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Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data
Linderman, George C., Rachh, Manas, Hoskins, Jeremy G., Steinerberger, Stefan, Kluger, Yuval
Published in Nature methods (01.03.2019)
Published in Nature methods (01.03.2019)
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Zero-preserving imputation of single-cell RNA-seq data
Linderman, George C., Zhao, Jun, Roulis, Manolis, Bielecki, Piotr, Flavell, Richard A., Nadler, Boaz, Kluger, Yuval
Published in Nature communications (11.01.2022)
Published in Nature communications (11.01.2022)
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Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden
Qing, Tao, Mohsen, Hussein, Marczyk, Michal, Ye, Yixuan, O’Meara, Tess, Zhao, Hongyu, Townsend, Jeffrey P., Gerstein, Mark, Hatzis, Christos, Kluger, Yuval, Pusztai, Lajos
Published in Nature communications (15.05.2020)
Published in Nature communications (15.05.2020)
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Inflammasome activation in infected macrophages drives COVID-19 pathology
Sefik, Esen, Qu, Rihao, Junqueira, Caroline, Kaffe, Eleanna, Mirza, Haris, Zhao, Jun, Brewer, J. Richard, Han, Ailin, Steach, Holly R., Israelow, Benjamin, Blackburn, Holly N., Velazquez, Sofia E., Chen, Y. Grace, Halene, Stephanie, Iwasaki, Akiko, Meffre, Eric, Nussenzweig, Michel, Lieberman, Judy, Wilen, Craig B., Kluger, Yuval, Flavell, Richard A.
Published in Nature (London) (16.06.2022)
Published in Nature (London) (16.06.2022)
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Ranking and combining multiple predictors without labeled data
Parisi, Fabio, Strino, Francesco, Nadler, Boaz, Kluger, Yuval
Published in Proceedings of the National Academy of Sciences - PNAS (28.01.2014)
Published in Proceedings of the National Academy of Sciences - PNAS (28.01.2014)
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PCGF Homologs, CBX Proteins, and RYBP Define Functionally Distinct PRC1 Family Complexes
Gao, Zhonghua, Zhang, Jin, Bonasio, Roberto, Strino, Francesco, Sawai, Ayana, Parisi, Fabio, Kluger, Yuval, Reinberg, Danny
Published in Molecular cell (10.02.2012)
Published in Molecular cell (10.02.2012)
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TrAp: a tree approach for fingerprinting subclonal tumor composition
Strino, Francesco, Parisi, Fabio, Micsinai, Mariann, Kluger, Yuval
Published in Nucleic acids research (01.09.2013)
Published in Nucleic acids research (01.09.2013)
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Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome
Raredon, Micha Sam Brickman, Yang, Junchen, Garritano, James, Wang, Meng, Kushnir, Dan, Schupp, Jonas Christian, Adams, Taylor S., Greaney, Allison M., Leiby, Katherine L., Kaminski, Naftali, Kluger, Yuval, Levchenko, Andre, Niklason, Laura E.
Published in Scientific reports (09.03.2022)
Published in Scientific reports (09.03.2022)
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Spatial epigenome–transcriptome co-profiling of mammalian tissues
Zhang, Di, Deng, Yanxiang, Kukanja, Petra, Agirre, Eneritz, Bartosovic, Marek, Dong, Mingze, Ma, Cong, Ma, Sai, Su, Graham, Bao, Shuozhen, Liu, Yang, Xiao, Yang, Rosoklija, Gorazd B., Dwork, Andrew J., Mann, J. John, Leong, Kam W., Boldrini, Maura, Wang, Liya, Haeussler, Maximilian, Raphael, Benjamin J., Kluger, Yuval, Castelo-Branco, Gonçalo, Fan, Rong
Published in Nature (London) (06.04.2023)
Published in Nature (London) (06.04.2023)
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Removal of batch effects using distribution-matching residual networks
Shaham, Uri, Stanton, Kelly P, Zhao, Jun, Li, Huamin, Raddassi, Khadir, Montgomery, Ruth, Kluger, Yuval
Published in Bioinformatics (Oxford, England) (15.08.2017)
Published in Bioinformatics (Oxford, England) (15.08.2017)
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Pembrolizumab for management of patients with NSCLC and brain metastases: long-term results and biomarker analysis from a non-randomised, open-label, phase 2 trial
Goldberg, Sarah B, Schalper, Kurt A, Gettinger, Scott N, Mahajan, Amit, Herbst, Roy S, Chiang, Anne C, Lilenbaum, Rogerio, Wilson, Frederick H, Omay, Sacit Bulent, Yu, James B, Jilaveanu, Lucia, Tran, Thuy, Pavlik, Kira, Rowen, Elin, Gerrish, Heather, Komlo, Annette, Gupta, Richa, Wyatt, Hailey, Ribeiro, Matthew, Kluger, Yuval, Zhou, Geyu, Wei, Wei, Chiang, Veronica L, Kluger, Harriet M
Published in The lancet oncology (01.05.2020)
Published in The lancet oncology (01.05.2020)
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Detection of differentially abundant cell subpopulations in scRNA-seq data
Zhao, Jun, Jaffe, Ariel, Li, Henry, Lindenbaum, Ofir, Sefik, Esen, Jackson, Ruaidhrí, Cheng, Xiuyuan, Flavell, Richard A., Kluger, Yuval
Published in Proceedings of the National Academy of Sciences - PNAS (01.06.2021)
Published in Proceedings of the National Academy of Sciences - PNAS (01.06.2021)
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Paracrine orchestration of intestinal tumorigenesis by a mesenchymal niche
Roulis, Manolis, Kaklamanos, Aimilios, Schernthanner, Marina, Bielecki, Piotr, Zhao, Jun, Kaffe, Eleanna, Frommelt, Laura-Sophie, Qu, Rihao, Knapp, Marlene S., Henriques, Ana, Chalkidi, Niki, Koliaraki, Vasiliki, Jiao, Jing, Brewer, J. Richard, Bacher, Maren, Blackburn, Holly N., Zhao, Xiaoyun, Breyer, Richard M., Aidinis, Vassilis, Jain, Dhanpat, Su, Bing, Herschman, Harvey R., Kluger, Yuval, Kollias, George, Flavell, Richard A.
Published in Nature (London) (23.04.2020)
Published in Nature (London) (23.04.2020)
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Humanized mouse liver reveals endothelial control of essential hepatic metabolic functions
Kaffe, Eleanna, Roulis, Manolis, Zhao, Jun, Qu, Rihao, Sefik, Esen, Mirza, Haris, Zhou, Jing, Zheng, Yunjiang, Charkoftaki, Georgia, Vasiliou, Vasilis, Vatner, Daniel F., Mehal, Wajahat Z., Yuval Kluger, Flavell, Richard A.
Published in Cell (31.08.2023)
Published in Cell (31.08.2023)
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Nlrp9b inflammasome restricts rotavirus infection in intestinal epithelial cells
Zhu, Shu, Ding, Siyuan, Wang, Penghua, Wei, Zheng, Pan, Wen, Palm, Noah W., Yang, Yi, Yu, Hua, Li, Hua-Bing, Wang, Geng, Lei, Xuqiu, de Zoete, Marcel R., Zhao, Jun, Zheng, Yunjiang, Chen, Haiwei, Zhao, Yujiao, Jurado, Kellie A., Feng, Ningguo, Shan, Liang, Kluger, Yuval, Lu, Jun, Abraham, Clara, Fikrig, Erol, Greenberg, Harry B., Flavell, Richard A.
Published in Nature (London) (29.06.2017)
Published in Nature (London) (29.06.2017)
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SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data
Dong, Mingze, Su, David G., Kluger, Harriet, Fan, Rong, Kluger, Yuval
Published in Nature communications (27.03.2025)
Published in Nature communications (27.03.2025)
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PD-L1 Studies Across Tumor Types, Its Differential Expression and Predictive Value in Patients Treated with Immune Checkpoint Inhibitors
Kluger, Harriet M., Zito, Christopher R., Turcu, Gabriela, Baine, Marina K., Zhang, Hongyi, Adeniran, Adebowale, Sznol, Mario, Rimm, David L., Kluger, Yuval, Chen, Lieping, Cohen, Justine V., Jilaveanu, Lucia B.
Published in Clinical cancer research (01.08.2017)
Published in Clinical cancer research (01.08.2017)
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A highly efficient and faithful MDS patient-derived xenotransplantation model for pre-clinical studies
Song, Yuanbin, Rongvaux, Anthony, Taylor, Ashley, Jiang, Tingting, Tebaldi, Toma, Balasubramanian, Kunthavai, Bagale, Arun, Terzi, Yunus Kasim, Gbyli, Rana, Wang, Xiaman, Fu, Xiaoying, Gao, Yimeng, Zhao, Jun, Podoltsev, Nikolai, Xu, Mina, Neparidze, Natalia, Wong, Ellice, Torres, Richard, Bruscia, Emanuela M., Kluger, Yuval, Manz, Markus G., Flavell, Richard A., Halene, Stephanie
Published in Nature communications (21.01.2019)
Published in Nature communications (21.01.2019)
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