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Rui Chen, Ph.D.

Associate Professor, Department of Molecular and Human Genetics

image: Rui Chen, Ph.D.Contact information


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 populations in the world with 40 million people who 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, Cep164and NMNAT1In 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 understanding molecular mechanism of diseases and identifying 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.


Mutations in PNPLA6 are linked to photoreceptor degeneration and various forms of childhood blindness., Kmoch, S., Majewski J., Ramamurthy V., Cao S., Fahiminiya S., Ren H., MacDonald I. M., Lopez I., Sun V., Keser V., et al. , Nature communications, 2015, Volume 6, p.5614, (2015) Abstract
Next-generation sequencing and novel variant determination in a cohort of 92 familial exudative vitreoretinopathy patients., Salvo, Jason, Lyubasyuk Vera, Xu Mingchu, Wang Hui, Wang Feng, Nguyen Duy, Wang Keqing, Luo Hongrong, Wen Cindy, Shi Catherine, et al. , Investigative ophthalmology & visual science, 2015, Volume 56, Issue 3, p.1937-46, (2015) Abstract
CRISPR-engineered mosaicism rapidly reveals that loss of Kcnj13 function in mice mimics human disease phenotypes., Zhong, Hua, Chen Yiyun, Li Yumei, Chen Rui, and Mardon Graeme , Scientific reports, 2015, Volume 5, p.8366, (2015) Abstract
Whole exome sequencing confirms the clinical diagnosis of Marfan syndrome combined with X-linked hypophosphatemia., Sheng, Xunlun, Chen Xue, Lei Bo, Chen Rui, Wang Hui, Zhang Fangxia, Rong Weining, Ha Ruoshui, Liu Yani, Zhao Feng, et al. , Journal of translational medicine, 2015, Volume 13, p.179, (2015) Abstract
Comprehensive molecular diagnosis of 67 Chinese Usher syndrome probands: high rate of ethnicity specific mutations in Chinese USH patients., Jiang, Lichun, Liang Xiaofang, Li Yumei, Wang Jing, Zaneveld Jacques Eric, Wang Hui, Xu Shan, Wang Keqing, Wang Binbin, Chen Rui, et al. , Orphanet journal of rare diseases, 2015, Volume 10, Issue 1, p.110, (2015) Abstract
FlyVar: a database for genetic variation in Drosophila melanogaster., Wang, Fei, Jiang Lichun, Chen Yong, Haelterman Nele A., Bellen Hugo J., and Chen Rui , Database : the journal of biological databases and curation, 2015, Volume 2015, (2015) Abstract
NGS-based Molecular diagnosis of 105 eyeGENE(®) probands with Retinitis Pigmentosa., Ge, Zhongqi, Bowles Kristen, Goetz Kerry, Scholl Hendrik P. N., Wang Feng, Wang Xinjing, Xu Shan, Wang Keqing, Wang Hui, and Chen Rui , Scientific reports, 2015, Volume 5, p.18287, (2015) Abstract
Comprehensive analysis of patients with Stargardt macular dystrophy reveals new genotype-phenotype correlations and unexpected diagnostic revisions., Zaneveld, Jacques, Siddiqui Sorath, Li Huajin, Wang Xia, Wang Hui, Wang Keqing, Li Hui, Ren Huanan, Lopez Irma, Dorfman Allison, et al. , Genetics in medicine : official journal of the American College of Medical Genetics, 2015 Apr, Volume 17, Issue 4, p.262-70, (2015) Abstract
ABCF1 extrinsically regulates retinal pigment epithelial cell phagocytosis., Guo, Feiye, Ding Ying, Caberoy Nora, Alvarado Gabriela, Wang Feng, Chen Rui, and Li Wei , Molecular biology of the cell, 2015 Apr 22, (2015) Abstract
ADIPOR1 is Mutated in Syndromic Retinitis Pigmentosa., Xu, Mingchu, Eblimit Aiden, Wang Jing, Li Jianli, Wang Feng, Zhao Li, Wang Xia, Xiao Ningna, Li Yumei, Wong Lee-Jun C., et al. , Human mutation, 2015 Dec 12, (2015) Abstract
Comprehensive Molecular Diagnosis of a Large Chinese Leber Congenital Amaurosis Cohort., Wang, Hui, Wang Xia, Zou Xuan, Xu Shan, Li Hui, Soens Zachry Tore, Wang Keqing, Li Yumei, Dong Fangtian, Chen Rui, et al. , Investigative ophthalmology & visual science, 2015 Jun, Volume 56, Issue 6, p.3642-55, (2015) Abstract
FOXO1 is Required for Binding of PR on IRF4, Novel Transcriptional Regulator of Endometrial Stromal Decidualization., Vasquez, Yasmin M., Mazur Erik C., Li Xilong, Kommagani Ramakrishna, Jiang Lichun, Chen Rui, Lanz Rainer B., Kovanci Ertug, Gibbons William E., and DeMayo Francesco J. , Molecular endocrinology (Baltimore, Md.), 2015 Mar, Volume 29, Issue 3, p.421-33, (2015) Abstract
Hemichordate genomes and deuterostome origins., Simakov, Oleg, Kawashima Takeshi, Marlétaz Ferdinand, Jenkins Jerry, Koyanagi Ryo, Mitros Therese, Hisata Kanako, Bredeson Jessen, Shoguchi Eiichi, Gyoja Fuki, et al. , Nature, 2015 Nov 26, Volume 527, Issue 7579, p.459-65, (2015) Abstract
Mutations in human IFT140 cause non-syndromic retinal degeneration., Xu, Mingchu, Yang Lizhu, Wang Feng, Li Huajin, Wang Xia, Wang Weichen, Ge Zhongqi, Wang Keqing, Zhao Li, Li Hui, et al. , Human genetics, 2015 Oct, Volume 134, Issue 10, p.1069-78, (2015) Abstract
Regulation of Drosophila eye development by the transcription factor Sine oculis., Jusiak, Barbara, Karandikar Umesh C., Kwak Su-Jin, Wang Feng, Wang Hui, Chen Rui, and Mardon Graeme , PloS one, 2014, Volume 9, Issue 2, p.e89695, (2014) Abstract
Drosophila eyes absent is required for normal cone and pigment cell development., Karandikar, Umesh C., Jin Meng, Jusiak Barbara, Kwak SuJin, Chen Rui, and Mardon Graeme , PloS one, 2014, Volume 9, Issue 7, p.e102143, (2014) Abstract
Genome-wide DNA binding pattern of the homeodomain transcription factor Sine oculis (So) in the developing eye of Drosophila melanogaster., Jusiak, Barbara, Wang Feng, Karandikar Umesh C., Kwak Su-Jin, Wang Hui, Chen Rui, and Mardon Graeme , Genomics data, 2014 Dec 1, Volume 2, p.153-155, (2014) Abstract
A homozygous missense mutation in NEUROD1 is associated with non-syndromic autosomal recessive retinitis pigmentosa., Wang, Feng, Li Huajin, Xu Mingchu, Li Hui, Zhao Li, Yang Lizhu, Zaneveld Jacques E., Wang Keqing, Li Yumei, Sui Ruifang, et al. , Investigative ophthalmology & visual science, 2014 Dec 4, (2014) Abstract
Onset of atonal expression in Drosophila retinal progenitors involves redundant and synergistic contributions of Ey/Pax6 and So binding sites within two distant enhancers., Zhou, Qingxiang, Zhang Tianyi, Jemc Jennifer C., Chen Yiyun, Chen Rui, Rebay Ilaria, and Pignoni Francesca , Developmental biology, 2014 Feb 1, Volume 386, Issue 1, p.152-64, (2014) Abstract
Large conserved domains of low DNA methylation maintained by Dnmt3a., Jeong, Mira, Sun Deqiang, Luo Min, Huang Yun, Challen Grant A., Rodriguez Benjamin, Zhang Xiaotian, Chavez Lukas, Wang Hui, Hannah Rebecca, et al. , Nature genetics, 2014 Jan, Volume 46, Issue 1, p.17-23, (2014) Abstract
Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements., Wang, Feng, Wang Hui, Tuan Han-Fang, Nguyen Duy H., Sun Vincent, Keser Vafa, Bowne Sara J., Sullivan Lori S., Luo Hongrong, Zhao Ling, et al. , Human genetics, 2014 Mar, Volume 133, Issue 3, p.331-45, (2014) Abstract
Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal., Sun, Deqiang, Luo Min, Jeong Mira, Rodriguez Benjamin, Xia Zheng, Hannah Rebecca, Wang Hui, Le Thuc, Faull Kym F., Chen Rui, et al. , Cell stem cell, 2014 May 1, Volume 14, Issue 5, p.673-88, (2014) Abstract
Large-scale identification of chemically induced mutations in Drosophila melanogaster., Haelterman, Nele A., Jiang Lichun, Li Yumei, Bayat Vafa, Sandoval Hector, Ugur Berrak, Tan Kai Li, Zhang Ke, Bei Danqing, Xiong Bo, et al. , Genome research, 2014 Oct, Volume 24, Issue 10, p.1707-18, (2014) Abstract
A missense mutation in HK1 leads to autosomal dominant retinitis pigmentosa., Wang, Feng, Wang Yandong, Zhang Bin, Zhao Li, Lyubasyuk Vera, Wang Keqing, Xu Mingchu, Li Yumei, Wu Frances, Wen Cindy, et al. , Investigative ophthalmology & visual science, 2014 Oct 14, (2014) Abstract
A Drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases., Yamamoto, Shinya, Jaiswal Manish, Charng Wu-Lin, Gambin Tomasz, Karaca Ender, Mirzaa Ghayda, Wiszniewski Wojciech, Sandoval Hector, Haelterman Nele A., Xiong Bo, et al. , Cell, 2014 Sep 25, Volume 159, Issue 1, p.200-14, (2014) Abstract

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