Contribution of transcriptional regulation to natural variations in Arabidopsis (2005)
Chen WJ, Chang H, Hudson ME, Kwan W-K, Li J, Estes B, Knoll D, Shi L, Zhu T
Genome Biology 6: R32

Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array (2005)
Hazen SP, Pathan MS, Sanchez A, Baxter I, Dunn M, Estes B, Chang HS, Zhu T, Kreps JA, Nguyen HT
Functional Integrative Genomics 5: 104-116

Networks of transcription factors with roles in environmental stress response (2004)
Chen WJ, Zhu T
Trends in Plant Science 9: 591-596

Phenotypic anchoring of gene expression changes during estrogen-induced uterine growth (2004)
Moggs JG, Tinwell H, Spurway T, Chang H-S, Pate I, Lim FL, Moore DJ, Soames A, Stuckey R, Currie R, Zhu T, Kimber I, Ashby J and Orphanides G
Environmental Health Perspectives Toxicogenomics 112: 1589-1606

Improving nutrition value of cereal grains by genomic approach (2004)
Shi L, Zhu T
In GENOMICS AND PROTEOMICS IN NUTRITION.
Moustaid-Moussa N, Berdanier CD Eds.
Marcel Dekker, New York ISBN: 0-8247-5430-1

Microchip based high throughput screening in chemical genomics (2004)
Khandurina J, Zhu T, Guttman A
In CHEMICAL GENOMICS.
Darvas F, Guttman A, Dorman G Eds.
Marcel Dekker, New York ISBN: 0-8247-5490-5

The transcriptome of rhizobacteria-induced systemic resistance in Arabidopsis (2004)
Verhagen BW, Glazebrook J, Zhu T, Chang HS, van Loon LC, Pieterse CM
Molecular Plant Microbe Interaction 17: 895-908

The response regulator arr2 integrates hormone and stress signaling in Arabidopsis (2004)
Hass C, Lohrmann J, Albrecht V, Sweere U, Yoo SD, Hwang I, Zhu T, Schfer E, Kudla J, Harter K
EMBO Journal 23: 3290-302

Gene expression signatures from three genetically separable R gene signaling pathways for downy mildew resistance (2004)
Eulgem T, Weigman VJ, Chang H-S, McDowell JM, Holub EB, Glazebrook J, Zhu T, Dangl JL
Plant Physiology 135: 1129-1144

Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation (2004)
Tepperman JM, Hudson ME, Khanna R, Zhu T, Chang H-S, Wang X, Quail PH
Plant Journal 38: 725-739

Finding unexpected patterns in microarray data (2003)
Perelman S, Mazzella MA, Muschietti J, Zhu T, Casal JJ
Plant Physiology 133: 1717-1725

Transcriptional responses to low temperature and their regulation in Arabidopsis (2003)
Zhu T, Provart NJ
Canadian Journal of Botany 81: 1168-1174

The genetic architecture of odor-guided behavior in Drosophila: epistasis and the transcriptome (2003)
Anholt RR, Dilda CL, Chang S, Fanara JJ, Kulkarni NH, Ganguly I, Rollmann SM, Kamdar KP, Mackay TF
Nature Genetics 35: 180-184

Expression Profiles of Arabidopsis thaliana in Mineral Deficiencies Reveal Novel Transporters Involved in Metal Homeostasis (2003)
Wintz H, Fox T, Wu Y-Y, Feng V, Chen W, Chang H-S, Zhu T, Vulpe C
Journal of Biological Chemistry 278: 47644-47653

Global analysis of gene expression using GeneChip microarrays (2003)
Zhu T
Current Opinion in Plant Biology 6: 418-425

Identification of nutrient partitioning genes participating in rice grain filling by singular value decomposition (SVD) of genome expression data (2003)
Anderson A, Hudson M, Chen W, Zhu T
BMC Genomics 4: 26

Crosstalk between cytosolic and plastidial pathways of isoprenoid biosynthesis in Arabidopsis thaliana (2003)
Laule O, Frholz A, Chang H-S, Zhu T, Wang X, Heifetz PB, Gruissem W, Lange BM
Proceedings of the National Academy of Sciences, U.S.A. 100: 6866-6871

Characterization of the Early Response of Arabidopsis to Alternaria brassicicola Infection Using Expression Profiling (2003)
van Wees SCM, Chang H-S, Zhu T, Glazebrook J
Plant Physology 132: 606-617

Gene Expression Phenotypes of Arabidopsis Associated with Sensitivity to Low Temperatures (2003)
Provart NJ, Gil P, Chen W, Han B, Chang H-S, Wang X, Zhu T
Plant Physology 132: 893-906

Topology of the network integrating salicylate and jasmonate signal transduction derived from global expression phenotyping (2003)
Glazebrook J, Chen W, Estes B, Chang H-S, Nawrath C, Mtraux J-P, Zhu T, Katagiri F
The Plant Journal 34: 217-228

Quantitative Nature of Arabidopsis Responses during Compatible and Incompatible Interactions with the Bacterial Pathogen Pseudomonas syringae (2003)
Tao Y, Xie Z, Chen W, Glazebrook J, Chang H-S, Han B, Zhu T, Katagiri F
The Plant Cell 15: 1-14

Diverse RNA viruses elicit the expression of common sets of genes in susceptible Arabidopsis thaliana plants (2003)
Whitham SA, Quan S, Chang H-S, Cooper B, Estes B, Zhu T, Wang X, Hou Y-M
The Plant Journal 33: 271-283

Large-Scale Identification of Single-Feature Polymorphisms in Complex Genomes (2003)
Borevitz JO, Liang D, Plouffe D, Chang H-S, Zhu T, Weigel D, Berry CC, Winzeler E, Chory J
Genome Research 13: 513-523

EMF Genes Maintain Vegetative Development by Repressing the Flower Program in Arabidopsis (2003)
Moon Y-H, Chen L, Pan RL, Chang H-S, Zhu T, Maffeo DM, Sung ZR
The Plant Cell 16: 681-693

Transcriptional control of nutrient partitioning during rice grain filling (2003)
Zhu T, Budworth P, Chen W, Provart N, Chang H-S, Guimil S, Su WP, Zou G, Wang X.
Plant Biotechnology Journal 1: 59-70

Finding Unexpected Patterns in Microarray Data (2003)
Susana Perelman, Mara Agustina Mazzella, Jorge Muschietti, Tong Zhu, and Jorge J.
Casal Plant Physiology 133: 1717-1725

Transcriptional responses to low temperature and their regulation in Arabidopsis (2003)
Tong Zhu and Nicholas J. Provart
Canadian Journal of Botany 81: 1168-1174

Expression Profiles of Arabidopsis thaliana in Mineral Deficiencies Reveal Novel Transporters Involved in Metal Homeostasis (2003)
Henri Wintz, Tama Fox, Ying-Ying Wu, Victoria Feng, Wenqiong Chen, Hur-Song Chang,Tong Zhu, and Chris Vulpe
Journal of Biological Chemistry 278: 47644-47653

Global analysis of gene expression using GeneChip microarrays (2003)
Tong Zhu
Current Opinion in Plant Biology 6: 418-425

Identification of nutrient partitioning genes participating in rice grain filling by singular value decomposition (SVD) of genome expression data (2003)
Abraham Anderson, Matthew Hudson, Wenqiong Chen, and Tong Zhu
BMC Genomics 4: 26

Crosstalk between cytosolic and plastidial pathways of isoprenoid biosynthesis in Arabidopsis thaliana (2003)
Oliver Laule, Andreas Frholz, Hur-Song Chang, Tong Zhu, Xun Wang, Peter B. Heifetz, Wilhelm Gruissem, and B. Markus Lange
Proceedings of the National Academy of Sciences, U.S.A. 100: 6866-6871

Characterization of the Early Response of Arabidopsis to Alternaria brassicicola Infection Using Expression Profiling (2003)
Saskia C.M. van Wees, Hur-Song Chang, Tong Zhu, and Jane Glazebrook
Plant Physology 132: 606-617

Gene Expression Phenotypes of Arabidopsis Associated with Sensitivity to Low Temperatures (2003)
Nicholas J. Provart, Wenqiong Chen, Bin Han, Hur-Song Chang, Xun Wang, and Tong Zhu
Plant Physology 132: 893-906

Topology of the Network Integrating Salicylate and Jasmonate Signal Transduction Derived from Global Expression Phenotyping (2003)
Jane Glazebrook, Wenqiong Chen, Bram Estes, Hur-Song Chang, Christiane Nawrath, Jean-Pierre Metraux, Tong Zhu and Fumiaki Katagiri
The Plant Journal 34: 217-228

Quantitative Nature of Arabidopsis Responses during Compatible and Incompatible Interactions with the Bacterial Pathogen Pseudomonas syringae (2003)
Yi Tao, Zhiyi Xie, Wenqiong Chen, Jane Glazebrook, Hur-Song Chang, Bin Han, Tong Zhu, Guangzhou Zou and Fumiaki Katagiri
The Plant Cell 15: 1-14

Diverse RNA Viruses Elicit the Expression of Common Sets of Genes in Susceptible Arabidopsis thaliana Plants (2003)
Steven A. Whitham, Sheng Quan, Hur-Song Chang, Bret Cooper, Bram Estes, Tong Zhu, Xun Wang and Yu-Ming Hou
The Plant Journal 33: 271-283

Large-Scale Identification of Single-Feature Polymorphisms in Complex Genomes (2003)
Justin O. Borevitz, David Liang, David Plouffe, Hur-Song Chang, Tong Zhu, Detlef Weigel, Charles C. Berry, Elizabeth Winzeler, and Joanne Chory
Genome Research 13: 513-523

EMF Genes Maintain Vegetative Development by Repressing the Flower Program in Arabidopsis (2003)
Yong-Hwan Moon, Lingjing Chen, Rong Long Pan, Hur-Song Chang, Tong Zhu, Daniel M. Maffeo, and Z. Renee Sung
The Plant Cell 16: 681-693

Transcriptional Control of Nutrient Partitioning during Rice Grain Filling (2003)
Tong Zhu, Paul Budworth, Wenqiong Chen, Nicholas Provart, Hur-Song Chang, Sonia Guimil, Wenpei Su, Bram Estes, Guangzhou Zou and Xun Wang
Plant Biotechnology Journal 1: 59-70

Distinct Regulation of Salinity and Genotoxic Stress Responses by Arabidopsis MAP Kinase Phosphatase 1 (2002)
Roman Ulm, Kazuya Ichimura,Tsuyoshi Mizoguchi, Scott C.Peck, Tong Zhu, Xun Wang, Kazuo Shinozaki and Jerzy Paszkowski
The EMBO Journal 21(23): 6483-6493

Distinct regulation of salinity and genotoxic stress responses by Arabidopsis MAP kinase phosphatase 1 (2002)
Ulm R, Ichimura K, Mizoguch T, Peck SC, Zhu T, Wang X, Shinozaki K, Paszkowski J.
The EMBO Journal 21: 6483-6493

Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress (2002)
Kreps J, Wu Y, Chang H-S, Zhu T, Wang X, Harper J
Plant Physiology 130: 2129-2141

Automated High-Throughput RNA Analysis by Capillary Electrophoresis (2002)
Khandurina J, Chang H-S, Wanders B, Guttman A
BioTechniques 32: 1226-1230

Transcription profiling of the early gravitropic response in Arabidopsis using high-density oligonucleotide probe microarrays (2002)
Moseyko N, Zhu T, Chang H-S, Wang X, Feldman LJ
Plant Physiology 130: 720-728

Analysis of differential gene expression by ligation specificity-based transcript profiling (2002)
Li B-Y, Kwan WK, Turgeon G, Wu J, Wang X, Li E, Zhu T, Shi L
Omics 6: 175-185

Transcriptional profiling reveals novel interactions between wounding, pathogen, abiotic stress, and hormonal responses in Arabidopsis (2002)
Cheong YH, Chang H-S, Gupta R, Wang X, Zhu T, Luan S
Plant Physiology 125: 661-677

Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses (2002)
Chen W, Provart NJ, Glazebrook J, Katagiri F, Chang HS, Eulgem T, Mauch F, Luan S, Zou G, Whitham SA, Budworth PR, Tao Y, Xie Z, Chen X, Lam S, Kreps JA, Harper JF, Si-Ammour A, Mauch-Mani B, Heinlein M, Kobayashi K, Hohn T, Dangl JL, Wang X, Zhu T
The Plant Cell 14: 559-574

Transcriptome Changes for Arabidopsis in Response to Salt, Osmotic, and Cold Stress (Dec, 2002)
Joel A. Kreps, Yajun Wu, Hur-Song Chang, Tong Zhu, Xun Wang, and Jeff F. Harper
Plant Physology 130: 2129-2141

Automated High-Throughput RNA Analysis by Capillary Electrophoresis (June, 2002)
Julia Khandurina, Hur-Song Chang, Bart Wanders, and Andrs Guttman
BioTechniques 32: 1226-1230

Transcription Profiling of the Early Gravitropic Response in Arabidopsis Using High-Density Oligonucleotide Probe Microarrays1[w] (October, 2002)
Nick Moseyko, Tong Zhu, Hur-Song Chang, Xun Wang, and Lewis J. Feldman*
Plant Physiology 130: 720-728

Analysis of Differential Gene Expression by Ligation Specificity-Based Transcript Profiling (2002)
BI-YU LI, WAI KING KWAN, GILLIAN TURGEON, JIANGUO WU, XUN WANG, E. LI, TONG ZHU, and LIANG SHI OMICS
A Journal of Integrative Biology 6(2): 175-185

Transcriptional Profiling Reveals Novel Interactions between Wounding, Pathogen, Abiotic Stress, and Hormonal Responses in Arabidopsis 1[w] (June, 2002)
Yong Hwa Cheong, Hur-Song Chang, Rajeev Gupta, Xun Wang, Tong Zhu*, and Sheng Luan
Plant Physiology 129: 661-677

Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses (Mar, 2002)
Wenqiong Chen, Nicholas Provart, Jane Glazebrook, Fumiaki Katagiri, Hur-Song Chang, Thomas Eulgem, Felix Mauch, Sheng Luan, Guangzhou Zou, Steve A. Whitham, Paul R. Budworth, Yi Tao, Zhiyi Xie, 1, Xi Chen, Steve Lam, Joel A. Kreps, Jeffery F. Harper, Azzedine Si-Ammour, Brigitte Mauch-Mani, Manfred Heinlein, Kappei Kobayashi, Thomas Hohn, Jeffery L. Dangl, Xun Wang and Tong Zhu
The Plant Cell 14: 559-574

Gene Expression Microarrays: Improvements and Applications Towards Agricultural Gene Discovery (Dec, 2001)
Tong Zhu, Hur-Song Chang, James Schmeits, Pedro Gil, Liang Shi, Paul Budworth, Guangzhou Zou, Xi Chen, and XunWang
JALA 6: 95-98

Multiple Transcription-Factor Genes Are Early Targets of Phytochrome A Signaling (July, 2001)
Tepperman JM, Zhu T, Chang H-S, Wang X, Quail PH
Proceedings of the National Academy of Sciences, U.S.A. 98: 9437-9442

Towards Elucidating Global Gene Expression in Developing Arabidopsis: Parallel Analysis of 8300 Genes (April, 2001)
Zhu T, Budworth P, Han B, Brown D, Chang H-S, Zou Z, Wang X
Plant Physiology and Biochemistry 39: 221-242

Gene expression microarrays: Improvements and applications towards agricultural gene discovery (2001)
Zhu T, Chang H-S, Schmeits J, Gil P, Shi L, Budworth P, Zou G, Chen X, Wang X
Journal of the Association for Laboratory Automation 6: 95-98

Multiple transcription-factor genes are early targets of phytochrome A signaling (2001)
Tepperman JM, Zhu T, Chang H-S, Wang X, Quail PH
Proceedings of the National Academy of Sciences, U.S.A. 98: 9437-9442

Towards elucidating global gene expression in developing Arabidopsis: parallel analysis of 8300 genes (2001)
Zhu T, Budworth P, Han B, Brown D, Chang H-S, Zou Z, Wang X
Plant Physiology and Biochemistry 39: 221-242

Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock (Dec. 2000)
Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA
Science 290(5499): 2110-3

Large-Scale Profiling of the Arabidopsis Transcriptome (Dec. 2000)
Zhu T, Wang X
Plant Physiology 124(4): 1472-1476

Orchestrated transcription of key pathways in Arabidopsis by the circadian clock (2000)
Harmer SL, Hogenesch JB, Straume M, Chang H-S, Han B, Zhu T, Wang X, Kreps JA, Kay SA
Science 290: 2110-2113.

Large-scale profiling of the Arabidopsis transcriptome (2000)
Zhu T, Wang X
Plant Physiology 124: 1472-1476.