Term of Graduation Student Name Adviser/Department Dissertation Title
Spring 2004 Bing, Nan Ina Hoeschele/ STAT/ VBI Statistical Analysis of Gene Expression Profile: Transcription Network Inference and Sample Classification
Spring 2006 Sha, Wei Pedro Mendes/ VBI Microarray data analysis methods and their applications to gene expression data analysis for Saccharomyces cerevisiae under oxidative stress
Spring 2007 Ruscio, Jory Zmuda David Bevan/ BCHM and Alexey Onufriev/ CSA (co-chairs) Molecular Modeling: Elucidation of Structure/Function Relationships of Proteins and DNA at the Atomic Resolution
Summer I 2007 Camacho, Diogo Mayo Pedro Mendes/ VBI In silico cell biology and biochemistry: a systems biology approach
Summer II 2007 MacKinnon, Kathryn David R Notter/ APSC (retired, prof emeritus now) Analysis of Inbreeding in a Closed Population of Crossbred Sheep
Fall 2007 Rajasimha, Harsha Karur David Samuels/ VBI (at Vanderbilt Univ now) Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation
Summer I 2008 Dyer, Matthew T M Murali/ CSA and Bruno Sobral/ VBI (co-chairs) Pathosystems Biology: Computational Prediction and Analysis of Host-Pathogen Protein Interaction Networks
Summer II 2008 Cortes Bermuda, Diego F. Vladimir Shulaev/ VBI (at Univ of North Texas now) Functional genomics through metabolite profiling and gene expression analysis in Arabidopsis thaliana
  Tuli, Leepika Vladimir Shulaev/ VBI Proteome Profiling of Saccharomyces cerevisae stress response to Cumene Hydroperoxide (CHP)
Fall 2008 Li, Shenghua John J Tyson/ BIOL Quantitative Modeling of the Molecular Mechanism Controlling the Asymmetric Cell Division Cycle in Caulobacter crescentus
  Zhang, Tongli John J Tyson/ BIOL Mathematical Models of Some Signaling Pathways Regulating Cell Survival and Death
Spring 2009 Krampis, Konstantino Mohammad Saghi-Maroof/ CSES Systems View Of The Soybean Genetic Mechanisms Involved In The Response To Plant Pathogen Infection
Fall 2009 Pokrzywa, Revonda Pedro Mendes/ VBI Systems Biology in an Imperfect World: Modeling Biological Systems with Incomplete Information
Spring 2010 Waller, Lachelle Brett Tyler/ PPWS/ VBI (at Oregon State Univ now) Transcriptional profiling of potential regulatory factors modulating defense mechanisms in soybean during Phytophthora sojae infection
  Wonnapinij, Passorn David Samuels/ VBI (at Vanderbilt Univ now) Theoretical and Statistical Approaches to Understand Human Mitochondrial DNA Heteroplasmy Inheritance
  Cai, Yizhi Jean Peccoud/ VBI GenoCAD: linguistic approaches to synthetic biology
Fall 2010 Cheng, Hui Pedro Mendes/ VBI New Dimensions: Integration and Visualization Methods Provide Insights into Systems Biology Data
  Krishnan, Arjun Andy Pereira/ CSES/ BIOL/ VBI (at Univ of Arkansas now) Systems Analysis of Stress Response in Plants
Spring 2011 Lewis, Bryan Leroy Stephen Eubank / NDSSL / VBI in silico Public Health: The Essential Role of Highly Detailed Simulations in Support of Public Health Decision-Making
  Kale, Shiv Dutt Brett Tyler/ PPWS/ VBI (at Oregon State Univ now) How Oomycete and Fungal Effectors Enter Host Cells and Promote Infection
  Falin, Lee J. Brett Tyler/ PPWS/ VBI (at Oregon State Univ now) Systems Uncertainty in Systems Biology & Gene Function Prediction
  Wu, Zhanghan John J Tyson/ BIOL Understanding molecular and cellular processes using statistical physics
  Singhania, Rajat John J Tyson/ BIOL Modeling Protein Regulatory Networks that Control Mammalian Cell Cycle Progression and that Exhibit Near-Perfect Adaptive Responses
  Dharmarajan, Lakshmi Biswarup Mukhopdyay/ VBI Structure-Function Studies on Two Phosphoenolpyruvate Carboxylases
Summer I 2011 Babiceanu, Mihaela Chris Lawrence/ BIOL/ VBI Analysis of the Allergenic Potential of the Ubiquitous Airborne Fungus Alternaria Using Bioinformatics
Fall 2011 Wendelsdorf, Katherine Madhav Marathe and Stephen Eubank / NDSSL-Barrett Group @ VBI (co-chairs) Models of the Mucosal Inflammatory and Regulatory Immune Pathways: The Role of Host Response in Microbial Persistence and Pathogenesis
  Lasher, Christopher D. T M Murali/ CSA and Padmavathy Rajagopalan/CHE (co-chairs) Discovering Contextual Connections Between Biological Processes using High-throughput Data
  Ravi, Janani John J Tyson/ BIOL Modeling the START Transition in the Budding Yeast Cell Cycle
  Laomettachit, Teeraphan John J Tyson/ BIOL Mathematical Modeling Approaches for Dynamical Analysis of Protein Regulatory Networks with Applications to the Budding Yeast Cell Cycle and the Circadian Rhythm in Cyanobacteria
Spring 2012 Yared Kidane Chris Lawrence/ BIOL/ VBI and T M Murali/ CSA The Landscape of Host Transcriptional Response Programs Commonly Perturbed by Infections Pathogens: Towards Host-Oriented Broad-Spectrum Drug Targets and Immunotherapeutic Interactions
  Shamira Shallom Harold Garner/ VBI/ BIOL/CSA/ VT Carilion School of Medicine A species independent universal bio-detection microarray for pathogen forensics and phylogenetic classification of microorganisms.
  Elaine Nsoesie Madhav Marathe/ NDSSL- VBI and Richard Beckman/ NDSSL-VBI Sensitivity Analysis and Forecasting in Network Epidemiology Models
Summer II 2012 Yan Fu Jianhua Xing/ BIOL and John Tyson/ BIOL (co-chairs) Computational Systems Biology Analysis of Cell Reprogramming and Activation Dynamics
Spring 2013 Timothy Driscoll David Bevan/BCHM and Joseph Gillespie/ U of MD (co-chairs) Host-Microbe Relations: A Phylogenomics-Driven Bioinformatic Approach to the Characterization of Microbial DNA from Heterogeneous Sequence Data
  Matthew W Lux Jean Peccoud/VBI Estimation of Gene Network Parameters from Imaging Cytometry Data
Fall 2013 Chun Chen John J Tyson/BIOL Systems Biology Study of Breast Cancer Endocrine Response and Resistance
  Hyunjin (Danielle) Choi Brett Tyler/VBI/PPWS (at Oregon State Univ now) An Interdisciplinary Approach: Computational Sequence Motif Search and Prediction of Protein Function with Experimental Validation
Spring 2014 Ha X. Dang Chris Lawrence/ BIOL/VBI Mold Allergomics Using Comparative and Machine Learning Approaches
  Gareth An Wei Highnam David Mittelman/ VBI/ BIOL Optimizing Analysis Pipelines for Improved Variant Discovery
  Shernita Lee Reinhard Laubenbacher/ VBI/MATH and Chris Lawrence/VBI/BIOL (co-chairs) Ironing Out the Host-fungal Interaction in Airway Epithelial Cells
  Matthew Morris Liwu Li/BIOL Molecular Mechanisms Responsible for the Dynamic Modulation of Macrophage Responses to Varying Dosages of Lipopolysaccharide
  Alexandra J Weisberg John Jelesko/PPWS Investigations into the Molecular Evolution of Plant Terpene, Alkaloid, and Urushiol Biosynthetic Enzymes
Summer I 2014 Adria Carbo Barrios Josep Bassangaya-Riera/ VBI Transdisciplinary Strategies to Study the Mechanisms of CD4+ T cell Differentiation and Heterogeneity
Summer II 2014 Hui Yi Ina Hoeschele/ VBI / STAT Assessment of Penalized Regression for Genome-wide Association  Studies
Fall 2014 Kartik Subramanian John J Tyson/ BIOL Spatiotemporal Model of the Asymmetric Division Cycle of Caulobacter crescentus
  Zalman Vaksman Harold Garner/ VBI/ BIOL/ CSA Somatic Microsatellite Variability in Cancer and DNA Repair Disorders
Spring 2015 Ed Dougherty James Turner/ MATH Computation and Numerics in Neurostimulation
  Caitlin Rivers Stephen Eubank/ VBI and Bryan Lewis/ VBI co-chairs Modeling Emerging Infectious Diseases for Public Health Decision Support
Summer I 2015 Monica Viladomiu Pujol Josep Bassaganya-Riera/ VBI Transdisciplinary Strategies for the Characterization of Mucosal Immune Responses
Summer II 2015 Casandra W. Philipson Josep Bassaganya-Riera/ VBI Systems Analysis and Characterization of Mucosal Immunity
Fall 2015 Pinyi Lu Josep Bassaganya-Riera/ VBI Computational Modeling-based Discovery of Novel Classes of Anti-inflammatory Drugs that Target Lanthionine Synthetase C-like Protein 2
  Eric Nordberg Allan Dickerman/ VBI Creating Scientific Software, with Application to Phylogenetics and Oligonucleotide Probe Design
Spring 2016 Delasa Aghamirzaie Ruth Green/ PPWS and Eva Colla'kova/PPWS Isoform-specific Expression During Embryo Development in Arabidopsis and Soybean
  Andrew Brantley Hall Jake Tu/ BIOCHEM Identification and Characterization of Y Chromosome and M Locus Genes in Anopheles and Aedes Mosquitoes Using the Chromosome Quotient Method
  Xiaofang Jiang Jake Tu/BIOCHEM Genomics and Transcriptomics Analysis of the Asian Malaria Mosquito Anopheles stephensi
  Nicholas Kinney Josep Bassaganya-Riera/ VBI Effects of Chromosome-Nuclear Envelope Attachments on 3D Genome Organization
  Richard Rosario Rodrigues Mark Williams/HORT Investigating Structure and Function of Rhizosphere Associated Microbial Communities in Natural and Managed Plant Systems
  Daniel Edward Sullivan Rebecca Wattam/VBI Evaluation of Word and Paragraph Embeddings and Analogical Reasoning as an Alternative to Term Frequency-Inverse Document Frequency-based Classification in Support of Biocuration
  Robin Varghese Shi Zheng/VTCRI Novel Prognostic Markers and Therapeutic Targets for Glioblastoma
  Hang Zhang Jianhua Xing/BIOL and John J Tyson/BIOL Theoretical and Computational Studies on the Dynamics and Regulation of Cell Phenotypic Transitions
Summer II 2016 Thero Modise Jensen/BIOL Genomic Instability and Gene Dosage Obscures Clues to Virulence Mechanisms of F. tularensis species
  Vinaya Vijayan Liqing Zhang/CS Understanding and Improving Identification of Somatic Variants
Fall 2016 Yufeng (Francis) Fang Brett Tyler/PPWS; at Oregon State Univ now Nuclear Localization and Genome Editing in The Oomycete Phytophthora sojae
Spring 2017 Lin Kang Pawel Michalak/VBI Comparative Genomics Insights into Speciation and Evolution in Hawaiian Drosophila
  Andrew Leber Josep Bassaganya-Riera/ VBI Systems Immunology Approaches for Precision Medicine
  Haktan Suren Jason Holliday/FOR (FREC) Sequence Capture as a Tool to Understand the Genomic Basis for Adaptation in Angiosperm and Gymnosperm Trees
  Karthik Raja Velmurugan Harold Garner/VBI/ BIOL/ CSA and David Bevan/BIOCHEM Novel Microsatellite Detection, Microsatellite Based Biomarker Discovery In Lung Cancer And The Exome-Wide Effects Of A Dysfunctional DNA Repair Mechanism


Yes - I am presently accepting student applications
No - I am not presently accepting student applications
Maybe - I would consider accepting an application from the right student