Bioinformatics - 2013

Franck, C. T., Nielsen, D. M., & Osborne, J. A. (2013). A method for detecting hidden additivity in two-factor unreplicated experiments. Computational Statistics & Data Analysis, 67, 95–104. https://doi.org/10.1016/j.csda.2013.05.002

Low, Y., Sedykh, A., Fourches, D., Golbraikh, A., Whelan, M., Rusyn, I., & Tropsha, A. (2013). Integrative Chemical–Biological Read-Across Approach for Chemical Hazard Classification. Chemical Research in Toxicology, 26(8), 1199–1208. https://doi.org/10.1021/TX400110F

Fourches, D., Muratov, E., Ding, F., Dokholyan, N. V., & Tropsha, A. (2013). Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches. Journal of Chemical Information and Modeling, 53(8), 1915–1922. https://doi.org/10.1021/CI400216Q

Zhang, L., Fourches, D., Sedykh, A., Zhu, H., Golbraikh, A., Ekins, S., … Tropsha, A. (2013). Discovery of Novel Antimalarial Compounds Enabled by QSAR-Based Virtual Screening. Journal of Chemical Information and Modeling, 53(2), 475–492. https://doi.org/10.1021/ci300421n

Fourches, D., & Tropsha, A. (2013). Using Graph Indices for the Analysis and Comparison of Chemical Datasets. Molecular Informatics, 32(9-10), 827–842. https://doi.org/10.1002/MINF.201300076

Ghosh, A., Wright, F. A., & Zou, F. (2013). Unified Analysis of Secondary Traits in Case–Control Association Studies. Journal of the American Statistical Association, 108(502), 566–576. https://doi.org/10.1080/01621459.2013.793121

Lonsdale, J., Thomas, J., Salvatore, M., Phillips, R., Lo, E., Shad, S., … Moore, H. F. (2013). The Genotype-Tissue Expression (GTEx) project. Nature Genetics, 45(6), 580–585. https://doi.org/10.1038/NG.2653

Sirenko, O., Cromwell, E. F., Crittenden, C., Wignall, J. A., Wright, F. A., & Rusyn, I. (2013). Assessment of beating parameters in human induced pluripotent stem cells enables quantitative in vitro screening for cardiotoxicity. Toxicology and Applied Pharmacology, 273(3), 500–507. https://doi.org/10.1016/J.TAAP.2013.09.017

Zhou, Y.-H., Mayhew, G., Sun, Z., Xu, X., Zou, F., & Wright, F. A. (2013). Space-time clustering and the permutation moments of quadratic forms. Stat, 2(1), 292–302. https://doi.org/10.1002/STA4.37

Byrnes, A. E., Wu, M. C., Wright, F. A., Li, M., & Li, Y. (2013). The Value of Statistical or Bioinformatics Annotation for Rare Variant Association With Quantitative Trait. Genetic Epidemiology, 37(7), 666–674. https://doi.org/10.1002/GEPI.21747

Phillippi, J., Xie, Y., Miller, D. R., Bell, T. A., Zhang, Z., Lenarcic, A. B., … Frelinger, J. A. (2013). Using the emerging Collaborative Cross to probe the immune system. Genes & Immunity, 15(1), 38–46. https://doi.org/10.1038/GENE.2013.59

Xiao, H., Ciavatta, D., Aylor, D. L., Hu, P., de Villena, F. P.-M., Falk, R. J., & Jennette, J. C. (2013). Genetically Determined Severity of Anti-Myeloperoxidase Glomerulonephritis. The American Journal of Pathology, 182(4), 1219–1226. https://doi.org/10.1016/j.ajpath.2012.12.006

Bobay, B. G., Digennaro, P., Scholl, E., Imin, N., Djordjevic, M. A., & McK Bird, D. (2013). Solution NMR studies of the plant peptide hormone CEP inform function. FEBS Letters, 587(24), 3979–3985. https://doi.org/10.1016/j.febslet.2013.10.033

Rotroff, D. M., Dix, D. J., Houck, K. A., Knudsen, T. B., Martin, M. T., McLaurin, K. W., … Judson, R. S. (2013). Using in vitro high throughput screening assays to identify potential endocrine-disrupting chemicals. Environmental Health Perspectives, 121(1), 7–14. https://doi.org/10.1289/ehp.1205065

Reif, D. M., Sypa, M., Lock, E. F., Wright, F. A., Wilson, A., Cathey, T., … Bioinformatics. (2013). ToxPi GUI: an interactive visualization tool for transparent integration of data from diverse sources of evidence. Bioinformatics, 29(3), 402–403. https://doi.org/10.1093/bioinformatics/bts686

Rotroff, D. M., Dix, D. J., Houck, K. A., Kavlock, R. J., Knudsen, T. B., Martin, M. T., … Judson, R. S. (2013). Real-time growth kinetics measuring hormone mimicry for ToxCast chemicals in T-47D human ductal carcinoma cells. Chemical Research in Toxicology, 26(7), 1097–1107. https://doi.org/10.1021/tx400117y

Judson, R., Kavlock, R., Martin, M., Reif, D., Houck, K., Knudsen, T., … Dix, D. (2013). Perspectives on validation of high-throughput assays supporting 21st century toxicity testing. Altex, 30(1), 51–66. Retrieved from http://europepmc.org/abstract/med/23338806

Kleinstreuer, N. C., Dix, D. J., Houck, K. A., Kavlock, R. J., Knudsen, T. B., Martin, M. T., … Judson, R. S. (2013). In vitro perturbations of targets in cancer hallmark processes predict rodent chemical carcinogenesis. Toxicological Sciences, 131(1), 40–55. https://doi.org/10.1093/toxsci/kfs285

Williams-DeVane, C. R., Reif, D. M., Cohen Hubal, E., Bushel, P. R., Hudgens, E. E., Gallagher, J. E., & Edwards, S. W. (2013). Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes. BMC Systems Biology, 7, 119. https://doi.org/10.1186/1752-0509-7-119

Motsinger-Reif, A. A., Zhu, H., Kling, M. A., Matson, W., Sharma, S., Fiehn, O., … Arnold, S. E. (2013). Comparing metabolomic and pathologic biomarkers alone and in combination for discriminating Alzheimer’s disease from normal cognitive aging. Acta Neuropathologica Communications, 1(1), 28. https://doi.org/10.1186/2051-5960-1-28

Houck, K. A., Richard, A. M., Judson, R. S., Martin, M. T., Reif, D. M., & Shah, I. (2013, February). ToxCast: Predicting Toxicity Potential Through High-Throughput Bioactivity Profiling. High-Throughput Screening Methods in Toxicity Testing, Vol. 2, p. 1–31. https://doi.org/10.1002/9781118538203.ch1

Sipes, N. S., Martin, M. T., Kothiya, P., Reif, D. M., Judson, R. S., Richard, A. M., … Knudsen, T. B. (2013). Profiling 976 ToxCast Chemicals across 331 Enzymatic and Receptor Signaling Assays. Chem. Res. Toxicol., 26(6), 878–895. https://doi.org/10.1021/tx400021f

Ducharme, N. A., Peterson, L. E., Benfenati, E., Reif, D., McCollum, C. W., JÅ, G., & Bondesson, M. (2013). Meta-analysis of toxicity and teratogenicity of 133 chemicals from zebrafish developmental toxicity studies. Reproductive Toxicology, 41, 98–108. https://doi.org/10.1016/j.reprotox.2013.06.070

Wambaugh, J. F., Setzer, R. W., Reif, D. M., Gangwal, S., Mitchell-Blackwood, J., Arnot, J. A., … E.A. (2013). High-throughput models for exposure-based chemical prioritization in the ExpoCast project. Environmental Science and Technology, 47(15), 8479–8488. https://doi.org/10.1021/es400482g

Wambaugh, J. F., Setzer, R. W., Pitruzzello, A. M., Liu, J., Reif, D. M., Kleinstreuer, N. C., … Lau, C. (2013). Dosimetric anchoring of in vivo and in vitro studies for perfluorooctanoate and perfluorooctanesulfonate. Toxicological Sciences, 136(2), 308–327. https://doi.org/10.1093/toxsci/kft204

Kleinstreuer, N., Dix, D., Rountree, M., Baker, N., Sipes, N., Reif, D., … Knudsen, T. (2013). A Computational Model Predicting Disruption of Blood Vessel Development. PLoS Comput Biol, 9(4), e1002996. https://doi.org/10.1371/journal.pcbi.1002996

Posner, L. P., Bailey, K. M., Richardson, E. Y., Motsinger-Reif, A. A., & Harms, C. A. (2013). ALFAXALONE ANESTHESIA IN BULLFROGS (LITHOBATES CATESBEIANA) BY INJECTION OR IMMERSION. JOURNAL OF ZOO AND WILDLIFE MEDICINE, 44(4), 965–971. https://doi.org/10.1638/2013-0090r.1

Zhang, J., Franks, R. G., Liu, X., Kang, M., Keebler, J. E. M., Schaff, J. E., … Xiang, Q.-Y. (2013). De novo Sequencing, Characterization, and Comparison of Inflorescence Transcriptomes of Cornus canadensis and C. florida (Cornaceae). PLOS ONE, 8(12). https://doi.org/10.1371/journal.pone.0082674

Lucky, A., Trautwein, M. D., Guenard, B. S., Weiser, M. D., & Dunn, R. R. (2013). Tracing the Rise of Ants - Out of the Ground. PLOS ONE, 8(12). https://doi.org/10.1371/journal.pone.0084012

Rotroff, D. M., Thomas, R., Breen, M., & Motsinger-Reif, A. A. (2013, December). Naturally occuring canine cancers: powerful models for stimulating pharmacogenomic advancement in human medicine. PHARMACOGENOMICS, Vol. 14, pp. 1929–1931. https://doi.org/10.2217/pgs.13.178

Davis, A. P., Wiegers, T. C., Roberts, P. M., King, B. L., Lay, J. M., Lennon-Hopkins, K., … Mattingly, C. J. (2013). A CTD-Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug-disease and drug-phenotype interactions. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/bat080

Dolezal, A. L., Obrian, G. R., Nielsen, D. M., Woloshuk, C. P., Boston, R. S., & Payne, G. A. (2013). Localization, morphology and transcriptional profile of Aspergillus flavus during seed colonization. MOLECULAR PLANT PATHOLOGY, 14(9), 898–909. https://doi.org/10.1111/mpp.12056

Supple, M. A., Hines, H. M., Dasmahapatra, K. K., Lewis, J. J., Nielsen, D. M., Lavoie, C., … Counterman, B. A. (2013). Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. GENOME RESEARCH, 23(8), 1248–1257. https://doi.org/10.1101/gr.150615.112

Guo, L., Tsai, S. Q., Hardison, N. E., James, A. H., Motsinger-Reif, A. A., Thames, B., … Piedrahita, J. A. (2013). Differentially expressed microRNAs and affected biological pathways revealed by modulated modularity clustering (MMC) analysis of human preeclamptic and IUGR placentas. PLACENTA, 34(7), 599–605. https://doi.org/10.1016/j.placenta.2013.04.007

Kaddurah-Daouk, R., Zhu, H., Sharma, S., Bogdanov, M., Rozen, S. G., Matson, W., … Arnold, S. E. (2013). Alterations in metabolic pathways and networks in Alzheimer’s disease. Translational Psychiatry, 3(4), e244–e244. https://doi.org/10.1038/TP.2013.18

Guo, Y. L., Pais, A., Weakley, A. S., & Xiang, Q. Y. (2013). Molecular phylogenetic analysis suggests paraphyly and early diversification of Philadelphus (Hydrangeaceae) in western North America: New insights into affinity with Carpenteria. Journal of Systematics and Evolution, 51(5), 545–563. https://doi.org/10.1111/jse.12041

Richards, K. L., Motsinger-Reif, A. A., Chen, H.-W., Fedoriw, Y., Fan, C., Nielsen, D. M., … Suter, S. E. (2013). Gene Profiling of Canine B-Cell Lymphoma Reveals Germinal Center and Postgerminal Center Subtypes with Different Survival Times, Modeling Human DLBCL. CANCER RESEARCH, 73(16), 5029–5039. https://doi.org/10.1158/0008-5472.can-12-3546

Tarigo, J. L., Scholl, E. H., Bird, D. M. K., Brown, C. C., Cohn, L. A., Dean, G. A., … Birkenheuer, A. J. (2013). A Novel Candidate Vaccine for Cytauxzoonosis Inferred from Comparative Apicomplexan Genomics. PLOS ONE, 8(8). https://doi.org/10.1371/journal.pone.0071233

Hertz, D. L., Roy, S., Motsinger-Reif, A. A., Drobish, A., Clark, L. S., McLeod, H. L., … Dees, E. C. (2013). CYP2C8*3 increases risk of neuropathy in breast cancer patients treated with paclitaxel. ANNALS OF ONCOLOGY, 24(6), 1472–1478. https://doi.org/10.1093/annonc/mdt018

Dai, H. Y., Charnigo, R. J., Becker, M. L., Leeder, J. S., & Motsinger-Reif, A. A. (2013). Risk score modeling of multiple gene to gene interactions using aggregated-multifactor dimensionality reduction. Biodata Mining, 6.

Motsinger-Reif, A. A., Jorgenson, E., Relling, M. V., Kroetz, D. L., Weinshilboum, R., Cox, N. J., & Roden, D. M. (2013). Genome-wide association studies in pharmacogenomics: Successes and lessons. Pharmacogenetics and Genomics, 23(8), 383–394.

Jenkins, C. N., Guenard, B., Diamond, S. E., Weiser, M. D., & Dunn, R. R. (2013). Conservation implications of divergent global patterns of ant and vertebrate diversity. DIVERSITY AND DISTRIBUTIONS, 19(8), 1084–1092. https://doi.org/10.1111/ddi.12090

Comeau, D. C., Dogan, R. I., Ciccarese, P., Cohen, K. B., Krallinger, M., Leitner, F., … Wilbur, W. J. (2013). BioC: a minimalist approach to interoperability for biomedical text processing. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/bat064

Su, Y., Nielsen, D., Zhu, L., Richards, K., Suter, S., Breen, M., … Osborne, J. (2013). Gene selection and cancer type classification of diffuse large-B-cell lymphoma using a bivariate mixture model for two-species data. Hum Genomics, 7, 2.

Siefert, A., Ravenscroft, C., Weiser, M. D., & Swenson, N. G. (2013). Functional beta-diversity patterns reveal deterministic community assembly processes in eastern North American trees. Global Ecology and Biogeography, 22(6), 682–691.

Jones, S., & Motsinger-Reif, A. (2013). Interview A discussion on genome-wide associations in pharmacogenomics. Pharmacogenomics, 14(4), 361–363.

Vargo, E. L., Leniaud, L., Swoboda, L. E., Diamond, S. E., Weiser, M. D., Miller, D. M., & Bagneres, A.-G. (2013). Clinal variation in colony breeding structure and level of inbreeding in the subterranean termites Reticulitermes flavipes and R.grassei. MOLECULAR ECOLOGY, 22(5), 1447–1462. https://doi.org/10.1111/mec.12166

Davis, A. P., Wiegers, T. C., Johnson, R. J., Lay, J. M., Lennon-Hopkins, K., Saraceni-Richards, C., … Mattingly, C. J. (2013). Text Mining Effectively Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database. PLOS ONE, 8(4). https://doi.org/10.1371/journal.pone.0058201