Bioinformatics - 2011

Reese, B. N., Payne, G. A., Nielsen, D. M., & Woloshuk, C. P. (2011). Gene Expression profile and response to maize kernels by Aspergillus flavus. Phytopathology, 101(7), 797–804. https://doi.org/10.1094/PHYTO-09-10-0261

O'Neil, B. H., Funkhouser, W. K., Calvo, B. F., Meyers, M. O., Kim, H. J., Goldberg, R. M., … Tepper, J. E. (2011). Nuclear Factor κ-Light Chain-Enhancer of Activated B Cells is Activated by Radiotherapy and is Prognostic for Overall Survival in Patients With Rectal Cancer Treated With Preoperative Fluorouracil-Based Chemoradiotheraphy. International Journal of Radiation Oncology*Biology*Physics, 80(3), 705–711. https://doi.org/10.1016/j.ijrobp.2010.02.063

Salzmann, C. A., Olivry, T. J. M., Nielsen, D. M., Paps, J. S., Harris, T. L., & Olby, N. J. (2011). Genome-wide linkage study of atopic dermatitis in West Highland White Terriers. BMC Genetics, 12(1), 37. https://doi.org/10.1186/1471-2156-12-37

Low, Y., Uehara, T., Minowa, Y., Yamada, H., Ohno, Y., Urushidani, T., … Tropsha, A. (2011). Predicting Drug-Induced Hepatotoxicity Using QSAR and Toxicogenomics Approaches. Chemical Research in Toxicology, 24(8), 1251–1262. https://doi.org/10.1021/tx200148a

Wright, F. A., Strug, L. J., Doshi, V. K., Commander, C. W., Blackman, S. M., Sun, L., … Cutting, G. R. (2011). Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2. Nature Genetics, 43(6), 539–546. https://doi.org/10.1038/ng.838

Gatti, D. M., Lu, L., Williams, R. W., Sun, W., Wright, F. A., Threadgill, D. W., & Rusyn, I. (2011). MicroRNA expression in the livers of inbred mice. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 714(1-2), 126–133. https://doi.org/10.1016/j.mrfmmm.2011.05.007

Taylor, C., Commander, C. W., Collaco, J. M., Strug, L. J., Li, W., Wright, F. A., … Corey, M. (2011). A novel lung disease phenotype adjusted for mortality attrition for cystic fibrosis Genetic modifier studies. Pediatric Pulmonology, 46(9), 857–869. https://doi.org/10.1002/ppul.21456

Thomas, F., Motsinger-Reif, A. A., Hoskins, J. M., Dvorak, A., Roy, S., Alyasiri, A., … McLeod, H. L. (2011). Methylenetetrahydrofolate reductase genetic polymorphisms and toxicity to 5-FU-based chemoradiation in rectal cancer. British Journal of Cancer, 105(11), 1654–1662. https://doi.org/10.1038/BJC.2011.442

Stock, S. P., Bird, D. M. K., Ghedin, E., & Goodrich-Blair, H. (2011). Abstracts of NEMASYM: The Third Nematode-Bacteria Symbioses Research Coordination Network Meeting. Symbiosis, 55(3), 97–109. https://doi.org/10.1007/s13199-011-0135-1

Shah, I., Houck, K., Judson, R. S., Kavlock, R. J., Martin, M. T., Reif, D. M., … Dix, D. J. (2011). Using Nuclear Receptor Activity to Stratify Hepatocarcinogens. PLoS ONE, 6(2). https://doi.org/10.1371/journal.pone.0014584

Sipes, N. S., Martin, M. T., Reif, D. M., Kleinstreuer, N. C., Judson, R. S., Singh, A. V., … Knudsen, T. B. (2011). Predictive models of prenatal developmental toxicity from ToxCast high-throughput screening data. Toxicological Sciences, 124(1), 109–127. https://doi.org/10.1093/toxsci/kfr220

Martin, M. T., Knudsen, T. B., Reif, D. M., Houck, K. A., Judson, R. S., Kavlock, R. J., & Dix, D. J. (2011). Predictive model of rat reproductive toxicity from ToxCast high throughput screening. Biology of Reproduction, 85(2), 327–339. https://doi.org/10.1095/biolreprod.111.090977

Hoover, K., Marceau, R., Harris, T., Hardison, N., Reif, D., & Motsinger-Reif, A. (2011). Optimization of grammatical evolution decision trees. Proceedings of the 13th annual conference companion on Genetic and evolutionary computation - GECCO '11, 35–36. https://doi.org/10.1145/2001858.2001879

Gallagher, J., Hudgens, E., Williams, A., Inmon, J., Rhoney, S., Andrews, G., … Hubal, E. C. (2011). Mechanistic indicators of childhood asthma (MICA) study: piloting an integrative design for evaluating environmental health. BMC Public Health, 11, 344. https://doi.org/10.1186/1471-2458-11-344

Joubert, B. R., Reif, D. M., Edwards, S. W., Leiner, K. A., Hudgens, E. E., Egeghy, P., … Hubal, E. C. (2011). Evaluation of genetic susceptibility to childhood allergy and asthma in an African American urban population. BMC Medical Genetics, 12, 25. https://doi.org/10.1186/1471-2350-12-25

Chandler, K. J., Barrier, M., Jeffay, S., Nichols, H. P., Kleinstreuer, N. C., Singh, A. V., … Knudsen, T. B. (2011). Evaluation of 309 Environmental Chemicals Using a Mouse Embryonic Stem Cell Adherent Cell Differentiation and Cytotoxicity Assay. PLoS ONE, 6(6), e18540. https://doi.org/10.1371/journal.pone.0018540

Kleinstreuer, N. C., Judson, R. S., Reif, D. M., Sipes, N. S., Singh, A. V., Chandler, K. J., … Knudsen, T. B. (2011). Environmental Impact on Vascular Development Predicted by High-Throughput Screening. Environ Health Perspect, 119(11), 1596–1603. https://doi.org/10.1289/ehp.1103412

Knudsen, T. B., Houck, K. A., Sipes, N. S., Singh, A. V., Judson, R. S., Martin, M. T., … Kavlock, R. J. (2011). Activity profiles of 309 ToxCast™ chemicals evaluated across 292 biochemical targets. Toxicology, 282(1-2), 1–15. https://doi.org/10.1016/j.tox.2010.12.010

The NIDDK central repository at 8 years-ambition, revision, use and impact. (2011). Database-The Journal of Biological Databases and Curation.

Beam, A. L., & Motsinger-Reif, A. A. (2011). Optimization of nonlinear dose- and concentration-response models utilizing evolutionary computation. Dose-Response, 9(3), 387–409.

Kaddurah-Daouk, R., Baillie, R. A., Zhu, H., Zeng, Z.-B., Wiest, M. M., Nguyen, U. T., … Krauss, R. M. (2011). Enteric Microbiome Metabolites Correlate with Response to Simvastatin Treatment. PLOS ONE, 6(10). https://doi.org/10.1371/journal.pone.0025482

Peters, E. J., Motsinger-Reif, A., Havener, T. M., Everitt, L., Hardison, N. E., Watson, V. G., … McLeod, H. L. (2011). Pharmacogenomic characterization of US FDA-approved cytotoxic drugs. PHARMACOGENOMICS, 12(10), 1407–1415. https://doi.org/10.2217/pgs.11.92

Fitzpatrick, M. C., Sanders, N. J., Ferrier, S., Longino, J. T., Weiser, M. D., & Dunn, R. (2011). Forecasting the future of biodiversity: a test of single- and multi-species models for ants in North America. ECOGRAPHY, 34(5), 836–847. https://doi.org/10.1111/j.1600-0587.2011.06653.x

Cohen, M. G., Rossi, J. S., Garbarino, J., Bowling, R., Motsinger-Reif, A. A., Schuler, C., … Gabriel, D. (2011). Insights into the inhibition of platelet activation by omega-3 polyunsaturated fatty acids: Beyond aspirin and clopidogrel. THROMBOSIS RESEARCH, 128(4), 335–340. https://doi.org/10.1016/j.thromres.2011.04.023

Angstadt, A. Y., Motsinger-Reif, A., Thomas, R., Kisseberth, W. C., Couto, C. G., Duval, D. L., … Breen, M. (2011). Characterization of Canine Osteosarcoma by Array Comparative Genomic Hybridization and RT-qPCR: Signatures of Genomic Imbalance in Canine Osteosarcoma Parallel the Human Counterpart. GENES CHROMOSOMES & CANCER, 50(11), 859–874. https://doi.org/10.1002/gcc.20908

Watson, V. G., Hardison, N. E., Harris, T., Motsinger-Reif, A., & McLeod, H. L. (2011). Genomic Profiling in CEPH Cell Lines Distinguishes between the Camptothecins and Indenoisoquinolines. MOLECULAR CANCER THERAPEUTICS, 10(10), 1839–1845. https://doi.org/10.1158/1535-7163.mct-10-0872

McFerrin, L. G., & Atchley, W. R. (2011). Evolution of the Max and Mlx Networks in Animals. GENOME BIOLOGY AND EVOLUTION, 3, 915–937. https://doi.org/10.1093/gbe/evr082

Tzeng, J.-Y., Zhang, D., Pongpanich, M., Smith, C., McCarthy, M. I., Sale, M. M., … Sullivan, P. F. (2011). Studying Gene and Gene-Environment Effects of Uncommon and Common Variants on Continuous Traits: A Marker-Set Approach Using Gene-Trait Similarity Regression. AMERICAN JOURNAL OF HUMAN GENETICS, 89(2), 277–288. https://doi.org/10.1016/j.ajhg.2011.07.007

Asher, G. N., Motsinger-Reif, A. A., Jonas, D. E., & Viera, A. J. (2011). Quality of reporting on randomised controlled trials of auriculotherapy for pain. ACUPUNCTURE IN MEDICINE, 29(2), 122–126. https://doi.org/10.1136/aim.2010.003475

Menke, S. B., Guenard, B., Sexton, J. O., Weiser, M. D., Dunn, R. R., & Silverman, J. (2011). Urban areas may serve as habitat and corridors for dry-adapted, heat tolerant species; an example from ants. URBAN ECOSYSTEMS, 14(2), 135–163. https://doi.org/10.1007/s11252-010-0150-7

Chang, K. Y., & Muddiman, D. C. (2011). Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms. BMC Genomics, 12.

Mathes, W. F., Aylor, D. L., Miller, D. R., Churchill, G. A., Chesler, E. J., Villena, F. P.-M., … Pomp, D. (2011). Architecture of energy balance traits in emerging lines of the Collaborative Cross. AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM, 300(6), E1124–E1134. https://doi.org/10.1152/ajpendo.00707.2010

Conrad, D. F., Keebler, J. E. M., DePristo, M. A., Lindsay, S. J., Zhang, Y. J., Casals, F., … Hurles, M. E. (2011). Variation in genome-wide mutation rates within and between human families. Nature Genetics, 43(7), 712–137.

Gamble, K. L., Motsinger-Reif, A. A., Hida, A., Borsetti, H. M., Servick, S. V., Ciarleglio, C. M., … Johnson, C. H. (2011). Shift work in nurses: Contribution of phenotypes and genotypes to adaptation. PLoS One, 6(4).

Dalzell, J. J., McVeigh, P., Warnock, N. D., Mitreva, M., Bird, D. M. K., Abad, P., … Maule, A. G. (2011). RNAi Effector Diversity in Nematodes. PLOS NEGLECTED TROPICAL DISEASES, 5(6). https://doi.org/10.1371/journal.pntd.0001176

Jenkins, C. N., Sanders, N. J., Andersen, A. N., Arnan, X., Bruehl, C. A., Cerda, X., … Dunn, R. R. (2011). Global diversity in light of climate change: the case of ants. DIVERSITY AND DISTRIBUTIONS, 17(4), 652–662. https://doi.org/10.1111/j.1472-4642.2011.00770.x

Zhu, H., & Li, L. (2011). Biological pathway selection through nonlinear dimension reduction. BIOSTATISTICS, 12(3), 429–444. https://doi.org/10.1093/biostatistics/kxq081

Stegen, J. C., Swenson, N. G., Enquist, B. J., White, E. P., Phillips, O. L., Jorgensen, P. M., … Vargas, P. N. (2011). Variation in above-ground forest biomass across broad climatic gradients. Global Ecology and Biogeography, 20(5), 744–754.

Thomas, R., Seiser, E. L., Motsinger-Reif, A., Borst, L., Valli, V. E., Kelley, K., … Breen, M. (2011). Refining tumor-associated aneuploidy through 'genomic recoding' of recurrent DNA copy number aberrations in 150 canine non-Hodgkin lymphomas. LEUKEMIA & LYMPHOMA, 52(7), 1321–1335. https://doi.org/10.3109/10428194.2011.559802

Hedan, B., Thomas, R., Motsinger-Reif, A., Abadie, J., Andre, C., Cullen, J., & Breen, M. (2011). Molecular cytogenetic characterization of canine histiocytic sarcoma: A spontaneous model for human histiocytic cancer identifies deletion of tumor suppressor genes and highlights influence of genetic background on tumor behavior. BMC Cancer, 11.

Watson, V. G., Motsinger-Reif, A., Hardison, N. E., Peters, E. J., Havener, T. M., Everitt, L., … McLeod, H. L. (2011). Identification and replication of loci involved in camptothecin-induced cytotoxicity using CEPH pedigrees. PLoS One, 6(5).

Winham, S. J., & Motsinger-Reif, A. A. (2011). The Effect of Retrospective Sampling on Estimates of Prediction Error for Multifactor Dimensionality Reduction. Annals of Human Genetics, 75, 46–61.

Tsai, S., Hardison, N. E., James, A. H., Motsinger-Reif, A. A., Bischoff, S. R., Thames, B. H., & Piedrahita, J. A. (2011). Transcriptional profiling of human placentas from pregnancies complicated by preeclampsia reveals disregulation of sialic acid acetylesterase and immune signalling pathways. PLACENTA, 32(2), 175–182. https://doi.org/10.1016/j.placenta.2010.11.014

Scholl, E. H., & Bird, D. M. K. (2011, February 22). Computational and phylogenetic validation of nematode horizontal gene transfer. BMC BIOLOGY, Vol. 9. https://doi.org/10.1186/1741-7007-9-9

Myers, R. A., Casals, F., Gauthier, J., Hamdan, F. F., Keebler, J., Boyko, A. R., … Stone, E. A. (2011). A population genetic approach to mapping neurological disorder genes using deep resequencing. PLoS Genetics, 7(2).

Winham, S., Wang, C., & Motsinger-Reif, A. A. (2011). A Comparison of Multifactor Dimensionality Reduction and L-1-Penalized Regression to Identify Gene-Gene Interactions in Genetic Association Studies. STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY, 10(1). https://doi.org/10.2202/1544-6115.1613