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馃寪
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kroy3/README.md

Kushal Raj Roy

Kushal Raj Roy

Computational biologist. PhD student in the iBio program at the University of Iowa, working on single-nucleus RNA-seq of the cochlea. Founder of Genoproteomics, a precision medicine venture bridging multi-omics, structural biology, and AI.

I build multi-omics integration methods, and I care about open science, reproducibility, and mentorship.

LinkedIn 路 ORCID


Currently

  • Developing a QC and analysis pipeline for single-nucleus RNA-seq in cochlear immunology, characterizing cell-type-specific transcriptional response and immune cell populations in the inner ear.


Multi-omics integration: layered molecular data converging through a graph network into clustered embeddings

Education
University of Iowa PhD in progress, Integrated Biology (iBio)
University of Houston MSc, Biochemistry
Savitribai Phule Pune University BSc, Microbiology

Publications

Peer-reviewed journal articles

  • Protein Function Prediction with Pretrained Transformers: Performance, Pitfalls, and Practical Guidance. Eurobiotech Journal, 2026. 10.2478/ebtj-2026-0005 路 Scopus-indexed

  • miRNA-mRNA Multi-omics Integration in Breast Cancer Staging. Advances in Biomarker Sciences and Technology, 2026. 10.1016/j.abst.2026.06.003

Accepted / in press

  • ReactionForge: A Temporal Graph Network for Suzuki-Miyaura Cross-Coupling Yield Prediction. International Journal of Complexity in Applied Science and Technology (Inderscience), 2026.

  • Machine Learning-Guided Catalyst Selection Reveals Nickel's Advantages Over Palladium in Suzuki-Miyaura Cross-Coupling. International Journal of Complexity in Applied Science and Technology (Inderscience), 2026.

Full record: ORCID 0000-0002-4664-7462

Tools
Languages Python 路 R 路 Bash 路 SQL
ML / Deep learning PyTorch 路 PyTorch Geometric 路 scikit-learn 路 HuggingFace Transformers
Single-cell & genomics Seurat 路 Scanpy 路 DESeq2 路 STAR 路 Snakemake 路 Nextflow
Omics & proteomics Waters UPLC-QDa 路 MassLynx 路 MaxQuant 路 STRING 路 Cytoscape
Data science Pandas 路 NumPy 路 Matplotlib 路 Seaborn 路 Plotly 路 Jupyter
Infrastructure Git 路 Docker 路 GitHub Actions 路 Conda 路 SLURM 路 AWS (S3/EC2)
Structural biology PyMOL 路 AlphaFold2

Outside the lab

Playing guitar, science documentaries, the history of molecular biology, and creative visual projects. Originally from Bangladesh, currently in Iowa City, IA.

GitHub stats

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