BU 2009-10 College of Engineering Bulletin

Boston University College of Engineering Bulletin

PhD Students Who Graduated During 2008/2009

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Bioinformatics
Biomedical Engineering
Computer Engineering
Electrical Engineering
Manufacturing Engineering
Materials Science & Engineering
Mechanical Engineering
Systems Engineering

Candidate	Dissertation Title	Professor
Bioinformatics
Ryan Douglas Brenke	“Efficient Algorithms for Modeling Macromolecular Interactions”	Professor Sandor Vajda, PhD
John Michael Brockman	“Analysis of Dendritic Targeting Elements and the Potential Impact of Alternative Polyadenylation”	Professor Joel H. Graber, PhD Professor Temple Smith, PhD
James Patrick Flanigon	“Sensitive Protein Detection Using PCR and Mass Spectrometry”	Professor Charles R. Cantor, PhD
Vincent A. Fusaro	“Prediction of High-Responding Peptides in Electrospray Mass Spectrometry”	Professor Jill Mesirov, PhD
Adam Matthew Gustafson	“Computational Prediction of Chemopreventive and Therapeutic Options in Cancer Using Whole-Genome Gene Expression Studies”	Professor Avrum Spira, MD
Soohyun Lee	“Computational Analysis of Human Genomic Sequence Variation and Drosophila Small RNA Transcriptome”	Professor Zhiping Weng, PhD
Bolan Linghu	“Gene Annotation and Disease Gene Prediction from an Integrated Functional Linkage Gene Network”	Professor Charles DeLisi, PhD
David Ronald Lorenz	“An Integrated Experimental/Computational Approach to Infer Gene Regulatory Networks: Application to a Model Prokaryote and Eukaryote”	Professor James Collins, DPhil
Denise Yuen Fung Mak	“Seed Modeling, Inverted Repeat Detection and Consensus RNA Secondary Structure Prediction”	Professor Gary Benson, PhD
Priyam Singh	“Characterization of Alternative mRNA 3'-Processing in Mouse Progenitor B-Cell Lymphoma”	Professor Joel H. Graber, PhD Professor Temple Smith, PhD
Chang-Jiun Wu	“Integrative Computational Analysis, Design and Validation of Cancer Biomarkers via Functional Modules and Pheno-Genomic Profiling”	Professor Simon Kasif, PhD
Yi Yu	“Localization of Genes Associated with Nicotine Dependence and Improved Random Forests Approaches for SNP Screening”	Professor Lindsay Farrer, PhD
TOP OF PAGE Biomedical Engineering
Gwo-Yu Chuang	“A Fast Fourier Transform Correlation Approach to Protein Mapping: Development and Applications”	Professor Sandor Vajda, PhD
Tara Lynn Deans	“An Engineered Synthetic Switch for Regulating Gene Expression in Mammalian Cells”	Professor James Collins, DPhil
Sophie Caroline Desbiens	“Therapeutic Agents for Cocaine Addiction: A Systems Pharmacology Approach”	Professor David H. Farb, PhD
Wynter Jóia Duncanson	“Targeted Polymer Ultrasound Contrast Agents for Molecular Imaging”	Professor Joyce Y. Wong, PhD
Daniel Kenneth Freeman	“Maintained Discharge and Adaptation Properties of Rat Retinal Ganglion Cells”	Professor Christopher L. Passaglia, PhD
Jane Marie Landolin	“DNA Sequence and Epigenetic Features that Drive Human Promoter Function”	Professor Zhiping Weng, PhD
ZhuangLi Liang	“Calcium Artifact Analysis and Multi-Component-Based Mitigation in Cardiac Multi-Detector Computed Tomography”	Professor W. Clement Karl, PhD
Kyle Patrick Lillis	“Development of Neural Recording Techniques and the Study of Epileptiform Activity in vitro”	Professor John White, PhD
Rapeechai Navawongse	“Extracellular Single Neuron Recording in Dorsal Cochlear Nucleus of Awake Gerbil”	Professor Herbert F. Voigt, PhD
Seth O. Newburg	“Mechanical Response of the Basilar Membrane to Lateral Micromanipulation”	Professor David C. Mountain, Jr., PhD
Kristy Thérèse Salisbury Palomares	“Mechanobiological Regulation of Cell Molecular Expression and Tissue Differentiation During Bone Healing”	Professor Elise Morgan, PhD
Harikrishnan Parameswaren	“Effect of Microscopic Structural Changes on Macroscopic Functional Properties: Imaging and Modeling the Lung Parenchyma in Three Dimensions”	Professor Béla Suki, PhD
Hemali Bharat Patel	“Decoding Transcriptional Regulatory Networks Activated During Stringent Response in Escherichia coli”	Professor Timothy S. Gardner, PhD
Jesse Brandt Wolinsky	“Prevention of Lung Tumor Recurrence Through Localized Drug Delivery via Paclitaxel-Eluting Glycerol-Based Polymeric Films”	Professor Mark W. Grinstaff, PhD
Computer Engineering
Ahmad Malih El Katerji	“BrainView: A Functional Neuroanatomy Knowledge System”	Professor David C. Mountain, Jr., PhD
Konrad Jan Kulikowski	“Codes and Circuits for Secure Hardware Design”	Professor Mark Karpovsky, PhD
Shan Lu	“A Nonlinear Multicompartmental Cochlear Model”	Professor Allyn E. Hubbard, PhD
Alexander Borisovitch Smirnov	“Asynchronous Micropipeline Synthesis System”	Professor Alexander Taubin, PhD
TOP OF PAGE Electrical Engineering
Suchin Aeron	“Sensing and Reconstruction of Sparse Phenomena Bounds and Algorithms”	Professor Venkatesh Saligrama, PhD
George Atia	“Robust Strategies for Cooperative and Cognitive Wireless Communication Systems”	Professor Venkatesh Saligrama, PhD
Shey-Sheen Chang	“Emergent Behavior Search in Complex Biosignals”	Professor S. Hamid Nawab, PhD
Marcos Andrés Diaz	“Particle-In-Cell Simulation of Electron Beam Instabilities in the Ionosphere and Implications for ISR Spectra”	Professor Joshua Semeter, PhD
Kristina Marie Driscoll	“Novel Nitride- and Silicon-Based Quantum Structures for Intersubband Light Emitting Devices”	Professor Roberto Paiella, PhD
Julia Rentz Dupuis	“Hyperspectral Fourier Transform Spectrometer for White Light Reflection Spectroscopy and Spectral Self Interference Fluorescence Microscopy”	Professor M. Selim Ünlü, PhD
Samuel Michael Keene	“Collision Recovery Techniques for Wireless LANs”	Professor Jeffrey B. Carruthers, PhD
Yan Li	“Ultrafast All-Optical Switching Based on Intersubband Transitions in Gallium Nitride/Aluminum Nitride Quantum-Well Waveguides”	Professor Roberto Paiella, PhD
I. Emre Özkumur	“Optical Interference Based Microarray Imaging for Label-Free Multi-Analyte Detection”	Professor M. Selim Ünlü, PhD
Eladio Rodriguez-Diaz	“Robust Classification Techniques and Their Application to Optical Spectroscopy in Medical Diagnostics”	Professor David Castañón, PhD
Onur Savas	“Consensus Algorithms for Power-Constrained Wireless Sensor Networks”	Professor Murat Alanyali, PhD
Alvin Gabriel Stern	“Design and Analysis of a Novel Avalanche Photodiode Array”	Professor Daniel C. Cole, PhD
Jason Bernard Stewart	“Development and Control of a New Class of Segmented Deformable Mirrors for Advanced Astronomical Imaging Applications”	Professor Thomas Bifano, PhD
Ayça Yalçın	“Spectral Fluorescence Measurements on Reflecting Surfaces Shedding Light onto Conformation and Orientation of Macromolecules”	Professor M. Selim Ünlü, PhD
Matthew David Zettergren	“Model-Based Optical and Radar Remote Sensing of Transport and Composition in the Auroral Ionosphere”	Professor Joshua Semeter, PhD
Manufacturing Engineering
Yaopeng Zhou	“Adaptive Optics Two-Photon Scanning Laser Fluorescence Microscopy”	Professor Thomas Bifano, PhD
Materials Science & Engineering
Haibing Wang	“Composite Mixed Ion-Electron Conducting (MIEC) Membranes for Hydrogen Generation and Separation”	Professor Srikanth Gopalan, PhD
Mechanical Engineering
Carlos Esteban Colosqui	“Theory and Lattice Boltzmann Simulations of Rapidly Oscillating Flows: Application to Nanofluidics”	Professor Victor Yakhot, PhD
Alia Winslow Foley	“Investigations of the Sound Generated by Supercavity Ventilation”	Professor Michael S. Howe, PhD
Zachary John Waters	“Sensing Resonant Objects in the Presence of Noise and Clutter Using Iterative Single-Channel Acoustic Time Reversal”	Professor Ronald A. Roy, PhD
Systems Engineering
Tarik Borogovac	“Constructive and Generic Control Variates for Monte Carlo Estimation”	Professor Pirooz Vakili, PhD
Dong Guo	“A New Statistical Localization Framework for Wireless Sensor Networks”	Professor Ioannis Ch. Paschalidis, PhD
Jianfeng Mao	“Dynamic Energy Management in Resource Limited Systems with Real-Time Constraints”	Professor Christos G. Cassandras, PhD
Xu Ning	“Control and Optimization Approaches for Power Management in Wireless Sensor Networks”	Professor Christos G. Cassandras, PhD
Chang-Chen Wu	“Production Planning and Quality of Service Allocation Across the Supply Chain in a Dynamic Lead Time Model”	Professor Michael Caramanis, PhD

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Published by Trustees of Boston University
One Silber Way
Boston, MA 02215

1 October 2009
Boston University
Questions
Credits

PhD Students Who Graduated During 2008/2009

Candidate

Dissertation Title

Professor

Bioinformatics

Biomedical Engineering

Computer Engineering

Electrical Engineering

Manufacturing Engineering

Materials Science & Engineering

Mechanical Engineering

Systems Engineering