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Molecular and Human Genetics

Houston, Texas

Department of Molecular and Human Genetics
Department of Molecular and Human Genetics
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Rui Chen, Ph.D.

Rui Chen, Ph.D.

Assistant Professor, Department of Molecular and Human Genetics

Other Positions

Assistant Professor, Program in Developmental Biology

Education

B.S., Tsinghua University, 1994
Ph.D., Baylor College of Medicine, 1999
Postdoc, Baylor College of Medicine, 2002

Research Interests

Our lab is broadly interested in developing and applying genomic technologies to understand the genetic networking underlying development biology and human diseases. Both experimental and computational approaches are used in combination to identify and model gene functions in both human patients and model organisms, including Drosophila and mice.

Identification of human retinal disease genes

One of the main focuses in our laboratory is to understand the molecular mechanism underlying human retinal disease. Collectively, ocular diseases affect large population with approximately 40 million people in the world are blind and another 100 million have substantial visual impairment. Together with our collaborators, we are currently working on identifying disease genes involved in several human retinal diseases, including Leber congenital amaurosis (LCA), Usher syndrome, retinitis pigmentosa (RP), and AMD. Recently, we have cloned Spata7 as a novel human retinal disease gene, whose mutations lead to LCA and RP. In addition, several novel disease loci have been mapped in our patient collection. To identify the mutation in these loci, we are applying the cutting edge NextGen sequencing technologies to perform both targeted and whole genome sequencing on these patient DNA samples.

Animal models for retinal disease and development

Model organisms including mouse and Drosophila melanogaster are useful tools to understand molecular mechanism of diseases and also identify genetic networks that control retinal development. Using mouse as the model organism, we have recently generated numerous knock out mice that mimic human retinal diseases. Genetic, genomic, and biochemical approaches to decipher the molecular function of these genes are currently underway. In Drosophila, a major effort in our laboratory is to understand the molecular mechanism of the early retinal cell fate determination process. A genome-wide, combinatorial approach, including gene expression profiling with both microarray and mRNA-Seq, comparative genomics at both DNA and mRNA level, and downstream target identification using ChIP-Seq, has been adopted. Strikingly, our data suggests a highly connected, dynamic genetic network. Further characterization as well as experimental validation and testing of the network will likely to provide significant contribution to our understanding the genetic mechanisms controlling retinal development in general.

Genomic technology development and applications

Introduction of new technologies often leads to breakthrough of scientific discoveries. Recently, the most exciting novel technology in molecular and genomic biology is the Next generation sequencing. To fully utilize this in our research, a set of protocols and software tools that specific for the NextGen technology have been developed among our laboratory and the collaborators, including RNA-Seq, miRNA-Seq, CNV-Seq, ChIP-Seq, chromatin profiling, and mutation detection. Currently, we are applying these tools to various research fields, including development, genetic disease gene cloning, and cancer biology.

Selected Publications

  1. Daines D, Wang H, Li Y, Han Y, Gibbs RA, Chen R (2009). High-throughput Multiplex Sequencing to Discover Copy Number Variants in Drosophila. Genetics 182(4): 935-41. [Pub Med]
  2. Wang H, den Hollander AI, Moayedi Y, Abulimiti A, Li Y, Collin RW, Hoyng CB, Lopez I, Bray M, Lewis RA, Lupski JR, Mardon G, Koenekoop RK, Chen R (2009). Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa. Am. J. Hum. Genet. 84(3): 380-7. [Pub Med]
  3. Li Y, Wang H, Peng J, Gibbs RA, Lewis RA, Lupski JR, Mardon G, Chen R (2009). Mutation survey of known LCA genes and loci in the Saudi Arabian population. Invest. Ophthalmol. Vis. Sci. 50(3): 1336-43. [Pub Med]
  4. Srivatsan A, Han Y, Peng J, Tehranchi AK, Gibbs R, Wang JD, Chen R (2008). High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet. 4(8): e1000139. [Pub Med]
  5. Ostrin EJ, Li Y, Hoffman K, Liu J, Wang K, Zhang L, Mardon G, Chen R (2006). Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless. Genome Res. 16(4): 466-76. [Pub Med]
  6. Havlak P, Chen R*, Durbin KJ, Egan A, Ren Y, Song XZ, Weinstock GM, Gibbs RA (2004). The Atlas Genome Assembly System. Genome Res. 14(4): 721-32. *Co-author [Pub Med]
  7. Rat Genome Sequencing Project Consortium (2004). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428(6982): 493-521. [Pub Med]
  8. Chen R, Bouck JB, Weinstock GM, Gibbs RA (2001). Comparing Vertebrate Whole-Genome Shotgun Reads to the Human Genome. Genome Res. 11(11): 1807-16. [Pub Med]
  9. Chen R, Amoui M, Zhang Z, Mardon G (1997). Dachshund and Eyes Absent Proteins Form a Complex and Function Synergistically To Induce Ectopic Eye Development in Drosophila. Cell 91(7): 893-903. [Pub Med]

More Publications (PubMed)

Contact Information

Rui Chen, Ph.D.
Human Genome Sequencing Center
Baylor College of Medicine
One Baylor Plaza, MS BCM226
Houston, TX, 77030, U.S.A.

Phone: 713-798-5194
Fax: 713-798-5741
E-mail:

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