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Structural and Computational Biology and Molecular Biophysics

Houston, Texas

A BCM research lab.
Structural and Computational Biology & Molecular Biophysics
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Rui Chen, Ph.D.

Rui Chen, Ph.D.

Assistant Professor, Department of Molecular and Human Genetics

Baylor College of Medicine


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 development biology and human diseases. Both experimental and computational approaches are used in combination to indentify and model gene functions in both human patients and modern organisms.

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 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 Stargardts'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 including mouse and Drosophilia melanogaster 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 to mimic human retinal diseases. Genetic, genomic, and biochemical approaches to decipher the molecular function of these genes are currently underway. In Drosophilia, 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 by RNA-Seq, comparative genomics at both DNA and mRNA level, and downstream target identification using ChlP-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 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

  • Nasser W, Santhanam B, Miranda ER, Parikh A, Juneja K, Rot G, Dinh C, Chen R, Zupan B, Shaulsky G and Kuspa A. Bacterial discrimination by dictyostelid amoebae reveals the complexity of ancient interspecies interactions. Curr Biol, 23(10):862-72 (2013). PubMed
  • Haase Gilbert E, Kwak SJ, Chen R and Mardon G. Drosophilia signal peptidase complex member Spase12 is required for development and cell differentiation. PLoS One, 8(4):e60908 (2013). PubMed
  • Huang Z, Chen K, Zhang J, Li Y, Wang H, Cui D, Tang J, Liu Y, Shi X, Li W, Liu D, Chen R, Sucgang RS and Pan X. A functional variomics tool for discovering drug-resistance genes and drug targets. Cell Rep, 3(2):577-85 (2013). PubMed
  • Zaneveld J, Wang F, Wang X and Chen R. Dawn of ocular gene therapy: implications for molecular diagnosis in retinal disease. Sci China Life Sci, 56(2):125-33 (2013). PubMed
  • Jusiak B, Abulimiti A, Haelterman N, Chen R and Mardon G. MAPK target sites of eyes absent are not required for eye development or survival in Drosophilia. PLoS One, 7(12):e50776 (2012). PubMed
  • Kriel A, Bittner AN, Kim SH, Liu K, Tehranchi AK, Zou WY, Rendon S, Chen R, Tu BP and Wang JD. Direct regulation of GTP homeostasis by (p)ppGpp: a critical component of viability and stress resistance. Mol Cell, 48(2):231-41 (2012). PubMed
  • Hawkins SM, Andreu-Vieyra CV, Kim TH, Jeong JW, Hodgson MC, Chen R, Creighton CJ, Lydon JP, Gunaratne PH, DeMayo FJ and Matzuk MM. Dysregulation of uterine signaling pathways in progesterone receptor-Cre knockout of dicer. Mol Endocrinol, 26(9):1552-66 (2012). PubMed

More Publications (PubMed)

Contact Information

Rui Chen, Ph.D.
Department: Human Genome Sequencing Center
Address: Baylor College of Medicine
One Baylor Plaza
Room N1519
Houston, TX, 77030, U.S.A.
Phone: 713-798-5194
Fax: 713-798-5741

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