Publications

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* Co-first authors # Co-corresponding authors

Preprint

1. Jiyuan Yang, Yang Qu, Nana Wei, Congcong Hu, Hua-Jun Wu#, Xiaoqi Zheng#. Spider: a flexible and unified framework for simulating spatial transcriptomics data.(Paper)

2. Congcong Hu, Nana Wei, Jiyuan Yang, Hua-Jun Wu#, Xiaoqi Zheng#. STCC: consensus clustering enhances spatial domain detection for spatial transcriptomics data.(Paper)

2024

31. Gangjian Wang*, Haojie Wang*, Xin Ji*, Tong Wange, Ye Zhang, Wenjie Jiang, Lin Meng, Hua-Jun Wu#, Xiaofang Xing#, and Jiafu Ji#. (2024). Intratumoral microbiome is associated with gastric cancer prognosis and therapy efficacy. Gut Microbes. (PDF)

30. Chunge Zhong*, Wen-Jie Jiang*, Yingjia Yao, Zexu Li, You Li, Shengnan Wang, Xiaofeng Wang, Wenjuan Zhu, Siqi Wu, Jing Wang, Shuangshuang Fan, Shixin Ma, Yeshu Liu, Han Zhang, Wenchang Zhao, Lu Zhao, Yi Feng, Zihan Li, Ruifang Guo, Li Yu, Fengyun Pei, Jun Hu, Xingzhi Feng, Zihuan Yang, Zhengjia Yang, Xueying Yang, Yue Hou, Danni Zhang, Dake Xu, Ren Sheng, Yihao Li, Lijun Liu, Hua-Jun Wu#, Jun Huang#, Teng Fei#. (2024). CRISPR screens reveal convergent targeting strategies against evolutionarily distinct chemoresistance in cancer. Nature Communications. (PDF)

2023

29. Jiang W-J*, Hu C, Lai F, Pang W, Yi X, Xu Q, Wang H, Zhou J, Zhu H, Zhong C, Kuang Z, Fan R， Shen J, Zhou X, Wang Y-J, Wong Catherine C. L#, Zheng X#, Wu H-J#. (2023). Assessing base-resolution DNA mechanics on the genome scale. Nucleic Acids Research. (PDF)(Code)(News)(Web)(Data1)(Data2)

28. Yao Y*, Zhang Y, Li Z, Chen Z, Wang X, Li Z, Yu L, Cheng X, Li W, Jiang W-J, Wu H-J, Feng Z, Sun J, Fei T# (2023) A deep learning-based drug repurposing screening and validation for anti-SARS-CoV-2 compounds by targeting the cell entry mechanism. Biochem Biophys Res Commun. 2023 Oct 1;675:113-121.(PDF)

27. Landshammer A*, Bolondi A*, Kretzmer H, Much C, Buschow R, Rose A, Wu H-J, Mackowiak SD, Braendl B, Giesselmann P, Tornisiello R, Parsi KM, Huey J, Mielke T, Meierhofer D, Maehr R, Hnisz D, Michor F, Rinn JL, Meissner A# (2023) T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation. eLife 12, e83077. (PDF)(Code)(Data)

2022

26. Wei N*, Nie Y, Liu L#, Zheng X#, Wu H-J#. Secuer: Ultrafast, scalable and accurate clustering of single-cell RNA-seq data.PLOS Computational Biology. 2022;18(12):e1010753. (PDF)(Code)(News)(Data)(Data)(Data)(Data)(Data)

25. Wu H-J*, Temko D*, Maliga Z*, Moreira A, Sei E, Minussi DC, Dean J, Lee C, Xu Q, Hochart G, Jacobson C, Yapp C, Schapiro D, Sorger P, Seeley EH, Navin N, Downey RJ, Michor F. Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients. Cell Genomics.2022;2(8):100165.(PDF)(Code)(Data)

2021

24. Wu H-J*, Landshammer A/*, Stamenova EK, Bolondi A, Kretzmer H, Meissner A, et al. Topological isolation of developmental regulators in mammalian genomes. Nature Communications. 2021;12(1):4897.(PDF)(Code)(Data)

2020

23. Shu S*, Wu H-J*, Ge JY, Zeid R, Harris IS, Jovanović B, et al. Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer. Molecular Cell. 2020;78(6):1096-113.e8.(PDF)(Data)

2019

22. Zhang W, Li Z, Wei N, Wu H-J, Zheng X. Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities. Bioinformatics. 2019;36(7):2017-24.(PDF)(Tool)

2018

21. Hinohara K*, Wu H-J*, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, et al. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer Cell. 2018;34(6):939-53.e9. (PDF)(Data)

20. Jun HJ*, Appleman VA*, Wu H-J*, Rose CM, Pineda JJ, Yeo AT, et al. A PDGFRα-driven mouse model of glioblastoma reveals a stathmin1-mediated mechanism of sensitivity to vinblastine. Nature Communications. 2018;9(1):3116.(PDF)(Data)

19. Cimino PJ, Kim Y, Wu H-J, Alexander J, Wirsching H-G, Szulzewsky F, et al. Increased HOXA5 expression provides a selective advantage for gain of whole chromosome 7 in IDH wild-type glioblastoma. Genes & development. 2018;32(7-8):512-23.(PDF)

2017

18. Han L*, Wu H-J*, Zhu H*, Kim K-Y, Marjani SL, Riester M, et al. Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucleic Acids Research. 2017;45(10):e77-e.(PDF)

17. Riester M*, Wu H-J*, Zehir A, Gönen M, Moreira AL, Downey RJ, et al. Distance in cancer gene expression from stem cells predicts patient survival. PLOS ONE. 2017;12(3):e0173589.(PDF)

16. Zheng X, Zhang N, Wu H-J, Wu H. Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies. Genome Biology. 2017;18(1):17(PDF)

2016

15. Wu H-J*, Michor F. A computational strategy to adjust for copy number in tumor Hi-C data. Bioinformatics. 2016;32(24):3695-701.(PDF)

14. Mahajan N, Wu H-J, Bennett RL, Troche C, Licht JD, Weber JD, et al. Sabotaging of the oxidative stress response by an oncogenic noncoding RNA. FASEB J. 2017;31(2):482-90.(PDF)

2015

13. Zhang N*, Wu H-J*, Zhang W, Wang J, Wu H, Zheng X. Predicting tumor purity from methylation microarray data. Bioinformatics. 2015;31(21):3401-5.(PDF)

2014

12. Zheng X*, Zhao Q*, Wu H-J*, Li W, Wang H, Meyer CA, et al. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biology. 2014;15(7):419.(PDF)

2013

11. Fu S, Lv Z, Gao Z, Wu H-J, Pang J, Zhang B, et al. De novo centromere formation on a chromosome fragment in maize. 2013;110(15):6033-6.(PDF)

10. Zhang B, Lv Z, Pang J, Liu Y, …, Wu H-J, et al. Formation of a Functional Maize Centromere after Loss of Centromeric Sequences and Gain of Ectopic Sequences The Plant Cell. 2013;25(6):1979-89.(PDF)

9. Wu H-J*, Wang Z-M*, Wang M, Wang X-J. Widespread Long Noncoding RNAs as Endogenous Target Mimics for MicroRNAs in Plants Plant Physiology. 2013;161(4):1875-84(PDF)

8. Ling H-Q, Zhao S, Liu D, Wang J, …, Wu H-J, …, Wang J, et al. Draft genome of the wheat A-genome progenitor Triticum urartu. Nature. 2013;496(7443):87-90(PDF)

2012

7. Li W, Shuai L, Wan H, Dong M, …, Wu H-J, Liu Z-H, et al.Androgenetic haploid embryonic stem cells produce live transgenic mice. Nature. 2012;490(7420):407-11.(PDF)

6. Wu H-J*, Ma Y-K*, Chen T, Wang M, Wang X-J. PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucleic Acids Research. 2012;40(W1):W22-W8.(PDF)

5. Wu H-J*, Zhang Z*, Wang J-Y*, Oh D-H*, Dassanayake M*, Liu B*, et al. Insights into salt tolerance from the genome of Thellungiella salsuginea. 2012;109(30):12219-24.(PDF)

4. Sheng C, Zheng Q, Wu J, …,Wu H-J, …,Wang X-J, et al. Direct reprogramming of Sertoli cells into multipotent neural stem cells by defined factors. Cell Research. 2012;22(1):208-18.(PDF)

2011

3. Tong M, Lv Z, Liu L, Zhu H, …, Wu H-J, …,Wang X-J, et al. Mice generated from tetraploid complementation competent iPS cells show similar developmental features as those from ES cells but are prone to tumorigenesis. Cell Research. 2011;21(11):1634-7.(PDF)

2010

2. Liu L, Luo G-Z, Yang W, …, Wu H-J,Wang Liu, et al. Activation of the Imprinted Dlk1-Dio3Region Correlates with Pluripotency Levels of Mouse Stem Cells. Journal of Biological Chemistry. 2010;285(25):19483-90.(PDF)

2009

1. Wuriyanghan H, Zhang B, …,Wu H-J, …,Wang X-J,et al. The Ethylene Receptor ETR2 Delays Floral Transition and Affects Starch Accumulation in Rice. The Plant Cell. 2009;21(5):1473-94.(PDF)