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4th-year PhD Student | Brown University | Deep Learning | Gene Regulation | Single-Cell and Spatial Omics | Foundation Models
My AI assistant - Elo - is in training and can occasionally make mistakes. He's fun to talk to though!
About Me
I am a 4th-year PhD student in Computational Biology at Brown University. I am advised by
Dr. Ritambhara Singh
and co-advised by
Dr. Erica Larschan
.
My research focuses on modeling gene regulation using multimodal datasets in different biological contexts
including learning and memory as well as dosage compensation using ML/DL applications.
Currently, I'm working on improving representations of single-cell and spatial foundation models using graph diffusion.
Before Brown, I studied RNA secondary structural design and transposable element evolution at the
Mathews
and the
Larracuente
Labs.
Outside of the lab, I enjoy cooking, doing community service, and learning about aquarium fish!
Selected Projects
DRIFT ↗
Diffusion-based Representation Integration for Foundation Models in Spatial Transcriptomics.
Odor-associated Learning and Memory ↗
Modeling gene regulatory mechanisms in olfactory cortex and hypothalamus under different odor conditions.
Synergistic Transcription Factor Control in Drosophila ↗
Multimodal modeling of Drosophila transcription factors involved in synapse formation and dosage compensation.
Publications
- Colin D. Baker, Tuan M. Pham, Pinar Demetci, Quang-Huy Tran, Ievgen Redko, Bjorn Sandstede, and Ritambhara Singh SCOT+: A Comprehensive Software Suite for Single-Cell Alignment Using Optimal Transport. (2025) [Bioinformatics Advances]
- Sara Zeppilli, Alonso O. Gurrola, Pinar Demetci, David H. Brann, Tuan M. Pham, Robin Attey, Noga Zilkha, et al. Single-cell genomics of the mouse olfactory cortex reveals contrasts with neocortex and ancestral signatures of cell type evolution. (2025) [Nature Neuroscience]
- Pham, Tuan M., Terrel Miffin, Hongying Sun, Kenneth K. Sharp, Xiaoyu Wang, Mingyi Zhu, Shuichi Hoshika, Raymond J. Peterson, Steven A. Benner, Jason D. Kahn, and David H. Mathews DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters. (2023) [ACS Synthetic Biology]
- James A Kentro, Gunjan Singh,Tuan M Pham , Justin Currie, Saniya Khullar, Audrey T Medeiros, Maria Tsiarli, Erica Larschan, Kate M O’Connor-Giles Conserved transcription factors coordinate synaptic gene expression through repression. (2025) [bioRxiv]
- Atishay Jain, Tuan M. Pham, David H. Laidlaw, Ying Ma, Ritambhara Singh Diffusion-based Representation Integration for Foundation Models Improves Spatial Transcriptomics Analysis. (2025) [bioRxiv]