一、国际期刊论文 (下划线代表通讯作者; *代表共同第一作者；#代表共同通讯作者)
Song K, Chen B, Cui Y, Zhou L, Chan KG, Zhang HY, He Ya-Wen. The Plant Defense Signal Salicylic Acid Activates the RpfB-Dependent Quorum Sensing Signal Turnover via Altering the Culture and Cytoplasmic pH in the Phytopathogen Xanthomonas campestris. mBio. 2022 Mar 7: e0364421.
Azad SM, Jin Y, Ser HL, Goh BH, Lee LH, Thawai C, He Ya-Wen. Biological insights into the piericidin family of microbial metabolites. Journal of Applied Microbiology. 2022, 132(2): 772-784.
Fang YL, Cui Y, Zhou L, Thawai C, Naqvi TA, Zhang HY, He Ya-Wen. H-NS family protein MvaU downregulates phenazine-1-carboxylic acid (PCA) biosynthesis via binding to an AT-rich region within the promoter of the phz2 gene cluster in the rhizobacterium Pseudomonas strain PA1201. Synth Syst Biotechnol. 2021, 6(4): 262-271.
Hui ML, Tan LT, Letchumanan V, He Ya-Wen, Fang CM, Chan KG, Law JW, Lee LH. The Extremophilic Actinobacteria: From Microbes to Medicine. Antibiotics (Basel). 2021 Jun 8;10(6):682.
Chen B, Li RF, Zhou L, Qiu JH, Song K, Tang JL, He Ya-Wen. The phytopathogen Xanthomonas campestris utilizes the divergently transcribed pobA/pobR locus for 4-hydroxybenzoic acid recognition and degradation to promote virulence. Molecular Microbiology, 2020 Nov;114(5):870-886.
Jin ZJ, Zhou L, Sun S, Cui Y, Song K, Zhang X, He Ya-Wen. Identification of a Strong Quorum Sensing- and Thermo-Regulated Promoter for the Biosynthesis of a New Metabolite Pesticide Phenazine-1-carboxamide in Pseudomonas strain PA1201. ACS Synthetic Biology. 2020 Jul 17;9(7):1802-1812.
He Ya-Wen, Cao XQ, Poplawsky AR Dr. Chemical structure, biological roles, biosynthesis and regulation of the yellow xanthomonadin pigments in the phytopathogen Xanthomonas. Molecular Plant Microbe Interactions. 2020, 33(5):705-714.
Sun S, Tan LT, Fang YL, Jin ZJ, Zhou L, Goh BH, Lee LH, Zhou J, He Ya-Wen. Overexpression of oxyR Increases Phenazine-1-Carboxylic Acid Biosynthesis via Small RNA phrS in the Rhizobacterium Strain Pseudomonas PA1201. Molecular Plant Microbe Interactions. 2020 Mar;33(3):488-498.
Cao XQ, Ouyang XY, Chen B, Song K, Zhou L, Jiang BL, Tang JL, Ji G, Poplawsky AR, He Ya-Wen. Genetic Interference Analysis Reveals that Both 3-Hydroxybenzoic Acid and 4-Hydroxybenzoic Acid Are Involved in Xanthomonadin Biosynthesis in the Phytopathogen Xanthomonas campestris pv. campestris. Phytopathology. 2020 Feb;110(2):278-286.
Keswani C, Singh HB, García-Estrada C, Caradus J, He Ya-Wen, Mezaache-Aichour S, Glare TR, Borriss R, Sansinenea E. Antimicrobial secondary metabolites from agriculturally important bacteria as next-generation pesticides. Applied Microbiology and Biotechnology. 2020 Feb;104(3):1013-1034.
Yang Q, Song L, Miao Z, Su M, Liang W, He Ya-Wen. Acetylation of BcHpt Lysine 161 Regulates Botrytis cinerea Sensitivity to Fungicides, Multistress Adaptation and Virulence. Front Microbiol. 2020 Jan 8;10: 2965.
Thawai C, Bunbamrung N, Pittayakhajonwut P, Chongruchiroj S, Pratuangdejkul J, He Ya-Wen, Tadtong S, Sareedenchai V, Prombutara P, Qian Y. A novel diterpene agent isolated from Microbispora hainanensis strain CSR-4 and its in vitro and in silico inhibition effects on acetylcholine esterase enzyme. Sci Rep. 2020 Jul 6;10(1):11058.
Law JW, Chan KG, He Ya-Wen, Khan TM, Ab Mutalib NS, Goh BH, Lee LH. Diversity of Streptomyces spp. from mangrove forest of Sarawak (Malaysia) and screening of their antioxidant and cytotoxic activities. Sci Rep. 2019 Dec 3;9(1):15262.
Chee PY, Mang M, Lau ES, Tan LT, He Ya-Wen, Lee WL, Pusparajah P, Chan KG, Lee LH, Goh BH. Epinecidin-1, an Antimicrobial Peptide Derived From Grouper (Epinephelus coioides): Pharmacological Activities and Applications. Front Microbiol. 2019 Nov 20;10:2631.
Keswani C, Singh HB, Hermosa R, García-Estrada C, Caradus J, He Ya-Wen, Mezaache-Aichour S, Glare TR, Borriss R, Vinale F, Sansinenea E. Antimicrobial secondary metabolites from agriculturally important fungi as next biocontrol agents. Appl Microbiol Biotechnol. 2019 Dec;103(23-24):9287-9303.
Zhou L, Li M, Wang XY, Liu H, Sun S, Chen H, Poplawsky A, He Ya-Wen. Biosynthesis of Coenzyme Q in the Phytopathogen Xanthomonas campestris via a Yeast-Like Pathway. Mol Plant Microbe Interact. 2019，32(2):217-226.
Diab AA, Cao XQ, Chen H, Song K, Zhou L, Chen B, He Ya-Wen. BDSF Is the Predominant In-Planta Quorum-Sensing Signal Used During Xanthomonas campestris Infection and Pathogenesis in Chinese Cabbage. Mol Plant Microbe Interact. 2019, 32(2):240-254.
Thawai C, He Ya-Wen, Tadtong S. Jishengella zingiberis sp. nov., isolated from root tissue of Zingiber montanum. Int J Syst Evol Microbiol. 2018 Oct; 68(10):3345-3350.
Cao, XQ, Zhou L, Chen B, He Ya-Wen. Biosynthesis of Xanthomonas yellow pigment xanthomonadins involves an ATP-dependent 3- HBA:ACP ligase and an unusual type II polyketide synthesis pathway. Molecular Microbiology. 2018, Oct; 110(1):16-32.
Qi X, Qu H, Yang D, Zhou L, He Ya-Wen, Yu Y, Qu J, Liu J. Lower respiratory tract microbial composition was diversified in Pseudomonas aeruginosa ventilator-associated pneumonia patients. Respir Res. 2018 Jul 27;19(1):139.
Fang Y L, Chen B, Zhou L, He Ya-Wen. The mechanism underlying the regulatory roles of anti-activator QslA on the biosynthesis of phenazine-1-carboxylic acid in Pseudomonas aeruginosa PA1201. Frontiers in Microbiology. 2018, Jul 25; 9:1584.
Zhou L, Sun S, Zhang W, He Ya-Wen. Ultra-Performance Liquid Chromatography/Mass Spectrometry for the Detection and Quantification of Diffusible Signal Factor (DSF) Family Quorum-Sensing Signals. Methods Mol Biol. 2018, 1673:97-105.
Sun S, Chen B, Jin ZJ, Zhou L, Fang YL, Thawai C, Rampioni G, He Ya-Wen. Characterization of the multiple molecular mechanisms underlying RsaL control of phenazine-1-carboxylic acid biosynthesis in the rhizosphere bacterium Pseudomonas aeruginosa PA1201. Molecular Microbiology. 2017, 104(6):931-947.
Zhou L, Wang X, Zhang W, Sun S, He Ya-Wen. Extraction, Purification and Quantification of Diffusible Signal Factor Family Quorum Sensing Signal Molecules in Xanthomonas. Bio-protocol, 2017, 7(6): e2190.
Zhou L, Zhang LH, Cámara M, He Ya-Wen. The DSF Family of Quorum Sensing Signals: Diversity, Biosynthesis, and Turnover in Xanthomonas. Trends in Microbiology. 2017, 25(4):293-303.
Sun S, Zhou L, Jin K, Jiang H, He Ya-Wen. Quorum sensing systems differentially regulate the production of phenazine-1-carboxylic acid in the rhizobacterium Pseudomonas aeruginosa PA1201. Scientific Reports, 2016, 6:30352.
Wang Xing-Yu, Zhou Lian, Yang J, Ji Guang-Hai, He Ya-Wen. The RpfB-Dependent Quorum Sensing Signal Turnover System Is Required for Adaptation and Virulence in the Pathogen Xanthomonas. Molecular Plant-Microbe Interactions. 2016, 29(3):220-30.
Zhou Lian, Jiang Haixia, Sun Shuang, Yang Dandan, Jin Kaiming, He Ya-Wen. Biotechnological potential of a rhizosphere Pseudomonas aeruginosa strain producing phenazine-1-carboxylic acid and phenazine-1-carboxamide. World Journal of Microbiology and Biotechnology, 2016, 32(3):50.
Zhou Lian*, Wang Xing-Yu*, Sun Shuang, Yang Li-Chao, Jiang Bo-Le, He Ya-Wen. Identification and Characterization of Naturally Occurring DSF-Family Quorum Sensing Signal Turnover System in the Phytopathogen Xanthomonas. Environmental Microbiology, 2015, 17(11):4646–4658.
Jin Kaiming*, Zhou Lian*, Jiang Haixia, Sun Shuang, Fang Yunling, Liu Jianhua, Zhang Xuehong, He Ya-Wen. Engineering the central biosynthetic and secondary metabolic pathways of Pseudomonas aeruginosa strain PA1201 to improve phenazine-1-carboxylic acid production. Metabolic Engineering, 2015, 32:30-38.
Wang Jia-Yuan*, Zhou Lian*, Chen Bo, Sun Shuang, Zhang Wei, Li Ming, Tang H, Jiang Bo-Le, Tang Ji-Liang, He Ya-Wen. A functional 4-hydroxybenzoate degradation pathway in the phytopathogen Xanthomonas campestris is required for full pathogenicity. Scientific Reports, 2015, 5: 18456.
Zhou Lian, Yu Yonghong, Chen Xiping, Diab AA, Ruan Lifang, He Jin, Wang Haihong#, He Ya-Wen#. The Multiple DSF-family QS Signals are synthesized from Carbohydrate and Branched-chain Amino Acids via the FAS Elongation Cycle. Scientific Reports, 2015, 5:13294.
Xu Shu, Pan X, Luo J, Wu J, Zhou Z, Liang X, He Ya-Wen, Zhou Mingguo. Effects of phenazine-1-carboxylic acid on the biology of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae. Pesticide Biochemistry and Physiology, 2015, 117:39-46.
Xu Jing, Zhou Lian, Venturi V, He Ya-Wen, Kojima M, Sakakibari H, Höfte M, De Vleesschauwer D. Phytohormone-mediated interkingdom signaling shapes the outcome of rice-Xanthomonas oryzae pv. oryzae interactions. BMC Plant Biology, 2015,15: 10.
Zhou Lian*, Wang Jia-Yuan*, Wang Jianhe, Poplawsky A, Lin Shuangjun, Zhu Bangshang, Chang Changqing, Zhou Tieling, Zhang Lian-Hui#, He Ya-Wen#. The diffusible factor (DF) synthase XanB2 is a bifunctional chorismatase that links the shikimate pathway to ubiquinone and xanthomonadins biosynthetic pathways. Molecular Microbiology, 2013, 87(1): 80-93.
Zhou Lian, Huang Tin-Wei, Sun Shuang, Wang Jia-Yuan, Chen Gongyou, Poplawsky AR, He Ya-Wen. The rice acterial pathogen Xanthomonas oryzae pv. oryzae produces 3-hydroxybenzoic acid and 4-hydroxybenzoic acid via XanB2 for use in xanthomonadin, ubiquinone and exopolysaccharide biosynthesis. Molecular Plant-Microbe Interactions. 2013, 26(10):1239-48.
Qian Guoliang, Wang Y, Liu Y, Xu F, He Ya-Wen, Du Liangcheng, Venturi V, Fan Jiaqing, Hu Boshi, Liu Fengquan. Lysobacter enzymogenes uses two distinct cell-cell signaling systems for differential regulation of secondary metabolite biosynthesis and colony morphology. Applied and Environmental Microbiology. 2013, 79(21): 6604-6616.
Wu Da-Qiang, Ye Jing, Ou Hong-Yu, Wei Xue, Huang Xianqing, He Ya-Wen# and Xu Yuquan#. Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18. BMC Genomics，2011, 12：438.
Zhou Lian, Vorholter FJ, He Ying-Qiang, Jiang Bo-Le, Tang Ji-Liang, Xu Yuquan, Puhler A#, He Ya-Wen#. Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris. BMC Genomics, 2011, 12(1):359.
He Ya-Wen#, Wu Jien, Zhou Lian, Yang Fan, Jiang Bo-Le, Tang Ji-Liang, Bai Linquan, Xu Yuquan, Deng Zixin, Zhang Lian-Hui#. Xanthomonas campestris diffusible factor is 3-hydroxybenzoic acid and associated with xanthomonadin biosynthesis, cell viability, antioxidant activity and systemic invasion. Molecular Plant-Microbe Interactions, 2011, 24(8):948-57.
He Ya-Wen*, Wu JE, Cha JS, Zhang LH (2010) Rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae produces multiple DSF-family signals in regulation of virulence factor production. BMC Microbiology, 10:187.
Cheng Z*, He Ya-Wen*, Lim SC*, Qamra R*, Walsh MA, Zhang LH, Song H (2010) Structural Basis of the Sensor-Synthase Interaction in Autoinduction of the Quorum Sensing Signal DSF Biosynthesis. Structure, 18(9):1199-1209.
Tao F, He Ya-Wen, Wu DH, Swarup S, Zhang LH (2010) The cyclic nucleotide monophosphate domain of Xanthomonas campestris global regulator Clp defines a new class of cyclic di-GMP effectors. The Journal of Bacteriology, 192(4):1020-9.
He Ya-Wen, Boon C, Zhou L, Zhang LH (2009) Co-regulation of Xanthomonas campestris virulence by quorum sensing and a novel two-component regulatory system RavS/RavR. Molecular Microbiology, 71(6):1464-1476.
He Ya-Wen, Zhang LH (2008) Quorum Sensing and Virulence Regulation in Xanthomonas campestris. FEMS Microbiology Reviews, 32: 842-857.
Boon C, Deng Y, Wang LH, He Ya-Wen, Xu JL, Fan Y, Pan SQ, Zhang LH (2008) A novel DSF-like signal from Burkholderia cenocepacia interferes with Candida albicans morphological transition. International Society of Microbial Ecology Journal (ISMEJ), 2(1):27-36.
He Ya-Wen, Ng YJ, Xu M, Lin K and Zhang LH (2007) Xanthomonas campestris cell-cell communication involves a nucleotide receptor protein Clp and a hierarchical signaling network. Molecular Microbiology, 64(2):281-292.
He Ya-Wen, Wang C, Zhou L, Song H, Dow JM, Zhang LH (2006) Dual signaling functions of the hybrid sensor kinase RpfC of Xanthomonas campestris involve either phosphorelay or receiver domain-protein interaction. The Journal of Biological Chemistry, 281:33414 – 33421.
Ryan RP, Fouhy Y, Lucey JF, Crossman LC, Spiro S, He Ya-Wen, Zhang LH, Heeb S, Camara M, Williams P, Dow JM (2006) Cell-cell signaling in Xanthomonas campestris involves an HD-GYP domain protein that functions in cyclic di-GMP turnover. Proceedings of National Academy of Science of USA, 103(17):6712-6717.
He Ya-Wen, Xu M, Lin K, Ng YJ, Wen CM, Wang LH, Liu ZD, Zhang HB, Dong YH, Dow JM and Zhang LH (2006) Genome scale analysis of diffusible signal factor regulon in Xanthomonas campestris pv. campestris: identification of novel cell-cell communication-dependent genes and functions. Molecular Microbiology, 59(2):610-622.
Wang LH, He Ya-Wen, Gao YF, Wu JE, Dong YH, Wang RB, He CZ, Wang SX, Weng LX, Xu JL, Tay L, Fang RX, Zhang LH (2004) A bacterial cell-cell communication signal with cross-kingdom structural analogs. Molecular Microbiology, 51(3):903-12.
Lo J, Lee S, Xu M, Liu F, Ruan H, Eun A, He Ya-Wen, Ma W, Wang W, Wen Z, Peng J (2003) 15,000 unique zebrafish est clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Genome Research, 13: 455-466.
Lee S, Cheng H, King KE, Wang W, He Ya-Wen, Hussain A, Lo J, Harberd NP, Peng J (2002) Gibberellin regulates Arabidopsis seed germination via RGL2, a GAI/RGA-like gene whose expression is up-regulated following imbibition. Genes and Development, 16:646-658.
He Ya-Wen and Loh CS (2002) Induction of early bolting in Arabidopsis thaliana by triacontanol, cerium and lanthanum is correlated with increased endogenous concentration of isopentenyl adenosine (iPAdos). Journal of Experimental Botany, 53 (368):505-512.
He Ya-Wen and Loh CS (2000) Cerium and lanthanum promote floral initiation and reproductive growth of Arabidopsis thaliana. Plant Science, 159:117-124.
二、中文期刊论文/综述
宋凯，郭晓春，陈博，何亚文. 植物病原黄单胞菌退出群体感应生理状态的分子机制和生物学意义. 微生物学报, 2021, 61(1): 68–76.
宋凯 周莲 何亚文. DSF-家族群体感应信号生物合成途径与调控机制研究进展. 微生物学通报. 2021, 48(4): 1239−1248.
崔 莹，宋 凯，何亚文. 假单胞菌代谢产物藤黄绿菌素化学结构、生物合成途径、调控机制及应用研究进展.中国生物防治学报, 2021, 37(1): 52-59.
邱嘉辉, 曹雪强, 宋凯, 陈博, 何亚文. 改造群体感应机制和菌黄素代谢途径生物合成“白原胶”. 基因组学与应用生物学. 2021, 40: 2118-2126.
郑哲麟，胡文达，何亚文*。微生物卤化酶及其应用研究进展。微生物前沿, 2020, 9(4)： 141-155。
崔莹，金子靖，何亚文。碳源影响水稻根际假单胞菌PA1201藤黄绿菌素的生物合成。微生学通报，2020，47（8）：2399-2408。
邱嘉辉，何亚文。微生物胞外多糖黄原胶的应用与研究进展。激光生物学报，2019， 28（5）：385-393。
陈慧 周莲 陈博 宋凯 郭晓春 何亚文*。天然氨基酸诱导野油菜黄单胞菌降解 DSF-家族群体感应 信号活性分析。微生物学通报，2019, 46(11): 2952−2962
曹雪强，何亚文。植物病原黄单胞菌菌黄素化学结构、生物学功能和生物合成机制研究进展。微生物前沿，2018，7（4）：156-164.
蒋海霞，周莲，何亚文。铜绿假单胞菌生防菌株代谢产物及其生防应用研究进展。微生物学通报，2015，42：1338-1349。
金凯明，周莲，蒋海霞，何亚文。微生物小基因组细胞工厂研究进展。生命科学，2015，7：883-891。
赵秀，朱小龙，何亚文，梁永恒。酿酒酵母中磷脂合成相关基因突变对细胞自噬和液泡形态的影响。南京农业大学学报, 2015,38(1):70-77.
方运玲，孙爽，申阅，何亚文。微生物源农药申嗪霉素的研制与应用。农药学学报，2014, 16（4）：387-393。
周莲，王杏雨，何亚文。植物病原黄单胞菌DSF信号依赖的群体感应记者及调控网络。中国农业科学，2013, 46（14）：2910-2922。
三、参与编写的著作/章节
(1) 何亚文，第五章：微生物源抗生素农药。见：《现代生物农药100问》。中国农业科学技术出版社，北京，2014年，第66-77页。
(2) He Ya-Wen, Chou Shan-Ho. Chapter 13. Cyclic di-GMP Regulation in Plant-Pathogenic Bacteria. In: Virulence Mechanisms of Plant-Pathogenic Bacteria (Edited by Wang N, Jones JB, Sundin GW). APS Press, St. Paul, Minnesota, USA, 2015, pp. 107-124.
(3) Zhou Lian, Sun Shuang, Zhang Wei, He Ya-Wen. Ultra-Performance Liquid Chromatography/Mass Spectrometry for the detection and quantification of Diffusible Signal Factor (DSF) family quorum sensing signals. In: Quorum Sensing Methods and Protocols (Edited by Livia Leoni, Giordano Rampioni). Humana Press, UK, 2017, pp. 97-106.
(4) He Ya-Wen, Qian Wei, Chou San-Ho. Chapter 25 Cyclic di-GMP Signaling in the Phytopathogen Xanthomonas campestris pv. campestris. In: S.-H. Chou et al. (eds.), Microbial Cyclic Di-Nucleotide Signaling. Springer Nature Switzerland AG2020, pp. 427-442.
四、专利：
（1）周莲，何亚文，高产吩嗪-1-羧酸和吩嗪-1-酰胺的根际假单胞菌。中国专利号ZL 2013 1 0511796.2，授权公告日：2016年2月10日。
（2）周莲，金凯明，何亚文。安全高效生产申嗪霉素的基因工程菌株及其应用。中国专利号ZL 2015 1 0056619.9，授权公告日：2018年02月09日。
（3）周莲，杨丹丹，何亚文。BDSF高产菌株及其发酵优化方法和应用。中国专利号：ZL201810002666.9，授权公告日：2020年11月06日。授权公告号：CN108342347B。
（4）何亚文，金子靖。低毒高产杀菌剂吩嗪-1-酰胺的基因工程菌株及培养方法和应用。专利号：ZL 2017 1 1125280.9。
（5）何亚文，邱嘉辉。一种高产白原胶的工程菌株及其构建与应用。申请号：CN201911141660.0；公开日：2020年2月11日，公开号：CN110777105A。
（6）何亚文. 一株高产杀粉蝶菌素A1和高效抑制植物病原黄单胞菌生长的链霉菌菌株。申请号：CN202011190782.1
（7）何亚文. 一株耐酸、耐盐、耐热、高效降解有机物的枯草芽孢杆菌及其在餐厨垃圾资源化中的应用.。申请号: 202110625225.6，申请公布号：CN113481118A。