| Year |
Citation |
Score |
| 2021 |
Li J, Bushel PR, Lin L, Day K, Wang T, DeMayo FJ, Wu SP, Li JL. Structural Equation Modeling of In silico Perturbations. Frontiers in Genetics. 12: 727532. PMID 34899830 DOI: 10.3389/fgene.2021.727532 |
0.314 |
|
| 2020 |
Sinha BK, Tokar EJ, Bushel PR. Elucidation of Mechanisms of Topotecan-Induced Cell Death in Human Breast MCF-7 Cancer Cells by Gene Expression Analysis. Frontiers in Genetics. 11: 775. PMID 32765594 DOI: 10.3389/Fgene.2020.00775 |
0.404 |
|
| 2020 |
Bushel PR, Ferguson SS, Ramaiahgari SC, Paules RS, Auerbach SS. Comparison of Normalization Methods for Analysis of TempO-Seq Targeted RNA Sequencing Data. Frontiers in Genetics. 11: 594. PMID 32655620 DOI: 10.3389/Fgene.2020.00594 |
0.381 |
|
| 2019 |
Kinyamu HK, Bennett BD, Bushel PR, Archer TK. Proteasome inhibition creates a chromatin landscape favorable to RNA Pol II processivity. The Journal of Biological Chemistry. PMID 31806706 DOI: 10.1074/Jbc.Ra119.011174 |
0.402 |
|
| 2019 |
Ramaiahgari SC, Auerbach SS, Saddler TO, Rice JR, Dunlap PE, Sipes NS, DeVito MJ, Shah RR, Bushel PR, Merrick BA, Paules RS, Ferguson SS. The Power of Resolution: Contextualized Understanding of Biological Responses to Liver Injury Chemicals using High-throughput Transcriptomics and Benchmark Concentration Modeling. Toxicological Sciences : An Official Journal of the Society of Toxicology. PMID 30850835 DOI: 10.1093/Toxsci/Kfz065 |
0.336 |
|
| 2018 |
Bushel PR, Paules RS, Auerbach SS. A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples. Frontiers in Genetics. 9: 485. PMID 30420870 DOI: 10.3389/Fgene.2018.00485 |
0.425 |
|
| 2018 |
Nguyen TT, Grimm SA, Bushel PR, Li J, Li Y, Bennett BD, Lavender CA, Ward JM, Fargo DC, Anderson CW, Li L, Resnick MA, Menendez D. Revealing a human p53 universe. Nucleic Acids Research. PMID 30107566 DOI: 10.1093/Nar/Gky720 |
0.397 |
|
| 2018 |
Lozoya OA, Martinez-Reyes I, Wang T, Grenet D, Bushel P, Li J, Chandel N, Woychik RP, Santos JH. Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation. Plos Biology. 16: e2005707. PMID 29668680 DOI: 10.1371/Journal.Pbio.2005707 |
0.31 |
|
| 2018 |
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. A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics. Plos One. 13: e0191105. PMID 29462216 DOI: 10.1371/Journal.Pone.0191105 |
0.475 |
|
| 2018 |
Santos JH, Lozoya OA, Martinez-Reyes I, Wang T, Grenet D, Bushel P, Li J, Chandel N, Woychik RP. Mitochondria impacts DNA methylation and gene expression through modulation of methionine and polyamine metabolism Biochimica Et Biophysica Acta (Bba) - Bioenergetics. 1859: e60. DOI: 10.1016/J.Bbabio.2018.09.179 |
0.357 |
|
| 2017 |
Funderburk KM, Auerbach SS, Bushel PR. Crosstalk between Receptor and Non-receptor Mediated Chemical Modes of Action in Rat Livers Converges through a Dysregulated Gene Expression Network at Tumor Suppressor Tp53. Frontiers in Genetics. 8: 157. PMID 29114260 DOI: 10.3389/Fgene.2017.00157 |
0.415 |
|
| 2017 |
Bennett BD, Bushel PR. goSTAG: gene ontology subtrees to tag and annotate genes within a set. Source Code For Biology and Medicine. 12: 6. PMID 28413437 DOI: 10.1186/S13029-017-0066-1 |
0.427 |
|
| 2017 |
Osgood RS, Upham BL, Bushel PR, Velmurugan K, Xiong KN, Bauer AK. Secondhand Smoke-Prevalent Polycyclic Aromatic Hydrocarbon Binary Mixture-Induced Specific Mitogenic and Pro-inflammatory Cell Signaling Events in Lung Epithelial Cells. Toxicological Sciences : An Official Journal of the Society of Toxicology. PMID 28329830 DOI: 10.1093/Toxsci/Kfx027 |
0.301 |
|
| 2016 |
Kim SH, Trinh AT, Larsen MC, Mastrocola AS, Jefcoate CR, Bushel PR, Tibbetts RS. Tunable regulation of CREB DNA binding activity couples genotoxic stress response and metabolism. Nucleic Acids Research. PMID 27431323 DOI: 10.1093/Nar/Gkw643 |
0.344 |
|
| 2016 |
Ciencewicki JM, Verhein KC, Gerrish KE, McCaw ZR, Li J, Bushel PR, Kleeberger SR. Effects of mannose-binding lectin on pulmonary gene expression and innate immune inflammatory response to ozone. American Journal of Physiology. Lung Cellular and Molecular Physiology. ajplung.00205.2015. PMID 27106289 DOI: 10.1152/Ajplung.00205.2015 |
0.352 |
|
| 2016 |
Li J, Bushel PR. EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data. Bmc Genomics. 17: 255. PMID 27004791 DOI: 10.1186/S12864-016-2584-7 |
0.361 |
|
| 2016 |
Bushel PR, Fannin RD, Gerrish K, Watkins PB, Paules RS. Blood gene expression profiling of an early acetaminophen response. The Pharmacogenomics Journal. PMID 26927286 DOI: 10.1038/Tpj.2016.8 |
0.435 |
|
| 2015 |
Fannin RD, Gerrish K, Sieber SO, Bushel PR, Watkins PB, Paules RS. Blood transcript immune signatures distinguish a subset of people with elevated serum ALT from others given acetaminophen. Clinical Pharmacology and Therapeutics. PMID 26690555 DOI: 10.1002/Cpt.328 |
0.347 |
|
| 2015 |
Yang J, Bennett BD, Luo S, Inoue K, Grimm SA, Schroth GP, Bushel PR, Kinyamu HK, Archer TK. LIN28A Modulates Splicing and Gene Expression Programs in Breast Cancer Cells. Molecular and Cellular Biology. 35: 3225-43. PMID 26149387 DOI: 10.1128/Mcb.00426-15 |
0.362 |
|
| 2015 |
Bourdon-Lacombe JA, Moffat ID, Deveau M, Husain M, Auerbach S, Krewski D, Thomas RS, Bushel PR, Williams A, Yauk CL. Technical guide for applications of gene expression profiling in human health risk assessment of environmental chemicals. Regulatory Toxicology and Pharmacology : Rtp. 72: 292-309. PMID 25944780 DOI: 10.1016/J.Yrtph.2015.04.010 |
0.409 |
|
| 2015 |
Davis M, Li J, Knight E, Eldridge SR, Daniels KK, Bushel PR. Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity. Frontiers in Genetics. 6: 14. PMID 25729387 DOI: 10.3389/Fgene.2015.00014 |
0.306 |
|
| 2015 |
Kinyamu HK, Yang J, Bennett B, Grimm S, Bushel P, Archer T. Abstract 1972: LIN28 gene targets are key mediators of breast cancer disease processes Cancer Research. 75: 1972-1972. DOI: 10.1158/1538-7445.Am2015-1972 |
0.348 |
|
| 2014 |
Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, Fang H, Hong H, Shen J, Su Z, Meehan J, Li X, Yang L, Li H, ?abaj PP, et al. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nature Biotechnology. 32: 926-32. PMID 25150839 DOI: 10.1038/Nbt.3001 |
0.4 |
|
| 2013 |
Williams-DeVane CR, Reif DM, Hubal EC, Bushel PR, Hudgens EE, Gallagher JE, Edwards SW. Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes. Bmc Systems Biology. 7: 119. PMID 24188919 DOI: 10.1186/1752-0509-7-119 |
0.341 |
|
| 2013 |
Huang L, Zhang HH, Zeng ZB, Bushel PR. Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification. Cancer Informatics. 12: 143-53. PMID 23966761 DOI: 10.4137/Cin.S10212 |
0.317 |
|
| 2013 |
Zhang L, Simpson DA, Innes CL, Chou J, Bushel PR, Paules RS, Kaufmann WK, Zhou T. Gene expression signatures but not cell cycle checkpoint functions distinguish AT carriers from normal individuals. Physiological Genomics. 45: 907-16. PMID 23943852 DOI: 10.1152/Physiolgenomics.00064.2013 |
0.401 |
|
| 2013 |
Lu J, Bushel PR. Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling. Gene. 527: 616-23. PMID 23845781 DOI: 10.1016/J.Gene.2013.06.052 |
0.384 |
|
| 2013 |
Davis BJ, Risinger JI, Chandramouli GV, Bushel PR, Baird DD, Peddada SD. Gene expression in uterine leiomyoma from tumors likely to be growing (from black women over 35) and tumors likely to be non-growing (from white women over 35). Plos One. 8: e63909. PMID 23785396 DOI: 10.1371/Journal.Pone.0063909 |
0.325 |
|
| 2012 |
Arana ME, Kerns RT, Wharey L, Gerrish KE, Bushel PR, Kunkel TA. Transcriptional responses to loss of RNase H2 in Saccharomyces cerevisiae. Dna Repair. 11: 933-41. PMID 23079308 DOI: 10.1016/J.Dnarep.2012.09.006 |
0.397 |
|
| 2012 |
Zhang L, Bushel PR, Chou J, Zhou T, Watkins PB. Identification of Identical Transcript Changes in Liver and Whole Blood during Acetaminophen Toxicity. Frontiers in Genetics. 3: 162. PMID 22973295 DOI: 10.3389/Fgene.2012.00162 |
0.416 |
|
| 2012 |
Bushel PR, McGovern R, Liu L, Hofmann O, Huda A, Lu J, Hide W, Lin X. Population differences in transcript-regulator expression quantitative trait loci. Plos One. 7: e34286. PMID 22479588 DOI: 10.1371/Journal.Pone.0034286 |
0.344 |
|
| 2012 |
Kerns RT, Bushel PR. The impact of classification of interest on predictive toxicogenomics. Frontiers in Genetics. 3: 14. PMID 22347226 DOI: 10.3389/Fgene.2012.00014 |
0.406 |
|
| 2012 |
Corton JC, Bushel PR, Fostel J, O'Lone RB. Sources of variance in baseline gene expression in the rodent liver. Mutation Research. 746: 104-12. PMID 22230429 DOI: 10.1016/J.Mrgentox.2011.12.017 |
0.446 |
|
| 2011 |
Chang C, Wang J, Zhao C, Fostel J, Tong W, Bushel PR, Deng Y, Pusztai L, Symmans WF, Shi T. Maximizing biomarker discovery by minimizing gene signatures. Bmc Genomics. 12: S6. PMID 22369133 DOI: 10.1186/1471-2164-12-S5-S6 |
0.411 |
|
| 2011 |
Hoenerhoff MJ, Pandiri AR, Lahousse SA, Hong HH, Ton TV, Masinde T, Auerbach SS, Gerrish K, Bushel PR, Shockley KR, Peddada SD, Sills RC. Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: similarities in the molecular landscape with human liver cancer. Toxicologic Pathology. 39: 678-99. PMID 21571946 DOI: 10.1177/0192623311407213 |
0.34 |
|
| 2011 |
Lu J, Kerns RT, Peddada SD, Bushel PR. Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays. Nucleic Acids Research. 39: e86. PMID 21525126 DOI: 10.1093/Nar/Gkr241 |
0.369 |
|
| 2010 |
Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, ... ... Bushel PR, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology. 28: 827-38. PMID 20676074 DOI: 10.1038/Nbt.1665 |
0.369 |
|
| 2010 |
Luo J, Schumacher M, Scherer A, Sanoudou D, Megherbi D, Davison T, Shi T, Tong W, Shi L, Hong H, Zhao C, Elloumi F, Shi W, Thomas R, Lin S, ... ... Bushel P, et al. A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data Pharmacogenomics Journal. 10: 278-291. PMID 20676067 DOI: 10.1038/Tpj.2010.57 |
0.334 |
|
| 2010 |
Fan X, Lobenhofer EK, Chen M, Shi W, Huang J, Luo J, Zhang J, Walker SJ, Chu TM, Li L, Wolfinger R, Bao W, Paules RS, Bushel PR, Li J, et al. Consistency of predictive signature genes and classifiers generated using different microarray platforms. The Pharmacogenomics Journal. 10: 247-57. PMID 20676064 DOI: 10.1038/tpj.2010.34 |
0.303 |
|
| 2009 |
Chou JW, Bushel PR. Discernment of possible mechanisms of hepatotoxicity via biological processes over-represented by co-expressed genes. Bmc Genomics. 10: 272. PMID 19538742 DOI: 10.1186/1471-2164-10-272 |
0.438 |
|
| 2009 |
Bushel PR. Clustering of gene expression data and end-point measurements by simulated annealing. Journal of Bioinformatics and Computational Biology. 7: 193-215. PMID 19226667 DOI: 10.1142/S021972000900400X |
0.322 |
|
| 2008 |
Lobenhofer EK, Auman JT, Blackshear PE, Boorman GA, Bushel PR, Cunningham ML, Fostel JM, Gerrish K, Heinloth AN, Irwin RD, Malarkey DE, Merrick BA, Sieber SO, Tucker CJ, Ward SM, et al. Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype. Genome Biology. 9: R100. PMID 18570634 DOI: 10.1186/Gb-2008-9-6-R100 |
0.383 |
|
| 2008 |
Huang L, Heinloth AN, Zeng ZB, Paules RS, Bushel PR. Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants. Bmc Genomics. 9: 288. PMID 18558008 DOI: 10.1186/1471-2164-9-288 |
0.387 |
|
| 2008 |
Boedigheimer MJ, Wolfinger RD, Bass MB, Bushel PR, Chou JW, Cooper M, Corton JC, Fostel J, Hester S, Lee JS, Liu F, Liu J, Qian HR, Quackenbush J, Pettit S, et al. Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories. Bmc Genomics. 9: 285. PMID 18549499 DOI: 10.1186/1471-2164-9-285 |
0.428 |
|
| 2008 |
Jin YH, Dunlap PE, McBride SJ, Al-Refai H, Bushel PR, Freedman JH. Global transcriptome and deletome profiles of yeast exposed to transition metals. Plos Genetics. 4: e1000053. PMID 18437200 DOI: 10.1371/Journal.Pgen.1000053 |
0.32 |
|
| 2008 |
Waters M, Stasiewicz S, Merrick BA, Tomer K, Bushel P, Paules R, Stegman N, Nehls G, Yost KJ, Johnson CH, Gustafson SF, Xirasagar S, Xiao N, Huang CC, Boyer P, et al. CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. Nucleic Acids Research. 36: D892-900. PMID 17962311 DOI: 10.1093/Nar/Gkm755 |
0.37 |
|
| 2007 |
Bushel PR, Heinloth AN, Li J, Huang L, Chou JW, Boorman GA, Malarkey DE, Houle CD, Ward SM, Wilson RE, Fannin RD, Russo MW, Watkins PB, Tennant RW, Paules RS. Blood gene expression signatures predict exposure levels. Proceedings of the National Academy of Sciences of the United States of America. 104: 18211-6. PMID 17984051 DOI: 10.1073/Pnas.0706987104 |
0.426 |
|
| 2007 |
Chou JW, Zhou T, Kaufmann WK, Paules RS, Bushel PR. Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes. Bmc Bioinformatics. 8: 427. PMID 17980031 DOI: 10.1186/1471-2105-8-427 |
0.459 |
|
| 2007 |
Zhou T, Chou J, Zhou Y, Simpson DA, Cao F, Bushel PR, Paules RS, Kaufmann WK. Ataxia telangiectasia-mutated dependent DNA damage checkpoint functions regulate gene expression in human fibroblasts. Molecular Cancer Research : McR. 5: 813-22. PMID 17699107 DOI: 10.1158/1541-7786.Mcr-07-0104 |
0.434 |
|
| 2007 |
Fostel JM, Burgoon L, Zwickl C, Lord P, Corton JC, Bushel PR, Cunningham M, Fan L, Edwards SW, Hester S, Stevens J, Tong W, Waters M, Yang C, Tennant R. Toward a checklist for exchange and interpretation of data from a toxicology study. Toxicological Sciences : An Official Journal of the Society of Toxicology. 99: 26-34. PMID 17442663 DOI: 10.1093/Toxsci/Kfm090 |
0.336 |
|
| 2007 |
Bushel PR, Wolfinger RD, Gibson G. Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes. Bmc Systems Biology. 1: 15. PMID 17408499 DOI: 10.1186/1752-0509-1-15 |
0.508 |
|
| 2007 |
Zhou T, Chou J, Mullen TE, Elkon R, Zhou Y, Simpson DA, Bushel PR, Paules RS, Lobenhofer EK, Hurban P, Kaufmann WK. Identification of primary transcriptional regulation of cell cycle-regulated genes upon DNA damage. Cell Cycle (Georgetown, Tex.). 6: 972-81. PMID 17404513 DOI: 10.4161/Cc.6.8.4106 |
0.431 |
|
| 2006 |
Zhou T, Chou JW, Simpson DA, Zhou Y, Mullen TE, Medeiros M, Bushel PR, Paules RS, Yang X, Hurban P, Lobenhofer EK, Kaufmann WK. Profiles of global gene expression in ionizing-radiation-damaged human diploid fibroblasts reveal synchronization behind the G1 checkpoint in a G0-like state of quiescence. Environmental Health Perspectives. 114: 553-9. PMID 16581545 DOI: 10.1289/Ehp.8026 |
0.406 |
|
| 2006 |
Innes CL, Heinloth AN, Flores KG, Sieber SO, Deming PB, Bushel PR, Kaufmann WK, Paules RS. ATM requirement in gene expression responses to ionizing radiation in human lymphoblasts and fibroblasts. Molecular Cancer Research : McR. 4: 197-207. PMID 16547157 DOI: 10.1158/1541-7786.Mcr-05-0154 |
0.385 |
|
| 2006 |
Xirasagar S, Gustafson SF, Huang CC, Pan Q, Fostel J, Boyer P, Merrick BA, Tomer KB, Chan DD, Yost KJ, Choi D, Xiao N, Stasiewicz S, Bushel P, Waters MD. Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application. Bioinformatics (Oxford, England). 22: 874-82. PMID 16410321 DOI: 10.1093/Bioinformatics/Btk045 |
0.367 |
|
| 2006 |
Leung E, Bushel PR. PAGE: phase-shifted analysis of gene expression. Bioinformatics (Oxford, England). 22: 367-8. PMID 16322047 DOI: 10.1093/Bioinformatics/Bti778 |
0.436 |
|
| 2005 |
Fostel J, Choi D, Zwickl C, Morrison N, Rashid A, Hasan A, Bao W, Richard A, Tong W, Bushel PR, Brown R, Bruno M, Cunningham ML, Dix D, Eastin W, et al. Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data. Toxicological Sciences : An Official Journal of the Society of Toxicology. 88: 585-601. PMID 16150882 DOI: 10.1093/Toxsci/Kfi315 |
0.316 |
|
| 2005 |
Chou JW, Paules RS, Bushel PR. Systematic variation normalization in microarray data to get gene expression comparison unbiased. Journal of Bioinformatics and Computational Biology. 3: 225-41. PMID 15852502 DOI: 10.1142/S0219720005001028 |
0.358 |
|
| 2005 |
Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, et al. Standardizing global gene expression analysis between laboratories and across platforms. Nature Methods. 2: 351-6. PMID 15846362 DOI: 10.1038/Nmeth754 |
0.397 |
|
| 2005 |
Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, et al. Addendum: Standardizing global gene expression analysis between laboratories and across platforms Nature Methods. 2: 477-477. DOI: 10.1038/nmeth0605-477a |
0.327 |
|
| 2004 |
Hamadeh HK, Jayadev S, Gaillard ET, Huang Q, Stoll R, Blanchard K, Chou J, Tucker CJ, Collins J, Maronpot R, Bushel P, Afshari CA. Integration of clinical and gene expression endpoints to explore furan-mediated hepatotoxicity. Mutation Research. 549: 169-83. PMID 15120969 DOI: 10.1016/J.Mrfmmm.2003.12.021 |
0.434 |
|
| 2004 |
Mattes WB, Pettit SD, Sansone SA, Bushel PR, Waters MD. Database development in toxicogenomics: issues and efforts. Environmental Health Perspectives. 112: 495-505. PMID 15033600 DOI: 10.1289/Ehp.6697 |
0.372 |
|
| 2003 |
Heinloth AN, Shackelford RE, Innes CL, Bennett L, Li L, Amin RP, Sieber SO, Flores KG, Bushel PR, Paules RS. ATM-dependent and -independent gene expression changes in response to oxidative stress, gamma irradiation, and UV irradiation. Radiation Research. 160: 273-90. PMID 12926986 DOI: 10.1667/Rr3047 |
0.323 |
|
| 2003 |
Heinloth AN, Shackelford RE, Innes CL, Bennett L, Li L, Amin RP, Sieber SO, Flores KG, Bushel PR, Paules RS. Identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiation. Molecular Carcinogenesis. 37: 65-82. PMID 12766906 DOI: 10.1002/Mc.10122 |
0.383 |
|
| 2003 |
Waters M, Boorman G, Bushel P, Cunningham M, Irwin R, Merrick A, Olden K, Paules R, Selkirk J, Stasiewicz S, Weis B, Van Houten B, Walker N, Tennant R. Systems toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base. Ehp Toxicogenomics : Journal of the National Institute of Environmental Health Sciences. 111: 15-28. PMID 12735106 |
0.343 |
|
| 2003 |
Steenbergen C, Afshari CA, Petranka JG, Collins J, Martin K, Bennett L, Haugen A, Bushel P, Murphy E. Alterations in apoptotic signaling in human idiopathic cardiomyopathic hearts in failure. American Journal of Physiology. Heart and Circulatory Physiology. 284: H268-76. PMID 12388275 DOI: 10.1152/Ajpheart.00707.2002 |
0.321 |
|
| 2002 |
Bushel PR, Hamadeh HK, Bennett L, Green J, Ableson A, Misener S, Afshari CA, Paules RS. Computational selection of distinct class- and subclass-specific gene expression signatures. Journal of Biomedical Informatics. 35: 160-70. PMID 12669979 DOI: 10.1016/S1532-0464(02)00525-7 |
0.473 |
|
| 2002 |
Amin RP, Hamadeh HK, Bushel PR, Bennett L, Afshari CA, Paules RS. Genomic interrogation of mechanism(s) underlying cellular responses to toxicants. Toxicology. 181: 555-63. PMID 12505366 DOI: 10.1016/S0300-483X(02)00481-X |
0.413 |
|
| 2002 |
Martinez JM, Afshari CA, Bushel PR, Masuda A, Takahashi T, Walker NJ. Differential toxicogenomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin in malignant and nonmalignant human airway epithelial cells. Toxicological Sciences : An Official Journal of the Society of Toxicology. 69: 409-23. PMID 12377990 DOI: 10.1093/Toxsci/69.2.409 |
0.431 |
|
| 2002 |
Hamadeh HK, Knight BL, Haugen AC, Sieber S, Amin RP, Bushel PR, Stoll R, Blanchard K, Jayadev S, Tennant RW, Cunningham ML, Afshari CA, Paules RS. Methapyrilene toxicity: anchorage of pathologic observations to gene expression alterations. Toxicologic Pathology. 30: 470-82. PMID 12187938 DOI: 10.1080/01926230290105712 |
0.455 |
|
| 2002 |
Lobenhofer EK, Bennett L, Cable PL, Li L, Bushel PR, Afshari CA. Regulation of DNA replication fork genes by 17beta-estradiol. Molecular Endocrinology (Baltimore, Md.). 16: 1215-29. PMID 12040010 DOI: 10.1210/Mend.16.6.0858 |
0.403 |
|
| 2002 |
Hamadeh HK, Bushel PR, Jayadev S, DiSorbo O, Bennett L, Li L, Tennant R, Stoll R, Barrett JC, Paules RS, Blanchard K, Afshari CA. Prediction of compound signature using high density gene expression profiling. Toxicological Sciences : An Official Journal of the Society of Toxicology. 67: 232-40. PMID 12011482 DOI: 10.1093/Toxsci/67.2.232 |
0.458 |
|
| 2002 |
Hamadeh HK, Bushel PR, Jayadev S, Martin K, DiSorbo O, Sieber S, Bennett L, Tennant R, Stoll R, Barrett JC, Blanchard K, Paules RS, Afshari CA. Gene expression analysis reveals chemical-specific profiles. Toxicological Sciences : An Official Journal of the Society of Toxicology. 67: 219-31. PMID 12011481 DOI: 10.1093/Toxsci/67.2.219 |
0.464 |
|
| 2002 |
Oh JS, Kucab JE, Bushel PR, Martin K, Bennett L, Collins J, DiAugustine RP, Barrett JC, Afshari CA, Dunn SE. Insulin-like growth factor-1 inscribes a gene expression profile for angiogenic factors and cancer progression in breast epithelial cells. Neoplasia (New York, N.Y.). 4: 204-17. PMID 11988840 DOI: 10.1038/Sj.Neo.7900229 |
0.395 |
|
| 2002 |
Hamadeh HK, Bushel P, Paules R, Afshari CA. Discovery in toxicology: mediation by gene expression array technology. Journal of Biochemical and Molecular Toxicology. 15: 231-42. PMID 11835620 DOI: 10.1002/Jbt.10006 |
0.356 |
|
| 2001 |
Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, Afshari C, Paules RS. Assessing gene significance from cDNA microarray expression data via mixed models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 8: 625-37. PMID 11747616 DOI: 10.1089/106652701753307520 |
0.577 |
|
| 2001 |
Lobenhofer EK, Bushel PR, Afshari CA, Hamadeh HK. Progress in the application of DNA microarrays. Environmental Health Perspectives. 109: 881-91. PMID 11673116 DOI: 10.1289/Ehp.01109881 |
0.33 |
|
| 2001 |
Bushel PR, Hamadeh H, Bennett L, Sieber S, Martin K, Nuwaysir EF, Johnson K, Reynolds K, Paules RS, Afshari CA. MAPS: a microarray project system for gene expression experiment information and data validation. Bioinformatics (Oxford, England). 17: 564-5. PMID 11395436 DOI: 10.1093/Bioinformatics/17.6.564 |
0.395 |
|
| 2001 |
Shcherbakova PV, Hall MC, Lewis MS, Bennett SE, Martin KJ, Bushel PR, Afshari CA, Kunkel TA. Inactivation of DNA mismatch repair by increased expression of yeast MLH1. Molecular and Cellular Biology. 21: 940-51. PMID 11154280 DOI: 10.1128/Mcb.21.3.940-951.2001 |
0.356 |
|
| 2001 |
Annab L, Kouprina N, Larionov V, Vojta P, Katoh M, Bushel P, Martin K, Oshimura M, Barrett JC, Afshari C. Combination of functional genomics approaches and microarray analyses to define candidate senescence genes Nature Genetics. 27: 37-37. DOI: 10.1038/86968 |
0.381 |
|
| 1995 |
Simonson MS, Walsh K, Kumar CC, Bushel P, Herman WH. Two proximal CArG elements regulate SM α-actin promoter, a genetic marker of activated phenotype of mesangial cells American Journal of Physiology - Renal Fluid and Electrolyte Physiology. 268. PMID 7733334 DOI: 10.1152/Ajprenal.1995.268.4.F760 |
0.301 |
|
| 1990 |
Wu J, Grindlay GJ, Bushel P, Mendelsohn L, Allan M. Negative regulation of the human epsilon-globin gene by transcriptional interference: role of an Alu repetitive element. Molecular and Cellular Biology. 10: 1209-16. PMID 2304465 DOI: 10.1128/Mcb.10.3.1209 |
0.4 |
|
| 1990 |
Bushel P, Rego K, Mendelsohn L, Allan M. Correlation between patterns of DNase I-hypersensitive sites and upstream promoter activity of the human epsilon-globin gene at different stages of erythroid development. Molecular and Cellular Biology. 10: 1199-208. PMID 2304464 DOI: 10.1128/Mcb.10.3.1199 |
0.342 |
|
| 1990 |
Lowndes NF, Bushel P, Mendelsohn L, Wu J, Yen MY, Allan M. A short, highly repetitive element in intron -1 of the human c-Ha-ras gene acts as a block to transcriptional readthrough by a viral promoter. Molecular and Cellular Biology. 10: 4990-5. PMID 2201911 DOI: 10.1128/Mcb.10.9.4990 |
0.315 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 2015 |
Verhein KC, McCaw Z, Gladwell W, Trivedi S, Bushel PR, Kleeberger SR. Novel Roles for Notch3 and Notch4 Receptors in Gene Expression and Susceptibility to Ozone-Induced Lung Inflammation in Mice. Environmental Health Perspectives. 123: 799-805. PMID 25658374 DOI: 10.1289/Ehp.1408852 |
0.3 |
|
| 2019 |
Davis M, Knight E, Eldridge SR, Li J, Bushel PR. Transcriptomic profiles of tissues from rats treated with anticancer drug combinations. Scientific Data. 6: 180306. PMID 30620345 DOI: 10.1038/Sdata.2018.306 |
0.29 |
|
| 2013 |
Madenspacher JH, Azzam KM, Gowdy KM, Malcolm KC, Nick JA, Dixon D, Aloor JJ, Draper DW, Guardiola JJ, Shatz M, Menendez D, Lowe J, Lu J, Bushel P, Li L, et al. p53 Integrates host defense and cell fate during bacterial pneumonia. The Journal of Experimental Medicine. 210: 891-904. PMID 23630228 DOI: 10.1084/Jem.20121674 |
0.286 |
|
| 2018 |
Duncan CG, Grimm SA, Morgan DL, Bushel PR, Bennett BD, Roberts JD, Tyson FL, Merrick BA, Wade PA. Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver. Scientific Reports. 8: 10138. PMID 29973619 DOI: 10.1038/S41598-018-28356-3 |
0.284 |
|
| 2012 |
Hewitt SC, Li L, Grimm SA, Chen Y, Liu L, Li Y, Bushel PR, Fargo D, Korach KS. Research resource: whole-genome estrogen receptor α binding in mouse uterine tissue revealed by ChIP-seq. Molecular Endocrinology (Baltimore, Md.). 26: 887-98. PMID 22446102 DOI: 10.1210/Me.2011-1311 |
0.278 |
|
| 1993 |
Kim JH, Bushel PR, Kumar CC. Smooth muscle alpha-actin promoter activity is induced by serum stimulation of fibroblast cells. Biochemical and Biophysical Research Communications. 190: 1115-21. PMID 8439311 DOI: 10.1006/Bbrc.1993.1165 |
0.277 |
|
| 2018 |
Bushel PR, Caiment F, Wu H, O'Lone R, Day F, Calley J, Smith A, Li J. RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database. Bmc Genomics. 19: 825. PMID 30453895 DOI: 10.1186/S12864-018-5220-X |
0.277 |
|
| 2018 |
Duncan CG, Kondilis-Mangum HD, Grimm SA, Bushel PR, Chrysovergis K, Roberts JD, Tyson FL, Merrick BA, Wade PA. Base-Resolution Analysis of DNA Methylation Patterns Downstream of Dnmt3a in Mouse Naïve B Cells. G3 (Bethesda, Md.). PMID 29326230 DOI: 10.1534/G3.117.300446 |
0.277 |
|
| 2014 |
Lowe JM, Menendez D, Bushel PR, Shatz M, Kirk EL, Troester MA, Garantziotis S, Fessler MB, Resnick MA. p53 and NF-κB coregulate proinflammatory gene responses in human macrophages. Cancer Research. 74: 2182-92. PMID 24737129 DOI: 10.1158/0008-5472.Can-13-1070 |
0.275 |
|
| 2012 |
Pandiri AR, Sills RC, Ziglioli V, Ton TV, Hong HH, Lahousse SA, Gerrish KE, Auerbach SS, Shockley KR, Bushel PR, Peddada SD, Hoenerhoff MJ. Differential transcriptomic analysis of spontaneous lung tumors in B6C3F1 mice: comparison to human non-small cell lung cancer. Toxicologic Pathology. 40: 1141-59. PMID 22688403 DOI: 10.1177/0192623312447543 |
0.273 |
|
| 2019 |
Grimm SA, Shimbo T, Takaku M, Thomas JW, Auerbach S, Bennett BD, Bucher JR, Burkholder AB, Day F, Du Y, Duncan CG, French JE, Foley JF, Li J, Merrick BA, ... ... Bushel PR, et al. DNA methylation in mice is influenced by genetics as well as sex and life experience. Nature Communications. 10: 305. PMID 30659182 DOI: 10.1038/S41467-018-08067-Z |
0.27 |
|
| 2003 |
Hodges LC, Cook JD, Lobenhofer EK, Li L, Bennett L, Bushel PR, Aldaz CM, Afshari CA, Walker CL. Tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cells. Molecular Cancer Research : McR. 1: 300-11. PMID 12612058 |
0.27 |
|
| 2015 |
Hewitt SC, Winuthayanon W, Pockette B, Kerns RT, Foley JF, Flagler N, Ney E, Suksamrarn A, Piyachaturawat P, Bushel PR, Korach KS. Development of phenotypic and transcriptional biomarkers to evaluate relative activity of potentially estrogenic chemicals in ovariectomized mice. Environmental Health Perspectives. 123: 344-52. PMID 25575267 DOI: 10.1289/Ehp.1307935 |
0.27 |
|
| 2011 |
Afshari CA, Hamadeh HK, Bushel PR. The evolution of bioinformatics in toxicology: advancing toxicogenomics. Toxicological Sciences : An Official Journal of the Society of Toxicology. 120: S225-37. PMID 21177775 DOI: 10.1093/Toxsci/Kfq373 |
0.269 |
|
| 2016 |
Manrai AK, Cui Y, Bushel PR, Hall M, Karakitsios S, Mattingly CJ, Ritchie M, Schmitt C, Sarigiannis DA, Thomas DC, Wishart D, Balshaw DM, Patel CJ. Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health. Annual Review of Public Health. PMID 28068484 DOI: 10.1146/Annurev-Publhealth-082516-012737 |
0.264 |
|
| 2016 |
Smith A, Calley J, Mathur S, Qian HR, Wu H, Farmen M, Caiment F, Bushel PR, Li J, Fisher C, Kirby P, Koenig E, Hall DG, Watson DE. The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog. Bmc Genomics. 17: 694. PMID 27576563 DOI: 10.1186/S12864-016-2956-Z |
0.264 |
|
| 2009 |
Bushel PR, Heard NA, Gutman R, Liu L, Peddada SD, Pyne S. Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle. Bmc Systems Biology. 3: 93. PMID 19758441 DOI: 10.1186/1752-0509-3-93 |
0.263 |
|
| 1995 |
Kumar CC, Kim J, Bushel P, Armstrong L, Catino JJ. Activation of smooth muscle α-actin promoter in ras-transformed cells by treatments with antimitotic agents: Correlation with stimulation of SRF:SRE mediated gene transcription Journal of Biochemistry. 118: 1285-1292. PMID 8720148 DOI: 10.1093/Oxfordjournals.Jbchem.A125020 |
0.257 |
|
| 2020 |
Bushel PR, Caiment F, Wu H, O'Lone R, Day F, Calley J, Smith A, Li J, Harrill AH. RATEmiRs: The Rat Atlas of Tissue-specific and Enriched miRNAs for Discerning Baseline Expression Exclusivity of Candidate Biomarkers. Rna Biology. PMID 32009518 DOI: 10.1080/15476286.2020.1724715 |
0.257 |
|
| 2020 |
Bisogno LS, Yang J, Bennett BD, Ward JM, Mackey LC, Annab LA, Bushel PR, Singhal S, Schurman SH, Byun JS, Nápoles AM, Pérez-Stable EJ, Fargo DC, Gardner K, Archer TK. Ancestry-dependent gene expression correlates with reprogramming to pluripotency and multiple dynamic biological processes. Science Advances. 6. PMID 33219026 DOI: 10.1126/sciadv.abc3851 |
0.256 |
|
| 2018 |
Bushel PR, Tong W. Editorial: Integrative Toxicogenomics: Analytical Strategies to Amalgamate Exposure Effects With Genomic Sciences. Frontiers in Genetics. 9: 563. PMID 30542369 DOI: 10.3389/Fgene.2018.00563 |
0.252 |
|
| 2014 |
Smith A, Calley J, Mathur S, Qian H, Farmen M, Engle S, Wu H, Caiment F, Bushel P, Li J, Watson D. The rat microRNA body atlas: Towards understanding serum microRNA changes and their utilisation as biomarkers of specific organ toxicity Toxicology Letters. 229: S22. DOI: 10.1016/J.Toxlet.2014.06.110 |
0.245 |
|
| 2009 |
Bushel PR, Nielsen D, Tong W. Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007). Bmc Proceedings. 3: S1. PMID 19278557 DOI: 10.1186/1753-6561-3-S2-S1 |
0.24 |
|
| 2011 |
Eggesbø M, Moen B, Peddada S, Baird D, Rugtveit J, Midtvedt T, Bushel PR, Sekelja M, Rudi K. Development of gut microbiota in infants not exposed to medical interventions. Apmis : Acta Pathologica, Microbiologica, Et Immunologica Scandinavica. 119: 17-35. PMID 21143523 DOI: 10.1111/J.1600-0463.2010.02688.X |
0.236 |
|
| 2001 |
Paules RS, Innes CL, Sieber SO, Shackelford RE, Heinloth AN, Deming PB, Cistulli CA, Bennett L, Bushel PR, Afshari CA, Kaufmann WK. ATM-dependent responses to DNA-damaging agents Nature Genetics. 27: 78-78. DOI: 10.1038/87240 |
0.235 |
|
| 2018 |
Muñoz MD, Della Vedova MC, Bushel PR, Ganini da Silva D, Mason RP, Zhai Z, Gomez Mejiba SE, Ramirez DC. The nitrone spin trap 5,5-dimethyl-1-pyrroline N-oxide dampens lipopolysaccharide-induced transcriptomic changes in macrophages. Inflammation Research : Official Journal of the European Histamine Research Society ... [Et Al.]. PMID 29589052 DOI: 10.1007/S00011-018-1141-Z |
0.221 |
|
| 2010 |
Huang J, Shi W, Zhang J, Chou JW, Paules RS, Gerrish K, Li J, Luo J, Wolfinger RD, Bao W, Chu TM, Nikolsky Y, Nikolskaya T, Dosymbekov D, Tsyganova MO, ... ... Bushel PR, et al. Genomic indicators in the blood predict drug-induced liver injury. The Pharmacogenomics Journal. 10: 267-77. PMID 20676066 DOI: 10.1038/tpj.2010.33 |
0.22 |
|
| 2020 |
Liu J, Castro L, Clayton NP, Bushel P, Li S, Yu L, Flagler ND, Scappini E, Yan Y, Dixon D. Bisphenol A and its analogues induce Fibrosis in a 3D Human Uterine Fibroid Model through TGF‐beta Signaling The Faseb Journal. 34: 1-1. DOI: 10.1096/Fasebj.2020.34.S1.06155 |
0.217 |
|
| 2022 |
Sinha BK, Tokar EJ, Li J, Bushel PR. Gene Expression Profiling Elucidates Cellular Responses to NCX4040 in Human Ovarian Tumor Cells: Implications in the Mechanisms of Action of NCX4040. Cancers. 15. PMID 36612280 DOI: 10.3390/cancers15010285 |
0.206 |
|
| 2022 |
Bushel PR, Ward J, Burkholder A, Li J, Anchang B. Mitochondrial-nuclear epistasis underlying phenotypic variation in breast cancer pathology. Scientific Reports. 12: 1393. PMID 35082309 DOI: 10.1038/s41598-022-05148-4 |
0.18 |
|
| 2022 |
Liu J, Yu L, Castro L, Yan Y, Clayton NP, Bushel P, Flagler ND, Scappini E, Dixon D. Short-term tetrabromobisphenol A exposure promotes fibrosis of human uterine fibroid cells in a 3D culture system through TGF-beta signaling. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 36: e22101. PMID 35032343 DOI: 10.1096/fj.202101262R |
0.176 |
|
| 2021 |
Jones W, Gong B, Novoradovskaya N, Li D, Kusko R, Richmond TA, Johann DJ, Bisgin H, Sahraeian SME, Bushel PR, Pirooznia M, Wilkins K, Chierici M, Bao W, Basehore LS, et al. A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency. Genome Biology. 22: 111. PMID 33863366 DOI: 10.1186/s13059-021-02316-z |
0.139 |
|
| 2011 |
Merrick BA, London RE, Bushel PR, Grissom SF, Paules RS. Platforms for biomarker analysis using high-throughput approaches in genomics, transcriptomics, proteomics, metabolomics, and bioinformatics. Iarc Scientific Publications. 121-42. PMID 22997859 |
0.137 |
|
| 2021 |
Deveson IW, Gong B, Lai K, LoCoco JS, Richmond TA, Schageman J, Zhang Z, Novoradovskaya N, Willey JC, Jones W, Kusko R, Chen G, Madala BS, Blackburn J, Stevanovski I, ... ... Bushel PR, et al. Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology. Nature Biotechnology. PMID 33846644 DOI: 10.1038/s41587-021-00857-z |
0.123 |
|
| 2013 |
Huda A, Bushel PR. Widespread Exonization of Transposable Elements in Human Coding Sequences is Associated with Epigenetic Regulation of Transcription. Transcriptomics: Open Access. 1. PMID 24860841 |
0.122 |
|
| 2021 |
Gong B, Li D, Kusko R, Novoradovskaya N, Zhang Y, Wang S, Pabón-Peña C, Zhang Z, Lai K, Cai W, LoCoco JS, Lader E, Richmond TA, Mittal VK, Liu LC, ... ... Bushel PR, et al. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. Genome Biology. 22: 109. PMID 33863344 DOI: 10.1186/s13059-021-02315-0 |
0.101 |
|
| 2013 |
Madenspacher JH, Azzam KM, Gowdy KM, Malcolm KC, Nick JA, Dixon D, Aloor JJ, Draper DW, Guardiola JJ, Shatz M, Menendez D, Lowe J, Lu J, Bushel P, Li L, et al. p53 integrates host defense and cell fate during bacterial pneumonia The Journal of Cell Biology. 201: i5-i5. DOI: 10.1083/JCB2014OIA5 |
0.062 |
|
| 2022 |
Foo ACY, Nesbit JB, Gipson SAY, Cheng H, Bushel P, DeRose EF, Schein CH, Teuber SS, Hurlburt BK, Maleki SJ, Mueller GA. Structure, Immunogenicity, and IgE Cross-Reactivity among Walnut and Peanut Vicilin-Buried Peptides. Journal of Agricultural and Food Chemistry. 70: 2389-2400. PMID 35139305 DOI: 10.1021/acs.jafc.1c07225 |
0.059 |
|
| Hide low-probability matches. |