Wang, D., Hou, S., Zhang, L. ..., Z. Zhang*.(2021) iMAP: integration of multiple single-cell datasets by
adversarial paired transfer networks. Genome Biol 22, 63 .(2021)
Zheng L, Z. Zhang*.(2021) Decoding the genetic basis of anti-tumor immunity. Immunity. 2021 Feb
9;54(2):199-201.
Cheng S, Li Z, Gao R, Xing B, Gao Y, Yang Y, Qin S, Zhang L, Ouyang H, Du P, Jiang L, Zhang B, Yang Y,
Wang X, Ren X, Bei JX, Hu X, Bu Z, Ji J, Z. Zhang*. (2021) A pan-cancer single-cell transcriptional atlas
of tumor infiltrating myeloid cells. Cell. 2021 Feb 4;184(3):792-809.e23
X. Ren,W. Wen ,X. Fan ,..., J. Chen, R. Jin, Z. Zhang*.(2021) COVID-19 immune features revealed by a
large-scale single-cell transcriptome atlas. Cell. 2021 Feb 3.
Liu Y, He S, Wang XL, Peng W, Chen QY, Chi DM, Chen JR, Han BW, Lin GW, Li YQ, Wang QY, Peng RJ, Wei PP,
Guo X, Li B, Xia X, Mai HQ, Hu XD, Zhang Z, Zeng YX, Bei JX. (2021)Tumour heterogeneity and intercellular
networks of nasopharyngeal carcinoma at single cell resolution. Nat Commun. 2021 Feb 2;12(1):741.
B. Liu, C. Li, Z. Li, D. Wang, X. Ren, and Z. Zhang*. (2020) An entropy-based metric for assessing the
purity of single cell populations, Nature Communications, 11:3155
X. Ren*, G. Zhong, Q. Zhang, L. Zhang, Y. Sun and Z. Zhang*. (2020) Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly. Cell Res. 2020 Sep;30(9):763-778.
Li J, Comeau HY, Zhang Z, Ren X.(2020) Landscape of transcript isoforms in single T cells infiltrating in non-small-cell lung cancer. J Genet Genomics. 2020 Jul 20;47(7):373-388.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.(2020) Pan-cancer analysis of whole genomes. Nature. 2020 Feb;578(7793):82-93.
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
Q. Zhang and Z. Zhang. (2020) Stepwise immune alterations in multiple myeloma progression.
Nature Cancer, (oi.org/10.1038/s43018-020-0063-1)
L. Zhang, Z. Li, K. M. Skrzypczynska, Q. Fang, W. Zhang, S. A. O’Brien, Y. He, L. Wang, Q. Zhang, A.
Kim, R. Gao, J. Orf, T. Wang, D. Sawant, J. Kang, D. Bhatt, D. Lu, C-M Li, A. Rapaport, K. Perez, Y. Ye,
S. Wang, X. Hu, X. Ren, W. Ouyang, Z. Shen*, J. G. Egen*, Z. Zhang. , and X. Yu*. (2020)
Single-cell
analyses inform mechanisms of myeloid-targeted therapies in colon cancer. Cell, 181:442-459
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
PCAWG Transcriptome Core Group, C. Calabrese, N. R. Davidson, D. Demircioğlu, N. A. Fonseca, Y. He, A.
Kahles, K-V Lehmann, F. Liu, Y. Shiraishi, C. M. Soulette, L. Urban, L. Greger, S. Li, D. Liu, M. D.
Perry, Q. Xiang, F. Zhang, J. Zhang, P. Bailey, S. Erkek, K. A. Hoadley, Y. Hou, M. R. Huska, H. Kilpinen,
J. O. Korbel, M. G. Marin, J. Markowski, T. Nandi, Q. Pan-Hammarström, C. S. Pedamallu, R. Siebert, S. G.
Stark, H. Su, P. Tan, S. M. Waszak, C. Yung, S. Zhu, P. Awadalla, C. J. Creighton, M. Meyerson, B. F.
Ouellette, K. Wu, H. Yang, PCAWG Transcriptome Working Group, A. Brazma*, A. N. Brooks*, J. Göke*, G.
Rätsch*, R. F. Schwarz*, O. Stegle*, Z. Zhang. & PCAWG Consortium. (2020) Genomic basis for RNA
alterations in cancer. Nature, 578:129-136
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*. Single cell epigenome sequencing technologies. Molecular Aspects of
Medicine, 59:
62-69 (2018) (Review) (*: Co-corresponding authors)
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)