Bioinformatics Portfolio

Selected computational projects

Independent analyses spanning single-cell multi-omics, cancer genomics, gene regulatory network inference, and CRISPR guide design , computation as a second instrument for asking biological questions. Each repository is open on GitHub.

Normalized validation confusion matrix across 15 leukocyte classes from the AML cytomorphology classifier

Hematopathology · Computational Cytology · Leukemic Cell Morphology

Morphological Leukocyte Phenotyping in Acute Myeloid Leukemia

Automated identification and phenotypic classification of 15 white blood cell lineages and blast stages in peripheral blood smears from AML patients.

Applied attention-based computational architectures to evaluate fine-grained cytological markers , chromatin condensation patterns, cytoplasmic granulation, and nuclear contour irregularities , achieving 94.7% accuracy aligned with standard cytopathological criteria.

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Multi-omic integration heatmap linking STAT1 ChIP-seq peaks to bulk and single-cell interferon-response gene expression

Transcriptomics · Epigenomics · Immune Gene Regulation

Multi-Omic Atlas of the STAT1 Interferon Response

Integrative multi-omic dissection of the transcriptional and epigenetic landscape mediated by STAT1 during interferon stimulation in human monocytes.

Built a reproducible workflow linking chromatin accessibility to downstream gene expression, mapping 800 STAT1 binding peaks across 710 genes and identifying 42 interferon-stimulated response genes with concordant epigenomic and transcriptomic evidence.

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Cell-type-specific gene regulatory network reconstructed from paired PBMC scRNA-seq and scATAC-seq data

Single-Cell Multi-Omics · Chromatin Dynamics · Immunogenomics

Gene Regulatory Network Inference in Immune Lineages

Decoding transcriptional regulatory hierarchies directly from paired single-cell RNA and ATAC sequencing (10x Genomics PBMC multiome).

Linked distal open chromatin peaks to cis-regulatory target promoters to reconstruct cell-type-specific regulatory networks, prioritizing key myeloid transcription factors such as AP-1 subunits (FOS, FOSB) and STAT1.

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Single-cell copy number heatmap showing clonal chromosomal amplifications in the HCC1954 breast cancer model

Cancer Genomics · Aneuploidy Profiling · Clonal Evolution

Single-Cell Genomic Copy Number Profiling in Breast Carcinoma

Inferring chromosomal copy number alterations (CNAs) and structural aneuploidies at single-cell resolution from genomic read distributions.

Implemented baseline diploid estimation, median normalization, and depth-based segmentation on the HCC1954 breast cancer model, successfully recovering hallmark clonal amplifications on chromosomes 1q and 3.

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Off-target risk landscape for candidate sgRNAs designed against the human HPRT1 locus

Genome Editing · Functional Genomics · Sequence Heuristics

Functional sgRNA Optimization for Targeted Gene Disruption

Quantitative target design and scoring of single-guide RNAs (sgRNAs) targeting the human HPRT1 gene locus.

Designed a multi-tier biological filtering scheme based on canonical PAM enumeration, GC-content bounds (40–60%), homopolymer exclusion, and seed-region efficiency scoring, validated against empirical knockout datasets from Doench et al. (2016).

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Differential expression heatmap of proliferation and estrogen-signaling transcripts across the GSE25066 chemotherapy response cohort

Molecular Oncology · Pharmacogenomics · Expression Biomarkers

Transcriptomic Biomarkers of Neoadjuvant Chemotherapy Response

Evaluating transcriptomic expression signatures predictive of pathologic complete response (pCR) to taxane-anthracycline chemotherapy in breast cancer.

Reanalyzed the clinical cohort GSE25066 (Symmans et al., 2010), extracting proliferation and estrogen signaling transcript modules that, combined with histopathological tumor parameters, reached an AUC of 0.79 in predicting treatment response.

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