Pierre Bushel

Adjunct Lecturer on Biostatistics

Department of Biostatistics

Other Affiliation

Senior Director, Computational Core and Computational Biology, BlueRock Therapeutics

Education

Ph.D., Bioinformatics, 2005, North Carolina State University
M.S., Molecular and Cellular Biology, 1989, Long Island University-Brooklyn campus
B.S., Zoology, 1984, University of Massachusetts-Amherst campus

Research

Dr. Bushel’s research focuses primarily on predictive genomics, underlying regulatory mechanisms of transcriptional networks, cancer genomics and gene biomarker discovery. He, his collaborators and associates use bioinformatics, computational biology, statistics and machine learning to address biological conditions and health concerns. In particular, he designs and implements analytical methodologies for integrative analyses of genomics, genetics, epigenetic, pathology images and other big data types. In addition, he develops software and databases for precision health informatics and deep learning for massive analysis of gene expression data.

PubMed Publications

Selected Publications

Jones W, Gong B, Novoradovskaya N, et al. A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency. Genome Biol. 2021 Apr 16;22(1):111.

Gong B, Li D, Kusko R, et al. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. Genome Biol. 2021 Apr 16;22(1):109.

Deveson IW, Gong B, Lai K, et al. SEQC2 Oncopanel Sequencing Working Group. Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology. Nat Biotechnol. 2021 Apr 12. doi: 10.1038/s41587-021-00857-z. Online ahead of print.

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. Front Genet. 2020 Jul 17;11:775.

Davis M, Knight E, Eldridge SR, Li J, Bushel PR. Transcriptomic profiles of tissues from rats treated with anticancer drug combinations. Sci Data. 2019 Jan 8;6:180306.

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. Front Genet. 2018 Oct 30;9:485

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. Front Genet. 2017 Oct 24;8:157.

Li J, Bushel PR. EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data. BMC Genomics. 2016 Mar 22;17(1):255.

Bushel PR, Fannin RD, Gerrish K, Watkins PB, Paules RS. Blood gene expression profiling of an early acetaminophen response. Pharmacogenomics J. 2016 Mar 1.

*Wang C, *Gong B, *Bushel PR, et al. SEQC Consortium, The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nat Biotechnol. 2014 Sep;32(9):926-32.

Huang L, Zhang HH, Zeng ZB, Bushel PR. Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification. Cancer Inform. 2013 Aug 4;12:143-53.

Lu J, Bushel PR. Dynamic expression of 3′ UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling. Gene. 2013 Sep 25;527(2):616-23.

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. 2012;7(3):e34286. Epub 2012 Mar 27.

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. 2009 Sept 16;3:93.

*Bushel, P.R., *Heinloth, A.N., Li, J., Huang, L., Chou, J.W., Boorman, G.A., Malarkey, D.E., Houle C.D., Ward S.M., Wilson R.E., Tennant R.W., Paules, R.S. Blood Gene Expression Signatures Predict Exposure Levels. PNAS 2007 Nov;104(46):18211-18216. Epub 2007 November 2.