BME faculty Senior Projects List 2014

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BME Faculty List of Possible Undergraduate Research Projects

Note to students. The projects listed in this matrix represent possible projects available to BME undergraduate students. We encourage you to contact listing faculty members for further information.

Last (link to website)
Lab Description Track Location Project title Project title Project title Project title
Jay Humphrey Vascular Mechanics and Mechanobiology Lab Biomechanics Malone Quantitative Histology Computational Hemodynamics Mechanobiological Assessments using Cell / Tissue Culture Computer-aided Experimentation
Evan Morris Neuroimaging of Addiction and Medications Development Imaging PET Center Imaging the Brain's Dopamine Response to Smoking Cigarettes Imaging the action of a Medication for Alcoholism. Build a Mock PET Scanner
Jim Duncan Biomedical Image Analysis
Imaging TAC
Image segmentation of biomedical structures
Quantification of cardiac (left ventricular) deformation from echocardiography
Prediction of tumor growth and response to radiotherapy from Magnetic Resonance Images

Richard Carson PET Technology and Applications Imaging PET Center
Awake Monkey PET Novel PET Algorithms for Carotid Arteries Multimodal Brain Networks in Cocaine Dependence Improved PET MR image registration


Larry Staib Medical Image Analysis Imaging TAC Magnetic Resonance Diffusion Weighted Image Analysis Imaging Biomarkers of Disease Machine learning for tissue classification

PET Center


Imaging TAC

Hemant Tagare
Imaging TAC

Angelica Gonzalez


Andre Levchenko

West Campus

Stuart Campbell
Biomechanics Malone

Fahmeed Hyder Functional and Molecular Imaging of the Brain Imaging
Calibrated fMRI for basal metabolism
Quantitative metabolic PET Liposomal BIRDS Dendrimeric BIRDS
Rong Fan Single-cell analysis for cancer research and immunology All tracks Malone Engineering Center Single-cell analysis of T cell response Genome editing and cancer development MicroPhysiological Systems High-content imaging for systems biology
Themis Kyriakides Extracellular Matrix, Tissue Engineering, and the Foreign Body Response Biomolecular Engineering, Tissue Engineering Amistad Migration Assays for Testing Next Generation Wound Healing Therapies Characterizing and Robustly Producing Keratinocyte Extracellular Matrix Effect of nanotopography on cell fusion
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Lab Descriptions


(Biomechanics Track) Our focus is on (i) developing computational models for understanding vascular disease progression and designing clinical interventions, (ii) using genetic, pharmacologic, and surgical models to elucidate mechanisms that underlie diverse vascular conditions, and (iii) using tissue engineered constructs to test hypotheses of mechanosensing and mechanoregulation of extracellular matrix.


(Bioimaging Track) The societal burden of misdiagnosed brain disorders and diseases is substantial. The Hyder lab is leading breakthroughs in quantitative and translational imaging technologies, based primarily on magnetic resonance methods, to visualize molecular processes of function and dysfunction at the laminar level.

A primary interest of the Hyder lab is to develop functional imaging techniques that relate neural activity to underlying laminar structure in health and disease. Emphasis is on fMRI, but other multi-modal fMRI methods in conjunction with MRS, electrophysiology, optical imaging, and PET are being sought for increased biomarker specificity. Specific areas of interest include (i) understanding the role of the extraordinarily high energy demands of ongoing and intrinsic activity within neural populations as potential for quantitative disease biomarker, (ii) advancing the spatiotemporal resolution of functional imaging to understand the relation of cellular metabolism in health and disease (e.g., healthy aging, Alzheimer’s disease, depression, epilepsy, schizophrenia), and (iii) developing advanced calibrated fMRI methods for using oxidative energy as an absolute index of neural activity, both with task and rest paradigms, across cortical and subcortical regions.

Another active interest in the Hyder lab is molecular imaging with magnetic resonance technologies where several disciplines connect, from chemistry and physics to material science and physiology. A new molecular imaging method, pioneered in the Hyder lab called BIRDS, combines high MRI spatial resolution with high MRS molecular specificity. The method, quite unconventionally, detects the paramagnetically-shifted and non-exchangeable protons from lanthanide (or transition) metal ion probes for high spatiotemporal resolution biosensing. Highly precise molecular imaging of temperature and pH is achievable with BIRDS. Current areas of relevance are (i) design of new molecular probes for BIRDS, (ii) early cancer detection and metastasis using absolute pH imaging, (iii) application of new probes for BIRDS as molecular targets for diseases (e.g., diabetes), and (iv) detection of tumor response to treatments (e.g., radiation, chemotherapy, heat).


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Project Descriptions


We use histology and immunohistology to quantify regional variations in the distributions of vascular cell phenotype, extracellular matrix, proteases, and cytokines to correlate with computational predictions. Primary focus – image analysis and histopathology.


Working with colleagues in our medical school, we use patient-specific computational models to study vascular disease mechanisms and their treatment. Primary focus - to use image reconstruction methods to create large scale computational models.


Assessments using Cell / Tissue Culture – We subject cultured cells and tissue engineered constructs to well defined mechanical stimuli and assess their mechanobiological responses. Primary focus – cell and tissue culture methods.


We use custom computer-controlled devices to perform theoretically motivated experiments. Primary goal – to design, build, and test new testing systems.


Quantification of cardiac (left ventricular) deformation from echocardiography: This work employs image feature detection and matching strategies for estimating local frame-to-frame displacements from image sequences, and then machine learning strategies to integrate the information to quantify strain in the left ventricle under different disease conditions. Biomechanical models of the heart can be used to help with the integration and close collaboration with clinical colleagues in cardiology is a key part of this work.


Image segmentation of biomedical structures: Here, the work involves the use of geometrical and statistical models of shape and mathematical optimization strategies to locate structure in images. The structure can range from finding cells or subcellular particles from high resolution microcope images to locating the endocardial surface of the heart from ultrasound or magnetic resonance images.


Prediction of tumor growth and response to radiotherapy from Magnetic Resonance Images: Sets of MR images are obtained from patients (in collaboration with Neurosurgeons and Neuroradiologists) and are assembled into a database. Pattern classification strategies can be developed and compared to other work in the literature to try to find parameters that can predict response to treatment.


Simulation studies to assess sensitivities required for fMRI and perfusion data to extract basal metabolism from calibrated fMRI data


Analysis of whole brain PET data of glucose and oxidative metabolism in the human brain in relation to blood flow


Development and/or characterization of newly developed probes encapsulated inside liposomes for BIRDS


Development and/or characterization of newly developed macromolecular-based probes for BIRDS


Perform, analyze, and develop the technology for awake monkey brain PET studies involving combined brain imaging (without head restraint) and behavioral tasks


Develop novel PET Algorithms to measure the activity in the carotid arteries which feed the brain


Analysis of PET (Dopamine) and fMRI data in subjects with Cocaine Dependence to determine altered brain networks


Improve the quality of image registration between PET and MR images for more accurate determination of small brain structures


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