People

Peggy Farnham

Peggy.Farnham[at]med.usc.edu

W.M. Keck Chair in Biochemistry
Professor and Chair of Biochemistry & Molecular Biology

 

I have been a leader in the genome-wide study of mammalian transcription factors by developing technologies that combine chromatin immunoprecipitation with genomic microarray hybridization (ChIP-chip assays) and with high throughput sequencing (ChIP-seq). My lab was the first to develop ChIP protocols for mammalian cells and for the study of tumors from cancer patients, focusing on key cancer pathways regulated by E2F, MYC, and b-catenin. More recently, my lab has been a major contributor to the production of ChIP-seq datasets in normal and tumor cells for site-specific factors, histone-modifying complexes, and modified histones, developing protocols that are widely used by the field. In addition to bench work, my lab has developed programs to assist in the analysis of genome-scale ChIP-chip and ChIP-seq data and to derive consensus motifs from experimentally identified binding sites. Current projects in my lab are focused on two aspects of cancer research, characterization of the genome-wide effects of epigenetic chemotherapeutic inhibitors and molecular characterization of cancer-associated enhancers. We have expertise in the use of genomic nucleases and artificial transcription factors based on zinc finger, TALEN, and CRISPR platforms.

 

I am a member of the ENCODE Consortium, whose goal is to map all the functional elements in the human genome, mainly focusing on cancer cell lines. I was also a member of the NIH Roadmap Epigenome Mapping Consortium, which just recently published epigenome for ~100 normal cell types. I have recently been funded as part of the PsychENCODE project, which is seeking to expand the ENCODE assays to the analysis of pyschiatric disorders. My contributions to technology development and genome-wide analyses have been recognized by appointment an AAAS Fellow and by receiving the ASBMB Herbert A. Sober Award for outstanding biochemical and molecular biological research. The Web of Science catalogs 162 of my publications and reports a current h-index of 64; over the last 10 years my publications have been cited an average of 884 times/year with 2200 citations in 2014.

 

USC Health Sciences Profile

Biosketch

Complete list of published work in PubMED as of January 2016

top


Robert Gao

gaorober[at]usc.edu

PhD Student

 

top


Phoebe Guo

yuguo[at]usc.edu

PhD Student

 

I am a graduate student in the Farnham lab. I earned my B.E. of Pharmaceutical Engineering from Tianjin University of Science and Technology in 2011 and M.S. of Biochemistry and Molecular Biology from University of Southern California in 2014. I have a long-standing passion for the health science field and I believe with the development of Next Generation Sequencing we are empowered like never before to crack the secret code of the human genome. My current research is focused on understanding the mechanistic aspects of prostate cancer risk loci identified by genome-wide association studies (GWAS).

CV

top


Fides Lay

flay[at]usc.edu

Postdoctoral Scholar

 

USC Health Sciences Profile

top


Zhifei Luo

zhifeilu[at]usc.edu

Masters Student

 

The advent of next-generation sequencing started the era of 'Omics' and novel high-throughput techniques and bioinformatic tools emerge every year, greatly accelerating biological research. As a Biochemistry and Molecular Biology Master student at the University of Southern California (USC), I am able to embrace the opportunity to be part of this revolution and work on cutting-edge research projects in both genomics and epigenomics. However, staying in the forefront to harness new techniques and interprete big data is very challenging, especially for students who exclusively work either at the bench or by performing computational analysis. Therefore, I have been shaping myself into a truly versatile researcher who can raise important biological questions, generate experimental data, develop bioinformatic methods to analyze data, test hypotheses, and finally answer the questions.

top


Carol Munoz

Carol.Munoz[at]med.usc.edu

Administrative Assistant

 

top


Suhn Kyong Rhie

rhie[at]usc.edu

Senior Research Associate

 

Dr. Suhn Rhie received her B.S. in Biochemistry, magna cum laude from the University of California, Los Angeles. She earned her PhD degree in Genetic, Molecular and Cellular Biology from the University of Southern California in 2013. She completed her postdoctoral training in the laboratory of Dr. Peter Laird, mainly characterizing heterogeneous tumor tissues of breast and prostate cancer patients as a leader of DNA methylation analysis for The Cancer Genome Atlas. Dr. Rhie joined Dr. Peggy Farnham's laboratory in 2015 as a Senior Research Associate and her current research focus is to investigate epigenomic dysregulation in human diseases. By integrating genomic and epigenomic data sets (e.g. ChIP-seq, RNA-seq, WGS, WGBS, NOMe-seq, HiC-seq) using bioinformatic tools, she studies the role of transcription factors and regulatory elements in human disease.

USC Health Sciences Profile

top


Heather Witt

hwitt[at]usc.edu

Research Specialist

 

top


Shannon Wood

s.wood[at]usc.edu

Research Specialist

 

top


Hang Yang

yanghang[at]usc.edu

Masters Student

 

top


Lijun Yao

lijunyao[at]usc.edu

Masters Student

 

I received my Bachelor’s Degree in China and entered the M.S. Program in Biochemistry and Molecular Biology at University of Southern California (USC) in August 2015. I joined Dr. Peggy Farnham's laboratory in October 2015, which is an excellent environment to develop scientific thinking patterns and learn a wide range of genomic and molecular techniques. The CRISPR/Cas9 technology empowers us to explore the function of risk enhancers associated with prostate cancer in a quite efficient manner. We are using advanced bioinformatics methods to analyze and interpret the effects of enhancer deletion upon the transcriptome and epigenome. The beauty of combining epigenetics and bioinformatics appeals to me very much. I have also just begun a project to identify the genes regulated by Zinc Finger Protein X-linked (ZFX) in multiple human cancer cell lines using ChIP-seq and RNA-seq.

top