CBB PhD Graduates

Jump to: 2022, 2021, 2020, 2019,
2018, 2017, 2016, 2015, 2014, 2013, 2012, 2011, 2010, 2009, 2008, 2007, 2006

* denotes December graduates

2022

Hussein Mohsen (2016 - 2022)

“Network Approaches to the Study of Genomic Variation in Cancer”


2021

David Chang (2016 - 2021)

“Natural language processing and graph representation learning for clinical data”

Scott Gigante (2017 - 2021)

“Diffusion-based approaches to visualization and exploration of high-dimensional
data”

Guannan Gong (2018 - 2021*)

“Next Generation Phenotyping in Clinical Trial based on Real-World Data”


2020

Dingjue (Frank) Ji (2015 - 2020)

“Integrative Analysis of Neuroimaging, Cognitive Functions and Genetics Data”

Xiaotong Li (2014 - 2020*)

“Clinical and Translational Cancer Research by Genomics and Transcriptomics Data
Analysis”

Kevin Lopez (2015 - 2020*)

“Machine Learning with Multimodal Data”

Jay Stanley (2016 - 2020)

“Geometric Data Organization: Algorithms and Applications”

Jun Zhao (2014 - 2020)

“Computational Methods for Single Cell RNA Sequencing Analysis”

Quan (Julian) Zhou (2015 - 2020)

“B Cell Clonal Lineage and Somatic Hypermutation Profiling Analysis”


2019

Mengting Gu (2013 - 2019)

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

Michael Klein (2012 - 2019)

“Two Novel Algorithms for Extracting Patient Specific Information from Tumor Biopsies. 1) GRAPE
(A Pathway Template Method to Characterize Tissue-Specific Functionality from Gene Expression
Profiles. 2) CRSO (A Tool for Identifying Driver Gene Combinations in Individual Cancer
Patients”

Donghoon Lee (2014 - 2019*)

“Leveraging Functional Genomic Data: Modeling Transcriptional Dynamics and Interpreting Disease
Genomes”

Ryan Powles (2014 - 2019)

“Picking Targets: Exploring Genomic Biomarkers of Breast Cancer Across Trials, Treatments, and
Tissues”

Alexandra Signoriello (2013 - 2019)

“Computational modeling of immune cells during tumor development using the deformable particle
model”

Ruijie Song (2012 - 2019)

“Volume- and Cell-Cycle-Aware Stochastic Modeling of Gene Networks”


2018

Daniel Gadala-Maria (2009 - 2018)

“Computational discovery of immunoglobulin genotypes from high-throughput B-cell receptor
sequencing data”

Jennifer Gaines (2013 - 2018)

“Computational Studies of Protein Structure”

Cong Liang (2012 - 2018)

“Mathematical modeling and data analysis in cell type evolutionary studies”


2017

Stefan Avey (2012 - 2017*)

“A Systems Approach to Understanding Influenza Infection and Vaccination Responses”

Christopher Fragoso (2012 - 2017)

“Computational Methods for Plant Population Genomics”

Namita Gupta (2011 - 2017)

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

Shantao Li (2012 - 2017*)

“Mining Large-scale Sequencing Reads to Learn Mutational Processes”

Mate Nagy (2011 - 2017)

“Advanced Information Retrieval and Extraction in Research and Clinical Settings”

Jason Vander Heiden (2011 - 2017)

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

Qian Wang (2012 - 2017*)

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


2016

Yuwei Cheng (2011 - 2016)

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

Xiu Huang (2010 - 2016)

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

Tingting Jiang (2011 - 2016*)

“Statistical and computational methods for integrative analysis in cancer genomics”


2015

Jieming Chen (2010 - 2015*)

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

Yao Fu (2010 - 2015)

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

Cong (Jason) Li (2010 - 2015)

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

Leon (Zhixiang) Lin (2010 - 2015)

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

Lucas Lochovsky (2008 - 2015*)

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

Kelly Stanton (2008 - 2015)

“Harmonic analysis of ChIP-seq”


2014

Mengjie Chen (2009 - 2014)

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

Xiaowei Chen (2008 - 2014)

“Statistical Modeling of Next Generation Sequence Data”

Matthew Holford (2009 - 2014)

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

Jing Leng (2008 - 2014)

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


2013

Christopher Bolen (2008 - 2013)

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

Ken Hui (2011 - 2013) [MD-PhD]

“Beyond GWAS: Translating the Genetics of Crohn’s Disease”

Haisu Ma (2008 - 2013)

“Statistical Modeling for Pathway-based Drug Target Discovery”

Taiwo Togun (2007 - 2013)

“A Multivariate Computational Framework to Identify Genomic Biomarkers in Cancer”

Mohamed Uduman (2006 - 2013)

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


2012

Raymond Auerbach (2007 - 2012*)

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

Jamie Duke (2006 - 2012*)

“Computational Modeling of Genome-Wide Mutation by AID”

Vijay Garla (2009 - 2012*)

“Kernel Methods and Semantic Techniques for Clinical Text Classification”

Lukas Haebegger (2007 - 2012)

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

Xinmeng Mu (2007 - 2012*)

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

Michael Sneddon (2006 - 2012)

“Overcoming Complexity in Systems Biology Modeling and Simulation”


2011

Jia Kang (2006 - 2011)

“Building Risk Prediction Model for Complex Genetic Disease Using High Dimensional Genetic
Data”

Karen Lostritto (2006 - 2011*)

“Piecewise Constant Estimation (Extensions of PartDSA and Applications to Cancer and
Epidemiological Studies”

ThaiBinh Luong (2005 - 2011*)

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

Pavithra Shivakumar (2005 - 2011)

“Predicting drug response and function using sub-structure analysis”

Chong Shou (2005 - 2011)

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


2010

Song Huang (2004 - 2010*)

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

Kevin Keating (2004 - 2010*)

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

Hugo Lam (2005 - 2010*)

“Computational Analysis on Genomic Variation (Detecting and Characterizing Structural Variants
in the Human Genome”

Laura Mustavich (2005 - 2010*)

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

Jill Rubinstein (2004 - 2010*)

“Translational Epigenetics (Applications of High-Throughput Genomic Technologies for Melanoma
Diagnostics and Treatment”

Sebastian Szpakowski (2005 - 2010*)

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


2009

David Ballard (2004 - 2009)

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

Tara Gianoulis (2003 - 2009)

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

Sujun Hua (2002 - 2009)

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

Sara Nichols (2003 - 2009*)

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


2008

Xiaowei Zhu (2002 - 2008*)

“Mapping Regulatory Networks Using Genomic and Proteomic Approaches”


2007

Valentin Dinu (2003 - 2007)

“Informatics Approaches to Translational Research (Management and Analysis of Clinical and High
Density Genomic Data”

Yin Liu (2002 - 2007*)

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

Tom Royce (2002 - 2007*)

“Tiling Microarray Informatics”


2006

Jill Rubinstein (2004 - 2006*) [MD-PhD]

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