Bioinformatics - 2015

Elkins, J. M., Fedele, V., Szklarz, M., Abdul Azeez, K. R., Salah, E., Mikolajczyk, J., … Zuercher, W. J. (2015). Comprehensive characterization of the Published Kinase Inhibitor Set. Nature Biotechnology, 34(1), 95–103. https://doi.org/10.1038/NBT.3374

Yang, J., Huang, T., Petralia, F., Long, Q., Zhang, B., Argmann, C., … Tu, Z. (2015). Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases. Scientific Reports, 5(1), 15145. https://doi.org/10.1038/SREP15145

Jansen, R., Penninx, B. W. J. H., Madar, V., Xia, K., Milaneschi, Y., Hottenga, J. J., … Sullivan, P. F. (2015). Erratum: Gene expression in major depressive disorder. Molecular Psychiatry, 21(3), 444–444. https://doi.org/10.1038/MP.2015.94

Jansen, R., Penninx, B. W. J. H., Madar, V., Xia, K., Milaneschi, Y., Hottenga, J. J., … Sullivan, P. F. (2015). Gene expression in major depressive disorder. Molecular Psychiatry, 21(3), 339–347. https://doi.org/10.1038/MP.2015.57

Alves, V. M., Muratov, E., Fourches, D., Strickland, J., Kleinstreuer, N., Andrade, C. H., & Tropsha, A. (2015). Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds. Toxicology and Applied Pharmacology, 284(2), 262–272. https://doi.org/10.1016/J.TAAP.2014.12.014

Isayev, O., Fourches, D., Muratov, E. N., Oses, C., Rasch, K., Tropsha, A., & Curtarolo, S. (2015). Materials Cartography: Representing and Mining Materials Space Using Structural and Electronic Fingerprints. Chemistry of Materials, 27(3), 735–743. https://doi.org/10.1021/CM503507H

Alves, V. M., Muratov, E., Fourches, D., Strickland, J., Kleinstreuer, N., Andrade, C. H., & Tropsha, A. (2015). Predicting chemically-induced skin reactions. Part II: QSAR models of skin permeability and the relationships between skin permeability and skin sensitization. Toxicology and Applied Pharmacology, 284(2), 273–280. https://doi.org/10.1016/J.TAAP.2014.12.013

Baker, N. C., Fourches, D., & Tropsha, A. (2015). Drug Side Effect Profiles as Molecular Descriptors for Predictive Modeling of Target Bioactivity. Molecular Informatics, 34(2-3), 160–170. https://doi.org/10.1002/MINF.201400134

Corvol, H., Blackman, S. M., Boëlle, P.-Y., Gallins, P. J., Pace, R. G., Stonebraker, J. R., … Knowles, M. R. (2015). Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis. Nature Communications, 6(1). https://doi.org/10.1038/NCOMMS9382

Eduati, F., Mangravite, L. M., Wang, T., Tang, H., Bare, J. C., Huang, R., … Saez-Rodriguez, J. (2015). Prediction of human population responses to toxic compounds by a collaborative competition. Nature Biotechnology, 33(9), 933–940. https://doi.org/10.1038/NBT.3299

Eduati, F., Mangravite, L. M., Wang, T., Tang, H., Bare, J. C., Huang, R., … Saez-Rodriguez, J. (2015). Erratum: Prediction of human population responses to toxic compounds by a collaborative competition. Nature Biotechnology, 33(10), 1109–1109. https://doi.org/10.1038/NBT1015-1109A

Rager, J. E., Tilley, S. K., Tulenko, S. E., Smeester, L., Ray, P. D., Yosim, A., … Fry, R. C. (2015). Identification of Novel Gene Targets and Putative Regulators of Arsenic-Associated DNA Methylation in Human Urothelial Cells and Bladder Cancer. Chemical Research in Toxicology, 28(6), 1144–1155. https://doi.org/10.1021/TX500393Y

Rotroff, D. M., Shahin, M. H., Gurley, S. B., Zhu, H., Motsinger-Reif, A., Meisner, M., … Kaddurah-Daouk, R. (2015). Pharmacometabolomic Assessments of Atenolol and Hydrochlorothiazide Treatment Reveal Novel Drug Response Phenotypes. CPT: Pharmacometrics & Systems Pharmacology, 4(11), 669–679. https://doi.org/10.1002/PSP4.12017

Crowley, J. J., Zhabotynsky, V., Sun, W., Huang, S., Pakatci, I. K., Kim, Y., … de Villena, F. P.-M. (2015). Erratum: Corrigendum: Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nature Genetics, 47(6), 690–690. https://doi.org/10.1038/NG0615-690A

Crowley, J. J., Zhabotynsky, V., Sun, W., Huang, S., Pakatci, I. K., Kim, Y., … Pardo-Manuel de Villena, F. (2015). Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nature Genetics, 47(4), 353–360. https://doi.org/10.1038/NG.3222

Bird, D. M., Williamson, V. M., & Opperman, C. H. (2015). Exploiting solved genomes of plant-parasitic nematodes to understand parasitism. In Advances in Botanical Research (Vol. 73, pp. 241–258). https://doi.org/10.1016/bs.abr.2014.12.008

Kollitz, E. M., Zhang, G., Hawkins, M. B., Whitfield, G. K., Reif, D. M., & Kullman, S. W. (2015). Molecular cloning, functional characterization, and evolutionary analysis of vitamin D receptors isolated from basal vertebrates. PLoS ONE, 10(4). https://doi.org/10.1371/journal.pone.0122853

Rovida, C., Asakura, S., Daneshian, M., Hofman-Huether, H., Leist, M., Meunier, L., … Hartung, T. (2015). Food for Thought...: Toxicity testing in the 21st century beyond environmental chemicals. Altex, 32(3), 171–181. https://doi.org/10.14573/altex.1506201

Motsinger, A. A., & Reif, D. M. (2015). Embracing complexity: Searching for gene-gene and gene environment interactions in genetic epidemiology. In Genomics and Proteomics: Principles, Technologies, and Applications (pp. 19–58). https://doi.org/10.1201/b18597

George, B. J., Reif, D. M., Gallagher, J. E., Williams-DeVane, C. R., Heidenfelder, B. L., Hudgens, E. E., … Edwards, S. W. (2015). Data-driven asthma endotypes defined from blood biomarker and gene expression data. PLoS ONE, 10(2). https://doi.org/10.1371/journal.pone.0117445

Meisner, M., & Reif, D. M. (2015). Computational Methods Used in Systems Biology. In Systems Biology in Toxicology and Environmental Health (pp. 85–115). https://doi.org/10.1016/B978-0-12-801564-3.00005-5

Ducharme, N. A., Reif, D. M., Gustafsson, J.-A., & Bondesson, M. (2015). Comparison of toxicity values across zebrafish early life stages and mammalian studies: Implications for chemical testing. Reproductive Toxicology, 55, 3–10. https://doi.org/10.1016/j.reprotox.2014.09.005

Loomis, D., Guyton, K., Grosse, Y., El, G. F., Bouvard, V., Benbrahim-Tallaa, L., … France. (2015). Carcinogenicity of lindane, DDT, and 2,4-dichlorophenoxyacetic acid. The Lancet. Oncology, 8. https://doi.org/10.1016/s1470-2045(15)00081-9

Wang, G. F., He, Y., Strauch, R., Olukolu, B. A., Nielsen, D., Li, X., & Balint-Kurti, P. J. (2015). Maize Homologs of Hydroxycinnamoyltransferase, a Key Enzyme in Lignin Biosynthesis, Bind the Nucleotide Binding Leucine-Rich Repeat Rp1 Proteins to Modulate the Defense Response. Plant Physiol, 169(3), 2230–2243.

Walter, V., Wright, F. A., & Nobel, A. B. (2015). Consistent testing for recurrent genomic aberrations. BIOMETRIKA, 102(4), 783–796. https://doi.org/10.1093/biomet/asv046

Odet, F., Pan, W., Bell, T. A., Goodson, S. G., Stevans, A. M., Yun, Z., … Deborah A. O'Brien. (2015). The Founder Strains of the Collaborative Cross Express a Complex Combination of Advantageous and Deleterious Traits for Male Reproduction. G3-GENES GENOMES GENETICS, 5(12), 2671–2683. https://doi.org/10.1534/g3.115.020172

Rebuli, M. E., Camacho, L., Adonay, M. E., Reif, D. M., Aylor, D. L., & Patisaul, H. B. (2015). Impact of Low-Dose Oral Exposure to Bisphenol A (BPA) on Juvenile and Adult Rat Exploratory and Anxiety Behavior: A CLARITY-BPA Consortium Study. TOXICOLOGICAL SCIENCES, 148(2), 341–354. https://doi.org/10.1093/toxsci/kfv163

Corvol, H., Blackman, S. M., Boelle, P. Y., Gallins, P. J., Pace, R. G., Stonebraker, J. R., … Patrone, M. V. (2015). Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis. Nature Communications, 6.

Reed, C. R., Ferguson, R. A., Peng, Y., Collier, B. R., Bradburn, E. H., Toms, A. R., … Hamill, M. E. (2015). Contact isolation is a risk factor for venous thromboembolism in trauma patients. JOURNAL OF TRAUMA AND ACUTE CARE SURGERY, 79(5), 833–837. https://doi.org/10.1097/ta.0000000000000835

Jackson, S., Nielsen, D. M., & Singh, N. D. (2015). Increased exposure to acute thermal stress is associated with a non-linear increase in recombination frequency and an independent linear decrease in fitness in Drosophila. BMC EVOLUTIONARY BIOLOGY, 15. https://doi.org/10.1186/s12862-015-0452-8

Abdo, N., Wetmore, B. A., Chappell, G. A., Shea, D., Wright, F. A., & Rusyn, I. (2015). In vitro screening for population variability in toxicity of pesticide-containing mixtures. ENVIRONMENT INTERNATIONAL, 85, 147–155. https://doi.org/10.1016/j.envint.2015.09.012

Roode, S. C., Rotroff, D., Avery, A. C., Suter, S. E., Bienzle, D., Schiffman, J. D., … Breen, M. (2015). Genome-wide assessment of recurrent genomic imbalances in canine leukemia identifies evolutionarily conserved regions for subtype differentiation. CHROMOSOME RESEARCH, 23(4), 681–708. https://doi.org/10.1007/s10577-015-9475-7

Hecht, E. S., Scholl, E. H., Walker, S. H., Taylor, A. D., Cliby, W. A., Motsinger-Reif, A. A., & Muddiman, D. C. (2015). Relative Quantification and Higher-Order Modeling of the Plasma Glycan Cancer Burden Ratio in Ovarian Cancer Case-Control Samples. JOURNAL OF PROTEOME RESEARCH, 14(10), 4394–4401. https://doi.org/10.1021/acs.jproteome.5b00703

Eduati, F., Mangravite, L. M., Wang, T., Tang, H., Bare, J. C., Huang, R. L., … Tice, R. R. (2015). Prediction of human population responses to toxic compounds by a collaborative competition. Nature Biotechnology, 33(9), 933–172.

Braga, R. C., Alves, V. M., Silva, M. F. B., Muratov, E., Fourches, D., Liao, L. M., … Andrade, C. H. (2015). Pred-hERG: A Novel web-Accessible Computational Tool for Predicting Cardiac Toxicity. MOLECULAR INFORMATICS, 34(10), 698–701. https://doi.org/10.1002/minf.201500040

Jack, J., Havener, T. M., McLeod, H. L., Motsinger-Reif, A. A., & Foster, M. (2015). Evaluating the role of admixture in cancer therapy via in vitro drug response and multivariate genome-wide associations. PHARMACOGENOMICS, 16(13), 1451–1463. https://doi.org/10.2217/pgs.15.85

Burke, M., Scholl, E. H., Bird, D. M. K., Schaff, J. E., Colman, S. D., Crowell, R., … Opperman, C. H. (2015). The plant parasite Pratylenchus coffeae carries a minimal nematode genome. NEMATOLOGY, 17(6), 621–637. https://doi.org/10.1163/15685411-00002901

Mele, M., Ferreira, P. G., Reverter, F., DeLuca, D. S., Monlong, J., Sammeth, M., … Calvo, M. (2015). The human transcriptome across tissues and individuals. Science, 348(6235), 660–665.

Fourches, D., Muratov, E., & Tropsha, A. (2015, August). Curation of chemogenomics data. https://doi.org/10.1038/nchembio.1881

Poorman, K., Borst, L., Moroff, S., Roy, S., Labelle, P., Motsinger-Reif, A., & Breen, M. (2015). Comparative cytogenetic characterization of primary canine melanocytic lesions using array CGH and fluorescence in situ hybridization. CHROMOSOME RESEARCH, 23(2), 171–186. https://doi.org/10.1007/s10577-014-9444-6

Shapiro, S. G., Raghunath, S., Williams, C., Motsinger-Reif, A. A., Cullen, J. M., Liu, T., … Breen, M. (2015). Canine urothelial carcinoma: genomically aberrant and comparatively relevant. CHROMOSOME RESEARCH, 23(2), 311–331. https://doi.org/10.1007/s10577-015-9471-y

Wang, K., Yu, S., Ji, X., Lakner, C., Griffing, A., & Thorne, J. L. (2015). Roles of Solvent Accessibility and Gene Expression in Modeling Protein Sequence Evolution. EVOLUTIONARY BIOINFORMATICS, 11. https://doi.org/10.4137/ebo.s22911

He, Y., Hoskins, J. M., Clark, S., Campbell, N. H., Wagner, K., Motsinger-Reif, A. A., & McLeod, H. L. (2015). Accuracy of SNPs to predict risk of HLA alleles associated with drug-induced hypersensitivity events across racial groups. PHARMACOGENOMICS, 16(8), 817–824. https://doi.org/10.2217/pgs.15.41

Didion, J. P., Morgan, A. P., Clayshulte, A. M.-F., Mcmullan, R. C., Yadgary, L., Petkov, P. M., … Villena, F. P.-M. (2015). A Multi-Megabase Copy Number Gain Causes Maternal Transmission Ratio Distortion on Mouse Chromosome 2. PLOS GENETICS, 11(2). https://doi.org/10.1371/journal.pgen.1004850

Rager, J. E., Tilley, S. K., Tulenko, S. E., Smeester, L., Ray, P. D., Yosim, A., … Del Razo, L. M. (2015). Identification of novel gene targets and putative regulators of arsenic-associated DNA methylation in human urothelial cells and bladder cancer. Chemical Research in Toxicology, 28(6), 1144–1155.

Abdo, N., Xia, M., Brown, C. C., Kosyk, O., Huang, R., Sakamuru, S., … Wright, F. A. (2015). Population-Based in Vitro Hazard and Concentration-Response Assessment of Chemicals: The 1000 Genomes High-Throughput Screening Study. ENVIRONMENTAL HEALTH PERSPECTIVES, 123(5), 458–466. https://doi.org/10.1289/ehp.1408775

Gonzalez, L. M., Fogle, C. A., Baker, W. T., Hughes, F. E., Law, J. M., Motsinger-Reif, A. A., & Blikslager, A. T. (2015). Operative factors associated with short-term outcome in horses with large colon volvulus: 47 cases from 2006 to 2013. EQUINE VETERINARY JOURNAL, 47(3), 279–284. https://doi.org/10.1111/evj.12273

Zhou, Y.-H., & Wright, F. A. (2015). Hypothesis testing at the extremes: fast and robust association for high-throughput data. BIOSTATISTICS, 16(3), 611–625. https://doi.org/10.1093/biostatistics/kxv007

O’Neal, W. K., Gallins, P., Pace, R. G., Dang, H., Wolf, W. E., Jones, L. C., … Knowles, M. R. (2015). Gene Expression in Transformed Lymphocytes Reveals Variation in Endomembrane and HLA Pathways Modifying Cystic Fibrosis Pulmonary Phenotypes. The American Journal of Human Genetics, 96(2), 318–328. https://doi.org/10.1016/J.AJHG.2014.12.022

Davis, A. P., Grondin, C. J., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B. L., … Mattingly, C. J. (2015). The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. NUCLEIC ACIDS RESEARCH, 43(D1), D914–D920. https://doi.org/10.1093/nar/gku935

Beam, A. L., Motsinger-Reif, A. A., & Doyle, J. (2015). An investigation of gene-gene interactions in dose-response studies with Bayesian nonparametrics. Biodata Mining, 8.

Knazovicky, D., Tomas, A., Motsinger-Reif, A., & Lascelles, B. D. X. (2015). Initial evaluation of nighttime restlessness in a naturally occurring canine model of osteoarthritis pain. PeerJ, 3.

Bird, D. M. K., Jones, J. T., Opperman, C. H., Kikuchi, T., & Danchin, E. G. J. (2015). Signatures of adaptation to plant parasitism in nematode genomes. PARASITOLOGY, 142, S71–S84. https://doi.org/10.1017/s0031182013002163