Zhenqiu Liu

Summary

Affiliation: University of Maryland
Country: USA

Publications

  1. ncbi request reprint Clustering gene expression data with kernel principal components
    Zhenqiu Liu
    Bioinformatics Cell, TATRC, 110 North Market Street, Frederick, MD 21701, USA
    J Bioinform Comput Biol 3:303-16. 2005
  2. pmc ErbB3 binding protein 1 represses metastasis-promoting gene anterior gradient protein 2 in prostate cancer
    Yuexing Zhang
    Greenebaum Cancer Center and Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    Cancer Res 70:240-8. 2010
  3. pmc Class prediction and feature selection with linear optimization for metagenomic count data
    Zhenqiu Liu
    University of Maryland Greenebaum Cancer Center, Baltimore, Maryland, USA
    PLoS ONE 8:e53253. 2013
  4. pmc Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data
    Zhenqiu Liu
    Department of Epidemiology and Public Health, University of Maryland Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Bioinformatics 27:3242-9. 2011
  5. pmc Gene and pathway identification with Lp penalized Bayesian logistic regression
    Zhenqiu Liu
    Division of Biostatistics, University of Maryland Greenebaum Cancer Center, 22 South Greene Street, Baltimore, MD 21201, USA
    BMC Bioinformatics 9:412. 2008
  6. pmc Survival prediction and gene identification with penalized global AUC maximization
    Zhenqiu Liu
    Division of Biostatistics, Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland 21201, USA
    J Comput Biol 16:1661-70. 2009
  7. doi request reprint Sparse support vector machines with Lp penalty for biomarker identification
    Zhenqiu Liu
    Division of Biostatistics and Bioinformatics, Department of Epidemiology and Preventive Medicine, Greenebaum Cancer Center, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
    IEEE/ACM Trans Comput Biol Bioinform 7:100-7. 2010
  8. ncbi request reprint Gene identification and survival prediction with Lp Cox regression and novel similarity measure
    Zhenqiu Liu
    University of Maryland Greenebaum Cancer Center, Baltimore, MD 21201, USA
    Int J Data Min Bioinform 3:398-408. 2009
  9. pmc Survival associated pathway identification with group Lp penalized global AUC maximization
    Zhenqiu Liu
    Greenebaum Cancer Center, University of Maryland, 22 South Greene Street, Baltimore, MD 21201, USA
    Algorithms Mol Biol 5:30. 2010
  10. doi request reprint ROC-based utility function maximization for feature selection and classification with applications to high-dimensional protease data
    Zhenqiu Liu
    Division of Biostatistics, University of Maryland Greenebaum Cancer Center, Baltimore, Maryland 21201, USA
    Biometrics 64:1155-61. 2008

Collaborators

Detail Information

Publications41

  1. ncbi request reprint Clustering gene expression data with kernel principal components
    Zhenqiu Liu
    Bioinformatics Cell, TATRC, 110 North Market Street, Frederick, MD 21701, USA
    J Bioinform Comput Biol 3:303-16. 2005
    ..A new algorithm based on KPCA and fuzzy C-means is proposed. Experiments with microarray data show that the proposed algorithms is in general superior to traditional algorithms...
  2. pmc ErbB3 binding protein 1 represses metastasis-promoting gene anterior gradient protein 2 in prostate cancer
    Yuexing Zhang
    Greenebaum Cancer Center and Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    Cancer Res 70:240-8. 2010
    ..Collectively, our results reveal an EBP1-Foxa-AGR2 signaling circuit with functional significance in metastatic prostate cancer...
  3. pmc Class prediction and feature selection with linear optimization for metagenomic count data
    Zhenqiu Liu
    University of Maryland Greenebaum Cancer Center, Baltimore, Maryland, USA
    PLoS ONE 8:e53253. 2013
    ..We evaluated the performance of our method on several real and simulation datasets. The proposed method can simultaneously identify features and predict classes with the metagenomic count data...
  4. pmc Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data
    Zhenqiu Liu
    Department of Epidemiology and Public Health, University of Maryland Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Bioinformatics 27:3242-9. 2011
    ..While several existing machine learning methods have been adapted for analyzing microbiome data recently, there is not yet an efficient and dedicated algorithm available for multiclass classification of human microbiota...
  5. pmc Gene and pathway identification with Lp penalized Bayesian logistic regression
    Zhenqiu Liu
    Division of Biostatistics, University of Maryland Greenebaum Cancer Center, 22 South Greene Street, Baltimore, MD 21201, USA
    BMC Bioinformatics 9:412. 2008
    ..Usually this parameter must be carefully tuned through cross-validation, which is time consuming...
  6. pmc Survival prediction and gene identification with penalized global AUC maximization
    Zhenqiu Liu
    Division of Biostatistics, Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland 21201, USA
    J Comput Biol 16:1661-70. 2009
    ..Software is available upon request from the first author...
  7. doi request reprint Sparse support vector machines with Lp penalty for biomarker identification
    Zhenqiu Liu
    Division of Biostatistics and Bioinformatics, Department of Epidemiology and Preventive Medicine, Greenebaum Cancer Center, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
    IEEE/ACM Trans Comput Biol Bioinform 7:100-7. 2010
    ..Biomarkers identified with our methods are compared with those from other methods in the literature. The software package in Matlab is available upon request...
  8. ncbi request reprint Gene identification and survival prediction with Lp Cox regression and novel similarity measure
    Zhenqiu Liu
    University of Maryland Greenebaum Cancer Center, Baltimore, MD 21201, USA
    Int J Data Min Bioinform 3:398-408. 2009
    ....
  9. pmc Survival associated pathway identification with group Lp penalized global AUC maximization
    Zhenqiu Liu
    Greenebaum Cancer Center, University of Maryland, 22 South Greene Street, Baltimore, MD 21201, USA
    Algorithms Mol Biol 5:30. 2010
    ....
  10. doi request reprint ROC-based utility function maximization for feature selection and classification with applications to high-dimensional protease data
    Zhenqiu Liu
    Division of Biostatistics, University of Maryland Greenebaum Cancer Center, Baltimore, Maryland 21201, USA
    Biometrics 64:1155-61. 2008
    ..Our main conclusion is that the performance of proposed algorithm is significantly better in most cases than the other classifiers tested. Software package in MATLAB is available upon request...
  11. ncbi request reprint Classification of proteomic data with multiclass Logistic Partial Least Squares algorithm
    Zhenqiu Liu
    Division of Biostatistics, Greenebaum Cancer Center, University of Maryland Medicine, 22 South Greene Street, Baltimore, MD 21201, USA
    Int J Bioinform Res Appl 4:1-10. 2008
    ..Wavelet decomposition and the proposed LPLS are applied to real life cancer data. Experimental comparisons show that LPLS with wavelet decomposition outperforms other methods in the analysis of MS data...
  12. doi request reprint Efficient support vector machine method for survival prediction with SEER data
    Zhenqiu Liu
    University of Maryland at Baltimore, Baltimore, MD, USA
    Adv Exp Med Biol 680:11-8. 2010
    ..It is easy to understand and efficient to use especially when applied to large datasets. Our method has been examined through both simulation and real data, and its performance is very good with limited experiments...
  13. ncbi request reprint Sparse logistic regression with Lp penalty for biomarker identification
    Zhenqiu Liu
    University of Maryland, USA
    Stat Appl Genet Mol Biol 6:Article6. 2007
    ..Our computational results show that Lp Logistic regression (p <1) outperforms the L1 logistic regression and SCAD SVM. Software is available upon request from the first author...
  14. pmc Kernel based methods for accelerated failure time model with ultra-high dimensional data
    Zhenqiu Liu
    University of Maryland Greenebaum Cancer Center, 22 South Greene Street, Baltimore, MD 21201, USA
    BMC Bioinformatics 11:606. 2010
    ..This two-step procedure may introduce bias and inaccuracy and lead us to miss biologically important genes...
  15. pmc Regularized F-measure maximization for feature selection and classification
    Zhenqiu Liu
    Division of Biostatistics, University of Maryland Greenebaum Cancer Center, Baltimore, MD 21201, USA
    J Biomed Biotechnol 2009:617946. 2009
    ..Our experiments with the benchmark, methylation, and high dimensional microarray data show that the performance of proposed algorithm is better or equivalent compared with the other popular classifiers in limited experiments...
  16. pmc Early detection of lung adenocarcinoma in sputum by a panel of microRNA markers
    Lei Yu
    Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201 1192, USA
    Int J Cancer 127:2870-8. 2010
    ..The sputum markers demonstrated the potential of translation to laboratory settings for improving the early detection of lung adenocarcinoma...
  17. pmc Altered miRNA expression in sputum for diagnosis of non-small cell lung cancer
    Ying Xie
    Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
    Lung Cancer 67:170-6. 2010
    ..82% sensitivity and 100.00% specificity by sputum cytology. The measurement of altered miRNA expression in sputum could be a useful noninvasive approach for the diagnosis of lung cancer...
  18. pmc Combined genetic analysis of sputum and computed tomography for noninvasive diagnosis of non-small-cell lung cancer
    Feng Jiang
    Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201 1192, USA
    Lung Cancer 66:58-63. 2009
    ..05). The integration of the genetic assay with CT led to improvements in noninvasive diagnosis of stage I NSCLCs, especially central tumors...
  19. pmc Post-transcriptional regulation of androgen receptor mRNA by an ErbB3 binding protein 1 in prostate cancer
    Hua Zhou
    Greenebaum Cancer Center, Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
    Nucleic Acids Res 38:3619-31. 2010
    ..Thus, decreases of EBP1 in prostate cancer could be important for the post-transcriptional up-regulation of AR contributing to aberrant AR expression and disease progression...
  20. pmc Small nucleolar RNA signatures as biomarkers for non-small-cell lung cancer
    Jipei Liao
    Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
    Mol Cancer 9:198. 2010
    ....
  21. doi request reprint Aldehyde dehydrogenase 1 is a tumor stem cell-associated marker in lung cancer
    Feng Jiang
    Department of Pathology, Greenbaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201 1192, USA
    Mol Cancer Res 7:330-8. 2009
    ..These findings offer an important new tool for the study of lung CSCs and provide a potential prognostic factor and therapeutic target for treatment of the patients with lung cancer...
  22. pmc ALDH1A1 is a marker for malignant prostate stem cells and predictor of prostate cancer patients' outcome
    Ting Li
    Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland 21201 1192, USA
    Lab Invest 90:234-44. 2010
    ..00093 and 0.00017, respectively). ALDH1A1 could be a prostate CSC-related marker. Measuring its expression might provide a potential approach to study tumorigenesis of PCa and predict outcome of the disease...
  23. pmc Anti-HDGF targets cancer and cancer stromal stem cells resistant to chemotherapy
    Jun Zhao
    Department of Oncology and Diagnostic Sciences, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
    Clin Cancer Res 19:3567-76. 2013
    ..The remainder will progress during initial treatment (primary resistance). In this study, we test whether the treatment can be improved by inhibiting hepatoma-derived growth factor (HDGF)...
  24. ncbi request reprint Genome-wide tagging SNPs with entropy-based Monte Carlo method
    Zhenqiu Liu
    Division of Biostatistics, University of Maryland Greenebaum Cancer Center, Baltimore, Maryland, USA
    J Comput Biol 13:1606-14. 2006
    ..Furthermore, the results show that CEMC is significantly better than random selection, and it also outperformed another block-free selection algorithm for the dataset considered...
  25. ncbi request reprint Magnetic enrichment of bronchial epithelial cells from sputum for lung cancer diagnosis
    Qi Qiu
    Department of Pathology, University of Maryland School of Medicine, 10 South Pine St, MSTF 7th Fl, Baltimore, MD 21201 1192, USA
    Cancer 114:275-83. 2008
    ..We propose to obtain concentrated and purified bronchial epithelial cells to improve early detection of lung cancer in sputum samples...
  26. pmc CDC25A(Q110del): a novel cell division cycle 25A isoform aberrantly expressed in non-small cell lung cancer
    Rania H Younis
    Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, United States of America
    PLoS ONE 7:e46464. 2012
    ..In this study we aimed to investigate the role of a novel CDC25A transcriptional variant, CDC25A(Q110del), on the regulation of the CDC25A protein, and its impact on prognosis of NSCLC patients...
  27. pmc Alterations in cell growth and signaling in ErbB3 binding protein-1 (Ebp1) deficient mice
    Yuexing Zhang
    Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
    BMC Cell Biol 9:69. 2008
    ..However, the physiological role of Ebp1 in the whole organism is not known. Therefore, we generated Ebp1-deficient mice carrying a gene trap insertion in intron 2 of the Ebp1 (pa2g4) gene...
  28. pmc Down-regulation of eIF4GII by miR-520c-3p represses diffuse large B cell lymphoma development
    Krystyna Mazan-Mamczarz
    Marlene and Stewart Greenebaum Cancer Center, Department of Medicine, University of Maryland, Baltimore, Maryland, United States of America
    PLoS Genet 10:e1004105. 2014
    ..Our results provide evidence that the tumor suppressor effect of miR-520c-3p is mediated through repression of translation while inducing senescence and that eIF4GII is a key effector of this anti-tumor activity. ..
  29. pmc Small nucleolar RNA signatures of lung tumor-initiating cells
    Kaiissar Mannoor
    Departments of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
    Mol Cancer 13:104. 2014
    ....
  30. pmc Differential response of the cynomolgus macaque gut microbiota to Shigella infection
    Anna M Seekatz
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 8:e64212. 2013
    ..These studies highlight the importance of further investigation into the possible protective role of the microbiota against enteric pathogens and consideration of host genetic backgrounds in conducting vaccine studies...
  31. pmc Microbial transformation from normal oral microbiota to acute endodontic infections
    William WL Hsiao
    University of Maryland School of Dentistry, Department of Endodontics, Prosthodontics and Operative Dentistry, Baltimore, MD 20201, USA
    BMC Genomics 13:345. 2012
    ..Bioinformatics tools and statistical tests with rigorous criteria were used to elucidate the spatial transition of the microbiota from normal to diseased sites...
  32. pmc Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome
    Margaret L Zupancic
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 7:e43052. 2012
    ....
  33. ncbi request reprint A novel multiple FISH array for the detection of genetic aberrations in cancer
    RuiYun Li
    Department of Surgery, The University of Maryland School of Medicine, Baltimore, 21201 1192, USA
    Lab Invest 86:619-27. 2006
    ..The technique may thus be a powerful laboratory strategy for cancer prevention and early detection and for improved patient management...
  34. pmc MiR-27a functions as a tumor suppressor in acute leukemia by regulating 14-3-3θ
    Kara A Scheibner
    Center for Stem Cell Biology and Regenerative Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
    PLoS ONE 7:e50895. 2012
    ..These data indicate that miR-27a contributes a tumor suppressor-like activity in acute leukemia cells via regulation of apoptosis, and that miR-27a and 14-3-3θ may be potential therapeutic targets...
  35. pmc Efficient feature selection and multiclass classification with integrated instance and model based learning
    Zhenqiu Liu
    Greenebaum Cancer Center and Department of Epidemiology and Public Health, University of Maryland at Baltimore, 655 W Baltimore Street, Baltimore, MD 21201, USA
    Evol Bioinform Online 8:197-205. 2012
    ..It performs well with limited computational experiments...
  36. pmc EBP1, an ErbB3-binding protein, is decreased in prostate cancer and implicated in hormone resistance
    Yuexing Zhang
    Greenebaum Cancer Center, University of Maryland School of Medicine, 655 West Baltimore Street, Baltimore, MD 21201, USA
    Mol Cancer Ther 7:3176-86. 2008
    ..Our data support a role for EBP1 in the development of hormone-refractory prostate cancer via inhibition of both AR- and HRG-stimulated growth and present a novel strategy for treating androgen-refractory prostate cancer...
  37. ncbi request reprint Structural Risk Minimisation based gene expression profiling analysis
    Xue Wen Chen
    Bioinformatics and Computational Life Sciences Laboratory, Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045, USA
    Int J Bioinform Res Appl 3:153-69. 2007
    ..The experimental results show that the proposed method produces significantly better performance than general wrapper methods that use cross validations...
  38. pmc A method for automatic identification of reliable heart rates calculated from ECG and PPG waveforms
    Chenggang Yu
    Bioinformatics Cell, Telemedicine and Advanced Technology Research Center, U S Army Medical Research and Materiel Command MRMC TATRC, 504 Scott Street, Ft Detrick, MD 21702 5012, USA
    J Am Med Inform Assoc 13:309-20. 2006
    ..The reliability is quantitatively expressed through a quality index (QI) for each HRr...
  39. pmc Multilocus LD measure and tagging SNP selection with generalized mutual information
    Zhenqiu Liu
    Department of Statistics, Ohio State University, Columbus, Ohio 43210 1247, USA
    Genet Epidemiol 29:353-64. 2005
    ..The results indicate that multilocus LD patterns can be captured well, and informative and nonredundant SNPs can be selected effectively from a large set of loci...

Research Grants2

  1. Statistical and Computational Methods for Systematically Mining the SNP and Gene
    Zhenqiu Liu; Fiscal Year: 2007
    ..We hope our researches have the impact of encouraging more people to contribute to this challenging problem. ..