Genetics - 2012

Huang, W., Richards, S., Carbone, M. A., Zhu, D., Anholt, R. R. H., Ayroles, J. F., … Mackay, T. F. C. (2012). Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proceedings of the National Academy of Sciences, 109(39), 15553–15559. https://doi.org/10.1073/pnas.1213423109

Mackay, T. F. C., Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., … Gibbs, R. A. (2012). The Drosophila melanogaster Genetic Reference Panel. Nature, 482(7384), 173–178. https://doi.org/10.1038/nature10811

Liberles, D. A., Teichmann, S. A., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., … Whelan, S. (2012). The interface of protein structure, protein biophysics, and molecular evolution. Protein Science, 21(6), 769–785. https://doi.org/10.1002/pro.2071

Péret, B., Swarup, K., Ferguson, A., Seth, M., Yang, Y., Dhondt, S., … Syed, A. (2012). AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during Arabidopsis development. The Plant Cell Online, 24(7), 2874–2885. https://doi.org/10.1105/tpc.112.097766

Ma, W., Halweg, C. J., Menendez, D., & Resnick, M. A. (2012). Differential effects of poly(ADP-ribose) polymerase inhibition on DNA break repair in human cells are revealed with Epstein-Barr virus. Proceedings of the National Academy of Sciences, 109(17), 6590–6595. https://doi.org/10.1073/pnas.1118078109

Silva, L. D. C. E., Wang, S., & Zeng, Z.-B. (2012). Composite Interval Mapping and Multiple Interval Mapping: Procedures and Guidelines for Using Windows QTL Cartographer. In Methods in Molecular Biology (pp. 75–119). https://doi.org/10.1007/978-1-61779-785-9_6

Trupp, M., Zhu, H., Wikoff, W. R., Baillie, R. A., Zeng, Z.-B., Karp, P. D., … Kaddurah-Daouk, R. (2012). Metabolomics Reveals Amino Acids Contribute to Variation in Response to Simvastatin Treatment. PLoS ONE, 7(7), e38386. https://doi.org/10.1371/journal.pone.0038386

Feng, C.-M., Liu, X., Yu, Y., Xie, D., Franks, R. G., & Xiang, Q.-Y. J. (2012). Evolution of bract development and B-class MADS box gene expression in petaloid bracts of cornus s. l. (cornaceae). New Phytologist, 196(2), 631–643. https://doi.org/10.1111/j.1469-8137.2012.04255.x

Klassen, H., Kiilgaard, J. F., Warfvinge, K., Samuel, M. S., Prather, R. S., Wong, F., … Young, M. J. (2012). Photoreceptor Differentiation following Transplantation of Allogeneic Retinal Progenitor Cells to the Dystrophic Rhodopsin Pro347Leu Transgenic Pig. STEM CELLS INTERNATIONAL, 2012. https://doi.org/10.1155/2012/939801

Silva, L. D. E., Wang, S. C., & Zeng, Z. B. (2012). Multiple trait multiple interval mapping of quantitative trait loci from inbred line crosses. BMC Genetics, 13.

O'Flaherty, S., & Klaenhammer, T. R. (2012). Influence of Exposure Time on Gene Expression by Human Intestinal Epithelial Cells Exposed to Lactobacillus acidophilus. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 78(14), 5028–5032. https://doi.org/10.1128/aem.00504-12

Kajikawa, A., Zhang, L., Long, J., Nordone, S., Stoeker, L., LaVoy, A., … Dean, G. (2012). Construction and Immunological Evaluation of Dual Cell Surface Display of HIV-1 Gag and Salmonella enterica Serovar Typhimurium FliC in Lactobacillus acidophilus for Vaccine Delivery. CLINICAL AND VACCINE IMMUNOLOGY, 19(9), 1374–1381. https://doi.org/10.1128/cvi.00049-12

Carroll, I. M., Ringel-Kulka, T., Siddle, J. P., Klaenhammer, T. R., & Ringel, Y. (2012). Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage. PLoS One, 7(10). https://doi.org/10.1371/journal.pone.0046953

Peret, B., Swarup, K., Ferguson, A., Seth, M., Yang, Y. D., Dhondt, S., … Laplaze, L. (2012). AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during arabidopsis development. Plant Cell, 24(7), 2874–2885.

Klaenhammer, T. R., Kleerebezem, M., Kopp, M. V., & Rescigno, M. (2012). The impact of probiotics and prebiotics on the immune system. NATURE REVIEWS IMMUNOLOGY, 12(10), 728–734. https://doi.org/10.1038/nri3312

Connallon, T., Singh, N. D., & Clark, A. G. (2012). Impact of Genetic Architecture on the Relative Rates of X versus Autosomal Adaptive Substitution. MOLECULAR BIOLOGY AND EVOLUTION, 29(8), 1933–1942. https://doi.org/10.1093/molbev/mss057

Zou, L. W., Susko, E., Field, C., & Roger, A. J. (2012). Fitting nonstationary general-time-reversible models to obtain edge-lengths and frequencies for the barry-hartigan model. Systematic Biology, 61(6), 927–940.

Rinella, E. S., & Threadgill, D. W. (2012). Efficacy of EGFR Inhibition Is Modulated by Model, Sex, Genetic Background and Diet: Implications for Preclinical Cancer Prevention and Therapy Trials. PLOS ONE, 7(6). https://doi.org/10.1371/journal.pone.0039552

Stasiuk, S. J., Scott, M. J., & Grant, W. N. (2012). Developmental plasticity and the evolution of parasitism in an unusual nematode, Parastrongyloides trichosuri. EvoDevo, 3(1). https://doi.org/10.1186/2041-9139-3-1

Felix, T. M., Hughes, K. A., Stone, E. A., Drnevich, J. M., & Leips, J. (2012). Age-specific variation in immune response in drosophila melanogaster has a genetic basis. Genetics, 191(3), 989–584.

Hines, H. M., Papa, R., Ruiz, M., Papanicolaou, A., Wang, C., Nijhout, H. F., … Reed, R. D. (2012). Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation. BMC Genomics, 13.

Welsh, C. E., Miller, D. R., Manly, K. F., Wang, J., McMillan, L., Morahan, G., … Villena, F. P.-M. (2012). Status and access to the Collaborative Cross population. MAMMALIAN GENOME, 23(9-10), 706–712. https://doi.org/10.1007/s00335-012-9410-6

Zhou, X., Sun, L. G., Huang, W., Cheng, W. H., & Jia, N. (2012). Precipitation in the Yellow River drainage basin and East Asian monsoon strength on a decadal time scale. Quaternary Research, 78(3), 486–491.

Li, L., Lim, S. F., Puretzky, A. A., Riehn, R., & Hallen, H. D. (2012). Near-field enhanced ultraviolet resonance Raman spectroscopy using aluminum bow-tie nano-antenna. Applied Physics Letters, 101(11).

Ardito, C. M., Gruener, B. M., Takeuchi, K. K., Lubeseder-Martellato, C., Teichmann, N., Mazur, P. K., … Siveke, J. T. (2012). EGF Receptor Is Required for KRAS-Induced Pancreatic Tumorigenesis. CANCER CELL, 22(3), 304–317. https://doi.org/10.1016/j.ccr.2012.07.024

Singh, N. D. (2012, October). Classical Genetics Meets Next-Generation Sequencing: Uncovering a Genome-Wide Recombination Drosophila melanogaster. PLOS GENETICS, Vol. 8. https://doi.org/10.1371/journal.pgen.1003024

Kaddurah-Daouk, R., Yuan, P., Boyle, S. H., Matson, W., Wang, Z., Zeng, Z. B., … Drevets, W. (2012). Cerebrospinal Fluid Metabolome in Mood Disorders-Remission State has a Unique Metabolic Profile. Scientific Reports, 2(1). https://doi.org/10.1038/srep00667

Andersen, J. M., Barrangou, R., Abou Hachem, M., Lahtinen, S. J., Goh, Y.-J., Svensson, B., & Klaenhammer, T. R. (2012). Transcriptional Analysis of Prebiotic Uptake and Catabolism by Lactobacillus acidophilus NCFM. PLOS ONE, 7(9). https://doi.org/10.1371/journal.pone.0044409

Threadgill, D. W., & Churchill, G. A. (2012). Ten Years of the Collaborative Cross. G3-GENES GENOMES GENETICS, 2(2), 153–156. https://doi.org/10.1534/g3.111.001891

Eversley, C. D., Yuying, X., Pearsall, R. S., & Threadgill, D. W. (2012). Mapping Six New Susceptibility to Colon Cancer (Scc) Loci Using a Mouse Interspecific Backcross. G3-GENES GENOMES GENETICS, 2(12), 1577–1584. https://doi.org/10.1534/g3.112.002253

Kelada, S. N. P., Aylor, D. L., Peck, B. C. E., Ryan, J. F., Tavarez, U., Buus, R. J., … Collins, F. S. (2012). Genetic Analysis of Hematological Parameters in Incipient Lines of the Collaborative Cross. G3-GENES GENOMES GENETICS, 2(2), 157–165. https://doi.org/10.1534/g3.111.001776

Bottomly, D., Ferris, M. T., Aicher, L. D., Rosenzweig, E., Whitmore, A., Aylor, D. L., … Heise, M. (2012). Expression quantitative trait loci for extreme host response to influenza a in pre-collaborative cross mice. G3-Genes Genomes Genetics, 2(2), 213–221.

Mustafi, R., Dougherty, U., Shah, H., Dehghan, H., Gliksberg, A., Wu, J., … Bissonnette, M. (2012). Both stromal cell and colonocyte epidermal growth factor receptors control HCT116 colon cancer cell growth in tumor xenografts. CARCINOGENESIS, 33(10), 1930–1939. https://doi.org/10.1093/carcin/bgs231

Liberles, D. A., Teichmann, S. A., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., … Lakner, C. (2012). [Review of The interface of protein structure, protein biophysics, and molecular evolution]. Protein Science, 21(6), 769–785.

Miko, I., Friedrich, F., Yoder, M. J., Hines, H. M., Deitz, L. L., Bertone, M. A., … Deans, A. R. (2012). On Dorsal Prothoracic Appendages in Treehoppers (Hemiptera: Membracidae) and the Nature of Morphological Evidence. PLOS ONE, 7(1). https://doi.org/10.1371/journal.pone.0030137

McFerrin, L. G., & Atchley, W. R. (2012). A novel N-terminal domain may dictate the glucose response of Mondo proteins. PLoS One, 7(4).

Sommer, J. R., Jackson, L. R., Simpson, S. G., Collins, E. B., Piedrahita, J. A., & Petters, R. M. (2012). Transgenic Stra8-EYFP pigs: a model for developing male germ cell technologies. TRANSGENIC RESEARCH, 21(2), 383–392. https://doi.org/10.1007/s11248-011-9542-6

Abou Hachem, M., Fredslund, F., Andersen, J. M., Larsen, R. J., Majumder, A., Ejby, M., … Svensson, B. (2012). Raffinose family oligosaccharide utilisation by probiotic bacteria: insight into substrate recognition, molecular architecture and diversity of GH36 alpha-galactosidases. BIOCATALYSIS AND BIOTRANSFORMATION, 30(3), 316–325. https://doi.org/10.3109/10242422.2012.674717

Concha, C., Edman, R. M., Belikoff, E. J., Schiemann, A. H., Carey, B., & Scott, M. J. (2012). Organization and expression of the Australian sheep blowfly (<i>Lucilia cuprina</i>) <i>hsp23</i>, <i>hsp24, hsp70</i> and <i>hsp83</i> genes. Insect Molecular Biology, 21(2), 169–180. https://doi.org/10.1111/j.1365-2583.2011.01123.x

Abo, R., Hebbring, S., Ji, Y., Zhu, H., Zeng, Z.-B., Batzler, A., … Weinshilboum, R. M. (2012). Merging pharmacometabolomics with pharmacogenomics using ‘1000 Genomes’ single-nucleotide polymorphism imputation. Pharmacogenetics and Genomics, 22(4), 247–253. https://doi.org/10.1097/fpc.0b013e32835001c9

Olarte, R. A., Horn, B. W., Dorner, J. W., Monacell, J. T., Singh, R., Stone, E. A., & Carbone, I. (2012). Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis. MOLECULAR ECOLOGY, 21(6), 1453–1476. https://doi.org/10.1111/j.1365-294x.2011.05398.x

Calsbeek, B. (2012). EXPLORING VARIATION IN FITNESS SURFACES OVER TIME OR SPACE. EVOLUTION, 66(4), 1126–1137. https://doi.org/10.1111/j.1558-5646.2011.01503.x

Law, S. H. W., Redelings, B. D., & Kullman, S. W. (2012). Comparative Genomics of Duplicate gamma-Glutamyl Transferase Genes in Teleosts: Medaka (Oryzias latipes), Stickleback (Gasterosteus aculeatus), Green Spotted Pufferfish (Tetraodon nigroviridis), Fugu (Takifugu rubripes), and Zebrafish (Danio rerio). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION, 318B(1), 35–49. https://doi.org/10.1002/jez.b.21439

Sze, S. H., Dunham, J. P., Carey, B., Chang, P. L., Li, F., Edman, R. M., … Tarone, A. M. (2012). A <i>de novo</i> transcriptome assembly of <i>Lucilia sericata</i> (Diptera: Calliphoridae) with predicted alternative splices, single nucleotide polymorphisms and transcript expression estimates. Insect Molecular Biology, 21(2), 205–221. https://doi.org/10.1111/j.1365-2583.2011.01127.x

Franzke, C.-W., Cobzaru, C., Triantafyllopoulou, A., Loeffek, S., Horiuchi, K., Threadgill, D. W., … Blobel, C. P. (2012). Epidermal ADAM17 maintains the skin barrier by regulating EGFR ligand-dependent terminal keratinocyte differentiation. JOURNAL OF EXPERIMENTAL MEDICINE, 209(6), 1105–1119. https://doi.org/10.1084/jem.20112258

Hung, H.-Y., Browne, C., Guill, K., Coles, N., Eller, M., Garcia, A., … Holland, J. B. (2012). The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population. HEREDITY, 108(5), 490–499. https://doi.org/10.1038/hdy.2011.103

Stone, E. A. (2012). Joint genotyping on the fly: Identifying variation among a sequenced panel of inbred lines. GENOME RESEARCH, 22(5), 966–974. https://doi.org/10.1101/gr.129122.111

Botero, C. A., & Rubenstein, D. R. (2012). Fluctuating environments, sexual selection and the evolution of flexible mate choice in birds. PLoS One, 7(2).

Khazaie, K., Zadeh, M., Khan, M. W., Bere, P., Gounari, F., Dennis, K., … Mohamadzadeh, M. (2012). Abating colon cancer polyposis by Lactobacillus acidophilus deficient in lipoteichoic acid. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109(26), 10462–10467. https://doi.org/10.1073/pnas.1207230109

Crowley, J. J., Kim, Y., Szatkiewicz, J. P., Pratt, A. L., Quackenbush, C. R., Adkins, D. E., … Sullivan, P. F. (2012). Genome-wide association mapping of loci for antipsychotic-induced extrapyramidal symptoms in mice. MAMMALIAN GENOME, 23(5-6), 322–335. https://doi.org/10.1007/s00335-011-9385-8

Stowe, S. D., Tucker, A. T., Thompson, R., Piper, A., Richards, J. J., Rogers, S. A., … Cavanagh, J. (2012). Evaluation of the toxicity of 2-aminoimidazole antibiofilm agents using both cellular and model organism systems. DRUG AND CHEMICAL TOXICOLOGY, 35(3), 310–315. https://doi.org/10.3109/01480545.2011.614620

Wu, S. T., Li, C. J., Huang, W., Li, W. Z., & Li, R. W. (2012). Alternative splicing regulated by butyrate in bovine epithelial cells. PLoS One, 7(6).

Shorter, J. R., & Rueppell, O. (2012). [Review of A review on self-destructive defense behaviors in social insects]. Insectes Sociaux, 59(1), 1–10.

Rinella, E. S., Bankaitis, E. D., & Threadgill, D. W. (2012). Dietary calcium supplementation enhances efficacy but also toxicity of EGFR inhibitor therapy for colon cancer. CANCER BIOLOGY & THERAPY, 13(3), 130–137. https://doi.org/10.4161/cbt.13.3.18690

Singh, N. D., & Shaw, K. L. (2012, January 3). On the scent of pleiotropy. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol. 109, pp. 5–6. https://doi.org/10.1073/pnas.1118531109

Morckel, A. R., Lusic, H., Farzana, L., Yoder, J. A., Deiters, A., & Nascone-Yoder, N. M. (2012). A photoactivatable small-molecule inhibitor for light-controlled spatiotemporal regulation of Rho kinase in live embryos. DEVELOPMENT, 139(2), 437–442. https://doi.org/10.1242/dev.072165

Cook, J. P., McMullen, M. D., Holland, J. B., Tian, F., Bradbury, P., Ross-Ibarra, J., … Flint-Garcia, S. A. (2012). Genetic Architecture of Maize Kernel Composition in the Nested Association Mapping and Inbred Association Panels. PLANT PHYSIOLOGY, 158(2), 824–834. https://doi.org/10.1104/pp.111.185033

Sommer, J. R., Chavali, V. R. M., Simpson, S. G., Ayyagari, R., & Petters, R. M. (2012). Cloning, characterization, and expression analysis of the pig (Sus scrofa) C1q tumor necrosis factor-related protein-5 gene. Molecular Vision, 18(12-14), 92–102.