Mehrdad Zandigohar
PhD candidate (Graduating in December) applying AI/ML to disease biology. Developed scRegulate (TF activity inference) and RAGulate (literature-guided TF validation). Collaborated with UIC, UCSF, and Northwestern to uncover new fibroblast and immune cell programs in fibroid tumors, hernia fibrosis, and wound healing.
Experience
University of Illinois Chicago
Spatial Transcriptomics in MED12/HMGA2 Fibroids (Collaboration with Northwestern) • 2025 – present
Discovered tumor-specific signaling rewiring and ligand-receptor interactions, highlighting genetic subtype–specific pathways.
- Cell type deconvolution and spatially resolved ligand-receptor analysis
- Subtype comparisons across MED12 vs. HMGA2 genetic variants
Single-Cell Atlas of Uterine Fibroids and Myometrium (Collaboration with UCSF) • 2021 – 2022
Processed 100k single-cell RNA-seq profiles from fibroid and myometrium tissue.
- Identified fibroblast and lymphatic-endothelial subtypes driving fibroid growth
- Lineage and cell-cell communication analyses
- Co-authored publication in Human Reproduction (41+ citations)
Transcription Factor Activity in Wound Healing (Immunology + Epigenomics) (Collaboration with UIC) • 2022 – 2024
Modeled macrophage TF programs in wound healing using scRNA-seq with ATAC/ChIP priors.
- Discovered regulators of impaired healing and fibrosis
- Published in The Journal of Immunology (Top Read Article, 2024)
Multi-omics and Spatial Transcriptomics in Disease Models: Role of progesterone action in inguinal hernia (Collaboration with Northwestern) • 2023 – 2025
Integrated scRNA-seq, scATAC-seq, and Xenium spatial data in mouse hernia models; discovered Pgr⁺ fibroblast subtype driving fibrosis.
- Processed and analyzed multi-omics and spatial datasets
- Pinpointed Pgr⁺ fibroblast subtype with TGF-β signaling linked to fibrosis and atrophy
- Handled GEO deposition, metadata curation, and reproducibility; co-authored JCI Insight
Graduate Research Assistant — Information Retrieval in Sparse & High-Dimensional Genomic Data • 2021 – 2023
Developed and benchmarked TF-IDF pipelines for scATAC-seq signal extraction, comparing PCA, LSI, and deep generative models.
- Improved retrieval of biological signal in sparse chromatin data
- First-author publication at IEEE BIBM 2022
Graduate Research Assistant — scRegulate: Interpretable Generative Model for TF Activity • 2023 – 2025
Built scRegulate, a generative model linking TF activity to scRNA-seq in disease models.
- Outperformed existing tools across perturb-seq and synthetic datasets
- Open-source package with docs, CI/CD, tutorials
- bioRxiv preprint (2025); under review (Bioinformatics); code
PhD Candidate — RAGulate: Retrieval-Augmented Generation for Literature-Guided Genomics • 2025 – present
Designed RAGulate to mine literature and validate TF-target predictions by integrating LLMs with regulatory priors.
- BioGPT/PubMedBERT with TFLink/GTRD for disease and context inference
- Open-source toolkit with documentation, following scRegulate principles
Education
University of Illinois Chicago
Doctor of Philosophy, Bioinformatics • 2020 — 2025
Southern Illinois University Edwardsville
Master of Science, Mechanical Engineering • 2018 — 2020
Sharif University of Technology
Bachelor of Science, Chemical Engineering • 2012 — 2017
Leadership & Technical Operations
Leadership in Lab Computing & Mentorship
University of Illinois Chicago • 2022 – present
- Infrastructure & operations: configured remote access; maintained 3 multi-user GPU servers (CUDA/Conda, upgrades) supporting ~10 researchers; managed job scheduling and user access
- Procurement & grants: led hardware procurement and setup; secured an NVIDIA GPU hardware grant (DGX Spark)
- Mentorship & collaboration: mentored 10+ trainees on GPU use, coding best practices, and workflows; built internal docs and streamlined reproducible pipelines
NVIDIA/scverse Accelerate Omics Hackathon
Remote on NVIDIA Brev • 2025
- Integrated Dask into decoupleR on NVIDIA Brev to parallelize TF activity on CPUs/GPUs; scaled to ~1M cells
Leadership & Service: Graduate Student Council Member
University of Illinois Chicago • 2022 – 2023
- Contributed to policy discussions and funding decisions; advocated graduate student needs across departments
Skills
Bioinformatics
Gene regulation (GRNs), peak calling, scRNA-seq, scATAC-seq, spatial transcriptomics, multi-omics, cell-cell communication, barcode decontamination, trajectory inference, biomarker discovery, GO/GSEA, comparative analysis
Bioinformatics Tools
Snakemake, Cell-Ranger/Space-Ranger/ARC, Scanpy, Seurat, Bioconductor, scverse
Infrastructure & DevOps
Git, Docker, Conda, Jupyter, AWS, CI/CD (GitHub Actions), SLURM, NVIDIA Brev
Programming
Python, R, Bash, MATLAB, C/C++, SQL
Data Science & ML
Deep learning, generative models (VAEs, transformers), retrieval-augmented generation (RAG), statistical modeling, data mining
ML Frameworks
PyTorch, Hugging Face (BioBERT/BioGPT/sentence-transformers), LlamaIndex
Distributed & GPU Computing
Dask, RAPIDS, PyTorch CUDA, cuDF/cuML, parallel I/O, GPU profiling
Recognition
Top Read Article: Transcription Factor Activity Regulating Macrophage Heterogeneity during Skin Wound Healing
• 2024
The Journal of Immunology
3rd Place, Oral Presentation
• 2023
5th Annual BME Research Symposium, UIC
Graduate Student Council (GSC) Award
• 2023-2025
University of Illinois at Chicago
NSF Student Travel Awards
• 2022
ACM-BCB & IEEE BIBM [AWD-003814; AWD-2131662]
2nd Place, Oral Presentation
• 2022
2nd Annual CBQB Research Day, UIC
Professional & Volunteer Services
Computational and Structural Biotechnology Journal (Elsevier)
Manuscript Reviewer • 2023
1 Manuscript.
Additional Links
Social Links
- Github: https://github.com/zandigohar
- LinkedIn: https://www.linkedin.com/in/zandigohar/
- Website: https://zandigohar.github.io/