Publications

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2022
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.
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.
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.
2023
Qian X, Srinivasan T, He J, Lu J, Jin Y, Gu H, Chen R. Ceramide compensation by ceramide synthases preserves retinal function and structure in a retinal dystrophy mouse model. Dis Model Mech. 2023 ;16(7).
Lu J, Zheng KQ, Bertrand RElaine, Quinlan J, Ferdous S, Srinivasan T, Oh S, Wang K, Chen R. Gene augmentation therapy to rescue degenerative photoreceptors in a Cwc27 mutant mouse model. Exp Eye Res. 2023 ;234:109596.
Chen Q, Sasikala-Appukuttan AKirshna, Husain Z, Shrivastava A, Spain M, Sendler ED, Daines B, Fischer S, Chen R, Cook TA, Friedrich M. Global Gene Expression Analysis Reveals Complex Cuticle Organization of the Tribolium Compound Eye. Genome Biol Evol. 2023 ;15(1).
Li J, Wang J, Ibarra IL, Cheng X, Luecken MD, Lu J, Monavarfeshani A, Yan W, Zheng Y, Zuo Z, Colborn SLynn Zayas, Cortez BSarahi, Owen LA, Tran NM, Shekhar K, Sanes JR, J Stout T, Chen S, Li Y, DeAngelis MM, Theis FJ, Chen R. Integrated multi-omics single cell atlas of the human retina. Res Sq. 2023 ;.
Liang Q, Cheng X, Wang J, Owen L, Shakoor A, Lillvis JL, Zhang C, Farkas M, Kim IK, Li Y, DeAngelis M, Chen R. A multi-omics atlas of the human retina at single-cell resolution. Cell Genom. 2023 ;3(6):100298.
Hussain HMuhammad J, Wang M, Huang A, Schmidt R, Qian X, Yang P, Marra M, Li Y, Pennesi ME, Chen R. Novel Pathogenic Mutations Identified from Whole-Genome Sequencing in Unsolved Cases of Patients Affected with Inherited Retinal Diseases. Genes (Basel). 2023 ;14(2).
Fu S, Fu J, Mobasher-Jannat A, Jadidi K, Li Y, Chen R, Imani S, Cheng J. Novel pathogenic variant in Iranian familial with inherited retinal dystrophies: genotype-phenotype correlation. 3 Biotech. 2023 ;13(6):166.
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.
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.
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.
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. 2023 ;.
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.
2024
Brock DC, Wang M, Hussain HMuhammad J, Rauch DE, Marra M, Pennesi ME, Yang P, Everett L, Ajlan RS, Colbert J, Porto FBelga Otto, Matynia A, Gorin MB, Koenekoop RK, Lopez I, Sui R, Zou G, Li Y, Chen R. Comparative analysis of in-silico tools in identifying pathogenic variants in dominant inherited retinal diseases. Hum Mol Genet. 2024 ;.
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. bioRxiv. 2024 ;.
Han JHoon, Rodenburg K, Hayman T, Calzetti G, Kaminska K, Quinodoz M, Marra M, Wallerich S, Allon G, Nagy ZZ, Knézy K, Li Y, Chen R, Barboni MTelles Sal, Yang P, Pennesi ME, L van den Born I, Varsányi B, Szabó V, Sharon D, Banin E, Ben-Yosef T, Roosing S, Koenekoop RK, Rivolta C. Loss-of-function variants in UBAP1L cause autosomal recessive retinal degeneration. Genet Med. 2024 ;:101106.