78 Search Results

q=Computational%20Biology

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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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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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Wyeth Bair , PhD

Email: wyeth0@uw.edu

Phone: (206) 221-8241

Dr. Bair's group integrates computational modeling and electrophysiology to study neural coding and cortical circuitry in the visual system. A primary focus of his work is the visual motion pathway. He is currently developing several integrated online resources to carry out his goals. These include the Neural Signal Archive, which contains neuronal data for public access; the Working Models site, which provides access to network models of the visual system; and the data system, which is a set of utilities for storing and analyzing spike trains.

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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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Trevor Bedford , PhD

Email: tbedford@fredhutch.org

Phone: (206) 667-6372

Dr. Bedford studies the dynamics of virus populations. This includes the questions of how strains spread through the world, strains evolve in response to immune pressure, and ultimately what makes a strain successful.

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Alice Berger , PhD

Email: ahberger@fredhutch.org

Phone: (206) 667-6281

The goal of the Berger laboratory is to enable precision medicine by systematically uncovering the molecular alterations in cancer, determining the function of these variant alleles, and understanding how these alleles modulate response to targeted or immune-based therapies. Although many of the genes involved in cancer have now been identified, a major challenge is discovering which specific alleles of these genes are involved and how these alleles modulate therapeutic response. We combine functional genomics, computational biology, biochemistry, and genetics to understand the mechanism of somatic cancer variants. Our goal is to identify drug targets and biomarkers and to translate this knowledge into clinical benefit for patients.

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Mark Binder , PhD

Email: mdbinder@uw.edu

Phone: (206) 543-2509

Dr. Binder's lab is presently investigating the dendritic mechanisms affecting the transfer of synaptic current to the soma of hypoglossal motoneurons recorded in rat brainstem slices. His team studies the voltage-dependance of the synaptic currents, what types of voltage-gated conductances on the dendrites affect the transfer of current to the soma and how concurrently-activated synaptic currents interact. They also use fluorescent imaging to determine the spatial distribution of the dendritic sodium, calcium, and mixed-cation channels. Binder's experimental projects are complemented by computer simulations using compartmental models of motoneurons with different types and distributions of dendritic conductances to help interpret the experimental data.

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Jesse Bloom , PhD

Email: jbloom@fredhutch.org

Phone: (206) 667-3622

Dr. Bloom studies the molecular evolution of proteins and viruses. Rapid evolution is a defining feature of many of the most medically problematic viral diseases, including influenza. Although this rapid evolution is usually bad from the perspective of public health, it offers a unique vantage from which to study a range of important questions in biology. His group takes an evolutionary perspective as we use a combination of experimental and computational techniques to study questions in virology, immunology, and protein biochemistry.

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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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Phil Bradley , PhD

Email: pbradley@fredhutch.org

Phone: (206) 667-7041

Dr. Bradley's research is focused on developing predictive models of molecular recognition using high-resolution structural modeling. His group is currently working to predict the specificity of protein-DNA and protein-peptide interactions. They develop and apply new algorithms for molecular modeling within the framework of the Rosetta software package, a set of tools for the prediction and design of protein structures and interactions.

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Robert Bradley , PhD

Email: rbradley@fredhutch.org

Phone: (206) 667-5662

Dr. Bradley uses genomics, sequence analysis, and molecular genetics to study the mechanistic origins and phenotypic consequences of alternative splicing and other RNA processing. He wants to identify diseases where RNA processing plays important, and previously unrecognized, roles. His laboratory studies pre-neoplastic diseases and cancers such as brain, prostrate and breast cancer.

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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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Brian Browning , PhD

Email: browning@uw.edu

Phone: (206) 685-8482

Dr. Browning's research is focused on the development of statistical and computational methods for analysis of large-scale genetic data from microarray genotyping and next-generation sequencing. These genetic data sets present computational and analytical challenges due to their size, and due to the complex patterns of inter-marker correlation in the data. Carefully engineered algorithms and software are necessary to extract the full information from these rich data sets.

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Elizabeth Buffalo , PhD

Email: ebuffalo@uw.edu

Phone: (206) 543-1432

Dr. Buffalo's general research focus is to contribute to a better understanding of the neural mechanisms involved in learning and memory. She uses neurophysiological techniques to record information, simultaneously, from multiple electrodes in the hippocampus and surrounding cortex in awake, behaving monkeys. She investigates how changes in neuronal activity correlate with the monkey's ability to learn and remember, and she's particularly interested in the activity of neuronal networks that underlie learning and memory processes.

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Alexei Chvetsov , PhD, DABR, MCCPM

Email: chvetsov@uw.edu

Phone: (206) 598-5971

Dr. Chvetsov's focus of clinical practice is Image-guided radiotherapy for lung and prostate tumors. His research interests include: optimization problems in radiotherapy planning; image-guided therapy using cone-beam CT; radiation biophysics and bioeffect planning; proton therapy planning. His most current work is on tumor-response parameters derived from imaging derived tumor-volume variation curves.

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Valerie Daggett , PhD

Email: daggett@u.washington.edu

Phone: (206) 685-7420

Dr. Daggett's research goal is to perform realistic molecular modeling studies relating to protein stability, function, and folding. Protein folding is one of the fundamental unsolved problems in molecular biology. A protein must assume a stable and precisely ordered conformation to perform its biological function properly. Although much is known of the structural details of the native folded conformation of proteins, very little is known about the actual folding process. An understanding of protein folding has important implications for all biological processes, including protein degradation, protein translocation, aging, and human diseases, including cancer and amyloid diseases.

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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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Paul Edlefsen , PhD

Email: pedlefse@scharp.org

Phone: (206) 667-4086

Dr. Edlefsen's research interests include statistical and computational methods for bioinformatics applications. He is also interested in statistical modeling techniques for genome science analysis.

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Evan Eichler , PhD

Email: eee@gs.washington.edu

Phone: (206) 543-9526

Dr. Eichler's long term research goal is to understand the evolution, pathology and mechanism(s) of recent gene duplication and DNA transposition within the human genome. His work involves the systematic discovery of these regions, the development of methods to assess their variation, the detection of signatures of rapid gene evolution and ultimately the correlation of this genetic variation with phenotypic differences within and between species.

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