Bioinformatics Portfolio
Original Work
Evaluation of mouse laryngeal inflammation upon low and high dose cigarette smoke exposures via NanoString analysis
This study, conducted as part of my professional work at Stanford University, examined the effects of low- and high-dose cigarette smoke exposures on murine larynges. The research employed bioinformatics methodologies, including differential gene expression analysis, functional enrichment, and network analysis, utilizing R programming and related tools. The NanoString nCounter inflammation panel was used to comprehensively evaluate inflammation and immune responses in the context of these exposures.
PublicationThe heatmap icon by Chenxin Li is licensed under CC-BY 4.0 Unported.
Academic Projects
The projects showcased here are computational analyses that may or may not include replicates of previously published work conducted by other researchers. While there may be minor differences due to dataset handling or tool versions, the core methodology and findings align closely with referenced studies when applicable. These projects utilize microarray and bulk RNA-seq datasets to explore differential gene expression patterns, and pathway enrichments. References to the original articles forming the basis of these projects can be found in the respective GitHub repository README files.
Calpain10 (CAPN10): Unraveling its Significance in Polycystic Ovary Syndrome (PCOS) and Insulin Resistance
This project investigated the role of the CAPN10 gene, a key contributor to insulin resistance and Type 2 Diabetes, in the context of PCOS. Conducted as part of the UTHealth BMI 5330: Introduction to Bioinformatics course, the project integrated bioinformatics tools and databases for genome annotation, variation analysis, gene expression profiling using R programming, and functional enrichment to explore the gene's functional impact and its association with metabolic disorders.
The DNA double helix icon by James-Lloyd is licensed under CC0.
Long-term IQOS Exposure Modulates Apoptosis and Cytokine Signaling Pathways: Genomic Insights from Mouse Lungs
This project examined the genomic effects of IQOS exposure on mouse lungs by utilizing a public microarray dataset obtained from the NCBI Gene Expression Omnibus (GEO). This work was conducted as part of the BMI 6313: Scientific Writing in Healthcare course at UTHealth. The project specifically included exploratory data analysis (EDA), differential expression analysis, as well as functional enrichment and network analysis.
Microarray-based Transcriptomic Analysis and Signature Extraction in Mice Lungs following 4 and 6 months of Cigarette Smoke (CS) Exposure
This project, part of the BMI 5333: Systems Medicine: Principles and Practice course at UTHealth, aimed to explore the transcriptomic changes in gene expression in mouse lung tissue caused by prolonged exposure to CS. The study utilized differential expression analysis, pathway enrichment analysis, network analysis, and hub gene identification, leveraging a publicly available microarray dataset from NCBI GEO.
Differential Expression Analysis: Responders vs. Non-Responders to Letrozole Treatment
This project focused on analyzing gene expression differences between two phenotypes—responders and non-responders to Letrozole treatment in breast cancer tumors, using a publicly available microarray dataset. The project was conducted as part of the BMI 5331: Foundations of Pharmacogenomics course at UTHealth.
The DNA microarray icon by Guillaume Paumier is licensed under CC-BY SA 3.0.
Transcriptomic Analysis of Respiratory Epithelial Cellular Responses Following Cigarette Smoke (CS) Exposures
In the context of the UTHealth BMI 5332: Statistical Analysis of Genomic Data, this class project focused on examining the transcriptomic profiles of air-liquid interface (ALI) cultures exposed to CS from various human and mouse airway cell types, utilizing bulk RNA sequencing datasets sourced from online databases.
Identification of Immunomodulatory Hub Genes and Cell Signatures in Mouse Lungs Exposed to Cigarette Smoke
As part of the Foundations of Biomedical Information Sciences II course at UTHealth, this project aimed to examine the temporal variations in immunomodulatory gene expression within mouse lungs that were subjected to varying durations of cigarette smoke exposure. The investigation utilized a publicly accessible bulk RNA sequencing dataset sourced from the NCBI GEO.
The genome sequencer icon by DBCLS is licensed under CC-BY 4.0 Unported.