CV
Education
- Ph.D. in Computational and Systems Biology, Washington University School of Medicine - Jul 2025 - current
- B.S. in Biomedical Engineering, University of Cincinnati - Aug 2020 - May 2025
Awards
- University of Cincinnati Dean’s List - 2020 - 2025
- DAAD RISE Germany scholarship - 2024
- Second Place, Trackerless 3D Freehand Ultrasound Reconstruction (TUS-REC) Challenge, MICCAI - 2024
- Mary Rowe Book Award for Study Abroad by University Honors Program - 2024
- College of Engineering and Applied Science Tribunal Research Scholarship - 2024
- Best Poster, Cincinnati Children’s Hospital Annual Immunology Retreat - 2023
- Excellent Award for Science Communication at University of Cincinnati Research Showcase - 2022
Work experience
- Computational Biology Research Assistant - Jan 2024 - Jun 2025 - Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Curate 2 single-cell RNA-sequencing datasets of brain tissues and cerebrospinal fluid in neurodegenerative disease patients, discovering marker genes in 7 brain cell populations and 11 immune cell types
- Apply elastic net regression and multiple testing correlation to elucidate cell-type specific enrichment of 50 biomarker proteins highly predictive of early onset of Alzheimer’s Disease in 3 proteomics blood datasets
- Computational Biology Research Assistant - Jan 2023 - Jun 2025 - Cincinnati Children’s Hospital, Cincinnati, OH, USA
- Integrated 150 bulk and single-cell next-generation sequencing epigenetics (ATAC-seq) and protein binding (ChIP- seq) assays in 20 cell lines, 2 primary immune cell types and 7 pluripotent stem cell stages using Python and R
- Devised novel multimodal deep learning models for predicting correct binding sites of 52 transcription factors from genome sequence and high-throughput epigenetics data, improving precision-recall of 50% over motif scanning
- Maintained and tested Nextflow high-throughput sequencing pipeline with peak calling, motif enrichment, and alignment to disease risk loci from GWAS studies, facilitating 6 research projects on autoimmune diseases
- Biomedical Imaging Research Assistant - May 2024 - Aug 2024 - German Cancer Research Center (DKFZ), Heidelberg, Germany
- Develop novel convolutional recurrent neural networks for 3D volume reconstruction and motion tracking from 1200 sensorless freehand B-mode ultrasound sequences of forearms
- Construct 3D segmentations of prostate tumors by image registration and digital processing on transrectal micro-ultrasound images and transverse histopathological slices from 20 patients
- Systems Biology Contributor - May 2023 - Dec 2023 - Google Summer of Code and Harvard University, Cambridge, MA, USA
- Studied systems biology approaches for modeling molecular pathways in drug-resistant cancer cell lines under drug perturbations
- Renovated published codebase from Tensorflow 1 to Pytorch, reproducing the dynamic systems model with correlation coefficient of 0.94 for predicting cell viability and expression levels of 99 proteins under 89 drug combinations
- Designed robust unit test cases with pytest, enabling implementation of automated CI/CD with Github Actions
- Applied updated codebase to analyze proteomics dataset of 90 single-drug perturbations and 7000 protein expressions in colorectal cancer cell lines, searching for novel synergistic drug combinations
- Biomedical Imaging Research Assistant - May 2022 - Dec 2022 - Washington University in St. Louis, St. Louis, MO, USA
- Fine-tuned residual network models for analysis of 1251 3D multimodal brain MRI images, achieving accuracy of 80% for tumor segmentations and 95% for segmentation quality grading
- Performed exploratory data analysis and curation from electronic health records to extract glioblastoma pathological data from 300 patients
- Biomedical Imaging Research Assistant - Oct 2021 - Dec 2022 - Cincinnati Children’s Hospital, Cincinnati, OH, USA
- Implemented image generative models for data augmentation of 2670 liver pediatric ultrasound images, enabling generation of synthetic healthy and diseased liver ultrasound datasets with 90% similarity to real images
- Conducted critical literature review of 40 publications, enabling comprehensive overview of current trends in computational liver ultrasound research
Skills
- Programming: Python, R, C++, MATLAB, Bash scripting, Linux, High Performance Computing
- Techonogies: Tensorflow, PyTorch, Nextflow, SnakeMake, Seurat, Scanpy
- Bioinformatics:
- High-throughput sequencing data analysis (RNA-seq, ATAC-seq, ChIP-seq)
- Population genetics data analysis (GWAS, meta-analysis)
- Nextflow pipeline development and deployment
- Data integration, visualization and presentation
- Biomedical Engineering:
- Biomedical signal processing
- Mathematical simulation, modeling, and optimization of disease transmissions
