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Jeffrey Chen

Research Profile

Physiology

Anatomy

Living Beings

Genes & Molecular Sequences

Procedures

Gene Expression Profiling

Chemicals & Drugs

Devices

Oligonucleotide Array Sequence Analysis

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Models, Genetic

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Publications

TOP 3
Jie Lu; Changqing Zhang; David C Baulcombe; Z Jeffrey Chen
Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds.
Marisa Miller; Changqing Zhang; Z Jeffrey Chen
Ploidy and Hybridity Effects on Growth Vigor and Gene Expression in Arabidopsis thaliana Hybrids and Their Parents.
Danny W-K Ng; Jie Lu; Z Jeffrey Chen
Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility.

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All Publications

2012: Jie Lu; Changqing Zhang; David C Baulcombe; Z Jeffrey Chen
Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(14):5529-34.
2012: Marisa Miller; Changqing Zhang; Z Jeffrey Chen
Ploidy and Hybridity Effects on Growth Vigor and Gene Expression in Arabidopsis thaliana Hybrids and Their Parents.
G3 (Bethesda, Md.) 2012;2(4):505-13.
2012: Danny W-K Ng; Jie Lu; Z Jeffrey Chen
Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility.
Current opinion in plant biology 2012;15(2):154-61.
2011: Danny W-K Ng; Gregory Palmer; Dorothea Tholl; Marvin Whiteley; Changqing Zhang; Marisa Miller; Z Jeffrey Chen
cis- and trans-Regulation of miR163 and target genes confers natural variation of secondary metabolites in two Arabidopsis species and their allopolyploids.
The Plant cell 2011;23(5):1729-40.
2011: Z Jeffrey Chen; Xueying Guan
Auxin boost for cotton.
Nature biotechnology 2011;29(5):407-9.
2011: Dustin Mayfield; Z Jeffrey Chen; J Chris Pires
Epigenetic regulation of flowering time in polyploids.
Current opinion in plant biology 2011;14(2):174-8.
2011: Misook Ha; Danny W-K Ng; Wen-Hsiung Li; Z Jeffrey Chen
Coordinated histone modifications are associated with gene expression variation within and between species.
Genome research 2011;21(4):590-8.
2011: Xueying Guan; Jinsuk J Lee; Mingxiong Pang; Xiaoli Shi; David M Stelly; Z Jeffrey Chen
Activation of Arabidopsis seed hair development by cotton fiber-related genes.
PloS one 2011;6(7):e21301.
2010: Kai Wang; Wangzhen Guo; Zaijie Yang; Yan Hu; Wenpan Zhang; Baoliang Zhou; David M Stelly; Z Jeffrey Chen; Tianzhen Zhang
Structure and size variations between 12A and 12D homoeologous chromosomes based on high-resolution cytogenetic map in allotetraploid cotton.
Chromosoma 2010;119(3):255-66.
2010: Doug J Hinchliffe; William R Meredith; Kathleen M Yeater; Hee Jin Kim; Andrew W Woodward; Z Jeffrey Chen; Barbara A Triplett
Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 2010;120(7):1347-66.
2010: Scott Jackson; Z Jeffrey Chen
Genomic and expression plasticity of polyploidy.
Current opinion in plant biology 2010;13(2):153-9.
2010: Z Jeffrey Chen
Molecular mechanisms of polyploidy and hybrid vigor.
Trends in plant science 2010;15(2):57-71.
2010: Yan Yuan Tseng; Z Jeffrey Chen; Wen-Hsiung Li
fPOP: footprinting functional pockets of proteins by comparative spatial patterns.
Nucleic acids research 2010;38(Database issue):D288-95.
2009: Misook Ha; Jie Lu; Lu Tian; Vanitharani Ramachandran; Kristin D Kasschau; Elisabeth J Chapman; James C Carrington; Xuemei Chen; Xiu-Jie Wang; Z Jeffrey Chen
Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(42):17835-40.
2009: Yan Yuan Tseng; Craig Dupree; Z Jeffrey Chen; Wen-Hsiung Li
SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns.
Nucleic acids research 2009;37(Web Server issue):W384-9.
2009: Misook Ha; Eun-Deok Kim; Z Jeffrey Chen
Duplicate genes increase expression diversity in closely related species and allopolyploids.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(7):2295-300.
2009: Zhongfu Ni; Eun-Deok Kim; Misook Ha; Erika Lackey; Jianxin Liu; Yirong Zhang; Qixin Sun; Z Jeffrey Chen
Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids.
Nature 2009;457(7227):327-31.
2009: Mingxiong Pang; Andrew W Woodward; Vikram Agarwal; Xueying Guan; Misook Ha; Vanitharani Ramachandran; Xuemei Chen; Barbara A Triplett; David M Stelly; Z Jeffrey Chen
Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.).
Genome biology 2009;10(11):R122.
2009: Robert T Gaeta; Suk-Young Yoo; J Chris Pires; Rebecca W Doerge; Z Jeffrey Chen; Thomas C Osborn
Analysis of gene expression in resynthesized Brassica napus Allopolyploids using arabidopsis 70mer oligo microarrays.
PloS one 2009;4(3):e4760.
2008: Misook Ha; Mingxiong Pang; Vikram Agarwal; Z Jeffrey Chen
Interspecies regulation of microRNAs and their targets.
Biochimica et biophysica acta 2008;1779(11):735-42.
2008: Meng Chen; Misook Ha; Erika Lackey; Jianlin Wang; Z Jeffrey Chen
RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids.
Genetics 2008;178(4):1845-58.
2007: Jinsuk J Lee; Andrew W Woodward; Z Jeffrey Chen
Gene expression changes and early events in cotton fibre development.
Annals of botany 2007;100(7):1391-401.
2007: Jianwei Zhao; Jianlin Wang; Lingling An; Rebecca W Doerge; Z Jeffrey Chen; Craig R Grau; Jinling Meng; Thomas C Osborn
Analysis of gene expression profiles in response to Sclerotinia sclerotiorum in Brassica napus.
Planta 2007;227(1):13-24.
2007: Z Jeffrey Chen; Lu Tian
Roles of dynamic and reversible histone acetylation in plant development and polyploidy.
Biochimica et biophysica acta 2007;1769(5-6):295-307.
2007: Misook Ha; Wen-Hsiung Li; Z Jeffrey Chen
External factors accelerate expression divergence between duplicate genes.
Trends in genetics : TIG 2007;23(4):162-6.
2007: Z Jeffrey Chen; Misook Ha; Douglas Soltis
Polyploidy: genome obesity and its consequences.
The New phytologist 2007;174(4):717-20.
2007: Joshua A Udall; Lex E Flagel; Foo Cheung; Andrew W Woodward; Ran Hovav; Ryan A Rapp; Jordan M Swanson; Jinsuk J Lee; Alan R Gingle; Dan Nettleton; Christopher D Town; Z Jeffrey Chen; Jonathan F Wendel
Spotted cotton oligonucleotide microarrays for gene expression analysis.
BMC genomics 2007;8():81.
2007: Z Jeffrey Chen
Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids.
Annual review of plant biology 2007;58():377-406.
2006: Jennifer A Tate; Zhongfu Ni; Anne-Cathrine Scheen; Jin Koh; Candace A Gilbert; David Lefkowitz; Z Jeffrey Chen; Pamela S Soltis; Douglas E Soltis
Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid.
Genetics 2006;173(3):1599-611.
2006: Jianlin Wang; Lu Tian; Hyeon-Se Lee; Z Jeffrey Chen
Nonadditive regulation of FRI and FLC loci mediates flowering-time variation in Arabidopsis allopolyploids.
Genetics 2006;173(2):965-74.
2006: Paulus M Fong; Lu Tian; Z Jeffrey Chen
Arabidopsis thaliana histone deacetylase 1 (AtHD1) is localized in euchromatic regions and demonstrates histone deacetylase activity in vitro.
Cell research 2006;16(5):479-88.
2006: Nian Wang; Shi-En Lu; Jianlin Wang; Z Jeffrey Chen; Dennis C Gross
The expression of genes encoding lipodepsipeptide phytotoxins by Pseudomonas syringae pv. syringae is coordinated in response to plant signal molecules.
Molecular plant-microbe interactions : MPMI 2006;19(3):257-69.
2006: Z Jeffrey Chen; Zhongfu Ni
Mechanisms of genomic rearrangements and gene expression changes in plant polyploids.
BioEssays : news and reviews in molecular, cellular and developmental biology 2006;28(3):240-52.
2006: Wenxiang Gao; Z Jeffrey Chen; John Z Yu; Russell J Kohel; James E Womack; David M Stelly
Wide-cross whole-genome radiation hybrid mapping of the cotton (Gossypium barbadense L.) genome.
Molecular genetics and genomics : MGG 2006;275(2):105-13.
2006: Jinsuk J Lee; Osama S S Hassan; Wenxilang Gao; Ning E Wei; Russell J Kohel; Xiao-Ya Chen; Paxton Payton; Sing-Hoi Sze; David M Stelly; Z Jeffrey Chen
Developmental and gene expression analyses of a cotton naked seed mutant.
Planta 2006;223(3):418-32.
2006: Jianlin Wang; Lu Tian; Hyeon-Se Lee; Ning E Wei; Hongmei Jiang; Brian Watson; Andreas Madlung; Thomas C Osborn; Rebecca W Doerge; Luca Comai; Z Jeffrey Chen
Genomewide nonadditive gene regulation in Arabidopsis allotetraploids.
Genetics 2006;172(1):507-17.
2005: Shi-En Lu; Nian Wang; Jianlin Wang; Z Jeffrey Chen; Dennis C Gross
Oligonucleotide microarray analysis of the salA regulon controlling phytotoxin production by Pseudomonas syringae pv. syringae.
Molecular plant-microbe interactions : MPMI 2005;18(4):324-33.
2005: Jianlin Wang; Jinsuk J Lee; Lu Tian; Hyeon-Se Lee; Meng Chen; Sheetal Rao; Edward N Wei; Rebecca W Doerge; Luca Comai; Z Jeffrey Chen
Methods for genome-wide analysis of gene expression changes in polyploids.
Methods in enzymology 2005;395():570-96.
2005: Craig S Pikaard; Sasha Preuss; Keith Earley; Richard Lawrence; Michelle S Lewis; Z Jeffrey Chen
Detecting differential expression of parental or progenitor alleles in genetic hybrids and allopolyploids.
Methods in enzymology 2005;395():554-69.
2005: J Spencer Johnston; Alan E Pepper; Anne E Hall; Z Jeffrey Chen; George Hodnett; Janice Drabek; Rebecca Lopez; H James Price
Evolution of genome size in Brassicaceae.
Annals of botany 2005;95(1):229-35.
2005: Lu Tian; M Paulus Fong; Jiyuan J Wang; Ning E Wei; Hongmei Jiang; Rebecca W Doerge; Z Jeffrey Chen
Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development.
Genetics 2005;169(1):337-45.
2004: Jianlin Wang; Lu Tian; Andreas Madlung; Hyeon-Se Lee; Meng Chen; Jinsuk J Lee; Brian Watson; Trevor Kagochi; Luca Comai; Z Jeffrey Chen
Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids.
Genetics 2004;167(4):1961-73.
2004: Wenxiang Gao; Z Jeffrey Chen; John Z Yu; Dwaine Raska; Russell J Kohel; James E Womack; David M Stelly
Wide-cross whole-genome radiation hybrid mapping of cotton (Gossypium hirsutum L.).
Genetics 2004;167(3):1317-29.
2004: Richard Lawrence; Keith Earley; Olga Pontes; Manuela Silva; Z Jeffrey Chen; Nuno Neves; Wanda Viegas; Craig S Pikaard
A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance.
Molecular cell 2004;13(4):599-609.
2004: Hyeon-Se Lee; Jianlin Wang; Lu Tian; Hongmei Jiang; Michael A Black; Andreas Madlung; Brian Watson; Lewis Lukens; J Chris Pires; Jiyuan J Wang; Luca Comai; Thomas C Osborn; Rebecca W Doerge; Z Jeffrey Chen
Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species.
Plant biotechnology journal 2004;2(1):45-57.
2004: M Mei; N H Syed; Wenxiang Gao; Peggy Thaxton; C Wayne Smith; David M Stelly; Z Jeffrey Chen
Genetic mapping and QTL analysis of fiber-related traits in cotton ( Gossypium).
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 2004;108(2):280-91.
2003: Olga Pontes; Richard Lawrence; Nuno Neves; Manuela Silva; Jae-Hyeok Lee; Z Jeffrey Chen; Wanda Viegas; Craig S Pikaard
Natural variation in nucleolar dominance reveals the relationship between nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(20):11418-23.
2003: Lu Tian; Jianlin Wang; M Paulus Fong; Meng Chen; Hongbin Cao; Stanton B Gelvin; Z Jeffrey Chen
Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 (AtHD1) expression.
Genetics 2003;165(1):399-409.
2001: Hyeon-Se Lee; Z Jeffrey Chen
Protein-coding genes are epigenetically regulated in Arabidopsis polyploids.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(12):6753-8.
2001: Lu Tian; Z Jeffrey Chen
Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(1):200-5.