People

Directors:

	Michael Olivier, Ph.D.   Dr. Olivier, Professor in the Department of Physiology, the Biotechnology and Bioengineering Center and Human and Molecular Genetics Center at the Medical College of Wisconsin, is the Principal Investigator and Director of the Wisconsin Center of Excellence in Genomics Science (CEGS).Dr. Olivier’s research has focused on the integration of genomics and proteomics technologies for the analysis of genome biology and common human diseases. His work at the Stanford Human Genome Center and MCW initially focused on the characterization of sequence variation in the human genome and has expanded to the integrated analysis of molecular and functional changes in cells, tissues, and organs as a result of disease-causing variants. As part of large-scale technology development efforts (Program for Genomic Applications and National Center for Proteomics Research), his lab develops methodologies, tools, and analysis approaches in genomics and proteomics.
	Lloyd Smith, Ph.D. Dr. Smith, W. L. Hubbell Professor of Chemistry at the University of Wisconsin in Madison, is the Co-Director of the Wisconsin Center of Excellence in Genomics Science (CEGS), along with Dr. Michael Olivier. His research focuses on the development of powerful new technologies to drive biological research, with particular focus on surface chemistries, mass spectrometry, and the emerging area of synthetic biology. Dr. Smith oversees all aspects of technology development for the CEGS, and coordinates the efforts of all other investigators at UW Madison.

Key Personnel:

Faculty
	Lisa Cirillo, Ph.D.  Dr. Cirillo is an Associate Professor in the Department of Cell Biology, Neurobiology and Anatomy at the Medical College of Wisconsin. She has considerable experience in the characterization and analysis of transcription factors and chromatin structure. Her research focuses on molecular mechanisms of liver development and function with a special focus on the role played by chromatin structure in the transcriptional regulation of liver genes. Dr. Cirillo is involved in technology development related to chromatin fragmentation and capture both in vitro and in vivo.
	Josh Coon, Ph.D.  Dr. Coon is an Associate Professor of Chemistry and Biomolecular Chemistry at UW-Madison. Dr. Coon’s research group develops next-generation protein measurement technologies and corresponding integrated informatics platforms to assimilate such data with gene- and transcript-level information. These essential technologies are explored and cultivated in the context of a cadre of driving biological problems, from basic to translational to clinical. As part of the CEGS team, Dr. Coon’s laboratory is developing high-throughput mass spectral analysis approaches that will allow the sensitive and efficient characterization of DNA-associated proteins as part of our novel technology.
	Steven Duncan, D. Phil. Dr. Duncan is the Marcus Professor of Human and Molecular Genetics and Vice-Chairman of the Department of Cell Biology, Neurobiology & Anatomy at the Medical College of Wisconsin. He is also director of the MCW Program in Regenerative Medicine and Stem Cell Biology. Dr. Duncan focuses his research interests on molecular mechanisms underlying mammalian development. He is the leading expert in the study of liver gene transcription, and he uncovered functional mechanisms by which HNF4, a liver-specific transcription factor, influences liver function and diabetes. He utilizes mouse knockout models and stem cells. Dr. Duncan’s effort as part of this CEGS is focused on the transition of the initial technology into mammalian cell systems.
	Audrey Gasch, Ph.D. Dr. Gasch is an Associate Professor of Genetics at UW Madison and a Member of the Genome Center of Wisconsin. Her research focus is investigating the role, regulation, and evolution of fungal genomic expression responses to stress, using yeast as a model system. Dr. Gasch is combining functional genomics and computational biology with traditional techniques in genetics and biochemistry to take a systems biology view of the eukaryotic response to environmental stress. She provides expertise on all Wisconsin CEGS research on yeast cells, including development of protocols and samples for microarray studies and comparison of mass-spec data to traditional genomic experiments.
	Andrew S. Greene, Ph.D. Dr. Greene is the Dr. Robert D. and Dr. Patricia E. Kern Professor of Biotechnology and Bioengineering and Professor of Physiology at the Medical College of Wisconsin. He is the Director of the Biotechnology and Bioengineering Center and the Innovation Center. His research spans the areas of molecular and cellular biology, genetics, proteomics, and technology development. Dr. Greene has considerable experience in statistical data analysis and bioinformatics as it relates to gene expression and proteomics. Dr. Greene participates in all efforts related to the technology development and coordinates bioinformatics and data analysis approaches to assess data quality and efficiency and specificity of the novel technology.
	Jozef Lazar, Ph.D.  Dr. Lazar is an Associate Professor in the Dermatology Department and member of the Human and Molecular Genetics Center at the Medical College of Wisconsin. He has considerable experience in physiology, cell and molecular biology, and molecular genetics, including characterization of gene expression and regulation of gene expression at the molecular level. Dr. Lazar is involved in the development of chromatin fragmentation and capture methodologies and transition from simple eukaryotic systems to more complex genomes.
	Shama Mirza, Ph.D.  Dr. Mirza is an Assistant Professor in the Department of Biochemistry at the Medical College of Wisconsin. She is an expert in mass spectrometry, and has developed numerous novel approaches to the quantitative analysis of biological samples using mass spectrometry. Dr. Mirza is assisting in the development of mass spectrometric analysis approaches of captured DNA protein complexes.
	Ronald Stewart, Ph.D. Dr. Stewart is the Bioinformatics Team Leader at the Wisconsin Institutes for Discovery at UW Madison, and Associate Director of Bioinformatics. Dr. Stewart’s areas of expertise include statistics, mathematics, computational biology, information technology, database development, and algorithm development. Dr. Stuart is involved in all aspects of data analysis and data integration, including statistical data quality assessment and integration of proteomic and gene expression data.
	Scott Terhune, Ph.D.   Dr. Terhune is Assistant Professor in the Department of Microbiology and Molecular Genetics at the Medical College of Wisconsin. His laboratory is part of the Biotechnology and Bioengineering Center, where he studies protein-protein interactions and protein complexes using mass spectrometry. Dr. Terhune’s research focuses on identifying viral-host protein interactions and the consequences of these interactions during herpesvirus infection. He is involved in the development of efficient DNA-protein complex capture strategies and in the adaptation of this technology to other biological systems.
Scientific Staff
	Brian Frey, Ph.D. Senior Scientist. Dr. Frey works on understanding the chemical reactions occurring during cross-linking and how those chemical changes affect the down-stream processes of purification, digestion, capture, and mass spectrometry.
	Hector Guillen Ahlers, Ph.D. Research Scientist Dr. Guillen-Ahlers has been working under direction of Dr. Olivier since 2010. His research focuses on the development and optimization of the chromatin isolation and capture technologies.
	Brian Halligan, Ph.D.  Dr. Halligan has been instrumental in the development of data analysis tools and protocols for mass spectral data at the National Center for Proteomics Research. He works closely with Dr. Olivier, Dr. Smith, Dr. Greene and other investigators on data analysis related to all aspects of MS analysis.
	Claudia Olivier, Ph.D.   Dr. Olivier has extensive teaching experience at the undergraduate level during her time as an Assistant Professor in the Department of Biological Sciences at the University of Wisconsin-Whitewater. Since joining the Biotechnology and Bioengineering Center at the Medical College of Wisconsin, she has been responsible for the organization and coordination of postdoctoral training efforts as well as career development activities within the Center.
	Mark Scalf, Ph.D. Associate Scientist. Dr. Scalf is developing and optimizing the tandem mass spectrometry proteomics-based methods.  He provides bench-level support to graduate students carrying-out the experimental work in developing the mass-spectrometry related components. He also coordinates data collection and analysis with the informatics group.
	Michael Shortreed, Ph.D. Senior Scientist. Dr. Shortreed provides bench-level support for the graduate students in developing surface capture assays. He will coordinate experiments involving informatics and array design with capture array development.
	Michael Westphall, Ph.D. Scientist. Dr. Westphall is an instrumentation innovator in the Coon lab. He specializes in improvements to mass spectrometric technology to increase sensitivity and throughput in proteomics analyses of samples produced by GENECAPP.
Postdoctoral Fellows:
	Akua Yalley, Ph.D., Cirillo Lab. Dr. Yalley purifies recombinant proteins needed for the project. She also performs chromatin immunoprecipitation assays to validate proteins bound to DNA.
	Michael Zickus, Ph.D., Olivier Lab. Dr. Zickus focuses his research on interfacing hybridization capture of DNA-bound protein complexes with mass spectral analysis for the identification of those proteins.
Graduate Students:
	Derek Baily, Coon Lab. His research focuses on sensitive and comprehensive mass-spectrometric identification of proteins captured through the GENECAPP process.
	Julia Kennedy-Darling, Smith Lab. Her research focuses on discovering new modulators of RNA polymerase by applying GENECAPP in E. coli.
	Rachel Knoener, Smith Lab. Her research focuses on addressing technical challenges in the GENECAPP process, including elimination of non-specific protein binding and improved capture efficiency.
	Gloria Kreitinger, Smith Lab. Her research focuses on achieving high sensitivity in mass spectrometric detection of proteins through development of SRM assays.
	Daniel Ladror, Smith Lab. His research focuses on developing model systems for optimizing various aspects of the GENECAPP process.
	Anna Larson , Smith Lab. Her research focuses on sensitive and comprehensive mass-spectrometric identification of proteins captured through the GENECAPP process.
	Fengjie Lui, Cirillo Lab. Her research focuses on chromatin and nucleosome biology.
	Yuan Yuan, Smith Lab. Her research focuses on improving the efficiency of each stage in the GENECAPP process.
Administration:
	Theresa Lins, M.S. Ms. Lins is the program coordinator for the Wisconsin Center of Excellence in Genomics Science. She coordinates administrative functions for the Center.