Genomics Faculty 2017

Name	Department/College	Research Interests
Kelly Brayton	Professor of Microbial Genomics, Department of Veterinary Microbiology and Pathology	My interest is in all aspects of microbial genomics: we do genome sequencing, comparative genomics, functional genomics, and high throughput RNA sequencing analysis. I primarily work with rickettsial bacteria Anaplasma spp., but have worked with unicellular eukaryotes as well. In addition we are exploring microbial diversity of ticks through microbiome and metagenomics analyses.
Shira Broschat	Electrical Engineering and Computer Science	My interest is in computational work using bioinformatics, machine learning, algorithm development, data analysis, and mathematical modeling techniques to further knowledge in microbiology. My main areas of interest are antimicrobial resistance, protein localization, and tick-borne pathogens such as Anaplasma marginale and Anaplasma phagocytophilum. The vast majority of my work involves genomes or proteomes available either at NCBI or sequenced at WSU.
Weihang Chai	Department of Biomedical Sciences, Elson S. Floyd College of Medicine	Maintaining the stability of genome is critical for preventing the development of cancer, premature aging, and certain neuro-degenerative diseases. Genome stability is constantly challenged by genotoxins present in the environment or introduced by human activities. We are particularly interested in understanding the mechanisms underlying how cells maintain genome stability in the presence of replication stress inducers using a combination of cell biology, molecular biology, and genomics approach.
Omar Cornejo	School of Biological Sciences	I am a population geneticist/genomicist by training. The research of my group generates and analyzes genomic data in order to: understand the evolutionary history of organisms, identify regions of the genomes under selection or identify genetic basis of phenotypes of interest. We work on a variety of systems and have generated/analyzed genomic data for humans, plants, microbes, etc. The ultimate goal of our research is understanding the processes that drive the evolution of genomic architecture of organisms. As a side note: I also teach a graduate class in population genomics (Methods in Population Genomics Biology 534) where students learn (in a workshop setting) how to go from raw sequence genome-wide data to the identification of SNPs and some basic population genetic analyses (population structure and summary statistics).
Stephen Ficklin	Department of Horticulture	I have two focus areas. First I am trying to grow a program in systems genetics. My efforts there seek to merge high-throughput data sets (particularly gene expression data) with genomic and genetic data to identify sets of genes underlying complex traits (of agricultural importance). My current emphasis is on development of novel computational algorithms for network construction and knowledge mining. Second, I seek to develop cyber-infrastructure that supports online community genome databases, including those hosted by other faculty here at WSU and abroad.
Caren Goldberg	Assistant Professor, Quantitative Spatial Ecology School of the Environment	My research program is expanding into conservation and landscape genomics using genotyping-by-sequencing approaches as well as metabarcoding of environmental samples. We address questions applicable to immediate resource management needs, primarily focusing on amphibians and other aquatic macroorganisms. I am interested in learning what infrastructure resources are being developed at WSU and in coordinating with other groups applying similar methods.
Zhihua Jiang	Animal Sciences; Vet Biomed	I would like to lead a campus-wide Genome Science seminar series initiative, provide our next generation transcriptome analysis tools to the community and develop a campus-wide program on transcriptome diversity and phenotype complexity if there are interests to do so.
Mike Kahn	Associate Director, Professor, Institute Of Biological Chemistry	My laboratory works on the genetics and physiology of Sinorhizobium meliloti, bacteria that fix nitrogen in symbiotic association with alfalfa. We were involved in annotation of the S. meliloti genome when it was a hard thing to do, have cloned all of the bacterial ORFs and are now examining expression and proteomes in free-living culture and symbiosis.
Joanna Kelley	School of Biological Sciences	My research area is evolutionary genomics. I utilize and develop technological and analytical methods for genome analysis, including full genome resequencing, de novo genome assembly and transcriptomics. We are interested in understanding how genomes change and diverge in response to extreme environments. To identify and characterize specific genes and pathways that underlie adaptive change, we combine statistical and genomic approaches with knowledge from organismal and ecological studies.
Doreen Main	Professor of Bioinformatics, Department of Horticulture	Development of workflows and online tools for processing and analysis of next generation sequence data; training of graduate students to process and analyze next generation sequence data; development of online community databases for genomics, genetics and breeding research; development of modules for the open-source, generic database Tripal platform; application and use of high performance computing in bioinformatics.
Michelle (Shelley) McGuire	School of Biological Sciences (Nutrition/Lactation Biology) Paul G. Allen School for Global Animal Health	Human milk is unarguably the only food ever truly "designed" to be consumed by humans, and its composition represents the foundation upon what we know about nutrient requirements during infancy. However, human milk composition varies greatly among women and populations and, although maternal diet is important for some nutrients, little is known about the factors driving these differences. The McGuire laboratory is interested in understanding the potential influence of genomic (evolutionary?) variation on human milk composition, and we hypothesize that there is in fact no "one-size-fits-all" construct when it comes to optimal nutrition during infancy.
Jon Oatley	College of Veterinary Medicine	My interest is in developing bioinformatics infrastructure to assist investigators with asking biological questions from sequencing data and assigning functional relevance through gene editing approaches. The past 10-15 years of research in genomics has generated a wealth of information and we are at the point of needing to assign functional relevance to understand disease states and produce foodstuffs with traits that will impact the manner in which the world population is fed for the next century.
Lucia Peixoto	College of Medicine, Spokane	My lab focuses on using genomic and computational biology approaches to study brain function. In particular, we are interested in understanding the underlying molecular basis of Autism Spectrum Disorders and their comorbidity with Intellectual Disability and Sleep Impairments. The lab uses mouse models for functional genomic studies of behavior and patient samples to study genetic contributions to disease.
John Wyrick	School of Molecular Biosciences	My interests are to use genomics methods to map DNA damage and repair across eukaryotic genomes. We are specifically interested in how chromatin and other DNA-binding proteins modulate damage formation and repair efficiency.
Devendra Shah	College of Veterinary Medicine	My interest is genomics of zoonotic bacterial pathogens that are transmitted from animals to people via food and other sources using wide spectrum of ecological niches including persistence in animal hosts, environment and foods. My primary focus is establishing genotype-to-phenotype associations as a prelude to provide mechanistic insights into bacterial proteins or pathways implicated in phenotypic traits such as host-association, pathogenesis, drug resistance, and adaptation to stress with the goal of discovery of new diagnostic markers, therapeutics and prophylactics for the detection, treatment and control of food- and water-borne zoonotic bacterial infections.
Stephen White	USDA-ARS, Animal Disease Research Unit; Dept. Veterinary Microbiology & Pathology	My group’s primary aim is to investigate host genomics of infectious disease susceptibility, particularly in livestock. We also are interested in pathogen and commensal genomics. Finally, we do some development and production trait genomics in livestock.
Mark Wildung	Scientific Assistant Sr., Lab Bioanalysis & Biotech	Generate and analyze genomic scale data for diverse clients of the WSU Genomics Core Lab. Projects range widely, all the way from micro and small RNA profiling to plant scale genomic assembly and include; prokaryotic and eukaryotic RNA-seq, ChIP-seq, de novo genome assembly, long amplicon analysis, mRNA isoform profiling, microbial community analysis, metagenomic reconstruction and assembly, and recently genome-wide mapping of DNA damage and repair. Our particular expertise is in solving previously unresolved genomic complexity and heterochromatin repeat structures.
Zhiwu Zhang	Crop and Soil Sciences	My interest is to innovate statistical methods and computing tools to advance genomic research toward the sustainability of food production and healthcare management. Particularly, my lab (http://zzlab.net) focuses on mapping genes through Genome Wide Association Studies and predictions of phenotypes and genetic merits by using genomic data.