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  • Showing 1-48 of 48 Results
2016
Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts.Ma, L., Chen Z., Huang da W., Kutty G., Ishihara M., Wang H., Abouelleil A., Bishop L., Davey E., Deng R., Deng X., Fan L., Fantoni G., FitzGerald M., Gogineni E., Goldberg JM, Handley G., Hu X., Huber C., Jiao X., et al. Nature communications, 2016/02/22, Volume 7, p.10740, (2016) Read More / View Supplemental Materials
Abstract
Genomic insights into the Ixodes scapularis tick vector of Lyme disease.Gulia-Nuss, M., Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J., Ribeiro JM, Megy K., Thimmapuram J., Miller JR, Walenz BP, Koren S., Hostetler JB, Thiagarajan M., Joardar VS, Hannick LI, Bidwell S., Hammond MP, et al. Nature communications, 2016/02/09, Volume 7, p.10507, (2016) Read More / View Supplemental Materials
Abstract
Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).Klionsky, DJ, Abdelmohsen K., Abe A., Abedin MJ, Abeliovich H., Acevedo Arozena A., Adachi H., Adams CM, Adams PD, Adeli K., Adhihetty PJ, Adler SG, Agam G., Agarwal R., Aghi MK, Agnello M., Agostinis P., Aguilar PV, Aguirre-Ghiso J., Airoldi EM, et al. Autophagy, 2016/01/02, Volume 12, Issue 1, p.1-222, (2016) Read More / View Supplemental Materials
2015
The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia.Muñoz, JF, Gauthier GM, Desjardins CA, Gallo JE, Holder J., Sullivan TD, Marty AJ, Carmen JC, Chen Z., Ding L., Gujja S., Magrini V., Misas E., Mitreva M., Priest M., Saif S., Whiston EA, Young S., Zeng Q., Goldman WE, et al. PLoS genetics, 2015/10/01, Volume 11, Issue 10, p.e1005493, (2015) Read More / View Supplemental Materials
Abstract
Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal.Cohen, KA, Abeel T., Manson McGuire A., Desjardins CA, Munsamy V., Shea TP, Walker BJ, Bantubani N., Almeida DV, Alvarado L., Chapman SB, Mvelase NR, Duffy EY, FitzGerald MG, Govender P., Gujja S., Hamilton S., Howarth C., Larimer JD, Maharaj K., et al. PLoS medicine, 2015/09/01, Volume 12, Issue 9, p.e1001880, (2015) Read More / View Supplemental Materials
Abstract
Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii.Farrer, RA, Desjardins CA, Sakthikumar S., Gujja S., Saif S., Zeng Q., Chen Y., Voelz K., Heitman J., May RC, Fisher MC, and Cuomo CA mBio, 2015/09/01, Volume 6, Issue 5, (2015) Read More / View Supplemental Materials
Abstract
Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus.Perlin, MH, Amselem J., Fontanillas E., Toh SS, Chen Z., Goldberg J., Duplessis S., Henrissat B., Young S., Zeng Q., Aguileta G., Petit E., Badouin H., Andrews J., Razeeq D., Gabaldón T., Quesneville H., Giraud T., Hood ME, Schultz DJ, et al. BMC genomics, 2015/06/16, Volume 16, Issue 1, p.461, (2015) Read More / View Supplemental Materials
Abstract
Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes.Desjardins, CA, Sanscrainte ND, Goldberg JM, Heiman D., Young S., Zeng Q., Madhani HD, Becnel JJ, and Cuomo CA Nature communications, 2015/05/13, Volume 6, p.7121, (2015) Read More / View Supplemental Materials
Abstract
Genetic and phenotypic intra-species variation in Candida albicans.Hirakawa, MP, Martinez DA, Sakthikumar S., Anderson MZ, Berlin A., Gujja S., Zeng Q., Zisson E., Wang JM, Greenberg JM, Berman J., Bennett RJ, and Cuomo CA Genome research, 2015/03/01, Volume 25, Issue 3, p.413-25, (2015) Read More / View Supplemental Materials
Abstract
2014
Genome update of the dimorphic human pathogenic fungi causing paracoccidioidomycosis.Muñoz, JF, Gallo JE, Misas E., Priest M., Imamovic A., Young S., Zeng Q., Clay OK, McEwen JG, and Cuomo CA PLoS neglected tropical diseases, 2014/12/01, Volume 8, Issue 12, p.e3348, (2014) Read More / View Supplemental Materials
Abstract
Evolution of invasion in a diverse set of fusobacterium species.Manson McGuire, A., Cochrane K., Griggs AD, Haas BJ, Abeel T., Zeng Q., Birren BW, Allen-Vercoe E., and Earl AM mBio, 2014/11/04, Volume 5, Issue 6, (2014) Read More / View Supplemental Materials
Abstract
Genome Sequence of Fusarium oxysporum f. sp. melonis Strain NRRL 26406, a Fungus Causing Wilt Disease on Melon.Ma, LJ, Shea T., Young S., Zeng Q., and Kistler HC Genome announcements, 2014/07/31, Volume 2, Issue 4, (2014) Read More / View Supplemental Materials
Abstract
Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251).Cuomo, CA, Rodriguez-Del Valle N., Perez-Sanchez L., Abouelleil A., Goldberg J., Young S., Zeng Q., and Birren BW Genome announcements, 2014/05/22, Volume 2, Issue 3, (2014) Read More / View Supplemental Materials
Abstract
Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.Janbon, G., Ormerod KL, Paulet D., Byrnes EJ 3rd, Yadav V., Chatterjee G., Mullapudi N., Hon CC, Billmyre RB, Brunel F., Bahn YS, Chen W., Chen Y., Goldberg J., Gujja S., Jones S., Kodira CD, Marra M., Mieczkowski PA, Schein JE, et al. PLoS genetics, 2014/04/01, Volume 10, Issue 4, p.e1004261, (2014) Read More / View Supplemental Materials
Abstract
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.Walker, BJ, Abeel T., Shea T., Priest M., Abouelliel A., Sakthikumar S., Cuomo CA, Zeng Q., Wortman J., Young SK, and Earl AM PloS one, 2014/01/01, Volume 9, Issue 11, p.e112963, (2014) Read More / View Supplemental Materials
Abstract
2013
High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides.Lebreton, F., Valentino MD, Duncan LB, Zeng Q., Manson McGuire A., Earl AM, and Gilmore MS Genome announcements, 2013/12/26, Volume 1, Issue 6, (2013) Read More / View Supplemental Materials
Abstract
Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains.Lebreton, F., McGuire AM, Godfrey P., Griggs A., Cheng L., Saif S., Young S., Zeng Q., Wortman J., Birren B., Earl AM, and Gilmore MS mBio, 2013/08/20, Volume 4, Issue 4, (2013) Read More / View Supplemental Materials
Abstract
Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily.Goldberg, JM, Griggs AD, Smith JL, Haas BJ, Wortman JR, and Zeng Q. Bioinformatics (Oxford, England), 2013/08/13, (2013) Read More / View Supplemental Materials
Abstract
Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica.Jiang, RH, de Bruijn I., Haas BJ, Belmonte R., Löbach L., Christie J., van den Ackerveken G., Bottin A., Bulone V., Díaz-Moreno SM, Dumas B., Fan L., Gaulin E., Govers F., Grenville-Briggs LJ, Horner NR, Levin JZ, Mammella M., Meijer HJ, Morris P., et al. PLoS genetics, 2013/06/01, Volume 9, Issue 6, p.e1003272, (2013) Read More / View Supplemental Materials
Abstract
Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.Desjardins, CA, Cerqueira GC, Goldberg JM, Dunning Hotopp JC, Haas BJ, Zucker J., Ribeiro JM, Saif S., Levin JZ, Fan L., Zeng Q., Russ C., Wortman JR, Fink DL, Birren BW, and Nutman TB Nature genetics, 2013/05/01, Volume 45, Issue 5, p.495-500, (2013) Read More / View Supplemental Materials
Abstract
Evolutionary dynamics of the accessory genome of Listeria monocytogenes.den Bakker, HC, Desjardins CA, Griggs AD, Peters JE, Zeng Q., Young SK, Kodira CD, Yandava C., Hepburn TA, Haas BJ, Birren BW, and Wiedmann M. PloS one, 2013/01/01, Volume 8, Issue 6, p.e67511, (2013) Read More / View Supplemental Materials
Abstract
2012
Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth.Cuomo, CA, Desjardins CA, Bakowski MA, Goldberg J., Ma AT, Becnel JJ, Didier ES, Fan L., Heiman DI, Levin JZ, Young S., Zeng Q., and Troemel ER Genome research, 2012/12/01, Volume 22, Issue 12, p.2478-88, (2012) Read More / View Supplemental Materials
Abstract
The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum.Neafsey, DE, Galinsky K., Jiang RH, Young L., Sykes SM, Saif S., Gujja S., Goldberg JM, Young S., Zeng Q., Chapman SB, Dash AP, Anvikar AR, Birren BW, Escalante AA, Barnwell JW, and Carlton JM Nature genetics, 2012/09/01, Volume 44, Issue 9, p.1046-50, (2012) Read More / View Supplemental Materials
Abstract
Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection.Henn, MR, Boutwell CL, Charlebois P., Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S., Zody MC, Erlich RL, Green LM, Berical A., Wang Y., Casali M., Streeck H., Bloom AK, Dudek T., Tully D., et al. PLoS pathogens, 2012/03/01, Volume 8, Issue 3, p.e1002529, (2012) Read More / View Supplemental Materials
Abstract
Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.Grad, YH, Lipsitch M., Feldgarden M., Arachchi HM, Cerqueira GC, FitzGerald M., Godfrey P., Haas BJ, Murphy CI, Russ C., Sykes S., Walker BJ, Wortman JR, Young S., Zeng Q., Abouelleil A., Bochicchio J., Chauvin S., Desmet T., Gujja S., et al. Proceedings of the National Academy of Sciences of the United States of America, 2012/02/21, Volume 109, Issue 8, p.3065-70, (2012) Read More / View Supplemental Materials
Abstract
Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.D'Souza, CA, Kronstad JW, Taylor G., Warren R., Yuen M., Hu G., Jung WH, Sham A., Kidd SE, Tangen K., Lee N., Zeilmaker T., Sawkins J., McVicker G., Shah S., Gnerre S., Griggs A., Zeng Q., Bartlett K., Li W., et al. mBio, 2012/01/06, Volume 2, Issue 1, p.e00342-10, (2012) Read More / View Supplemental Materials
Abstract
Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection.Martinez, DA, Oliver BG, Gräser Y., Goldberg JM, Li W., Martinez-Rossi NM, Monod M., Shelest E., Barton RC, Birch E., Brakhage AA, Chen Z., Gurr SJ, Heiman D., Heitman J., Kosti I., Rossi A., Saif S., Samalova M., Saunders CW, et al. mBio, 2012/01/01, Volume 3, Issue 5, (2012) Read More / View Supplemental Materials
Abstract
2011
High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)).Earl, AM, Desjardins CA, FitzGerald MG, Arachchi HM, Zeng Q., Mehta T., Griggs A., Birren BW, Toney NC, Carr J., Posey J., and Butler WR Standards in genomic sciences, 2011/12/31, Volume 5, Issue 3, p.389-97, (2011) Read More / View Supplemental Materials
Abstract
Glioblastoma-Derived Epidermal Growth Factor Receptor Carboxyl-Terminal Deletion Mutants Are Transforming and Are Sensitive to EGFR-Directed Therapies.Cho, J., Pastorino S., Zeng Q., Xu X., Johnson W., Vandenberg S., Verhaak R., Cherniack AD, Watanabe H., Dutt A., Kwon J., Chao YS, Onofrio RC, Chiang D., Yuza Y., Kesari S., and Meyerson M. Cancer research, 2011/12/15, Volume 71, Issue 24, p.7587-96, (2011) Read More / View Supplemental Materials
Abstract
Approaches to Fungal Genome Annotation.Haas, BJ, Zeng Q., Pearson MD, Cuomo CA, and Wortman JR Mycology, 2011/10/03, Volume 2, Issue 3, p.118-141, (2011) Read More / View Supplemental Materials
Abstract
Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis.Desjardins, CA, Champion MD, Holder JW, Muszewska A., Goldberg J., Bailão AM, Brigido MM, Ferreira ME, Garcia AM, Grynberg M., Gujja S., Heiman DI, Henn MR, Kodira CD, León-Narváez H., Longo LV, Ma LJ, Malavazi I., Matsuo AL, Morais FV, et al. PLoS genetics, 2011/10/01, Volume 7, Issue 10, p.e1002345, (2011) Read More / View Supplemental Materials
Abstract
Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development.Holder, JW, Ulrich JC, DeBono AC, Godfrey PA, Desjardins CA, Zucker J., Zeng Q., Leach AL, Ghiviriga I., Dancel C., Abeel T., Gevers D., Kodira CD, Desany B., Affourtit JP, Birren BW, and Sinskey AJ PLoS genetics, 2011/09/01, Volume 7, Issue 9, p.e1002219, (2011) Read More / View Supplemental Materials
Abstract
Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea.Amselem, J., Cuomo CA, van Kan JA, Viaud M., Benito EP, Couloux A., Coutinho PM, de Vries RP, Dyer PS, Fillinger S., Fournier E., Gout L., Hahn M., Wincker P., Anthouard V., Chen Z., Danchin EG, Dasilva C., Güldener U., Henrissat B., et al. PLoS genetics, 2011/08/01, Volume 7, Issue 8, p.e1002230, (2011) Read More / View Supplemental Materials
Abstract
Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens.Klosterman, SJ, Subbarao KV, Kang S., Veronese P., Gold SE, Thomma BP, Chen Z., Henrissat B., Lee YH, Park J., Garcia-Pedrajas MD, Barbara DJ, Anchieta A., de Jonge R., Santhanam P., Maruthachalam K., Atallah Z., Amyotte SG, Paz Z., Inderbitzin P., et al. PLoS pathogens, 2011/07/01, Volume 7, Issue 7, p.e1002137, (2011) Read More / View Supplemental Materials
Abstract
Full-length transcriptome assembly from RNA-Seq data without a reference genome.Grabherr, MG, Haas BJ, Yassour M., Levin JZ, Thompson DA, Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., Di Palma F., Birren BW, Nusbaum C., Lindblad-Toh K., Friedman N., et al. Nature biotechnology, 2011/05/15, Volume 29, Issue 7, p.644-52, (2011) Read More / View Supplemental Materials
Abstract
2010
Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.Brister, JR, Bao Y., Kuiken C., Lefkowitz EJ, Le Mercier P., Leplae R., Madupu R., Scheuermann RH, Schobel S., Seto D., Shrivastava S., Sterk P., Zeng Q., Klimke W., and Tatusova T. Viruses, 2010/10/01, Volume 2, Issue 10, p.2258-68, (2010) Read More / View Supplemental Materials
Abstract
Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.Neafsey, DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E., Hung CY, McMahan C., White J., Sykes S., Heiman D., Young S., Zeng Q., Abouelleil A., Aftuck L., Bessette D., Brown A., FitzGerald M., Lui A., Macdonald JP, et al. Genome research, 2010/07/01, Volume 20, Issue 7, p.938-46, (2010) Read More / View Supplemental Materials
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A catalog of reference genomes from the human microbiome.Human Microbiome Jumpstart Reference Strains, Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M., Sodergren E., Chinwalla AT, Feldgarden M., Gevers D., Haas BJ, Madupu R., Ward DV, Birren BW, Gibbs RA, Methe B., Petrosino JF, et al. Science (New York, N.Y.), 2010/05/21, Volume 328, Issue 5981, p.994-9, (2010) Read More / View Supplemental Materials
Abstract
High-quality draft genome sequences of 28 Enterococcus sp. isolates.Palmer, KL, Carniol K., Manson JM, Heiman D., Shea T., Young S., Zeng Q., Gevers D., Feldgarden M., Birren B., and Gilmore MS Journal of bacteriology, 2010/05/01, Volume 192, Issue 9, p.2469-70, (2010) Read More / View Supplemental Materials
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Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.Ma, LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A., Dufresne M., Freitag M., Grabherr M., Henrissat B., Houterman PM, Kang S., Shim WB, Woloshuk C., Xie X., Xu JR, Antoniw J., Baker SE, Bluhm BH, Breakspear A., et al. Nature, 2010/03/18, Volume 464, Issue 7287, p.367-73, (2010) Read More / View Supplemental Materials
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Analysis of high-throughput sequencing and annotation strategies for phage genomes.Henn, MR, Sullivan MB, Stange-Thomann N., Osburne MS, Berlin AM, Kelly L., Yandava C., Kodira C., Zeng Q., Weiand M., Sparrow T., Saif S., Giannoukos G., Young SK, Nusbaum C., Birren BW, and Chisholm SW PloS one, 2010/02/05, Volume 5, Issue 2, p.e9083, (2010) Read More / View Supplemental Materials
Abstract
2009
Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives.Sharpton, TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R., Kodira CD, Neafsey DE, Zeng Q., Hung CY, McMahan C., Muszewska A., Grynberg M., Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, et al. Genome research, 2009/10/01, Volume 19, Issue 10, p.1722-31, (2009) Read More / View Supplemental Materials
Abstract
Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication.Ma, LJ, Ibrahim AS, Skory C., Grabherr MG, Burger G., Butler M., Elias M., Idnurm A., Lang BF, Sone T., Abe A., Calvo SE, Corrochano LM, Engels R., Fu J., Hansberg W., Kim JM, Kodira CD, Koehrsen MJ, Liu B., et al. PLoS genetics, 2009/07/01, Volume 5, Issue 7, p.e1000549, (2009) Read More / View Supplemental Materials
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Evolution of pathogenicity and sexual reproduction in eight Candida genomes.Butler, G., Rasmussen MD, Lin MF, Santos MA, Sakthikumar S., Munro CA, Rheinbay E., Grabherr M., Forche A., Reedy JL, Agrafioti I., Arnaud MB, Bates S., Brown AJ, Brunke S., Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D., Hoyer LL, et al. Nature, 2009/06/04, Volume 459, Issue 7247, p.657-62, (2009) Read More / View Supplemental Materials
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Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies.Champion, MD, Zeng Q., Nix EB, Nano FE, Keim P., Kodira CD, Borowsky M., Young S., Koehrsen M., Engels R., Pearson M., Howarth C., Larson L., White J., Alvarado L., Forsman M., Bearden SW, Sjöstedt A., Titball R., Michell SL, et al. PLoS pathogens, 2009/05/01, Volume 5, Issue 5, p.e1000459, (2009) Read More / View Supplemental Materials
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2007
Genome sequence of Aedes aegypti, a major arbovirus vector.Nene, V., Wortman JR, Lawson D., Haas B., Kodira C., Tu ZJ, Loftus B., Xi Z., Megy K., Grabherr M., Ren Q., Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J., Sinkins SP, Hogenkamp DG, Amedeo P., et al. Science (New York, N.Y.), 2007/06/22, Volume 316, Issue 5832, p.1718-23, (2007) Read More / View Supplemental Materials
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2006
DNA sequence and analysis of human chromosome 8.Nusbaum, C., Mikkelsen TS, Zody MC, Asakawa S., Taudien S., Garber M., Kodira CD, Schueler MG, Shimizu A., Whittaker CA, Chang JL, Cuomo CA, Dewar K., FitzGerald MG, Yang X., Allen NR, Anderson S., Asakawa T., Blechschmidt K., Bloom T., et al. Nature, 2006/01/19, Volume 439, Issue 7074, p.331-5, (2006) Read More / View Supplemental Materials
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2005
DNA sequence and analysis of human chromosome 18.Nusbaum, C., Zody MC, Borowsky ML, Kamal M., Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA, Dewar K., FitzGerald MG, Yang X., Abouelleil A., Allen NR, Anderson S., Bloom T., Bugalter B., Butler J., Cook A., DeCaprio D., et al. Nature, 2005/09/22, Volume 437, Issue 7058, p.551-5, (2005) Read More / View Supplemental Materials
Abstract
  • Showing 1-48 of 48 Results