Publications

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Lindsey ARI, Kelkar YD, Wu X, Sun D, Martinson EO, Yan Z, Rugman-Jones PF, Hughes DST, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Ye G, Gibbs RA, Richards S, Yi SV, Stouthamer R, Werren JH. Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum. BMC Biol. 2018 ;16(1):54.
Newton ILG, Clark ME, Kent BN, Bordenstein SR, Qu J, Richards S, Kelkar YD, Werren JH. Comparative Genomics of Two Closely Related Wolbachia with Different Reproductive Effects on Hosts. Genome Biol Evol. 2016 ;8(5):1526-42.
Lermi NOzirmak, Gray SB, Bowen CM, Reyes-Uribe L, Dray BK, Deng N, Harris RA, Raveendran M, Benavides F, Hodo CL, Taggart MW, Maresso KColbert, Sinha KM, Rogers J, Vilar E. Comparative molecular genomic analyses of a spontaneous rhesus macaque model of mismatch repair-deficient colorectal cancer. PLoS Genet. 2022 ;18(4):e1010163.
Rogers J, Gibbs RA. Comparative primate genomics: emerging patterns of genome content and dynamics. Nat Rev Genet. 2014 ;15(5):347-59.
Ansari-Lari MA, Oeltjen JC, Schwartz S, Zhang Z, Muzny DM, Lu J, Gorrell JH, Chinault AC, Belmont JW, Miller W, Gibbs RA. Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. Genome Res. 1998 ;8(1):29-40.
Levin ML, Chatterjee A, Pragliola A, Worley KC, Wehnert M, Zhuchenko O, Smith RF, Lee CC, Herman GE. A comparative transcription map of the murine bare patches (Bpa) and striated (Str) critical regions and human Xq28. Genome Res. 1996 ;6(6):465-77.
Chen Z-X, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AMaria, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim Y-A, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu L-L, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu Y-Q, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 ;24(7):1209-23.
Chen R, Bouck JB, Weinstock GM, Gibbs RA. Comparing vertebrate whole-genome shotgun reads to the human genome. Genome Res. 2001 ;11(11):1807-16.
Ziegler TE, Kapoor A, Binkley NC, Rice KS, Rogers J, Jolly CJ, Phillips-Conroy JE. Comparison of vitamin D metabolites in wild and captive baboons. Am J Primatol. 2018 ;80(12):e22935.
Duan Y, Zhou L, Hall DG, Li W, Doddapaneni H, Lin H, Liu L, Vahling CM, Gabriel DW, Williams KP, Dickerman A, Sun Y, Gottwald T. Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics. Mol Plant Microbe Interact. 2009 ;22(8):1011-20.
Matejková P, Strouhal M, Smajs D, Norris SJ, Palzkill T, Petrosino JF, Sodergren E, Norton JE, Singh J, Richmond TA, Molla MN, Albert TJ, Weinstock GM. Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays. BMC Microbiol. 2008 ;8:76.
Prall TM, Karl JA, Varghese JM, Baker DA, Minor NR, Raveendran M, Harris RA, Rogers J, Wiseman RW, O'Connor DH. Complete Genomic Assembly of Mauritian Cynomolgus Macaque Killer Ig-like Receptor and Natural Killer Group 2 Haplotypes. J Immunol. 2024 ;212(11):1754-1765.
Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, Misquitta L, Schaefer CF, Buetow KH, Bonner TI, Yankie L, Ward M, Phan L, Astashyn A, Brown G, Farrell C, Hart J, Landrum M, Maidak BL, Murphy M, Murphy T, Rajput B, Riddick L, Webb D, Weber J, Wu W, Pruitt KD, Maglott D, Siepel A, Brejova B, Diekhans M, Harte R, Baertsch R, Kent J, Haussler D, Brent M, Langton L, Comstock CLG, Stevens M, Wei C, van Baren MJ, Salehi-Ashtiani K, Murray RR, Ghamsari L, Mello E, Lin C, Pennacchio C, Schreiber K, Shapiro N, Marsh A, Pardes E, Moore T, Lebeau A, Muratet M, Simmons B, Kloske D, Sieja S, Hudson J, Sethupathy P, Brownstein M, Bhat N, Lazar J, Jacob H, Gruber CE, Smith MR, McPherson J, Garcia AM, Gunaratne PH, Wu J, Muzny DM, Gibbs RA, Young AC, Bouffard GG, Blakesley RW, Mullikin J, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJM, Holt RA, Marra MA, Lu S, Yang S, Hartigan J, Graf M, Wagner R, Letovksy S, Pulido JC, Robison K, Esposito D, Hartley J, Wall VE, Hopkins RF, Ohara O, Wiemann S. The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 ;19(12):2324-33.
Jensen A, Swift F, de Vries D, Beck RMD, Kuderna LFK, Knauf S, Chuma IS, Keyyu JD, Kitchener AC, Farh K, Rogers J, Marques-Bonet T, Detwiler KM, Roos C, Guschanski K. Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation. Mol Biol Evol. 2023 ;40(12).
Bakken TE, Miller JA, Ding S-L, Sunkin SM, Smith KA, Ng L, Szafer A, Dalley RA, Royall JJ, Lemon T, Shapouri S, Aiona K, Arnold J, Bennett JL, Bertagnolli D, Bickley K, Boe A, Brouner K, Butler S, Byrnes E, Caldejon S, Carey A, Cate S, Chapin M, Chen J, Dee N, Desta T, Dolbeare TA, Dotson N, Ebbert A, Fulfs E, Gee G, Gilbert TL, Goldy J, Gourley L, Gregor B, Gu G, Hall J, Haradon Z, Haynor DR, Hejazinia N, Hoerder-Suabedissen A, Howard R, Jochim J, Kinnunen M, Kriedberg A, Kuan CL, Lau C, Lee C-K, Lee F, Luong L, Mastan N, May R, Melchor J, Mosqueda N, Mott E, Ngo K, Nyhus J, Oldre A, Olson E, Parente J, Parker PD, Parry S, Pendergraft J, Potekhina L, Reding M, Riley ZL, Roberts T, Rogers B, Roll K, Rosen D, Sandman D, Sarreal M, Shapovalova N, Shi S, Sjoquist N, Sodt AJ, Townsend R, Velasquez L, Wagley U, Wakeman WB, White C, Bennett C, Wu J, Young R, Youngstrom BL, Wohnoutka P, Gibbs RA, Rogers J, Hohmann JG, Hawrylycz MJ, Hevner RF, Molnár Z, Phillips JW, Dang C, Jones AR, Amaral DG, Bernard A, Lein ES. A comprehensive transcriptional map of primate brain development. Nature. 2016 ;535(7612):367-75.
Jin M, Eblimit A, Pulikkathara M, Corr S, Chen R, Mardon G. Conditional knockout of retinal determination genes in differentiating cells in Drosophila. FEBS J. 2016 ;283(15):2754-66.
Eblimit A, Agrawal SAkshay, Thomas K, Anastassov IAssenov, Abulikemu T, Moayedi Y, Mardon G, Chen R. Conditional loss of Spata7 in photoreceptors causes progressive retinal degeneration in mice. Exp Eye Res. 2018 ;166:120-130.
Perelygin AA, Kammerer CM, Stowell NC, Rogers J. Conservation of human chromosome 18 in baboons (Papio hamadryas): a linkage map of eight human microsatellites. Cytogenet Cell Genet. 1996 ;75(4):207-9.
Harris RA, Raveendran M, Lyfoung DT, Sedlazeck FJ, Mahmoud M, Prall TM, Karl JA, Doddapaneni H, Meng Q, Han Y, Muzny DM, Wiseman RW, O'Connor DH, Rogers J. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus. Gigascience. 2022 ;11.
Foote AD, Liu Y, Thomas GWC, Vinar T, Alföldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Qin X, Qu J, Raney BJ, Vijay N, Wolf JBW, Hahn MW, Muzny DM, Worley KC, M Gilbert TP, Gibbs RA. Convergent evolution of the genomes of marine mammals. Nat Genet. 2015 ;47(3):272-5.
Marom R, Burrage LC, Venditti R, Clément A, Blanco-Sánchez B, Jain M, Scott DA, Rosenfeld JA, V Sutton R, Shinawi M, Mirzaa G, DeVile C, Roberts R, Calder AD, Allgrove J, Grafe I, Lanza DG, Li X, Joeng KSang, Lee Y-C, Song I-W, Sliepka JM, Batkovskyte D, Washington M, Dawson BC, Jin Z, Jiang M-M, Chen S, Chen Y, Tran AA, Emrick LT, Murdock DR, Hanchard NA, Zapata GE, Mehta NR, Weis MAnn, Scott AA, Tremp BA, Phillips JB, Wegner J, Taylor-Miller T, Gibbs RA, Muzny DM, Jhangiani SN, Hicks J, Stottmann RW, Dickinson ME, Seavitt JR, Heaney JD, Eyre DR, Westerfield M, De Matteis MAntonietta, Lee B. COPB2 loss of function causes a coatopathy with osteoporosis and developmental delay. Am J Hum Genet. 2021 ;108(9):1710-1724.
Dennenmoser S, Sedlazeck FJ, Iwaszkiewicz E, Li X-Y, Altmüller J, Nolte AW. Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. Mol Ecol. 2017 ;26(18):4712-4724.
Brasó-Vives M, Povolotskaya IS, Hartasánchez DA, Farré X, Fernandez-Callejo M, Raveendran M, Harris RA, Rosene DL, Lorente-Galdos B, Navarro A, Marques-Bonet T, Rogers J, Juan D. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet. 2020 ;16(5):e1008742.
Degenhardt JD, de Candia P, Chabot A, Schwartz S, Henderson L, Ling B, Hunter M, Jiang Z, Palermo RE, Katze M, Eichler EE, Ventura M, Rogers J, Marx P, Gilad Y, Bustamante CD. Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta). PLoS Genet. 2009 ;5(1):e1000346.
Lindstrand A, Frangakis S, Carvalho CMB, Richardson EB, McFadden KA, Willer JR, Pehlivan D, Liu P, Pediaditakis IL, Sabo A, Lewis RAlan, Banin E, Lupski JR, Davis EE, Katsanis N. Copy-Number Variation Contributes to the Mutational Load of Bardet-Biedl Syndrome. Am J Hum Genet. 2016 ;99(2):318-36.