Lei Chen

Summary

Country: China

Publications

  1. doi request reprint Analysis of the chemical toxicity effects using the enrichment of Gene Ontology terms and KEGG pathways
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People s Republic of China Electronic address
    Biochim Biophys Acta 1860:2619-26. 2016
  2. ncbi request reprint OPMSP: A Computational Method Integrating Protein Interaction and Sequence Information for the Identification of Novel Putative Oncogenes
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, People s Republic of China
    Protein Pept Lett 23:1081-1094. 2016
  3. ncbi request reprint Identification of compound-protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, People s Republic of China
    Mol Genet Genomics 291:2065-2079. 2016
  4. doi request reprint Identifying novel protein phenotype annotations by hybridizing protein-protein interactions and protein sequence similarities
    Lei Chen
    School of Life Sciences, Shanghai University, Shanghai, 200444, People s Republic of China
    Mol Genet Genomics 291:913-34. 2016
  5. ncbi request reprint Predicting the types of metabolic pathway of compounds using molecular fragments and sequential minimal optimization
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People s Republic of China
    Comb Chem High Throughput Screen 19:136-43. 2016
  6. doi request reprint A computational method for the identification of new candidate carcinogenic and non-carcinogenic chemicals
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People s Republic of China
    Mol Biosyst 11:2541-50. 2015
  7. doi request reprint Prediction and analysis of cell-penetrating peptides using pseudo-amino acid composition and random forest models
    Lei Chen
    College of Life Science, Shanghai University, Shanghai, 200444, People s Republic of China
    Amino Acids 47:1485-93. 2015
  8. pmc Prediction of cancer drugs by chemical-chemical interactions
    Jing Lu
    Department of Medicinal Chemistry, School of Pharmacy, Yantai University, Yantai, Shandong, People s Republic of China
    PLoS ONE 9:e87791. 2014
  9. doi request reprint A hybrid method for prediction and repositioning of drug Anatomical Therapeutic Chemical classes
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People s Republic of China
    Mol Biosyst 10:868-77. 2014
  10. doi request reprint Prediction of drug target groups based on chemical-chemical similarities and chemical-chemical/protein connections
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People s Republic of China Electronic address
    Biochim Biophys Acta 1844:207-13. 2014

Collaborators

Detail Information

Publications46

  1. doi request reprint Analysis of the chemical toxicity effects using the enrichment of Gene Ontology terms and KEGG pathways
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People s Republic of China Electronic address
    Biochim Biophys Acta 1860:2619-26. 2016
    ..Better understanding of the mechanisms underlying various toxicity effects can help eliminate unqualified candidate drugs in early stages, allowing researchers to focus their attention on other more viable candidates...
  2. ncbi request reprint OPMSP: A Computational Method Integrating Protein Interaction and Sequence Information for the Identification of Novel Putative Oncogenes
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, People s Republic of China
    Protein Pept Lett 23:1081-1094. 2016
    ..Six of these genes-ESR1, CDK9, SEPT2, HOXA10, LMX1B, and NR2C2-are extensively discussed. Several lines of evidence indicate that they may be novel oncogenes...
  3. ncbi request reprint Identification of compound-protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, People s Republic of China
    Mol Genet Genomics 291:2065-2079. 2016
    ..Our results indicate that compound-protein interactions are related to biological processes involving immune, developmental and hormone-associated pathways...
  4. doi request reprint Identifying novel protein phenotype annotations by hybridizing protein-protein interactions and protein sequence similarities
    Lei Chen
    School of Life Sciences, Shanghai University, Shanghai, 200444, People s Republic of China
    Mol Genet Genomics 291:913-34. 2016
    ....
  5. ncbi request reprint Predicting the types of metabolic pathway of compounds using molecular fragments and sequential minimal optimization
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People s Republic of China
    Comb Chem High Throughput Screen 19:136-43. 2016
    ..We also make predictions using some compounds with unknown metabolic pathways and choose 17 compounds for analysis. The results indicate that the method proposed may become a useful tool in predicting and analyzing metabolic pathways. ..
  6. doi request reprint A computational method for the identification of new candidate carcinogenic and non-carcinogenic chemicals
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People s Republic of China
    Mol Biosyst 11:2541-50. 2015
    ..In addition, several candidate carcinogenic/non-carcinogenic chemicals exhibit structural dissimilarity with validated carcinogenic/non-carcinogenic chemicals...
  7. doi request reprint Prediction and analysis of cell-penetrating peptides using pseudo-amino acid composition and random forest models
    Lei Chen
    College of Life Science, Shanghai University, Shanghai, 200444, People s Republic of China
    Amino Acids 47:1485-93. 2015
    ..In parallel, an optimal random forest prediction model was built. We hope that our findings will provide new resources for the study of cell-penetrating peptides. ..
  8. pmc Prediction of cancer drugs by chemical-chemical interactions
    Jing Lu
    Department of Medicinal Chemistry, School of Pharmacy, Yantai University, Yantai, Shandong, People s Republic of China
    PLoS ONE 9:e87791. 2014
    ..Encouraged by the promising results, the method may become a useful tool to the prediction of drugs indications. ..
  9. doi request reprint A hybrid method for prediction and repositioning of drug Anatomical Therapeutic Chemical classes
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People s Republic of China
    Mol Biosyst 10:868-77. 2014
    ..It was conceivable that the proposed method could be used as an efficient tool to identify ATC-classes of novel drugs or to discover novel uses of known drugs. ..
  10. doi request reprint Prediction of drug target groups based on chemical-chemical similarities and chemical-chemical/protein connections
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People s Republic of China Electronic address
    Biochim Biophys Acta 1844:207-13. 2014
    ..This article is part of a Special Issue entitled: Computational Proteomics, Systems Biology & Clinical Implications. Guest Editor: Yudong Cai. ..
  11. ncbi request reprint A two-step similarity-based method for prediction of drug's target group
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, People s Republic of China
    Protein Pept Lett 20:364-70. 2013
    ..The results show that using graph representation to encode drug is a good choice in this area. We expect that this contribution will provide some help to understand drug-target interaction network...
  12. ncbi request reprint Analysis of metabolic pathway using hybrid properties
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, People s Republic of China
    Protein Pept Lett 19:99-107. 2012
    ..26%. It is anticipated that this novel approach and encouraging result may give meaningful illumination to investigate this important topic...
  13. pmc Prediction of effective drug combinations by chemical interaction, protein interaction and target enrichment of KEGG pathways
    Lei Chen
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
    Biomed Res Int 2013:723780. 2013
    ..These important features may help to gain insights into the mechanisms of drug combinations, and the proposed prediction model could become a useful tool for screening possible drug combinations. ..
  14. pmc Identifying chemicals with potential therapy of HIV based on protein-protein and protein-chemical interaction network
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China
    PLoS ONE 8:e65207. 2013
    ..All these indicate that our method as presented in this paper is quite promising. The method may become a useful tool, or at least plays a complementary role to the existing method, for identifying novel anti-HIV drugs...
  15. pmc Predicting drugs side effects based on chemical-chemical interactions and protein-chemical interactions
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
    Biomed Res Int 2013:485034. 2013
    ....
  16. pmc The Use of Gene Ontology Term and KEGG Pathway Enrichment for Analysis of Drug Half-Life
    Yu Hang Zhang
    School of Life Sciences, Shanghai University, Shanghai 200444, People s Republic of China
    PLoS ONE 11:e0165496. 2016
    ..This analysis confirmed our results and may show evidence for a new method in studying drug half-lives and building effective computational methods for the prediction of drug half-lives...
  17. pmc Prediction of protein-protein interaction sites by random forest algorithm with mRMR and IFS
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 7:e43927. 2012
    ..It is anticipated that our prediction method will become a useful tool for identifying PPI sites, and that the feature analysis described in this paper will provide useful insights into the mechanisms of interaction...
  18. pmc Analysis of Gene Expression Profiles in the Human Brain Stem, Cerebellum and Cerebral Cortex
    Lei Chen
    School of Life Sciences, Shanghai University, Shanghai, 200444, China
    PLoS ONE 11:e0159395. 2016
    ..As a whole, the results of our study will improve our ability to predict and understand genes related to brain regionalization and function. ..
  19. pmc The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer
    Lei Chen
    College of Life Science, Shanghai University, Shanghai, 200444, People s Republic of China College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, People s Republic of China
    PLoS ONE 10:e0128696. 2015
    ..A final analysis of these new chemicals in the context of the current literature indicates that several chemicals are strongly linked to lung cancer. ..
  20. pmc Gene expression profiling gut microbiota in different races of humans
    Lei Chen
    School of Life Sciences, Shanghai University, Shanghai 200444, People s Republic of China
    Sci Rep 6:23075. 2016
    ..Our analyses of extracted genes support the widely accepted hypotheses that eating habits, living environments and metabolic levels in different races can influence the characteristics of the gut microbiome. ..
  21. pmc A hybrid computational method for the discovery of novel reproduction-related genes
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, People s Republic of China
    PLoS ONE 10:e0117090. 2015
    ..The in-depth analysis of the high confidence novel reproduction genes revealed hidden mechanisms of reproduction and provided guidelines for further experimental validations. ..
  22. pmc Gene Ontology and KEGG Pathway Enrichment Analysis of a Drug Target-Based Classification System
    Lei Chen
    College of Life Science, Shanghai University, Shanghai, People s Republic of China College of Information Engineering, Shanghai Maritime University, Shanghai, People s Republic of China
    PLoS ONE 10:e0126492. 2015
    ..Our results provide for the first time the biological relevance among drugs, targets and biological functions, which serves as a new basis for future DTI predictions. ..
  23. doi request reprint Analysis of protein pathway networks using hybrid properties
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
    Molecules 15:8177-92. 2010
    ..88%. It is anticipated that, this novel approach and encouraging result, although preliminary yet, may stimulate extensive investigations into this important topic...
  24. pmc Predicting Anatomical Therapeutic Chemical (ATC) classification of drugs by integrating chemical-chemical interactions and similarities
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, China
    PLoS ONE 7:e35254. 2012
    ....
  25. doi request reprint Validating the performance of one-time decomposition for fMRI analysis using ICA with automatic target generation process
    Shengnan Yao
    Digital Image and Intelligent Computation Laboratory, College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
    Magn Reson Imaging 31:970-5. 2013
    ..Furthermore, the ROC (Receiver Operating Characteristic) power analysis also denoted the better signal reconstruction performance of ATGP-ICA than that of RDICA...
  26. doi request reprint Deciphering the effects of gene deletion on yeast longevity using network and machine learning approaches
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    Biochimie 94:1017-25. 2012
    ..Moreover, it has not escaped our notice that, after some modification, the current model can also be used to study many other phenotype prediction problems from the angle of systems biology...
  27. pmc Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property
    Tao Huang
    Institute of Systems Biology, Shanghai University, Shanghai, People s Republic of China
    PLoS ONE 6:e25297. 2011
    ..It is anticipated that our report may stimulate a series of follow-up investigations in this new and challenging area...
  28. ncbi request reprint Using compound similarity and functional domain composition for prediction of drug-target interaction networks
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, China
    Med Chem 6:388-95. 2010
    ..23%, 94.74%, 97.80%, and 97.51%, respectively, indicating that compound similarity and functional domain composition are very effective to predict drug-target interaction networks...
  29. pmc Analysis of tumor suppressor genes based on gene ontology and the KEGG pathway
    Jing Yang
    The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine SJTUSM and Shanghai Institutes for Biological Sciences SIBS, Chinese Academy of Sciences CAS, Shanghai, People s Republic of China
    PLoS ONE 9:e107202. 2014
    ..We hope these findings can help in building effective prediction methods for identifying TSGs and thereby, promoting the discovery of effective cancer treatments. ..
  30. pmc Identification of novel candidate drivers connecting different dysfunctional levels for lung adenocarcinoma using protein-protein interactions and a shortest path approach
    Lei Chen
    School of Life Sciences, Shanghai University, Shanghai 200444, People s Republic of China
    Sci Rep 6:29849. 2016
    ..Several candidate genes remained, which are deemed to be related to two different levels of cancer. The analyses confirmed our assertions that some have the potential to contribute to the tumorigenesis process on multiple levels. ..
  31. pmc Discovery of new candidate genes related to brain development using protein interaction information
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People s Republic of China
    PLoS ONE 10:e0118003. 2015
    ..Of the final identified genes, several have been reported to be associated with brain development, indicating the effectiveness of the method, whereas several of the others may have potential roles in brain development. ..
  32. pmc Computational analysis of HIV-1 resistance based on gene expression profiles and the virus-host interaction network
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 6:e17291. 2011
    ..These proteins may be useful targets for AIDS prevention or therapy, as intervention in these pathways could disrupt communication with virus-targeted proteins and HIV-1 infection...
  33. pmc Predicting chemical toxicity effects based on chemical-chemical interactions
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, China
    PLoS ONE 8:e56517. 2013
    ..50%, substantially higher than the rate of 25.43% achieved by random guesses. Encouraged by the promising results, we expect that our method will become a useful tool in screening out drugs with high toxicity...
  34. pmc Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, PR China
    BMC Bioinformatics 11:293. 2010
    ....
  35. doi request reprint SACICA: a sparse approximation coefficient-based ICA model for functional magnetic resonance imaging data analysis
    Nizhuan Wang
    Digital Image and Intelligent Computation Laboratory, Shanghai Maritime University, Shanghai 201306, China
    J Neurosci Methods 216:49-61. 2013
    ..In addition, the SACICA combined with Fast-FENICA proposed by Wang et al. (2012) was demonstrated to conduct the group analysis effectively on the resting-state data set...
  36. pmc A Shortest-Path-Based Method for the Analysis and Prediction of Fruit-Related Genes in Arabidopsis thaliana
    Liucun Zhu
    School of Life Sciences, Shanghai University, Shanghai, People s Republic of China
    PLoS ONE 11:e0159519. 2016
    ..The described analyses indicate that several of the discovered genes are associated with fruit fertilization, development and maturation in Arabidopsis thaliana. ..
  37. doi request reprint Identification of Genes Associated with Breast Cancer Metastasis to Bone on a Protein-Protein Interaction Network with a Shortest Path Algorithm
    Yu Dong Cai
    School of Life Sciences, Shanghai University, Shanghai 200444 People s Republic of China
    J Proteome Res . 2017
    ..Eighteen putative genes were identified by the method and were extensively analyzed. The confirmation results indicate that these genes participate in metastasis...
  38. pmc Prediction of multi-type membrane proteins in human by an integrated approach
    Guohua Huang
    Institute of Systems Biology, Shanghai University, Shanghai, China Department of Mathematics, Shaoyang University, Shaoyang, Hunan, China
    PLoS ONE 9:e93553. 2014
    ..New metrics for evaluating performances of methods dealing with multi-label problems were also presented. The program of the method is available upon request. ..
  39. pmc Finding candidate drugs for hepatitis C based on chemical-chemical and chemical-protein interactions
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, People s Republic of China
    PLoS ONE 9:e107767. 2014
    ..Hopefully, this proposed method could provide new insights into the discovery of candidate drugs for the treatment of HCV and other diseases. ..
  40. doi request reprint Interferon-microRNA signalling drives liver precancerous lesion formation and hepatocarcinogenesis
    Yingcheng Yang
    International Co operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, China Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
    Gut 65:1186-201. 2016
    ..However, little is known about the mechanisms by which precancerous lesions are initiated and their physiological significance...
  41. doi request reprint A novel approach for fMRI data analysis based on the combination of sparse approximation and affinity propagation clustering
    Tianlong Ren
    Digital Image and Intelligent Computation Laboratory, College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
    Magn Reson Imaging 32:736-46. 2014
    ..This proposed clustering analysis method is expected to have wide applicability. ..
  42. doi request reprint Interleukin-1β/Iinterleukin-1 receptor-associated kinase 1 inflammatory signaling contributes to persistent Gankyrin activation during hepatocarcinogenesis
    Bo Su
    International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute Hospital, Shanghai, China Central Laboratory, Thoracic Surgery Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
    Hepatology 61:585-97. 2015
    ..Inhibition of phospho-JNK impairs IL-1β/IRAK-1 signaling-mediated up-regulation of Gankyrin...
  43. doi request reprint Epigenetic modification of MiR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4
    Liang Li
    International Co operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, China National Center for Liver Cancer, Shanghai, China
    Gut 64:156-67. 2015
    ..Liver tumour-initiating cells (T-ICs) are critical for hepatocarcinogenesis. However, the underlying mechanism regulating the function of liver T-ICs remains unclear...
  44. doi request reprint MUC15 inhibits dimerization of EGFR and PI3K-AKT signaling and is associated with aggressive hepatocellular carcinomas in patients
    Ruo Yu Wang
    International Co operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Shanghai, China The Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
    Gastroenterology 145:1436-48.e1-12. 2013
    ..However, little is known about the role of MUC15 in pathogenesis of hepatocellular carcinoma (HCC)...
  45. pmc Cancer incidence and mortality in patients with type 2 diabetes treated with human insulin: a cohort study in Shanghai
    Yunjuan Gu
    Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People s Hospital, Shanghai, China
    PLoS ONE 8:e53411. 2013
    ..The aim was to investigate the association between human insulin and cancer incidence and mortality in Chinese patients with type 2 diabetes...
  46. doi request reprint A fast-FENICA method on resting state fMRI data
    Nizhuan Wang
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
    J Neurosci Methods 209:1-12. 2012
    ..This proposed effective group analysis method is expected to have wide applicability...