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Journal Article
Naval-Sanchez M, Nguyen Q, McWilliam S, Porto-Neto LR, Tellam R, Vuocolo T, Reverter A, Perez-Enciso M, Brauning R, Clarke S, McCulloch A, Zamani W, Naderi S, Rezaei HReza, Pompanon F, Taberlet P, Worley KC, Gibbs RA, Muzny DM, Jhangiani SN, Cockett N, Daetwyler H, Kijas J. Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds. Nat Commun. 2018 ;9(1):859.
Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton J-A, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SMJ, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristensen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, V Oddy H, Nicholas FW, McEwan JC, Kijas J, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP. The sheep genome illuminates biology of the rumen and lipid metabolism. Science. 2014 ;344(6188):1168-1173.
Bouck JB, Metzker ML, Gibbs RA. Shotgun sample sequence comparisons between mouse and human genomes. Nat Genet. 2000 ;25(1):31-3.
Butler DJ, Mozsary C, Meydan C, Danko D, Foox J, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Westover CD, Ryon K, Young B, Bhattacharya C, Ruggiero P, Langhorst BW, Tanner N, Gawrys J, Meleshko D, Xu D, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Schwartz RE, Iftner A, Bezdan D, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Hajirasouliha I, Horner SM, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Levy S, Wu S, Tatonetti N, Imielinski M, Rennert H, Mason CE. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions. bioRxiv. 2020 ;.
Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin C-S, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat Commun. 2021 ;12(1):1660.
Friedman JM, Bombard Y, Carleton B, Issa AM, Knoppers B, Plon SE, Rahimzadeh V, Relling MV, Williams MS, van Karnebeek C, Vears D, Cornel MC. Should secondary pharmacogenomic variants be actively screened and reported when diagnostic genome-wide sequencing is performed in a child?. Genet Med. 2024 ;26(2):101033.
Voevodin A, Samilchuk E, Allan J, Rogers J, Broussard S. Simian T-lymphotropic virus type 1 (STLV-1) infection in wild yellow baboons (Papio hamadryas cynocephalus) from Mikumi National Park, Tanzania. Virology. 1997 ;228(2):350-9.
Chen D, Ge J, Wang L, Gao Q, Ma P, Li N, Li D-Q, Wang Z. A simple and evolutional approach proven to recanalise the nasolacrimal duct obstruction. Br J Ophthalmol. 2009 ;93(11):1438-43.
Garsin DA, Sifri CD, Mylonakis E, Qin X, Singh KV, Murray BE, Calderwood SB, Ausubel FM. A simple model host for identifying Gram-positive virulence factors. Proc Natl Acad Sci U S A. 2001 ;98(19):10892-7.
Civitello AB, Richards S, Gibbs RA. A simple protocol for the automation of DNA cycle sequencing reactions and polymerase chain reactions. DNA Seq. 1992 ;3(1):17-23.
Lee I, Razaghi R, Gilpatrick T, Molnar M, Gershman A, Sadowski N, Sedlazeck FJ, Hansen KD, Simpson JT, Timp W. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing. Nat Methods. 2020 ;17(12):1191-1199.
Andersson B, Lu J, Shen Y, Wentland MA, Gibbs RA. Simultaneous shotgun sequencing of multiple cDNA clones. DNA Seq. 1997 ;7(2):63-70.
Estécio MRH, Gallegos J, Dekmezian M, Lu Y, Liang S, Issa J-PJ. SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters. Mol Cancer Res. 2012 ;10(10):1332-42.
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.
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.
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.
Cotton RT, Li D, Scherer SE, Muzny DM, Hodges SE, Catania RL, Witkiewicz AK, Brody JR, Kennedy EP, Yeo CJ, F Brunicardi C, Gibbs RA, Gingras M-C, Fisher WE. Single nucleotide polymorphism in RECQL and survival in resectable pancreatic adenocarcinoma. HPB (Oxford). 2009 ;11(5):435-44.
Lemon WJ, Swinton CH, Wang M, Berbari N, Wang Y, You M. Single nucleotide polymorphism (SNP) analysis of mouse pulmonary adenoma susceptibility loci 1-4 for identification of candidate genes. J Med Genet. 2003 ;40(4):e36.
Yan Y, Wang M, Lemon WJ, You M. Single nucleotide polymorphism (SNP) analysis of mouse quantitative trait loci for identification of candidate genes. J Med Genet. 2004 ;41(9):e111.
Morrison AC, Bare LA, Luke MM, Pankow JS, Mosley TH, Devlin JJ, Willerson JT, Boerwinkle E. Single nucleotide polymorphisms associated with coronary heart disease predict incident ischemic stroke in the atherosclerosis risk in communities study. Cerebrovasc Dis. 2008 ;26(4):420-4.
Yakub I, Lillibridge KM, Moran A, Gonzalez OY, Belmont J, Gibbs RA, Tweardy DJ. Single nucleotide polymorphisms in genes for 2'-5'-oligoadenylate synthetase and RNase L inpatients hospitalized with West Nile virus infection. J Infect Dis. 2005 ;192(10):1741-8.
Lu J, Kishida K, Cruz JDe Asis, Lohrenz T, Deering DTreadwell, Beauchamp M, P Montague R. Single stimulus fMRI produces a neural individual difference measure for Autism Spectrum Disorder. Clin Psychol Sci. 2015 ;3(3):422-432.
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.