Establishing the infrastructure for functional annotation of farmed animal genomes
Lead Research Organisation:
University of Edinburgh
Department Name: The Roslin Institute
Abstract
Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in agriculture, improving animal health and welfare, contributing to medical research and increasing our understanding of natural and wild animal populations.
High quality annotated genome sequences ("sequence of DNA nucleotides that make up the genetic material of an organism") provide an important framework for the discovery of genetic variation ("genotype") in that sequence linked to variation in the characteristics ("phenotype") of an animal. Genome sequences are available for many domesticated animals, including poultry (chicken, turkey and duck), livestock (cattle, pig, goat and sheep), fish (cod, tilapia and salmon) and companion animals (dog and horse). Today technology to sequence DNA is both rapid and relatively cheap and allowed the development of a wide range of assays based on generating short or long sequences. High quality, annotated genomes are critical to the analysis of these assays, including RNA-seq analysis of a cells RNA ("read off the genome, encoding information to synthesise proteins or regulate gene expression"), Methyl-seq analysis of the location of covalent modifications (methyl-groups) to the genome or ChIP-seq analysis of proteins bound to the genome that activate or repress gene expression. Identifying the functional elements within the genome that code for proteins, non-coding RNAs or regulate gene expression is essential for understanding the phenotypic consequences encoded in the genome.
Annotated genome sequences are freely available on-line through Ensembl, NCBI and UCSC. We have used the Ensembl system to establish high quality annotations of animal genomes based on mostly cDNA and comparative data from other species. Whilst 70-90% of protein coding elements can be identified, there is little information on non-coding RNA genes many of which are suspected to regulate gene expression. Comparing the number of annotated RNAs read from genes in the human, mouse and domesticated animal genomes shows that the complexity of RNAs in domesticated animals is underestimated. Even less is known of regulatory sequences, which is a significant barrier to understanding the link between genotype and phenotype.
The importance of this challenge is recognised by the EU-US Animal Biotechnology Working Group, which is promoting the need for transnational coordinated functional annotation of animal genomes. Following a workshop of over 100 scientists in San Diego (2014) an international consortium the "Functional Annotation of ANimal Genomes or FAANG" was launched. The FAANG project aims to provide experimental data to comprehensively annotate domesticated animal genomes.
We will establish the data infrastructure to support these goals. The infrastructure will comprise hardware and compute capacity at Roslin/TGAC/EMBL-EBI together with software to enable the functional annotation of animal genomes. The infrastructure will support a Data Coordination Centre (DCC) and Data Analysis Centres (DACs). DCC will store data and analyses from the FAANG consortium subject to quality control checks. DACs will seek to minimise redundant analysis of data. Standard bioinformatics pipelines for quality control of assay-by-sequence data (ChIP-Seq, RNA-Seq, and Methyl-seq), tools for validation of sample identity and a number of primary analysis pipelines (to map location of RNAs for protein coding/non-coding RNAs and regulatory features) will be developed.
A high quality annotated genome is a key source of information and critical for contemporary research in the biological sciences. It is valuable not only to academic researchers, but also to scientists working in animal breeding, animal health and pharmaceutical industries. This project is concerned with the infrastructure for delivering high quality annotated reference genomes to enable research on economically important animals.
High quality annotated genome sequences ("sequence of DNA nucleotides that make up the genetic material of an organism") provide an important framework for the discovery of genetic variation ("genotype") in that sequence linked to variation in the characteristics ("phenotype") of an animal. Genome sequences are available for many domesticated animals, including poultry (chicken, turkey and duck), livestock (cattle, pig, goat and sheep), fish (cod, tilapia and salmon) and companion animals (dog and horse). Today technology to sequence DNA is both rapid and relatively cheap and allowed the development of a wide range of assays based on generating short or long sequences. High quality, annotated genomes are critical to the analysis of these assays, including RNA-seq analysis of a cells RNA ("read off the genome, encoding information to synthesise proteins or regulate gene expression"), Methyl-seq analysis of the location of covalent modifications (methyl-groups) to the genome or ChIP-seq analysis of proteins bound to the genome that activate or repress gene expression. Identifying the functional elements within the genome that code for proteins, non-coding RNAs or regulate gene expression is essential for understanding the phenotypic consequences encoded in the genome.
Annotated genome sequences are freely available on-line through Ensembl, NCBI and UCSC. We have used the Ensembl system to establish high quality annotations of animal genomes based on mostly cDNA and comparative data from other species. Whilst 70-90% of protein coding elements can be identified, there is little information on non-coding RNA genes many of which are suspected to regulate gene expression. Comparing the number of annotated RNAs read from genes in the human, mouse and domesticated animal genomes shows that the complexity of RNAs in domesticated animals is underestimated. Even less is known of regulatory sequences, which is a significant barrier to understanding the link between genotype and phenotype.
The importance of this challenge is recognised by the EU-US Animal Biotechnology Working Group, which is promoting the need for transnational coordinated functional annotation of animal genomes. Following a workshop of over 100 scientists in San Diego (2014) an international consortium the "Functional Annotation of ANimal Genomes or FAANG" was launched. The FAANG project aims to provide experimental data to comprehensively annotate domesticated animal genomes.
We will establish the data infrastructure to support these goals. The infrastructure will comprise hardware and compute capacity at Roslin/TGAC/EMBL-EBI together with software to enable the functional annotation of animal genomes. The infrastructure will support a Data Coordination Centre (DCC) and Data Analysis Centres (DACs). DCC will store data and analyses from the FAANG consortium subject to quality control checks. DACs will seek to minimise redundant analysis of data. Standard bioinformatics pipelines for quality control of assay-by-sequence data (ChIP-Seq, RNA-Seq, and Methyl-seq), tools for validation of sample identity and a number of primary analysis pipelines (to map location of RNAs for protein coding/non-coding RNAs and regulatory features) will be developed.
A high quality annotated genome is a key source of information and critical for contemporary research in the biological sciences. It is valuable not only to academic researchers, but also to scientists working in animal breeding, animal health and pharmaceutical industries. This project is concerned with the infrastructure for delivering high quality annotated reference genomes to enable research on economically important animals.
Technical Summary
High quality, annotated reference genomes are essential for contemporary biological research. Reference genome sequences have been established for farmed animal species, including chicken, cattle, sheep, goat, pig, turkey, duck, dog, horse and most recently tilapia. However, unannotated genome sequences are not immediately useful. We have used the Ensembl system to establish high quality annotations of these genomes based on the data available at the time, mostly cDNA and comparative data from other species. However these annotations are incomplete, with transcriptomes that lack details of transcript isoforms and transcriptional start sites, and more critically the identity of regulatory regions is essentially absent from the annotation of all these genomes.
We will establish the data infrastructure critical to the coordinated functional annotation of animal genomes and the success of the international "Functional Annotation of ANimal Genomes" (FAANG) project. The goals of FAANG are to provide experimental data to comprehensively annotate transcriptomes and regulatory regions in farmed animals. The infrastructure will comprise substantial hardware and compute capacity at Roslin and TGAC allied to existing hardware at EMBL-EBI together with software to enable the functional annotation of farmed animal genomes and linking genotype (sequence) to phenotype.
The infrastructure will support a Data Coordination Centre (DCC) and Data Analysis Centres (DACs). DCC will store data and analyses after quality control checks. DACs will seek to minimise redundant analysis of data. We will establish standard analysis pipelines across multiple sites to ensure distributed analyses are comparable.
Bioinformatics pipelines for quality control of assay by sequence data (ChIP-Seq, RNA-Seq, and Methylation studies), tools for validation of sample identity and a number of primary analyses (transcriptome and epigenetic marks and other regulatory features) will be developed.
We will establish the data infrastructure critical to the coordinated functional annotation of animal genomes and the success of the international "Functional Annotation of ANimal Genomes" (FAANG) project. The goals of FAANG are to provide experimental data to comprehensively annotate transcriptomes and regulatory regions in farmed animals. The infrastructure will comprise substantial hardware and compute capacity at Roslin and TGAC allied to existing hardware at EMBL-EBI together with software to enable the functional annotation of farmed animal genomes and linking genotype (sequence) to phenotype.
The infrastructure will support a Data Coordination Centre (DCC) and Data Analysis Centres (DACs). DCC will store data and analyses after quality control checks. DACs will seek to minimise redundant analysis of data. We will establish standard analysis pipelines across multiple sites to ensure distributed analyses are comparable.
Bioinformatics pipelines for quality control of assay by sequence data (ChIP-Seq, RNA-Seq, and Methylation studies), tools for validation of sample identity and a number of primary analyses (transcriptome and epigenetic marks and other regulatory features) will be developed.
Planned Impact
Who will benefit?
The primary beneficiaries from this proposal to establish the data infrastructure to develop the Functional Annotation of ANimal Genome (FAANG) resources will be researchers in academia and industry in the UK and throughout the world. The initial meeting of over 100 scientists in San Diego in Jan 2014, convened to discuss the FAANG concept, indicates the level of interest in the resources to be developed and managed by the FAANG consortium.
Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in the animal sector of agriculture, contributing to medical research by providing animal models, improving animal health and welfare and informing understanding of natural and wild animal populations.
The world's leading animal breeding companies, of which some of the largest are UK companies, have in-house genetics expertise. Thus, these companies have the expertise to exploit the information captured and disseminated through FAANG consortium.
Evidence of the value of animal genomes to the pharmaceutical sector is provided by their recent investments in sequencing the pig and dog genomes, as well as the use of the chick as a developmental model underpinned by an annotated genome sequence.
Suppliers of species specific 'omics tools such as expression arrays, SNP chips and proteomics systems will benefit from access to annotated genomes, with links to features (e.g. probes) on their products.
There are potential indirect benefits to the wider public addressing the food security agenda, as discussed below.
How will they benefit?
The proposed FAANG resources will enable research to dissect the genetic control of economically important (and complex) traits in farmed animals including feed efficiency and susceptibility to infectious diseases.
This enabling of genetics research in farmed animals will facilitate advanced genetic improvement for these species. For example, there will be opportunities to develop more realistic and powerful models to predict breeding values from genome-wide genotypes produced either from high density SNP panels or full/partial genome sequences. Genetic improvement of farmed animals is a key means of addressing the food security agenda.
The utility of 'omics technology products, such as expression microarrays and SNP chips are greatly enhanced when the features on these products can be linked to a well-annotated genome sequence and other information sources. For example, probe sets for Affymetrix arrays and SNPs on Affymetrix and Illumina chips can be linked to annotated genes and genome locations respectively, thus enabling more effective use of these products. Well-annotated genomes facilitate the design of capture probes for exome sequencing; current developers of such products include Agilent and Roche Nimblegen. In particular, these sectors will be able to probe both the coding and the less characterised non-coding RNA genes.
Academic and other researchers will benefit from the ability to link the read-out from assay by sequence assays to an annotated genome sequence. Without such a frame of reference such assays are of limited value. For example, all RNA-seq studies need a comprehensive set of gene models to assay at the level of specific transcript isoforms not just at the gene level.
The impacts on research will be delivered within the timeframe of the proposed project and continue thereafter on an international scale. There will be direct impacts on staff through training and outeach activities in bioinformatics. The indirect impacts, for example, on the food security agenda and the wider public will take longer. However, the time to impact for genetic tests for susceptibility to inherited or infectious diseases in animals with their positive impacts on animal welfare can be short, within 1 to 3 years.
The primary beneficiaries from this proposal to establish the data infrastructure to develop the Functional Annotation of ANimal Genome (FAANG) resources will be researchers in academia and industry in the UK and throughout the world. The initial meeting of over 100 scientists in San Diego in Jan 2014, convened to discuss the FAANG concept, indicates the level of interest in the resources to be developed and managed by the FAANG consortium.
Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in the animal sector of agriculture, contributing to medical research by providing animal models, improving animal health and welfare and informing understanding of natural and wild animal populations.
The world's leading animal breeding companies, of which some of the largest are UK companies, have in-house genetics expertise. Thus, these companies have the expertise to exploit the information captured and disseminated through FAANG consortium.
Evidence of the value of animal genomes to the pharmaceutical sector is provided by their recent investments in sequencing the pig and dog genomes, as well as the use of the chick as a developmental model underpinned by an annotated genome sequence.
Suppliers of species specific 'omics tools such as expression arrays, SNP chips and proteomics systems will benefit from access to annotated genomes, with links to features (e.g. probes) on their products.
There are potential indirect benefits to the wider public addressing the food security agenda, as discussed below.
How will they benefit?
The proposed FAANG resources will enable research to dissect the genetic control of economically important (and complex) traits in farmed animals including feed efficiency and susceptibility to infectious diseases.
This enabling of genetics research in farmed animals will facilitate advanced genetic improvement for these species. For example, there will be opportunities to develop more realistic and powerful models to predict breeding values from genome-wide genotypes produced either from high density SNP panels or full/partial genome sequences. Genetic improvement of farmed animals is a key means of addressing the food security agenda.
The utility of 'omics technology products, such as expression microarrays and SNP chips are greatly enhanced when the features on these products can be linked to a well-annotated genome sequence and other information sources. For example, probe sets for Affymetrix arrays and SNPs on Affymetrix and Illumina chips can be linked to annotated genes and genome locations respectively, thus enabling more effective use of these products. Well-annotated genomes facilitate the design of capture probes for exome sequencing; current developers of such products include Agilent and Roche Nimblegen. In particular, these sectors will be able to probe both the coding and the less characterised non-coding RNA genes.
Academic and other researchers will benefit from the ability to link the read-out from assay by sequence assays to an annotated genome sequence. Without such a frame of reference such assays are of limited value. For example, all RNA-seq studies need a comprehensive set of gene models to assay at the level of specific transcript isoforms not just at the gene level.
The impacts on research will be delivered within the timeframe of the proposed project and continue thereafter on an international scale. There will be direct impacts on staff through training and outeach activities in bioinformatics. The indirect impacts, for example, on the food security agenda and the wider public will take longer. However, the time to impact for genetic tests for susceptibility to inherited or infectious diseases in animals with their positive impacts on animal welfare can be short, within 1 to 3 years.
Organisations
- University of Edinburgh (Lead Research Organisation)
- Agrocampus Ouest (Collaboration)
- Moredun Research Institute (Collaboration)
- Swedish University of Agricultural Sciences (Collaboration)
- ETH Zurich (Collaboration)
- International Livestock Research Institute (ILRI) (Collaboration)
- Oregon State University (Collaboration)
- Functional Annotation of ANimal Genomes (FAANG) (Collaboration)
- Diagenode (Collaboration)
- University of Liege (Collaboration)
- Polish Academy of Sciences (Collaboration)
- Iowa State University (Collaboration)
- Arizona State University (Collaboration)
- Utrecht University (Collaboration)
- Centre for Genomic Regulation (CRG) (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- University of Limoges (Collaboration)
- UNIVERSITY OF ABERDEEN (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- University of Leipzig (Collaboration)
- UNIVERSITY OF BIRMINGHAM (Collaboration)
- Edinethics (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- Kenya Agriculture & Livestock Research Organization (KALRO) (Collaboration)
- University of Alberta (Collaboration)
- Aarhus University (Collaboration)
- HARVARD UNIVERSITY (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- Faculdade de Medicina de Marília (Collaboration)
- Martin Luther University of Halle-Wittenberg (Collaboration)
- Scotland's Rural College (Collaboration)
- European Federation of Animal Science (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- University of East Anglia (Collaboration)
- Wageningen University & Research (Collaboration)
- University of Delaware (Collaboration)
- National Institute of Allergy and Infectious Diseases (NIAID) (Collaboration)
- Weizmann Institute of Science (Collaboration)
- Leibniz Association (Collaboration)
- University of California, Davis (Collaboration)
- University of Arkansas (Collaboration)
- Charoen Pokphand Group (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- Natural Resources Institute Finland (Collaboration)
Publications
Warren WC
(2017)
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure.
in G3 (Bethesda, Md.)
Roumpeka DD
(2017)
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data.
in Frontiers in genetics
Yao Y
(2017)
Activation of gga-miR-155 by reticuloendotheliosis virus T strain and its contribution to transformation.
in The Journal of general virology
Archibald A
(2020)
An improved pig reference genome sequence to enable pig genetics and genomics research
in GigaScience
Mick Watson
(2017)
Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism
in University of Edinburgh
Andersson L
(2015)
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.
in Genome biology
Mwangi WN
(2017)
Differentially expressed genes during spontaneous lytic switch of Marek's disease virus in lymphoblastoid cell lines determined by global gene expression profiling.
in The Journal of general virology
Aken BL
(2017)
Ensembl 2017.
in Nucleic acids research
Ruffier M
(2017)
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.
in Database : the journal of biological databases and curation
| Description | The primary purpose of this grant was to provide the physical computing infrastructure and software to support contributors to the Functional Annotation of Animal Genomes (FAANG) project. Hardware The hardware for the infrastructure that has been established with this capital grant comprises: TGAC (now the Earlham Institute) Storage 330TB of primary high-performance scale-out EMC Isilon storage. The 330TB storage is mirrored for resiliency (total raw storage with filesystem overheads is 749TB). Compute: Purchased 5 high-end HPC quad socket servers (one server with 512GB RAM and 4 servers with 256GB RAM - 200 total cores) and 4 dual socket servers (each with 128GB RAM - 96 total cores) Networking: Purchased necessary Infiniband and Ethernet switching cables for storage and compute infrastructure. Also required rack expansion infrastructure. The complete storage hardware has been successfully integrated within TGAC's existing storage infrastructure and the compute hardware. Roslin, University of Edinburgh Storage: 1 PB of high performance data storage has been installed with optimisation as required to meet ongoing usage demands, including provision of caching capacity for DataStore mounts, as well as dedicated quotas for high performance working space and fully backed-up. Compute: High performance compute has been installed comprising 16x nodes with 512RAM, 12x nodes with 512GB RAM, 8x nodes with 768RAM, 2x nodes with 2TB RAM, 2x nodes with 3TB RAM and 3x nodes with 2x K80 GPGPU to deliver a flexible high performance compute capability for a range of tasks in sequence analyses and functional genome annotation Networking: Purchased necessary network cabling for storage and compute infrastructure and expansion of the rack infrastructure. The storage and compute solutions are fully integrated within the University of Edinburgh's Eddie 3 HPC Storage and Compute systems. EMBL-EBI In addition, the EMBL-EBI has purchased 500TB of disk to facilitate the sharing of data within the animal genomics community, both through public release and intra-project collaboration. This is available for use now, and is intended to supplement the established data archives at EMBL-EBI. Software A goal of this project was to improve the performance of the software pipelines for the FAANG project. We largely focussed on bioinformatics tools and pipelines for improved transcript reconstruction and gene annotation. RNA transcript sequence data from the two main sequencing technology platforms (Illumina and Pacific Biosciences) have different characteristics which present different challenges to the analysis pipelines. The Illumina platforms yield very large volumes of highly accurate sequences at low cost, but the reads are too short to span a transcript. In contrast, the PacBio IsoSeq protocol yields long reads with the potential to capture complete transcripts, but with a high (15%) primary error rate. TGAC (now the Earlham Institute) have developed the following software and pipelines. Portcullis: is a command line utility that calculates a comprehensive set of junction metrics on all potential splice junctions derived from aligned RNA-Seq reads and uses customizable filtering strategies to produce files compatible with transcript reconstruction tools such as Cufflinks and Augustus. Portcullis is capable of analysing all the splicing junctions defined by 170 million aligned RNA-Seq reads in less than one hour, using a relatively low amount of resources: 10 GB of peak RAM using 10 threads. Mikado: has a novel algorithm that leverages transcript assemblies generated by multiple methods to define expressed loci, select a representative transcript and provide a more accurate and comprehensive set of gene models than existing approaches. Mikado can also utilize blast data to score transcripts based on homology support and to identify and split chimeric transcripts. Optionally junction confidence data as provided by Portcullis can be used to assess the assembled transcripts. An overall score is generated for each transcript and the highest scoring transcript selected at each defined loci. Additional transcripts (splice variants) compatible with the representative transcript are then returned based on user configurable criteria e.g. transcripts with sufficient CDS overlap or excluding transcripts with retained introns or which meet criteria for nonsense mediated decay targeting. Our approach is also amenable to incorporating Illumina assembled transcripts and those generated from long read technologies such as Pacbio. Mikado can aid filtering of incorrectly aligned Pacbio reads. miRCat2 MiRCat and other similar algorithms suffer from false positive and negative predictions and have not scaled well. We are working on a new release of the software, trained using large-scale sequencing data from wildtype small RNA populations and genetic mutants in the miRNA pathway (Dicer and Drosha) from a variety of animal species. Initial results show significant improvements in run-time, memory usage and accuracy. Trinity: we have adopted the Allinea MAP and Intel Vtune profiling tools to exhaustively profile the performance of Trinity at runtime to highlight key compute and I/O bottlenecks and specifically target performance tuning to regions of the code that contribute most to the runtime performance. Initial profiling has indicated that the I/O characteristics of Trinity can be better managed. Roslin have been working on the following: Pacific Bioscience Isoseq long read transcriptome sequencing pipeline: While PacBio raw error rates are around 15%, a unique feature of Isoseq is that a single read can cover a transcript multiple times. This allows for a primary error correction step where the multiple passes of the transcript are aligned to remove errors. Subsequently, a further level of error correction can be performed by finding highly similar sequences and aligning them together (Iterative Clustering for Error correction, ICE). We have been collaborating with Pacific Biosciences to develop these pipelines. There is a publicly available version of the error correction pipeline available from Pacific Biosciences and a more customized version at Roslin which will be published for public research use. For species with a good genome assembly, a third level of error correction can be performed. By mapping the transcript sequences to the genome, we can attain the reference version of the transcript which is free of errors on the reference level. We have developed the pipeline for this third level of error correction and implemented it in a project using Isoseq data. We have also been developing pipelines for handling the data after error correction, locating the genomic position of each transcript, grouping transcripts into gene models, and running analyses to predict putative functions such as identifying coding and non-coding RNA, pseudogenes, and nonsense mediated decay products. RNA-Seq benchmarking: Specifically we have published a paper which benchmarks the performance of popular RNA-Seq algorithms, identifies genome alignment as a major source of errors and driven by multi-mapped reads (http://www.genomebiology.com/2015/16/1/177). We propose two solutions to the "multi-map" problem, both of which have implementations available on GitHub: - peakRescue (https://github.com/rnaseq/peakRescue) is a software tool that "rescues" multi-mapped reads to single genes, with improved performance compared to other algorithms. - MMG (https://github.com/mw55309/RNAfreak) is an approach which recognises that some reads are impossible to assign to a single gene, and assigns them instead to "groups" of genes; these groups can then be tested for differential expression. Finally, we are benchmarking RNA-Seq tools to assess how well they perform in the presence of incomplete transcriptomes and genomes (https://github.com/rnaseq/degraTrans). EMBL-EBI We have been working to improve the Ensembl gene annotation system. As part of this award, the assembly loading and QC phase have been converted to the Ensembl eHive pipeline management system (EEPMS) and been successfully tested. The EEPMS is a pipeline management solution developed and maintained by the Ensembl Project that allows for high levels of pipeline automation, graphical monitoring of pipeline progress and ease of configuration. We have shown that a process that required one to two weeks of work for a single species can now be set up for multiple species in a matter of minutes, with the whole process running in a fully automated manner over the course of 2-5 days. The code for the pipeline is available: https://github.com/Ensembl We are also developing data analysis pipelines based on standards defined by the ENCODE project and the International Human Epigenome Consortium (IHEC). These pipelines will be used across functional genomics datasets generated across species involved in FAANG. The working groups are adapting pipelines where necessary to maximize the integrated analyses of datasets. Currently, groups are establishing best practices, documenting and testing developed pipeline with pre-existing data. (http://www.ebi.ac.uk/seqdb/confluence/display/FAANG/FAANG+Wiki+Home) We view the deposition of analysis results with the EMBL-EBI data archives as important to open science. To facilitate this, we have built a software library to help build the metadata required for submitting data to the archives. Where new codebases are being created, the code is being released under an Apache license though the FAANG git organisation https://github.com/FAANG/. Some of these projects also extend the Ensembl and ReseqTrack codebases which are also hosted in github (https://github.com/Ensembl, https://github.com/EMBL-EBI-GCA/reseqtrack). The analysis pipelines are being developed in a coordinated with collaborators across the Functional Annotation of Animal Genomes (FAANG) project. We are participating in the regular (at least monthly) discussions of the FAANG Bioinformatics and Data Analysis group which is co-chaired by Mick Watson (Roslin Co-I). |
| Exploitation Route | The computing hardware and software are being used by scientists engaged in genome research at The Roslin Institute, EMBL-EBI, the Earlham Institute and beyond and in particular by contributors to the Functional Annotation of Animal Genomes consortium. Publications that are outputs from analyses performed on this compute resource have also been reported as outputs from this award. |
| Sectors | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software) |
| Description | PoreCamp Texas |
| Geographic Reach | North America |
| Policy Influence Type | Influenced training of practitioners or researchers |
| URL | http://porecamp.github.io/texas/ |
| 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 | (BovReg) - BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Amount | € 6,033,458 (EUR) |
| Funding ID | 815668 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 09/2019 |
| End | 08/2023 |
| 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 | AQUA-FAANG: Advancing European Aquaculture by Genome Functional Annotation |
| Amount | £668,211 (GBP) |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 05/2019 |
| End | 04/2023 |
| Description | Bioinformatics and Biological Resources Fund |
| Amount | £791,463 (GBP) |
| Funding ID | BB/N019202/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2016 |
| End | 10/2020 |
| Description | Bioinformatics and Biological Resources Fund |
| Amount | £884,274 (GBP) |
| Funding ID | BB/M011461/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2015 |
| End | 07/2019 |
| Description | Ensembl - adding value to animal genomes through high quality annotation |
| Amount | £378,425 (GBP) |
| Funding ID | BB/S020152/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2019 |
| End | 07/2022 |
| Description | Ensembl - adding value to animal genomes through high quality annotation |
| Amount | £368,856 (GBP) |
| Funding ID | BB/S02008X/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2019 |
| End | 07/2022 |
| Description | European Commission H2020-SFS30-2018-2020 Sustainable Food Security: The regulatory GENomE of SWine and CHicken: functional annotation during development |
| Amount | € 6,000,000 (EUR) |
| Funding ID | 817998 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 07/2019 |
| End | 06/2023 |
| Description | General Scheme - Jeff Schoenebeck - Fit for Purpose: A Reference Genome to Empower Canine Health Research |
| Amount | £199,937 (GBP) |
| Funding ID | 5126826 |
| Organisation | Dogs Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2018 |
| End | 03/2021 |
| Description | National Institute of Food and Agriculture Default Scheme - Alan Archibald - Consortium funding - Emily Clark - Ovine FAANG Project |
| Amount | £46,415 (GBP) |
| Funding ID | 2017-67016-26301 |
| Organisation | U.S. Department of Agriculture USDA |
| Department | National Institute for Food and Agriculture |
| Sector | Public |
| Country | United States |
| Start | 04/2017 |
| End | 03/2020 |
| Title | Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen |
| Description | This dataset represents 913 draft bacterial and archaeal genomes assembled from over 800 gigabases of rumen metagenomic sequence data derived from 43 Scottish cattle, using both metagenomic binning and Hi-C-based proximity-guided assembly. Most of these genomes represent previously unsequenced strains and species. The draft genomes contain over 1.2 million predicted protein sequences, and 69,000 proteins predicted to be involved in carbohydrate metabolism. ## Relation to earlier versions ## This data is referenced by Watson et al. (In Submission). A previous paper, in bioRXiv, referenced the earlier dataset "Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism" https://datashare.is.ed.ac.uk/handle/10283/2772. This in turn was superseded by the more recent version Hi-C genomes from "Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism" https://datashare.is.ed.ac.uk/handle/10283/2911. The paper underwent many rounds of review, the first-round revised paper referenced the second (Hi-C) dataset and the final, accepted version will reference the DOI of this dataset. The datasets changed in nature and in name during this process. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | The dataset is expected to underpin global rumen microbiome research in the next 5-10 years |
| URL | https://datashare.is.ed.ac.uk/handle/10283/3009 |
| Title | Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism |
| Description | The cow rumen is a specialised organ adapted for the efficient breakdown of plant material into energy and nutrients, and it is the rumen microbiome that encodes the enzymes responsible. Many of these enzymes are of huge industrial interest. Despite this, rumen microbes are under-represented in the public databases. Here we present 220 high quality bacterial and archaeal genomes assembled directly from 768 gigabases of rumen metagenomic sequence data. Comparative analysis with current publicly available genomes reveals that the majority of these represent previously unsequenced strains and species of bacteria and archaea. The genomes contain over 13,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in the public databases. Inclusion of the 220 genomes presented here improves metagenomic read classification by 2-3-fold, both in our data and in other publicly available rumen datasets. This release improves the coverage of rumen microbes in the public databases, and represents a hugely valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | This dataset is expected to underpin research in rumen microbiomes over the next 5-10 years |
| URL | https://datashare.is.ed.ac.uk/handle/10283/2772 |
| Title | Common warthog (Phacochoerus africanus) reference genome sequence |
| Description | De novo assembly of a chromosome-level reference genome of the common warthog (Phacochoerus africanus). For the warthog assembly DNA was isolated from Pulmonary Alveolar Macrophages derived from a female individual. DNA long reads were isolated by Edinburgh Genomics and sequencing was done using Pacific Biosciences Sequel instruments at Pacific Biosciences and at Edinburgh Genomics. A total of 44 SMRT cells yielded 150Gbp of raw data with a read N50 of 13.9kbp, providing about 60x coverage of the genome. Contig level assembly was generated using Falcon and Falcon-unzip, reconstructing the 2.4 Gbp long genome in 1,500 contigs (with contig N50 of 3.2Mbp). Scaffolding was done using optical mapping data produced by Deep Seq on a Bionano Saphyr instrument, using Bionano Solve software. This was followed by scaffolding based on proximity ligation method. The Hi-C library was created using Dovetail Genomics' Hi-C library preparation kit. Refining the scaffolds were done with Dovetail Genomics' HiRise pipeline. Gaps in the assembly were filled with PBJelly using the PacBio long-read dataset. Error correction was done with Pilon, based on an Illumina short read library generated from the same warthog individual. The mitochondrial (MT) DNA was assembled from filtered, MT specific, PacBio long-read sequences using the Flye assembler and was error corrected with Illumina short-read data with Pilon. Data use: The assembly sequence is made publicly available by Prof. Alan L. Archibald, University of Edinburgh, Roslin Institute and Royal (Dick) School of Veterinary Studies, Midlothian, UK, under the terms of the Toronto Statement (Nature 2009, 461: 168) with the following understanding: Users are free to analyse these data if the providers of these data are properly cited, any whole genome analyses should follow guidelines outlined in the Ft. Lauderdale agreement on the use of this assembly and any redistribution of the data should carry this notice. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | None as yet |
| URL | https://www.ncbi.nlm.nih.gov/assembly/GCA_016906955.1/ |
| 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 | PRJEB14552 |
| Description | The MHC region contains many genes that are key regulators of both innate and adaptive immunity including the polymorphic MHCI and MHCII genes. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation that determines the nature of immune responses. Currently our knowledge of the bovine MHCI repertoire is limited with only the Holstein-Friesian breed having been studied in any depth. Traditional methods of MHCI genotyping are of low resolution and laborious and this has been a major impediment to a more comprehensive analysis of the MHCI repertoire of other cattle breeds. Next-generation sequencing (NGS) technologies have been used to enable high throughput and much higher resolution MHCI typing in a number of species. In this study we have developed a MiSeq platform approach and requisite bioinformatics pipeline to facilitate typing of bovine MHCI repertoires. The method was validated initially on a cohort of Holstein-Friesian animals and then demonstrated to enable characterisation of MHCI repertoires in African cattle breeds, for which there was limited or no available data. During the course of these studies we identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire. Construction protocol: Total RNAs were extracted from white blood cell pellets prepared form blood obtained by venepuncture using Tri-reagent (Sigma-Aldrich, Dorset) and cDNA prepared using the Reverse Transcription Kit (Promega, WI); both according to the manufacturer's protocols. PCR amplification was performed with the Phusion HF PCR kit (NEB, Herts.) using bovine MHCI primers that included Illumina sequencing primer annealing sites, multiple sample identifier tags (D501-508 and D701-712) and Illumina ligation adaptors. PCR products from ~96 animals were pooled to form a library which was then sequenced on the Illumina Miseq platform. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | These data represent a reference dataset of novel MHC alleles in cattle and may underpin research into cattle immunogenetic diversity for many years in the future |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB14552 |
| Title | PRJEB14979 |
| Description | Marek's Disease Virus (MDV) is a widespread alphaherpesvirus of poultry that causes Marek's disease (MD) characterised by fatal visceral CD4+ TCRaß+ T cell tumours at high incidence in susceptible hosts. As is the case with many virus-induced tumours, immortal cell lines harbouring viral genome have been generated from ex vivo cultures of MD tumours. As readily-available sources of large numbers of cells of a uniform type, MDV-transformed lymphoblastoid cell lines (LCL) have proved extremely valuable in studying virus-host interaction. While the viral genome is held in a latent state in most of the cells, a minor population of cells display spontaneous reactivation identifiable by the expression of lytic viral genes such as pp38. The process of spontaneous reactivation in these cell populations offers the opportunity for investigating the biological processes involved in the reactivation events. For this, we used two lymphoblastoid cell lines derived from lymphomas induced by pRB1B-UL47eGFP, a recombinant MDV engineered to express EGFP fused with the UL47. We used Fluorescence-activated cell sorting (FACS) to purify the rare EGFP-positive cell population with spontaneously activating viral genome from the majority EGFP-negative cells and analysed their gene expression profiles by RNA-sequencing using Illumina HiSeq2500. The reads generated were mapped using TopHat and gene expression levels were analysed by edgeR. Ingenuity pathway analysis software on more than 2000 differentially-expressed genes between the lytically infected (EGFP-positive) and latently infected (EGFP-negative) cell populations was used identify major biological pathways involved in the reactivation. These studies revealed that amongst others, transcripts directly involved in T activation such as CD3 complex, CD28, ICOS, phospholipase C, CD3 complex were down-regulated following reactivation of the virus in the LCL. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | These data detail the gene expression changes during spontaneous activation of MDV and will be useful to researchers investigating the mechanism of action of this important virus, as well as in vaccine design |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB14979 |
| Title | PRJEB21624 |
| Description | This is one of the largest rumen metagenomics datasets ever released and represents 43 Scottish cattle from diverse breeds, different in methane emissions and feed conversion ratio. These data were used to assemble over 913 novel rumen microbial genomes. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | These data were used to assemble over 913 novel rumen microbial genomes, which are expected to impact global rumen microbiome research over the next 5-10 years |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB21624 |
| Title | Supporting data for "An improved pig reference genome sequence to enable pig genetics and genomics research" |
| Description | The domestic pig ( Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited its utility. We present two annotated highly contiguous chromosome-level genome assemblies created with more recent long read technologies and a whole genome shotgun strategy, one for the same Duroc female (Sscrofa11.1) and one for an outbred, composite breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. These highly contiguous assemblies plus annotation of a further 11 short read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | http://gigadb.org/dataset/100732 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Aarhus University |
| Country | Denmark |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Centre for Genomic Regulation (CRG) |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Diagenode |
| Country | Belgium |
| Sector | Private |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | ETH Zurich |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Edinethics |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | European Federation of Animal Science |
| Country | Italy |
| Sector | Public |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Faculdade de Medicina de Marília |
| Country | Brazil |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Versailles |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Leibniz Association |
| Department | Leibniz Institute for Farm Animal Biology |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Martin Luther University of Halle-Wittenberg |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Natural Resources Institute Finland |
| Country | Finland |
| Sector | Public |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Polish Academy of Sciences |
| Department | Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences |
| Country | Poland |
| Sector | Public |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | University of Alberta |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | University of Edinburgh |
| Department | The Roslin Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | University of Liege |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | University of Limoges |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Utrecht University |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Wageningen University & Research |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| 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 | Charoen Pokphand (CP) group |
| Organisation | Charoen Pokphand Group |
| Country | Thailand |
| Sector | Private |
| PI Contribution | Charoen Pokphand (CP) group are a large Asian conglomerate with an interest in farming, food production and feed additives. They have placed one of their staff members with me for PhD training, fully funded by them. We are training the staff member in laboratory and bioinformatics techniques related to microbiome research in chickens. |
| Collaborator Contribution | CP provide access to large chicken flocks both in at their farms and in their production facility. This enables us to study chicken breeds in the actual environments in which they live throughout Asia. |
| Impact | This is a multi-disciplinary project involving both laboratory and computational techniques. The major outcome so far include a review paper (http://aem.asm.org/content/early/2018/01/29/AEM.02627-17.abstract) and the technology transfer from our group into the commercial partner. |
| Start Year | 2017 |
| Description | David Griffiths, Moredun |
| Organisation | Moredun Research Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We have been working with David Griffiths at The Moredun Research Institute since 2011 in the study of ovine pulmonary adenocarcinoma |
| Collaborator Contribution | David Griffiths is an expert in the study of ovine pulmondary adenocarcinoma, how the virus functions and how we might design intervention strategies such as vaccines. My group is expert in the use of genomics and bioinformatics and together we are using sequencing to understand how the virus interacts with its host |
| Impact | NA |
| Start Year | 2011 |
| Description | EMBL-EBI collaboration with the Functional Analysis of ANimal Genomes (FAANG) Consortium |
| Organisation | Functional Annotation of ANimal Genomes (FAANG) |
| Country | Global |
| Sector | Charity/Non Profit |
| PI Contribution | We participate in conference calls on the analysis of data. Peter Harrison co-chairs the Metadata and Data Sharing Committee and is a member of the FAANG steering committee. The objective of the Metadata and Data Sharing committee is to recommend standard methods to record information for all samples, experiments and analyses carried out by FAANG consortium members; recommend best practice for data archiving; and define data sharing methodologies that encourage sharing within the FAANG consortium and rapid public release of raw data and analysis results. |
| Collaborator Contribution | There are numerous partners that are part of this collaboration. They contribute data, tools, and other expertise. |
| Impact | The collaboration is still in the early stages, and we are aiming to get funding for this work. FAANG aims to: Standardize core assays and experimental protocols Coordinate and facilitate data sharing Establish an infrastructure for analysis of these data Provide high quality functional annotation of animal genomes |
| Start Year | 2014 |
| Description | Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | "The Animal Functional Genomics Resource" project is a collaboration between EMBL-EBI and The Roslin Institute and is supported through linked BBSRC grants to these two partners. The EMBL-EBI and Roslin Institute partners are also active members of the Functional Annotation of ANimal Genomes (FAANG) working group on Metadata and Data Sharing (M&DS). The Roslin partners bring knowledge of the target farmed animal species and exemplar datasets with which to test the draft data and metadata standards developed by the M&DS working group. The Roslin partners have also tested the systems for capturing metadata and for pre-publication data sharing. |
| Collaborator Contribution | The EMBL-EBI partners are developing and hosting the FAANG Data Portal (http://data.faang.org/home). The EMBL-EBI partners are also developing common data submission tools and QC tools. Scientists from EMBL-EBI and the University of Delaware co-chair the Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group. Scientists at Iowa State University provide links to the FAANG Bioinformatics and Data Analysis working group and to the USDA NRSP8 Bioinformatics Coordinator. Ninety-three of the 398 individuals who have joined as 'contributors' to the Functional Annotation of ANimal Genomes (FAANG) consortium have self-identified as members of the Metadata and Data Sharing (M&DS) Working group. For the sake of brevity only a few key partners are named here. |
| Impact | The FAANG Data Sharing Statement (https://www.faang.org/data-share-principle) and guidance on data submission (https://www.ebi.ac.uk/seqdb/confluence/display/FAANG/FAANG+Archive+Submission+guidelines) |
| Start Year | 2016 |
| Description | Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group |
| Organisation | Iowa State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | "The Animal Functional Genomics Resource" project is a collaboration between EMBL-EBI and The Roslin Institute and is supported through linked BBSRC grants to these two partners. The EMBL-EBI and Roslin Institute partners are also active members of the Functional Annotation of ANimal Genomes (FAANG) working group on Metadata and Data Sharing (M&DS). The Roslin partners bring knowledge of the target farmed animal species and exemplar datasets with which to test the draft data and metadata standards developed by the M&DS working group. The Roslin partners have also tested the systems for capturing metadata and for pre-publication data sharing. |
| Collaborator Contribution | The EMBL-EBI partners are developing and hosting the FAANG Data Portal (http://data.faang.org/home). The EMBL-EBI partners are also developing common data submission tools and QC tools. Scientists from EMBL-EBI and the University of Delaware co-chair the Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group. Scientists at Iowa State University provide links to the FAANG Bioinformatics and Data Analysis working group and to the USDA NRSP8 Bioinformatics Coordinator. Ninety-three of the 398 individuals who have joined as 'contributors' to the Functional Annotation of ANimal Genomes (FAANG) consortium have self-identified as members of the Metadata and Data Sharing (M&DS) Working group. For the sake of brevity only a few key partners are named here. |
| Impact | The FAANG Data Sharing Statement (https://www.faang.org/data-share-principle) and guidance on data submission (https://www.ebi.ac.uk/seqdb/confluence/display/FAANG/FAANG+Archive+Submission+guidelines) |
| Start Year | 2016 |
| Description | Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group |
| Organisation | University of Delaware |
| Department | Department of Animal and Food Sciences |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | "The Animal Functional Genomics Resource" project is a collaboration between EMBL-EBI and The Roslin Institute and is supported through linked BBSRC grants to these two partners. The EMBL-EBI and Roslin Institute partners are also active members of the Functional Annotation of ANimal Genomes (FAANG) working group on Metadata and Data Sharing (M&DS). The Roslin partners bring knowledge of the target farmed animal species and exemplar datasets with which to test the draft data and metadata standards developed by the M&DS working group. The Roslin partners have also tested the systems for capturing metadata and for pre-publication data sharing. |
| Collaborator Contribution | The EMBL-EBI partners are developing and hosting the FAANG Data Portal (http://data.faang.org/home). The EMBL-EBI partners are also developing common data submission tools and QC tools. Scientists from EMBL-EBI and the University of Delaware co-chair the Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group. Scientists at Iowa State University provide links to the FAANG Bioinformatics and Data Analysis working group and to the USDA NRSP8 Bioinformatics Coordinator. Ninety-three of the 398 individuals who have joined as 'contributors' to the Functional Annotation of ANimal Genomes (FAANG) consortium have self-identified as members of the Metadata and Data Sharing (M&DS) Working group. For the sake of brevity only a few key partners are named here. |
| Impact | The FAANG Data Sharing Statement (https://www.faang.org/data-share-principle) and guidance on data submission (https://www.ebi.ac.uk/seqdb/confluence/display/FAANG/FAANG+Archive+Submission+guidelines) |
| Start Year | 2016 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Agrocampus Ouest |
| Country | France |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Arizona State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Centre for Genomic Regulation (CRG) |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Rennes Centre |
| Country | France |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Toulouse |
| Country | France |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Harvard University |
| Department | Harvard Medical School |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Iowa State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Kenya Agriculture & Livestock Research Organization (KALRO) |
| Country | Kenya |
| Sector | Private |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Medical Research Council (MRC) |
| Department | Medical Research Council (MRC) Centre Cambridge |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | National Institute of Allergy and Infectious Diseases (NIAID) |
| Country | United States |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | National Institutes of Health (NIH) |
| Department | National Institute of Environmental Health Sciences |
| Country | United States |
| Sector | Public |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Oregon State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Swedish University of Agricultural Sciences |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of Arkansas |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of California, Davis |
| Department | UC Davis Genome Cente |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of Delaware |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of Leipzig |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | University of Nottingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | International Avian RNA-Seq Consortium |
| Organisation | Weizmann Institute of Science |
| Country | Israel |
| Sector | Academic/University |
| PI Contribution | I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries). |
| Collaborator Contribution | Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome. |
| Impact | Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6. |
| Start Year | 2011 |
| Description | PoreCamp |
| Organisation | University of Birmingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | PoreCamp is a training programme in nanopore sequencing run via a collaboration between Universities of Edinburgh, Birmingham and Nottingham |
| Collaborator Contribution | The first PoreCamp was a training course run for users of the Oxford Nanopore MinION, taking place over 5 days in December 2015. Users were trained in library preparation, sequencing and bioinformatics. A second PoreCamp occurred in Exeter in 2016. A third PoreCamp occured in Texas in 2017. |
| Impact | Well over 200 students trained to date |
| Start Year | 2015 |
| Description | PoreCamp |
| Organisation | University of Nottingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | PoreCamp is a training programme in nanopore sequencing run via a collaboration between Universities of Edinburgh, Birmingham and Nottingham |
| Collaborator Contribution | The first PoreCamp was a training course run for users of the Oxford Nanopore MinION, taking place over 5 days in December 2015. Users were trained in library preparation, sequencing and bioinformatics. A second PoreCamp occurred in Exeter in 2016. A third PoreCamp occured in Texas in 2017. |
| Impact | Well over 200 students trained to date |
| Start Year | 2015 |
| 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 |
| 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 | EBI pipeline to produce standardised reference datasets |
| Description | EMBL-EBI has built a software pipeline to produce standardised reference datasets based on a genome assembly and the full complement of annotated genes: this will be the foundation for comparable analyses across multiple species. At present it includes support for files for common genomics tools, including alignment indexes for genomic and transcriptomic mapping. This will be extended to support the analysis methods chosen by the FAANG community. The pipeline also measures how 'mappable' each position in a genome is. This is then used to support the production of normalised signal tracks from functional data, which is very useful for simplifying comparisons between different experiments. |
| Type Of Technology | Software |
| Year Produced | 2015 |
| Open Source License? | Yes |
| Impact | To date this pipeline has only been used internally by our group at EBI, however we anticipate uptake by the research community in the future. |
| URL | https://github.com/FAANG/ |
| Title | Improvements to Ensembl gene annotation pipeline |
| Description | EMBL-EBI has improved the Ensembl gene annotation system. The Ensembl Project produces annotation for many vertebrate species, and has previously taken a major role in annotation for farmed animals including sheep and pig. The improvements that Ensembl has been working on relate to the initial 'genome preparation' phase of our gene annotation pipeline, where the genome assembly information is loaded into an Ensembl relational database framework. The loaded assembly is quality controlled by comparing it to the original assembly files to ensure loading has been successful. Genomic features, such as repeat regions and regions showing evidence of protein coding potential, are then annotated on the loaded assembly. These steps are the precursor to full gene annotation of the target species. As part of this award, the assembly loading and QC phase have been converted to the Ensembl eHive pipeline management system (EEPMS) and been successfully tested. The EEPMS is a pipeline management solution developed and maintained by the Ensembl Project that allows for high levels of pipeline automation, graphical monitoring of pipeline progress and ease of configuration. This will allow the genome preparation phase of the annotation process to scale to larger number of species than Ensembl is currently able to annotate. We have also converted our feature annotation analyses to the EEPMS and successfully tested it. We have shown that a process that required one to two weeks of work for a single species can now be set up for multiple species in a matter of minutes, with the whole process running in a fully automated manner over the course of 2-5 days. |
| Type Of Technology | Software |
| Year Produced | 2015 |
| Open Source License? | Yes |
| Impact | The impact to date has been internal, due to our improvements in the annotation pipeline. However, this work will be very important for the farmed animal community going forward. The next phase of this project will involve building a test suite of modules to ensure that any alterations to the pipeline do not lead to errors in the output. The final phase is to make the pipeline available in the form of an installer or a container for use by the community. |
| URL | https://github.com/Ensembl |
| Title | MAGpy |
| Description | Recent advances in bioinformatics have enabled the rapid assembly of genomes from metagenomes (MAGs), and there is a need for reproducible pipelines that can annotate and characterise thousands of genomes simultaneously. Here we present MAGpy, a Snakemake pipeline that takes FASTA input and compares MAGs to several public databases, checks quality, assigns a taxonomy and draws a phylogenetic tree. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | This software was used to annotate 913 metagenome assembled genomes from the cattle rumen, a dataset which is expected to underpin rumen metagenomics research for the next 5-10 years |
| URL | https://datashare.is.ed.ac.uk/handle/10283/3009 |
| Description | Animal Microbiome Congress London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Mick Watson presented his work on functional microbiome analysis at the Animal Microbiome Congress London. Attendees included industry/business, farmers, professional practitioners and academics |
| Year(s) Of Engagement Activity | 2017 |
| 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 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 | 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 | Creation of multiple genome alignments and clade-based tools to facilitate the study of speciation and adaptation in birds |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk at EOU215: Badajoz, Spain, August 2105. Roundtable 7 (Genetics): Creation of multiple genome alignments and clade-based tools to facilitate the study of speciation and adaptation in birds |
| Year(s) Of Engagement Activity | 2015 |
| Description | EBI attendance at FAANG workshop, Washington (USA), October 2015 |
| 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 | Laura Clarke attended the GO-FAANG meeting and gave a presentation on 'FAANG: Status on Data storage and analysis challenges'. The meeting aimed to build plans to fund the work of the international FAANG consortium and inform policy makers. |
| Year(s) Of Engagement Activity | 2015 |
| Description | EBI attendance at PAG XXIV, San Diego, USA, January 2016 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Laura Clarke gave a poster presentation on 'FAANG - Metadata and Data Sharing Committee' at the Plant and Animal Genomes conference. The poster raised awareness among the research community of the FAANG activities and in particular the committee that Laura Clarke is a part of. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Evonik research day |
| 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 my work on precision analysis of microbiomes to Evonik, an international company with over 13000 employees and with interests in chemical and food production. This was part of a one day workshop with Evonik, hosted by Roslin and focused on microbiomes |
| Year(s) Of Engagement Activity | 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 | ISAG 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Mick Watson presented work on cutting edge techniques that can be used to analyse metagenomics sequence data. ISAG is the international society for animal genetics and this was the very first microbiome session. In attendance were industry practitioners and academics |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.isag.us/2017/ |
| Description | Mick Watson Roslin Industry Day |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Mick Watson presented on how genomic technologies are transforming biological research, to an audience of industry and professional practitioners invited to The Roslin Institute to discuss science and policy |
| Year(s) Of Engagement Activity | 2016 |
| Description | Non-Model Avian Genomics Fit for Purpose - the End of the Model Organism? |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk: Non-Model Avian Genomics Fit for Purpose - the End of the Model Organism? Avian Genomes: Plant & Animal Genomes, San Diego, Jan 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | PAG 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Mick Watson gave a talk at PAG 2017 on Comparison of Methods for Functional and Phylogenetic Characterisation of Rumen Metagenomic Data. Attendees include industry, professional practitioners and academics |
| Year(s) Of Engagement Activity | 2017 |
| Description | PAG 2018 microbiome talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I gave a talk on microbiome bioinformatics at PAG 2018 in San Diego in the microbiome session. PAG includes attendees from industry, farming and academia. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Past, Present and Future of Genomics in Poultry Breeding. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk: Past, Present and Future of Genomics in Poultry Breeding. 25th World's Poultry Congress, Beijing, 5-9 September, 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | 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 | 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 | Rumen microbiome article in Farmer's Weekly |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Mick Watson was personally interviewed for an article in Farmer's weekly on the potential impact of our rumen microbiome work (doi:10.1038/s41467-018-03317-6) on breeding for production traits in beef and dairy cattle. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.fwi.co.uk/livestock/rumen-genotyping-advances-enhance-cattle-breeding.htm |
| Description | Rumen microbiome work in the national press (print editions) |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Various articles about our rumen microbiome work appeared in the national press, including: Scottish Daily Express, Scottish Sun, The Scotsman and the Press and Journal |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.pressandjournal.co.uk/fp/business/farming/1427948/cow-digestion-discovery-could-boost-pr... |
| Description | Rumen microbiome work on National Public Radio (NPR) in the USA |
| 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 | Our rumen microbiome work was featured on NPR.org, (National Public Radio), a US news network that has over 7 million followers on Twitter and reaches millions of people online and via radio. The article was immediately syndicated across an additional ~40 NPR-associated websites |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.npr.org/sections/thesalt/2018/03/06/589997622/mysteries-of-the-moo-crobiome-could-tweaki... |
| 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 | The Chicken and other Avian Genomes: new insights and opportunities for all from high throughput sequencing and bioinformatics. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk: the Chicken and other Avian Genomes: new insights and opportunities for all from high throughput sequencing and bioinformatics. In "Avian Model Systems 9: a new integrative platform", Taipei, Taiwan, 38 March to 3 April, 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Various articles on rumen microbiome work |
| 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 | Various online websites picked up our press release on our rumen microbiome work (doi:10.1038/s41467-018-03317-6) including: https://phys.org/news/2018-02-dna-cow-stomachs-aid-meat.html https://www.sciencedaily.com/releases/2018/02/180228085347.htm http://www.labmanager.com/news/2018/02/dna-study-of-cow-stomachs-could-aid-meat-and-dairy-production#.WpwhWOjFLZs https://www.technologynetworks.com/genomics/news/cows-guts-could-hold-secrets-to-more-meat-and-milk-298080 http://www.sciencenewsline.com/news/2018030111510072.html https://www.eurekalert.org/pub_releases/2018-02/uoe-dso022718.php http://biofuelsdigest.com/nuudigest/2018/02/28/cow-stomach-microbes-could-hold-key-for-increased-food-and-biofuel-production/ |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.sciencedaily.com/releases/2018/02/180228085347.htm |