Publications

Peer-Reviewed Research Articles

Published as Fu, X. and Fu, A. X. *Equal contribution; †corresponding author.

A foundation model of transcription across human cell types
Fu, X.*†, Mo, S.*, Buendia, A.*, et al.
Nature 637, 965–973 (2025)
Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease
Fu, A. X., Lui, K. N.-C., Tang, C. S.-M., et al.
Genome Research 30, 1618–1632 (2020)
Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data
Su, J., Reynier, J.-B., Fu, X., et al.
Genome Biology 24, 291 (2023)
Hypomorphic and dominant-negative impact of truncated SOX9 dysregulates Hedgehog-Wnt signaling, causing campomelia
Au, T. Y. K., Yip, R. K. H., Wynn, S. L., Tan, T. Y., Fu, A. X., et al.
PNAS 120, e2208623119 (2023)
Genome-wide association analyses identified novel susceptibility loci for pulmonary embolism among Han Chinese population
Zhang, Z., Li, H., …, Fu, X., et al.
BMC Medicine 21, 153 (2023)
A unified framework for integrative study of heterogeneous gene regulatory mechanisms
Cao, Q., Zhang, Z., Fu, A. X., et al.
Nature Machine Intelligence 2, 447–456 (2020)
Identification of genes associated with Hirschsprung disease, based on whole-genome sequence analysis, and potential effects on enteric nervous system development
Tang, C. S.-M., Li, P., Lai, F. P.-L., Fu, A. X., et al.
Gastroenterology 155, 1908–1922.e5 (2018)
Dual roles of an Arabidopsis ESCRT component FREE1 in regulating vacuolar protein transport and autophagic degradation
Gao, C., Zhuang, X., Cui, Y., Fu, X., et al.
PNAS 112, 1886–1891 (2015)

Reviews and Perspectives

Illuminating the noncoding genome in cancer using artificial intelligence
Alvarez-Torres, M. d. M., Fu, X., and Rabadan, R.
Cancer Research 85, 2368–2375 (2025)
Understanding variants of unknown significance: the computational frontier
Fu, X. and Rabadan, R.
The Oncologist 29, 653–657 (2024)

Preprints and Unpublished Manuscripts

Mapping the genetic landscape of the DNA damage response with Cas12a-based combinatorial knockout screens
Hayward, S. B., Vaitsiankova, A., …, Fu, X., …, and Ciccia, A.
Accepted in principle, Nature Biotechnology. Preprint: bioRxiv (2026)
Decoding the gene regulatory landscape through multimodal learning of protein–DNA interactions
Tan, J.*, Fu, X.*, Ling, X.*, et al.
bioRxiv (2025; revised January 18, 2026)
Computational structure prediction methods enable the systematic identification of oncogenic mutations
Fu, X., Reglero, C., Swamy, V., et al.
bioRxiv (2022)
Nucleosome-scale p53–hormone receptor grammar links cancer and primate evolution
Fu, X.*†, Cai, Q.*, Satya, P., Rabadan, R.†, and Levine, A. J.†
Unpublished manuscript (2026)

Workshop Contributions

Multi-modal self-supervised pre-training for large-scale genome data
Mo, S., Fu, X., Hong, C., et al.
NeurIPS AI for Science Workshop (2021)