Students in Training and Alumni
Students of Bioengineering
| Tatsuya Arai |
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Alum Tatsuya Arai completed Ph.D. with Specialization in Multi-Scale Biology in 2013. Dissertation "In Vivo Biomechanics of Human Pulmonary Circulation" |
| Amran Asadi |
MD/PhD scholar Amran Asadi completed the Specialization in Multi-Scale Biology and conferred the Ph.D. in 2015. He continues training for the MD |
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| Nirupama (Pam) Bhattacharya |
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Alum, Nirupama (Pam) earned her PhD with Specialization in Multi-Scale Biology in Fall, 2014. |
| Britton Boras |
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Alum Britton Boras earned the PhD with Specialization in Multi-Scale Biology in 2015. Dissertation "A Multi-Scale Modeling Approach to Understanding PKA Activation in Cardiac Myocytes" |
| Eric Carruth |
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Alum Eric Carruth completed his PhD in June, 2018. His research has focused on developing and parameterizing models of the biomechanics of the heart. Our group uses diffusion tensor imaging (DTI) in the rat heart to... more |
| Shruti Davey |
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Alum Shruti Davey completed her degree in 2016-17. The experimental plan for my research includes three aims: 1) to quantitatively characterize the deformation of the fiber networks within collagen gels during cell... more |
| Samson Fong |
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My goal is to create a data-driven whole cell model. To do this, I aim to develop a comprehensive approach to data integration that allow... more |
| Nickolas Forsch |
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My research airms include: improving the update scheme for coupling the myocyte electromechanics ODEs with the finite element biomechanics PDEs based on the relationship of solution convergence to computational cost... more |
| Matthew Gonzales |
Alum and MD/PhD scholar Dr. Gonzales earned his Ph.D. in 2013, MD in 2015 and is conducting post graduate training at UCLA Medical Center. Thesis title: Rotor Termination in a Patient-Specific Model of Atrial... more |
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| Jeffry Granados |
To optimize the expression of differentiation markers, organoid growth, and functional 3D transport to be measured with quantitative radiolabel assays, fluorescence assays, and confocal microscopy together with... more |
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| Valerie Griffeth |
Alum and MD/PhD scholar, Dr. Griffeth was awarded the MD in 2015, PhD with Specialization in Multi-Scale Biology in 2013. She is conducting post graduate trraining with Oregon Health and Science University Medicine... more |
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| Jia Guo |
Alum Jia Guo earned the PhD with Specialization in Multi-Scale Biology in 2014 |
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| Kara Johnson |
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High Throughput Profiling of Protein Interactions with Nucleic Acid Barcodes |
| Amanda Li |
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Alum Amanda Li completed the PhD Specialization in September, 2016. Her thesis was Noncovalent Interactions: Evaluation of Computational Methods and Characterization of Molecular Binding |
| Esther Lim |
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The goal of my project is to understand how cancer cells modulate sphingolipid metabolism to facilitate tumor survival and metastasis. We aim to identify sphingolipid metabolism genes that are essential for in vivo... more |
| Christopher MacDonald |
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Alum Christopher MacDonald completed his PhD in 2011, thesis Calcium Dynamics in Astrocytes: From Ocillations to Alzheimer's |
| Sara McArdle |
Alum Sara McArdle earned the PhD with Specialization in Multi-Scale Biology in 2015. |
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| Kimberly McCabe |
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The major aim of my research project is to use computational simulation to elucidate mechanisms by which dATP aids in myocyte contraction. This process will also help uncover any possible negative side effects of... more |
| Seth Parker |
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Alum Seth Parker earned the PhD with Specialization in Multi-Scale Biology in September of 2016, thesis Regulation of Mitochondrial Metabolism by the LKB1 Tumor. He has accepted a postdoctoral training... more |
| Emily Pfeiffer |
Alum Emily Pfeiffer was awarded the PhD with Specialization in Multi-Scale Biology in 2013. |
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| Justin Plaut |
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DNA Nanostructure-Decorated Oncolytic Virus: Protecting against Antibody Neutralization and Enhancing Tumor Tropism |
| Vishwajith Ramesh |
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Developing a Reliable Stroke Evaluation System with 3D Depth Tracking and Computer Vision |
| Nikhil Rao |
Alum Nikhil Rao earned his PhD with Specialization in Multi-Scale Biology in 2014 |
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| Helen Saad |
Alum Helen Saad completed her PhD with Specialization in Multi-Scale Biology in 2013. |
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| Samir Saidi |
Aim 1: Design and build a two-photon microscope that utilizes both remote focusing (Fig. 2D) [2] and adaptive optics [3] to compensate for optical aberrations created when large axial displacements from the objective... more |
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| Aaron Simon |
Alum and MD/PhD scholar, Dr. Aaron Simon completed his MD in 2016, PhD with Specialization in Multi-Scale Biology in 2014; and is conducting post graduate training with University of California, Davis Medical Center... more |
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| Jessica Ungerleider |
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Nanoparticles for targeted drug delivery in peripheral artery disease. |
| William Valdez |
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In collaboration with the cardiac mechanics research group, I plan to comprehensively relate acute physiological responses of cardiomyocytes to longer-term transcriptional regulation of hypertrophy through modeling... more |
| Christopher Villongco |
Alum Christopher Villongco completed his PhD with Specialization in Multi-Scale Biology June, 2015. |
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| Kevin Vincent |
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Alum Kevin Vincent completed the Ph.D. Specialization in Multi-scale Biology in 2016. Thesis: Structural contributions to fibrillatory rotors in a patient-derived computational model of the atria |
Students of Biomedical Sciences
| Loren Brown |
Alum, Loren Brown completed the Specialization program and conferred his degree in 2014. |
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| Ilean Chai |
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Alum Ilean Chai completed her degree in 2017. Her research focus involved utilizing techniques from traditiona\ virology, structural biology, cell biology, molecular biology, biochemistry and mass spectrometry; and... more |
| Samantha Jones |
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Samantha Jones earned her PhD in June, 2018, research expertise in The Role of Nonsense-mediated mRNA Decay in Neural Development. My work was focused on showing that the effects of UPF3A depletion or... more |
| Gleb Martovetsky |
Alum, Gleb Mortovetsky earned the Ph.D. Specialization in Multi-Scale Biology in 2016 |
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| Devendra Mistry |
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Alum Devendra Mistry earned the PhD Specialization in Multi-Scale Biology in 2011 with thesis The Mollecular Mechanism Underlying the Gondaotropin Releasing Hormone Pulse Sesitivity of Follicle Stimulating... more |
| Jonathan Okerblom |
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Alum Jonathan Okerblom earned his PhD with Specialization in Multi-scale Biology in September, 2017. Approximately 2-3 million years ago, our human ancestors lost the function of CMAH– a gene that remains... more |
| Steve Rees |
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My project currently has three objectives. I will begin by first determining how current POPs interact with P-gp at the molecular level, which will require P-gp co-crystallization with these compounds. From these... more |
| Eleen Shum |
Alum Eleen Shum earned the Ph.D. with Specialization in Multi-Scale Biology in 2015. Dissertation "Physiological Role of the UPF3 in Gene Paralogs in Nonsense-Mediated RNA Decay" |
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| Eric Wang |
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My long term goal is to bridge the gap between molecular and cellular neurobiology with systems-level neuroscience. In particular, I want to understand how biochemical changes in specific subsets of neurons can exert... more |
| Jacob Wozniak |
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High-Resolution Cellular Mapping of Host-Pathogen Spaciotemporal Protein Dynamics |
Students of Biological Sciences
| Evan Campbell |
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In Dr. Brenda Bloodgood's lab, Evan Campbell investigates cellular mechanisms underlying activity-dependent gene expression in hippocampal neurons and how synaptic activity is communicated to the nucleus. ... more |
| Eileen Gonzalez |
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Cytoskeletal and Mitochondrial Mechanisms of Neuronal Development Influenced by Normal and Excess Glutamate Conditions Using Approaches that Combine Molecular Biology with Advanced Cellular Imaging |
| Anna Guzikowski |
We aim to study how external, environmental stimuli in the form of stress can exert influence on chemical substrates through modification of RNAs and exert influence on a larger scale via impact upon gene expression... more |
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| Phillip Kyriakakis |
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Alum Phillip Kyriakakis completed the Ph.D. with Specialization in Multi-Scale Biology in 2014. Dissertation "Glk1p, an actin-like metabolic enzyme that forms glucose regulated filaments" |
| Regina Powers |
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My thesis project revolves around one such protein, called navigator 1 (NAV1), as it has been shown that it is important in the development of neurons. |
| Natalia Slepak |
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Determine if Npas4 is required for sharpening orientation tuning in the adult; if required for maintaining orientation tuning in adults; and if Npas4 mediated circuit remodeling promotes visual learning. |
| Nathan (Kannis) Solberg |
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Alum Nathan Solberg, research is in area of Alzheimer's utilizing a hybrid of cellular, mollecular, systems and computational methods. |
Students of Chemistry and Biochemistry
| Chris Fisher |
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There are numerous pathways through which influenza A can enter a host cell to begin infection.... more |
| Dimitrios Floros |
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Alum Dimitri Floros completed his UCSD degree in 2015-16. His research project: develop an agar based co-culture system of plant and soil microbes; use MS-based techniquest to investigate the spatial organization... more |
| Isaiah Gomez |
Alum Isaiah Gomez completed his UCSD degree in 2015-16. Research Project: to show that large data sets of mass spectra from marine microbial species can be quickly analyzed and known compounds be dereplicated as a... more |
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| Kristofer Haushalter |
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Alum Kristofer Haushalter completed the PhD with Specialization in Multi-scale Biology in Dec 2016, thesis "Mechanisms for Non-canonical PKA Signaling Regulation in the Heart". |
| Alexandra Heyneman |
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Comparing Ensemble-Averaged and Single Framed Electrostatics for Brownian Dynamics Simulations |
| Sophia Hirakis |
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Multi-scale sub-cellular modeling of calcium dynamics in the dyadic cleft of cardiomyocytes using Monte Carlo Simulations |
| Benjamin Jagger |
Drug Target Systems, with two aims: 1. Calculation of Dissassociation Rates Using SEEKR; and 2. Implementation of an Accelerated Milestoning Approach. |
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| Chris Lee |
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My goal is to use multi-scale computational models of viral surfaces to simulate key events in the host-switching process. |
| Heidi Leonard |
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Nanostructured porous silicon for drug delivery. |
| Charles Lin |
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40% of drug candidates that enter clinical trials fail due to poor permeability through cell membranes. Despite this, a detailed understanding of small molecule and peptide membrane... more |
| Chi-Wei Man |
Linker of Nucleoskeleton and Cytoskeleton (LINC) Complex |
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| Daniel Mermelstein |
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Dan Mermelstein, alum as of June, 2018, completed his dissertation titled Improvements and Applications of Alchemical Free Energy, Constant pH and Accelerated Molecular Dynamics Calculations in the AMBER Molecular... more |
| Vincent Metzger |
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Alum, Vincent Metzger completed his PhD with Specialization in Multi-Scale Biology in 2014. Dissertation "Insights from Molecular Simulations and Multi-Scale Mathematical Modeling of Biological Systems" |
| Jesse Meyer |
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Alum Jesse Meyer, earned his PhD with Specialization in Multi-Scale Biology in 2015. Dissertation "Novel Proteomics Methods for Increased Sensitivity, Greater Proteome Coverage, and Global Profiling of Endogenous... more |
| Zhengtao Qin |
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Alum Qin Zhengtao completed his PhD with Specialization in Multi-Scale Biology in 2014. Dissertation "Molecular Imaging Probes for Positive Emission Tomography and Optimal Imaging of Sentinel Lymph Node and Tumor"... more |
| Kartik Lakshmi Rallapalli |
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Many-Body representation of base-editing CRISPR-Cas9 The goal of my research is to use multi-scale computational simulation models to study the structural and energetic changes induced due to specific... more |
| Andrew Rudd |
I aim to develop tools to allow for programmed division of artificial vesicles, an area that is incredibly lacking in the field. To accomplish this, I plan to explore small membrane binding proteins known to induce... more |
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| Reta Sarsam |
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Biochemical and Structural Characterization of Fragile X Related Protein 1 |
| Christian Seitz |
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Valuable work has been done linking smaller scale biological simulation programs, but much less work has been done on larger scale... more |
| Lorilee Tallorin |
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Alum Lori Tallorin completed her PhD with Specialization in Multi-Scale Biology in 2016 (sr). My research involves redirecting small molecules for malaria: inhibitors of enoyl-ACP reductase for Plasmodium Falciparum... more |
| Jeff Wagner |
I propose to make a scalable data integration tool for structural biology and biophysics |
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| Nathaniel Wood Cohan |
Alum Nathaniel Wood Cohan conferred his degree in 2013. His research goal: "Pushing sub-tomogram averaging into plastic: A study of LRRK2, a Parkinson's disease related protein, and its interaction with the... more |
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| Jane Yang |
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Alum, Jane Yang completed the Ph.D. with Specialization in Multi-Scale Biology in 2013. Dissertation, Investigating Microbial Metabolites with Novel Mass Spectrometry Tools. She is currently a Clinical Chemist. |
Students of Mechanical & Aerospace Engineering
| Abhay Bangalore |
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Alum Abhay Bangalore completed his PhD Specialization in Multi-scale Biology in 2017. His research focus: Towards a Fluid-Structure-Growth and Remodeling Framework to Simulate Vein Graft Failure Post Coronary Artery... more |
| Miriam Bell |
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My current research focuses on computationally modelling calcium signaling in dendritic spines located on neurons. I'm specifically interested in how geometry affects the spatial and temporal dynamics of AMPA... more |
| Ernesto Criado Hidalgo |
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My current research is focused in developing novel experimental and computational techniques to measure inter-cellular forces during tissue development. Cells can sense their physical surroundings and translate... more |
| Manuel Gomez |
Alum, Manuel Gomez-Gonzalez completed his PhD with Specialization in Multi-Scale Biology in 2015. Dissertation, One- and Two-Point Particle Tracking Microrheology of Complex Viscoelastic Fluids |
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| Benjamin Regner |
Alum, Benjamin Regner earned his PhD with Specialization in Multi-Scale Biology in 2014. |
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| Kai Szeto |
Alum Kai Szeto earned his degree in 2014, having researched mechanisms to understand and develop therapies for skeletal functioning. |
Students of NanoEngineering
| Michael Getz |
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Conducting research within the Chemical Engineering Program of the NanoEngineering Department: This proposed plan aims to identify the design principles associated with noncanonical signaling through G-protein... more |
| Allen Leung |
Although my research focuses and makes models for single cell organisms, perhaps the most incredible aspect of life is its ability for single-celled organisms to self-organize and differentiate to achieve a higher... more |
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| Irem Ustunol |
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Irem's specific focus in the major is biomedical nanotechnology. She is interested in... more |
Students of Neuroscience
| Olubankole Aladesuyi Arogundade |
Determine the connectivity of VP Cholinergic Neurons; and the role of VP chol. neurons in mediating biochemical responses to stress. |
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| Jeffrey Bush |
Jeff Bush: Completed his PhD in Spring Quarter, 2018. His dissertation is Spatial Distribution of Subcellular Organelles in Hippocampal Dendrites from High-Resolution EM Images and involved multiscale modeling of... more |
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| Bethanny Danskin |
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Research interest: Exploring how decision is encoded in cortex, specifically using calcium imaging and optogenetics to trace... more |
| Paxon Frady |
Alum, E. Paxon Frady completed his Ph.D. in 2014 "Activity Mapping the Leech Nervous System" |
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| Tom Gillespie |
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l plan to conduct research into how to represent, visualize, and organize the incredible diversity of types of data produced in neuroscience. My objective is two-fold. The fist is to make it possible to search and... more |
| Eulanca Liu |
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The physiological basis of the blood oxygenation level dependent (BOLD) signal in functional magnetic resonance imaging (fMRI) |
| Anja Payne Higgins |
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Understanding how Npas4 regulates neuronal spiking in vivo will provide new insights into the mystery of how memory is generated and preserved. |
