Publications

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Journal Article
Jeong M, Sun D, Luo M, Huang Y, Challen GA, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim S-B, Yang L, Ko M, Chen R, Göttgens B, Lee J-S, Gunaratne P, Godley LA, Darlington GJ, Rao A, Li W, Goodell MA. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat Genet. 2014 ;46(1):17-23.
Devlin DJ, Zaneveld SAgrawal, Nozawa K, Han X, Moye AR, Liang Q, Harnish JMichael, Matzuk MM, Chen R. Knockout of mouse receptor accessory protein 6 leads to sperm function and morphology defects†. Biol Reprod. 2020 ;102(6):1234-1247.
Chen R, Mardon G. Keeping an eye on the fly genome. Dev Biol. 2005 ;282(2):285-93.
Coppieters F, Ascari G, Dannhausen K, Nikopoulos K, Peelman F, Karlstetter M, Xu M, Brachet C, Meunier I, Tsilimbaris MK, Tsika C, Blazaki SV, Vergult S, Farinelli P, Van Laethem T, Bauwens M, De Bruyne M, Chen R, Langmann T, Sui R, Meire F, Rivolta C, Hamel CP, Leroy BP, De Baere E. Isolated and Syndromic Retinal Dystrophy Caused by Biallelic Mutations in RCBTB1, a Gene Implicated in Ubiquitination. Am J Hum Genet. 2016 ;99(2):470-80.
DuPont M, Jones EM, Xu M, Chen R. Investigating the disease association of USH2A p.C759F variant by leveraging large retinitis pigmentosa cohort data. Ophthalmic Genet. 2018 ;39(2):291-292.
Zhao L, Chen Y, Bajaj AOnkar, Eblimit A, Xu M, Soens ZT, Wang F, Ge Z, Jung SYun, He F, Li Y, Wensel TG, Qin J, Chen R. Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes. Genome Res. 2016 ;26(5):660-9.
Yeung K, Wang F, Li Y, Wang K, Mardon G, Chen R. Integrative genomic analysis reveals novel regulatory mechanisms of eyeless during Drosophila eye development. Nucleic Acids Res. 2018 ;46(22):11743-11758.
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 ;.
Dharmat R, Liu W, Ge Z, Sun Z, Yang L, Li Y, Wang K, Thomas K, Sui R, Chen R. IFT81 as a Candidate Gene for Nonsyndromic Retinal Degeneration. Invest Ophthalmol Vis Sci. 2017 ;58(5):2483-2490.
Jin M, Aibar S, Ge Z, Chen R, Aerts S, Mardon G. Identification of novel direct targets of Drosophila Sine oculis and Eyes absent by integration of genome-wide data sets. Dev Biol. 2016 ;415(1):157-167.
Wang Y, Brahmakshatriya V, Zhu H, Lupiani B, Reddy SM, Yoon B-J, Gunaratne PH, Kim JHwan, Chen R, Wang J, Zhou H. Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach. BMC Genomics. 2009 ;10:512.
Qian X, Wang J, Wang M, Igelman AD, Jones KD, Li Y, Wang K, Goetz KE, Birch DG, Yang P, Pennesi ME, Chen R. Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases. Front Genet. 2021 ;12:647400.
Millo T, Rivera A, Obolensky A, Marks-Ohana D, Xu M, Li Y, Wilhelm E, Gopalakrishnan P, Gross M, Rosin B, Hanany M, Webster A, Tracewska AMaria, Koenekoop RK, Chen R, Arno G, Schueler-Furman O, Roosing S, Banin E, Sharon D. Identification of autosomal recessive novel genes and retinal phenotypes in members of the solute carrier (SLC) superfamily. Genet Med. 2022 ;24(7):1523-1535.
Soens ZT, Li Y, Zhao L, Eblimit A, Dharmat R, Li Y, Chen Y, Naqeeb M, Fajardo N, Lopez I, Sun Z, Koenekoop RK, Chen R. Hypomorphic mutations identified in the candidate Leber congenital amaurosis gene CLUAP1. Genet Med. 2016 ;18(10):1044-51.
Wang F, Li H, Xu M, Li H, Zhao L, Yang L, Zaneveld JE, Wang K, Li Y, Sui R, Chen R. A homozygous missense mutation in NEUROD1 is associated with nonsyndromic autosomal recessive retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2014 ;56(1):150-5.
Daines B, Wang H, Li Y, Han Y, Gibbs RA, Chen R. High-throughput multiplex sequencing to discover copy number variants in Drosophila. Genetics. 2009 ;182(4):935-41.
Srivatsan A, Han Y, Peng J, Tehranchi AK, Gibbs RA, Wang JD, Chen R. High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet. 2008 ;4(8):e1000139.
Zhou Q, Yao F, Wang F, Li H, Chen R, Sui R. A heterozygous mutation in RPGR associated with X-linked retinitis pigmentosa in a patient with Turner syndrome mosaicism (45,X/46,XX). Am J Med Genet A. 2018 ;176(1):214-218.
Simakov O, Kawashima T, Marlétaz F, Jenkins J, Koyanagi R, Mitros T, Hisata K, Bredeson J, Shoguchi E, Gyoja F, Yue J-X, Chen Y-C, Freeman RM, Sasaki A, Hikosaka-Katayama T, Sato A, Fujie M, Baughman KW, Levine J, Gonzalez P, Cameron C, Fritzenwanker JH, Pani AM, Goto H, Kanda M, Arakaki N, Yamasaki S, Qu J, Cree A, Ding Y, Dinh HH, Dugan S, Holder M, Jhangiani SN, Kovar CL, Lee SL, Lewis LR, Morton D, Nazareth LV, Okwuonu G, Santibanez J, Chen R, Richards S, Muzny DM, Gillis A, Peshkin L, Wu M, Humphreys T, Su Y-H, Putnam NH, Schmutz J, Fujiyama A, Yu J-K, Tagawa K, Worley KC, Gibbs RA, Kirschner MW, Lowe CJ, Satoh N, Rokhsar DS, Gerhart J. Hemichordate genomes and deuterostome origins. Nature. 2015 ;527(7579):459-65.
Wang J, Zhao L, Wang X, Chen Y, Xu M, Soens ZT, Ge Z, Wang PRonghan, Wang F, Chen R. GRIPT: a novel case-control analysis method for Mendelian disease gene discovery. Genome Biol. 2018 ;19(1):203.
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).
Gunasekara CJ, C Scott A, Laritsky E, Baker MS, MacKay H, Duryea JD, Kessler NJ, Hellenthal G, Wood AC, Hodges KR, Gandhi M, Hair AB, Silver MJ, Moore SE, Prentice AM, Li Y, Chen R, Coarfa C, Waterland RA. A genomic atlas of systemic interindividual epigenetic variation in humans. Genome Biol. 2019 ;20(1):105.
Ostrin EJ, Li Y, Hoffman K, Liu J, Wang K, Zhang L, Mardon G, Chen R. Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless. Genome Res. 2006 ;16(4):466-76.
Jusiak B, Wang F, Karandikar UC, Kwak S-J, Wang H, Chen R, Mardon G. Genome-wide DNA binding pattern of the homeodomain transcription factor Sine oculis (So) in the developing eye of . Genom Data. 2014 ;2:153-155.
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, J Venter C, Woodage T, Smith D, Lee H-M, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, K Durbin J, Simons R, Ren Y, Song X-Z, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQian, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, M Albà M, Abril JF, Guigó R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee Y-A, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, T Andrews D, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, J Venter C, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VBing, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 ;428(6982):493-521.