致力于黑曲霉等工业微生物的系统与合成生物学研究，重点开发系统生物学技术与高通量基因组编辑技术，整合多组学数据，解析黑曲霉等工业微生物的独特分子机制，辅以计算机设计开发创建新型细胞工厂，实现工业化菌株的个性化定制，推动传统发酵行业的升级换代与绿色发展。在Microb Biotechnol、ACS Synth Biol、Biotechnol J、Microb Cell Fact与Biotechnol Biofuels等杂志上发表SCI论文20篇，申请发明专利8项,其中授权2项。

代表论著：

1） Zheng X, Cairns TC, Ni X, Zhang L, Zhai H, Meyer V, Zheng P, Sun J. Comprehensively dissecting the hub regulation of PkaC on high-productivity and pellet macromorphology in citric acid producing Aspergillus niger. Microb Biotechnol. 2022 Feb 25. doi: 10.1111/1751-7915.14020.

2）Zheng X, Zheng P, Sun J. CRISPR/Cas-based genome editing in Aspergillus niger. Sheng Wu Gong Cheng Xue Bao. 2021 Mar 25;37(3):980-990.

3）Zhang L^#, Zheng X^#, Cairns TC, Zhang Z, Wang D, Zheng P, Sun J. Disruption or reduced expression of the orotidine-5'-decarboxylase gene pyrG increases citric acid production: a new discovery during recyclable genome editing in Aspergillus niger. Microb Cell Fact. 2020 Mar 24;19(1):76.

4）Zheng X, Zheng P, Zhang K, Cairns TC, Meyer V, Sun J, Ma Y. 5S rRNA Promoter for Guide RNA Expression Enabled Highly Efficient CRISPR/Cas9 Genome Editing in Aspergillus niger. ACS Synth Biol. 2019 Jul 19;8(7):1568-1574. 

5） Zheng X, Yu J, Cairns TC, Zhang L, Zhang Z, Zhang Q, Zheng P, Sun J, Ma Y. Comprehensive Improvement of Sample Preparation Methodologies Facilitates Dynamic Metabolomics of Aspergillus niger. Biotechnol J. 2019 Mar;14(3):e1800315.

6）Zheng X, Zheng P, Sun J. Systems biology for industrial biotechnology. Sheng Wu Gong Cheng Xue Bao. 2019 Oct 25;35(10):1955-1973.

7） Tong Z^#, Zheng X^#, Tong Y, Shi YC, Sun J. Systems metabolic engineering for citric acid production by Aspergillus niger in the post-genomic era. Microb Cell Fact. 2019 Feb 4;18(1):28.

8） Zheng X, Zheng P, Sun J, Zhang K, Ma Y. Heterologous and endogenous U6 snRNA promoters enable CRISPR/Cas9 mediated genome editing in Aspergillus niger. Fungal Biol Biotechnol. 2018 Feb 8;5:2.

9）Zhang Q^#, Zheng X^#, Wang Y, Yu J, Zhang Z, Dele-Osibanjo T, Zheng P, Sun J, Jia S, Ma Y. Comprehensive optimization of the metabolomic methodology for metabolite profiling of Corynebacterium glutamicum. Appl Microbiol Biotechnol. 2018 Jun 6.

10）Cairns TC, Zheng X, Feurstein C, Zheng P, Sun J, Meyer V. A Library of Aspergillus niger Chassis strains for morphology engineering connects strain fitness and filamentous growth with submerged macromorphology. Front Bioeng Biotechnol. 2022 Jan 17;9:820088.

11）Cairns TC, Zheng X, Zheng P, Sun J, Meyer V. Turning Inside Out: Filamentous Fungal Secretion and Its Applications in Biotechnology, Agriculture, and the Clinic. J Fungi (Basel). 2021 Jul 2;7(7):535.

12） Cairns TC, Zheng X, Zheng P, Sun J, Meyer V. Moulding the mould: understanding and reprogramming filamentous fungal growth and morphogenesis for next generation cell factories. Biotechnol Biofuels. 2019 Apr 2;12:77.

13） Cairns TC^#, Feurstein C^#, Zheng X, Zheng P, Sun J, Meyer V. A quantitative image analysis pipeline for the characterization of filamentous fungal morphologies as a tool to uncover targets for morphology engineering: a case study using aplD in Aspergillus niger. Biotechnol Biofuels. 2019 Jun 15;12:149.

14） Wang X, Li Q, Sun C, Cai Z, Zheng X, Guo X, Ni X, Zhou W, Guo Y, Zheng P, Chen N, Sun J, Li Y, Ma Y. GREACE-assisted adaptive laboratory evolution in endpoint fermentation broth enhances lysine production by Escherichia coli. Microb Cell Fact. 2019 Jun 11;18(1):106.