Publications

Selected Publications

Liu, J., Manabe, H., Qian, W., Wang, Y., Gu, Y., Chu, A. K. Y., Gadhvi, G., Song, Y., Ono, N., Welch, J. D. "CytoSignal Detects Locations and Dynamics of Ligand-Receptor Signaling at Cellular Resolution from Spatial Transcriptomic Data". Accepted at: Nature Genetics, 2026. DOI
Gu, Y.*, Liu, J.*, Lee, H. K., Li, C., Lu, L., Moline, J., Guan, R., Welch, J. D. "Topological Velocity Inference from Spatial Transcriptomic Data Maps Cell Fate Transition in Space and Time". In: Nature Biotechnology, 1-12 (2025). DOI
Matsushita, Y.*, Liu, J.*, Chu, A. K. Y., Tsutsumi-Arai, C., Nagata, M., Arai, Y., Ono, W., Yamamoto, K., Saunders, T. L., Welch, J. D., Ono, N. "Bone marrow endosteal stem cells dictate active osteogenesis and aggressive tumorigenesis". In: Nature Communications, 14.1 (2023), p. 2383. DOI
Liu, J.*, Gao, C.*, Sodicoff, J., Kozareva, V., Macosko, E. Z., Welch, J. D. "Jointly defining cell types from multiple single-cell datasets using LIGER". In: Nature Protocols, 15.11 (2020), pp. 3632-3662. DOI

* co-first author; # co-corresponding author

Liu, J., Manabe, H., Qian, W., Wang, Y., Gu, Y., Chu, A. K. Y., Gadhvi, G., Song, Y., Ono, N., Welch, J. D. “CytoSignal Detects Locations and Dynamics of Ligand-Receptor Signaling at Cellular Resolution from Spatial Transcriptomic Data”. Accepted at: Nature Genetics, 2026. DOI

Gu, Y.*, Liu, J.*, Lee, H. K., Li, C., Lu, L., Moline, J., Guan, R., Welch, J. D. “Topological Velocity Inference from Spatial Transcriptomic Data Maps Cell Fate Transition in Space and Time”. In: Nature Biotechnology, 1-12 (2025). DOI
Liu, J.#, Wang, Y., Li, C., Gu, Y., Ono, N., Welch, J. D.# “CytoSimplex: Visualizing Single-cell Fates and Transitions on a Simplex”. In: Bioinformatics (2025), btaf119. DOI
Zhang, H., Patrick, M. T., Zhao, J., Zhai, X., Liu, J., Li, Z., Gu, Y., Welch, J., Zhou, X., Modlin, R. L., Tsoi, L. C., Gudjonsson, J. E. “Techniques and analytic workflow for spatial transcriptomics and its application to allergy and inflammation”. In: Journal of Allergy and Clinical Immunology, 155.3 (2025), pp. 678-687. DOI

Gu, Y.*, Liu, J.*, Li, C., Welch, J. D. “Mapping Cell Fate Transition in Space and Time”. In: 28th International Conference on Research in Computational Molecular Biology (RECOMB), 2024. DOI

Matsushita, Y.*, Liu, J.*, Chu, A. K. Y., Tsutsumi-Arai, C., Nagata, M., Arai, Y., Ono, W., Yamamoto, K., Saunders, T. L., Welch, J. D., Ono, N. “Bone marrow endosteal stem cells dictate active osteogenesis and aggressive tumorigenesis”. In: Nature Communications, 14.1 (2023), p. 2383. DOI
Matsushita, Y., Liu, J., Chu, A. K. Y., Ono, W., Welch, J. D., Ono, N. “Endosteal stem cells at the bone-blood interface: A double-edged sword for rapid bone formation”. In: BioEssays, 46.3 (2023), p. 2300173. DOI

Alghamri, M. S., McClellan, B. L., Avvari, R. P., Thalla, R., Carney, S., Hartlage, C. S., Haase, S., Ventosa, M., Taher, A., Kamran, N., Zhang, L., Faisal, S. M., Nunnez, F. J., Garcia-Fabiani, M. B., Al-Holou, W. N., Orringer, D., Hervey-Jumper, S., Heth, J., Patil, P. G., Eddy, K., Merajver, S. D., Ulintz, P. J., Welch, J. D., Gao, C., Liu, J., Nunez, G., Hambardzumyan, D., Lowenstein, P. R., Castro, M. G. “G-CSF secreted by mutant IDH1 glioma stem cells abolishes myeloid cell immunosuppression and enhances the efficacy of immunotherapy”. In: Science Advances, 7.40 (2021), eabh3243. DOI
Gao, C., Liu, J., Kriebel, A. R., Preissl, S., Luo, C., Castanon, R., Sandoval, J., Rivkin, A., Nery, J. R., Behrens, M. M., Ecker, J. R., Ren, B., Welch, J. D. “Iterative single-cell multi-omic integration using online learning”. In: Nature Biotechnology, 39.8 (2021), pp. 1000-1007. DOI

Liu, J.*, Gao, C.*, Sodicoff, J., Kozareva, V., Macosko, E. Z., Welch, J. D. “Jointly defining cell types from multiple single-cell datasets using LIGER”. In: Nature Protocols, 15.11 (2020), pp. 3632-3662. DOI