R Chen

Summary

Affiliation: Texas Medical Center
Country: USA

Publications

  1. ncbi request reprint The DNA sequence, annotation and analysis of human chromosome 3
    Donna M Muzny
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 440:1194-8. 2006
  2. pmc Conserved developmental transcriptomes in evolutionarily divergent species
    Anup Parikh
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Genome Biol 11:R35. 2010
  3. pmc Integrated analysis of mutations, miRNA and mRNA expression in glioblastoma
    Hua Dong
    State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
    BMC Syst Biol 4:163. 2010
  4. pmc Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies
    Riccardo Papa
    Department of Biology, University of Puerto Rico Rio Piedras, San Juan, Puerto Rico
    BMC Genomics 9:345. 2008
  5. pmc Comparing vertebrate whole-genome shotgun reads to the human genome
    R Chen
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 11:1807-16. 2001
  6. pmc Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project
    Rui Chen
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 14:679-84. 2004
  7. ncbi request reprint Demonstration of dose-dependent global and regional cocaine-induced reductions in brain blood flow using a novel approach to quantitative single photon emission computerized tomography
    B Johnson
    Clinical Laboratory and Experimental Alcohol Research Center, University of Texas Health Science Center at Houston, USA
    Neuropsychopharmacology 18:377-84. 1998
  8. pmc Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution
    Stephen Richards
    Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas 77030, USA
    Genome Res 15:1-18. 2005
  9. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
  10. ncbi request reprint The finished DNA sequence of human chromosome 12
    Steven E Scherer
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 440:346-51. 2006

Detail Information

Publications28

  1. ncbi request reprint The DNA sequence, annotation and analysis of human chromosome 3
    Donna M Muzny
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 440:1194-8. 2006
    ....
  2. pmc Conserved developmental transcriptomes in evolutionarily divergent species
    Anup Parikh
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Genome Biol 11:R35. 2010
    ..The social amoebae Dictyostelium discoideum and Dictyostelium purpureum have similar developmental morphologies although their genomes are as divergent as those of man and jawed fish...
  3. pmc Integrated analysis of mutations, miRNA and mRNA expression in glioblastoma
    Hua Dong
    State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
    BMC Syst Biol 4:163. 2010
    ....
  4. pmc Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies
    Riccardo Papa
    Department of Biology, University of Puerto Rico Rio Piedras, San Juan, Puerto Rico
    BMC Genomics 9:345. 2008
    ..melpomene. To this end we have undertaken comparative mapping and targeted genomic sequencing in both species. This paper reports on a comparative analysis of genomic sequences linked to color pattern mimicry genes in Heliconius...
  5. pmc Comparing vertebrate whole-genome shotgun reads to the human genome
    R Chen
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 11:1807-16. 2001
    ..This approach can also be applied to other mammalian genomes for gene finding. These data predicted approximately 42,500 genes in the human, slightly more than reported previously...
  6. pmc Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project
    Rui Chen
    Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 14:679-84. 2004
    ..Combined with the assembled BAC fingerprint map, a set of BAC clones that covered >97% of the genome was identified and used in the RGSP...
  7. ncbi request reprint Demonstration of dose-dependent global and regional cocaine-induced reductions in brain blood flow using a novel approach to quantitative single photon emission computerized tomography
    B Johnson
    Clinical Laboratory and Experimental Alcohol Research Center, University of Texas Health Science Center at Houston, USA
    Neuropsychopharmacology 18:377-84. 1998
    ..Additionally, identifying the site-specific effects of cocaine provides targets for the development of putative therapeutic medications to attenuate or minimize ischemic stroke in cocaine addicts...
  8. pmc Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution
    Stephen Richards
    Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas 77030, USA
    Genome Res 15:1-18. 2005
    ..Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila...
  9. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  10. ncbi request reprint The finished DNA sequence of human chromosome 12
    Steven E Scherer
    Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 440:346-51. 2006
    ..The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents...
  11. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  12. ncbi request reprint A clone-array pooled shotgun strategy for sequencing large genomes
    W W Cai
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 11:1619-23. 2001
    ..It is immediately applicable to the sequencing of mouse, rat, zebrafish, and other important genomes, and can be managed in a cooperative fashion to take advantage of a distributed international DNA sequencing capacity...
  13. ncbi request reprint Keeping an eye on the fly genome
    Rui Chen
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Dev Biol 282:285-93. 2005
    ....
  14. pmc The Atlas genome assembly system
    Paul Havlak
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 14:721-32. 2004
    ..Atlas was used to assemble a draft DNA sequence of the rat genome; its major components including overlapper and split-scaffold are also being used in pure WGS projects...
  15. pmc High-throughput multiplex sequencing to discover copy number variants in Drosophila
    Bryce Daines
    Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Genetics 182:935-41. 2009
    ..The approach we describe is immediately applicable to the systematic exploration of copy number variation in model organisms and humans...
  16. ncbi request reprint Dual regulation and redundant function of two eye-specific enhancers of the Drosophila retinal determination gene dachshund
    Kartik S Pappu
    Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Development 132:2895-905. 2005
    ..Our results suggest that the two eye enhancers act redundantly and in concert with each other to integrate distinct upstream inputs and direct the eye-specific expression of dac...
  17. pmc Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless
    Edwin J Ostrin
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 16:466-76. 2006
    ..These results suggest that the integrated strategy of computational biology, genomics, and genetics is a powerful approach to identify direct downstream targets for any transcription factor genome-wide...
  18. ncbi request reprint Dachshund and eyes absent proteins form a complex and function synergistically to induce ectopic eye development in Drosophila
    R Chen
    Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, USA
    Cell 91:893-903. 1997
    ..We propose that a conserved regulatory network, rather than a linear hierarchy, controls retinal specification and involves multiple protein complexes that function during distinct steps of eye development...
  19. pmc Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing
    Hui Wang
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 20:981-8. 2010
    ..Introduction of this and other sequencing-based methods for mutation cloning will enable broader usage of forward genetics screens and have significant impacts in the field of model organisms such as Drosophila...
  20. ncbi request reprint Mechanism of hedgehog signaling during Drosophila eye development
    Kartik S Pappu
    Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
    Development 130:3053-62. 2003
    ..Moreover, while the effects of Hh are primarily concentration dependent in other tissues, hh signaling in the eye acts as a binary switch to initiate retinal morphogenesis by inducing expression of the tissue-specific factor Eya...
  21. pmc High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies
    Anjana Srivatsan
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
    PLoS Genet 4:e1000139. 2008
    ....
  22. pmc The DNA sequence of the human X chromosome
    Mark T Ross
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 434:325-37. 2005
    ..Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence...
  23. ncbi request reprint Genetic analysis in patients with left ventricular noncompaction and evidence for genetic heterogeneity
    Yanlin Xing
    Department of Pediatrics, Toyama Medical and Pharmaceutical University, 2630 Sugitani, Toyama 930 0194, Japan
    Mol Genet Metab 88:71-7. 2006
    ..LVNC, like other forms of inherited cardiomyopathy, is a genetically heterogeneous disease, associated with variable clinical symptoms and can be inherited as an autosomal or X-linked recessive disorder...
  24. ncbi request reprint [Osteocalcin and type I collagen mRNA expression of rat marrow stromal cells under induction condition]
    Huaiqing Chen
    Institute of Biomedical Engineering, West China Medical Center, Sichuan University, Chengdu 610041, China
    Hua Xi Yi Ke Da Xue Xue Bao 33:200-3. 2002
    ..To investigate osteocalcin and type I collagen mRNA expression of rat marrow stromal cells under induction condition...
  25. ncbi request reprint Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring
    Jacek P Dworzanski
    Geo Centers, Inc, Aberdeen Proving Ground, Maryland 21010 0068, USA
    Anal Chem 76:2355-66. 2004
    ....
  26. ncbi request reprint Identification and functional characterization of JWA polymorphisms and their association with risk of gastric cancer and esophageal squamous cell carcinoma in a Chinese population
    Wei Yan Tang
    Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, China
    J Toxicol Environ Health A 70:885-94. 2007
    ..Further studies are needed to substantiate the biological significance and related mechanisms underlying the associations...
  27. ncbi request reprint Mass spectrometry-based proteomics combined with bioinformatic tools for bacterial classification
    Jacek P Dworzanski
    Geo Centers, Inc, Aberdeen Proving Ground, Maryland 21010 0068, USA
    J Proteome Res 5:76-87. 2006
    ..It is shown that, if a sufficient amount of sequence information is obtained from the MS/MS experiments, a bacterial sample can be classified to a strain level by using this proteomics method, leading to its positive identification...
  28. pmc Simultaneous detection of microsatellite repeats and SNPs in the macrophage migration inhibitory factor (MIF) gene by thin-film biosensor chips and application to rural field studies
    Xiao bo Zhong
    Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
    Nucleic Acids Res 33:e121. 2005
    ..We also present data supporting significant population stratification of the low- versus high-expression forms of MIF that may bear on the role of this gene in infectious diseases...

Research Grants9

  1. Genome-wide Dissection of the Retinal Determination Network
    Rui Chen; Fiscal Year: 2007
    ..Since both ey and many of its downstream genes are highly conserved in humans and many developmental parallels exist between Drosophila and mammalian retina, this work will directly impact our understanding of human retinal development. ..
  2. Genome-wide Dissection of the Retinal Determination Network
    Rui Chen; Fiscal Year: 2009
    ....
  3. Genetics of Early Onset Retinal Diseases
    Rui Chen; Fiscal Year: 2010
    ....
  4. Genetics of Early Onset Retinal Diseases
    Rui Chen; Fiscal Year: 2011
    ....