Zhang XK, Wang FF, Yang NH, Chen NZ, Hu YM, Peng XJ*, Shen SH*. 2023. Bioinformatics analysis and function prediction of NBS-LRR gene family in Broussonetia papyrifera. Biotechnology Letters, 45(1): 13-31

Hu YM, Peng XJ*, Shen SH* 2022. Identification and investigation of the genetic variations and candidate genes responsible for seed weight via GWAS in Paper mulberry. International Journal of Molecular Sciences, 23: 12520

Tang F, Zhang D, Chen NZ, Peng XJ*, Shen SH*. 2022. Genome-wide analysis of BpYABs and function identification involving in the leaf and silique development in transgenic Arabidopsis. International Journal of Molecular Sciences, 23: 1670

Su YL, Peng XJ*, Shen SH*. 2022. Identification of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in paper mulberry and their potential roles in response to cold stress. Computational Biology and Chemistry, 97: 107622

Wang FF, Chen NZ*, Shen SH*. 2022. iTRAQ-Based quantitative proteomics analysis reveals the mechanism of golden-yellow leaf mutant in hybrid paper mulberry. International Journal of Molecular Sciences, 23: 127

Wang FF, Su YL, Chen NZ*, Shen SH*. 2021. Genome- wide analysis of the UGT gene family and identification of flavonoids in Broussonetia papyrifera. Molecules, 26: 3449

Hu YM, Peng XJ, Wang FF, Chen PL, Zhao ML, Shen SH*. 2021. Natural population re-sequencing detects the genetic basis of local adaptation to low temperature in a woody plant. Plant Molecular Biology, 105: 585-599

Zhang BH，Chen NZ，Peng XJ*, Shen SH*. 2021. Identification of the PP2C gene family in paper mulberry (Broussonetia papyrifera) and its roles in the regulation mechanism of the response to cold stress. Biotechnology letters, 43(5): 1089-1102

Zhao ML, Peng XJ, Chen NZ*, Shen SH*. 2020. Genome-wide identification of the TCP gene family in Broussonetia papyrifera and functional analysis of BpTCP8, 14 and 19 in shoot branching. Plants, 9: 1301

Chen PL, Hu YM, Tang F, Zhao ML, Peng XJ*, Shen SH*. 2020. Cooperation between Broussonetia papyrifera and symbiotic fungal community to improve host local adaptability. Applied Microbiology and Biotechnology, 86: e00464-20

Chen PL, Zhao ML, Tang F, Hu YM, Peng XJ*, Shen SH*. 2020. The effect of plant compartments on the Broussonetia papyrifera-associated fungal and bacterial communities. Applied Microbiology and Biotechnology, 104: 3627-3641

Chen PL, Zhao ML, Tang F, Hu YM, Peng XJ*, Shen SH*. 2019. The effect of environment on the microbiome associated with the roots of a native woody plant under different climate types in China. Applied Microbiology and Biotechnology, 103: 3899-3913

Peng XJ, Liu H, Chen PL, Tang F, Hu YM, Wang FF, Pi Z, Zhao ML, Chen NZ, Chen H, Zhang XK, Yan XQ, Liu M, Fu XJ, Zhao GF, Yao P, Wang LL, Dai H, Li XM, Xiong W, Xu WC, Zheng HK, Yu HY*, Shen SH*. 2019. A chromosome-scale genome assembly of paper mulberry (Broussonetia papyrifera) and genetic basis of its forage and papermaking usage. Molecular Plant, 12: 661-677

Liu H, Wang FF, Peng XJ, Huang JH, Shen SH*. 2019. Global phosphoproteomic analysis reveals the defense and response mechanisms of Jatropha curcas seedling under chilling stress. International Journal of Molecular Sciences, 20: 208

Wu QQ, Peng XJ, Yang MF, Zhang WP, Frank BD, Norman U, Jing YX*, Shen SH*. 2018. Rhizobia promote the growth of rice shoots by targeting cell signaling, division and expansion. Plant Molecular Biology, 97: 507-523

Tang F, Chen NZ, Zhao ML, Wang YC, He RP, Peng XJ*, Shen SH*. 2017. Identification and functional divergence analysis of WOX gene family in paper mulberry. International Journal of Molecular Sciences, 18: 1782

Pi Z, Zhao ML, Peng XJ, Shen SH*. 2017. Phosphoproteomic analysis of paper mulberry reveals phosphorylation functions in chilling tolerance. Journal of Proteome Research, 16:1944-1961

Peng XJ, Wang Q, Liu H, Shen SH*. 2017. Phylogenetic and functional analysis of the basic transcription factor gene BTF3 from Jatropha curcas. Plant Growth Regulation, 82: 247-257

Wang YY, Ji KX, Shen SH, Chen H*. 2016. Probing molecular events associated with early development of thylakoid membranes by comparative proteomics and low temperature fluorescence. Journal of Proteomics, 143: 401-415

Peng XJ, Liu H, Wan D, Shen SH*. 2016. Genome-wide identification of the Jatropha curcas MYB family and functional analysis of the abiotic stress responsive gene JcMYB2. BMC Genomics, 17: 251

Peng XJ, Wu QQ, Teng LH, Tang F, Pi Z, Shen SH*. 2015. Transcriptional regulation of the paper mulberry under cold stress as revealed by a comprehensive analysis of transcription factors. BMC Plant Biology, 15: 108

Peng XJ, Teng LH, Yan XQ, Zhao ML, Shen SH*. 2015. The cold responsive mechanism of the paper mulberry: Decreased photosynthesis capacity and increased starch accumulation. BMC Genomics, 16: 898

Liu H, Wang CP, Chen F, Shen SH*. 2015. Proteomic analysis of oil bodies in mature Jatropha curcas seeds with different lipid content. Journal of Proteomics, 113: 403-414

Peng XJ, Wang YC, He RP, Zhao ML, Shen SH*. 2014. Global transcriptomics identification and analysis of transcriptional factors in different tissues of the paper mulberry. BMC Plant Biology, 14 (1): 194

Peng XJ, Teng LH, Wang XM, Wang YC, Shen SH*.2014. De novo assembly of expressed transcripts and global transcriptomics analysis of seedling in paper mulberry (Broussonetia kazinoki x Broussonetia papyifera). PLoS ONE, 9(5): e97487

Sun JW, Peng XJ, Fan WH, Tang MJ, Liu J, Shen SH*. 2014. Functional analysis of BpDREB2 gene involved in salt and drought response from a woody plant Broussonetia papyrifera. Gene, 535: 140-149

Liu H, Wang CP, Liu GS*, Shen SH*. 2013. Proteomic analysis of the seed development in Jatropha curcas: from carbon flux to the lipid accumulation. Journal of Proteomics, 91: 23-40

Wang XQ, Han F, Yang MF, Yang PF, Shen SH*. 2013. Exploring the response of rice (Oryza sativa) leaf to gibberellins: a proteomicstrategy. Rice, 6: 17

Zhang MD*, Shen SH. 2013. Effective protein extraction protocol forproteomics studies of Jerusalem artichokeleaves. Journal of Separation Science, 36: 2203-2209

Ji KX, Wang YY, Sun WN, Lou QJ, Mei HW, Shen SH, Chen H*. 2012. Drought-responsive mechanisms in rice genotypes with contrasting drought tolerance during reproductive stage. Journal of Plant Physiology, 169: 336-344

Chen Q, Zhang MD, Shen SH*. 2011. Effect of salt on malondialdehyde and antioxidant enzymes in seedling roots of Jerusalem artichoke (Helianthus tuberosus L.). Acta Physiologiae Plantarum, 33: 273-278

Zhang MD, Chen Q, Shen SH*. 2011. Physiological responses of two Jerusalem artichoke cultivars to drought stress induced by polyethylene glycol. Acta Physiologiae Plantarum, 33: 313-318

Fan WH, Cui WT, Li XF, Chen SY, Liu GS*, Shen SH*. 2011. Proteomics analysis of rice seedling responses to ovine saliva. Journal of Plant Physiology, 68: 500-509

Peng XJ, Ma XY, Fan WH, Su M, Cheng LQ, Iftekhar A, Lee BH, Qi DM, Shen SH*, Liu GS*. 2011. Improved drought and salt tolerance of Arabidopsis thaliana by transgenic expression of a novel DREB gene from Leymus chinensis. Plant Cell Reports, 30: 1493-1502

He DL, Han C, Yao JL, Shen SH and Yang PF*. 2011. Constructing the metabolic and regulatory pathways in germinating rice seeds through proteomic approach. Proteomics, 11:  2693–2713

Chen Q, Zhang MD, Shen SH*. 2011. Comparison of protein extraction methods suitable for proteomics analysis in seedling roots of Jerusalem artichoke under salt (NaCl) stress. African Journal of Biotechnology, 10: 7650-7657

Yang J, Yang MF, Zhang WP, Chen F, Shen SH*. 2011. A putative flowering-time-related Dof transcription factor gene, JcDof3, is controlled by the circadian clock in Jatropha curcas. Plant Science, 181: 667-674

Liu H, Yang ZL, Yang MF, Shen SH*. 2011. The differential proteome of endosperm and embryo from mature seed of Jatropha curcas. Plant Science, 181: 660-666

Tang MJ, Liu XF, Deng HP*, Shen SH*. 2011. Over-expression of JcDREB, a putative AP2/EREBP domain-containing transcription factor gene in woody biodiesel plant Jatropha curcas, enhances salt and freezing tolerance in transgenic Arabidopsis thalia. Plant Science, 181: 623-631

Li XJ, Yang MF, Zhu Y, Liang Y, ShenSH*. 2011. Proteomic analysis of salt stress responses in rice shoot. Journal of Plant Biology, 54: 384-395

Liu Y, Chen H, Zhuang DF, Jiang D, Liu J, Wu GJ, Yang MF*, Shen SH*. 2010. Characterization of a DRE-binding transcription factor from asparagus (Asparagus officinalis L.), and its overexpression in Arabidopsis resulting in salt- and drought-resistant transgenic plants. International Journal of Plant Sciences, 171: 12-23

Ji KX, Chi F, Yang MF, Shen SH*, Jing YX*, Cheng HP and Dazzo FB. 2010. Movement of Rhizobia inside tobacco and lifestyle alternation from endophytes to free-living Rhizobia on leaves. Journal of Microbiology and Biotechnology, 20: 238-244

Li XJ, Yang MF, Chen H, Qu LQ, Chen F, Shen SH*. 2010. Abscisic acid pretreatment enhances salt tolerance of rice seedlings: Proteomic evidence. BBA-Proteins and Proteomics, 1804: 929-940

Chi F, Yang PF, Han F, Jing YX*, Shen SH*. 2010. Proteomic analysis of rice seedlings infected by Sinorhizobium meliloti 1021. Proteomics, 10: 1861-1874

Yang J, Yang MF, Wang D, Chen F* and Shen SH*. 2010. JcDof1, a Dof transcription factor gene, is associated with the light-mediated circadian clock in Jatropha curcas. Physiologia Plantarum, 139: 324-334

Pan XL*, Jiang QY, Pan QY, Wen XF, Shi YD, Wang YJ, Pan TY, Xie SG, Zhang GY, Wu SJ, Chai YF, Zhang C, Wu ZX and Shen SH*. 2009. Proteomic analysis of ‘hybrid necrosis’ in wheat (Triticum aestivum) leaves. Functional Plant Biology, 36: 251-259

Zhang CX, Zhao X, Han F, Yang MF*, Jing YX, Chida T, Shen SH*. 2009. Comparative proteome analysis of two antagonist Bacillus subtilis strains. Journal of Microbiology and Biotechnology, 19: 351-358

Yang MF, Liu YJ, Liu Y, Chen H*, Chen F, Shen SH*. 2009. Proteomic analysis of oil mobilization in seed germination and postgermination development of Jatropha curcas. Journal of Proteome Research, 8: 1441-1451

Wang XQ, Yang PF, Liu Z, Liu WH, Hu Y, Chen H, Kuang TY, Pei ZM, Shen SH, He YK*. 2009. Exploring the mechanism of Physcomitrella patens desiccation tolerance through a proteomic strategy. Plant Physiology, 149: 1739-1750

Liu H, Liu YJ, Yang MF*, Shen SH*. 2009. A Comparative analysis of embryo and endosperm proteome from seeds of Jatropha curcas. Journal of Integrative Plant Biology, 51: 850-857

Wang XQ, Yang PF, Liu Z, Xu Y, Kuang TY, Shen SH*, He YK*. 2009. Proteomic analysis of the cold stress response in the moss, Physcomitrella patens. Proteomics, 9: 4529-4538

Han F, Chen H, Li XJ, Yang MF*, Liu Ge*, Shen SH*. 2009. A comparative proteomic analysis of rice seedlings under various high-temperature stresses. BBA-Proteins and Proteomics, 1794: 1625-1634

Zhang CX, Zhao X, Jing YX, Chida T, Chen H, Shen SH*. 2008. Phenotypic and biological properties of two antagonist Bacillus subtilis strains. World Journal of Microbiology Biotechnology, 24: 2179-2181

Wang XQ, Yang PF, Gao Q, Liu XL, Kuang TY, Shen SH*, He YK*. 2008. Proteomic analysis of the response to high-salinity stress in Physcomitrella patens, 228: 167-177

Jiang QY, Chen H, Pan XL*, Pan QY, Shi YH, Li XR, Zhang GY, Wang YJ, Xie SG, Shen SH*. 2008. Proteomic analysis of wheat (T. aestivum L) hybrid necrosis. Plant Science, 175: 394-403

Lu P, Chen LJ, Li GX, Shen SH, Wang LL, Jiang QY*, Zhang JF. 2007. Influence of furfural concentration on growth and ethanol yield of Saccharomyces kluyveri. Journal of Environmental Sciences.19: 1528-1532

Yang PF, Chen H, Liang Y, Shen SH*. 2007. Proteomic analysis of de-etiolated rice seedlings upon exposure to light. Proteomics, 7: 2459-2468

Yang PF, Li XJ, Wang XQ, Chen H, Chen F, Shen SH*. 2007. Proteomic analysis of rice (Oryza sativa) seeds during germination. Proteomics, 7: 3358-3368

Liang Y, Chen H, Tang MJ and Shen SH*. 2007. Proteome analysis of an ectomycorrhizal fungus Boletus edulis under salt shock. Mycological Research, 111: 939-946

Liang Y, Chen H, Tang MJ, Yang PF, Shen SH*. 2007. Responses of Jatropha curcas seedlings to cold stress: photosynthesis related proteins and chlorophyll fluorescence characteristics. Physiologia Plantarum, 131: 508-517

Tang MJ, Sun JW, Liu Y, Chen F, Shen SH*. 2007. Isolation and functional characterization of the JcERF gene, a putative AP2/EREBP domain-containing transcription factor, in woody oil plant Jatropha curcas. Plant Molecular Biology, 63: 419-428

Han WW, Shen SH*, Tai PD. 2007. Proteome analysis of inhibitory effect of gadolinium on Sinorhizobium fredii. Journal of Rare Earths, 25: 106-110

Yang PF, Shen SH*, Kuang TY. 2006. A comparative analysis of the endosperm proteins separated by two-dimensional electrophoresis for two cultivars of hybrid rice (Oryza sativa L.). Journal of Integrative Plant Biology, 48: 1028-1033

Zuo P, Chen H*, Wu YS, Shen SH, Wang P, Ai XC, Zhang JP*, Li LB, Kuang TY. 2006. Effects of different aggregation forms of LHC II from Bryopsis corticulans on the excited state properties of Chl a. Chinese Science Bulletin, 51: 1444-1451

Zhou XJ, Liang Y, Chen H, Shen SH*, Jing YX*. 2006. Effects of rhizobia inoculation and nitrogen fertilization on soybean photosynthetic physiology. Photosynthetica, 44: 530-535

Chen YM, Chen T, Shen SH, Zheng MZ, Guo YM, Lin JX*, Baluska F, Samaj J. 2006. Differential display proteomic analysis of Picea meyeri pollen germination and pollen tube growth after actin depolymerization by latrunculin B. The Plant Journal, 47: 174-195

Yang PF, Liang Y, Shen SH*, Kuang TY. 2006. Proteome analysis of rice uppermost internodes at the milky stage. Proteomics, 6: 3330-3338

Yang PF, Li XJ, Liang Y, Jing YX, Shen SH*, Kuang TY. 2006. Proteomic analysis of the response of Liangyoupeijiu (A super high-yield hybrid rice) seedlings to cold stress. Journal of Integrative Plant Biology, 48: 945-951

Lü SY, Jing YX, Shen SH, Zhao HY, Ma LQ, Zhou XJ, Ren Q，Li YF*. 2005. Antiporter Gene from Hordum brevisubulatum (Trin.) Link and Its Overexpression in Transgenic Tobaccos. Journal of Integrative Plant Biology, 47: 343-349

Chi F, Shen SH, Cheng HP, Jing YX*, Yanni YG. and Dazzo FB. 2005. Ascending migration of endophytic Rhizobia from roots to leaves inside rice plants and assessment of their benefits to the growth physiology of rice. Applied and Environmental Microbiology, 71: 7271-7278

Chen H*, Shen SH, Liang Y, Leng J, Tang MJ, Gong YD. 2005. Evidence for dissociation of chlorophyll b from the main light-harvesting complex in the oligomerization state isolated from marine alga, Bryopsis corticulans. Biochimica et Biophysica Acta- Bioenergetics, 1707: 170-179

Tang MJ，Lü SY, Jing YX, Zhou XJ, Sun JW, Shen SH*. 2005. Isolation and identification of a cold-inducible gene encoding a putative DRE-binding transcription factor from Festuca arundinacea. Plant Physiology and Biochemistry, 43: 233-239

Qi SW, Yang PF, Jing YX, Shen SH* & Yang SS*. 2004. A proteomic analysis of bacterial strain Sinorhizobium fredii RT19 subjected to salt shock. Chinese Science Bulletin, 49: 1828-1833

Chen H*, Shen SH, He JF, Leng J, Li LB & Kuang TY. 2004. A light-harvesting siphonaxanthin- chlorophyll a/b-protein complex of marine green alga, Bryopsis corticulans. Chinese Science Bulletin, 49: 1936-1941

Yang GX, Jan A, Shen SH, Yazaki J, Ishikawa M, Shimatani Z, Kishimoto N, Kikuchi S, Matsumoto H and Komatsu S*. 2004. Microarray analysis of brassinosteroids- and gibberellin-regulated gene expression in rice seedlings. Molecular Genetics and Genomics, 271:468-478

Shen SH and Jing YX*. 2003. Present status and development on biological nitrogen fixation research in China. Chinese Science Bulletin, 48: 954-960

Yang GX, Shen SH, Yang SH, Komatsu S*. 2003. OsCDPK13, a calcium-dependent protein kinase gene from rice, is induced in response to cold and gibberellin. Plant Physiology and Biochemistry, 41: 369-374

Shen SH*, Jing YX, Kuang TY. 2003. Proteomics approach to identify wound-response related proteins from rice leaf sheath. Proteomics, 3: 527-535

Shen SH, Sharma A, Komatsu S*. 2003. Characterization of Proteins Responsive to Gibberellin in the Leaf-Sheath of Rice (Oryza sativa L.) Seedling Using Proteome Analysis. Biological Pharmaceutical Bulletin, 26: 129-136

Komatsu S*, Konishi H, Shen SH, Yang GX. 2003. Rice proteomics: a step toward functional analysis of the rice genome. Molecular Cellular & Proteomics, 2: 2-10

Shen SH, Matsubae M, Takao T, Komatsu S*. 2002. A proteomics analysis of leaf sheath from rice. Journal of Biochemistry, 132: 613-620

沈世华*, 彭献军, 陈乃芝. 2020. 杂交构树产业扶贫实践与成效. 中国科学院院刊，第 35 卷（增刊 2）：57-65

沈世华*, 彭献军, 段瑞, 熊伟. 2018. 科技引领创新 产业助力扶贫——杂交构树扶贫工程在山东菏泽的成效与启示. 中国科学院院刊，33：979-986

彭献军, 沈世华*. 2018. 构树：一种新型木本模式植物。植物学报，53：372-381

邳植, 沈世华*. 2018. 构树作为新兴的蛋白饲料原料的研究。饲料工业，39：23-28

胡艳敏, 彭献军, 沈世华*. 2018. 从古代科技史角度审视构树的多重文化内涵及应用价值. 北京林业大学学报，17：38-4

彭献军, 王金山, 沈世华*. 2016. 运用杂交构树进行尾矿生态修复和矿区绿化. 天津农业科学, 22(12): 111-119

著作专著：     

[1]  沈世华，2011。微生物蛋白质组学研究进展。李俊、沈德龙、林先贵主编，农业微生物研究与产业化进展。北京：科学出版社

[2] 沈世华等译，2013。H. Thiellement, M. Zivy, C. Damerval, V. Méchin主编，植物蛋白质组学-实验指南。北京：科学出版社。

[3] 沈世华、邓华平编著，2016。构树栽培及饲用技术。北京：中国农业科技技术出版社。

[4] 沈世华、罗朝立主编，2023。构树扶贫工程——我国生态农牧业发展的新探索。北京：中国文联出版社。

[5] 沈世华主编，2023。中国杂交构树产业发展蓝皮书（2022）。北京：研究出版社。

[6] 沈世华主编，2024。中国杂交构树产业发展蓝皮书（2023）。北京：研究出版社。