2024

Li M, Wu Q, Guo F, Ouyang Y, Ao D, You S, Liu Y. (2024) A versatile, rapid agrobacterium-mediated transient expression system for functional genomics studies in cannabis seedling. Planta. DOI:10.1007/s00425-024-04448-5

You S, Yao S, Chen X, Hou Q, Liu Z, Lei G, Xie X, Liang Z, Yuchi Z , You M, Liu Y, Xiong L. (2024). CRISPR/Cas9-Mediated Knockout of the PxJHBP Gene Resulted in Increased Susceptibility to Bt Cry1Ac Protoxin and Reduced Lifespan and Spawning Rates in Plutella xylostella. Journal of Agricultural and Food Chemistry. DOI: 10.1021/acs.jafc.3c08721.

Huang X, Chen W, Zhao Y, Chen J, Ouyang Y, Li M, Gu Y, Wu Q, Cai S, Guo F, Ao D, Zhu P, You S, Vasseur L, Liu Y. (2024) Deep learning-based quantification and transcriptomic profiling reveal a methyl jasmonate‐mediated glandular trichome formation pathway in Cannabis sativa. The Plant Journal. DOI:  10.1111/tpj.16663.

Wang W, Li Y, Cai C and Zhu Q.(2024) Auxin response factors fine-tune lignin biosynthesis in response to mechanical bending in bamboo. New Phytol.241:1161-1176.

2023

Jiang B,Zhong Z,Gu L,Zhang X,Wei J,Ye C,Lin G,Qu G,Xiang X,Wen C,Gateas M,Bailey-Serres J,Wang Q,He C, Wang X and Lin C. (2023)Light-induced LLPS of the CRY2/SPA1/FIO1 complex regulating mRNA methylation and chlorophyll homeostasis in Arabidopsis.Nature Plants. https://doi.org/10.1038/s41477-023-01580-0.

Jia J, Chen L, Yu W, Cai S, Su S, Xiao X, Tang X, Jiang X, Chen D, Fang Y, Wang J, Luo X, Li J, Huang Y and Su J.（2023）The novel nematicide chiricanine A suppresses Bursaphelenchus xylophilus pathogenicity in Pinus massoniana by inhibiting Aspergillus and its secondary metabolite, sterigmatocystin. Front. Plant Sci.14:1257744. doi: 10.3389/fpls.2023.1257744.

Dang X, Zhu L, Ren H, Lin D. (2023) Methods to Visualize and Quantify Cortical Microtubule Arrays in Arabidopsis Conical Cells. Methods Mol Biol. 2604:317-325.

Jin Y,Wang B,Bao M,Li Y,Xiao S,Wang Y,Zhang J,Zhao L,Zhang H,Hsu Y,Li M,Gu L. (2023) Development of an efficient expression system with large cargo capacity for interrogation of gene function in bamboo based on bamboo mosaic virus. J Integr Plant Biol.https://doi.org/10.1111/jipb.13468.

Wang Y,Wang H,Wang H,Zhou R,Wu J,Zhang Z,Jin Y,Li T,Kohnen M,Liu X,Wei W,Chen K,Gao Y,Ding J,Zhang H,Liu B,Lin C,Gu L. (2023) Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo (Phyllostachys edulis). Genomics, Proteomics & Bioinformatics. https://doi.org/10.1016/j.gpb.2023.01.007.

Zhang Y,Wei Y,Meng J,Wang Y,Nie S,Zhang Z,Wang Y,Gao Y,Wu J,Li T,Liu X,Zhang H,Gu L. (2023) Chromosome-scale de novo genome assembly and annotation of three representative Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana . Plant Journal. https://doi.org/10.1111/tpj.16201 .

Liao J,Deng B,Yang Q,Li Y,Zhang Y,Cong J,Wang X,Kohnen M,Liu Z,Lu M,Lin D,Gu L,Liu B.(2023) Insights into Cryptochrome Modulation of ABA Signaling to Mediate Dormancy Regulation in Marchantia polymorpha. New Phytol.238(4):1479-1497.

2022

Huang T, Kramer EM, Lin D.(2022) Editorial: Petal Development: From Cell Biology to EvoDevo. Front Plant Sci. Jun 15;13:951442. doi: 10.3389/fpls.2022.951442.

Chen B, Dang X, Bai W, Liu M, Li Y, Zhu L, Yang Y, Yu P, Ren H, Huang D, Pan X, Wang H, Qin Y, Feng S, Wang Q, Lin D. (2022) The IPGA1-ANGUSTIFOLIA module regulates microtubule organisation and pavement cell shape in Arabidopsis. New Phytol. 236(4):1310-1325.

Li T,Wang H,Zhang Y,Wang H,Zhang Z,Liu X,Zhang Z,Liu K,Yang D,Zhang H,Gu L.(2022) Comprehensive profiling of epigenetic modifications in fast-growing moso bamboo shoots. Plant Physiology. https://doi.org/10.1093/plphys/kiac525.

Ren H,Rao J,Tang M,Li Y,Dang X,Lin D.(2022) PP2A interacts with KATANIN to promote microtubule organization and conical cell morphogenesis. J Integr Plant Biol. https://www.jipb.net/EN/10.1111/jipb.13281.

Gao Y,Liu X,Jin Y,Wu J,Li S,Li Y,Chen B,Zhang Y,Wei L,Li W,Li R,Lin C,Reddy A,Jaiswal R,Gu L.(2022) Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of Populus trichocarpa. Plant Physiology. https://doi.org/10.1093/plphys/kiac272.

Liu S, Zhang L, Gao L, Chen Z, Bie Y, Zhao Q, Zhang S, Hu X, Liu Q, Wang X, Wang Q. (2022) Differential photoregulation of the nuclear and cytoplasmic CRY1 in Arabidopsis. New Phytologist. (doi: 10.1111/nph.18007).

Zhang Z,Wang H,Wu J,Jin Y,Xiao S,Li T,Liu X,Zhang H,Zhang Z,Su J,Liu J,Wang X,Gao Y,Ma X and Gu L. (2022) Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata.Frontiers in Genetics. https://doi.org/10.3389/fgene.2022.843269.

Zheng Y,Yang D,Rong J,Chen L,Zhu Q,He T,Chen L,Ye J,Fan L,Gao Y,Zhang H,Gu L.(2022) Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma Bamboo (Dendrocalamus latiflorus Munro). Journal of Integrative Plant Biology.64(3):649-670.

Cai S, Jia J, He C, Zeng L, Fang Y, Qiu G, Lan X, Su J, He X.(2022) Multi-Omics of Pine Wood Nematode Pathogenicity Associated With Culturable Associated Microbiota Through an Artificial Assembly Approach. Frionters in Plant Science. doi: 10.3389/fpls.2021.798539.

2021

Wang X, Jiang B, Gu L, Chen Y, Mora M, Zhu M, Noory E, Wang Q, Lin C.(2021) A photoregulatory mechanism of the circadian clock in Arabidopsis.Nature Plants.7(10):1397-1408.

Chen Y, Hu X, Liu S, Su T, Huang H, Ren H, Gao Z, Wang X, Lin D, Wohlschlegel JA, Wang Q, Lin C.(2021) Regulation of Arabidopsis photoreceptor CRY2 by two distinct E3 ubiquitin ligases.Nature Communications.12(1):2155. doi: 10.1038/s41467-021-22410-x.

Wu Y,Wang Q,Qu J,Liu W,Gao X,Li X,Yang,X,Lin C,Shuai J. (2021) Different response modes and cooperation modulations of blue-light receptors in photomorphogenesis. Plant Cell Environ. 44:1802–1815.

Xiang M,Ding W,Wu C,Wang W,Ye S,Cai C,Hu X,Wang N,Bai W,Tang X,Zhu C,Xu Q,Zheng Y,Ding Z,Lin C,Zhu Q. (2021) Production of purple Ma bamboo (Dendrocalamus latiflorus Munro) with enhanced drought and cold stress tolerance by engineering anthocyanin biosynthesis.Planta.254(3):50. doi: 10.1007/s00425-021-03696-z.

Liu Y,Duan X,Zhao X,Ding W,Wang Y,Xiong Y. (2021) Diverse nitrogen signals activate convergent ROP2-TOR signaling in Arabidopsis.Developmental Cell.56(9):1283-1295.

Liu Y,Xiong Y.(2021) Liquid culture system for efficient depletion of the endogenous nutrients in Arabidopsis seedlings.Star Protocols.2(4):100922. doi: 10.1016/j.xpro.2021.100922.

Zhu T,Tang W,Chen D,Li J,Su J. (2021) Identification of a novel efficient transcriptional activation domain from Chinese fir (Cunninghamia lanceolata).Journal of Genetics and Genomics.48(3):257-259.

Piao M,Zou J,Li Z,Zhang J,Yang L,Yao N,Li Y,Tang H,Zhang L,Yang D,Yang Z,Du X,Zuo Z. (2021) The Arabidopsis HY2 Gene Acts as a Positive Regulator of NaCl Signaling during Seed Germination.International Journal of Molecular Sciences.22(16):9009.

doi: 10.3390/ijms22169009.

Zou J,Li Z,Tang H,Zhang L,Li J,Li Y,Yao N,Li Y,Yang D,Zuo Z. (2021) Arabidopsis LSH8 positively regulates ABA signaling by changing the expression pattern of ABA responsive proteins. International Journal of Molecular Sciences.22(19):10314.doi: 10.3390/ijms221910314.

Chen K,Hu K,Xi F,Wang H,Kohnen M,Gao P,Liao J,Wei W,Liu X,Zhang H,Gu L.(2021) High-efficient and transient transformation of Moso Bamboo (Phyllostachys edulis) and Ma Bamboo (Dendrocalamus latiflorus Munro). Journal of Plant Biology. https://doi.org/10.1007/s12374-020-09294-y.

Wang H,Liu S,Dai X,Yang Y,Luo Y,Gao Y,Liu X,Wei W,Wang H,Xu X,Reddy A,Jaiswal P,Li W,Liu B,Gu L.(2021)PSDX: A comprehensive multi-omics association database of Populus trichocarpa with a focus on the secondary growth in response to stresses. Frontiers in Plant Science. 20;12:655565.doi: 10.3389/fpls.2021.655565.

Liu X,Gao Y,Liao J,Miao M,Chen K,Xi F,Wei W,Wang H,Wang Y,Xi X, Reddy A ,Gu L.(2021) Genome-wide profiling of circular RNAs, alternative splicing, and R-loops in stem-differentiating xylem of Populus trichocarpa. J Integr Plant Biol .63(7):1294-1308. 

Lin Z,Guo C,Lou S,Jin S,Zeng W,Guo Y,Fang J,Xu Z,Zuo Z,Ma L.(2021) Functional analyses unveil the involvement of moso bamboo (Phyllostachys edulis) group I and II NIN-LIKE PROTEINS in nitrate signaling regulation. Plant Science .306:110862.doi: 10.1016/j.plantsci.2021.110862.

Wu B,Liang A,Zhang H,Zhu T,Zhou Z,Yang D,Tang W,Li J,Su J. (2021)Application of Conventional UAV-based High-throughput Object Detection in the Early Diagnosis of Pine Wilt Disease by Deep Learning.Forest Ecology and Management.https://doi.org/10.1016/j.foreco.2021.118986.

Tu M,Wang W,Yai N,Cai,C,Liu Y,Lin C,Zuo Z,Zhu Q.(2021) The transcriptional dynamics during de novo shoot organogenesis of Ma bamboo (Dendrocalamus latiflorus Munro): implication of the contributions of abiotic stress response in this process.The Plant Journal. https://doi.org/10.1111/tpj.15398.

Fu L, Liu Y, Qin G, Wu P, Zi H, Xu Z, Zhao X, Wang Y, Li Y, Yang S, Peng C, Wong CCL, Yoo SD, Zuo Z, Liu R, Cho YH, Xiong Y. (2021) The TOR-EIN2 axis mediates nuclear signalling to modulate plant growth. Nature.doi: 10.1038/s41586-021-03310-y. 

Wang J,Wu B,Kohnen MV,Lin D,Yang C,Wang X,Qiang,A,Liu W,Kang J,Li H,Shen J,Yao T,Su J,Li B and Gu L.(2021) Classification of Rice Yield Using UAV-Based Hyperspectral Imagery and Lodging Feature. Plant Phenomics. https://doi.org/10.34133/2021/9765952.

Liu Y, Zhu P, Cai S, Haughn G, Page JE. (2021) Three novel transcription factors involved in cannabinoid biosynthesis in Cannabis sativa L. Plant Mol Biol. doi: 10.1007/s11103-021-01129-9. 

Cai S, Zhang Z, Huang S, Bai X, Huang Z, Zhang YJ, Huang L, Tang W, Haughn G, You S, Liu Y. (2021) CannabisGDB: a comprehensive genomic database for Cannabis Sativa L. Plant Biotechnol J. doi: 10.1111/pbi.13548. 

Zhang Z, Wang H, Wang Y, Xi F, Wang H, Kohnen MV, Gao P, Wei W, Chen K, Liu X, Gao Y, Han X, Hu K, Zhang H, Zhu Q, Zheng Y, Liu B, Ahmad A, Hsu YH, Jacobsen SE, Gu L. (2021) Whole genome characterization of chronological age-associated changes in methylome and circular RNAs in moso bamboo (Phyllostachys edulis) from vegetative to floral growth. Plant J. doi: 10.1111/tpj.15174. 

Gao Y, Liu X, Wu B, Wang H, Xi F, Kohnen MV, Reddy ASN, Gu L. (2021) Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing. Genome Biol.22(1):doi: 10.1186/s13059-020-02241-7.

2020

Wang Q,Lin C.（2020）Mechanisms of Cryptochrome-Mediated Photoresponses in Plants.Annu Rev Plant Biol. 71:103-129.

Wang Q,Lin C.（2020）A structural view of plant CRY2 photoactivation and inactivation. Nat Struct Mol Biol. 27(5):401-403. 

Fu L,Wang P,Xiong Y.（2020）Target of Rapamycin Signaling in Plant Stress Responses.Plant Physiology. 182(4):1613-1623.

Liu Y,Wu C,Hu X,Gao H,Wang Y,Luo H,Cai S,Li G,Zheng Y,Lin C,Zhu Q.（2020）Transcriptome profiling reveals the crucial biological pathways involved in cold response in Moso bamboo (Phyllostachys edulis).Tree physiology. 40(4):538-556.

Dang X,Chen B,Liu F,Ren H,Liu X,Zhou J,Qin Y,Lin D.（2020）Auxin signaling-mediated apoplastic pH modification functions in petal conical cell shaping.Cell Reports. 30(11):3904-3916.

Liu Q , Su T, He W, Ren H , Liu S, Chen Y , Gao L, Hu X , Lu H, Cao S , Huang Y , Wang X , Wang Q, Lin C.（2020）Photooligomerization Determines Photosensitivity and Photoreactivity of Plant Cryptochromes.Molecular Plant. 13(3):398-413.

Liu H,Su T,He W,Wang Q,Lin C.(2020) The Universally Conserved Residues Are Not Universally Required for Stable Protein Expression or Functions of Cryptochromes. Molecular Biology and Evolution.37(2):327-340.

Ye S,Chen G ,Kohnen MV,Wang W,Cai C,Ding W,Wu C,Gu L,Zheng Y,Ma X,Lin C,Zhu Q.(2019) Robust CRISPR/Cas9 mediated genome editing and its application in manipulating plant height in the first generation of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro). Plant Biotechnology Journal. Dec 19. doi: 10.1111/pbi.13320.

Ye W, Wang T, Wei W, Lou S, Lan F, Zhu S, Li Q, Ji G, Lin C, Wu X, Ma L.(2020) The Full-Length Transcriptome of Spartina alterniflora Reveals the Complexity of High Salt Tolerance in Monocotyledonous Halophyte. Plant Cell Physiol.61(5):882-896. 

Yuan X, Xu P, Yu Y, Xiong Y. (2020) Glucose-TOR signaling regulates PIN2 stability to orchestrate auxin gradient and cell expansion in Arabidopsis root. Proc Natl Acad Sci U S A. 117(51):32223-32225. 

Cai C, Wang W, Ye S, Zhang Z, Ding W, Xiang M, Wu C, Zhu Q. (2020) Overexpression of a Novel Arabidopsis Gene SUPA Leads to Various Morphological and Abiotic Stress Tolerance Alternations in Arabidopsis and Poplar. Front Plant Sci. doi: 10.3389/fpls.2020.560985. PMID: 33281837; PMCID: PMC7688997.

Ye X, Tu M, Piao M, Yang L, Zhou Z, Li Z, Lin M, Yang Z, Zuo Z. (2020) Using phage-assisted continuous evolution (PACE) to evolve human PD1. Exp Cell Res. doi: 10.1016/j.yexcr.2020.112244. 

Dang X, Zhu L, Lin D. (2020) Live imaging of microtubules in petal conical cells. Methods Cell Biol. 160:253-261. 

Zhang Z, Yang X, Cheng L, Guo Z, Wang H, Wu W, Shin K, Zhu J, Zheng X, Bian J, Li Y, Gu L, Zhu Q, Wang ZY, Wang W. (2020) Physiological and transcriptomic analyses of  brassinosteroid function in moso bamboo (Phyllostachys edulis) seedlings.Planta.doi: 10.1007/s00425-020-03432-z. PMID: 32712728.

Wang Y, Wang H, Xi F, Wang H, Han X, Wei W, Zhang H, Zhang Q, Zheng Y, Zhu Q, Kohnen MV, Reddy ASN, Gu L. (2020) Profiling of circular RNA N6 -methyladenosine in moso bamboo (Phyllostachys edulis) using nanopore-based direct RNA sequencing. J Integr Plant Biol. 62(12):1823-1838. 

Guo Z, Zhang Z, Yang X, Yin K, Chen Y, Zhang Z, Shin K, Zhu Q, Wang ZY, Wang W. (2020) PSBR1, encoding a mitochondrial protein, is regulated by brassinosteroid in moso bamboo (Phyllostachys edulis). Plant Mol Biol.103(1-2):63-74. 

2019

Zhao L,Zhang H,Kohnen M,Prasad K V,Gu L,Reddy A S.（2019）Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing .Frontiers in Genetics.3(21): 10:253. doi: 10.3389/fgene.2019.00253.

Wang T,Li Q,Lou S,Yang Y,Peng L,Lin Z,Hu Q,Ma L.（2019）GSK3/ shaggy-like kinase 1 ubiquitously regulates cell growth from Arabidopsis to Moso bamboo (Phyllostachys edulis).Plant Science.283:290-300.

Wu B,Zhang H,Lin L,Wang H,Gao Y,Zhao L,Chen Y,Chen R,Gu L.（2019）A similarity searching system for biological phenotype images using deep convolutional encoder-decoder architecture. Current Bioinformatics.14(7):628-639.

Potok M E,Wang Y,Xu L,Zhong Z,Liu W,Feng S,Naranbaatar B,Rayatpisheh S,Wang Z,Wohlschlegel J A,Ausin I,Jacobsen S E.（2019）Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. Nature Communications. 10(1): 3352.

doi: 10.1038/s41467-019-11291-w.

Zhu Q,Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E.（2019）Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis.Development.146(17): dev175919.doi: 10.1242/dev.175919.

Wang Q,Lin C.（2019）Photoreceptor signaling: when COP1 meets VPs.EMBO JOURNAL. 38(18):e102962.doi: 10.15252/embj.2019102962.

Yang Z, Chen L, Kohnen M V , Xiong B , Zhen X , Liao J , Oka Y , Zhu Q, Gu L , Lin C , Liu B.（2019）Identification and Characterization of the PEBP Family Genes in Moso Bamboo (Phyllostachys heterocycla).Scientific  Reports. 9(1):14998.doi: 10.1038/s41598-019-51278-7.

Zou X,Liang A,Wu B,Su J.（2019）UAV-based high-throughput approach for fast growing Cunninghamia lanceolata (Lamb.) cultivar screening by machine learning.Forests.10(9):815.

Li Y,Lin B,Zhu P,Zhang H,Su J.（2019）The interactions of PhSPL17 and PhJAZ1 mediate the on- and off-year moso bamboo (Phyllostachys heterocycla) resistance to the Pantana phyllostachysae larval feeding.Pest Manag Science. 76(4):1588-1595.

Zhang N,Meng Y,Li X,Zhou Y,Ma L,Fu L, Schwarzländer M,Liu H,Xiong Y.（2019）Metabolite-mediated TOR signaling regulates the circadian clock in Arabidopsis.PNAS. 116(51):25395-25397.

Wang H, Wang H, Zhang H, Liu S, Wang Y, Gao Y, Xi F, Zhao L, Liu B, Reddy ASN, Lin C, Gu L.(2019) The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species.Bioinformatics. 35(17):3119-3126. 

Yu X, Wang Y, Kohnen MV, Piao M, Tu M, Gao Y, Lin C, Zuo Z, Gu L.(2019) Large Scale Profiling of Protein Isoforms Using Label-Free Quantitative Proteomics Revealed the Regulation of Nonsense-Mediated Decay in Moso Bamboo (Phyllostachys edulis).

Cells. 8(7): pii: E744. doi: 10.3390/cells8070744.

Wang Y, Gao Y, Zhang H, Wang H, Liu X, Xu X, Zhang Z, Kohnen MV, Hu K, Wang H, Xi F, Zhao L, Lin C, Gu L.(2019) Genome-Wide Profiling of Circular RNAs in the Rapidly Growing Shoots of Moso Bamboo(Phyllostachys edulis).Plant Cell Physiol. 60(6):1354-1373.

Yang Z, Chen L, Kohnen MV, Xiong B, Zhen X, Liao J, Oka Y, Zhu Q, Gu L, Lin C, Liu B. (2019)Identification and Characterization of the PEBP Family Genes in Moso Bamboo (Phyllostachys heterocycla). Sci Rep. 9(1):14998. doi: 10.1038/s41598-019-51278-7.

Yang Y, Huang W, Wu E, Lin C, Chen B, Lin D.(2019) Cortical Microtubule Organization during Petal Morphogenesis in Arabidopsis.Int J Mol Sci. 20(19):pii: E4913. doi: 10.3390/ijms20194913.

Zhang N,Meng Y,Li X,Zhou Y,Ma L,Fu L, Schwarzländer M ,Liu H,Xiong Y.(2019) Metabolite-mediated TOR signaling regulates the circadian clock in Arabidopsis. Proc Natl Acad Sci U S A.116(51):25395-25397.

Wang T ,Yang Y,Lou S, Wei W,Zhao Z, Ren Y, Lin C, Ma L. (2019) Genome-Wide Characterization and Gene Expression Analyses of GATA Transcription Factors in Moso Bamboo (Phyllostachys edulis). Int. J. Mol. Sci. 21(1): pii: E14. doi: 10.3390/ijms21010014.

Liu Y,Wu C,Hu X,Gao H,Wang Y,Luo H,Sen C,Li G,Zheng Y,Lin C,Zhu Q.(2019)Transcriptome profiling reveals the crucial biological pathways involved in cold response in Moso bamboo (Phyllostachys edulis). Tree Physiology. Dec 20.doi:10.1093/treephys/tpz133.

Yang Y, Chen B, Dang X, Zhu L, Rao J, Ren H, Lin C, Qin Y, Lin D. (2019) Arabidopsis IPGA1 is a microtubule-associated protein essential for cell expansion during petal morphogenesis. J Exp Bot. pii: erz284. doi: 10.1093/jxb/erz284.
Ye G, Zhang H,Chen B, Nie S, Liu H, Gao W, Wang H, Gao Y, Gu L.(2019) De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia providesinsight into secondary growth.Plant J. 97(4):779-794.

Gao  Y, Xi F, Zhang H, Liu X, Wang H, Zhao L, Reddy A, Gu L.(2019)  Single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) in plants:  The status of the bioinformatics tools to unravel the transcriptome  complexity.Current Bioinformatics. 14(7):566-573.

2018

Dang X, Yu P, Li Y, Yang Y, Zhang Y, Ren H, Chen B, Lin D.（2018）Reactive oxygen species mediate conical cell shaping in Arabidopsis thaliana petals. PLoS Genetics. 14(10):e1007705.

Yang L,MO W,Yu X,Yao N,Zhou Z,Fan X,Zhang L,Piao M,Li S,Yang D,Lin C and Zuo Z.(2018) Reconstituting Arabidopsis CRY2 Signaling Pathway in Mammalian Cells Reveals Regulation of Transcription by Direct Binding of CRY2 to DNA.Cell Reports.24:585-593.

Wang Q,Liu Q,Wang X,Zuo Z,Oka Y and Lin C.(2018) New insights into the mechanisms of phytochrome-cryptochrome coaction.New Phytologist.217:547–551.

Wang Q, Zuo Z, Wang X, Liu Q, Gu L, Oka Y, Lin C.(2018) Beyond the photocycle – how cryptochromes regulate photoresponses in plants?.Current Option in Plant Biology. 45:120-126.

Zhang H, Wang H, Zhu Q, Gao Y, Wang H, Zhao L, Wang Y, Xi F, Wang W, Yang Y, Lin C, Gu L.(2018) Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications.BMC plant biology.18(1):125. doi: 10.1186/s12870-018-1336-z.

2017

Wang X,Wang Q,Han Y,Liu Q,Gu L,Yang Z,Su J,Liu B,Zuo Z,He W,Wang J,Liu B,Minami M,Kim J,Oka Y and Lin C. (2017) A CRY–BIC negative-feedback circuitry regulating blue light sensitivity of Arabidopsis.The Plant Journal.92:426-436.
Wang W,Gu L,Ye S,Zhang H,Cai C,Xiang M,Gao Y,Wang Q,Lin C and Zhu Q. (2017) Genome-wide analysis and transcriptomic profiling of the auxin biosynthesis,transport and signaling family genes in moso bamboo (Phyllostachys heterocycla).BMC Genomics.18:870 DOI 10.1186/s12864-017-4250-0.

Liu K, Niu Y, Konishi M, Wu Y, Du H, Chung H, Li L, Boudsocq M, McCormack M, Maekawa S, Ishida T, Zhang C, Shokat K, Yanagisawa S and Sheen J.(2017) Discovery of nitrate–CPK–NLP signaling in central nutrient–growth networks.Nature.545:311-316.

Liu Q, Wang Q, Deng W, Wang X, Piao M, Cai D, Li Y , Barshop W, Yu X, Zhou T, Liu B, Oka Y, Wohlschlegel J, Zuo Z and Lin C.(2017) Molecular basis for blue light-dependent phosphorylation of Arabidopsis cryptochrome 2.Nature Communications.doi: 10.1038/ncomms15234.

Ren H, Dang X, Cai X, Yu P, Li Y, Zhang S, Liu M, Chen B, Lin D.（2017）Spatio-temporal orientation of microtubules controls conical cell shape in Arabidopsis thaliana petals. PLoS Genetics.13(6): e1006851. doi: 10.1371/journal.pgen.1006851.

Ye S ,Cai C, Ren H, Wang W, Xiang M, Tang X, Zhu C, Yin T, Zhang L and Zhu Q.(2017) An Efficient Plant Regeneration and Transformation System of Ma Bamboo (Dendrocalamus latiflorus Munro) Started from Young Shoot as Explant.Frontiers Plant Science.8:1298 doi:10.3389/fpls.2017.01298.

Wang T, Wang H, Cai D, Gao Y, Zhang H, Wang Y, Lin C, Ma L and Gu L.(2017) Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis). The Plant Journal.doi: 10.1111/tpj.13597.

Gao Y, Wang H, Zhang H, Wang Y, Chen J, Gu L.(2018) PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq. Bioinformatics.34(9):1580-1582.

Zhang H, Lin C and Gu L.(2017) Light Regulation of Alternative Pre-mRNA Splicing in Plants. Photochem Photobiol. 93(1):159-165.

2016

Wang Q,Zuo Z ,Wang X,Gu L , Yoshizumi T,Yang,Z ,Liu Q,Liu W,Han Y J,Liu B, Wohlschlegel J A, Matsui M, Oka Y and Lin C .(2016) Photoactivation and inactivation mechanisms of Arabidopsis cryptochrome 2.Science.354:343-347.

Liu Q,Wang Q,Liu B,Wang W,Wang X,Park J,Yang Z,Du X,Bian M and Lin C.(2016) The Blue Light-Dependent Polyubiquitination and Degradation of Arabidopsis Cryptochrome2 Requires Multiple E3 Ubiquitin Ligases.Plant Cell Physiol.57(10):2175-2186.

Ren H,Dang X ,Yang Y,Huang D,Liu M,Gao X,Lin D.(2016) SPIKE1 Activates ROP GTPase to Modulate Petal Growth and Shape.Plant Physiol.172(1):358-371.

Ausin I，Feng S，Yu C, Liu W, Kuo HY, Jacobsen EL, Zhai J, Gallego-Bartolome J, Wang L, Egertsdotter U, Street NR, Jacobsen SE and Wang H. (2016) DNA methylome of the 20-gigabase Norway spruce genome.Proc. Nat. Acad. Sci. U. S. A. doi/10.1073/pnas.1618019113.

Groth M, Moissiard G, Wirtz M, Wang H, Garcia-Salinas C, Ramos-Parra P A, Bischof S, Feng S, Cokus SJ, John A, Smith DC, Zhai J, Hale CJ, Long JA, Hell R, Diaz de la Garza RI, Jacobsen SE. (2016) MTHFD1 controls DNA methylation in Arabidopsis.Nature Communications.7:11640.

Harris CJ, Husmann D, Liu W, Kasmi FE, Wang H, Papikian A, Pastor WA, Moissiard G, Vashisht AA, Dang JL, Wohlschlegel JA, Jacobsen SE. (2016) Arabidopsis AtMORC4 and AtMORC7 Form Nuclear Bodies and Repress a Large Number of Protein-Coding Genes.PLOS Genetics.doi:10.1371/journal.pgen.1005998.

Yang L,Wang X,Deng W ,Mo W ,Gao J,Liu Q,Zhang C ,Wang Q,Lin C and Zuo Z .(2016) Using HEK293T Expression System to Study Photoactive Plant Cryptochromes.Frontiers in Plant Science.27(7): 940. doi: 10.3389.

Liu B,Yang Z,Gomez A,Liu B,Lin C ,Oka Y.(2016) Signaling mechanisms of plant cryptochromes in Arabidopsis thaliana.J Plant Res.129(2):137-148.

Zhu Q, Benková E.(2016) Seedlings' Strategy to Overcome a Soil Barrier.Trends Plant Science.pii: S1360-1385(16)30113-3.

Chaiwanon J, Wang W, Zhu JY,Oh E, Wang ZY. (2016) Information Integration and Communication in Plant Growth Regulation.Cell.164(6):1257-1268.

2015

Zhai J, Bischof S, Wang H, Feng S, Lee TF, Teng C, Chen X, Park SY, Liu L, Gallego-Bartolome J, Liu W, Henderson IR, Meyers BC, Ausin I, Jacobsen SE.（2015）A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis.Cell.163(2):445-455.

Wang H, Beyene G, Zhai J, Feng S, Fahlgren N, Taylor NJ, Bart R, Carrington JC, Jacobsen SE, Ausin I.(2015) CG gene body DNA methylation changes and evolution of duplicated genes in cassava.Proc Natl Acad Sci U S A.112(44):13729-13734.

Jie Gao., Xu Wang., Meng Zhang., Mingdi Bian., Weixian Deng., Zecheng Zuo., Zhenming Yang.,Dongping Zhong and Chentao Lin.(2015) Trp triad-dependent rapid photoreduction is not required for the function of Arabidopsis CRY1.Proc Natl Acad Sci U S A.112(29):9135-9140.

Wang Q., Barshop W.D., Bian M., Vashisht A.A., He R., Yu X., Liu B., Nguyen P., Liu X., Zhao X., Wohlschlegel J.A and Lin C. (2015) The Blue Light-Dependent Phosphorylation of the CCE Domain Determines the Photosensitivity of Arabidopsis CRY2.Mol Plant. 8: 631-643.

Xuehua Zhong., Christopher J. Hale., Minh Nguyen., Israel Ausin., Martin Groth., Jonathan Hetzela., Ajay A. Vashisht., Ian R. Henderson., James A. Wohlschlegel and Steven E. Jacobsen. (2015) DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis.Proc Natl Acad Sci U S A.112: 911-916.

2014

Wang, X., Wang, Q., Nguyen, P., Lin, C. (2014) Cryptochrome-mediated light responses in plants.Enzymes.35:167-89. doi: 10.1016/B978-0-12-801922-1.00007-5.

Martin Groth.,Hume Stroud.,Suhua Feng.,Maxim V.C.Greenberg.,Ajay A.Vashisht.,James A.Wohlschlege.,Steven E.Jacobsen and Israel Ausin.(2014) SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation.Proc Natl Acad Sci U S A.111(49):17666-17671.

Wenfei Wang and Zhi-Yong Wang.(2014) At the Intersection of Plant Growth and Immunity.Cell Host & Microbe.15:400-402.

Wenfei Wang., Ming-Yi Bai and Zhi-Yong Wang.(2014) The brassinosteroid signaling network-a paradigm of signal integration.Current Opinion in Plant Biology.21:147-153.