Bioinformatics - 2008

Hulgan, T., Tebas, P., Canter, J. A., Mulligan, K., Haas, D. W., Dubé, M., … Kallianpur, A. R. (2008). Hemochromatosis Gene Polymorphisms, Mitochondrial Haplogroups, and Peripheral Lipoatrophy during Antiretroviral Therapy. The Journal of Infectious Diseases, 197(6), 858–866. https://doi.org/10.1086/528697

Olby, N. J., Harris, T., Mehta, P. M., Breen, M., Thomas, R., Myers, R., & Nielsen, D. (2008). Linkage Analysis in American Staffordshire Terriers with Hereditary Cerebellar Cortical Degeneration. Journal of Veterinary Internal Medicine, 22(3), 723–724.

Smith, C. A., Robertson, D., Yates, B., Nielsen, D. M., Brown, D., Dean, R. A., & Payne, G. A. (2008). The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus. Current Genetics, 54(5), 241–269. https://doi.org/10.1007/s00294-008-0215-9

Tetko, I. V., Sushko, I., Pandey, A. K., Zhu, H., Tropsha, A., Papa, E., … Varnek, A. (2008). Critical Assessment of QSAR Models of Environmental Toxicity against Tetrahymena pyriformis: Focusing on Applicability Domain and Overfitting by Variable Selection. Journal of Chemical Information and Modeling, 48(9), 1733–1746. https://doi.org/10.1021/ci800151m

Zhu, H., Tropsha, A., Fourches, D., Varnek, A., Papa, E., Gramatica, P., … Tetko, I. V. (2008). Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis. Journal of Chemical Information and Modeling, 48(4), 766–784. https://doi.org/10.1021/ci700443v

Sullivan, P. F., Lin, D., Tzeng, J.-Y., van den Oord, E., Perkins, D., Stroup, T. S., … Close, S. L. (2008). Genomewide association for schizophrenia in the CATIE study: results of stage 1. Molecular Psychiatry, 13(6), 570–584. https://doi.org/10.1038/mp.2008.25

Ghosh, A., Zou, F., & Wright, F. A. (2008). Estimating Odds Ratios in Genome Scans: An Approximate Conditional Likelihood Approach. The American Journal of Human Genetics, 82(5), 1224. https://doi.org/10.1016/j.ajhg.2008.04.004

Ghosh, A., Zou, F., & Wright, F. A. (2008). Estimating Odds Ratios in Genome Scans: An Approximate Conditional Likelihood Approach. The American Journal of Human Genetics, 82(5), 1064–1074. https://doi.org/10.1016/j.ajhg.2008.03.002

Lee, S., Sullivan, P. F., Zou, F., & Wright, F. A. (2008). Comment on a Simple and Improved Correction for Population Stratification. The American Journal of Human Genetics, 82(2), 524–526. https://doi.org/10.1016/j.ajhg.2007.10.014

Tsai, S., Hardison, N., Bischoff, S., Thames, B., Jamessd, A., Motsinger-Reif, A., & Piedrahita, J. (2008). 262: Molecular signatures of preeclampsia in human term placentas. American Journal of Obstetrics and Gynecology, 199(6), S84. https://doi.org/10.1016/j.ajog.2008.09.290

Schaff, J. E., Mbeunkui, F., Blackburn, K., Bird, D. M. K., & Goshe, M. B. (2008). SILIP: A novel stable isotope labeling method for in planta quantitative proteomic analysis. Plant Journal, 56(5), 840–854. https://doi.org/10.1111/j.1365-313X.2008.03639.x

Reif, D. M., McKinney, B. A., & Motsinger, A. A. (2008). Genetic basis for adverse events after smallpox vaccination (Journal of Infectious Diseases (2008) 198, (16-22)). Journal of Infectious Diseases, 198(5). https://doi.org/10.1086/590918

Reif, D. M., McKinney, B. A., Motsinger, A. A., Chanock, S. J., Edwards, K. M., Rock, M. T., … Crowe, Jr., J. E. (2008). Genetic Basis for Adverse Events after Smallpox Vaccination. The Journal of Infectious Diseases, 198(1), 16–22. https://doi.org/10.1086/588670

Hardison, N. E., Fanelli, T. J., Dudek, S. M., Reif, D. M., Ritchie, M. D., & Motsinger-Reif, A. A. (2008). A balanced accuracy fitness function leads to robust analysis using grammatical evolution neural networks in the case of class imbalance. Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08, 353–354. https://doi.org/10.1145/1389095.1389159

Motsinger-Reif, A. A., Reif, D. M., Fanelli, T. J., & Ritchie, M. D. (2008). A Comparison of Analytical Methods for Genetic Association Studies. GENETIC EPIDEMIOLOGY, 32(8), 767–778. https://doi.org/10.1002/gepi.20345

Choi, S. C., Redelings, B. D., & Thorne, J. L. (2008). Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 363(1512), 3931–3939. https://doi.org/10.1098/rstb.2008.0167

Schaff, J. E., Mbeunkui, F., Blackburn, K., Bird, D. M., & Goshe, M. B. (2008). A sequence-anchored genetic linkage map for the moss, Physcomitrella patens. Plant Journal, 56(5), 840–854.

Opperman, C. H., Bird, D. M., Williamson, V. M., Rokhsar, D. S., Burke, M., Cohn, J., … Windham, E. (2008). Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(39), 14802–14807. https://doi.org/10.1073/pnas.0805946105

Prugnolle, F., Mcgee, K., Keebler, J., & Awadalla, P. (2008). Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents. BMC Evolutionary Biology, 8.

Nielsen, D. M., Suchindran, S., & Smith, C. P. (2008). Does strong linkage disequilibrium guarantee redundant association results? Genetic Epidemiology, 32(6), 546–552. https://doi.org/10.1002/gepi.20328

Grossman, I., Sullivan, P. F., Walley, N., Liu, Y., Dawson, J. R., Gumbs, C., … Goldstein, D. B. (2008). Genetic determinants of variable metabolism have little impact on the clinical use of leading antipsychotics in the CATIE study. GENETICS IN MEDICINE, 10(10), 720–729. https://doi.org/10.1097/GIM.0b013e3181863239

Huang, L., Heinloth, A. N., Zeng, Z. B., Paules, R. S., & Bushel, P. R. (2008). Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants. BMC Genomics, 9.

Leehey, M. A., Berry-Kravis, E., Goetz, C. G., Zhang, L., Hall, D. A., Li, L., … Hagerman, P. J. (2008). FMR1 CGG repeat length predicts motor dysfunction in premutation carriers. Neurology (Minneapolis, Minn.), 70(16), 1397–1402.

Aylor, D. L., & Zeng, Z. B. (2008). From classical genetics to quantitative genetics to systems biology: Modeling epistasis. PLoS Genetics, 4(3).

Zhang, L., Martin, E. R., Chung, R.-H., Li, Y.-J., & Morris, R. W. (2008). X-LRT: A likelihood approach to estimate genetic risks and test association with X-linked markers using a case-parents design. GENETIC EPIDEMIOLOGY, 32(4), 370–380. https://doi.org/10.1002/gepi.20311

Kim, Y., Feng, S., & Zeng, Z.-B. (2008). Measuring and partitioning the high-order linkage disequilibrium by multiple order Markov chains. GENETIC EPIDEMIOLOGY, 32(4), 301–312. https://doi.org/10.1002/gepi.20305

Motsinger-Reif, A. A., Dudek, S. M., Hahn, L. W., & Ritchie, M. D. (2008). Comparison of approaches for machine-learning optimization of neural networks for detecting gene-gene interactions in genetic epidemiology. GENETIC EPIDEMIOLOGY, 32(4), 325–340. https://doi.org/10.1002/gepi.20307