Genetics - 2007

Weake, V. M., & Scott, M. J. (2007). The non-dosage compensated Lsp1α gene of Drosophila melanogaster escapes acetylation by MOF in larval fat body nuclei, but is flanked by two dosage compensated genes. BMC Molecular Biology, 8(1), 35. https://doi.org/10.1186/1471-2199-8-35

Schaff, J. E., Nielsen, D. M., Smith, C. P., Scholl, E. H., & Bird, D. M. K. (2007). Comprehensive Transcriptome Profiling in Tomato Reveals a Role for Glycosyltransferase in Mi-Mediated Nematode Resistance. Plant Physiology, 144(2), 1079–1092. https://doi.org/10.1104/pp.106.090241

Cary, J. W., OBrian, G. R., Nielsen, D. M., Nierman, W., Harris-Coward, P., Yu, J., … Calvo, A. M. (2007). Elucidation of veA-dependent genes associated with aflatoxin and sclerotial production in Aspergillus flavus by functional genomics. Applied Microbiology and Biotechnology, 76(5), 1107–1118. https://doi.org/10.1007/s00253-007-1081-y

Propper, C., Willoughby, M., Halpern, C. T., Carbone, M. A., & Cox, M. (2007). Parenting quality, DRD4, and the prediction of externalizing and internalizing behaviors in early childhood. Developmental Psychobiology, 49(6), 619–632. https://doi.org/10.1002/dev.20249

Chekanova, J. A., Gregory, B. D., Reverdatto, S. V., Chen, H., Kumar, R., Hooker, T., … Peng, Q. (2007). Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the< i> Arabidopsis</i> Transcriptome. Cell, 131(7), 1340–1353. https://doi.org/10.1016/j.cell.2007.10.056

Zeng, Z. B. (2007). The Hill–Robertson effect is a consequence of interplay between linkage, selection and drift: a commentary on ‘The effect of linkage on limits to artificial selection’ by W. G. Hill and A. Robertson. Genetics Research, 89(5-6), 309–310. https://doi.org/10.1017/s0016672308009506

Riedl, C. A. L., Riedl, M., Mackay, T. F. C., & Sokolowski, M. B. (2007). Genetic and behavioral analysis of natural variation in Drosophila melanogaster pupation position. FLY, 1(1), 23–32. https://doi.org/10.4161/fly.3830

Conkling, M. A., Song, W., & Mendu, N. (2007). Regulation of quinolate phosphoribosyl transferase expression. Washington, DC: U.S. Patent and Trademark Office.

Mendu, N., Bland, M., Wolfe, S., Hebrank, J., & Mahato, D. (2007). Methods for injecting avian eggs. Washington, DC: U.S. Patent and Trademark Office.

Gibson, G., & Goldstein, D. B. (2007). Human genetics: The hidden text of genome-wide associations. Current Biology, 17(21), R929–932.

Ronan C. O'Malley, Alonso, J. M., Kim, C. J., Leisse, T. J., & Ecker, J. R. (2007). An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome. NATURE PROTOCOLS, 2(11), 2910–2917. https://doi.org/10.1038/nprot.2007.425

Lawton-Rauh, A., Robichaux, R. H., & Purugganan, M. D. (2007). Diversity and divergence patterns in regulatory genes suggest differential gene flow in recently derived species of the Hawaiian silversword alliance adaptive radiation (Asteraceae). MOLECULAR ECOLOGY, 16(19), 3995–4013. https://doi.org/10.1111/j.1365-294X.2007.03445.x

Carroll, I. M., Andrus, J. M., Bruno-Barcena, J. M., Klaenhammer, T. R., Hassan, H. M., & Threadgill, D. S. (2007). Anti-inflammatory properties of Lactobacillus gasseri expressing manganese superoxide dismutase using the interleukin 10-deficient mouse model of colitis. AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY, 293(4), G729–G738. https://doi.org/10.1152/ajpgi.00132.2007

Hsieh, W.-P., Passador-Gurgel, G., Stone, E. A., & Gibson, G. (2007). Mixture modeling of transcript abundance classes in natural populations. GENOME BIOLOGY, 8(6). https://doi.org/10.1186/gb-2007-8-6-r98

Ghosh, F., Engelsberg, K., English, R. V., & Petters, R. M. (2007). Long-term neuroretinal full-thickness transplants in a large animal model of severe retinitis pigmentosa. GRAEFES ARCHIVE FOR CLINICAL AND EXPERIMENTAL OPHTHALMOLOGY, 245(6), 835–846. https://doi.org/10.1007/s00417-006-0437-9

Sturino, J. M., & Klaenhammer, T. R. (2007). Inhibition of bacteriophage replication in Streptococcus thermophilus by subunit poisoning of primase. MICROBIOLOGY-SGM, 153, 3295–3302. https://doi.org/10.1099/mic.0.2007/007567-0

Dobson, A. E., Sanozky-Dawes, R. B., & Klaenhammer, T. R. (2007). Identification of an operon and inducing peptide involved in the production of lactacin B by Lactobacillus acidophilus. JOURNAL OF APPLIED MICROBIOLOGY, 103(5), 1766–1778. https://doi.org/10.1111/j.1365-2672.2007.03417.x

Arguello-Astorga, G., Ascencio-Ibanez, J. T., Dallas, M. B., Orozco, B. M., & Hanley-Bowdoin, L. (2007). High-frequency reversion of geminivirus replication protein mutants during infection. JOURNAL OF VIROLOGY, 81(20), 11005–11015. https://doi.org/10.1128/JVI.00925-07

Caicedo, A. L., Williamson, S. H., Hernandez, R. D., Boyko, A., Fledel-Alon, A., York, T. L., … Purugganan, M. D. (2007). Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLOS GENETICS, 3(9), 1745–1756. https://doi.org/10.1371/journal.pgen.0030163

Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., … al. (2007). [Review of Evolution of genes and genomes on the Drosophila phylogeny]. Nature, 450(7167), 203–218.

Melchinger, A. E., Utz, H. F., Piepho, H.-P., Zeng, Z.-B., & Schoen, C. C. (2007). The role of epistasis in the manifestation of heterosis: A systems-oriented approach. GENETICS, 177(3), 1815–1825. https://doi.org/10.1534/genetics.107.077537

Bushel, P. R., Wolfinger, R. D., & Gibson, G. (2007). Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes. BMC SYSTEMS BIOLOGY, 1. https://doi.org/10.1186/1752-0509-1-15

Moser, J. M., Carbone, I., Arasu, P., & Gibson, G. (2007). Impact of population structure on genetic diversity of a potential vaccine target in the canine hookworm (Ancylostoma caninum). JOURNAL OF PARASITOLOGY, 93(4), 796–805. https://doi.org/10.1645/GE-1096R.1

Wang, P., Lyman, R. F., Shabalina, S. A., Mackay, T. F. C., & Anholt, R. R. H. (2007). Association of polymorphisms in odorant-binding protein genes with variation in olfactory response to benzaldehyde in Drosophila. GENETICS, 177(3), 1655–1665. https://doi.org/10.1534/genetics.107.079731

Yang, R., Gao, H., Wang, X., Zhang, J., Zeng, Z.-B., & Wu, R. (2007). A semiparametric approach for composite functional mapping of dynamic quantitative traits. GENETICS, 177(3), 1859–1870. https://doi.org/10.1534/genetics.107.077321

Pfeiler, E. A., & Klaenhammer, T. R. (2007). [Review of The genomics of lactic acid bacteria]. TRENDS IN MICROBIOLOGY, 15(12), 546–553. https://doi.org/10.1016/j.tim.2007.09.010

Mather, K. A., Caicedo, A. L., Polato, N. R., Olsen, K. M., McCouch, S., & Purugganan, M. D. (2007). The extent of linkage disequilibrium in rice (Oryza sativa L.). GENETICS, 177(4), 2223–2232. https://doi.org/10.1534/genetics.107.079616

Bockhorst, J., Lu, F., Janes, J. H., Keebler, J., Gamain, B., Awadalla, P., … Smith, J. D. (2007). Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA. MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 155(2), 103–112. https://doi.org/10.1016/j.molbiopara.2007.06.007

Lai, C.-Q., Leips, J., Zou, W., Roberts, J. F., Wollenberg, K. R., Parnell, L. D., … Mackay, T. F. C. (2007). Speed-mapping quantitative trait loci using microarrays. NATURE METHODS, 4(10), 839–841. https://doi.org/10.1038/NMETH1084

Smith, C. A., Woloshuk, C. P., Robertson, D., & Payne, G. A. (2007). Silencing of the aflatoxin gene cluster in a diploid strain of Aspergillus flavus is suppressed by ectopic aflR expression. GENETICS, 176(4), 2077–2086. https://doi.org/10.1534/genetics.107.073460

Conkling, M., & Li, Y. (2007). Putrescine-n-methyltransferase promoter. Washington, DC: U.S. Patent and Trademark Office.

Conkling, M., & Li, Y. (2007). Plant promoter sequence. Washington, DC: U.S. Patent and Trademark Office.

Irsigler, A. S. T., Costa, M. D., Zhang, P., Reis, P. A. B., Dewey, R. E., Boston, R. S., & Fontes, E. P. B. (2007). Expression profiling on soybean leaves reveals integration of ER- and osmotic-stress pathways. BMC GENOMICS, 8. https://doi.org/10.1186/1471-2164-8-431

Durmaz, E., & Klaenhammer, T. R. (2007). AbiZ phage resistance gene. Washington, DC: U.S. Patent and Trademark Office.

Li, H., He, Z., Lu, G., Lee, S. C., Alonso, J., Ecker, J. R., & Luan, S. (2007). A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis. PLANT CELL, 19(8), 2403–2416. https://doi.org/10.1105/tpc.107.053579

Lewis, R. S., Linger, L. R., Wolff, M. F., & Wernsman, E. A. (2007). The negative influence of N-mediated TMV resistance on yield in tobacco: linkage drag versus pleiotropy. THEORETICAL AND APPLIED GENETICS, 115(2), 169–178. https://doi.org/10.1007/s00122-007-0552-y

Patel, M., Farzana, L., Robertson, L. K., Hutchinson, J., Grubbs, N., Shepherd, M. N., & Mahaffey, J. W. (2007). The appendage role of insect disco genes and possible implications on the evolution of the maggot larval form. DEVELOPMENTAL BIOLOGY, 309(1), 56–69. https://doi.org/10.1016/j.ydbio.2007.06.017

Sommer, J. R., Collins, E. B., Estrada, J. L., & Petters, R. M. (2007). Synchronization and superovulation of mature cycling gilts for the collection of pronuclear stage embryos. ANIMAL REPRODUCTION SCIENCE, 100(3-4), 402–410. https://doi.org/10.1016/j.anireprosci.2006.10.010

Estrada, J., Sommer, J., Collins, B., Mir, B., Martin, A., York, A., … Piedrahita, J. A. (2007). Swine generated by somatic cell nuclear transfer have increased incidence of intrauterine growth restriction (IUGR). CLONING AND STEM CELLS, 9(2), 229–236. https://doi.org/10.1089/clo.2006.0079

Szalma, S. J., Hostert, B. M., LeDeaux, J. R., Stuber, C. W., & Holland, J. B. (2007). QTL mapping with near-isogenic lines in maize. THEORETICAL AND APPLIED GENETICS, 114(7), 1211–1228. https://doi.org/10.1007/s00122-007-0512-6

Thorne, J. L. (2007). Protein evolution constraints and model-based techniques to study them. CURRENT OPINION IN STRUCTURAL BIOLOGY, 17(3), 337–341. https://doi.org/10.1016/j.sbi.2007.05.006

Korves, T. M., Schmid, K. J., Caicedo, A. L., Mays, C., Stinchcombe, J. R., Purugganan, M. D., & Schmitt, J. (2007). Fitness effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field. AMERICAN NATURALIST, 169(5), E141–E157. https://doi.org/10.1086/513111

Stone, E. A., & Sidow, A. (2007). Constructing a meaningful evolutionary average at the phylogenetic center of mass. BMC BIOINFORMATICS, 8. https://doi.org/10.1186/1471-2105-8-222

Wang, Z., Smith, C. E., & Atchley, W. R. (2007). Application of complex demodulation on bZIP and bHLH-PAS protein domains. Mathematical Biosciences, 207(2), 204–218. https://doi.org/10.1016/j.mbs.2007.01.004

Welchman, D. P., Mathies, L. D., & Ahringer, J. (2007). Similar requirements for CDC-42 and the PAR-3/PAR-6/PKC-3 complex in diverse cell types. DEVELOPMENTAL BIOLOGY, 305(1), 347–357. https://doi.org/10.1016/j.ydbio.2007.02.022

Choi, S. C., Hobolth, A., Robinson, D. M., Kishino, H., & Thorne, J. L. (2007). Quantifying the impact of protein tertiary structure on molecular evolution. MOLECULAR BIOLOGY AND EVOLUTION, 24(8), 1769–1782. https://doi.org/10.1093/molbev/msm097

Thorne, J. L., Choi, S. C., Yu, J., Higgs, P. G., & Kishino, H. (2007). Population genetics without intraspecific data. MOLECULAR BIOLOGY AND EVOLUTION, 24(8), 1667–1677. https://doi.org/10.1093/molbev/msm085

Cartwright, R. A. (2007). Ngila: global pairwise alignments with logarithmic and affine gap costs. BIOINFORMATICS, 23(11), 1427–1428. https://doi.org/10.1093/bioinformatics/btm095

Shultz, R. W., Tatineni, V. M., Hanley-Bowdoin, L., & Thompson, W. F. (2007). [Review of Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice(1[W][OA])]. Plant Physiology, 144(4), 1697–1714.

Large, E. E., & Mathies, L. D. (2007). Chromatin regulation and sex determination in Caenorhabditis elegans. TRENDS IN GENETICS, 23(7), 314–317. https://doi.org/10.1016/j.tig.2007.04.002

Pfeiler, E. A., Azcarate-Peril, M. A., & Klaenhammer, T. R. (2007). Characterization of a novel bile-inducible operon encoding a two-component regulatory system in Lactobacillus acidophilus. JOURNAL OF BACTERIOLOGY, 189(13), 4624–4634. https://doi.org/10.1128/JB.00337-07

Lai, C.-Q., Parnell, L. D., Lyman, R. F., Ordovas, J. A., & Mackay, T. F. C. (2007). Candidate genes affecting Drosophila life span identified by integrating microarray gene expression analysis and QTL mapping. MECHANISMS OF AGEING AND DEVELOPMENT, 128(3), 237–249. https://doi.org/10.1016/j.mad.2006.12.003

Mackay, T. F. C., & Anholt, R. R. H. (2007). Ain't misbehavin? Genotype-environment interactions and the genetics of behavior. TRENDS IN GENETICS, 23(7), 311–314. https://doi.org/10.1016/j.tig.2007.03.013

Ehrenreich, I. M., Stafford, P. A., & Purugganan, M. D. (2007). The genetic architecture of shoot branching in Arabidopsis thaliana: A comparative assessment of candidate gene associations vs. quantitative trait locus mapping. GENETICS, 176(2), 1223–1236. https://doi.org/10.1534/genetics.107.071928

Rollmann, S. M., Yamamoto, A., Goossens, T., Zwarts, L., Callaerts-Vegh, Z., Callaerts, P., … Anholt, R. R. H. (2007). The early developmental gene Semaphorin 5c contributes to olfactory behavior in adult Drosophila. GENETICS, 176(2), 947–956. https://doi.org/10.1534/genetics.106.069781

Hawkins, E. C., Birkenheuer, A. J., Marr, H. S., Rogala, A. R., Large, E. E., & Adler, K. B. (2007). Quantification of mucin gene expression in tracheobronchial epithelium of healthy dogs and dogs with chronic bronchitis. AMERICAN JOURNAL OF VETERINARY RESEARCH, 68(4), 435–440. https://doi.org/10.2460/ajvr.68.4.435

Jordan, C. V., Shen, W., Hanley-Bowdoin, L. K., & Robertson, D. (2007). Geminivirus-induced gene silencing of the tobacco retinoblastoma-related gene results in cell death and altered development. PLANT MOLECULAR BIOLOGY, 65(1-2), 163–175. https://doi.org/10.1007/s11103-007-9206-3

Fink, R. C., Evans, M. R., Porwollik, S., Vazquez-Torres, A., Jones-Carson, J., Troxell, B., … Hassan, H. M. (2007). FNR is a global regulator of virulence and anaerobic metabolism in Salmonella enterica serovar typhimurium (ATCC 14028s). JOURNAL OF BACTERIOLOGY, 189(6), 2262–2273. https://doi.org/10.1128/JB.00726-06

Mylona, P. V., Polidoros, A. N., & Scandalios, J. G. (2007). Antioxidant gene responses to ROS-generating xenobiotics in developing and germinated scutella of maize. JOURNAL OF EXPERIMENTAL BOTANY, 58(6), 1301–1312. https://doi.org/10.1093/jxb/erl292

Stepanova, A. N., Yun, J., Likhacheva, A. V., & Alonso, J. M. (2007). Multilevel interactions between ethylene and auxin in Arabidopsis roots. PLANT CELL, 19(7), 2169–2185. https://doi.org/10.1105/tpc.107.052068

Redelings, B. D., & Suchard, M. A. (2007). Incorporating indel information into phylogeny estimation for rapidly emerging pathogens. BMC Evolutionary Biology, 7.

Hall, M. C., Dworkin, I., Ungerer, M. C., & Purugganan, M. (2007). Genetics of microenvironmental canalization in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America, 104(34), 13717–13722.

Fan, C., Xiang, Q.-Y., Remington, D. L., Purugganan, M. D., & Wiegmann, B. M. (2007). Evolutionary patterns in the antR-Cor gene in the dwarf dogwood complex (Cornus, Cornaceae). GENETICA, 130(1), 19–34. https://doi.org/10.1007/s10709-006-0016-3

Sanchez, J. J., Goodman, M. M., & Stuber, C. W. (2007). Racial diversity of maize in Brazil and adjacent areas. Maydica, 52(1), 13–30.

Zhao, W., Duscher, G., Rozgonyi, G., Zikry, M. A., Chopra, S., & Ozturk, M. C. (2007). Quantitative nanoscale local strain profiling in embedded SiGe metal-oxide-semiconductor structures. APPLIED PHYSICS LETTERS, 90(19). https://doi.org/10.1063/1.2738188

Gibson, G. (2007). Human evolution: Thrifty genes and the dairy queen. Current Biology, 17(8), R295–296.

Durmaz, E., & Klaenhammer, T. R. (2007). Abortive phage resistance mechanism AbiZ speeds the lysis clock to cause premature lysis of phage-infected Lactococcus lactis. JOURNAL OF BACTERIOLOGY, 189(4), 1417–1425. https://doi.org/10.1128/JB.00904-06

Passador-Gurgel, G., Hsieh, W.-P., Hunt, P., Deighton, N., & Gibson, G. (2007). Quantitative trait transcripts for nicotine resistance in Drosophila melanogaster. NATURE GENETICS, 39(2), 264–268. https://doi.org/10.1038/ng1944

Lin, Y.-M., Fang, S.-C., & Thorne, J. L. (2007). A tabu search algorithm for maximum parsimony phylogeny inference. EUROPEAN JOURNAL OF OPERATIONAL RESEARCH, 176(3), 1908–1917. https://doi.org/10.1016/j.ejor.2005.10.031

Lewis, R. S., Milla, S. R., & Kernodle, S. P. (2007). Analysis of an introgressed Nicotiana tomentosa genomic region affecting leaf number and correlated traits in Nicotiana tabacum. THEORETICAL AND APPLIED GENETICS, 114(5), 841–854. https://doi.org/10.1007/s00122-006-0482-0

Atchley, W. R., & Zhao, J. (2007). Molecular architecture of the DNA-binding region and its relationship to classification of basic helix-loop-helix proteins. MOLECULAR BIOLOGY AND EVOLUTION, 24(1), 192–202. https://doi.org/10.1093/molbev/msl143

Callanan, M. J., Russell, W. M., & Klaenhammer, T. R. (2007). Modification of Lactobacillus beta-glucuronidase activity by random mutagenesis. GENE, 389(2), 122–127. https://doi.org/10.1016/j.gene.2006.10.022

Klaenhammer, T. R., Azcarate-Peril, M. A., Altermann, E., & Barrangou, R. (2007, March). Influence of the dairy environment on gene expression and substrate(1-3). JOURNAL OF NUTRITION, Vol. 137, pp. 748S–750S. https://doi.org/10.1093/jn/137.3.748s

Mu, J., Awadalla, P., Duan, J., McGee, K. M., Keebler, J., Seydel, K., … Su, X.-zhuan. (2007). Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome. NATURE GENETICS, 39(1), 126–130. https://doi.org/10.1038/ng1924

Zou, W., Aylor, D. L., & Zeng, Z. B. (2007). eQTL Viewer: visualizing how sequence variation affects genome-wide transcription. BMC Bioinformatics, 8(7).

Hsieh, W.-P., Chu, T.-M., & Wolfinger, R. (2007). Comparison of statistical performance of univariate and bivariate mixed models for Affymetrix (R) probe level data. JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION, 77(3), 251–264. https://doi.org/10.1080/10629360600826398