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C. Li, B. Liu, B. Kang, Z. Liu, Y. Liu, C. Chen, X. Ren*, and Z. Zhang. . SciBet as a portable and fast single cell type identifier. Nature Communications, 11:1818

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R. Bernards, E. Jaffee, J. A. Joyce, S. W. Lowe, E. R. Mardis, S. J. Morrison, K. Polyak, C. L. Sears, K. H. Vousden, and Z. Zhang. (2020) A roadmap for the next decade in cancer research. Nature Cancer, 1:12-17

R. Yang, S. Cheng, N. Luo, R. Gao, K. Yu, B. Kang, L. Wang, Q. Zhang, Q. Fang, L. Zhang, C. Li, A. He, X. Hu, J. Peng*, X. Ren*, and Z. Zhang. . (2020) Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis. Genome Biology, 21:2

X. Wang, Y. He, Q. Zhang, X. Ren, and Z. Zhang. (2020) Direct comparative analysis of 10X Genomics Chromium and Smart-seq2. Genome, Proteome and Bioinformatics, (accepted)

F. Liu, Y. Zhang, L. Zhang, Z. Li, Q. Fang, R. Gao, and Z. Zhang. (2019) Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data. Genome Biology, 20:242

Q. Zhang, Y. He, N. Luo, S. J. Patel, Y. Han, R. Gao, M. Modak, S. Carotta, C. Haslinger, D. Kind, G. W. Peet, G. Zhong, S. Lu, W. Zhu, Y. Mao, M. Xiao, M. Bergmann, X. Hu, S. P. Kerkar, A. B. Vogt, S. Pflanz, K. Liu*, J. Peng*, X. Ren*, and Z. Zhang. (2019) Landscape and dynamics of single immune cells in hepatocellular carcinoma. Cell, 179:829-845.

F. Liu, Y. Zhang, L. Zhang, Z. Li, Q. Fang, R. Gao, and Z. Zhang. (2019) Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data. Genome Biology, 20:242

H. Yang, L. Xia, J. Chen, S. Zhang, V. Martin, Q. Li, S. Lin, J. Chen, J. Calmette, M. Lu, L. Fu, J. Yang, Z. Pan, K. Yu, J. He, E.Morand, G. Schlecht-Louf, R. Krzysiek, L. Zitvogel, B. Kang, Z. Zhang, A. Leader, P. Zhou, L. Lanfumey, M. Shi, G. Kroemer, and Y. Ma. (2019) Stress–glucocorticoid–TSC22D3 axis compromises therapy-induced antitumor immunity. Nature Medicine, 26:1428-1441.

X. Ren and Z. Zhang. (2019) Understanding tumor-infiltrating lymphocytes by single cell RNA sequencing. Advances in Immunology, 144:217-245

Y. Zhang, L. Zheng, L. Zhang, X. Hu, X. Ren, and Z. Zhang (2019) Deep single-cell RNA sequencing data of individual T cells from treatment-naïve colorectal cancer patients. Scientific Data, 6:131.

A. Kim, C-J Han, I. Driver, A. Olow, A. K. Sewell, Z. Zhang, W. Ouyang, J. G. Egen, and X. Yu. (2019) LILRB1 blockade enhances bispecific T cell engager antibody-induced tumor cell killing by effector CD8+ T cells. The Journal of Immunology, 203:1076-1087

Z. Tang, B. Kang, C. Li, T. Chen, and Z. Zhang. (2019) GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis. Nucleic Acids Research, 47:W556-W560

L. Zhang and Z. Zhang. (2019) Recharacterizing tumor-infiltrating lymphocytes by single-cell RNA sequencing. Cancer Immunology Research, 7:1040-1046.

R. Xue, L. Chen, C. Zhang, M. Fujita, R. Li, S.-M. Yan, C. K. Ong, X. Liao, Q. Gao, S. Sasagawa, Y. Li, J. Wang, H. Guo, Q.-T. Huang, Q. Zhong, J. Tan, L. Qi, W. Gong, Z. Hong, M. Li, J. Zhao, T. Peng, Y. Lu, K. H. T. Lim, A. Boot, A. Ono, K. Chayama, Z. Zhang, S. G. Rozen, B. T. Teh, X. W. Wang, H. Nakagawa, M.-S. Zeng, F. Bai, and N. Zhang. (2019) Genomic and Transcriptomic Profiling of Combined Hepatocellular and Intrahepatic Cholangiocarcinoma Reveals Distinct Molecular Subtypes. Cancer cell, 35:932-947

X. Ren*, L. Zheng, and Z. Zhang. . (2019) SSCC: a computational framework for rapid and accurate clustering of large-scale single cell RNA-seq data. Genome, Proteome and Bioinformatics, 17:201-210

C. Zheng, L. Zheng, J.-K. Yoo, H. Guo, Y. Zhang, X. Guo, B. Kang, R. Hu, J. Y. Huang, Q. Zhang, Z. Liu, M. Dong, X. Hu, W. Ouyang*, J. Peng*, and Z. Zhang. . (2017) Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing. Cell, 169(7), 1342–1356

Z. Tang, C. Li, B. Kang, G. Gao, C. Li, and Z. Zhang. (2017) GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Research, 45(W1):W98-W102

Wen L*, Tang Fuchou*. Human Germline Cell Development: from the Perspective of Single-Cell Sequencing. Molecular Cell, 76: 320-328 (2019)(Review)(*: Co-corresponding authors)

Wen L*, Tang Fuchou*. Boosting the power of single-cell analysis. Nature Biotechnology, 36: 408-409 (2018) (Preview) (*: Co-corresponding authors)

Wen L*, Tang Fuchou*. Single-cell sequencing in stem cell biology. Genome Biology 17: 71 (2016) (*: Co-corresponding authors) (Review)

Tang Fuchou, Lao K, Surani MA. Development and applications of single-cell transcriptome analysis. Nature Methods 8: S6-S11 (2011) (Review)

Yang L, Ma Z, Cao C, Zhang Y, Wu X, Lee R, Hu B, Wen L, Ge H, Huang Y*, Lao K*, Tang Fuchou*. MR-seq: measuring a single cell’s transcriptome repeatedly by RNA-seq. Science Bulletin, 62: 391-398 (2017) (*: Co-corresponding authors)

Tang Fuchou, Barbacioru C, Nordman E, Li B, Xu N, Bashkirov VI, Lao K, Surani MA. RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nature Protocols 5: 516-535 (2010)

Tang Fuchou*, Barbacioru C*, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA. mRNA-Seq whole transcriptome analysis of a single cell. Nature Methods 6: 377 - 382 (2009) (*: Co-first authors)

Tang Fuchou, Hajkova P, Barton SC, O`Carroll D, Lee C, Lao K, Surani MA. 220-plex microRNA expression profile of a single cell. Nature Protocols 1: 1154 - 1159 (2006)

Wang S, Zheng Y, Li J, Yu Y, Zhang W, Song M, Liu Z, Min Z, Hu H, Jing Y, He X, Sun L, Ma L, Esteban CR, Chan P, Qiao J, Zhou Q, Izpisua Belmonte JC*, Qu J*, Tang Fuchou*, Liu GH*. Single-Cell Transcriptomic Atlas of Primate Ovarian Aging. Cell, 180: 585-600 (2020) (*: Co-corresponding authors)

Soares E, Xu Q, Li Q, Qu J, Zheng Y, Raeven HHM, Brandao KO, Petit I, van den Akker WMR, van Heeringen SJ, Aberdam D, Tang Fuchou*, Zhou H*. Single-cell RNA-seq identifies a reversible mesodermal activation in abnormally specified epithelia of p63 EEC syndrome. Proc Natl Acad Sci U S A, 116: 17361-17370 (2019) (*: Co-corresponding authors)

Hu Y, Wang X, Hu B, Mao Y, Chen Y, Yan L, Yong J, Dong J, Wei Y, Wang W, Wen L, Qiao J*, Tang Fuchou*. Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis. PLoS Biology, 17: e3000365 (2019) (*: Co-corresponding authors)

Cui Y, Zheng Y, Liu X, Yan L, Fan X, Yong J, Hu Y, Dong J, Li Q, Wu X, Gao S, Li J, Wen L, Qiao J*, Tang Fuchou*. Single-cell transcriptome analysis maps the developmental track of the human heart. Cell Reports, 26: 1934–1950 (2019) (*: Co-corresponding authors)

Ji Q, Zheng Y, Zhang G, Hu Y, Fan X, Hou Y, Wen L, Li L, Xu Y, Wang Y*, Tang Fuchou*. Single-cell RNA-seq analysis reveals the progression of human osteoarthritis. Annals of the Rheumatic Diseases, 78: 100-110 (2019) (*: Co-corresponding authors)

Bian S, Hou Y, Zhou X, Li X, Yong J, Wang Y, Wang W, Yan J, Hu B, Guo H, Wang J, Gao S, Mao Y, Dong J, Zhu P, Xiu D, Yan L, Wen L, Qiao J*, Tang Fuchou*, Fu W*. Single-cell multiomics sequencing and analyses of human colorectal cancer. Science, 362: 1060-1063 (2018) (*: Co-corresponding authors)

Wang P, Chen Y, Yong J, Cui Y, Wang R, Wen L, Qiao J*, Tang Fuchou*. Dissecting the global dynamic molecular profiles of human fetal kidney development by single-cell RNA sequencing. Cell Reports, 24: 3554-3567 (2018) (*: Co-corresponding authors)

Wang M, Liu X, Chang G, Chen Y, An G, Yan L, Gao S, Xu Y, Cui Y, Dong J, Chen Y, Fan X, Hu Y, Song K, Zhu X, Gao Y, Yao Z, Bian S, Hou Y, Lu J, Wang R, Fan Y, Lian Y, Tang W, Wang Y, Liu J, Zhao L, Wang L, Liu Z, Yuan R, Shi Y, Hu B, Ren X, Tang Fuchou*, Zhao XY*, Qiao J*. Single-cell RNA sequencing analysis reveals sequential cell fate transition during human spermatogenesis. Cell Stem Cell, 23: 599-614 (2018) (*: Co-corresponding authors)

Chen Y, Zheng Y, Gao Y, Lin Z, Yang S, Wang T, Wang Q, Xie N, Hua R, Liu M, Sha J, Griswold MD, Li J*, Tang Fuchou*, Tong MH*. Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis. Cell Research, 28: 879–896 (2018)

Li L, Guo F, Gao Y, Ren Y, Yuan P, Yan L, Li R, Liang Y, Li J, Hu B, Gao J, Wen L, Tang Fuchou*, Qiao J*. Single-cell multi-omics sequencing of human early embryos. Nature Cell Biology, 20: 847-858 (2018) (*: Co-corresponding authors)

Fan X, Dong J, Zhong S, Wei Y, Wu Q, Yan L, Yong J, Sun L, Wang X, Zhao Y, Wang W, Yan J, Wang X*, Qiao J*, Tang Fuchou*. Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis. Cell Research, 28: 730-745 (2018) (*: Co-corresponding authors)

Gao S, Yan L, Wang R, Li J, Yong J, Zhou X, Wei Y, Wu X, Wang X, Fan X, Yan J, Zhi X, Gao Y, Guo H, Jin X, Wang W, Mao Y, Wang F, Wen L, Fu W, Ge H*, Qiao J*, Tang Fuchou*. Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing. Nature Cell Biology, 20: 721-734 (2018) (*: Co-corresponding authors)

Zhong S, Zhang S, Fan X, Wu Q, Yan L, Dong J, Zhang H, Li L, Sun L, Pan N, Xu X, Tang Fuchou*, Zhang J*, Qiao J*, Wang X*. A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. Nature, 555: 524-528 (2018) (*: Co-corresponding authors)

Zhu P, Guo H, Ren Y, Hou Y, Dong J, Li R, Lian Y, Fan X, Hu B, Gao Y, Wang X, Wei Y, Liu P, Yan J, Ren X, Yuan P, Yuan Y, Yan Z, Wen L, Yan L*, Qiao J*, Tang Fuchou*. Single-cell DNA methylome sequencing of human preimplantation embryos. Nature Genetics, 50: 12-19 (2018) (*: Co-corresponding authors)

Dong J, Hu Y, Fan X, Wu X, Mao Y, Hu B, Guo H, Wen L, Tang Fuchou*. Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis. Genome Biology, 19: 31 (2018) (*: Corresponding author)

Guo F*, Li L, Li J, Wu X, Hu B, Zhu P, Wen L, Tang Fuchou*. Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells. Cell Research, 27: 967-988 (2017) (Cover story) (*: Co-corresponding authors)

Li L, Dong J, Yan L, Yong J, Liu X, Hu Y, Fan X, Wu X, Guo H, Wang X, Zhu X, Li R, Yan J, Wei Y, Zhao Y, Wang W, Ren Y, Yuan P, Yan Z, Hu B, Guo F, Wen L, Tang Fuchou*, Qiao J*. Single-cell RNA-seq analysis maps development of human germline cells and gonadal niche interactions. Cell Stem Cell, 20: 858-873 (2017) (*: Co-corresponding authors)

Zhu C, Gao Y, Guo H, Xia B, Song J, Wu X, Zeng H, Kee K, Tang Fuchou*, Yi C*. Single-cell 5-formylcytosine landscapes of mammalian early embryos and ESCs at single-base resolution. Cell Stem Cell, 20: 720-731 (2017) (*: Co-corresponding authors)

Zhou F, Li X, Wang W, Zhu P, Zhou J, He W, Ding M, Xiong F, Zheng X, Li Z, Ni Y, Mu X, Wen L, Cheng T, Lan Y, Yuan W*, Tang Fuchou*, Liu B*. Tracing haematopoietic stem cell formation at single-cell resolution. Nature, 533: 487-492 (2016) (*: Co-corresponding authors)

Zhu C, Gao Y, Guo H, Xia B, Song J, Wu X, Zeng H, Kee K, Tang Fuchou*, Yi C*. Single-cell 5-formylcytosine landscapes of mammalian early embryos and ESCs at single-base resolution. Cell Stem Cell, 20: 720-731 (2017) (*: Co-corresponding authors)

Hou Y, Guo H, Cao C, Li X, Hu B, Zhu P, Wu X, Wen L, Tang Fuchou*, Huang Y*, Peng J*. Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Research 26: 304-319 (2016) (*: Co-corresponding authors)

Fan X, Zhang X, Wu X, Guo H, Hu Y, Tang Fuchou*, Huang Y*. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biology 16: 148 (2015) (*: Co-corresponding authors)

Guo H, Zhu P, Guo F, Li X, Wu X, Fan X, Wen L*, Tang Fuchou*. Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing. Nature Protocols 10: 645-659 (2015) (*: Co-corresponding authors)

Wen L, Tang Fuchou*. Reconstructing complex tissues from single-cell analyses. Cell 157: 771-773 (2014)

Streets AM, Zhang X, Cao C, Pang Y, Wu X, Xiong L, Yang L, Fu Y, Zhao L*, Tang Fuchou*, Huang Y*. Microfluidic single-cell whole-transcriptome sequencing. Proc Natl Acad Sci U S A 111: 7048-7053 (2014) (*: Co-corresponding authors)

Guo H, Zhu P, Wu X, Li X, Wen L, Tang Fuchou*. Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Research 23: 2126-2135 (2013) (*: Corresponding author)

Yan L, Yang M, Guo H, Yang L, Wu J, Li R, Liu P, Lian Y, Zheng X, Yan J, Huang J, Li M, Wu X, Wen L, Lao K, Li R*, Qiao J*, Tang Fuchou*. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nature Structural & Molecular Biology 20: 1131-1139 (2013) (*: Co-corresponding authors)

Tang Fuchou, Barbacioru C, Bao S, Lee C, Nordman E, Wang X, Lao K, Surani MA. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell 6: 468 - 478 (2010)