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1. Full Text Interactive roles of chromatin regulation and circadian clock function in plants
by Chen, Z. Jeffrey and Mas, Paloma
Genome Biology, ISSN 1474-7596, 03/2019, Volume 20, Issue 1, pp. 62 - 12
Circadian rhythms in transcription ultimately result in oscillations of key biological processes. Understanding how transcriptional rhythms are generated in... 
REVERSIBLE HISTONE ACETYLATION | LEAF SENESCENCE | DNA METHYLATION PATTERNS | ARABIDOPSIS-THALIANA | INTEGRATE LIGHT | RHYTHMS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | GENE-EXPRESSION | DOWN-REGULATION | H2B MONOUBIQUITINATION | JMJC DOMAIN | Arabidopsis - genetics | Arabidopsis Proteins - metabolism | Arabidopsis Proteins - genetics | Gene Expression Regulation, Plant | Chromatin Assembly and Disassembly | Circadian Clocks | Arabidopsis - metabolism | Circadian rhythms | Senescence | Transcription factors | Transcription | Gene regulation | Oscillations | Hybrid vigor | Domestication | Genomes | Circadian rhythm | Gene expression | Chromatin remodeling | Proteins | Cell cycle | DNA methylation | Epigenetics | Vigor
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2. Full Text Molecular mechanisms of polyploidy and hybrid vigor
by Chen, Z. Jeffrey
Trends in Plant Science, ISSN 1360-1385, 2010, Volume 15, Issue 2, pp. 57 - 71
Hybrids such as maize ( ) or domestic dog ( ) grow bigger and stronger than their parents. This is also true for allopolyploids such as wheat ( spp.) or frog... 
OVERDOMINANT EPISTATIC LOCI | PRIMARY GENETIC-BASIS | ALLELIC VARIATION | ARABIDOPSIS CIRCADIAN CLOCK | INBREEDING DEPRESSION | TRANS-ACTING SIRNAS | STARCH DEGRADATION | MAIZE HYBRIDS | INTERSPECIFIC HYBRIDIZATION | ELITE RICE HYBRID | PLANT SCIENCES | Polyploidy | Animals | RNA Interference | Humans | Gene Expression Regulation, Plant | Models, Genetic | Hybrid Vigor | Circadian Rhythm | Gene expression | Analysis
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3. Full Text Genomic and epigenetic insights into the molecular bases of heterosis
by Chen, Z. Jeffrey
Nature Reviews Genetics, ISSN 1471-0056, 07/2013, Volume 14, Issue 7, pp. 471 - 482
Heterosis, also known as hybrid vigour, is widespread in plants and animals, but the molecular bases for this phenomenon remain elusive. Recent studies in... 
DIRECTED DNA METHYLATION | ALLELIC VARIATION | ARABIDOPSIS CIRCADIAN CLOCK | NATURAL VARIATION | WIDE ANALYSIS | GENETICS & HEREDITY | QUANTITATIVE TRAIT LOCUS | GENE-EXPRESSION | HISTONE MODIFICATIONS | NUCLEOLAR DOMINANCE | RNA-POLYMERASE | Metabolomics | Genome-Wide Association Study | Polyploidy | Hybrid Vigor - genetics | Genes, Plant | Epigenesis, Genetic | Genomics | Gene Expression Profiling | Biomass | Systems Biology | Ploidies | Alleles | Gene Expression Regulation, Plant | Transcription, Genetic | Models, Genetic | Plant Physiological Phenomena | Genome | Epigenetic inheritance | Care and treatment | Genetic aspects | Research | Heterosis
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4. Full Text COP1 SUPPRESSOR 4 promotes seedling photomorphogenesis by repressingCCA1andPIF4expression inArabidopsis
by Zhao, Xianhai and Jiang, Yan and Li, Jian and Huq, Enamul and Chen, Z. Jeffrey and Xu, Dongqing and Deng, Xing Wang
Proceedings of the National Academy of Sciences, ISSN 0027-8424, 11/2018, Volume 115, Issue 45, pp. 11631 - 11636
CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and DE-ETIOLATED 1 (DET1) are founding components of two central repressor complexes of photomorphogenesis that... 
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5. Full Text Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids
by Chen, Z. Jeffrey
Annual Review of Plant Biology, ISSN 1543-5008, 2007, Volume 58, Issue 1, pp. 377 - 406
Polyploidy, or whole-genome duplication (WGD), is an important genomic feature for all eukaryotes, especially many plants and some animals. The common... 
Evolution | Polyploidy | RNA interference | Epigenetic regulation | Nonadditive gene expression | ARABIDOPSIS-THALIANA | DNA METHYLATION | CHROMOSOMAL DUPLICATION | nonadditive gene expression | evolution | epigenetic regulation | MICROARRAY ANALYSIS | PLANT SCIENCES | SELF-INCOMPATIBILITY | polyploidy | GENOME EVOLUTION | DUPLICATE GENES | SEGMENTAL DUPLICATIONS | FLOWERING PLANTS | NUCLEOLAR DOMINANCE | Phenotype | Plants - genetics | Fertility | Epigenesis, Genetic | Genetic Speciation | Alleles | Gene Expression Regulation, Plant | Gene Silencing | Gene Dosage | Models, Genetic | Genome, Plant
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6. COP1 SUPPRESSOR 4 promotes seedling photomorphogenesis by repressing CCA1 and PIF4 expression in Arabidopsis
by Xianhai Zhao and Yan Jiang and Jian Li and Enamul Huq and Z Jeffrey Chen and Dongqing Xu and Xing Wang Deng
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 11/2018, Volume 115, Issue 45, p. 11631
CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and DE-ETIOLATED 1 (DET1) are founding components of two central repressor complexes of photomorphogenesis that... 
Morphogenesis | Circadian rhythms | Gene silencing | Repressing | Darkness | Phenotypes | Genetic suppression | Flowers & plants | Circadian rhythm | Mutation | Photomorphogenesis | Seedlings
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7. Full Text Asymmetrical changes of gene expression, small RNA s and chromatin in two resynthesized wheat allotetraploids
by Jiao, Wu and Yuan, Jingya and Jiang, Shan and Liu, Yanfeng and Wang, Lili and Liu, Mingming and Zheng, Dewei and Ye, Wenxue and Wang, Xiue and Chen, Z. Jeffrey
The Plant Journal, ISSN 0960-7412, 03/2018, Volume 93, Issue 5, pp. 828 - 842
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8. Diurnal down-regulation of ethylene biosynthesis mediates biomass heterosis
by Qingxin Song and Atsumi Ando and Dongqing Xu and Lei Fang and Tianzhen Zhang and Enamul Huq and Hong Qiao and Xing Wang Deng and Z Jeffrey Chen
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 05/2018, Volume 115, Issue 21, p. 5606
Heterosis is widely applied in agriculture; however, the underlying molecular mechanisms for superior performance are not well understood. Ethylene... 
Circadian rhythms | Plants (botany) | Hybrids | 1-Aminocyclopropane-1-carboxylate synthase | Genes | Gene regulation | Ethylene | Parents | Interspecific | Biosynthesis | Biomass | Hybridization | Gene expression | Diurnal | Heterosis | Fruits | Mutants | Ripening | Signaling | Molecular modelling | Plant growth | Agriculture | Vigor | Elongation
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9. Full Text Epigenetic and developmental regulation in plant polyploids
by Song, Qingxin and Chen, Z Jeffrey
Current Opinion in Plant Biology, ISSN 1369-5266, 04/2015, Volume 24, pp. 101 - 109
Polyploidy or whole-genome duplication occurs in some animals and many flowering plants, including many important crops such as wheat, cotton and oilseed rape.... 
GROWTH VIGOR | PHENOTYPIC VARIATION | DNA METHYLATION | GENE-EXPRESSION | RESYNTHESIZED BRASSICA-NAPUS | HYBRIDIZATION | ARABIDOPSIS | CYTOSINE METHYLATION | NUCLEOLAR DOMINANCE | MOLECULAR-MECHANISMS | PLANT SCIENCES | Plant Proteins - genetics | DNA Methylation | Polyploidy | Histones - genetics | Plant Development | Plants - genetics | Epigenesis, Genetic | Plant Proteins - metabolism | Histones - metabolism | Epigenetic inheritance | Methylation | Gene expression | Laws, regulations and rules | Genes | Genomics | Evolution | Plants | Wheat | development | polyploidy | DNA methylation | transposons | gene expression | epigenetics | small RNAs
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10. Full Text Dynamic Roles for Small RNAs and DNA Methylation during Ovule and Fiber Development in Allotetraploid Cotton
: e1005724
by Qingxin Song and Xueying Guan and Z Jeffrey Chen
PLoS Genetics, ISSN 1553-7390, 12/2015, Volume 11, Issue 12
  DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites via distinct pathways.... 
Bias | DNA methylation | Epigenetics | Genomes | Roles | Cotton | Textile fibers | Gene expression | Deoxyribonucleic acid--DNA
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11. Full Text Genomic and expression plasticity of polyploidy
by Jackson, Scott and Chen, Z Jeffrey
Current Opinion in Plant Biology, ISSN 1369-5266, 2010, Volume 13, Issue 2, pp. 153 - 159
Polyploidy or whole genome duplication (WGD) occurs throughout the evolutionary history of many plants and some animals, including crops such as wheat, cotton,... 
PHENOTYPIC VARIATION | EVOLUTION | HEXAPLOID WHEAT | DUPLICATE GENES | BRASSICA-NAPUS | GENE-EXPRESSION | ARABIDOPSIS ALLOTETRAPLOIDS | PLANTS | ALLOPOLYPLOIDS | NUCLEOLAR DOMINANCE | PLANT SCIENCES | Biological Evolution | Polyploidy | Genome, Plant - genetics | Plants - genetics | Hybridization, Genetic | Gene Expression Regulation, Plant | Models, Genetic | nonadditive gene expression | crops | polyploidy | paleopolyploidy | epigenetics | small RNAs
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12. Full Text Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
by Zhang, Tianzhen and Hu, Yan and Jiang, Wenkai and Fang, Lei and Guan, Xueying and Chen, Jiedan and Zhang, Jinbo and Saski, Christopher A and Scheffler, Brian E and Stelly, David M and Hulse-Kemp, Amanda M and Wan, Qun and Liu, Bingliang and Liu, Chunxiao and Wang, Sen and Pan, Mengqiao and Wang, Yangkun and Wang, Dawei and Ye, Wenxue and Chang, Lijing and Zhang, Wenpan and Song, Qingxin and Kirkbride, Ryan C and Chen, Xiaoya and Dennis, Elizabeth and Llewellyn, Danny J and Peterson, Daniel G and Thaxton, Peggy and Jones, Don C and Wang, Qiong and Xu, Xiaoyang and Zhang, Hua and Wu, Huaitong and Zhou, Lei and Mei, Gaofu and Chen, Shuqi and Tian, Yue and Xiang, Dan and Li, Xinghe and Ding, Jian and Zuo, Qiyang and Tao, Linna and Liu, Yunchao and Li, Ji and Lin, Yu and Hui, Yuanyuan and Cao, Zhisheng and Cai, Caiping and Zhu, Xiefei and Jiang, Zhi and Zhou, Baoliang and Guo, Wangzhen and Li, Ruiqiang and Chen, Z Jeffrey
Nature Biotechnology, ISSN 1087-0156, 05/2015, Volume 33, Issue 5, pp. 531 - 537
Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1... 
GENOME SEQUENCE | CELL-WALL | EVOLUTION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BRASSICA-NAPUS | ANNOTATION | GENE-EXPRESSION | ARABIDOPSIS | PREDICTION | REVEALS | TOOL | Cotton Fiber | Tetraploidy | Plant Proteins - genetics | Base Sequence | Gossypium - genetics | Chromosome Mapping | High-Throughput Nucleotide Sequencing | Genome, Plant | Plant Proteins - biosynthesis | Sequence Analysis, DNA | Polyploidy | Nucleotide sequencing | Identification and classification | Methods | DNA sequencing | Cotton | Crops | Genomes
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