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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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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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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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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Circulating Cytokines Predict Immune-Related Toxicity in Melanoma Patients Receiving Anti-PD-1-Based Immunotherapy von Lim, Su Y, Lee, Jenny H, Gide, Tuba N, Menzies, Alexander M, Guminski, Alexander, Carlino, Matteo S, Breen, Edmond J, Yang, Jean Y H, Ghazanfar, Shila, Kefford, Richard F, Scolyer, Richard A, Long, Georgina V, 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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Ensemble deep learning in bioinformatics von Cao, Yue, Geddes, Thomas Andrew, Yang, Jean Yee Hwa, Yang, Pengyi

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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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Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE von Lin, Yingxin, Wu, Tung-Yu, Chen, Xi, Wan, Sheng, Chao, Brian, Xin, Jingxue, Yang, Jean, Wong, Wing H, Wang, Y X Rachel

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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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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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Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2 von Humphrey, Sean J., Yang, Guang, Yang, Pengyi, Fazakerley, Daniel J., Stöckli, Jacqueline, Yang, Jean Y., James, David E.

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A benchmark study of simulation methods for single-cell RNA sequencing data von Cao, Yue, Yang, Pengyi, Yang, Jean Yee Hwa

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3D reconstruction of spatial expression von Lin, Yingxin, 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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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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Distinct Molecular Profiles and Immunotherapy Treatment Outcomes of V600E and V600K BRAF -Mutant Melanoma von Pires da Silva, Inês, Wang, Kevin Y X, Wilmott, James S, Holst, Jeff, Carlino, Matteo S, Park, John J, Quek, Camelia, Wongchenko, Matthew, Yan, Yibing, Mann, Graham, Johnson, Douglas B, McQuade, Jennifer L, Rai, Rajat, Kefford, Richard F, Rizos, Helen, Scolyer, Richard A, Yang, Jean Y H, Long, Georgina V, Menzies, Alexander M

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Deep multimodal graph-based network for survival prediction from highly multiplexed images and patient variables von Fu, Xiaohang, Patrick, Ellis, Yang, Jean Y.H., Feng, David Dagan, Kim, Jinman

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