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* denotes December graduates
2023
“Computational and Evolutionary Approaches for Translational Cancer Research”
“Multi-scale gene regulation analysis with ChIP-seq and beyond”
“Learning latent representations for biological molecules & their properties”
2022
“Identifying immunological biomarkers in massive public data”
“Leverage eQTLs to Understand Genetic Etiology of Human Diseases”
“Network Approaches to the Study of Genomic Variation in Cancer”
“A Peak Through the Noise: Capturing Biological Heterogeneity in Aging with Our Machine Learning Toolkit”
“Identification of Genetic Implications in Psychiatric Disorders”
“Making the Most of Polygenic Risk Scores (PRS): Risk Decompositions, Cross-Population Predictions, and Clinical Applications”
“Leveraging Omics Data for Better Treatment: Computational Methods for Biomarker Identification, Drug Repositioning, and Polypharmacy Risk Assessment”
“Dissecting the Impact of Clonal Hematopoiesis on age-related disease”
“Statistical Methods for Genetic Prediction of Complex Traits in Single and Multiple Populations”
2021
“Natural language processing and graph representation learning for clinical data”
“Diffusion-based approaches to visualization and exploration of high-dimensional data”
“Next Generation Phenotyping in Clinical Trial based on Real-World Data”
2020
“Integrative Analysis of Neuroimaging, Cognitive Functions and Genetics Data”
“Clinical and Translational Cancer Research by Genomics and Transcriptomics Data Analysis”
“Machine Learning with Multimodal Data”
“Geometric Data Organization: Algorithms and Applications”
“Computational Methods for Single Cell RNA Sequencing Analysis”
“B Cell Clonal Lineage and Somatic Hypermutation Profiling Analysis”
2019
“A Transferable Framework for Large-Scale Genome Annotation with Applications in Disease Studies”
“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”
“Leveraging Functional Genomic Data: Modeling Transcriptional Dynamics and Interpreting Disease Genomes”
“Picking Targets: Exploring Genomic Biomarkers of Breast Cancer Across Trials, Treatments, and Tissues”
“Computational modeling of immune cells during tumor development using the deformable particle model”
“Volume- and Cell-Cycle-Aware Stochastic Modeling of Gene Networks”
2018
“Computational discovery of immunoglobulin genotypes from high-throughput B-cell receptor sequencing data”
“Computational Studies of Protein Structure”
“Mathematical modeling and data analysis in cell type evolutionary studies”
2017
“A Systems Approach to Understanding Influenza Infection and Vaccination Responses”
“Computational Methods for Plant Population Genomics”
“Computational Identification of B Cell Clones in High-Throughput Immunoglobulin Sequencing Data”
“Mining Large-scale Sequencing Reads to Learn Mutational Processes”
“Advanced Information Retrieval and Extraction in Research and Clinical Settings”
“Computation Methods for the Analysis of B Cell Repertoires and Application to Human Autoimmunity”
“Statistical Methods of post-GWAS analysis incorporating multiple phenotypes, transcriptome variations, and biological networks”
2016
“Statistical and computational methods on GWAS and post-GWAS analysis to identify genetic basis of intracranial aneurysm”
“Some statistical methods on analyzing gene expression and DNA sequencing data towards detection and interpretation of cancer biomarkers”
“Statistical and computational methods for integrative analysis in cancer genomics”
2015
“Variant Interpretation in Personal Genomes using Repeat Protein Sequences, Networks and Allele-Specific Analyses”
“Computational Methods for Estimating Functional Consequences of Genetic Variants and Application to Cancer Genomics”
“Some statistical methods for joint analysis of high dimensional genomics data”
“Some statistical methods for spatial-temporal brain gene expression data”
“LARVA—an Integrative Framework for Large-scale Analysis of Recurrent Variants in Noncoding Annotations—and Other Tools”
“Harmonic analysis of ChIP-seq”
2014
“Some Statistical Methods for Integrative Analysis in Epigenetics and Cancer Genomics”
“Statistical Modeling of Next Generation Sequence Data”
“Using Semantic Web Tools to Create an Integrated Framework for Biomedical Research”
“Studying the Evolution of Gene Regulation Using Next-Generation Sequencing (Computational Methods and Data Integration”
2013
“Computational analysis of blood transcriptional signatures in the study of HCV susceptibility, infection, and therapy response”
“Beyond GWAS: Translating the Genetics of Crohn’s Disease”
“Statistical Modeling for Pathway-based Drug Target Discovery”
“A Multivariate Computational Framework to Identify Genomic Biomarkers in Cancer”
“Computational Methods for Detecting Antigen-Driven Selection in Ig Sequences”
2012
“Elucidating Transcriptional Regulation Using High-Throughput Sequencing, Data Integration, and Computational Methods”
“Computational Modeling of Genome-Wide Mutation by AID”
“Kernel Methods and Semantic Techniques for Clinical Text Classification”
“Computational Methodologies for Transcript Analysis in the Age of Next-Generation DNA Sequencing”
“A Computational Genomics Study (Characterizing Genomic Variants in Non-coding Regions of the Human Genome”
“Overcoming Complexity in Systems Biology Modeling and Simulation”
2011
“Building Risk Prediction Model for Complex Genetic Disease Using High Dimensional Genetic Data”
“Piecewise Constant Estimation (Extensions of PartDSA and Applications to Cancer and Epidemiological Studies”
“Improving Biomedical Information Retrieval Using Term Identification and Concurrent Image and Text Processing”
“Predicting drug response and function using sub-structure analysis”
“Computational Analysis on Biological Networks:Measuring Evolutionary Rewiring & Predicting Regulatory Relationship”
2010
“High-dimensional Gene expression Classification and genome-wide association Studies of Complex Traits”
“Semi-automated Model Building for RNA Crystallography (A Directed Rotameric Approach to Building the RNA Backbone”
“Computational Analysis on Genomic Variation (Detecting and Characterizing Structural Variants in the Human Genome”
“Integrating Genomic and Kinetic Data to Elucidate Mechanisms of Alcohol Dependence”
“Translational Epigenetics (Applications of High-Throughput Genomic Technologies for Melanoma Diagnostics and Treatment”
“Towards Intelligent Integration of Information from High-Throughput Studies of Human Genomes”
2009
“Integration of Genomic Data to Identify Genes and Pathways Associated with Disease”
“Mining Biological Complexity (Cross Integration of Large-Scale Metagenomics, Environmental, and Chemical Datasets”
“Genomic Studies on Nuclear Receptor-Mediated Transcriptional Networks in Breast Cancer Cells”
“High-throughput Methods in Computer-aided Drug Design Pertaining to Flexibility, Selectivity and Lipophilicity”
2008
“Mapping Regulatory Networks Using Genomic and Proteomic Approaches”
2007
“Informatics Approaches to Translational Research (Management and Analysis of Clinical and High Density Genomic Data”
“Statistical Modeling of Biological Interactions in Eukaryotes using Genomics and Proteomics Data”
“Tiling Microarray Informatics”
2006
“Translational Epigenetics: Applications of High-Throughput Genomic Technologies for Melanoma Diagnostics and Treatment”