Hari, A., AbdulHameed, M.D.M., Balik-Meisner, M., Mav, D., Phadke, D.P., Scholl, E.H., Shah, R., Casey, W.M., Auerbach, S., Wallqvist, A. & Pannala, V.R. (2024). Exposure to PFAS chemicals induces sex-dependent alterations in key rate-limiting steps of lipid metabolism in liver steatosis. Frontiers in Toxicology 6 – 2024.

Hogberg, H.T., Tsaioun, K., Breidenbach, J.D., Elmore, B., Filipovska, J., Garcia-Reyero, N., Hargreaves, A.J., Joshi, O., Omeragic, E., Plant, S., Ram, R., Virmani, I., Waspe, J. & Macmillan, D.S. (2024). A systematic scoping review of the neurological effects of COVID-19. Neurotoxicology 2024 May 17:S01610813X(24)00041-X.

Cong, G., Patton, R.M., Chao, F., Svoboda, D.L., Casey, W.M., Schmitt, C.P., Murphy, C., Erickson, J.N., Combs, P. & Auerbach, S.S. (2024). Completion of the DrugMatrix Toxicogenomics Database using ToxComl. bioRxiv 2024.03.26.586669.

Ford, L.C., Lin, H-C., Tsai, H-H. D., Zhou, Y-H., Wright, F.A., Sedykyh, A., Shah, R.R., Chiu, W.A. & Rusyn, I. (2024). Hazard and risk characterization of 56 structurally diverse PFAS using a targeted battery of broad coverage assays using six human cell types. Toxicology 503:153763.

Lloyd, D., House, J.S., Akhtari, F.S., Schmitt, C.P., Fargo, D.C., Scholl, E.H., Phillips, J., Choksi, S., Shah, R., Hall, J.E. & Motsinger-Reif, A. (2024). Interactive data sharing for multiple questionnaire-based exposome-wide association studies and exposome correlations in the Personalized Environment and Genes Study. Exposome, Feb 12;4(1):osae003. PMCID: PMC10899804

Lloyd, D., House, J.S., Akhtari, F.S., Schmitt, C.P., Fargo, D.C., Scholl, E.H., Phillips, J., Choksi, S., Shah, R., Hall, J.E. & Motsinger-Reif, A. (2024). Questionnaire-based exposome-wide association studies for common diseases in the personalized environment and genes study. Exposome, osae002.

Schmidt, L., Finnerty Mutlu, A.N., Elmore, R., Olorisade, B.K., Thomas, J. & Higgins, J.P.T. (2023). Data extraction methods for systematic review (semi)automation: Update of a living systematic review [version 2; peer review: 3 approved]. F1000 Research, 10:401. PMCID: PMC8361807

Pike, C.M., Zwarycz, B., McQueen, B.E., Castillo, M., Barron, C., Morowitz, J.M., Levi, J.A., Phadke, D., Balik-Meisner, M., Mav, D., Shah, R., Cunningham Glasspoole, D.L., Laetham, R., Thelin, W., Bunger, M.K. & Boazak, E.M., (2023). Characterization and optimization of variability in a human colonic epithelium culture model. bioRxiv, Sep 22:2023.09.22.559007. PMCID: PMC10542543

Green, A.J., Truong, L., Thunga, P., Leong, C., Hancock, M., Tanguay, R.L.; Reif, D.M. (2023). Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies. bioRxiv, Sep 17:2023.09.13.557544. PMCID: PMC10515950

Schmidt, L., Sinyor, M., Webb, R.T., Marshall, C., Knipe, D., Eyles, E.C., John, A., Gunnell, D. & Higgins, J.P.T. (2023). A narrative review of recent tools and innovations toward automating living systematic reviews and evidence syntheses. Zeitschrift für Evidenz, Fortbildung und Qualität im Gesundheitswesen (ZEFQ), 181: 65-75

Foley, J.F., Elgart, B., Phadke. D., Mav, D., Tripodi, I., Clausen, N., Weick, M., Gladwell, W., Gerrish, K., Shah, R., Merrick, B.A. (2023). Whole exome and transcript profiling of liver following aflatoxin B1 exposure in rats. Journal of Applied Toxicology 2023; 1-13.

Tripodi, I.J., Schmidt, L., Howard, B.E., Mav, D. & Shah, R. (2023). A Tissue-Specific and Toxicology-Focused Knowledge Graph. Information, 14(2), 91.

Kidd, B., Wang, K., Xu, Y, & Ni, Y. (2023). Federated Learning for Sparse Bayesian Models with Applications to Electronic Health Records and Genomics. Pacific Symposium on Biocomputing, 28:484-495. PMCID: PMC9782716.

Liu, L., Zhou, Y., Liu, Z., Li, J., Hu, L., He, L., Gao, G., Kidd, B., Walsh, A., Jiang, R., Wu, C., Zhang, K. & Xie, L. (2022). Osr1 Regulates Macrophage-mediated Liver Inflammation in Nonalcoholic Fatty Liver Disease Progression. Cellular and Molecular Gastroenterology and Hepatology, 27; S2352-345X(22)00261-2.

Dunnick, J.K., Pandiri, A.R., Shockley, K.R., Herbert, R., Mav, D., Phadke, D., Shah, R.R. & Merrick, B.A. (2022). Single nucleotide polymorphism patterns associated with a cancer resistant phenotype. Experimental and Molecular Pathology, 104812 (Accepted, in press).

Blake, B., Miller, C.N., Nguyen, H., Phan, T.P., Phadke, D.P., Balik-Meisner, M.R., Mav, D., Shah, R.R. & Fenton, S.E. (2022). Transcriptional pathways linked to fetal and maternal hepatic dysfunction caused by gestational exposure to perfluorooctanoic acid (PFOA) or hexafluoropropylene oxide-dimer acid (HFPO-DA or GenX) in CD-1 mice. Ecotoxicology and Environmental Safety (Accepted, in press).

Tandon, A., Howard, B., Ramaiahgari, S., Maharana, A., Ferguson, S., Shah, R. & Merrick, A. (2022). Deep learning image analysis of high-throughput toxicology assay images. SLAS Discovery, 27(1), 27-38. PMCID: PMC8955414

Brandner, S., McAleenan, A., Jones, H.E., Kernohan, A., Robinson, T., Schmidt, L., Dawson, S., Kelly, C., Leal, E.S., Faulkner, C.L., Palmer, A., Wragg, C., Jefferies, S., Vale, L., Higgins, J.P.T. & Kurian, K.M. (2022). Diagnostic accuracy of 1p/19q codeletion tests in oligodendroglioma: a comprehensive meta-analysis based on a Cochrane systematic review. Neuropathology and Applied Neurobiology, 48(4), e12790. PMCID: PMC9208578

Brownstein, N.C., Cai, J., Smith, S., Diatchenko, L., Slade, G.D. & Bair, E. (2022). Modeling secondary phenotypes conditional on genotypes in case-control studies. Stats, 5(1), 203-214.

Everett LJ; Mav D; Phadke DP; Balik-Meisner M; Shah R.R. (2022). Impact of Aligner, Normalization Method, and Sequencing Depth on TempO-seq Accuracy. Bioinformatics and Biology Insights 16:1-12.

Lam J; Elmore R; Howard B; Shah R. (2022). Low-calorie sweeteners and health outcomes: an evaluation of rapid versus traditional evidence mapping. BMC Research Notes 15:65.

Schmidt L; Olorisade B; McGuinness L; Thomas J. and Higgins, J. (2021). Data extraction methods for systematic review (semi)automation: A living systematic review. F1000Research 10, p.401.

Eyles E; Moran P; Okolie C; Dekel D; Macleod-Hall C; Webb R; Schmidt, L; Knipe D; Sinyor M; McGuinness L; Arensman E; Hawton K; O’Connor R; Kapur N; O’Neill S; Olorisade B; Cheng H; Higgins J; John A. and Gunnell D. (2021). Systematic review of the impact of the COVID-19 pandemic on suicidal behaviour amongst health and social care workers across the world. Journal of Affective Disorders Reports 6, p.100271.

John A; Eyles E; Webb R; Okolie C; Schmidt L; Arensman E; Hawton K; O’Connor R; Kapur N; Moran P; O’Neill S; McGuinness L; Olorisade B; Dekel D; Macleod-Hall C; Cheng H; Higgins J. and Gunnell D. (2021). The impact of the COVID-19 pandemic on self-harm and suicidal behaviour: update of living systematic review. F1000Research 9, p.1097.

Tandon A; Howard B; Ramaiahgari S; Maharana A; Ferguson S; Shah R; Merrick A. (2021). “Deep Learning Image Analysis of High-Throughput Toxicology Assay Images.” SLAS Discovery 27(1): 29-38.

Foley JF; Elgart B; Merrick BA; Phadke DP; Cook ME; Malphurs JA; Solomon GG; Shah RR; Fessler MB; Miller FW; Gerrish KE. (2021). “Whole genome sequencing of low input circulating cell-free DNA obtained from normal human subjects.” Physiological Reports 9:e14993.

Sedykh AY; Shah RR; Kleinstreuer NC; Auerbach SS; Gombar VK (2021). “Saagar-A New, Extensible Set of Molecular Substructures for QSAR/QSPR and Read-Across Predictions.” Chemical Research in Toxicology 34(2):634-640

Elmore R; Schmidt L; Lam J; Howard BE; Tandon A; Norman C; Phillips J; Shah M; Patel S; Albert T; Taxman DJ;Shah RR; (2020). “Risk and Protective Factors in the COVID-19 Pandemic: A Rapid Evidence Map.” Frontiers in Public Health 8 (787).

Mav D; Phadke DP; Balik-Meisner MR; Merrick BA; Auerbach S; Niemeijer M; Huppelschoten S; Baze A; Parmentier C; Richert L; van de Water B; Shah RR; Paules RS (2020). “Utility of Extrapolating Human S1500+ Genes to the Whole Transcriptome: Tunicamycin Case Study.” Bioinformatics and Biology Insights 14: 1-14.

Gwinn WM; Auerbach SS; Parham F; Stout MD; Waidyanatha S; Mutlu E; Collins B; Paules RS; Merrick BA; Ferguson S; Ramaiahgari S; Bucher JR; Sparrow B; Toy H; Gorospe J; Machesky N; Shah RR; Balik-Meisner MR; Mav D; Phadke DP; Roberts G; DeVito MJ (2020). “Evaluation of 5-day in vivo rat liver and kidney with high-throughput transcriptomics for estimating benchmark doses of apical outcomes.” Toxicological Sciences; kfaa081

Ma J; Bair E; Motsinger-Reif A. (2020). “Nonlinear Dose-Response Modeling of High-Throughput Screening Data Using an Evolutionary Algorithm.” Dose-Response April-June 2020: 1-10.

Bell S; Abedini J; Ceger P; Chang X; Cook B; Karmaus AL; Lea I; Mansouri K; Phillips J; McAfee E; Rai R; Rooney J; Sprankle C; Tandon A; Allen D; Casey W; Kleinstreuer N. (2020). “An integrated chemical environment with tools for chemical safety testing.” Toxicology in Vitro 67, 104916.

Yan X; Sedykh A; Wang W; Yan B; Zhu H (2020). “Construction of a web-based nanomaterial database by big data curation and modeling friendly nanostructure annotations.” Nature Communications 11; 2519

Merrick BA; Phadke DP; Bostrom MA; Shah RR; Wright GM; Wang X; Gordon O; Pelch KE; Auerbach SS; Paules RS; DeVito MJ; Waalkes MP; Tokar EJ (2020). “KRAS-retroviral fusion transcripts and gene amplification in arsenic-transformed, human prostate CAsE-PE cancer cells.” Toxicology and Applied Pharmacology; 397;115017

Howard BE; Phillips J; Tandon A; Maharana A; Elmore R; Mav D; Sedykh A; Thayer K; Merrick BA; Walker V; Rooney A; Shah RR (2020). “SWIFT-Active Screener: accelerated document screening through active learning and integrated recall estimation.” Environment International; 138;105623

Liu G; Yan X; Sedykh A; Pan X; Zhao X; Yan B; Zhu H (2020). “Analysis of model PM2. 5-induced inflammation and cytotoxicity by the combination of a virtual carbon nanoparticle library and computational modeling.” Ecotoxicology and Environmental Safety; 15;191:110216

Phillips J.R.,  Svoboda D.L., Tandon A., Patel S., Sedykh A., Mav D., Kuo B., Yauk C.L., Longlonog Y., Thomas R.S., Gift J.S., Davis J.A., Olszyk L., Merrick B.A., Paules R.S., Parham F., Saddler T., Shah R.R., and Auerbach S.S. (2019) BMDExpress 2: enhanced transriptomic dose-response analysis workflow.  Bioinformatics 35(10): 1780-1782.

Kovi RC; Bhusari S; Mav D; Shah RR; Ton TV; Hoenerhoff MJ; Sills RC; Pandiri AR (2019). “Genome-wide promoter DNA methylation profiling of hepatocellular carcinomas arising either spontaneously or due to chronic exposure to Ginkgo biloba extract (GBE) in B6C3F1/N mice.” Archives of Toxicology; 93(8):2219-2235

Yan X; Sedykh A; Wang W; Yan B; Zhu H (2019). “Novel nanodescriptors applied in QNAR: Combination of virtual nanomaterial library and geometrical structure of nanomaterial.” Abstracts of Papers of the American Chemical Society; 257

Witt KL; Hsieh JH; Smith-Roe SL; Xia M; Sedykh A; Huang R; Auerbach S; Tice RR (2019). “Assessment of Genotoxicity Potential Using High Throughput Screening Approaches: The Tox21 Experience.” Environmental and Molecular Mutagenesis; 60:37-38

Merrick BA, Phadke DP, Bostrom MA, Shah RR, Wright GM, Wang X, Gordon O, Pelch KE, Auerbach SS, Paules RS, DeVito MJ, Waalkes MP, Tokar EJ (2019). “Arsenite malignantly transforms human prostate epithelial cells in vitro by gene amplification of mutated KRAS.” PLoS One; 14(4), e0215504

Lam J, Howard BE, Thayer K, Shah RR (2019). “Low-calorie sweeteners and health outcomes: A demonstration of rapid evidence mapping (rEM).” Environment International; 123:451-458

Balik-Meisner MR, Mav D, Phadke DP, Everett L, Shah RR, Tal T, Shepard PJ, Merrick BA, Paules RS (2019). “Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics.” Zebrafish

Ramaiahgari SC, Auerbach SS, Saddler TO, Rice JR, Dunlap PE, Sipes NS, DeVito MJ, Shah RR, Bushel PR, Merrick BA, Paules RS, Ferguson SS. (2019). “The Power of Resolution: Contextualized Understanding of Biological Responses to Liver Injury Chemicals using High-throughput Transcriptomics and Benchmark Concentration Modeling.” Toxicological Sciences

Hubbard TD, Hsieh JH, Rider CV, Sipes NS, Sedykh A, Collins BJ, Auerbach SS, Xia M, Huang R, Walker NJ, DeVito MJ (2019). “Using Tox21 High-Throughput Screening Assays for the Evaluation of Botanical and Dietary Supplements.” Applied in vitro toxicology; 5(1)

Yan X, Sedykh A, Wang W, Zhao X, Yan B, Zhu H (2019). “In silico profiling nanoparticles: predictive nanomodeling using universal nanodescriptors and various machine learning approaches.” Nanoscale; 11(17): 8352-8362

Hsieh JH, Smith-Roe S, Huang R, Sedykh A, Shockley K, Auerbach SS, Merrick BA, Xia M, Tice RR, Witt K (2019). “Identifying Compounds with Genotoxicity Potential Using Tox21 High Throughput Screening Assays.” Chemical Research in Toxicology

Wang W, Yan X, Zhao L, Russo DP, Wang S, Liu Y, Sedykh A, Zhao X, Yan B, Zhu H (2019). “Universal nanohydrophobicity predictions using virtual nanoparticle library.” Journal of cheminformatics; 11(1):6

Glynn C, Tokdar ST, Howard B, Banks DL (2019). “Bayesian analysis of dynamic linear topic models.” Bayesian Analysis; 14(1):53-80

Svoboda DL, Saddler T, Auerbach SS (2019). “An Overview of National Toxicology Program’s Toxicogenomic Applications: DrugMatrix and ToxFX.” Advances in Computational Toxicology, 141-157

Pelch K, Wignall JA, Goldstone AE, Ross PK, Blain RB, Shapiro AJ, Holmgren SD, Hsieh JH, Svoboda D, Auerbach SS, Parham FM, Masten SA, Walker V, Rooney A, Thayer KA (2019). “A Scoping Review of the Health and Toxicological Activity of Bisphenol A (BPA) Structural Analogues and Functional Alternatives.” Toxicology

Truong L, Zaikova T, Baldock BL, Balik-Meisner M, To K, Reif DM; Kennedy ZC, Hutchison JE, Tanguay RL (2019). “Systematic determination of the relationship between nanoparticle core diameter and toxicity for a series of structurally analogous gold nanoparticles in zebrafish.” Nanotoxicology

Foley JF, Phadke DP, Hardy O, Hardy S, Miller V, Madan A, Howard K, Kruse K, Lord C, Ramaiahgari S, Solomon GG, Shah RR, Pandiri AR, Herbert RA, Sills RC, Merrick BA (2018). “Whole exome sequencing in the rat.” BMC genomics; 19(1), 487

Auerbach SS, Xu M, Merrick BA, Hoenerhoff MJ, Phadke D, Taxman DJ, Shah R, Hong HL, Ton T, Kovi RC, Sills RC, Pandiri AR (2018). “Exome Sequencing of Fresh-frozen or Formalin-fixed Paraffin-embedded B6C3F1/N Mouse Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Chemical Exposure.” Toxicology pathology; doi:/10.1177/0192623318789398

La MK, Sedykh A, Fourches D, Muratov E, Tropsha (2018). “Predicting Adverse Drug Effects from Literature-and Database-Mined Assertions”. Drug Safety; pp 1-14

Wignall JA, Muratov E, Sedykh A, Guyton KZ, Tropsha A, Rusyn I, Chiu WA (2018). “Conditional Toxicity Value (CTV) Predictor: An In Silico Approach for Generating Quantitative Risk Estimates for Chemicals”. Environmental health perspectives; 126(5):057008-057008

Mav D, Shah RR, Howard BE, Auerbach SS, Bushel PR, Collins JB, Gerhold DL, Judson RS, Karmaus AL, Maull EA, Mendrick DL, Merrick BA, Sipes NS, Svoboda D, Paules RS (2018).  “A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics.” PLoS One; 13-2, e0191105

Cocce KJ, Jasper JS, Everett LJ, Wardell SE, Westerling T, Krebs T, Baldi R, Wright TM, Yllanes A, Blitzer JT, Logsdon D, Rakiec D, Ruddy D, Hyslop T, Jiang L, Hall A, Marks JR, Crawford GE, Brown M, McDonell DP, Norris JD (2018). “GRHL2: key lineage determining factor collaborates with FOXA1 to establish targetable collateral pathway in endocrine therapy-resistant breast cancer”. Molecular Biology and Evolution; Volume 35, Issue 1, Pages 50–65

Li R, Grimm SA, Mav D, Gu H, Djukovic D, Shah R, Merrick BA, Raftery D, Wade PA (2018). “Transcriptome and DNA Methylome Analysis in a Mouse Model of Diet-Induced Obesity Predicts Increased Risk of Colorectal Cancer”. Cell Rep, 2018 Jan 16;22(3):624-637. doi: 10.1016/j.celrep.2017.12.071

Merrick BA, Chang JS, Phadke DP, Bostrom MA, Shah RR, Wang X, Gordon O, Wright GM (2018). “HAfTs are novel lncRNA transcripts from aflatoxin exposure”. PLoS One, 2018 Jan 19;13(1): e0190992. doi: 10.1371/journal.pone.0190992

Balik-Meisner M, Truong L, Scholl EH, Tanguay RL, Reif DM (2018). “Population genetic diversity in zebrafish lines.” Mammalian Genome; 24 Jan 2018; doi: 10.1007/s00335-018-9735-x

Hardy CM, Burke MK, Everett LJ, Han MV, Lantz KM, Gibbs AG (2018). “Genome-wide analysis of starvation-selected Drosophila melanogaster—A genetic model of obesity”. Molecular Biology and Evolution 2018, 35(1):50-65

Pelch KE; Wignall JA; Goldstone AE; Ross PK; Blain RB; Shapiro AJ; Holmgren SD; Hsieh JH; Svoboda D; Auerbach SS; Parham FM; Masten SA; Thayer KA (2017). “NTP Research Report on Biological Activity of Bisphenol A (BPA) Structural Analogues and Functional Alternatives: Research Report 4.” National Toxicology Program, Research Triangle Park (NC)

Reif DM, Balik-Meisner M, Truong L, Scholl EH, Du JK La, Tanguay RL (2017). “Gene-Environment Interactions Associated with Differential Susceptibility to Chemical Exposure.” Environmental and Molecular Mutagenesis; Vol. 58, pp. S32-S32

Maharana A, Nsoesie EO (2017). “Using Deep Learning to Examine the Association between the Built Environment and Neighborhood Adult Obesity Prevalence.” arXiv preprint arXiv:1711.00885. (submitted)

Shimbo T, Dunnick JK, Brix A, Mav D, Shah R, Roberts JD, Wade PA (2017). “DNA Methylation Changes in Tbx3 in a Mouse Model Exposed to Polybrominated Diphenyl Ethers”. Int J Toxicol, 2017 May/Jun;36(3):229-238. doi: 10.1177/1091581817706676.

Wang W, Sedykh A, Sun H, Zhao L, Russo DP, Zhou H, Yan B, Zhu H (2017). “Predicting Nano-Bio Interactions by Integrating Nanoparticle Libraries and Quantitative Nanostructure Activity Relationship Modeling”. ACS Nano. 2017 Dec 26;11(12):12641-12649. doi: 10.1021/acsnano.7b07093

Maharana A, Nguyen QC, Nsoesie EO (2017). “Using Deep Learning and Satellite Imagery to Quantify the Impact of the Built Environment on Neighborhood Crime Rates.” arXiv preprint arXiv:1710.05483. (submitted)

Maharana A, Yetisgen M (2017). “Clinical Event Detection with Hybrid Neural Architecture.” BioNLP 2017:351-5

Henly S, Tuli G, Kluberg SA, Hawkins JB, Nguyen QC, Anema A, Maharana A, Brownstein JS, Nsoesie EO (2017). “Disparities in digital reporting of illness: A demographic and socioeconomic assessment.” Preventive medicine, 101:18-22.

Singh A, Foley J, Tandon A, Phadke D, Kinyamu H, Archer T (2017). “A role for BRG1 regulated genes during development of the lymphatic system”. Oncotarget, 2017 Jul 4;8(33):54925-54938. doi: 10.18632/oncotarget.18976

Sipes NS, Wambaugh JF, Pearce R, Auerbach SS, Wetmore BA, Hsieh JH, Shapiro AJ, Svoboda D, DeVito MJ, Ferguson SS (2017). “An Intuitive Approach for Predicting Potential Human Health Risk with the Tox21 10k Library”. Environ Sci Technol. 2017 Sep 19;51(18):10786-10796. doi: 10.1021/acs.est.7b00650

Bell SM, Phillips J, Sedykh A, Tandon A, Sprankle C, Morefield SQ, Shapiro A, Allen D, Shah R, Maull EA, Casey WM, Kleinstreuer NC (2017). “An Integrated Chemical Environment to Support 21st Century Toxicology”. “Environmental Health Perspectives, 54501,1.

Garlapow ME, Everett LJ, Zhou S, Gearhart AW, Fay KA, Huang W, Morozova TV, Arya GH, Turlapati L, St Armour GE, Hussain YN, McAdams SE, Fochler S, Mackay TF (2017). “Genetic and genomic response to selection for food consumption in Drosophila melanogaster”. Behavior Genetics 2017, Volume 47, Issue 2, pp 227-243

Shimbo T, Dunnick JK, Brix A, Mav D, Shah RR, Wade PA (2017). “DNA Methylation Changes in Tbx3 in a Mouse Model Exposed to Polybrominated Diphenyl Ethers”. Int J Toxicol 2017 doi 10.1177/1091581817706676

Ferguson SS, Ramaiahgari SC, Saddler T, Rice J, Dunlap P, Sipes N, Shah R, Merrick A, Bushel P, DeVito MJ, Paules RS (2017). “Development of organotypic culture systems to link pathway perturbations with phenotypic responses.” Environmental and Molecular Mutagenesis; Vol. 58, pp. S26-S26

Hsieh J-H, Huang R, Lin J-A, Sedykh A, Zhao J, Tice RR, Paules R S, Xia M, Auerbach SS (2017). “Real-time cell toxicity profiling of Tox21 10K compounds reveals cytotoxicity dependent toxicity pathway linkage”. PloS one; 12(7): e0181291.  doi 10.1371/journal.pone.0181291

Zhao L, Wang W, Sedykh A, Zhu H (2017). “Experimental errors in QSAR modeling sets: What we can do and what we cannot do”. ACS omega; 2(6):2805-2812. doi: 10.1021/acsomega.7b00274

Howard BE, Phillips J, Miller K, Tandon A, Mav D, Shah MR, Holmgren S, Pelch KE, Rooney AA, Macleod M, Shah RR, Thayer K (2016). “SWIFT-Review: A Text-mining Workbench for Systematic Review.” Syst Rev. 2016 May 23;5(1):87. doi: 10.1186/s13643-016-0263-z.

Nsoesie EO, Flor L, Hawkins J, Maharana A, Skotnes T, Marinho F, Brownstein JS (2016). “Social media as a sentinel for disease surveillance: what does sociodemographic status have to do with it?”. PLoS currents; 8.

Shorter JR, Dembeck LM, Everett LJ, Morozova TV, Arya GH, Turlapati L, St Armour GE, Schal C, Mackay TF, Anholt RR (2016). “Obp56h modulates mating behavior in Drosophila melanogaster”. G3 2016, 6(10):3335-3342.

Alves V, Muratov E, Capuzzi S, Politi R, Low Y, Braga R, Zakharov AV, Sedykh A, Mokshyna E, Farag S, Andrade C, Kuz’min V, Fourches D, Tropsha A (2016). “Alarms about structural alerts”. Green Chem. 2016 Aug 21;18(16):4348-4360. doi: 10.1039/C6GC01492E.

Singh AP, Foley JF, Rubino M, Boyle MC, Tandon A, Shah R, Archer TK (2016). “BRG1 enables rapid growth of the early embryo by suppressing genes that regulate apoptosis and cell growth arrest.” Mol Cell Biol; 16 May 2016; doi:10.1128/MCB.01101-15.

Glynn C, Tokdar S, Banks D, Howard BE (2016). “Bayesian Analysis of Dynamic Linear Topic Models.” (submitted).

Recio L, Phillips S, Davis J, Shah R, Marroni D, Friedman M (2016).  “Transcriptional Profiling in Testes of Rats Exposed to Acrylamide Reveals Actin Filaments, Protein Catabolism and Cell Proliferation” Society of Toxicology Meeting, New Orleans, Louisiana, March 13—17, 2016.

Shah R (2016). “Integration of Epigenomics Data with Other “-Omics” Datasets in Translational Toxicology Studies.” Society of Toxicology Meeting, New Orleans, Louisiana, March 13—17, 2016.

Howard BE, Phillips J, Miller K, Thayer K, Shah R (2016). “Mining the Tox21 Literature with SWIFT-Review.” Society of Toxicology Meeting, New Orleans, Louisiana, March 13—17, 2016.

Miller K, Howard BE, Phillips J, Shah M, Mav D, Shah R (2016). “SWIFT-Active Screener: Reducing Literature Screening Effort Through Machine Learning for Systematic Reviews.” Society of Toxicology Meeting, New Orleans, Louisiana, March 13—17, 2016.

Howard BE, Miller K, Phillips J, Thayer K, Shah R (2016). “Evaluation of the Literature Prioritization Capabilities of SWIFT-Review, a Tool for Conducting Systematic Reviews of Environmental Health Questions.” Society of Toxicology Meeting, New Orleans, Louisiana, March 13—17, 2016.

Rotroff DM, Oki NO, Liang X, Yee SW, Stocker SL, Corum DG, Meisner M, Fiehn  O, Motsinger-Reif  AA, Giacomini KM, Kaddurah-Daouk R (2016). “Pharmacometabolomic Assessment of Metformin in Non-diabetic, African Americans,” Frontiers in Pharmacology, vol. 7, p. 135, Jun. 2016

Auerbach S, Filer D, Reif D, Walker VR, Blumberg B, Clegg D, Holloway AC, Schlezinger J, Scheri RC, Srinivasan S, White MF, Svoboda D, Judson R, Bucher JR, Thayer KA (2016). (in press) “Prioritizing environmental chemicals for obesity and diabetes outcomes research: A screening approach using ToxCast high throughput data.” Environmental Health Perspectives.

Yang WE, Suchindran S, Nicholson BP, McClain MT, Burke T, Ginsburg GS, Harro CD, Chakraborty S, Sack DA, Woods CW, Tsalik EL (2016). “Transcriptomic Analysis of the Host Response and Innate Resilience to Enterotoxigenic Escherichia coli Infection in Humans.” J Infect Dis. 2016 Jan 18. pii: jiv593.

Chen S, Hsieh JH, Huang R, Sakamuru S, Hsin LY, Xia M, Shockley KR, Auerbach S, Kanaya N, Lu H, Svoboda D, Witt KL, Merrick BA, Teng CT, Tice RR (2015). “Cell-Based High-Throughput Screening for Aromatase Inhibitors in the Tox21 10K Library.” Toxicol Sci. 2015 Oct;147(2):446-57. doi: 10.1093/toxsci/kfv141.

Adler M, Ramm S, Hafner M, Muhlich JL, Gottwald EM, Weber E, Jaklic A, Ajay AK, Svoboda D, Auerbach S, Kelly EJ, Himmelfarb J, Vaidya VS (2015). “A Quantitative Approach to Screen for Nephrotoxic Compounds In Vitro.” J Am Soc Nephrol. 2015 Aug 10. pii: ASN.2015010060.

Lewis DA, Suchindran S, Beckman MG, Hooper WC, Grant AM, Heit JA, Manco-Johnson M, Moll S, Philipp CS, Kenney K, De Staercke C, Pyle ME, Chi JT, Ortel TL. (2015). “Whole blood gene expression profiles distinguish clinical phenotypes of venous thromboembolism.” Thromb Res. 2015 Apr;135(4):659-65.

Li JH, Suchindran S, Shah SH, Kraus WE, Ginsburg GS, Voora D (2015). Pharmacogenomics. 2015 Apr;16(5):449-58.

Qiu LQ, Abey S, Harris S, Shah R, Gerrish KE, Blackshear PJ (2015). “Global analysis of posttranscriptional gene expression in response to sodium arsenite.”  Environmental Health Perspectives. 2015 Apr; 123(4):324-30.

Srirangan S, Sauer M-L, Howard B, Dvora M, Dums J, Backman P, Sederoff H (2015). “Interaction of Temperature and Photoperiod Increases Growth and Oil Content in the Marine Microalgae Dunaliella viridis.” PLoS ONE 10(5): e0127562. doi:10.1371/journal.pone.0127562.

Kim MT, Huang R, Sedykh A, Wang W, Xia M, Zhu H (2015). “Mechanism profiling of hepatotoxicity caused by oxidative stress using the antioxidant response element reporter gene assay models and big data”. Environmental Health Perspectives, 2015, ASAP

Rotroff DM, Shahin  MH, Gurley  SB, Zhu H, Reif AM, Meisner M, Beitelshees  AL, Fiehn O, Johnson  JA, Elbadawi-Sidhu M, Frye  RF, Gong Y, Weng L, Cooper-DeHoff  RM, Kaddurah-Daouk R (2015). “Pharmacometabolomic Assessments of Atenolol and Hydrochlorothiazide Treatment Reveal Novel Drug Response Phenotypes,” CPT Pharmacometrics & Systems Pharmacology, vol. 4, no. 11, pp. 669–79, Nov. 2015

Meisner M, Reif DM (2015). “Computational Methods Used in Systems Biology,” in Systems Biology in Toxicology and Environmental Health, Rebecca C. Fry, Ed. Chapel Hill, NC: Academic Press, 2015, p. 85-115

Soccio RE, Chen ER, Rajapurkar SR, Safabakhsh P, Marinis JM, Dispirito JR, Emmett MJ, Briggs ER, Fang B, Everett LJ, Lim HW, Won KJ, Steger DJ, Wu Y, Civelek M, Voight BF, Lazar MA (2015). “Genetic variation determines PPARγ function and antidiabetic drug response in vivo”. Cell 2015, 162(1):33-44

Wang W, Kim M, Sedykh A, Zhu H (2015). “Developing enhanced blood-brain barrier permeability models: Integrating external bio-assay data in QSAR modeling”. Pharmaceutical Research, 2015, 32(9), 3055-3065

Hsieh J-H, Sedykh A, Huang R, Xia M, Tice RR (2015). “A Data analysis pipeline accounting for artifacts in Tox21 quantitative high throughput screening assays”. Journal of Biomolecular Screening, 2015, 20(7), 887-897

Lucas, J, Dressman HK, Suchindran S, Chute JP (2014). “A translatable predictor of human radiation exposure.”  Plos One 2014.

Nelson ER, Wardell SE, Jasper JS, Park S, Suchindran S, Howe MK, Carver NJ, Pillai RV, Sullivan PM, Sondhi V, Umetani M, Geradts J, McDonnell DP (2014). “27-Hydroxycholesterol links hypercholesterolemia and breast cancer pathophysiology.” Science. 2013 Nov 29;342(6162):1094-8.

Auerbach SS, Phadke DP, Mav D, Holmgren S, Gao Y, Xie B, Shin JH, Shah RR, Merrick AB, Tice RR (2014). “RNA-seq-based toxicogenomic assessment of fresh frozen and formalin-fixed tissues yields similar mechantistic insights.” J. Appl. Toxicol.; Published online, doi: 10.1002/jat.3068.

Li  R, Grimm SA, Chrysovergis K, Kosak J, Wang X, Burkholder A, Jandardhan K, Mav D, Shah R, Eling TE, Wade PA  (2014). “Obesity, rather than diet, drives epigenetic alterations in colonic epithelium resembling cancer progression.” Cell Metabolism; 19(4)p-702-711.

Li  R, Mav D, Grimm S, Jothi R, Shah R, Wade P (2014). “Fine-tuning of epigenetic regulation with respect to promoter CpG content in a cell type-specific manner.” Epigenetics; 9(5).

Coarfa C, Pichot C, Jackson A, Tandon A, Amin V, Raghuraman S, Paithankar S, Lee AV, McGuire SE, Milosavljevic A (2014). “Analysis of interactions between theepigenome and structural mutability of the genome using Genboree Workbench tools.” BMC Bioinformatics. 2014;15 Suppl 7:S2. doi: 10.1186/1471-2105-15-S7-S2.

SEQC/MAQC-III Consortium (2014). “A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.” Nature Biotechnology. 32, 903–914 (2014).

Wang, C., Gong, B., Bushel, P.R., Thierry-Mieg, J., Thierry-Mieg, D., Xu, J., Fang, H., Hong, H., Shen, J., Su, Z., Meehan, J., Li, X., Yang, L., Li, H., Labaj, P.P., Kreil, D.P., Megherbi, D., Gaj, S., Caiment, F., van Delft, J., Kleinjans, J., Scherer, A., Devanarayan, V., Wang, J., Yang, Y., Qian, H.R., Lancashire, L.J., Bessarabova, M., Nikolsky, Y., Furlanello, C., Chierici, M., Albanese, D., Jurman, G., Riccadonna, S., Filosi, M., Visintainer, R., Zhang, K.K., Li, J., Hsieh, J.H., Svoboda, D.L., Fuscoe, J.C., Deng, Y., Shi, L., Paules, R.S., Auerbach, S.S., Tong, W (2014). “The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.” Nat Biotechnol. 9: 926-932.

Hodgson E, Wallace AD, Shah RR, Choi K, Joo H (2014). “Human variation and risk assessment: microarray and other studies utilizing human hepatocytes and human liver subcellular preparations.” J Biochem Mol Toxicol. 2014 Jan; 28(1):1-10.

Sprague B, Shi Q, Kim MT, Zhang L, Sedykh A, Ichiishi E, Tokuda H, Lee KH, Zhu H (2014). “Design, synthesis and experimental validation of novel potential chemopreventive agents using random forest and support vector machine binary classifiers”. Journal of Computer-Aided Molecular Design, 2014, 28(6), 631-646

Fang B, Everett LJ, Jager J, Briggs E, Armour SM, Feng D, Roy A, Gerhart-Hines Z, Sun Z, Lazar MA (2014). “Circadian enhancers coordinate multiple phases of rhythmic gene transcription in vivo”. Cell 2014, 159(5):1140-1152 (*co-first authors)

Shin S, Le Lay J, Everett LJ, Gupta R, Rafiq K, Kaestner KH (2014). “CREB mediates the insulinotropic and anti-apoptotic effects of GLP-1 signaling in adult mouse β-cells”. Molecular Metabolism 2014, 3(8):803-812

Turner JR, Ray R, Lee B, Everett L, Xiang J, Jepson C, Kaestner KH, Lerman C, Blendy JA (2014). “Evidence from mouse and man for a role of Neuregulin 3 in nicotine dependence”. Molecular Psychiatry 2014, 19(7):801-810

Low Y, Sedykh A, Rusyn I, Tropsha A (2014). “Integrative approaches for predicting in vivo effects of chemicals from their structural descriptors and the results of short-term biological assays”. Current Topics in Medicinal Chemistry, 2014, 14(11), 1356-1364

Thompson C, Sedykh A, Nicol M, Muratov E, Fourches D, Tropsha A, Kashuba A (2014). “Cheminformatics analysis to identify predictors of antiviral drug penetration into the female genital tract”. AIDS Research and Human Retroviruses, 2014, 30(11), 1058-1064

Zhu H, Zhang J, Kim M, Boison A, Sedykh A, Moran K (2014). “Big data in chemical toxicity research: the use of high-throughput screening assays to identify potential toxicants”. Chemical Research in Toxicolgy, 2014, 27(10), 1643-1651

Everett LJ and Lazar MA (2014). Nuclear receptor Rev-erbα: up, down, and all around. Trends in Endocrinology and Metabolism 2014, 25(11):586-592

Sun Z, Feng D, Fang B, Mullican SE, You SH, Lim HW, Everett LJ, Nabel CS, Li Y, Selvakumaran V, Won KJ, Lazar MA (2013). “Deacetylase-independent function of HDAC3 in transcription and metabolism requires Nuclear Receptor Corepressor”. Molecular Cell 2013, 52(6):769-782

Gerhart-Hines Z, Feng D, Emmett MJ, Everett LJ, Loro E, Briggs ER, Bugge A, Hou C, Ferrara C, Seale P, Pryma DA, Khurana TS, Lazar MA (2013). “The nuclear receptor Rev-erbα controls circadian thermogenic plasticity”. Nature 2013, 503(7476):410-413

Plasschaert RN, Vigneau S, Tempera I, Gupta R, Maksimoska J, Everett L, Davuluri R, Marmorstein R, Lieberman PM, Schultz D, Hannenhalli S, Bartolomei MS (2013). “CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation”. Nucleic Acids Research 2013, 42(2):774-789

Everett LJ, Le Lay J, Lukovac S, Bernstein D, Steger DJ, Lazar MA, Kaestner KH (2013). “Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver”. BMC Genomics 2013, 14:337

Bramswig NC, Everett LJ, Schug J, Dorrell C, Liu C, Luo Y, Streeter PR, Naji A, Grompe M, Kaestner KH (2013). “Epigenomic plasticity enables human pancreatic α to β cell reprogramming”. The Journal of Clinical Investigation 2013, 123(3):1275-1284

Everett LJ and Lazar MA (2013). Cell-specific integration of nuclear receptor function at the genome. WIREs Systems Biology and Medicine 2013, 5(5):615-629

Shimbo T, Du Y, Grimm S, Dhasarathy A, Mav D, Shah R, Shi H, Wade PA (2013). “MBD3 localizes at promoters, gene bodies and enhancers of active genes.” PLoS Genet; 9(12):e1004028. doi:10.1371/journal.pgen.1004028.

Lai A, Mav D, Shah R, Grimm S, Phadke D, Hatzi K, Melnick A, Geigerman C, Sobol S, Jaye D, Wade P. (2013). “DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B cell activation.” Genome Res; Published online, doi:10.1101/gr.155473.113.

Smith L, Tandon A, Shah R, Mav D, Scoltock A, Cidlowski J.  (2013) “Deep sequencing identification of novel glucocorticoid-responsive miRNAs in apoptotic primary lymphocytes.” PLoS ONE; 8(10): e78316. doi:10.1371/journal.pone.0078316.

Roberts SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D, Stojanov P, Kiezun A, Kryukov GV, Carter SL, Saksena G, Harris S, Shah RR, Resnick MA, Getz G, Gordenin DA (2013). “An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers.” Nat Genet. 2013 Sep; 45(9):970-6.

Merrick A, Phadke D, Auerbach S, Mav D, Stiegelmeyer S, Shah R, Tice R. (2013) “RNA-seq profiling reveals novel hepatic gene expression pattern in Aflatoxin B1 treated rats.” PLoS ONE; 8(4) e61758.

Howard BE, Hu Q, Babaoglu AC, Chandra M, Borghi M, Tan X, He L, Winter-Sederoff H, Gassmann W, Veronese P, Heber S (2013). “High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants.” PLoS One, 8(10) e74183.

Kim M, Sedykh A, Chakravarti SK, Saiakhov R, Zhu H (2013). “Critical evaluation of human oral bioavailability for pharmaceutical drugs by using various cheminformatics approaches”. Pharmaceutical Research, 2013, 31(4), 1002-1014

Zhu X-W, Sedykh A, Liu S-S (2014). “Hybrid in silico models for drug-induced liver injury using chemical descriptors and in vitro cell-imaging information”. Journal of Applied Toxicology, 2014, 34(3), 281-288

Low Y, Sedykh A, Fourches D, Golbraikh A, Whelan M, Rusyn I, Tropsha A (2013). “Integrative chemical-biological read-across approach for chemical hazard classification”. Chemical Research in Toxicology, 2013, 26(8), 1199-1208

Zhang L, Sedykh A, Tripathi A, Zhu H, Afantitis A, Mouchlis V, Rusyn I, Tropsha A (2013). “Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and structure-based virtual screening approaches”. Toxicology and Applied Pharmacology, 2013, 272(1), 67-76

Yang K, Koeck K, Sedykh A, Tropsha A, Brouwer K L R (2013). “An Updated review on drug-induced cholestasis: Mechanisms and investigation of physicochemical properties and pharmacokinetic parameters”. Journal of Pharmaceutical Sciences, 2013, 102(9), 3037-57

Zhu X-W, Sedykh A, Zhu H, Liu S-S, Tropsha A (2013). “The use of pseudo-equilibrium constant affords improved QSAR models of human plasma protein binding”. Pharmaceutical Research, 2013, 30(7), 1790-1798.

Zhang L, Zhu H, Fourches D, Sedykh A, Golbraikh A, Ekins S, Clark J, Connelly M, Signal M, Hodges M, Guiguemde A, Guy R, Tropsha A (2013). “Discovery of novel antimalarial compounds enabled by QSAR-based virtual screening”. Journal of Chemical Information and Modeling, 2013, 53(2), 475-492

Sedykh A, Fourches D, Duan J, Hucke O, Garneau M, Zhu H, Bonneau P, Tropsha A (2013). “Human intestinal transporter database: QSAR modeling and virtual profiling of drug uptake, efflux and interactions”. Pharmaceutical Research, 2013, 30(4), 996-1007.

Roberts S, Sterling J, Thompson C, Harris S, Mav D, Shah R, Klimczak L, Kryukov G, Mlac E, Milecskowski P, Resnick M, Gordenin D.  (2012) “Clustered mutations in yeast and in human cancers can arise from long single strand DNA regions.” Mol Cell; 46(4):424-35.

Burd CJ, Ward JM, Crusselle-Davis VJ, Kissling GE, Phadke DP, Shah RR, Archer TK (2012). “Analysis of chromatin dynamics during glucocorticoid receptor activation.” Mol Cell Biol 32(10):1805-17.

Riehle K, Coarfa C, Jackson A, Ma J, Tandon A, Paithankar S, Raghuraman S, Mistretta TA, Saulnier D, Raza S, Diaz MA, Shulman R, Aagaard K, Versalovic J, Milosavljevic A (2012). “The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences.” BMC Bioinformatics. 2012;13 Suppl 13:S11. doi: 10.1186/1471-2105-13-S13-S11.

Gunaratne PH, Coarfa C, Soibam B, Tandon A (2012). “miRNA data analysis: next-gen sequencing. Methods.” Mol Biol. 2012;822:273-88. doi: 10.1007/978-1-61779-427-8_19.

Annab LA, Bortner CD, Sifre MI, Collins JM, Shah RR, Dixon D, Karimi Kinyamu H, Archer TK. (2012). “Differential Responses to Retinoic Acid and Enocrine Disruptor Compounds of Subpopulations within Human Embryonic Stem Cell Lines Differentiation.” Differentiation, 2012 Nov;84(4):330-43.

Solimeo R, Zhang J, Kim M, Sedykh A, Zhu H (2012). “Predicting chemical ocular toxicity using combinatorial QSAR approach”. Chemical Research in Toxicology, 2012, 25(12), 2763-2769.

Cern A, Golbraikh A, Sedykh A, Tropsha A, Barenholz Y, Goldblum A (2012). “Quantitative structure-property relationship modeling of remote liposome loading of drugs”. Journal of Controlled Release, 2012, 160(2), 147-157.

Rusyn I, Sedykh A, Low Y, Guyton K, Tropsha A (2012). “Predictive modeling of chemical hazard by integrating numerical descriptors of chemical structures and short-term toxicity assay data”. Toxicological Sciences, 2012, 127(1), 1-9.

Lock E, Abdo N, Huang R, Xia M, Kosyk O, O’Shea S, Zhou Y-H, Sedykh A, Tropsha A, Austin C, Tice R, Wright F, Rusyn I (2012). “Quantitative high-throughput screening for chemical toxicity in a population-based in vitro model”. Toxicological Sciences, 2012, 126(2), 578-588.

O’Hanlon T, Rider L, Gan L, Fanin R, Paules RS, Umbach D, Weinberg C, Shah R, Mav D, Gourley M, Miller F. (2011) “Gene expression profiles from discordant monozygotic twings suggest that molecular pathways are shared among multiple systemic autoimmune diseases.” Arthritis Res Ther; 13(2):R69.

Dhasarathy A, Phadke D, Mav D, Shah R, Wade P.  (2011) “The transcription factors Snail and Slug activate the transfrorming growth factor-beta signaling pathway in breast cancer.” PLoS ONE; 6(10):e25614.

Sun Z, Feng D, Everett LJ, Bugge A, Lazar MA (2011). Circadian Epigenomic Remodeling and Hepatic Lipogenesis: Lessons from HDAC3. Cold Spring Harbor Symposia on Quantitative Biology 2011, 76:49-55

Howard BE, Veronese P, Heber S (2011). “Improved RNA-Seq Read Partitions in Linear Models for Isoform Quantification.” BIBM 2011, Atlanta, GA, p 151-154.

Benjamin AM, Suchindran S, Pearce K, Rowell J, Lien LF, Guyton JR, McCarthy JJ (2011). “Gene by sex interaction for measures of obesity in the framingham heart study.” Journal of Obesity 2011.

Hsieh J-H, Yin S, Liu S, Sedykh A, Dokholyan N, Tropsha, A (2011). “Combined application of cheminformatics- and physical force field-based scoring functions improves binding affinity prediction for CSAR datasets”. Journal of Chemical Information and Modeling, 2011, 51(9), 2027-2035.

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”. Chemical Research in Toxicology, 2011, 24, 1251-1262.

Sedykh A, Zhu H, Tang H, Zhang L, Richard A, Rusyn I, 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”. Environmental Health Perspectives, 2011, 119(3), 364-370.

Li JH, Lao XQ, Tillmann HL, Rowell J, Patel K, Thompson A, Suchindran S, Muir AJ, Guyton JR, Gardner SD, McHutchison JG, McCarthy JJ (2010). “Interferon-lambda genotype and low serum low-density lipoprotein cholesterol levels in patients with chronic hepatitis C infection.” Hepatology 2010; 51(6).

Chiba-Falek O, Nichols M, Suchindran S, Guyton J, Ginsburg GS, Barrett-Connor E, McCarthy JJ (2010). “Impact of gene variants on sex-specific regulation of human Scavenger receptor class B type 1 (SR-BI) expression in liver and association with lipid levels in a population-based study.” BMC Med Genet. 2010;11:9.

Suchindran S, Rivedal D, Guyton JR, Milledge T, Gao X, Benjamin A, Rowell J, Ginsburg G, McCarthy JJ (2010). “Genome-wide association study of Lp-PLA(2) activity and mass in the Framingham Heart Study.” Plos Genetics 2010; 6 (4).

McCarthy JJ, Li JH, Thompson A, Suchindran S, Lao XQ, Patel K, Tillmann HL, Muir AJ, McHutchison JG (2010). “Replicated association between an IL28B gene variant and a sustained response to pegylated interferon and ribavirin.” Gastroenterology. 2010;138(7):2307-14.

Everett L, Hansen M, Hannenhalli S (2010). Regulating the regulators: Modulators of transcription factor activity. Methods in Molecular Biology 2010, 674:297-312

Lai A, Fatemi M, Dhasarathy A, Malone C, Sobol E, Geigerman C, Kaye D, Mav D, Shah R, Li L, Wade P (2010) “DNA methylation prevents CTCF-mediated silencing of oncogene BCL6 in B cell lymphomas.” J Exper Med; 207(9):1939-50.

Baniwal S, Khalid O, Gabet Y, Shah R, Purcell D, Mav D, Kohn-Gabet A, Shi Y, Coetzee G, Frenkel B.  (2010) “Runx2 transcriptome of prostate cancer cells:insights into invasiveness amd bone matastasis.” Mol Cancer; 9:258.

Auerbach S, Irwin R, Mav D, Shah R, Vallent M, Boorman G (2010). “Predicting the hepatocarcinogenic potential of alkenylbenzene flavoring agents using toxicogenomics and machine learning.” Toxicol Appl Pharm; 243(3):300-314.

S. Auerbach, R. Thomas, R. Shah, H. Xu, M. Vallant, A. Nyska, J. Dunnick (2010). “Comparative phenotypic assessment of cardiac pathology, physiology and gene expression in C3H/HeJ, C57BL/6J, and B6C3F1/J mice.” Toxicologic Pathology, 38:923-942, Nov 2010.

L. Smith, R. Shah, J. Cidlowski (2010). “Glucocorticoids modulate microRNA expression and processing during lymphocyte apoptosis, Journal of Biological Chemistry.” jbc.M110.162123, Sept. 16, 2010.

W Shi, M Bessarabova, D Dosymbekov, Z Dezso, T Nikolskaya, M Dudoladova, T Serebryiskaya, A Bugrim, R Brennan, R. Shah, J Dopazo, M Chen, Y Deng, T Shi, G Jurman, C Furlanello, R Thomas, C Corton, W Tong, L Shi, and Y Nikolsky (2010). “Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes”. The Pharmacogenomics Journal, 10, pg: 310–323, April 2010.

R. Fannin, M. Russo, T. Oconnell, K. Gerrish, J Winnike, J Macdonald, J Newton, S. Malik, S. Sieber, J. Parker, R. Shah, T. Zhou, P. Watkins and R. Paules (2010). “Acetaminophen dosing of humans results in blood transcriptome and metabolome changes consistent with impaired oxidative phosphorylation.” Hepatology, Jan 2010; pg:227-236.

Heber S, Howard BE (2010). “Genome Rearrangements.” In Pevsner P (Ed.), Bioinformatics for Biologists (p 167-188). Cambridge, UK: Cambridge University Press.

Howard BE, Heber S (2010). “Toward Reliable Isoform Quantification using RNA-Seq Data.”  BMC Bioinformatics 11(Suppl 3):S6.

Nakagawa-Goto K, Chang P-C, Lai C-Y, Hung H-Y, Chen T-H, Wu P-C, Zhu H, Sedykh A, Bastow K, Lee K-H (2010). “Antitumor agents. 280. Multidrug resistance-selective Desmosdumotin B analogues”. Journal of Medicinal Chemistry, 2010, 53, 6699–6705.

Wang C, Meisner M (2010). “Dynamic Data Visualization,” Case Studies in Business, Industry and Government Statistics, vol. 4, no. 1, pp. 9–22, 2010.

Throne P, Cohn R, Mav D, Arbes S, Zeldin D. (2009) “Predictors of endotoxin levels in U.S. housing.” Environ Health Persp; 117(5):763-771.

Suchindran S, Vana AM, Shaffer RA, Alcaraz JE, McCarthy JJ (2009). “Racial differences in the interaction between family history and risk factors associated with diabetes in the National Health and Nutritional Examination Survey, 1999-2004.” Genetics in Medicine 2009; 11(7):542.

Howard BE, Sick B, Heber S (2009). “Unsupervised Assessment of Microarray Data Quality Using a Gaussian Mixture Model.”  BMC Bioinformatics 10:191.

Howard BE, Heber S (2009). “Towards Reliable Isoform Quantification using RNA-Seq Data.”  BIBM 2009, Washington DC, p 130-135.

Howard BE, Sick B, Heber S (2009). “Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression.”  In Mandoiu I, Narasimhan G, Zhang Y (Eds.), Proceedings of the 5th International Symposium on Bioinformatics Research and Applications (ISBRA 2009), Ft. Lauderdale, FL, p 18-27.

Kim J, Zhao S, Howard B, Heber S (2009). “Mining of cis-Regulatory Motifs Associated with Tissue-specific Alternative Splicing.”  In Mandoiu I, Narasimhan G, Zhang Y (Eds.), Proceedings of the 5th International Symposium on Bioinformatics Research and Applications (ISBRA 2009), Ft. Lauderdale, FL, p. 260-271.

Zhu H, Martin T M, Lin Y, Sedykh A, Young M D, Tropsha A (2009). “QSAR Modeling of Rat Acute Toxicity by Oral Exposure”. Chemical Research in Toxicology, 2009, 22, 1913-1921.

Leiss J, Lyden J, Mathews R, Sitzman K, Vanderpuije A, Mav D, Kendram M, Klein C, Humphrey C. (2008) “Blood exposure incidence rates from the North Carolina Study of Home Care and Hospice Nurses.” Am J Indust Med; 52(2):99-104.

Berman R, Pessah I, Mouton P, Mav D, Harry J.  (2008) “Low-level neonatal Thimerosal exposure: Further evaluation of altered neurotoxic potential in SJL Mice.” Toxicol Sci; 101(2):294-309.

Nielsen DM, Suchindran S, and Smith CP (2008).  “Does strong linkage disequilibrium guarantee redundant association results.” Genetic Epidemiology 2008; 32 (6): 546-52.

Chaganty N, Mav D. (2007) “Estimation methods for analyzing longitudinal data occurring in biomedical research.” C5777 Computational Methods in Biomedical Research, Chapman & Hall/CRC, NY, 371-400.

Barboriak D, DesJardins A, Rich J, Phadke DP, Friedman H, Vredenburgh J (2007). “Treatment of Recurrent Glioblastoma Multiforme with Bevacizimab and Irinotecan Leads to Rapid Decreases in Tumor Plasma Volume and Ktrans.” Radiological Society of North America Scientific Assembly and Annual Meeting.

Howard BE, Perera I, Im YJ, Winter-Sederoff H, Sick B, and Heber S. (2007). “Quality Assessment of Affymetrix GeneChip Data using the EM Algorithm and a Naive Bayes Classifier.”  In  Yang JY, Yang MQ, Zhu MM, Zhang Y, Arabnia HR, et al. (Eds.), Proceedings of the IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE 2007), Cambridge, MA, p. 232-237.

Barboriak D, Phadke DP (2007). “Dynamic Susceptibility Contrast MR Analysis Software for Evaluation of Perfusion Parameters in Patients with Brain Tumors.”, Electronic exhibit, American Society of Neuroradiology.

G. Muse, D. Gilchrist, S. Nechaev, R. Shah, J. Parker, S. Grissom, J. Zeitlinger and K. Adelman (2007). “RNA polymerase is poised for development across the genome.” Nature Genetics, Dec 2007 9(12):1507-11.

Sedykh A, Klopman G (2007).” Data analysis and alternative modeling of MITI-I aerobic biodegradation”. SAR & QSAR in Environmental Research, 2007, 18(7), 693-709.

Frahm JL, Howard BE, Heber S, Muddiman DC (2006). “Accessible Proteomics Space and its Implications for Peak Capacity for Zero-, One- and Two- Dimensional Separations Coupled with FT-ICR and TOF Mass Spectrometry.” Journal of Mass Spectrometry, 41:3, 281-288.

Suchindran S (2006).  “An introduction to bioinformatics and its relationship to data mining.” Biostatistical Aspects of Health and Population. 2006.

Everett L, Wang LS, Hannenhalli S (2006). “Dense subgraph computation via stochastic search: application to detect transcriptional modules”. Bioinformatics 2006, 22(14):e117-123

Sedykh A, Klopman G (2006). “A structural analogue approach to the prediction of LogP”. Journal of Chemical Information and Modeling, 2006, 46 (4): 1598-1603.

Zamorano R, Suchindran S, Gainer JV (2005).  “The 3′-untranslated region of the type 2 bradykinin receptor is a potent regulator of gene expression.”  Am J Physiol Renal Physiol 2005; 290(2):456-464.

Zhu H, Sedykh A, Chakravarti S K, and Klopman G (2005). “A new group contribution approach to the calculation of LogP”. Current Computer-Aided Molecular Design, 2005, 1: 3-9.

Iannone, M.A., Simmons, C.A., Kadwell, S.H., Svoboda, D.L., Vanderwall, D.E., Deng, S.-J., Consler, T.G., Shearin, J., Gray, J.G, and Pearce, K.H (2004). “Correlation between in Vitro Peptide Binding Profiles and Cellular Activities for Estrogen Receptor-Modulating Compounds.” Mol. Endocrinol., 18: 1064-1081.

Boros E, Everett L. (2004) “Optimal protein encoding. DIMACS Technical Report”, DTR 2004-55, November 2004.

W. Pendergraft, G. Preston, R. Shah, A. Tropsha, C. Carter, J. Jennette and R. Falk (2004). “Autoimmunity is triggered by cPR-3(105-201), a protein complementary to human autoantigen proteinase-3.” Nature Medicine, 2004 Jan; 10(1):72-79.

S. Edavettal, K. Carrick, R. Shah, L. Pederson, A. Tropsha, R. Marshall Pope and J. Liu. (2004). “A conformational change in heparan sulfate 3-O-sulfotransferase-1 is induced by binding to heparan sulfate.” Biochemistry, 2004; 43(16):4680-4688.

J. Huan, W. Wang, A. Washington, J. Prins, R. Shah, and A. Tropsha (2004). “Accurate classification of protein structural families using coherent subgraph analysis, Pacific Symposium on Biocomputing.” 2004; 9:411-422.

Mav D and Chaganty N.  (2004) “Bivariate models for identifying differentially expressed genes in microarray experiments.” J Stat Theory Appl ; 3(2):111-124.

Howard B, Sheppard J (2004). “The Royal Road Not Taken: A Re-examination of the Reasons for GA Failure on R1.”  In Deb, K., et al. (Eds.), Genetic and Evolutionary Computation – GECCO 2004, (pp 1208-1219), Seattle, WA: Springer.

Klopman G, Sedykh A (2002). “An MCASE approach to the search of a cure for Parkinson’s disease”. BMC Pharmacology 2002, 2.

Kalpakis K, Gada (Phadke) D, Puttagunta V (2001). “Distance Measures for Effective Clustering of ARIMA Time-Series”, Proceedings of the IEEE International Conference on Data Mining.

Sedykh A, Saiakhov R, Klopman G. META V (2001). “A model of photodegradation for the prediction of photoproducts of chemicals under natural-like conditions”. Chemosphere 2001, 45: 971-981.

S. Iyer, R. Shah, A. Sharma, D. Jendrossek and A. Desai (2000). “Purification of Aspergillus fumigatus (Pdf1) Poly (a-hydroxybutyrate) (PHB) Depolymerase Using a New, Single-Step Substrate Affinity Chromatography Method: Characterization of the PHB Depolymerase Exhibiting Novel Self-Aggregation Behavior.” Journal of Polymers and the Environment, 2000 Oct; 8(4):197-203.

Vaidya V, Deshpande V, Gada (Phadke) D, Shirole B (1999). “Statistical approach to feature extraction for numeral recognition from degraded documents”, Proceedings of the Fifth International Conference on Document Analysis and Recognition.

Saiakhov R, Sedykh A, Galkin V, Cherkasov R (1999). “Basicity and reactivity of alpha-aminophosphonates”. Theoretical investigation. Phosphorus, Sulfur, and Silicon and the related elements 1999, 147, 363-363.

Saiakhov R, Sedykh A, Galkin V, Cherkasov R (1999). “New applications of the frontal steric effect model: IV. Optimization of molecular structure”. Russian Journal of Organic Chemistry 1999, 35(5): 666-669.

Raleigh JA, Chou SC, Tables L, Suchindran S, Varia MA, Horsman MR (1998). “Relationship of hypoxia to metallothionein expression in murine tumors.”  Int J Radiat Oncol Biol Phy 1998; 42:727-730.

Totowa, NJ, Svoboda, D.L. and J.-M.V. Vos (1998). “Postreplication Repair/Replicative Bypass Assay.” In DNA Repair Protocols, D.S. Henderson, Editor. The Humana Press, Inc.

Svoboda, D.L., Briley, L.P., and Vos, J.-M.H (1998). “Defective Bypass Replication of a Leading Strand Cyclobutane Thymine Dimer in Xeroderma Pigmentosum Variant Cell Extracts.” Cancer Res. 58: 2445-2448.

Thomas, D.C., Svoboda, D.L., Vos, J.-M.H., and Kunkel, T. A. (1996). “Strand Specificity of Mutagenic Bypass Replication of DNA Containing Psoralen Monoadducts in a Human Cell Extract.” Mol. Cell. Biol., 16(5), 2537-2544.

Svoboda, D.L., and Vos, J.-M.H. (1995). “Differential Replication of a Single, UV-Induced Lesion in the Leading or Lagging Strand by a Human Cell Extract:  Fork Uncoupling or Gap Formation.” Proc. Natl. Acad. Sci., USA., 1995, 92, 11975-11979.

Svoboda, D.L., Smith, C.A., Taylor, J.-S., and Sancar, A. J (1993). “Effect of Sequence, Adduct Type, and Opposing Lesions on the Binding and Repair of Ultraviolet Photodamage by DNA Photolyase and (A)BC Excinuclease.” Biol. Chem., 268, 1069410700.

Svoboda, D.L., Taylor, J.-S., Hearst, J.E., and Sancar, A. J. (1993). “DNA Repair by Eukaryotic Nucleotide Excision Nuclease:  Removal of Thymine Dimer and Psoralen Monoadduct by HeLa Cell Free Extract and of Thymine Dimer by Xenopus Laevis Oocytes.” Biol. Chem., 268, 1931-1936.

Huang, J.C., Svoboda, D.L., Reardon, J.T., and Sancar, A (1992). “Human Nucleotide Excision Nuclease Removes Thymine Dimers from DNA by Incision of the 22nd Phosphodiester Bond 5’ and the 6th Phosphodiester Bond 3’ to the Photodimer.” Proc. Natl. Acad. Sci., USA, 89, 3664-3668.

Taylor, J.-S., Garrett, D.S., Brockie, I.R., Svoboda, D.L., and Telser, J (1990). “1H NMR Assignment and Melting Temperature Study of Cis,Syn- and Trans,SynThymine Dimer Containing Duplexes of d(CGTATTATGC)•d(GCATAATACG).” Biochemistry, 29, 8858-8866.

Gaspar, P.P., Boo, B.H., and Svoboda D.L. (1987). “Evidence from a Hot Atom Experiment for the Silylsilylene to Disilene Rearrangement:  SiH3SiH: –> SiH2 =SiH2.” J. Phys. Chem., 91, 5011-5013.

Gaspar, P.P., Berowitz, D.M., Strongin, D.R., Svoboda, D.L., Tuchler, M.B., Ferrieri, R.A., and Wolf A.P. (1986). “Reactions of Recoiling 11C Atoms with Toluene.” J. Phys. Chem., 90, 4691-46