Rui Chen

Dr. Rui Chen



Associate Professor, Baylor College of Medicine

B.S., Tsinghua University, 1994
Ph.D., Baylor College of Medicine, 1999
Postdoc, Baylor College of Medicine, 2000-02

Functional genomics of visual system development and diseases; High throughput technology

Our lab is broadly interested in developing and applying genomic technologies to understand the genetic networking underlying developmental 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 a large population; 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, mutations in which lead to LCA and RP. In addition, several novel disease loci have been mapped in our patient collection. To identify the mutations 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 a significant contribution to our understanding of 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 is specific for the NextGen technology has been developed among our laboratory and our 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

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 Research 16:466-476.

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 Genetics 4:e1000139.

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. American Journal of Human Genetics 84:380-387.

Daines B, Wang H, Li Y, Han Y, Gibbs R, Chen R (2009) High-throughput multiplex sequencing to discover copy number variants in Drosophila. Genetics 182:935-941.

Wang H, Chattopadhyay A, Li Z, Daines B, Li Y, Gao C, Gibbs R, Zhang K, Chen R (2010) Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Research 20:981-988.

Daines B, Wang H, Wang L, Li Y, Han Y, Emmert D, Gelbart W, Wang X, Li W, Gibbs R, Chen R (2011) The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Research 21:315-324.

Wang H, Chen X, Dudinsky L, Patenia C, Chen Y, Li Y, Wei Y, Abboud EB, Al-Rajhi AA, Lewis RA, Lupski JR, Mardon G, Gibbs RA, Perkins BD, Chen R (2011) Exome capture sequencing identifies a novel mutation in BBS4. Molecular Vision 17:3529-3540.

Wang X, Wang H, Cao M, Li Z, Chen X, Patenia C, Gore A, Abboud EB, Al-Rajhi AA, Lewis RA, Lupski JR, Mardon G, Zhang K, Muzny D, Gibbs RA, Chen R (2011) Whole-exome sequencing identifies ALMS1, IQCB1, CNGA3, and MYO7A mutations in patients with Leber congenital amaurosis. Human Mutation 32:1450-1459.

Koenekoop RK, Wang H, Majewski J, Wang X, Lopez I, Ren H, Chen Y, Li Y, Fishman GA, Genead M, Schwartzentruber J, Solanki N, Traboulsi EI, Cheng J, Logan CV, McKibbin M, Hayward BE, Parry DA, Johnson CA, Nageeb M, Poulter JA, Mohamed MD, Jafri H, Rashid Y, Taylor GR, Keser V, Mardon G, Xu H, Inglehearn CF, Fu Q, Toomes C, Chen R (2012) Mutations in NMNAT1 cause Leber congenital amaurosis and identify a new disease pathway for retinal degeneration. Nature Genetics 44:1035-1039.

Contact Information

Rui Chen, Ph.D.

Department of Molecular and Human Genetics
Baylor College of Medicine
One Baylor Plaza N1519
Houston, Texas 77030, U.S.A.

Tel: (713) 798-5194
Fax: (713) 798-5741

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