Chichun Tan and Ying Ma# (2025). “A Spatially Informed Matrix Normal Model for Gene Co-expression Analysis in Spatial Transcriptomics Studies.” Nucleic Acids ResearchLink
Guo, Yuanchuan; Jun S. Liu#; Huimin Cheng#; Ying Ma# (2025). “JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics.” NeurIPS 2025 (accepted) link
Ying Ma# (2025). “Bridging histology and spatial gene expression across scales.” Nature Methods (commentary paper) Link
Andrew Yang, Joshua Woo, Ryan Zhang, Alan Mach, Prem Ramkumar, Ying Ma# (2025). “Tool-wielding language-model-based agent offers conversational exploration of clinical tabular data.” Preprint. Link
Atishay Jain, Tuan M. Pham, David H. Laidlaw, Ying Ma, Ritambhara Singh (2025). “Diffusion-based Representation Integration for Foundation Models Improves Spatial Transcriptomics Analysis.” preprintlink
Atishay Jain, David H. Laidlaw, Ying Ma, Ritambhara Singh (2025). “Improved Spatial Transcriptomics Clustering with Nested Graph Neural Networks.” ACM-BCB 2025 (accepted) link
Houcheng Li; Huicong Zhang; Pengju Zhao; Qi Zhang; Senlin Zhu; Tao Shi; Ya-Nan Wang; Jing-Sheng Lu; Liu Yang; John F. O’Grady; David E. MacHugh; Yu Wang; Zhenyu Wei; Xuemei Lu; Ming-Shan Wang; Bo Han; Weijie Zheng; Ao Chen; Shamima Akter; Nayan Bhowmik; Ying Ma; Ransom L. Baldwin; Congjun Li; Jicai Jiang; Li Ma; Christian Maltecca; Junjian Wang; Mian Gong; Xiaoning Zhu; Qing Lin; Yang Xi; Di Zhu; Jinyan Teng; Dailu Guan; Bingxing An; Jilong Ren; Yali Hou; Fei Wang; Bingjie Li; Laurent A.F. Frantz; Greger Larson; Zexi Cai; Goutam Sahana; Yu Jiang; Huizeng Sun; Dongxiao Sun; George E. Liu; Lingzhao Fang (2025). “An atlas of cell type specific regulatory effects in cattle.” Preprint. Link
Yağmur Halezeroğlu; Brenda M. Chiang; Stephanie Adame; Aheli Chattopadhyay; Ying Ma; Jeff Barry; Katrina Abuabara (2025). “Atopic dermatitis is a risk factor for total joint arthroplasty surgical site infections.” Journal of the European Academy of Dermatology and Venereology. Link
Huimin Li; Bencong Zhu; Xi Jiang; Ying Ma; Lin Xu; Qiwei Li (2025). “Robust Bayesian Integrative Modeling of Single Cell and Spatially Resolved Transcriptomics Data.” Preprint. Link
Nell Klimpert; Mihaly Kollo; David H. Brann; Chichun Tan; David Barry; Ying Ma; Andreas T. Schaefer; Alexander Fleischmann (2025). “3D spatial transcriptomics reveals the molecular structure of input and output pathways in the mouse olfactory bulb.” Preprint. Link
Jianhong Chen; Ying Ma; Xubo Yue (2025). “Temporal Causal Discovery in Dynamic Bayesian Networks Using Federated Learning.” IEEE Transactions on Artificial Intelligencelink
2024
Ying Ma; Xiang Zhou (2024). “Accurate and Efficient Integrative Reference-Informed Spatial Domain Detection for Spatial Transcriptomics.” Nature Methods. Link
Yanghong Guo; Bencong Zhu; Chen Tang; Ruichen Rong; Ying Ma; Guanghua Xiao; Lin Xu; Qiwei Li (2024). “BayeSMART: Bayesian clustering of multi-sample spatially resolved transcriptomics data.” Briefings in Bioinformatics. Link
2022
Ying Ma; Snehal Patil; Xiang Zhou; Bhramar Mukherjee; Lars G. Fritsche (2022). “ExPRSweb: An online repository with polygenic risk scores for common health-related exposures.” The American Journal of Human Genetics. PDF
Zhao, Peiyao; Jiaqiang Zhu; Ying Ma; Xiang Zhou (2022). “Modeling zero inflation is not necessary for spatial transcriptomics.” Genome Biology. DOI
Ying Ma; Xiang Zhou (2022). “Spatially informed cell type deconvolution for spatial transcriptomics.” Nature Biotechnology. Link
2021
Ying Ma; Xiang Zhou (2021). “Genetic prediction of complex traits with polygenic scores: a statistical review.” Trends in Genetics. Link
Fritsche, Lars G.; Ying Ma; Daiwei Zhang; Maxwell Salvatore; Seunggeun Lee; Xiang Zhou; Bhramar Mukherjee (2021). “On cross-ancestry cancer polygenic risk scores.” PLOS Genetics. Link
Fritsche, Lars G.; Snehal Patil; Lauren J. Beesley; Peter VandeHaar; Maxwell Salvatore; Ying Ma; Robert B. Peng; Daniel Taliun; Xiang Zhou; Bhramar Mukherjee (2021). “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. PDF
2020
Ying Ma; Shiquan Sun; Xuequn Shang; Evan T. Keller; Mengjie Chen; Xiang Zhou (2020). “Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies.” Nature Communications. Link
2019
Sun, Shiquan; Jiaqiang Zhu; Ying Ma; Xiang Zhou (2019). “Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis.” Genome Biology. Link
