Staphylococcus aureus host interactions and adaptation
Howden, Benjamin P., Giulieri, Stefano G., Wong Fok Lung, Tania, Baines, Sarah L., Sharkey, Liam K., Lee, Jean Y. H., Hachani, Abderrahman, Monk, Ian R., Stinear, Timothy P.
Published in Nature reviews. Microbiology (01.06.2023)
Published in Nature reviews. Microbiology (01.06.2023)
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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
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Published in Nature communications (20.04.2020)
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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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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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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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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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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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Cryptic susceptibility to penicillin/β-lactamase inhibitor combinations in emerging multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages
Ba, Xiaoliang, Raisen, Claire L., Restif, Olivier, Cavaco, Lina Maria, Vingsbo Lundberg, Carina, Lee, Jean Y. H., Howden, Benjamin P., Bartels, Mette D., Strommenger, Birgit, Harrison, Ewan M., Larsen, Anders Rhod, Holmes, Mark A., Larsen, Jesper
Published in Nature communications (14.10.2023)
Published in Nature communications (14.10.2023)
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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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Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis
Lee, Jean Y. H., Monk, Ian R., Gonçalves da Silva, Anders, Seemann, Torsten, Chua, Kyra Y. L., Kearns, Angela, Hill, Robert, Woodford, Neil, Bartels, Mette D., Strommenger, Birgit, Laurent, Frederic, Dodémont, Magali, Deplano, Ariane, Patel, Robin, Larsen, Anders R., Korman, Tony M., Stinear, Timothy P., Howden, Benjamin P.
Published in Nature microbiology (01.10.2018)
Published in Nature microbiology (01.10.2018)
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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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Zinc-binding to the cytoplasmic PAS domain regulates the essential WalK histidine kinase of Staphylococcus aureus
Monk, Ian R., Shaikh, Nausad, Begg, Stephanie L., Gajdiss, Mike, Sharkey, Liam K. R., Lee, Jean Y. H., Pidot, Sacha J., Seemann, Torsten, Kuiper, Michael, Winnen, Brit, Hvorup, Rikki, Collins, Brett M., Bierbaum, Gabriele, Udagedara, Saumya R., Morey, Jacqueline R., Pulyani, Neha, Howden, Benjamin P., Maher, Megan J., McDevitt, Christopher A., King, Glenn F., Stinear, Timothy P.
Published in Nature communications (11.07.2019)
Published in Nature communications (11.07.2019)
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Genomic Insights Into Last-Line Antimicrobial Resistance in Multidrug-Resistant Staphylococcus and Vancomycin-Resistant Enterococcus
Turner, Adrianna M, Lee, Jean Y H, Gorrie, Claire L, Howden, Benjamin P, Carter, Glen P
Published in Frontiers in microbiology (16.03.2021)
Published in Frontiers in microbiology (16.03.2021)
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Within-host evolution of bovine Staphylococcus aureus selects for a SigB-deficient pathotype characterized by reduced virulence but enhanced proteolytic activity and biofilm formation
Marbach, Helene, Mayer, Katharina, Vogl, Claus, Lee, Jean Y. H., Monk, Ian R., Sordelli, Daniel O., Buzzola, Fernanda R., Ehling-Schulz, Monika, Grunert, Tom
Published in Scientific reports (17.09.2019)
Published in Scientific reports (17.09.2019)
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