Differential Expression Analysis (DESeq2/limma), Pathway Enrichment (GSEA/KEGG), and custom high-res visualizations (Volcano plots, Heatmaps).
Unsupervised clustering, UMAP/t-SNE dimensionality reduction, and cell type annotation using Scanpy and Seurat.
Scalable cloud-native workflow generation using Nextflow and WDL/Cromwell for AWS and Google Cloud environments.
Parsing VCF files, prioritizing pathogenic somatic/germline variants via Ensembl VEP, and pharmacogenomics reporting.
Detecting resistance genes in bacterial genomes using CARD/ResFinder databases and generating epidemiological reports.
Deploying Large Language Models (LLMs) and RAG architecture for automated PubMed literature mining and systematic reviews.
Structural bioinformatics and Cheminformatics. Visualizing AlphaFold models and molecular drug-binding pockets.
Analyzing 16S rRNA taxonomic abundances, calculating Alpha/Beta diversity, and modeling dysbiosis via 3D PCoA.
Processing framework for 10x Genomics Visium spatial tissue coordinates. Computes spatial weight matrices and Moran's I spatial autocorrelation per gene.
Parses predicted aligned error (PAE) matrices from EMBL-EBI AlphaFold DB API (UniProt P04637). Evaluates structured core domains vs intrinsically disordered regions.
Single-cell mRNA splicing dynamics solver based on scVelo pancreas benchmark. Fits linear degradation constant gamma and computes velocity vectors.
Processed bacterial genomes to detect AMR genes. Delivered comprehensive heatmaps mapping resistance mechanisms to drug classes.
Leveraged LLM/RAG architecture connected to the PubMed API to autonomously extract data and summarize cohorts for a clinical meta-analysis.
Processed raw RNA-seq counts to identify DEGs. Delivered publication-ready interactive Volcano plots and clustered heatmaps.
Performed clustering on 10X Genomics scRNA-seq data to map immune cell trajectories and discover novel rare cell biomarkers.
Visualized AlphaFold predicted structures to evaluate the impact of clinical missense mutations on drug binding affinity.
Filtered human Whole Exome Sequencing (WES) VCF files using Ensembl VEP to prioritize pathogenic variants for oncology targeted therapy.
Integrated IGV technology to visually verify BAM/VCF somatic mutations across hg38 human reference assemblies.
Automated microarray data retrieval and generated GSEA ridge plots mapping significantly enriched KEGG pathways in tumor samples.
Designed a scalable Cromwell WDL pipeline for GATK Somatic Variant Calling, ready for deployment on AWS Batch / Google Cloud Life Sciences.
Calculated Alpha/Beta diversity from 16S microbiome ASV tables, delivering interactive 3D PCoA projections and taxonomy bar charts.
Preserves spatial cellular architecture in tissue sections without dissociation. Computes Delaunay spatial contact graphs, Moran's I spatial autocorrelation for spatially variable genes (SVGs), and maps cell-cell ligand-receptor communication networks within tumor microenvironments.
Extends 3D protein structure prediction to multi-chain complex systems (Protein-DNA, Protein-RNA, Protein-Ligand). Parses 2D Predicted Aligned Error (PAE) matrices to decouple inter-chain domain confidence from intra-chain errors and computes solvent-accessible surface area (SASA) burial.
Calculates time-resolved single-cell transcriptomic velocity vectors from ratios of unspliced pre-mRNA to spliced mature mRNA. Fits kinetic differential equations and applies CellRank absorbing Markov chains to predict cell fate decisions in stem cell differentiation and tumor evolution.