Yerkes Nonhuman Primate Genomics Core

 

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The genome sequences of human3, chimpanzee4, Indian rhesus macaque5, orangutan6, Chinese rhesus macaque2 and cynomolgus macaque2 are published, and sequencing of several more primate species is underway. The mission of the Yerkes Nonhuman Primate Genomics Core (GenCore) is to provide researchers at the Yerkes National Primate Research Center (YNPRC), Emory Vaccine Center (EVC) and greater Emory community with access to cutting edge high throughput genomic technologies including Next Generation sequencing (NGS) and microarray. The GenCore laboratory features an Illumina HiSeq1000 System, an Affymetrix GeneChip platform and an Agilent Bioanalyzer. The GenCore offers a diverse set of assays, including NGS applications: RNAseq, targeted resequencing, ChIP-seq and miRNA sequencing. The GenCore staff consists of two full time Research Specialists and one full time bioinformaticists and provides researchers with ‘start-to-finish’ service, assisting in assay design, sample preparation, quality assessment, data analysis and bioinformatics support. Ongoing projects in the GenCore laboratory include gene expression profiling of several pre-clinical HIV vaccine candidates, transcriptomic analysis of multiple primate malaria species, targeted sequencing of multiple genomic regions for their effects on behavior, and comparative miRNA analysis.

How To Use GenCore

For more information please contact:

Co-directors:

 

Dr. Zach Johnson zpjohns@emory.edu 404-727-1832

 

Dr. Steven Bosinger steven.bosinger@emory.edu 404-727-7216


Personnelfrom left: Steve Bosinger, Joana Yu, Zach Johnson, Nirav Patel, Gregory Tharp

Dr. Steven Bosinger
Co-Director

Dr. Bosinger received his doctorate in Microbiology & Immunology from the University of Western Ontario in London, Canada. Dr. Bosinger was a recipient of a Canadian Institutes of Health Research Fellowship in HIV&AIDS, and conducted his postdoctoral training at the University of Pennsylvania with Dr. Guido Silvestri. In 2008, Dr. Bosinger received a Young Investigator Award from the Global HIV Vaccine Enterprise for his work characterizing the immune response to SIV in natural host monkeys at a genome-wide level. Dr. Bosinger has been conducting studies utilizing transcriptomics in SIV monkey model species since 2000, and has published genetic studies using several different model NHP species, including cynomolgus and rhesus macaques, sooty mangabeys and African green monkeys. Currently, Dr. Bosinger’s research is focused on understanding the mechanisms by which nonpathogenic species avoid disease during HIV/SIV infection and identifying correlates of immunity in candidate HIV vaccines. 

Dr. Zach Johnson
Co-Director

Dr. Johnson received his doctorate from the University of Texas and spent eight years training at the Southwest National Primate Research Center before joining the Yerkes Research Center.

Dr. Johnson studies how genetic variation influences complex disease phenotypes, especially those that manifest themselves in the brain. Researchers in the Johnson lab study inherit social complexity present in multiple nonhuman primate species to better model phenotypes related to anxiety and other mental illnesses in humans. In the near future, the lab team will begin to use touch screen kiosks within large social groups of rhesus macaques to examine the effects of genetic variation on cognitive function and learning.

Other studies in the Johnson lab include examining the effects of genetic factors on diet choice and total caloric intake in the rhesus macaque, as well as the interactions between diets, genome wide gene expression, gut microbial flora composition and obesity phenotypes.

Additionally, Dr. Johnson is studying the major histocompatability complex (MHC) region of the sooty mangabey genome for possible clues as to why these natural hosts of simian immunodeficiency virus (SIV) thrive despite high viral loads.

Dr. Johnson collaborates with a number of researchers at Yerkes, including Drs. James Else, Kai McCormack and Mark Wilson.

Nirav Patel
Lab Manager

Mr. Patel has over 5 years of research experience in laboratories running diverse -omics platforms. Nirav graduated from the University of Queensland in Australia with a Masters in Biotechnology. His graduate research involved studying differential protein expression in A549 cells infected with wild type and mutated RSV at the State-of-the art proteomics facility at the Queensland Institute of Medical Research, Brisbane. Nirav has extensive experience with wide array of molecular biology techniques. As a GenCore manager, Nirav is primarily responsible for day-to-day oversight of the core operations, including developing and optimizing new protocols, training new staff, overseeing quality in assay data and monitoring project progress and ensuring scheduled deadlines are met. 

Gregory Tharp
Bioinformaticist

Mr. Tharp has been working in bioinformatics and computational support for genetic research for the past 4 years. Starting in Dr James Thomas’ lab in the Department of Human Genetics at Emory in 2008, Greg worked with and developed new analytical tools for the analysis of sequencing, assembly, alignment, expression and statistics of genetic assays. Greg implemented and maintained the computational infrastructure of the Thomas lab including the implementation of a local mirror of the UCSC genomics browser. He is currently the senior data analyst for the Yerkes Non-Human Primate Genomics Core Laboratory (NHP GCL) where he performs analysis on both gene expression microarray assays and sequencing results from our Illumina HiSeq 1000 system. He is also responsible for the design and maintenance of the NHP GCL computational infrastructure which consists of a multi-core IlluminaCompute server, the instrument controllers for both the Illlumina HiSeq 1000 and the Affymetrix GCS3000 system as well as numerous Windows and OS-X based workstations for other instrument and technician support. He has had a 25 year career as an engineering systems analyst working on developing and evaluating engineering systems in academic and government research at the University of California, Berkeley and the California Institute of Technology’s Jet Propulsion Laboratory as well as working independently and for a small contracting firm as a research engineering consultant.

Joana Yu
Research Specialist

Ms Yu has worked for over 4 years in viral-related research and has specialized technical experience in fluorescence microscopy, flow cytometry, and microarray gene expression as an undergraduate research assistant at the Georgia Institute of Technology investigating the delivery of single-molecule sensitive fluorescent probes essential for targeting viruses such as, respiratory syncytial virus and influenza.  During this time, she gathered probe delivery data for an array of varying cell types utilizing a novel method of intracellular delivery with a bacterial toxin, streptolyocin-O.

In 2011, Joana joined the Yerkes National Primate Research Center at Emory as a research specialist.  Joana worked on numerous studies involved in the progression of SIV, simian immunodeficiency virus, infection in non-human primates as a model for HIV infection and the progression of AIDS. In the Yerkes Genomics Core, Joana has performed RNA purification on a wide variety of samples derived from NHPs, including whole blood/PAXgene tubes, PBMCs, rectal mucosa, vaginal biopsies and subsets of sorted cells (tetramer+ CD8 cells, sorted CD8 T cells, CD4 T cells. Joana has performed Affymetrix microarray analysis on hundreds of samples from NHPs from varying tissue sources. Joana has extensive experience performing microarrays for very technically challenging NHP/SIV vaccine studies.

Lab Space with Nirav at work