Modelling Cellular and Tissue Systems
Lead Research Organisation:
University of Edinburgh
Department Name: The Roslin Institute
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The aim of this theme is to use information derived from high throughput technologies such as microarrays and molecular imaging to develop predictive models of cellular and tissue behaviour, and of the function of individual gene products within cellular systems. In particular, this theme aims to provide a framework in which to efficiently identify the function of candidate genes underlying simple or complex traits. The objectives of the theme are: To conduct evolutionary comparisons of transcription networks (transcript and microarray focused). To reverse engineer regulatory networks. To dissect microRNA regulatory networks. To model cellular and tissue systems in diseases.
Planned Impact
unavailable
Organisations
- University of Edinburgh (Lead Research Organisation)
- University of Glasgow (Collaboration)
- Agrocampus Ouest (Collaboration)
- Swedish University of Agricultural Sciences (Collaboration)
- Arizona State University (Collaboration)
- Iowa State University (Collaboration)
- Centre for Genomic Regulation (CRG) (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- Oregon State University (Collaboration)
- University of Leipzig (Collaboration)
- Sanford-Burnham Medical Research Institute (Collaboration)
- Royal Veterinary College (RVC) (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- Kenya Agriculture & Livestock Research Organization (KALRO) (Collaboration)
- HARVARD UNIVERSITY (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- University of East Anglia (Collaboration)
- University of California, Davis (Collaboration)
- University of Delaware (Collaboration)
- National Institute of Allergy and Infectious Diseases (NIAID) (Collaboration)
- University of Arkansas (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- Weizmann Institute of Science (Collaboration)
People |
ORCID iD |
| Alan Archibald (Principal Investigator) |
Publications
Ait-Ali T
(2008)
Dynamic differential regulation of innate immune transcripts during the infection of alveolar macrophages by the porcine reproductive and respiratory syndrome virus.
in Developments in biologicals
Anderson C
(2016)
A strategy to discover new organizers identifies a putative heart organizer.
in Nature communications
Archibald A
(2008)
Animal genomics for animal health report: critical needs, problems to be solved, potential solutions, and a roadmap for moving forward.
in Developments in biologicals
Audzevich T
(2017)
Pre/pro-B cells generate macrophage populations during homeostasis and inflammation.
in Proceedings of the National Academy of Sciences of the United States of America
Baillie JK
(2011)
Somatic retrotransposition alters the genetic landscape of the human brain.
in Nature
Clark EL
(2017)
A high resolution atlas of gene expression in the domestic sheep (Ovis aries).
in PLoS genetics
Clark EL
(2017)
A high resolution atlas of gene expression in the domestic sheep (Ovis aries).
in PLoS genetics
Doig TN
(2013)
Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment.
in BMC genomics
Freeman T
(2010)
Systems Biology for Signaling Networks
Freeman TC
(2010)
The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways.
in BMC systems biology
| Description | Development and application of the modified Edinburgh Pathway Notation, a graphical pathway modelling language. In particular, its application to the type 1 interferon pathway has formed the basis for further computational modelling of the system. By modifying a Petri net-based approach to run stochastic flow simulations, the dynamic behaviour of this pathway and the transcriptional network it controls are now being modelled. Development and application of BioLayout Express3D. This tool supports the construction and clustering of large network graphs in 3-dimensional space based on the correlation coefficient between individual gene profiles. It provides a very powerful means to visualise and explore large amounts of data e.g. transcriptomics data and exceptional resolution in defining co-expression networks. The tool and its application for elucidating networks underlying cancer development using meta-analyses of data will be expanded upon during the review. The building of a transcriptional network model for human monocyte differentiation using sequence- and hybridisation-based expression profiling tools, driven by Institute PIs (Hume and Faulkner), in collaboration with the Riken Institute (Japan). The proposition and confirmation of a previously unknown source of transcriptional and regulatory complexity in mammals: transposed elements RNAs (teRNAs). Development of testable models predicting follicle patterning of hair and feathers. |
| Exploitation Route | In addition to the contribution to the understanding of complex biological systems, this project supported the development of analysis tools such as BioLayout Express which have been subsequently been used by researchers around the world. |
| Sectors | Agriculture Food and Drink |
| Description | Adapted yeast for superior carbon conversion |
| Amount | £573,511 (GBP) |
| Funding ID | 100962 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2011 |
| End | 07/2014 |
| Description | BBSRC - DTG |
| Amount | £80,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2009 |
| End | 09/2012 |
| Description | BBSRC-DTG |
| Amount | £85,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2010 |
| End | 09/2014 |
| Description | BBSRC-DTG |
| Amount | £85,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2011 |
| End | 09/2015 |
| Description | BBSRC-DTG |
| Amount | £80,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2008 |
| End | 09/2012 |
| Description | Biotek2021: The Atlantic salmon genome sequence as a tool for precision breeding |
| Amount | kr 1,500,000 (NOK) |
| Funding ID | Researcher project - BIOTEK2021 |
| Organisation | Research Council of Norway |
| Department | BIOTEK2021 |
| Sector | Public |
| Country | Norway |
| Start | 02/2012 |
| End | 02/2016 |
| Description | Response Mode: Unravelling the networks that regulate seasonal rhythmicity in the epigenome |
| Amount | £1,200,000 (GBP) |
| Funding ID | BB/N015347/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2016 |
| End | 12/2019 |
| Description | Roslin Institute |
| Amount | £120,000 (GBP) |
| Organisation | University of Edinburgh |
| Department | The Roslin Institute |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 09/2009 |
| End | 09/2013 |
| Description | Self funding |
| Amount | £100,000 (GBP) |
| Organisation | Government of Malaysia |
| Sector | Public |
| Country | Malaysia |
| Start | 01/2008 |
| End | 12/2011 |
| Title | Pathway modelling app |
| Description | There is a need for formalised diagrams that both summarise current biological pathway knowledge and support modelling approaches that explain and predict their behaviour. Here, we present a new, freely available modelling framework that includes a biologist friendly pathway modelling language (mEPN), a simple but sophisticated method to support model parameterisation using available biological information; a stochastic flow algorithm that simulates the dynamics of pathway activity; and a 3-D visualisation engine that aids understanding of the complexities of a system's dynamics. We present example pathway models that illustrate of the power of approach to depict a diverse range of systems. |
| Type Of Material | Model of mechanisms or symptoms - in vitro |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | This approach has been used to model a range of biological systems and we are slowly seeing in an increasing number of people adopting the method. |
| URL | https://www.virtuallyimmune.org/ |
| Title | Virtually Immune |
| Description | Virtually Immune is a resource that aims to support the graphical and computational modelling of immune pathways. The tools and resources presented there are primarily designed for biologists, both to use and to allow them to develop their own models of systems of interest to them. Virtually Immune introduces: a standardised system for presenting pathway knowledge a user-friendly platform for modelling pathway resources which capture and collate information from hundreds of papers a platform for knowledge exchange within the scientific community |
| Type Of Material | Database/Collection of data |
| Year Produced | 2014 |
| Provided To Others? | Yes |
| Impact | As a result of setting up this website as part of the phase 1 of the NCR's Crack it challenge we are beginning to guide people to it as a resource for our modelling efforts. Two papers in preparation describing the tools and our modelling approach. |
| URL | http://www.virtuallyimmune.org/ |
| Description | BioLayout Express3D project |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Together we have worked as a team in developing the BioLayout tool with almost all of the coding has been performed in Edinburgh. |
| Collaborator Contribution | Advice, shared publications, ideas. |
| Impact | Outcomes from this work include the tool itself, numerous publications by ourselves and others. The original paper published in PLoS Comp Biol (2007) has been cited 243 times and the Nature Protocols paper (2009) has been cited 239 times (Google Scholar, Feb 2019). This was a multidisciplinary collaboration involving biologists, computer scientists, software engineers and mathematicians.The codebase for this software was licensed from the University of Edinburgh by Kajeka Ltd a UoE spinout company (www.kajeka.com). |
| Start Year | 2006 |
| Description | Endocrine control of bone growth and development |
| Organisation | University of Glasgow |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Provided laboratory and animal model skills and expertise to various projects |
| Collaborator Contribution | Provided clinical insight |
| Impact | Dobie R, Ahmed SF, Staines KA, Pass C, Jasim S, MacRae VE, Farquharson C (2015) Increased linear bone growth by GH in the absence of SOCS2 is independent of IGF-1. J Cell Physiol 230:2796-806. Holgersen K, Dobie R, Farquharson C, Ahmed SF, Hansen AK, and Thomas Lindebo Holm TL (2015) Increased bone loss during piroxicam accelerated colitis in the interleukin-10 k.o. mouse model. Inflamm. Bowel Diseases: 21:257-66. Huesa C, Zhu D, Glover JD, Ferron M, Karsenty G, Milne EM, Millan JL, Ahmed SF, Farquharson C, Morton NM, MacRae VE. (2014) Deficiency of the bone mineralization inhibitor NPP1 protects against obesity and diabetes. Dis Model Mech. 12:1341-1350. Dobie R, MacRae VE, Huesa C, Van't Hof R, Ahmed SF, Farquharson C (2014) Direct stimulation of bone mass by increased GH signalling in osteoblasts of Socs2-/- mice. J Endocrinol. 223:93-106. Pass C, MacRae VE, Huesa C, Ahmed SF, Farquharson C 2012 SOCS2 is the critical regulator of GH action in murine growth plate chondrogenesis. 2012 J Bone Miner Res. 27:1055-1066. Owen HC, Ahmed SF, Farquharson C. 2009. Chondrocyte p21WAF1/CIP1 expression is increased by Dexamethasone but does not contribute to Dexamethasone-induced growth retardation in vivo. Calcified Tissue International 85:326-334. Owen HC, Roberts SJ, Ahmed SF, Farquharson C 2008 Dexamethasone-induced expression of the glucocorticoids response gene lipocalin 2 in chondrocytes. Am J Physiol Endocrinol Metab. 294:E1023-34. MacRae VE, Ahmed SF, Mushtaq T, Farquharson C 2007. IGF-I signalling in bone growth: Inhibitory actions of dexamethasone and IL-1ß. Growth Hormone and IGF-I Research 17:435-439. MacRae VE, Wong SC, Smith W, Gracie A, McInnes I, Galea P, Gardner-Medwin J, Farquharson C, Ahmed SF. 2007. Cytokine profiling and in vitro studies of murine bone growth using biological fluids from children with juvenile idiopathic arthritis. Clin. Endocrinol 67:442-448. Owen H, Miner JN, Ahmed SF, Farquharson C. 2007. The Growth Plate Sparing Effects of the Selective Glucocorticoid Receptor Modulator, AL-438. Mol Cell Endocrinology 264:164-170. MacRae VE, Burdon T, Ahmed SF, Farquharson C 2006. Ceramide inhibition of chondrocytes proliferation and bone growth is IGF-I independent. J Endocrinology 191:369-377. MaCrae V, Farquharson C, Ahmed SF. 2006 The Restricted Potential For Recovery Of Growth Plate Chondrogenesis And Longitudinal Bone Growth Following Exposure To Pro-inflammatory Cytokines. J Endocrinology 189: 319-328. Mushtaq T, Bijman P, Ahmed SF, Farquharson C.2004. Insulin like growth factor-I augments chondrocyte hypertrophy and reverses glucocorticoid mediated growth retardation in fetal mice metatarsal cultures. Endocrinology 145:2478-86. Mushtaq T, Farquharson C, Seawright E, Ahmed SF. 2002. Glucocorticoid effects on chondrogenesis, differentiation and apoptosis in the murine ATDC5 cell line. J Endocrinol. 175:705-13. 2012-2014. Medical Research Scotland. Investigating the Regulation of Insulin Signalling in Bone by PC-1. £147,056 2010-2013. MRC. CSF1 and the control of postnatal growth and organ development in the rat. £650,000 2004 - 2006. Novo Nordisk Ltd, Industrial Support. Inflammatory cytokines in juvenile idiopathic arthritis. £180,000 |
| Description | Endocrine control of bone growth and development |
| Organisation | University of Glasgow |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Provided laboratory and animal model skills and expertise to various projects |
| Collaborator Contribution | Provided clinical insight |
| Impact | Dobie R, Ahmed SF, Staines KA, Pass C, Jasim S, MacRae VE, Farquharson C (2015) Increased linear bone growth by GH in the absence of SOCS2 is independent of IGF-1. J Cell Physiol 230:2796-806. Holgersen K, Dobie R, Farquharson C, Ahmed SF, Hansen AK, and Thomas Lindebo Holm TL (2015) Increased bone loss during piroxicam accelerated colitis in the interleukin-10 k.o. mouse model. Inflamm. Bowel Diseases: 21:257-66. Huesa C, Zhu D, Glover JD, Ferron M, Karsenty G, Milne EM, Millan JL, Ahmed SF, Farquharson C, Morton NM, MacRae VE. (2014) Deficiency of the bone mineralization inhibitor NPP1 protects against obesity and diabetes. Dis Model Mech. 12:1341-1350. Dobie R, MacRae VE, Huesa C, Van't Hof R, Ahmed SF, Farquharson C (2014) Direct stimulation of bone mass by increased GH signalling in osteoblasts of Socs2-/- mice. J Endocrinol. 223:93-106. Pass C, MacRae VE, Huesa C, Ahmed SF, Farquharson C 2012 SOCS2 is the critical regulator of GH action in murine growth plate chondrogenesis. 2012 J Bone Miner Res. 27:1055-1066. Owen HC, Ahmed SF, Farquharson C. 2009. Chondrocyte p21WAF1/CIP1 expression is increased by Dexamethasone but does not contribute to Dexamethasone-induced growth retardation in vivo. Calcified Tissue International 85:326-334. Owen HC, Roberts SJ, Ahmed SF, Farquharson C 2008 Dexamethasone-induced expression of the glucocorticoids response gene lipocalin 2 in chondrocytes. Am J Physiol Endocrinol Metab. 294:E1023-34. MacRae VE, Ahmed SF, Mushtaq T, Farquharson C 2007. IGF-I signalling in bone growth: Inhibitory actions of dexamethasone and IL-1ß. Growth Hormone and IGF-I Research 17:435-439. MacRae VE, Wong SC, Smith W, Gracie A, McInnes I, Galea P, Gardner-Medwin J, Farquharson C, Ahmed SF. 2007. Cytokine profiling and in vitro studies of murine bone growth using biological fluids from children with juvenile idiopathic arthritis. Clin. Endocrinol 67:442-448. Owen H, Miner JN, Ahmed SF, Farquharson C. 2007. The Growth Plate Sparing Effects of the Selective Glucocorticoid Receptor Modulator, AL-438. Mol Cell Endocrinology 264:164-170. MacRae VE, Burdon T, Ahmed SF, Farquharson C 2006. Ceramide inhibition of chondrocytes proliferation and bone growth is IGF-I independent. J Endocrinology 191:369-377. MaCrae V, Farquharson C, Ahmed SF. 2006 The Restricted Potential For Recovery Of Growth Plate Chondrogenesis And Longitudinal Bone Growth Following Exposure To Pro-inflammatory Cytokines. J Endocrinology 189: 319-328. Mushtaq T, Bijman P, Ahmed SF, Farquharson C.2004. Insulin like growth factor-I augments chondrocyte hypertrophy and reverses glucocorticoid mediated growth retardation in fetal mice metatarsal cultures. Endocrinology 145:2478-86. Mushtaq T, Farquharson C, Seawright E, Ahmed SF. 2002. Glucocorticoid effects on chondrogenesis, differentiation and apoptosis in the murine ATDC5 cell line. J Endocrinol. 175:705-13. 2012-2014. Medical Research Scotland. Investigating the Regulation of Insulin Signalling in Bone by PC-1. £147,056 2010-2013. MRC. CSF1 and the control of postnatal growth and organ development in the rat. £650,000 2004 - 2006. Novo Nordisk Ltd, Industrial Support. Inflammatory cytokines in juvenile idiopathic arthritis. £180,000 |
| Description | Functional aspects of skeletal mineralisation |
| Organisation | Royal Veterinary College (RVC) |
| Department | Pathobiology and Population Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have supplied the genetically altered mouse model and expertise into various aspects of bone analysis |
| Collaborator Contribution | They have provided expertise in determining the effects of mechanical loading on skeletal architecture and geometry |
| Impact | Ahmed Al-Jazzar A,, Javaheri B, Prideaux M, Boyde A, Scudamore C, Cherifi C, Hay E, Hopkinson M, Boyd M, Cohen-Solal M, Farquharson C, Pitsillides A (2016) Dmp1 promoter-driven Diphtheria toxin receptor Transgene expression directs unforeseen effects in multiple tissues. Int J Mol Sci 26;18(1). pii: E29 Staines KA, Prideaux M, Buttle DJ, Pitsillides AA, Farquharson C (2016) E11/Podoplanin Protein Stabilization through Inhibition of the proteasome promotes osteocyte differentiation in murine in vitro models. J Cell Physiol. 231:1392-404. Staines KA, Madi K, Mirczuk SM, Parker S, Burleigh A, Poulet B, Hopkinson M, Bodey AJ, Fowkes RC, Farquharson C, Lee PD, Pitsillides AA (2016) Endochondral growth defect and deployment of transient chondrocyte behaviours underlie osteoarthritis onset in a natural murine model. Arthritis Rheumatol. 68:880-91. Zaman G, Staines K, Farquharson C, Newton PT, Dudhia J, Chenu C, Pitsillides AA, Dhoot GK (2016) Expression of Sulf1 and Sulf2 in cartilage, bone and endochondral fracture healing. Histochem Cell Biol 145:67-79. Javaheri B, Carriero A, Staines KA, Chang Y-M, Houston DA, Oldknow KJ, Millan JL, Bassir Kazeruni N, Salmon P, Shefelbine S, Farquharson C, Pitsillides, AA (2015) Phospho1 deficiency transiently modifies bone architecture yet produces consistent modification in osteocyte differentiation and vascularization with ageing Bone 81:277-91 Prideaux M, Staines KA, Jones ER, Riley GP, Pitsillides AA, Farquharson C (2015) MMP and TIMP temporal gene expression during osteocytogenesis (2015). Gene Expr Patterns. 18(1-2):29-36. Zhu D, Mackenzie NC, Millan JL, Farquharson C, Macrae VE 2013 A protective role for FGF-23 in local defence against disrupted arterial wall integrity? Mol Cell Endocrinol. 372(1-2):1-11. Prideaux M, Loveridge N, Pitsillides AA, Farquharson C 2012 Extracellular Matrix Mineralization Promotes E11/gp38 Glycoprotein Expression and Drives Osteocytic Differentiation. PLoS One. 7(5):e36786. Rawlinson SCF, Murray DH, Wright CDP, Mosely JR, Bredl JC, Loveridge N, Leterrier C, Constantin P, Saxon LK, Farquharson C*, Pitsillides AA*. 2009 Genetic selection for fast growth generates bone architecture characterised for enhanced periosteal expansion and limited consolidation of the cortices but a diminution in early responses to mechancial loading Bone. 45:357-366. (* Joint last author). MacRae VE, Horvat S, Pells S, Dale, H Collinson RS, Pitsillides AA, Ahmed SF, Farquharson C. 2009 Increased bone mass, altered trabecular architecture and modified growth plate organization in the growing skeleton of SOCS2 deficient mice. J Cell Physiol 218:276-284. 2014-2016. Arthritis Research UK. Subchondral bone sclerosis in OA is driven by defective mineralisation and osteocyte formation. £179,458. |
| Start Year | 2009 |
| 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 | PHOSPHO1 regulation of bone mineralisation |
| Organisation | Sanford-Burnham Medical Research Institute |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | Generated and supplied the genetically modified mice and also expertise in bone analysis |
| Collaborator Contribution | Provided additional genetically modified mice and expertise in Matrix Vesicle analysis |
| Impact | Zweifler L, Ao M, Yadav M, Kuss P, Narisawa S, Kolli T, Wimer HF, Farquharson C, Somerman MJ, Millán JL, Foster BL (2016) Role of PHOSPHO1 in periodontal development and function. J Dent Res 95:742-51. Yadav MC, Bottini M, Cory E, Bhattacharya MAK, Kuss P, Narisawa S, Sah RL, Beck L, Faadel B, Farquharson C, Millán JL (2016) Skeletal mineralization deficits and impaired biogenesis of chondrocyte-derived matrix vesicles in Phospho1/Pit1 double knockout mice. J. Bone Min. Res 31:1275-86. Rodriguez-Florez N, Mukadam Q, Garcia-Tunon E, Saiz E, Oldknow KJ, Farquharson C, Millán JL, Boyde A, Sandra J. Shefelbine SJ (2015) Extremes of toughness: an investigation of the mineral in ductile and brittle mouse bone. J Bone Min Res 30:786-95. Javaheri B, Carriero A, Staines KA, Chang Y-M, Houston DA, Oldknow KJ, Millan JL, Bassir Kazeruni N, Salmon P, Shefelbine S, Farquharson C, Pitsillides, AA (2015) Phospho1 deficiency transiently modifies bone architecture yet produces consistent modification in osteocyte differentiation and vascularization with ageing Bone 81:277-91 Huesa C, Houston D, Kiffer-Moreira T, Yadav MC, Millan JL, Farquharson C (2015) The Functional co-operativity of Tissue-Nonspecific Alkaline Phosphatase (TNAP) and PHOSPHO1 during initiation of Skeletal Mineralization. Biochemistry and Biophysics Reports 4:196-201 Carriero A, Bruse JL, Oldknow KJ, Millán JL, Farquharson C, Shefelbine SJ. (2014) Reference point indentation is not indicative of stress intensity fracture toughness in mouse bone. Bone 69:174-179. Bravo Y, Teriete P, Dhanya R-P, Dahl R, Lee PS, Kiffer-Moreira T, Ganji SR, Sergienko E, Smith LH, Farquharson C, Millán JL, Cosford NDP (2014) Design, Synthesis and Evaluation of Benzoisothiazolones as Selective Inhibitors of PHOSPHO1, Bioorganic & Medicinal Chemistry Letters Bioorg Med Chem Lett 24:4308-11. Yadav MC, Huesa C, Narisawa S, Hoylaerts MF, Moreau A, Farquharson C, Millán JL (2014) Zhu D, Mackenzie NCW, Millan JL, Lerman D, Dweck MR, Newby DE, Farquharson C, MacRae VE (2014). Up-regulation of IGF2 during vascular calcification. J Mol. Endocrinol 52:77-85. Ablation of osteopontin prevents the skeletal deformities in Phospho1-/- mice. J.Bone Min. Res. 29:2369-2381. Huesa C, Zhu D, Glover JD, Ferron M, Karsenty G, Milne EM, Millan JL, Ahmed SF, Farquharson C, Morton NM, MacRae VE. (2014) Deficiency of the bone mineralization inhibitor NPP1 protects against obesity and diabetes. Dis Model Mech. 12:1341-1350 McKee MD, Yadav MC, Foster BL, Somerman MJ, Farquharson C, Millán JL. (2013) Compounded PHOSPHO1/ALPL Deficiencies Reduce Dentin Mineralization. J Dent Res. 92:721-7. Kiffer-Moreira T, Yadav MC, Zhu D, Narisawa S, Sheen C, Stec B, Cosford ND, Dahl R, Farquharson C, Hoylaerts MF, Macrae VE, Millán JL. 2013 Pharmacological inhibition of PHOSPHO1 suppresses vascular smooth muscle cell calcification. J Bone Miner Res. 28:81-91. Zhu D, Mackenzie NC, Millan JL, Farquharson C, Macrae VE 2013 A protective role for FGF-23 in local defence against disrupted arterial wall integrity? Mol Cell Endocrinol. 372(1-2):1-11. Mackenzie NCW, Zhu D, Milne EM, van't Hof R, Martin, A, Quarles, LD, Millán JL, Farquharson C, MacRae VE. 2012 Altered Bone Development and an Increase in FGF-23 Expression in Enpp1-/- mice. PLoS One 7(2):e32177 Zhu D, Mackenzie NCW, Millán JL, Farquharson C, MacRae VE. 2011 The Appearance and Modulation of Osteocyte Marker Expression During Calcification of Vascular Smooth Muscle Cells. PLoS One 6(5): e19595. Huesa C, Yadav MC, Finnilä MAJ, Goodyear SR, Robins SP, Tanner KE, Aspden RM, Millán JL and Farquharson C. 2011 PHOSPHO1 is essential for mechanically competent mineralization and the avoidance of spontaneous fractures. Bone 48:1066-74. Yadav MC, Simão AM, Narisawa S, Huesa C, McKee MD, Farquharson C, Millán JL. 2011 Loss of skeletal mineralization by the simultaneous ablation of PHOSPHO1 and alkaline phosphatase function - A unified model of the mechanisms of initiation of skeletal calcification. J Bone Miner Res. 26:286-297. Ciancaglini P, Yadav MC, Simão AMS Narisawa S, Pizauro JM, Farquharson C, Hoylaerts MF, Millán JL. 2010 Kinetic analysis of substrate utilization by native and TNAP-, NPP1- or PHOSPHO1-deficient matrix vesicles. J Bone Min Res. 25:716-23. Macrae V, Davey M, Mcteir L, Narisawa S, Yadav M, Millan JL, Farquharson C. 2010 Inhibition of PHOSPHO1 activity results in impaired skeletal mineralization during limb development of the chick. Bone. 46:1146-55. Roberts SJ, Narisawa S, Harmey D, Millán JL, Farquharson C 2007. Functional Involvement of PHOSPHO1 in Matrix Vesicle-Mediated Skeletal Mineralization. J Bone Min Res 22:617-627. 2006 - 2011. National Institutes for Health, USA. Mechanisms of initiation of skeletal mineralisation. £1,000,000 |
| Start Year | 2007 |
| Title | Graphia Professional |
| Description | This is a network analysis tool designed for the analysis of biological data. It is a commercial product produced by Kajeka Ltd a company founded on the IP and know how behind BioLayout Express3D. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2015 |
| Open Source License? | Yes |
| Impact | This is the first product of Kajeka Ltd and sales of it will help support the company as it grows. |
| URL | https://kajeka.com/graphia-professional/ |
| Title | Virtually Immune - Pathway Modelling Resource |
| Description | With data and information on biological systems growing quickly, ordering this wealth of knowledge into models has become of paramount importance. This is particularly so in the case of the immune system where the sheer complexity of components, cells and stimuli that can activate or suppress its activity are a hindrance to advancing our understanding of infectious and inflammatory disease. Virtually Immune is a resource that aims to support the graphical and computational modelling of immune pathways. The tools and resources presented here are primarily designed for biologists, both to use and to allow them to develop their own models of systems of interest to them. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | The website and pathway resources supported by it are presented to the community for exploration and reuse. Two papers describing the approach to modelling and how models can be used for simulating the activity of pathways are given below. O'Hara L., Livigni A., Theo T., Boyer B., Angus T., Wright D., Chen S-H., Raza S., Barnett M.W., Digard P., Smith L.B. and Freeman T.C. Modelling the Structure and Dynamics of Biological Pathways. PLoS Biol. 14(8):e1002530 (2016). Livigni A., O'Hara L., Polak, M.E., Angus T., Wright D., Smith L.B. and Freeman T.C. A Graphical and Computational Modelling Platform for Biological Pathways. Nature Protocols 13(4):705-722 (2018). |
| URL | https://www.virtuallyimmune.org/ |
| Company Name | Graphia |
| Description | Graphia develops software that is capable of efficiently analysing and plotting large amounts of data from a variety of sources. The company claims that its software can be used by both experienced data analysts and non-specialist. |
| Year Established | 2014 |
| Impact | The company is still at an early stage in its development but is beginning to gain commercial traction and clients for the software. We have won one Scottish Enterprise grant and have submitted a second for the development of our next generation software. We also secured seed investment of £230k last year. We are collaborating with academic scientists who develop network analysis algorithms or who use network analysis in their work. We have a number of ongoing discussions with major pharmaceutical and platform providers. |
| Website | http://kajeka.com |
| Description | ChickAtlas: a comparative gene expression atlas of the vertebrate embryo |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a research talk "ChickAtlas: a comparative gene expression atlas of the vertebrate embryo" as part of a BARD workshop: affecting early life poultry development to improve domestic flow livestock, Jerusalem, Israel (2011). Aim was to report on novel ways to study chick embryos. Outcome was a number of collaborations. |
| Year(s) Of Engagement Activity | 2011 |
| Description | Chicken genome update, consortia for RNAseq, SNPs and more ... |
| 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 Avian Model Systems 7. Talk: Chicken genome update, consortia for RNAseq, SNPs and more " 14-19 Nov, Nagoya, Japan 2012. |
| Year(s) Of Engagement Activity | 2012 |
| Description | Roslin Institute Open days |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Several hundred children and parents attended a demonstration on "bone" and the "skeleton". This involved participation by the children Great interest from the audience |
| Year(s) Of Engagement Activity | 2010,2011,2012,2013 |
| Description | The 6th International chick meeting, Edinburgh (2011) Avian Genome Evolution |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Organised conference and presented a talk "Avian Genome Evolution" at the 6th International chick meeting, Edinburgh (2011). Aim was to inform, build network, seek collaborations, etc. in the avian research community. Further consortia (e.g. the chicken RNAseq consortium) and projects were created. |
| Year(s) Of Engagement Activity | 2011 |
| Description | The chicken genome 10 years on. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Keynote lecture: chicken genome - 10 years on. Avian Model Systems - the 8th International Meeting, Cold Spring Harbour, USA, 4-8th March, 2014. CSHL Leading Strand - Keynote Lecture Series (http://theleadingstrand.cshl.edu/Course/Keynote/2014/AVIAN/150 The chicken genome 10 years on - BBSRC (http://www.bbsrc.ac.uk/news/events/1403-chicken-genome.aspx) |
| Year(s) Of Engagement Activity | 2014 |
| Description | Transcriptional and Epigenetic Regulation of Seasonal Timing. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited lecture: Transcriptional and Epigenetic Regulation of Seasonal Timing. In "Evolution of seasonal timers". The 64th NIBB Conference, Okazaki Conference Centre, Okazaki, Japan. 22-24 April, 2016. |
| Year(s) Of Engagement Activity | 2016 |