Data Science Insitute
Center for Computational Molecular Biology
Honors Thesis Archive
2025 Honors Theses
- Lisa Duan, CSF Metabolomic Signatures Predict Shunt Surgery Outcomes for Patients with Normal Pressure Hydrocephalus (NPH)
- Kanayo Duru, Machine Learning in Multi-Parametric Modeling of Treatment Outcomes for Colorectal Cancer
- Brian Ji, Development of a Closed-Loop Deep Brain Stimulation Approach via Comprehensive Spectral Signatures
- Dravid Navale, Characterization of Cellular Landscapes of Right Atrium Remodeling in Pulmonary Hypertension
- Michael Sun, Variational Graph Auto-Encoder Based Learning for Inferring Recurrence-Driven Interactions in Glioblastoma
- Helen Xie, Decoding the Tumor Immune Microenvironment in Neuroblastoma: An Integrative Transcriptomic Analysis
2024 Honors Theses
- Madeleine Pittigher, Identification of Genomic Markers for use in Haploid Selection Mapping to Define Loci Conferring Reproductive Success at Varying Temperatures in Arabidopsis thaliana
- Kikuyo Shaw, Developing an Agent-Based Model for Infectious Disease Spread in an Indoor Setting
- Jasmine Shum, Exploring Underlying Mechanisms of Co-Transcriptional Regulation Through RNA- and DNA-Protein Interactions
- Smriti Vaidyanathan, Computational Analysis of the Impact of GA-binding Transcription Factor CLAMP on Splicing Condensate Dynamics in Drosophila
- Neal Yin, Adaptive Significance of Amphicarpy as a Bet-hedging Strategy in American Hog-peanut
- Kaleb Zuckerman, COATswga: A fast primer design toolkit for optimizing genome coverage and specificity in selective whole genome amplification
2023 Honors Theses
- Julie Karam, Using Machine Learning to Classify Subtypes and Predict Clinical Features of Breast Cancer Using Genomic Data
- Alexander Le, Development and Comparative Analysis of Counterfactual Explanations Using Autoencoder-Based Approaches for Single-Cell Data
- David Inho Lee, Application of LSTM Autoencoders on HIV-1 RNA Sequence to Create Latent Space Representations forViral Subtyping
- Michelle Mai, Exploring the Association of Vitamin D Supplementation on Psoriasis Disease Activity
- Yuan Pu, Deep Learning Models with Attention Mechanism for Predicting Gene Expression from Epigenetic Data in Glioblastoma Stem Cells
- Priyanka Solanky, Scaling Biological Models of Striatal Dopamine using Deep Neural Networks
- Ivo Su, Detecting EEG Bio-Markers in Obsessive Compulsive Disorder Patients through the Multi Source Interference Task: Preliminary Analysis
- Merih Deniz Toruner, Predicting Glioblastoma Multiforme (GBM) Gene Expression from Epigenetic Markers and Super Enhancers
2022 Honors Theses
- Jonathan Arditi, Entropy Analysis of m6A Transcriptomic Profile in Entacapone-Treated Glioblastoma Stem Cells
- Ji Yun (Estelle) Han, Explaining Patterns of Widespread Loss of Heterozygosity in Cancer
- Samuel Maffa, Quantitative Analysis of Mathematical Models of Pattern Formation
- Ijeoma Meremikwu, Temporal Haplotype Changes of Vaccine Candidates for Malaria
- Justin Sanders, Deep Generative and Predictive Modeling of Single Cell RNA Seq Time Series Data
- Selena Zhang, Heritability estimates are stable across different tranches of the UK Biobank
2021 Honors Theses
- Daniel Ben-Isvy, Multilocus Informativeness: A Novel Method for Fine Mapping Disease-Causing Variants in Genome-Wide Association Studies
- Kelly Clark, A HiC map of the senescent genome at kilobase resolution reveals novel associations between chromatin changes and gene expression
- Marlene Goetz, Alternative Splicing Analysis of Tripeptidyl Peptidase 1 Mutations in CLN2 Batten Disease Models
- Ishaani Khatri, Evaluation of quantitative magnetic resonance imaging to predict intracranial hypertension in neonates by machine learning
- Xavier Loinaz, Exploring Graph-Based Neural Networks for Modeling Long-Range Epigenetic Gene Regulation
- Isaac Nathoo, XvsY: pipeline to identify shared and distinct genomic signatures from multiple expression and protein-DNA interaction data sets over time
- Aris Paschalidis, coiaf: Complexity Of Infection Estimation with Allele Frequencies
- Toni Sagayaraj, Image-Like Graph Representations for Improved Molecular Property Prediction
2020 Honors Theses
- Hersh Gupta, Exploration of possible molecular mechanisms of action of clinical effects of opioids in lung adenocarcinoma and triple negative breast cancer through RNA sequencing
- Samuel Hinthorn, Finding Pearls in the Literature Ocean: CIS-Lexicon Ontology Search Engine (CLOSE) for Gene Regulatory Networks of the Regulatory Gene
- Jaison Jain, A Bioinformatic Exploration of Unique Biological Features in Sciara Coprophila
- Amy Wang, Comparative Analysis of Fusion Detection Algorithms
- Elizabeth Woo, The Effects of Genetic Variants on Protein Structure and their Associations with Preeclampsia
- Elliot Youth, Post-Infarction Dysregulation of Cardiac Redox Balance:
Novel Avenues for Cardiovascular Disease Treatment
2019 Honors Theses
- Carleen Jeffers, Automating Pathology with Deep Learning
- Lena Joesch-Cohen, Exome Sequence Variation in X-Linked Intellectual Disability Genes in the Control Population
- Jay Khurana, Pan-Cancer Analysis of Collagen Variants Shows Associations with Patient Outcomes
- Sarah Kim, Developing New Strategies to Analyze Exercise-Induced Quiescence in C. Elegans
- Shosana Rosenzweig, Valproic Acid Alters Transcriptional and Signaling Pathways in First Trimester Stem Cell Derived Human Neurons
2018 Honors Theses
- Arun Das, Approaches in Genomic Privacy