Lixin Cheng (程立新)

Address: Shenzhen People’s Hospital, Shenzhen, China.

Email: easonlcheng@gmail.com

ORCID: 0000-0002-9427-383X

GoogleScholar

ResearchGate

RA recruitment: I am looking for Postdoc and Research Assistants to work together computational biology and bioinformatics. Please email me if interested.

Research Interests:

• Diagnostic and prognostic biomarker identification
• Machine learning algorithms
• Data integration and transfer learning
• Systems biololgy and network analysis
• Multiomics

Education:

• Jan 2014 – Jan 2018, PhD (Computational Biology), Department of Computer Science and Engineering, The Chinese University of Hong Kong.
• 2008 – 2011, MPhil (Bioinformatics), College of Bioinformatics Science and Technology, Harbin Medical University.
• 2003 – 2008, BSc (Biotechnology), Department of Biotechnology, Harbin Medical University.

Selected Publications:

(* corresponding author; # co-first author; IF, Impact Factor)

• Nana Jin#, Chuanchuan Nan#, Wanyang Li#, Peijing Lin, Yu Xin, Jun Wang, Yuelong Chen, Yuanhao Wang, Kaijiang Yu, Changsong Wang, Chunbo Chen*, Qingshan Geng*, Lixin Cheng*.
  PAGE-based transfer learning from single-cell to bulk sequencing enhances model generalization for sepsis diagnosis.
  Briefings in Bioinformatics, 2025. Full Text

• Pengfei Huang†, Yanqi Liu†, Yue Li†, Yu Xin†, Chuanchuan Nan†, Yinghao Luo, Yating Feng, Nana Jin, Yahui Peng, Dawei Wang, Yang Zhou, Feiyu Luan, Xinran Wang, Xibo Wang, Hongxu Li, Yuxin Zhou, Weiting Zhang, Yuhan Liu, Mengyao Yuan, Yuxin Zhang, Yuchen Song, Yu Xiao, Lifeng Shen, Kaijiang Yu*, Mingyan Zhao*, Lixin Cheng*, Changsong Wang*.
  Metabolomics- and proteomics-based multiomics integration reveals early metabolite alterations in sepsis-associated acute kidney injury.
  BMC Medicine 2025. Full Text

• Ran Wang, Yan Qian, Xiaojing Guo, Fangda Song, Zhiqiang Xiong, Shirong Cai, Xiuwu Bian, Man Hon Wong, Qin Cao*, Lixin Cheng*, Gang Lu*, Kwong Sak Leung*.
  STModule: identifying tissue modules to uncover spatial components and characteristics of transcriptomic landscapes.
  Genome Medicine 2025. Full Text

• Shuojia Wang, Zikuan Yang, Yilin Chen, Jing Zhu, Lin Kang*, Lixin Cheng*.
  Longitudinal association between multimorbidity, participating activity and cognitive function: cross-lagged mediation analysis.
  The Journals of Gerontology: Series A, 2025.

• Jiayue Qiu, Nana Jin, Lixin Cheng*, Chen Huang*. iDICss robustly predicts melanoma immunotherapy response by synergizing genomic and transcriptomic knowledge via independent component analysis.
  Clinical and Translational Medicine, 2025. Full Text

• Han Yin, Zihan Gao, Mengyang Jia, Cheng Jiang, Yuanhao Wang, Dahui Xue, Jingnan Huang, Huhao Feng, Nana Jin, Jingjin Liu*, Lixin Cheng*, Qingshan Geng*. Diminished salivary cortisol response to mental stress predict all-cause mortality in general population.
  Journal of Psychosomatic Research, 2025. Full Text

• Dian Meng, Yu Feng, Kaishen Yuan, Zitong Yu, Qin Cao, Lixin Cheng*, Xubin Zheng*.
  scMMAE: masked cross-attention network for single-cell multimodal omicsfusion to enhance unimodal omics.
  Briefings in Bioinformatics, 2025. Full Text

• Xubin Zheng, Dian Meng, Duo Chen, Wan-Ki Wong, Ka-Ho To, Lei Zhu, JiaFei Wu, Yining Liang, Kwong-Sak Leung, Man-Hon Wong, and Lixin Cheng*.
  scCaT: An explainable capsulating architecture for sepsis diagnosis transferring from single-cell RNA sequencing.
  PLOS Computational Biology, 2024. Full Text

• Ning Zhang#, Fengxia Yang#, Pengfei Zhao#, Nana Jin, Haonan Wu, Tao Liu, Qingshan Geng*, Xiaojun Yang*, and Lixin Cheng*.
  MrGPS: a m6A-related gene pair signature to predict the prognosis and immunological impact of glioma patients.
  Briefings in Bioinformatics, 2024. Full Text

• Ying Li#, Jing Gao#, Xubin Zheng#, Guole Nie, Jican Qin, Haiping Wang, Tao He, Åsa Wheelock, Chuan-Xing Li*, Lixin Cheng*, Xun Li*.
  Diagnostic prediction of portal vein thrombosis in chronic cirrhosis patients using data-driven precision medicine model.
  Briefings in Bioinformatics, 2024. Full Text

• Jun Wang, Marc Horlacher, Lixin Cheng*, Ole Winther*.
  DeepLocRNA: An interpretable deep learning model for predicting RNA subcellular localisation with domain-specific transfer-learning.
  Bioinformatics, 2024 Full Text

• Jize Xie#, Xubin Zheng#, Jianlong Yan#, Qizhi Li, Nana Jin, Shuojia Wang, Pengfei Zhao, Shuai Li, Wanfu Ding*, Lixin Cheng*, Qingshan Geng*.
  Deep learning model to discriminate diverse infection types based on pairwise analysis of host gene expression.
  iScience, 2024 Full Text

• Shuojia Wang, Yilin Chen, Lijiao Xiong, Nana Jin, Pengfei Zhao, Zhen Liang*, Lixin Cheng*, Lin Kang*.
  Multimorbidity measures associated with cognitive function among community dwelling older Chinese adults.
  Alzheimer’s & Dementia, 2024 (IF=13) Full Text

• Shuojia Wang, Chengyuan Yu, Jing Zhu, Pengfei Zhao, Nana Jin, Lixin Cheng*, Lin Kang*.
  Multimorbidity patterns, leisure activities, and cognitive function: A population-based longitudinal study.
  The Journals of Gerontology: Series A, 2024 Full Text

• Yining Liang, Jiayue Zhang, Dehong Luo*, Lixin Cheng*, Yijin Wang*.
  Deregulation of immune response contributing to fulminant hepatitis in HEV infected pregnant women.
  Journal of Medical Virology, 2024

• Xubin Zheng#, Nana Jin#, Qiong Wu#, Ning Zhang, Haonan Wu, Yuanhao Wang, Rui Luo, Tao Liu, Wanfu Ding*, Qingshan Geng*, Lixin Cheng*.
  Less is more: relative rank is more informative than absolute abundance for compositional NGS data.
  Briefings in Functional Genomics, 2024

• Nana Jin, Lixin Cheng*, Qingshan Geng*.
  Multiomics on Mental Stress-Induced Myocardial Ischemia: A Narrative Review.
  Heart and Mind, 2024

• Qizhi Li#, Xubin Zheng#, Jize Xie#, Ran Wang, Mengyao Li, Man-Hon Wong, Kwong-Sak Leung, Shuai Li, Qingshan Geng*, and Lixin Cheng*.
  bvnGPS: a generalizable diagnostic model for acute bacterial and viral infection using integrative host transcriptomics and pretrained neural networks.
  Bioinformatics, 2023 (IF=6.9) Full Text

• Ran Wang, Xubin Zheng, Fangda Song, Man Hon Wong, Kwong Sak Leung, and Lixin Cheng*.
  Deciphering associations between gut microbiota and clinical factors using microbial modules.
  Bioinformatics, 2023 (IF=6.9) Full Text

• Lixin Cheng#*, Haonan Wu#, Xubin Zheng, Ning Zhang, Pengfei Zhao, Ran Wang, Qiong Wu, Tao Liu, Xiaojun Yang, and Qingshan Geng*.
  GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion.
  Bioinformatics, 2023 (IF=6.9) Full Text

• Xiaojun Liu#, Chengyin Hong#, Yichun Jiang#, Wei Li, Youlian Chen, Yonghui Ma, Pengfei Zhao, Tiyuan Li, Huaisheng Chen*, Xueyan Liu*, and Lixin Cheng*.
  Co-expression module analysis reveals high expression homogeneity for both coding and non-coding genes in sepsis.
  BMC Genomics, 2023 (IF=4.4) Full Text

• Jun Wang*, Marc Horlacher, Lixin Cheng, Ole Winther.
  RNA trafficking and subcellular localization – a review of mechanisms, experimental and predictive methodologies.
  Briefings in Bioinformatics, 2023. (IF=9.5) Full Text

• Qiong Wu#, Xubin Zheng#, Kwong-Sak Leung, Man-Hon Wong, Stephen Kwok-Wing Tsui*, and Lixin Cheng*.
  meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data.
  Bioinformatics, 2022 (IF=6.9) Full Text

• Ran Wang, Xubin Zheng, Jun Wang, Shibiao Wan, Fangda Song, Man-Hon Wong, Kwong-Sak Leung, and Lixin Cheng*.
  Improving bulk RNA-seq classification by transferring gene signature from single cells in acute myeloid leukemia.
  Briefings in Bioinformatics, 2022. (IF=14) Full Text

• Haili Li#, Xubin Zheng#, Jing Gao, Kwong-Sak Leung, Man-Hon Wong, Shu Yang, Yakun Liu, Ming Dong, Huimin Bai, Xiufeng Ye*, and Lixin Cheng*.
  Whole transcriptome analysis reveals non-coding RNA’s competing endogenous gene pairs as novel form of motifs in serous ovarian cancer.
  Computers in Biology and Medicine, 2022 (IF=6.9) Full Text

• Xueyan Liu, Yong Xu, Ran Wang, Sheng Liu, Jun Wang, YongLun Luo, Kwong-Sak Leung, and Lixin Cheng*.
  A network-based algorithm for the identification of moonlighting non-coding RNAs and its application in sepsis.
  Briefings in Bioinformatics, 2021. (IF=11.6) Full Text

• Yueran Yang#, Yu Zhang#, Shuai Li, Xubin Zheng, Man-Hon Wong, Kwong-Sak Leung, and Lixin Cheng*.
  A robust and generalizable immune-related signature for sepsis diagnostics.
  IEEE/ACM Transactions in Computational Biology and Bioinformatics, 2021. Full Text

• Xubin Zheng, Kwong-Sak Leung, Man-Hon Wong, and Lixin Cheng*.
  Long non-coding RNA Pairs to Assist in Diagnosing Sepsis.
  BMC Genomics, 2021.(IF=3.9) Full Text

• Honglong Wu#, Xuebin Wang#, Mengtian Chu, Dongfang Li, Lixin Cheng*, Ke Zhou*.
  HCMB: A stable and efficient algorithm for processing the normalization of highly sparse Hi-C contact data.
  Computational and Structural Biotechnology Journal, 2021. (IF=7.2) Full Text

• Lixin Cheng#*, Yonglun Zeng#, Shuai Hu, Ning Zhang, Kenneth C.P. Cheung, Baiying Li, Kwong-Sak Leung, Liwen Jiang*.
  Systematic prediction of autophagy-related proteins using Arabidopsis thaliana interactome data.
  Plant Journal 2021. (IF=6.4) Full Text

• Yang Song, Suzhu Zhu, Ning Zhang, and Lixin Cheng*.
  Blood circulating miRNA pairs as a robust signature for early detection of esophageal cancer.
  Front. Oncol., 2021. (IF=6.2) Full Text

• Xubin Zheng#, Qiong Wu#, Haonan Wu#, Man-Hon Wong, Kwong Sak Leung, Xueyan Liu*, and Lixin Cheng*.
  Evaluating the consistency of gene methylation in liver cancer using bisulfite sequencing data.
  Front. Cell Dev. Biol., 2021. (IF=6.6) Full Text

• Xueyan Liu#, Xubin Zheng#, Jun Wang#, Ning Zhang, Kwong-Sak Leung, Xiufeng Ye*, and Lixin Cheng*.
  A long non-coding RNA signature for diagnostic prediction of sepsis upon ICU admission.
  Clinical and Translational Medicine, 2020. (IF=7.9) Full Text

• Sheng Liu, Wenjing Zhao, Xueyan Liu*, and Lixin Cheng*.
  Metagenomic analysis of the gut microbiome in atherosclerosis patients identify cross-cohort microbial signatures and potential therapeutic target.
  FASEB Journal, 2020. (IF=5.0) Full Text

• Linting Li, Min Liu, Ludan Yue, Rui Wang, Ning Zhang, Yujie Liang, Liang Zhang, Lixin Cheng*, Jiang Xia*, Ruibing Wang*.
  Host–Guest Protein Assembly for Affinity Purification of Methyllysine Proteomes.
  Analytical Chemistry, 2020. (IF=6.8) Full Text

• Lixin Cheng#, Chuanchuan Nan#, Lin Kang#, Ning Zhang, Sheng Liu, Huaisheng Chen, Chengying Hong, Youlian Chen, Zhen Liang*, Xueyan Liu*.
  Whole blood transcriptomic investigation identifies long non-coding RNAs as regulators in sepsis.
  Journal of Translational Medicine, 2020. (IF=4.1) Full Text

• Jun Wang, Xiuqing Zhang, Lixin Cheng*, Yonglun Luo*.
  An overview and metanalysis of Machine and Deep Learning-Based CRISPR gRNADesign Tools.
  RNA Biology, 2019. (IF=5.5) Full Text

• Jun Wang, Xi Xiang, Lars Bolund, Xiuqing Zhang, Lixin Cheng*, Yonglun Luo*.
  GNL-Scorer: A generalized model for predicting CRISPR on-target activity by machine learning and featurization.
  Journal of Molecular Cell Biology, 2019. (IF=4.7) Full Text

• Xueyan Liu#, Nan Li#, Sheng Liu, Jun Wang, Ning Zhang, Xubin Zheng, Kwong-Sak Leung, and Lixin Cheng*.
  Normalization methods for the analysis of unbalanced transcriptome data: a review.
  Frontier in Biotechnology and Bioengineering, 2019. (IF=5.1) Full Text

• Lixin Cheng, Pengfei Liu, Dong Wang*, and Kwong-Sak Leung*.
  Exploiting locational and topological overlap model to identify modules in human protein interaction network.
  BMC Bioinformatics, 2019. (IF=2.2) Full Text

• Lixin Cheng*, Kwong-Sak Leung*.
  Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome.
  Bioinformatics, 2018. (IF=7.3) Full Text

• Lixin Cheng*, Kwong-Sak Leung*.
  Quantification of non-coding RNA target localization diversity and its application in cancers.
  Journal of Molecular Cell Biology, 2017. (IF=6.0) Full Text

• Lixin Cheng, Pengfei Liu, and Kwong-Sak Leung*.
  SMILE: a novel procedure for subcellular module identification with localization expansion.
  IET System Biology, 2017 (Also in ACM-BCB 2017) Full Text

• Lixin Cheng, Kaili Fan, Yan Huang, Dong Wang*, and Kwong-Sak Leung*.
  Full characterization of localization diversity in human protein interactome.
  Journal of Proteome Research, 2017. (IF=4.3) Full Text

• Lixin Cheng#, Xuan Wang#, Pak-Kan Wong, Kwan-Yeung Lee, Le Li, Bin Xu, Dong Wang*, and Kwong-Sak Leung*.
  ICN: A normalization method for gene expression data considering the over-expression of informative genes.
  Molecular BioSystems, 2016. (IF=2.8) Full Text

• Lixin Cheng, Leung-Yau Lo, Nelson Tang*, Dong Wang*, and Kwong-Sak Leung*.
  CrossNorm: a novel normalization strategy for microarray data in cancers.
  Scientific Reports, 2016. (IF=5.6) Full Text

Conference:

• Lixin Cheng, Pengfei Liu, and Kwong-Sak Leung.
  SMILE: a novel procedure for subcellular module identification with localization expansion.
  ACM-BCB’17, August 20-23, 2017, Boston, MA, USA.