Dr Xin Wang (王鑫博士)

PhD (Cambridge), Postdoc (Harvard)

Associate Professor
Associate Head
Assistant Head (Postgraduate Education)

Dr Xin Wang

Contact Information

Office: 1B-102, 1/F, Block 1,
To Yuen Building
Phone: +852 3442-2367
Fax: +852 3442-0549
Email: xin.wang@cityu.edu.hk
Web: Personal Homepage
CityU Scholars

Research Interests

  • Cancer genomics
  • Prognostic and predictive biomarkers
  • Regulatory networks
  • Therapeutic targets
  • Bioinformatic tools

Dr Wang is a computational biologist. He was trained as a computer scientist initially in China. Impressed by the beauty of Life Sciences and importance of cancer research, he decided to dedicate to the interdisciplinary field of computational biology. Dr Wang pursued his PhD at the University of Cambridge Department of Oncology and Cancer Research UK Cambridge Institute, where his research was concerned with how to infer intracellular signalling pathways from phenotyping screens. In collaboration with experimental oncologists, he also identified three molecularly distinct colon cancer subtypes using an unsupervised classification approach. From 2013 to 2015, Dr Wang did his postdoc training at Harvard Medical School Department of Biomedical Informatics, where he learned advanced techniques in next-generation sequencing data analysis.

Dr Wang's major research interest is to better understand the biology underlying cancer using quantitative approaches. Especially, he has more passion in projects that bridge basic biological studies and clinical research. He has rich experience in integrative analysis of multilevel (epi)genomic data and clinical outcomes for dissecting cancer heterogeneity. Currently, his research consists of four parts:

  1. identifying and characterizing molecularly distinct cancer subtypes that are in relation to clinical responses;
  2. identifying prognostic and predictive cancer biomarkers that are more accessible in the clinic;
  3. identifying potential therapeutic targets using network-based approaches;
  4. developing bioconductor packages and web tools for analyzing next-generation sequencing data (SPP2), high-throughput screens (HTSanalyzeR), etc.

Selected Publications

( co-first author; * co-corresponding author)

  1. Huang H, Shao X, Xie Y, Wang T, Zhang Y, Wang X*, Deng X*, An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa, Nature Communications 2019,10: 2931
  2. Kandimalla R, Gao F, Li Y, Huang H, Ke J, Deng X, Zhao L, Zhou S, Goel A*, and Wang X*, RNAMethyPro: A biologically conserved signature of N6-methyladenosine regulators for predicting survival at pan-cancer level, npj Precision Oncology 2019, 3:13.
  3. Kandimalla R, Ozawa T, Gao F, Wang X*, Goel A* and the T1 Colorectal Cancer Study Group, Gene Expression Signature in Surgical Tissues and Endoscopic Biopsies Identifies High-risk T1 Colorectal Cancers, Gastroenterology 2019, DOI: 10.1053/j.gastro.2019.02.027
  4. Izumi D, Gao F, Toden S, Sonohara F, Kanda M, Ishimoto T, Kodera Y, Wang X*, Baba H and Goel A*, A genome-wide transcriptomic approach identifies a novel gene expression signature for the detection of lymph node metastasis in patients with early stage gastric cancer, EBioMedicine 2019, pii: S2352-3964(19)30063-5
  5. Chen H, Gao F , He M, Ding XF, Wong AM, Sze SC, Yu AC, Sun T, Chan AWH, Wang X*, Wong N*, Long-read RNA Sequencing identifies Novel Splice Variants in Hepatocellular Carcinoma and Tumor‐specific Isoforms, Hepatology 2019; doi:10.1002/hep.30500 (co-corresponding author)
  6. Lin X, Duan X, Jacobs C, Ullmann J, Chan CY, Chen S, Cheng SH, Zhao WN, Poduri A, Wang X*, Haggarty SJ*, Shi P*, High-throughput Brain Activity Mapping and Machine Learning as a Foundation for Systems Neuropharmacology, Nature Communications 2018;9:5142. (co-corresponding author)
  7. Xu Z, Fang P, Xu B, Lu Y, Xiong J, Gao F, Wang X, Fan J, Shi P*, High-throughput Three-dimensional Chemotactic Assays Reveal Steepness-dependent Complexity in Neuronal Sensation to Molecular Gradients, Nature Communications 2018;9: 4745.
  8. Zhao L, Wang W, Xu L, Yi T, Zhao X, Wei Y, Vermeulen L, Goel A, Zhou S* and Wang X*, Integrative network biology analysis identifies miR-508-3p as the determinant for the mesenchymal identity and a strong prognostic biomarker of ovarian cancer, Oncogene 2018, doi:10.1038/s41388-018-0577-5 (co-corresponding author)
  9. He L, Gomes AP, Wang X, Yoon SO, Lee G, Nagiec M, Cho S, Chavez A, Islam T, Yu Y, Asara JM, Kim BY, Blenis J. mTORC1 Promotes Metabolic Reprogramming by the Suppression of GSK3-Dependent Foxk1 Phosphorylation. Molecular Cell 2018, doi:10.1016/j.molcel.2018.04.024
  10. Kandimalla R, Gao F, Matsuyama T, Ishikawa T, Uetake H, Takahashi N, Yamada Y, Becerra C, Kopetz S, Wang X* and Goel A*. Genome-wide discovery and identification of a novel miRNA signature for recurrence prediction in stage II and III colorectal cancer. Clin Cancer Res 2018, doi:10.1158/1078-0432.CCR-17-3236
  11. Wang W, Kandimalla R, Huang H, Zhu L, Li Y, Gao F, Goel A*, Wang X*, Molecular subtyping of colorectal cancer: recent progress, new challenges and emerging opportunities, Seminars in Cancer Biology 2018, doi:10.1016/j.semcancer.2018.05.002
  12. Zhao L, Huang S, Mei S, Yang Z, Xu L, Zhou N, Yang Q, Shen Q, Wang W, Le X, Lau WB, Lau B, Wang X, Yi T, Zhao X, Wei Y, Warner M, Gustafsson JA, Zhou S. Pharmacological activation of estrogen receptor beta augments innate immunity to suppress cancer metastasis. PNAS 2018, 115(16):E3673-E3681
  13. Zhao L, Wang W, Huang S, Yang Z, Xu L, Yang Q, Zhou X, Wang J, Shen Q, Wang C, Le X, Feng M, Zhou N, Lau WB, Lau B, Yao S, Yi T, Wang X, Zhao X, Wei Y and Zhou S. The RNA binding protein SORBS2 suppresses metastatic colonization of ovarian cancer by stabilizing tumor-suppressive immunomodulatory transcripts. Genome Biology 2018, 19(1):35
  14. Sonohara F, Gao F, Iwata N, Kanda M, Koike M, Takahashi N, Yamada Y, Kodera Y, Wang X*, Goel A*, Genome-wide Discovery of a Novel Gene-expression Signature for the Identification of Lymph Node Metastasis in Esophageal Squamous Cell Carcinoma, Annals of Surgery 2017, doi:10.1097/SLA.0000000000002622
  15. Xu Z, Wang W, Ren Y, Zhang W, Fang P, Huang L, Wang X and Shi P. Regeneration of cortical tissue from brain injury by implantation of defined molecular gradient of semaphorin 3A. Biomaterials 2018;157: 125-135, doi: 10.1016/j.biomaterials.2017.12.010
  16. Linnekamp JF, van Hooff SR, Prasetyanti PR, Kandimalla R, Buikhuisen JY, Fessler E, Ramesh P, Lee KAST, van Bochove GGW, de Jong JH, Cameron K, van Leersum R, Rodermond HM, Franitza M, Nürnberg P, Mangiapane LR, Wang X, Clevers H, Vermeulen L, Stassi G and Medema JP, Consensus Molecular Subtypes of colorectal cancer are recapitulated in in vitro and in vivo models, Cell Death and Differentiation 2018, doi:10.1038/s41418-017-0011-5
  17. Ozawa T, Kandimalla R, Gao F, Nozawa H, Hata K, Nagata H, Okada S, Izumi D, Baba H, Fleshman J, Wang X, Watanabe T, Goel A, A microRNA Signature Associated With Metastasis of T1 Colorectal Tumors to Lymph Nodes, Gastroenterology 2017, doi: 10.1053/j.gastro.2017.11.275
  18. Wang Y, Lin X, Chen X, Chen X, Xu Z, Zhang W, Liao Q, Duan X, Wang X, Liu M, Wang F, He J & Shi P, Tetherless near-infrared control of brain activity in behaving animals using fully implantable upconversion microdevices, Biomaterials 2017, 142, 136-148, doi: 10.1016/j.biomaterials.2017.07.017
  19. Yu VWC, Yusuf RZ, Oki T, Wu J, Saez B, Wang X, Cook C, Baryawno N, Ziller MJ, Lee E, Gu H, Meissner A, Lin CP, Kharchenko PV, Scadden DT, Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells, Cell 2016, 167(5):1310-1322
  20. Trinh A, Trumpi K, De Sousa E Melo F, Wang X, de Jong JH, Fessler E, Kuppen PJK, Reimers MS, Swets M, Koopman M, Nagtegaal I, Jansen M, Hooijer GKJ, Offerhaus GJ, Kranenburg O, Punt CJ, Medema JP, Markowetz F, Vermeulen L, Practical and Robust Identification of Molecular Subtypes in Colorectal Cancer by Immunohistochemistry, Clinical Cancer Research 2016, doi: 10.1158/1078-0432.CCR-16-0680
  21. Fessler E, Drost J, van Hooff SR, Linnekamp JF, Wang X, Jansen M, De Sousa E Melo F, Prasetyanti PR, IJspeert JEG, Franitza M, Nürnberg P, van Noesel CJM, Dekker E, Vermeulen L, Clevers H, and Medem JP, TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype, EMBO Molecular Medicine 2016, 8(7): 745–760, doi: 10.15252/emmm.201606184
  22. Fessler E, Jansen M, De Sousa E Melo F, Zhao L, Prasetyanti PR, Rodermond H, Kandimalla R, Linnekamp JF, Franitza M, van Hooff SR, de Jong JH, Oppeneer SC, van Noesel CJM, Dekker E, Stassi G, Wang X*, Medema JP*, and Vermeulen L*, A multidimensional network approach reveals microRNAs as determinants of the mesenchymal colorectal cancer subtype, Oncogene 2016, doi: 10.1038/onc.2016.134 (co-corresponding author)
  23. Masuda T, Wang X, Maeda M, Canver MC, Sher F, Funnell APW, Fisher C, Suciu M, Martyn GE, Norton LJ, Zhu C, Kurita R, Nakamura Y, Xu J, Higgs DR, Crossley M, Bauer DE, Orkin SH, Kharchenko PV, Maeda T, Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin, Science 2016, 351(6270):285-289
  24. Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L & Sabine Tejpar, The consensus molecular subtypes of colorectal cancer, Nature Medicine 2015, 10.1038/nm.3967
  25. Alekseyenko AA, Walsh EM, Wang X, Grayson AR, Hsi PT, Kharchenko PV, Kuroda MI, and French CA, The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains, Genes Dev 2015, 29: 1507-1523
  26. Wang X and Markowetz F, "Joining the dots–network analysis of gene perturbation data", book chapter, In Systems Genetics: linking phenotype and genotype, Markowetz F and Boutros M, Cambridge University Press, 2015
  27. Sadanandam A, Wang X, Felipe de Sousa E, Gray JW, Vermeulen L, Hanahan D, & Medema JP, Reconciliation of classification systems defining molecular subtypes of colorectal cancer, Cell Cycle 2014, 13(3): 353-357
  28. De Sousa E Mello, F, Wang X, Jansen M, Fessler E, Trinh A, et al., Poor prognosis colon cancer is defined by a distinct molecular subtype and develops from serrated precursor lesions, Nature Medicine 2013, 19(5): 614-618
  29. Wang X, Yuan K, Hellmayr C, Liu W and Markowetz F, Reconstructing evolving signaling networks by hidden Markov nested effects models, Annals of Applied Statistics 2014, 8(1): 448-480
  30. Mulder KW, Wang X, Escriu C, Ito Y, Schwarz RF, Gillis J, et al., Diverse epigenetic strategies interact to control epidermal differentiation. Nature Cell Biology 2012, 14(7):753-763
  31. Wang X, Castro MA, Mulder KW and Markowetz F, Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations. PLoS Computational Biology 2012, 8(6):e1002566
  32. Castro MA, Wang X, Fletcher M, Ponder BAJ, Meyer KB, Markowetz F, RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations, Genome Biology 2012, 13:R29
  33. Wang X, Terfve C, Rose JC, Markowetz F, HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens. Bioinformatics 2011, 27(6):879