| 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 |
0.426 |
|
| 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 |
0.399 |
|
| 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 |
0.383 |
|
| 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 |
0.368 |
|
| 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 |
0.369 |
|
| 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 |
0.335 |
|
| 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 |
0.507 |
|
| 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 |
0.435 |
|
| 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 |
0.433 |
|
| 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 |
0.576 |
|
| 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 |
0.394 |
|
| 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 |
|
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