scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning
Lin, Yingxin, Wu, Tung-Yu, Wan, Sheng, Yang, Jean Y. H., Wong, Wing H., Wang, Y. X. Rachel
Published in Nature biotechnology (01.05.2022)
Published in Nature biotechnology (01.05.2022)
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Transcriptional downregulation of MHC class I and melanoma de- differentiation in resistance to PD-1 inhibition
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
Published in Nature communications (20.04.2020)
Published in Nature communications (20.04.2020)
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Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2
Humphrey, Sean J., Yang, Guang, Yang, Pengyi, Fazakerley, Daniel J., Stöckli, Jacqueline, Yang, Jean Y., James, David E.
Published in Cell metabolism (04.06.2013)
Published in Cell metabolism (04.06.2013)
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Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2
Lin, Yingxin, Cao, Yue, Willie, Elijah, Patrick, Ellis, Yang, Jean Y. H.
Published in Nature communications (17.07.2023)
Published in Nature communications (17.07.2023)
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Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis
Geddes, Thomas A, Kim, Taiyun, Nan, Lihao, Burchfield, James G, Yang, Jean Y H, Tao, Dacheng, Yang, Pengyi
Published in BMC bioinformatics (24.12.2019)
Published in BMC bioinformatics (24.12.2019)
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BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data
Fu, Xiaohang, Lin, Yingxin, Lin, David M., Mechtersheimer, Daniel, Wang, Chuhan, Ameen, Farhan, Ghazanfar, Shila, Patrick, Ellis, Kim, Jinman, Yang, Jean Y. H.
Published in Nature communications (13.01.2024)
Published in Nature communications (13.01.2024)
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The impact of device-assisted therapies on the gut microbiome in Parkinson’s disease
Lubomski, Michal, Xu, Xiangnan, Holmes, Andrew J., Yang, Jean Y. H., Sue, Carolyn M., Davis, Ryan L.
Published in Journal of neurology (01.02.2022)
Published in Journal of neurology (01.02.2022)
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Scalable workflow for characterization of cell-cell communication in COVID-19 patients
Lin, Yingxin, Loo, Lipin, Tran, Andy, Lin, David M, Moreno, Cesar, Hesselson, Daniel, Neely, G Gregory, Yang, Jean Y H
Published in PLoS computational biology (01.10.2022)
Published in PLoS computational biology (01.10.2022)
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Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development
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
Published in BMC genomics (04.12.2017)
Published in BMC genomics (04.12.2017)
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PD-L1 Expression and Immune Escape in Melanoma Resistance to MAPK Inhibitors
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
Published in Clinical cancer research (15.10.2017)
Published in Clinical cancer research (15.10.2017)
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Imputation of plasma lipid species to facilitate integration of lipidomic datasets
Dakic, Aleksandar, Wu, Jingqin, Wang, Tingting, Huynh, Kevin, Mellett, Natalie, Duong, Thy, Beyene, Habtamu B., Magliano, Dianna J., Shaw, Jonathan E., Carrington, Melinda J., Inouye, Michael, Yang, Jean Y., Figtree, Gemma A., Curran, Joanne E., Blangero, John, Simes, John, Giles, Corey, Meikle, Peter J.
Published in Nature communications (20.02.2024)
Published in Nature communications (20.02.2024)
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LC-N2G: a local consistency approach for nutrigenomics data analysis
Xu, Xiangnan, Solon-Biet, Samantha M, Senior, Alistair, Raubenheimer, David, Simpson, Stephen J, Fontana, Luigi, Mueller, Samuel, Yang, Jean Y H
Published in BMC bioinformatics (17.11.2020)
Published in BMC bioinformatics (17.11.2020)
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Clonal evolution in liver cancer at single-cell and single-variant resolution
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
Published in Journal of hematology and oncology (02.02.2021)
Published in Journal of hematology and oncology (02.02.2021)
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Distinct Molecular Profiles and Immunotherapy Treatment Outcomes of V600E and V600K BRAF -Mutant Melanoma
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
Published in Clinical cancer research (15.02.2019)
Published in Clinical cancer research (15.02.2019)
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scDC: single cell differential composition analysis
Cao, Yue, Lin, Yingxin, Ormerod, John T, Yang, Pengyi, Yang, Jean Y H, Lo, Kitty K
Published in BMC bioinformatics (24.12.2019)
Published in BMC bioinformatics (24.12.2019)
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Targeting activating mutations of EZH2 leads to potent cell growth inhibition in human melanoma by derepression of tumor suppressor genes
Tiffen, Jessamy C, Gunatilake, Dilini, Gallagher, Stuart J, Gowrishankar, Kavitha, Heinemann, Anja, Cullinane, Carleen, Dutton-Regester, Ken, Pupo, Gulietta M, Strbenac, Dario, Yang, Jean Y, Madore, Jason, Mann, Graham J, Hayward, Nicholas K, McArthur, Grant A, Filipp, Fabian V, Hersey, Peter
Published in Oncotarget (29.09.2015)
Published in Oncotarget (29.09.2015)
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Viral Integration Plays a Minor Role in the Development and Prognostication of Oral Squamous Cell Carcinoma
Satgunaseelan, Laveniya, Strbenac, Dario, Tadi, Sahithi, Nguyen, Kevin, Wykes, James, Palme, Carsten E, Low, Tsu-Hui Hubert, Yang, Jean Y H, Clark, Jonathan R, Gupta, Ruta
Published in Cancers (24.10.2022)
Published in Cancers (24.10.2022)
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Integrated single cell data analysis reveals cell specific networks and novel coactivation markers
Ghazanfar, Shila, Bisogni, Adam J, Ormerod, John T, Lin, David M, Yang, Jean Y H
Published in BMC systems biology (05.12.2016)
Published in BMC systems biology (05.12.2016)
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