This project analyzes the long non-coding RNA UCA1 in non-small cell lung cancer (NSCLC) using TCGA RNA-seq data. It includes data preprocessing, normalization, differential expression analysis, and visualization. Key outputs are UCA1 expression patterns, PCA plots, heatmap
End-to-end oncology RWE pipeline: synthetic EHR data (Synthea) harmonized to the OMOP CDM, an NSCLC cohort built with dbt and PostgreSQL, and survival analysis in R, benchmarked against SEER registry data. Includes data-quality checks and a documented case where the synthetic data failed validation. Methods demo, not real patient data.
Plasma cell-free DNA hydroxymethylomes discriminate disease state in EGFR-mutant non-small cell lung cancer.
A collection of code related to my MS thesis in Bioinformatics at SDSU
Strict held-out CP/CPR/CPRD/RD survival modeling reference implementation for the ACRIN 6668/RTOG 0235 secondary analysis.
Gene expression analysis to identify biomarkers for early lung cancer detection (SCLC & NSCLC)
Single-cell RNA-seq analysis of CD8 T cell functional states in lung cancer - two-dataset portfolio examining tumor-associated exhaustion in LUAD and its association with anti-PD-1 immunotherapy response in NSCLC.
NSCLC Radiomics: Survival Time prediction using CT-extracted features and clinical data.
PubChem API scraper for EGFR inhibitors including SMILES, MW, Lipinski Ro5 compliance across 3 TKI generations
Patient-aware benchmark of frozen scGPT versus Scanpy/PCA on 29,614 NSCLC single cells with held-out evaluation and sample-level analysis
Somatic mutations in TCGA lung adenocarcinoma — maftools workflow
Erhobene Datenelemente zum Lungenkrebspatientenpfad im Forschungsprojekt MiHUB
Single-cell and bulk RNA-seq analysis of T cell functional states associated with immunotherapy response in NSCLC.
Analysis code for NSCLC radiosensitivity radiogenomics and CT radiomic surrogate modeling.
Bayesian NMA of advanced NSCLC treatments across 10 studies using gemtc and JAGS — fixed/random effects models, DIC model selection, SUCRA rankings, full league table, node-splitting consistency check, and heterogeneity estimation for NICE STA submissions.
PERSIST (PERsister-State In-Silico Targeting): residual-state modelling of single-cell drug response for combination therapy prediction in EGFR-mutant NSCLC and TNBC
MSc Data Analytics Thesis: Unsupervised Feature Extraction for Assessing Recurrence of Lung Cancer
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