Selected peer-reviewed journal articles: 

Xiangyu Deng, Zengxin Li, Wei Zhang*. 2012. Transcriptome sequencing of Salmonella enterica serovar Enteritidis under desiccation and starvation stress in peanut oil. Food Microbiology (UK) 30:311-315.

Yingshu He, Dongjing Guo, Jingyun Yang, Mary Lou Tortorello, Wei Zhang*. 2011. Survival and heat resistance of Salmonella enterica and Escherichia coli O157:H7 in peanut butter. Applied and Environmental Microbiology 77:8434-8438.
Jia Wen, Xiangyu Deng, Zengxin Li, Edward G. Dudley, Ramaswamy C. Anatheswaran, Stephen J. Knabel, Wei Zhang*. 2011. Transcriptomic response of Listeria monocytogenes during transition to the long-term-survival phase. Applied and Environmental Microbiology 77:5966-5972. 

Kaiping Deng, Siyun Wang, Xiaoqian Rui, Wei Zhang, Mary Lou Tortorello*. 2011. Functional analysis of ycfR and ycfQ in Escherichia coli O157:H7 linked to outbreaks associated with fresh produce. Applied and Environmental Microbiology 77:3952-3959. 

Pina M. Fratamico*, Siyun Wang, Xianghe Yan, Wei Zhang, Yuesheng Li. 2010. Differential gene expression of Escherichia coli O157:H7 in ground beef extract compared to tryptic soy broth. Journal of Food Science. 76:M79-M87. 

Xiangyu Deng, Adam M. Phillippy, Zengxin Li, Steven L. Salzberg, Wei Zhang*. 2010. Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification. BMC Genomics 11:500 

Siyun Wang, Adam M. Phillippy, Kaiping Deng, Xiaoqian Rui, Mary Lou Tortorello, Wei Zhang*. 2010. Transcriptomic responses of Salmonella enterica Enteritidis and Typhimurium to chlorine-based oxidative stress. Applied and Environmental Microbiology 76:5013-5024. 

Siyun Wang, Kaiping Deng, Sam Zaremba, Xiangyu Deng, Chiahui Lin, Qian Wang, Mary Lou Tortorello, Wei Zhang*. 2009. Transcriptomic response of Escherichia coli O157:H7 to oxidative stress. Applied and Environmental Microbiology 75: 6110-6123. 

Adam M. Phillippy*, Xiangyu Deng, Wei Zhang, Steven L. Salzberg. 2009. Efficient oligonucleotide probe selection for pan genomic tiling arrays. BMC Bioinformatics 10:293. 

Shannon D. Manning, Alifiya S. Motiwala, A. Cody Springman, Weihong Qi, David W. Lacher, Lindsey M. Ouellette, Janice M. Mladonicky, Patricia Somsel, James T. Rudrik, Stephen E. Dietrich, Wei Zhang, Bala Swaminathan, David Alland, Thomas S. Whittam*. 2008. Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proceedings of National Academy of Sciences U.S.A. 105:4868-4873 

Xinyi He, Hongyu Ou, Yu Qing, Xiufen Zhou, Jun Wu, Jingdan Liang, Wei Zhang, Kumar Rajakumar, Zixin Deng*. 2007. Analysis of a genomic island housing dnd gene clusters which encodes S modification system in Streptomyces lividans. Molecular Microbiology 65:1034-1048.

Hui Cai, Beatriz T. Rodríguez, Wei Zhang, Jeff R. Broadbent and James L. Steele*. 2007. Genotypic and phenotypic characterization of Lactobacillus casei strains from different ecological niches suggests frequent recombination and niche specificity. Microbiology 153:2655-2665.

Yi Chen, Wei Zhang, Stephen J. Knabel*. 2007. Multi-virulence-locus sequence typing identifies single nucleotide polymorphisms which differentiate epidemic clones and outbreak strains of Listeria monocytogenes. Journal of Clinical Microbiology 45: 835-846. 

Wei Zhang*, Weihong Qi, Thomas J. Albert, Alifiya S. Motiwala, David Alland, Eija K. Hyytia-Trees, Efrain M. Ribot, Patricia I. Fields, Thomas S. Whittam and Bala Swaminathan. 2006. Probing genomic diversity and evolution of Escherichia coli O157 by single-nucleotide polymorphisms. Genome Research 16:757-767.
Book Chapters 

Wei Zhang*, Joseph Wade, Edward Dudley. 2011. Chapter 10. Genomic and transcriptomic analysis of foodborne bacterial pathogens. In: Wei Zhang, Martin Wiedmann (eds.), Genomics of Foodborne Bacterial Pathogens. In: Food Microbiology and Food Safety book series. Springer, New York, USA. 640 p. 48 illus., 31 in color., ISBN 978-4419-7685-7, Hardcover.
Bala Swaminathan*, Didier Cabanes, Wei Zhang, Pascale Cossart. 2007. Chapter 21: Listeria monocytogenes. p. 457-491. In: Doyle MP, Beuchat LR, Montville TJ, (eds.), Food Microbiology: Fundamentals and Frontiers, 3rd ed. ASM Press, Washington DC, USA