Xiaobo Zhou

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Identification of a chronic obstructive pulmonary disease genetic determinant that regulates HHIP
    Xiaobo Zhou
    Channing Laboratory, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Hum Mol Genet 21:1325-35. 2012
  2. pmc Clld7, a candidate tumor suppressor on chromosome 13q14, regulates pathways of DNA damage/repair and apoptosis
    Xiaobo Zhou
    The Channing Laboratory, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
    Cancer Res 70:9434-43. 2010
  3. pmc Gene expression analysis uncovers novel hedgehog interacting protein (HHIP) effects in human bronchial epithelial cells
    Xiaobo Zhou
    Channing Division of Network Medicine, Department of Medicine, Brigham and Women s Hospital, and Harvard Medical School, Boston, MA, USA
    Genomics 101:263-72. 2013
  4. pmc Context based mixture model for cell phase identification in automated fluorescence microscopy
    Meng Wang
    Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, 3rd Floor, 1249 Boylston, Boston, MA 02215, USA
    BMC Bioinformatics 8:32. 2007
  5. ncbi request reprint Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy
    Meng Wang
    Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, 3rd Floor, 1249 Boylston, Boston, MA 02215, USA
    Bioinformatics 24:94-101. 2008
  6. pmc Automated neurite extraction using dynamic programming for high-throughput screening of neuron-based assays
    Yong Zhang
    Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, Boston, MA 02215, USA
    Neuroimage 35:1502-15. 2007
  7. ncbi request reprint Dendritic spine detection using curvilinear structure detector and LDA classifier
    Yong Zhang
    Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, Boston, MA 02215, USA
    Neuroimage 36:346-60. 2007
  8. ncbi request reprint Towards automated cellular image segmentation for RNAi genome-wide screening
    Xiaobo Zhou
    Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, 3rd Floor, 1249 Boylston, Boston, MA 02215, USA
    Med Image Comput Comput Assist Interv 8:885-92. 2005
  9. ncbi request reprint Automated axon tracking of 3D confocal laser scanning microscopy images using guided probabilistic region merging
    Ranga Srinivasan
    Harvard Center for Neurodegeneration and Repair Center for Bioinformatics, Harvard Medical School, Boston, MA, USA
    Neuroinformatics 5:189-203. 2007
  10. ncbi request reprint Cancer classification and prediction using logistic regression with Bayesian gene selection
    Xiaobo Zhou
    Harvard Center for Neurodegeneration and Repair, Center for Bioinformatics, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
    J Biomed Inform 37:249-59. 2004

Collaborators

Detail Information

Publications28

  1. pmc Identification of a chronic obstructive pulmonary disease genetic determinant that regulates HHIP
    Xiaobo Zhou
    Channing Laboratory, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Hum Mol Genet 21:1325-35. 2012
    ..Together, our findings reveal one mechanism through which SNPs upstream of the HHIP gene modulate the expression of HHIP and functionally implicate reduced HHIP gene expression in the pathogenesis of COPD...
  2. pmc Clld7, a candidate tumor suppressor on chromosome 13q14, regulates pathways of DNA damage/repair and apoptosis
    Xiaobo Zhou
    The Channing Laboratory, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
    Cancer Res 70:9434-43. 2010
    ..Furthermore, depletion of Clld7 in normal human epithelial cells conferred resistance to apoptosis triggered by DNA damage. Taken together, the biological actions of Clld7 are consistent with those of a tumor suppressor...
  3. pmc Gene expression analysis uncovers novel hedgehog interacting protein (HHIP) effects in human bronchial epithelial cells
    Xiaobo Zhou
    Channing Division of Network Medicine, Department of Medicine, Brigham and Women s Hospital, and Harvard Medical School, Boston, MA, USA
    Genomics 101:263-72. 2013
    ..Thus, we identified potential HHIP targets in human bronchial epithelial cells that may contribute to COPD pathogenesis...
  4. pmc Context based mixture model for cell phase identification in automated fluorescence microscopy
    Meng Wang
    Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, 3rd Floor, 1249 Boylston, Boston, MA 02215, USA
    BMC Bioinformatics 8:32. 2007
    ..Existing methods are limited in dealing with such time-lapse data sets while manual analysis is not feasible. This paper presents statistical data analysis and statistical pattern recognition to perform this task...
  5. ncbi request reprint Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy
    Meng Wang
    Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, 3rd Floor, 1249 Boylston, Boston, MA 02215, USA
    Bioinformatics 24:94-101. 2008
    ....
  6. pmc Automated neurite extraction using dynamic programming for high-throughput screening of neuron-based assays
    Yong Zhang
    Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, Boston, MA 02215, USA
    Neuroimage 35:1502-15. 2007
    ..All these properties make the proposed algorithm attractive for high-throughput screening of neuron-based assays...
  7. ncbi request reprint Dendritic spine detection using curvilinear structure detector and LDA classifier
    Yong Zhang
    Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, Boston, MA 02215, USA
    Neuroimage 36:346-60. 2007
    ..We evaluate the proposed approach by comparing with the manual results in terms of backbone length, spine number, spine length, and spine density...
  8. ncbi request reprint Towards automated cellular image segmentation for RNAi genome-wide screening
    Xiaobo Zhou
    Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, 3rd Floor, 1249 Boylston, Boston, MA 02215, USA
    Med Image Comput Comput Assist Interv 8:885-92. 2005
    ..K-nearest neighbor classifier (KNN) is employed to perform cell phenotype classification. Experimental results indicate that the proposed approach can be used to identify cell phenotypes of RNAi genome-wide screens...
  9. ncbi request reprint Automated axon tracking of 3D confocal laser scanning microscopy images using guided probabilistic region merging
    Ranga Srinivasan
    Harvard Center for Neurodegeneration and Repair Center for Bioinformatics, Harvard Medical School, Boston, MA, USA
    Neuroinformatics 5:189-203. 2007
    ..The results are validated with the manual tracking results while the robustness of the algorithm is compared with the published repulsive snake algorithm...
  10. ncbi request reprint Cancer classification and prediction using logistic regression with Bayesian gene selection
    Xiaobo Zhou
    Harvard Center for Neurodegeneration and Repair, Center for Bioinformatics, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
    J Biomed Inform 37:249-59. 2004
    ..Finally, the robustness and sensitivity properties of the proposed method are also investigated...
  11. pmc Identification of SNP-containing regulatory motifs in the myelodysplastic syndromes model using SNP arrays and gene expression arrays
    Jing Fan
    Department of Electrical and Computer Engineering, Northeastern University, Boston, MA 02115, USA
    Chin J Cancer 32:170-85. 2013
    ....
  12. doi request reprint Cellular phenotype recognition for high-content RNA interference genome-wide screening
    Jun Wang
    Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, Boston, Massachusetts, USA
    J Biomol Screen 13:29-39. 2008
    ..Moreover, the authors applied this approach to analyze the whole high-content fluorescence images of Drosophila cells for further HCS-based gene function analysis...
  13. pmc A time-series method for automated measurement of changes in mitotic and interphase duration from time-lapse movies
    Frederic D Sigoillot
    Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 6:e25511. 2011
    ..However, extraction of quantitative information by manual inspection of time-lapse movies is too time-consuming to be useful for analysis of large experiments...
  14. ncbi request reprint A novel tracing algorithm for high throughput imaging Screening of neuron-based assays
    Yong Zhang
    Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, Boston, MA 02215, United States
    J Neurosci Methods 160:149-62. 2007
    ..Detailed results on experimental validation of the proposed method and on its comparative performance with other proposed schemes are included...
  15. ncbi request reprint Tracking molecular particles in live cells using fuzzy rule-based system
    Shan Jiang
    HCNR Center for Bioinformatics, Harvard Medical School and Brigham and Women s Hospital, Boston, Massachusetts 02215, USA
    Cytometry A 71:576-84. 2007
    ..Results show that this method can accurately track most of the particles in the high volume images...
  16. ncbi request reprint A computerized cellular imaging system for high content analysis in Monastrol suppressor screens
    Xiaobo Zhou
    Harvard Center for Neurodegeneration and Repair Center for Bioinformatics, Harvard Medical School, 1249 Boylston, Boston, MA 02215, USA
    J Biomed Inform 39:115-25. 2006
    ..The results are validated and evaluated by comparing the performance of HCS-MMA with visual analysis, as well as clustering of the drug compounds under evaluation...
  17. pmc Protein structure similarity from Principle Component Correlation analysis
    Xiaobo Zhou
    Center for Neurodegeneration and Repair, Center for Bioinformatics, Harvard Medical School, Boston, MA 02215, USA
    BMC Bioinformatics 7:40. 2006
    ..We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities...
  18. ncbi request reprint Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis
    Michael H Cho
    Channing Division of Network Medicine, Brigham and Women s Hospital, Boston, MA, USA Division of Pulmonary and Critical Care Medicine, Brigham and Women s Hospital, Boston, MA, USA Electronic address
    Lancet Respir Med 2:214-25. 2014
    ..We sought to identify risk loci for moderate to severe and severe COPD with data from several cohort studies...
  19. pmc Faslodex inhibits estradiol-induced extracellular matrix dynamics and lung metastasis in a model of lymphangioleiomyomatosis
    Chenggang Li
    Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Am J Respir Cell Mol Biol 49:135-42. 2013
    ..Faslodex inhibits the estradiol-induced lung metastasis of TSC2-deficient cells. Targeting estrogen receptors with Faslodex may be of efficacy in the treatment of LAM. ..
  20. ncbi request reprint Expression of a viral oncoprotein in normal human epithelial cells triggers an autophagy-related process: is autophagy an "Achilles' heel" of human cancers?
    Xiaobo Zhou
    Department of Medicine, Infectious Diseases Division, Brigham and Women s Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
    Autophagy 5:578-9. 2009
    ....
  21. pmc A novel peak detection approach with chemical noise removal using short-time FFT for prOTOF MS data
    Shuqin Zhang
    HCNR CBI, Harvard Medical School and Brigham and Women s Hospital, Boston, MA, USA
    Proteomics 9:3833-42. 2009
    ..Our method is easily implemented and is highly effective to define peaks that will be used for disease classification or to highlight potential biomarkers...
  22. pmc Boosting alternating decision trees modeling of disease trait information
    Kuang Yu Liu
    HCNR Center for Bioinformatics, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02215, USA
    BMC Genet 6:S132. 2005
    ..In conclusion, our findings suggest that the ADTrees method may offer a more accurate representation of the disease status that allows for better detection of linkage evidence...
  23. pmc Human papillomavirus type 16 E7 oncoprotein associates with the cullin 2 ubiquitin ligase complex, which contributes to degradation of the retinoblastoma tumor suppressor
    Kyungwon Huh
    The Channing Laboratory 861, Brigham and Women s Hospital, 181 Longwood Avenue, Boston, MA 02115, USA
    J Virol 81:9737-47. 2007
    ..Hence, we propose that the HPV16 E7-associated cullin 2 ubiquitin ligase complex contributes to aberrant degradation of the pRB tumor suppressor in HPV16 E7-expressing cells...
  24. ncbi request reprint Automated segmentation, classification, and tracking of cancer cell nuclei in time-lapse microscopy
    Xiaowei Chen
    HCNR Center for Bioinformatics, Harvard Medical School, Boston, MA 02115, USA
    IEEE Trans Biomed Eng 53:762-6. 2006
    ..Experimental results show that the proposed method is efficient and effective in cell tracking and phase identification...
  25. pmc Expression of the human papillomavirus type 16 E7 oncoprotein induces an autophagy-related process and sensitizes normal human keratinocytes to cell death in response to growth factor deprivation
    Xiaobo Zhou
    Brigham and Women s Hospital and Department of Medicine, Harvard Medical School, USA
    Virology 385:192-7. 2009
    ..These findings indicate that even under normal culture conditions, HPV16 E7 expression triggers metabolic stress that may result in autophagy, a pathway implicated in carcinogenesis...
  26. ncbi request reprint Bayesian variable selection for gene expression modeling with regulatory motif binding sites in neuroinflammatory events
    Kuang Yu Liu
    HCNR Center for Bioinformatics, Harvard Medical School, Boston, Massachusetts 02215, USA
    Neuroinformatics 4:95-117. 2006
    ....
  27. pmc Comprehensive genetic assessment of a functional TLR9 promoter polymorphism: no replicable association with asthma or asthma-related phenotypes
    Nancy E Lange
    Channing Laboratory, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    BMC Med Genet 12:26. 2011
    ..We performed detailed genetic association studies of the functional variant rs5743836 with asthma susceptibility and asthma-related phenotypes in three independent cohorts...
  28. ncbi request reprint Mutual information-based feature selection in studying perturbation of dendritic structure caused by TSC2 inactivation
    Xiaobo Zhou
    HCNR Center for Bioinformatics, Harvard Medical School, Boston, Massachusetts 02215, USA
    Neuroinformatics 4:81-94. 2006
    ..Finally, we explored the application of pattern recognition method in a small sample with richer feature properties, namely bootstrap mutual information estimation and a mutual information- based feature selection method...