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Tang J, Liang S, Alam S, Cheng W, Zhang Y, and Ma J.
A meta-interaction basis for cell-cell communication in tissues.
bioRxiv, https://doi.org/10.64898/2026.09.21.753369
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Zhang Y†, Lu X†, Kunisky AK‡, Alam S‡, Tang J‡, Zhang R‡, Wang S, Zhang H, Baroudi J, Ichcho W, Jia D, Ghorbanikalateh S, Ghorbanikalateh S, Wang S, Bennett DA, Mathys H*, Duan Z*, and Ma J*.
Single-cell multiomics connects 3D genome and transcriptome alterations in Alzheimer's disease.
Science, 393(6809):eadz1652, 2026.
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Deshpande A, Bei Z, Ma J*, and Krieger S*.
MIMYR: Generative modeling of missing tissue in spatial transcriptomics.
bioRxiv, https://doi.org/10.1101/2025.11.24.690239
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Liu S, Tang J, Ma J*, and Liang S*.
TissueNarrator: Generative Modeling of Spatial Transcriptomics with Large Language Models.
bioRxiv, https://doi.org/10.1101/2025.11.24.690325
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Haber E†, Alam S†, Ho N†, Liu R, Trop E, Liang S, Yang M, Krieger S*, and Ma J*.
HEIMDALL: A modular framework for tokenization in single-cell foundation models.
bioRxiv, https://doi.org/10.1101/2025.11.09.687403
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Krieger S, Haber E, and Ma J.
EYKTHYR reveals transcriptional regulators of spatial gene programs.
bioRxiv, https://doi.org/10.1101/2025.05.19.654884
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Alam S, Zhou T, Haber E, Chidester B, Liu S, and Chen F, and Ma J.
POPARI: Modeling multisample variation in spatial transcriptomics.
bioRxiv, https://doi.org/10.1101/2025.05.08.652741
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Liang S, Tang J, Wang G, and Ma J.
STEAMBOAT: Attention-based multiscale delineation of cellular interactions in tissues.
bioRxiv, https://doi.org/10.1101/2025.04.06.647437
RECOMB, 2025.
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Haber E, Deshpande A, Ma J*, and Krieger S*.
Unified integration of spatial transcriptomics across platforms with LLOKI.
Genome Research, 35(12):2722-2733, 2025.
RECOMB, 2025.
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Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z*, and Ma J*.
GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells.
Nature Genetics, 56(8):1701-1711, 2024.
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Xiong K†, Zhang R†, and Ma J.
scGHOST: Identifying single-cell 3D genome subcompartments.
Nature Methods, 21(5):814-822, 2024.
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Chidester B†, Zhou T†, Alam S, and Ma J.
SPICEMIX enables integrative single-cell spatial modeling of cell identity.
Nature Genetics, 55(1):78-88, 2023. [Cover Article]
RECOMB, 2021.
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Zhang R†, Zhou T†, and Ma J.
Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi.
Cell Systems, 13(10):P798-807.E6, 2022. [Cover Article]
RECOMB, 2022.
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Zhang R, Zhou T, and Ma J.
Multiscale and integrative single-cell Hi-C analysis with Higashi.
Nature Biotechnology, 40:254–261, 2022.