W. Evan Johnson, Ph.D.


Associate Professor of Medicine


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: wej@bu.edu
Office: E645
Phone: 617-638-2541

Research Interests

Applications in precision genomic medicine, epigenomics, transcription regulation, next-generation sequencing and microarray analysis, 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, Bayesian networks

Selected Publications

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 20: a complete computational framework for strain identification in environmental or clinical sequencing samples. Microbiome. 2014;2:33. PubMed PMID: 25225611; PubMed Central PMCID: PMC4164323.

Hong C, Clement NL, Clement S, Hammoud SS, Carrell DT, Cairns BR, Snell Q, Clement MJ, Johnson WE. Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data. BMC Bioinformatics. 2013 Nov 21;14:337. PubMed PMID: 24261665; PubMed Central PMCID: PMC3924334.

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.

Piccolo SR, Sun Y, Campbell JD, Lenburg ME, Bild AH, Johnson WE. A single-sample microarray normalization method to facilitate personalized-medicine workflows. Genomics. 2012 Dec;100(6):337-44. PubMed PMID: 22959562; PubMed Central PMCID: PMC3508193.

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.

Johnson WE, Welker NC, Bass BL. Dynamic linear model for the identification of miRNAs in next-generation sequencing data. Biometrics. 2011 Dec;67(4):1206-14. PubMed PMID: 21385162; PubMed Central PMCID: PMC3116054.

Clement NL, Clement MJ, Snell Q, Johnson WE. Parallel Mapping Approaches for GNUMAP. IPDPS. 2011;PubMed PMID: 23396612; PubMed Central PMCID: PMC3565456.

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; 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 W, Liu X, Liu JS. Doubly-Stochastic Continuous-Time Hidden Markov Analysis of Genome Tiling Arrays. The annals of applied statistics. 2009; 3:1183-1203.

Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS. Model-based analysis of two-color arrays (MA2C). Genome Biol. 2007;8(8):R178. PubMed PMID: 17727723; PubMed Central PMCID: PMC2375008.

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.