Assistant Professor, Departments of Molecular and Human Genetics and Program in Developmental Biology

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

RESEARCH INTERESTS:

Our lab is broadly interested in studying and modeling the genetic networks underlying human ocular diseases and controlling vision development. Taking a system biology approach, both experimental and computational approaches are used in parallel to identify and model gene functions during retinal development in both human and model organisms.

Currently, our lab is focusing on identify novel genes involved in Leber congenital amaurosis (LCA) , the most common hereditary cause of visual impairment in infants and children. LCA is a set of inherited, early onset retinopathies that affect about 1 in 15,000 in the general U.S. population and account for more than five percent of all retinal dystrophies. Unfortunately, to date, no medical or surgical intervention has been shown to alter the natural course of LCA, nor has any pharmacologic therapy shown effect on modulating or moderating its progression. Currently, mutations in at least thirteen genes have been associated with recessive LCA, which account for about 63 percent of all cases. To clone additional LCA disease genes, in collaboration with Dr. James Lupski and Dr. Richard Lewis, we have collected DNA samples from 38 consanguineous Saudi Arabian and 80 North American families with recessive LCA. Currently, direct sequencing as well as whole genome linkage scan using the 300K SNP array platform is in progress for these families. So far, two novel disease loci have been identified and mutation identification using a candidate gene approach of these two loci is ongoing.

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. In Drosophila, a major effort in our laboratory is to understand the molecular mechanism of the early retinal cell fate determination process. Retinal cell fate determination is the early phase during fly eye development and only a handful genes (RD genes) are known to control this process. To better understand the underlying genetic network, microarray experiments were conducted to identify novel genes that function among or immediately downstream of the RD gene group. A combinatorial approach of comparative genomics, computational biology and genetic epistasis analysis is used to further identify potential direct downstream targets of the RD genes. In collaboration with Dr. Graeme Mardon, systematic modeling as well as direct experimental studies of the function of these genes is currently underway.

Finally, developing novel applications that take advantage of the new sequencing technologies, such as Solexa and 454, is another focus of our lab. The unparallel high throughput provided by these next generation sequencing tools provide unique opportunities for better understanding many fundamental questions in molecular biology and genetics. Currently, we are focusing on applying these technologies to understanding the molecular mechanism of gene regulation network during retinal development.

SELECTED PUBLICATIONS:

1. 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: 466-476.

2. Chen R, Mardon G (2005). Keeping an eye on the fly genome. Dev Biol. 282: 285-293.

3. Chen R, Sodergren E, Weinstock GM, Gibbs RA (2004). Dynamic Building of a BAC Clone Tiling Path for the Rat Genome Sequencing Project. Genome Res. 14: 679-684.

4. 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: 721-732. *co-author

5. Rat Genome Sequencing Project Consortium (2004). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493-521.

6. Pappu KS, Chen R, Middlebrooks BW, Woo C, Heberlein U, Mardon G (2003). Mechanism of hedgehog signaling during Drosophila eye development. Development 130: 3053-3062.

7. Chen R, Bouck JB, Weinstock GM, Gibbs RA (2001). Comparing Vertebrate Whole-Genome Shotgun Reads to the Human Genome. Genome Res. 11: 1807-1816.

8. Chen R, Halder G, Zhang Z, Mardon G (1999). Signaling by the TGF-b homolog decapentaplegic functions reiteratively within the network of genes controlling retinal cell fate determination in Drosophila. Development 126: 935-943.

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: 893-903.

For more publications, see listing on Pub Med.

CONTACT INFORMATION:

Rui Chen, Ph.D
Department of Molecular and Human Genetics
Baylor College of Medicine
One Baylor Plaza, Rm. N1519
Houston, Texas 77030, U.S.A.
Mail Stop: BCM226

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

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