# First Author, *Corresponding Author

1. Yue Huang^#; Jing Guo^#; Xueshuai Han^#; Yang Zhao; Xuejing Li; Peiqi Xing; Yulou Liu; Yingxuan Sun; Song Wu; Xuan Lv; Lei Zhou; Yazhuo Zhang; Chuzhong Li*; Weiyan Xie*; Zhaoqi Liu*; Splicing diversity enhances the molecular classification of pituitary neuroendocrine tumors, Nature Communications, 2025, 16(1): 1552

2.Xinzhi Wu^#; Xueshuai Han^#; Haibo Zhu^#; Mingxuan Li; Lei Gong; Sicheng Jing; Weiyan Xie*; Zhaoqi Liu*; Chuzhong Li*; Yazhuo Zhang*; Single-cell transcriptomics identify a novel macrophage population associated with bone invasion in pituitary neuroendocrine tumors, Journal of Experimental & Clinical Cancer Research, 2025, 44(1): 27

3. Minu Seong^#; Pedro Bak‐Gordon; Zhaoqi Liu; Peter D Canoll; James L Manley*; Splicing dysregulation in glioblastoma alters the function of cell migration‐related genes, Glia, 2025, 73(2): 215-270

4.Jingru Sui^#; Dan Guo; Xiao Wen; Lei Zhou; Yue Huang; Haoyu Yu; Jinyu Chen; Zhaoqi Liu*; Systematic Characterization of Splicing Dysregulation in Pan Solid Tumor Transcriptome, Advanced science, 2024, 12(4): e2405626

5.Xueshuai Han^#; Jingru Sui^#; Kui Nie; Yang Zhao; Xuan Lv; Jindou Xie; Leonard Tan; Rex K. H. Au-Yeung; Jiao Ma; Giorgio Inghirami; Olivier Elemento; Wayne Tam* ; Zhaoqi Liu*; Tumor evolution analysis uncovered immune-escape related mutations in relapse of diffuse large B-cell lymphoma, Leukemia, 2024, 38(10): 2276-2280

6.Xueshuai Han^#; Zhaoqi Liu*; Aberrant somatic hypermutation at super-enhancer drives B cell lymphoma transformation, Genomics, Proteomics & Bioinformatics, 2024, 22(4): qzae015

7. Isaac Wakiro^#; Yue Huang#; Xuejing Yang; Xueqin Xie; Hanzhi Luo; Kathryn Chang; Aspen Pierson; Emily Batchelor; Yuanming Cheng; Diu TT Nguyen; Zhaoqi Liu*; Michael G Kharas*; Rbmx Regulates YTHDC1 Nuclear Condensates to Promote Nascent Transcription in Acute Myeloid Leukemia, Blood, 2024, 144(Supplement 1): 627-627

8.Kausik Regunath^#; Vitalay Fomin; Zhaoqi Liu; Pingzhang Wang; Mainul Hoque; Bin Tian; Raul Rabadan*; Carol Prives*; Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types, Molecular Cancer Research, 2024, 22(6): 555-571

9.Jian Zhang^#; Jindou Xie^#; Ji Huang; Xiangyang Liu; Ruihong Xu; Jonas Tholen; Wojciech P.Galej; Liang Tong; James L. Manley*; Zhaoqi Liu* ; Characterization of the SF3B1–SUGP1 interface reveals how numerous cancer mutations cause mRNA missplicing, Genes & Development, 2023, 37: 1-16

10.Song Wu^#; Yue Huang^#; Mochen Zhang; Zheng Gong; Guoliang Wang; Xinchang Zheng; Wenting Zong; Wei Zhao; Peiqi Xing; Rujiao Li*; Zhaoqi Liu*; Yiming Bao*; ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers, Nucleic Acids Research, 2023, 51(D1): D1196-D1204

11.Nan Han^#; Zhaoqi Liu*；Targeting alternative splicing in cancer immunotherapy，Frontiers in Cell and Developmental Biology, 2023, 11: 1232146

12.Quanhua Mu^#; Ruichao Chai^#; Bo Pang; Yingxi Yang; Hanjie Liu; Zheng Zhao; Zhaoshi Bao; Dong Song; Zhihan Zhu; Mengli Yan; Biaobin Jiang; Zongchao Mo; Jihong Tang; Jason K Sa; Hee Jin Cho; Yuzhou Chang; Kaitlin Hao Yi Chan; Danson Shek Chun Loi; Sindy Sing Ting Tam; Aden Ka Yin Chan; Angela Ruohao Wu; Zhaoqi Liu; Wai Sang Poon; Ho Keung Ng; Danny Tat Ming Chan; Antonio Iavarone*; Do-Hyun Nam*; Tao Jiang*; Jiguang Wang*; Identifying predictors of glioma evolution from longitudinal sequencing, Science translational medicine, 2023, 15(716): eadh4181

13.Hao Guo^#; Jin Xu^#; Peiqi Xing^#; Qilong Li; Donghai Wang; Chao Tang; Bruno Palhais; Juliette Roels; Jiaxu Liu; Sa Pan; Jinyan Huang; Zhaoqi Liu; Ping Zhu; Tom Taghon; Guoliang Qing; Pieter Van Vlierberghe*; Hudan Liu*; RNA helicase DHX15 exemplifies a unique dependency in acute leukemia, Haematologica, 2023, 108(8): 2029–2043

14.Jian Zhang^#; Ji Huang; Ke Xu; Peiqi Xing; Yue Huang; Zhaoqi Liu; Liang Tong; James L. Manley*; DHX15 is involved in SUGP1-mediated RNA mis-splicing by mutant SF3B1 in cancer, Proceedings of the National Academy of Sciences 2022, 119 (49) : e2216712119.

15.Yen K. Lieu^#*; Zhaoqi Liu;Abdullah M. Alig; Xin Weih; Alex Pensond; Jian Zhanga; Xiuli Anh; Raul Rabadand; Azra Razab; James L. Manleya*; Siddhartha Mukherjee*; SF3B1 mutant-induced missplicing of MAP3K7 causes anemia in myelodysplastic syndromes, Proceedings of the National Academy of Sciences 2022, 119(1): e2111703119.

16.Zhaoqi Liu^#*, Raul Rabadan*；Computing the role of alternative splicing in cancer, Trends in cancer, 2021,7(4): 347-358

17.Bo Liu^#; Zhaoqi Liu^#; Sisi Chen; Michelle Ki; Caroline Erickson; Jorge S. Reis-Filho;Benjamin H. Durham; Qing Chang; Elisa de Stanchina; Yiwei Sun; Raul Rabadan; Omar Abdel-Wahab*; Sarat Chandarlapaty* ; Mutant SF3B1 promotes AKT and NF-kB driven mammary tumorigenesis, The Journal of Clinical Investigation, 2021, 131(1): e138315

18.Camila Prieto^#; Diu Nguyen^#; Zhaoqi Liu; Justin Wheat; Alexendar Perez; Saroj Gourkanti; Timothy Chou; Anthony Velleca; Thomas Rohwetter; Ersilia Barin; Arthur Chow; James Taggart; Katerina Hoskova; Meera Dhodapkar; Alexandra Schurer; Trevor S Barlowe; Ly P Vu; Christina Leslie; Ulrich Steidl; Raul Rabadan*; Michael G Kharas*; Transcriptional control of CBX5 by the RNA-binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia, Nature Cancer, 2021, 2(7): 741-757

19.Delin Chen^#; Bo Chu^#; Xin Yang; Zhaoqi Liu; Ying Jin; Ning Kon; Raul Rabadan; Xuejun Jiang; Brent R. Stockwell; Wei Gu*; iPLA2β-mediated lipid detoxification controls p53-driven ferroptosis independent of GPX4, Nature Communications, 2021,12(1): 3644

20.Mai Sato^#; Andrew Walter Liebau; Zhaoqi Liu; Lizhi Liu; Raul Rabadan; Jean Gautier*; The UVSSA complex alleviates MYC-driven transcription stress, Journal of Cell Biology, 2021, 220 (2): e201807163.

21.Zhaoqi Liu^#; Ioan Filip; Karen Gomez; Dewaldt Engelbrecht; Shabnum Meer; Pooja N. Lalloo;Pareen Patel; Yvonne Perner; Junfei Zhao; Jiguang Wang; Laura Pasqualucci*; Raul Rabadan*; Pascale Willem*; Genomic Characterization of HIV-Associated Plasmablastic Lymphoma Identifies Pervasive Mutations in the JAK–STAT Pathway, Blood Cancer Discovery, 2020, 1(1): 112-125

22.Zhaoqi Liu^#; Akihide Yoshimi^#*; Jiguang Wang; Hana Cho; Stanley Chun-Wei Lee; Michelle Ki;Lillian Bitner; Timothy Chu; Harshal Shah; Bo Liu; Anthony R. Mato; Peter Ruvolo; Giulia Fabbri; Laura Pasqualucci; Omar Abdel-Wahab; Raul Rabadan*; Mutations in the RNA Splicing Factor SF3B1Promote Tumorigenesis through MYC Stabilization, Cancer Discovery, 2020, 10(6): 806-821

23.Zhaoqi Liu^#; Jian Zhang^#; Yiwei Sun; Tomin E. Perea-Chamblee; James L. Manley*; Raul Rabadan*; Pan-cancer analysis identifies mutations in SUGP1 that recapitulate mutant SF3B1 splicing dysregulation, Proceedings of the National Academy of Sciences, 2020, 117(19): 10305-10312

24.Danilo Fiore^#; Luca Vincenzo Cappelli^#; Paul Zumbo; Jude M Phillips; Zhaoqi Liu; Shuhua Cheng; Liron Yoffe; Paola Ghione; Federica Di Maggio; Ahmet Dogan; Inna Khodos; Elisa de Stanchina; Joseph Casano;Clarisse Kayembe; Wayne Tam; Doron Betel; Robin Foa’; Leandro Cerchietti; Raul Rabadan; Steven Horwitz; David M Weinstock; Giorgio Inghirami*; A novel JAK1 mutant breast implant-associated anaplastic large cell lymphoma patient-derived xenograft fostering pre-clinical discoveries, Cancers, 2020, 12(6): 1603

25.Luis Arnes^#*; Zhaoqi Liu^#; Jiguang Wang^#; Carlo Maurer; Irina Sagalovskiy; Marta SanchezMartin;Nikhil Bommakanti; Diana C Garofalo; Dina A Balderes; Lori Sussel; Kenneth P Olive*; Raul Rabadan *; Comprehensive characterization of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma, Gut, 2019, 68(3): 499-511

26.Suji Han^#; Hyemi Shin^#; Jin-Ku Lee^#; Zhaoqi Liu; Raul Rabadan; Jeongwu Lee; Jihye Shin; Cheolju Lee; Heekyoung Yang; Donggeon Kim; Sung Heon Kim; Jooyeon Kim; Jeong-Woo Oh; Doo-Sik Kong; Jung-Il Lee; Ho Jun Seol; Jung Won Choi; Hyun Ju Kang*; Do-Hyun Nam*; Secretome analysis of patient-derived GBM tumor spheres identifies midkine as a potent therapeutic target, Experimental & molecular medicine, 2019, 51(12): 1-11

27.Jian Zhang^#; Abdullah M Ali; Yen K Lieu; Zhaoqi Liu; Jianchao Gao;Raul Rabadan; Azra Raza; Siddhartha Mukherjee*; James L Manley*; Disease-causing mutations in SF3B1 alter splicing by disrupting interaction with SUGP1, Molecular cell , 2019, 76(1): 82-95. e7

28.Jin-Ku Lee^#; Zhaoqi Liu^#; Jason K. Sa^#; Sang Shin^#; Jiguang Wang^#; Mykola Bordyuh; Hee Jin Cho; Oliver Elliott; Timothy Chu; Seung Won Choi; Daniel I. S. Rosenbloom; In-Hee Lee; Yong Jae Shin; Hyun Ju Kang; Donggeon Kim; Sun Young Kim; Moon-Hee Sim; Jusun Kim; Taehyang Lee; Yun Jee Seo; Hyemi Shin; Mijeong Lee; Sung Heon Kim; Yong-Jun Kwon; Jeong-Woo Oh; Minsuk Song; Misuk Kim;Doo-Sik Kong; Jung Won Choi; Ho Jun Seol; Jung-Il Lee; Seung Tae Kim; Joon Oh Park; Kyoung-Mee Kim; Sang-Yong Song; Jeong-Won Lee; Hee-Cheol Kim; Jeong Eon Lee; Min Gew Choi; Sung Wook Seo; Young Mog Shim; Jae Ill Zo; Byong Chang Jeong; Yeup Yoon; Gyu Ha Ryu; Nayoung K. D. Kim; Joon Seol Bae; Woong-Yang Park; Jeongwu Lee; Roel G. W. Verhaak; Antonio Iavarone; Jeeyun Lee*; Raul Rabadan*; Do-Hyun Nam*; Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy, Nature Genetics, 2018, 50(10): 1399-1411

29. Magdolna Djurec^#; Osvaldo Graña; Albert Lee; Kevin Troulé; Elisa Espinet; Lavinia Cabras; Carolina Navas; María Teresa Blasco; Laura Martín-Díaz; Miranda Burdiel; Jing Li, Zhaoqi Liu; Mireia Vallespinós; Francisco Sanchez-Bueno; Martin R Sprick; Andreas Trumpp; Bruno Sainz; Fátima Al-Shahrour; Raul Rabadan; Carmen Guerra*; Mariano Barbacid*; Saa3 is a key mediator of the protumorigenic properties of cancer-associated fibroblasts in pancreatic tumors, Proceedings of the National Academy of Sciences, 2018, 115(6) : E1147-E1156

30.Jin-Ku Lee^#; Jiguang Wang^#; Jason K Sa^#; Erik Ladewig^#; Hae-Ock Lee; In-Hee Lee; Hyun Ju Kang; Daniel S Rosenbloom; Pablo G Camara; Zhaoqi Liu; Patrick van Nieuwenhuizen; Sang Won Jung; Seung Won Choi; Junhyung Kim; Andrew Chen; Kyu-Tae Kim; Sang Shin; Yun Jee Seo; Jin-Mi Oh; Yong Jae Shin; Chul-Kee Park; Doo-Sik Kong; Ho Jun Seol; Andrew Blumberg; Jung-Il Lee; Antonio Iavarone; Woong-Yang Park*; Raul Rabadan* & Do-Hyun Nam*; Spatiotemporal genomic architecture informs precision oncology in glioblastoma, Nature Genetics, 2017, 49(4), 594-599

31.Jiguang Wang^#; Emanuela Cazzato; Erik Ladewig; Veronique Frattini; Daniel I S Rosenbloom; Sakellarios Zairis; Francesco Abate; Zhaoqi Liu; Oliver Elliott; Yong-Jae Shin; Jin-Ku Lee; In-Hee Lee; Woong-Yang Park; Marica Eoli; Andrew J Blumberg; Anna Lasorella; Do-Hyun Nam*; Gaetano Finocchiaro*; Antonio Iavarone *; Raul Rabadan*; Clonal evolution of glioblastoma under therapy, Nature Genetics, 2016, 48(7): 768-776

32.Xuemei Ning^#; Zhaoqi Liu; Shihua Zhang*; Local community extraction in directed networks, Physica A: Statistical Mechanics and its Applications, 2016, 452: 258-265

33.Zhaoqi Liu^#; Shihua Zhang*; Tumor characterization and stratification by integrated molecular profiles reveals essential pan-cancer features, BMC genomics, 2015,16: 1-12

34.Meng Zou^#; Zhaoqi Liu; Xiang-Sun Zhang; Yong Wang*; NCC-AUC: an AUC optimization method to identify multi-biomarker panel for cancer prognosis from genomic and clinical data, Bioinformatics, 2015, 31(20): 3330-3338

35.Xiaofeng Dai^#; Zhaoqi Liu; Shihua Zhang*; Over-expression of EPS15 is a favorable prognostic factor in breast cancer, Molecular bioSystems, 2015, 11(11): 2978-2985