Publications

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Cheverud JM, Hager R, Roseman C, Fawcett G, Wang B, Wolf JB. Genomic imprinting effects on adult body composition in mice. Proc Natl Acad Sci U S A. 2008 ;105(11):4253-8.
Pearce SL, Clarke DF, East PD, Elfekih S, Gordon KHJ, Jermiin LS, McGaughran A, Oakeshott JG, Papanicolaou A, Perera OP, Rane RV, Richards S, Tay WT, Walsh TK, Anderson A, Anderson CJ, Asgari S, Board PG, Bretschneider A, Campbell PM, Chertemps T, Christeller JT, Coppin CW, Downes SJ, Duan G, Farnsworth CA, Good RT, Han LB, Han YC, Hatje K, Horne I, Huang YP, Hughes DST, Jacquin-Joly E, James W, Jhangiani S, Kollmar M, Kuwar SS, Li S, Liu N-Y, Maibeche MT, Miller JR, Montagne N, Perry T, Qu J, Song SV, Sutton GG, Vogel H, Walenz BP, Xu W, Zhang H-J, Zou Z, Batterham P, Edwards OR, Feyereisen R, Gibbs RA, Heckel DG, McGrath A, Robin C, Scherer SE, Worley KC, Wu YD. Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. BMC Biol. 2017 ;15(1):63.
Timms KM, Ansari-Lari MA, Morris W, Brown SN, Gibbs RA. The genomic organization of Isopeptidase T-3 (ISOT-3), a new member of the ubiquitin specific protease family (UBP). Gene. 1998 ;217(1-2):101-6.
Jones SN, Ansari-Lari MA, Hancock AR, Jones WJ, Gibbs RA, Donehower LA, Bradley A. Genomic organization of the mouse double minute 2 gene. Gene. 1996 ;175(1-2):209-13.
Frank TS, Sun X, Zhang Y, Yang J, Fisher WE, Gingras M-C, Li M. Genomic profiling guides the choice of molecular targeted therapy of pancreatic cancer. Cancer Lett. 2015 ;363(1):1-6.
Rokita JLynne, Rathi KS, Cardenas MF, Upton KA, Jayaseelan J, Cross KL, Pfeil J, Egolf LE, Way GP, Farrel A, Kendsersky NM, Patel K, Gaonkar KS, Modi A, Berko ER, Lopez G, Vaksman Z, Mayoh C, Nance J, McCoy K, Haber M, Evans K, McCalmont H, Bendak K, Böhm JW, Marshall GM, Tyrrell V, Kalletla K, Braun FK, Qi L, Du Y, Zhang H, Lindsay HB, Zhao S, Shu J, Baxter P, Morton C, Kurmashev D, Zheng S, Chen Y, Bowen J, Bryan AC, Leraas KM, Coppens SE, Doddapaneni H, Momin Z, Zhang W, Sacks GI, Hart LS, Krytska K, Mosse YP, Gatto GJ, Sanchez Y, Greene CS, Diskin SJ, Vaske OMorozova, Haussler D, Gastier-Foster JM, E Kolb A, Gorlick R, Li X-N, C Reynolds P, Kurmasheva RT, Houghton PJ, Smith MA, Lock RB, Raman P, Wheeler DA, Maris JM. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design. Cell Rep. 2019 ;29(6):1675-1689.e9.
Rogers J. Genomic resources for rhesus macaques (Macaca mulatta). Mamm Genome. 2022 ;33(1):91-99.
Li J, Jiang T, Mao J-H, Balmain A, Peterson L, Harris C, Rao PH, Havlak P, Gibbs R, Cai W-W. Genomic segmental polymorphisms in inbred mouse strains. Nat Genet. 2004 ;36(9):952-4.
Wang Y, Zhang Y, Yang J, Ni X, Liu S, Li Z, Hodges SE, Fisher WE, Brunicardi FC, Gibbs RA, Gingras M-C, Li M. Genomic sequencing of key genes in mouse pancreatic cancer cells. Curr Mol Med. 2012 ;12(3):331-41.
Chiou KL, Janiak MC, Schneider-Crease IA, Sen S, Ayele F, Chuma IS, Knauf S, Lemma A, Signore AV, D'Ippolito AM, Abebe B, Haile AAzanaw, Kebede F, Fashing PJ, Nguyen N, McCann C, Houck ML, Wall JD, Burrell AS, Bergey CM, Rogers J, Phillips-Conroy JE, Jolly CJ, Melin AD, Storz JF, Lu A, Beehner JC, Bergman TJ, Snyder-Mackler N. Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas. Nat Ecol Evol. 2022 ;6(5):630-643.
Gibbs RA, Rogers J. Genomics: Gorilla gorilla gorilla. Nature. 2012 ;483(7388):164-5.
Fuller ZL, Haynes GD, Richards S, Schaeffer SW. Genomics of natural populations: Evolutionary forces that establish and maintain gene arrangements in Drosophila pseudoobscura. Mol Ecol. 2017 ;26(23):6539-6562.
Schaeffer SW, Richards S, Fuller ZL. Genomics of natural populations: gene conversion events reveal selected genes within the inversions of Drosophila pseudoobscura. G3 (Bethesda). 2024 ;14(10).
Fuller ZL, Haynes GD, Richards S, Schaeffer SW. Genomics of Natural Populations: How Differentially Expressed Genes Shape the Evolution of Chromosomal Inversions in Drosophila pseudoobscura. Genetics. 2016 ;204(1):287-301.
Vinson A, Mahaney MC, Diego VP, Cox LA, Rogers J, VandeBerg JL, Rainwater DL. Genotype-by-diet effects on co-variation in Lp-PLA2 activity and LDL-cholesterol concentration in baboons fed an atherogenic diet. J Lipid Res. 2008 ;49(6):1295-302.
Wang X, Charng W-L, Chen C-A, Rosenfeld JA, Shamsi AAl, Al-Gazali L, McGuire M, Mew NAh, Arnold GL, Qu C, Ding Y, Muzny DM, Gibbs RA, Eng CM, Walkiewicz M, Xia F, Plon SE, Lupski JR, Schaaf CP, Yang Y. Germline mutations in ABL1 cause an autosomal dominant syndrome characterized by congenital heart defects and skeletal malformations. Nat Genet. 2017 ;49(4):613-617.
Carbone L, R Harris A, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, De Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LDW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, Hallers Bten, Terhune E, Thomas GWC, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA. Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014 ;513(7517):195-201.
Ahola V, Lehtonen R, Somervuo P, Salmela L, Koskinen P, Rastas P, Välimäki N, Paulin L, Kvist J, Wahlberg N, Tanskanen J, Hornett EA, Ferguson LC, Luo S, Cao Z, de Jong MA, Duplouy A, Smolander O-P, Vogel H, McCoy RC, Qian K, Chong WSwee, Zhang Q, Ahmad F, Haukka JK, Joshi A, Salojärvi J, Wheat CW, Grosse-Wilde E, Hughes D, Katainen R, Pitkänen E, Ylinen J, Waterhouse RM, Turunen M, Vähärautio A, Ojanen SP, Schulman AH, Taipale M, Lawson D, Ukkonen E, Mäkinen V, Goldsmith MR, Holm L, Auvinen P, Frilander MJ, Hanski I. The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nat Commun. 2014 ;5:4737.
Dederich DA, Okwuonu G, Garner T, Denn A, Sutton A, Escotto M, Martindale A, Delgado O, Muzny DM, Gibbs RA, Metzker ML. Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomes. Nucleic Acids Res. 2002 ;30(7):e32.
Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FEnnes, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CChuen, Lee J, Tan P, Lim WKhong, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MHeide, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKai-How, Bonet TMarques. A global catalog of whole-genome diversity from 233 primate species. Science. 2023 ;380(6648):906-913.
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).
Bélanger L, Frain M, Baril P, Gingras MC, Bartkowiak J, Sala-Trepat JM. Glucocorticosteroid suppression of alpha1-fetoprotein synthesis in developing rat liver. Evidence for selective gene repression at the transcriptional level. Biochemistry. 1981 ;20(23):6665-72.
Ahmed KMokim, Veeramachaneni R, Deng D, Putluri N, Putluri V, Cardenas MF, Wheeler DA, Decker WK, Frederick AI, Kazi S, Sikora AG, Sandulache VC, Frederick MJ. Glutathione peroxidase 2 is a metabolic driver of the tumor immune microenvironment and immune checkpoint inhibitor response. J Immunother Cancer. 2022 ;10(8).
Worley KC. A golden goat genome. Nat Genet. 2017 ;49(4):485-486.
Blackshear PJ, Graves JP, Stumpo DJ, Cobos I, Rubenstein JLR, Zeldin DC. Graded phenotypic response to partial and complete deficiency of a brain-specific transcript variant of the winged helix transcription factor RFX4. Development. 2003 ;130(19):4539-52.