To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company.
Impact Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Bern
Country Switzerland 
Sector Academic/University 
PI Contribution I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database.
Collaborator Contribution To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company.
Impact Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of California, Davis
Country United States 
Sector Academic/University 
PI Contribution I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database.
Collaborator Contribution To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company.
Impact Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Helsinki
Country Finland 
Sector Academic/University 
PI Contribution I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database.
Collaborator Contribution To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company.
Impact Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Liege
Country Belgium 
Sector Academic/University 
PI Contribution I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database.
Collaborator Contribution To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company.
Impact Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Minnesota
Country United States 
Sector Academic/University 
PI Contribution I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database.
Collaborator Contribution To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company.
Impact Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Pennsylvania
Country United States 
Sector Academic/University 
PI Contribution I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database.
Collaborator Contribution To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company.
Impact Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Rennes 1
Country France 
Sector Academic/University 
PI Contribution I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database.
Collaborator Contribution To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company.
Impact Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Saskatchewan
Country Canada 
Sector Academic/University 
PI Contribution I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database.
Collaborator Contribution To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company.
Impact Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Sydney
Country Australia 
Sector Academic/University 
PI Contribution I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database.
Collaborator Contribution To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company.
Impact Publications in preparation.
Start Year 2016
 
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 Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Harvard University
Department Harvard Medical School
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Iowa State University
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Kenya Agriculture & Livestock Research Organization (KALRO)
Country Kenya 
Sector Private 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Medical Research Council (MRC)
Department Medical Research Council (MRC) Centre Cambridge
Country United Kingdom 
Sector Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation National Institute of Allergy and Infectious Diseases (NIAID)
Country United States 
Sector Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation National Institute of Environmental Health Sciences
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 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 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. 
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 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 Kajeka Ltd 
Description The biological sciences generate vast amounts of data from numerous analytical platforms; the data is big, complex and multi-layered. Like all big data, its analysis and correct interpretation represent a significant challenge. Kajeka produces a data analysis platform for the visualization and analysis of numerical matrices and networks. Our network analysis tools provide a rapid analysis pipelines producing visually intuitive network representations of data structure, whatever the source, allowing you to make more effective, more efficient, data-driven decisions - quickly. Company offering network analysis tools for the analysis of primarily of omics data. The company's first product, Graphia Professional, is based on IP and know how behind BioLayout Express3D. The company are now (Feb 2019) about to release a new network analysis platform for the analysis of biological data called Graphia. 
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://www.kajeka.com
 
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 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 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 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 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 Past, Present and Future of Genomics in Poultry Breeding. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk: Past, Present and Future of Genomics in Poultry Breeding. 25th World's Poultry Congress, Beijing, 5-9 September, 2016.
Year(s) Of Engagement Activity 2016
 
Description Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk at the 8th International Conference on Genomics (ICG-8). Talk: Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing. 29 Oct - 1 Nov 2013, Shenzhen, China.
Year(s) Of Engagement Activity 2013
 
Description 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 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 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 6th International chick meeting, Edinburgh (2011) Avian Genome Evolution 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Organised conference and presented a talk "Avian Genome Evolution" at the 6th International chick meeting, Edinburgh (2011). Aim was to inform, build network, seek collaborations, etc. in the avian research community. Further consortia (e.g. the chicken RNAseq consortium) and projects were created.
Year(s) Of Engagement Activity 2011
 
Description The chicken 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