Rui Chen, Ph.D.

Visiting Professor

(713) 798-5194

Email

ruichen@bcm.edu

Positions

Visiting Professor: Molecular and Human Genetics
Baylor College of Medicine

Joint Professor: HGSC:Faculty-General/Basic
Baylor College of Medicine
Houston, TX, US

Professor: Ophthalmology
University of California Irvine
Irvine, California, United States

Education

BS from Tsinghua University: 01/1994 - Beijing, China, People's Rep

PhD from Baylor College Of Medicine: 01/1999 - Houston, TX, United States

Post-Doctoral Fellowship at Baylor College Of Medicine: 01/2002 - Houston, United States

Professional Statement

With over 30 million variants in the human genome, which ones are important? Through the lens of human variation and diseases, we focus on advancing our ability to identify, assess, and predict variants with functional consequences using an interdisciplinary approach.

The Chen lab uses innovative genetics and genomics, single cell omics, computational, and imaging tools to understand the connection between genetic variants and human diseases, using the visual system as the model.

We pursue these goals in the following areas:
• Identify genes and mutations underlying human diseases.
• Systematically predict and assess the function consequence of genetic variants across the genome.
• Investigate the changes in transcriptome and epigenome during development and under disease condition at single-cell resolution.
• Develop novel therapeutics, including gene therapy, genome editing, and neural regeneration, for treating the diseases.

Genetics of disease
Genetics plays important role in human visual disorders that affect more than 30 million people in the United States alone. The Chen lab aims at characterizing the genetic factors underlying the neural degenerative diseases in the human visual system, including both the inherited to age related retinal degenerative diseases. A combination of next generation sequencing, single cell omics, patient derived iPSC and retinal organoid, mice and non human primate models, and machine learning and deep learning technologies are used.

Single cell omics
The Chen lab is leading the effort of the constructing the cell atlas of the visual system as part of the Human Cell Atlas (HCA) project (https://www.humancellatlas.org/biological-networks/). Building on this foundation, we aim at gaining insights of the development and the disease of the visual system as the single cell resolution.

Therapeutics
The Chen lab is applying what has been learnt from the genetics to develop novel therapeutics treating human retinal degenerative diseases.

Websites

VIICTR Publications List

Department of Molecular and Human Genetics

Welcome to visit our lab webpage

BCM lab page

Selected Publications

Liang Q, Dharmat R, Owen L, Shakoor A, Li Y, Kim S, Vitale A, Kim I, Morgan D, Liang S, Wu N, Chen K, DeAngelis MM, Chen R. " Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling.. " Nat Commun.. 2019 ; 10 : 5743.
Moshiri A, Chen R, Kim S, Harris RA, Li Y, Raveendran M, Davis S, Liang Q, Pomerantz O, Wang J, Garzel L, Cameron A, Yiu G, Stout JT, Huang Y, Murphy CJ, Roberts J, Gopalakrishna KN, Boyd K, Artemyev NO, Rogers J, Thomasy SM. " A nonhuman primate model of inherited retinal disease " J Clin Invest. 2019 Feb 1; 129 (2) : 863-874.
Pubmed PMID: 30667376.
Kim S, Lowe A, Dharmat R, Lee S, Owen LA, Wang J, Shakoor A, Li Y, Morgan DJ, Hejazi AA, Cvekl A, DeAngelis MM, Zhou ZJ, Chen R*, Liu W. " Generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids. " Proc Natl Acad Sci U S A. 2019 May 28; 116 (22) : 10824-10833.
Pubmed PMID: 31072937.
Jun Wang, Li Zhao, Xia Wang, Yong Chen, Mingchu Xu, Zachry T. Soens, Zhongqi Ge, Peter Ronghan Wang, Fei Wang and Rui Chen. " GRIPT: a novel case-control analysis method for Mendelian disease gene discovery " Genome Biology. 2018 ; 19 : 203.
Pubmed PMID: 30477545.
Dharmat R, Eblimit A, Robichaux MA, Zhang Z, Nguyen TT, Jung SY, He F, Jain A, Li Y, Qin J, Overbeek P, Roepman R, Mardon G, Wensel TG, Chen R. " SPATA7 maintains a novel photoreceptor-specific zone in the distal connecting cilium. " J Cell Biol. 2018 Aug 6; 217 (2851-2865)
Pubmed PMID: 29899041.
Xu M, Xie YA, Abouzeid H, Gordon CT, Fiorentino A, Sun Z, (…), Chen R, Allikmets R, Schorderet DF. " Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies. " Am J Hum Genet. 2017 Aug 6; 217 (8) : 2851-2865.
Pubmed PMID: 28285769.
Li Zhao, Yiyun Chen, Amol Onkar Bajaj, Aiden Eblimit, Mingchu Xu, Zachry T. Soens, Feng Wang, Zhongqi Ge, Sung Yun Jung, Feng He, Yumei Li, Theodore G. Wensel, Jun Qin, Rui Chen. " Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes. " Genome Research. 2016 May ; 26 (5) : 660-9.
Pubmed PMID: 26912414.
Arno G, Agrawal SA, Eblimit A, Bellingham J, Xu M, Wang F, Chakarova C, Parfitt DA, (...), Chen R. " Mutations in REEP6 Cause Autosomal-Recessive Retinitis Pigmentosa. " Am J Hum Genet. 2016 Dec 1; 99 (6) : 1305-1315.
Pubmed PMID: 27889058.
Koenekoop RK, Wang H, Majewski J, Wang X, ...; 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. " Mutations in NMNAT1 cause Leber congenital amaurosis and identify a new disease pathway for retinal degeneration " Nat Genet. 2012 Sep ; 44 (9) : 1035-9.
Pubmed PMID: 22842230.
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. " Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa " Am J Hum Genet. 2009 Mar ; 84 (3) : 380-7.
Pubmed PMID: 19268277.