Publications

†: Co-first/co-last author

Preprint

  • Zhang, D. †, Rubio Rodríguez-Kirby, L. †, Lin, Y., Song, M., Wang, L., …, & Zhao, H., Castelo-Branco, G., Fan, R. (2024) Spatial dynamics of mammalian brain development and neuroinflammation by multimodal tri-omics mapping. [paper]

  • Lim, S.Y., Lin, Y., Lee, J.H., Pedersen, B., Stewart, A., Scolyer, R.A., Long, G.V., Yang, J.Y.H., Rizos, H. (2024) Single-cell RNA sequencing reveals melanoma cell state-dependent heterogeneity of response to MAPK inhibitors. [paper]

  • Hsu, I. U., Lin, Y., Guo, Y., Xu, Q. J., Shao, Y., Wang, R. L., Yin, D., Zhao, J., Young, L.H., Zhao, H., Zhang, L., Chang, R. B. (2023) Differential developmental blueprints of organ-intrinsic nervous systems. [paper]

  • Cao, Y., Yu, L., Torkel, M., Kim, S., Lin, Y., Yang, P., Speed, T., Ghazanfar, S., Yang, J.Y.H. (2023) The current landscape and emerging challenges of benchmarking single-cell methods. [paper]

  • Yin, D., Cao, Y., Chen, J., Mak, C.L.Yl, Yu, K.H.O., Lin, Y. †, Ho, J. W. K. †, Yang, J.Y.H. †. (2022) Covidscope: An atlas-scale COVID-19 resource for single-cell meta analysis at sample and cell levels. [paper]

Publication

Methodologies and tools

  • 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 [paper]

  • Fu, X.†, Lin, Y.†, Lin, D., Mechtersheimer, D., Wang, C., Ameen, F., Ghazanfar, S., Patrick, E., Kim, J. and Yang, J.Y.H. (2024) Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data. Nature Communications [paper]

  • Lin, Y.†, Wu, T.Y.†, Chen, X.†, Wan, S., Chao, B., Xin, J., Yang, J.Y.H., Wong, W.H. and Wang, Y.R. (2024) Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE. Genome Research [paper]

  • Lin, Y., Cao, Y., Willie, E., Patrick, E., Yang, J.Y.H. (2023) Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2. Nature Communications [paper]

  • Lin, Y.†, Wu, T.Y.†, Wan, S., Yang, J.Y.H., Wong, W.H., and Wang, Y.X.R.(2022) scJoint: transfer learning for data integration of single-cell RNA-seq and ATAC-seq. Nature Biotechnology. [package][paper]

  • Cao, Y., Lin, Y., Patrick, E., Yang, P., and Yang, J.Y.H. (2022) scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction. Bioinformatics. [package][paper]

  • Kim, H.J., Wang, K.Y., Chen, C., Lin, Y., Tam, P., Lin, D.M., Yang, J.Y.H. and Yang, P. (2021) Uncovering cell identity through differential stability with Cepo. Nature Computational Science. [package][paper]

  • 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. [package][paper]

  • 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. Molecular Systems Biology. [package][shiny][paper]

  • 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. [package][shiny][paper]

  • 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. [package] [paper]

  • Lin, Y., Ghazanfar, S., Strbenac, D., Wang, A., Patrick, E., Lin, D., Speed, T., Yang, J.Y.H. & Yang, P. (2019) Evaluating stably expressed genes in single cells. GigaScience. [package] [paper]

  • Cao, Y.†, Lin, Y.†, Ormerod, J., Yang, P., Yang, J.Y.H. & Lo, K. (2019) scDC: single cell differential composition analysis. BMC Bioinformatics. [package] [paper]

  • Kim, T., Chen, I.R., Lin, Y., Wang, A.Y.Y., Yang, J.Y.H. and Yang, P. (2019) Impact of similarity metrics on single-cell RNA-seq data clustering. Briefings in bioinformatics, 20(6), pp.2316-2326. [paper]

Applications

Single-cell

  • Cao, Y., Tran, A., Kim, H., Robertson, N., Lin, Y., Torkel, M., Yang, P., Patrick, E., Ghazanfar, S., Yang, J.Y.H. (2023) Thinking process templates for constructing data stories with SCDNEY. [paper]
  • Lin, Y., Loo, L., Tran, A., Moreno, C., Hesselson D., Neely, G., and Yang, J.Y.H. (2022) Characterization of cell-cell communication in COVID-19 patients. PLoS Computational Biology. [paper]
  • He, J.†, Lin, Y.†, Meng M., Li J., Yang, J.Y.H., Wang H. (2021) Construction of a human cell landscape of COVID-19 infection at single-cell level. Aging and disease. [paper]
  • Su, X., Zhao, L., Shi, Y., Zhang, R., Long, Q., Bai, S., Luo, Q., Lin, Y., Zou, X., Ghazanfar, S. and Tao, K., … & Han, Z.G. (2021) Clonal evolution in liver cancer at single-cell and single-variant resolution. Journal of hematology & oncology.[paper]
  • Su, X., Long, Q., Bo, J., Shi, Y., Zhao, L.N., Lin Y., Luo, Q., Ghazanfar, S., Zhang, C., Liu, Q., Wang, L., He, K., He, J., Cui, X., Yang, J.Y.H., Han, Z.G., Yang, G., and Sha, J.J. (2020) Mutational and transcriptomic landscapes of a rare human prostate basal cell carcinoma. The Prostate. [paper]

Other omics

  • Martinez, A. P., Chung, A. C., Huang, S., Bisogni, A. J., Lin, Y., Cao, Y., … & Lin, D. M. (2023) Pcdh19 mediates olfactory sensory neuron coalescence during postnatal stages and regeneration. Iscience, 26(11).

Kidney transplant

  • Philipoff, A. †, Lin, Y.†, Teixeira-Pinto, A., Gately, R., Craig, J.C., …, Wong, G. & Lim, W. (2024) Antecedent Cardiac Arrest Status of Donation After Circulatory Determination of Death (DCDD) Kidney Donors and the Risk of Delayed Graft Function After Kidney Transplantation: A Cohort Study. Transplantation. [paper]

  • Lin, Y., Teixeira-Pinto, A., Craig, J., Opdam, H., Chapman, J., Pleass, H., Carter, A., Rogers N., Davies, C., McDonald, S., Yang, J., Lim, W., and Wong, G. (2023) Trajectories of systolic blood pressure decline in kidney transplant donors prior to circulatory death and delayed graft function. Clinical Kidney Journal. [paper]

  • Zhang, Y., Hu, A., Lin, Y., Cao, Y., Muller, S., Wong, G., and Yang, J.Y.H. (2023) simKAP: Simulation framework for the kidney allocation process with decision making model. Scientific Reports [paper]

  • Lin, Y., Teixeira-Pinto, A., Opdam, H., Chapman, J. R., Craig, J. C., Rogers, N., … & Wong, G. (2022) Nonutilization of Kidneys From Donors After Circulatory Determinant of Death. Transplantation Direct. [paper]

  • Lim, W.H., Ooi E., Pankaj, A., Teixeira-Pinto, A., Lin, Y., … & Wong, G. (2022) The incidence of cancer recurrence and new cancer following commencement of dialysis. Clinical Kidney Journal. [paper]

  • Chung, E., Blazek, K., Teixeira-Pinto, A., Sharma, A., Kim, S., Lin, Y., … & Wong, G. (2022) Predictive Models for Recurrent Membranous Nephropathy After Kidney Transplantation. Transplantation Direct. [paper]

Review & news

  • Kim, D., Tran, A., Kim, H.J., Lin, Y., Yang, J.Y.H. and Yang, P. (2023) Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data. npj Systems Biology and Applications. [paper]

  • Lin, Y. and Yang, J.Y. (2022) 3D reconstruction of spatial expression. Nature Methods. [paper]