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Chang S, Zhao W, Ma Y, Sandstede B, Singh R.
"Cell type-specific gene regulatory network inference from single cell transcriptomics with ctOTVelo." bioRxiv : the preprint server for biology, 2026.
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Jain A, Pham TM, Laidlaw DH, Ma Y, Singh R.
"Diffusion-based Representation Integration for Foundation Models Improves Spatial Transcriptomics Analysis." International Conference on Intelligent Systems for Molecular Biology (ISMB), 2026.
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Klimpert N, Kollo M, Brann DH, Tan C, Barry D, Ma Y, Schaefer AT, Fleischmann A.
"3D spatial transcriptomics reveals the molecular structure of input and output pathways in the mouse olfactory bulb." bioRxiv : the preprint server for biology, 2025.
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Tan, Chichun, Ma, Ying.
"A spatially informed matrix normal model for gene co-expression analysis in spatial transcriptomics studies." Nucleic Acids Research, vol. 53, no. 22, 2025.
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Ma Y.
"Bridging histology and spatial gene expression across scales." Nature methods, vol. 22, no. 9, 2025, pp. 1765-1767.
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Chen, Jianhong, Ma, Ying, Yue, Xubo.
"Federated Learning of Dynamic Bayesian Network via Continuous Optimization from Time Series Data." IEEE Transactions on Artificial Intelligence, 2025, pp. 1-18.
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Jain, Atishay, Laidlaw, David, Ma, Ying, Singh, Ritambhara.
"Improved Spatial Transcriptomics Clustering with Nested Graph Neural Networks." Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2025, pp. 1-10.
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Guo, Yuanchuan, Liu, Jun S., Cheng, Huimin, Ma, Ying.
"JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics." Conference on Neural Information Processing Systems (NeurIPS 2025), 2025.
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Yang, Andrew, Woo, Joshua, Zhang, Ryan, Mach, Alan, Ramkumar, Prem, Ma, Ying.
"Tool-wielding language-model-based agent offers conversational exploration of clinical tabular data." npj Artificial Intelligience , 2025.
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Ma Y, Zhou X.
"Accurate and efficient integrative reference-informed spatial domain detection for spatial transcriptomics." Nature methods, vol. 21, no. 7, 2024, pp. 1231-1244.
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Ma, Ying, Patil, Snehal, Zhou, Xiang, Mukherjee, Bhramar, Fritsche, Lars G.
"ExPRSweb: An online repository with polygenic risk scores for common health-related exposures." The American Journal of Human Genetics, vol. 109, no. 10, 2022, pp. 1742-1760.
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Zhao, Peiyao, Zhu, Jiaqiang, Ma, Ying, Zhou, Xiang.
"Modeling zero inflation is not necessary for spatial transcriptomics." Genome Biology, vol. 23, no. 1, 2022.
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Ma, Ying, Zhou, Xiang.
"Spatially informed cell-type deconvolution for spatial transcriptomics." Nature Biotechnology, vol. 40, no. 9, 2022, pp. 1349-1359.
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Ma, Ying, Zhou, Xiang.
"Genetic prediction of complex traits with polygenic scores: a statistical review." Trends in Genetics, vol. 37, no. 11, 2021, pp. 995-1011.
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Fritsche, Lars G., Ma, Ying, Zhang, Daiwei, Salvatore, Maxwell, Lee, Seunggeun, Zhou, Xiang, Mukherjee, Bhramar.
"On cross-ancestry cancer polygenic risk scores." PLOS Genetics, vol. 17, no. 9, 2021, pp. e1009670.
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Fritsche, Lars G., Patil, Snehal, Beesley, Lauren J., VandeHaar, Peter, Salvatore, Maxwell, Ma, Ying, Peng, Robert B., Taliun, Daniel, Zhou, Xiang, Mukherjee, Bhramar.
"Cancer PRSweb: An Online Repository with Polygenic Risk Scores for Major Cancer Traits and Their Evaluation in Two Independent Biobanks." The American Journal of Human Genetics, vol. 107, no. 5, 2020, pp. 815-836.
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Ma, Ying, Sun, Shiquan, Shang, Xuequn, Keller, Evan T., Chen, Mengjie, Zhou, Xiang.
"Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies." Nature Communications, vol. 11, no. 1, 2020.
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Sun, Shiquan, Zhu, Jiaqiang, Ma, Ying, Zhou, Xiang.
"Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis." Genome Biology, vol. 20, no. 1, 2019.
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