Kushal Raj Roy

Biochemist working at the interface of single-cell transcriptomics and machine learning. My doctoral research in the Sung Lab uses single-nucleus RNA sequencing of the cochlea to resolve cell-type-specific transcriptional responses to cisplatin ototoxicity, characterize cochlear immune cell populations, and study blood-labyrinth barrier function, supported by a reproducible QC and analysis pipeline I build and maintain. In parallel, I develop and evaluate deep learning and generative AI methods for multi-omics data: miRNA-mRNA integration for cancer staging, pretrained protein language models for function prediction, multi-omics deep learning and single-cell foundation models for infectious disease, and equivariant and temporal graph neural networks for molecular prediction.

The aim connecting both lines is to use integrated multi-omics data and modern AI models to explain how individual cell types respond to injury and disease.

Ph.D. Student; PI: Dr. Cathy Yea Won Sung - University of Iowa, Department of Biology (Sung Lab) - Iowa City, IA, USA

(2026)

• Analyze single-nucleus RNA-seq of the cochlea to identify cell-type-specific transcriptional responses to cisplatin-induced ototoxic injury.
• Characterize cochlear immune cell populations, including macrophage subsets, and their transcriptional states after injury.
• Investigate blood-labyrinth barrier function and the immune and vascular cell programs associated with it.
• Build and maintain a reproducible QC and analysis pipeline for multi-organ single-nucleus transcriptomic data (ambient RNA and doublet assessment, filtering, normalization, integration, annotation) on Linux/SLURM HPC.

Graduate Research Assistant - University of Houston (Wang Lab) - Houston, TX, USA

(2025-01 - 2025-12)

• Single-molecule FRET analysis of ribosomal translocation and elongation factor function; built analysis workflows for conformational-state data.
• Maintained and optimized UPLC-MS methods (Waters UPLC-QDa) for RNA and oligonucleotide quality control.

Project Intern - Savitribai Phule Pune University - Pune, India

(2019-11 - 2020-11)

• Screened small-molecule inhibitors of human islet amyloid polypeptide aggregation; INS-1E cell culture, western blotting of AKT and Bax/Bcl-2 signaling, and molecular dynamics simulation.

Summer Research Intern - Savitribai Phule Pune University - Pune, India

(2019-04 - 2019-08)

• Small-molecule discovery research targeting sickle cell disease.

Graduate Teaching Assistant - University of Houston, Department of Biology and Biochemistry - Houston, TX, USA

(2022-08 - 2024-12)

• Led Biochemistry I (BCHS 3304) recitations, exam reviews, and office hours on enzyme kinetics, pH/pKa, and bioenergetics.
• Taught General Chemistry I and II (CHEM 1106, 1112), Organic Chemistry, and Introductory Biology (BIOL 1106) laboratory sections; graded lab reports.
• Mentored Welch Foundation undergraduate summer research interns.

Instructor - LearningPotato Education, Pune - Pune

(2018-01 - 2019-04)

• School-level biology and chemistry.

Ph.D. - Integrated Biology (iBio) - University of Iowa (2026)

M.Sc. - Biochemistry - University of Houston (2022 - 2025)

M.Sc. - Biochemistry - Fergusson College (Autonomous) (2018 - 2020)

B.Sc. - Microbiology - Savitribai Phule Pune University (2014 - 2018)