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Publications

2012
Atlas2 Cloud: a framework for personal genome analysis in the cloud., Evani, Uday S., Challis Danny, Yu Jin, Jackson Andrew R., Paithankar Sameer, Bainbridge Matthew N., Jakkamsetti Adinarayana, Pham Peter, Coarfa Cristian, Milosavljevic Aleksandar, et al. , BMC genomics, 2012, Volume 13 Suppl 6, p.S19, (2012) Abstract
Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms., Lu, James T., Wang Yi, Gibbs Richard A., and Yu Fuli , Genome biology, 2012, Volume 13, Issue 2, p.R15, (2012) Abstract
Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes., Qin, Xiang, Galloway-Peña Jessica R., Sillanpaa Jouko, Roh Jung Hyeob, Nallapareddy Sreedhar R., Chowdhury Shahreen, Bourgogne Agathe, Choudhury Tina, Muzny Donna M., Buhay Christian J., et al. , BMC microbiology, 2012, Volume 12, p.135, (2012) Abstract
Genomic and SNP analyses demonstrate a distant separation of the hospital and community-associated clades of Enterococcus faecium., Galloway-Peña, Jessica, Roh Jung Hyeob, Latorre Mauricio, Qin Xiang, and Murray Barbara E. , PloS one, 2012, Volume 7, Issue 1, p.e30187, (2012) Abstract
Human genome sequencing in health and disease., Gonzaga-Jauregui, Claudia, Lupski James R., and Gibbs Richard A. , Annual review of medicine, 2012, Volume 63, p.35-61, (2012) Abstract
Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma., Creighton, Chad J., Hernandez-Herrera Anadulce, Jacobsen Anders, Levine Douglas A., Mankoo Parminder, Schultz Nikolaus, Du Ying, Zhang Yiqun, Larsson Erik, Sheridan Robert, et al. , PloS one, 2012, Volume 7, Issue 3, p.e34546, (2012) Abstract
An integrative variant analysis suite for whole exome next-generation sequencing data., Challis, Danny, Yu Jin, Evani Uday S., Jackson Andrew R., Paithankar Sameer, Coarfa Cristian, Milosavljevic Aleksandar, Gibbs Richard A., and Yu Fuli , BMC bioinformatics, 2012, Volume 13, p.8, (2012) Abstract
MAPK target sites of eyes absent are not required for eye development or survival in Drosophila., Jusiak, Barbara, Abulimiti Abuduaini, Haelterman Nele, Chen Rui, and Mardon Graeme , PloS one, 2012, Volume 7, Issue 12, p.e50776, (2012) Abstract
Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology., English, Adam C., Richards Stephen, Han Yi, Wang Min, Vee Vanesa, Qu Jiaxin, Qin Xiang, Muzny Donna M., Reid Jeffrey G., Worley Kim C., et al. , PloS one, 2012, Volume 7, Issue 11, p.e47768, (2012) Abstract
Mis-assembled "segmental duplications" in two versions of the Bos taurus genome., Zimin, Aleksey V., Kelley David R., Roberts Michael, Marçais Guillaume, Salzberg Steven L., and Yorke James A. , PloS one, 2012, Volume 7, Issue 8, p.e42680, (2012) Abstract
PDX-1 is a therapeutic target for pancreatic cancer, insulinoma and islet neoplasia using a novel RNA interference platform., Liu, Shi-He, Rao Donald D., Nemunaitis John, Senzer Neil, Zhou Guisheng, Dawson David, Gingras Marie-Claude, Wang Zhaohui, Gibbs Richard, Norman Michael, et al. , PloS one, 2012, Volume 7, Issue 8, p.e40452, (2012) Abstract
Phosphorylated and sumoylation-deficient progesterone receptors drive proliferative gene signatures during breast cancer progression., Knutson, Todd P., Daniel Andrea R., Fan Danhua, Silverstein Kevin At, Covington Kyle R., Fuqua Suzanne A. W., and Lange Carol A. , Breast cancer research : BCR, 2012, Volume 14, Issue 3, p.R95, (2012) Abstract
PNPLA3 polymorphisms and liver aminotransferase levels in a Mexican American population., Li, Quan, Qu Hui-Qi, Rentfro Anne R., Grove Megan L., Mirza Shaper, Lu Yang, Hanis Craig L., Fallon Michael B., Boerwinkle Eric, Fisher-Hoch Susan P., et al. , Clinical and investigative medicine. Médecine clinique et experimentale, 2012, Volume 35, Issue 4, p.E237-45, (2012) Abstract
REGγ is associated with multiple oncogenic pathways in human cancers., He, Jing, Cui Long, Zeng Yu, Wang Guangqiang, Zhou Ping, Yang Yuanyuan, Ji Lei, Zhao Yanyan, Chen Jiwu, Wang Zhuo, et al. , BMC cancer, 2012, Volume 12, p.75, (2012) Abstract
Transcriptional enhancers in protein-coding exons of vertebrate developmental genes., Ritter, Deborah I., Dong Zhiqiang, Guo Su, and Chuang Jeffrey H. , PloS one, 2012, Volume 7, Issue 5, p.e35202, (2012) Abstract
Treponema pallidum infection in the wild baboons of East Africa: distribution and genetic characterization of the strains responsible., Harper, Kristin N., Fyumagwa Robert D., Hoare Richard, Wambura Philemon N., Coppenhaver Dorian H., Sapolsky Robert M., Alberts Susan C., Tung Jenny, Rogers Jeffrey, Kilewo Morris, et al. , PloS one, 2012, Volume 7, Issue 12, p.e50882, (2012) Abstract
TWIST represses estrogen receptor-alpha expression by recruiting the NuRD protein complex in breast cancer cells., Fu, Junjiang, Zhang Lianmei, He Tao, Xiao Xiuli, Liu Xiaoyan, Wang Li, Yang Luquan, Yang Manman, Zhang Tiandan, Chen Rui, et al. , International journal of biological sciences, 2012, Volume 8, Issue 4, p.522-32, (2012) Abstract
Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster., Ober, Ulrike, Ayroles Julien F., Stone Eric A., Richards Stephen, Zhu Dianhui, Gibbs Richard A., Stricker Christian, Gianola Daniel, Schlather Martin, Mackay Trudy F. C., et al. , PLoS genetics, 2012, Volume 8, Issue 5, p.e1002685, (2012) Abstract
Whole genome sequence of Treponema pallidum ssp. pallidum, strain Mexico A, suggests recombination between yaws and syphilis strains., Pětrošová, Helena, Zobaníková Marie, Čejková Darina, Mikalová Lenka, Pospíšilová Petra, Strouhal Michal, Chen Lei, Qin Xiang, Muzny Donna M., Weinstock George M., et al. , PLoS neglected tropical diseases, 2012, Volume 6, Issue 9, p.e1832, (2012) Abstract
Estrogen Receptor-Positive Breast Cancer Cells Drive CAFs to Secrete Leptin and Support Tumor Invasiveness, Barone, Ines, Catalano Stefania, Gelsomino Luca, Panza Salvatore, Marsico Stefania, Giordano Cinzia, Bonofiglio Daniela, Casaburi Ivan, Covington Kyle R., Fuqua Suzanne, et al. , The FASEB Journal, Volume 26, p.142–7, (2012)
Increasing the number of URMS in genomic science; (1854F)., Murray, D., Whittington D., and Gibbs R. , 62nd Annual Meeting of The American Society of Human Genetics, San Francisco, California, (2012)
Targeting Thyroid Receptor b in Estrogen Receptor Negative Breast Cancer, Gu, G., Covington K., Rechoum Y., O'Malley B., Mangelsdorf D., Minna J., Webb P., and Fuqua S. , Cancer Research, Volume 72, Number 24 Supplement 3, (2012)
Whole Exome Sequencing of Polycythemia Vera Reveals Novel Recurrent Somatic and Germline Variation, Wang, Linghua, Swierczek Sabina, Piterkova Lucie, Hickman Kimberly, Wheeler David A., and Prchal Josef T. , Blood, Volume 120, Number 21, (2012)


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