Author details

Full Name

Pierre R Bushel

Affiliation

ORCID

Career Start Year

1990

Papers

117

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
35082309	Mitochondrial-nuclear epistasis underlying phenotypic variation in breast cancer pathology.	Scientific Reports	2022
35404422	A Collaborative Initiative to Establish Genomic Biomarkers for Assessing Tumorigenic Potential to Reduce Reliance on Conventional Rodent Carcinogenicity Studies.	Toxicol Sci	2022
36612280	Gene Expression Profiling Elucidates Cellular Responses to NCX4040 in Human Ovarian Tumor Cells: Implications in the Mechanisms of Action of NCX4040.		2022
35032343	Short-term tetrabromobisphenol A exposure promotes fibrosis of human uterine fibroid cells in a 3D culture system through TGF-beta signaling.	FASEB Journal	2022
35139305	Structure, Immunogenicity, and IgE Cross-Reactivity among Walnut and Peanut Vicilin-Buried Peptides.	Journal of Agricultural and Food Chemistry	2022
34899830	Structural Equation Modeling of In silico Perturbations.	Front Genet	2021
33846644	Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology.	Nat Biotechnol	2021
33863366	A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency.	Genome Biol	2021
33863344	Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.	Genome Biol	2021
33219026	Ancestry-dependent gene expression correlates with reprogramming to pluripotency and multiple dynamic biological processes.	Sci Adv	2020
32009518	RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs for discerning baseline expression exclusivity of candidate biomarkers.	RNA Biol	2020
31806706	Proteasome inhibition creates a chromatin landscape favorable to RNA Pol II processivity.	Journal of Biological Chemistry	2020
32655620	Comparison of Normalization Methods for Analysis of TempO-Seq Targeted RNA Sequencing Data.	Front Genet	2020
32765594	Elucidation of Mechanisms of Topotecan-Induced Cell Death in Human Breast MCF-7 Cancer Cells by Gene Expression Analysis.	Frontiers in Genetics	2020
30850835	The Power of Resolution: Contextualized Understanding of Biological Responses to Liver Injury Chemicals Using High-throughput Transcriptomics and Benchmark Concentration Modeling.	Toxicol Sci	2019
30620345	Transcriptomic profiles of tissues from rats treated with anticancer drug combinations.	Scientific data	2019
29589052	The nitrone spin trap 5,5-dimethyl-1-pyrroline N-oxide dampens lipopolysaccharide-induced transcriptomic changes in macrophages.	Inflammation Research	2018
30453895	RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database.	BMC Genomics	2018
29973619	Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver.	Sci Rep	2018
30107566	Revealing a human p53 universe.	Nucleic Acids Res	2018
30542369	Editorial: Integrative Toxicogenomics: Analytical Strategies to Amalgamate Exposure Effects With Genomic Sciences.	Front Genet	2018
30420870	A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples.	Front Genet	2018
29668680	Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation.	PLoS Biol	2018
29462216	A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics.	PLoS One	2018
29326230	Base-Resolution Analysis of DNA Methylation Patterns Downstream of <i>Dnmt3a</i> in Mouse NaÃ¯ve B Cells.	G3 (Bethesda)	2018
28068484	Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health.	Annu Rev Public Health	2017
28413437	goSTAG: gene ontology subtrees to tag and annotate genes within a set.	Source Code for Biology and Medicine	2017
28329830	Secondhand Smoke-Prevalent Polycyclic Aromatic Hydrocarbon Binary Mixture-Induced Specific Mitogenic and Pro-inflammatory Cell Signaling Events in Lung Epithelial Cells.	Toxicological Sciences	2017
29114260	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.	Front Genet	2017
26927286	Blood gene expression profiling of an early acetaminophen response.	Pharmacogenomics J	2017
27576563	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	2016
27106289	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	2016
27431323	Tunable regulation of CREB DNA binding activity couples genotoxic stress response and metabolism.	Nucleic Acids Research	2016
27004791	EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data.	BMC Genomics	2016
26690555	Blood transcript immune signatures distinguish a subset of people with elevated serum ALT from others given acetaminophen.	Clin Pharmacol Ther	2016
26149387	LIN28A Modulates Splicing and Gene Expression Programs in Breast Cancer Cells.	Mol Cell Biol	2015
25658374	Novel Roles for Notch3 and Notch4 Receptors in Gene Expression and Susceptibility to Ozone-Induced Lung Inflammation in Mice.	Environmental Health Perspectives	2015
25575267	Development of phenotypic and transcriptional biomarkers to evaluate relative activity of potentially estrogenic chemicals in ovariectomized mice.	Environ Health Perspect	2015
25729387	Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity.	Frontiers in Genetics	2015
25944780	Technical guide for applications of gene expression profiling in human health risk assessment of environmental chemicals.	Regul Toxicol Pharmacol	2015
25150839	The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.	Nat Biotechnol	2014
24737129	p53 and NF-ÎºB coregulate proinflammatory gene responses in human macrophages.	Cancer Research	2014
24860841	Widespread Exonization of Transposable Elements in Human Coding Sequences is Associated with Epigenetic Regulation of Transcription.		2013
23943852	Gene expression signatures but not cell cycle checkpoint functions distinguish AT carriers from normal individuals.	Physiological Genomics	2013
23845781	Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling.	Gene	2013
24188919	Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes.	BMC Syst Biol	2013
23966761	Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification.	Cancer Informatics	2013
23785396	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	2013
23630228	p53 Integrates host defense and cell fate during bacterial pneumonia.	Journal of Experimental Medicine	2013
22230429	Sources of variance in baseline gene expression in the rodent liver.	Mutat Res	2012