Includes over 250 transcriptomics and genomics papers published from 2009 to 2011 in plants, animals, and other non-human species; sorted by species.

1. P u b l i c a t i o n s
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).

2. 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).

3. 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).

4. 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).

5. 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).

6. 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).

7. 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).

8. 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).

9. 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).
Pontin M. A., et al. Transcriptome changes in grapevine (Vitis vinifera L.) cv. Malbec leaves induced by
ultraviolet-B radiation. BMC Plant Biology 10:224 (2010).
Schlauch K. A., Grimplet J., Cushman J., Cramer G. R. Transcriptomics analysis methods: microarray data
processing, analysis and visualization using the Affymetrix GeneChip®
Vitis vinifera Genome Array. Chapter 22 in
Methodologies and Results in Grapevine Research, edited by Delrot S, Or E., Grando S., Medrano H., Bavaresco
L., Springer, pp 317-34 (2010).
Lettuce
Schwember A. R., Bradford K. J. Quantitative trait loci associated with longevity of lettuce seeds under
conventional and controlled deterioration storage conditions. Journal of Experimental Botany 61(15):4423-4436
(2010).
Maize and sorghum
Makarevitch I., Harris C. Aneuploidy causes tissue-specific qualitative changes in global gene expression patterns
in maize. Plant Physiology 152:927-38 (2010).
Mall T. K. Evaluation of novel input output traits in sorghum through biotechnology. PhD dissertation, University
of Nebraska (2010).
Zheng J., et al. Genome-wide transcriptome analysis of two maize inbred lines under drought stress.
Plant Molecular Biology 72(4-5):407-21 (2010).
Zhao G., et al. Gibberellin-induced mesocotyl elongation in deep-sowing tolerant maize inbred line 3681-4.
Plant Breeding 129(1):87-91 (2010).
Xing G., et al. Identification and characterization of a novel hybrid upregulated long non-protein coding RNA in
maize seedling roots. Plant Science 179(4):356-63 (2010).
Medicago
Naoumkina M. A., et al. Genomic and coexpression analyses predict multiple genes involved in triterpene saponin
biosynthesis in Medicago truncatula. The Plant Cell 22:850-66 (2010).
Benedito V. A., et al. Genomic inventory and transcriptional analysis of Medicago truncatula transporters.

10. Plant Physiology 152:1716-30 (2010).
Holmes P., Djordjevic M. A., Imin N. Global gene expression analysis of in vitro root formation in Medicago
truncatula. Functional Plant Biology 37(12):1117-31 (2010).
Henckel K., Küster H., Stutz L. J., Goesmann A. MediPlEx − a tool to combine in silico & experimental gene
expression profiles of the model legume Medicago truncatula. BMC Research Notes 3(1):262.
Gaige A. R., Ayella A., Shuai B. Methyl jasmonate and ethylene induce partial resistance in Medicago truncatula
against the charcoal rot pathogen Macrophomina phaseolina. Physiological and Molecular Plant Pathology 74(5-
6):412-8 (2010).
Franken P. Molecular-physiological aspects of the AM symbiosis post penetration. Chapter 5 in Arbuscular
Mycorrhizas: Physiology and Function, edited by Koltai H, Kapulnik, Y., Springer, p 93-116 (2010).
Friesen M. L., et al. Population genomic analysis of Tunisian Medicago truncatula reveals candidates for local
adaptation. Plant Journal 63(4):623-35 (2010).
Poplar
Gou J., et al. Gibberellins Regulate Lateral root formation in Populus through interactions with auxin and other
hormones. The Plant Cell 22:623-39 (2010).
Hamanshi E. T., et al. Intraspecific variation in the Populus balsamifera drought transcriptome. Plant, Cell &
Environment 33(10):1742-55 (2010).
Behnke, K., et al. RNAi-mediated suppression of isoprene emission in poplar transiently impacts phenolic
metabolism under high temperature and high light intensities: a transcriptomic and metabolomic analysis.
Plant Molecular Biology 74(1-2):61-75 (2010).
Ding, M., et al. Salt-induced expression of genes related to Na+
/K+
and ROS homeostasis in leaves of salt-
resistant and salt-sensitive poplar species. Plant Molecular Biology 73(3):251-69 (2010).
Grisel N., et al. Transcriptome responses to aluminum stress in roots of aspen (Populus tremula). BMC Plant
Biology 10:185 (2010).
Porcine
Nielsen K. B., Kruhøffer M., Holm I. E., Jørgensen A. L., Nielsen A. L. Identification of genes differentially
expressed in the embryonic pig cerebral cortex before and after appearance of gyration. BMC Research Notes
3:127 (2010).
Li F. N., et al. Chloride intracellular channel 5 modulates adipocyte accumulation in skeletal muscle by inhibiting
preadipocyte differentiation. Journal of Cellular Biochemistry 110(4):1013-21 (2010).
Stoltz D. A., et al. Cystic fibrosis pigs develop lung disease and exhibit defective bacterial eradication at birth.
Science Translational Medicine 2(29):29ra31 (2010).
Malkevich N., McCarron R. M., Mahon R. T. Decompression from saturation using oxygen: its effect on DCS and
RNA in large swine. Aviation, Space, and Environmental Medicine 81(1):15-21 (2010).
Østrup E., Bauersachs S., Blum H., Wolf E., Hyttel P. Differential endometrial gene expression in pregnant and
nonpregnant sows. Biology of Reproduction 83(2):277-85 (2010).
Fernandez-Rodriguez A., et al. Differential gene expression in ovaries of pregnant pigs with high and low
prolificacy levels and identification of candidate genes for litter size. Biology of Reproduction 83(2):277-85
(2010).
Li Y., Xu Z., Li H., Xiong Y., Zuo B. Differential transcriptional analysis between red and white skeletal muscle of
Chinese Meishan pigs. International Journal of Biological Sciences 6(4):350-60 (2010).
Martijn C., Wiklund L. Effect of methylene blue on the genomic response to reperfusion injury induced by cardiac
arrest and cardiopulmonary resuscitation in porcine brain. BMC Medical Genomics 3:27 (2010).
Kordus R. J. Expression of DIO2 in the porcine ovary. PhD dissertation, University of South Carolina, (2010).

11. Srikanchai T., Murani E., Wimmers K., Ponsuksili S. Four loci differentially expressed in muscle tissue depending
on water-holding capacity are associated with meat quality in commercial pig herds. Molecular Biology Reports
37(1):595-601 (2010).
Wimmers K., Murani E., Ponsuksili S. Functional genomics and genetical genomics approaches towards
elucidating networks of genes affecting meat performance in pigs. Brief Functional Genomics 9(3):251-8 (2010).
LaVoie H. A., Kordus R. J., Nguyen J. B., Barth J. L., Hui Y. Y. GATA depletion impacts insulin-like growth factor 1
mRNA and protein levels in luteinizing porcine granulosa cells. Biology of Reproduction 83(6):1015-26 (2010).
Byrne G., Schmoeckel M., Reichart B., McGregor C. G. A. Gene array studies in orthotopic pig to baboon cardiac
xenotransplantation. Xenotransplantation 17(2):115–6 (2010).
Bahls M., et al. Gene expression differences in the brachial and femoral arteries of Rapacz familial
hypercholesterloemic swine at birth are related to atherosusceptibility. The FASEB Journal 24(suppl):1039.1
(2010).
Barb C. R., et al. Gene expression in hypothalamus, liver, and adipose tissues and food intake response to
melanocortin-4 receptor agonist in pigs expressing melanocortin-4 receptor mutations. Physiological Genomics
41(3):254-68 (2010).
Jiang C. et al. Gene expression profiling of skeletal muscle of nursing piglets. International Journal of Biological
Sciences 6(7):627-38 (2010).
Lee G., et al. Genomic expression profiling in lymph nodes with lymphoid depletion from porcine circovirus 2-
infected pigs. Journal of General Virology 91(Pt 10):2585-91 (2010).
Zhou G., et al. Global comparison of gene expression profiles between intramuscular and subcutaneous
adipocytes of neonatal landrace pig using microarray. Meat Science 86(2):440-50 (2010).
Ponsuksili S., Murani E., Schwerin M., Schellander K., Wimmers K. Identification of expression QTL (eQTL) of
genes expressed in porcine M. longissimus dorsi and associated with meat quality traits. BMC Genomics 11:572
(2010).
Tian F., et al. Immune events associated with high level protection against Schistosoma japonicum infection in
pigs immunized with UV-attenuated cercariae. PLoS One 5(10):e13408 (2010).
doi:10.1371/journal.pone.0013408
Peters S. M., et al. In vitro identification and verification of inflammatory biomarkers in swine. Veterinary
Immunology and Immunopathology Article 139(1):67-72 (2010).
Jameel M. N., et al. Long-term functional improvement and gene expression changes after bone marrow-derived
multipotent progenitor cell transplantation in myocardial infarction. American Journal of Physiology − Heart and
Circulatory Physiology 298(5):H1348-56 (2010).
Tuggle C. K., et al. Methods for transcriptomic analyses of the porcine host immune response: application to
Salmonella infection using microarrays. Veterinary Immunology and Immunopathology 138(4):280-91 (2010).
van Malenstein, H., et al. Molecular analysis of sepsis-induced changes in the liver: microarray study in a porcine
model of acute fecal peritonitis with fluid resuscitation. Shock 34(4):427-36 (2010).
Andersson M. On the immune response in porcine enteric diseases, with special reference to swine Dysentery,
proliferative enteropathy and PMWS. PhD dissertation, Swedish University of Agricultural Sciences, Uppsala
(2010).
Wimmers K., Murani E., Ponsuksili S. Pre- and postnatal differential gene expression with relevance for meat and
carcass traits in pigs − a review. Animal Science Papers and Reports 28(2):115-22 (2010).
Wang S., et al. Rapid and dynamic alterations of gene expression profiles of adult porcine bone marrow-derived
stem cell in response to hypoxia. Stem Cell Research 4(2):117-28 (2010).

12. Li R., et al. Response of swine spleen to Streptococcus suis infection revealed by transcription analysis. BMC
Genomics 11:556 (2010).
Tsapara A., et al. The RhoA activator GEF-H1/Lfc is a transforming growth factor-β target gene and
effector that regulates a-smooth muscle actin expression and cell migration. Molecular Biology of the Cell
21(6):860-70 (2010).
Tomás A., Fernandes L. T., Sánchez A., Segalés J. Time course differential gene expression in response to
porcine circovirus type 2 subclinical infection. Veterinary Research 41(1):12 (2010).
Rice
Wang L., et al. A dynamic gene expression atlas covering the entire life cycle of rice. Plant Journal 61(5):752-66
(2010).
Wang J., et al. A global analysis of QTLs for expression variations in rice shoots at the early seedling stage.
The Plant Journal 63(6):1063-74 (2010).
Yan W.-H., et al. A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and
heading date in rice. Molecular Plant. Published online December 10, 2010. doi:10.1093/mp/ssq070.
Su C.-F., et al. A novel MYBS3-dependent pathway confers cold tolerance in rice. Plant Physiology
153(1):145-58.
Ning J., Li X., Hicks L. M., Xiong L. A Raf-like MAPKKK gene DSM1 mediates drought resistance through reactive
oxygen species scavenging in rice. Plant Physiology 152(2):876-90 (2010).
Horiuchi Y., et al. A simple optimization can improve the performance of single feature polymorphism detection
by Affymetrix expression arrays. BMC Genomics 11:315 (2010).
Wright M. H., et al. ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and
highly homozygous populations. Bioinformatics 26(23):2952–60 (2010).
Taylor N. L., et al. Analysis of the rice mitochondrial carrier family reveals anaerobic accumulation of a basic
amino acid carrier involved in arginine metabolism during seed germination. Plant Physiology 154(2):691-704
(2010).
Allen A. M., Lexer C., Hiscock S. J. Comparative analysis of pistil transcriptomes reveals conserved and novel
genes expressed in dry, wet and semi-dry stigmas. Plant Physiology 154(3):1347-60 (2010).
Jain M., Ghanashyam C., Bhattacharjee A. Comprehensive expression analysis suggests overlapping and specific
roles of rice glutathione S-transferase genes during development and stress responses. BMC Genomics 11:73
(2010).
Narsai R., Ivanova A., Ng S., Whelan J. Defining reference genes in Oryza sativa using organ, development,
biotic and abiotic transcriptome datasets. BMC Plant Biology 10:56 (2010).
Wang K., et al. DEP and AFO regulate reproductive habit in rice. PLoS Genetics 6(1):e1000818 (2010).
Liu F., et al. Gene expression profiles deciphering rice phenotypic variation between Nipponbare (japonica) and
93-11 (indica) during oxidative stress. PLoS One 5(1):e8632 (2010).
Wei L. Q., et al. Genome-scale analysis and comparison of gene expression profiles in developing and germinated
pollen in Oryza sativa. BMC Genomics 11:338 (2010).
Ma H., Zhao J. Genome-wide identification, classification, and expression analysis of the arabinogalactan protein
gene family in rice (Oryza sativa L.). Journal of Experimental Botany 61(10):2647-68 (2010).
Garg R., Jhanwar S., Tyagi A. K., Jain M. Genome-wide survey and expression analysis suggest diverse roles of
glutaredoxin gene family members during development and response to various stimuli in rice. DNA Research
17(6):353-367 (2010).
Zhao X., Huang J., Yu H., Wang L., Xie W. Genomic survey, characterization and expression profile analysis of
the peptide transporter family in rice (Oryza sativa L.). BMC Plant Biology 10:92 (2010).

13. Deshmukh R., et al. Identification of candidate genes for grain number in rice (Oryza sativa L.). Functional &
Integrative Genomics 10(3):339-47 (2010). doi:10.1007/s10142-010-0167-2
Deshmukh R., et al. Modulation of transcription factor and metabolic pathway genes in response to water-deficit
stress in rice. Functional and Integrative Genomics 10(3):339-47 (2010).
Swarbreck S. M., Defoin-Platel M., Hindle M., Saqi M., Habash D. Z. New perspectives on glutamine synthetase in
grasses. Journal of Experimental Botany. Published online December 13, 1010. doi:10.1093/jxb/erq356.
Singh A., Giri J., Kapoor S., Tyagi A. K., Pandey G. K. Protein phosphatase complement in rice: genome-wide
identification and transcriptional analysis under abiotic stress conditions and reproductive development. BMC
Genomics 11:435 (2010).
Widodo M. R., et al. Response to zinc deficiency of two rice lines with contrasting tolerance is determined by root
growth maintenance and organic acid exudation rates, and not by zinc-transporter activity. New Phytologist
186(2):400-14 (2010).
Fujita M., et al. Rice expression atlas in reproductive development. Plant & Cell Physiology 51(12):2060-81
(2010).
Cotsaftis O., et al. Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress.
Molecular Plant. Published online November 1, 2010. doi: 10.1093/mp/ssq056.
Yaish M. W., et al. The APETALA-2-like transcription factor OsAP2-39 controls key interactions between abscisic
acid and gibberellin in rice. PLoS Genetics 6(9):e1001098 (2010).
Ficklin S. P., Luo F., Feltus F. A. The association of multiple interacting genes with specific phenotypes in rice
using gene coexpression networks. Plant Physiology 154(1):13-24 (2010).
Guo J., Wang F., Song J., Sun W. Zhang X. S. The expression of Orysa;CycB1;1 is essential for endosperm
formation and causes embryo enlargement in rice. Planta 231(2):293-303 (2010).
Marcela S., Sawers R., Oakeley E., Angliker H., Paszkowski U. Tissue-adapted invasion strategies of the rice blast
fungus Magnaporthe oryzae. The Plant Cell 22(9):3177-87 (2010).
Jha G., Patel H. K., Dasgupta M., Palaparthi R., Sonti R. V. Transcriptional profiling of rice leaves undergoing a
hypersensitive response like reaction induced by Xanthomonas oryzae pv. oryzae cellulase. Rice 3(1):1-21
(2010).
Qin H., et al. Transcriptomics analysis identified candidate genes colocalized with seed dormancy QTLs in rice
(Oryza sativa L.). Journal of Plant Biology 53(5):330-7 (2010).
Soybean
Bolon Y.-T., et al. Complementary genetic and genomic approaches help characterize the linkage group I seed
protein QTL in soybean. BMC Plant Biology 10:41 (2010).
Mensack M. M., et al. Evaluation of diversity among common beans (Phaseolus vulgaris L.) from two centers of
domestication using 'omics' technologies. BMC Genomics 11(1):686 (2010).
Narikawa T., et al. Expression of the stress-related genes for glutathione S-transferase and ascorbate peroxidase
in the most-glycinin-deficient soybean cultivar Tousan205 during seed maturation. Bioscience, Biotechnology,
and Biochemistry 74(9):1976-9 (2010).
Mochida K., et al. Genome-wide analysis of two-component systems and prediction of stress-responsive two-
component system members in soybean. DNA Research 17(5):303-24 (2010).
Gillespie K. M. Genomic and biochemical investigation of soybean antioxidant metabolism in response to growth
at elevated carbon dioxide and elevated ozone. PhD dissertation, University of Illinois at Urbana-Champaign
(2010).
Ge Y., et al. Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment. BMC
Plant Biology 10:153 (2010).

14. Koch M., et al. Rhizobial adaptation to hosts, a new facet in the legume root-nodule symbiosis. Molecular Plant-
Microbe Interactions 23(6):784-90 (2010).
Hudson K. A. The circadian clock-controlled transcriptome of developing soybean seeds. The Plant Genome
3(1):3-13 (2010).
Waller L. M. Transcriptional profiling of potential regulatory factors modulating defense mechanisms in soybean
during Phytophthora sojae infection. PhD disseration, Virginia Polytechnic Institute and State University (2010).
Das S., Ehlers J .D., Close T. J., Roberts P. A. Transcriptional profiling of root-knot nematode induced feeding
sites in cowpea (Vigna unguiculata L. Walp.) using a soybean genome array. BMC Genomics 11:480 (2010).
Tobacco
Edwards K. D., et al. TobEA: an atlas of tobacco gene expression from seed to senescence. BMC Genomics
11:142 (2010).
Tomato
Nashilevitz S., et al. An orange ripening mutant links plastid NAD(P)H dehydrogenase complex activity to central
and specialized metabolism duringtomato fruit maturation. The Plant Cell 22(6):1977-97 (2010).
Ozaki S., et al. Coexpression analysis of tomato genes and experimental verification of coordinated expression of
genes found in a functionally enriched coexpression module. DNA Research 17(2):105–16 (2010).
Sun W., et al. Comparative transcriptomic profiling of a salt-tolerant wild tomato species and a salt-sensitive
tomato cultivar. Plant & Cell Physiology 51(6):997-1006 (2010).
López-Ráez J. A., et al. Hormonal and transcriptional profiles highlight common and differential host responses to
arbuscular mycorrhizal fungi and the regulation of the oxylipin pathway. Journal of Experimental Botany
61(10):2589-601 (2010).
Meir S., et al. Microarray analysis of the abscission-related transcriptome in the tomato flower abscission zone in
response to auxin depletion. Plant Physiology 154(4):1929-56 (2010).
Hanssen I. M., Thomma B. P. Pepino mosaic virus: a successful pathogen that rapidly evolved from emerging to
endemic in tomato crops. Molecular Plant Pathology 11(2):179-89 (2010).
Ruzicka D. R., Barrios-Masias F. H., Hausmann N. T., Jackson L. E., Schachtman D. P. Tomato root transcriptome
response to a nitrogen-enriched soil patch. BMC Plant Biology 10:75 (2010).
Garrido G., Morcillo R. J., Rodríguez J. A., Bote J. A. Variations in the mycorrhization characteristics in roots of
wild-type and ABA-deficient tomato are accompanied by specific transcriptomic alterations. Molecular Plant-
Microbe Interactions 23(5):651-64 (2010).
Wheat
Bozkurt T. O., McGrann G. R., MacCormack R., Boyd L. A., Akkaya M. S. Cellular and transcriptional responses of
wheat during compatible and incompatible race-specific interactions with Puccinia striiformis f. sp. tritici.
Molecular Plant Pathology 11(5):625–40 (2010).
Tang Z., Zhang L., Yang D., Zhao C., Zheng Y. Cold-stress contributes to aberrant cytokinesis during male
meiosis I in a wheat thermosensitive genic male sterile line. Plant, Cell & Environment. Published online
November 10, 2010. doi:10.1111/j.1365-3040.2010.02250.x.
Lee T. G., Lee Y. J., Kim D. Y., Seo Y. W. Comparative physical mapping between wheat chromosome arm 2BL
and rice chromosome 4. Genetica 138(11-12):1277-96 (2010).
Sharma S., et al. Delineating the structural, functional and evolutionary relationships of sucrose phosphate
synthase gene family II in wheat and related grasses. BMC Plant Biology 10:134 (2010).
Chagué V., et al. Genome-wide gene expression changes in genetically stable synthetic and natural wheat
allohexaploids. New Phytologist 187(4):1181-94.

15. Long, X.-Y., et al. Genome-wide identification and evaluation of novel internal control genes for Q-PCR based
transcript normalization in wheat. Plant Molecular Biology 74(3):307-11 (2010).
Unver T., Bakar M., Shearman R., Budak, H. Genome-wide profiling and analysis of Festuca arundinacea miRNAs
and transcriptomes in response to foliar glyphosate application. Molecular Genetics and Genomics 283(4):397-
413 (2010).
Akhunova A. R., Matniyazov R. T., Liang H., Akhunov E. D. Homoeolog-specific transcriptional bias in
allopolyploid wheat. BMC Genomics 11:505 (2010).
Ugarte C. C., Trupkin S. A., Ghiglione H., Slafer G., Casal J. J. Low red/far-red ratios delay spike and stem
growth in wheat. Journal of Experimental Botany 61(11):3152-62 (2010).
Lulin M., et al. Molecular cloning and characterization of an up-regulated UDP-glucosyltransferase gene induced
by DON from Triticum aestivum L. cv. Wangshuibai. Molecular Biology Reports 37(2):785-95.
Gao Z., et al. Overexpressing a putative aquaporin gene from wheat, TaNIP, enhances salt tolerance in
transgenic Arabidopsis. Plant & Cell Physiology 51(5):767-75 (2010).
Winfield M. O., Lu C., Wilson I. D., Coghill J. A., Edwards K. J. Plant responses to cold: transcriptome analysis of
wheat. Plant Biotechnology Journal 8(7):749-71 (2010).
Liu X., et al. Reactive oxygen species are involved in plant defense against a gall midge. Plant Physiology
152(2):985-99 (2010).
Stephenson, T. J., McIntyre C. L., Collet, C., Xue, G.-P. TaNF-YC11, one of the light-upregulated NF-YC members
in Triticum aestivum, is co-regulated with photosynthesis-related genes. Functional & Integrative Genomics
10(2)265-76 (2010).
Romeuf I., et al. wDBTF: an integrated database resource for studying wheat transcription factor families.
BMC Genomics 11:185 (2010).
Affymetrix, Inc. +1-888-362-2447  Affymetrix UK Ltd. +44-(0)1628-552550  Affymetrix Japan K.K. +81-(0)3-6430-4020
Panomics Products +1-877-PANOMICS www.panomics.com  USB Products +1-800-321-9322 www.usb.affymetrix.com
www.affymetrix.com Please visit our website for international distributor contact information.
For Research Use Only. Not for use in diagnostic procedures.
P/N F184 Rev. 1
©2011-12 Affymetrix, Inc. All rights reserved.