Lingxi CHEN (陈凌曦)

  Assistant Professor

  Biomedical Sciences

  City University of Hong Kong

  Email: lingxi.chen@cityu.edu.hk

  Google Scholar • GitHub

About

I joined the City University of Hong Kong as an Assistant Professor in the Department of Biomedical Sciences, starting in Dec 2023. I obtained BSc and MSc in Computer Science from University of Nottingham and University College London. I completed my PhD and PostDoc in Computer Science from City University of Hong Kong.

My research primarily focuses on computational biology and computational veterinary medicine algorithms and platforms, specializing in Genome Structural Aberrations, Single-Cell and Spatial Multi-Omics, AI in Healthcare, and Online Biomedical Platforms. I am passionate about applying computer science and artificial intelligence to address critical open challenges in biomedical science.

1. Genomic Structural Aberrations
To develop specialized tools for the detection and analysis of genomic aberrations, such as single nucleotide variations (SNVs), copy number variations (CNVs), and complex structural variations (CSVs). To identify the aberration biomarkers associated with multiple cancers and complex diseases for precision medicine.
2. Single-Cell and Spatial Omics
To design computational algorithms tailored for the analysis of bulk, single-cell, and spatial omics data. To address the challenges such as imputing missing data, dimension reduction, clustering, data integration, and more.
3. AI in Healthcare
To build diagnostic and prognostic AI models for various conditions, including cancer and complex diseases in humans and animals.
4. Online Biomedical Platforms
To create user-friendly online webservers and databases that offer integrated analysis pipelines and interactive visualization interfaces. To enable non-bioinformaticians to explore complex biological data with simple mouse operations.


PhD Opportunity

If you are interested in pursuing a PhD degree related to computational biology or computational veterinary medicine, please send an email to lingxi.chen@cityu.edu.hk. State briefly why you are interested in your Personal Statement and attach a CV, including information about your education and research.

General Requirement
  • GPA 3.6+/4.0, average grade 85+ (compulsory)
  • IELTS 6.5+ (compulsory)
  • Having background from programming/algorithm side (Computer Science, Data Science, Artifical Intelligence, Software Engineering, etc.) or domain side (Biomedical Science, Biology, etc.) For students with a primary background in computer science, active coding contributions to open-source projects are preferred. For students with a biomedical background, priority will be given to those who have first-author papers in SCI-indexed journals.
  • Passion for Learning: We are looking for individuals with a strong desire to expand their knowledge in both computer science and biomedical science.
  • Desire for Lifelong Research: Our ideal candidates aspire to make a significant impact in research and view a PhD as the beginning of a lifelong research career.

    • Available PhD Programme
  • PhD Programme in Biomedical Sciences at CityU HK, highly competitive applicants may apply for Hong Kong PhD Fellowship Scheme (HKPFS). 
  • 3+1 Interdisciplinary PhD Programme between CityU HK and Cornell University’s College of Veterinary Medicine, the research should related to computational biology/veterinary medicine.
  • Joint PhD Programme between CityU HK and Partner Mainland University, applicants must be PhD candidates from the following university:
    • 北京航空航天大学 中南大学 大连理工大学 复旦大学 哈尔滨工业大学 华中科技大学 吉林大学 南京大学 南开大学 中国人民大学 上海交通大学 山东大学 华南理工大学 东南大学 四川大学 南方科技大学 天津大学 同济大学 中国科学院大学 中国科学技术大学 西安交通大学 厦门大学 武汉大学 浙江大学

    Benefits
  • Monthly stipend of around 18,000 HKD (4 years).
  • 17 days of HK statutory public holidays and 24 days of annual leave.
  • Encouragement to attend international academic conferences with a reimbursement of up to HKD 10,000 for travel expenses.


    • Selected Publications

    Note: † joint first author. * corresponding author.

    IF-Defense

    Deciphering complex breakage-fusion-bridge genome rearrangements with Ambigram
    Chaohui Li†, Lingxi Chen†, Guangze Pan, Wenqian Zhang, and Shuai Cheng Li*
    Nature Communications. 2023.
    [Paper]  [Code] 

    IF-Defense

    Smurf: embedding single-cell rna-seq data with matrix factorization preserving self-consistency
    Juhua Pu† , Bingchen Wang† , Xingwu Liu* , Lingxi Chen* , and Shuai Cheng Li*
    Briefings in Bioinformatics. 2023.
    [Paper]  [Code] 

    IF-Defense

    Incorporating cell hierarchy to decipher the functional diversity of single cells
    Lingxi Chen, Shuai Cheng Li*
    Nucleic Acids Research. 2022.
    [Paper]  [Code] 

    IF-Defense

    Somatic variant analysis suite: copy number variation clonal visualization online platform for large-scale single-cell genomics
    Lingxi Chen†, Yuhao Qing†, Ruikang Li†, Chaohui Li†, Hechen Li, Xikang Feng, and Shuai Cheng Li*
    Briefings in Bioinformatics. 2021.
    [Paper]  [Website] 

    IF-Defense

    Machine learning based early warning system enables accurate mortality risk prediction for covid-19
    Yue Gao†, Guang-Yao Cai†, Wei Fang†, Hua-Yi Li†, Si-Yuan Wang†, Lingxi Chen†, Yang Yu, et al.
    Nature Communications. 2020.
    [Paper]  [Code] 

    IF-Defense

    DeepMF: Deciphering the latent patterns in omics profiles with a deep learning method
    Lingxi Chen†, Jiao Xu†, and Shuai Cheng Li∗
    BMC Bioinformatics. 2019.
    [Paper]  [Code] 


    Professional Activities

    Journal Reviewer
  • Bioinformatics
  • Briefings in Bioinformatics
  • Frontiers in Oncology
  • BMC Bioinformatics
    •

    Last updated: Dec, 2023 by Lingxi Chen