skip to content »

Molecular and Human Genetics

Houston, Texas

Department of Molecular and Human Genetics
Department of Molecular and Human Genetics
not shown on screen

Rui Chen, Ph.D.

Rui Chen, Ph.D.

Associate Professor of Molecular and Human Genetics

Other Positions

Associate Professor, Program in Developmental Biology


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

Research Interests

Our lab focuses on understanding the molecular mechanisms underlying human diseases. Both experimental and computational approaches are used in combination to identify and model gene functions in both human patients and model organisms.

Identification of human retinal disease genes

Collectively, ocular diseases affect large population in the world with 40 million people are blind and another 100 million with substantial visual impairment. Together with our collaborators, we are currently working on identifying genes involved in several human retinal diseases, such as Leber congenital amaurosis (LCA), Usher syndrome, retinitis pigmentosa (RP), cone and rod dystrophy, and Stargardt’s disease. Recently, we have cloned three novel human retinal disease genes, including Spata7, Cep164, and NMNAT1. 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 coupled with functional analysis to these patient samples.

Animal models for retinal disease and development

Model organisms such as mouse are useful tools to understand molecular mechanism of diseases and also identify genetic networks controlling retinal development. Using mouse as the model organism, we have recently generated numerous mouse models for the novel disease genes identified by our group that mimic human retinal diseases. Genetic, genomic, and biochemical approaches to decipher the molecular function of these genes are currently underway.

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. Wang X, Wang H, Sun V, Tuan HF, Keser V, Wang K, Ren H, Lopez I, Zaneveld JE, Siddiqui S, Bowles S, Khan A, Salvo J, Jacobson SG, Iannaccone A, Wang F, Birch D, Heckenlively JR, Fishman GA, Traboulsi EI, Li Y, Wheaton D, Koenekoop RK, Chen R (2013). Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing. J. Med. Genet. 50(10): 674-88. PubMed PMID: 23847139
  2. Li Y, Jiang Y, Chen Y, Karandikar U, Hoffman K, Chattopadhyay A, Mardon G, Chen R (2013). optix functions as a link between the retinal determination network and the dpp pathway to control morphogenetic furrow progression in Drosophila. Dev. Biol. 381(1): 50-61. PubMed PMID: 23792115
  3. 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; Finding of Rare Disease Genes (FORGE) Canada Consortium, 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. Nat. Genet. 44(9): 1035-9. PubMed PMID: 22842230
  4. 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. Mol. Vis. 17: 3529-40. PubMed PMID: 22219648
  5. 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. Hum. Mutat. 32(12): 1450-9. PubMed PMID: 21901789
  6. 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 Res. 21(2): 315-24. PubMed PMID: 21177959
  7. 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 Res. 20(7): 981-8. PubMed PMID: 20472684
  8. 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. PubMed PMID: 19528327
  9. 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. PubMed PMID: 19268277

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 this page to a friend