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Professor Wang, John Junwen

BS (HZAU); MS (Jiangnan); MCIT (UPenn); PhD (UW-Seattle)

Professor Wang, John Junwen - HKU Faculty of Dentistry 香港大學牙醫學院

Profile

Title
  • Professor
    教授
Division
Applied Oral Sciences & Community Dental Care
E-mail
junwen@hku.hk
Phone
+852 2859 0128
Biography
Professor Wang is currently a professor in Faculty of Dentistry, the University of Hong Kong (HKU). He was a full Professor of Biomedical Informatics at Mayo Clinic in Arizona, and affiliate Professor at Arizona State University, USA. He obtained his PhD from University of Washington, Masters from University of Pennsylvania, USA and Jiangnan University, and BE from Huazhong Agricultural University, China. Prof. Wang’s research interests are in Bioinformatics, gene regulatory network construction, AI and methodology development for data analysis. He has published over 130 papers in journals such as Nature genetics, Nature Communications, Nature Machine Intelligence, Circulation, NAR, Bioinformatics, and has obtained funding from RGC of Hong Kong, and NIH of USA as project leaders. He was an ISI top 1% cited scholar, an outstanding young researcher awardee at HKU, and is currently an associate editor of Journal of Cancer Immunology, Immunotherapy.
Research Theme
Population Oral Health
Areas of Research Expertise
  • Bioinformatics
  • Precision Dentistry/Medicine
  • Systems Biology
  • Artificial intelligence
  • Drug Discovery
Research Profile
Publication & Awards
Publications

    Article

  • Mudappathi Rekha, Patton Tatiana, Chen Hai, Yang Ping, Sun Zhifu, Wang Panwen, Shi Chang Xin, Wang Junwen, Liu Li. reg-eQTL: Integrating transcription factor effects to unveil regulatory variants, American Journal of Human Genetics 2025; 112(3): 659-674 doi:10.1016/j.ajhg.2025.01.015
  • Liu Yong, Zhong Le, Yan Bin, Chen Zhuobin, Yu Yanjia, Yu Dan, Qin Jing, Wang Junwen. A self-attention-driven deep learning framework for inference of transcriptional gene regulatory networks, Briefings in Bioinformatics 2025; 26(1) doi:10.1093/bib/bbae639
  • Blechter B, Hsiung CA, Wang X, Zhang H, Seow WJ, Shi J, Chatterjee N, Kim HN, Wong MP, Hong YC, Wong JYY, Dai J, Hosgood HD, Wang Z, Chang IS, Choi J, Wang J, Song M, Hu W, Zheng W, Kim JH, Zhou B, Albanes D, Shin MH, Chung LP, An SJ, Zheng H, Yatabe Y, Zhang XC, Kim YT, Shu XO, Kim YC, Vermeulen RCH, Bassig BA, Chang J, Man Ho JC, Ji BT, Kubo M, Daigo Y, Momozawa Y, Kamatani Y, Honda T, Kunitoh H, Watanabe SI, Miyagi Y, Nakayama H, Matsumoto S, Tsuboi M, Goto K, Yin Z, Takahashi A, Goto A, Minamiya Y, Shimizu K, Tanaka K, Wu T, Wei F, Su J, Kim YH, Oh IJ, Fun Lee VH, Su WC, Chen YM, Chang GC, Chen KY, Huang MS, Lin HC, Seow A, Park JY, Kweon SS, Chen CJ, Gao YT, Wu C, Qian B, Lu D, Liu J, Jeon HS, Hsiao CF, Sung JS, Tsai YH, Jung YJ, Guo H, Hu Z, Chen TY, Burdett L, Yeager M, Hutchinson A, Berndt SI, Wu W, Wang J, Choi JE, Park KH, Sung SW, Liu L, Kang CH, Chen CH, Xu J, Guan P, Tan W, Wang CL, Loon Sihoe AD, Chen Y, Choi YY, Kim JS, Yoon HI, Cai Q, Park IK, Xu P, He Q, Chen CY, Wu J, Lim WY, Chen KC, Chan JKC, Li J, Chen H, Yu CJ, Jin L, Fraumeni JF, Liu J, Landi MT, Yamaji T, Yang Y, Hicks B, Wyatt K, Li SA, Ma H, Song B, Wang Z, Cheng S, Li X, Ren Y, Iwasaki M, Zhu J, Jiang G, Fei K, Wu G, Chien LH, Tsai FY, Yu J, Stevens VL, Yang PC, Lin D, Chen K, Wu YL, Matsuo K, Rothman N, Shiraishi K, Shen H, Chanock SJ, Kohno T, Lan Q. Polygenic Risk Score and Lung Adenocarcinoma Risk Among Never-Smokers by EGFR Mutation Status: A Brief Report, Journal of Thoracic Oncology 2025; 20(4): 521-530 doi:10.1016/j.jtho.2024.11.019
  • Ren Y, Xiong W, Feng C, Yu D, Wang X, Yang Q, Yu S, Zhang H, Huo B, Jiang H, Li Z, Wang J, Su YX, Yang P, Liao Y, Zhong Q, Wang J. Multi-omics insights into the molecular signature and prognosis of hypopharyngeal squamous cell carcinoma, Communications Biology 2025; 8(1) doi:10.1038/s42003-025-07700-0
  • Zhu T, Shen Q, Shen L, Wang Y, Zhu B, Ma L, Feng S, Wang C, Yan S, Li J, Chen Z, Zhou J, Huang H, Li B, Shen Z, Wang Q, Wang J, Gwinner W, Scheffner I, Rong S, Yang B, Wang J, Haller H, Han X, Guo G, Yin Z, Jin J, Lan HY, Chen J, Jiang H. Senescence-induced p21high macrophages contributed to CD8+ T cells-related immune hyporesponsiveness in kidney transplantation via Zfp36/IL-27 axis, Cell Discovery 2025; 11(1) doi:10.1038/s41421-025-00784-2
  • Mudappathi R, Maguire A, Yi ES, Peng Y, Kachergus JM, Khoor A, Tan K, Zaniletti I, Wampfler JA, Lou Y, Reck Dos Santos PA, D'Cunha J, Sun Z, Liu L, Jelinek DF, Wang J, Tazelaar HD, Thompson EA, Yang P. Spatially defined intratumoral immune biomarkers predict recurrent versus second primary tumors in non-small cell lung cancer, Precision clinical medicine 2025; 8(1) doi:10.1093/pcmedi/pbaf001
  • Gile Jennifer J, Mondello Patrizia, Wang Zixing, Li Ying, Bansal Radhika, Gandhi Sangeetha, Zhang Henan, Babadi Elham, Martinez Kodi, McCoy Gabrielle, Shao Zuoyi, Regan Kevin, Hathcock Matthew A, Wang Panwen, Wang Junwen, Al Saleh Abdullah S, Ruan Gordon, Ansell Stephen M, Bennani N Nora, Johnston Patrick B, Paludo Jonas, Villasboas-Bisneto Jose C, Khurana Arushi, Durani Urshila, Wang Yucai, Hampel Paul J, Rosenthal Allison, Munoz Javier, Moreno Eider, Castro Januario E, Murthy Hemant S, Kharfan-Dabaja Mohamed, Kenderian Saad S, Kim Jenny J, Shen Rhine, Mattie Mike, Lin Yi, Witzig Thomas E. Hypomagnesemia in lymphoma patients receiving CAR T therapy correlates with immune dysfunction and decreased survival, Experimental Hematology and Oncology 2025; 14(1) doi:10.1186/s40164-025-00623-w
  • Wang Panwen, Yu Yue, Dong Haidong, Zhang Shuwen, Sun Zhifu, Zeng Hu, Mondello Patrizia, Kocher Jean-Pierre A, Wang Junwen, Asmann Yan W, Lin Yi, Li Ying. Immunopipe: a comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline, NAR Genom Bioinform 2025; 7(2) doi:10.1093/nargab/lqaf063
  • Guan Jiahui, Xie Peilin, Meng Dian, Yao Lantian, Yu Dan, Chiang Ying Chih, Lee Tzong Yi, Wang Junwen. ToxiPep: Peptide toxicity prediction via fusion of context-aware representation and atomic-level graph, Computational and Structural Biotechnology Journal 2025; 27: 2347-2358 doi:10.1016/j.csbj.2025.05.039
  • Li Ziying, Zhang Wei, Yang Menglin, Zheng Shiqi, Zhang Yanlin, Huang Weiying, Tan Yanting, Wang Hanhua, Zhou Guoyong, Wang Wei, Wang Junwen, Li Rui, Huang Yanhua, Peng Jie. Fermented Lentinus edodes improves insulin sensitivity in dam and offspring mice via activation of the hepatic PI3K/AKT signaling pathway, British Journal of Nutrition 2025; 1-14 doi:10.1017/S0007114525103796
  • Lin Xiang, Ren Jianlan, Gao Le, Wang Junwen, Wei Zhi. scDILT: A Model-Based and Constrained Deep Learning Framework for Single-Cell Data Integration, Label Transferring, and Clustering , IEEE Transactions on Computational Biology and Bioinformatics 2025; 22(3): 1083-1094 doi:10.1109/TCBBIO.2025.3553068
  • Guan Jiahui, Yao Lantian, Xie Peilin, Zhao Zhihao, Meng Dian, Lee Tzong Yi, Wang Junwen, Chiang Ying Chih. Graph-RPI: predicting RNA–protein interactions via graph autoencoder and self-supervised learning strategies , Briefings in Bioinformatics 2025; 26(3) doi:10.1093/bib/bbaf292
  • Loo Ai Leen Shu Jen, Cen Rong, Wang Junwen, Wu Zhaoming, Duncan Henry Fergus, Lee Angeline Hui Cheng, Zhang Chengfei. Symptom correlation and spatial distribution of inflammatory mediators in pulpitis—A preliminary study, International Endodontic Journal 2025; doi:10.1111/iej.14275
  • Wang Panwen, Dong Haidong, Yu Yue, Zhang Shuwen, Sun Zhifu, Kocher Jean-Pierre A, Wang Junwen, Yi Lin, Li Ying. Abstract 4959: Immunopipe: A comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline, Cancer Research 2024; 84(6_Supplement) doi:10.1158/1538-7445.AM2024-4959
  • Tang Ling, Nyarige Verah, Li Pengsheng, Wang Junwen, Zhu Wuqiang. Identification of circular RNAs regulating cardiomyocyte proliferation in neonatal pig hearts, JCI Insight 2024; 9(15) doi:10.1172/jci.insight.175625
  • Wang Junlin, Lam Pui Ying, Su Yuxiong, Wang Junwen. Abstract 3553: OralDB, A integrative data portal for oral and oropharyngeal cancer omics and clinical research, Cancer Research 2024; 84(6) doi:10.1158/1538-7445.AM2024-3553
  • Lee Brian N, Wang Junwen, Hall Molly A, Kim Dokyoon, Stites Shana D, Shen Li. Sex modifies effects of imaging and CSF biomarkers on cognitive and functional outcomes: a study of Alzheimer's disease, Neurobiology of Aging 2024; 133: 67-77 doi:10.1016/j.neurobiolaging.2023.10.002
  • Wang Jun, Zheng Shiqi, Li Ziying, Tang Yimei, Huang Yanhua, Wang Junwen, Li Rui, Peng Jie. Pentadecanoic acid (C15:0, PA) induces mild maternal glucose intolerance and promotes the growth of the offspring partly through up-regulating liver PPARα and MAPK signaling pathways, Food and Function 2024; 15(23): 11400-11414 doi:10.1039/d4fo03970j
  • Jin Xiaohong, Chen Zimeng, Yu Dan, Jiang Qianhui, Chen Zhuobin, Yan Bin, Qin Jing, Liu Yong, Wang Junwen. TPepPro: a deep learning model for predicting peptide-protein interactions, Bioinformatics 2024; 41(1) doi:10.1093/bioinformatics/btae708
  • Bhardwaj V, Yang ZZ, Jalali S, Villasboas JC, Mudappathi R, Wang J, Mukherjee P, Paludo J, Tang X, Kim HJ, Krull JE, Wenzl K, Novak AJ, Mondello P, Ansell SM. Expanded tumor-associated polymorphonuclear myeloid-derived suppressor cells in Waldenstrom macroglobulinemia display immune suppressive activity, Blood Cancer Journal 2024; 14(1) doi:10.1038/s41408-024-01173-w
  • Du Shujuan, Chen Xiaoting, Han Xiao, Wang Yuyan, Yu Dan, Li Ying, Zhu Caixia, Tong Yin, Gao Shujun, Wang Junwen, Wei Fang, Cai Qiliang. Lactate Induces Tumor Progression via LAR Motif-Dependent Yin-Yang 1 Degradation, Molecular Cancer Research 2024; 22(10): 957-972 doi:10.1158/1541-7786.MCR-23-0583
  • Yang ZZ, Kim HJ, Wu HY, Tang XY, Yu Y, Krull J, Larson DP, Moore RM, Maurer MJ, Pavelko KD, Jalali S, Pritchett JC, Mudappathi R, Wang JW, Villasboas JC, Mondello P, Novak AJ, Ansell SM. T-cell phenotype including CD57+ T follicular helper cells in the tumor microenvironment correlate with a poor outcome in follicular lymphoma, Blood Cancer Journal 2023; 13(1) doi:10.1038/s41408-023-00899-3
  • Wu JF, Su Y, Chen YX, Zhu WH, Reiman EM, Caselli RJ, Chen KW, Thompson PM, Wang JW, Wang YL, Alzheimers Dis Neuroimaging. A Surface-Based Federated Chow Test Model for Integrating APOE Status, Tau Deposition Measure, and Hippocampal Surface Morphometry, Journal of Alzheimer's Disease 2023; 93(3): 1153-1168 doi:10.3233/JAD-230034
  • Shi JX, Shiraishi K, Choi JY, Matsuo K, Chen TY, Dai JC, Hung RJ, Chen KX, Shu XO, Kim YT, Landi MT, Lin DX, Zheng W, Yin ZH, Zhou BS, Song B, Wang JC, Seow WJ, Song L, Chang IS, Hu W, Chien LH, Cai QY, Hong YC, Kim HN, Wu YL, Wong MP, Richardson BD, Funderburk KM, Li SL, Zhang TW, Breeze C, Wang ZM, Blechter B, Bassig BA, Kim JH, Albanes D, Wong JYY, Shin MH, Chung LP, Yang Y, An SJ, Zheng H, Yatabe Y, Zhang XC, Kim YC, Caporaso NE, Chang J, Ho JCM, Kubo M, Daigo Y, Song M, Momozawa Y, Kamatani Y, Kobayashi M, Okubo K, Honda T, Hosgood DH, Kunitoh H, Patel H, Watanabe S, Miyagi Y, Nakayama H, Matsumoto S, Horinouchi H, Tsuboi M, Hamamoto R, Wang JW, et al. Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population, Nature Communications 2023; 14(1) doi:10.1038/s41467-023-38196-z
  • Farina JM, Chen Y, Jaroszewski DE, Bostoros P, Wang J. Genetic variants in pectus excavatum, Journal of Pediatric Surgery 2023; 58(3): 600-601 doi:10.1016/j.jpedsurg.2022.10.038
  • Flick Matthew, Weiskittel Taylor, Meng-Lin Kevin, D'Angelo Fulvio, Caruso Francesca, Ensign Shannon, Blomquist Mylan, Wang Luija, Sereduk Christopher, de Leon Gustavo, Nespodzany Ashley, Urcuyo Javier, Gonzalez Ashlynn, Curtin Lee, Singleton Kyle, Anil Aliya, Simmineh Natenael, Lewis Erika, Noviello Teresa, Patel Reyna, Wang Panwen, Wang Junwen, et al. Abstract 5621: Multi-parametric MRI maps regional heterogeneity of high grade glioma phenotypes, Cancer Research 2023; 83(7 Suppl) doi:10.1158/1538-7445.AM2023-5621
  • Lee BN, Wang J, Nho K, Saykin AJ, Shen L. Discovering Precision AD Biomarkers with Varying Prognosis Effects in Genetics Driven Subpopulations, AMIA Joint Summits on Translational Science proceedings 2023; 340-349
  • Hu Leland S, D’Angelo Fulvio, Weiskittel Taylor M, Caruso Francesca P, Fortin Ensign Shannon P, Blomquist Mylan R, Flick Matthew J, Wang Lujia, Sereduk Christopher P, Meng-Lin Kevin, de Leon Gustavo, Nespodzany Ashley, Urcuyo Javier C, Gonzales Ashlyn C, Curtin Lee, Lewis Erika M, Singleton Kyle W, Dondlinger Timothy, Anil Aliya, Semmineh Natenael B, Noviello Teresa, Patel Reyna A, Wang Panwen, Wang Junwen, Eschbacher Jennifer M, Hawkins-Daarud Andrea, Jackson Pamela R, Grunfeld Itamar S, Elrod Christian, Mazza Gina L, McGee Sam C, Paulson Lisa, Clark-Swanson Kamala, Lassiter-Morris Yvette, Smith Kris A, Nakaji Peter, Bendok Bernard R, Zimmerman Richard S, Krishna Chandan, Patra Devi P, Patel Naresh P, Lyons Mark, Neal Matthew, Donev Kliment, Mrugala Maciej M, Porter Alyx B, Beeman Scott C, Jensen Todd R, Schmainda Kathleen M, Zhou Yuxiang, Baxter Leslie C, Plaisier Christopher L, Li Jing, Li Hu, Lasorella Anna, Quarles C Chad, Swanson Kristin R, Ceccarelli Michele, Iavarone Antonio, Tran Nhan L. Integrated molecular and multiparametric MRI mapping of high-grade glioma identifies regional biologic signatures, Nature Communications 2023; 14(1): 6066 doi:10.1038/s41467-023-41559-1
  • Xu Hang, Yi Xianfu, Fan Xutong, Wu Chengyue, Wang Wei, Chu Xinlei, Zhang Shijie, Dong Xiaobao, Wang Zhao, Wang Jianhua, Zhou Yao, Zhao Ke, Yao Hongcheng, Zheng Nan, Wang Junwen, Chen Yupeng, Plewczynski Dariusz, Sham Pak Chung, Chen Kexin, Huang Dandan, Li Mulin Jun. Inferring CTCF-binding patterns and anchored loops across human tissues and cell types, Patterns 2023; 4(8) doi:10.1016/j.patter.2023.100798
  • Yang P, Mudappathi R, Maguire A, Yi J, Yanxi C, Zaniletti I, Kumar A, Wampfler J, Reck dos Santos P, Lou Y, D'Cunha J, Liu L, Diane J, Wang J, Tazelaar H. P1.24-09 Spatially Defined Immune Response Signatures in 5μm Tumor Section of Resected T1-2N0M0 Lung Cancer Predict Clinical Outcome, Journal of Thoracic Oncology 2023; 18(11, Supplement): 263-264 doi:10.1016/j.jtho.2023.09.446
  • Ahmadinejad Navid, Troftgruben Shayna, Wang Junwen, Chandrashekar Pramod B., Dinu Valentin, Maley Carlo, Liu Li. Accurate Identification of Subclones in Tumor Genomes, Molecular Biology and Evolution 2022; 39(7): article no. msac136-article no. msac136 doi:10.1093/molbev/msac136
  • Mohamadi Ahmad, Cheng Tianfan, Jin Lijian, Wang Junwen, Sun Hongzhe, Koohi-Moghadam Mohamad. An ensemble 3D deep-learning model to predict protein metal-binding site, Cell Reports Physical Science 2022; 3(9): article no. 101046-article no. 101046 doi:10.1016/j.xcrp.2022.101046
  • Shen Qixia, Teng Lisha, Wang Yucheng, Guo Luying, Xu Feng, Huang Hongfeng, Xie Wenqing, Zhou Qin, Chen Ying, Wang Junwen, Mao Youying, Chen Jianghua, Jiang Hong. Integrated genomic, transcriptomic and metabolomic analysis reveals MDH2 mutation-induced metabolic disorder in recurrent focal segmental glomerulosclerosis, Frontiers in Immunology 2022; 13: article no. 962986-article no. 962986 doi:10.3389/fimmu.2022.962986
  • Ferrer A, Mudappathi R, Lasho T, Carr RM, Fernandez JA, Finke C, Gangat N, Abraham RS, Binder M, Mangaonkar AA, Wang JW, Patnaik MM. Longitudinal Single Cell Multiomic Analysis of a Patient with GATA2 Haploinsufficiency with ASXL1 Mutant Clonal Hematopoiesis, Blood 2022; 140 doi:10.1182/blood-2022-167808
  • Tang XY, Yang ZZ, Kim HJ, Anagnostou T, Yu Y, Wu XS, Chen J, Krull JE, Wenzl K, Mondello P, Bhardwaj V, Wang JW, Novak AJ, Ansell SM. Phenotype, Function, and Clinical Significance of CD26+ and CD161+Tregs in Splenic Marginal Zone Lymphoma, Clinical Cancer Research 2022; 28(19): 4322-4335 doi:10.1158/1078-0432.CCR-22-0977
  • Wu Jianfeng, Chen Yanxi, Wang Panwen, Caselli Richard, Thompson Paul, Wang Junwen, Wang Yalin. Integrating Transcriptomics, Genomics, and Imaging in Alzheimer's Disease: A Federated Model, Frontiers in Radiology 2022; 1 doi:10.3389/fradi.2021.777030
  • Lee Brian N, Wang Junwen, Shen Li. Identifying precision AD biomarkers with varying prognosis effects in genetics driven subpopulations, Alzheimer's & Dementia: The Journal of the Alzheimer's Association 2022; 17(S4) doi:10.1002/alz.053201
  • Ensign Shannon P Fortin, D'Angelo Fulvio, Caruso Francesca P, Sereduk Christopher, Singleton Kyle, Eschbacher Jennifer, Mazza Gina, Mrugala Maciej, Porter Alyx, Bendok Bernard, Zimmerman Richard, Smith Kris, Nakaji Peter, Swanson Kamala, Wang Junwen, Semmineh Nathenael, Quarles Christopher, Lasorella Anna, Swanson Kristin, Ceccarelli Michele, Iavarone Antonio, Hu Leland, Tran Nhan L. Abstract 770: Multiregional imaging and genomic analysis in high-grade IDH-mutant astrocytoma identifies intratumor subclones with aggressive features, Cancer Research 2022; 82(12 Supplement) doi:10.1158/1538-7445.AM2022-770
  • Miller Aunay, Wang Junwen, Loftus Joseph, Tran Nhan. Abstract 1556: Long non-coding RNA WNT5A-AS1 shows sex-dimorphic differences in survival for males with glioblastoma, Cancer Research 2022; 82(12) doi:10.1158/1538-7445.AM2022-1556
  • Miller Aunay, Wang Junwen, Loftus Joseph, Tran Nhan. 426 Long non-coding RNA WNT5A-AS1 shows sex-dimorphic differences in survival for males with glioblastoma, Journal of Clinical and Translational Science 2022; 6(S1): 83-83 doi:10.1017/cts.2022.247
  • Hu Leland S., Wang Lujia, Hawkins-Daarud Andrea, Eschbacher Jennifer M., Singleton Kyle W., Jackson Pamela R., Clark-Swanson Kamala, Sereduk Christopher P., Peng Sen, Wang Panwen, Wang Junwen, Baxter Leslie C., Smith Kris A., Mazza Gina L., Stokes Ashley M., Bendok Bernard R., Zimmerman Richard S., Krishna Chandan, Porter Alyx B., Mrugala Maciej M., Hoxworth Joseph M., Wu Teresa, Tran Nhan L., Swanson Kristin R., Li Jing. Uncertainty quantification in the radiogenomics modeling of EGFR amplification in glioblastoma, Scientific Reports 2021; 11(1): article no. 3932-article no. 3932 doi:10.1038/s41598-021-83141-z
  • Hasan Md Mahmudul, Nair Sumi Sukumaran, O’Leary Jacqueline G., Thompson-Snipes Lu Ann, Nyarige Verah, Wang Junwen, Park Walter, Stegall Mark, Heilman Raymond, Klintmalm Goran B., Joo Hye Mee, Oh Sang Kon. Implication of TIGIT+ human memory B cells in immune regulation, Nature Communications 2021; 12(1): article no. 1534-article no. 1534 doi:10.1038/s41467-021-21413-y
  • Gong Binsheng, Li Dan, Kusko Rebecca, Novoradovskaya Natalia, Zhang Yifan, Wang Shangzi, Pabón-Peña Carlos, Zhang Zhihong, Lai Kevin, Cai Wanshi, LoCoco Jennifer S., Best Hunter, Bhandari Ambica, Bisgin Halil, Blackburn James, Blomquist Thomas M., Deveson Ira W., Boardman Lisa, Burgher Blake, Butler Daniel J., Chang Chia Jung, Marella Narasimha, Chaubey Alka, Chen Tao, Chierici Marco, Chin Christopher R., Close Devin, Conroy Jeffrey, Duncan Daniel, Coleman Jessica Cooley, Eterovic Agda Karina, Fan Xiaohui, Martín-Arenas Rubén, Foox Jonathan, Furlanello Cesare, Ghosal Abhisek, Scherer Andreas, Glenn Sean, Guan Meijian, Haag Christine, Hang Xinyi, Happe Scott, Hennigan Brittany, Megherbi Dalila B., Hipp Jennifer, Hong Huixiao, Horvath Kyle, Hu Jianhong, Schulze Egbert, Hung Li Yuan, Jarosz Mirna, Kerkhof Jennifer, Kipp Benjamin, Kreil David Philip, Meng Qingchang, Łabaj Paweł, Lapunzina Pablo, Li Peng, Li Quan Zhen, Li Weihua, Sebra Robert, Li Zhiguang, Liang Yu, Liu Shaoqing, Liu Zhichao, Mieczkowski Piotr A., Ma Charles, Shaknovich Rita, Morrison Tom, Muzny Donna, Ning Baitang, Parsons Barbara L., Xiao Wenzhong, Paweletz Cloud P., Pirooznia Mehdi, Qu Wubin, Raymond Amelia, Rindler Paul, Ringler Rebecca, Shi Qiang, Sadikovic Bekim, Shi Tieliu, Silla-Castro Juan Carlos, Xu Shibei, Smith Melissa, López Mario Solís, Song Ping, Lader Eric, Stetson Daniel, Strahl Maya, Stuart Alan, Supplee Julianna, Szankasi Philippe, Tan Haowen, Yang Mary, Tang Lin ya, Tao Yonghui, Thakkar Shraddha, Thierry-Mieg Danielle, Richmond Todd A., Thierry-Mieg Jean, Thodima Venkat J., Thomas David, Tichý Boris, Tom Nikola, Ying Jianming, Garcia Elena Vallespin, Verma Suman, Walker Kimbley, Wang Charles, Wang Junwen, Mittal Vinay K., Wang Yexun, Wen Zhining, Wirta Valtteri, Wu Leihong, Yip Shun H., Xiao Chunlin, Liu Liang Chun, Zhang Guangliang, Zhang Sa, Zhao Meiru, Zheng Yuanting, Craig Daniel J., Zhou Xiaoyan, Mason Christopher E., Mercer Timothy, Tong Weida, Shi Leming, Jones Wendell, Johann Donald J., Xu Joshua, Willey James C., Bushel Pierre R., Crawford Erin, Yu Ying, Xu Chang, Chen Guangchun, Burgess Daniel, Cawley Simon, Giorda Kristina, Haseley Nathan, Qiu Fujun, Wilkins Katherine, Arib Hanane, del Pozo Angela, Attwooll Claire, Babson Kevin, Bao Longlong, Bao Wenjun, Lucas Anne Bergstrom. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions, Genome Biology 2021; 22(1): article no. 109-article no. 109 doi:10.1186/s13059-021-02315-0
  • Qin Jing, Hu Yaohua, Yao Jen Chih, Leung Ricky Wai Tak, Zhou Yongqiang, Qin Yiming, Wang Junwen. Cell fate conversion prediction by group sparse optimization method utilizing single-cell and bulk OMICs data, Briefings in Bioinformatics 2021; 22(6): article no. bbab311-article no. bbab311 doi:10.1093/bib/bbab311
  • Yao Hongcheng, Liang Qian, Qian Xinyi, Wang Junwen, Sham Pak Chung, Li Mulin Jun. Methods and resources to access mutation-dependent effects on cancer drug treatment, Briefings in Bioinformatics 2020; 21(6): 1886-1903 doi:10.1093/bib/bbz109
  • Chandrashekar Pramod, Ahmadinejad Navid, Wang Junwen, Sekulic Aleksandar, Egan Jan B., Asmann Yan W., Kumar Sudhir, Maley Carlo, Liu Li. Somatic selection distinguishes oncogenes and tumor suppressor genes, Bioinformatics 2020; 36(6): 1712-1717 doi:10.1093/bioinformatics/btz851
  • Qu Lihui, Lu Yingying, Ying Meike, Li Bingjue, Weng Chunhua, Xie Zhoutao, Liang Ludan, Lin Chuan, Yang Xian, Feng Shi, Wang Yucheng, Shen Xiujin, Zhou Qin, Chen Ying, Chen Zhimin, Wu Jianyong, Lin Weiqiang, Shen Yi, Qin Jing, Xu Hang, Xu Feng, Wang Junwen, Chen Jianghua, Jiang Hong, Huang Hongfeng. Correction: Tacrolimus dose requirement based on the CYP3A5 genotype in renal transplant patients, Oncotarget 2020; 11(16): 1474-1477 doi:10.18632/oncotarget.27561
  • Dong Qunxi, Zhang Jie, Li Qingyang, Wang Junwen, Leporé Natasha, Thompson Paul M., Caselli Richard J., Ye Jieping, Wang Yalin. Integrating Convolutional Neural Networks and Multi-Task Dictionary Learning for Cognitive Decline Prediction with Longitudinal Images, Journal of Alzheimer's Disease 2020; 75(3): 971-992 doi:10.3233/JAD-190973
  • Li Bingjue, Zhu Chaohong, Dong Lihua, Qin Jing, Xiang Wenyu, Davidson Alan J., Feng Shi, Wang Yucheng, Shen Xiujin, Weng Chunhua, Wang Cuili, Zhu Tingting, Teng Lisha, Wang Junwen, Englert Christoph, Chen Jianghua, Jiang Hong. ADAM10 mediates ectopic proximal tubule development and renal fibrosis through Notch signalling, Journal of Pathology 2020; 252(3): 274-289 doi:10.1002/path.5517
  • Huang Dandan, Yi Xianfu, Zhou Yao, Yao Hongcheng, Xu Hang, Wang Jianhua, Zhang Shijie, Nong Wenyan, Wang Panwen, Shi Lei, Xuan Chenghao, Li Miaoxin, Wang Junwen, Li Weidong, Kwan Hoi Shan, Sham Pak Chung, Wang Kai, Li Mulin Jun. Ultrafast and scalable variant annotation and prioritization with big functional genomics data, Genome Research 2020; 31(12): 1789-1801 doi:10.1101/gr.267997.120
  • Koohi-Moghadam M, Borad MJ, Tran NL, Swanson KR, Boardman LA, Sun H, Wang JW. MetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers, Bioinformatics 2019; 35(19): 3812-3814 doi:10.1093/bioinformatics/btz123
  • Wang Bingbing, Wang Panwen, Parobchak Nataliya, Treff Nathan, Tao Xin, Wang Junwen, Rosen Todd. Integrated RNA-seq and ChIP-seq analysis reveals a feed-forward loop regulating H3K9ac and key labor drivers in human placenta, Placenta 2019; 76: 40-50 doi:10.1016/j.placenta.2019.01.010
  • Wang Junwen, Wang Kai, Liu Xiaoming, Sham Pak, Zhao Zhongming. Next-Generation Sequencing in Human Genetic Studies: Genome Technologies and Applications to Human Genetic Studies, Human Heredity 2019; 83(3): 105-106 doi:10.1159/000494818
  • Poon NYE, Hao B, Guan D, Li J, Lu J, Yang Y, Wu B, Wu CM, Webb SE, Liang Y, Miller AL, Yao X, Wang J, Yan B, Boheler KR. Integrated transcriptomic and regulatory network analyses identify microRNA-200c as a novel repressor of human pluripotent stem cell-derived cardiomyocyte differentiation and maturation, Cardiovascular Research 2018; 114(6): 894-906 doi:10.1093/cvr/cvy019
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  • Wang Z, Zhu B, Zhang M, Parikh H, Jia J, Chung CC, Sampson JN, Hoskins JW, Hutchinson A, Burdette L, Ibrahim A, Hsing AW, Hsiung CA, Hu N, Adjei AA, Gross M, Ruder AM, Hu W, Hu Z, Huang MS, Wang C, Canzian F, Lim WY, Hunter DJ, Simon M, Inskip PD, Ma J, Ito H, Jacobs EJ, Ryu JS, Jacobs KB, Yang HP, Cao G, Kim YC, Jenab M, Ji BT, Koh WP, Ahlbom A, Johansen C, Johansson M, Southey MC, Johnson A, Sanson M, Caporaso NE, Kaaks R, Prescott J, Gastier-Foster JM, Kamat AM, Yang PC, Kamineni A, Kohno T, Malats N, Kolonel LN, Kooperberg C, Carrato A, Kratz CP, Yu CJ, Aldrich M, Krogh V, Kunitoh H, Stampfer M, Cortessis VK, Kurtz RC, Shen H, Kurucu N, Arslan AA, Lan Q, Ambrosone CB, Lathrop M, Wang J, Schned A, Mannisto S, Marina N, Mastrangelo G, Matsuo K, Crawford ED, Kitahara CM, McGlynn KA, Austin MA, Berndt SI, McKean-Cowdin R, Gorlick R, McNeill LH, Gillanders EM, McWilliams RR, Gaziano JM, Melin BS, Carreon T, Amos C, Meltzer PS, Cussenot O, Mensah JE, Miao X, Wang SS, Michaud DS, Ye Y, Khanna C, Stattin P, Carta A, Mondul AM, Moore LE, Muir K, Niwa S, Gerhard DS, Lissowska J, Beane Freeman LE, Olson SH, Orr N, Andersson U, Chang GC, Sierri S, Panico S, Yeboah ED, Park JY, Stern MC, Patel AV, Patino-Garcia A, Weiderpass E, Pavanello S, Davis FG, Risch HA, Peeters PH, Peplonska B, Schumacher FR, Giffen CA, Peters U, Petersen GM, Yin Z, Picci P, Weinstein SJ, Andriole G, Van Den Eeden SK, Lecanda F, Pike MC, De Vivo I, Porru S, Schwartz AG, Stevens VL, Schwartz KL, Schwenn M, Scotlandi K, Duell EJ, Goggins M, Arici C, Seow A, Yu K, Khaw KT, Serra C, Wu X, Serra M, Sesso HD, Giovannucci EL, Severi G, Chang IS, Wentzensen N, Stolzenberg-Solomon RZ, Stram DO, Strom SS, Su WC, Kim C, Sund M, Grossman HB, Hallmans G, Sung SW, Lindstrom S, Swerdlow A, Li D, Baris D, Lee KM, Tan W, Hautman C, Tanaka H, Albanes D, Tang W, Tang ZZ, Chang-Claude J, Tardon A, Ding T, Pu X, Yuan JM, Tay E, Taylor PR, Tettey Y, Thomas DM, Lee MP, Spector L, Haiman CA, Tirabosco R, Barkauskas DA, Goldstein AM, Yatabe Y, Tjonneland A, Dinney CP, Tobias GS, Zanetti KA, Toro JR, Travis RC, Che X, Trichopoulos D, Kim IS, Troisi R, Truelove A, Wheeler W, Le Marchand L, Tsai YH, Tucker MA, Di Stefano AL, Tumino R, Chen CJ, Gonzalez C, Shen M, Bassig BA, Kim YH, Van Den Berg D, White E, Zeleniuch-Jacquotte A, Wiencke JK, Wolk A, Wolpin BM, Klein AP, Greene MH, Wong MP, Elena JW, Purdue MP, Wrensch M, Conti D, Berg CD, Wu C, Liao LM, Wu T, Chen CY, Zheng W, Bertazzi PA, Zhou B, Mirabello L, Qiao YL, Savage SA, Liu J, Amiano P, Kraft P, Chanock SJ, Siddiq A, Grubb R, Shete S, Yeager M, Garcia-Closas R, Landi MT, Giles GG, Shi J, Chatterjee N, Amundadottir LT, Kim YT, Vermeulen R, Fan JH, Biritwum RB, Black A, Blot W, Boeing H, Shiraishi K, Ying C, Boffetta P, Gu J, Lin D, Deng X, Bolton K, Kang CH, Boutron-Ruault MC, Feigelson HS, Bracci PM, Brennan P, Brinton LA, Rajaraman P, Brotzman M, Bueno-de-Mesquita HB, Chen CH, Shu XO, Buring JE, Butler MA, Jung YJ, Cai Q, Lin J, Wu YL, Guan P, Riboli E, Cancel-Tassin G, Chen C, Feychting M, Chen KY, Chen YM, Chokkalingam AP, Linet MS, Chu LW, Klein R, Vineis P, Clavel-Chapelon F, Karagas M, Raj PS, Colditz GA, Sierrasesumaga L, Colt JS, Figueroa JD, Hankinson SE, Flanagan AM, Fraumeni JF, Visvanathan K, Freedman ND, Spitz M, Gokgoz N, Fridley BL, Fuchs CS, Ljungberg B, Wunder JS, Gago-Dominguez M, Lau CC, Gallinger S, Lerner SP, Gao YT, Gapstur SM, Garcia-Closas M, Rodabough RJ, Kogevinas M, Harris CC, Hartge P, Hattinger C, Hayes RB, Xiang YB, Diver WR, He Q, Lloreta J, Sihoe ADL, Helman L, Andrulis IL, Henderson BE, Allen NE, Henriksson R, Abnet CC, Hoffman-Bolton J, Vogel U, Hohensee C, Holly EA, Xu J, Hong YC, Hoover RN, Rothman N, Hosgood HD, Silverman DT, Cook MB, Lu D, Wang C, Hsiao CF. Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33., Human molecular genetics 2014; 23(24): 6616-6633 doi:10.1093/hmg/ddu363
  • YALAMANCHILI HK, LI Z, WANG P, Wong MP, Yao JJ, Wang JJ. SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples, Nucleic Acids Research 2014; 42(15) doi:10.1093/nar/gku577
  • Xu M, Zhao GN, Lv X, Liu G, WANG Y, Hao DL, Wang JJ, Liu DP, Liang CC. CTCF controls HOXA cluster silencing and mediates PRC2-repressive higher-order chromatin structure in NT2/D1 cells, Molecular and Cellular Biology 2014; doi:10.1128/MCB.00567-14
  • Pan X, Papasani M, Hao Y, Calamito M, Wei F, Quinn WJ, Basu A, Wang J, Hodawadekar S, Zaprazna K, Liu H, Shi Y, Allman D, Cancro M, Atchison ML. YY1 controls Igκ repertoire and B-cell development, and localizes with condensin on the Igκ locus, EMBO Journal 2013; 32(8): 1168-1182 doi:10.1038/emboj.2013.66
  • Wang T, Mao X, Li H, Qiao S, Xu A, Wang JJ, Lei S, Liu Z, Ng JKF, Wong GTC, Vanhoutte PMGR, Irwin MG, Xia Z. N-Acetylcysteine and allopurinol up-regulated the Jak/STAT3 and PI3K/Akt pathways via adiponectin and attenuated myocardial postischemic injury in diabetes, Free Radical Biology & Medicine 2013; 63: 291-303 doi:10.1016/j.freeradbiomed.2013.05.043
  • Li J, Wang Y, Xia Z, Sham PC, Wang JJ. GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications, Nucleic Acids Res 2013; 41(W1): W150-W158 doi:10.1093/nar/gkt456
  • Lei S, Li H, Xu J, Liu Y, Gao X, Wang JJ, Ng JKF, Lau WB, Ma XL, Rodrigues B, Irwin MG, Xia Z. Hyperglycemia-Induced Protein Kinase Cβ2 Activation Induces Diastolic Cardiac Dysfunction in Diabetic Rats by Impairing Caveolin-3 Expression and Akt/eNOS Signaling, Diabetes 2013; 62(7): 2318-28 doi:10.2337/db12-1391
  • QIN J, LI MJ, WANG P, Wong NS, Wong MP, Xia Z, Tsao GSW, Zhang MQ, Wang JJ. ProteoMirExpress: inferring microRNA and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data, Molecular and Cellular Proteomics 2013; 12(11): 3379-3387 doi:10.1074/mcp.O112.019851
  • CHENG T, XIA W, WANG P, HUANG F, Wang JJ, Sun H. Histidine-rich proteins in prokaryotes: metal homeostasis and environmental habitat-related occurrence, Metallomics 2013; 5(10): 1423-1429 doi:10.1039/C3MT00059A
  • Li H, Liu Z, Wang JJ, Wong GT, Cheung CW, Zhang L, Chen C, Xia Z, Irwin MG. Susceptibility to myocardial ischemia reperfusion injury at early stage of type 1 diabetes in rats, Cardiovascular Diabetology 2013; 12(1): article no. 133-article no. 133 doi:10.1186/1475-2840-12-133
  • Wang P, Lai WF, Li J, Xu F, Yalamanchili HK, Lovell-Badge R, Wang JJ. Inference of gene-phenotype associations via protein-protein interaction and orthology, PLoS ONE 2013; 8(10): e77478-e77478 doi:10.1371/journal.pone.0077478
  • Liu J, Xiao Z, Wong SK, Tin PC, Ho KY, Wang JJ, Sham MH, Wong MP. Lung cancer tumorigenicity and drug resistance are maintained through ALDH(hi)CD44(hi) tumor initiating cells, Oncotarget 2013; 4(10): 1698-1711
  • Song Y, Karasugi T, Cheung KMC, Chiba K, Ho DWH, Miyake A, Kao PYP, Sze KL, Yee FYA, Takahashi A, Kawaguchi Y, Mikami Y, Matsumoto M, Togawa D, Kanayama M, Shi D, Dai J, Jiang Q, Wu C, Tian W, Wang N, Leong JCY, Luk KDK, Yip SP, Cherny SS, Wang JJ, Mundlos S, Kelempisioti A, Eskola PJ, Mannikko M, Makela P, Karppinen J, Jarvelin MR, O'Reilly PF, Kubo M, Kimura T, Kubo T, Toyoma Y, Mizuta H, Cheah KSE, Tsunoda T, Sham PC, Ikegawa S, Chan D. Lumbar disc degeneration is linked to a carbohydrate sulfotransferase 3 variant., Journal of Clinical Investigation 2013; 123: 4909-4917 doi:10.1172/JCI69277
  • Liu Jing, Xiao Zhijie, Wong Sunny Kit Man, Tin Vicky Pui Chi, Ho Ka Yan, Wang Junwen, Sham Mai Har, Wong Maria Pik. Lung cancer tumorigenicity and drug resistance are maintained through ALDHhiCD44hi tumor initiating cells, Oncotarget 2013; 4(10): 1686-1699 doi:10.18632/oncotarget.20917
  • Zhang G, Zhou B, Wang W, Zhang M, Zhao Y, Wang Z, Yang L, Zhai j, Feng CG, Wang JJ, Chen X. A functional single-nucleotide polymorphism in the promoter of the gene encoding interleukin 6 is associated with susceptibility to tuberculosis, Journal of Infectious Diseases 2012; 205(11): 1697-1704 doi:10.1093/infdis/jis266
  • Li MJ, Wang P, Liu X, Lim EL, Wang Z, Yeager M, Wong MP, Sham PC, Chanock SJ, Wang J. GWASdb: A database for human genetic variants identified by genome-wide association studies, Nucleic Acids Research 2012; 40(D1): D1047-D1054 doi:10.1093/nar/gkr1182
  • Zhang Y, Liao S, Yang M, Liang X, Poon MW, Wong CY, Wang J, Zhou Z, Cheong SK, Lee CN, Tse HF, Lian Q. Improved Cell Survival and Paracrine Capacity of Human Embryonic Stem Cell-Derived Mesenchymal Stem Cells Promote Therapeutic Potential for Pulmonary Arterial Hypertension., Cell Transplantation 2012; 21 doi:10.3727/096368912X653020
  • Li MJ, Sham PC, Wang J. Genetic variant representation, annotation and prioritization in the post-GWAS era, Cell Research 2012; 22(10): 1505-1508 doi:10.1038/cr.2012.106
  • Xu F, Wang W, Wang P, Li J, Sham PC, Wang JJ. A fast and accurate SNP detection algorithm for next-generation sequencing data, Nature Communications 2012; 3: 1258-1258 doi:10.1038/ncomms2256
  • Lan Q, Hsiung CA, Matsuo K, Hong YC, Seow A, Wang Z, Hosgood HD, Chen K, Wang JC, Chatterjee N, Hu W, Yin Z, Wu C, An SJ, Qian B, Lee VHF, Hsiao CF, Lu D, Sung JS, Kim JH, Gao YT, Li Y, Tsai YH, Jung YJ, Guo H, Hu Z, Chen YM, Hutchinson A, Wang WC, Klein R, Chung CC, Oh IJ, Choi JE, Chen KY, Berndt SI, He X, Wu W, Chang J, Liu L, Zhang XC, Huang MS, Zheng H, Wang J, Su WC, Zhao X, Park KH, Sung SW, Kang CH, Shu XO, Hu L, Chen CH, Pao W, Dong J, Kim YC, Yang TY, Xu J, Guan P, Chen CY, Tan W, Su J, Wang CL, Li H, Sihoe ADL, Kim C, Zhao Z, Chen Y, Choi YY, Hung JY, Kim JS, Vermeulen R, Yoon HI, Cai Q, Lin CC, Park IK, He Q, Xu P, Perng RP, Kohno T, Wu J, Kweon SS, Lim WY, Chen KC, Chow WH, Zhou B, Ji BT, Chan JKC, Chu M, Li YJ, Wong MP, Yokota J, Li J, Chen H, Xiang YB, Yu CJ, Shin MH, Kunitoh H, Wu G, Jin L, Lo YL, Shiraishi K, Zheng W, Chen YH, Lin HC, Wu T, Wu YL, Fraumeni JF, Yang PC, Lin D, Chanock SJ, Caporaso N, Rothman N, Park JY, Chen CJ, Kim YH, Liu J, Kim YT, Landi MT, Shen H, Lawrence C, Burdett L, Yeager M, Yuenger J, Jacobs KB, Chang IS, Mitsudomi T, Jeon HS, Kim HN, Chang GC, Bassig BA, Tucker M, Wei F. Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia, Nature Genetics 2012; 44(12): 1330-1335 doi:10.1038/ng.2456
  • Qin J, Li MJ, Wang P, Zhang MQ, Wang J. ChIP-Array: Combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor, Nucleic Acids Research 2011; 39(SUPPL. 2): W430-W436 doi:10.1093/nar/gkr332
  • Zhang G, Chen X, Chan L, Zhang M, Zhu B, Wang L, Zhu X, Zhang J, Zhou B, Wang J. An SNP selection strategy identified IL-22 associating with susceptibility to tuberculosis in Chinese, Scientific Reports 2011; 1: 20-20 doi:10.1038/srep00020
  • Wang W, Zhi W, Lam TW, Wang JJ. Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions, Scientific Reports 2011; 1, article no. 55 doi:10.1038/srep00055
  • Wu HJ, Wu W, Sun HY, Qin GW, Wang HB, Wang P, Yalamanchili HK, Wang J, Tse HF, Lau CP, Vanhoutte PM, Li GR. Acacetin causes a frequency- and use-dependent blockade of hKv1.5 channels by binding to the S6 domain, Journal of Molecular and Cellular Cardiology 2011; 51(6): 966-973 doi:10.1016/j.yjmcc.2011.08.022
  • Yang S, Yalamanchili HK, Li X, Yao KM, Sham PC, Zhang MQ, Wang J. Correlated evolution of transcription factors and their binding sites, Bioinformatics 2011; 27(21): 2972-2978 doi:10.1093/bioinformatics/btr503
  • Wang LY, Wang P, Li MJ, Qin J, Wang X, Zhang MQ, Wang J. EpiRegNet: Constructing epigenetic regulatory network from high throughput gene expression data for humans, Epigenetics 2011; 6(12): 1505-1512 doi:10.4161/epi.6.12.18176
  • Wang JJ. A database of genetic variants in microRNA genes and their putative functional roles in gene regulation, Human Mutation 2011; 33(1): vii-vii
  • Li MJ, Sham PC, Wang J. FastPval: A fast and memory efficient program to calculate very low P-values from empirical distribution, Bioinformatics 2010; 26(22): 2897-2899 doi:10.1093/bioinformatics/btq540
  • Wei F, Zaprazna K, Wang J, Atchison ML. PU.1 can recruit BCL6 to DNA to repress gene expression in germinal center B cells, Molecular and Cellular Biology 2009; 29(17): 4612-4622 doi:10.1128/MCB.00234-09
  • Tseng H, Chou W, Wang J, Zhang X, Zhang S, Schultz RM. Mouse ribosomal RNA genes contain multiple differentially regulated variants, PLoS ONE 2008; 3(3) doi:10.1371/journal.pone.0001843
  • Wang J, Ungar LH, Tseng H, Hannenhalli S. MetaProm: A neural network based meta-predictor for alternative human promoter prediction, BMC Genomics 2007; 8(374): 1-13 doi:10.1186/1471-2164-8-374
  • Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE, Wacholder S, Wang Z, Welch R, Hutchinson A, Wang J, Yu K, Chatterjee N, Orr N, Willett WC, Colditz GA, Ziegler RG, Berg CD, Buys SS, Mccarty CA, Feigelson HS, Calle EE, Thun MJ, Hayes RB, Tucker M, Gerhard DS, Fraumeni JF, Hoover RN, Thomas G, Chanock SJ. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer, Nature Genetics 2007; 39(7): 870-874 doi:10.1038/ng2075
  • Vardhanabhuti S, Wang J, Hannenhalli S. Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation, Nucleic Acids Research 2007; 35(10): 3203-3213 doi:10.1093/nar/gkm201
  • Zhang S, Wang J, Tseng H. Basonuclin regulates a subset of ribosomal RNA genes in HaCAT cells, PLoS ONE 2007; 2(9) doi:10.1371/journal.pone.0000902
  • Wang J, Hannenhalli S. A mammalian promoter model links cis elements to genetic networks, Biochemical and Biophysical Research Communications 2006; 347(1): 166-177 doi:10.1016/j.bbrc.2006.06.062
  • Wang J, Zhang S, Schultz RM, Tseng H. Search for basonuclin target genes, Biochemical and Biophysical Research Communications 2006; 348(4): 1261-1271 doi:10.1016/j.bbrc.2006.07.198
  • Hannenhalli S, Putt ME, Gilmore JM, Wang J, Parmacek MS, Epstein JA, Morrisey EE, Margulies KB, Cappola TP. Transcriptional genomics associates FOX transcription factors with human heart failure, Circulation 2006; 114(12): 1269-1276 doi:10.1161/CIRCULATIONAHA.106.632430
  • Wang J, Feng JA. NdPASA: A novel pairwise protein sequence alignment algorithm that incorporates neighbor-dependent amino acid propensities, Proteins: Structure, Function and Genetics 2005; 58(3): 628-637 doi:10.1002/prot.20359
  • Wang J, Hannenhalli S. Generalizations of Markov model to characterize biological sequences, BMC Bioinformatics 2005; 6 doi:10.1186/1471-2105-6-219
  • Li W, Wang J, Feng JA. NdPASA: A pairwise sequence alignment server for distantly related proteins, Bioinformatics 2005; 21(19): 3803-3805 doi:10.1093/bioinformatics/bti619
  • Rupp B, Wang J. Predictive models for protein crystallization, Methods 2004; 34(3): 390-407 doi:10.1016/j.ymeth.2004.03.031
  • Wang J, Feng JA. Exploring the sequence patterns in the α-helices of proteins, Protein Engineering 2003; 16(11): 799-807 doi:10.1093/protein/gzg101

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    Book Chapter

  • Yan B, Wang P, Wang JJ, Boheler KR. Discovery of surface target proteins linking drugs, molecular markers, gene regulation, protein networks, and disease by using a web-based platform Targets-search . The Surfaceome: Methods and Protocols. New York, NY: Humana Press; 2018:331-344.
  • Wang W, Xu F, Wang JJ. Assessment of Mapping and SNP-Detection Algorithms for Next-Generation Sequencing Data in Cancer Genomics . Next generation sequencing in cancer research. Volume 1, Decoding the cancer genome. New York: Springer; 2013:301-317.

    • Conference Paper

  • Wu Jianfeng, Su Yi, Reiman Eric M., Caselli Richard J., Chen Kewei, Thompson Paul M., Wang Junwen, Wang Yalin. Investigating the Effect of Tau Deposition and Apoe on Hippocampal Morphometry in Alzheimer's Disease: A Federated Chow Test Model, Proceedings - International Symposium on Biomedical Imaging 2022; 2022-March doi:10.1109/ISBI52829.2022.9761576
  • Bhardwaj V, Jalali S, Villasboas JC, Yang ZZ, Tang XY, Mukherjee P, Mondello P, Kim H, Mudappathi R, Wang JW, Krull JE, Wenzl K, Novak AJ, Ansell SM. Increased Tumor-Associated CD66b+ Myeloid-Derived Suppressor Cells in Waldenstrom Macroglobulinemia Inhibit T-Cell Immune Function, 64th ASH Annual Meeting (10/12/2022-13/12/2022, New Orleans) 2022; 140 doi:10.1182/blood-2022-166450
  • Wu Y, Luo R, Lam TW, Ting HF, Wang J. Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long reads, The 11th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) Proceedings 2020; article No. 15:1-article No. 15:7 doi:10.1145/3388440.3412457
  • Chan YS, Lam TF, Jiang Y, Wu LK, Ma CW, Wang JJ. Orexin delays activity-dependent maturation of the vestibular system in rats, 11th FENS Forum of Neuroscience 2018; 691-691
  • Qin Y, Ng RK, Ng TW, Tong KK, Au TYK, Niu B, Tan Z, Yip MS, Wang JJ, Sham PC, Cheah KSE. Genome-wide identification of active enhancers in the developing mouse nucleus pulposus, Hong Kong Inter-University Postgraduate Symposium in Biochemical Sciences, 2017 2017;
  • Yip SH, Wang P, Kocher JP, Sham PC, Wang JJ. Linnorm: Improved statistical analysis for single cell RNA-seq expression data, Hong Kong Inter-University Postgraduate Symposium in Biochemical Sciences, 2017 2017;
  • Jiang Y, Lam TF, Ma CW, Shum DKY, Wang JJ, Chan YS. Orexin regulates synaptic transmission in the central vestibular system, International Behavorial Neuroscience Society Annual Meeting, 2017 2017; 148-149
  • Gao XY, Xu H, Ho JCM, Chan OSH, Xu F, Wang JW, Lee VHF, Tin VPC, Xiao ZJ, Wang SQ, Yam JWP, Wong MP. Whole-exome sequencing reveals tyrosine kinase-resistant mutations in pretreatment EGFR-mutant lung adenocarcinomas, Cancer Research 2017; 77(13) doi:10.1158/1538-7445.AM2017-LB-274
  • Jiang Y, Ma CW, Wang JJ, Chan YS. Orexin modulates inhibitory synaptic transmission of vestibular nuclear neurons in rats, Neuroscience Symposium & HKSN 2016 Annual Scientific Conference 2016; 37, abstract no. P16-37, abstract no. P16
  • Wang P, Lian Q, Wang YL, Zhang M, Xia Z, Wang J. EATdb: a database of human enhancers and their putative targets, Annual Clinical Genetics Meeting by the American College of Medical Genetics and Genomics, ACMG 2015 2015;
  • Wang P, Qin J, Qin Y, Zhu Y, Wang LY, Li MJ, Zhang MQ, Wang JJ. ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks, Mathematics, Computer and Life Sciences Interdisciplinary Research Young Scholars Forum 2015;
  • Wang P, Qin J, Qin Y, Zhu Y, Wang LY, Li MJ, Zhang MQ, Wang JJ. ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks, ISMB/ECCB 2015 Joint Conference 2015;
  • Liu Z, Li MJ, Wang P, Wong MP, Yeager M, Sham PC, Chanock SJ, Xia Z, Wang JJ. A comprehensive database for GWAS¬identified human genetic variants: an update of GWASdb, ACMG 2015 Annual Clinical Genetics Meeting 2015;
  • Zhu Y, Wang JJ, Qin J. The role of FOXM1 and Kaiso in non-small-cell lung carcinoma (NSCLC), ISMB/ECCB 2015 Joint Conference 2015;
  • Wong MP, Gao X, Kwan TK, Xu H, Tin VPC, Wang JJ, Xiao Z, Xu F. Application of whole exome sequencing in metachronous lung cancers evaluation, Conference of the European Association for Cancer Research, EACR 2015 2015;
  • Qin Y, Koohimoghadam M, Wang P, Qin J, Wang JJ. Machine learning based gene regulatory network inferring with genetics and epigenetics features, Research Postgraduate Symposium, RPS 2015 2015;
  • Wang Y, LI J, Wang JJ. Analysis of long-range chromatin interaction and how transcription factors are involved to regulate gene expression, CSHL Winter Biotechnology Conference on Systems Biology 2014;
  • Wang Y, Wang J. Analysis of long-range chromatin interaction and how transcription factors are involved to regulate gene expression, Hong Kong Inter-University Biochemistry Postgraduate Symposium 2014; 23, poster no. 21-23, poster no. 21
  • Wang Y, Wang P, Xia Z, Lian Q, Zhang MQ, Wang JJ. EATdb: a database of human enhancers and their putative targets, Research Postgraduate Symposium, RPS 2014 2014;
  • Li ML, Wang LY, Sham PC, Zhang MQ, Liu SJ, Wang JJ. Exploring the genome-wide roles of transcription factors and their complexes in chromosome interaction, Annual Meeting of the American Society of Human Genetics, ASHG 2014 2014; 368, abstract 1639M-368, abstract 1639M
  • Wang P, Li MJ, Liu X, Wang JJ. MapIn: an Interactive Mapping tool for biological descriptors, International Conference on Systems Biology & the Translational Bioinformatics Conference, ISB/TBC 2014 2014;
  • Li MJ, Wu J, Jiang P, Li W, Zhu Y, Fernandez D, Ryan RJH, Chen Y, Wang JJ, Liu JS, Liu XS. Exploring functional variation affecting miRNA and ceRNA regulation in humans, Conference of Program in Quantitative Genomics, PQG 2014 2014; doi:10.1101/016865
  • Wang Y, Xu F, Hu L, Quan Q, Tsang CN, Chu IK, Wang JJ. An integrated metalloproteomic analysis depicts the proteomic features of helicobacter pylori in response to Bi(III), International Conference on Biological Inorganic Chemistry, ICBIC-17 2014;
  • Wang Y, Xu F, Hu L, Quan Q, Tsang CN, Chu IK, Wang JJ, Sun H. An integrated metalloproteomic analysis depicts the proteomic features of Helicobacter pylori in response to Bi(III), Asian Conference on Coordination Chemistry, ACCC-5 2014;
  • Yalamanchili HK, Yan B, Li MJ, Qin J, Zhao Z, Chin FYL, Wang JJ. Inferring gene regulatory network from variable delay high temporal data, ISMB/ECCB 2013 Joint Conference 2013;
  • Wang Y, Zhang MQ, Wang JJ. Global landscape of histone modifications contributes to cellular identity determination by affecting gene expression dynamics, Mathematics, Computer and Life Sciences Interdisciplinary Research Young Scholars Forum 2013;
  • Li J, Wang Y, Xia Z, Sham PC, Wang JJ. GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications, Mathematics, Computer & Life Sciences Interdisciplinary Research Young Scholars Forum 2013;
  • Li J, Wang Y, Zhang MQ, Wang JJ. Systematic analysis of the role of transcription regulators in distal interactions, Gordon Conference on Posttranslational Modification Networks: Phosphosignaling 2013;
  • Xu F, Wang W, Wang P, Li J, Sham PC, Wang JJ. FaSD: a efficient model to detect SNPs for NGS data, Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013 2013;
  • Wang W, Xu F, Wang P, Li MJ, Sham PC, Wang JJ. Assessment of aligner and SNP caller for next generation sequencing and a fast and accurate SNP detection method, ISMB/ECCB 2013 Joint Conference 2013;
  • Qin J, Li MJ, Wang P, Wong NS, Wong MP, Xia Z, Tsao GSW, Zhang MQ, Wang JJ. ProteoMirExpress: inferring microRNA-centered regulatory networks from high-throughput proteomic and transcriptome data, ISMB-ECCB 2013 Joint Conference 2013;
  • Li J, Wang Y, Wang JJ. dbPSHP: a database of recent positive selection across human population, Annual International Conference on Computational and Systems Biology, ICCSB 2013 2013;
  • Li J, Wang Y, Xia ZY, Sham PC, Wang JJ. GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations and chromosome states, Research Postgraduate Symposium, RPS 2013 2013;
  • Yalamanchili HK, Li Z, Yao JJ, Wang JJ. Recovering isoform specific gene regulatory networks from RNA-SEQ data, Research Postgraduate Symposium, RPS 2013 2013;
  • Wang W, Wei ZHI, Lam TW, Wang JJ. Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions, Hong Kong Inter-University Postgraduate Symposium 2012;
  • Wang Y, Wang P, Li J, Qin J, Wang X, Zhang MQ, Wang JJ. EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans, Hong Kong Inter-University Postgraduate Symposium 2012;
  • Yalamanchili HK, Xiao QW, Wang JJ. A Novel Neural Response Algorithm for Protein Function Prediction, Hong Kong Inter-University Postgraduate Symposium 2012;
  • Yalamanchili HK, Xiao QW, Wang J. A novel neural response algorithm for protein function prediction, BMC Systems Biology 2012; 6(suppl. 1, article no. S19) doi:10.1186/1752-0509-6-S1-S19
  • Xu F, Wang W, Wang P, Sham PC, Wang JJ. A fast and accurate SNP detection algorithm for next-generation sequencing data, Hong Kong Inter-University 2012 Postgraduate Symposium on Life Science 2012;
  • Xu F, Wang W, Wang P, Sham PC, Wang JJ. A fast and accurate SNP detection algorithm for next-generation sequencing data, HKU 2012 Research Postgraduate Seminar Series 2012;
  • Song Y, Karasugi T, Cheung KMC, Chiba K, Ho DWH, Miyake A, Kao PYP, Sze KL, Yee AFY, Takahashi A, Kawaguchi Y, Mikami Y, Matsumoto M, Togawa D, Kanayama M, Shi D, Dai J, Jiang Q, Wu C, Tian W, Wang NA, Leong JCY, Luk KDK, Yip SP, Cherny SS, Wang JJ, Mundlos S, Kelempisioti A, Eskola PJ, Mannikko M, Makela P, Karppinen J, Jarvelin MR, O Reilly PF, Kubo M, Kimura T, Kubo T, Toyama Y, Mizuta H, Cheah KSE, Tsunoda T, Sham PC, Ikegawa S, Chan D. Identification of a functional variant in CHST3 associated with the susceptibility for lumbar disc degeneration, Symposium of the Hong Kong Society for Developmental Biology, HKSDB 2012 2012;
  • Yalamanchili HK, Wang JJ. Gene regulatory network inference from high frequency time series data, Research Postgraduate Symposium, RPS 2012 2012;
  • Qin J, Li MJ, Wang P, Wang JJ. Integrative approach for omic data analysis and gene regulatory network construction, Research Postgraduate Symposium, RPS 2012 2012;
  • Wang W, Xu F, Wang JJ. Assessment of aligner and SNP caller for next generation sequencing and a fast and accurate SNP detection method, Research Postgraduate Symposium, RPS 2012 2012;
  • Wang Y, Zhang MQ, Wang JJ. Global landscape of histone modifications contributes to cellular identity determination by affecting gene expression dynamics, Genome Informatics 2012 2012;
  • Yalamanchili HK, Xiao QW, Wang JJ. A Novel Neural Response Algorithm for Protein Function Prediction, IEEE BIBM 2012 2012;
  • Wang JJ. Integrative analysis of high throughput data for regulatory network construction, BIT’s 2nd Annual World Congress of Molecular & Cell Biology 2012;
  • Wang JJ. Constructing epigenetic regulatory networks from high throughput gene expression and ChIP-seq data, Annual World Congress of Regenerative Medicine & Stem cell 2012;
  • Wang JJ. A fast and accurate SNP detection algorithm for next-generation-sequencing data, IEEE International Conference on Systems Biology (ISB) 2012;
  • Yalamanchili HK, Wang J, Xiao QW. NRProF: Neural response based protein function prediction algorithm, Proceedings of the IEEE International Conference on Systems Biology, ISB 2011 2011; 33-40 doi:10.1109/ISB.2011.6033117
  • Qin J, Li MJ, Wang P, Zhang MQ, Wang JJ. ChIP-array: combinatory analysis of ChIP-seq/chip and microarray gene expression data, CSHAsia 2011 Conference on High Throughput Biology 2011;
  • Qin J, Li MJ, Wang P, Zhang MQ, Wang JJ. ChIP-array: gene regulation network construction from ChIP-seq/chip and mRNA expression data, Hong Kong Inter-University Biochemistry Postgraduate Symposium 2011;
  • Wang Y, Wang P, Li J, Qin J, Wang XW, Zhang MQ, Wang JJ. EpiRegNet: constructing epigenetic regulatory networks from high throughput gene expression data for humans, Hong Kong Inter-University Biochemistry Postgraduate Symposium 2011;
  • Wang W, Wei Z, Lam TW, Wang JJ. Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions, Hong Kong Inter-University Biochemistry Postgraduate Symposium 2011;
  • Yalamanchili HK, Xiao QW, Wang JJ. ProF: neural response based protein function prediction algorithm, Hong Kong Inter-University Biochemistry Postgraduate Symposium 2011;
  • Wang W, Wei Z, Lam TW, Wang JJ. Assessment of next generation sequencing analysis tools shows lower coverage and poorer SNP-calling quality in the CpG islands and regulatory regions in cancer genome, Research Postgraduate Symposium, RPS 2011 2011;
  • Qin J, Li J, Wang JJ. ProteoMirExpress: inferring microRNA activities from mRNA and protein expression data, Research Postgraduate Symposium, RPS 2011 2011;
  • Wang Y, Wang P, Qin J, Wang XW, Zhang MQ, Wang JJ. EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans, Research Postgraduate Symposium, RPS 2011 2011;
  • Yalamanchili HK, Xiao QW, Wang JJ. NRProF: neural response based protein function prediction algorithm, Research Postgraduate Symposium, RPS 2011 2011;
  • Xu F, Wang W, Wang P, Sham PC, Wang JJ. FaSD: a fast and accurate SNP detection algorithm for next-generation sequencing data, Research Postgraduate Symposium, RPS 2011 2011;
  • Wang W, Wei ZHI, Lam TW, Wang JJ. Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions, IEEE International Conference on Systems Biology 2011;
  • Wang W, Wei Z, Lam TW, Wang JJ. Assessment of next generation sequencing analysis tools shows lower coverage and poorer SNP-calling quality in the CpG islands and regulatory regions, Frontiers in Biomedical Research Conference 2011;
  • Qin J, Li J, Wang P, Zhang MQ, Wang JJ. ChIP-Array: Gene Regulation Network Construction from ChIP-seq/chip and mRNA expression data, IEEE International Conference on Systems Biology 2011;
  • Wang Y, Wang P, Li J, Qin J, Wang XW, Zhang MQ, Wang JJ. EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans, IEEE International Conference on Systems Biology 2011;
  • Wang Y, Wang P, Li J, Qin J, Wang XW, Zhang MQ, Wang JJ. EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans, CSHAsia 2011 Conference on Bioinformatics of Human and Animal Genomics 2011;
  • Li J, Wang JJ. FastPval: a fast and memory efficient program to calculate very low p-values from empirical distribution, IEEE International Conference on Systems Biology (ISB) 2011; Paper ID: 28-Paper ID: 28
  • Yang S, Li XR, Yalamanchili HK, Wang JJ. Co-evolution of transcription factors and their binding sites, Hong Kong Inter-University Biochemistry Postgraduate Symposium 2010;
  • Wang JJ, Yang S, Yalamanchili HK, Li X. Co-evolution of transcription factor and its binding sites, CSHL Meeting on Systems Biology 2010;
  • Yang S, Agrawal K, Lam TW, Sham PC, Cheah K, Wang J. A novel profile hidden Markov model to predict microRNAs and their targets simultaneously, Annual International Conference on Computational Systems Bioinformatics, CSB 2010 2010;
  • Yu CL, Chan WY, Wang J, Nicholls JM, Peiris JSM, Mason RJ, Chan MCW. Avian influenza H5N1 and seasonal H1N1 virus infection and innate host responses in human alveolar type II epithelial cells and macrophages, ISIRV Options-7 Conference 2010;
  • Wang JJ. Prediction of transcription factor binding sites from protein sequence through protein-DNA co-evolution, CSH Asia Conference on Computational Biology 2010;
  • Yang S, Agrawal KR, Lam TW, Sham PC, Cheah KSE, Wang JJ. Novel Profile Hidden Markov Model to Predict MicroRNAs and their Targets Simutaneously, Research Postgraduate Symposium, RPS 2009 2009;

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Honours & Awards
  • 2013. Sham PC, WANG Yan, Wong MP, LI Jun, Wang JJ, Xia Z. The best poster presentation award: The 5th International Conference on Computational and Systems Biology, SUSTC, Shenzhen, Nov15, 2013.
  • 2013. Wang JJ. Outstanding Young Researcher Award (2011-2012): The University of Hong Kong.
  • 2012. Wang JJ. Individual advancement award for national science & tech project: Shenzhen virtual university campus.
  • 2009. Wang JJ. Gold Medal Winner: International Genetically Engineered Machine Competition (IGEM’09), MIT.
  • 2005. Wang JJ. NIH NRSA Computational Genomics Training Fellowship: University of Pennsylvania.
  • 1998. Wang JJ. Institute of Food Technologists Scholastic Award: University of Washington.
  • 1997. Wang JJ. Claire & Egtvedt Fellow: University of Washington.

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Knowledge Exchange
  • 01 June 2013: Wang John Junwen. 瞄準目標，不懈追求 -與港大傑出科研工作者獎獲得者王俊文博士之訪談錄.
  • 13 March 2013: Wang John Junwen. video for outstanding young researcher awardees.
  • 11 December 2012: Wang John Junwen. 科研協作系列之背靠祖國.
Grants
  • Project Title: Unravelling the single-cell developmental atlas during degradation of the dental lamina: implications for whole-tooth regeneration in diphyodont species
    Grant Type: General Research Fund (GRF) 2025/26
    Funding Year: 2025
    Amount: HK$1,381,520
    Principal Investigator: Professor Zhang, Chengfei
    Co-investigator(s): Professor Wu Zhaoming, Professor Hu Mingxin, Professor Wang Junwen John
  • Project Title: Discovering prognostic biomarkers for pulpotomy outcome in permanent mature teeth with irreversible pulpitis
    Grant Type: General Research Fund (GRF) 2023/24
    Funding Year: 2023
    Amount: HK$1,532,000
    Principal Investigator: Professor Zhang, Chengfei
    Co-investigator(s): Professor Wang Junwen John, Professor Wu Zhaoming, Professor Lee Angeline Hui Cheng, Professor Zhang Gao
  • Project Title: A spatiotemporal analysis of the m6A RNA modification mechanism in senescence-associated alveolar bone remodelling
    Grant Type: General Research Fund (GRF) 2023/24
    Funding Year: 2023
    Amount: HK$1,117,540
    Principal Investigator: Professor Yang, Yanqi
    Co-investigator(s): Professor Jin Lijian, Professor Wang Junwen John, Dr. HU Zhekai, Professor Matsuo Koichi
  • Project Title: A bioinformatics platform to decode causal effects of germline alterations in oral and oropharynx cancers
    Grant Type: Collaborative Research Fund (CRF) - Group Research Project 2023/2024
    Funding Year: 2023
    Amount: HK$2,936,465
    Principal Investigator: Professor Wang, Junwen John
    Co-principal investigator(s): Professor Su Yuxiong, Dr Fan Xiaodan, Professor Guan Xin-Yuan, Professor Lee Victor Ho Fun
  • Project Title: Bioinformatics/AI to decode Molecular determinants of sex differences in head and neck cancers
    Grant Type: Seed Fund for PI Research – Basic Research
    Funding Year: 2023
    Amount: HK$39,520
    Principal Investigator: Professor Wang, Junwen John
  • Project Title: Early Childhood Caries Prediction by Using Multimodal Machine Learning
    Grant Type: Health and Medical Research Fund 2023
    Funding Year: 2023
    Amount: HK$1,496,878
    Principal Investigator: Dr Liu, Pei
    Co-investigator(s): Professor Huang Shi, Professor Wang Junwen John, Professor Yiu Cynthia Kar Yung, Professor Lo Edward Chin Man, Professor Wong May Chun Mei
  • Project Title: AI/informatic methods to annotate the function of genetic variants in protein coding regions
    Grant Type: Seed Fund for Basic Research for New Staff
    Funding Year: 2022
    Amount: HK$150,000
    Principal Investigator: Professor Wang, Junwen John
  • Project Title: The functional roles of minerals and vitamins in human diseases – an AI/informatics approach
    Grant Type: Seed Fund for Collaborative Research
    Funding Year: 2022
    Amount: HK$400,000
    Principal Investigator: Professor Wang, Junwen John
    Co-principal investigator(s): Emeritus Professor Flemmig Thomas Frank, Professor McGrath Colman, Professor Lee Victor Ho Fun, Professor Zhang Gao, Professor Yang Yanqi, Professor Su Yuxiong
  • Project Title: PKCß2 over-activation reduces cardiac tolerance to ischemia-reperfusion injury in diabetic rodents by downregulating caveolin-3 and modulating cardiomyocyte autophagy
    Grant Type: General Research Fund (GRF)
    Funding Year: 2015
    Amount: HK$860,359
    Principal Investigator: Dr Xia, Zhengyuan
    Co-investigator(s): Professor Wang Junwen John, Professor Xu Aimin, Professor Vanhoutte Paul Michel Georges Remi, Dr Yue Jianbo, Professor Irwin Michael Garnet
  • Project Title: Deriving nucleus pulposus progenitors to facilitate vertebral joint repair
    Grant Type: General Research Fund (GRF)
    Funding Year: 2015
    Amount: HK$814,907
    Principal Investigator: Dr Leung, Victor Yu Leong
    Co-investigator(s): Dr Sakai Daisuke, Professor Wang Junwen John, Emeritus Professor Chan Danny, Professor Cheung Kenneth Man Chee
  • Project Title: Antimicrobial activities of bismuth complexes beyond H. pylori
    Grant Type: General Research Fund (GRF)
    Funding Year: 2015
    Amount: HK$1,058,362
    Principal Investigator: Professor Sun, Hongzhe
    Co-investigator(s): Professor Wang Junwen John
  • Project Title: Translating intra-tumoural genetic heterogeneity to identify cancer progression genes in lung adenocarcinoma
    Grant Type: Health and Medical Research Fund - Full Grant
    Funding Year: 2015
    Amount: HK$1,196,608
    Principal Investigator: Dr Wong, Maria Pik
    Co-investigator(s): Professor Lee Victor Ho Fun, Professor Wang Junwen John, Professor Lee Elaine Yuen Phin, Professor Fong Daniel Yee Tak, Professor Sham Pak Chung, Dr Leung Kin Chung
  • Project Title: Epigenetic function of TET2 in the transcriptional regulation of MLL-rearranged leukemia
    Grant Type: Health and Medical Research Fund - Full Grant
    Funding Year: 2015
    Amount: HK$1,200,000
    Principal Investigator: Dr Ng, Ray Kit
    Co-investigator(s): Professor Wang Junwen John
  • Project Title: A novel computational framework to identify transcription factor-DNA interaction for cancer genomics
    Grant Type: General Research Fund (GRF)
    Funding Year: 2014
    Amount: HK$1,282,684
    Principal Investigator: Professor Sham, Pak Chung
    Co-investigator(s): Dr Yao Kwok Ming, Dr Wong Maria Pik, Professor Wang Junwen John
  • Project Title: The role and mechanisms of tumor initiating cells regulation by nuclear factor of activated T-cells (NFAT) pathway in non-small cell lung cancer
    Grant Type: General Research Fund (GRF)
    Funding Year: 2014
    Amount: HK$881,856
    Principal Investigator: Dr Wong, Maria Pik
    Co-investigator(s): Professor Wang Junwen John
  • Project Title: Identification of cancer metastasis and drug resistance pathways through comparison of primary and metastatic lung adenocarcinomas by next generation sequencing analysis
    Grant Type: Health and Medical Research Fund - Full Grant
    Funding Year: 2013
    Amount: HK$1,000,000
    Principal Investigator: Dr Wong, Maria Pik
    Co-investigator(s): Dr Au Siu Kie, Professor Wang Junwen John, Professor Sham Pak Chung, Professor Lee Victor Ho Fun, Dr Sihoe Dart Loon Alan, Dr Chan Siu Hong
  • Project Title: Identifying critical transitions and gene regulatory networks controlling phases of chondrocyte differentiation in the growth plate
    Grant Type: NSFC/RGC Joint Research Scheme
    Funding Year: 2013
    Amount: HK$1,125,000
    Principal Investigator: Emeritus Professor Cheah, Kathryn Song Eng
    Co-principal investigator(s): Professor Zhang Michael Q Co-investigator(s): Professor Wang Junwen John, Dr Gao Juntao, Emeritus Professor Chan Danny, Dr Gu Jin, Dr Ng Ray Kit
  • Project Title: Functional Analyses of How Genomic Variation Affects Personal Risk for Degenerative Skeletal Disorders
    Grant Type: Theme-based Research Scheme
    Funding Year: 2012
    Amount: HK$63,750,000
    Principal Investigator: Emeritus Professor Cheah, Kathryn Song Eng
    Co-principal investigator(s): Professor Zhang Michael Qiwei, Professor Chan Barbara Pui, Emeritus Professor Luk Keith Dip Kei, Emeritus Professor Chan Danny, Professor Cheung Kenneth Man Chee, Professor Sham Pak Chung, Professor Jin Dong-Yan, Dr Lam Yun Wah, Dr Lian Qizhou Co-investigator(s): Dr Cherny Stacey Shawn, Dr Ng Ray Kit, Dr Samartzis Dino, Professor Huang Jiandong, Professor Wang Junwen John, Dr Song You-qiang
  • Project Title: Systems biology approach to understand gene regulatory network of lung cancer pathogenesis
    Grant Type: National Natural Science Foundation of China (NSFC) - Major Research Project
    Funding Year: 2012
    Amount: HK$1,130,400
    Principal Investigator: Professor Wang, Junwen John
    Co-investigator(s): Dr Liu Jing, Dr. WANG Yan, Dr. XU Feng, Dr. QIN Jing, Dr. WANG Weixin, Mr Liu Xiaorong, Dr Wong Maria Pik, Dr. WANG Panwen, Dr. LI Jun
  • Project Title: Understanding the co-evolutionary relationship between transcription factors and their DNA binding sites for bHLH family in eukaryotes
    Grant Type: General Research Fund (GRF)
    Funding Year: 2011
    Amount: HK$950,000
    Principal Investigator: Professor Wang, Junwen John
    Co-investigator(s): Dr Yao Kwok Ming
  • Project Title: Investigation of tumor-propagating cells and stemness/differentiation axis pathways in non-small cell lung cancers
    Grant Type: General Research Fund (GRF)
    Funding Year: 2011
    Amount: HK$900,000
    Principal Investigator: Dr Wong, Maria Pik
    Co-investigator(s): Professor Sham Mai Har, Professor Wang Junwen John
  • Project Title: Outstanding Young Researcher Award 2011-12
    Grant Type: Outstanding Young Researcher Award
    Funding Year: 2011
    Amount: HK$300,000
    Principal Investigator: Professor Wang, Junwen John
  • Project Title: Understanding genetic and epigenetic features of active promoters in human/mouse embryonic stem cells
    Grant Type: NSFC/RGC Joint Research Scheme
    Funding Year: 2010
    Amount: HK$756,000
    Principal Investigator: Professor Wang, Junwen John
    Co-principal investigator(s): Professor Zhang Michael Qiwei Co-investigator(s): Dr Wang Xiao Wo
  • Project Title: A Novel Hidden Markov Model to Predict microRNAs and their Targets Simultaneously and its Application to the Epstein-Barr virus
    Grant Type: Research Fund for the Control of Infectious Diseases - Full Grants
    Funding Year: 2010
    Amount: HK$982,485
    Principal Investigator: Professor Wang, Junwen John
    Co-investigator(s): Professor Tsao George Sai Wah
  • Project Title: Evolution and functional specialization of alternative promoters in humans
    Grant Type: General Research Fund (GRF)
    Funding Year: 2009
    Amount: HK$850,230
    Principal Investigator: Professor Wang, Junwen John
    Co-investigator(s): Professor Huang Jiandong
  • Project Title: Attending and presentation in AACR
    Grant Type: Conference Support for Teaching Staff
    Funding Year: 0
    Amount: HK$18,000
    Principal Investigator: Professor Wang, Junwen John

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Invited Lectures & Keynote Speeches
  • 01 August 2014: Decoding genetic and epigenetic networks for vitamin C mediated cell reprogramming. ChemEpInformatics: In the pursuit of epidrugs using chemoinformatics and computational approaches, ACS National meeting, San Francisco, CA, August 10-14, 2014.
  • 01 May 2014: Integrative analysis of OMICs big data for network inference. Youth forum for interdisciplinary research in math, computer science and life sciences (http://omicslab.genetics.ac.cn/youthforum/ ), Beijing, China, May 24-25, 2014.
  • 01 March 2014: Integrative analysis of OMICs data for functional genomics. Nephrology update West lake forum (http://www.westlakeforum.net/), Hangzhou, China, March 27-29, 2014.
  • 01 August 2013: GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications. ISB 2013, Huangshan, Anhui, China, 23 August, 2013.
  • 01 July 2013: Genetic variations in the next generation: detection, prioritizing and functional annotation. ISMB/ECCB 2013, Berlin, Germany, 23 July, 2013.
  • 01 June 2013: Bioinformatics tools for next generation sequencing data analysis and gene regulatory network inference. HUST-HKU Genetics & Bioinformatics Symposium, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, China, 4 June 2013.
  • 01 June 2013: Systems biology approaches for integrative analysis of next generation sequencing data. School of Food Science & Technology, Huazhong Agricultural University, Wuhan, China, 5 June, 2013.
  • 01 April 2013: Detection, Reprioritizing and Functional Annotation of Genetic Variations for Next Generation Sequencing data. State Key Lab of Systems Biology, CAS, Shanghai, China, 19 April 2013..
  • 01 April 2013: Bioinformatics tools for next generation sequencing data analysis and gene regulatory network inference. Key Laboratory of Medical Molecular Virology, Fudan University Shanghai Medical School, Shanghai, China, 23 April 2013.
  • 01 April 2013: Bioinformatics tools for next generation sequencing data analysis. Department of Food Science & Engineering, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China, 22 April 2013.
  • 01 December 2012: A fast and accurate SNP detection algorithm for NGS data. ISCB-Asia, Shenzhen, China, 17-19 December 2012.
  • 01 December 2012: Co-chair for Regulatory Networks in Stem Cells Session, in RMSC-2012, Guangzhou, China, Dec. 2-4. .
  • 01 December 2012: Constructing epigenetic regulatory networks from high throughput gene expression and ChIP-seq data. 5th annual world congress of regenerative medicine & stem cell-2012, Guangzhou, China, 1-4 December 2012..
  • 01 December 2012: Genetic Variations in the Next Generation: Detection, Reprioritizing and Functional Annotation. Frontier in Biomedical Research 2012, Faculty of Medicine, The University of Hong Kong, Hong Kong, China, 14 December 2012..
  • 01 November 2012: Integrative analysis of genomic data for gene function inference. Institute for Nutritional Sciences, SIBS, Shanghai, China, 15 November 2012..
  • 01 September 2012: From genomics to proteomics: Integrative analysis of OMICs data for functional genomics. School of Biological Science, The University Of Hong Kong, Hong Kong, China, 7 September 2012..
  • 01 August 2012: Discovery of functional genetic variants in the post-GWAS era. IEEE International Conference on Systems Biology, Xi’an, China, Aug 18-20.
  • 01 August 2012: From genomics to proteomics: Integrative analysis of OMICs data for functional genomics. School of Computer, Wuhan University, Wuhan, China, 23 Aug..
  • 01 August 2012: A fast and accurate SNP detection algorithm for NGS data . IEEE International Conference on Systems Biology, Xi’an, China, Aug 18-20.
  • 01 May 2012: A fast and accurate SNP detection algorithm for next-generation sequencing data. Tsinghua University, Beijing, China. May 21.
  • 01 May 2012: Integrative analysis of high throughput data for regulatory network construction. BIT’s 2nd Annual World Congress of Molecular & Cell Biology, Beijing, China. May 18.
  • 01 May 2012: Co-chair for Gene Expression and Regulations Session, in CMCB-2012, May 18-22, Beijing, China.. .
  • 01 May 2012: Integrative analysis of OMICs data for cancer genomics. PUMC, Beijing, China. May 17.
  • 01 May 2012: Integrative analysis of OMICs data for regulatory network inference. HKU-McGill Symposium, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China. May 3.
  • 01 January 2012: Integrative analysis of OMICs data for cancer genomics. Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China. Jan. 31.
  • 01 September 2011: FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution. IEEE International Conference on Systems Biology, Zhuhai, China, Sept 2- 4.
  • 01 July 2011: Bioinformatics and systems biology research in JJWangLab@HKU. School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China. July 19.
  • 01 May 2011: Co-evolution of Transcription Factors and Their Binding Sites. School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China. May. 20.
  • 01 March 2011: Co-evolution of Transcription Factors and Their Binding Sites. TNLIST, Tsinghua University, Beijing, China. Mar. 23.
  • 01 November 2010: Gene regulation, stem cells and cancer genomics. Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China. Nov. 24.
  • 01 October 2010: Prediction of transcription factor binding sites from protein sequence through protein-DNA co-evolution. CSH-Asia Conferences, Computational Biology. Cold Spring Harbor Asia, Suzhou, China. Oct. 1.
  • 01 October 2010: Application of bioinformatics in stem cell study. Stem Cell & Regenerative Medicine Consortium (SCRMC), The University of Hong Kong, Hong Kong, China, Oct. 12.
  • 01 April 2010: Prediction of DNA binding sites from transcription factor protein sequence through co-evolution, College of Information Science & Technology, Drexel University, Philadelphia, PA, USA. April 2 . .
  • 01 April 2010: A novel profile-HMM to predict microRNAs and their targets simultaneously, Department of Computer Sciences, New Jersey Institute of Technology, Newark, NJ, USA. April 5. .
  • 01 March 2010: Co-evolution of Transcription Factors and Their Binding Sites, Center for Bioinformatics & Dept. of Genetics, University of Pennsylvania, Philadelphia, PA, USA. March 30 . .
  • 01 March 2010: A novel profile-HMM to predict microRNA-target interaction, Dept. of Computer and Information Sciences, University of Delaware, Newark, DE, USA. March, 31. .
  • 01 March 2010: Next-generation sequencing and Cancer genomics. PLA Military Academy of Medical Sciences, Beijing, China. Mar. 24.
  • 01 May 2009: Computational methods for prediction of promoters and transcription factor binding sites. Institute of Biochemistry and Cell Biology, Shanghai, May 14.
  • 10 November 2008: Computational methods for prediction of alternative promoters and transcription factor binding sites.. School of Computing, National University of Singapore, Singapore. November 10.

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HKU Committee Appointments
  • 01 August 2022-Present: Faculty of Dentistry, Board of the. The teachers who are members of the Faculty and who are full-time employees of the University
  • 03 March 2008-15 April 2016: Faculty of Medicine, Board of the. The teachers who are members of the Faculty and who are full-time employees of the University

Note

  • All publication and awards data are automatically fetched periodically from the HKU Scholars Hub.