Publications

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Filters: Keyword is Sequence Analysis, RNA  [Clear All Filters]
2022
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.
2021
Conley BA, Staudt L, Takebe N, Wheeler DA, Wang L, Cardenas MF, Korchina V, Zenklusen JClaude, McShane LM, Tricoli JV, Williams PM, Lubensky I, O'Sullivan-Coyne G, Kohn E, Little RF, White J, Malik S, Harris LN, Mann B, Weil C, Tarnuzzer R, Karlovich C, Rodgers B, Shankar L, Jacobs PM, Nolan T, Berryman SM, Gastier-Foster J, Bowen J, Leraas K, Shen H, Laird PW, Esteller M, Miller V, Johnson A, Edmondson EF, Giordano TJ, Kim B, S Ivy P. The Exceptional Responders Initiative: Feasibility of a National Cancer Institute Pilot Study. J Natl Cancer Inst. 2021 ;113(1):27-37.
Zhang Y, Chen F, Donehower LA, Scheurer ME, Creighton CJ. A pediatric brain tumor atlas of genes deregulated by somatic genomic rearrangement. Nat Commun. 2021 ;12(1):937.
2020
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.
2019
Park YH, Snook JD, Ostrin EJ, Kim S, Chen R, Frankfort BJ. Transcriptomic profiles of retinal ganglion cells are defined by the magnitude of intraocular pressure elevation in adult mice. Sci Rep. 2019 ;9(1):2594.
2017
Moss TJ, Qi Y, Xi L, Peng B, Kim T-B, Ezzedine NE, Mosqueda ME, Guo CC, Czerniak BA, Ittmann M, Wheeler DA, Lerner SP, Matin SF. Comprehensive Genomic Characterization of Upper Tract Urothelial Carcinoma. Eur Urol. 2017 ;72(4):641-649.
Nandakumar P, Tin A, Grove ML, Ma J, Boerwinkle E, Coresh J, Chakravarti A. MicroRNAs in the miR-17 and miR-15 families are downregulated in chronic kidney disease with hypertension. PLoS One. 2017 ;12(8):e0176734.
Chhibber A, French CE, Yee SW, Gamazon ER, Theusch E, Qin X, Webb A, Papp AC, Wang A, Simmons CQ, Konkashbaev A, Chaudhry AS, Mitchel K, Stryke D, Ferrin TE, Weiss ST, Kroetz DL, Sadee W, Nickerson DA, Krauss RM, George AL, Schuetz EG, Medina MW, Cox NJ, Scherer SE, Giacomini KM, Brenner SE. Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. Pharmacogenomics J. 2017 ;17(2):137-145.
2016
Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, Charpiot E, Adelmann CH, Ching G, Nguyen TN, Nicholas C, Thomas VD, Migden M, MacFarlane D, Thompson E, Shen J, Takata Y, McNiece K, Polansky MA, Abbas HA, Rajapakshe K, Gower A, Spira A, Covington KR, Xiao W, Gunaratne P, Pickering C, Frederick M, Myers JN, Shen L, Yao H, Su X, Rapini RP, Wheeler DA, Hawk ET, Flores ER, Tsai KY. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nat Commun. 2016 ;7:12601.
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.
2015
Vasquez YM, Mazur EC, Li X, Kommagani R, Jiang L, Chen R, Lanz RB, Kovanci E, Gibbons WE, DeMayo FJ. FOXO1 is required for binding of PR on IRF4, novel transcriptional regulator of endometrial stromal decidualization. Mol Endocrinol. 2015 ;29(3):421-33.
Roy A, Kumar V, Zorman B, Fang E, Haines KM, Doddapaneni H, Hampton OA, White S, Bavle AA, Patel NR, Eldin KW, M Hicks J, Rakheja D, Leavey PJ, Skapek SX, Amatruda JF, Nuchtern JG, Chintagumpala MM, Wheeler DA, Plon SE, Sumazin P, D Parsons W. Recurrent internal tandem duplications of BCOR in clear cell sarcoma of the kidney. Nat Commun. 2015 ;6:8891.
Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, Thomas MJ, Kelly S, Weiss JM, Raveendran M, Muzny DM, Gibbs RA, Rogers J, Schroth GP, Katze MG, Mason CE. Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). Nucleic Acids Res. 2015 ;43(Database issue):D737-42.
2014
Xia Z, Donehower LA, Cooper TA, Neilson JR, Wheeler DA, Wagner EJ, Li W. Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. Nat Commun. 2014 ;5:5274.
2012
Highlander SK. High throughput sequencing methods for microbiome profiling: application to food animal systems. Anim Health Res Rev. 2012 ;13(1):40-53.
2011
Daines B, Wang H, Wang L, Li Y, Han Y, Emmert D, Gelbart W, Wang X, Li W, Gibbs RA, Chen R. The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res. 2011 ;21(2):315-24.