Publications & Preprints
Research on computational gene regulation, spatial transcriptomics, and machine learning methods for multi-omic analysis.
Preprints
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J. Rahmat, T. Pham, and A. M. Larracuente.
kmerRRR: A k-mer based tool for functional genomics in Repeat Rich Regions.
(2026)
A computational tool for analyzing k-mer patterns in repeat-rich genomic regions, enabling functional genomics studies in highly repetitive DNA sequences.
[bioRxiv] -
Z. S. Warner, S. Negm, P. Wynn, T. Pham, L. Zaki, G. Giri,
P. B. Frandsen, A. M. Larracuente, and J. S. Sproul.
Satellite DNA dynamics across phylogenetic scales in ground beetles and other insects.
(2026)
Comparative genomic analysis of satellite DNA evolution across insect species, revealing patterns of repeat dynamics and their role in genome evolution.
[bioRxiv] -
A. Jain*, T.M. Pham*, D. H. Laidlaw, Y. Ma, and R. Singh.
Diffusion-based Representation Integration for Foundation Models Improves Spatial Transcriptomics Analysis.
(2025)
DRIFT: A scalable diffusion framework that integrates spatial topology into pretrained foundation models, enabling improved spatial transcriptomics analysis witho[...]
[Bioinformatics] -
J. A. Kentro, G. Singh, T.M. Pham, J. Currie, S. Khullar,
A. T. Medeiros, M. Tsiarli, E. Larschan, and K. M. O'Connor-Giles.
Conserved transcription factors coordinate synaptic gene expression through repression.
(2025)
This work uses graph neural networks and gene regulatory network inference to identify conserved transcription factors controlling synapse formation in Drosoph[...]
[bioRxiv]
Peer-Reviewed Publications
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C. D. Baker, T.M. Pham, P. Demetci, Q.-H. Tran, I. Redko,
B. Sandstede, and R. Singh.
SCOT+: A Comprehensive Software Suite for Single-Cell Alignment Using Optimal Transport.
(2025)
Software implementing optimal transport methods for single-cell alignment and multi-omic data integration, enabling scalable computational approaches to gene regu[...]
[Bioinformatics Advances] -
S. Zeppilli, A. O. Gurrola, P. Demetci, D. H. Brann, T.M. Pham,
R. Attey, N. Zilkha, et al.
Single-cell genomics of the mouse olfactory cortex reveals contrasts with neocortex
and ancestral signatures of cell type evolution.
(2025)
Uses single-cell RNA-sequencing and gene regulatory network inference (optimal transport and graph neural networks) to characterize gene regulation and cell type [...]
[Nature Neuroscience] -
T.M. Pham, T. Miffin, H. Sun, K. K. Sharp, X. Wang, M. Zhu,
S. Hoshika, R. J. Peterson, S. A. Benner, J. D. Kahn, and D. H. Mathews.
DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs
Including Loop and Mismatch Thermodynamic Parameters.
(2023)
Advances RNA and DNA structure design by integrating expanded synthetic nucleotide alphabets with thermodynamic modeling, relevant to understanding RNA secondary[...]
[ACS Synthetic Biology]