Alumni
The UC San Diego Libraries provide access to official copies of all UC San Diego dissertations. Search the UC San Diego Libraries Catalog for UC San Diego Bioinformatics dissertations.
Jennifer Nguyen
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Using multi-omic QTL analysis in fetal-like pancreatic progenitor cells to characterize diabetes-associated regulatory variants during early development
Abstract: Link
Advisor(s): Kelly Frazer , Lucila Ohno-Machado
Adam Officer
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Multimodal Data Integration Applied to Cancer Evolution and Signaling
Abstract: Link
Advisor(s): Pablo Tamayo , J. Silvio Gutkind
Anh Pham
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Strengthening Health Research Workflow for Research-Oriented Sharing, Predictive Modeling, and Cross-Institutional Collaboration
Abstract: Link
Advisor(s): Tsung-Ting Kuo , Lucila Ohno-Machado
Alexander Wenzel
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Expanding the applicability of gene set enrichment analysis with data-driven gene set refinement and adaptation for sparse data
Abstract: Link
Advisor(s): Jill Mesirov
Fatemeh Amrollahi
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Generalizeable Risk Predictive Deep Learning Models
Abstract: Link
Advisor(s): Shamim Nemati , Gabriel Wardi
Email: ochapman@ucsd.edu
Owen Chapman
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Inter- and intratumoral heterogeneity of circular extrachromosomal DNA in medulloblastoma and other pediatric cancers
Abstract: Link
Advisor(s): Jill Mesirov , Bing Ren
Jihoon Kim
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Data Standardization, Federated Learning, and Informed Consent Algorithms and Tools to Honor Patient Privacy and Preferences in Clinical Research
Abstract: Link
Advisor(s): Lucila Ohno-Machado , Tsung-Ting Kuo
Email: f5yuan@ucsd.edu
Nancy Yuan
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Using Machine Learning to Elucidate Disease Heterogeneity and Improve Prognostication in Patients with COPD
Abstract: Link
Advisor(s): Terry Gaasterland , Tsung-Ting Kuo
Andrea Castro
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Determinants for Effective Neoantigen Based Anti-Tumor Immune Response
Abstract: Link
Advisor(s): Hannah Carter , Ludmil Alexandrov
Nathaniel Delos Santos
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Score-based Transcription Factor Motif Enrichment Strategies for Analysis of Transcriptional Regulation of Immune Response
Abstract: Link
Advisor(s): Christopher Benner , Melissa Gymrek
Kevin Blansit
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Advancing Cardiovascular MRI Acquisition Through Deep Convolutional Neural Network-Based Localization
Abstract: Link
Advisor(s): Albert Hsiao
Argus Athanas-Crannell
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Leveraging Longitudinal Data for Predictive Modeling in Clinical and Mental Health Settings
Abstract: Link
Advisor(s): Nicholas Schork , Lucila Ohno-Machado
Michelle Dow
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Integrative Multi-omics Analysis to Understand Cancer and Anticancer Therapy
Abstract: Link
Advisor(s): Hannah Carter
Yingxiang Huang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Preservation of Patient Level Privacy : Federated Classification and Calibration Models
Abstract: Link
Advisor(s): Lucila Ohno-Machado
Margaret Donovan
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Understanding the cellular heterogeneity in fetal-like and adult tissues to study cell-type-specific functional genetic variation
Abstract: Link
Advisor(s): Kelly Frazer
Jing Zhang
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Supporting Diabetes Patient Decisional Needs Through Online Health Communities
Abstract: Link
Advisor(s): Vineet Bafna , Michael Hogarth
Stephanie Feudjio Feupe
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Deep Characterization of the Contribution of Short Tandem Repeats Across Tissues
Abstract: Link
Advisor(s): Melissa Gymrek , Vineet Bafna
Kemal Eren
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Understanding the evolution of HIV-1 Env through computational analysis and visualization of long-read amplicon sequences
Abstract: Link
Advisor(s): Joel Wertheim , Siavash Mirarab
Email: w2wei@ucsd.edu
Wei Wei
Degree Conferred: Ph.D. Bioinformatics and Systems Biology with a Specialization in Biomedical InformaticsThesis: Information Retrieval in Biomedical Research: From Articles to Datasets
Abstract: Link
Advisor(s): Lucila Ohno-Machado , Xiaoqian Jiang
Email: edlevy@ucsd.edu
Eric Levy
Degree Conferred: Ph.D. Bioinformatics and Systems BiologyThesis: Molecular immune signatures of T-cell infiltration in cancer
Abstract: Link
Advisor(s): Lucila Ohno-Machado , Olivier Harismendy
Next Position: Personalis, Senior Bioinformatics Scientist