Works matching AU Z Jeffrey Chen

Results: 67

fPOP: footprinting functional pockets of proteins by comparative spatial patterns.

Published in:

Nucleic Acids Research, 2010, v. 38, p. D288, doi. 10.1093/nar/gkp900

By:

Yan Yuan Tseng;
Chen, Z. Jeffrey;
Wen-Hsiung Li

Publication type:

Article

SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_2, p. W384, doi. 10.1093/nar/gkp308

By:

Tseng, Yan Yuan;
Dupree, Craig;
Chen, Z. Jeffrey;
Li, Wen-Hsiung

Publication type:

Article

International plant molecular biology: a bright future for green science.

Published in:

Genome Biology, 2012, v. 13, n. 11, p. 323, doi. 10.1186/gb-2012-13-11-323

By:

Sibum Sung;
Huq, Enamul;
Z Jeffrey Chen

Publication type:

Article

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.

Published in:

Theoretical & Applied Genetics, 2010, v. 120, n. 7, p. 1347, doi. 10.1007/s00122-010-1260-6

By:

Hinchliffe, Doug;
Meredith, William R.;
Yeater, Kathleen M.;
Hee Jin Kim;
Woodward, Andrew W.;
Chen, Z. Jeffrey;
Triplett, Barbara A.

Publication type:

Article

Arabidopsis thaliana histone deacetylase 1 (AtHD1) is localized in euchromatic regions and demonstrates histone deacetylase activity in vitro.

Published in:

Cell Research, 2006, v. 16, n. 5, p. 479, doi. 10.1038/sj.cr.7310059

By:

Fong, Paulus M.;
Lu Tian;
Chen, Z. Jeffrey

Publication type:

Article

Cytoplasmic genome contributions to domestication and improvement of modern maize.

Published in:

BMC Biology, 2024, v. 22, n. 1, p. 1, doi. 10.1186/s12915-024-01859-4

By:

Cao, Shuai;
Zhang, Huanhuan;
Liu, Yang;
Sun, Yi;
Chen, Z. Jeffrey

Publication type:

Article

Polyploidy: genome obesity and its consequences.

Published in:

2007

By:

Chen, Z. Jeffrey;
Ha, Misook;
Soltis, Douglas

Publication type:

Report

Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation.

Published in:

BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1708-9

By:

Tuttle, John R.;
Gyoungju Nah;
Duke, Mary V.;
Alexander, Danny C.;
Xueying Guan;
Qingxin Song;
Chen, Z. Jeffrey;
Scheffler, Brian E.;
Haigler, Candace H.

Publication type:

Article

Analysis of gene expression profiles in response to Sclerotinia sclerotiorum in Brassica napus.

Published in:

Planta: An International Journal of Plant Biology, 2007, v. 227, n. 1, p. 13, doi. 10.1007/s00425-007-0586-z

By:

Zhao, Jianwei;
Wang, Jianlin;
An, Lingling;
Doerge, R. W.;
Chen, Z. Jeffrey;
Grau, Craig R.;
Meng, Jinling;
Osborn, Thomas C.

Publication type:

Article

Developmental and gene expression analyses of a cotton naked seed mutant.

Published in:

Planta: An International Journal of Plant Biology, 2006, v. 223, n. 3, p. 418, doi. 10.1007/s00425-005-0098-7

By:

Lee, Jinsuk J.;
Hassan, Osama S. S.;
Wenxilang Gao;
Wei, Ning E.;
Kohel, Russell J.;
Xiao-Ya Chen;
Payton, Paxton;
Sing-Hoi Sze;
Stelly, David M.;
Chen, Z. Jeffrey

Publication type:

Article

Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids.

Published in:

2009

By:

Ni, Zhongfu;
Kim, Eun-Deok;
Ha, Misook;
Lackey, Erika;
Liu, Jianxin;
Zhang, Yirong;
Sun, Qixin;
Chen, Z. Jeffrey

Publication type:

Letter

Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-06275-6

By:

Wang, Fang;
Han, Tongwen;
Jeffrey Chen, Z.

Publication type:

Article

Altered chromatin architecture and gene expression during polyploidization and domestication of soybean.

Published in:

Plant Cell, 2021, v. 33, n. 5, p. 1430, doi. 10.1093/plcell/koab081

By:

Wang, Longfei;
Jia, Guanghong;
Jiang, Xinyu;
Cao, Shuai;
Chen, Z Jeffrey;
Song, Qingxin

Publication type:

Article

Temporal Regulation of the Metabolome and Proteome in Photosynthetic and Photorespiratory Pathways Contributes to Maize Heterosis.

Published in:

Plant Cell, 2020, v. 32, n. 12, p. 3706, doi. 10.1105/tpc.20.00320

By:

Li, Zhi;
Zhu, Andan;
Song, Qingxin;
Chen, Helen Y.;
Harmon, Frank G.;
Chen, Z. Jeffrey

Publication type:

Article

Rice Circadian Clock Regulates Tiller Growth and Panicle Development Through Strigolactone Signaling and Sugar Sensing.

Published in:

Plant Cell, 2020, v. 32, n. 10, p. 3124, doi. 10.1105/tpc.20.00289

By:

Wang, Fang;
Han, Tongwen;
Song, Qingxin;
Ye, Wenxue;
Song, Xiaoguang;
Chu, Jinfang;
Li, Jiayang;
Chen, Z. Jeffrey

Publication type:

Article

B-BOX DOMAIN PROTEIN28 Negatively Regulates Photomorphogenesis by Repressing the Activity of Transcription Factor HY5 and Undergoes COP1-Mediated Degradation.

Published in:

Plant Cell, 2018, v. 30, n. 9, p. 2006, doi. 10.1105/tpc.18.00226

By:

Lin, Fang;
Jiang, Yan;
Li, Jian;
Yan, Tingting;
Fan, Liumin;
Liang, Jiansheng;
Chen, Z. Jeffrey;
Xu, Dongqing;
Deng, Xing Wang

Publication type:

Article

Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis in Arabidopsis Intraspecific Hybrids.

Published in:

Plant Cell, 2014, v. 26, n. 6, p. 2430, doi. 10.1105/tpc.113.115980

By:

Ng, Danny W.-K.;
Miller, Marisa;
Yu, Helen H.;
Huang, Tien-Yu;
Kim, Eun-Deok;
Lu, Jie;
Xie, Qiguang;
McClung, C. Robertson;
Chen, Z. Jeffrey

Publication type:

Article

Ploidy variation induces butterfly effect on chromatin topology in wheat.

Published in:

Plant Journal, 2024, v. 119, n. 5, p. 2450, doi. 10.1111/tpj.16932

By:

Jiao, Wu;
Lu, Kening;
Wen, Mingxing;
Mao, Junrong;
Ni, Zhongfu;
Chen, Z. Jeffrey;
Wang, Xiue;
Song, Qingxin;
Yuan, Jingya

Publication type:

Article

Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1229-8

By:

Qingxin Song;
Tianzhen Zhang;
Stelly, David M.;
Chen, Z. Jeffrey

Publication type:

Article

Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat.

Published in:

BMC Biology, 2020, v. 18, n. 1, p. N.PAG, doi. 10.1186/s12915-020-00909-x

By:

Yuan, Jingya;
Jiao, Wu;
Liu, Yanfeng;
Ye, Wenxue;
Wang, Xiue;
Liu, Bao;
Song, Qingxin;
Chen, Z. Jeffrey

Publication type:

Article

Genome-Wide Dosage-Dependent and -Independent Regulation Contributes to Gene Expression and Evolutionary Novelty in Plant Polyploids.

Published in:

Molecular Biology & Evolution, 2015, v. 32, n. 9, p. 2351, doi. 10.1093/molbev/msv116

By:

Xiaoli Shi;
Changqing Zhang;
Dae Kwan Ko;
Jeffrey Chen, Z.

Publication type:

Article

RNAi of met1 Reduces DNA Methylation and Induces Genome-Specific Changes in Gene Expression and Centromeric Small RNA Accumulation in Arabidopsis Allopolyploids.

Published in:

Genetics, 2008, v. 178, n. 4, p. 1845, doi. 10.1534/genetics.107.086272

By:

Meng Chen;
Ha, Misook;
Lackey, Erika;
Jianlin Wang;
Chen, Z. Jeffrey

Publication type:

Article

Evolution and Expression of Homeologous Loci in Tragopogon miscellus (Asteraceae), a Recent and Reciprocally Formed Allopolyploid.

Published in:

Genetics, 2006, v. 173, n. 3, p. 1599, doi. 10.1534/genetics.106.057646

By:

Tate, Jennifer A.;
Zhongfu Ni;
Scheen, Anne-Cathrine;
Jin Koh;
Gilbert, Candace A.;
Lefkowitz, David;
Chen, Z. Jeffrey;
Soltis, Pamela S.;
Soltis, Douglas E.

Publication type:

Article

Nonadditive Regulation of FRI and FLC Loci Mediates flowering-Time Variation in Arabidopsis Allopolyploids.

Published in:

Genetics, 2006, v. 173, n. 2, p. 965, doi. 10.1534/genetics.106.056580

By:

Jianlin Wang;
Lu Tian;
Hyeon-Se Lee;
Z. Jeffrey Chen

Publication type:

Article

Genomewide Nonadditive Gene Regulation in Arabidopsis Allotetraploids.

Published in:

Genetics, 2006, v. 172, n. 1, p. 507, doi. 10.1534/genetics.105.047894

By:

Jianlin Wang;
Lu Tian;
Hyeon-Se Lee;
Wei, Ning E.;
Hongmei Jiang;
Watson, Brian;
Madlung, Andreas;
Osborn, Thomas C.;
Doerge, R. W.;
Comai, Luca;
Chen, Z. Jeffrey

Publication type:

Article

Reversible Histone Acetylation and Deacetylation Mediate Genome-Wide, Promoter-Dependent and Locus-Specffic Changes in Gene Expression During Plant Development.

Published in:

Genetics, 2005, v. 169, n. 1, p. 337, doi. 10.1534/genetics.104.033142

By:

Lu Tian;
Fong, M. Paulus;
Wang, Jiyuan J.;
Wei, Ning E.;
Jiang, Hongmei;
Doerge, R. W.;
Chen, Z. Jeffrey

Publication type:

Article

Stochastic and Epigenetic Changes of Gene Expression in Arabidopsis Polyploids.

Published in:

Genetics, 2004, v. 167, n. 4, p. 1961, doi. 10.1534/genetics.104.027896

By:

Jianlin Wang;
Lu Tian;
Madlung, Andreas;
Hyeon-Se Lee;
Meng Chen;
Lee, Jinsuk J.;
Watson, Brian;
Kagochi, Trevor;
Comai, Luca;
Chen, Z. Jeffrey

Publication type:

Article

Wide-Cross Whole-Genome Radiation Hybrid Mapping of Cotton (Gossypium hirsutum L.).

Published in:

Genetics, 2004, v. 167, n. 3, p. 1317, doi. 10.1534/genetics.103.020479

By:

Wenxiang Gao;
Chen, Z. Jeffrey;
Yu, John Z.;
Raska, Dwaine;
Kohel, Russell J.;
Womack, James E.;
Stelly, David M.

Publication type:

Article

Genetic Control of Developmental Changes Induced by Disruption of Arabidopsis Histone Deacetylase 1 (AtHD1) Expression.

Published in:

Genetics, 2003, v. 165, n. 1, p. 399, doi. 10.1093/genetics/165.1.399

By:

Lu Tian;
Jianlin Wang, Joachim;
M. Paulus Fong, Joachim;
Meng Chen;
Hongbin Cao, Joachim;
Gelvin, Stanton B.;
Chen, Z. Jeffrey

Publication type:

Article

RNA polymerase I transcription in a Brassica interspecific hybrid and its progenitors: Tests of...

Published in:

Genetics, 1999, v. 152, n. 1, p. 451, doi. 10.1093/genetics/152.1.451

By:

Frieman, Matthew;
Chen, Jeffrey Z.

Publication type:

Article

Protein nonadditive expression and solubility contribute to heterosis in Arabidopsis hybrids and allotetraploids.

Published in:

Frontiers in Plant Science, 2023, p. 1, doi. 10.3389/fpls.2023.1252564

By:

June, Viviana;
Dongqing Xu;
Papoulas, Ophelia;
Boutz, Daniel;
Marcotte, Edward M.;
Chen, Z. Jeffrey

Publication type:

Article

Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton.

Published in:

Plant Journal, 2006, v. 47, n. 5, p. 761, doi. 10.1111/j.1365-313X.2006.02829.x

By:

Samuel Yang, S.;
Foo Cheung;
Lee, Jinsuk J.;
Misook Ha;
Wei, Ning E.;
Sing-Hoi Sze;
Stelly, David M.;
Thaxton, Peggy;
Triplett, Barbara;
Town, Christopher D.;
Chen, Z. Jeffrey

Publication type:

Article

Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02614-0

By:

Cao, Shuai;
Wang, Longfei;
Han, Tongwen;
Ye, Wenxue;
Liu, Yang;
Sun, Yi;
Moose, Stephen P.;
Song, Qingxin;
Chen, Z. Jeffrey

Publication type:

Article

Genomic and epigenetic insights into the molecular bases of heterosis.

Published in:

Nature Reviews Genetics, 2013, v. 14, n. 7, p. 471, doi. 10.1038/nrg3503

By:

Chen, Z. Jeffrey

Publication type:

Article

Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species.

Published in:

Plant Biotechnology Journal, 2004, v. 2, n. 1, p. 45, doi. 10.1046/j.1467-7652.2003.00048.x

By:

Lee, Hyeon‐Se;
Wang, Jianlin;
Tian, Lu;
Jiang, Hongmei;
Black, Michael A.;
Madlung, Andreas;
Watson, Brian;
Lukens, Lewis;
Pires, J. Chris;
Wang, Jiyuan J.;
Comai, Luca;
Osborn, Thomas C.;
Doerge, R. W.;
Chen, Z. Jeffrey

Publication type:

Article

Gene Expression Changes and Early Events in Cotton Fibre Development.

Published in:

Annals of Botany, 2007, v. 100, n. 7, p. 1391, doi. 10.1093/aob/mcm232

By:

Jinsuk J. Lee;
Andrew W. Woodward;
Z. Jeffrey Chen

Publication type:

Article

BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping.

Published in:

G3: Genes | Genomes | Genetics, 2015, v. 5, n. 6, p. 1095, doi. 10.1534/g3.115.017749

By:

Hulse-Kemp, Amanda M.;
Ashraf, Hamid;
Stoffel, Kevin;
Xiuting Zheng;
Saski, Christopher A.;
Scheffler, Brian E.;
Fang, David D.;
Chen, Z. Jeffrey;
Van Deynze, Allen;
Stelly, David M.

Publication type:

Article

Evolution of Genome Size in Brassicaceae.

Published in:

Annals of Botany, 2005, v. 95, n. 1, p. 229, doi. 10.1093/aob/mci016

By:

JOHNSTON, J. SPENCER;
PEPPER, ALAN E.;
HALL, ANNE E.;
CHEN, Z. JEFFREY;
HODNETT, GEORGE;
DRABEK, JANICE;
LOPEZ, REBECCA;
PRICE, H. JAMES

Publication type:

Article

Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis.

Published in:

Nature Communications, 2015, v. 6, n. 7, p. 7453, doi. 10.1038/ncomms8453

By:

Miller, Marisa;
Song, Qingxin;
Shi, Xiaoli;
Juenger, Thomas E.;
Chen, Z. Jeffrey

Publication type:

Article

SCARECROW-LIKE15 interacts with HISTONE DEACETYLASE19 and is essential for repressing the seed maturation programme.

Published in:

Nature Communications, 2015, v. 6, n. 7, p. 7243, doi. 10.1038/ncomms8243

By:

Gao, Ming-Jun;
Li, Xiang;
Huang, Jun;
Gropp, Gordon M.;
Gjetvaj, Branimir;
Lindsay, Donna L.;
Wei, Shu;
Coutu, Cathy;
Chen, Zhixiang;
Wan, Xiao-Chun;
Hannoufa, Abdelali;
Lydiate, Derek J.;
Gruber, Margaret Y.;
Chen, Z. Jeffrey;
Hegedus, Dwayne D.

Publication type:

Article

Control of cotton fibre elongation by a homeodomain transcription factor GhHOX3.

Published in:

Nature Communications, 2014, v. 5, n. 11, p. 5519, doi. 10.1038/ncomms6519

By:

Shan, Chun-Min;
Shangguan, Xiao-Xia;
Zhao, Bo;
Zhang, Xiu-Fang;
Chao, Lu-men;
Yang, Chang-Qing;
Wang, Ling-Jian;
Zhu, Hua-Yu;
Zeng, Yan-Da;
Guo, Wang-Zhen;
Zhou, Bao-Liang;
Hu, Guan-Jing;
Guan, Xue-Ying;
Chen, Z. Jeffrey;
Wendel, Jonathan F.;
Zhang, Tian-Zhen;
Chen, Xiao-Ya

Publication type:

Article

miR828 and miR858 regulate homoeologous MYB2 gene functions in Arabidopsis trichome and cotton fibre development.

Published in:

Nature Communications, 2014, v. 5, n. 1, p. 3050, doi. 10.1038/ncomms4050

By:

Guan, Xueying;
Pang, Mingxiong;
Nah, Gyoungju;
Shi, Xiaoli;
Ye, Wenxue;
Stelly, David M.;
Chen, Z. Jeffrey

Publication type:

Article

Transcriptome analysis of extant cotton progenitors revealed tetraploidization and identified genome-specific single nucleotide polymorphism in diploid and allotetraploid cotton.

Published in:

BMC Research Notes, 2014, v. 7, p. 1, doi. 10.1186/1756-0500-7-493

By:

Xueying Guan;
Gyoungju Nah;
Qingxin Song;
Udall, Joshua A.;
Stelly, David M.;
Chen, Z. Jeffrey

Publication type:

Article

Imprinting but not cytonuclear interactions determines seed size heterosis in Arabidopsis hybrids.

Published in:

Plant Physiology, 2024, v. 195, n. 2, p. 1214, doi. 10.1093/plphys/kiae061

By:

June, Viviana;
Song, Xiaoya;
Chen, Z Jeffrey

Publication type:

Article

Temporal Regulation of the Metabolome and Proteome in Photosynthetic and Photorespiratory Pathways Contributes to Maize Heterosis.

Published in:

Plant Physiology, 2020, v. 184, n. 4, p. 3706, doi. 10.1105/tpc.20.00320

By:

Zhi Li;
Andan Zhu;
Qingxin Song;
Chen, Helen Y.;
Harmon, Frank G.;
Chen, Z. Jeffrey

Publication type:

Article

Histone Modifications Define Expression Bias of Homoeologous Genomes in Allotetraploid Cotton.

Published in:

Plant Physiology, 2016, v. 172, n. 3, p. 1760, doi. 10.1104/pp.16.01210

By:

Dewei Zheng;
Wenxue Ye;
Qingxin Song;
Fangpu Han;
Tianzhen Zhang;
Chen, Z. Jeffrey

Publication type:

Article

Heterologous protein-DNA interactions lead to biased allelic expression of circadian clock genes in interspecific hybrids.

Published in:

Scientific Reports, 2017, p. 45087, doi. 10.1038/srep45087

By:

Ng, Danny W-K.;
Chen, Helen H. Y.;
Chen, Z. Jeffrey

Publication type:

Article

Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02094-0

By:

Song, Qingxin;
Ando, Atsumi;
Jiang, Ning;
Ikeda, Yoko;
Chen, Z. Jeffrey

Publication type:

Article

Phytohormonal Networks Promote Differentiation of Fiber Initials on Pre-Anthesis Cotton Ovules Grown In Vitro and In Planta.

Published in:

PLoS ONE, 2015, v. 10, n. 4, p. 1, doi. 10.1371/journal.pone.0125046

By:

Kim, Hee Jin;
Hinchliffe, Doug J.;
Triplett, Barbara A.;
Chen, Z. Jeffrey;
Stelly, David M.;
Yeater, Kathleen M.;
Moon, Hong S.;
Gilbert, Matthew K.;
Thyssen, Gregory N.;
Turley, Rickie B.;
Fang, David D.

Publication type:

Article

Activation of Arabidopsis Seed Hair Development by Cotton Fiber-Related Genes.

Published in:

PLoS ONE, 2011, v. 6, n. 7, p. 1, doi. 10.1371/journal.pone.0021301

By:

Guan, Xueying;
Lee, Jinsuk J.;
Pang, Mingxiong;
Shi, Xiaoli;
Stelly, David M.;
Chen, Z. Jeffrey

Publication type:

Article