Rui Chen
Professor, Ophthalmology
School of Medicine
School of Medicine
Ph.D., Baylor College of Medicine, 1999, Developmental Biology and Genetics
University of California, Irvine
5141 California Avenue
Room 245
Irvine, CA 92697
5141 California Avenue
Room 245
Irvine, CA 92697
Research Interests
Genomics, Single Cell Omics, Visual System, Gene Therapy
Websites
Research Abstract
We pursue the goals in the following areas:
1) Identify genes and mutations underlying human diseases.
2) Systematically predict and assess the function consequence of genetic variants across the genome.
3) Investigate the changes in transcriptome and epigenome during development and under disease condition at single-cell resolution.
4) Develop novel therapeutics, including gene therapy, genome editing, and neural regeneration, for treating the diseases.
1) Identify genes and mutations underlying human diseases.
2) Systematically predict and assess the function consequence of genetic variants across the genome.
3) Investigate the changes in transcriptome and epigenome during development and under disease condition at single-cell resolution.
4) Develop novel therapeutics, including gene therapy, genome editing, and neural regeneration, for treating the diseases.
Short Biography
Dr. Chen, a professor at the Gavin Herbert Eye Institute - Center for Translational Vision Research in the department of Ophthalmology at University of California, Irvine. His research utilizes genetics, genomics, model systems, and bioinformatics to unravel the genetic basis of human retinal diseases. Additionally, Dr. Chen is leading the effort of creating the human eye's single-cell atlas for the Human Cell Atlas project, employing cutting-edge single-cell omics and spatial transcriptomics technologies.
Publications
Zuo Z, Cheng X, Ferdous S, Shao J, Li J, Bao Y, Li J, Lu J, Jacobo Lopez A, Wohlschlegel J, Prieve A, Thomas MG, Reh TA, Li Y, Moshiri A, Chen R. Single cell dual-omic atlas of the human developing retina. Nat Commun. 2024 Aug 9;15(1):6792. doi: 10.1038/s41467-024-50853-5. PMID: 39117640; PMCID: PMC11310509
Li J, Choi J, Cheng X, Ma J, Pema S, Sanes JR, Mardon G, Frankfort BJ, Tran NM, Li Y, Chen R. Comprehensive single-cell atlas of the mouse retina. iScience. 2024 May 8;27(6):109916. doi: 10.1016/j.isci.2024.109916. PMID: 38812536; PMCID: PMC11134544.
Wang J, Wang M, Moshiri A, Harris RA, Raveendran M, Nguyen T, Kim S, Young L, Wang K, Wiseman R, O'Connor DH, Johnson Z, Martinez M, Montague MJ, Sayers K, Lyke M, Vallender E, Stout T, Li Y, Thomasy SM, Rogers J, Chen R. Genetic diversity of 1,845 rhesus macaques improves genetic variation interpretation and identifies disease models. Nat Commun. 2024 Jul 5;15(1):5658. doi: 10.1038/s41467-024-49922-6. PMID: 38969634; PMCID: PMC11226599.
Jun Wang, Xuesen Cheng, Qingnan Liang, Leah A. Owen, Jiaxiong Lu, Yiqiao Zheng, Meng Wang, Shiming Chen, Margaret M. DeAngelis, Yumei Li, Rui Chen Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation Genome Biology, 2023 DOI : 10.1186/s13059-023-03111-8
Choi J, Li J, Ferdous S, Liang Q, Moffitt JR, Chen R. Spatial organization of the mouse retina at single cell resolution by MERFISH. Nat Commun. 2023 Aug 15;14(1):4929. doi: 10.1038/s41467-023-40674-3. PMID: 37582959; PMCID: PMC10427710
Dou J, Tan Y, Kock KH, Wang J, Cheng X, Tan LM, Han KY, Hon CC, Park WY, Shin JW, Jin H, Wang Y, Chen H, Ding L, Prabhakar S, Navin N, Chen R, Chen K. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nat Biotechnol. 2023 Aug 17. doi: 10.1038/s41587-023-01873-x PMID: 37592035
Wang J, Liu H, Bertrand RE, Sarrion-Perdigones A, Gonzalez Y, Venken KJT, Chen R. A novel statistical method for interpreting the pathogenicity of rare variants. Genetics in Medicine. 2021 Jan;23(1):59-68. doi: 10.1038/s41436-020-00948-3. Epub 2020 Sep 4. PMID: 32884132; PMCID: PMC7796914.
Li J, Choi J, Cheng X, Ma J, Pema S, Sanes JR, Mardon G, Frankfort BJ, Tran NM, Li Y, Chen R. Comprehensive single-cell atlas of the mouse retina. iScience. 2024 May 8;27(6):109916. doi: 10.1016/j.isci.2024.109916. PMID: 38812536; PMCID: PMC11134544.
Wang J, Wang M, Moshiri A, Harris RA, Raveendran M, Nguyen T, Kim S, Young L, Wang K, Wiseman R, O'Connor DH, Johnson Z, Martinez M, Montague MJ, Sayers K, Lyke M, Vallender E, Stout T, Li Y, Thomasy SM, Rogers J, Chen R. Genetic diversity of 1,845 rhesus macaques improves genetic variation interpretation and identifies disease models. Nat Commun. 2024 Jul 5;15(1):5658. doi: 10.1038/s41467-024-49922-6. PMID: 38969634; PMCID: PMC11226599.
Jun Wang, Xuesen Cheng, Qingnan Liang, Leah A. Owen, Jiaxiong Lu, Yiqiao Zheng, Meng Wang, Shiming Chen, Margaret M. DeAngelis, Yumei Li, Rui Chen Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation Genome Biology, 2023 DOI : 10.1186/s13059-023-03111-8
Choi J, Li J, Ferdous S, Liang Q, Moffitt JR, Chen R. Spatial organization of the mouse retina at single cell resolution by MERFISH. Nat Commun. 2023 Aug 15;14(1):4929. doi: 10.1038/s41467-023-40674-3. PMID: 37582959; PMCID: PMC10427710
Dou J, Tan Y, Kock KH, Wang J, Cheng X, Tan LM, Han KY, Hon CC, Park WY, Shin JW, Jin H, Wang Y, Chen H, Ding L, Prabhakar S, Navin N, Chen R, Chen K. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nat Biotechnol. 2023 Aug 17. doi: 10.1038/s41587-023-01873-x PMID: 37592035
Wang J, Liu H, Bertrand RE, Sarrion-Perdigones A, Gonzalez Y, Venken KJT, Chen R. A novel statistical method for interpreting the pathogenicity of rare variants. Genetics in Medicine. 2021 Jan;23(1):59-68. doi: 10.1038/s41436-020-00948-3. Epub 2020 Sep 4. PMID: 32884132; PMCID: PMC7796914.
Link to this profile
https://faculty.uci.edu/profile/?facultyId=7279
https://faculty.uci.edu/profile/?facultyId=7279
Last updated
09/25/2024
09/25/2024