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)

• 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. (IF=9.5) 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. (IF=9.5) 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 (IF=6.9)

• 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

• Baiying Li#, Yonglun Zeng#, Wenhan Cao, Wenxin Zhang, Lixin Cheng, Haidi Yin, Qian Wu, Xiangfeng Wang, Yan Huang, Wilson Chun Yu Lau, Zhong-Ping Yao, Yusong Guo*, Liwen Jiang*.
  A distinct giant coat protein complex II vesicle population in Arabidopsis thaliana.
  Nature Plants, 2021. 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

• Miao Liu, Sicong He, Lixin Cheng, Jianan Qu, and Jiang Xia*.
  Phase-Separated Multienzyme Biosynthesis.
  Biomacromolecules, 2020 (IF=6.1)

• 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

• Kenneth Cheung, Silvia Fanti, Claudio Mauro, GS Wang, Anitha Nair, HM Fu, Silvia Angeletti, Silvia Spoto, Marta Fogolari, Francesco romano, Dunja Aksentijevic, WW Liu, BY Li, Lixin Cheng, LW Yang, Juho Vuononvirta, Thanushiyan Poobalasingam, David Smith, Massimo Ciccozzi, Egle Solito, Federica Marelli-Berg.
  Preservation of microvascular barrier function requires CD31 receptor-induced metabolic reprogramming.
  Nat Commun. 2020 Jul 17;11(1):3595.

• 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

• Qiong Zhao, Jinbo Shen, Caiji Gao, Yong Cui, Yongyi Wang, Jie Cui, Lixin Cheng, Wenhan Cao, Ying Zhu, Shuxian Huang, Qianzi Zhou, Cheuk Ka Leong, King Pong Leung, Xuemei Chen & Liwen Jiang*.
  RST1 is a FREE1 Suppressor that Negatively Regulates Vacuolar Trafficking in Arabidopsis.
  Plant Cell, 2019.

• 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.