Publications

ARK-Genomics Staff included as a collaborating authors

  1. Schnettler, E., Donald, C.L., Human, S., Watson, M., Siu, R.W., Mcfarlane, M., Fazakerley, J.K., Kohl, A., and Fragkoudis, R. (2013). Knockdown of piRNA pathway proteins results in enhanced Semliki Forest virus production in mosquito cells. J Gen Virol.
  2. Schnettler, E., Ratinier, M., Watson, M., Shaw, A.E., Mcfarlane, M., Varela, M., Elliott, R.M., Palmarini, M., and Kohl, A. (2012). RNA interference targets arbovirus replication in Culicoides cells. J Virol.
  3. Wilkie, G.S., Davison, A.J., Watson, M., Kerr, K., Sanderson, S., Bouts, T., Steinbach, F., and Dastjerdi, A. (2013). Complete genome sequences of elephant endotheliotropic herpesviruses 1A and 1B determined directly from fatal cases. J Virol.
  4. Freeman TC, Ivens A, Baillie JK, Beraldi D, Barnett MW, Dorward D, Downing A, Fairbairn L, Kapetanovic R, Raza S, Tomoiu A, Alberio R, Wu C, Su AI, Summers KM, Tuggle CK, Archibald AL, Hume DA. (2012) A gene expression atlas of the domestic pig. BMC Biol. 10:90. doi: 10.1186/1741-7007-10-90
  5. Hocking PM, Morrice DM, Law AS, Burt DW (2012) Many quantitative trait loci for feather growth in an F(2) broiler × layer cross collocate with body weight loci. Br Poult Sci. 53(2):162-7
  6. Richardson, E. J. & Watson, M. (2012) The automatic annotation of bacterial genomes. Brief Bioinform.
  7. Yao, Y., Smith, L. P., Petherbridge, L., Watson, M. & Nair, V. (2012) Novel microRNAs encoded by duck enteritis virus. J Gen Virol.
  8. Egan, S. A., Ward, P. N., Watson, M., Field, T. R. & Leigh, J. A. (2012) Vru (Sub0144) controls expression of proven and putative virulence determinants and alters the ability of Streptococcus uberis to cause disease in dairy cattle. Microbiology.
  9. Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, Heutink P, Carninci P, Jeddeloh JA, Faulkner GJ (2011). Somatic retrotransposition alters the genetic landscape of the human brain. Nature. 479(7374):534-7
  10. Gunaratne, P. H., Creighton, C. J., Watson, M. & Tennakoon, J. B. (2010) Large-scale integration of MicroRNA and gene expression data for identification of enriched microRNA-mRNA associations in biological systems. Methods Mol Biol, 667, 297-315.
  11. Gunaratne, P. H., Lin, Y. C., Benham, A. L., Drnevich, J., Coarfa, C., Tennakoon, J. B., Creighton, C. J., Kim, J. H., Milosavljevic, A., Watson, M., Griffiths-Jones, S. & Clayton, D. F. (2011) Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain. BMC Genomics, 12, 277.
  12. Harvey, P. C., Watson, M., Hulme, S., Jones, M. A., Lovell, M., Berchieri, A., JNR., Young, J., Bumstead, N. & Barrow, P. (2011) Salmonella enterica serovar Typhimurium colonizing the lumen of the chicken intestine are growing slowly and up-regulate a unique set of virulence and metabolism genes. Infect. Immun., IAI.01390-10.
  13. Mwangi, W. N., Beal, R. K., Powers, C., WU, X., Humphrey, T., Watson, M., Bailey, M., Friedman, A. & Smith, A. L. (2010) Regional and global changes in TCRalphabeta T cell repertoires in the gut are dependent upon the complexity of the enteric microflora. Dev Comp Immunol, 34, 406-17.
  14. Richardson, E. J., Limaye, B., Inamdar, H., Datta, A., Manjari, K. S., Pullinger, G. D., Thomson, N. R., Joshi, R. R., Watson, M. & Stevens, M. P. (2011) Genome Sequences of Salmonella enterica Serovar Typhimurium, Choleraesuis, Dublin, and Gallinarum Strains of Well- Defined Virulence in Food-Producing Animals. J Bacteriol, 193, 3162-3.
  15. Warren W.C., Clayton D.F., Ellegren H., Arnold A.P., Hillier L.W., Künstner A., Searle S., White S., Vilella A.J., Fairley S., Heger A., Kong L., Ponting C.P., Jarvis E.D., Mello C.V., Minx P., Lovell P., Velho T.A., Ferris M., Balakrishnan C.N., Sinha S., Blatti C., London S.E., Li Y., Lin Y.C., George J., Sweedler J., Southey B., Gunaratne P., Watson M., Nam K., Backström N., Smeds L., Nabholz B., Itoh Y., Whitney O., Pfenning A.R., Howard J., Völker M., Skinner B.M., Griffin D.K., Ye L., McLaren W.M., Flicek P., Quesada V., Velasco G., Lopez-Otin C., Puente X.S., Olender T., Lancet D., Smit A.F., Hubley R., Konkel M.K., Walker J.A., Batzer M.A., Gu W., Pollock D.D., Chen L., Cheng Z., Eichler E.E., Stapley J., Slate J., Ekblom R., Birkhead T., Burke T., Burt D., Scharff C., Adam I., Richard H., Sultan M., Soldatov A., Lehrach H., Edwards S.V., Yang S.P., Li X., Graves T., Fulton L., Nelson J., Chinwalla A., Hou S., Mardis E.R., Wilson R.K. (2010) The genome of a songbird. Nature, 464, 757-62.
  16. Widdison, S., Siddiqui, N., Easton, V., Lawrence, F., Ashley, G., Werling, D., Watson, M. & Coffey, T. J. (2010) The bovine chemokine receptors and their mRNA abundance in mononuclear phagocytes. BMC Genomics, 11, 439.
  17. Widdison, S., Watson, M. & Coffey, T. J. (2011) Early response of bovine alveolar macrophages to infection with live and heat-killed Mycobacterium bovis. Dev Comp Immunol, 35, 580-91.
  18. Smith J, Speed D, Hocking PM, Talbot RT, Degen WG, Schijns VE, Glass EJ, Burt DW. Development of a chicken 5 K microarray targeted towards immune function. BMC Genomics. 2006 Mar 13;7:49.
  19. The chicken talpid3 gene encodes a novel protein essential for Hedgehog signaling. Davey MG, Paton IR, Yin Y, Schmidt M, Bangs FK, Morrice DR, Smith TG, Buxton P, Stamataki D, Tanaka M, Münsterberg AE, Briscoe J, Tickle C, Burt DW.Genes Dev. 2006 May 15;20(10):1365-77.
  20. The Talpid3 gene (KIAA0586) encodes a centrosomal protein that is essential for primary cilia formation. Yin Y, Bangs F, Paton IR, Prescott A, James J, Davey MG, Whitley P, Genikhovich G, Technau U, Burt DW, Tickle C. Development. 2009 Feb;136(4):655-64. Epub 2009 Jan 14.
  21. Genini S, Nguyen TT, Malek M, Talbot R, Gebert S, Rohrer G, Nonneman D, Stranzinger G, Vögeli P. Radiation hybrid mapping of 18 positional and physiological candidate genes for arthrogryposis multiplex congenita on porcine chromosome 
  22. Anim Genet.2006 Jun;37(3):239-44. Jensen K, Talbot R, Paxton E, Waddington D, Glass EJ. Development and validation of a bovine macrophage specific cDNA microarray. BMC Genomics. 2006 Sep 1;7:224.
  23. Zhang F, Hopwood P, Abrams CC, Downing A, Murray F, Talbot R, Archibald A, Lowden S, Dixon LK. Macrophage transcriptional responses following in vitro infection with a highly virulent African swine fever virus isolate. J Virol. 2006 Nov;80(21):10514-21.
  24. Analysis of talpid3 and wild-type chicken embryos reveals roles for Hedgehog signalling in development of the limb bud vasculature. Davey MG, James J, Paton IR, Burt DW, Tickle C. Dev Biol. 2007 Jan 1;301(1):155-65. Epub 2006 Aug 10.
  25. A QTL for osteoporosis detected in an F2 population derived from White Leghorn chicken lines divergently selected for bone index. Dunn IC, Fleming RH, McCormack HA, Morrice D, Burt DW, Preisinger R, Whitehead CC. Anim Genet. 2007 Feb;38(1):45-9.
  26. Roe AJ, Tysall L, Dransfield T, Wang D, Fraser-Pitt D, Mahajan A, Constandinou C, Inglis N, Downing A, Talbot R, Smith DG, Gally DL. Analysis of the expression, regulation and export of NleA-E in Escherichia coli O157 : H7. Microbiology. 2007 May;153(Pt 5):1350-60.
  27. Quantitative trait loci for bone traits segregating independently of those for growth in an F2 broiler x layer cross. Sharman PW, Morrice DR, Law AS, Burt DW, Hocking PM. Cytogenet Genome Res. 2007;117(1-4):296-304.
  28. de Koning DJ, Alan Archibald A. and Haley CS Livestock genomics: bridging the gap between mice and men Trends in Biotechnology Volume 25, Issue 11, November 2007, Pages 483-489
  29. Burt DW. Emergence of the Chicken as a Model Organism: Implications for Agriculture and Biology Poult Sci 2007. 86:1460-1471
  30. Martin SA, Taggart JB, Seear P, Bron JE, Talbot R, Teale AJ, Sweeney GE, Høyheim B, Houlihan DF, Tocher DR, Zou J, Secombes CJ. Interferon type I and type II responses in an Atlantic salmon (Salmo salar) SHK-1 cell line by the salmon TRAITS/SGP microarray. Physiol Genomics. 2007 Dec 19;32(1):33-44. Epub 2007 Sep 5.
  31. Jensen K, Paxton E, Waddington D, Talbot R, Darghouth MA, Glass EJ. Differences in the transcriptional responses induced by Theileria annulata infection in bovine monocytes derived from resistant and susceptible cattle breeds. Int J Parasitol. 2008 Mar;38(3-4):313-25. Epub 2007 Sep 18.  
  32. Griffin DK, Robertson LB, Tempest HG, Vignal A, Fillon V, Crooijmans RP, Groenen MA, Deryusheva S, Gaginskaya E, Carré W, Waddington D, Talbot R, Völker M, Masabanda JS, Burt DW. Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution. BMC Genomics. 2008 Apr 14;9:168.
  33. Anderson CA, Maclean A, Dunnigan MG, Pelosi AJ, Murray V, McKee I, McDonald G, Burt DW, Morrice DR, Muir WJ, Visscher PM, Blackwood DH. A genome-wide linkage study in families with major depression and co-morbid unexplained swelling. Am J Med Genet B Neuropsychiatr Genet. 2008 Apr 5;147(3):356-62.
  34. Taggart JB, Bron JE, Martin SA, Seear PJ, Høyheim B, Talbot R, Carmichael SN,  Villeneuve LA, Sweeney GE, Houlihan DF, Secombes CJ, Tocher DR, Teale AJ. A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray. J Fish Biol. 2008 Jun;72(9):2071-2094.
  35. Dupré SM, Burt DW, Talbot R, Downing A, Mouzaki D, Waddington D, Malpaux B, Davis JR, Lincoln GA, Loudon AS. Identification of melatonin-regulated genes in the ovine pituitary pars tuberalis, a target site for seasonal hormone control. Endocrinology. 2008 Nov;149(11):5527-39. Epub 2008 Jul 31.  
  36. Forsyth NR, Kay A, Hampson K, Downing A, Talbot R, McWhir J. Transcriptome alterations due to physiological normoxic (2% O2) culture of human  embryonic stem cells. Regen Med. 2008 Nov;3(6):817-33.
  37. Identification of chromosomal regions associated with growth and carcass traits in an F full sib intercross line originating from a cross of chicken lines divergently selected on body weight. Ter?i? D, Holcman A, Dov? P, Morrice DR, Burt DW, Hocking PM, Horvat S. Anim Genet. 2009 May 16. [Epub ahead of print]
  38. Graham G., Sharp PJ, Li Q., Wilson PW., Talbot RT, Downing AC. and Boswell T. HSP90B1, a thyroid hormone-responsive heat shock protein gene involved in photoperiodic signalling Brain Research Bulletin Volume 79, Issues 3-4, 29 May 2009, Pages 201-207
  39. Ait-Ali T, Wilson AW, Finlayson H, Carré W, Ramaiahgari SC, Westcott DG, Waterfall M, Frossard JP, Baek KH, Drew TW, Bishop SC, Archibald AL. Functional analysis of the porcine USP18 and its role during porcine arterivirus replication. Gene. 2009 Jun 15;439(1-2):35-42. Epub 2009 Mar 11. 
  40. New hypotheses on the function of the avian shell gland derived from microarray analysis comparing tissue from juvenile and sexually mature hens. Dunn IC, Wilson PW, Lu Z, Bain MM, Crossan CL, Talbot RT, Waddington D. Gen Comp Endocrinol. 2009 Sep 1;163(1-2):225-32. Epub 2009 Mar 20.      
  41. Seear PJ, Carmichael SN, Talbot R, Taggart JB, Bron JE, Sweeney GE. Differential Gene Expression During Smoltification of Atlantic Salmon (Salmo salar L.): a First Large-Scale Microarray Study Mar Biotechnol (NY). 2009 Jul 8. [Epub ahead of print]
 
Publications with ARK-Genomics (acknowledged) contributions
  1. Gunn-Moore FJ, Hill M, Davey F, Herron LR, Tait S, Sherman D, Brophy PJ. A functional FERM domain binding motif in neurofascin. Mol Cell Neurosci. 2006 Dec;33(4):441-6. Epub 2006 Oct 12
  2. aman M. Das, Nick J. Van Hateren, Gareth R. Howell, Elizabeth R. Farrell, Fiona K. Bangs, Victoria C. Porteous, Elizabeth M. Manning, Michael J. McGrew, Kyoji Ohyama, Melanie A. Sacco, Pam A. Halley, Helen M. Sang, Kate G. Storey, Marysia Placzek, Cheryll Tickle, Venugopal K. Nair and Stuart A. Wilson A robust system for RNA interference in the chicken using a modified microRNA operon  Developmental Biology Volume 294, Issue 2, 15 June 2006, Pages 554-563     
  3. Construction of a normalized Bos taurus and Bos indicus macrophage-specific cDNA library K. Jensen, D. Speed, E. Paxton, J. L. Williams and E. J. Glass  Animal Genetics Volume 37, Issue 1, Pages 75-77      
  4. Eva Tiecke, Fiona Bangs, Rudiger Blaschke, Elizabeth R. Farrell, Gudrun Rappold and Cheryll Tickle, Expression of the short stature homeobox gene Shox is restricted by proximal and distal signals in chick limb buds and affects the length of skeletal elements  Developmental Biology Volume 298, Issue 2, 15 October 2006, Pages 585-596      
  5. Gene expression profiling of hereditary exencephaly in chickens Jaszczak, K. - Sazanov, A. A. - Sacharczuk, M. - Korczak, M. - Sazanova, A. L. - Parada, R. - Malewski, T. Animal Genetics Volume 37, Issue 3, Pages 253-257      
  6. Guo H, Liu WS, Takasuga A, Eyer K, Landrito E, Xu SZ, Gao X, Ren HY. Mapping of the CCK, PSMC2, PSMC4, PSMD1, CPB1 and PSPH genes in cattle. Anim Genet. 2006 Feb;37(1):73-5.      
  7. Hämmerle B, Tejedor FJ  A novel function of DELTA-NOTCH signalling mediates the transition from proliferation to neurogenesis in neural progenitor cells. PLoS One. 2007 Nov 14;2(11):e1169.     
  8. Del Barrio MG, Taveira-Marques R, Muroyama Y, Yuk DI, Li S, Wines-Samuelson M, Shen J, Smith HK, Xiang M, Rowitch D, Richardson WD. A regulatory network involving Foxn4, Mash1 and delta-like 4/Notch1 generates V2a and V2b spinal interneurons from a common progenitor pool. Development. 2007 Oct;134(19):3427-36. Epub 2007 Aug 29.      
  9. Jaffrézic F, de Koning DJ, Boettcher PJ, Bonnet A, Buitenhuis B, Closset R, Déjean S, Delmas C, Detilleux JC, Dovc P, Duval M, Foulley JL, Hedegaard J, Hornshøj H, Hulsegge I, Janss L, Jensen K, Jiang L, Lavric M, Lê Cao KA, Lund MS, Malinverni R, Marot G, Nie H, Petzl W, Pool MH, Robert-Granié C, San Cristobal M, van Schothorst EM, Schuberth HJ, Sørensen P, Stella A, Tosser-Klopp G, Waddington D, Watson M, Yang W, Zerbe H, Seyfert HM. Analysis of the real EADGENE data set: comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (open access publication). Genet Sel Evol. 2007 Nov-Dec;39(6):633-50. Epub 2007 Dec 6.      
  10. Szczerbal I, Chmurzynska A, Switonski M. Cytogenetic mapping of eight genes encoding fatty acid binding proteins (FABPs) in the pig genome. Cytogenet Genome Res. 2007;118(1):63-6.     
  11. Graham A, Blentic A, Duque S, Begbie J. Delamination of cells from neurogenic placodes does not involve an epithelial-to-mesenchymal transition. Development. 2007 Dec;134(23):4141-5. Epub 2007 Oct 24.      
  12. Nimmagadda S, Geetha-Loganathan P, Pröls F, Scaal M, Christ B, Huang R. Expression pattern of Dll4 during chick embryogenesis. Histochem Cell Biol. 2007 Aug;128(2):147-52. Epub 2007 Jun 29.     
  13. Wathes DC, Fenwick M, Cheng Z, Bourne N, Llewellyn S, Morris DG, Kenny D, Murphy J, Fitzpatrick R. Influence of negative energy balance on cyclicity and fertility in the high producing dairy cow. Theriogenology. 2007 Sep 1;68 Suppl 1:S232-41. Epub 2007 May 2. Review.     
  14. Wathes DC, Abayasekara DR, Aitken RJ. Polyunsaturated fatty acids in male and female reproduction. Biol Reprod. 2007 Aug;77(2):190-201. Epub 2007 Apr 18. Review.      
  15. J.-F. Hocquette, S. Lehnert, W. Barendse, I. Cassar-Malek and B. Picard  Recent advances in cattle functional genomics and their application to beef quality animal, Volume 1, Issue 01, February 2007, pp 159-173      
  16. Glass EJ, Jensen K. Resistance and susceptibility to a protozoan parasite of cattle--gene expression differences in macrophages from different breeds of cattle. Vet Immunol Immunopathol. 2007 Nov 15;120(1-2):20-30. Epub 2007 Jul 25. Review.     
  17. Hytönen VP, Määttä JA, Niskanen EA, Huuskonen J, Helttunen KJ, Halling KK, Nordlund HR, Rissanen K, Johnson MS, Salminen TA, Kulomaa MS, Laitinen OH, Airenne TT. Structure and characterization of a novel chicken biotin-binding protein A (BBP-A). BMC Struct Biol. 2007 Mar 7;7:8.     
  18. Twine R. Thinking across species--a critical bioethics approach to enhancement. Theor Med Bioeth. 2007;28(6):509-23.      
  19. Cogburn LA., Porter TE.,  Duclos MJ, Simon J., Burgess SC., Zhull JJ, Cheng HH., J. Dodgson JB. and Burnside J. Functional Genomics of the Chicken—A Model Organism Poult Sci 2007. 86:2059-2094      
  20. Genetical Genomics: Combining Gene Expression with Marker Genotypes in Poultry D. J. de Koning, C. P. Cabrera and C. S. Haley  Poult Sci 2007. 86:1501-1509      
  21. Ben-Yair R, Kalcheim C. Notch and bone morphogenetic protein differentially act on dermomyotome cells to generate endothelium, smooth, and striated muscle. J Cell Biol. 2008 Feb 11;180(3):607-18.      
  22. Malashichev Y, Christ B, Pröls F. Avian pelvis originates from lateral plate mesoderm and its development requires signals from both ectoderm and paraxial mesoderm. Cell Tissue Res. 2008 Mar;331(3):595-604. Epub 2007 Dec 18.      
  23. Szczerbal I, Chmurzynska A. Chromosomal localization of nine porcine genes encoding transcription factors involved in adipogenesis. Cytogenet Genome Res. 2008;121(1):50-4. Epub 2008 May 7.      
  24. Antonio Abellán and Loreta Medina Expression of cLhx6 and cLhx7/8 suggests a pallido-pedunculo-preoptic origin for the lateral and medial parts of the avian bed nucleus of the stria terminalis Brain Research BulletinVolume 75, Issues 2-4, 18 March 2008, Pages 299-304     
  25. Towers M, Mahood R, Yin Y& Tickle C Integration of growth and specification in chick wing digit-patterning Nature 452, 882-886 (17 April 2008)  
  26. Fisher ME, Clelland AK, Bain A, Baldock RA, Murphy P, Downie H, Tickle C, Davidson DR, Buckland RA. Integrating technologies for comparing 3D gene expression domains in the developing chick limb. Dev Biol. 2008 May 1;317(1):13-23. Epub 2008 Feb 7.     
  27. Leaver MJ, Villeneuve LA, Obach A, Jensen L, Bron JE, Tocher DR, Taggart JB. Functional genomics reveals increases in cholesterol biosynthetic genes and highly unsaturated fatty acid biosynthesis after dietary substitution of fish oil with vegetable oils in Atlantic salmon (Salmo salar). BMC Genomics. 2008 Jun 24;9:299.     
  28. Triana-Baltzer GB, Liu Z, Gounko NV, Berg DK. Multiple cell adhesion molecules shaping a complex nicotinic synapse on neurons. Mol Cell Neurosci. 2008 Sep;39(1):74-82. Epub 2008 Jun 4.      
  29. Jensen K., de Miranda Santos IKF and Glass EJ Using genomic approaches to unravel livestock (host)–tick–pathogen interactions Trends in Parasitology Volume 23, Issue 9, September 2007, Pages 439-444                 
  30. Marín F, Aroca P, Puelles L. Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Dev Biol. 2008 Nov 15;323(2):230-47. Epub 2008 Aug 27.      
  31. S. Druyan, J. E. de Oliveira and C. M. Ashwell Focused Microarrays as a Method to Evaluate Subtle Changes in Gene Expression Poult Sci 2008. 87:2418-2429      
  32. Mende M, Christophorou NA, Streit A. Specific and effective gene knock-down in early chick embryos using morpholinos but not pRFPRNAi vectors. Mech Dev. 2008 Nov-Dec;125(11-12):947-62. Epub 2008 Sep 3.      
  33. Watkins C, McKellar A, Jensen K, George A, Jones D, Sharp MJ, Stevenson K, Hopkins J. Development and validation of an oligonucleotide microarray for immuno-inflammatory genes of ruminants. Vet Res Commun. 2008 Dec;32(8):647-57. Epub 2008 Jun 20.      
  34. Le Bihan-Duval E., Berri C., Pitel F., Nadaf J., Sibut V., Gigaud V. and Duclos M Approches combinées de génomique positionnelle et expressionnelle pour l’étude des gènes contrôlantla qualité de la viande chez les volailles INRA Prod. Anim.,2008, 21 (2), 159-166      
  35. Désert C, Duclos MJ, Blavy P, Lecerf F, Moreews F, Klopp C, Aubry M, Herault F, Le Roy P, Berri C, Douaire M, Diot C, Lagarrigue S. Transcriptome profiling of the feeding-to-fasting transition in chicken liver. BMC Genomics. 2008 Dec 17;9:611.      
  36. Wastling JM, Xia D, Sohal A, Chaussepied M, Pain A, Langsley G. Proteomes and transcriptomes of the Apicomplexa – Where’s the message? International Journal for Parasitology Volume 39, Issue 2, 15 January 2009, Pages 135-143      
  37. Gossner AG.  and Hopkins J. Incremental generation of an EST set for the analysis of scrapie pathogenesis Small Ruminant Research Volume 81, Issue 1, January 2009, Pages 75-78      
  38. Wang Y, Sun H, Shen P, Zhang X, Xia X, Xia B. Effective inhibition of replication of infectious bursal disease virus by miRNAs delivered by vectors and targeting the VP2 gene. J Virol Methods. 2009 Jan 31. [Epub ahead of print]      
  39. Clinically failed eggs as a source of normal human embryo stem cells. De Sousa PA, Gardner J, Sneddon S, Pells S, Tye BJ, Dand P, Collins DM, Stewart K, Shaw L, Przyborski S, Cooke M, McLaughlin KJ, Kimber SJ, Lieberman BA, Wilmut I, Brison DR. Stem Cell Res. 2009 Feb 6. [Epub ahead of print]      
  40. Entrican G, Lunney JK, Rutten VP, Baldwin CL. A current perspective on availability of tools, resources and networks for veterinary immunology Vet Immunol Immunopathol. 2009 Mar 15;128(1-3):24-9. Epub 2008 Oct 17      
  41. Powell F, Lawson M, Rothwell L, Kaiser P.  Development of reagents to study the turkey's immune response: Identification and molecular cloning of turkey CD4, CD8alpha and CD28. Dev Comp Immunol. 2009 Apr;33(4):540-6. Epub 2008 Nov 12      
  42. Sánchez-Guardado LO, Ferran JL, Mijares J, Puelles L, Rodríguez-Gallardo L, Hidalgo-Sánchez M. Raldh3 gene expression pattern in the developing chicken inner ear. J Comp Neurol. 2009 May 1;514(1):49-65.      
  43. Wang Y, Sun H, Shen P, Zhang X, Xia X. Effective inhibition of infectious bursal disease virus replication by recombinant avian adeno-associated virus-delivered microRNAs. J Gen Virol. 2009 Jun;90(Pt 6):1417-22. Epub 2009 Mar 4.      
  44. Hu X, Gao Y, Feng C, Liu Q, Wang X, Du Z, Wang Q, Li N. Advanced technologies for genomic analysis in farm animals and its application for QTL mapping. Genetica. 2009 Jun;136(2):371-86. Epub 2008 Dec 18. Review.      
  45. Hu X, Yu Gao Y, Feng C, Liu Q, o Wang X, Du Z, Wang Q and Li N Advanced technologies for genomic analysis in farm animals and its application for QTL mapping Journal Genetica  Volume 136, Number 2 / June, 2009      
  46. Wathes DC, Cheng Z, Chowdhury W, Fenwick MA, Fitzpatrick R, Morris DG, Patton J, Murphy JJ. Negative energy balance alters global gene expression and immune responses in the uterus of postpartum dairy cows. Physiol Genomics. 2009 Jun 30. [Epub ahead of print]      
  47. Hedegaard J, Arce C, Bicciato S, Bonnet A, Buitenhuis B, Collado-Romero M, Conley LN, Sancristobal M, Ferrari F, Garrido JJ, Groenen MA, Hornshøj H, Hulsegge I, Jiang L, Jiménez-Marín A, Kommadath A, Lagarrigue S, Leunissen JA, Liaubet L, Neerincx PB, Nie H, Poel J, Prickett D, Ramirez-Boo M, Rebel JM, Robert-Granié C, Skarman A, Smits MA, Sørensen P, Tosser-Klopp G, Watson M. Methods for interpreting lists of affected genes obtained in a DNA microarray experiment. BMC Proc. 2009 Jul 16;3 Suppl 4:S5.      
  48. Neerincx PB, Casel P, Prickett D, Nie H, Watson M, Leunissen JA, Groenen MA, Klopp C. Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis. BMC Proc. 2009 Jul 16;3 Suppl 4:S1.      
  49. Neerincx PB, Rauwerda H, Nie H, Groenen MA, Breit TM, Leunissen JA. OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity. BMC Proc. 2009 Jul 16;3 Suppl 4:S4.      
  50. Szczerbal I, Foster HA, Bridger JM. The spatial repositioning of adipogenesis genes is correlated with their expression status in a porcine mesenchymal stem cell adipogenesis model system. Chromosoma. 2009 Jul 8. [Epub ahead of print]      
  51. Abellán A, Medina L. Subdivisions and derivatives of the chicken subpallium based on expression of LIM and other regulatory genes and markers of neuron subpopulations during development. J Comp Neurol. 2009 Aug 1;515(4):465-501.
 
Meeting Abstracts
  1. Optimisation of print buffer and processing protocols for use on both contact and non-contact microarrayers. Alison Downing1, Stephen Carmichael1, Susan Seaton2, Richard Talbot1 Advances in Microarray Technology 3rd Annual meeting; Edinburgh 2007      
  2. Production of Farm Animal Microarrays Alison Downing, Stephen Carmichael, Sarah Smith, Dave Burt, Alan Archibald and Richard Talbot, 3rd International Symposium of Farm Animal Genomics, Edinburgh 2008      
  3. Synthesising Technologies for Microarray Quality Optimisation – Dr Karen Allison, Alison Downing, Katie McDaniel  Advances in Microarray Technology 4th meeting; Barcelona 2008      
  4. Investigating the ovine abomasal response to Teladorsagia circumcincta challenge Pamela A. Knight, Alan D. Pemberton, Susan E. Griffith, Judith M. Pate, Richard T. Talbot, Sarah Smith, David Waddington, Alan L. Archibald., W. David Smith, Ivan W. Morrison and Hugh R.P. Miller AVTRW conference March 2008 York      
  5. The innate immune response of the ovine abomasal mucosa to the gastric nematode Teladorsagia circumcincta; novel findings from gene expression profiling. Pamela A. Knight, Susan E. Griffith, Alan D. Pemberton, Jeremy K. Brown, Judith M. Pate, Richard T. Talbot, Sarah Smith, David Waddington, Alan L. Archibald., W. David Smith, Hugh R.P. Miller and Ivan W. Morrison AVTRW conference March 2009 York      
  6. Producing a meaningful picture of microarray data through statistics D.Mouzaki, R. Talbot, D. Waddington 3rd International Symposium of Farm Animal Genomics, Edinburgh 2008      
  7. Polymorphism Detection Strategies David Morrice, Dawn Windsor, Karen Troup, Caroline Gilhooly, Dave Burt and Richard Talbot. 3rd International Symposium of Farm Animal Genomics, Edinburgh 2008      
  8. Production of sheep cDNA microarray Sarah Smith, David W Smith, Pam Knight, Alison Downing, Stephen Carmichael, Richard Talbot, Alan Archibald 3rd International Symposium of Farm Animal Genomics, Edinburgh 2008      
  9. EST clones for Farm Animals Stephen Carmichael, Caroline Gilhooly, Karen Troup, David Morrice, Mark Fell, Dave Burt, Alan Archibald and Richard Talbot 3rd International Symposium of Farm Animal Genomics, Edinburgh 2008      
  10. Transcriptomic analysis of Atlantic salmon (Salmo salar) head kidney cells infected with infectious pancreatic necrosis virus William Starkey, James Bron, John Taggart, Jacqueline Ireland, Tony Ellis, Richard Talbot, Stephen Carmichael, Randolph Richards, Alan Teale 3rd International Symposium of Farm Animal Genomics, Edinburgh 2008      
  11. K. Jensen, R. Talbot, D. Waddington and E.J. Glass Monocytes from disease resistant and susceptible cattle display distinct transcriptome profiles during Theileria annulata infection Veterinary Immunology and Immunopathology Volume 128, Issues 1-3, 15 March 2009, Page 216      
  12. Efstathios S. Giotis, Dave W. Burt, Alistair N.J. Scott, Alison Downing, Richard T. Talbot, Lisa Rothwell, Pete Kaiser, Elizabeth J. Glass and Daniel Todd Transcriptomic analysis of the Chicken Anaemia Virus (CAV)-induced immunosuppression Veterinary Immunology and Immunopathology Volume 128, Issues 1-3, 15 March 2009, Page 244
 
Conference proceedings including ARK-Genomics work
  1. Towards a molecular genetic tool for health and performance monitoring of Atlantic salmon (Salmo salar): The TRAITS 17K cDNA microarray  A.J. Teale, A.L. Archibald, J.E. Bron, D.W. Burt, D.F. Houlihan, B. Høyheim, S.A.M. Martin, F.D. Murray, C.J. Secombes, P.J. Seear, G.E. Sweeney, J.B. Taggart, R. Talbot, D.R. Tocher and X. Zheng Aquaculture Volume 272, Supplement 1, 2007, Pages S313-S314      
  2. Tatjana Sjakste and Ziedonis Gr?slis Contributions of genomics and bioinformatics in animal breeding 12 TH BALTIC ANIMAL BREEDING CONFERENCE (2007) Pascual-Font, A.; Merchan, A.; Maranillo, E.; Brillas, J.; Sanudo, J. R.; Valderrama-Canales, F. J. Morphometry of the recurrent laryngeal nerves of the rat Journal of Anatomy. 210(5):624, May 2007.      
  3. de Koning DJ, Jaffrézic F, Lund MS, Watson M, Channing C, Hulsegge I, Pool MH, Buitenhuis B, Hedegaard J, Hornshøj H, Jiang L, Sørensen P, Marot G, Delmas C, Lê Cao KA, San Cristobal M, Baron MD, Malinverni R, Stella A, Brunner RM, Seyfert HM, Jensen K, Mouzaki D, Waddington D, Jiménez-Marín A, Pérez-Alegre M, Pérez-Reinado E, Closset R, Detilleux JC, Dovc P, Lavric M, Nie H, Janss L The EADGENE Microarray Data Analysis Workshop (Open Access publication) Genet. Sel. Evol. 39 (2007) 621-631      
  4. Colette Désert, Pierre Blavy, Francois Moreews, Michel Duclos, Pascale Leroy, Madeleine Douaire and Christian Diot  Transcriptome Profiling Of Feeding-To-Fasting Transition In Chicken Liver Using A Chicken 20K Oligo Microarray International Plant & Animal Genomes XVI Conference (2008)  
  5. Tamsyn M Crowley, Volker R Haring, Simon Burggraaf  and Robert J Moore Application of chicken microarrays for gene expression analysis in other avian species BMC Genomics 2009, 10(Suppl 2):S3      
  6. Christophe Klopp, Francois Moreews, Marc Aubry, Sandrine Lagarrigue Contribution To The Annotations Of The Chicken 20K Oligo Microarray Of ARK-Genomics International Plant & Animal Genomes XVI Conference (2008)      
  7. T. Acamovic and AJ Cowieson The effect of xylanase, amylase and protease on the metabolisable energy of various varieties of maize when precision-fed to broiler chickens British Poultry Abstracts Volume 4, Number 1, (April 2008), 1—36   
       
Books 
  1. Burt DW The Chicken Genome Vertebrate Genomes; Karger, 2006, vol 2, pp 123-137      
  2. Tatjana Sauka-Spenglera and Meyer Barembauma  Gain-and loss-of-function approaches in the chick embryo (Chapter 12) Methods in Cell Biology.Volume 87, Edition: 2 - 2008 -Pages 237-256   Avian Embryology, 2008 (chapter 12)      
  3. Laura S Gammill and Vivian M Lee  Gene Discovery: Macroarrays and Microarrays (Chapter 16) Methods in Cell Biology.Volume 87, Edition: 2 - 2008 -    
  4. Ivor Mason  The Avian Embryo Molecular Embryology ISSN 1064-3745 (Print) 1940-6029 (Online)  Volume Volume 461      
  5. Nick J. Van Hateren, Rachel S. Jones and Stuart A. Wilson  RNA Interference in Chicken Embryos Electroporation and Sonoporation in Developmental Biology 2009 Springer Japan   
       
News Items  
  1. S.LAGARRIGUE and  M. DUCLOS Evaluation of the eQTL (expression QTL) approach to identify genesresponsible for quantitative trait variation Séminaire AGENAE / GENANIMAL 2007 15-16 octobre au VVF Dourdan (91)Bilan des projets GENANIMAL 2003-2006     
  2. M. G. Diskin, S. Childs , D. A. Kenny, and J. M. Sreenan Studies relating to Polyunsaturated Fatty Acid (PUFA) Supplementation and Fertility in Cattle TAEGASC report 2008: http://www.teagasc.ie/research/reports/sheep/5358/eopr-5358.asp     
  3. Tracey Duncombe, BBSRC and Professor Alan Teale,University of Stirling FISH AND DNA CHIPS AQUACULTURE HEALTH International ISSUE 7 NOVEMBER 2006    
  4. Suryakant Mishra Current Status and Research Priorities inPoultry Biotechnology to 2020 Poultry Research Priorities to 2020, 2006 – Citeseer    
  5. Christine Silvy L’agriculture sur Internet   Cahiers Agricultures. Volume 16, Number 3, Mai-Juin 2007   
    
Other Publications          
  1. Jessica Lynn Read Snyder (North Carolina State University) Genomic Analysis of the Influence of Selenium Sources in Broiler Chickens Challenged with an Enteric Avian Reovirus Thesis (MSc, North Carolina State University) 2009     
  2. Michel de Haan, Debbie Wilhelmus, Ingrid van Dixhoorn, Roel Veerkamp, Rita Hoving en Mari Smits How can genomics add value in dairy cattle farming? Areas where innovative genomics solutions are welcomed, will be used to focus genomics research Applied genomics in dairy cattle farming   Perspectief voor genomica in de melkveehouderij (2008) Rapport 126     
  3. Tomi Jukkola (University of Helsinki) FGFR1 regulated gene-expression, cell proliferation and differentiation in the developing midbrain and hindbrain Dissertationes bioscientiarum molecularium Universitatis Helsingiensis in Viikki 17/2007