Publications

  1. Abell, A.N., Jordan, N.V., Huang, W., Prat, A., Midland, A.A., Johnson, N.L., Granger, D.A., Mieczkowski, P.A., Perou, C.M., Gomez, S.M., Li, L., and Johnson, G.L. (2011) MAP3K4/CBP-Regulated H2B Acetylation Controls Epithelial-Mesenchymal Transition in Trophoblast Stem Cells. Cell Stem Cell. 8:525-37
  2. Adams, T.M., and Nobel, A.B. (2010) Uniform convergence of Vapnik-Chervonenkis classes under ergodic sampling. Annals of Probability 38(4):1345–1367.
  3. Bradford, B.U., Lock, E.F., Kosyk, O., Kim, S.K., Uehara, T., Harbourt, D., DeSimone, M., Threadgill, D.W., Tryndyak, V., Pogribny, I.P., Bleyle, L., Koop, D.R. and Rusyn, I. (2011) Inter-strain differences in the liver effects of trichloroethylene in a multi-strain panel of inbred mice. Toxicol Sci 120:206-217.
  4. Choi, K., and Gomez, S.M. (2009) Comparison of phylogenetic trees through alignment of embedded evolutionary distances. BMC Bioinformatics 10:423.
  5. Doolittle, J.M., and Gomez, S.M. (2011) Mapping protein interactions between Dengue virus and its human and insect hosts. PLoS Neglected Tropical Diseases, 5(2):e954
  6. Doolittle, J.M. and Gomez, S.M. (2010) Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virology J, 7:82.
  7. Duncan, J.S., Whittle, M.C., Nkamura, K., Abell, A.N., Midland, A.A., Zawistowksi, J.S., Johnson, N.L., Granger, D.A., Jordan, N.V., Darr, D., Usary, J., Major, B., He, X., Hoadley, K., Sharpless, N.E., Perou, C.M., Gomez, S.M., Jin, J., Frye, S.V., Earp, H.S., Graves, L.M., and Johnson, G.L. (2012) Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple negative breast cancer. (accepted in Cell).
  8. Fourches, D., Barnes, J.C., Day, N.C., Bradley, P., Reed, J.Z., and Tropsha, A. (2010) Cheminformatics analysis of assertions mined from literature that describe drug-induced liver injury in different species. Chem Res Toxicol 23:171-183.
  9. Garcia, G.J.M., Picher, M., Zuo, P., Okada, S.F., Lazarowski, E.R., Button, B., Boucher, R.C., and Elston, T.C. (2011) Computational model for the regulation of extracellular ATP and adenosine in airway epithelia. In: Purinergic Regulation of Respiratory Diseases (M. Picher and R.C. Boucher, eds.), Chapter 3, Springer Publishing.
  10. Gatti, D.M., Barry, W.T., Nobel, A.B., Rusyn, I., and Wright, F.A. (2010) Heading down the wrong pathway: On the influence of correlation within gene sets. BMC Genomics 11:574.
  11. Gatti, D.M., Harrill, A.H., Wright, F.A., Threadgill, D.W., and Rusyn, I. (2009) Replication and Narrowing of Gene Expression Quantitative Trait Loci using Inbred Mice. Mammalian Genome 20:437-446.
  12. Gatti, D.M., Lu, L., Williams, R.W., Sun, W., Wright, F.A., Threadgill, D.W., and Rusyn, I. (2011) MicroRNA expression in the livers of inbred mice. Mutat Res 714:126-133
  13. Gatti DM, Shabalin AA, Lam TC, Wright FA, Rusyn I, and Nobel A. (2009) FastMap: Fast eQTL mapping in homozygous populations. Bioinformatics 4: 482-489.
  14. Gatti, D.M., Zhao, N., Chesler, E.J., Bradford, B.U., Shabalin, A., Yordanova, R., Lu, L., and Rusyn, I. (2010) Sex-specific gene expression in BXD mouse liver. Physiol Genomics 42:456-468.
  15. Golbraikh, A., Wang, X.S., Zhu, H., and Tropsha, A. (2012) Predictive QSAR Modeling: Methods and Applications in Drug Discovery and Chemical Risk Assessment. In: Handbook of Computational Chemistry, Shukla and Leshinkii, Eds, Springer (in press).
  16. Harrill, A.H., Gatti, D.M., Threadgill, D.W., and Rusyn, I. (2009) Population-Based Discovery of Toxicogenomics Biomarkers for Hepatotoxicity Using a Laboratory Strain Diversity Panel. Toxicological Sciences 110:235-243.
  17. Lee S, Wright FA, Zou F. (2011) Control of population stratification by correlation-selected principal components. Biometrics. 67:967-974.
  18. Lock, E.F., Abdo, N. Huang, R., Xia, M., Kosyk, O., O’Shea, S.H., Zhou, Y.H., Sedykh, A., Tropsha, A., Austin, C.P., Tice, R.R., Wright, F.A., and Rusyn, I. (2012) Quantitative high-throughput screening for chemical toxicity in a population-based in vitro model. Toxicol Sci. 126(2), 578–588 (2012)
  19. Low, Y., Uehara, T., Minowa, Y., Yamada, H., Ohno, Y., Urushidani, T., Sedykh, A., Muratov, E., Kuz'min, V., Fourches, D., Zhu, H., Rusyn, I., Tropsha, A. (2011) Predicting Drug-Induced Hepatotoxicity Using QSAR and Toxicogenomics Approaches. Chem Res Toxicol. 24(8):1251-62.
  20. Martinez, S.M., Bradford, B.U., Soldatow, V.Y., Kosyk, O., Sandot, A., Witek, R., Kaiser, R., Stewart, T., Amaral, K., Freeman, K., Black, C., LeCluyse, E.L., Ferguson, S.S., and Rusyn, I. (2010) Evaluation of an in vitro toxicogenetic mouse model for hepatotoxicity. Toxicol Appl Pharmacol 249:208-216.
  21. O’Shea, S.H., Schwarz, J., Kosyk, O., Ross, P.K., Ha, M.J., Wright, F.A., and Rusyn, I. (2011) In vitro screening for population variability in chemical toxicity. Toxicol Sci 119:398-407.
  22. Pogribny, I.P., Starlard-Davenport, A., Tryndyak, V., Han, T., Ross, S.A., Rusyn, I., and Beland, F.A., Difference in expression of hepatic microRNAs is associated with strain-specific susceptibility to dietary nonalcoholic steatohepatitis in mice. Lab Invest 90:1437-1446, 2010.
  23. Rodgers, A.D., Zhu, H., Fourches, D., Rusyn, I., and Tropsha, A. (2010) Modeling Liver-Related Adverse Effects of Drugs Using kNN QSAR Method. Chem Res Toxicol 23:724-732.
  24. Ross, P.K., Woods, C.G., Bradford, B.U., Kosyk, O., Gatti, D.M., Cunningham, M.L., and Rusyn, I. (2009) Time-course comparison of xenobiotic activators of CAR and PPARalpha in mouse liver. Toxicol Appl Pharmacol 235:199-207.
  25. Rusyn, I., and Daston, G.P. (2010) Computational Toxicology: Realizing the Promise of the Toxicity Testing in the 21st Century. Environ Health Persp 118:1047-1050.
  26. Rusyn, I., Gatti, D.M., Wiltshire, T., Kleeberger, S.R., and Threadgill, D.W. (2010) Toxico-genetics: population-based testing of drug and chemical safety in mouse models. Pharmacogenomics 11:1127-1136.
  27. Rusyn, I., Sedykh, A., Low, Y., Guyton, K.Z., Tropsha, A. (2012) Predictive modeling of chemical hazard by integrating numerical descriptors of chemical structures and short-term toxicity assay data. Toxicol Sci 127(1), 1–9 (2012).
  28. Sedykh A, Zhu H, Tang H, Zhang L, Richard A, Rusyn I, and Tropsha A. (2011). Use of in vitro HTS-Derived Concentration-Response Data as Biological Descriptors Improves the Accuracy of QSAR Models of in vivo Toxicity. Environ. Health Perspect. 119:364-370.
  29. Shabalin, A.A., Weigman, V.J., Perou, C.M., and Nobel, A.B. (2009) Finding Large Average Submatrices in High Dimensional Data. Annals of Applied Statistics 3:985-1012.
  30. Staab, J., O’Connell, T.M. and Gomez, S.M. (2010) Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS). BMC Bioinformatics 2010, 11:123.
  31. Strychalski, W., Adalsteinsson, D., and Elston, T.C. (2010) A cut-cell method form modeling spatial sytems of biochemical reactions in arbitrary cell geometries. Comm Appl Math Comp Sci 5:31-53.
  32. Strychalski, W., Adalsteinsson, D., and Elston, T.C. (2010) Simulating biochemical networks in complex moving geometries. SIAM J Sci Comput 32(5): 3039–3070.
  33. Sun, W. A. (2012) Statistical Framework for eQTL Mapping Using RNA-seq Data. Biometrics (in press).
  34. Sun, W., Buck, M.J., Patel, M., and Davis, I.J. (2010) Improved ChIP-chip analysis by mixture model approach. BMC Bioinformatics 10:173.
  35. Sun, W., and Wright, F.A. (2010) A geometric interpretation of the permutation p-value and its application in eQTL studies. Annals of Applied Statistics 4(2):1014–1033.
  36. Sun W, Xie W, Xu F, Grunstein M, and Li KC. (2009) Pattern recognition in tiling array ChIP-chip data by segmental semi-Markov model, with application in nucleosome free region study. PLoS ONE, 4(3) e4721.
  37. Sushko I, Novotarskyi S, Körner R, Pandey AK, Cherkasov A, Li J, Gramatica P, Hansen K, Schroeter T, Müller KR, Xi L, Liu H, Yao X, Öberg T, Hormozdiari F, Dao P, Sahinalp C, Todeschini R, Polishchuk P, Artemenko A, Kuz'min V, Martin TM, Young DM, Fourches D, Muratov E, Tropsha A, Baskin I, Horvath D, Marcou G, Muller C, Varnek A, Prokopenko VV, Tetko IV. (2010). Applicability domains for classification problems: benchmarking of distance to models for ames mutagenicity set. J Chem Inf Model. 50:2094-2111.
  38. Tsygankov D, Liu Y, Sanoff HK, Sharpless NE and Elston TC. (2009) A quantitative model for age-dependent expression of the p16INK4a tumor suppressor. PNAS, 106:16562-16567.
  39. Weinreb, G.E., Kapustina, M.T., Jacobson, K., and Elston, T.C. (2009) In silico generation of alternative hypotheses using causal mapping (CMAP). PLoS One, 4:e5378.
  40. Walter, V., Nobel, A.B., and Wright, F.A. (2011) DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors. Bioinformatics 27:678-685.
  41. Wright, F.A., Shabalin, A., and Rusyn, I. (2012) Computational tools for discovery and interpretation of expression quantitative trait loci. Pharmacogenomics 13:343-352, 2012.
  42. Xia, K., Shabalin, A.A., Huang, S., Madar, V., Zhou, Y.H., Wang, W., Zou, F., Sun, W., Sullivan, P.F., Wright, F.A. (2012) seeQTL: a searchable database for human eQTLs. Bioinformatics. 28:451-452.
  43. Xu, K., Morgan, K.T., Elston, T.C., and Gomez, S.M. (2011) A whole-body model for glycogen regulation reveals a critical role for substrate cycling in maintaining blood glucose homeostasis. PLoS Computational Biology. 7:e1002272.
  44. Zhou, Y., Xia, K., and Wright, F.A. (2011) A powerful and flexible approach to the analysis of RNA sequence count data. Bioinformatics 27:2672-2678.
  45. Zhu, H., Martin, T.M., Ye, L., Young, D.M., and Tropsha, A. (2009) Combinatorial QSAR modeling of rat acute toxicity by oral exposure. Chem Res Toxicol 22:1913-1921.
  46. Zhu H, Rusyn I, Richard A, Tropsha A. (2008) Use of cell viability assay data improves the prediction accuracy of conventional quantitative structure-activity relationship models of animal carcinogenicity. Environ. Health Perspect. 116: 506-513.
  47. Zhu, H., Ye, L., Richard, A., Golbraikh, A., Wright, F.A., Rusyn, I., and Tropsha, A. (2009) A novel two-step hierarchical quantitative structure activity relationship modeling workflow for predicting acute toxicity of chemicals in rodents. Envr Health Persp 117:1257-1264.
  48. Zou, F., Lee, S., Knowles, M.R., Wright, F.A. (2010) Quantification of population structure using correlated SNPs by shrinkage principal components. Hum Hered 70:9-22.