Publications

^† indicates co-first author.

Peer-Reviewed Publications

1. Clarke, H.A.^†, Ma, X.^†, Shedlock, C.J.^†, et al. Spatial mapping of the brain metabolome lipidome and glycome. Nature Communications, 16, 4373 (2025).
2. Ma, X.^†, Shedlock, C.J.^†, Medina, T.^†, et al. AI-driven framework to map the brain metabolome in three dimensions. Nature Metabolism (2025).
3. Clarke, H.A., Hawkinson, T.R., Clarke, H., et al., Ma, X. Glycogen drives tumour initiation and progression in lung adenocarcinoma. Nature Metabolism (2025).
4. Ma, X., Thela, S.R., Zhao, F., et al. Deep5hmC: predicting genome-wide 5-hydroxymethylcytosine landscape via a multimodal deep learning model. Bioinformatics, 40(9), btae528 (2024).
5. Zhao, F., Ma, X., Yao, B., et al. Scada: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data. PLOS Computational Biology, 20(8) (2024).

Manuscripts Under Revision

1. Rodriguez-Palma, E., Gomez, K., Calderon-Rivera, A., et al., Ma, X., et al. A peptidomimetic inhibitor of moesin alleviates chronic pain by suppressing NaV1.7 and NaV1.8 channels. Science Translational Medicine (under revision).
2. Ribas, R., Tang, Q., Caffee, S., et al., Ma, X., Chen, L., Sun, R., et al. Mass Spectrometry-based Spatial Imaging of the Cochlea. Journal of the American Society for Mass Spectrometry (under revision).
3. Guarnieri, J.W., Maghsoudi, Z., Kim, J., et al., Ma, X., et al. Guardians of the Mitochondria: Space Mitochondria 2.0 Systemic Analysis Reveals Bioenergetic Dysregulation Across Species. Cell (under revision).
4. Ma, X., Allison, D., Macedo, J.K.A., et al. Machine learning-based prediction of clinical outcomes in glioblastoma using glycomics features. Computational and Structural Biotechnology Journal (under revision).
5. Ma, X., Jin, W., Lu, Q., et al. Reference-Informed Detection of Spatial Domains Using Weak Supervision for Spatial Transcriptomics. Genome Research (under revision).

Manuscripts Under Review

1. Jin, W., Zhao, F., Ma, X., et al. DeepCNet: An interpretable deep learning model for inferring cell type-specific promoter-enhancer interactions from single-cell multiome data. Nature Communications (under review).
2. Hawkinson, T.R., Liu, Z., Ribas, R.A., et al., Ma, X. Hyper-Glycosylation as a Central Metabolic Driver of Alzheimer's Disease. Nature Metabolism (under review).

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