Publications
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About BarleyBase/PLEXdb | Cite or use BarleyBase/PLEXdb

Publications about BarleyBase/PLEXdb

BarleyBase/PLEXdb: A Unified Expression Profiling Database for Plants and Plant Pathogens

Wise RP, Caldo RA, Hong L, Shen L, Cannon EK, Dickerson JA.

Pages 347-363 In Methods in Molecular Biology, Vol. 406, Plant Bioinformatics - Methods and Protocols. Edwards D. ed. Humana Press, Totowa, NJ. 2007.

Please cite PLEXdb using this paper if your publication uses tools or data from PLEXdb.

 

BarleyBase — An expression profiling database for plant genomics

Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise and Julie A. Dickerson

Nucleic Acids Research, 2005, Vol. 33, Database issue D614-D618

PubMed: 15608273

 

BarleyExpress: a web-based submission tool for enriched microarray database annotations

Tang X, Shen L, Dickerson JA.

Bioinformatics 2005 21(3):399-401

PubMed: 15347571

 

 

Publications which cite or use PLEXdb/BarleyBase
(Also includes publications that support data in PLEXdb)

A dynamic gene expression atlas covering the entire life cycle of rice.

Wang L, Xie W, Chen Y, Tang W, Yang J, Ye R, Liu L, Lin Y, Xu C, Xiao J, Zhang Q.

The Plant Journal (2010) 61, 752–766

PubMed: 20003165

PLEXdb:

 

DEP and AFO regulate reproductive habit in rice..

Wang K, Tang D, Hong L, Xu W, Huang J, Li M, Gu M, Xue Y, Cheng Z.

PLoS Genet 2010 Jan 22;6(1):e1000818.

PubMed: 20107517

PLEXdb: browse OS33 experiment data

 

Structural and functional characterization of a winter malting barley .

María Muñoz-Amatriaín , L. Cistué, Y. Xiong, H. Bilgic, A. D. Budde, M. R. Schmitt, K. P. Smith, P. M. Hayes and G. J. Muehlbauer

Theoretical and Applied Genetics 120(5): 971-984 (2010)

PubMed: 19960335

PLEXdb: browse BB76 experiment data

 

Physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings.

Zheng L, Huang F, Narsai R, Wu J, Giraud E, He F, Cheng L, Wang F, Wu P, Whelan J, Shou H

Plant Physiol. 2009 Sep;151(1):262-74. Epub 2009 Jul 15.

PubMed: 19605549

PLEXdb: browse OS31 experiment data

 

Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools..

Sreenivasulu N, Usadel B, Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close TJ, Stitt M, Graner A, Wobus U

Plant Physiol 2008 Apr;146(4):1738-58.

PubMed: 18281415

PLEXdb: browse BB85 experiment data
browse BB86 experiment data

 

Differentially expressed genes during malting and correlation with malting quality phenotypes in barley (Hordeum vulgare L.)..

Lapitan NL, Hess A, Cooper B, Botha AM et al.

Theor Appl Genet 2009 Mar;118(5):937-52.

PubMed: 19132335

PLEXdb: browse BB87 experiment data

 

SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip..

Fujisawa H, Horiuchi Y, Harushima Y, Takada T et al.

BMC Bioinformatics 2009 May 6;10:131.

PubMed: 19419536

PLEXdb: browse OS29 experiment data

 

Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice..

Jain M, Khurana JP.

FEBS J 2009 Jun;276(11):3148-62.

PubMed: 19490115

PLEXdb: browse OS28 experiment data

 

Glycinebetaine-induced water-stress tolerance in codA-expressing transgenic indica rice is associated with up-regulation of several stress responsive genes..

Kathuria H, Giri J, Nataraja KN, Murata N et al.

Plant Biotechnol J 2009 Aug;7(6):512-26

PubMed: 19490479

PLEXdb: browse OS27 experiment data

 

Transcriptome Analysis of a Wheat Near-Isogenic Line Pair Carrying Fusarium Head Blight-Resistant and -Susceptible Alleles.

Haiyan Jia, Seungho Cho, Gary J. Muehlbauer

Molecular Plant-Microbe Interactions 22(11):1366-1378 (2009).

PLEXdb: browse TA20 experiment data

 

Wild barley expresses distinct sets of genes in response to pathogens of different trophic lifestyles..

Millett, B.P., Y. Xiong, S. Dahl, B.J. Steffenson, G.J. Muehlbauer.

Physiol. & Mol. Plant Path. (2009)

PLEXdb: browse BB61 experiment data

 

Drought response in the spikes of barley: gene expression in the lemma, palea, awn, and seed..

Tilahun Abebe1, Kalpalatha Melmaiee1, Virginia Berg and Roger P. Wise.

Functional & Integrative Genomics : epub ahead of print (Nov 2009).

PLEXdb: browse BB89 experiment data

 

Comparative Transcriptional Profiling Established the Awn as the Major Photosynthetic Organ of the Barley Spike While the Lemma and the Palea Primarily Protect the Seed .

Tilahun Abebe, Roger P. Wise, and Ronald W. Skadsen.

Plant Genome 2:247-259 (2009).

PLEXdb: browse BB73 experiment data

 

Transcript-Based Cloning of RRP46, a Regulator of rRNA Processing and R Gene-Independent Cell Death in Barley-Powdery Mildew Interactions. .

Xi L, Moscou MJ, Meng Y, Xu W, Caldo RA, Shaver M, Nettleton D, Wise RP.

The Plant Cell 21:3280-3295 (2009).

PubMed: 19861556

PLEXdb: browse BB46 experiment data

 

Expansion and diversification of the Populus R2R3-MYB family of transcription factors.

Wilkins O, Nahal H, Foong J, Provart NJ et al

Plant Physiol 2009 Feb;149(2):981-93

PubMed: 19091872

PLEXdb: browse PT2 experiment data

 

Wheat blast: histopathology and transcriptome reprogramming in response to adapted and nonadapted Magnaporthe isolates .

Hale A. Tufan, Graham R. D. McGrann, Andreas Magusin, Jean-Benoit Morel, Lucie Miché, Lesley A. Boyd

New Phytologist Volume 184(2):473-484 (2009).

PLEXdb: browse TA24 experiment data

 

Gene expression in grapevine cultivars in response to Bois Noir phytoplasma infection..

Albertazzi G., Caffagni A., Milc J.A., Francia E., Roncaglia E., Ferrari F., Tagliafico E., Stefani E., Pecchioni N.(2009)

Plant Science 176: 792-804 .

PLEXdb: browse VV14 experiment data

 

Ripening-Regulated Susceptibility of Tomato Fruit to Botrytis cinerea Requires NOR But Not RIN or Ethylene.

Cantu D, Blanco-Ulate B, Yang L, Labavitch JM et al

Plant Physiol 2009 Jul;150(3):1434-49

PubMed: 19465579

PLEXdb: browse LE3 experiment data

 

Novel Genes of Fusarium graminearum That Negatively Regulate Deoxynivalenol Production and Virulence.

D. M. Gardiner, K. Kazan, and J. M. Manners.

Mol Plant Microbe Interact. 2009 Dec;22(12):1588-600.

PubMed: 19888824

PLEXdb: browse FG14 experiment data

 

Lr34-mediated leaf rust resistance in wheat: transcript profiling reveals a high energetic demand supported by transient recruitment of multiple metabolic pathways.

Bolton MD, Kolmer JA, Xu WW, Garvin DF

Mol Plant Microbe Interact 2008 Dec;21(12):1515-27

PubMed: 18986248

PLEXdb: browse TA32 experiment data

 

Gene expression analysis of the wheat response to infection by Fusarium pseudograminearum.

Desmond, O.J., Manners, J.M., Schenk, P.M., Mclean, D.J. and Kazan K

Physiological and Molecular Plant Pathology. doi:10.1016/j.pmpp.2008.12.001

PLEXdb: browse TA31 experiment data

 

Molecular dissection of variation in carbohydrate metabolism related to water-soluble carbohydrate accumulation in stems of wheat.

Xue GP, McIntyre CL, Jenkins CL, Glassop D et al

Plant Physiol 2008 Feb;146(2):441-54

PubMed: 18083795

PLEXdb: browse TA30 experiment data

 

Suppression of Soybean Oleosin Produces Micro-Oil Bodies that Aggregate into Oil Body/ER Complexes.

Schmidt, MA and Herman, EM

Molecular Plant Advance Access published on September 15, 2008. doi:10.1093/mp/ssn049

PLEXdb: browse GM22 experiment data

 

Gene expression analysis in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow) in an early growth stage..

Panthee DR, Yuan JS, Wright DL, Marois JJ et al.

Funct Integr Genomics 2007 Oct;7(4):291-301

PubMed: 17318271

PLEXdb: browse GM12 experiment data

 

Genome-wide analysis of gene expression in soybean shoot apical meristem.

Haerizadeh F, Wong CE, Singh MB, Bhalla PL

Plant Mol Biol 2009 Apr;69(6):711-27

PubMed: 19115044

PLEXdb: browse GM20 experiment data

 

Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array.

Das S, Bhat PR, Sudhakar C, Ehlers JD et al

BMC Genomics 2008 Feb 28;9:107

PubMed: 18307807

PLEXdb: browse GM19 experiment data

 

Molecular processes underlying the floral transition in the soybean shoot apical meristem.

Wong CE, Singh MB, Bhalla PL

Plant J 2009 Mar;57(5):832-45

PubMed: 18980639

PLEXdb: browse GM18 experiment data

 

The genetics of barley low-tillering mutants: absent lower laterals (als)..

Dabbert T, Okagaki RJ, Cho S, Boddu J, Muehlbauer GJ.

Theor Appl Genet. 2009 May;118(7):1351-60.

PubMed: 19241055

PLEXdb: browse BB47 experiment data

 

Effect of transgenes on global gene expression in soybean is within the natural range of variation of conventional cultivars.

Cheng KC, Beaulieu J, Iquira E, Belzile FJ et al

J Agric Food Chem 2008 May 14;56(9):3057-6

PubMed: 18433101

PLEXdb: browse GM16 experiment data

 

A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R.

Gregory Alvord W, Roayaei JA, Quiñones OA, Schneider KT

Brief Bioinform 2007 Nov;8(6):415-31

PubMed: 17906332

PLEXdb: browse GM15 experiment data

 

Transcriptional analysis of the sweet orange interaction with the citrus canker pathogens Xanthomonas axonopodis pv. citri and Xanthomonas axonopodis pv. aurantifolii..

RAÚL ANDRÉS CERNADAS, LUCIANA RODRIGUES CAMILLO AND CELSO EDUARDO BENEDETTI

MOLECULAR PLANT PATHOLOGY (2008) 9 ( 5 )

PubMed: 19018992

PLEXdb:

 

Transcriptome profiling in hybrid poplar following interactions with Melampsora rust fungi.

Azaiez A, Boyle B, Levée V, Séguin A

Mol Plant Microbe Interact 2009 Feb;22(2):190-200

PubMed: 19132871

PLEXdb: browse PT1 experiment data

 

Differential expression of genes in the leaves of sugarcane in response to sugar accumulation.

McCormick A, Cramer M, Watt D

ropical Plant Biology, Volume 1, Number 2, June 2008 , pp. 142-158(17)

PLEXdb: browse SO1 experiment data

 

Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat.

Crismani W, Baumann U, Sutton T, Shirley N et al

BMC Genomics 2006 Oct 19;7:267

PubMed: 17052357

PLEXdb: browse TA27 experiment data

 

Barley elicits a similar early basal defence response during host and non-host interactions with Polymyxa root parasites.

Graham R. D. McGrann, Belinda J. Townsend, John F. Antoniw, Michael J. C. Asher, Effie S. Mutasa-Göttgens

European Journal of Plant Pathology 123(1):5-15

PLEXdb: browse BB74 experiment data
browse BB75 experiment data

 

Genome-wide transcriptional analysis of super-embryogenic Medicago truncatula explant cultures.

Imin N, Goffard N, Nizamidin M, Rolfe BG

BMC Plant Biol 2008 Oct 27;8:110

PubMed: 18950541

PLEXdb: browse ME3 experiment data

 

Transcriptional profiling of Medicago truncatula meristematic root cells.

Holmes P, Goffard N, Weiller GF, Rolfe BG et al

BMC Plant Biol 2008 Feb 27;8:21

PubMed: 18302802

PLEXdb: browse ME2 experiment data

 

Gene expression analyses in individual grape (Vitis vinifera L.) berries during ripening initiation reveal that pigmentation intensity is a valid indicator of developmental staging within the cluster.

Lund ST, Peng FY, Nayar T, Reid KE et al

Plant Mol Biol 2008 Oct;68(3):301-15

PubMed: 18642093

PLEXdb: browse VV15 experiment data

 

Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome.

A Aprile, A M Mastrangelo, A M De Leonardis, G Galiba, E Roncaglia, F Ferrari, L De Bellis, L Turchi, G Giuliano, L Cattivelli

BMC Genomics 2009, 10:279.

PLEXdb: browse TA23 experiment data

 

Comparative transcriptomics in the Triticeae.

Andreas W Schreiber, Tim Sutton, Rico A Caldo, Elena Kalashyan, Ben Lovell, Gwenda Mayo, Gary J Muehlbauer, Arnis Druka, Robbie Waugh, Roger P Wise, Peter Langridge and Ute Baumann

BMC Genomics 2009, 10:285.

PubMed: 19558723

PLEXdb: browse BB3 experiment data
browse TA3 experiment data

 

Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion..

Batista R, Saibo N, Lourenço T, Oliveira MM.

Proc Natl Acad Sci U S A 2008 Mar 4;105(9):3640-5

PubMed: 18303117

PLEXdb: browse OS24 experiment data

 

Highly sensitive and high-throughput analysis of plant hormones using MS-probe modification and liquid chromatography-tandem mass spectrometry: an application for hormone profiling in Oryza sativa.

Kojima M, Kamada-Nobusada T, Komatsu H, Takei K et al

Plant Cell Physiol 2009 Apr 20

PubMed: 19369275

PLEXdb: browse OS23 experiment data

 

OsLIC, a Novel CCCH-Type Zinc Finger Protein with Transcription Activation, Mediates Rice Architecture via Brassinosteroids Signaling.

Wang L, Xu Y, Zhang C, Ma Q et al

PLoS ONE 2008;3(10):e3521

PubMed: 18953406

PLEXdb: browse OS22 experiment data

 

Global patterns of gene expression in rice cultivars undergoing a susceptible or resistant interaction with the parasitic plant Striga hermonthica..

Swarbrick PJ, Huang K, Liu G, Slate J et al.

New Phytol 2008 May 26.

PubMed: 18507775

PLEXdb: browse OS19 experiment data

 

Control of rice grain-filling and yield by a gene with a potential signature of domestication..

Wang E, Wang J, Zhu X, Hao W et al.

Nat Genet 2008 Nov;40(11):1370-4

PubMed: 18820698

PLEXdb: browse OS17 experiment data

 

Genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice..

Li M, Xu W, Yang W, Kong Z et al.

Plant Physiol 2007 Aug;144(4):1797-812.

PubMed: 17556504

PLEXdb: browse OS16 experiment data

 

Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice..

Huang L, Sun Q, Qin F, Li C et al

Plant Physiol 2007 Jul;144(3):1508-19

PubMed: 17468215

PLEXdb: browse OS15 experiment data

 

Transcript profiling of the anoxic rice coleoptile..

Lasanthi-Kudahettige R, Magneschi L, Loreti E, Gonzali S et al.

Plant Physiol 2007 May;144(1):218-31

PubMed: 17369434

PLEXdb: browse OS14 experiment data

 

Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism..

Hirose N, Makita N, Kojima M, Kamada-Nobusada T et al.

Plant Cell Physiol 2007 Mar;48(3):523-39.

PubMed: 17293362

PLEXdb: browse OS13 experiment data

 

Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism..

Hirose N, Makita N, Kojima M, Kamada-Nobusada T et al.

Plant Cell Physiol 2007 Mar;48(3):523-39

PubMed: 17293362

PLEXdb: browse OS12 experiment data

 

Natural variation for alleles under epigenetic control by the maize chromomethylase zmet2..

Makarevitch I, Stupar RM, Iniguez AL, Haun WJ et al.

Genetics 2007 Oct;177(2):749-60.

PubMed: 17660570

PLEXdb: browse ZM26 experiment data

 

Pep1, a secreted effector protein of Ustilago maydis, is required for successful invasion of plant cells..

Doehlemann G, van der Linde K, Assmann D, Schwammbach D et al.

PLoS Pathog 2009 Feb;5(2):e1000290.

PubMed: 19197359

PLEXdb: browse ZM24 experiment data

 

Profiling expression changes caused by a segmental aneuploid in maize..

Makarevitch I, Phillips RL, Springer NM

BMC Genomics 2008 Jan 10;9:7.

PubMed: 18186930

PLEXdb: browse ZM23 experiment data

 

Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis..

Stupar RM, Gardiner JM, Oldre AG, Haun WJ et al.

BMC Plant Biol 2008 Apr 10;8:33

PubMed: 18402703

PLEXdb: browse ZM21 experiment data

 

Nonadditive expression and parent-of-origin effects identified by microarray and allele-specific expression profiling of maize endosperm..

Stupar RM, Hermanson PJ, Springer NM.

Plant Physiol 2007 Oct;145(2):411-25.

PubMed: 17766400

PLEXdb: browse ZM17 experiment data

 

Nonadditive expression and parent-of-origin effects identified by microarray and allele-specific expression profiling of maize endosperm..

Stupar RM, Hermanson PJ, Springer NM

Plant Physiol 2007 Oct;145(2):411-25.

PubMed: 17766400

PLEXdb: browse ZM16 experiment data

 

Microarray analysis of the interaction between the aphid Rhopalosiphum padi and host plants reveals both differences and similarities between susceptible and partially resistant barley lines..

Delp G, Gradin T, Ahman I, Jonsson LM.

Mol Genet Genomics 2009 Mar;281(3):233-48.

PubMed: 19085010

PLEXdb: browse BB71 experiment data

 

Using Genomics to Study Legume Seed Development.

Brandon H. Le, Javier A. Wagmaister , Tomokazu Kawashima, Anhthu Q. Bui, John J. Harada, and Robert B. Goldberg

Plant Physiology

PLEXdb: browse GM10 experiment data

 

Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid..

Stupar RM, Springer NM

Gentics 2006 Aug;173(4):2199-210

PubMed: 16702414

PLEXdb: browse ZM12 experiment data

 

Susceptibility of rice to the blast fungus, Magnaporthe grisea..

Ribot C, Hirsch J, Balzergue S, Tharreau D, Nottéghem JL, Lebrun MH, Morel JB.

J Plant Physiol. 2008 Jan;165(1):114-24

PubMed: 17905473

PLEXdb: browse OS7 experiment data

 

Transcriptome Analysis of Cold Acclimation in Barley Albina and Xantha Mutants.

Jan T. Svensson, Cristina Crosatti, Chiara Campoli, Roberto Bassi, Antonio Michele Stanca, Timothy J. Close and Luigi Cattivelli

Plant Physiology May 2006, Vol. 141, pp. 257–270

PubMed: 16603669

PLEXdb: browse BB65 experiment data

 

F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress..

Jain M, Nijhawan A, Arora R, Agarwal P et al.

Plant Physiol 2007 Apr;143(4):1467-83.

PubMed: 17293439

PLEXdb: browse OS5 experiment data

 

A gene expression map of Arabidopsis thaliana development.

Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU

Nat Genet. 2005 May;37(5):501-6. Epub 2005 Apr 3

PubMed: 15806101

PLEXdb: browse AT40 experiment data
browse AT41 experiment data

 

Microarray Analysis of Late Response to Boron Toxicity in Barley (Hordeum vulgare L.) Leaves.

Öz MT, Y?lmaz R, Eyido?an F, de Graaff L, Yücel M, Öktem HA ? Mehmet Tufan OZ, Remziye YILMAZ, Fusun EYIDOGAN, Leo de GRAAFF, Meral YUCEL, 2, Huseyin Avni OKTEM

Turkish Journal of Agriculture and Forestry, 33: 191-202, 2009.

PLEXdb: browse BB63 experiment data

 

Blufensin1 negatively impacts Basal defense in response to barley powdery mildew..

Meng Y, Moscou MJ, Wise RP.

Plant Physiol. 2009 Jan;149(1):271-85..

PubMed: 19005086

PLEXdb: browse BB10 experiment data

 

Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes.

Michael Gore,* Peter Bradbury, René Hogers, Matias Kirst, Esther Verstege, Jan van Oeveren, Johan Peleman, Edward Buckler, and Michiel van Eijk

The Plant Genome [A Supplement to Crop Science].Crop Sci. 47(S2) S135–S148 .July 2007 No. 2.

PubMed: not in pubmed

PLEXdb: browse ZM10 experiment data

 

A gene expression atlas of the model legume Medicago truncatula.

Vagner Benedito, Ivone Torez-Jerez, Jeremy Murray, Andry Andriankaja, Stacey Allen, Klementina Kakar, Maren Wandrey, Jerome Verdier, Helene Zuber, Thomas Ott, Sandra Moreau, Andreas Niebel, Tancred Frickey, Georg Weiller, Ji He, Xinbin Dai, Patrick Zhao, Yuhong Tang, and Michael Udvardi

The Plant Journal

PubMed: 18410479

PLEXdb: browse ME1 experiment data

 

Diversification of Lrk/Tak kinase gene clusters is associated with subfunctionalization and cultivar-specific transcript accumulation in barley.

Hu P, Wise RP

2008. Functional & Integrative Genomics

PubMed: 18414912

 

Transcriptional regulation by a NAC (NAM-ATAF1,2-CUC2) transcription factor attenuates ABA signalling for efficient basal defence towards Blumeria graminis f.sp. hordei in Arabidopsis. .

Jensen MK, Hagedorn PH, de Torres-Zabala M, Grant MR, Rung JH, Collinge DB, Lyngkjaer MF

Plant J. 2008 Aug 6. [Epub ahead of print]

PubMed: 18694460

PLEXdb: browse AT31 experiment data

 

Transcriptome analysis of high-temperature adult-plant resistance conditioned by Yr39 during the wheat–Puccinia striiformis f. sp. tritici interaction .

Tristan E Coram, Matthew L. Settles and Xianming Chen

MOLECULAR PLANT PATHOLOGY (2008) 9(4), 479-493

PubMed: 18705862

PLEXdb: browse TA11 experiment data

 

Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus.

Tristan E. Coram, Matthew L. Settles, Meinan Wang and Xianming Chen

Theoretical and Applied Genetics. 2008 May 10

PubMed: 18470504

 

Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots.

Elke Mangelsen, Joachim Kilian, Kenneth W Berendzen, Uner H Kolukisaoglu, Klaus Harter, Christer Jansson and Dierk Wanke

BMC Genomics, 2008, 9:194

PubMed: 18442363

 

Comparative transcriptome profiling of near-isogenic barley (Hordeum vulgare) lines differing in the allelic state of a major grain protein content locus identifies genes with possible roles in leaf senescence and nitrogen reallocation..

Aravind K. Jukanti, Nancy M. Heidlebaugh, David L. Parrott, Isabelle A. Fischer, Kate McInnerney and Andreas M. Fischer

New Phytologist 177(2):333-349 (Jan 2008).

PubMed: 18028296

PLEXdb: browse BB53 experiment data

 

Global gene regulation by Fusarium transcription factors Tri6 and Tri10 reveals adaptations for toxin biosynthesis..

Seong, K., Pasquali, M., Song, J., Hilburn, K., McCormick, S., Dong, Y., Xu, J.-R. and Kistler, H.C.

Molecular Microbiology 72: 354-367 (2009).

PubMed: 19320833

PLEXdb: browse FG10 experiment data
browse FG11 experiment data

 

Parallel expression profiling of barley-stem rust interactions.

Zhang L, Castell-Miller C, Dahl S, Steffenson B, Kleinhofs A.

Funct Integr Genomics. 2008 Jan 15 [Epub ahead of print]..

PubMed: 18196301

PLEXdb: browse BB49 experiment data

 

Powdery Mildew Induces Defense-Oriented Reprogramming of the Transcriptome in a Susceptible But Not in a Resistant Grapevine.

Raymond W.M. Fung, Martin Gonzalo, Csaba Fekete, Laszlo G. Kovacs, Yan He, Ellen Marsh, Lauren M. McIntyre, Daniel P. Schachtman and Wenping Qiu

Plant Physiol. 2008 Jan;146(1):236-49

PubMed: 17993546

PLEXdb: browse VV12 experiment data
browse VV13 experiment data

 

Transcript profiling in host-pathogen interactions.

Wise RP, Moscou MJ, Bogdanove AJ, Whitham SA

2007. Annual Review of Phytopathology 45: 329-369.

PubMed: 17480183

PLEXdb: browse BB4 experiment data

 

Transcriptome analysis of the wheat-Puccinia striiformis f. sp. tritici interaction.

TRISTAN E. CORAM, MEINAN WANG AND XIANMING CHEN

MOLECULAR PLANT PATHOLOGY 9 (2): 157-169 (2008).

PubMed: 18705849

PLEXdb: browse TA9 experiment data

 

Stress-responsive ATAF1 negatively regulates ABA signalling for efficeint basal defence in Arabidopsis.

Michael K. Jensen, Peter H. Hagedorn, Marta de Torres-Zabala, Murray R. Grant, Jesper H. Rung, David B. Collinge, and Michael F. Lyngkjaer

 

Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at veraison..

Stefania Pilati, Michele Perazzolli, Andrea Malossini, Alessandro Cestaro, Lorenzo Dematte, Paolo Fontana, Antonio Dal Ri, Roberto Viola, Riccardo Velasco, Claudio Moser.

BMC Genomics 8 (1), 428 (2007).

PubMed: 18034875

PLEXdb: browse VV11 experiment data

 

The L-type calcium channel, Cch1, affects ascospore discharge and mycelial growth in the filamentous fungus Gibberella zeae (anamorph Fusarium graminearum) .

Hallen HE, Trail F

Eukaryotic Cell 2008 Feb;7(2):415-24

PubMed: 18083828

PLEXdb: browse FG6 experiment data

 

Transcriptome analysis of trichothecene-induced gene expression in barley..

Boddu J, Cho S, Muehlbauer GJ

Mol Plant Microbe Interact. 2007 Nov;20(11):1364-75

PubMed: 17977148

PLEXdb: browse BB52 experiment data

 

Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development.

Deluc LG, Grimplet J, Wheatley MD, Tillett RL, Quilici DR, Osborne C, Schooley DA, Schlauch KA, Cushman JC, Cramer GR

BMC Genomics. 2007 Nov 22;8(1):429

PubMed: 18034876

PLEXdb: browse VV5 experiment data

 

Conidial germination in the filamentous fungus Fusarium graminearum.

Seong KY, Zhao X, Xu JR, Güldener U, Kistler HC

Fungal Genetics and Biology. 2007 Sep 14

PubMed: 17950638

PLEXdb: browse FG7 experiment data

 

Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation.

Potokina E, Druka A, Luo Z, Wise R, Waugh R, Kearsey M

The Plant Journal. 2007 Oct 18

PubMed: 17944808

PLEXdb: browse BB21 experiment data

 

Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines.

Bilgic, H., Cho, S., Garvin, D.F., and Muehlbauer, G.J.

2007. Genome 50(9):898-906

PubMed: 18059553

PLEXdb: browse BB55 experiment data

 

Steam-girdling of barley (Hordeum vulgare) leaves leads to carbohydrate accumulation and accelerated leaf senescence, facilitating transcriptomic analysis of senescence-associated genes.

Parrott DL, McInnerney K, Feller U, Fischer AM

2007 New Phytologist 176: 56–69

PubMed: 17803641

PLEXdb: browse BB50 experiment data

 

Mapping translocation breakpoints using a wheat microarray.

Bhat, P.R., Lukaszewski, A , Cui, X., Xu, J., Wanamaker, S., Svensson, JT., Waines, G.,. and Close, TJ.

Nucleic Acids Research (2007) 35 (9):2936-2943.

PubMed: 17439961

 

A Low Phytic Acid Barley Mutation Alters Seed Gene Expression.

David E. Bowen, Edward J. Souza, Mary J. Guttieri, Victor Raboy, and Jianming Fu

Crop Sci 2007;47 S-149-S-159.

PLEXdb: browse BB22 experiment data

 

SFP Genotyping From Affymetrix Arrays Is Robust But Largely Detects Cis-acting Expression Regulators.

Z. W. Luo, E. Potokina, A. Druka, R. Wise, R. Waugh and M. J. Kearsey

Genetics, Vol. 176, 789-800, June 2007, Copyright © 2007 doi:10.1534/genetics.106.067843

PubMed: 17409081

PLEXdb: browse BB21 experiment data

 

Distinct biphasic mRNA changes in response to Asian soybean rust infection.

Martijn van de Mortel, Justin C. Recknor, Michelle A. Graham, Dan Nettleton, Jaime D. Dittman, Rex T. Nelson, Cláudia V. Godoy, Ricardo V. Abdelnoor, Álvaro M.R. Almeida, Thomas J. Baum, Steven A. Whitham

Molecular Plant-Microbe Interactions (2007) Volume 20, Issue 8, pages 887-899. doi:10.1094/MPMI-20-8-0887

PubMed: 17722693

PLEXdb: browse GM2 experiment data

 

Tissue-specific mRNA expression profiling in grape berry tissues.

Grimplet J, Deluc LG, Tillett RL, Wheatley MD, Schlauch KA, Cramer GR, Cushman JC

BMC Genomics. 2007 Jun 21;8(1):187

PubMed: 17584945

PLEXdb: browse VV3 experiment data

 

Identifying regions of the wheat genome controlling seed development by mapping expression quantitative trait loci.

Jordan MC, Somers DJ and Banks TW

Plant Biotechnology J. 2007. 5:442-453

PubMed: 17388792

 

Gene expression associated with compatible viral diseases in grapevine cultivars.

Espinoza C, Vega A, Medina C, Schlauch K, Cramer G, Arce-Johnson P

Funct Integr Genomics 2007 Apr;7(2):95-110. Epub 2006 Jun 15

PubMed: 16775684

PLEXdb: browse VV7 experiment data

 

Estimating the number of true null hypotheses from a histogram of p-values.

Nettleton D, Hwang JTG, Caldo RA, Wise RP

2006. Journal of Agricultural, Biological, and Environmental Statistics 11: 337-356.

PLEXdb: browse BB4 experiment data

 

Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles.

Cramer GR, Ergul A, Grimplet J, Tillett RL, Tattersall EA, Bohlman MC, Vincent D, Sonderegger J, Evans J, Osborne C, Quilici D, Schlauch KA, Schooley DA, Cushman JC

Functional & integrative genomics

PubMed: 17136344

PLEXdb: browse VV2 experiment data

 

Rpr1, a gene required for Rpg1-dependent resistance to stem rust in barley.

Zhang L, Fetch T, Nirmala1 J, Schmierer D, Brueggeman R, Steffenson B, Kleinhofs A

TAG Theoretical and Applied Genetics. Volume 113, Number 5 / September, 2006

PubMed: 16832646

PLEXdb: browse BB28 experiment data

 

Stage-specific suppression of basal defense discriminates barley plants containing fast- and delayed-acting Mla powdery mildew resistance alleles.

Caldo RA, Nettleton D, Peng J, Wise RP

Molecular Plant-Microbe Interactions. 2006 Sep;19(9):939-47

PubMed: 16941898

PLEXdb: browse BB2 experiment data
browse BB4 experiment data

 

Genetic diversity contribution to errors in short oligonucleotide microarray analysis.

Kirst M, Caldo R, Casati P, Tanimoto G, Walbot V, Wise RP,5 and Buckler ES

Plant Biotechnology Journal. Online Early. doi:10.1111/j.1467-7652.2006.00198.x.

PLEXdb:

 

Transcriptome Analysis of Cold Acclimation in Barley Albina and Xantha Mutants.

Svensson JT, Crosatti C, Campoli C, Bassi R, Stanca AM, Close TJ, Cattivelli L

Plant Physiology 2006 May;141(1):257-70. Epub 2006 Apr 7.

PubMed: 16603669

 

Transcriptome Analysis of the Barley - Fusarium graminearum Interaction.

Boddu J, Cho S, Kruger WM, and Muehlbauer GJ

Molecular Plant-Microbe Interactions. 2006 April;19(4):407-417.

PubMed: 16610744

PLEXdb: browse BB9 experiment data

 

An atlas of gene expression from seed to seed through barley development.

Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R

Functional & Integrative Genomics. 2006 Mar

PubMed: 16547597

PLEXdb: browse BB3 experiment data

 

Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta.

Guldener U, Seong KY, Boddu J, Cho S, Trail F, Xu JR, Adam G, Mewes HW, Muehlbauer GJ, Kistler HC

Fungal Genetics and Biology. 2006 Mar 10

PubMed: 16531083

PLEXdb: browse FG1 experiment data
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Genetic Regulation of Gene Expression During Shoot Development in Arabidopsis.

DeCook R, Lall S, Nettleton D and Howell SH

Genetics. 2006 Feb;172(2):1155-1164.

PubMed: 15956669

PLEXdb: browse AT10 experiment data

 

Transcriptome analysis and physical mapping of barley genes in wheat-barley chromosome addition lines.

Cho S, Garvin DF, Muehlbauer GJ

Genetics. 2006 Feb;172(2):1277-85.

PubMed: 16322516

PLEXdb: browse BB8 experiment data

 

Expression analysis of barley (Hordeum vulgare L.) during salinity stress.

Walia H, Wilson C, Wahid A, Condamine P, Cui X, Close TJ

Functional & Integrative Genomics. 2006 Mar;6(2):143-156

PubMed: 16450154

 

Comparative Transcriptional Profiling of Two Contrasting Rice Genotypes under salinity stress during the vegetative growth stage.

Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, Close TJ

2005 Oct;139(2):822-35. Epub 2005 Sep 23

PubMed: 16183841

 

A comparative analysis of transcript abundance using SAGE and Affymetrix arrays.

Ibrahim AF, Hedley PE, Cardle L, Kruger W, Marshall DF, Muehlbauer GJ, Waugh R

Functional & Integrative Genomics. 2005 Jul;5(3):163-74.

PubMed: 15714318

 

Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit.

Cui X, Xu J, Asghar R, Condamine P, Svensson JT, Wanamaker S, Stein N, Roose M, and Close TJ

Bioinformatics Advance Access published online on August 23, 2005.

PubMed: 16118260

 

Single-feature polymorphism discovery in the barley transcriptome.

Rostoks N, Borevitz JO, Hedley PE, Russell J, Mudie S, Morris J, Cardle L, Marshall DF, Waugh R

Genome Biology. 2005, June;6(6).

PubMed: 15960806

PLEXdb: browse BB3 experiment data

 

Transcriptome profiling of the response of Arabidopsis thaliana suspension culture cells to sucrose starvation.

Contento AL, Kim SJ and Bassham DC

Plant Physiology, 135(4), 2330-47.

PubMed: 15310832

PLEXdb: browse AT8 experiment data

 

Interaction-Dependent Gene Expression in Mla-Specified Response to Barley Powdery Mildew.

Rico A. Caldo, Dan Nettleton and Roger P. Wise

Plant Cell. 16:2514-2528 (2004).

PubMed: 15319481

PLEXdb: browse BB4 experiment data
browse BB46 experiment data

 

Cutting Edge Transcriptome Analysis: It's All about Design.

Nancy A. Eckardt, News and Reviews Editor

Plant Cell. 16:2249-2251 (2004).

 

A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning.

Mitra RM, Gleason CA, Edwards A, Hadfield J, Downie JA, Oldroyd GE, Long SR

Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4701-5

PubMed: 15070781

PLEXdb: browse BB5 experiment data

 

A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age.

Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP

Plant Physiol. 2004 Mar;134(3):960-8.

PubMed: 15020760

PLEXdb: browse BB1 experiment data