Publications
Selected publications and preprints.
Preprints
- 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) [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) [bioRxiv]
Publications
- 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) [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) [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) [ACS Synthetic Biology]