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Supplementary data for our genomics publications could be found
in the Yale Plant Genomics Group.

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: Full Text Available

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· Jang S, Marchal V, Panigrahi KC, Wenkel S, Soppe W, Deng XW, Valverde F, Coupland G.

Arabidopsis COP1 shapes the temporal pattern of CO accumulation conferring a photoperiodic flowering response.

EMBO J. 2008 Apr 23;27(8):1277-88. Epub 2008 Apr 3.

· Li L, He H, Zhang J, Wang X, Bai S, Stolc V, Tongprasit W, Young ND, Yu O, Deng XW.

Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays.

Genome Biol. 2008 Mar 19;9(3):R57. [Epub ahead of print]

· Chen H, Zhang J, Neff MM, Hong SW, Zhang H, Deng XW, Xiong L.

Integration of light and abscisic acid signaling during seed germination and early seedling development.

Proc Natl Acad Sci U S A 2008 Mar 18;105(11):4495-500. Epub 2008 Mar 10.

· Li X, Wang X, He K, Ma Y, Su N, He H, Stolc V, Tongprasit W, Jin W, Jiang J, Terzaghi W, Li S & Deng XW

High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression

Plant Cell 2008; Epub Feb 8. 2008. Suppl. Dataset 1, 2.

· Lee JH, Terzaghi W, Gusmaroli G, Charron JBF, Yoon HJ, Chen H, He YJ, Xiong Y & Deng XW.

Characterization of Arabidopsis and Rice DWD Proteins and Their Roles as Substrate Receptors for CUL4-RING E3 Ubiquitin Ligases

Plant Cell 2008; Epub Jan 25 2008 Suppl. Dataset 1a, 1b, 2.

· Feng S, Martinez C, Gusmaroli G, Wang Y, Zhou J, Wang F, Chen L, Yu L, Iglesias-Pedraz JM, Kircher S, Schafer E, Fu X, Fan LM & Deng XW.

Coordinated regulation of Arabidopsis thaliana development by light and gibberellins

Nature 2008 Jan 24; 451(475-479).

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· Gong W, He K, Covington M, Dinesh-Kumar SP., Snyder M, Harmer SL, Zhu YX & Deng XW.

The Development of Protein Microarrays and Their Applications in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors

Molecular Plant 2007 Oct23; [Epub ahead of print].

· Rubio V and Deng XW.

Standing on the Shoulders of GIGANTEA

Science 2007 Oct 12; 318(5848): 206 - 207.

· Menon S, Chi H, Zhang H, Deng XW, Flavell RA, Wei N.

COP9 signalosome subunit 8 is essential for peripheral T cell homeostasis and antigen receptor¨Cinduced entry into the cell cycle from quiescence

Nat Immunol. 2007 Nov; 8(11):1236-45. Epub 2007 Sep 30.

Supplementary information

· Han B, Xue Y, Li J, Deng XW, Zhang Q.

Rice functional genomics research in China.

Philos Trans R Soc Lond B Biol Sci. 2007 Jun 29;362(1482):1009-21.

· Pick E, Lau OS, Tsuge T, Menon S, Tong Y, Dohmae N, Plafker SM, Deng XW, Wei N.

Mammalian DET1 regulates Cul4A activity and forms stable complexes with E2 ubiquitin-conjugating enzymes.

Mol Cell Biol. 2007 Jul;27(13):4708-19. Epub 2007 Apr 23.

· Qin G, Gu H, Ma L, Peng Y, Deng XW, Chen Z, Qu LJ.

Disruption of phytoene desaturase gene results in albino and dwarf phenotypes in Arabidopsis by impairing chlorophyll, carotenoid, and gibberellin biosynthesis

Cell Res. 2007 (17): 471-482. Epub 2007 May 8.

· Li L, Wang X, Sasidharan R., Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng XW.

Global Identification and Characterization of Transcriptionally Active Regions in the Rice Genome

PLoS ONE. 2007; 2(3): e294.

· Jiao Y, Deng XW.

A genome-wide transcriptional activity survey of rice transposable element-related genes

Genome Biology. 2007 8(2):R28. Epub 2007 Feb 27.

· Lee J, He K, Stolc V, Lee H, Figueroa P, Gao Y, Tongprasit W, Zhao H, Lee I, Deng XW.

Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development.

Plant Cell. 2007 Mar; 19: 731-749. Epub 2007 Mar 2.

Editorial Comment

· Jiao Y, Lau OS, Deng XW.

Light-regulated transcriptional networks in higher plants.

Nat Rev Genet. 2007 Mar;8(3):217-30.

· Gusmaroli G, Figueroa P, Serino G, Deng XW.

Role of the MPN Subunits in COP9 Signalosome Assembly and Activity, and Their Regulatory Interaction with Arabidopsis Cullin3-Based E3 Ligases.

Plant Cell. 19(2):564-81. Epub 2007 Feb 16.

· Zhou J, Wang X, Jiao Y, Qin Y, Liu X, He K, Chen C, Ma L, Wang J, Xiong L, Zhang Q, Fan L, Deng XW.

Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle

Plant Mol Biol. 2007 Mar;63(5):591-608. Epub 2007 Jan 16.

· Bai S, Zhong X, Ma L, Zheng W, Fan LM, Wei N, Deng XW.

A simple and reliable assay for detecting specific nucleotide sequences in plants using optical thin-film biosensor chips

Plant J. 2007 Jan; 49 (2): 354-366. Epub 2006 Dec 6.

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· Chen H, Karplus VJ, Ma H, Deng XW.

Plant Biology Research Comes of Age in China.

Plant Cell. 2006 Nov;18(11):2855-64.

· Su N, He K, Jiao Y, Chen C, Zhou J, Li L, Bai S, Li X, Deng XW.

Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice.

Plant Mol Biol. 2006 Oct 28; [Epub ahead of print]

· Wang X, He H, Li L, Chen R, Deng XW, Li S

NMPP: a user-customized NimbleGen microarray data processing pipeline.

Bioinformatics. 2006 Dec; 22(23): 2955-7. Epub 2006 Oct 12.

· Lee JH, Deng XW, Kim WT

Possible role of light in the maintenance of EIN3/EIL1 stability in Arabidopsis seedlings.

Biochem Biophys Res Commun. 2006 Nov; 350(2): 484-491. Epub 2006 Sep 25.

· Chen, H, Shen Y, Tang X, Yu L, Wang J, Guo L, Zhang Y, Zhang H, Feng S, Strickland E, Zheng N, and Deng XW

Arabidopsis CULLIN4 Forms an E3 Ubiquitin Ligase with RBX1 and the CDD Complex in Mediating Light Control of Development

Plant Cell 2006;18(8):1991-2004. Epub 2006 July 14.

· Guo L, Yin B, Zhou J, Li X, Deng XW

Development of rabbit monoclonal and polyclonal antibodies for detection of site-specific histone modifications and their application in analyzing overall modification levels.

Cell Research. 2006 May; 16(5): 519-27. Epub 2006 May 15

· Dong L, Wang L, Zhang Y, Zhang Y, Deng X, Xue Y.

An auxin-inducible F-box protein CEGENDUO negatively regulates auxin-mediated lateral root formation in Arabidopsis.

Plant Mol Biol. 2006 Mar; 60(4): 599-615.

· Yi C, Li S, Wang J, Wei N, Deng XW.

Affinity purification reveals the association of WD40 protein constitutive photomorphogenic 1 with the hetero-oligomeric TCP-1 chaperonin complex in mammalian cells.

Int J Biochem Cell Biol. 2006; 38(7): 1076-83. Epub 2006 Feb 8.

· Li J, Zhu S, Song X, Shen Y, Chen H, Yu J, Yi K, Liu Y, Karplus VJ, Wu P, Deng XW.

A Rice Glutamate Receptor-Like Gene Is Critical for the Division and Survival of Individual Cells in the Root Apical Meristem.

Plant Cell. 2006 Feb; 18(2):340-9. Epub 2005 Dec 23.

· Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, Deng XW.

Genome-wide transcription analyses in rice using tiling microarrays.

Nature Genetics. 2006 Jan; 38: 124 – 129. Epub Dec 20.

· Datta S, Hettiarachchi GH, Deng XW, Holm M.

Arabidopsis CONSTANS-LIKE3 Is a Positive Regulator of Red Light Signaling and Root Growth.

Plant Cell. 2006 Jan;18(1):70-84. Epub 2005 Dec 9.

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· Jiao Y, Ma L, Strickland E, Deng XW.

Conservation and Divergence of Light-Regulated Genome Expression Patterns during Seedling Development in Rice and Arabidopsis.

Plant Cell. 2005 Dec; 17(12):3239-56. Epub 2005 Nov 11.

· Kraft E, Stone SL, Ma L, Su N, Gao Y, Lau OS, Deng XW, Callis J.

Genome Analysis and Functional Characterization of the E2 and RING-Type E3 Ligase Ubiquitination Enzymes of Arabidopsis.

Plant Physiol. 2005 Dec; 139(4):1597-611.

· Feng JX, Liu D, Pan Y, Gong W, Ma LG, Luo JC, Deng XW, Zhu YX.

An Annotation Update via cDNA Sequence Analysis and Comprehensive Profiling of Developmental, Hormonal or Environmental Responsiveness of the Arabidopsis AP2/EREBP Transcription Factor Gene Family.

Plant Mol Biol. 2005 Dec; 59(6):853-68.

· Wang X, Li L, Chen C, Wang J, Li S, and Deng XW

Analysis of oligo hybridization properties by high-resolution tiling arrays in rice.

Proceeding report, 5th International Rice Genetics Symposium, 2005: 65-76. 19-23 November, 2005; Manila, Philippines.

· Shen Y, Feng S, Ma L, Lin R, Qu LJ, Chen Z, Wang H, Deng XW.

Arabidopsis FHY1 Protein Stability Is Regulated by Light via Phytochrome A and 26S Proteasome.

Plant Physiol. 2005 Nov; 139: 1234–1243.

· Zhang S, Chen C, Li L, Meng L, Singh J, Jiang N, Deng XW, He ZH, Lemaux PG.

Evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family.

Plant Physiol. 2005 139(3):1107-24.

· Stolc V, Li L, Wang X, Li X, Su N, Tongprasit W, Han B, Xue Y, Li J, Snyder1 M, Gerstein M, Wang J, Deng XW.

A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.

Plant Molecular Biology. 2005 Sep; 59(1):137–149.

· Yi C, Deng XW.

COP1 - from plant photomorphogenesis to mammalian tumorigenesis.

Trends Cell Biol. 2005 Nov; 15 (11): 618-625.

· Ma L, Chen C, Liu X，Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X, Bao J, Li J, Pedersen S, Bolund L, Zhao H, Yuan L, Wong GKS, Wang J, Deng XW, Wang J.
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis.

Genome Research. 2005 September; 15(9):1274-1283.

· Yi C, Li S, Chen X, Wiemer EAC, Wang J, Wei N, Deng XW.

Major Vault Protein, in Concert with Constitutively Photomorphogenic 1, Negatively Regulates c-Jun–Mediated Activator Protein 1 Transcription in Mammalian Cells.

Cancer Res. 2005 July; 65(13): 5835 – 5840.

· Menon S, Rubio V, Wang X, Deng XW, Wei N.

Purification of the COP9 Signalosome from Porcine Spleen, Human Cell Lines, and Arabidopsis thaliana Plants

Methods Enzymol 2005; 398:468-481.

· Li L, Deng XW.
It runs in the family: regulation of brassinosteroid signaling by the BZR1-BES1 class of transcription factors.
Trends Plant Sci. 2005 Jun; 10(6): 266-8.

· Li L, Wang X, Xia M, Stolc V, Su N, Peng Z, Li S, Wang J, Wang X, Deng XW.
Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture.
Genome Biol. 2005 Jun ;6(6):R52. Epub 2005 May 27.

· Jiao Y, Jia P, Wang X, Su N, Yu S, Zhang D, Ma L, Feng Q, Jin Z, Li L, Xue Y, Cheng Z, Zhao H, Han B, Deng XW.
A Tiling Microarray Expression Analysis of Rice Chromosome 4 Suggests a Chromosome-Level Regulation of Transcription.
Plant Cell. 2005 June; 17(6):1641-57. Epub 2005 Apr 29.

· Ma L, Sun N, Liu X, Jiao Y, Zhao H, Deng XW.
Organ-Specific Expression of Arabidopsis Genome during Development.
Plant Physiol. 2005 May;138(1):80-91.