Academic Background

Research Interest

Publication

1. Chen, S. †, Lin, Y. †, Yang, H. †, Li. Z., Li. S., Chen, D., …, & Liu, H., 2025. A CD26+ tendon stem cell population contributes to tendon repair and heterotopic ossification. Nature Communications, 16(1), 749.
2. Li, H. †, Lin, Y. †, He, W., Han, W., Xu, X., Xu, C., Gao, E., Zhao, H., Gao, X., 2024. SANTO: a coarse-to-fine stitching and alignment method for spatial omics. Nature Communications, 15(1), 6048.
3. Fu, X. †, Lin, Y. †, Lin, D., Mechtersheimer, D., Wang, C., Ameen, F., … & Yang, J. Y. H., 2024. BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data. Nature Communications, 15(1), 509.
4. Lin, Y., Cao, Y., Willie, E., Patrick, E. and Yang, J.Y.H., 2023. Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2. Nature Communications, 14(1), 4272.
5. Lin, Y.†, Wu, T.Y.†, Chen, X.†, Wan, S., Chao, B., Xin, J., Yang, J.Y.H., Wong, W.H., Wang, Y.X.R., 2023. Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE. Genome Research, 34(1), 119-133.
6. Lin, Y. †, Wu, T.Y. †, Wan, S., Yang, J.Y.H., Wong, W.H., and Wang, Y.X.R., 2022. scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning. Nature Biotechnology, 40(5), 703-710.
7. Lin, Y., Cao, Y., Kim, H.J., Salim, A., Speed, T., Lin, D.M., Yang, P. and Yang, J.Y.H., 2020. scClassify: sample size estimation and multiscale classification of cells using single and multiple reference. Mol. Syst. Biol., 16(6), e9389.
8. Ghazanfar, S., Lin, Y., Su, X., Lin, D.M., Patrick, E., Han, Z.G., Marioni, J.C. and Yang, J.Y.H., 2020. Investigating higher order interactions in single-cell data with scHOT. Nature Methods, 17(8), 799-806.
9. Kim, H.J. †, Lin, Y. †, Geddes, T.A., Yang, J.Y.H. and Yang, P., 2020. CiteFuse enables multi-modal analysis of CITE-seq data, Bioinformatics, 36(14), 4137-4143.
10. Lin, Y., Ghazanfar, S., Wang, K.Y., Gagnon-Bartsch, J.A., Lo, K.K., Su, X., Han, Z.G., Ormerod, J.T., Speed, T.P., Yang, P. and Yang, J.Y.H., 2019. scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets. Proceedings of the National Academy of Sciences, 116(20), 9775-9784.
12. † indicates co-first author/equal contribution

Major Research Grants

• 2024 – 2027 Australian National Health and Medical Research Council (NHMRC) Ideas Grant – Title: Precision-based strategies to overcome treatment resistance in dedifferentiated melanoma.

Honours and Awards

Professional Services

• Reviewer for Nature, Nature Methods, Nature Biotechnology, Nature Communications, Nature Computational Science, Genome Biology, Briefings in bioinformatics, Kidney international, Kidney international reports, Computational and Structural Biotechnology Journal, PLoS Computational Biology, Journal of Genetics and Genomics, GigaScience.

Research group/personal website links

• https://yingxinlin.github.io/