Projects - Summer 2009
Please note: We are including opportunities with bioengineering-related faculty at UC San Francisco! This is an exciting opportunity to work with faculty not usually accessible to Berkeley undergrads. However, students working with UCSF faculty must be able to commute to San Francisco 5 days per week during the summer. UCSF campuses are accessible by public transit, and by a network of free UCSF shuttles, but there may be significant commute time and some transit expense. Driving to and parking at UCSF is often not possible.
Seung-Wuk Lee
Research Area: Biomaterials
Campus: UC Berkeley
Department: Bioengineering
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, phone: 486-4628
Lab Description: We are developing novel functional materials using biological basic building blocks (DNA, protein, virus, cell) to address challenging problems in nanoscience and tissue engineering, with a focus on self-assembly of functional nanoscale structures and materials.
Desired student knowledge or qualifications: Biological and chemical skills
Lab experience
Expect to work 40hr/week
Optional project description:
Theresa Head-Gordon
Research Area: Biomaterials
Campus: UC Berkeley
Department: Bioengineering
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, phone: (510) 666-2744
Lab Description: The simultaneous revolutions in molecular biology, scientific computing, and nanotechnology is giving rise to new interdisciplinary research opportunities at the interfaces of engineering, chemistry, biology, physics, mathematics and computational science. The projects worked on by the Head-Gordon lab are united under a general theme of understanding and developing engineering strategies to impact biological function with topics ranging from protein aggregation disease, biomaterials assembly, and glassy dynamics of nanomaterials.
Desired student knowledge or qualifications: tbd
Optional project description:
Valerie Marie Weaver
Research Area: Biomechanics
Campus: UCSF Parnassus
Department: Department of Surgery
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, phone: 415/476-3826
Lab Description: My group studies the role of mechanical force in stem cell fate, tissue development and tumor evolution/pathogenesis. We are looking for one enthusiastic student who is interested in exploring the role of cell and matrix force in cell migration/invasion as it pertains to breast cancer.
Desired student knowledge or qualifications: prefer junior or senior with knowledge of cell culture and some basic cell biology and/or physiology, need to understand basics of mechanics - the intensity of the work is such that summer school enrollment is not advisable, desire a full time summer employment with possibility of extended work into the school year if desired.
Optional project description: We are looking for a student with an interest in studying durotaxis in 2 and 3 dimensions and generating traction force measurements - and someone who is willing to learn some basic cell biology and molecular manipulations - they will be working under the guidance of a postdoctoral fellow with supervision from the mentor - valerie weaver - if good progress is made the student will be encouraged to prepare/submit a presentation for the annual american association for cell biology
Bernard Halloran
Research Area: Biomechanics
Campus: UCSF VA Medical Center
Department: Medicine
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, phone: 415-750-6928
Lab Description: We focus on how bone senses and responds to mechanical loading and how aging affects this process.
Desired student knowledge or qualifications: Must be willing to work with animals and have a car
Optional project description: Mechanical loading of bone
David Rempel
Research Area: Biomechanics
Campus: UCB Richmond Field Station
Department: Bioengineering
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, phone: 510-665-3403
Lab Description: The laboratory does workplace biomechanics studies to improve the design of tools and workstation. Past research has included design of keyboards, computer mice, pipettors, office chairs, construction work.
Desired student knowledge or qualifications: Expected work hours are 40 per week during usual work hours and sometimes on weekend.
Optional project description: Optimal Location for Touch Screens. A research project with human subjects to determine the optimal location for computer touch screens that considers the shoulder muscle load as well as neck muscle load. Project involves interacting with subjects, collecting data in lab (location RFS), analyzing data, assisting with data analysis and manuscript preparation.
Jenni Buckley
Research Area: Biomechanics
Campus: UCSF - SF General
Department: UCSF Orthopaedic Surgery
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, phone: 415-206-8295
Lab Description: We perform biomechanical tests on human cadaveric tissue to test new orthopaedic devices, such as total joint replacements, suture anchors, fracture plates/nails, and spinal fusion systems.
Desired student knowledge or qualifications: Students must be comfortable working with heavy machinery and human cadavers. Prior machine shop experience is a plus, but not a requirement. We are looking for motivated, hands-on individuals who work well in a team environment.
Optional project description: The student will work closely with one of our project managers (spine or trauma team). Initial tasks will include anatomical dissections, specimen preparation for mechanical testing, and learning the basics of materials testing machines. The student will be given more independent tasks as the internship progresses, and depending on performance will be given the opportunity to continue their work in the lab for the upcoming school year.
Clifton M. Schor
Research Area: Computational Biology
Campus: UC Berkeley
Department: Optometry
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, phone: 642-1130
Lab Description: 1) Studies of visual perception during eye movements and motion perception
2) Studies of aberrations of the eye, measured with a wave front sensor, during attempts to focus. Results are related to prosthetic ocular lenses that correct cataract.
Desired student knowledge or qualifications: Matlab skills are very useful. Interest in either visual perception, or in prosthetic ocular devices for focusing.
Optional project description: see above
Sarah Nelson
Research Area: Imaging
Campus: UCSF Mission Bay
Department: Bioengineering
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, phone: 415 476 6383
Lab Description: My research program is focused on the development of techniques for acquisition and quantitative analysis of MR imaging and spectral data. This includes the interpretation of in vivo data obtained using whole body scanners ranging in field strength from 1.5T to 7T. The increase in sensitivity at higher field strength brings a number of challenges in terms of the design and optimization of hardware and software components. The objective of such research is to implement novel strategies for obtaining MR data that are applicable to understanding normal physiology and elucidating the underlying mechanisms of disease progression and response to therapy. This has required an understanding of the biological basis of different diseases and an appreciation of the issues that are important for the management of individual patients. Translating these needs into basic bioengineering problems means that the underlying principles of MR physics must be combined with the design of new algorithms for post-processing and quantitative interpretation of the resulting multi-dimensional and multi-faceted imaging data. The students and fellows in this research group come from a wide variety of different backgrounds with expertise in mathematics, physics, computer analysis, biology and chemistry. Applications that are being considered include the study of patients with brain tumors, prostate cancer and neurological diseases.
Desired student knowledge or qualifications: Experience in programming and algorithm development is preferred. Full time participation is not an absolute requirement but would allow completion of a more meaningful project.
Optional project description: Depends on the skills of the student.
Srikantan Nagarajan
Research Area: Imaging
Campus: UCSF Parnassus
Department: Radiology and Biomedical Imaging
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, phone: 4154764982
Lab Description: My laboratory is involved in development of machine learning algorithms for brain imaging and brain computer interfaces. We are also involved in several basic neuroscience and clinical projects applying functional brain imaging. Specifically, I am interested in determining the neural mechanisms underlying speech feedback procesing, speech motor control and auditory perceptual learning.
Desired student knowledge or qualifications: MATLAB programming skills, Some ideas about basic signal processing and stochastic processes, expected to work full-time during the summer.
Optional project description: I have some MATLAB programming projects involving testing of machine learning algorithms on simulations and real data. I also want some programming efforts to improve a software called NUTMEG that my laboratory distributes as open-source.
Colin Studholme
Research Area: Imaging
Campus: UCSF Parnassus
Department: Radiology and Biomedical Imaging
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, phone: 415 353 9064
Lab Description: The Biomedical Image Computing group at UCSF
are developing and applying mathematical and
computational techniques to quantify human brain
development from MRI acquired in utero from fetuses and
in vivo from premature babies.
We have two 5 year NIH funded research projects in
these areas.
For further information our group website is at:
http://radiology.ucsf.edu/bicg
Desired student knowledge or qualifications: An interest in computing applied and medical imaging.
Experience in programming and image processing would be useful.
Hours per week at UCSF campus are reasonably flexible.
(given the commute from Berkeley)
Optional project description: A previous summer student has worked on methods to map
the cortical thickness of the human fetal brain in order to
detect and understand cortical abnormalities.
This could be extended or a new project area developed.
Xiaoliang Zhang
Research Area: Imaging
Campus: UCSF Mission Bay
Department: Radiology
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, phone: 415-514-4801
Lab Description: The research in our lab focuses on development of fast imaging (mainly parallel imaging) and high field MR technology for humans and experimental animals. For more info, please go to www.radiology.ucsf.edu/zhanglab
Two months research target for each student: one conference paper
Desired student knowledge or qualifications: good writing skills, strong math, knowledge in circuit design (or RF circuit design), passion and motivation in research.
Optional project description:
Martin Banks
Research Area: Imaging
Campus: UC Berkeley
Department: Vision Science, Optometry
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, phone: 510-642-9341
Lab Description: We do basic and applied research on human vision. Research areas include a) determining how 3d percepts are constructed, b) determining how the brain integrates information from different senses, c) development and evaluation of 3d displays and graphics techniques.
Desired student knowledge or qualifications: Skills would include familiarity with Matlab and OpenGL. Good math skills. Hours flexible, but would like 20 hours or more per week.
Optional project description: There are a few possibilities ranging from basic research on human vision to applied research on how different displays and graphics techniques affect visual performance and aesthetics.
Thomas Budinger
Research Area: Nanotechnology and Instrumentation
Campus: UC Berkeley - LBL
Department: BIOE
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, phone: 510-486-5435
Lab Description: Three projects:
1. Using 25 nm magnetite particles, we are researching a new method of treating breast and other cancers. The particles become extremely hot when exposed to an oscillating magnetic field. These particles stimulate cancer cells to release proteins to which the immune system responds and hopefully kills tumors. We plan to inject these particles directly into tumors. Both animal and human studies are planned. We have the particles and the 150kHz oscillating magnetic field instrument.
2. A material science project endeavors to discover new crystals that are efficient detectors of radiation. This involves use of spectrometers, synthesis of proposed chemical compounds, diffraction and luminosity measurements, and crystal growing3
3. My associate Dr. Peng is leading a project to perfect a method whereby the tongue can control computers and other devices by wireless communications. We have invented the device and are starting experiments with human volunteers.
Desired student knowledge or qualifications: One student needs to have skills in either electrical circuits or skills in materials such as polymers. This is for the tongue touch wireless controller.
One student needs to have laboratory skills in animal research or knowledge or immunology or experience in instrument measurements such as digital oscilloscopes.
Optional project description: My laboratory has a very large variety of projects that require additional workers. The projects range from imaging with radioisotopes, magnetic resonance imaging, electronic devices to aid the handicapped, new radiation detector projects, a project to measure metabolism in algae directed toward optimizing biofuel production and projects using radiotracers to help in soil remediation.
Dan Fletcher
Research Area: Nanotechnology and Instrumentation
Campus: UC Berkeley
Department: Bioengineering
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, phone:
Lab Description: "The Fletcher Lab studies the mechanics and dynamics of cell movements and shape changes involved in tissue development and repair. For these studies, we develop new instrumentation and measurement technologies to quantify cell and molecular mechanics. Our tools include optical microscopy, atomic force microscopy (AFM), optical trapping, and microfabrication, as well as biophysical modeling and simulation. Based on our understanding of cell and molecular mechanics, we are developing medical devices that aid in clinical diagnosis and treatment of disease."
Desired student knowledge or qualifications: Full time, experience or interest in microfluidics, optical microscopy, and image processing.
Optional project description:
Mahesh H. Mankani MD
Research Area: Tissue Engineering
Campus: UCSF - SF General
Department: Surgery
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, phone: 415-206-8814
Lab Description: The long-term goal of my lab has been to establish an interdisciplinary program to treat patients’ bone abnormalities with cell-based therapies. We have an active research program to establish the safety and efficacy of using human bone marrow stromal cells (BMSCs) to heal focal bone defects in patients. This program is currently focused on understanding how ceramic scaffolds influence BMSC to express a bone phenotype in vivo. We are also interested in determining the role that BMSCs play in the abnormal bone formation of osteoporosis, focusing on the role of PTHrP expression in BMSCs. This work involves cell culture, gene and protein analysis using standard techniques, and some animal work with mice.
Desired student knowledge or qualifications: I am interested in working with students who are curious, bright, and hard-working. Ideally, the students would have worked in a research lab before, even on an unpaid basis. Student who possess experience with performing cell culture, PCR, immuno-histochemistry, or in situ hybridization will be favored, but these skills are not requirements. I’m interested in having the student work 36-40 hours per week, more-or-less during business hours, on at least 4 days of the week. I would ideally like students who are not distracted by concurrent summer school obligations; that said, I’m willing to consider students who are planning on attending summer school classes only in the evenings and on weekends.
Optional project description: I have some flexibility with projects, so I’ll try to match the project to the goals and interests of the student.
Stefan Habelitz
Research Area: Tissue Engineering
Campus: UCSF Parnassus
Department: Preventive and Restorative Dental Sciences
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, phone: 415-5140818
Lab Description: Design of scafolds for co-culture systems
Desired student knowledge or qualifications: needs strong background in cell culture work
Optional project description: You will explore different designs of thin biological and biodegradable membranes to be used in co-culture systms with dental stem cells.
Chris Anderson
Research Area: Tissue Engineering
Campus: UC Berkeley
Department: Bioengineering
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, phone: 510-666-3611
Lab Description: My lab develops the foundational technologies and applications for Synthetic Biology, a ground-up approach to genetic engineering. More information is available at our group website: https://andersonlab.qb3.berkeley.edu/
Desired student knowledge or qualifications: The candidate should have a desire to pursue synthetic biology research. Expect to work 40 hours per week and although summer school can be discussed, do not assume it is compatible with the work schedule.
Optional project description:
Song Li
Research Area: Tissue Engineering
Campus: UC Berkeley
Department: Bioengineering
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, phone: (510) 666-2799
Lab Description: Our research involves multidisciplinary approaches and collaborations with both academia and industry. Current research topics include:
* Stem cell and tissue engineering
* Micro/nanotechnology
* Mechanobiology/mechanotransduction
Desired student knowledge or qualifications: tbd
Optional project description: tbd
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