Chun Ye

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Discovering tightly regulated and differentially expressed gene sets in whole genome expression data
    Chun Ye
    Bioinformatics Program, University of California San Diego, La Jolla, CA 92093 0404, USA
    Bioinformatics 23:e84-90. 2007
  2. pmc Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast
    Chun Ye
    Bioinformatics Program, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 5:e1000311. 2009
  3. pmc Orthologous repeats and mammalian phylogenetic inference
    Ali Bashir
    Bioinformatics Program, University of California San Diego, La Jolla, California 92093 0114, USA
    Genome Res 15:998-1006. 2005
  4. pmc Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches
    Jae Hoon Sul
    Computer Science Department, University of California, Los Angeles, California, USA
    PLoS Genet 9:e1003491. 2013
  5. ncbi request reprint Assessing computational tools for the discovery of transcription factor binding sites
    Martin Tompa
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:137-44. 2005
  6. ncbi request reprint Molecular evolution of growth hormone gene family in old world monkeys and hominoids
    Chun Ye
    Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
    Gene 350:183-92. 2005
  7. ncbi request reprint Independent origin of the growth hormone gene family in New World monkeys and Old World monkeys/hominoids
    Ying Li
    Laboratory of Molecular Evolution and Genome Diversity, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
    J Mol Endocrinol 35:399-409. 2005
  8. ncbi request reprint PKD1 inhibits cancer cells migration and invasion via Wnt signaling pathway in vitro
    Ke Zhang
    State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, and School of Life Science, Sichuan University, Chengdu 610041, China
    Cell Biochem Funct 25:767-74. 2007

Detail Information

Publications8

  1. ncbi request reprint Discovering tightly regulated and differentially expressed gene sets in whole genome expression data
    Chun Ye
    Bioinformatics Program, University of California San Diego, La Jolla, CA 92093 0404, USA
    Bioinformatics 23:e84-90. 2007
    ..We present a new method based on notions of tight regulation and differential expression to look for sets of genes which appear to be significantly affected by genetic variation...
  2. pmc Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast
    Chun Ye
    Bioinformatics Program, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 5:e1000311. 2009
    ..The software package implementing the algorithms discussed in this work is available as a MATLAB package upon request...
  3. pmc Orthologous repeats and mammalian phylogenetic inference
    Ali Bashir
    Bioinformatics Program, University of California San Diego, La Jolla, California 92093 0114, USA
    Genome Res 15:998-1006. 2005
    ..With rapid expansion of available partial sequence data, computational analysis of repetitive elements holds great promise for the future of phylogenetic inference...
  4. pmc Effectively identifying eQTLs from multiple tissues by combining mixed model and meta-analytic approaches
    Jae Hoon Sul
    Computer Science Department, University of California, Los Angeles, California, USA
    PLoS Genet 9:e1003491. 2013
    ..Additionally, our method provides an interpretation framework that accurately predicts whether an eQTL has an effect in a particular tissue...
  5. ncbi request reprint Assessing computational tools for the discovery of transcription factor binding sites
    Martin Tompa
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:137-44. 2005
    ..The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools...
  6. ncbi request reprint Molecular evolution of growth hormone gene family in old world monkeys and hominoids
    Chun Ye
    Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
    Gene 350:183-92. 2005
    ..Our results disclosed the complex history of the primate growth hormone gene family and raised intriguing questions on the consequences of these evolutionary events...
  7. ncbi request reprint Independent origin of the growth hormone gene family in New World monkeys and Old World monkeys/hominoids
    Ying Li
    Laboratory of Molecular Evolution and Genome Diversity, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
    J Mol Endocrinol 35:399-409. 2005
    ..Detailed analysis of the evolution of pseudogenes showed that the evolutionary pattern of this gene family in platyrrhines is in agreement with the so-called birth-and-death process...
  8. ncbi request reprint PKD1 inhibits cancer cells migration and invasion via Wnt signaling pathway in vitro
    Ke Zhang
    State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, and School of Life Science, Sichuan University, Chengdu 610041, China
    Cell Biochem Funct 25:767-74. 2007
    ..And we also showed that PC-1 regulated these processes in a process that may be at least partially through the Wnt pathway. Collectively, our data suggest that PKD1 may act as a novel member of the tumor suppressor family of genes...