Bioinformatics - 2017

Legge, S. E., Hamshere, M. L., Ripke, S., Pardinas, A. F., Goldstein, J. I., Rees, E., … Walters, J. T. R. (2017). Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia. Molecular Psychiatry, 22(10), 1502–1508. https://doi.org/10.1038/MP.2016.97

Fourches, D. (2017). Reaction: Molecular Modeling for Novel Antibacterials. Chem, 3(1), 13–14. https://doi.org/10.1016/J.CHEMPR.2017.06.016

Kuenemann, M. A., & Fourches, D. (2017). Cheminformatics Modeling of Amine Solutions for Assessing their CO2Absorption Properties. Molecular Informatics, 36(7), 1600143. https://doi.org/10.1002/MINF.201600143

Genetic effects on gene expression across human tissues. (2017). Nature, 550(7675), 204–213. https://doi.org/10.1038/NATURE24277

Li, X., Kim, Y., Tsang, E. K., Davis, J. R., Damani, F. N., Chiang, C., … Montgomery, S. B. (2017). The impact of rare variation on gene expression across tissues. Nature, 550(7675), 239–243. https://doi.org/10.1038/NATURE24267

Tukiainen, T., Villani, A.-C., Yen, A., Rivas, M. A., Marshall, J. L., Satija, R., … MacArthur, D. G. (2017). Landscape of X chromosome inactivation across human tissues. Nature, 550(7675), 244–248. https://doi.org/10.1038/NATURE24265

Tan, M. H., Li, Q., Shanmugam, R., Piskol, R., Kohler, J., Young, A. N., … Li, J. B. (2017). Dynamic landscape and regulation of RNA editing in mammals. Nature, 550(7675), 249–254. https://doi.org/10.1038/NATURE24041

St John-Williams, L., Blach, C., Toledo, J. B., Rotroff, D. M., Kim, S., Klavins, K., … Kaddurah-Daouk, R. (2017). Targeted metabolomics and medication classification data from participants in the ADNI1 cohort. Scientific Data, 4(1). https://doi.org/10.1038/SDATA.2017.140

Nho, K., Dehkordi, S. M., Motsinger-Reif, A., Baillie, R. A., Bhattacharyya, S., Tenenbaum, J. D., … Kaddurah-Daouk, R. F. (2017). GUT DERIVED BILE ACID METABOLITES CORRELATE WITH STRUCTURAL AND FUNCTIONAL NEUROIMAGING MEASURES IN ALZHEIMER’S DISEASE. Alzheimer's & Dementia, 13(7), P543–P544. https://doi.org/10.1016/J.JALZ.2017.07.131

Toledo, J. B., Arnold, M., Kastenmüller, G., Chang, R., Baillie, R. A., Han, X., … Kaddurah-Daouk, R. (2017). Metabolic network failures in Alzheimer's disease: A biochemical road map. Alzheimer's & Dementia, 13(9), 965–984. https://doi.org/10.1016/J.JALZ.2017.01.020

Rotroff, D. M., Pijut, S. S., Marvel, S. W., Jack, J. R., Havener, T. M., Pujol, A., … Motsinger‐Reif, A. A. (2017). Genetic Variants in
            HSD17B3
            ,
            SMAD3
            , and
            IPO11
            Impact Circulating Lipids in Response to Fenofibrate in Individuals With Type 2 Diabetes. Clinical Pharmacology & Therapeutics, 103(4), 712–721. https://doi.org/10.1002/CPT.798

Urkasemsin, G., Nielsen, D. M., Singleton, A., Arepalli, S., Hernandez, D., Agler, C., & Olby, N. J. (2017). Genetics of Hereditary Ataxia in Scottish Terriers. Journal of Veterinary Internal Medicine, 31(4), 1132–1139. https://doi.org/10.1111/jvim.14738

Zhang, G., Truong, L., Tanguay, R. L., & Reif, D. M. (2017). Integrating Morphological and Behavioral Phenotypes in Developing Zebrafish. The Rights and Wrongs of Zebrafish: Behavioral Phenotyping of Zebrafish, pp. 259–272. https://doi.org/10.1007/978-3-319-33774-6_12

Watson, A. T. D., Planchart, A., Mattingly, C. J., Winkler, C., Reif, D. M., & Kullman, S. W. (2017). Embryonic exposure to TCDD impacts osteogenesis of the axial skeleton in Japanese medaka, Oryzias latipes. Toxicological Sciences, 155(2), 485–496. https://doi.org/10.1093/toxsci/kfw229

Roell, K. R., Reif, D. M., & Motsinger-Reif, A. A. (2017). An introduction to terminology and methodology of chemical synergy-perspectives from across disciplines. Frontiers in Pharmacology, 8(APR). https://doi.org/10.3389/fphar.2017.00158

Zhang, G., Roell, K. R., Truong, L., Tanguay, R. L., & Reif, D. M. (2017). A data-driven weighting scheme for multivariate phenotypic endpoints recapitulates zebrafish developmental cascades. Toxicology and Applied Pharmacology, 314, 109–117. https://doi.org/10.1016/j.taap.2016.11.010

Zhang, G., Truong, L., Tanguay, R. L., & Reif, D. M. (2017). A New Statistical Approach to Characterize Chemical-Elicited Behavioral Effects in High-Throughput Studies Using Zebrafish. PLOS ONE, 12(1). https://doi.org/10.1371/journal.pone.0169408

Borrel, A., & Fourches, D. (2017). RealityConvert: a tool for preparing 3D models of biochemical structures for augmented and virtual reality. BIOINFORMATICS, 33(23), 3816–3818. https://doi.org/10.1093/bioinformatics/btx485

Carter, J. E., Motsinger-Reif, A. A., Krug, W. V., & Keene, B. W. (2017). The Effect of Heart Disease on Anesthetic Complications During Routine Dental Procedures in Dogs. JOURNAL OF THE AMERICAN ANIMAL HOSPITAL ASSOCIATION, 53(4), 206–213. https://doi.org/10.5326/jaaha-ms-6512

St John-Williams, L., Blach, C., Toledo, J. B., Rotroff, D. M., Kim, S., Klavins, K., … Saykin, A. J. (2017). Data descriptor: Targeted metabolomics and medication classification data from participants in the ADNI1 cohort. Scientific Data, 4.

Holterman, M., Karegar, A., Mooijman, P., Megen, H., Elsen, S., Vervoort, M. T. W., … Helder, J. (2017). Disparate gain and loss of parasitic abilities among nematode lineages. PLOS ONE, 12(9). https://doi.org/10.1371/journal.pone.0185445

Teferedegne, B., Rotroff, D. M., Macauley, J., Foseh, G., Lewis, G., Motsinger-Rief, A., & Lewis, A. M., Jr. (2017, October 4). Assessment of potential miRNA biomarkers of VERO-cell tumorigenicity in a new line (AGMK1-9T7) of African green monkey kidney cells. VACCINE, Vol. 35, pp. 5503–5509. https://doi.org/10.1016/j.vaccine.2017.04.004

House, J. S., Grimm, F. A., Jima, D. D., Zhou, Y. H., Rusyn, I., & Wright, F. A. (2017). A Pipeline for high-throughput concentration response modeling of gene expression for toxicogenomics. Frontiers in Genetics, 8.

Aguet, F., Brown, A. A., Castel, S. E., Davis, J. R., He, Y., Jo, B., … Nedzel, J. L. (2017). Genetic effects on gene expression across human tissues. Nature, 550(7675), 204-.

Knecht, A. L., Truong, L., Marvel, S. W., Reif, D. M., Garcia, A., Lu, C., … Tanguay, R. L. (2017). Transgenerational inheritance of neurobehavioral and physiological deficits from developmental exposure to benzo[a]pyrene in zebrafish. TOXICOLOGY AND APPLIED PHARMACOLOGY, 329, 148–157. https://doi.org/10.1016/j.taap.2017.05.033

Henriquez, A., House, J., Miller, D. B., Snow, S. J., Fisher, A., Ren, H., … Kodavanti, U. P. (2017). Adrenal-derived stress hormones modulate ozone-induced lung injury and inflammation. TOXICOLOGY AND APPLIED PHARMACOLOGY, 329, 249–258. https://doi.org/10.1016/j.taap.2017.06.009

Venkatratnam, A., Furuya, S., Kosyk, O., Gold, A., Bodnar, W., Konganti, K., … Rusyn, I. (2017). Editor's Highlight: Collaborative Cross Mouse Population Enables Refinements to Characterization of the Variability in Toxicokinetics of Trichloroethylene and Provides Genetic Evidence for the Role of PPAR Pathway in Its Oxidative Metabolism. TOXICOLOGICAL SCIENCES, 158(1), 48–62. https://doi.org/10.1093/toxsci/kfx065

Chiu, W. A., Wright, F. A., & Rusyn, I. (2017). A tiered, Bayesian approach to estimating population variability for regulatory decision-making. Altex-Alternatives to Animal Experimentation, 34(3), 377–388.

Rudra, P., Zhou, Y. H., & Wright, F. A. (2017). A procedure to detect general association based on concentration of ranks. Stat, 6(1), 88–101.

Nguyen, T. V., Reuter, J. M., Gaikwad, N. W., Rotroff, D. M., Kucera, H. R., Motsinger-Reif, A., … Schmidt, P. J. (2017). The steroid metabolome in women with premenstrual dysphoric disorder during GnRH agonist-induced ovarian suppression: effects of estradiol and progesterone addback. Translational Psychiatry, 7(8), e1193–e1193. https://doi.org/10.1038/TP.2017.146

Toms, A., & Barrangou, R. (2017). On the global CRISPR array behavior in class I systems. BIOLOGY DIRECT, 12. https://doi.org/10.1186/s13062-017-0193-2

Toledo, J. B., Arnold, M., Kastenmuller, G., Chang, R., Baillie, R. A., Han, X. L., … Motsinger-Reif, A. (2017). Metabolic network failures in Alzheimer's disease: A biochemical road map. Alzheimers & Dementia, 13(9), 965–984.

Kuenemann, M. A., & Fourches, D. (2017). Cheminformatics modeling of amine solutions for assessing their CO2 absorption properties. Molecular Informatics, 36(7).

Ash, J., & Fourches, D. (2017). Characterizing the Chemical Space of ERK2 Kinase Inhibitors Using Descriptors Computed from Molecular Dynamics Trajectories. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 57(6), 1286–1299. https://doi.org/10.1021/acs.jcim.7b00048

Mochizuki, H., Motsinger-Reif, A., Bettini, C., Moroff, S., & Breen, M. (2017). Association of breed and histopathological grade in canine mast cell tumours. VETERINARY AND COMPARATIVE ONCOLOGY, 15(3), 829–839. https://doi.org/10.1111/vco.12225

Lee, S., Sun, W., Wright, F. A., & Zou, F. (2017). An improved and explicit surrogate variable analysis procedure by coefficient adjustment. BIOMETRIKA, 104(2), 303–316. https://doi.org/10.1093/biomet/asx018

Guo, Y., Fudali, S., Gimeno, J., DiGennaro, P., Chang, S., Williamson, V. M., … Nielsen, D. M. (2017). Networks Underpinning Symbiosis Revealed Through Cross-Species eQTL Mapping. Genetics, 206(4), 2175–2184. https://doi.org/10.1534/genetics.117.202531

Tilley, S. K., Reif, D. M., & Fry, R. C. (2017). Incorporating ToxCast and Tox21 datasets to rank biological activity of chemicals at Superfund sites in North Carolina. ENVIRONMENT INTERNATIONAL, 101, 19–26. https://doi.org/10.1016/j.envint.2016.10.006

Liu, X., Finucane, H. K., Gusev, A., Bhatia, G., Gazal, S., O'Connor, L., … Price, A. L. (2017). Functional Architectures of Local and Distal Regulation of Gene Expression in Multiple Human Tissues. AMERICAN JOURNAL OF HUMAN GENETICS, 100(4), 605–616. https://doi.org/10.1016/j.ajhg.2017.03.002

Kuenemann, M. A., Szymczyk, M., Chen, Y., Sultana, N., Hinks, D., Freeman, H. S., … Vinueza, N. R. (2017). Weaver's historic accessible collection of synthetic dyes: a cheminformatics analysis. CHEMICAL SCIENCE, 8(6), 4334–4339. https://doi.org/10.1039/c7sc00567a

Jansen, R., Hottenga, J.-J., Nivard, M. G., Abdellaoui, A., Laport, B., Geus, E. J., … Boomsma, D. I. (2017). Conditional eQTL analysis reveals allelic heterogeneity of gene expression. HUMAN MOLECULAR GENETICS, 26(8), 1444–1451. https://doi.org/10.1093/hmg/ddx043

Muratov, E., Lewis, M., Fourches, D., Tropsha, A., & Cox, W. C. (2017). Computer-assisted decision support for student admissions based on their predicted academic performance. American Journal of Pharmaceutical Education, 81(3).

McLaughlin, C. M., Marks, S. L., Dorman, D. C., Motsinger-Reif, A., & Hanel, R. M. (2017). Thromboelastographic monitoring of the effect of unfractionated heparin in healthy dogs. JOURNAL OF VETERINARY EMERGENCY AND CRITICAL CARE, 27(1), 71–81. https://doi.org/10.1111/vec.12526

Shorter, J. R., Odet, F., Aylor, D. L., Pan, W., Kao, C.-Y., Fu, C.-P., … Villena, F. P.-M. (2017). Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross. GENETICS, 206(2), 557–572. https://doi.org/10.1534/genetics.116.199596

Marvel, S. W., Rotroff, D. M., Wagner, M. J., Buse, J. B., Havener, T. M., McLeod, H. L., & Motsinger-Reif, A. A. (2017). Common and rare genetic markers of lipid variation in subjects with type 2 diabetes from the ACCORD clinical trial. PeerJ, 5.

Roell, K. R., Reif, D. M., & Motsinger-Reif, A. A. (2017). [Review of An introduction to terminology and methodology of chemical synergy-perspectives from across disciplines]. Frontiers in Pharmacology, 8.

Driessche, G., & Fourches, D. (2017). Adverse drug reactions triggered by the common HLA-B*57:01 variant: A molecular docking study. Journal of Cheminformatics, 9.

Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., King, B. L., McMorran, R., … Mattingly, C. J. (2017). The Comparative Toxicogenomics Database: update 2017. NUCLEIC ACIDS RESEARCH, 45(D1), D972–D978. https://doi.org/10.1093/nar/gkw838

Rotroff, D. M., Marvel, S. W., Jack, J. R., Havener, T. M., Doria, A., Shah, H. S., … Motsinger-Reif, A. A. (2017). Common genetic variants in neurobeachin (nbea) are associated with metformin drug response in individuals with type 2 diabetes in the accord clinical trial. Clinical Pharmacology & Therapeutics, Vol. 101, pp. S9–9.

Prevatt, B.-S., Desmarais, S. L., & Janssen, P. A. (2017). Lifetime substance use as a predictor of postpartum mental health. ARCHIVES OF WOMENS MENTAL HEALTH, 20(1), 189–199. https://doi.org/10.1007/s00737-016-0694-5