Publications

Tumor-specific lncRNA IGF1R-AS1 trans-regulates chromatin interactions associated with oncogenic MYC signaling

Yongyong Yang#, Ting-You Wang#, Joshua Fry#, Yingming Li#, Qingshu Meng#, Nathan E. Patchen, Abhirami Ramakrishnan, et al.

Nature Communications, 2026, 17(1). (#Co-first authors)

Paper

A genomic language model for chimera artifact detection in Nanopore direct RNA sequencing

Yangyang Li#, Ting-You Wang#, Qingxiang Guo, Yanan Ren, Xiaotong Lu, Qi Cao, Rendong Yang.

Nature Communications, 2026, 17(1), 1864. (#Co-first authors)

Paper

Ketone drink enhances therapeutic efficacy in prostate cancer by targeting EZH2

Chaehyun Yum, Richard Schaefer, Rui Wang, Ting-You Wang, Xiaotong Lu, Qi Liu, et al.

Oncogenesis, 2025, 14(1), 24.

Paper

Androgen receptor-regulated lncRNA PRCAT71 promotes AR signaling through the interaction with KHSRP in prostate cancer

Yongyong Yang, Ting-You Wang, Qianru Li, Jiawen Lu, Yanan Ren, Adam B. Weiner, Joshua Fry, et al.

Science Advances, 2025, 11(15).

Paper

EZH2 directly methylates PARP1 and regulates its activity in cancer

Qingshu Meng, Jiangchuan Shen, Yanan Ren, Qi Liu, Rui Wang, Qiaqia Li, Weihua Jiang, Quan Wang, Yixiang Zhang, Jonathan Trinidad, Xiaotong Lu, Tingyou Wang, Yanqiang Li, et al.

Science Advances, 2024, 10(48).

Paper

Comparative analyses of gene networks mediating cancer metastatic potentials across lineage types

Sheng Wang, Emily K Stroup, Ting-You Wang, Rendong Yang, Zhe Ji.

Briefings in Bioinformatics, 2024, 25(4).

Paper

Chapter 5: Detecting Medium and Large Insertions and Deletions with transIndel

Ting-You Wang and Rendong Yang.

Variant Calling - Methods and Protocols, Humana, New York, NY, 2022, vol 2493.

Paper

Opposing transcriptional programs of KLF5 and AR emerge during therapy for advanced prostate cancer

Meixia Che, Aashi Chaturvedi, Sarah Munro, Samuel Pitzen, Alexander Ling, Weijie Zhang, Joshua Mentzer, Sheng-Yu Ku, Loredana Puca, Yanyun Zhu, Andries Bergman, Tesa Severson, Colleen Forster, Yuzhen Liu, Jacob Hildebrand, Mark Daniel, Ting-You Wang et al.

Nature Communications, 2021, 12, 6377.

Paper

A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes

Ting-You Wang, Qi Liu, Yanan Ren, Sk. Kayum Alam, Li Wang, Zhu Zhu, Luke H. Hoeppner, Scott M. Dehm, Qi Cao, Rendong Yang.

Molecular Cell, 2021, 81:2246-2260 e2212. (Highlighted in Cancer Immunology Research, June 1, 2021)

Paper

Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo

Ting-You Wang and Rendong Yang.

STAR Protocols, 2021, 2, 100788.

Paper

LncGSEA: a versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data

Yanan Ren, Ting-You Wang, Leah Anderton, Qi Cao, Rendong Yang.

BMC Genomics, 2021, 22(1):574.

Paper

Identification of 38 novel loci for systemic lupus erythematosus and genetic heterogeneity between ancestral groups

Yong-Fei Wang, Yan Zhang, Zhiming Lin, Huoru Zhang, Ting-You Wang, Yujie Cao, David L Morris, et al.

Nature Communications, 2021, 12, 772.

Paper

ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation

Ting-You Wang, Rendong Yang.

GigaScience, 2020, 9.

Paper

RAS internal tandem duplication disrupts GTPase-activating protein (GAP) binding to activate oncogenic signaling

Andrew C Nelson, Thomas J Turbyville, Srisathiyanarayanan Dharmaiah, Megan Rigby, Rendong Yang, Ting-You Wang, John Columbus, et al.

Journal of Biological Chemistry, 2020, 295, 9335-9348.

Paper

Identification of regulatory modules that stratify lupus disease mechanism through integrating multi-omics data

Ting-You Wang, Yong-Fei Wang, Yan Zhang, Jiangshan Jane Shen, Mengbiao Guo, Jing Yang, et al.

Molecular Therapy - Nucleic Acids, 2020, 19, 318-329.

Paper

ScanNeo: identifying indel derived neoantigens using RNA-Seq data

Ting-You Wang, Li Wang, Sk. Kayum Alam, Luke H. Hoeppner, Rendong Yang.

Bioinformatics, 2019, 35(20), 4159-4161.

Paper

HLA-IMPUTER: an easy to use web application for HLA imputation and association analysis using population-specific reference panels

Jiangshan Shen, Chao Yang, Yong-Fei Wang, Ting-You Wang, Mengbiao Guo, et al.

Bioinformatics, 2018, 35(7), 1244-1246.

Paper

Identification of ST3AGL4, MFHAS1, CSNK2A2 and CD226 as loci associated with systemic lupus erythematosus (SLE) and evaluation of SLE genetics in drug repositioning

Yong-Fei Wang, Yan Zhang, Zhengwei Zhu, Ting-You Wang, David L Morris, Jiangshan Jane Shen, et al.

Annals of the Rheumatic Diseases, 2018, 77(7):1078-1084.

Paper

Regulatory and evolutionary signatures of sex-biased genes on both the X chromosome and the autosomes

Jiangshan Shen, Ting-You Wang, Wanling Yang.

Biology of Sex Differences, 2017, 8(1):35.

Paper

Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus

David L Morris, Yujun Sheng, Yan Zhang, Yong-Fei Wang, Zhengwei Zhu, Philip Tombleson, Lingyan Chen, Deborah S Cunninghame Graham, James Bentham, Amy L Roberts, Ruoyan Chen, Xianbo Zuo, Tingyou Wang, Leilei Wen, Chao Yang, Lu Liu, Lulu Yang, Feng Li, Yuanbo Huang, Xianyong Yin, Sen Yang, Lars Rönnblom, Barbara G Fürnrohr, Reinhard E Voll, Georg Schett et al.

Nature Genetics, 2016, 48, 940-946.

Paper

Meta-analysis of GWAS on two Chinese populations followed by replication identifies novel genetic variants on the X chromosome associated with systemic lupus erythematosus

Yan Zhang, Jing Zhang, Jing Yang, Yongfei Wang, Lu Zhang, Xianbao Zuo, Liangdan Sun, Hai-Feng Pan, Nattiya Hirankarn, Tingyou Wang, Ruoyan Chen, Dingge Ying, et al.

Human Molecular Genetics, 2015, 24(1), 274-284.

Paper

Chromosome-8-Coded Proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with Partial Immunohistochemical Verifications

Yang Liu, Wantao Ying, Zhe Ren, Wei Gu, Yang Zhang, Guoquan Yan, Pengyuan Yang, Yinkun Liu, Xuefei Yin, Cheng Chang, Jing Jiang, Fengxu Fan, Chengpu Zhang, Ping Xu, Quanhui Wang, Bo Wen, Liang Lin, Tingyou Wang, Chaoqin Du et al.

Journal of Proteome Research, 2014, 13(1), 126-136.

Paper

Qualitative and quantitative expression status of the human chromosome 20 genes in cancer tissues and the representative cell lines

Quanhui Wang#, Bo Wen#, Guangrong Yan#, Junying Wei#, Liqi Xie#, Shaohang Xu, Dahai Jiang, Tingyou Wang, Ruo Zhou, Haiyi Zhao et al.

Journal of Proteome Research, 2013, 12(1), 151-161. (#Co-first authors)

Paper

A predicted protein-protein interaction network of the filamentous fungus Neurospora crassa

Ting-You Wang, Fei He, Qi-Wen Hu, Ziding Zhang.

Molecular BioSystems, 2011, 7, 2278-2285.

Paper