Li, Feng

Lab Introduction

Our research laboratory studies the biology and evolution of emerging RNA viruses of humans and animals with clinical relevance. The other component of our research program centers on viral cross-species transmission and pathogenesis. A large portion of our efforts is on zoonotic and equine viruses. New knowledge emerging from our studies will be instrumental to design of next-generation antiviral therapeutics and vaccines, which will contribute to future pandemic preparedness and response. RNA viruses that are currently under investigation in our laboratory include influenza viruses (human and equine and other animals), rotaviruses (human and equine), Zika virus and HIV-1 (human), West Nile viruses (human and equine), equine infectious anemia virus, and equine arteritis virus.

One growing interest in our laboratory is to map the inter- and intra-host genetic variations in viral populations and assess whether these polymorphisms affect viral antigenicity, virulence, and transmission to new hosts. The other emerging topic in our laboratory is to utilize next-generation sequence technology for rapid detection and characterization of new vial pathogens emerging in horses.

Identification of emerging and reemerging viral pathogens in horses

This project will utilize the MiSeq platform to detect, sequence, and characterize viral pathogens that cause diseases in horses. We will first sequence viral genomes and then conduct a de novo genome assembly using Miseq read data to determine the draft full-length of viral genomes.

Personnel:

Feng Li (Faculty), Dan Wang (Faculty)

Chithra Sreenivasan (Post-doc)

Ahsan Naveed (Post-doc)

Shalini Soni (Post-doc)

Tirth Uprety (Graduate RA)

Lianne Eertink (Graduate GRA)  

Computational methods:

Sequence read analysis and mapping, transcriptome assembly, sequence annotation and validation, and phylogenetic analysis

Software:

Discovering new viral pathogens. CLC Genomics workstation, Trinity, HiSat2, SAMtools, RSEM, NCBI BLAST, BLAST2G0, BEAST, and OmicsBox

Next-generation sequencing analysis of cellular responses to viral infections

This project will enable the identification of cellular genes and their networks that may correlate disease severity or protection following viral infections of in vitro cell cultures and animals. 

Personnel:

Feng Li (Faculty)

Dan Wang (Faculty)

Chithra Sreenivasan (Post-doc)

Ahsan Naveed (Post-doc)

Shalini Soni (Post-doc)

Tirth Uprety (Graduate RA)

Lianne Eertink (Graduate GRA) 

Computational Methods:

Sequence read analysis and mapping, transcriptome assembly, sequence annotation and validation, and differential expression analysis.

Software:

Identifying cellular genes and their network as potential correlates of disease or protection during viral infection:  FastQC, GSNAP, HTSeq, DESeq, SAMtools, and cufflinks

Computational Methods:

Most of the computational methods can be accessible through the internet free of charge.  Our department has purchased CLC Genomics workstation, and we are in the process of acquiring the OmicsBox for our MiSeq data analysis.

Software: 

FastQC, GSNAP, HTSeq, DESeq, SAMtools, and cufflinks or similar software will be used in our transcriptome analysis.

UK and non-UK collaborators:

Grants:

Publications: