Xin Chen

Summary

Affiliation: University of California
Country: USA

Publications

  1. 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
  2. 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
  3. pmc Inactivation of Spry2 accelerates AKT-driven hepatocarcinogenesis via activation of MAPK and PKM2 pathways
    Chunmei Wang
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
    J Hepatol 57:577-83. 2012
  4. pmc Functional crosstalk between AKT/mTOR and Ras/MAPK pathways in hepatocarcinogenesis: implications for the treatment of human liver cancer
    Chunmei Wang
    Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, San Francisco, CA, USA
    Cell Cycle 12:1999-2010. 2013
  5. 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
  6. pmc Mapping environment-specific quantitative trait loci
    Xin Chen
    Department of Statistics, University of California, Riverside, California 92521, USA
    Genetics 186:1053-66. 2010
  7. pmc AKT (v-akt murine thymoma viral oncogene homolog 1) and N-Ras (neuroblastoma ras viral oncogene homolog) coactivation in the mouse liver promotes rapid carcinogenesis by way of mTOR (mammalian target of rapamycin complex 1), FOXM1 (forkhead box M1)/SKP2,
    Coral Ho
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
    Hepatology 55:833-45. 2012
  8. pmc Indian hedgehog regulates intestinal stem cell fate through epithelial-mesenchymal interactions during development
    Cynthia Kosinski
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA
    Gastroenterology 139:893-903. 2010
  9. 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
  10. pmc Oncogene-specific formation of chemoresistant murine hepatic cancer stem cells
    Edward Kai Hua Chow
    Department of Microbiology and Immunology, G W Hooper Research Foundation, University of California, San Francisco, CA 94143, USA
    Hepatology 56:1331-41. 2012

Collaborators

Detail Information

Publications40

  1. 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...
  2. 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...
  3. pmc Inactivation of Spry2 accelerates AKT-driven hepatocarcinogenesis via activation of MAPK and PKM2 pathways
    Chunmei Wang
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
    J Hepatol 57:577-83. 2012
    ..The goal of the present study was to investigate the eventual biochemical and genetic crosstalk between activated AKT and inactivation of Spry2 during liver cancer development by using in vivo and in vitro approaches...
  4. pmc Functional crosstalk between AKT/mTOR and Ras/MAPK pathways in hepatocarcinogenesis: implications for the treatment of human liver cancer
    Chunmei Wang
    Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, San Francisco, CA, USA
    Cell Cycle 12:1999-2010. 2013
    ....
  5. 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...
  6. pmc Mapping environment-specific quantitative trait loci
    Xin Chen
    Department of Statistics, University of California, Riverside, California 92521, USA
    Genetics 186:1053-66. 2010
    ..Only 1 marker had both the main and the Q × E interaction effects. Each of the other markers had either a main effect or a Q × E interaction effect but not both...
  7. pmc AKT (v-akt murine thymoma viral oncogene homolog 1) and N-Ras (neuroblastoma ras viral oncogene homolog) coactivation in the mouse liver promotes rapid carcinogenesis by way of mTOR (mammalian target of rapamycin complex 1), FOXM1 (forkhead box M1)/SKP2,
    Coral Ho
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
    Hepatology 55:833-45. 2012
    ....
  8. pmc Indian hedgehog regulates intestinal stem cell fate through epithelial-mesenchymal interactions during development
    Cynthia Kosinski
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA
    Gastroenterology 139:893-903. 2010
    ..We examined the role of Indian hedgehog (Ihh) in mesenchymal organization and the mechanisms by which perturbations in epithelial-mesenchymal interactions affect ISC fate...
  9. 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...
  10. pmc Oncogene-specific formation of chemoresistant murine hepatic cancer stem cells
    Edward Kai Hua Chow
    Department of Microbiology and Immunology, G W Hooper Research Foundation, University of California, San Francisco, CA 94143, USA
    Hepatology 56:1331-41. 2012
    ..Accordingly, SP cells and their tumor-initiating subset were more resistant than non-SP cells to chemotherapeutics that are effluxed by MDR1...
  11. 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)...
  12. doi request reprint A stochastic expectation and maximization algorithm for detecting quantitative trait-associated genes
    Haimao Zhan
    Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
    Bioinformatics 27:63-9. 2011
    ..The correlations between gene expressions and quantitative traits are essential for understanding the functions of genes and dissecting gene regulatory networks...
  13. 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...
  14. 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...
  15. 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...
  16. pmc Hydrodynamic transfection for generation of novel mouse models for liver cancer research
    Xin Chen
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California Liver Center, University of California, San Francisco, California Electronic address
    Am J Pathol 184:912-23. 2014
    ..Furthermore, it can be used as an in vivo transfection method to study biochemical cross talks among multiple pathways along hepatocarcinogenesis and to test the therapeutic potential of drugs against liver cancer...
  17. 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
    ....
  18. doi request reprint Amacrine-to-amacrine cell inhibition: Spatiotemporal properties of GABA and glycine pathways
    Xin Chen
    Department of Molecular and Cell Biology, University of California, Berkeley, USA
    Vis Neurosci 28:193-204. 2011
    ..Surprisingly, neither of these amacrine cell classes received sustained local GABAergic inhibition, commonly found in an earlier study of ganglion cells...
  19. 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...
  20. pmc TiProD: the Tissue-specific Promoter Database
    Xin Chen
    Centre of Bioinformatics, College of Life Sciences, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China
    Nucleic Acids Res 34:D104-7. 2006
    ..We have defined a measure for tissue-specificity that allows the user to discriminate between ubiquitously and specifically expressed genes. The database is accessible at http://tiprod.cbi.pku.edu.cn:8080/index.html...
  21. ncbi request reprint Deriving an ontology for human gene expression sources from the CYTOMER database on human organs and cell types
    Holger Michael
    Department of Bioinformatics, Faculty of Medicine, Georg August University Goettingen, Goldschmidtstr 1, D 37077 Goettingen, Germany
    In Silico Biol 5:61-6. 2005
    ..The ontology has been transferred to the OWL format and is freely available for download at http://cytomer/bioinf.med.uni-goettingen.de...
  22. 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...
  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. 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
    ....
  25. 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
    ....
  26. ncbi request reprint [IRE_FINDER-computational search of iron response element in human and mouse UTRs]
    Xin Chen
    College of Life Science, Peking University, Beijing 100871, China
    Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 34:743-7. 2002
    ..Here we use an improved computation method performing a comprehensive search of IRE in human and mouse genes. We try to catalog potential human and mouse IRE containing genes, at the same time identify potential U1A5 IREs...
  27. 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...
  28. 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...
  29. 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...
  30. 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
    ....
  31. 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...
  32. 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...
  33. 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
    ....
  34. 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...
  35. doi request reprint IGF-I (CA) repeat polymorphisms and risk of cancer: a meta-analysis
    Xin Chen
    Laboratory of Gene Function, School of Life Science, East China Normal University, Shanghai, People s Republic of China
    J Hum Genet 53:227-38. 2008
    ..However, a larger single study is required to further evaluate the association IGF-I (CA)19 polymorphisms and the cancer risk in a specific population...
  36. 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)...
  37. 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...
  38. 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...
  39. 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...
  40. ncbi request reprint Structure-based combinatorial library design: methodologies and applications
    Mary Pat Beavers
    Computer Assisted Drug Discovery, R W Johnson Pharmaceutical Research Institute, Raritan, NJ 08869, USA
    J Mol Graph Model 20:463-8. 2002
    ..Examples of the successful application of these methodologies are highlighted, demonstrating their performances within the practical drug discovery process...