Genetics - 2009 Concha, C., & Scott, M. J. (2009). Sexual Development in Lucilia cuprina (Diptera, Calliphoridae) Is Controlled by the Transformer Gene. Genetics, 182(3), 785–798. https://doi.org/10.1534/genetics.109.100982 Concha, C., & Scott, M. J. (2009). Sexual development in Lucilia cuprina (Diptera, Calliphoridae) is controlled by the transformer gene. Genetics, 182(3), 785–798. Kim, Y., Feng, S., & Zeng, Z.-B. (2009). Measuring and partitioning the high-order linkage disequilibrium by multiple order Markov chains. Genetic Epidemiology, 33(2), 181–181. https://doi.org/10.1002/gepi.20349 Bushel, P. R., Nielsen, D., & Tong, W. (2009). Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007). BMC Proceedings, 3(S2). https://doi.org/10.1186/1753-6561-3-s2-s1 Lopez-Ochoa, L., Nash, T. E., Ramirez-Prado, J., & Hanley-Bowdoin, L. (2009). Isolation of Peptide Aptamers to Target Protein Function. In Methods in Molecular Biology (pp. 333–360). https://doi.org/10.1007/978-1-59745-557-2_19 Tsuchisaka, A., Yu, G., Jin, H., Alonso, J. M., Ecker, J. R., Zhang, X., … Theologis, A. (2009). A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana. Genetics, 183(3), 979–1003. https://doi.org/10.1534/genetics.109.107102 Kumar, S., & Thompson, W. F. (2009). Plant Genome Engineering Using Zinc Finger Nucleases. In Molecular Techniques in Crop Improvement (pp. 579–590). https://doi.org/10.1007/978-90-481-2967-6_24 Gibson, G. (2009). It takes a genome: How a clash between our genes and modern life is making us sick. Upper Saddle River, N.J. : Pearson Education. Weber, A. L., Zhao, Q., McMullen, M. D., & Doebley, J. F. (2009). Using association mapping in teosinte to investigate the function of maize selection-candidate genes. PLoS One, 4(12). Hobolth, A., & Stone, E. A. (2009). SIMULATION FROM ENDPOINT-CONDITIONED, CONTINUOUS-TIME MARKOV CHAINS ON A FINITE STATE SPACE, WITH APPLICATIONS TO MOLECULAR EVOLUTION. ANNALS OF APPLIED STATISTICS, 3(3), 1204–1231. https://doi.org/10.1214/09-AOAS247 Kennerly, E. M., Idaghdour, Y., Olby, N. J., Munana, K. R., & Gibson, G. (2009). Pharmacogenetic association study of 30 genes with phenobarbital drug response in epileptic dogs. PHARMACOGENETICS AND GENOMICS, 19(12), 911–922. https://doi.org/10.1097/FPC.0b013e3283307cba Dougherty, U., Cerasi, D., Taylor, I., Kocherginsky, M., Tekin, U., Badal, S., … Bissonnette, M. (2009). Epidermal Growth Factor Receptor Is Required for Colonic Tumor Promotion by Dietary Fat in the Azoxymethane/Dextran Sulfate Sodium Model: Roles of Transforming Growth Factor-alpha and PTGS2. CLINICAL CANCER RESEARCH, 15(22), 6780–6789. https://doi.org/10.1158/1078-0432.CCR-09-1678 Goering, L. M., Hunt, P. K., Heighington, C., Busick, C., Pennings, P. S., Hermisson, J., … Gibson, G. (2009). Association of orthodenticle with Natural Variation for Early Embryonic Patterning in Drosophila melanogaster. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION, 312B(8), 841–854. https://doi.org/10.1002/jez.b.21299 Ruedi, E. A., & Hughes, K. A. (2009). Age, but not experience, affects courtship gene expression in male Drosophila melanogaster. PLoS One, 4(7). Stoeker, L., Nordone, S., LaVoy, A., Tallon, R., Klaenhammer, T., & Dean, G. (2009). Toll-like receptor activation profiles of wild-type, recombinant, and mutant Lactobacillus: implications for vaccine design. RETROVIROLOGY, Vol. 6. https://doi.org/10.1186/1742-4690-6-s3-p133 Edwards, A. C., & Mackay, T. F. C. (2009). Quantitative Trait Loci for Aggressive Behavior in Drosophila melanogaster. GENETICS, 182(3), 889–897. https://doi.org/10.1534/genetics.109.101691 Santa-Maria, M. C., Chou, C.-J., Yencho, G. C., Haigler, C. H., Thompson, W. F., Kelly, R. M., & Sosinski, B. (2009). Plant cell calcium-rich environment enhances thermostability of recombinantly produced alpha-amylase from the hyperthermophilic bacterium Thermotoga maritime. Biotechnology and Bioengineering, 104(5), 947–956. https://doi.org/10.1002/bit.22468 Dackor, J., Caron, K. M., & Threadgill, D. W. (2009). Placental and Embryonic Growth Restriction in Mice With Reduced Function Epidermal Growth Factor Receptor Alleles. GENETICS, 183(1), 207–218. https://doi.org/10.1534/genetics.109.104372 Gunderson, S., Nordone, S., LaVoy, A., Zhang, L., Klaenhammer, T., & Dean, G. (2009). Immunogenicity of Lactobacillus gasseri-FliC as an oral mucosal vaccine adjuvant for HIV. RETROVIROLOGY, Vol. 6. https://doi.org/10.1186/1742-4690-6-s3-p163 Ehrenreich, I. M., Hanzawa, Y., Chou, L., Roe, J. L., Kover, P. X., & Purugganan, M. D. (2009). Candidate Gene Association Mapping of Arabidopsis Flowering Time. GENETICS, 183(1), 325–335. https://doi.org/10.1534/genetics.109.105189 Halladay, A. K., Amaral, D., Aschner, M., Bolivar, V. J., Bowman, A., DiCicco-Bloom, E., … Threadgill, D. W. (2009, September). Animal models of autism spectrum disorders: Information for neurotoxicologists. NEUROTOXICOLOGY, Vol. 30, pp. 811–821. https://doi.org/10.1016/j.neuro.2009.07.002 Conkling, M. A., Song, W., & Mendu, N. (2009). Regulation of quinolate phosphoribosyl transferase expression. Klaenhammer, T. R., Russell, W. M., Altermann, E., & Azcarate-Peril, A. (2009). Nucleic acid sequences encoding two-component sensing and regulatory proteins, antimicrobial proteins and uses therefor. Klaenhammer, T. R., Altermann, E., Azcarate-Peril, M. A., McAuliffe, O., & Russell, W. M. (2009). Lactobacillus acidophilus nucleic acid sequences encoding stress-related proteins and uses therefor. Klaenhammer, T. R., Russell, W. M., Altermann, E., & Buck, B. L. (2009). Lactobacillus acidophillus nucleic acid sequences encoding cell surface protein homologues and uses therefore. Munger, S. C., Aylor, D. L., Syed, H. A., Magwene, P. M., Threadgill, D. W., & Capel, B. (2009). Elucidation of the transcription network governing mammalian sex determination by exploiting strain-specific susceptibility to sex reversal. GENES & DEVELOPMENT, 23(21), 2521–2536. https://doi.org/10.1101/gad.1835809 Barrangou, R., Azcarate-Peril, A., Altermann, E., Duong, T., & Klaenhammer, T. R. (2009). Compositions comprising promoter sequences and methods of use. Morozova, T. V., Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. A., Lyman, R. E., … Anholt, R. R. H. (2009). Alcohol Sensitivity in Drosophila: Translational Potential of Systems Genetics. GENETICS, 183(2), 733–745. https://doi.org/10.1534/genetics.109.107490 Need, A. C., Attix, D. K., McEvoy, J. M., Cirulli, E. T., Linney, K. L., Hunt, P., … Goldstein, D. B. (2009). [Review of A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB]. Human Molecular Genetics, 18(23), 4650–4661. Bird, D. M. K., Williamson, V. M., Abad, P., McCarter, J., Danchin, E. G. J., Castagnone-Sereno, P., & Opperman, C. H. (2009). The Genomes of Root-Knot Nematodes. ANNUAL REVIEW OF PHYTOPATHOLOGY, Vol. 47, pp. 333–351. https://doi.org/10.1146/annurev-phyto-080508-081839 Buck, B. L., Azcarate-Peril, M. A., & Klaenhammer, T. R. (2009). Role of autoinducer-2 on the adhesion ability of Lactobacillus acidophilus. JOURNAL OF APPLIED MICROBIOLOGY, 107(1), 269–279. https://doi.org/10.1111/j.1365-2672.2009.04204.x Engelbrektson, A., Korzenik, J. R., Pittler, A., Sanders, M. E., Klaenhammer, T. R., Leyer, G., & Kitts, C. L. (2009). Probiotics to minimize the disruption of faecal microbiota in healthy subjects undergoing antibiotic therapy. JOURNAL OF MEDICAL MICROBIOLOGY, 58(5), 663–670. https://doi.org/10.1099/jmm.0.47615-0 Stone, E. A., & Griffing, A. R. (2009). On the Fiedler vectors of graphs that arise from trees by Schur complementation of the Laplacian. LINEAR ALGEBRA AND ITS APPLICATIONS, 431(10), 1869–1880. https://doi.org/10.1016/j.laa.2009.06.024 Schaffer, H. E., Averitt, S. F., Hoit, M. I., Peeler, A., Sills, E. D., & Vouk, M. A. (2009, July). NCSU's Virtual Computing Lab: A Cloud Computing Solution. COMPUTER, Vol. 42, pp. 94–97. https://doi.org/10.1109/mc.2009.230 Reininga, J. M., Nielsen, D., & Purugganan, M. D. (2009). Functional and geographical differentiation of candidate balanced polymorphisms in Arabidopsis thaliana. MOLECULAR ECOLOGY, 18(13), 2844–2855. https://doi.org/10.1111/j.1365-294X.2009.04206.x Choi, S. C., Stone, E. A., Kishino, H., & Thorne, J. L. (2009). Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci. Gene, 441(1-2), 45–52. https://doi.org/10.1016/j.gene.2008.07.020 Harbison, S. T., & Sehgal, A. (2009). Energy stores are not altered by long-term partial sleep deprivation in Drosophila melanogaster. PLoS One, 4(7). Weir, B. S., Hill, W. G., Zhu, J., & Zeng, Z.-B. (2009, June). The Third International Conference of Quantitative Genetics. GENETICA, Vol. 136, pp. 211–212. https://doi.org/10.1007/s10709-008-9315-1 Lamm, K. S., & Redelings, B. D. (2009). Reconstructing ancestral ranges in historical biogeography: properties and prospects. JOURNAL OF SYSTEMATICS AND EVOLUTION, 47(5), 369–382. https://doi.org/10.1111/j.1759-6831.2009.00042.x Harrill, A. H., Ross, P. K., Gatti, D. M., Threadgill, D. W., & Rusyn, I. (2009). Population-Based Discovery of Toxicogenomics Biomarkers for Hepatotoxicity Using a Laboratory Strain Diversity Panel. TOXICOLOGICAL SCIENCES, 110(1), 235–243. https://doi.org/10.1093/toxsci/kfp096 Dackor, J., Li, M., & Threadgill, D. W. (2009). Placental overgrowth and fertility defects in mice with a hypermorphic allele of epidermal growth factor receptor. MAMMALIAN GENOME, 20(6), 339–349. https://doi.org/10.1007/s00335-009-9189-2 Uronis, J. M., & Threadgill, D. W. (2009). [Review of Murine models of colorectal cancer]. MAMMALIAN GENOME, 20(5), 261–268. https://doi.org/10.1007/s00335-009-9186-5 Stone, E. A., & Ayroles, J. F. (2009). Modulated Modularity Clustering as an Exploratory Tool for Functional Genomic Inference. PLOS GENETICS, 5(5). https://doi.org/10.1371/journal.pgen.1000479 Ikeda, Y., Men, S., Fischer, U., Stepanova, A. N., Alonso, J. M., Ljung, K., & Grebe, M. (2009). Local auxin biosynthesis modulates gradient-directed planar polarity in Arabidopsis. NATURE CELL BIOLOGY, 11(6), 731–U70. https://doi.org/10.1038/ncb1879 Shultz, R. W., Lee, T.-J., Allen, G. C., Thompson, W. F., & Hanley-Bowdoin, L. (2009). Dynamic Localization of the DNA Replication Proteins MCM5 and MCM7 in Plants. PLANT PHYSIOLOGY, 150(2), 658–669. https://doi.org/10.1104/pp.109.136614 Goh, Y. J., Azcarate-Peril, M. A., O'Flaherty, S., Durmaz, E., Valence, F., Jardin, J., … Klaenhammer, T. R. (2009). Development and Application of a upp-Based Counterselective Gene Replacement System for the Study of the S-Layer Protein SlpX of Lactobacillus acidophilus NCFM. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 75(10), 3093–3105. https://doi.org/10.1128/AEM.02502-08 Shen, W., Reyes, M. I., & Hanley-Bowdoin, L. (2009). Arabidopsis Protein Kinases GRIK1 and GRIK2 Specifically Activate SnRK1 by Phosphorylating Its Activation Loop. PLANT PHYSIOLOGY, 150(2), 996–1005. https://doi.org/10.1104/pp.108.132787 Richards, J. J., Reyes, S., Stowe, S. D., Tucker, A. T., Ballard, T. E., Mathies, L. D., … Melander, C. (2009). Amide Isosteres of Oroidin: Assessment of Antibiofilm Activity and C. elegans Toxicity. JOURNAL OF MEDICINAL CHEMISTRY, 52(15), 4582–4585. https://doi.org/10.1021/jm900378s Lewis, R. S., & Kernodle, S. P. (2009). A method for accelerated trait conversion in plant breeding. THEORETICAL AND APPLIED GENETICS, 118(8), 1499–1508. https://doi.org/10.1007/s00122-009-0998-1 Zou, W., & Zeng, Z.-B. (2009). Multiple interval mapping for gene expression QTL analysis. GENETICA, 137(2), 125–134. https://doi.org/10.1007/s10709-009-9365-z Liang, L.-J., Weiss, R. E., Redelings, B., & Suchard, M. A. (2009). Improving phylogenetic analyses by incorporating additional information from genetic sequence databases. BIOINFORMATICS, 25(19), 2530–2536. https://doi.org/10.1093/bioinformatics/btp473 Dworkin, I., Kennerly, E., Tack, D., Hutchinson, J., Brown, J., Mahaffey, J., & Gibson, G. (2009). Genomic Consequences of Background Effects on scalloped Mutant Expressivity in the Wing of Drosophila melanogaster. GENETICS, 181(3), 1065–1076. https://doi.org/10.1534/genetics.108.096453 Stepanova, A. N., & Alonso, J. M. (2009). [Review of Ethylene signaling and response: where different regulatory modules meet]. CURRENT OPINION IN PLANT BIOLOGY, 12(5), 548–555. https://doi.org/10.1016/j.pbi.2009.07.009 Wang, T., & Zeng, Z.-B. (2009). Contribution of genetic effects to genetic variance components with epistasis and linkage disequilibrium. BMC GENETICS, 10. https://doi.org/10.1186/1471-2156-10-52 Cartwright, R. A. (2009). Antagonism between local dispersal and self-incompatibility systems in a continuous plant population. MOLECULAR ECOLOGY, 18(11), 2327–2336. https://doi.org/10.1111/j.1365-294X.2009.04180.x Lee, D., Yu, M., Lee, E., Kim, H., Yang, Y., Kim, K., … Threadgill, D. W. (2009). Tumor-specific apoptosis caused by deletion of the ERBB3 pseudo-kinase in mouse intestinal epithelium. JOURNAL OF CLINICAL INVESTIGATION, 119(9), 2702–2713. https://doi.org/10.1172/JCI36435 Carroll, I. M., Threadgill, D. W., & Threadgill, D. S. (2009). [Review of The gastrointestinal microbiome: a malleable, third genome of mammals]. MAMMALIAN GENOME, 20(7), 395–403. https://doi.org/10.1007/s00335-009-9204-7 Pfeiler, E. A., & Klaenhammer, T. R. (2009). Role of Transporter Proteins in Bile Tolerance of Lactobacillus acidophilus. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 75(18), 6013–6016. https://doi.org/10.1128/AEM.00495-09 Jacquet, B. V., Patel, M., Iyengar, M., Liang, H., Therit, B., Salinas-Mondragon, R., … Ghashghaei, H. T. (2009). Analysis of neuronal proliferation, migration and differentiation in the postnatal brain using equine infectious anemia virus-based lentiviral vectors. GENE THERAPY, 16(8), 1021–1033. https://doi.org/10.1038/gt.2009.58 Barrick, C. J., Roberts, R. B., Rojas, M., Rajamannan, N. M., Suitt, C. B., Kevin D. O'Brien, … Threadgill, D. W. (2009). Reduced EGFR causes abnormal valvular differentiation leading to calcific aortic stenosis and left ventricular hypertrophy in C57BL/6J but not 129S1/SvImJ mice. AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY, 297(1), H65–H75. https://doi.org/10.1152/ajpheart.00866.2008 Harrill, A. H., Watkins, P. B., Su, S., Ross, P. K., Harbourt, D. E., Stylianou, I. M., … Threadgill, D. W. (2009). Mouse population-guided resequencing reveals that variants in CD44 contribute to acetaminophen-induced liver injury in humans. GENOME RESEARCH, 19(9), 1507–1515. https://doi.org/10.1101/gr.090241.108 La Merrill, M., Kuruvilla, B. S., Pomp, D., Birnbaum, L. S., & Threadgill, D. W. (2009). Dietary Fat Alters Body Composition, Mammary Development, and Cytochrome P450 Induction after Maternal TCDD Exposure in DBA/2J Mice with Low-Responsive Aryl Hydrocarbon Receptors. ENVIRONMENTAL HEALTH PERSPECTIVES, 117(9), 1414–1419. https://doi.org/10.1289/ehp.0800530 Johnson, C. S., Wernsman, E. A., & LaMondia, J. A. (2009). Effect of a Chromosome Segment Marked by the Ph-p Gene for Resistance to Phytophthora nicotianae on Reproduction of Tobacco Cyst Nematodes. PLANT DISEASE, 93(3), 309–315. https://doi.org/10.1094/PDIS-93-3-0309 Mohamadzadeh, M., Duong, T., Sandwick, S. J., Hoover, T., & Klaenhammer, T. R. (2009). Dendritic cell targeting of Bacillus anthracis protective antigen expressed by Lactobacillus acidophilus protects mice from lethal challenge. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106(11), 4331–4336. https://doi.org/10.1073/pnas.0900029106 Bird, D. M., & Opperman, C. H. (2009). [Review of The secret(ion) life of worms]. GENOME BIOLOGY, 10(1). https://doi.org/10.1186/gb-2009-10-1-205 Ayroles, J. F., Carbone, M. A., Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., … Mackay, T. F. C. (2009). Systems genetics of complex traits in Drosophila melanogaster. NATURE GENETICS, 41(3), 299–307. https://doi.org/10.1038/ng.332 Pfeiler, E., Castrezana, S., Reed, L. K., & Markow, T. A. (2009). Genetic, ecological and morphological differences among populations of the cactophilic Drosophila mojavensis from southwestern USA and northwestern Mexico, with descriptions of two new subspecies. JOURNAL OF NATURAL HISTORY, 43(15-16), 923–938. https://doi.org/10.1080/00222930802610535 Harbison, S. T., Carbone, M. A., Ayroles, J. F., Stone, E. A., Lyman, R. F., & Mackay, T. F. C. (2009). Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep. NATURE GENETICS, 41(3), 371–375. https://doi.org/10.1038/ng.330 Azcarate-Peril, M. A., Tallon, R., & Klaenhammer, T. R. (2009). Temporal gene expression and probiotic attributes of Lactobacillus acidophilus during growth in milk. JOURNAL OF DAIRY SCIENCE, 92(3), 870–886. https://doi.org/10.3168/jds.2008-1457 Caicedo, A. L., Richards, C., Ehrenreich, I. M., & Purugganan, M. D. (2009). Complex Rearrangements Lead to Novel Chimeric Gene Fusion Polymorphisms at the Arabidopsis thaliana MAF2-5 Flowering Time Gene Cluster. MOLECULAR BIOLOGY AND EVOLUTION, 26(3), 699–711. https://doi.org/10.1093/molbev/msn300 Kim, Y. J., Feng, S., & Zeng, Z. B. (2009). Measuring and partitioning the high-order linkage disequilibrium by multiple order Markov chains (vol 32, pg 301, 2008). Genetic Epidemiology, Vol. 33, pp. 181–181. Schroeter, J., & Klaenhammer, T. (2009). [Review of Genomics of lactic acid bacteria]. FEMS MICROBIOLOGY LETTERS, 292(1), 1–6. https://doi.org/10.1111/j.1574-6968.2008.01442.x Wang, T., Jacob, H., Ghosh, S., Wang, X., & Zeng, Z.-B. (2009). A Joint Association Test for Multiple SNPs in Genetic Case-Control Studies. GENETIC EPIDEMIOLOGY, 33(2), 151–163. https://doi.org/10.1002/gepi.20368 Bitto, E., Bingman, C. A., Bittova, L., Houston, N. L., Boston, R. S., Fox, B. G., & Phillips, G. N., Jr. (2009). X-ray structure of ILL2, an auxin-conjugate amidohydrolase from Arabidopsis thaliana. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 74(1), 61–71. https://doi.org/10.1002/prot.22124 Ventura, M., O'Flaherty, S., Claesson, M. J., Turroni, F., Klaenhammer, T. R., Sinderen, D., & Paul W. O'Toole. (2009). [Review of Genome-scale analyses of health-promoting bacteria: probiogenomics]. NATURE REVIEWS MICROBIOLOGY, 7(1), 61–U77. https://doi.org/10.1038/nrmicro2047 Cartwright, R. A. (2009). Problems and Solutions for Estimating Indel Rates and Length Distributions. MOLECULAR BIOLOGY AND EVOLUTION, 26(2), 473–480. https://doi.org/10.1093/molbev/msn275 Goh, Y. J., & Klaenhammer, T. R. (2009). [Review of Genomic features of Lactobacillus species]. Frontiers in Bioscience, 14, 1362–1386. Kumar, S., & Thompson, W. F. (2009). Simultaneous excision of two transgene flanking sequences and resolution of complex integration loci. PLANT MOLECULAR BIOLOGY, 69(1-2), 23–32. https://doi.org/10.1007/s11103-008-9402-9