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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.
Marafi D, Kozar N, Duan R, Bradley S, Yokochi K, Mutairi FAl, Saadi NWaill, Whalen S, Brunet T, Kotzaeridou U, Choukair D, Keren B, Nava C, Kato M, Arai H, Froukh T, Faqeih EAli, AlAsmari AM, Saleh MM, Vairo FPinto E, Pichurin PN, Klee EW, Schmitz CT, Grochowski CM, Mitani T, Herman I, Calame DG, Fatih JM, Du H, Coban-Akdemir Z, Pehlivan D, Jhangiani SN, Gibbs RA, Miyatake S, Matsumoto N, Wagstaff LJ, Posey JE, Lupski JR, Meijer D, Wagner M. A reverse genetics and genomics approach to gene paralog function and disease: Myokymia and the juxtaparanode. Am J Hum Genet. 2022 ;109(9):1713-1723.
Li-Byarlay H, Li Y, Stroud H, Feng S, Newman TC, Kaneda M, Hou KK, Worley KC, Elsik CG, Wickline SA, Jacobsen SE, Ma J, Robinson GE. RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee. Proc Natl Acad Sci U S A. 2013 ;110(31):12750-5.
Jordan VK, Beck TF, Hernandez-Garcia A, Kundert PN, Kim B-J, Jhangiani SN, Gambin T, Starkovich M, Punetha J, Paine IS, Posey JE, Li AH, Muzny DM, Hsu C-W, Lashua AJ, Sun X, Fernandes CJ, Dickinson ME, Lally KP, Gibbs RA, Boerwinkle E, Lupski JR, Scott DA. The role of FREM2 and FRAS1 in the development of congenital diaphragmatic hernia. Hum Mol Genet. 2018 ;27(12):2064-2075.
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Oeyen JPhilip, Baa-Puyoulet P, Benoit JB, Beukeboom LW, Bornberg-Bauer E, Buttstedt A, Calevro F, Cash EI, Chao H, Charles H, Chen M-JMay, Childers C, Cridge AG, Dearden P, Dinh H, Doddapaneni H, Dolan A, Donath A, Dowling D, Dugan S, Duncan E, Elpidina EN, Friedrich M, Geuverink E, Gibson JD, Grath S, Grimmelikhuijzen CJP, Große-Wilde E, Gudobba C, Han Y, Hansson BS, Hauser F, Hughes DST, Ioannidis P, Jacquin-Joly E, Jennings EC, Jones JW, Klasberg S, Lee SL, Lesný P, Lovegrove M, Martin S, Martynov AG, Mayer C, Montagné N, Moris VC, Munoz-Torres M, Murali SCanchi, Muzny DM, Oppert B, Parisot N, Pauli T, Peters RS, Petersen M, Pick C, Persyn E, Podsiadlowski L, Poelchau MF, Provataris P, Qu J, Reijnders MJMF, von Reumont BMarcus, Rosendale AJ, Simão FA, Skelly J, Sotiropoulos AG, Stahl AL, Sumitani M, Szuter EM, Tidswell O, Tsitlakidis E, Vedder L, Waterhouse RM, Werren JH, Wilbrandt J, Worley KC, Yamamoto DS, van de Zande L, Zdobnov EM, Ziesmann T, Gibbs RA, Richards S, Hatakeyama M, Misof B, Niehuis O. Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. Genome Biol Evol. 2020 ;12(7):1099-1188.
Salerno W, Havlak P, Miller J. Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments. Proc Natl Acad Sci U S A. 2006 ;103(35):13121-5.
Rahbar MH, Samms-Vaughan M, Loveland KA, Ardjomand-Hessabi M, Chen Z, Bressler J, Shakespeare-Pellington S, Grove ML, Bloom K, Pearson DA, Lalor GC, Boerwinkle E. Seafood consumption and blood mercury concentrations in Jamaican children with and without autism spectrum disorders. Neurotox Res. 2013 ;23(1):22-38.
Hughes JF, Skaletsky H, Pyntikova T, Koutseva N, Raudsepp T, Brown LG, Bellott DW, Cho T-J, Dugan-Rocha S, Khan Z, Kremitzki C, Fronick C, Graves-Lindsay TA, Fulton L, Warren WC, Wilson RK, Owens E, Womack JE, Murphy WJ, Muzny DM, Worley KC, Chowdhary BP, Gibbs RA, Page DC. Sequence analysis in reveals pervasiveness of X-Y arms races in mammalian lineages. Genome Res. 2020 ;30(12):1716-1726.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 ;432(7018):695-716.
Sucgang R, Chen G, Liu W, Lindsay R, Lu J, Muzny D, Shaulsky G, Loomis W, Gibbs R, Kuspa A. Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium. Nucleic Acids Res. 2003 ;31(9):2361-8.
Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LDW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, Munson KM, DeVogelaere E, Armstrong J, Diekhans M, Walker JA, Tomlinson C, Graves-Lindsay TA, Kremitzki M, Salama SR, Audano PA, Escalona M, Maurer NW, Antonacci F, Mercuri L, Maggiolini FAM, Catacchio CRita, Underwood JG, O'Connor DH, Sanders AD, Korbel JO, Ferguson B, H Kubisch M, Picker L, Kalin NH, Rosene D, Levine J, Abbott DH, Gray SB, Sanchez MM, Kovacs-Balint ZA, Kemnitz JW, Thomasy SM, Roberts JA, Kinnally EL, Capitanio JP, Skene JHPate, Platt M, Cole SA, Green RE, Ventura M, Wiseman RW, Paten B, Batzer MA, Rogers J, Eichler EE. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science. 2020 ;370(6523).
Christian BT, Fox AS, Oler JA, Vandehey NT, Murali D, Rogers J, Oakes TR, Shelton SE, Davidson RJ, Kalin NH. Serotonin transporter binding and genotype in the nonhuman primate brain using [C-11]DASB PET. Neuroimage. 2009 ;47(4):1230-6.
Kalin NH, Shelton SE, Fox AS, Rogers J, Oakes TR, Davidson RJ. The serotonin transporter genotype is associated with intermediate brain phenotypes that depend on the context of eliciting stressor. Mol Psychiatry. 2008 ;13(11):1021-7.
Mubiru JN, Garcia-Forey M, Cavazos N, Hemmat P, Dick EJ, Owston MA, Bauer CA, Shade RE, Rogers J. Serum prostate specific antigen changes in cynomolgus monkeys (Macaca fascicularis) on a high sugar high fat diet. Prostate. 2012 ;72(5):469-75.
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.
Sodergren E, Shen Y, Song X, Zhang L, Gibbs RA, Weinstock GM. Shedding genomic light on Aristotle's lantern. Dev Biol. 2006 ;300(1):2-8.
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.
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.
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.
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.