Publications

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He J, Cui L, Zeng Y, Wang G, Zhou P, Yang Y, Ji L, Zhao Y, Chen J, Wang Z, Shi T, Zhang P, Chen R, Li X. REGγ is associated with multiple oncogenic pathways in human cancers. BMC Cancer. 2012 ;12:75.
Pearce W, Chen R, Jain N. Reply. Ophthalmology. 2019 ;126(7):e51-e52.
Lopez AJacobo, Kim S, Qian X, Rogers J, J Stout T, Thomasy SM, La Torre A, Chen R, Moshiri A. Retinal organoids derived from rhesus macaque iPSCs undergo accelerated differentiation compared to human stem cells. Cell Prolif. 2022 ;55(4):e13198.
Qian X, Srinivasan T, He J, Chen R. The Role of Ceramide in Inherited Retinal Disease Pathology. Adv Exp Med Biol. 2023 ;1415:303-307.
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Chen Y, Zhao L, Wang Y, Cao M, Gelowani V, Xu M, Agrawal SA, Li Y, Daiger SP, Gibbs RA, Wang F, Chen R. SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data. BMC Bioinformatics. 2017 ;18(1):147.
MacKay H, Gunasekara CJ, Yam K-Y, Srisai D, Yalamanchili HKrishna, Li Y, Chen R, Coarfa C, Waterland RA. Sex-specific epigenetic development in the mouse hypothalamic arcuate nucleus pinpoints human genomic regions associated with body mass index. Sci Adv. 2022 ;8(39):eabo3991.
Alam J, Yaman E, Silva GCristal Vi, Chen R, de Paiva CS, Stepp MAnn, Pflugfelder SC. Single cell analysis of short-term dry eye induced changes in cornea immune cell populations. Front Med (Lausanne). 2024 ;11:1362336.
Zuo Z, Cheng X, Ferdous S, Shao J, Li J, Bao Y, Li J, Lu J, Lopez AJacobo, 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 ;15(1):6792.
Raja KKumar Boll, Yeung K, Shim Y-K, Li Y, Chen R, Mardon G. A single cell genomics atlas of the Drosophila larval eye reveals distinct photoreceptor developmental timelines. Nat Commun. 2023 ;14(1):7205.
Raja KKumar Boll, Yeung K, Li Y, Chen R, Mardon G. A single cell RNA sequence atlas of the early Drosophila larval eye. BMC Genomics. 2024 ;25(1):616.
Yeung K, Raja KKumar Boll, Shim Y-K, Li Y, Chen R, Mardon G. Single cell RNA sequencing of the adult Drosophila eye reveals distinct clusters and novel marker genes for all major cell types. Commun Biol. 2022 ;5(1):1370.
Dharmat R, Kim S, Li Y, Chen R. Single-Cell Capture, RNA-seq, and Transcriptome Analysis from the Neural Retina. Methods Mol Biol. 2020 ;2092:159-186.
Zhang K, Gao M, Chong Z, Li Y, Han X, Chen R, Qin L. Single-cell isolation by a modular single-cell pipette for RNA-sequencing. Lab Chip. 2016 ;16(24):4742-4748.
Wang J, Cheng X, Liang Q, Owen LA, Lu J, Zheng Y, Wang M, Chen S, DeAngelis MM, Li Y, Chen R. 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 Biol. 2023 ;24(1):269.
Li Y, Ren P, Dawson A, Vasquez HG, Ageedi W, Zhang C, Luo W, Chen R, Li Y, Kim S, Lu HS, Cassis LA, Coselli JS, Daugherty A, Shen YH, LeMaire SA. Single-Cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expression Patterns in Control and Aneurysmal Human Aortic Tissue. Circulation. 2020 ;142(14):1374-1388.
Li J-M, Kim S, Zhang Y, Bian F, Hu J, Lu R, Pflugfelder SC, Chen R, Li D-Q. Single-Cell Transcriptomics Identifies a Unique Entity and Signature Markers of Transit-Amplifying Cells in Human Corneal Limbus. Invest Ophthalmol Vis Sci. 2021 ;62(9):36.
Li D-Q, Kim S, Li J-M, Gao Q, Choi J, Bian F, Hu J, Zhang Y, Li J, Lu R, Li Y, Pflugfelder SC, Miao H, Chen R. Single-cell transcriptomics identifies limbal stem cell population and cell types mapping its differentiation trajectory in limbal basal epithelium of human cornea. Ocul Surf. 2021 ;20:20-32.
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(1):5743.
Dou J, Tan Y, Kock KHong, Wang J, Cheng X, Tan LMin, Han KYeon, Hon C-C, Park W-Y, 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. 2024 ;42(5):803-812.
Eblimit A, Nguyen T-MT, Chen Y, Esteve-Rudd J, Zhong H, Letteboer S, van Reeuwijk J, Simons DL, Ding Q, Wu KMan, Li Y, Van Beersum S, Moayedi Y, Xu H, Pickard P, Wang K, Gan L, Wu SM, Williams DS, Mardon G, Roepman R, Chen R. Spata7 is a retinal ciliopathy gene critical for correct RPGRIP1 localization and protein trafficking in the retina. Hum Mol Genet. 2015 ;24(6):1584-601.
Lu J, Xiong K, Qian X, Choi J, Shim Y-K, Burnett J, Mardon G, Chen R. Spata7 is required for maintenance of the retinal connecting cilium. Sci Rep. 2022 ;12(1):5575.
Dharmat R, Eblimit A, Robichaux MA, Zhang Z, Nguyen T-MT, Jung SYun, 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 ;217(8):2851-2865.
Zhi D, Chen R. Statistical guidance for experimental design and data analysis of mutation detection in rare monogenic mendelian diseases by exome sequencing. PLoS One. 2012 ;7(2):e31358.
Pew BK, Harris RA, Sbrana E, Guaman MCuevas, Shope C, Chen R, Meloche S, Aagaard K. Structural and transcriptomic response to antenatal corticosteroids in an Erk3-null mouse model of respiratory distress. Am J Obstet Gynecol. 2016 ;215(3):384.e1-384.e89.
Wen S, Wang M, Qian X, Li Y, Wang K, Choi J, Pennesi ME, Yang P, Marra M, Koenekoop RK, Lopez I, Matynia A, Gorin M, Sui R, Yao F, Goetz K, Porto FBelga Otto, Chen R. Systematic assessment of the contribution of structural variants to inherited retinal diseases. Hum Mol Genet. 2023 ;32(12):2005-2015.