| Assessing gene significance from cDNA microarray expression data via mixed models RD Wolfinger, G Gibson, ED Wolfinger, L Bennett, H Hamadeh, P Bushel, ... Journal of computational biology 8 (6), 625-637, 2001 | 1383 | 2001 |
| The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models L Shi, G Campbell, WD Jones, F Campagne, Z Wen, SJ Walker, Z Su, ... Nature biotechnology 28 (8), 827-838, 2010 | 883 | 2010 |
| A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium Nature biotechnology 32 (9), 903-914, 2014 | 873 | 2014 |
| Standardizing global gene expression analysis between laboratories and across platforms Toxicogenomics Research Consortium Weis BK weis@ niehs. nih. gov 1 b Nature methods 2 (5), 351-356, 2005 | 608 | 2005 |
| The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance C Wang, B Gong, PR Bushel, J Thierry-Mieg, D Thierry-Mieg, J Xu, ... Nature biotechnology 32 (9), 926-932, 2014 | 558 | 2014 |
| Gene expression analysis reveals chemical-specific profiles HK Hamadeh, PR Bushel, S Jayadev, K Martin, O DiSorbo, S Sieber, ... Toxicological Sciences 67 (2), 219-231, 2002 | 550 | 2002 |
| A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data J Luo, M Schumacher, A Scherer, D Sanoudou, D Megherbi, T Davison, ... The pharmacogenomics journal 10 (4), 278-291, 2010 | 364 | 2010 |
| Prediction of compound signature using high density gene expression profiling HK Hamadeh, PR Bushel, S Jayadev, O DiSorbo, L Bennett, L Li, ... Toxicological Sciences 67 (2), 232-240, 2002 | 339 | 2002 |
| Statistical analysis of a gene expression microarray experiment with replication MK Kerr, CA Afshari, L Bennett, P Bushel, J Martinez, NJ Walker, ... Statistica Sinica, 203-217, 2002 | 273 | 2002 |
| p53 and NF-κB coregulate proinflammatory gene responses in human macrophages JM Lowe, D Menendez, PR Bushel, M Shatz, EL Kirk, MA Troester, ... Cancer research 74 (8), 2182-2192, 2014 | 192 | 2014 |
| Development of gut microbiota in infants not exposed to medical interventions M Eggesbø, B Moen, S Peddada, D Baird, J Rugtveit, T Midtvedt, ... Apmis 119 (1), 17-35, 2011 | 192 | 2011 |
| Global transcriptome and deletome profiles of yeast exposed to transition metals YH Jin, PE Dunlap, SJ McBride, H Al-Refai, PR Bushel, JH Freedman PLoS genetics 4 (4), e1000053, 2008 | 188 | 2008 |
| Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology IW Deveson, B Gong, K Lai, JS LoCoco, TA Richmond, J Schageman, ... Nature biotechnology 39 (9), 1115-1128, 2021 | 185 | 2021 |
| Tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cells LC Hodges, JD Cook, EK Lobenhofer, L Li, L Bennett, PR Bushel, ... Molecular Cancer Research 1 (4), 300-311, 2003 | 182 | 2003 |
| The evolution of bioinformatics in toxicology: advancing toxicogenomics CA Afshari, HK Hamadeh, PR Bushel Toxicological Sciences 120 (suppl_1), S225-S237, 2011 | 175 | 2011 |
| CEBS—Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data M Waters, S Stasiewicz, B Alex Merrick, K Tomer, P Bushel, R Paules, ... Nucleic acids research 36 (suppl_1), D892-D900, 2007 | 166 | 2007 |
| Database development in toxicogenomics: issues and efforts. WB Mattes, SD Pettit, SA Sansone, PR Bushel, MD Waters Environmental health perspectives 112 (4), 495-505, 2004 | 160 | 2004 |
| Methapyrilene toxicity: anchorage of pathologic observations to gene expression alterations HK Hamadeh, BL Knight, AC Haugen, S Sieber, RP Amin, PR Bushel, ... Toxicologic pathology 30 (4), 470-482, 2002 | 157 | 2002 |
| Blood gene expression signatures predict exposure levels PR Bushel, AN Heinloth, J Li, L Huang, JW Chou, GA Boorman, ... Proceedings of the National Academy of Sciences 104 (46), 18211-18216, 2007 | 147 | 2007 |
| A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics D Mav, RR Shah, BE Howard, SS Auerbach, PR Bushel, JB Collins, ... PloS one 13 (2), e0191105, 2018 | 138 | 2018 |
