Publications

Huidong Chen, Jayoung Ryu, Michael E Vinyard, Adam Lerer, Luca Pinello (2023). SIMBA: SIngle-cell eMBedding Along with features. Nature Methods.

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Haichuan Hu, Zofia Piotrowska, Patricia J. Hare, Huidong Chen, Hillary E. Mulvey, Aislinn Mayfield, Sundus Noeen, Krystina Kattermann, Max Greenberg, August Williams, Amanda K. Riley, Jarad J. Wilson, Ying-Qing Mao, Ruo-Pan Huang, Mandeep K. Banwait, Jeffrey Ho, Giovanna S. Crowther, Lida P. Hariri, Rebecca S. Heist, David P. Kodack, Luca Pinello, Alice T. Shaw, Mari Mino-Kenudson, Aaron N. Hata, Lecia V. Sequist, Cyril H. Benes, Matthew J. Niederst, Jeffrey A. Engelman (2021). Three subtypes of lung cancer fibroblasts define distinct therapeutic paradigms. Cancer Cell.

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David F. Stein, Huidong Chen, Michael E. Vinyard, Qian Qin, Rebecca D. Combs, Qian Zhang, Luca Pinello (2021). singlecellVR: Interactive Visualization of Single-Cell Data in Virtual Reality. Front. genet.

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Lingfei Wang, Qian Zhang, Qian Qin, Nikolaos Trasanidis, Michael Vinyard, Huidong Chen, Luca Pinello (2021). Current progress and potential opportunities to infer single-cell developmental trajectory and cell fate. Curr. Opin. Syst. Biol..

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Carman Man-Chung Li, Hana Shapiro, Christina Tsiobikas, Laura M. Selfors, Huidong Chen, Jennifer Rosenbluth, Luca Pinello, Kaitlin Moore, Kushali P. Gupta, G. Kenneth Gray, Yaara Oren, Michael J. Steinbaugh, Jennifer L. Guerriero, Aviv Regev, Joan S. Brugge (2020). Aging-associated alterations in mammary epithelia and stroma revealed by single-cell RNA sequencing. Cell Rep..

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Ik Soo Kim, Jingyi Wu, Gilbert J. Rahme, Sofia Battaglia, Atray Dixit, Elizabeth Gaskell, Huidong Chen, Luca Pinello, Bradley E. Bernstein (2020). Parallel single-cell RNA-seq and genetic recording reveals lineage decisions in developing embryoid bodies. Cell Rep..

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Luca Albergante, Evgeny Mirkes, Jonathan Bac, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander Gorban, Andrei Zinovyev (2020). Robust and scalable learning of complex intrinsic dataset geometry via ElPiGraph. Entropy.

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Huidong Chen, Caleb Lareau, Tommaso Andreani, Michael E. Vinyard, Sara P. Garcia, Kendell Clement, Miguel A. Andrade-Navarro, Jason D. Buenrostro, Luca Pinello (2019). Assessment of computational methods for the analysis of single-cell ATAC-seq data. Genome Biol..

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Huidong Chen, Luca Albergante, Jonathan Y. Hsu, Caleb A. Lareau, Giosuè Lo Bosco, Jihong Guan, Shuigeng Zhou, Alexander N. Gorban, Daniel E. Bauer, Martin J. Aryee, David M. Langenau, Andrei Zinovyev, Jason D. Buenrostro, Guo-Cheng Yuan, Luca Pinello (2019). Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nat. Commun..

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Xiaoping Han, Haide Chen, Daosheng Huang, Huidong Chen, Lijiang Fei, Chen Cheng, He Huang, Guo-Cheng Yuan, Guoji Guo (2018). Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing. Genome Biol..

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Qin Tang, Sowmya Iyer, Riadh Lobbardi, John C. Moore, Huidong Chen, Caleb Lareaun, Christine Hebert, McKenzie L. Shaw, Cyril Neftel, Mario L. Suva, Craig J. Ceol, Andre Bernards, Martin Aryee, Luca Pinello, Iain A. Drummond, David M. Langenau (2017). Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing. J. Exp. Med..

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Lan Jiang, Huidong Chen, Luca Pinello, Guo-Cheng Yuan (2016). GiniClust: detecting rare cell types from single-cell gene expression data with Gini index. Genome Biol..

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Huidong Chen, Jihong Guan, Shuigeng Zhou (2015). Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. TCBB.

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