CBB Graduates

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Ruijie Song – PhD, May 2019 (entered 2012)


Mengting Gu – PhD, May 2019 (entered 2013)

Dissertation: “A Transferable Framework for Large-Scale Genome Annotation with Applications in Disease Studies”

Michael Klein – PhD, May 2019 (entered 2012)


Alexandra Signoriello – May 2019 PhD (entered 2013)



Namita Gupta - PhD, May 2017 (entered 2011)

Dissertation: ”Computational Identification of B Cell Clones in High-Throughput Immunoglobulin Sequencing Data”

Christopher Fragoso - PhD, May 2017 (entered 2012)

Dissertation: ”Computational Methods for Plant Population Genomics”

Jason Vander Heiden - PhD, May 2017 (entered 2011)

Dissertation: ”Computation Methods for the Analysis of B Cell Repertoires and Application to Human Autoimmunity”

Mate Nagy - PhD, May 2017 (entered 2011)

Dissertation: ”Advanced Information Retrieval and Extraction in Research and Clinical Settings”

Qian Wang - PhD, December 2017 (entered 2012)

Dissertation: ”Statistical Methods of post-GWAS analysis incorporating multiple phenotypes, transcriptome variations, and biological networks”

Stefan Avey - PhD, December 2017 (entered 2012)

Dissertation: ”A Systems Approach to Understanding Influenza Infection and Vaccination Responses”


Xiu Huang - PhD, May 2016 (entered 2010)

Dissertation: ”Some statistical methods on analyzing gene expression and DNA sequencing data towards detection and interpretation of cancer biomarkers”

Yuwei Cheng - PhD, May 2016 (entered 2011)

Dissertation: ”Statistical and computational methods on GWAS and post-GWAS analysis to identify genetic basis of intracranial aneurysm”

Tingting Jiang - PhD, December 2016 (entered 2011)

Dissertation: ”Statistical and computational methods for integrative analysis in cancer genomics”

Leon (Zhixiang) Lin - PhD, May 2015 (entered 2010)

Dissertation: ”Some statistical methods for spatial-temporal brain gene expression data”

Cong (Jason) Li - PhD, May 2015 (entered 2010)

Dissertation: ”Some statistical methods for joint analysis of high dimensional genomics data”

Yao Fu - PhD, May 2015 (entered 2010)

Dissertation: ”Computational Methods for Estimating Functional Consequences of Genetic Variants and Application to Cancer Genomics”

Kelly Stanton - PhD, May 2015 (entered 2008)

Dissertation: ”Harmonic analysis of ChIP-seq”

Lucas Lochovsky - PhD, December 2015 (entered 2008)

Dissertation: ”LARVA—an Integrative Framework for Large-scale Analysis of Recurrent Variants in Noncoding Annotations—and Other Tools”

Jieming Chen - PhD, December 2015 (entered 2010)

Dissertation: ”Variant Interpretation in Personal Genomes using Repeat Protein Sequences, Networks and Allele-Specific Analyses”

Xiaowei Chen - PhD, May 2014 (entered 2008)

Dissertation: ”Statistical Modeling of Next Generation Sequence Data”

Jing Leng - PhD, May 2014 (entered 2008)

Dissertation: ”Studying the Evolution of Gene Regulation Using Next-Generation Sequencing: Computational Methods and Data Integration”

Mengjie Chen - PhD, May 2014 (entered 2009)

Dissertation: ”Some Statistical Methods for Integrative Analysis in Epigenetics and Cancer Genomics”

Matthew Holford - PhD, May 2014 (entered 2009)

Dissertation: ”Using Semantic Web Tools to Create an Integrated Framework for Biomedical Research”

Haisu Ma - PhD, May 2013 (entered 2008)

Dissertation: ”Statistical Modeling for Pathway-based Drug Target Discovery”

Mohamed Uduman - PhD, May 2013 (entered 2006)

Dissertation: ”Computational Methods for Detecting Antigen-Driven Selection in Ig Sequences”

Taiwo Togun - PhD, May 2013 (entered 2007)

Dissertation: ”A Multivariate Computational Framework to Identify Genomic Biomarkers in Cancer”

Christopher Bolen - PhD, May 2013 (entered 2008)

Dissertation: ”Computational analysis of blood transcriptional signatures in the study of HCV susceptibility, infection, and therapy response”

Michael Sneddon - PhD, May 2012 (entered 2006)

Dissertation: ”Overcoming Complexity in Systems Biology Modeling and Simulation”

Lukas Haebegger - PhD, May 2012 (entered 2007)

Dissertation: ”Computational Methodologies for Transcript Analysis in the Age of Next-Generation DNA Sequencing”

Raymond Auerbach - PhD, December 2012 (entered 2007)

Dissertation: ”Elucidating Transcriptional Regulation Using High-Throughput Sequencing, Data Integration, and Computational Methods”

Jamie Duke - PhD, December 2012 (entered 2006)

Dissertation: ”Computational Modeling of Genome-Wide Mutation by AID”

Vijay Garla - PhD, December 2012 (entered 2009)

Dissertation: ”Kernel Methods and Semantic Techniques for Clinical Text Classification”

Xinmeng Mu - PhD, December 2012 (entered 2007)

Dissertation: ”A Computational Genomics Study: Characterizing Genomic Variants in Non-coding Regions of the Human Genome”

Pavithra Shivakumar - PhD, May 2011 (entered 2005)

Dissertation: ”Predicting drug response and function using sub-structure analysis.”

Chong Shou - PhD, May 2011 (entered 2005)

Dissertation: ”Computational Analysis on Biological Networks:Measuring Evolutionary Rewiring & Predicting Regulatory Relationship”

Jia Kang - PhD, May 2011 (entered 2006)

Dissertation: ”Building Risk Prediction Model for Complex Genetic Disease Using High Dimensional Genetic Data.”

Karen Lostritto - PhD, December 2011 (entered 2006)

Dissertation: ”Piecewise Constant Estimation: Extensions of PartDSA and Applications to Cancer and Epidemiological Studies”

ThaiBinh Luong - PhD, December 2011 (entered 2005)

Dissertation: ”Improving Biomedical Information Retrieval Using Term Identification and Concurrent Image and Text Processing”

Song Huang - PhD, December 2010 (entered 2004)

Dissertation: ”High-dimensional Gene expression Classification and genome-wide association Studies of Complex Traits”

Hugo Lam - PhD, December 2010 (entered 2005)

Dissertation: ”Computational Analysis on Genomic Variation: Detecting and Characterizing Structural Variants in the Human Genome”

Kevin Keating - PhD, December 2010 (entered 2004)

Dissertation: ”Semi-automated Model Building for RNA Crystallography: A Directed Rotameric Approach to Building the RNA Backbone”

Jill Rubinstein - PhD, December 2010 (entered 2004)

Dissertation: ”Translational Epigenetics: Applications of High-Throughput Genomic Technologies for Melanoma Diagnostics and Treatment”

Laura Mustavich - PhD, December 2010 (entered 2005)

Dissertation: ”Integrating Genomic and Kinetic Data to Elucidate Mechanisms of Alcohol Dependence”

Sebastian Szpakowski - PhD, December 2010 (entered 2005)

Dissertation: ”Towards Intelligent Integration of Information from High-Throughput Studies of Human Genomes”

Sujun Hua - PhD, May 2009 (entered 2002)

Dissertation: ”Genomic Studies on Nuclear Receptor-Mediated Transcriptional Networks in Breast Cancer Cells”

Tara Gianoulis - PhD, May 2009 (entered 2003)

Dissertation: ”Mining Biological Complexity: Cross Integration of Large-Scale Metagenomics, Environmental, and Chemical Datasets”

David Ballard - PhD, May 2009 (entered 2004)

Dissertation: ”Integration of Genomic Data to Identify Genes and Pathways Associated with Disease”

Sara Nichols - PhD, December 2009 (entered 2003)

Dissertation: ”High-throughput Methods in Computer-aided Drug Design Pertaining to Flexibility, Selectivity and Lipophilicity”

Xiaowei Zhu - PhD, December 2008 (entered 2002)

Dissertation: ”Mapping Regulatory Networks Using Genomic and Proteomic Approaches”


Valentin Dinu - PhD, May 2007 (entered 2003)

Dissertation: ”Informatics Approaches to Translational Research: Management and Analysis of Clinical and High Density Genomic Data”

Yin Liu - PhD, December 2007 (entered 2002)

Dissertation: ”Statistical Modeling of Biological Interactions in Eukaryotes using Genomics and Proteomics Data”

Tom Royce - PhD, December 2007 (entered 2002)

Dissertation: ”Tiling Microarray Informatics”