Publications · Jiazhang Cai

Published (15)

1.WEST is an ensemble method for spatial transcriptomics analysis

Cai, J., Cheng, H., Wu, S., Zhong, W., Yuan, G. C., & Ma, P. (2024). Cell Reports Methods, 4(11).

2.Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniques

Cai, J., Wu, S., Cheng, H., Zhong, W., Yuan, G. C., & Ma, P. (2025). STAR Protocols, 6(1).

3.The microbiome and metatranscriptome of a panel from the Sarracenia mapping population reveal complex assembly and function involving host influence

Cai, J., Mohsin, I., Rogers, W., Zhang, M., Jiang, L., Malmberg, R., & Alabady, M. (2024). Frontiers in Plant Science, 15, 1445713.

DOI ›

4.Subsampling in large graphs using Ricci curvature

Wu, S., Cheng, H., Cai, J., Ma, P., & Zhong, W. (2023). International Conference on Learning Representations (ICLR).

OpenReview ›

5.MultiCOP: an association analysis of microbiome and metabolome relationships

Wang, Z., Fang, L., Cai, J., Ma, P., & Zhong, W. (2024). Statistics in Biosciences, 1-21.

6.Large language models for bioinformatics

Ruan, W., Lyu, Y., Zhang, J., Cai, J., Shu, P., Ge, Y., et al. & Liu, T. (2026). Quantitative Biology, 14(1), e70014.

7.Knowledge distillation and dataset distillation of large language models: emerging trends, challenges, and future directions

Fang, L., Yu, X., Cai, J., Chen, Y., Wu, S., Liu, Z., et al. & Ma, P. (2026). Artificial Intelligence Review, 59(1), 17.

8.Incidence of hypernatremia in dogs treated with single dose activated charcoal for acute toxicant ingestion: multi-center retrospective study (2018 to 2023)

Young, T., Walton, R. A., Cheng, P., Cai, J., Mochel, J. P., & Peterson, K. (2025). Frontiers in Veterinary Science, 12, 1547076.

9.Utilization of peripheral glucose and lactate differences in the diagnosis of feline arterial thromboembolism: a multi-center study

Yee, M., Guillaumin, J., 't Hoen, M., Cai, J., Mochel, J., & Walton, R. (2024). Frontiers in Veterinary Science, 11, 1505479.

10.Transmucosal detomidine gel induces emesis in approximately half of cats presenting for dietary indiscretion

Neufeld, M. R., Hanson, K. R., Mochel, J. P., Cai, J., Raffe, M. R., Handel, A., & Julius, T. (2026). Journal of the American Veterinary Medical Association, 1(aop), 1-6.

11.A preliminary investigation in dogs to evaluate for post-anesthetic lung ultrasound findings suggestive of atelectasis

Wheeler, E., Kraus, B. H., Mochel, J., Cai, J., Ciou, M., Lu, M., & Ward, J. (2025). Veterinary Anaesthesia and Analgesia, 52(1), 124-e13.

12.Tensor analysis of animal behavior by matricization and feature selection

Wang, B., Cai, J., Fang, L., Tsujikawa, M., Ma, P., & Leung, Y. F. (2025). Computers in Biology and Medicine, 197, 110959.

13.Multicenter retrospective evaluation of the use of lyophilized platelets in dogs

Nugen, S., Walton, R. A., Smith, R., Cai, J., Mochel, J. P., & Mays, E. L. (2026). Journal of Veterinary Emergency and Critical Care.

14.Incidence of hypernatremia in dogs treated with multi-dose activated charcoal for acute toxicant ingestion: multi-center retrospective study (2018 to 2023)

Gabriel, L., Walton, R. A., Young, T., Cai, J., Mochel, J. P., & Peterson, K. (2025). Frontiers in Veterinary Science, 12, 1584162.

15.The association between non-depolarizing neuromuscular blockade agents and survival to discharge in dogs undergoing mechanical ventilation: a multi-center retrospective study of 227 dogs (2010 to 2020)

Ngo, L., Walton, R., Wolf, J., Levy, N., Ludwik, T., Thevelein, B., Blong, A., Cai, J., & Mochel, J. (2025). Frontiers in Veterinary Science, 12, 1539138.

Accepted / In press (1)

16.Multi-teacher Bayesian knowledge distillation for protein localization prediction with uncertainty quantification

Fang, L., Chen, Y., Cai, J., Zhong, W., & Ma, P. (2026). Journal of the American Statistical Association, Case Studies (in press).

Under review (3)

17.SpaDiff: denoising for sequence-based spatial transcriptomics via diffusion process

Cai, J., Chen, Y., Fang, L., Zhong, W., Yuan, G. C., & Ma, P. (2025). Cell Reports Methods (under review).

18.Pseudo-time reconstruction for analyzing transmission direction in COVID-19 contact-tracing data

Cai, J., Feng, Y., Cheng, H., Ge, Y., Guo, Z., Huang, H., et al. & Shen, Y. (2025). Epidemics (under review).

19.Double generative learning for tackling the curse of dimensionality in causal inference

Lu, H., Cheng, H., Fang, L., Cai, J., Zeng, P., Ma, P., & Zhong, W. (2026). Journal of the American Statistical Association (under review).

Preprints (2)

20.Alignment and safety in large language models: safety mechanisms, training paradigms, and emerging challenges

Lu, H., Fang, L., Zhang, R., Li, X., Cai, J., Cheng, H., et al. & Ma, P. (2025). arXiv:2507.19672.

21.MicroRNA expression in asymptomatic welders: implications for biomarker discovery for environmentally-linked neurodegenerative disorders

Bargues-Carot, A., Prado-Rico, J., Kawasawa, Y. I., Cai, J., Yanosky, J. D., Zenitsky, G., et al. & Huang, X. (2025). medRxiv.