Xiaobo Zhou

Summary

Publications

  1. pmc Computational modeling of 3D tumor growth and angiogenesis for chemotherapy evaluation
    Lei Tang
    Department of Translational Imaging, The Methodist Hospital Research Institute, Houston, Texas, United States of America
    PLoS ONE 9:e83962. 2014
  2. pmc Systematically studying kinase inhibitor induced signaling network signatures by integrating both therapeutic and side effects
    Hongwei Shao
    Department of Radiology, Wake Forest School of Medicine, Winston Salem, North Carolina, United States of America Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui, P R China
    PLoS ONE 8:e80832. 2013
  3. pmc Discovering transcription and splicing networks in myelodysplastic syndromes
    Hongyan Wang
    Center for Bioinformatics and Systems Biology, Division of Radiologic Sciences, Wake Forest University Baptist Medical Center, Winston Salem, North Carolina, United States of America
    PLoS ONE 8:e79118. 2013
  4. pmc Multi-scale agent-based modeling on melanoma and its related angiogenesis analysis
    Jun Wang
    College of Computer and Information Science, Southwest University, Chongqing 400715, China
    Theor Biol Med Model 10:41. 2013
  5. pmc SNVHMM: predicting single nucleotide variants from next generation sequencing
    Jiawen Bian
    Department of Diagnostic Radiology, Center for Bioinformatics and Systems Biology, Wake Forest University School of Medicine, Winston Salem 27103, NC, USA
    BMC Bioinformatics 14:225. 2013
  6. ncbi request reprint Multipotential differentiation of human urine-derived stem cells: potential for therapeutic applications in urology
    Shantaram Bharadwaj
    Wake Forest Institute of Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, North Carolina, USA
    Stem Cells 31:1840-56. 2013
  7. pmc Multi-scale agent-based brain cancer modeling and prediction of TKI treatment response: incorporating EGFR signaling pathway and angiogenesis
    Xiaoqiang Sun
    Department of Radiology, The Methodist Hospital Research Institute, Weil Cornell Medical College, Houston, TX 77030, USA
    BMC Bioinformatics 13:218. 2012
  8. pmc Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach
    Huiming Peng
    Center for Bioinformatics and Systems Biology and Department of Radiology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA, Department of Radiology, The Methodist Hospital Research Institute, Houston, TX 77030, USA, Department of Pathology, The Methodist Hospital Research Institute, Houston, TX 77030, USA, Proteomics Programmatic Core Laboratory, The Methodist Hospital Research Institute, Houston, TX 77030, USA, College of Computer and Information Science, Southwest University, Chongqing 400715, China, Department of Pathology, Florida Hospital, Orlando, FL 32803, USA
    Bioinformatics 30:1899-907. 2014
  9. pmc Accuracy of a computer-aided surgical simulation protocol for orthognathic surgery: a prospective multicenter study
    Sam Sheng Pin Hsu
    Department of Oral and Maxillofacial Surgery, The Methodist Hospital Research Institute, and Department of Pediatric Surgery, The University of Texas Health Science Center, Houston, TX 77030, USA
    J Oral Maxillofac Surg 71:128-42. 2013
  10. doi request reprint A systematic modeling study on the pathogenic role of p38 MAPK activation in myelodysplastic syndromes
    Huiming Peng
    Department of Radiology, The Methodist Hospital, The Methodist Hospital Research Institute, and Weill Cornell Medical College, Houston, TX, USA
    Mol Biosyst 8:1366-74. 2012

Collaborators

Detail Information

Publications27

  1. pmc Computational modeling of 3D tumor growth and angiogenesis for chemotherapy evaluation
    Lei Tang
    Department of Translational Imaging, The Methodist Hospital Research Institute, Houston, Texas, United States of America
    PLoS ONE 9:e83962. 2014
    ....
  2. pmc Systematically studying kinase inhibitor induced signaling network signatures by integrating both therapeutic and side effects
    Hongwei Shao
    Department of Radiology, Wake Forest School of Medicine, Winston Salem, North Carolina, United States of America Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui, P R China
    PLoS ONE 8:e80832. 2013
    ..Furthermore, this integration strategy can be easily extended to other specific cell lines to be a powerful tool for drug screen before clinical trials. ..
  3. pmc Discovering transcription and splicing networks in myelodysplastic syndromes
    Hongyan Wang
    Center for Bioinformatics and Systems Biology, Division of Radiologic Sciences, Wake Forest University Baptist Medical Center, Winston Salem, North Carolina, United States of America
    PLoS ONE 8:e79118. 2013
    ..Many of these networks were enriched in the herpes simplex infection pathway which involves many splicing factors, and pathways in cancers and acute or chronic myeloid leukemia. ..
  4. pmc Multi-scale agent-based modeling on melanoma and its related angiogenesis analysis
    Jun Wang
    College of Computer and Information Science, Southwest University, Chongqing 400715, China
    Theor Biol Med Model 10:41. 2013
    ..Thus, we proposed a novel multi-scale agent-based computational model that integrates the angiogenesis into tumor growth to study the response of melanoma cancer under combined drug treatment...
  5. pmc SNVHMM: predicting single nucleotide variants from next generation sequencing
    Jiawen Bian
    Department of Diagnostic Radiology, Center for Bioinformatics and Systems Biology, Wake Forest University School of Medicine, Winston Salem 27103, NC, USA
    BMC Bioinformatics 14:225. 2013
    ..However, for data with low sequencing depth, the efficiency of such algorithms remains poor and needs to be improved...
  6. ncbi request reprint Multipotential differentiation of human urine-derived stem cells: potential for therapeutic applications in urology
    Shantaram Bharadwaj
    Wake Forest Institute of Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, North Carolina, USA
    Stem Cells 31:1840-56. 2013
    ..USCs may be useful in cell-based therapies and tissue engineering applications, including urogenital reconstruction...
  7. pmc Multi-scale agent-based brain cancer modeling and prediction of TKI treatment response: incorporating EGFR signaling pathway and angiogenesis
    Xiaoqiang Sun
    Department of Radiology, The Methodist Hospital Research Institute, Weil Cornell Medical College, Houston, TX 77030, USA
    BMC Bioinformatics 13:218. 2012
    ....
  8. pmc Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach
    Huiming Peng
    Center for Bioinformatics and Systems Biology and Department of Radiology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA, Department of Radiology, The Methodist Hospital Research Institute, Houston, TX 77030, USA, Department of Pathology, The Methodist Hospital Research Institute, Houston, TX 77030, USA, Proteomics Programmatic Core Laboratory, The Methodist Hospital Research Institute, Houston, TX 77030, USA, College of Computer and Information Science, Southwest University, Chongqing 400715, China, Department of Pathology, Florida Hospital, Orlando, FL 32803, USA
    Bioinformatics 30:1899-907. 2014
    ..However, how the p38 mitogen-activated protein kinase signaling pathway is involved in drug resistance, in particular the roles that the various p38 isoforms play, remains largely unknown...
  9. pmc Accuracy of a computer-aided surgical simulation protocol for orthognathic surgery: a prospective multicenter study
    Sam Sheng Pin Hsu
    Department of Oral and Maxillofacial Surgery, The Methodist Hospital Research Institute, and Department of Pediatric Surgery, The University of Texas Health Science Center, Houston, TX 77030, USA
    J Oral Maxillofac Surg 71:128-42. 2013
    ..The purpose of this prospective multicenter study was to assess the accuracy of a computer-aided surgical simulation (CASS) protocol for orthognathic surgery...
  10. doi request reprint A systematic modeling study on the pathogenic role of p38 MAPK activation in myelodysplastic syndromes
    Huiming Peng
    Department of Radiology, The Methodist Hospital, The Methodist Hospital Research Institute, and Weill Cornell Medical College, Houston, TX, USA
    Mol Biosyst 8:1366-74. 2012
    ..Our study suggests that the combination of molecular biological studies and systematic modeling is a powerful tool for comprehensive investigation of the complex cellular mechanisms involved in MDS pathogenesis...
  11. pmc Targeting the biophysical properties of the myeloma initiating cell niches: a pharmaceutical synergism analysis using multi-scale agent-based modeling
    Jing Su
    Department of Radiology, The Wake Forest School of Medicine, Winston Salem, North Carolina, United States of America
    PLoS ONE 9:e85059. 2014
    ..We concluded that targeting the biophysical properties of stem cell niches is of high clinical potential since it may re-sensitize tumor initiating cells to chemotherapies and reduce risks of cancer relapse...
  12. pmc A system mathematical model of a cell-cell communication network in amyotrophic lateral sclerosis
    Hongwei Shao
    Methodist Hospital Research Institute, 6670 Bertner Avenue, Houston, USA
    Mol Biosyst 9:398-406. 2013
    ..In the future, if we combine the side effects of different therapies, this model can be used to optimize the therapeutic strategies so that they can effectively improve survival rates and quality of life for patients with ALS...
  13. pmc A computational model for compressed sensing RNAi cellular screening
    Hua Tan
    Department of Radiology, The Methodist Hospital Research Institute, Weill Medical College of Cornell University, Houston, TX 77030, USA
    BMC Bioinformatics 13:337. 2012
    ..The traditional RNAi screening scheme, in which one siRNA is designed to knockdown one specific mRNA target, needs a large library of siRNAs and turns out to be time-consuming and expensive...
  14. pmc Incremental kernel ridge regression for the prediction of soft tissue deformations
    Binbin Pan
    The Methodist Hospital Research Institute, Houston, Texas, USA
    Med Image Comput Comput Assist Interv 15:99-106. 2012
    ..Thus, our model is biomechanical relevant and statistical relevant. Validation on eleven patients demonstrates the effectiveness and efficiency of our method...
  15. pmc MRI-based prediction of pulsed high-intensity focused ultrasound effect on tissue transport in rabbit muscle
    Brian E O'Neill
    Department of Translational Imaging, The Methodist Hospital Research Institute, Houston, Texas, USA
    J Magn Reson Imaging 38:1094-102. 2013
    ..To design an algorithm for optimizing pulsed high intensity focused ultrasound (p-HIFU) treatment parameters to maximize tissue transport while minimizing thermal necrosis based on MR image guidance...
  16. pmc NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq
    Zheng Xia
    Department of Radiology, The Methodist Hospital Research Institute, Houston, TX 77030, USA
    BMC Bioinformatics 12:162. 2011
    ..Novel study on isoform inference and estimation purely from RNA-Seq without annotation information is desirable...
  17. pmc FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq
    Chenglin Liu
    Department of Diagnostic Radiology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA
    BMC Bioinformatics 14:193. 2013
    ..Gene fusions, which result from abnormal chromosome rearrangements, are a pathogenic factor in cancer development. The emerging RNA-Seq technology enables us to detect gene fusions and profile their features...
  18. ncbi request reprint A novel network and sparsity constraint regression model for functional module identification in genomic data analysis
    Zheng Xia
    Department of Radiology, The Methodist Hospital Research Institute, Houston, TX 77030, USA
    Int J Data Min Bioinform 8:311-25. 2013
    ..Many of those findings are confirmed by published literature...
  19. pmc An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data
    Guangxu Jin
    Systems Medicine and Bioengineering Department, Cornell University, Houston, TX 77030, USA
    Bioinformatics 27:i310-6. 2011
    ..In this article, we propose an enhanced Petri-Net (EPN) model to recognize the synergistic effects of drug combinations from the molecular response profiles, i.e. drug-treated microarray data...
  20. pmc Systems modeling of anti-apoptotic pathways in prostate cancer: psychological stress triggers a synergism pattern switch in drug combination therapy
    Xiaoqiang Sun
    Department of Radiology, Wake Forest School of Medicine, Winston Salem, North Carolina, United States of America School of Mathematical Science, Beijing Normal University, Beijing, P R China
    PLoS Comput Biol 9:e1003358. 2013
    ....
  21. doi request reprint In vitro evaluation of new approach to digital dental model articulation
    Yu Bing Chang
    Surgical Planning Laboratory, Department of Oral and Maxillofacial Surgery, Methodist Hospital Research Institute, Houston, TX, USA
    J Oral Maxillofac Surg 70:952-62. 2012
    ..The purpose of the present study was to evaluate the accuracy of our newly developed approach to digital dental model articulation...
  22. pmc Cytokine combination therapy prediction for bone remodeling in tissue engineering based on the intracellular signaling pathway
    Xiaoqiang Sun
    Department of Radiology, The Methodist Hospital Research Institute, Weil Cornell Medical College, Houston, TX 77030, USA
    Biomaterials 33:8265-76. 2012
    ..We revealed the characteristics of cytokine combinations of Wnt/BMP2 which could be used to guide the design of in vivo bone scaffolds and the clinical treatment of some diseases such as osteoporosis...
  23. pmc Interleukin-2 Functions in Anaplastic Large Cell Lymphoma Cells through Augmentation of Extracellular Signal-Regulated Kinases 1/2 Activation
    Masanori Ito
    Department of Pathology, The Methodist Hospital and The Methodist Hospital Research Institute, Houston, TX, USA
    Int J Biomed Sci 7:181-90. 2011
    ..Our findings demonstrate that IL-2 signaling plays a functional role in ALCL cells, and enhances lymphoma cell survival by increasing activation of the ERK1/2 pathway...
  24. pmc Skeletal myogenic differentiation of urine-derived stem cells and angiogenesis using microbeads loaded with growth factors
    Guihua Liu
    Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC 27157, USA
    Biomaterials 34:1311-26. 2013
    ..This approach could potentially be used for cell therapy in the treatment of stress urinary incontinence...
  25. pmc Detection and characterization of regulatory elements using probabilistic conditional random field and hidden Markov models
    Hongyan Wang
    Department of Radiology, The Methodist Hospital Research Institute, Houston, TX 77030, USA
    Chin J Cancer 32:186-94. 2013
    ....
  26. doi request reprint Peak tree: a new tool for multiscale hierarchical representation and peak detection of mass spectrometry data
    Peng Zhang
    Department of Electronics Engineering and Information Science, University of Science and Technology of China, PO Box 4, Hefei, Anhui 230027, P R China
    IEEE/ACM Trans Comput Biol Bioinform 8:1054-66. 2011
    ..The benefits from our peak-tree-based system for MS disease analysis are also proved on real SELDI data...
  27. pmc Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes
    Dominik Beck
    Bioengineering and Bioinformatics Program, Department of Pathology, The Methodist Hospital Research Institute, Weill Cornell Medical College, Houston, TX, 77030, USA
    BMC Med Genomics 4:19. 2011
    ..Little is known about small regulatory RNAs and how they contribute to pathogenesis, progression and transcriptome changes in MDS...