Skip to content
View kroy3's full-sized avatar
🌐
Learning
🌐
Learning
7 followers · 75 following

Achievements

Achievement: Pull SharkAchievement: Quickdraw

Achievements

Achievement: Pull SharkAchievement: Quickdraw

Block or report kroy3

Block user

Prevent this user from interacting with your repositories and sending you notifications. Learn more about blocking users.

You must be logged in to block users.

Content in all repositories owned by your account will be closed.
Maximum 250 characters. Please don’t include any personal information such as legal names or email addresses. Markdown is supported. This note will only be visible to you.
Report abuse

Contact GitHub support about this user’s behavior. Learn more about reporting abuse.

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

Popular repositories Loading

  1. statistics-for-data-scientists statistics-for-data-scientists Public

    Forked from andrewgbruce/statistics-for-data-scientists

    Code and data associated with the book "Statistics for Data Scientists: 50 Essential Concepts"

    R 1

  2. Topo2D Topo2D Public

    Python 1

  3. ReactionForge ReactionForge Public

    Python 1

  4. kushalrajroy kushalrajroy Public

    Config files for my GitHub profile.

  5. SSAGES SSAGES Public

    Forked from SSAGESproject/SSAGES

    Software Suite for Advanced General Ensemble Simulations

    C++

  6. code code Public

    Forked from dataprofessor/code

    Compilation of R and Python programming codes on the Data Professor YouTube channel.

    Jupyter Notebook