Integrative Physiology, Systems Biology & Synthetic Biology
Contents
- Faculty
- Description
- Research at UW
- Career Opportunities
- Degree Programs
- Sample Programs
- Subspecialty Areas & Suggested Coursework
- Summary
Faculty
Core Faculty
- Jim Bassingthwaighte, MD, PhD
- Martin Kushmerick, MD, PhD
- Michael Regnier, PhD
- Jay Rubinstein , MD, PhD
- Herb Sauro, PhD
- Wendy Thomas, PhD
Other Faculty: see below.
Description
- Produce the next generation of leaders in computational and integrative bioengineering. The postgenomic era is the era of quantitative systems biology and integrative modeling from molecule to human.
- Understand, predict and control biological systems. Basic scientific knowledge provides the basis for therapeutic intervention as in drug delivery and in evaluation of patients in the intensive care unit.
- Build student skills attractive to employers in biosystems, biotransport, biomechanics, biosignals, biochemical and metabolic engineering and medical sciences.
- Use computational methods to solve problems resulting from disease or injury, like improved software for diagnosis from clinical imaging, for prosthesis and tissue development, robotic control in surgery.
- Train students to apply sophisticated quantitative analysis to solving bioengineering’s next challenges. These range from defining biochemical and gene regulatory systems to the delivery of pharmaceutics and the stimulation of tissue regrowth.
- Develop new insight into the nature of biological processes by uncovering the complexity of human pathophysiology with the aid of computational modeling and experimental studies.
Research centers & projects
- National Simulation Resource for Mass Transport and Exchange (NSR) http://nsr.bioeng.washington.edu/
- Physiome Project http://www.physiome.org/
- Vascular Imaging Laboratory http://www.rad.washington.edu/research/our-research/groups/vil
- biological sciences from genes to cells to systems to intact organisms in the environment.
- engineering mathematics, modeling and simulation analysis, and data analysis
- biomechanics, signals, bioinstrumentation and biosensors
Selected current research
- Modeling software engineering and biosystem modeling languages: Develop simulation analysis technologies and interfaces for Web-based operation and international collaborations. Multiscale models capture and integrate knowledge from 1000's of studies into a self consistent schema allowing prediction and testing; the model concepts are distributed worldwide e.g. www.phsyiome.org) to foster collaboration in improving them.
- The physiome project: a large multi-institutional effort to develop databases of anatomic and physiologic information for quantitative integrative analysis of the function of living organisms. This links with programs in Europe, Japan and Australasia. http://www.physiome.org/
- Quantitative image analysis: positron emission tomography (PET) of intraorgan blood lfows and metabolism, magnetic resonance imaging (MRI) analysis of atherosclerotic plaque, ultrasound for tissue characterization, development of software for automated tracking of cellular dynamics, gene transcription, or axon growth. http://faculty.washington.edu/afolch/
- Molecular motion: study of the chemo-mechanics, kinetics and regulation of motor and signaling proteins at the level of protein-protein interactions, and at the cellular and systemic levels. Molecular mechanics of contraction in heart and skeletal muscle; conformational changes in proteins with reactions. http://www.bioeng.washington.edu/regnier/
- Kinetic models of energetics of cells and organs in vivo: signaling, regulation and interaction of molecular and cellular mechanisms in metabolism to sustain and restore energy balance in muscle. Cellular metabolic changes are central to the robustness of biological systems in response to environmental perturbation or partial system failure. Multicomponent systems models assist in defining useful therapy. http://depts.washington.edu/bioe/people/core/kushmerick/kushmerick.html
Pharmaceutical and device industries: An increased demand for efficiency in research and drug development, implantable tissues and devices means industry is seeking graduates with computational and integrative bioengineering training. New companies are emerging focusing on genetics, acquired, and infectious diseases. Systems analysis, feedback and control systems, and operational analysis are important aspects of designing large projects.
Academia: There is a great need for quantitative analysis and integration of knowledge in order to predict and understand phenotype and functioning of the organism as a result of the giant strides made in understanding the genome and proteome.
Degree Programs
Course credit requirements for MS and PhD degrees are those listed for the department (see also below). These will be more or less evenly spread among bioengineering courses, engineering courses offered by other departments, and biological courses offered by other departments. Bioengineering courses will aim at conveying in detail some specific areas of research and expose the students to a variety of state of the art, current enabling technologies (i.e. software and hardware; typically, more than one). The thesis and research topics might be in any area related to the expertise of the faculty, and will most likely be among currently funded research areas. Other programs on the UW campus in related areas are:
- Biomedical and Health Informatics
- Computational Molecular Biology
- Statistical Genetics
- Biomolecular Structure and Design
- Quantitative Ecology and Resource Management
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Subspecialty Areas & Suggested Coursework
Below are sample programs and suggested subspecialty areas. The course listings given below will assist you by suggesting what a particular program might target.
Guidelines:
- In consultation with their faculty advisor, students carefully design their own programs to achieve their long-term goals.
- Making early choices maximizes opportunities and minimizes duration of the program.
- Students are encouraged to select courses from the following subspecialty areas as fulfillment of the required 16 elective credits
- BIOEN 540: Biosystem Identification (4)
- BIOEN 542: Computer Simulation in Biology (3)
- BIOEN 584: Computational and Integrative Biosystems (4)
- STAT 524: Design of Medical Studies (3) (requires STAT 421)
- AMATH: 503: Mathematical Biology I (3)
- CSE 403: Software Engineering (4)
- PCEUT 501: Advanced Pharmacokinetics (5)
- PCEUT 502: Advanced Pharmacokinetics Concepts (4)
- BIOEN 540: Biosystem Identification (4)
- BIOEN 545: Fractals and Chaos in Biology (3)
- BIOEN 584: Computational and Integrative Biosystems (4)
- AMATH 503: Mathematical Biology I (3)
- CHEM E 475: Computer Analysis in Chemical Engineering (3)
- ME 431: Advanced Fluid Mechanics (4) (requires ME 333: Introduction to Fluid Mechanics (4))
- ME 533: Fluid Mechanics I (3)
- ME 534: Fluid Mechanics II (3)
- STAT 390: Probability and Statistics in Engineering and Science (4)
- AMATH 503: Mathematical Biology I (3)
- AMATH 504: Mathematical Biology II (3)
- BIOEN 540: Biosystem Identification (4)
- BIOEN 584: Computational and Integrative Biosystems (4)
- CONJ 531: Signaling Mechanisms in Excitable Cells (1.5)
- CONJ 532: Signal Transduction from the Cell Membrane to the Nucleus (1.5)
- CSE 403: Software Engineering (4)
- STAT 390: Probability and Statistics in Engineering and Science (4)
- BIOEN 540: Biosystem Identification (4)
- BIOEN 513: Current Topics in Cardiac Physiology(1)
- BIOEN 584: Computational & Integrative Biosystems (4)
- AMATH 503: Mathematical Biology I (3)
- ME 478: Finite Element Analysis (4)
- ME 599: Biomechanics Seminar (1)
- STAT 390: Probability and Statistics in Engineering & Science (4)
- ZOOL 440: Biomechanics (4)
- AMATH 584: Applied Linear Algebra and Introductory Numerical Methods (5)
- BIOEN 540: Biosystem Identification (4)
- BIOEN 584: Computational and Integrative Biosystems (4)
- STAT 524: Design of Medical Studies (3)
- BIOST 534: Statistical Computing (3)
- CSE 403: Software Engineering (4)
- CSE 544: Principles of Database Systems (3)
- STAT 390: Probability and Statistics Engineering and Science (4)
Summary
- Offers conceptual approaches to engineering as applied to biology, an important skill for every student.
- Provides a set of tools to bioengineers and develops synergistic associations across research areas.
- Trains graduate students in a growiing field.
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