Xinxia Peng

Bio

Please visit our lab website: https://penglab.cvm.ncsu.edu

I joined NC State in July 2016 as Dean’s Faculty Excellence cluster hire, in the field of “Translational Genomics of Infectious Diseases”. Currently I am an Associate Professor of Infectious disease in the Department of Molecular Biomedical Sciences, and a member of NC State Bioinformatics Research Center (https://brc.ncsu.edu).

I am a computational biologist interested in high-throughput omics data analysis and method development, and its application in infectious disease and immunology. After receiving my Ph.D. in Computational Biology and Bioinformatics, I worked as a Bioinformatics Manager at Seattle BioMed (now Center for Infectious Disease Research), where I performed transcriptomics and proteomics data analyses to improve malaria vaccine design and to identify drug targets. In 2008 I joined the University of Washington as a computational research scientist, and began using systems approaches to study virus-host interactions and viral pathogenesis. I was promoted to a Research Assistant Professor in the University of Washington Department of Microbiology in 2012.

As an early adopter of deep sequencing technologies, I have discovered some novel aspects of pathogen‐host interactions. For example, by analyzing transcriptome deep sequencing data (RNA‐seq), I authored the first report that long noncoding RNAs (lncRNAs) are related to virus infection and innate immunity in 2010. I have also led large scale collaborative efforts including the completion of the domestic ferret genome sequencing project and the development of a centralized nonhuman primate (NHP) reference transcriptome resource by deep sequencing complete transcriptomes of multiple NHP species. Prior to joining NC State, I also served as the lead computational biologist for the NIAID NHP Functional Genomics Core for AIDS Vaccine Research and Development. I am continuously actively involved in both HIV/AIDS research and other areas of infectious disease research.

CERTIFICATIONS

Ph.D., Life Sciences: Computational Biology and Bioinformatics, University of Tennessee – Oak Ridge National Laboratory Graduate School of Genome Science and Technology, Oak Ridge, TN, 2005
M.S., Computer Science, University of Tennessee, Knoxville, TN, 2004
M.S., Foods and Nutrition, University of Georgia, Athens, GA, 2001
M.S., Biochemistry and Molecular Biology, East China Normal University, Shanghai, China, 1999
B.S., Biology, East China Normal University, Shanghai, China, 1996

Area(s) of Expertise

COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, INFECTIOUS DISEASES
noncoding RNA, immunity, and target identification
Microbiome, immunity, and vaccine efficacy
Complex immune genes: genetic variation and transcriptional regulation
Genomics for infectious disease animal models: non-human primates and ferret

Publications

• Cervicovaginal microbial features predictsChlamydia trachomatisspread to the upper genital tract of infected women , (2024)
• Human long noncoding RNA,VILMIR,is induced by major respiratory viral infections and modulates the host interferon response , (2024)
• Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques , (2024)
• Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques , MICROBIOLOGY SPECTRUM (2024)
• Alternative splicing and genetic variation of mhc-e: implications for rhesus cytomegalovirus-based vaccines , COMMUNICATIONS BIOLOGY (2022)
• Phylogeny-guided microbiome OTU-specific association test (POST) , MICROBIOME (2022)
• Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques , JOURNAL OF IMMUNOLOGY (2022)
• Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution , NUCLEIC ACIDS RESEARCH (2021)
• Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen , JOURNAL OF THE ROYAL SOCIETY INTERFACE (2021)
• Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy , PLOS PATHOGENS (2021)

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