Publications

Agricultural publications

Bioinformatics McCarthy F. M., et al. AgBase: supporting functional modeling in agricultural organisms. Nucleic Acids Research 39(suppl 1):D497-506 (2011).

Ogata Y., Suzuki H., Sakurai N., Shibata D. CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics 26(9):1267-8 (2010).

Baginsky S., Hennig L., Zimmermann P., Gruissem W. Gene expression analysis, proteomics, and network discovery. Plant Physiology 152:402-10 (2010).

Mochida K., Shinozaki K. Genomics and bioinformatics resources for crop improvement. Plant and Cell Physiology 51(4):497–523 (2010).

Zeisel A., Amir A., Köstler W. J., Domany E. Intensity dependent estimation of noise in microarrays improves detection of differentially expressed genes. BMC Bioinformatics 11:400 (2010).

Sakurai N., et al. KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Research 39(suppl 1):D677-84 (2011).

Watson-Haigh N. S., Kadarmideen H. N., Reverter A. PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches. Bioinformatics 26(3):411-3 (2010).

Lohse M., et al. Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis. Plant Physiology 153(2):642-51 (2010).

Dai X., et al. TrichOME: a comparative omics database for plant trichomes. Plant Physiology 152(1):44–54 (2010).

Multiple organisms Oikawa A., et al. An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development. PLoS One 5(11):e15481 (2010).

Narsai R., Castleden I., Whelan J. Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana. BMC Plant Biology 10:262 (2010).

Dinkins, R. D., Barnes A., Waters W. Microarray analysis of endophyte-infected and endophyte-free tall fescue. Journal of Plant Physiology 167(14):1197-1203 (2010).

Anopheles/Plasmodium White B. J. Ecological genomics of the malaria mosquito Anopheles gambiae. PhD dissertation, University of Notre Dame (2010).

White B. J., Cheng C., Simard F., Costantini C., Besansky N. Genetic association of physically unlinked islands of genomic divergence in incipient species of Anopheles gambiae. Molecular Ecology 19(5):925–39 (2010).

Mu J., et al. Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs. Nature Genetics 42(3):268-71 (2010).

Arabidoposis Das, Ma., et al. A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and Brassica napus. Plant Molecular Biology 72(4-5):545-56 (2010).

Seymour G. B., et al. A SEPALLATA gene is involved in the development and ripening of strawberry (Fragaria×ananassa Duch.) fruit, a non-climacteric tissue. Journal of Experimental Botany. Published online November 29, 2010. doi:10.1093/jxb/erq360.

Kato N., He H., Steger A. P. A systems model of vesicle trafficking in Arabidopsis pollen tubes. Plant Physiology 152(2):590–601 (2010).

Rehrauer H. et al. AGRONOMICS1: A new resource for Arabidopsis transcriptome profiling. Plant Physiology 152(2):487-99 (2010).

Gilding E. K., Marks M. D. Analysis of purified glabra3-shapeshifter trichomes reveals a role for NOECK in regulating early trichome morphogenic events. Plant Journal 64(2):304-17 (2010).

Truman W. M., Bennett M. H., Turnbull C. G. N., Grant M. R. Arabidopsis auxin mutants are compromised in systemic acquired resistance and exhibit aberrant accumulation of various indolic compounds. Plant Physiology 152:1562-73 (2010).

Li L., Ye H., Guo H., Yin Y. Arabidopsis IWS1 interacts with transcription factor BES1 and is involved in plant steroid hormone brassinosteroid regulated gene expression. Proceedings of the National Academy of Sciences of the United States of America 107(8):3918–23 (2010).

Zakrzewska-Placzek M., Souret F. F., Sobczyk G. J., Green P. J., Kufel J. Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA. Nucleic Acids Research 38(13):4487-502 (2010).

Matsui A, et al. Arabidopsis tiling array analysis to identify the stress-responsive genes. Methods in Molecular Biology 639:141-55 (2010).

Borghi L., et al. Arabidopsis RETINOBLASTOMA-RELATED is required for stem cell maintenance, cell differentiation, and lateral organ production. Plant Cell 22:1792-811 (2010).

Liu J.-X., Howell S. H. bZIP28 and NF-Y transcription factors are activated by ER stress and assemble into a transcriptional complex to regulate stress response genes in Arabidopsis. Plant Cell 22:782-96 (2010).

Ruhlmann J. M., Kram B. W., Carter C. J. CELL WALL INVERTASE 4 is required for nectar production in Arabidopsis. Journal of Experimental Botany 61(2):395-404 (2010).

Chen K., Zhang Y., Tang T., Shi S. Cis-regulatory change and expression divergence between duplicate genes formed by genome duplication of Arabidopsis thaliana. Chinese Science Bulletin 55(22):2359-65 (2010).

Hannah M. A., et al. Combined transcript and metabolite profiling of Arabidopsis grown under widely variant growth conditions facilitates the identification of novel metabolite-mediated regulation of gene expression. Plant Physiology 152:2120-9 (2010).

Tsuchiya T., Eulgem T. Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana development. BMC Plant Biology (10):203 (2010).

Liu D., et al. cpSecA, a thylakoid protein translocase subunit, is essential for photosynthetic development in Arabidopsis. Journal of Experimental Botany 61(6):1655-69 (2010).

Rowe H. C., et al. Deficiencies in jasmonate-mediated plant defense reveal quantitative variation in Botrytis cinerea pathogenesis. PLoS Pathogens 6(4):e1000861 (2010).

Pantelides I. S., Tjamos S. E., Paplomatas E. J. Ethylene perception via ETR1 is required in Arabidopsis infection by Verticillium dahlia. Molecular Plant Pathology 11(2):191–202 (2010).

Kleindt C. K., Stracke R., Mehrtens F., Weisshaar B. Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Research Notes 3:255 (2010).

Juenger T. E., et al. Exploring genetic and expression differences between physiologically extreme ecotypes: comparative genomic hybridization and gene expression studies of Kas-1 and Tsu-1 accessions of Arabidopsis thaliana. Plant, Cell & Environment 33(8):1268-84 (2010).

Okamoto M. Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays. Plant Journal 62(1):39-51 (2010).

Le B. H., et al. Global analysis of gene activity during Arabidopsis seed development and identification of seed- specific transcription factors. Proceedings of the National Academy of Sciences of the United States of America 107(18):8063-70 (2010).

Laubinger S., et al. Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome. Proceedings of the National Academy of Sciences of the United States of America. 107(41):17466–73 (2010).

Streitner C., Hennig L., Korneli C., Staiger D. Global transcript profiling of transgenic plants constitutively overexpressing the RNA-binding protein AtGRP7. BMC Plant Biology 10:221 (2010).

Xiao Y. L., et al. High throughput generation of promoter reporter (GFP) transgenic lines of low expressing genes in Arabidopsis and analysis of their expression patterns. Plant Methods 6:18 (2010).

Licausi F., et al. HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana. The Plant Journal 62(2):302–15 (2010).

Drews G. N., Wang D., Steffen J. G., Schumaker K. S., Yadegari R. Identification of genes expressed in the angiosperm female gametophyte. Journal of Experimental Botany. Published online November 39, 2010. doi:10.1093/jxb/erq385.

Kinoshita N., et al. Identification of growth insensitive to ABA3 (gia3), a recessive mutation affecting ABA signaling for the control of early post-germination growth in Arabidopsis thaliana. Plant and Cell Physiology 51(2):239-51 (2010).

Xiao Y., Yu X., Chen J., Di P., Chen W., Zhang L. IiSDD1, a gene responsive to autopolyploidy and environmental factors in Isatis indigotica. Molecular Biology Reports 37(2):987-94 (2010).

Larue C. T., Wen J., Walker J. C. Interactions between a NAC-domain transcription factor and the putative small protein encoding DVL/ROT gene family. Plant Molecular Biology Reporter 28(1):162-8 (2010).

Sun Y., et al. Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis. Developmental Cell 19(5):765-77 (2010).

Nelson D. C., et al. Karrikins enhance light responses during germination and seedling development in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 107(15):7095-100 (2010).

Chandran D., Inada N., Hather G., Kleindt, C. K. Wildermuth M. C. Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators. Proceedings of the National Academy of Sciences of the United States of America 107(1):460-5 (2010).

Jülke, S., Ludwig-Müller, J. Modulation of lipid transfer proteins alters clubroot development in Arabidopsis thaliana. Acta Horticulturae 867:165-72 (2010).

Wang Y.-H., Warren J. T., Jr. Mutations in retrotransposon AtCOPIA4 compromises resistance to Hyaloperonospora parasitica in Arabidopsis thaliana. Genetics and Molecular Biology 33(1):135-40 (2010).

Yant L., et al. Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2. The Plant Cell 22(7):2156-70 (2010).

Sharabi-Schwager M., Lers A., Samach A., Guy C. L., Porat R. Overexpression of the CBF2 transcriptional activator in Arabidopsis delays leaf senescence and extends plant longevity. Journal of Experimental Botany 61(1):261-73 (2010).

Sharabi-Schwager M., Samach A, Porat R. Overexpression of the CBF2 transcriptional activator in Arabidopsis suppresses the responsiveness of leaf tissue to the stress hormone ethylene. Plant Biology (Stuttgart) 12(4):630-8 (2010).

Jung H.-S., Chory J. Signaling between chloroplasts and the nucleus: can a systems biology approach bring clarity to a complex and highly regulated pathway? Plant Physiology 152(2):453-9 (2010).

Che P., et al. Signaling from the endoplasmic reticulum activates brassinosteroid signaling and promotes acclimation to stress in Arabidopsis. Science Signaling 3(141):ra69 (2010).

Childs L. H., et al. Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana. BMC Genomics 11:188 (2010).

Holman T. J. et al. Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two- cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray. Plant Methods 6:9 (2010).

Santuari L., et al. Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays. Genome Biology 11(1):R4(2010).

Xu J., et al. The ABORTED MICROSPORES regulatory network is required for postmeiotic male reproductive development in Arabidopsis thaliana. The Plant Cell 22:91-107 (2010).

Xie Y.-D., et al. The Arabidopsis gene SIGMA FACTOR-BINDING PROTEIN 1 plays a role in the salicylate- and jasmonate-mediated defence responses. Plant, Cell & Environment 33(5):828–39 (2010).

Moldovan D., Spriggs A., Dennis E. S., Wilson I. W. The hunt for hypoxia responsive natural antisense short interfering RNAs. Plant Signal Behavior 5(3):247–51 (2010).

Jaspers P., et al. The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants. BMC Genomics 11:170 (2010).

Matthes M. C., et al. The transcriptome of cis-jasmone-induced resistance in Arabidopsis thaliana and its role in indirect defence. Planta 232(5):1163-80 (2010).

Tchagang A., et al. Towards a temporal modeling of the genetic network controlling systemic acquired resistance in Arabidopsis thaliana. National Research Council, Canada Publications Archive. http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/ctrl?action=rtdoc&an=15261149&lang=en

Tiwari S., et al. Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana. BMC Plant Biology 10:72 (2010).

Weisman D., Alkio M., Colón-Carmona A. Transcriptional responses to polycyclic aromatic hydrocarbon-induced stress in Arabidopsis thaliana reveal the involvement of hormone and defense signaling pathways. BMC Plant Biology 10:59 (2010).

Bhattarai K. K., Atamian H. S., Kaloshian I., Eulgem T. WRKY72-type transcription factors contribute to basal immunity in tomato and Arabidopsis as well as gene-for-gene resistance mediated by the tomato R gene Mi-1. The Plant Journal 63(2):229–40 (2010).

Aspergillus Georgianna D. R., et al. Beyond aflatoxin: four distinct expression patterns and functional roles associated with Aspergillus flavus secondary metabolism gene clusters. Molecular Plant Pathology 11(2):213–26 (2010).

Reese B. N., Payne G. A., Woloshuk C. P. Effect of maize kernels maturation on transcriptional activity in Aspergillus flavus. Phytopathology 100(6, suppl 1):S108 (2010). van den Berg R. A., et al. Identification of modules in Aspergillus niger by gene co-expression network analysis. Fungal Genetics and Biology 47(6):539–50 (2010).

Axolotl Page R. B., Boley M.A., Smith J. J., Putta S., Voss S. R. Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development. BMC Evolutionary Biology 10:199 (2010).

Barley Lacerenza J. A., Parrott D. L., Fischer A. M. A major grain protein content locus on barley (Hordeum vulgare L.) chromosome 6 influences flowering time and sequential leaf senescence. Journal of Experimental Botany 61(11):3137-3149 (2010).

Liu Z., Faris J. D., Edwards M. C., and Friesen T. L. Development of expressed sequence tag (EST)-based markers for genomic analysis of a barley 6H region harboring multiple net form net blotch resistance genes. The Plant Genome 3(1):41-52 (2010).

Kwasniewski M., Janiak A., Mueller-Roeber B., Szarejko I. Global analysis of the root hair morphogenesis transcriptome reveals new candidate genes involved in root hair formation in barley. Journal of Plant Physiology 167(13):1076-83 (2010).

Petti C., Khan M., Doohan F. Lipid transfer proteins and protease inhibitors as key factors in the priming of barley responses to Fusarium head blight disease by a biocontrol strain of Pseudomonas fluorescens. Functional & Integrative Genomics 10(4):619-27 (2010).

Chen, K., Tian S., Yandell B. S., Kaeppler S. M., An, Y. C. Loss-of-function of DELLA protein SLN1 activates GA signaling in barley aleurone. Acta Physiologiae Plantarum 32(4):789-800 (2010).

Ma, X., et al. Physcion, a natural anthraquinone derivative, enhances the gene expression of leaf-specific thionin of barley against Blumeria graminis. Pest Management Science 66(7):718-24 (2010).

Zalewski W., Galuszka P., Gasparis S., Orczyk W., Nadolska-Orczyk A. Silencing of the HvCKX1 gene decreases the cytokinin oxidase/dehydrogenase level in barley and leads to higher plant productivity. Journal of Experimental Botany 61(6):1839-51 (2010).

Mangelsen E., et al. Transcriptome analysis of high-temperature stress in developing barley caryopses: early stress responses and effects on storage compound biosynthesis. Molecular Plant. Published online October 5, 2010. doi:10.1093/mp/ssq058.

Bovine Aston K. I., et al. Abnormal levels of transcript abundance of developmentally important genes in various stages of preimplantation bovine somatic cell nuclear transfer embryos. Cellular Reprogramming 12(1):23-32 (2010).

Shimizu T., et al. Actions and interactions of progesterone and estrogen on transcriptome profiles of the bovine endometrium. Physiological Genomics 42A(4):290-300 (2010).

Caires K., Oatley J., McLean D. Cellular, molecular and genomic mechanisms regulating testis function in livestock. Chapter 12 in Reproductive Genomics in Domestic Animals, edited by Jiang A., Ott T. L., Wiley- Blackwell, pp 269-90 (2010).

Günther J., et al. Comparative kinetics of E. coli vs. S. aureus specific activation of key- immune pathways in mammary epithelial cell: S. aureus elicits a delayed response dominated by IL-6, but not by IL-1A or TNF-a. Infection and Immunity. Published online November 29, 2010. doi:10.1128/IAI.01071-10.

Tian J., et al. Delineating the angiogenic gene expression profile prior to pulmonary vascular remodeling in a lamb model of congenital heart disease. Physiological Genomics. Published online October 26, 2010. doi:10.1152/physiolgenomics.00135.2010.

Zhang Y.-Y., et al. Differentially expressed genes in skeletal muscle tissues from castrated Qinchuan cattle males compared with those from intact males. Livestock Science 135(1):220-3 (2011).

Joseph S. J., et al. Effect of diet supplementation on the expression of bovine genes associated with fatty acid synthesis and metabolism. Bioinformatics and Biology Insights 4:19-31(2010).

Carter F., et al. Effect of elevated circulating progesterone concentration on bovine blastocyst development and global transcriptome following endoscopic transfer of in vitro produced embryos to the bovine oviduct. Biology of Reproduction 83(5):707-19 (2010).

Skiba M., Glowinski F., Koczan D., Mettenleiter T. C., Karger A. Gene expression profiling of Pseudorabies virus (PrV) infected bovine cells by combination of transcript analysis and quantitative proteomic techniques. Veterinary Microbiology 143(1):14-20 (2010).

Peacock C. Host and parasite genomics, an Australasian perspective. Parasite Immunology 32(8):599–606 (2010).

Berry, S. D., et al. Mapping a quantitative trait locus for the concentration of β-lactoglobulin in milk, and the effect of β-lactoglobulin genetic variants on the composition of milk from Holstein-Friesian x Jersey crossbred cows. New Zealand Veterinary Journal 58(1):1-5 (2010).

Hou X., Li Q., Huang T. Microarray analysis of gene expression profiles in the bovine mammary gland during lactation. Science China Life Sciences 53(2):248-56 (2010).

McCarthy S. D. et al. Negative energy balance and hepatic gene expression patterns in high-yielding dairy cows during the early postpartum period: a global approach. Physiological Genomics 42A(3):188-99 (2010).

Riley L. G., et al. The influence of extracellular matrix and prolactin on global gene expression profiles of primary bovine mammary epithelial cells in vitro. Animal Genetics 41(1):55–63 (2010).

Piper E. K., et al. Tick-susceptible Bos taurus cattle display an increased cellular response at the site of larval Rhipicephalus (Boophilus) microplus attachment, compared with tick-resistant Bos indicus cattle. International Journal for Parasitology 40(4):431-41 (2010).

Minogue B. M., Richardson S. M., Zeef L. A., Freemont A. J., Hoyland J. A. Transcriptional profiling of bovine intervertebral disc cells: implications for identification of normal and degenerate human intervertebral disc cell phenotypes. Arthritis Research & Therapy 12(1):R22 (2010).

Feugang J. M. et al. Transcriptome analysis of bull spermatozoa: implications for male fertility. Reproductive BioMedicine Online 21(3):312-24 (2010).

Huang W., Yandell B. S., Khatib H. Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development. BMC Genomics 11:23 (2010).

Lee S.-H., et al. Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo (Korean Cattle). BMC Genomics 11:623 (2010).

Brassica Love C. G., et al. A Brassica exon array for whole-transcript gene expression profiling. PLoS One 5(9):e12812 (2010).

Canine and others Gallardo-Arrieta F., et al. A transcriptional signature associated with the onset of benign prostate hyperplasia in a canine model. Prostate 70(13):1402-12 (2010).

Kil D. Y., Vester Boler B. M., Apanavicius C. J., Schook L. B., Swanson K. S. Age and diet affect gene expression profiles in canine liver tissue. PLoS One 5(10):e13319 (2010).

Goldstein O., et al. An ADAM9 mutation in canine cone-rod dystrophy 3 establishes homology with human cone- rod dystrophy 9. Molecular Vision 16:1549-69 (2010).

Ke X., et al. Assessment of the functionality of genome-wide canine SNP arrays and implications for canine disease association studies. Animal Genetics. Published online Novemer 11, 2010. doi:10.1111/j.1365- 2052.2010.02132.x.

Wood M. W., Breitschwerdt E. B., Gookin J. L. Autocrine effects of interleukin-6 mediate acute-phase pro- inflammatory and tissue reparative transcriptional responses of canine bladder mucosa. Infection and Immunity. Published online November 29, 2010. doi:10.1128/IAI.01102-10.

Töyli M., Rosberg-Kulha L., Capra J., Vuoristo J., Eskelinen S. Different responses in transformation of MDCK cells in 2D and 3D culture by v-Src as revealed by microarray techniques, RT-PCR and functional assays. Laboratory Investigation 90(6):915–28 (2010).

Danesha A., et al. Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation. Virology 409(1):102-12 (2010).

O'Donoghue L. E., et al. Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome. BMC Cancer 10:506 (2010).

Mathias R. A., et al. Extracellular remodelling during oncogenic Ras-induced epithelial-mesenchymal transition facilitates MDCK cell migration. Journal of Proteome Research 9(2):1007–19 (2010).

Mahoney J .A., Fisher J C., Snyder S. A., Hauck M. L. Feasibility of using gene expression analysis to study canine soft tissue sarcomas. Mammalian Genome 21(11-12):577-82 (2010).

Kil D. Y., Vester Boler B. M., Apanavicius C. J., Schook L. B., Swanson K. S. Gene expression profiles of colonic mucosa in healthy young adult and senior dogs. PLoS One 5(9):e12882 (2010).

Tamburini B. A. et al. Gene expression profiling identifies inflammation and angiogenesis as distinguishing features of canine hemangiosarcoma. BMC Cancer 10:619 (2010).

Kropatsch R., et al. Generalized progressive retinal atrophy in the Irish Glen of Imaal Terrier is associated with a deletion in the ADAM9 gene. Molecular and Cellular Probes 24(6):357-63 (2010).

Meurs K. M., et al. Genome-wide association identifies a deletion in the 3′ untranslated region of striatin in a canine model of arrhythmogenic right ventricular cardiomyopathy. Human Genetics 128(3):315-24 (2010).

Fang Y., et al. Molecular characterization of in vivo adjuvant activity in influenza-vaccinated ferrets. Journal of Virology Published online June 9, 2010. doi:10.1128/JVI.02305-09.

Jiang B., et al. Neuroinflammation in advanced canine glaucoma. Molecular Vision 16:2092–108 (2010).

Grant R. W., Vester Boler B. M., Ridge T. K., Graves T. K., Swanson K. S. Obese canine skeletal muscle transcriptome exhibits altered inflammatory signaling. The FASEB Journal 24(suppl):934.4 (2010).

Ojaimi C., Kinugawa S., Recchia F. A., Hintze T. H. Oxidant-NO dependent gene regulation in dogs with type I diabetes: impact on cardiac function and metabolism. Cardiovascular Diabetology 9:43 (2010).

Suematsu N., et al. Potential mechanisms of low sodium diet–induced cardiac disease: superoxide-NO in the heart. Circulation Research 106(3):593-600 (2010).

Ostrander E. A., et al. Tracking genes and finding mutations: finding genes for complex traits in the domestic dog (Canis familiaris). Genome Biology 11:I23 (2010).

Chicken Cavill R., et al. A combined metabonomic and transcriptomic approach to investigate metabolism during development in the chick chorioallantoic membrane. Journal of Proteome Research 9(6):3126–34 (2010).

Maślikowski B. M., et al. Cellular processes of v-Src transformation revealed by gene profiling of primary cells − implications for human cancer. BMC Cancer 10:41 (2010).

Mao W., Hunt H. D., Cheng H. H. Cloning and functional characterization of chicken stem cell antigen 2. Developmental & Comparative Immunology 34(3):360-68 (2010).

Yoshimura T., Sharp P. J. Genetic and molecular mechanisms of avian photoperiodism. Chapter 18 in Photoperiodism: the Biological Calendar, edited by Nelson R. J., Denlinger D. L, Somers D. E. Oxford University Press, pp 446-61 (2010).

Richards M. P., Proszkowiec-Weglarz M., Rosebrough R. W., McMurtry J. P., Angel R. Effects of early neonatal development and delayed feeding immediately post-hatch on the hepatic lipogenic program in broiler chicks. Comparative Biochemistry and Physiology − Part B: Biochemistry & Molecular Biology 157(4):374-88 (2010).

Frucht C. S., et al. Gene expression analysis of forskolin treated basilar papillae identifies microRNA181a as a mediator of proliferation. PLoS One 5(7):e11502 (2010).

Soulet F., et al. Gene signatures in wound tissue as evidenced by molecular profiling in the chick embryo model. BMC Genomics 11:495 (2010).

Akizu N., Estarás C., Guerrero L., Martí E., Martínez-Balbás M. A. H3K27me3 regulates BMP activity in developing spinal cord. Development 137(17):2915-25 (2010).

Miranda-Rottmann S., Kozlov A. S., Hudspeth A. J. Highly specific alternative splicing of transcripts encoding BK channels in the chicken's cochlea is a minor determinant of the tonotopic gradient. Molecular and Cellular Biology 30(14):3646-60 (2010).

Kimura W., et al. Identification of region-specific genes in the early chicken endoderm. Gene Expression Patterns. Published online November 23, 2010. doi:10.1016/j.gep.2010.11.002

Heidari M., et al. Marek's disease virus-induced immunosuppression: array analysis of chicken immune response gene expression profiling. Viral Immunology 23(3):309-19 (2010).

Albon J., et al. Microarray analysis of gene expression in the corneal epithelium during development. Investigative Ophthalmology & Visual Science 51:E-Abstract 3752 (2010).

Pesevski Z., et al. Molecular analysis of normal and hypoplastic chick embryonic ventricles. The FASEB Journal 24(suppl):lb15 (2010).

Mank J. E., Nam K., Brunström B., Ellegren H. Ontogenetic complexity of sexual dimorphism and sex-specific selection. Molecular Biology and Evolution 27(7):1570-8 (2010).

Alinikula J. Regulation of B cell gene expression and function by Ikaros, Helios and Bcl6. PhD dissertation, University of Turku, Finland (2010).

Zhang S. O., Mathur S., Hattem G., Tassy O., Pourquié O. Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos. BMC Genomics 11:13 (2010).

Mořkovský L., et al. The chicken Z chromosome is enriched for genes with preferential expression in ovarian somatic cells. Journal of Molecular Evolution 70(2):129-36 (2010).

Degletagne C., et al. Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays. BMC Genomics 11(1):344 (2010).

Alev C. et al. Transcriptomic landscape of the primitive streak. Development 137(17):2863-74 (2010).

Ciraci C., Tuggle C. K., Wannemuehler M. J., Nettleton D., Lamont S. J. Unique genome-wide transcriptome profiles of chicken macrophages exposed to Salmonella-derived endotoxin. BMC Genomics 11:545 (2010).

Cotton Sun, Q., et al. Gene expression profiling during gland morphogenesis of a mutant and a glandless upland cotton. Molecular Biology Reports 37(7):3319-25 (2010).

Christianson J. A., Llewellyn D. J., Dennis E. S., Wilson I. W. Global gene expression responses to waterlogging in roots and leaves of cotton (Gossypium hirsutum L.). Plant and Cell Physiology 51(1):21-37 (2010).

Entamoeba histolytica Bussa S. N., et al. Members of the Entamoeba histolytica transmembrane kinase family play non-redundant roles in growth and phagocytosis. International Journal for Parasitology 40(7):833-43 (2010).

Fusarium graminearum Liu X., Tang W.-H., Zhao X.-M., Chen L. A network approach to predict pathogenic genes for Fusarium graminearum. PLoS One 5(10):e13021 (2010).

Min K., et al. A novel gene, ROA, is required for normal morphogenesis and discharge of ascospores in Gibberella zeae. Eukaryotic Cell 9(10):1495-503 (2010).

Walter S., Nicholson P., Doohan F. M. Action and reaction of host and pathogen during Fusarium head blight disease. New Phytologist 185(1):54–66 (2010).

Wong P., et al. FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum. Nucleic Acids Research 39(suppl 1):D637-9 (2011).

Stephens A. Molecular analysis of fungal pathogenicity in crown rot disease of wheat caused by Fusarium graminearum. PhD dissertation, The University of Queensland (2010).

Gardiner D. M., Kazan K., Manners J. M. Novel genes of Fusarium graminearum that negatively regulate deoxynivalenol production and virulence. Molecular Plant-Microbe Interactions 22(12):1588-600 (2009).

Kumar L., Breakspear A., Kistler C., Ma L.-J., Xie X. Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes. BMC Genomics 11:208 (2010).

Grape Gao F., et al. A functional EDS1 ortholog is differentially regulated in powdery mildew resistant and susceptible grapevines and complements an Arabidopsis eds1 mutant. Planta 231(5):1037-47 (2010).

Cramer G. R. Abiotic stress and plant responses from the whole vine to the genes. Australian Journal of Grape and Wine Research 16(suppl s1):86-93 (2010).

Koyama, K., Sadamatsu, K., Goto-Yamamoto, N. Abscisic acid stimulated ripening and gene expression in berry skins of the Cabernet Sauvignon grape. Functional & Integrative Genomics 10(3):367-81 (2010).

Sreekantan L., et al. Differential floral development and gene expression in grapevines during long and short photoperiods suggests a role for floral genes in dormancy transitioning. Plant Molecular Biology 73(1-2):191-205 (2010).

Sasapu A., Su Y., Qiu W. Functional analyses of a grapevine mitogen-activated protein kinase kinase gene. Australian Journal of Grape and Wine Research 16(supp s1):A12 (2010).

Gambetta G. A., Matthews M. A., Shaghasi T. A., McElrone A. J., Castellarin S. D. Sugar and abscisic acid signaling orthologs are activated at the onset of ripening in grape. Planta 232(1):219-34 (2010).

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