Xin Chen

Summary

Affiliation: University of California
Country: USA

Publications

  1. doi request reprint Dynamics of MRI-Guided thermal ablation of VX2 tumor in paraspinal muscle of rabbits
    Xin Chen
    Radiation Oncology Department, University of California at San Francisco, 1600 Divisadero Street, Suite 0130, San Francisco, CA 94115, USA
    IEEE Trans Biomed Eng 55:1004-14. 2008
  2. ncbi request reprint RNA interference as therapeutics for hepatocellular carcinoma
    Chuanrui Xu
    Department of Bioengineering and Therapeutic Science, University of California, San Francisco, CA 94143, USA
    Recent Pat Anticancer Drug Discov 6:106-15. 2011
  3. doi request reprint Chromosomal changes in fibrolamellar hepatocellular carcinoma detected by array comparative genomic hybridization
    Sanjay Kakar
    Department of Pathology, University of California, San Francisco, CA, USA
    Mod Pathol 22:134-41. 2009
  4. pmc New tools for functional genomic analysis
    Xin Chen
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
    Drug Discov Today 14:754-60. 2009
  5. pmc Chromosomal abnormalities determined by comparative genomic hybridization are helpful in the diagnosis of atypical hepatocellular neoplasms
    Sanjay Kakar
    Department of Pathology, University of California, San Francisco, 4150 Clement Street, San Francisco, CA 94121, USA
    Histopathology 55:197-205. 2009
  6. ncbi request reprint Array-based comparative genomic hybridization reveals recurrent chromosomal aberrations and Jab1 as a potential target for 8q gain in hepatocellular carcinoma
    Mohini A Patil
    Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
    Carcinogenesis 26:2050-7. 2005
  7. ncbi request reprint An integrated data analysis approach to characterize genes highly expressed in hepatocellular carcinoma
    Mohini A Patil
    Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
    Oncogene 24:3737-47. 2005
  8. pmc Distinct pathways of genomic progression to benign and malignant tumors of the liver
    Aaron D Tward
    G W Hooper Foundation and Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 104:14771-6. 2007
  9. ncbi request reprint Hedgehog signaling in human hepatocellular carcinoma
    Mohini A Patil
    Department of Biopharmaceutical Sciences and Liver Center, University of California, San Francisco, California 94143 0446, USA
    Cancer Biol Ther 5:111-7. 2006
  10. pmc Bmi1 functions as an oncogene independent of Ink4A/Arf repression in hepatic carcinogenesis
    Chuan Rui Xu
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94143, USA
    Mol Cancer Res 7:1937-45. 2009

Collaborators

Detail Information

Publications44

  1. doi request reprint Dynamics of MRI-Guided thermal ablation of VX2 tumor in paraspinal muscle of rabbits
    Xin Chen
    Radiation Oncology Department, University of California at San Francisco, 1600 Divisadero Street, Suite 0130, San Francisco, CA 94115, USA
    IEEE Trans Biomed Eng 55:1004-14. 2008
    ..The combined use of MR image monitoring and model simulation has the potential for improving pretreatment planning and real-time prediction of lesion-size dynamics for guidance of thermal ablation of tumors...
  2. ncbi request reprint RNA interference as therapeutics for hepatocellular carcinoma
    Chuanrui Xu
    Department of Bioengineering and Therapeutic Science, University of California, San Francisco, CA 94143, USA
    Recent Pat Anticancer Drug Discov 6:106-15. 2011
    ..Here, we summarized the progress of RNAi therapeutics in HCC treatment, relevant patents, potential challenges and prospects in the future...
  3. doi request reprint Chromosomal changes in fibrolamellar hepatocellular carcinoma detected by array comparative genomic hybridization
    Sanjay Kakar
    Department of Pathology, University of California, San Francisco, CA, USA
    Mod Pathol 22:134-41. 2009
    ..The favorable outcome in some fibrolamellar carcinomas may be due to absent or low number of cytogenetic aberrations...
  4. pmc New tools for functional genomic analysis
    Xin Chen
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
    Drug Discov Today 14:754-60. 2009
    ..Using human liver cancer as an example, we provide further information of how these genomic approaches can be applied in cancer research...
  5. pmc Chromosomal abnormalities determined by comparative genomic hybridization are helpful in the diagnosis of atypical hepatocellular neoplasms
    Sanjay Kakar
    Department of Pathology, University of California, San Francisco, 4150 Clement Street, San Francisco, CA 94121, USA
    Histopathology 55:197-205. 2009
    ..To explore the utility of cytogenetic abnormalities in the distinction of hepatic adenoma (HA) and well-differentiated hepatocellular carcinoma (HCC)...
  6. ncbi request reprint Array-based comparative genomic hybridization reveals recurrent chromosomal aberrations and Jab1 as a potential target for 8q gain in hepatocellular carcinoma
    Mohini A Patil
    Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
    Carcinogenesis 26:2050-7. 2005
    ....
  7. ncbi request reprint An integrated data analysis approach to characterize genes highly expressed in hepatocellular carcinoma
    Mohini A Patil
    Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
    Oncogene 24:3737-47. 2005
    ..This approach of integrating other biological information with gene expression in the analysis helps select aberrantly expressed genes in HCC that may be further studied for their diagnostic or therapeutic utility...
  8. pmc Distinct pathways of genomic progression to benign and malignant tumors of the liver
    Aaron D Tward
    G W Hooper Foundation and Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 104:14771-6. 2007
    ....
  9. ncbi request reprint Hedgehog signaling in human hepatocellular carcinoma
    Mohini A Patil
    Department of Biopharmaceutical Sciences and Liver Center, University of California, San Francisco, California 94143 0446, USA
    Cancer Biol Ther 5:111-7. 2006
    ..The study therefore, for the first time, provides evidence that hedgehog signaling may be activated in some HCC tumors. The results also indicate that the hedgehog pathway may be a new candidate for therapeutic targeting in HCC...
  10. pmc Bmi1 functions as an oncogene independent of Ink4A/Arf repression in hepatic carcinogenesis
    Chuan Rui Xu
    Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94143, USA
    Mol Cancer Res 7:1937-45. 2009
    ..In summary, our study shows that Bmi1 can cooperate with other oncogenic signals to promote hepatic carcinogenesis in vivo. Yet Bmi1 functions independent of Ink4A/Arf repression in liver cancer development...
  11. pmc S-nitrosylation from GSNOR deficiency impairs DNA repair and promotes hepatocarcinogenesis
    Wei Wei
    Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
    Sci Transl Med 2:19ra13. 2010
    ..Thus, our data suggest that GSNOR deficiency, through dysregulated S-nitrosylation, may promote HCC, possibly by inactivating a DNA repair system...
  12. pmc Synergistic role of Sprouty2 inactivation and c-Met up-regulation in mouse and human hepatocarcinogenesis
    Susie A Lee
    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
    Hepatology 52:506-17. 2010
    ..Coordinated deregulation of Spry2 and c-Met signaling may be a pivotal oncogenic mechanism responsible for unrestrained activation of ERK and AKT pathways in human hepatocarcinogenesis...
  13. doi request reprint Optimisation-based thermal treatment planning for catheter-based ultrasound hyperthermia
    Xin Chen
    Thermal Therapy Research Group, Department of Radiation Oncology, University of California at San Francisco, San Francisco, California 94143 1708, USA
    Int J Hyperthermia 26:39-55. 2010
    ....
  14. doi request reprint Integration of genomic analysis and in vivo transfection to identify sprouty 2 as a candidate tumor suppressor in liver cancer
    Susie A Lee
    Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
    Hepatology 47:1200-10. 2008
    ..In addition, we demonstrate that the integration of genomic analysis and in vivo transfection is a powerful tool to identify genes that are important during hepatic carcinogenesis...
  15. ncbi request reprint Magnetic resonance imaging and model prediction for thermal ablation of tissue
    Xin Chen
    Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106, USA
    J Magn Reson Imaging 26:123-32. 2007
    ..To monitor and predict tissue temperature distributions and lesion boundaries during thermal ablation by combining MRI and thermal modeling methods...
  16. ncbi request reprint Automatic tracing of vocal-fold motion from high-speed digital images
    Yuling Yan
    Department of Mechanical Engineering, University of Hawaii Manoa, Honolulu, HI 96822, USA
    IEEE Trans Biomed Eng 53:1394-400. 2006
    ..The performance, effectiveness and validation of our approach is demonstrated using representative, high-speed imaging recordings of subjects having normal and pathological voices...
  17. doi request reprint Radiologic and histologic characterization of silk fibroin as scaffold coating for rabbit tracheal defect repair
    Yusu Ni
    Department of Otolaryngology, Eye and ENT Hospital of Shanghai Medical School, Fudan University, Shanghai, China
    Otolaryngol Head Neck Surg 139:256-61. 2008
    ..To explore the feasibility of silk fibroin as a biomaterial coating used in tracheal defect reconstruction...
  18. doi request reprint A computationally efficient method for automatic registration of orthogonal x-ray images with volumetric CT data
    Xin Chen
    ADSIP Research Centre, University of Central Lancashire, Preston, UK
    Phys Med Biol 53:967-83. 2008
    ..12 mm for translation and 0.61 +/- 0.29 degrees for rotation within the capture range has been achieved. For the tested phantom data, the algorithm has also shown to be robust without being affected by artificial markers in the image...
  19. doi request reprint Shield effect of silicate on adsorption of proteins onto silicon-doped hydroxyapatite (100) surface
    Xin Chen
    Department of Chemistry, Zhejiang University, Hangzhou 310027, PR China
    Biomaterials 29:2423-32. 2008
    ....
  20. doi request reprint W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data
    Xin Chen
    School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
    Bioinformatics 24:1121-8. 2008
    ..Thus, learning an accurate PWM to characterize the binding sites of a specific TF is a fundamental problem that plays an important role in modeling regulatory motifs and also in discovering the regulatory targets of TFs...
  21. doi request reprint Study of transmembrane potentials on cellular inner and outer membrane--frequency response model and its filter characteristic simulation
    Chenguo Yao
    State Key Laboratory of Power Transmission Equipment and System Security and New Technology, College of Electrical Engineering, Chongqing University, Chongqing 400044, China
    IEEE Trans Biomed Eng 55:1792-9. 2008
    ..Therefore, the frequency response model could help to choose reasonable window parameters for the application of a nanosecond pulsed electric field to tumor treatment...
  22. doi request reprint Continuous monitoring of sonomyography, electromyography and torque generated by normal upper arm muscles during isometric contraction: sonomyography assessment for arm muscles
    Jun Shi
    Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong
    IEEE Trans Biomed Eng 55:1191-8. 2008
    ..The potential values of SMG together with EMG to provide a more comprehensive assessment for the muscle functions should be further investigated with more subjects and more muscle groups...
  23. ncbi request reprint Expression profiling identifies chemokine (C-C motif) ligand 18 as an independent prognostic indicator in gastric cancer
    Suet Yi Leung
    Department of Pathology, The University of Hong Kong, Queen Mary Hospital, China
    Gastroenterology 127:457-69. 2004
    ..We previously analyzed gene-expression patterns in 90 gastric adenocarcinomas by using complementary DNA microarrays and prioritized a list of genes whose expression levels predict patient outcome...
  24. doi request reprint Insight from molecular modeling into different conformation and SAR of natural steroids and unnatural 7-oxa-steroids
    Fu An Kang
    Johnson and Johnson Pharmaceutical Research and Development, LLC, 665 Stockton Drive, Exton, PA 19341, USA
    Bioorg Med Chem Lett 18:3687-90. 2008
    ..The unnatural 7-oxa-steroids were orally active in a rat complement C3 assay and showed comparable pharmacokinetic and metabolic profiles to those of the natural steroid, mifepristone...
  25. ncbi request reprint Electronic post-compensation of WDM transmission impairments using coherent detection and digital signal processing
    Xiaoxu Li
    CREOL, The College of Optics and Photonics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816 2700, USA
    Opt Express 16:880-8. 2008
    ..Transmission of 10 x 10 Gbit/s binary-phase-shift-keying (BPSK) signals at a channel spacing of 20 GHz over 800 km dispersion shifted fiber (DSF) has been demonstrated numerically...
  26. ncbi request reprint Wide band single polarization and polarization maintaining fibers using stress rods and air holes
    Xin Chen
    Science and Technology Division, Corning Incorporated, SP AR 01 2, Corning, NY 14831, USA
    Opt Express 16:12060-8. 2008
    ..As a result, fibers with very large single polarization bandwidth as well as larger effective area are identified...
  27. ncbi request reprint Frequency response model and simulation of transmembrane potentials on cellular inner and outer membranes
    Xin Chen
    Key Laboratory of High Voltage Engineering and Electrical New Technology, Ministry of Education, Chongqing University, Chongqing, 400044 China
    Conf Proc IEEE Eng Med Biol Soc 2007:5819-22. 2007
    ..The experimental result agrees well with the simulation. Therefore, the simulation result provides a theoretical guidance to choosing reasonable window parameters for application of nanosecond pulse to tumor treatment...
  28. ncbi request reprint DNACompress: fast and effective DNA sequence compression
    Xin Chen
    Computer Science Department, University of California, Santa Barbara, CA 99106, USA
    Bioinformatics 18:1696-8. 2002
    ..While achieving the best compression ratios for DNA sequences, our new DNACompress program significantly improves the running time of all previous DNA compression programs...
  29. ncbi request reprint Can an in silico drug-target search method be used to probe potential mechanisms of medicinal plant ingredients?
    Xin Chen
    Department of Computational Science, National University of Singapore, Blk S17, Level 7, 3 Science Drive 2, Singapore 117543
    Nat Prod Rep 20:432-44. 2003
    ....
  30. ncbi request reprint Synthesis and biological evaluation of novel macrocyclic bis-7-azaindolylmaleimides as potent and highly selective glycogen synthase kinase-3 beta (GSK-3 beta) inhibitors
    Lan Shen
    Drug Discovery Division, Johnson and Johnson Pharmaceutical Research and Development, L L C, 1000 Route 202, PO Box 300, Raritan, NJ 08869, USA
    Bioorg Med Chem 12:1239-55. 2004
    ....
  31. ncbi request reprint Computer prediction of drug resistance mutations in proteins
    Zhi Wei Cao
    Bioinformatics and Drug Design Group, Department of Computational Science, National University of Singapore, Blk Soc 1, Level 7, Singapore 117543
    Drug Discov Today 10:521-9. 2005
    ..Several protein structure- and sequence-based computer methods have been explored for mechanistic study and prediction of resistance mutations. These methods and their usefulness are reviewed here...
  32. ncbi request reprint Intrabody three-dimensional position sensor for an ultrasound endoscope
    Shinichi Tamura
    Division of Interdisciplinary Image Analysis, Osaka University Medical School, Suita City, Japan
    IEEE Trans Biomed Eng 49:1187-94. 2002
    ..The system may be envisaged as a kind of global positioning system for intrabody navigation...
  33. ncbi request reprint Quantitative analysis of brain optical images with 2D C0 complexity measure
    Yang Cao
    Center for Brain Science Research, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, PR China
    J Neurosci Methods 159:181-6. 2007
    ..This suggests that 2D C0 could be used as a new quantitative measure for analyzing the intrinsic signal optical images...
  34. ncbi request reprint A general framework for biclustering gene expression data
    Haifeng Li
    Center of Excellence in Genomic Science, University of Southern California, Los Angeles, CA 90089, USA
    J Bioinform Comput Biol 4:911-33. 2006
    ..The preliminary experiments on simulated as well as real data show that our approach is very versatile and promising...
  35. ncbi request reprint Matching-pursuit/split-operator-Fourier-transform simulations of excited-state nonadiabatic quantum dynamics in pyrazine
    Xin Chen
    Department of Chemistry, Yale University, New Haven, CT 06520 8107, USA
    J Chem Phys 125:124313. 2006
    ..The reported results show that the generalized MP/SOFT method is a practical and accurate approach to model nonadiabatic reaction dynamics in polyatomic systems...
  36. ncbi request reprint Assignment of orthologous genes via genome rearrangement
    Xin Chen
    Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
    IEEE/ACM Trans Comput Biol Bioinform 2:302-15. 2005
    ..The simulation results demonstrate that SOAR, in general, performs better than the iterated exemplar algorithm in terms of computing the reversal distance and assigning correct orthologs...
  37. ncbi request reprint Support vector machines approach for predicting druggable proteins: recent progress in its exploration and investigation of its usefulness
    Lian Yi Han
    Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Blk Soc 1, Level 7, 3 Science Drive 2, Singapore 117543
    Drug Discov Today 12:304-13. 2007
    ....
  38. ncbi request reprint Computerized tomography based on DEI refraction information
    Yi Sun
    Department of Electronics Engineering of Dalian University of Technology, Dalian, Liao Ning, PR China
    Comput Med Imaging Graph 31:383-9. 2007
    ..Using these two methods, two samples of weak absorption are reconstructed with the experimental data obtained at Beijing Synchrotron Radiation Facility (BSRF)...
  39. ncbi request reprint Does drug-target have a likeness?
    Xin Chen
    College of Life Science, Zhejiang University, Hangzhou, Zhejiang, PR China
    Methods Inf Med 46:360-6. 2007
    ..In this work, we propose that a disease-independent property of proteins, "drug-target likeness", can be explored to facilitate the genomic scale target screening in the post-genomic age...
  40. ncbi request reprint A modified PSO structure resulting in high exploration ability with convergence guaranteed
    Xin Chen
    Department of Electromechanical Engineering, Faculty of Science and Technology, University of Macau, Taipa, Macao SAR, China
    IEEE Trans Syst Man Cybern B Cybern 37:1271-89. 2007
    ..quot; Finally, a series of benchmarks is proposed to verify the feasibility of PSO-CREV...
  41. ncbi request reprint Learning position weight matrices from sequence and expression data
    Xin Chen
    School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
    Comput Syst Bioinformatics Conf 6:249-60. 2007
    ..These large-scale tests demonstrate that W-AlignACE is an effective tool for discovering TF binding sites from gene expression or ChIP-chip data and, in particular, has the ability to find very weak motifs...
  42. ncbi request reprint Learning the drug target-likeness of a protein
    Huan Xu
    College of Life Science, Zhejiang University, Zijinhua Road, Hangzhou, Zhejiang, P R China
    Proteomics 7:4255-63. 2007
    ....
  43. ncbi request reprint MSOAR: a high-throughput ortholog assignment system based on genome rearrangement
    Zheng Fu
    Department of Computer Science and Engineering, University of California, Riverside, California 92521, USA
    J Comput Biol 14:1160-75. 2007
    ..These test results indicate that our approach is very promising for genome-wide ortholog assignment. Supplemental material and MSOAR program are available at http://msoar.cs.ucr.edu...
  44. ncbi request reprint Performance of similarity measures in 2D fragment-based similarity searching: comparison of structural descriptors and similarity coefficients
    Xin Chen
    Computer Assisted Drug Discovery, Johnson and Johnson Pharmaceutical Research and Development, L L C, Raritan, New Jersey 08869, and Spring House, Pennsylvania 19477, USA
    J Chem Inf Comput Sci 42:1407-14. 2002
    ....