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Zhen Su, Ph.D. - Publications

Affiliations: 
2003 University of Arizona, Tucson, AZ 
Area:
Environmental Sciences, Molecular Biology
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74 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Cao Y, Yan H, Sheng M, Liu Y, Yu X, Li Z, Xu W, Su Z. KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome. Bmc Plant Biology. 24: 177. PMID 38448830 DOI: 10.1186/s12870-024-04860-9  0.316
2023 Xue T, Liu L, Zhang X, Li Z, Sheng M, Ge X, Xu W, Su Z. Genome-Wide Investigation and Co-Expression Network Analysis of SBT Family Gene in . International Journal of Molecular Sciences. 24. PMID 36982835 DOI: 10.3390/ijms24065760  0.324
2022 Li Z, Hu Y, Ma X, Da L, She J, Liu Y, Yi X, Cao Y, Xu W, Jiao Y, Su Z. WheatCENet: A database for comparative co-expression networks analysis of allohexaploid wheat and its progenitors. Genomics, Proteomics & Bioinformatics. PMID 35660007 DOI: 10.1016/j.gpb.2022.04.007  0.303
2022 Yang J, Yan H, Liu Y, Da L, Xiao Q, Xu W, Su Z. GURFAP: A Platform for Gene Function Analysis in . Frontiers in Genetics. 13: 823966. PMID 35495163 DOI: 10.3389/fgene.2022.823966  0.35
2022 Sheng M, Ma X, Wang J, Xue T, Li Z, Cao Y, Yu X, Zhang X, Wang Y, Xu W, Su Z. KNOX II Transcription Factor HOS59 Functions in Regulating Rice Grain Size. The Plant Journal : For Cell and Molecular Biology. PMID 35167131 DOI: 10.1111/tpj.15709  0.319
2021 Ma X, Yan H, Yang J, Liu Y, Li Z, Sheng M, Cao Y, Yu X, Yi X, Xu W, Su Z. PlantGSAD: a comprehensive gene set annotation database for plant species. Nucleic Acids Research. PMID 34534340 DOI: 10.1093/nar/gkab794  0.324
2021 Xiao Q, Li Z, Qu M, Xu W, Su Z, Yang J. LjaFGD: Lonicera japonica functional genomics database. Journal of Integrative Plant Biology. PMID 33982879 DOI: 10.1111/jipb.13112  0.303
2020 Sheng M, She J, Xu W, Hong Y, Su Z, Zhang X. HpeNet: Co-expression Network Database for Transcriptome Assembly of Pall. Frontiers in Genetics. 11: 570138. PMID 33193666 DOI: 10.3389/fgene.2020.570138  0.317
2020 Yang J, Xiao Q, Xu J, Da L, Guo L, Huang L, Liu Y, Xu W, Su Z, Yang S, Pan Q, Jiang W, Zhou T. GelFAP: Gene Functional Analysis Platform for . Frontiers in Plant Science. 11: 563237. PMID 33193491 DOI: 10.3389/fpls.2020.563237  0.314
2020 Zhao N, Zhang K, Wang C, Yan H, Liu Y, Xu W, Su Z. Systematic Analysis of Differential H3K27me3 and H3K4me3 Deposition in Callus and Seedling Reveals the Epigenetic Regulatory Mechanisms Involved in Callus Formation in Rice. Frontiers in Genetics. 11: 766. PMID 32765593 DOI: 10.3389/Fgene.2020.00766  0.433
2020 Zhao N, Sheng M, Zhao J, Ma X, Wei Q, Song Q, Zhang K, Xu W, Sun C, Liu F, Su Z. Over-Expression of Delays Leaf Senescence in Rice ( L.). Frontiers in Bioengineering and Biotechnology. 8: 471. PMID 32509751 DOI: 10.3389/Fbioe.2020.00471  0.433
2020 Wang J, Ma X, Yang J, Hui Y, She J, Tian T, Li Z, Xu W, Gao Z, Su Z, Zhao H. Coexpression Analysis Reveals Dynamic Modules Regulating the Growth and Development of Cirri in the Rattans ( and ). Frontiers in Genetics. 11: 378. PMID 32477399 DOI: 10.3389/Fgene.2020.00378  0.43
2020 Zhao G, Song Y, Wang Q, Yao D, Li D, Qin W, Ge X, Yang Z, Xu W, Su Z, Zhang X, Li F, Wu J. Salt Tolerance Is Enhanced by Overexpression of JAZ1. Frontiers in Bioengineering and Biotechnology. 8: 157. PMID 32211392 DOI: 10.3389/Fbioe.2020.00157  0.446
2019 Da L, Liu Y, Yang J, Tian T, She J, Ma X, Xu W, Su Z. AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. Frontiers in Plant Science. 10: 1333. PMID 31695717 DOI: 10.3389/Fpls.2019.01333  0.427
2019 Fang Y, Chen L, Lin K, Feng Y, Zhang P, Pan X, Sanders J, Wu Y, Wang XE, Su Z, Chen C, Wei H, Zhang W. Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice. Genome Research. PMID 31262943 DOI: 10.1101/Gr.246009.118  0.342
2019 Yan H, Sheng M, Wang C, Liu Y, Yang J, Liu F, Xu W, Su Z. AtSPX1-mediated transcriptional regulation during leaf senescence in Arabidopsis thaliana. Plant Science : An International Journal of Experimental Plant Biology. 283: 238-246. PMID 31128694 DOI: 10.1016/J.Plantsci.2019.03.005  0.414
2019 Yan H, Liu Y, Zhang K, Song J, Xu W, Su Z. Chromatin State-Based Analysis of Epigenetic H3K4me3 Marks of in Response to Dark Stress. Frontiers in Genetics. 10: 306. PMID 31001332 DOI: 10.3389/Fgene.2019.00306  0.411
2019 She J, Yan H, Yang J, Xu W, Su Z. croFGD: Functional Genomics Database. Frontiers in Genetics. 10: 238. PMID 30967897 DOI: 10.3389/Fgene.2019.00238  0.444
2018 Yang J, Liu Y, Yan H, Tian T, You Q, Zhang L, Xu W, Su Z. PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins. Frontiers in Genetics. 9: 590. PMID 30555515 DOI: 10.3389/Fgene.2018.00590  0.408
2018 Ma X, Zhao H, Xu W, You Q, Yan H, Gao Z, Su Z. Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development. Frontiers in Genetics. 9: 574. PMID 30542370 DOI: 10.3389/Fgene.2018.00574  0.434
2018 Tian T, You Q, Yan H, Xu W, Su Z. MCENet: A database for maize conditional co-expression network and network characterization collaborated with multi-dimensional omics levels. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 30057343 DOI: 10.1016/J.Jgg.2018.05.007  0.384
2018 Dong Z, Yu J, Li H, Huang W, Xu L, Zhao Y, Zhang T, Xu W, Jiang J, Su Z, Jin W. Transcriptional and epigenetic adaptation of maize chromosomes in Oat-Maize addition lines. Nucleic Acids Research. PMID 29579310 DOI: 10.1093/Nar/Gky209  0.429
2017 Liu Y, Tian T, Zhang K, You Q, Yan H, Zhao N, Yi X, Xu W, Su Z. PCSD: a plant chromatin state database. Nucleic Acids Research. PMID 29040761 DOI: 10.1093/Nar/Gkx919  0.346
2017 You Q, Yi X, Zhang K, Wang C, Ma X, Zhang X, Xu W, Li F, Su Z. Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation. Scientific Reports. 7: 9098. PMID 28831143 DOI: 10.1038/S41598-017-09680-6  0.393
2017 Liu Y, Zhang W, Zhang K, You Q, Yan H, Jiao Y, Jiang J, Xu W, Su Z. Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness. Scientific Reports. 7: 4093. PMID 28642500 DOI: 10.1038/S41598-017-04524-9  0.405
2017 Zhao H, Zhao S, Fei B, Liu H, Yang H, Dai H, Wang D, Jin W, Tang F, Gao Q, Xun H, Wang Y, Qi L, Yue X, ... ... Su Z, et al. Announcing the Genome Atlas of Bamboo and Rattan (GABR) project: promoting research in evolution and in economically and ecologically beneficial plants. Gigascience. PMID 28637269 DOI: 10.1093/Gigascience/Gix046  0.334
2017 Tian T, Liu Y, Yan H, You Q, Yi X, Du Z, Xu W, Su Z. agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Research. PMID 28472432 DOI: 10.1093/Nar/Gkx382  0.309
2017 Zhang K, Xu W, Wang C, Yi X, Su Z. Differential deposition of H2A.Z in rice seedling tissue during the day-night cycle. Plant Signaling & Behavior. 0. PMID 28151037 DOI: 10.1080/15592324.2017.1286438  0.363
2017 You Q, Xu W, Zhang K, Zhang L, Yi X, Yao D, Wang C, Zhang X, Zhao X, Provart NJ, Li F, Su Z. ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. Nucleic Acids Research. 45: D1090-D1099. PMID 28053168 DOI: 10.1093/Nar/Gkw910  0.419
2016 You Q, Yan H, Liu Y, Yi X, Zhang K, Xu W, Su Z. A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data. Functional & Integrative Genomics. PMID 28032247 DOI: 10.1007/S10142-016-0541-9  0.322
2016 You Q, Zhang L, Yi X, Zhang K, Yao D, Zhang X, Wang Q, Zhao X, Ling Y, Xu W, Li F, Su Z. Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum. Scientific Reports. 6: 38436. PMID 27922095 DOI: 10.1038/Srep38436  0.426
2016 Fang Y, Wang L, Wang X, You Q, Pan X, Xiao J, Wang XE, Wu Y, Su Z, Zhang W. Histone modifications facilitate the coexpression of bidirectional promoters in rice. Bmc Genomics. 17: 768. PMID 27716056 DOI: 10.1186/S12864-016-3125-0  0.412
2016 Zhang K, Xu W, Wang C, Yi X, Zhang W, Su Z. Differential deposition of H2A.Z in combination with histone modifications within related genes in rice callus and seedling. The Plant Journal : For Cell and Molecular Biology. PMID 27643852 DOI: 10.1111/Tpj.13381  0.352
2016 Tian T, You Q, Zhang L, Yi X, Yan H, Xu W, Su Z. SorghumFDB: sorghum functional genomics database with multidimensional network analysis. Database : the Journal of Biological Databases and Curation. 2016. PMID 27352859 DOI: 10.1093/Database/Baw099  0.46
2016 Ma X, Fu Y, Zhao X, Jiang L, Zhu Z, Gu P, Xu W, Su Z, Sun C, Tan L. Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing. Scientific Reports. 6: 27425. PMID 27251022 DOI: 10.1038/Srep27425  0.303
2016 Zhang K, Song Q, Wei Q, Wang C, Zhang L, Xu W, Su Z. Down-regulation of OsSPX1 caused semi-male sterility, resulting in reduction of grain yield in rice. Plant Biotechnology Journal. PMID 26806409 DOI: 10.1111/Pbi.12527  0.399
2015 Yu J, Zhang Y, Di C, Zhang Q, Zhang K, Wang C, You Q, Yan H, Dai SY, Yuan JS, Xu W, Su Z. JAZ7 negatively regulates dark-induced leaf senescence in Arabidopsis. Journal of Experimental Botany. PMID 26547795 DOI: 10.1093/Jxb/Erv487  0.405
2015 Xu W, Di C, Zhou S, Liu J, Li L, Liu F, Yang X, Ling Y, Su Z. Rice transcriptome analysis to identify possible herbicide quinclorac detoxification genes. Frontiers in Genetics. 6: 306. PMID 26483837 DOI: 10.3389/Fgene.2015.00306  0.424
2015 Miao Z, Xu W, Li D, Hu X, Liu J, Zhang R, Tong Z, Dong J, Su Z, Zhang L, Sun M, Li W, Du Z, Hu S, Wang T. De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway. Bmc Genomics. 16: 818. PMID 26481731 DOI: 10.1186/S12864-015-2019-X  0.405
2015 Guo J, Shi G, Guo X, Zhang L, Xu W, Wang Y, Su Z, Hua J. Transcriptome analysis reveals that distinct metabolic pathways operate in salt-tolerant and salt-sensitive upland cotton varieties subjected to salinity stress. Plant Science : An International Journal of Experimental Plant Biology. 238: 33-45. PMID 26259172 DOI: 10.1016/J.Plantsci.2015.05.013  0.356
2015 Zhang L, Guo J, You Q, Yi X, Ling Y, Xu W, Hua J, Su Z. GraP: platform for functional genomics analysis of Gossypium raimondii. Database : the Journal of Biological Databases and Curation. 2015: bav047. PMID 25982315 DOI: 10.1093/Database/Bav047  0.398
2015 Yi X, Zhang Z, Ling Y, Xu W, Su Z. PNRD: a plant non-coding RNA database. Nucleic Acids Research. 43: D982-9. PMID 25398903 DOI: 10.1093/Nar/Gku1162  0.316
2014 Meng Y, Ma N, Zhang Q, You Q, Li N, Ali Khan M, Liu X, Wu L, Su Z, Gao J. Precise spatio-temporal modulation of ACC synthase by MPK6 cascade mediates the response of rose flowers to rehydration. The Plant Journal : For Cell and Molecular Biology. 79: 941-50. PMID 24942184 DOI: 10.1111/Tpj.12594  0.351
2014 Yu J, Zhang Z, Wei J, Ling Y, Xu W, Su Z. SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways. Bmc Genomics. 15: 271. PMID 24712981 DOI: 10.1186/1471-2164-15-271  0.367
2013 Wang C, Wei Q, Zhang K, Wang L, Liu F, Zhao L, Tan Y, Di C, Yan H, Yu J, Sun C, Chen WJ, Xu W, Su Z. Down-regulation of OsSPX1 causes high sensitivity to cold and oxidative stresses in rice seedlings. Plos One. 8: e81849. PMID 24312593 DOI: 10.1371/Journal.Pone.0081849  0.376
2013 Yi X, Du Z, Su Z. PlantGSEA: a gene set enrichment analysis toolkit for plant community. Nucleic Acids Research. 41: W98-103. PMID 23632162 DOI: 10.1093/Nar/Gkt281  0.419
2013 Zhang X, Yao D, Wang Q, Xu W, Wei Q, Wang C, Liu C, Zhang C, Yan H, Ling Y, Su Z, Li F. mRNA-seq analysis of the Gossypium arboreum transcriptome reveals tissue selective signaling in response to water stress during seedling stage. Plos One. 8: e54762. PMID 23382961 DOI: 10.1371/Journal.Pone.0054762  0.382
2013 Du Z, Li H, Wei Q, Zhao X, Wang C, Zhu Q, Yi X, Xu W, Liu XS, Jin W, Su Z. Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. Molecular Plant. 6: 1463-72. PMID 23355544 DOI: 10.1093/Mp/Sst018  0.4
2013 Liu F, Xu W, Song Q, Tan L, Liu J, Zhu Z, Fu Y, Su Z, Sun C. Microarray-assisted fine-mapping of quantitative trait loci for cold tolerance in rice. Molecular Plant. 6: 757-67. PMID 23267004 DOI: 10.1093/Mp/Sss161  0.358
2012 Zhang G, Zhang Y, Su Z. CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana. Bmc Bioinformatics. 13: 332. PMID 23256889 DOI: 10.1186/1471-2105-13-332  0.307
2012 Yao D, Wei Q, Xu W, Syrenne RD, Yuan JS, Su Z. Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis. Bmc Bioinformatics. 13: S10. PMID 23046216 DOI: 10.1186/1471-2105-13-S15-S10  0.377
2011 Li D, Zhang Y, Hu X, Shen X, Ma L, Su Z, Wang T, Dong J. Transcriptional profiling of Medicago truncatula under salt stress identified a novel CBF transcription factor MtCBF4 that plays an important role in abiotic stress responses. Bmc Plant Biology. 11: 109. PMID 21718548 DOI: 10.1186/1471-2229-11-109  0.376
2011 Yao D, Zhang X, Zhao X, Liu C, Wang C, Zhang Z, Zhang C, Wei Q, Wang Q, Yan H, Li F, Su Z. Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of cotton (Gossypium hirsutum L.). Genomics. 98: 47-55. PMID 21569837 DOI: 10.1016/J.Ygeno.2011.04.007  0.422
2011 Xu W, Yang R, Li M, Xing Z, Yang W, Chen G, Guo H, Gong X, Du Z, Zhang Z, Hu X, Wang D, Qian Q, Wang T, Su Z, et al. Transcriptome phase distribution analysis reveals diurnal regulated biological processes and key pathways in rice flag leaves and seedling leaves. Plos One. 6: e17613. PMID 21407816 DOI: 10.1371/Journal.Pone.0017613  0.431
2010 Ling Y, Du Z, Zhang Z, Su Z. ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome. Bmc Genomics. 11: 580. PMID 20955618 DOI: 10.1186/1471-2164-11-580  0.385
2010 Di C, Xu W, Su Z, Yuan JS. Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function. Bmc Bioinformatics. 11: S22. PMID 20946606 DOI: 10.1186/1471-2105-11-S6-S22  0.404
2010 Yang R, Su Z. Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation. Bioinformatics (Oxford, England). 26: i168-74. PMID 20529902 DOI: 10.1093/Bioinformatics/Btq189  0.323
2010 Wei LQ, Xu WY, Deng ZY, Su Z, Xue Y, Wang T. Genome-scale analysis and comparison of gene expression profiles in developing and germinated pollen in Oryza sativa. Bmc Genomics. 11: 338. PMID 20507633 DOI: 10.1186/1471-2164-11-338  0.424
2010 Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Research. 38: W64-70. PMID 20435677 DOI: 10.1093/Nar/Gkq310  0.375
2010 Liu F, Xu W, Wei Q, Zhang Z, Xing Z, Tan L, Di C, Yao D, Wang C, Tan Y, Yan H, Ling Y, Sun C, Xue Y, Su Z. Gene expression profiles deciphering rice phenotypic variation between Nipponbare (Japonica) and 93-11 (Indica) during oxidative stress. Plos One. 5: e8632. PMID 20072620 DOI: 10.1371/Journal.Pone.0008632  0.414
2010 Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z. PMRD: plant microRNA database. Nucleic Acids Research. 38: D806-13. PMID 19808935 DOI: 10.1093/Nar/Gkp818  0.344
2009 Li D, Su Z, Dong J, Wang T. An expression database for roots of the model legume Medicago truncatula under salt stress. Bmc Genomics. 10: 517. PMID 19906315 DOI: 10.1186/1471-2164-10-517  0.369
2009 Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN, Yuan JS. Novel software package for cross-platform transcriptome analysis (CPTRA). Bmc Bioinformatics. 10: S16. PMID 19811681 DOI: 10.1186/1471-2105-10-S11-S16  0.369
2009 Zhao L, Liu F, Xu W, Di C, Zhou S, Xue Y, Yu J, Su Z. Increased expression of OsSPX1 enhances cold/subfreezing tolerance in tobacco and Arabidopsis thaliana. Plant Biotechnology Journal. 7: 550-61. PMID 19508276 DOI: 10.1111/J.1467-7652.2009.00423.X  0.409
2009 Du Z, Zhou X, Li L, Su Z. plantsUPS: a database of plants' Ubiquitin Proteasome System. Bmc Genomics. 10: 227. PMID 19445698 DOI: 10.1186/1471-2164-10-227  0.403
2009 Peng ZY, Zhou X, Li L, Yu X, Li H, Jiang Z, Cao G, Bai M, Wang X, Jiang C, Lu H, Hou X, Qu L, Wang Z, Zuo J, ... ... Su Z, et al. Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis. Nucleic Acids Research. 37: D975-82. PMID 19015126 DOI: 10.1093/Nar/Gkn873  0.408
2008 Zhou X, Su Z. tCal: transcriptional probability calculator using thermodynamic model. Bioinformatics (Oxford, England). 24: 2639-40. PMID 18796477 DOI: 10.1093/Bioinformatics/Btn494  0.322
2008 Wang Y, Zhang WZ, Song LF, Zou JJ, Su Z, Wu WH. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiology. 148: 1201-11. PMID 18775970 DOI: 10.1104/Pp.108.126375  0.411
2008 Liu F, Xu W, Tan L, Xue Y, Sun C, Su Z. Case study for identification of potentially indel-caused alternative expression isoforms in the rice subspecies japonica and indica by integrative genome analysis. Genomics. 91: 186-94. PMID 18037265 DOI: 10.1016/J.Ygeno.2007.10.001  0.421
2008 He F, Kang J, Zhou X, Su Z, Qu L, Gu H. Variation at the transcriptional level among Chinese natural populations of Arabidopsis thaliana in response to cold stress Chinese Science Bulletin. 53: 2989-2999. DOI: 10.1007/S11434-008-0403-5  0.398
2007 Zhou X, Su Z. EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species. Bmc Genomics. 8: 246. PMID 17645808 DOI: 10.1186/1471-2164-8-246  0.328
2007 Hou ZC, Xu GY, Su Z, Yang N. Purifying selection and positive selection on the myxovirus resistance gene in mammals and chickens. Gene. 396: 188-95. PMID 17467195 DOI: 10.1016/J.Gene.2007.03.017  0.31
2006 Jia J, Fu J, Zheng J, Zhou X, Huai J, Wang J, Wang M, Zhang Y, Chen X, Zhang J, Zhao J, Su Z, Lv Y, Wang G. Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings. The Plant Journal : For Cell and Molecular Biology. 48: 710-27. PMID 17076806 DOI: 10.1111/J.1365-313X.2006.02905.X  0.419
2003 Su Z, Cushman JH, Curry JE. Computer simulation of anisotropic diffusion in monolayer films in mica slit pores Journal of Chemical Physics. 118: 1417-1422. DOI: 10.1063/1.1531073  0.601
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