Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data von Yu, Lijia, Cao, Yue, Yang, Jean Y H, Yang, Pengyi

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Transcriptional downregulation of MHC class I and melanoma de- differentiation in resistance to PD-1 inhibition von Lee, Jenny H., Shklovskaya, Elena, Lim, Su Yin, Carlino, Matteo S., Menzies, Alexander M., Stewart, Ashleigh, Pedersen, Bernadette, Irvine, Malama, Alavi, Sara, Yang, Jean Y. H., Strbenac, Dario, Saw, Robyn P. M., Thompson, John F., Wilmott, James S., Scolyer, Richard A., Long, Georgina V., Kefford, Richard F., Rizos, Helen

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Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2 von Lin, Yingxin, Cao, Yue, Willie, Elijah, Patrick, Ellis, Yang, Jean Y. H.

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Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis von Geddes, Thomas A, Kim, Taiyun, Nan, Lihao, Burchfield, James G, Yang, Jean Y H, Tao, Dacheng, Yang, Pengyi

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Scalable workflow for characterization of cell-cell communication in COVID-19 patients von Lin, Yingxin, Loo, Lipin, Tran, Andy, Lin, David M, Moreno, Cesar, Hesselson, Daniel, Neely, G Gregory, Yang, Jean Y H

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BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data von Fu, Xiaohang, Lin, Yingxin, Lin, David M., Mechtersheimer, Daniel, Wang, Chuhan, Ameen, Farhan, Ghazanfar, Shila, Patrick, Ellis, Kim, Jinman, Yang, Jean Y. H.

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Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development von Su, Xianbin, Shi, Yi, Zou, Xin, Lu, Zhao-Ning, Xie, Gangcai, Yang, Jean Y H, Wu, Chong-Chao, Cui, Xiao-Fang, He, Kun-Yan, Luo, Qing, Qu, Yu-Lan, Wang, Na, Wang, Lan, Han, Ze-Guang

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Clonal evolution in liver cancer at single-cell and single-variant resolution von Su, Xianbin, Zhao, Linan, Shi, Yi, Zhang, Rui, Long, Qi, Bai, Shihao, Luo, Qing, Lin, Yingxin, Zou, Xin, Ghazanfar, Shila, Tao, Kun, Yang, Guoliang, Wang, Lan, He, Kun-Yan, Cui, Xiaofang, He, Jian, Wu, Jiao-Xiang, Han, Bo, Yan, Bin, Deng, Biao, Wang, Na, Li, Xiaolin, Yang, Pengyi, Hou, Shangwei, Sun, Jielin, Yang, Jean Y. H., Chen, Jinhong, Han, Ze-Guang

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scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning von Lin, Yingxin, Wu, Tung-Yu, Wan, Sheng, Yang, Jean Y. H., Wong, Wing H., Wang, Y. X. Rachel

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LC-N2G: a local consistency approach for nutrigenomics data analysis von Xu, Xiangnan, Solon-Biet, Samantha M., Senior, Alistair, Raubenheimer, David, Simpson, Stephen J., Fontana, Luigi, Mueller, Samuel, Yang, Jean Y. H.

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3D reconstruction of spatial expression von Lin, Yingxin, Yang, Jean Y. H.

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Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis von Ghazanfar, Shila, Vuocolo, Tony, Morrison, Janna L, Nicholas, Lisa M, McMillen, Isabella C, Yang, Jean Y H, Buckley, Michael J, Tellam, Ross L

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The impact of device-assisted therapies on the gut microbiome in Parkinson’s disease von Lubomski, Michal, Xu, Xiangnan, Holmes, Andrew J., Yang, Jean Y. H., Sue, Carolyn M., Davis, Ryan L.

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Lipidomics Profiling and Risk of Coronary Artery Disease in the BioHEART-CT Discovery Cohort von Zhu, Dantong, Vernon, Stephen T, D'Agostino, Zac, Wu, Jingqin, Giles, Corey, Chan, Adam S, Kott, Katharine A, Gray, Michael P, Gholipour, Alireza, Tang, Owen, Beyene, Habtamu B, Patrick, Ellis, Grieve, Stuart M, Meikle, Peter J, Figtree, Gemma A, Yang, Jean Y H

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Cross-Platform Omics Prediction procedure: a statistical machine learning framework for wider implementation of precision medicine von Wang, Kevin Y. X., Pupo, Gulietta M., Tembe, Varsha, Patrick, Ellis, Strbenac, Dario, Schramm, Sarah-Jane, Thompson, John F., Scolyer, Richard A., Muller, Samuel, Tarr, Garth, Mann, Graham J., Yang, Jean Y. H.

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PD-L1 Expression and Immune Escape in Melanoma Resistance to MAPK Inhibitors von Kakavand, Hojabr, Rawson, Robert V, Pupo, Gulietta M, Yang, Jean Y H, Menzies, Alexander M, Carlino, Matteo S, Kefford, Richard F, Howle, Julie R, Saw, Robyn P M, Thompson, John F, Wilmott, James S, Long, Georgina V, Scolyer, Richard A, Rizos, Helen

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scDC: single cell differential composition analysis von Cao, Yue, Lin, Yingxin, Ormerod, John T, Yang, Pengyi, Yang, Jean Y H, Lo, Kitty K

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Evaluating stably expressed genes in single cells von Lin, Yingxin, Ghazanfar, Shila, Strbenac, Dario, Wang, Andy, Patrick, Ellis, Lin, David M, Speed, Terence, Yang, Jean Y H, Yang, Pengyi

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The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies von Lubomski, Michal, Xu, Xiangnan, Holmes, Andrew J, Muller, Samuel, Yang, Jean Y H, Davis, Ryan L, Sue, Carolyn M

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