Publications

• Sequential emergence and contraction of epithelial subtypes in the prenatal human choroid plexus revealed by a stem cell model 

H. Masters, S. Wang, C. Tu, Q. Nguyen, Y. Sha, MK Karikomi et al.

Nature Communications, 16(1), 2025

• LMNA-related dilated cardiomyopathy: single-cell transcriptomics during patient-derived iPSC differentiation support cell type and lineage-specific dysregulation of gene expression and development for cardiomyocytes and epicardium-derived cells with Lamin A/C haploinsufficiency

M. V. Zaragoza, T.A. Bui, H.P. Widyastuti, M. Mehrabi, Z. Cang, Y. Sha, A. Grosberg, Q. Nie. 

Cells, 13(17), 1479, 2024

• Reconstructing growth and dynamic trajectories from single-cell transcriptomics Data

Y. Sha, Y. Qiu, P. Zhou, Q. Nie. 

Nature Machine Intelligence, 6(1), 25-39, 2024

• NeuralGene: Inferring gene regulation and cell fate dynamics from Neural ODEs

Y. Sha#, Y. Qiu#, Q. Nie. (#: co-first)

Journal of Machine Learning for Modeling and Computing 4, no. 3, 2023

• Single-cell analysis of human basal cell carcinoma reveals novel regulators of tumor growth and the tumor microenvironment

C. Guerrero-Juarez, G. Lee, Y. Liu, S. Wang, M. Karikomi, Y. Sha, R. Chow, T. Nguyen et al. 

Science Advances 8, no.23, 2022

• A study of gene expression, structure, and contractility of iPSC-derived cardiac myocytes from a family with heart disease due to LMNA mutation

M. Mehrabi, T. A. Morris, Z. Cang, C. H. Nguyen, Y. Sha, M. N. Asad, N. Khachikyan et al.

Annals of biomedical engineering 49, no. 12 3524-3539, 2021

• Inference of intercellular communications and multilayer gene-regulations of epithelial–mesenchymal transition from single-cell transcriptomic data

Y. Sha, S. Wang, F. Bocci, P. Zhou, Q. Nie. 

Frontiers in genetics, 11, 1700, 2021

• Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data

Y. Sha, S. Wang, P. Zhou, Q. Nie. 

Nucleic Acids Research, 48(17), Pages 9505-9530, 2020

• Intermediate cell states in epithelial-to-mesenchymal transition

Y. Sha, D. Haensel, G. Guitierrez, H. Du, X. Dai, Q. Nie. 

Physical Biology, 18:16(2):021001, 2019