Guo, Yuanchuan; Jun S. Liu#; Huimin Cheng#; Ying Ma# (2025). “JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics.” NeurIPS 2025 (accepted).
Chichun Tan and Ying Ma# (2025). “A Spatially Informed Matrix Normal Model for Gene Co-expression Analysis in Spatial Transcriptomics Studies.” Nucleic Acids Research (accepted).
Ying Ma# (2025). “Bridging histology and spatial gene expression across scales.” Nature Methods (commentary paper) Link
Jain, Atishay; David H. Laidlaw; Ying Ma; R. Singh (2025). “Improved Spatial Transcriptomics Clustering with Nested Graph Neural Networks.” ACM-BCB 2025 (accepted).
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.” Preprint. IEEE Transactions on Artificial Intelligence (accepted)
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
