W. Evan Johnson, Ph.D.

Evan-Blur

Associate Professor of Medicine and Biostatistics

Education

B.S., Summa Cum Laude, Mathematics, Southern Utah University, Cedar City, Utah, 2002
M.S., Statistics, Brigham Young University, Provo, Utah, 2003
M.A., Biostatistics, Harvard University, Cambridge, Massachusetts, 2006
Ph.D., Biostatistics, Harvard University, Cambridge, Massachusetts,  2007

Contact Information

Email: “my initials” AT bu.edu
Office: E609
Phone: 617-638-2541

Research Interests

Applications in precision genomic medicine, metagenomics, infectious disease diagnostics, batch effects, genomic data analysis, tumor heterogeneity and cancer research

Methodology: Bayesian methods, factor analysis and structural equations models, Hidden Markov models, dynamic programming, nonparametric regression, mixture models, high-performance and parallel computing, and Bayesian networks

Selected Publications

Google Scholar: https://scholar.google.com/citations?user=PI6bhY4AAAAJ&hl=en

MyNCBI: http://www.ncbi.nlm.nih.gov/myncbi/browse/collection/41689720/

Piccolo SR, Hoffman LM, Conner T, Shrestha G, Cohen AL, Marks JR, Neumayer LA, Agarwal CA, Beckerle MC, Andrulis IL, Spira AE, Moos PJ, Buys SS, Johnson WE, Bild AH. Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility. Mol Syst Biol. 2016 Mar 10;12(3):860. PubMed PMID: 26969729.

Piccolo SR, Andrulis IL, Cohen AL, Conner T, Moos PJ, Spira AE, Buys SS, Johnson WE, Bild AH. Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility. BMC Med Genomics. 2015 Nov 4;8:72. doi: 10.1186/s12920-015-0145-6. PubMed PMID: 26538066; PubMed Central PMCID: PMC4634735.

Castro-Nallar E, Shen Y, Freishtat RJ, Pérez-Losada M, Manimaran S, Liu G, Johnson WE, Crandall KA. Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities. BMC Med Genomics. 2015 Aug 16;8:50. PubMed PMID: 26277095; PubMed Central PMCID: PMC4537781.

Shen Y, Rahman M, Piccolo SR, Gusenleitner D, El-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE. ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways. Bioinformatics. 2015 Jun 1;31(11):1745-53. PubMed PMID: 25617415; PubMed Central PMCID: PMC4443674.

Byrd AL, Perez-Rogers JF, Manimaran S, Castro-Nallar E, Toma I, McCaffrey T, Siegel M, Benson G, Crandall KA, Johnson WE. Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. BMC Bioinformatics. 2014 Aug 4;15:262. PubMed PMID: 25091138; PubMed Central PMCID: PMC4131054.

Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE. PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples. Microbiome. 2014;2:33. PubMed PMID: 25225611; PubMed Central PMCID: PMC4164323.

Bild AH, Chang JT, Johnson WE, Piccolo SR. A field guide to genomics research. PLoS Biol. 2014 Jan;12(1):e1001744. PubMed PMID: 24409093; PubMed Central PMCID: PMC3883637.

Piccolo SR, Withers MR, Francis OE, Bild AH, Johnson WE. Multiplatform single-sample estimates of transcriptional activation. Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17778-83. PubMed PMID: 24128763; PubMed Central PMCID: PMC3816418.

Francis OE, Bendall M, Manimaran S, Hong C, Clement NL, Castro-Nallar E, Snell Q, Schaalje GB, Clement MJ, Crandall KA, Johnson WE. Pathoscope: species identification and strain attribution with unassembled sequencing data. Genome Res. 2013 Oct;23(10):1721-9. PubMed PMID: 23843222; PubMed Central PMCID: PMC3787268.

Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012 Mar 15;28(6):882-3. PubMed PMID: 22257669; PubMed Central PMCID: PMC3307112.

Cohen AL, Soldi R, Zhang H, Gustafson AM, Wilcox R, Welm BE, Chang JT, Johnson E, Spira A, Jeffrey SS, Bild AH. A pharmacogenomic method for individualized prediction of drug sensitivity. Mol Syst Biol. 2011 Jul 19;7:513. PubMed PMID: 21772261; PubMed Central PMCID: PMC3159972.

Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet. 2010 Oct;11(10):733-9. PubMed PMID: 20838408; NIHMSID: NIHMS282727; PubMed Central PMCID: PMC3880143.

Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE. The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. Bioinformatics. 2010 Jan 1;26(1):38-45. PubMed PMID: 19861355.

Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007 Jan;8(1):118-27. PubMed PMID: 16632515.

Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12457-62. PubMed PMID: 16895995; PubMed Central PMCID: PMC1567901.