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Neil Abernathy , PhD

Email: neila@u.washington.edu

Phone: (206) 616-2813

Dr. Abernathy's current research interests are public health informatics standards, epidemic models, and molecular epidemiology in the context of global health; scientific and social networks as they pertain to collaborative research; novel 3-D imaging displays; Environmental interventions for infectious disease; high-throughput biology; and evolutionary game theory.

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Erica Anderson-Nissen , PhD

Email: eanderse@fhcrc.org

Phone: +27 (0)21 202 2228

Dr. Andersen-Nissen is interested in studying the influence of early innate immune responses to HIV vaccines on subsequent adaptive immune responses elicited. In addition, she studies systems biology analyses of how immune responses are shaped.

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Steve Andrews , PhD

Email: sandrews@fredhutch.org

Phone: (206) 667-7007

Dr. Andrews's research is in the interdisciplinary field of systems biology. His interests are in the combination of physics, chemistry, and biology methods to investigate organization within biological systems, on size scales that typically range from a few proteins to many cells. Results are yielding insights into how the highly structured macroscopic world of living organisms is built from the stochastic microscopic world of individual molecules. He is also providing an improved conceptual foundation for medical and biotechnology developments, with impacts on topics such as drug discovery, personalized medicine, biofuel generation, and bioremediation.

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Justin Ashworth , PhD

Email: Justin.Ashworth@systemsbiology.org

Phone: (206) 732-2179

Dr. Ashworth is interested in the modeling and prediction of molecular and genetic variations in cellular systems, and the ways in which the functions and interactions of proteins are "designed" in nature to yield cellular physiologies and adaptations. Recently I have been studying gene regulation of new microorganisms and the functional roles of mutations in cellular systems in order to relate our biophysical understanding of molecular function and evolution to systems-level characteristics.

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Nitin Baliga , PhD

Email: nbaliga@systemsbiology.org

Phone: (206) 732-1266

Dr. Baliga leads a group which builds predictive models of complex biological phenomena that can be used to guide cells in the fight against disease, they have established numerous collaborations to apply this methodology to wide-ranging problems from climate change to cancer. In ongoing research, Dr. Baliga is applying advanced methods to the study of brain cancer (glioblastoma multiforme) to gain insights into human disease to improve prevention, diagnosis, prognosis and treatment.

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Karl Bohringer , PhD

Email: karlb@u.washington.edu

Phone: (206) 221-5177

Dr. Bohringer's current research interests include micromanipulation and microassembly, as well as biomedical implants and bioMEMS for single-cell genomics and proteomics. There are two major research themes in his work: Controlling surfaces and interfacial forces at the micro and nano scale, including systems for controlled self-assembly of microcomponents, programmable surfaces whose local properties (for example, hydrophobicity) can be changed on demand, and MEMS actuator arrays and microrobots for moving tiny objects; Joining MEMS and biology by integrating new biomaterials into MEMS processes and devices, biomedical sensor implants, and microfluidic chips for handling and analyzing biological samples. Dr. Bohringer is also interested in discussing ideas for leveraging the unique capabilities of the Washington Nanofabrication Facility for research programs in the biomedical field.

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Hamid Bolouri , PhD

Email: hbolouri@fredhutch.org

Phone: (206) 667-2748

Dr. Bolouri is interested in understanding how gene regulatory interactions control cellular state and identity, both in normal development and in diseases such as cancer. A particular focus of his lab is the development and use of integrative computational systems biology methods to map gene regulatory networks from whole genome data: currently they are working on identification of cis-regulatory sequence variations in childhood Acute Myeloid Leukemia.

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Karol Bomsztyk , MD

Email: karolb@uw.edu

Phone: (206) 616-7949

Dr. Bomstyzk areas of research interest include pathogenesis of bacterial, fungal and parasitic diseases; epigenetics of inflammation and infection; and epigenetics of HIV infection.

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Roger Brent , PhD

Email: rbrent@fredhutch.org

Phone: (206) 667-1482

Dr. Brent studies the quantitative operation of the systems that living cells use to sense, represent, transmit, and act upon information to make decisions that determine their future fates. He specifically studies prototypic cell signaling systems in budding yeast and the pheromone response system; he has extended similar work to systems operating in single cells of tissues in a metazoan, Caenorhabditis elegans.

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Roger Bumgarner , PhD

Email: rogerb@u.washington.edu

Phone: (206) 732-6137

Dr. Bumgarner's research is focused on the creation of tools to connect expression data to biological meaning and the application of these tools to understanding host-virus interactions and the host innate immune response.

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Yong Chi , PhD

Email: ychi@fredhutch.org

Phone: (206) 667-5255

Currently, Dr. Chi is a staff scientist in the laboratory of Dr. Bruce Clurman in the Clinical Research Division of the Fred Hutch and is also affiliated with the laboratory of Dr. Robert Moritz at ISB. He has been developing proteomics-based tools to facilitate biological research. Specifically, he has pursued a proteomics approach to systematically identify the direct substrates of protein kinases. Mapping kinase and substrate relationships is critical for elucidating kinases functions and their signaling pathways. Despite the enormous interests and efforts in the field, it has remained a technical challenge, and the progress has been slow. He developed an in vitro-based method for proteome-wide identification of protein kinase substrates in cell lysates. This method utilized tools in biology, protein chemistry, and mass spectrometry and identified an unprecedented large number of candidate substrates for the human CDK2 kinase. Current in vitro and in vivo approaches suffer the shortcoming of large false-positive identifications due to non-physiological settings or indirect hits. He is now working on a cell-based approach that would minimize false-positive identifications due to the non-physiological settings while maintaining direct kinase-substrate relationships.

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Daniel Chiu , PhD

Email: chiu@u.washington.edu

Phone: (206) 543-1655

Dr. Chiu is a professor of engineering at UW whose research focus is on developing and applying single-molecule methods for probing complex biological systems, specifically synaptic functioning and single-cell biology. The Chiu group is interested in studying both the biophysical properties of single proteins in the context of a cell, as well as using the sensitivities achieved in single-molecule detection for biotechnological applications, such as in high-throughput screening, in the separation and detection of trace biological molecules from single cells (e.g., signaling proteins), and in the development of ultrasensitive sensors.

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Charles Cobbs , MD

Email: charles.cobbs@swedish.org

Phone: (206) 320-2028

The goal of the work in Dr. Cobb's laboratory is to explore the role that human cytomegalovirus (HCMV) plays in human cancer. Dr. Cobbs discovered and first published that HCMV infection is present in nearly 100% of human glioblastomas, as well as a high percentage of other solid tumors (including colon and prostate). The focus of his work now is to elucidate patterns of HCMV gene expression in human tumors, and to determine how the expression of HCMV gene products can promote oncogenesis in tumors that are infected. Dr. Cobb's work has led to clinical trials of antiviral therapies for human glioblastomas, which are leading to increased survival in glioblastoma patients.

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Eric Deutsch , PhD

Email: Eric.Deutsch@systemsbiology.org

Phone: (206) 732-1397

Dr. Deutsch's research focus is mainly software development for the analysis and integration of data for systems biology research. He is the lead designer for the Systems Biology Experiment Analysis Management System (SBEAMS) and he contributes the development of minimum information standards, data formats, and databases for proteomics as chair of the HUPO Proteomics Standards Initiative (PSI). Dr. Deutsch is also the leader of the Trans-Proteomic Pipeline project, which aims to provide a free and open-source suite of tools for the processing and analysis of proteomics tandem mass spectrometry data, and he heads the Peptide Atlas Project, which aims to collect proteomics mass spectrometry data from labs around the world to synthesize a master list of observed peptides and proteins and disseminate the results back to the community.

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Zhijun Duan , PhD

Email: zjduan@uw.edu

Phone: (206) 543-3363

Dr. Duan's research is focused on the relationship between the form and function of human genomes during development and tumorigenesis. One of the striking features of the eukaryotic nucleus is that chromosomes adopt preferred conformations that vary across different tissues and developmental stages.

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Maitreya Dunham , PhD

Email: maitreya@u.washington.edu

Phone: (206) 543-2338

Dr. Dunham's research combines experimental evolution with genomic analysis and comparative functional genomics to study the structure and function of genetic networks in yeast. Her particular interests are in how additions and subtractions in gene and chromosome copy number lead to phenotypes.

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Stan Fields , PhD

Email: fields@u.washington.edu

Phone: (206) 616-4522

Dr. Fields is interested in developing technologies, especially those to analyze protein function. In the last decade, genome sequences have led to the prediction of large complements of proteins, ranging from a few thousand in bacterial species to more than 20,000 for humans and other mammalian species.

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David Fredricks , MD

Email: dfredric@fredhutch.org

Phone: (206) 667-1935

Dr. Fredricks's lab has identified several fastidious bacterial species that are useful markers of BV and are associated with adverse health outcomes. They are using novel cultivation methods to propagate some of these bacteria in the lab, and study how indigenous microbes interact with each other and the human host. He is currently looking for collaboration in molecular biology, microbiology, immunology, and cell biology. He is also looking for collaborators to focus on clinical epidemiology by studying microbial ecology in different human hosts.

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Stephen Friend , MD, PhD

Email: friend@sagebase.org

Phone: (206) 667-2101

Dr. Stephen Friend is a world leader in efforts to make large scale, data-intensive biology more openly accessible to citizens and the entire research community in order to accelerate scientific progress. He is a co-founder of Sage Bionetworks, a nonprofit institute working to create an open-access Internet database for researchers worldwide to share their genomic data. Sage bionetworks is hosted by Fred Hutchinson Cancer research Center and its goal to build predictive models of cancer.

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Gustavo Glusman , PhD

Email: gustavo.glusman@systemsbiology.org

Phone: (206) 732-1273

Dr. Glusman uses computational approaches to investigate genome structure and evolution; multi-gene families; prediction and discovery of genes and transcripts; genes not coding for proteins; visualization of complex data; and image analysis. His algorithms are contributing to the discovery of genes that are not easily identified using standard procedures, to the interpretation of large-scale transcriptomic and genomic data, and to the study of disease genetics.

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