LifeX

LifeX institute is just started in 2025, so currently no paper affiliated with LifeX have been published. But we do have several paper affiliated with LifeX are being reviewed in journals.

LifeX institute is led by Dr. Shifu Chen, and following are part of his publications:

Recent publicationsย (*ย corresponding author๏ผŒ#ย co-first author): ย ย 

  1. Yujie Shi, Bo Hu, Shuaiqiang Gao, Xiang Xia, Xikai Deng, Wenjian Qin, Mingyan Xu, Jia Gu,ย Shifu Chen*. Application of Quantitative Histomorphometric Features in Computational Pathology. Interdisciplinary Medicine. 2024.
  2. Ying Jin,ย et al,ย Shifu Chen,ย et al, Rui-Hua Xu. A phase II clinical trial of toripalimab in advanced solid tumors with polymerase epsilon/polymerase delta (POLE/POLD1) mutation. Signal Transduction and Targeted Therapy. 2024.
  3. Mingyao Lai, Tianhao Mu, Ming Liu, Qingjun Hu, Juan Li, Tanxiao Huang, Yingmei Li,ย Shifu Chen*, Linbo Cai. Personalized therapy guided by longitudinal liquid biopsies for treatment of leptomeningeal disease from lung adenocarcinoma: A case report. Oncology Letters. 2024.
  4. Lei Wang, Meng Diao, Zheng Zhang, Minlin Jiang,ย Shifu Chen, Deping Zhao, Zhenguo Liu, Caicun Zhou. Comparison of the somatic genomic landscape between central-and peripheral-type non-small cell lung cancer. Lung Cancer. 2024.
  5. Bosen Zhu, Ming Liu, Tianhao Mu, Wentao Li, Junqi Ren, Xiangtao Li, Yi Liang, Ziyi Yang, Yulin Niu,ย Shifu Chen*, Junqiong Lin. Quadruple primary tumors in a lynch syndrome patient surviving more than 26 years with genetic analysis: a case report and literature review. Frontiers in Oncology. 2024.
  6. Shifu Chen*, Yaru Chen, Zhouyang Wang, Wenjian Qin, Jing Zhang, Heera Nand, Jishuai Zhang, Jun Li, Xiaoni Zhang, Xiaoming Liang and Mingyan Xu, Efficient sequencing data compression and FPGA acceleration based on a two-step framework, Frontiers in Genetics.
  7. Limin Xu, Jing Zhang, Yiqian He, Qianqian Yang, Tianhao Mu, Qiushi Guo, Yingqiang Li, Tian Tong,ย Shifu Chen*, Richard D. Ye*, ย ScRNAPip: A systematic and dynamic pipeline for single-cell RNA sequencing analysis,ย iMeta, 2023.
  8. Shifu, Chen*,ย Ultrafast one pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta (2023): e107.
  9. Guowu, Wu, et al.,ย Shifu Chen*, The genomic characteristics of RET fusion positive tumors in Chinese non-small cell lung cancer (NSCLC) patients. Journal of Cancer Research and Clinical Oncology 149.3 (2023): 1019-1028.
  10. Jingxian Duan, et al,ย Shifu Chen, Lei Zhang. Single-cell RNA-seq Revealed that Altered Tumor Infiltrating Lymphocytes in Cirrhotic Liver Indicate Development of Hepatocellular Carcinoma. Journal of Clinical and Translational Hepatology, 2023.
  11. Huaichao Luo, Ruiling Zu, Ziru Huang, Yingqiang Li, Yulin Liao, Wenxin Luo, Peng Zhou, Dongsheng Wang,ย Shifu Chen*, Weimin Li* & Jian Huang*, Characteristics and significance of peripheral blood T-cell receptor repertoire features in patients with indeterminate lung nodules. Signal Transduction and Targeted Therapy.
  12. Qi Zhao#, Feng Wang#, Yan-Xing Chen#,ย Shifu Chen#ย et al , Comprehensive profiling of 1015 patientsโ€™ exomes reveals genomic-clinical associations in colorectal cancer. Nature Communications, 2022.
  13. Feng Wang, et al,ย Shifu Chenย et al, Genomic temporal heterogeneity of circulating tumour DNA in unresectable metastatic colorectal cancer under first-line treatment. Gut, 2021
  14. Shifu Chen* et al. A Computational Toolset for Rapid Identification of SARS-CoV-2, other Viruses, and Microorganisms from Sequencing Data.ย Briefing in Bioinformatics
  15. Yayi He et al.,ย Shifu Chenย et al., Caicun Zhou.ย Mutational Profile Evaluates Response and Survival to Firstโ€Line Chemotherapy in Lung Cancer.ย Advanced Science. 2021
  16. Yayi He et al.,ย Shifu Chenย et al., Caicun Zhou.ย Genomic and transcriptional alterations in first-line chemotherapy exert a potentially unfavorable influence on subsequent immunotherapy in NSCLC.ย Theranostics. 2021
  17. Bing Wang et al.,ย Shifu Chenย et al., Hongbin Xu.ย The mutational landscape and prognostic indicators of pseudomyxoma peritonei originating from the ovary.ย International Journal of Cancer. 2021
  18. Shaokun Liu et al,ย Shifu Chen*.ย The Genomic Characteristics of ALK Fusion Positive Tumors in Chinese NSCLC Patients.ย Frontiers in Oncology, 2020.
  19. Jixian Li et al.,ย Shifu Chen*, Da Wu*. Targeted deep sequencing helps distinguish independent primary tumors from intrapulmonary metastasis for lung cancer diagnosis.ย Journal of Cancer Research and Clinical Oncology, 2020.
  20. Jingxian Duan et al.ย Shifu Chen*, Genetic Biomarkers For Hepatocellular Carcinoma In The Era Of Precision Medicine,ย Journal of hepatocellular carcinoma, 2019.
  21. Kaibin Huang et al,ย Shifu Chen*, Ligang Xia. Circulating tumor DNA sequencing for colorectal cancers: A comparative analysis of colon cancer and rectal cancer data.ย Cancer Biomarkersย 2019,ย DOI: 10.3233/CBM-190257
  22. Jingxian Duan et al,ย Shifu Chen*. Genetic Biomarkers For Hepatocellular Carcinoma In The Era Of Precision Medicine.ย Journal of Hepatocellular Carcinoma, 2019, DOI: 10.2147/JHC.S224849
  23. Jainfei Yao et al,ย Shifu Chen, Lele Song. Comprehensive analysis of POLE and POLD1 Gene Variations identifies cancer patients potentially benefit from immunotherapy in Chinese population.ย Scientific Reports, 2019, DOI: 10.1038/s41598-019-52414-z
  24. Shifu Chen*, Yanqing, Yaru Chen, et al.ย gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data.ย BMC Bioinformatics, 2019,ย DOI: 10.1186/s12859-019-3280-9
  25. Shifu Chen*, Yanqing Zhou, Yaru Chen, Jia Gu. fastp: an ultra-fast all-in-one FASTQ preprocessor.ย Bionformatics, 2018. DOI10.1093/bioinformatics/bty560.ย 
  26. Anqi Chen et al.,ย Shifu Chen,ย et al. Robust Detection of Urothelial Bladder Carcinoma Via Microfluidic Immunoassay and Single-Cell DNA Copy Number Alteration Analysis of Captured Urinary Exfoliated Tumor Cells.ย Cancer Researchย 78.14 (2018): 4073-4085. Web. 21 Aug. 2018.
  27. Shifu Chen*, Ming Liu, Tanxiao Huang, Wenting Liao, Mingyan Xu, Jia Gu. GeneFuse: detection and visualization of target gene fusions from DNA sequencing data.ย International Journal of Biological Sciences; 14(8):843-848. doi:10.7150/ijbs.24626..
  28. Shifu Chen*, Ming Liu, Yanqing Zhou. Bioinformatics Analysis for Cell-Free Tumor DNA Sequencing Data.ย Computational Systems Biology: Methods and Protocols, Methods in Molecular Biology, vol. 1754. 2018.ย DOIย 10.1007/978-1-4939-7717-8.ย 
  29. Jun Li, Renzhong Liu, Cuihong Huang,ย Shifu Chen, Mingyan Xu, The Introduction and Clinical Application of Cell-Free Tumor DNA.ย Computational Systems Biology: Methods and Protocols, Methods in Molecular Biology, vol. 1754. 2018.ย DOIย 10.1007/978-1-4939-7717-8.
  30. Xiao Sun,ย Tanxiao Huang,ย Fangsheng Cheng,ย Kaibing Huang,ย Ming Liu,ย Wan He,ย Mingwei Li,ย Xiaoni Zhang,ย Mingyan Xu,ย Shifu Chen*,ย Ligang Xia.ย Monitoring colorectal cancer following surgery using plasma circulating tumor DNA.ย Oncology Letters, 2018.
  31. Ruilian Xu,ย Guolin Zhong,ย Tanxiao Huang,ย Wan He,ย Cheng Kong,ย Xiaoni Zhang,ย Ying Wang,ย Ming Liu,ย Mingyan Xu,ย Shifu Chen*.ย Sequencing of circulating tumor DNA for dynamic monitoring of gene mutations in advanced non-small cell lung cancer.ย Oncology Letters, 15, 3726-3734.ย 2018
  32. Shifu Chen*, Tanxiao Huang, Tiexiang Wen, Hong Li, Mingyan Xu, Jia Gu.ย MutScan: Fast detection and visualization of target mutations by scanning FASTQ data. Jan 2018,ย BMC Bioinformaticsย 19(1)
  33. Tiexiangย Wen, Fengย Yang,ย Jia Gu,ย Shifu Chen,ย Lei Wang,ย Yaoqin Xie, An adaptive kernel regression method for 3D ultrasound reconstruction using speckle prior and parallel GPU implementation.ย Neurocomputing. Vol 275, 31 January 2018, Pages 208-223
  34. Shifu Chen, Tanxiao Huang, Yanqing Zhou, Yue Han, Mingyan Xu and Jia Gu.ย AfterQC: automatic filtering, trimming, error removing and quality control for fastq data.ย BMC Bioinformaticsย Vol 18 Suppl 4, 2017.ย 
  35. ย Shifu Chen,ย Mingย Liu, Xiaoni Zhang, Renwen Long, Yixing Wang, Yue Han, Shiwei Zhang and ย Jia Gu. SeqMaker: A Study of Cell-free DNA Fragmentation Pattern and Its Application in DNA Sample Type Classification.ย IEEE/ACM Transactions on Computational Biology and Bioinformatics.ย 2017