Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data von Linderman, George C., Rachh, Manas, Hoskins, Jeremy G., Steinerberger, Stefan, Kluger, Yuval

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Zero-preserving imputation of single-cell RNA-seq data von Linderman, George C., Zhao, Jun, Roulis, Manolis, Bielecki, Piotr, Flavell, Richard A., Nadler, Boaz, Kluger, Yuval

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DeepSurv: personalized treatment recommender system using a Cox proportional hazards deep neural network von Katzman, Jared L, Shaham, Uri, Cloninger, Alexander, Bates, Jonathan, Jiang, Tingting, Kluger, Yuval

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Ranking and combining multiple predictors without labeled data von Parisi, Fabio, Strino, Francesco, Nadler, Boaz, Kluger, Yuval

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Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden von Qing, Tao, Mohsen, Hussein, Marczyk, Michal, Ye, Yixuan, O’Meara, Tess, Zhao, Hongyu, Townsend, Jeffrey P., Gerstein, Mark, Hatzis, Christos, Kluger, Yuval, Pusztai, Lajos

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Inflammasome activation in infected macrophages drives COVID-19 pathology von 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.

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PCGF Homologs, CBX Proteins, and RYBP Define Functionally Distinct PRC1 Family Complexes von Gao, Zhonghua, Zhang, Jin, Bonasio, Roberto, Strino, Francesco, Sawai, Ayana, Parisi, Fabio, Kluger, Yuval, Reinberg, Danny

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TrAp: a tree approach for fingerprinting subclonal tumor composition von Strino, Francesco, Parisi, Fabio, Micsinai, Mariann, Kluger, Yuval

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Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome von 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.

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Removal of batch effects using distribution-matching residual networks von Shaham, Uri, Stanton, Kelly P, Zhao, Jun, Li, Huamin, Raddassi, Khadir, Montgomery, Ruth, Kluger, Yuval

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PD-L1 Studies Across Tumor Types, Its Differential Expression and Predictive Value in Patients Treated with Immune Checkpoint Inhibitors von 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

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Detection of differentially abundant cell subpopulations in scRNA-seq data von Zhao, Jun, Jaffe, Ariel, Li, Henry, Lindenbaum, Ofir, Sefik, Esen, Jackson, Ruaidhrí, Cheng, Xiuyuan, Flavell, Richard A., Kluger, Yuval

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Paracrine orchestration of intestinal tumorigenesis by a mesenchymal niche von 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.

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Spatial epigenome–transcriptome co-profiling of mammalian tissues von 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

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A highly efficient and faithful MDS patient-derived xenotransplantation model for pre-clinical studies von 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

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Nlrp9b inflammasome restricts rotavirus infection in intestinal epithelial cells von 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.

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Gating mass cytometry data by deep learning von Li, Huamin, Shaham, Uri, Stanton, Kelly P, Yao, Yi, Montgomery, Ruth R, Kluger, Yuval

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Genome-wide remodeling of the epigenetic landscape during myogenic differentiation von Asp, Patrik, Blum, Roy, Vethantham, Vasupradha, Parisi, Fabio, Micsinai, Mariann, Cheng, Jemmie, Bowman, Christopher, Kluger, Yuval, Dynlacht, Brian David

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Humanized mouse liver reveals endothelial control of essential hepatic metabolic functions von 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.

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Three-Dimensional Reconstruction Pre-Training as a Prior to Improve Robustness to Adversarial Attacks and Spurious Correlation von Yamada, Yutaro, Zhang, Fred Weiying, Kluger, Yuval, Yildirim, Ilker

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