Bio-X fellowships

The Bio-X Fellowships are made possible by various gifts in order to promote interdisciplinary research for promising scientists working on projects that bridge the gap between biology and other fields, such as , engineering, computer science, and chemistry.

Researchers are encouraged to work collaboratively with professors in different departments or schools, drawing on expertise campus-wide.

NEW ADVANCES IN SCIENCE AND ENGINEERING Bio-X Fellowships

Bio-X Graduate Student Fellowships 2004 & 2005 2-5 Bio-X Pfizer Graduate Student Fellowship 2005 5 Bio-X Graduate Student Fellowships 2006 6-8 Bio-X Endowed Graduate Fellowships 2006 8 Bio-X Graduate Student Fellowships 2007, 2008, 2009 9-14 Bio-X SIGF in Human Health Awards 2008 & 2009 14-15 Medtronic Fellow, Skippy Frank Fellow, Amgen Fellow 16 Bio-X Bioengineering Graduate Fellowships 17-22 Bio-X Postdoctoral Fellowships 23-24

Bio-X Graduate Student Fellowships 2004

Relly Brandman autonomously controlled. His focus was to Chemical & Systems Biology improve the controllability of such instru- ments by creating novel algorithms that rely upon solid mechanics models as well as multi- ple sensory inputs.

Professor Vijay Pande (Chemistry) Graduated 2009 Samuel Kim Research Scientist at Simprota Corporation Chemistry Inhibitors and activators of proteins can be used to uncover how cells work and to develop new drugs and therapies. The focus of Relly’s project was to develop and use computational tools to design modulators specific for particular proteins that will then be Professor Richard Zare (Chemistry) experimentally tested. Graduated 2009 Postdoctoral Scholar at POSTECH (South Korea) David Camarillo Microfluidic platforms for single-cell analysis Mechanical Engineering have been developed. The protein chip allows for manipulating individual cyanobacteria cells and quantitatively detecting the proteins in light-harvesting antenna complexes. The DNA chip enables the amplification of genomic DNA from an environmental cyanobacterium Professor Kenneth Salisbury (Computer Science) and downstream genetic analysis. These plat- Graduated 2008 forms, with proper adaptations and improve- Senior Controls Engineer at Hansen Medical ments, will be used to explore the origin and David’s research was in the area of biomedical dynamics of the cell-to-cell heterogeneity device innovation, specializing in robotically enhanced surgery. He developed technologies found in a microbial population or community. for flexible robotic manipulators. These instru- ments can be tele-operated by a physician or

Page 2 Bio-X Graduate Student Fellowships 2004

Andy Loening Leslie Meltzer Bioengineering, Neurosciences, Medicine Neurobiology

Profs. Theo Palmer (Neurosurgery) and Karl Professor Sanjiv Sam Gambhir (Radiology, Deisseroth (Bioengineering, Psychiatry) Bioengineering) Graduated 2008 Graduated 2006 Medical Information Manager at Actelion Radiologist at Stanford Hospital Pharmaceuticals US Andy’s research focused on devel- Leslie’s research explored the oping a new class of probes for in wiring of new stem cell-derived vivo receptor imaging consisting of neurons into intact circuits using bioluminescent proteins fused to techniques bridging bioengineering, receptor ligands. Preliminary work neurosurgery, and computer had focused on optimizing the science. She investigated the bioluminescent proteins for this following critical questions: 1) How purpose through rational and ran- are new stem cell-derived neurons dom mutagenesis approaches. wired into the adult mammalian Work was then ongoing to develop brain? 2) How does wiring of new the ligand/bioluminescent fusion neurons according to these rules proteins and to validate them both impact memory storage in compu- in vitro and in vivo. tational neural networks? and 3) How does wiring of new neu- Sergio Moreno rons in this way impact memory Physics storage in behaving animals?

Sara Zhao Mechanical Engineering Profs. Michael Levitt () and Sebastian Doniach (Applied Physics) Sergio works in Prof. Levitt's group developing a novel computational Professor Beth Pruitt (Mechanical framework to study large-scale Engineering) protein movements as they ex- Graduated 2005 plore their energy landscapes. The Mechanotransduction, the process method will be applied to proteins by which cells convert mechanical under experimental study in Prof. stimuli into cellular signals, is im- Frydman's lab. portant in many areas of physiolo- gy, medicine, and medical device They expect that this interdiscipli- design. The goal of Beth’s project nary collaboration will be very was to study the MEC-4 channel beneficial to both experimentalists complex that mediates sensory and theoreticians as it will help mechanotransduction of touch understand particular protein sys- receptor neurons. A biomolecular tems and will provide insight into model would be developed to the general mechanisms by which describe the mechanism of MEC-4 proteins fold and perform their channel complex as mechanorecep- biological functions. tor and its critical role in the whole-cell behavior.

Page 3 Bio-X Graduate Student Fellowships 2005

Afsheen Afshar David Myung Electrical Engineering, Chemical Engineering and Medicine Ophthalmology

Professor Krishna Shenoy (Electrical Engineering) Profs. Curtis Frank (Chemical Engineering) and Graduated 2008 Christopher Ta (Ophthalmology) Medical Student at Graduated 2008 Afsheen’s research with the Shenoy group Corneal blindness affects millions worldwide involved the design and implementation of and requires a corneal transplant. An engi- neural prosthetics that patients can use. He neered artificial cornea has the potential to focused his efforts on the paradigm of point-to- replace the need for human donor tissue point movements, such as those done by typing while providing better surgical outcomes. on a keyboard. Specifically, he developed inno- David’s project was the design, fabrication, vative computational models and algorithms and characterization of an artificial cornea that help elucidate how the brain plans and based on a novel class of hydrogel polymer executes movement. He was concurrently alloys. These “biomimetic” materials have working on improving the electronic infrastruc- demonstrated great potential for emulating ture that could support an extremely fast (i.e., the transparency, biomechanics, and realtime) and accurate 'virtual keyboard' that regenerative capacity of a human cornea. would allow a patient to type by planning move- His aims were to characterize the unique ments to desired keys at desired times. Finally, properties of these polymers, engineer them he collaborated with neurosurgeon Dr. Jaimie to promote integration with host corneal Henderson to apply their work to a Parkinson's tissue, and finally to study the cellular Disease patient population. Afsheen hoped to response to them in vitro. bring all these avenues together to help create a real, useful prosthetic.

Georgios Asimenos Computer Science Rachel Kalmar Neurosciences

Professor (Computer Science) Graduated 2009 Profs. Krishna Shenoy (Electrical Engineering) and William Newsome (Neurobiology) Georgios was developing a next-generation Rachel is interested in understanding how whole-genome alignment pipeline in order to ensembles of neurons collectively encode and harvest the enormous wealth of genomic data transmit information, and how this neural that is becoming available; mainly the 12 Dro- activity underlies complex behavior and sophila genomes and the impending 20 mamma- cognition. Using a combination of behavioral, lian genomes. He used these alignments to physiological and computational approaches, predict putative functional elements based on she will explore how the brain computes constraint of evolution. The challenge was not values, how this computation drives decision only to identify such elements, but to under- making, and the applications of this value stand how they act in the context of specific assessment in the context of neural prosthetic biological systems. He also investigated new development. high-throughput experimental techniques to study predicted elements during development of the Drosophila embryo.

Page 4 Bio-X Graduate Student Fellowships 2005

Jules VanDersarl Yufeng Yang Materials Science Neurosciences & Engineering

Profs. Nicholas Melosh (Materials Science Professor Bingwei Lu (Pathology) & Engineering) and Michael Longaker Graduated 2009 (Surgery) Assistant Professor at Fuzhou University Jules is involved in exploring new The goal of Yufeng’s project was to methods to use nanoscale elec- examine the dopaminergic neuron tronics to direct stem cell differen- associated neural circuitry in fruit tiation in an effort to better under- fly (Drosophila) models of stand and control the spatial and Parkinson's disease, using a temporal events that occur during combination of genetics, electro- differentiation. They are developing physiology, behavioral analysis and an active electronic chip that computational modeling stores signaling chemicals within approaches. nano-reservoirs and releases them when activated with an electronic signal.

This chip will allow them to extend the spatial and temporal control of soluble signals down to an individu- al cell for unprecedented control over the local cellular environment.

Bio-X Pfizer Graduate Student Fellowship

Vincent Chu creation of computational tools to Applied Physics model these effects, and experi- mental verification of new theories. Research in this area may lead to new drug designs, molecular sensor designs, and increased knowledge Professor Sebastian Doniach (Applied of gene regulation. Physics) Ion atmospheres play an important role in the function and formation of tertiary structure in charged nucleic acids. However, current understanding of electrostatics around nucleic acids is poorly understood. Vincent’s research is focused on advancing the theory of nucleic acid electrostatics, the

Page 5 Bio-X Graduate Student Fellowships 2006

Edith Arnold Ian Chen Mechanical Engineering Bioengineering, Medicine

Profs. Scott Delp (Bioengineering, Mechanical Engineering) and Garry Gold (Radiology) Professor Sanjiv Sam Gambhir (Bioengineering, Musculoskeletal modeling and simulation tools Radiology) are powerful resources for both basic research Graduated 2008 and clinical applications. However, current Stem cell therapy has emerged over the past models incorporate a major simplification by decade as a promising treatment for conges- representing muscles as single lines following tive heart failure. Current clinical studies on the effective line of action. In Edith’s research, cell therapy lack an objective method to non- she will develop a modeling pipeline that incor- invasively assess the survival and migration of porates diffusion tensor magnetic resonance stem cells following implantation. The goal of imaging to create three-dimensional finite ele- Ian’s project is to develop a novel multimodal- ment models of muscle representing the geom- ity reporter gene for labeling stem cells and etry and architecture of muscle fibers. These monitoring their behaviors in living subjects models will be used to explore the functional using a combination of positron emission implications of altered muscle architecture and tomography (PET), optical bioluminescence to simulate surgical treatments designed to imaging, and magnetic resonance imaging treat movement abnormalities. (MRI). Efforts are underway to develop and validate such a reporter gene in terms of its ability to lead to highly specific and sensitive Jennifer Blundo imaging signals which are reflective of stem Mechanical Engineering cell viability. The development and characteri- zation of such reporter genes should provide a valuable tool for investigators in the future to accurately assess the efficacy of stem cell therapy in humans. Professor Christopher Jacobs (Mechanical Engineering) The powerful potential of stem cell therapy motivates a better understanding of the basic Sanjay Dastoor mechanisms regulating developmental biology. Mechanical Engineering The role of mechanical and electrical forces in the adult physiology and pathology has been well documented, and Jennifer is interested in what clues these phenomena may hold for generating robust, terminally differentiated stem Profs. Mark Cutkosky (Mechanical Engineering) and Scott cells. The pluripotent capacity of human em- Delp (Bioengineering, Mechanical Engineering) bryonic stem cells makes them an attractive Sanjay is researching the application of artifi- source for cell-based myocardial therapy. Spe- cial muscles to robotics and prosthetics cifically, the delivery of cardiac myocytes, which through a novel manufacturing method. Elec- constitute 70-80% of the adult myocardium, tric motors lack many of the dynamic charac- may restore tissue viability and function to teristics of biological muscle, limiting their use ischemic tissue damaged by a heart attack. Her in biomimetic devices. Electroactive polymer research is motivated by the limitations of actuators are a promising alternative, with current methods to derive cardiac myocytes muscle-like performance, light weight, low from stem cells. The aim is to increase the cost, and silent operation. He is developing differentiation yield of cardiac myocytes methods for fabricating these actuators using through electromechanical conditioning and shape deposition manufacturing, which allows ultimately the in vivo performance of myocardial customized geometries, heterogeneous cell-transplants. materials, and embedded components.

Page 6 Bio-X Graduate Student Fellowships 2006

Katy Keenan tion by an order-of-magnitude by Mechanical using off-the-shelf graphics pro- Engineering, cessing units (GPUs) as cost- Radiology effective high performance co- processor. This technology will enable the use of advanced recon- Profs. Scott Delp (Bioengineering, Mechanical Engineering), Garry Gold struction methods that improve (Radiology), and Gary Beaupre the accuracy of the scans, resulting (Mechanical Engineering) in more reliable diagnosis. The goal of Katy’s work is to bet- ter diagnose cartilage health, ena- bling early detection of diseases such as osteoarthritis. Currently, Aaron Wang because cartilage disease cannot be Bioengineering, diagnosed early, there is no metric Medicine of cartilage health to non-invasively evaluate restorative therapies. She is combining magnetic resonance imaging techniques with mechanical Profs. Charles Taylor (Bioengineering, testing of ex vivo cartilage to devel- Mechanical Engineering) and David Liang op a correlation between imaging (Cardiovascular Medicine) Graduated 2009 parameters and mechanical proper- Development of a novel portable ties of cartilage. Several of the ultrasound cuff with an automated novel MRI techniques she is using, bleed detection algorithm for e.g. sodium, T1rho and bound pool would be useful for medics in the fraction maps, are being developed field. The goal of Aaron’s study at Stanford. She will translate the was to evaluate a detection strate- correlation between imaging pa- gy for internal bleeding that em- rameters and mechanical proper- ploys a well-established theoretical ties to in vivo imaging of human biofluid model, the power patients. law. This law characterizes normal

blood flow rates through an arteri-

al tree by its bifurcation geome-

try. By detecting flows that deviate Guillem Pratx from the model, they hypothesized Electrical that vascular abnormalities could Engineering be localized. Their bleed detection

metric demonstrated good sensitiv-

ity and specificity in computational

bleed simulations, in vivo rabbit Professor Craig Levin (Radiology) Positron emission tomography bleed models, and human case (PET) is a medical imaging modality studies in dialysis patients. that has the powerful capability to non-invasively interrogate cellular and molecular processes occurring deep within the tissue of living subjects. However, advanced image reconstruction methods require more computation than is available in a typical clinical setting. Hence, the goal of Guillem’s work has been to accelerate the reconstruc-

Page 7 Bio-X Graduate Student Fellowships 2006

Peggy Yao to bind to. However, only a small number of Biomedical Informatics conformations can be obtained experimental- ly, while existing simulation techniques are often too expensive to broadly sample folded conformation space. Peggy’s research will focus on designing new methods to efficiently Professor Jean-Claude Latombe (Computer Science) sample protein conformations. She will use In the study of protein-ligand binding, the con- the linkage model together with rigidity analy- formational selection theory suggests that a sis to develop a new, efficient protein confor- protein exists as an ensemble of rapidly inter- mation sampling method taking steric clash converting folded conformations and that a into account. ligand selects the most proper conformations

Bio-X Endowed Graduate Fellowships 2006

Namiko Abe technology platform which combines yeast Biomedical Fellow surface display and cell-free protein synthesis Neurosciences to engineer proteins for enhanced biological efficacy. It will be demonstrated by evolving epidermal growth factor, which plays a role in the healing process and has great therapeutic potential for wound repair and regenerative Professor Tobias Meyer (Chemical & Systems Biology) medicine. Graduated 2007

Although phosphoinositides(PIs) represent a minor fraction of cellular lipids, they are integral components of cell membranes. Recent Daniel Kimmel evidence suggests that PIs have not only a Affymetrix Fellow structural role but may also act as important Neurosciences, Medicine second messengers during membrane trafficking events. The Meyer laboratory in collaboration with Tom Wandless's group developed a chem- ically-inducible translocation strategy to rapidly Professor William Newsome (Neurobiology) synthesize or degrade specific PIs at the plasma When we make decisions, we must consider membrane. She planned to make improve- both the costs and benefits associated with ments upon this chemical strategy while devel- each choice. In the world of economics, this oping new bioengineered probes to manipulate problem is often solved by reducing costs and levels of different PIs in specific membrane benefits to a common currency, namely mon- compartments. She then used these tools to ey. The Newsome laboratory believes the investigate the role of specific PI species in brain solves the problem similarly by repre- various steps of receptor-mediated endocytosis senting benefit, cost and net value as discrete as well as the synaptic vesicle cycle. neural signals. To test this, they make eco- nomic offers to monkeys while they record from or manipulate the activity of neurons Bertrand Lui underlying the animals' decision to accept or Lubert Stryer Fellow reject their offers. Their results will shed light Bioengineering on the neural basis of value.

Profs. Jennifer Cochran (Bioengineering) and James Swartz (Chemical Engineering) The goal of Bertrand’s research is to develop a

Page 8 Bio-X Graduate Student Fellowships 2007

Kelsey Clark weakness, bony deformities, or Neurosciences joint tightness—contribute to a patient’s crouch gait and should be corrected with treatment.

Professor Tirin Moore (Neurobiology) The visual world contains far more information than we can process Frances Lau or respond to at any one time. Electrical How does the brain select specific Engineering stimuli to enter awareness and guide behavior? In addition, goal- driven behavior-- from baking a cake to changing lanes on the free- Profs. Craig Levin (Radiology) and Mark way-- often involves 'holding in Horowitz (Electrical Engineering, Computer mind' certain facts about the state Science) of the world. How is task-relevant Frances is developing an ultra-high information selected for entry into resolution Positron Emission To- memory and maintained in the mography (PET) system dedicated absence of continued sensory to breast cancer imaging. PET is a input? To what extent are the non-invasive, in-vivo, molecular same neural circuits involved in imaging technology that has shown processing sensory stimuli used to promise for early identification of maintain and manipulate breast cancer due to its ability to remembered stimuli? visualize biochemical changes in malignant tissue well before struc- tural changes occur. She applies hardware design and signal integrity Jennifer Hicks concepts to develop data acquisi- Mechanical tion electronics that read out and Engineering process the small signals detected. She is also using ideas from high speed data communication circuits to propose and design a novel integrated circuit for a future PET Professor Scott Delp (Bioengineering, system. Mechanical Engineering) Many children with cerebral palsy walk with a crouched posture that prevents them from moving safely and efficiently. Since the body is a complex dynamic system, it is difficult for clinicians to determine why a patient walks in a crouch gait and prescribe an appropriate treat- ment plan using the current set of tests and assessment tech- niques. The goal of Jennifer’s re- search is to develop objective tools based on biomechanical simulation and statistical modeling to identify which factors—including muscle

Page 9 Bio-X Graduate Student Fellowships 2007

Cory McLean Computer Science Larry Wang Materials Science & Engineering

Professor Gill Bejerano (Developmental Biology) Profs. Sarah Heilshorn (Materials Science & Engineering) Evolution of cis-regulatory elements may drive and Andrew Spakowitz (Chemical Engineering) the majority of anatomical evolution, yet the The goal of Larry’s research project is to mechanisms of cis-regulation of gene expres- understand the structural and behavioral sion are poorly understood. Cory has uncov- characteristics of quaternary ered a number of interesting non-coding ge- using the coat-vesicle protein clathrin. This nomic regions within vertebrates using the study employs two major approaches in computational tools of high-performance com- parallel: development of a theoretical model puting, statistics, and natural language pro- using Brownian dynamics simulation to predict cessing. He is also investigating roles for ma- quaternary structure and in vitro self-assembly chine learning in the discovery of a genomic experiments to observe and control the signature of cis-regulatory elements. Transgenic quaternary structure. Clathrin proteins per- experiments performed in collaboration with form their biological functions by self- the Kingsley laboratory will help to elucidate assembling into cages, and recent reports have the roles of these elements in vertebrate evolu- begun to elucidate the structure of the individ- tion. ual clathrin molecule and have provided a more detailed static picture of the in vivo assembly.

Rebecca Taylor Kitchener Wilson Mechanical Engineering Bioengineering

Profs. Ellen Kuhl (Mechanical Engineering) and Beth Pruitt Profs. Joe Wu (Radiology) and Paul Yock (Bioengineering, (Mechanical Engineering) Mechanical Engineering) After a heart attack, the heart has limited ability Kitchener’s research focuses on characterizing to repair itself. Because cardiomyocytes (CMs) human embryonic stem cell differentiation and are difficult to culture in vitro, there are few transplantation, with a specific focus on options for creating tissue patches to repair the cardiovascular tissue regeneration. He is using heart. Dynamic cell culture, which provides genomic and proteomic methodologies such synchronized electric field pacing and cyclic as DNA microarrays and highly sensitive strain, holds promise for enabling the creation protein arrays to better understand the of stem cell-derived CM grafts with regenera- regulatory networks that govern stem cell tive capacity for healing an infracted heart. Our behavior, as well as in vivo molecular imaging computational models and newly developed techniques to assess their engraftment in tools utilizing stretchable microelectrode arrays mouse models of disease. Of particular inter- and micropatterned silicone substrates will est is the cardiac stem cell “niche,” or micro- enable engineers and biologists to create environment within heart tissue, that enhanced cell culture platforms for both basic promotes their regenerative capacity. and translational research into CM growth.

Page 10 Bio-X Graduate Student Fellowships 2008

Mario Diaz de Tyler Hillman la Rosa Genetics, Chemical MSTP Engineering

Professor Andrew Spakowitz (Chemical Professor Matt Scott (Developmental Engineering) Biology) The Spakowitz lab examines how Tyler’s focus is on understanding proteins find their target sites on how cells communicate with one DNA, a process central to proper another to influence fate decisions cellular function and survival. Of during embryo development and particular interest is the role that tumor formation. In particular, he DNA conformation, including studies the gene regulatory interac- supercoiling and higher-order tions controlled by the mammalian chromatin organization, plays in Hedgehog signaling pathway. He this search. They have developed a completed a high-throughput RNA novel theoretical framework to interference screen in search of address this phenomenon on line- novel genes that regulate Hedge- ar, supercoiled, and nucleosomal hog signaling in mammals which DNA, and their predictions will be resulted in the identification of subsequently verified experimental- several genes whose loss results in ly. The resulting elucidation of the robust and reproducible inhibition mechanisms behind target site of Hedgehog signaling. He is now localization will provide fundamen- following up these hits to better tal knowledge of gene regulation understand how they might regu- processes and the of late this important developmental protein-DNA interactions. and oncogenic signaling pathway.

Lisa Gunaydin Ian Marshall Neurosciences Civil & Environmental Engineering

Professor Alfred Professor Karl Deisseroth (Bioengineering, Spormann (Civil & Psychiatry) Environmental Engineering, Chemical Elucidating the neurobiological Engineering) basis of social behavior is critical to Complex microbial communities understanding normal human be- play an important role in a range of havior and its dysregulation in environments, including the biodeg- psychiatric diseases like autism. Lisa radation of toxic compounds in is studying the neural circuits in- groundwater, interactions in the volved in social behavior using light human gut affecting health, and the -activated microbial opsins that contribution of agriculture to glob- their lab has engineered for fast al atmospheric methane concentra- optical control of neural activi- tions. Ian is applying novel molecu- ty. These optogenetic tools pro- lar methods, specifically, tiling vide high spatiotemporal resolution DNA microarray, to query the in probing the activity of specific presence and expression of func- cell types within large neuronal tional genes from a wide range of populations, which will help eluci- microbes in the environment to date the basic circuit dynamics better understand interspecies underlying this complex behavior. microbial interactions.

Page 11 Bio-X Graduate Student Fellowships 2008

Andreas Rauschecker changes at targeted sites within our genome Neurosciences, MSTP and a chemical technology to expand and control hematopoietic stem cells outside of living animals. These projects address major challenges for researchers and clinicians in- volved with genetic manipulation and stem cell Professor Brian Wandell (Psychology) biology. Both projects take advantage of our Andreas’s work uses several modern imaging expertise in molecular biology and synthetic modalities, including fMRI, DTI, and electro- organic chemistry and interface with imaging, physiological recordings, to understand the immunology, and regenerative medicine. neural basis of reading. More than a fifth of the US population reads below their age level and dyslexia is the most common learning disabil- Brian Wilt ity. In many cases, the visual system of the Applied Physics brain is unable to decode visual patterns into words. Their lab studies the neural mecha- nisms behind this decoding process in the nor- mal human brain. To complement this work, they also look at patients who are either sud- Profs. Mark Schnitzer (Biology, denly unable to read due to a tumor, stroke, or Applied Physics) and Karl Deisseroth (Bioengineering, epilepsy, or who have never been able to read Psychiatry) (developmental dyslexia). In order to crack the neural code, we require new tools for probing and perturbing neural circuitry in vivo. Brian is interested in incor- Mark Sellmyer porating these new techniques into his lab’s Chemical & Systems Biology, expertise with in vivo fluorescence microen- Medicine doscopy. In particular, he is studying innova- tive strategies for light delivery in optical stimulation experiments with channelrhodop- sin and halorhodopsin. He also has interests Profs. Tom Wandless (Chemical & Systems Biology) and in novel, fully-automated data analysis tech- Michael Longaker (Surgery) niques for calcium imaging data. His studies Mark is interested in developing chemical tools concentrate on visual and motor systems, for improving bioscience research and medical with a particular emphasis on cerebellar ataxia therapies. Specifically, he is working on a tech- mouse models. These projects draw on his nology to improve our ability to make genetic background in physics, optics, applied math,

Bio-X Graduate Student Fellowships 2009

Aakash Basu that introduces negative supercoils into DNA. Applied Physics He is developing and using single molecule assays to follow the activity of one motor molecule as a function of solution conditions and mechanical perturbations such as tension and torque. Through this study, he wishes to Professor Zev Bryant (Bioengineering) gain a broad understanding of how chemical Aakash’s goal is to understand how molecular reactions are coupled to mechanical move- motors couple ATP hydrolysis to the produc- ments, and the general principles that govern tion of mechanical work. In particular, he is the functioning of molecular motors. attempting to understand the mechanochemis- try of DNA gyrase – a type II Topoisomerase

Page 12 Bio-X Graduate Student Fellowships 2009

Elsa Birch Christine Chemical McLeavey Engineering Neurosciences

Professor Markus Covert (Bioengineering) Profs. Scott Delp (Bioengineering, Mechani- Although viral genomes are rela- cal Engineering) and Karl Deisseroth tively short and well studied there (Bioengineering, Psychiatry) Optogenetic technology allows one are no reliable treatments for viral to control the activity of individual infection. This is because the com- plexity of infection is largely gov- neurons with pulses of light by genetically inserting photo- erned by the host machinery that activated proteins into the desired the virus commandeers order to replicate. Understanding the role neuron. A cation channel, Chan- nelrhodopsin-2 (ChR2), stimulates of host genes in infection is there- the neuron when exposed to blue fore crucial to the development of new treatment strategies. Elsa’s light, while NpHR, a chloride lab presents a differential equation pump, inactivates the neuron when exposed to yellow light. This population model of E. coli infec- tion by bacteriophage lambda. technology has been used to study When fit to experimental infection brain circuitry, but it will be the first effort to control peripheral timecourse data for E. coli knock- neurons to study the peripheral outs, the parameters of this model give insight into the particular role nervous system.

of host genes in infection. Alia Schoen

Graham Dow Materials Science & Biology Engineering

Professor Sarah Heilshorn (Materials Science & Engineering) Professor Dominique Bergmann (Biology) The Heilshorn lab intends to devel- Plants are dependent on their op clathrin as a protein-based ability to sense and respond to template for the creation of hierar- their surrounding environment. In chically ordered inorganic such processes, stomata play a nanostructures. Combining theo- crucial role by controlling the flux retical and experimental methods of gases between plants atmos- to gain insight into kinetic and phere. Stomatal development and thermodynamic processes that function have been independently regulate the self-assembly of clath- described at a molecular and physi- rin will enable the prediction and ological level, but there remains a formation of ordered 2D and 3D void in explaining fundamental nanostructured materials. They connections between those para- anticipate these to be widely appli- digms, especially the environmental cable to other self-assembly sys- inputs that direct both. The goal of tems. They will develop rational the Bergmann lab is to elucidate design of bi-functional peptides to these multi-scale relationships bridge the biologic-inorganic inter- controlling stomata to improve our face, to enable efficient formation understanding of plant systems and screening of nanostructured biology and plant-environment materials for a range of applica- interactions. tions. Page 13 Bio-X Graduate Student Fellowships 2009

Jong Min Sung Noureddine Tayebi Applied Physics Electrical Engineering

Professor James Spudich (Biochemistry) Profs. Nicholas Melosh (Materials Science & Engineering) The objective of Jong’s research is to obtain a and Ricardo Dolmetsch (Neurobiology) precise correlation between the mechanical, Autism spectrum disorders (ASDs) cause structural and biochemical aspects of actomyo- language and social impairments in children. sin interactions associated with human beta- Gene mutations can cause ASDs by altering cardiac myosin cardiomyopathies at a single signaling pathways of Ca2+ ions in neurons molecule level. Our hypothesis is that the implicated with ASDs. To detect such altera- structural changes caused by the mutations will tions, the “patch-clamp” technique, which cause malfunctions of beta-cardiac myosin, in allows for high-resolution current measure- terms of 1) force generation roles (step size, ments in ion channels, is used. However, low force), 2) enzymatic roles (actin-activated throughput and the destructive nature of the ATPase), and 3) coordination between them. technique prevent observing communications To clarify with molecular precision which as- between neurons and long experiment longev- pects of chemo-mechanical transduction are ity. To mitigate these problems, Noureddine altered by selected HCM familial mutations, we is helping to develop novel chip-based patch- will directly measure individual actomyosin clamp arrays where “nanoposts” are nonde- interactions using a variety of single molecule structively fused into neuron membranes. This tools. allows the study of long-term genetic- mutation effects and communication abnor- malities between neurons.

Bio-X SIGFs in Human Health 2008

Viviana Melinda Cromie Gradinaru Mechanical Neurosciences Engineering

Profs. Karl Deisseroth Profs. Scott Delp (Bioengineering, Mechanical Engineering) (Bioengineering, Psychiatry) and Jaimie Henderson and Mark Schnitzer (Biology, Applied Physics) (Neurosurgery) Melinda’s goal is to understand the fundamental Deep brain stimulation (DBS) is a powerful behavior of muscle by imaging sarcomeres, the therapeutic option for intractable movement smallest units of muscle tissue that contract to and affective disorders (Parkinson's disease, generate force. Sarcomeres have never been tremor, depression). However, due to the imaged in humans because they are smaller than nonspecificity of electrical stimulation, DBS the resolution of current clinical imaging modal- has variable efficacy and can lead to serious ities. Using a novel microendoscopy system, side effects, such as speech impairment or their laboratory imaged sarcomeres in humans paresis. Viviana’s research uses precise bioen- for the first time. Melinda’s current work is to gineering tools to address a critical question in use this newly developed system to quantify the neurosurgery field: how does DBS exerts muscle contractile behavior in healthy humans its therapeutic effects? By using a cell-type and in individuals with spinal cord injury to specific optical deep brain stimulator devel- improve surgical treatments that restore mus- oped in the Deisseroth lab, her research cle function. investigates the role of specific cell types in PD pathology. These findings could be used to improve the parameters for electrode place- ment and stimulation in patients. Page 14 Bio-X SIGFs in Human Health 2009

Liang Liang Peter Olcott Applied Physics Bioengineering

Profs. Liqun Luo (Biology) and Mark Profs. Craig Levin (Radiology) and Robert Schnitzer (Biology, Applied Physics) Feigelson (Materials Science & Engineering) Liang is interested in the organiza- PET is a non-invasive, in-vivo, func- tion and information processing tional, molecular imaging technolo- principles of neural circuits. She gy that is an important tool for uses the fruit fly olfactory system clinical disease management and as a model to study the functional pre-clinical small animal research. connections in the central nervous Peter wishes to improve the time system and to characterize where resolution by more than an order and how the olfactory information of magnitude over the current is integrated and transformed. She generation of time-of-flight (ToF) is incorporating advanced fly genet- PET systems by investigating readily ics, light-activated microbial opsins available non-linear photonic mate- and genetically-encoded calcium rials for use as a ToF PET detector, indicators to manipulate and rec- instead of scintillation crystals. ord neuronal activity with high These materials are not based on spatiotemporal resolution. The fluorescence and have the potential novel noninvasive optogenetic to enable sub-millimeter localiza- approach will help us to better tion. This would revolutionize PET understand the neural coding in the imaging and greatly improve its olfactory circuitry and to gain performance for characterizing insight into the organization princi- early disease. ples of neural systems. Shawn Ouyang Li Ma Chemical & Statistics Systems Biology

Professor James Chen (Chemical & Systems Professor Wing Wong (Statistics) Biology) Epistasis has long been speculated Zebrafish have the unique ability to to play important roles in the regenerate several of its tissues, epidemiology of common diseases. including those of the heart, retina, Current approaches to testing spinal cord, and fins. Understanding interactions have achieved limited the molecular mechanisms that success and are most ineffective in underlie this process should pro- the presence of genetic heteroge- vide insights into how tissue regen- neity--when people have (clinically) eration is achieved and reveal the same disease for different strategies for their reactivation in genetic reasons. Li’s research fo- humans. Shawn’s goal is to deci- cuses on developing statistical and pher the molecular and cellular computational methods for testing events associated with larval tail interactions that are robust to regeneration. He has identified genetic heterogeneity. They will several genes that are upregulated use large scale computation to or downregulated in posterior cells seek genetic patterns that account after the tail is amputated and is for a small proportion of the pa- working to determine the roles of tients. these genes in the regenerative process. Page 15 Bio-X Medtronic Fellow 2008 Gaurav To overcome these limitations, a currently Krishnamurthy important research goal is to create bioengi- Mechanical neered autologous tissue valves. A key com- Engineering ponent of this thrust is to understand more completely the structure and function of native valves. Toward this end, using Profs. D. Craig Miller (Cardiothoracic Surgery) and radiopaque marker technology and inverse Ellen Kuhl (Mechanical Engineering) finite element analysis that Gaurav has Mitral valve disease affects ~3 million adults each quantified, for the first time, the material year in the . Surgical valve repair is parameters of the anterior mitral leaflet in preferred, but valve replacement can be re- the beating heart. quired. Replacement involves implantation of a mechanical or tissue valve, which is associated with anticoagulation/thromboembolic complica- tions and less than ideal durability, respectively.

Bio-X Skippy Frank Fellow 2009 Adam de la Zerda various proteins specific to a particular dis- Skippy Frank Fellow ease, indicating the molecular characteristics Electrical Engineering of the disease (e.g., whether breast cancer is responding to a chemotherapy or not). He designs a photo-acoustic imaging instrument and a number of molecular contrast agents Professor Sanjiv Sam Gambhir that produce a photoacoustic signal upon (Bioengineering, Radiology) binding to breast cancer cells. His final goal is In Adam’s research, he develops a new technique to integrate the imaging instrument with the for non-invasive imaging of living subjects called cancer-detecting contrast agents by testing 'Photo-acoustic Molecular Imaging'. Using this them on mice carrying a human breast technique, physicians will be able to monitor

Amgen Fellow 2009

Sanaz Saatchi ing technology, coupled with computational Bioengineering analysis and molecular biology techniques, Sanaz’s work with the laboratories of Charles Taylor and Paul Yock will character- ize the three-dimensional nanometric tissue structure changes and biological events oc- Profs. Charles Taylor (Bioengineering) and curring within a blood vessel wall during Paul Yock (Bioengineering) aneurysm development in an unprecedented Abdominal aortic aneurysms (AAA) are a life- manner. These studies will improve their threatening degenerative disease. A better un- understanding of aneurysm development and derstanding of the pathological mechanisms that may assist in the identification of potential lead to aneurysm formation is essential for the therapeutic targets. development of effective preventative therapies. Through the use of a novel high resolution imag-

Page 16 Bio-X Bioengineering Graduate Fellowships 2004

Amanda Adam Gross- Malone man Professor Christopher Profs. Terence Jacobs Sanger (Pediatric (Mechanical Neurosurgery), Scott Engineering) Delp (Bioengineering, Mechanical Graduated 2007 Engineering) and Krishna Shenoy (Electrical It is well documented that bone Engineering) responds to changes in load with Adam studies children with severe corresponding changes in size and movement disorders in order to density. The Jacob lab believes that generate hypotheses as to the Oscillatory Fluid Flow (OFF), gen- biological cause for their erated by pressure gradients in the disorders. He will collect data lacunar cannicular network, is a from each child—ranging from potent physiological signal that is simple MRI and CT scans to more recognized by bone cells as an complex kinesthetic analyses. The anabolic stimulus. While it is data will help shed light on the known that bone cells respond to specific locations in the brain that fluid flow with various intracellular may be malfunctioning. Using this chemical responses, the actual information, Adam will design mechanism that transduces the further experiments to test these physical extracellular signal to a hypotheses and provide insight for chemical intracellular one is not yet better treatments and potential known. cures for these diseases. In partic- ular, Adam is interested in deter- Amanda hoped to determine the mining how and why deep brain actual molecules that take part in stimulation is an effective treat- this conversion from a mechanical ment for some dystonic children signal to a chemical one. Her hy- and what parameters of the stimu- pothesis was that this mecha- lation can be adapted to optimize notransduction event could be the benefits of DBS in these chil- linked to integrins and the phos- dren. phorylation of Focal Adhesion Kinase (FAK). FAK is a good candi- date for a mechanotrasduction molecule in bone cells because it has both structural and enzymatic function and has proved relevant in mechanotransduction in other cell types.

Page 17 Bio-X Bioengineering Graduate Fellowships 2005

Virginia Chu Stephen Lee Professor Terence Sanger (Pediatric Professor Jennifer Cochran Neurosurgery) (Bioengineering)

Graduated 2009 The Cochran lab uses directed evolution and Virginia worked in Dr. Sanger's group to develop yeast display to create novel protein mutants a theoretical model for human motor learning. In for therapeutics in wound healing and cancer particular, she was interested in studying motor applications. Stephen’s current project inves- learning in children and young adults. Various tigates mutants of human epidermal growth aspects of motor learning were explored to help factor (EGF), a protein involved in both of shed light on the important elements of motor these pathways. In vitro assays are being used learning. Virginia also studied children with se- to study the migratory and proliferative vere movement disorders in order to learn more effects of EGF on murine and human fibro- about the missing pieces that lead to various blasts. His goal is to demonstrate an EGF motor learning deficits. Using this information, mutant with improved migration and prolif- she intended to study “correction” methods to eration over wildtype to ultimately test in compensate for the missing pieces in light of the mice in vivo. model. With a greater understanding of the motor learning deficits, Virginia hoped to develop medical devices and training paradigms to help children with movement disorders learn Prasheel Lillaney and further develop their motor skills. Professor Rebecca Fahrig (Radiology)

Mindy Chang Professor Tirin Moore (Neurobiology) The goal of Prasheel’s project is to build a hybrid X-Ray/MRI system that will allow Interventional Radiologists more versatility in how they approach various procedures that require MR or X-Ray guidance, while still Mindy is interested in using signal processing and maintaining the image quality and perfor- computational modeling approaches to under- mance offered by a conventional MRI or X- stand neural circuits. Her current project ray system. Prasheel is currently modeling involves population analysis of neurons in the the electron beam optics in X-ray tubes and visual cortex that encode color and orientation determining how the electron beam is affect- information. Future research will focus on mech- ed by the presence of the strong MR fringe anisms of visual attention in modulating neural field. He is also developing different X-ray representations of sensory input. tube motor designs that would allow for better tube performance in the hybrid sys- tem.

Page 18 Bio-X Bioengineering Graduate Fellowships 2006

Angela Wu Murtaza Mogri Professor Stephen Professor Karl Quake Deisseroth (Bioengineering) (Bioengineering, Psychiatry)

Chromatin immunoprecipitation Deep brain stimulation (DBS) is a (ChIP) is a powerful assay used to therapeutic option for intractable probe DNA–protein interactions. neurological and psychiatric disor- Traditional methods of implement- ders, including Parkinson's disease. ing this assay are cumbersome and Because of the heterogeneity of require a large number of cells, brain tissue, it has been challenging making it difficult to study rare to elucidate the underlying mecha- cancer and stem cells. The Quake nisms of DBS. Using , lab has designed a microfluidic which employs light activated con- device (named AutoChIP) to per- ductance regulators expressed in form sensitive ChIP analysis on low specific cell types, The Deisseroth cell numbers in a rapid, automated laboratory tested a multitude of fashion while preserving the speci- suggested mechanisms, systemati- ficity of the assay. The recently cally driving or inhibiting an array demonstrated AutoChIP results of circuit elements in freely moving from 2,000 cells were comparable parkinsonian rodents. Since the to conventional ChIP methods therapeutic effects could be ac- using 50,000–500,000 cells. She is counted for by stimulation of corti- using this device to study oncogene cal axons, they are developing addiction in cancer cells and to do noninvasive methods for stimulat- profiling of cancer stem cells. She ing these axons as a potential believes that their device provides treatment for Parkinson’s disease. a solution to the need for a high sensitivity, rapid, and automated ChIP assay, and in doing so will change the way we study cancer, and enable studies of cancer stem cells that were not possible previously.

Bio-X Bioengineering Graduate Fellowships 2007

Sheng Ding formation, and potentially control (1 year award) the structure and function of the Professor Annelise new tissue. Her research project is Barron to create protein polymer hydro- (Bioengineering) gels that are enzymatically cross-

linked as tissue engineering scaf-

folds. These new hydrogels are Tissue engineering is an exciting biocompatible and biodegradable. and revolutionary strategy to over- Using genetic engineering, they can come the problem of donor short- modify these hydrogels for particu- age in tissue transplantation. The lar requirements for specific tissue Barron lab investigates appropriate engineering applications by careful- scaffolds mimicking the natural ly designing the amino acid se- extracellular matrices, which deliv- quence, chain length, and block er the cells to the desired site, spacing of the protein polymers. provide a space for new tissue Page 19 Bio-X Bioengineering Graduate Fellowships 2007 Jacob Hughey Min-Sun Son Professor Markus Covert Professor Marc Levenston (Bioengineering) (Mechanical Engineering)

Min-Sun’s work in the Soft Tissue Biome- The goal of Jacob’s work is to provide a quanti- chanics Laboratory under Dr. Marc Le- tative understanding of the intricate circuitry venston involves studying gene expressions that controls how cells interact with their envi- of various proteins such as collagen, aggre- ronment. Currently he is focusing on the TNF- can, and aggrecanase in the immature and induced response of the NF-κB network, which mature bovine menisci. These proteins are is crucially involved in cell proliferation and the known to have important roles in meniscus innate immune response and is misregulated in degeneration. The meniscus does not have many cancers. He is using live cell imaging and much regenerative capabilities and has been mathematical modeling to explain how the correlated with cartilage degeneration, or dynamics of the network depend on TNF osteoarthritis. Therefore, comparing the dose. This research will lead to greater under- protein expression levels in mature and standing of how cells sense and respond to the immature tissue will provide helpful insight in intensity of environmental signals fully understanding the mechanism of degen-

eration. She is also looking at different re- Jayodita Sanghvi gions in the meniscus, which are subject to Professor Markus Covert (Bioengineering) different kinds of mechanical forces in the knee.

Nan Xiao Professor Charles Taylor (Bioengineering, Mechanical Jayodita has been developing a computational Engineering) model of the smallest known bacterium, which describes the dynamics of every molecule in the cell and includes the function of every gene. The model involves the integrated understand- Computational simulations of blood flow ing metabolism, replication, transcription, trans- dynamics (hemodynamics) enable detailed, lation, regulation, and more. She has also been quantitative investigation of the role of he- developing means to experimentally validate the modynamic factors in vascular disease. In model. Manipulation of the virtual cell will ena- order to construct realistic, patient-specific ble a better understanding of cell physiology models of blood flow, data from non-invasive and help uncover unknown cell mechanisms. measurements must be used to improve the Future expansion of the model may help predict reliability of the simulation. Currently, the cell responses to drugs and environmental goal of the Taylor laboratory is to couple stresses, or provide insight on how to engineer vessel wall-motion data from sequences of cells to perform desired functions. CT images with a 3-D computational model incorporating the fluid-structure interaction between blood and blood vessel in order to minimize the differences between observa- tion and simulation. Accomplishing this goal will bring them one step closer to producing realistic, personalized blood flow models that may have important applications in the treat- ment of vascular disease.

Page 20 Bio-X Bioengineering Graduate Fellowships 2008

Mihalis cell, just as electronic memory Kariolis systems are crucial for the modern Professor Jennifer computer. Cochran (Bioengineering)

Grace Tang Using yeast surface display and Professor directed evolution, the Cochran lab engineers novel proteins for use in (Bioengineering, applications ranging from cancer Genetics) therapy and imaging to wound healing. Mihalis’s research is fo- cused on engineering the Agouti- related protein(AgRP) for binding In recent years, technological ad- to the integrin, αIIbβ3. This integ- vancements have enabled the crea- rin is highly expressed on the plate- tion of structural genomics initia- let membrane and when activated tives worldwide. The collective it engenders aggregation and subse- aim is to increase the structural quent clot formation. Though knowledge of proteins and to essential to wound healing, aber- achieve a thorough coverage of rant platelet aggregation can lead protein structure space. Target to myocardial infarctions, embo- selection is therefore focused on lisms and strokes. Engineering proteins with low sequence homol- AgRP to bind specifically to the ogy to existing structures; howev- αIIbβ3 integrin would limit platelet er, this has come at the cost of an activation and subsequently lessen increasing number of structures the risk of ischemic events. with unknown function. Traditional methods for functional inference are unreliable at low Ton sequence homology. Grace aims Subsoontorn to use machine learning algorithms Professor in combination with molecular Drew Endy dynamics to detect local three- (Bioengineering) dimensional patterns for functional inference.

Ton is developing a design frame- work for genetically encoded memory. The memory system is built from in vivo machineries and functions inside a living cell. Partic- ularly, he is exploring two alterna- tive approaches: multistabilities of gene expression and site-specific DNA modifications. The challenges are to have fast mechanisms for encoding and decoding information and to have stable storages under stochastic environment inside a cell. This technology will be critical for engineering increasingly more complicated behaviors of a living

Page 21 Bio-X Bioengineering Graduate Fellowships 2009

Incoming Bioengineering Fellows spend one year in rotation through labs of their choice before committing to a research project.

Kathryn Montgomery Yen-Hsiang Wang

Kathryn plans to study the mechanics of bioen- Molecular Imaging could allow in vivo investi- gineering, especially the investigation of cellular gation of biomedical reactions, which is responses to mechanical stimuli. These types of useful in both drug development and clinical studies have many applications in the realm of studies. Molecular Magnetic Resonance Imag- biomaterials and regenerative medicine. Tissue ing (mMRI) shows a high potential in this engineering relies on a solid base of biomechan- field due to high anatomical resolution. ical information. From the molecular to the organism level, biomechanics plays a major role Current research in mMRI focus on the in all systems. design of contrast agents, but not much address on the related pulse sequences. Yen- Hsiang’s research interest is to find out a Rebecca Snyder new mMRI method by both optimizing con- trast agents and its pulse sequence. Develop- ing fast imaging techniques used for hyperpo-

larized Magnetic Resonance Spectroscopy would be a suitable beginning for him to understand the methodology behind.

While obtaining my PhD in Bioengineering Rebecca plans to pursue research in orthopedic tissue engineering by studying the effects of BIO - X AT STANFORD scaffold material properties on the differentia- tion of stem cells. By utilizing her knowledge of TO EDUCATE... the materials paradigm and biological response pathways, she intends to incorporate varying TO DISCOVER …. materials within a single tissue scaffold to pro- mote heterogeneous differentiation in response T O I N V E N T . … to biomechanical signals.

This work can provide a construct that closely mimics the extensive collaboration of various cell types within a given biologic space. Such detailed study of host-tissue interactions could impact the development of devices ranging from pacemakers to orthopedic implants.

Page 22 Bio-X Postdoctoral Fellowships 2005

Tiffany Sergey Chung Solomatin Radiology Chemistry

Profs. Steve Chu (Physics, Applied Physics) Profs. Jianghong Rao (Radiology) and Sanjiv and Daniel Herschlag (Biochemistry, Chem- Sam Gambhir (Bioengineering, Radiology) istry, and Chemical Engineering)

Tiffany designed small molecule Sergey’s research will involve the probes for in vivo imaging of apop- use of single-molecule Fluores- tosis. Because apoptosis takes cence Resonance Energy Transfer place through activation of caspa- (sm-FRET) to explore the folding ses, she will develop a biolumines- dynamics of RNA. In the cence imaging system that can Herschlag and Chu labs, Sergey is directly image the activation of the using synthetic and characterization caspases in vivo. techniques to determine distance changes between labeled sites on a ribozyme molecule.

Page 23 Bio-X Postdoctoral Fellowships 2007

Genentech Fellowship Bio-X Postdoctoral Fellowship

Shilpa Sambashivan Elena Rykhlevskaia Chemical & Systems Biology Psychiatry

Professor Axel Brunger (Molecular & Cellular Physiology, Profs. Vinod Menon (Psychiatry, Neurosciences) and Brian Neurology & Neurological Sciences) Wandell (Psychology) The Endoplasmic Reticulum Associated Degra- Elena is interested in connectivity aspects of dation pathway is an important quality control brain organization. She develops data mining pathway that is essential for clearing misfolded algorithms for analysis and modeling of in vivo proteins from cells in a timely manner thus human brain imaging data to understand how preventing the accumulation of toxic aggre- different brain areas interact as part of a large- gates. Aberrant functioning of the ERAD scale network. Her lab works with the Cogni- Pathway has been linked to several diseases tive and Systems Neuroscience Lab, and the including Parkinson’s disease. The pathway is Vision, Imaging Science and Technology Activi- highly evolved with specific branches of the ties Lab. To capture the structural back bone pathway dedicated to the clearance of misfold- of brain networks, they use diffusion tensor ed proteins in different cellular locations. imaging (DTI), while functional magnetic reso- Employing biochemical assays and structural nance imaging (fMRI) is used to infer activity techniques like X-ray , single- synchronization and information flow among molecule studies and electron microscopy, the key network nodes (at rest, or when The Brunger lab is interested in determining performing a task). She is particularly fascinat- the molecular interactions between misfolded ed with the changes in structural and function- proteins and the various components of the al aspects of brain network connectivity due ERAD-L pathway. to brain development and aging.

Bio-X Postdoctoral Fellowships 2009

Yu-Shan Lin Tristan Ursell Chemistry Bioengineering

Professor Vijay Pande (Chemistry) Professor Kerwyn Huang (Bioengineering) Mounting research evidence suggests that Tristan’s research has concentrated on the soluble oligomers of amyloid beta (Aβ) pep- mesoscopic scale, where proteins, lipids, and tide play a causal role in Alzheimers disease. their aggregates are examined as mechanical This research project describes an interdisci- elements that respond to stresses in the envi- plinary approach to provide valuable insight ronment. His goal is to probe the importance into the important problem of Aβ oligomeri- of physical and mechanical forces in mecha- zation. The Pande lab proposes to utilize nisms driving cellular organization by integrat- advanced simulation techniques to provide ing approaches from experimental cell biology, structural, thermodynamic, and kinetic infor- biochemistry, and with theoretical mation on the structure and oligomerization studies based on mechanics, statistical physics, of Aβ peptides. They shall obtain testable and . As a consequence, spectroscopic predictions by integrating their it will benefit from natural collaborations with simulations with theoretical vibrational spec- faculty from the Schools of Medicine and troscopy. Engineering. Page 24 Bio-X Fellows—Where are they now?

The Bio-X Fellowship Program has completed three rounds of funding and has seen a number of students graduate and pursue their careers after Stanford. Below are some highlights from our recent graduates.

Amanda Malone, Ph.D. Vice President and Director of Research and Development Auritec Pharmaceuticals, Inc.

Auritec is a small self-owned pharmaceutical company specializing in im- proving the dosage dependence of FDA-approved drugs. Amanda writes grants and manages research projects which are aimed at reducing the effective dosages required for drugs which may be currently available on the market.

“The Bio-X Program and Fellowship allowed me to do riskier research for my Ph.D. because we didn’t have outside funding for that [specific] pro- ject. I think it directly contributed to the success of that work, specifically in the publication of the work in the Proceedings of the National Acade- my of Sciences.”

David Myung, Ph.D. President and CEO (co-founder) Biomimedica, Inc.

Biomimedica, Inc., based in Berkeley, is an early stage, venture backed start-up developing a novel orthopaedic joint repair technology. The idea for the company came out of materials characterization work that David pursued during his graduate research while sponsored by the Bio-X Pro- gram.

“One of the many ways Bio-X led me to what I’m doing now is by getting me initially connected to people in the device and venture community, and these connections led to others that helped get the company started and funded.”

Leslie Meltzer, Ph.D. Medical Information Manager Actelion Pharmaceuticals US

Actelion is an emerging biopharmaceutical company that develops novel therapies for highly unmet medical needs. As a Manager in Medical Infor- mation, Leslie provides technical and scientific support to physicians, sales managers, commercial affiliates and customers.

“The diversity of science [in Bio-X and the Clark Center] enables you to become a real generalist—to feel comfortable jumping into a new field. My work in Bio-X, the Neurosciences Program, and at Stanford allowed me to look for something interesting [when ready to graduate], knowing that I had the ability to learn quickly, solve problems, and work with re-

Page 25 Past Bio-X Graduate Fellowships Graduated Bio-X Fellows:

Student Department Degree, Year

Namiko Abe Neurosciences M. S., 2007 Afsheen Afshar Electrical Engineering Ph. D., 2008 Georgios Asimenos Computer Science Ph. D., 2009 Relly Brandman Chemical & Systems Biology Ph. D., 2009 Virginia Chu Bioengineering Ph. D., 2009 Vincent Chu Applied Physics Ph. D., 2009 David Camarillo Mechanical Engineering Ph. D., 2008 Ian Chen Bioengineering Ph. D., 2008 Samuel Kim Chemistry Ph. D., 2009 Andreas Loening Bioengineering Ph. D., 2006 Amanda Malone Bioengineering Ph. D., 2007 Leslie Meltzer Neurobiology Ph. D., 2008 David Myung Chemical Engineering Ph. D., 2008 Aaron Wang Bioengineering Ph. D., 2009 Yufeng Yang Neurosciences Ph. D., 2009 Sara Zhao Mechanical Engineering M. S., 2005

Completed fellowships:

Student Department Yr completed

Jennifer Blundo Mechanical Engineering 2009 Stephen Lee Bioengineering 2007 Sergio Moreno Physics 2007 Mindy Chang Bioengineering 2008 Sheng Ding Bioengineering 2008 Adam Grossman Bioengineering 2008 Rachel Kalmar Neurosciences 2008 Prasheel Lillaney Bioengineering 2008 Murtaza Mogri Bioengineering 2008 Guillem Pratx Electrical Engineering 2009 Jayodita Sanghvi Bioengineering 2008 Jules VanDersarl Materials Science & Engineering Aut 2008 Yufeng Yang Neurosciences 2008 Larry Wang Materials Science & Engineering 2008 Sanjay Dastoor Mechanical Engineering 2009 Kathryn Keenan Mechanical Engineering 2009 Angela Wu Bioengineering 2009 Daniel Kimmel Neurobiology 2009 Bertrand Lui Bioengineering 2009

Page 26 Current Bio-X Fellows

Current Bio-X Graduate Fellows:

Student Department Edith Arnold Mechanical Engineering Peggy Yao Biomedical Informatics Kelsey Clark Neurosciences Jennifer Hicks Mechanical Engineering Jacob Hughey Bioengineering Frances Lau Electrical Engineering Cory McLean Computer Science Min-Sun Son Bioengineering Rebecca Taylor Mechanical Engineering Kitchener Wilson Bioengineering Nan Xiao Bioengineering Mario Diaz de la Rosa Chemical Engineering Lisa Gunaydin Neurosciences Tyler Hillman Genetics, Medicine Mihalis Kariolis Bioengineering Ian Marshall Civil & Environmental Engineering Andreas Rauschecker Neurosciences, Psychology Mark Sellmyer Chemical & Systems Biology Ton Subsoontorn Bioengineering Grace Tang Bioengineering Brian Wilt Applied Physics Aakash Basu Applied Physics Elsa Birch Chemical Engineering Graham Dow Biology Christine McLeavey Neurosciences Alia Schoen Materials Science & Engineering Jong Min Sung Applied Physics Noureddine Tayebi Electrical Engineering

Bio-X Endowed and SIGF Fellows:

Student Department Neurobiology Melinda Cromie Mechanical Engineering Liang Liang Applied Physics Li Ma Statistics Peter Olcott Bioengineering Shawn Ouyang Chemical & Systems Biology

Industry sponsored awards: Student Department Guarav Krishnamurthy (Medtronic Foundation) Mechanical Engineering Adam de la Zerda (Skippy Frank Foundation) Electrical Engineering Sanaz Saatchi( Amgen) Bioengineering

Page 27 Professor Carla Shatz Director of Bio-X James H. Clark Center 318 Campus Drive, W157 [email protected] Heideh Fattaey, Ph.D. Director of Operations and Programs James H. Clark Center 318 Campus Drive, S356

[email protected]

Jill Sakata, Ph.D. Bio-X Education and Fellowship Manager 318 Campus Drive, S135 Olgalydia Urbano-Winegar [email protected] Bioengineering Student Services Manager 318 Campus Drive, S166

[email protected]

Bio-X Program

To learn more about the Bio-X Program at Stanford, please visit the Bio-X website at:

http://biox.stanford.edu

Cover art provided by: Murtaza Mogri, Viviana Gradinaru, and Karl Deisseroth Brochure designed by F. Sincock