New members 2021-09.

  • Chen Tianhang, Shuai Yi, Ye Zhengqian joined our group as new PhD students in September!
  • Song Kai, Xue Hua joined our group as a Postdoc in October!

New members 2020-09.

  • Li Jiang, Wang Lishi, Wang Xiangeng and Zhang Xianrui joined our group as new PhD students in September!

Congratulations to QI Lin for his paper recently published in Science Advances!

  • Congratulations to QI Lin for his paper recently published in Science Advances!
  • More could be found in news section.

New members 2019-09.

  • Rayna joined our group as a joint PhD student in June!
  • Guiyuan,Lingli,Yuni and Tan joined our group as new PhD students in September!

'The 3rd international symposium on the frontiers of stress medicine'

  • Dr. Wang was invited to give a talk in 'The 3rd international symposium on the frontiers of stress medicine' in Chengdu, Sichuan, China.

Congratulations to Huang Hao for his paper recently published in Nature Communications!

  • Congratulations to Huang Hao for his paper recently published in Nature Communications!
  • More could be found in news section.

Congratulations to Gao Feng for his paper recently published in Gastroenterology!

  • Congratulations to Gao Feng for his paper recently published in Gastroenterology!
  • More could be found in news section.

Visiting the Sixth Affiliated Hospital of Sun Yat-sen University!

  • Dr. Wang and Prof. Michael Yang were invited to visit the Sixth Affiliated Hospital of Sun Yat-sen University by vice president of the hospital Wu Xiaojian!

Visiting Peking University Shenzhen Hospital!

  • Dr. Wang and Prof. Michael Yang were invited to visit Peking University Shenzhen Hospital by Prof. Shubin Wang.

Congratulations to Duan Xin for his paper recently published and highlighted in Nature Communications!

  • Congratulations to Duan Xin for his paper recently published and highlighted in Nature Communications!
  • More could be found in news section.

Graduation Ceremony

  • Feng Gao became the first graduate of Joint PhD Program with Cornell University!
  • Congratulate Feng and wish him a bright future!

New members 2018-09

  • Lin and Miaomiao joined our group as new PhD students in September!
  • Yi joined our group as a new PhD student in November!
  • Zhongxu joined our group as a new PhD student in March 2019!
  • Welcome them!

A Multi-disciplinary Symposium on Translational Multi-omics and Precision Medicine

Prof Nathalie Wong and Prof Ajay Goel gave keynote talks!

Uncovering intratumor heterogeneity with Dirichlet processes

We invited Dr. KeYuan from University of Glasgow to give a seminar!

New members 2017-09

  • Hao and Ying joined our group as new PhD students in September!
  • Lin joined our group as a Research Assistant in October!
  • Welcome them!

Research Interest

Our major research interest is to better understand the biology underlying cancer using quantitative approaches. Especially, we have more passion in projects that bridge basic biological studies and clinical research.

Integrative Analysis

We have rich experience in integrative analysis of multilevel (epi)genomic data and clinical outcomes for dissecting cancer heterogeneity.

Subtyping

Identifying and characterizing molecularly distinct cancer subtypes that are in relation to clinical responses.

Biomarkers

Identifying prognostic and predictive cancer biomarkers that are more accessible in the clinic.

Therapeutic targets

Identifying potential therapeutic targets using network-based approaches.

Packages/tools

Developing bioconductor packages and web tools for analyzing next-generation sequencing data (SPP2), high-throughput screens (HTSanalyzeR), etc.

Members

We always welcome outsanding bioinformatics students to join our lab. Please see Contact for details.

  • Postdoctoral Fellow, Harvard Medical School, Dr. Peter Kharchenko PhD, Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Dr. Florian Markowetz.

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

    Xin WANG

    Assistant Professor, Biomedical Sciences, City University HK

  • Feng is mainly focusing on applying artificial intelligence technologies such as deep learning to cancer research, including but not limited to patient stratification, biomarker and target discovery.

    Linkedin: https://hk.linkedin.com/in/feng-gao-3b7bb33a

    Feng GAO

    Joint PhD Student with Cornell University

  • Wei is currently working on cancer prognosis prediction, including building a new model to predict relapse and identifying predictive biomarkers.

    Wei WANG

    PhD Student. M.S in Microbiology

  • Xin DUAN has expertise at image processing and is currently working on drug screening using brain image in zebrafish model.

    Xin DUAN

    Research Asistant. M.E in Pattern Recognition

  • Yuchen started focusing on bioinformatics during master study. Now his interests are mainly on cancer-specific regulatory network analysis and data mining problems in epigenetics.

    Yuchen ZHANG

    PhD Student. M.E in Pattern Recognition

  • Lina is devoting herself to applying bioinformatics into epigenetics.

    Lina ZHU

    Joint PhD Student with Cornell University.

  • Hao is mainly focusing on applying bioinformatics to cancer research.

    Hao HUANG

    Joint PhD Student with Cornell University.

  • Ying is currently working on analyzing intra-tumor and inter-tumor heterogeneity and developing a model for a combinatorial prognostic biomarker.

    Ying LI

    PhD Student. M.S in Bioinformatics

  • Lin was started to get involved in research of bioinformatics during his master study. He is currently working on integrate analysis of multi-omic data.

    Lin QI

    PhD Student. M.E in Pattern Recognition

  • Miaomiao is currently focousing on cancer subtyping classification and prognosis prediction.

    Miaomiao Tan

    PhD Student. M.S in transgenic science

  • Yi is currently working on database creating and drug screening by analyzing brain activity maps of zebrafish model.

    Yi Cao

    PhD Student. M.S in Pattern Recognition

  • Zhongxu is working on cancer genomics analysis, biomarker development and neoantigen prediction.

    Zhongxu Zhu

    PhD Student. M.S in Bioinformatics

  • Rayna is working on biomarker development based on nanopore sequencing technology.

    (Rayna) Yu CHEN

    PhD Student. M.S in Biotherapy

  • Lingli is currently working on method development for cancer subtyping and single-cell sequencing data analysis.

    Lingli He

    PhD Student. M.S in Statistics

  • Tan is working on cancer genomics and bioinformatics.

    Tan Wu

    PhD Student. M.S in Bioinformatics

Recent Publications

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Integrative network biology analysis identifies miR-508-3p as the determinant for the mesenchymal identity and a strong prognostic biomarker of ovarian cancer.

on May 2631, 26118

Authors Zhao L†, Wang W†, Xu L, Yi T, Zhao X, Wei Y, Vermeulen L, Goel A, Zhou S* and Wang X* Oncogene 2018, doi:https://doi.org/10.1038/s41388-018-0577-5 Abstract Ovarian cancer is a heterogeneous malignancy that poses tremendous clinical challenge. Based on unsupervised classification of whole-genome gene expression profiles, four molecular subtypes of ovarian cancer were recently identified. However, single-driver molecular events specific to these subtypes have not been clearly elucidated. We aim to characterize the regulatory mechanisms underlying the poor prognosis mesenchymal subtype of ovarian cancer using a systems biology approach, involving a variety of molecular modalities including gene and microRNA expression profiles.

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High-throughput Brain Activity Mapping and Machine Learning as a Foundation for Systems Neuropharmacology.

on May 331, 3118

Authors Lin X†, Duan X†, Jacobs C, Ullmann J, Chan CY, Chen S, Cheng SH, Zhao WN, Poduri A, Wang X*, Haggarty SJ*, Shi P* Nature Communications 2018, doi:https://doi.org/10.1038/s41467-018-07289-5 Abstract Technologies for mapping the spatial and temporal patterns of neural activity have advanced our understanding of brain function in both health and disease. An important application of these technologies is the discovery of next-generation neurotherapeutics for neurological and psychiatric disorders.

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mTORC1 Promotes Metabolic Reprogramming by the Suppression of GSK3-Dependent Foxk1 Phosphorylation.

on May 731, 7068

Authors 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. Molecular Cell 2018, doi:https://doi.org/10.1016/j.molcel.2018.04.024 Abstract Highlights mTORC1 suppresses GSK3-dependent Foxk1 phosphorylation Foxk1 phosphorylation promotes 14-3-3 binding and nuclear exclusion Foxk1 transcriptionally regulates Hif1α expression Foxk1 and Hif1α contribute to mTORC1-regulated metabolic reprogramming Summary The mammalian Target of Rapamycin Complex 1 (mTORC1)-signaling system plays a critical role in the maintenance of cellular homeostasis by sensing and integrating multiple extracellular and intracellular cues.

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Molecular subtyping of colorectal cancer: recent progress, new challenges and emerging opportunities.

on May 1731, 17058

Authors Wang W†, Kandimalla R†, Huang H†, Zhu L, Li Y, Gao F, Goel A*,Wang X* Seminars in Cancer Biology 2018, doi:10.1016/j.semcancer.2018.05.002 Abstract Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. Similar to many other malignancies, CRC is a heterogeneous disease, making it a clinical challenge for optimization of treatment modalities in reducing the morbidity and mortality associated with this disease. A more precise understanding of the biological properties that distinguish patients with colorectal tumors, especially in terms of their clinical features, is a key requirement towards a more robust, targeted-drug design, and implementation of individualized therapies.

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Our Collaborations