Bioinformatics - 2012

Sedykh, A., Fourches, D., Duan, J., Hucke, O., Garneau, M., Zhu, H., … Tropsha, A. (2012). Human Intestinal Transporter Database: QSAR Modeling and Virtual Profiling of Drug Uptake, Efflux and Interactions. Pharmaceutical Research, 30(4), 996–1007. https://doi.org/10.1007/S11095-012-0935-X

Emond, M. J., Louie, T., Emerson, J., Zhao, W., Mathias, R. A., Knowles, M. R., … Bamshad, M. J. (2012). Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis. Nature Genetics, 44(8), 886–889. https://doi.org/10.1038/ng.2344

Sun, L., Rommens, J. M., Corvol, H., Li, W., Li, X., Chiang, T. A., … Strug, L. J. (2012). Multiple apical plasma membrane constituents are associated with susceptibility to meconium ileus in individuals with cystic fibrosis. Nature Genetics, 44(5), 562–569. https://doi.org/10.1038/ng.2221

Che, R., Motsinger-Reif, A. A., & Brown, C. C. (2012). Loss of Power in Two-Stage Residual-Outcome Regression Analysis in Genetic Association Studies. Genetic Epidemiology, n/a-n/a. https://doi.org/10.1002/gepi.21671

Thomas, V. P., Fudali, S. L., Schaff, J. E., Liu, Q., Scholl, E. H., Opperman, C. H., … Williamson, V. M. (2012). A sequence-anchored linkage map of the plant-parasitic nematode meloidogyne hapla reveals exceptionally high genome-wide recombination. G3: Genes, Genomes, Genetics, 2(7), 815–824. https://doi.org/10.1534/g3.112.002261

Judson, R. S., Martin, M. T., Egeghy, P., Gangwal, S., Reif, D. M., Kothiya, P., … A.M. (2012). Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System. International Journal of Molecular Sciences, 13(2), 1805–1831. https://doi.org/10.3390/ijms13021805

Padilla, S., Corum, D., Padnos, B., Hunter, D. L., Beam, A., Houck, K. A., … Reif, D. M. (2012). Zebrafish developmental screening of the ToxCast™ Phase I chemical library. Reproductive Toxicology, 33(2), 174–187. https://doi.org/10.1016/j.reprotox.2011.10.018

Kavlock, R., Chandler, K., Houck, K., Hunter, S., Judson, R., Kleinstreuer, N., … Dix, D. (2012). Update on EPA’s ToxCast Program: Providing High Throughput Decision Support Tools for Chemical Risk Management. Chem. Res. Toxicol., 25(7), 1287–1302. https://doi.org/10.1021/tx3000939

Gangwal, S., Reif, D. M., Mosher, S., Egeghy, P. P., Wambaugh, J. F., Judson, R. S., & Hubal, E. A. C. (2012). Incorporating exposure information into the toxicological prioritization index decision support framework. Science of The Total Environment, 435-436, 316–325. https://doi.org/10.1016/j.scitotenv.2012.06.086

Dix, D. J., Houck, K. A., Judson, R. S., Kleinstreuer, N. C., Knudsen, T. B., Martin, M. T., … Kavlock, R. J. (2012). Incorporating biological, chemical, and toxicological knowledge into predictive models of toxicity. Toxicological Sciences, 130(2), 440–441. https://doi.org/10.1093/toxsci/kfs281

Gory, J. J., Sweeney, H. C., Reif, D. M., & Motsinger-Reif, A. A. (2012). A comparison of internal model validation methods for multifactor dimensionality reduction in the case of genetic heterogeneity. BMC Research Notes, 5(1), 623. https://doi.org/10.1186/1756-0500-5-623

Hoover, K., Marceau, R., Harris, T., Reif, D., & Motsinger-Reif, A. (2012). A comparison of GE optimized neural networks and decision trees. Proceedings of the fourteenth international conference on Genetic and evolutionary computation conference companion - GECCO Companion '12, 611–614. https://doi.org/10.1145/2330784.2330885

Brown, C. C., Havener, T. M., Medina, M. W., Krauss, R. M., McLeod, H. L., & Motsinger-Reif, A. A. (2012). Multivariate methods and software for association mapping in dose-response genome-wide association studies. Biodata Mining, 5.

Wu, C. H., Arighi, C. N., Cohen, K. B., Hirschman, L., Krallinger, M., Lu, Z., … Wilbur, W. J. (2012, December 5). BioCreative-2012 Virtual Issue. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/bas049

Davis, A. P., Johnson, R. J., Lennon-Hopkins, K., Sciaky, D., Rosenstein, M. C., Wiegers, T. C., & Mattingly, C. J. (2012). Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database. Database-The Journal of Biological Databases and Curation.

Che, R. L., Motsinger-Reif, A. A., & Brown, C. C. (2012). Loss of power in two-stage residual-outcome regression analysis in genetic association studies.

Wiegers, T. C., Davis, A. P., & Mattingly, C. J. (2012). Collaborative biocuration-text-mining development task for document prioritization for curation. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/bas037

Swenson, N. G., Enquist, B. J., Pither, J., Kerkhoff, A. J., Boyle, B., Weiser, M. D., … Reich, P. B. (2012). The biogeography and filtering of woody plant functional diversity in North and South America. Global Ecology and Biogeography, 21(8), 798–808.

Hu, J., Ge, H. Y., Newman, M., & Liu, K. J. (2012). OSA: a fast and accurate alignment tool for RNA-Seq. Bioinformatics, 28(14), 1933–1934.

Brown, C. C., Havener, T. M., Medina, M. W., Auman, J. T., Mangravite, L. M., Krauss, R. M., … Motsinger-Reif, A. A. (2012). A genome-wide association analysis of temozolomide response using lymphoblastoid cell lines shows a clinically relevant association with MGMT. PHARMACOGENETICS AND GENOMICS, 22(11), 796–802. https://doi.org/10.1097/fpc.0b013e3283589c50

Funk-Keenan, J., Sacco, J., Wong, Y. Y., Rasmussen, S., Motsinger-Reif, A., & Trepanier, L. A. (2012). Evaluation of Polymorphisms in the Sulfonamide Detoxification Genes CYB5A and CYB5R3 in Dogs with Sulfonamide Hypersensitivity. JOURNAL OF VETERINARY INTERNAL MEDICINE, 26(5), 1126–1133. https://doi.org/10.1111/j.1939-1676.2012.00965.x

He, Y. J., Misher, A. D., Irvin, W., Motsinger-Reif, A., McLeod, H. L., & Hoskins, J. M. (2012). Assessing the utility of whole genome amplified DNA as a template for DMET Plus array. Clinical Chemistry and Laboratory Medicine, 50(8), 1329–1334.

Walker, J. M., Hanel, R. M., Hansen, B. D., & Motsinger-Reif, A. A. (2012, December). Comparison of venous sampling methods for thromboelastography in clinically normal dogs. AMERICAN JOURNAL OF VETERINARY RESEARCH, Vol. 73, pp. 1864–1870. https://doi.org/10.2460/ajvr.73.12.1864

King, B. L., Davis, A. P., Rosenstein, M. C., Wiegers, T. C., & Mattingly, C. J. (2012). Ranking Transitive Chemical-Disease Inferences Using Local Network Topology in the Comparative Toxicogenomics Database. PLOS ONE, 7(11). https://doi.org/10.1371/journal.pone.0046524

Kaddurah-Daouk, R., McEvoy, J., Baillie, R., Zhu, H. J., Yao, J. K., Nimgaonkar, V. L., … Nasrallah, H. A. (2012). Impaired plasmalogens in patients with schizophrenia. Psychiatry Research, 198(3), 347–352.

Kaddurah-Daouk, R., Yuan, P. X., 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.

Ravel, J., Gajer, P., Fu, L., Mauck, C. K., Koenig, S. S. K., Sakamoto, J., … Zeichner, S. L. (2012). Twice-Daily Application of HIV Microbicides Alters the Vaginal Microbiota. MBIO, 3(6). https://doi.org/10.1128/mbio.00370-12

Hertz, D. L., Motsinger-Reif, A. A., Drobish, A., Winham, S. J., McLeod, H. L., Carey, L. A., & Dees, E. C. (2012). CYP2C8*3 predicts benefit/risk profile in breast cancer patients receiving neoadjuvant paclitaxel. BREAST CANCER RESEARCH AND TREATMENT, 134(1), 401–410. https://doi.org/10.1007/s10549-012-2054-0

Sacco, J. C., Abouraya, M., Motsinger-Reif, A., Yale, S. H., McCarty, C. A., & Trepanier, L. A. (2012). Evaluation of polymorphisms in the sulfonamide detoxification genes NAT2, CYB5A, and CYB5R3 in patients with sulfonamide hypersensitivity. PHARMACOGENETICS AND GENOMICS, 22(10), 733–740. https://doi.org/10.1097/fpc.0b013e328357a735

Conner, B. J., Hanel, R. M., Hansen, B. D., Motsinger-Reif, A. A., Asakawa, M., & Swanson, C. R. (2012, May). Effects of acepromazine maleate on platelet function assessed by use of adenosine diphosphate activated- and arachidonic acid-activated modified thromboelastography in healthy dogs. AMERICAN JOURNAL OF VETERINARY RESEARCH, Vol. 73, pp. 595–601. https://doi.org/10.2460/ajvr.73.5.595

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

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: selective serotonin reuptake inhibitor response pharmacogenomics. PHARMACOGENETICS AND GENOMICS, 22(4), 247–253. https://doi.org/10.1097/fpc.0b013e32835001c9

Guenard, B., Weiser, M. D., & Dunn, R. R. (2012). Global models of ant diversity suggest regions where new discoveries are most likely are under disproportionate deforestation threat. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109(19), 7368–7373. https://doi.org/10.1073/pnas.1113867109

Brown, C., Oki, N. O., Hariani, G., & Motsinger-Reif, A. A. (2012). A predictive model for Efavirenz dosing. Pharmacogenomics, 13(2), 137–138.

Kaspari, M., & Weiser, M. D. (2012). Energy, taxonomic aggregation, and the geography of ant abundance. Ecography, 35(1), 65–72.

Lessard, J.-P., Borregaard, M. K., Fordyce, J. A., Rahbek, C., Weiser, M. D., Dunn, R. R., & Sanders, N. J. (2012). Strong influence of regional species pools on continent-wide structuring of local communities. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 279(1727), 266–274. https://doi.org/10.1098/rspb.2011.0552