Bioinformatics - 2014

Goldstein, J. I., Fredrik Jarskog, L., Hilliard, C., Alfirevic, A., Duncan, L., Fourches, D., … Sullivan, P. F. (2014). Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles. Nature Communications, 5(1). https://doi.org/10.1038/NCOMMS5757

Cherkasov, A., Muratov, E. N., Fourches, D., Varnek, A., Baskin, I. I., Cronin, M., … Tropsha, A. (2014). QSAR Modeling: Where Have You Been? Where Are You Going To? Journal of Medicinal Chemistry, 57(12), 4977–5010. https://doi.org/10.1021/JM4004285

Mu, Q., Jiang, G., Chen, L., Zhou, H., Fourches, D., Tropsha, A., & Yan, B. (2014). Chemical Basis of Interactions Between Engineered Nanoparticles and Biological Systems. Chemical Reviews, 114(15), 7740–7781. https://doi.org/10.1021/CR400295A

Golbraikh, A., Muratov, E., Fourches, D., & Tropsha, A. (2014). Data Set Modelability by QSAR. Journal of Chemical Information and Modeling, 54(1), 1–4. https://doi.org/10.1021/CI400572X

Blatt, J., Farag, S., Corey, S. J., Sarrimanolis, Z., Muratov, E., Fourches, D., … Janzen, W. P. (2014). Expanding the scope of drug repurposing in pediatrics: The Children's Pharmacy Collaborative™. Drug Discovery Today, 19(11), 1696–1698. https://doi.org/10.1016/J.DRUDIS.2014.08.003

Wright, F. A., Sullivan, P. F., Brooks, A. I., Zou, F., Sun, W., Xia, K., … Boomsma, D. I. (2014). Heritability and genomics of gene expression in peripheral blood. Nature Genetics, 46(5), 430–437. https://doi.org/10.1038/NG.2951

Lange, L. A., Hu, Y., Zhang, H., Xue, C., Schmidt, E. M., Tang, Z.-Z., … Sturcke, A. (2014). Whole-Exome Sequencing Identifies Rare and Low-Frequency Coding Variants Associated with LDL Cholesterol. The American Journal of Human Genetics, 94(2), 233–245. https://doi.org/10.1016/J.AJHG.2014.01.010

Bushnell, P. J., Tatum-Gibbs, R., McKee, J. M., Evansky, P. A., Higuchi, M., MLin, M. T., … Boyes, W. K. (2014). ToxiFly: Can fruit flies be used to identify toxicity pathways for airborne chemicals? Neurotoxicology and Teratology, 43, 89. https://doi.org/10.1016/J.NTT.2014.04.045

Guo, Y., Bird, D. M. K., & Nielsen, D. M. (2014). Improved structural annotation of protein-coding genes in the Meloidogyne hapla genome using RNA-Seq. Worm, 3(1), e29158. https://doi.org/10.4161/worm.29158

Olukolu, B. A., Wang, G.-F., Vontimitta, V., Venkata, B. P., Marla, S., Ji, J., … Johal, G. (2014). A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways. PLoS Genetics, 10(8), e1004562. https://doi.org/10.1371/journal.pgen.1004562

Motsinger-Reif, A. A., Zhu, H., Kling, M. A., Matson, W., Sharma, S., Fiehn, O., … Arnold, S. E. (2014). Comparing metabolomic and pathologic biomarkers alone and in combination for discriminating Alzheimer's disease from normal cognitive aging. Acta Neuropathologica Communications, 2(1). https://doi.org/10.1186/2051-5960-1-28

Filer, D., Patisaul, H. B., Schug, T., Reif, D., & Thayer, K. (2014). Test driving ToxCast: Endocrine profiling for 1858 chemicals included in phase II. Current Opinion in Pharmacology, 19, 145–152. https://doi.org/10.1016/j.coph.2014.09.021

Huang, R., Sakamuru, S., Martin, M. T., Reif, D. M., Judson, R. S., Houck, K. A., … Xia, M. (2014). Profiling of the Tox21 10K compound library for agonists and antagonists of the estrogen receptor alpha signaling pathway. Scientific Reports, 4. https://doi.org/10.1038/srep05664

Rotroff, D. M., Martin, M. T., Dix, D. J., Filer, D. L., Houck, K. A., Knudsen, T. B., … Judson, R. S. (2014). Predictive endocrine testing in the 21st century using in vitro assays of estrogen receptor signaling responses. Environmental Science and Technology, 48(15), 8706–8716. https://doi.org/10.1021/es502676e

Kleinstreuer, N. C., Yang, J., Berg, E. L., Knudsen, T. B., Richard, A. M., Martin, M. T., … Houck, K. A. (2014). Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms. Nature Biotechnology, 32(6), 583–591. https://doi.org/10.1038/nbt.2914

Truong, L., Reif, D. M., St, M. L., Geier, M. C., Truong, H. D., & Tanguay, R. L. (2014). Multidimensional in vivo hazard assessment using zebrafish. Toxicological Sciences, 137(1), 212–233. https://doi.org/10.1093/toxsci/kft235

Wilson, A., Reif, D. M., & Reich, B. J. (2014). Hierarchical dose-response modeling for high-throughput toxicity screening of environmental chemicals. Biom, 70(1), 237–246. https://doi.org/10.1111/biom.12114

Rotroff, D. M., Wetmore, B. A., Dix, D. J., Ferguson, S. S., Clewell, H. J., Houck, K. A., … Thomas, R. S. (2014). Erratum to Incorporating human dosimetry and exposure into High-throughput in Vitro Toxicity Screening [Toxicological sciences 137, 2, (2014), 499]. Toxicological Sciences, 137(2). https://doi.org/10.1093/toxsci/kft185

Rotroff, D., Jack, J., Campbell, N., Clark, S., & Motsinger-Reif, A. A. (2014). PGxClean: a quality control GUI for the Affymetrix DMET chip and other candidate gene studies with non-biallelic alleles. Biodata Mining, 7.

Kelada, S. N. P., Carpenter, D. E., Aylor, D. L., Chines, P., Rutledge, H., Chesler, E. J., … Collins, F. S. (2014). Integrative Genetic Analysis of Allergic Inflammation in the Murine Lung. AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY, 51(3), 436–445. https://doi.org/10.1165/rcmb.2013-0501oc

Beam, A. L., Motsinger-Reif, A., & Doyle, J. (2014). Bayesian neural networks for detecting epistasis in genetic association studies. BMC Bioinformatics, 15.

Li, J., Hu, J., Newman, M., Liu, K. J., & Ge, H. Y. (2014). RNA-seq analysis pipeline based on oshell environment. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(5), 973–978.

Bucknoff, M. C., Hanel, R. M., Marks, S. L., Motsinger-Reif, A. A., & Suter, S. E. (2014). Evaluation of thromboelastography for prediction of clinical bleeding in thrombocytopenic dogs after total body irradiation and hematopoietic cell transplantation. AMERICAN JOURNAL OF VETERINARY RESEARCH, 75(5), 425–432. https://doi.org/10.2460/ajvr.75.5.425

Griffing, A. R., Lynch, B. R., & Stone, E. A. (2014). Structural properties of the minimum cut of partially-supplied graphs. DISCRETE APPLIED MATHEMATICS, 177, 152–157. https://doi.org/10.1016/j.dam.2014.05.043

Jack, J. R., Motsinger-Reif, A. A., Koutros, S., Alavanja, M. C., Freeman, L. E. B., & Hoppin, J. A. (2014). Single-Nucleotide Polymorphism Data Support the General Unrelatedness of the Males in the Agricultural Health Study. CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION, 23(10), 2192–2195. https://doi.org/10.1158/1055-9965.epi-14-0276

Tomas, A., Marcellin-Little, D. J., Roe, S. C., Motsinger-Reif, A., & Lascelles, B. D. X. (2014). Relationship Between Mechanical Thresholds and Limb Use in Dogs With Coxofemoral Joint OA-Associated Pain and the Modulating Effects of Pain Alleviation From Total Hip Replacement on Mechanical Thresholds. VETERINARY SURGERY, 43(5), 542–548. https://doi.org/10.1111/j.1532-950x.2014.12160.x

Ginn, J., Sacco, J., Wong, Y. Y., Motsinger-Reif, A., Chun, R., & Trepanier, L. A. (2014). Positive association between a glutathione-S-transferase polymorphism and lymphoma in dogs. VETERINARY AND COMPARATIVE ONCOLOGY, 12(3), 227–236. https://doi.org/10.1111/vco.12000

Thomas, R., Borst, L., Rotroff, D., Motsinger-Reif, A., Lindblad-Toh, K., Modiano, J. F., & Breen, M. (2014). Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma. CHROMOSOME RESEARCH, 22(3), 305–319. https://doi.org/10.1007/s10577-014-9406-z

Dolezal, A. L., Shu, X., OBrian, G. R., Nielsen, D. M., Woloshuk, C. P., Boston, R. S., & Payne, G. A. (2014). Aspergillus flavus infection induces transcriptional and physical changes in developing maize kernels. Frontiers in Microbiology, 5. https://doi.org/10.3389/fmicb.2014.00384

Jack, J., Rotroff, D., & Motsinger-Reif, A. (2014). Lymphoblastoid Cell Lines Models of Drug Response: Successes and Lessons from this Pharmacogenomic Model. CURRENT MOLECULAR MEDICINE, 14(7), 833–840. https://doi.org/10.2174/1566524014666140811113946

Wang, X., Zhang, D., & Tzeng, J.-Y. (2014). Pathway-Guided Identification of Gene-Gene Interactions. ANNALS OF HUMAN GENETICS, 78(6), 478–491. https://doi.org/10.1111/ahg.12080

Hu, J., & Tzeng, J.-Y. (2014). Integrative gene set analysis of multi-platform data with sample heterogeneity. BIOINFORMATICS, 30(11), 1501–1507. https://doi.org/10.1093/bioinformatics/btu060

Rutledge, H., Aylor, D. L., Carpenter, D. E., Peck, B. C., Chines, P., Ostrowski, L. E., … Kelada, S. N. P. (2014). Genetic Regulation of Zfp30, CXCL1, and Neutrophilic Inflammation in Murine Lung. GENETICS, 198(2), 735–U376. https://doi.org/10.1534/genetics.114.168138

LeVine, D. N., Birkenheuer, A. J., Brooks, M. B., Nordone, S. K., Bellinger, D. A., Jones, S. L., … Key, N. S. (2014). A novel canine model of immune thrombocytopenia: has immune thrombocytopenia (ITP) gone to the dogs? BRITISH JOURNAL OF HAEMATOLOGY, 167(1), 110–120. https://doi.org/10.1111/bjh.13005

Wright, F. A., Sullivan, P. F., Brooks, A. I., Zou, F., Sun, W., Xia, K., … Hottenga, J. J. (2014). Heritability and genomics of gene expression in peripheral blood. Nature Genetics, 46(5), 430–437.

Lee, S., Zou, F., & Wright, F. A. (2014). Convergence of sample eigenvalues, eigenvectors, and principal component scores for ultra-high dimensional data. BIOMETRIKA, 101(2), 484–490. https://doi.org/10.1093/biomet/ast064

Agler, C., Nielsen, D. M., Urkasemsin, G., Singleton, A., Tonomura, N., Sigurdsson, S., … Olby, N. J. (2014). Canine hereditary ataxia in old english sheepdogs and gordon setters is associated with a defect in the autophagy gene encoding RAB24. PLoS Genet, 10(2), e1003991.

Wiegers, T. C., Davis, A. P., & Mattingly, C. J. (2014). Web services-based text-mining demonstrates broad impacts for interoperability and process simplification. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/bau050

Comeau, D. C., Batista-Navarro, R. T., Dai, H.-J., Dogan, R. I., Yepes, A. J., Khare, R., … Wilbur, W. J. (2014). BioC interoperability track overview. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/bau053

Che, R. L., Jack, J. R., Motsinger-Reif, A. A., & Brown, C. C. (2014). An adaptive permutation approach for genome-wide association study: Evaluation and recommendations for use. Biodata Mining, 7.

Chiu, W. A., Campbell, J. L., Jr., Clewell, H. J., III, Zhou, Y.-H., Wright, F. A., Guyton, K. Z., & Rusyn, I. (2014). Physiologically Based Pharmacokinetic (PBPK) Modeling of Interstrain Variability in Trichloroethylene Metabolism in the Mouse. ENVIRONMENTAL HEALTH PERSPECTIVES, 122(5), 456–463. https://doi.org/10.1289/ehp.1307623

Hertz, D. L., Roy, S., Jack, J., Motsinger-Reif, A. A., Drobish, A., Clark, L. S., … McLeod, H. L. (2014). Genetic heterogeneity beyond CYP2C8*3 does not explain differential sensitivity to paclitaxel-induced neuropathy. BREAST CANCER RESEARCH AND TREATMENT, 145(1), 245–254. https://doi.org/10.1007/s10549-014-2910-1

Arighi, C. N., Wu, C. H., Cohen, K. B., Hirschman, L., Krallinger, M., Valencia, A., … Wiegers, T. C. (2014, May 22). BioCreative-IV virtual issue. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/bau039

Brown, C. C., Havener, T. M., Medina, M. W., Jack, J. R., Krauss, R. M., McLeod, H. L., & Motsinger-Reif, A. A. (2014). Genome-wide association and pharmacological profiling of 29 anticancer agents using lymphoblastoid cell lines. PHARMACOGENOMICS, 15(2), 137–146. https://doi.org/10.2217/pgs.13.213

Lockhart, L. E., Motsinger-Reif, A. A., Simpson, W. M., & Posner, L. P. (2014). Prevalence of onychectomy in cats presented for veterinary care near Raleigh, NC and educational attitudes toward the procedure. VETERINARY ANAESTHESIA AND ANALGESIA, 41(1), 48–53. https://doi.org/10.1111/vaa.12077

Chen, H.-W., Small, G. W., Motsinger-Reif, A., Suter, S. E., & Richards, K. L. (2014). VH1-44 gene usage defines a subset of canine B-cell lymphomas associated with better patient survival. VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY, 157(3-4), 125–130. https://doi.org/10.1016/j.vetimm.2013.10.020