Publications

Preprints

Coalescent-Based Time-Stratified Statistics Reveal Population Structure Dynamics using the Ancestral Recombination Graph

bioRxiv

Deng, Y., Pritchard, J. K., & Spence, J. P. (2026).

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

bioRxiv

Rocha, J. L., Lou, R. N., Adam, C. L., Hebbar, P., Ferguson, S., ... Deng, Y., et al. (2026).

Population-scale Ancestral Recombination Graphs with tskit 1.0

arXiv

Jeffery, B., Wong, Y., Thornton, K., Tsambos, G., Bisschop, G., Deng, Y., et al. (2026).

Tree Thinking in the Genomic Era: Unifying Models Across Cells, Populations, and Species

arXiv

Deng, Y., Zhan, S. H., Zhang, Y., Zhang, C., & Chen, B. (2025).

Robustness of Ancestral Recombination Graph Inference Tools to Phasing Errors

bioRxiv

Wang, L.^†, Deng, Y.^*, & Nielsen, R.^* (2025).

^† Undergraduate mentee    ^* Co-corresponding authors

Published Articles

2025

A general framework for branch length estimation in Ancestral Recombination Graphs

Proceedings of the National Academy of Sciences

Deng, Y., DeWitt, W. S., Song, Y. S., & Nielsen, R. (2025).

Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes

Nature Genetics

Deng, Y., Nielsen, R., & Song, Y. S. (2025).

Inference and applications of ancestral recombination graphs

Nature Reviews Genetics

Nielsen, R., Vaughn, A. H., & Deng, Y. (2025).

A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact

Genetics

Deng, Y., Nielsen, R., & Song, Y. S. (2025).

2023

CherryML: scalable maximum likelihood estimation of phylogenetic models

Nature Methods

Prillo, S., Deng, Y., Boyeau, P., Li, X., Chen, P.-Y., & Song, Y. S. (2023).

2022

Evaluation of methods for estimating coalescence times using ancestral recombination graphs

Genetics

Brandt, D. Y. C., Wei, X., Deng, Y., Vaughn, A. H., & Nielsen, R. (2022).

2021

The distribution of waiting distances in ancestral recombination graphs

Theoretical Population Biology

Deng, Y., Song, Y. S., & Nielsen, R. (2021).

2018

Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy

Nature Communications

Li, A., Yin, X., Xu, B., Wang, D., Han, J., Wei, Y., Deng, Y., Xiong, Y., & Zhang, Z. (2018).