W. Evan Johnson, Ph.D.

Evan-Blur

Assistant Professor of Medicine

Education

B.S., Summa Cum Laude, Mathematics, Physics Minor, 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 personalized 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

Lyon GJ, Jiang T, Van Wijk R, Wang W, y Bodily P, Xing J, Tian L, Robison R, Clement M, Yang L, Zhang P, Liu Y, Moore B, Glessner J, Elia J, Reimherr F, van Solinge W, Yandell M, Hakonarson H, Wang J, Johnson WE, Wei Z, Wang K (2011). Exome Sequencing and Unrelated Findings in the context of Complex Disease Research: Ethical and Clinical Implications. Discovery Medicine, 12(62).

Cohen AL, Soldi R, Zhang H, Gustafson AM, Wilcox R, Welm BE, Chang JT, Johnson WE , Spira A, Jeffrey SS, Bild AH (2011). MATCH: Merging genomic and pharmacologic Analyses for Therapy CHoice. Molecular Systems Biology 7: 513.

Rope AF, Wang K, Evjenth R, Xing K, Johnston JJ, Swenson JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM Stevens CA, Jiang T, Schank C, Fain HD, Robison R, Dalley B, Chin S, South TS, Pysher TJ, Jorde LB, Hakonarson H, Lillehaug JR, Biesecker LG, Yandell M, Arnesen T, Lyon GJ (2011). Using VAAST to Identify an X-Linked Disorder Resulting in Lethality in Male Infants Due to N-Terminal Acetyltransferase Deficiency. American Journal of Human Genetics 10.1016/j.ajhg.2011.05.017.

Warf MB, Johnson WE, Bass BL (2011). Improved annotation of C. elegans  microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer. RNA 17: 563-577.

Johnson WE, Welker NC, Bass BL (2011). Dynamic Linear Model for the Identi_cation of miRNAs in Next-generation Sequencing Data. Biometrics 67: doi: 10.1111/j.1541-0420.2010.01570.x.

Leek JT, Scharpf R, Corrada-Bravo H, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA (2010). Tackling the widespread and critical impact of batch effects in high-throughput data. Nature Reviews Genetics 11, 733-739.

Rai K, Sarkar S, Broadbent T, Voas M, Grossman KF, Dehghanizadeh S, Hagos F, Li Y, Toth RK, Chidester S, y Bahr TM, Johnson WE, Sklow B, Burt R, Cairns BR, Jones DA (2010). DNA Demethylase Activity Maintains Zebrafish Intestinal Cells in a Progenitor-like State Following Loss of APC. Cell 142(6): 930-942.

Thyagarajan B, Blaszczak AG, Chandler KJ, Watts JL, Johnson WE, Graves BJ (2010) ETS-4 Is a Transcriptional Regulator of Life Span in Caenorhabditis elegans. PLoS Genetics 6 (9): e1001125.

Clement N, Snell Q, Clement M, Hollenhorst PC, Parwar J, Graves BJ, Cairns BR, Johnson WE (2010). The GNUMAP Algorithm: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing. Bioinformatics, 26(1): 38-45

Hollenhorst PC, Chandler KJ, Poulsen RL, Johnson WE, Speck NA, Graves BJ (2009). DNA specificity determinants associate with distinct transcription factor functions. PLoS Genetics, 5(12):e1000778.

Johnson WE, Liu JS, Liu XS (2009). Doubly-stochastic continuous-time Hidden Markov approach for applications on genome tiling arrays. Annals of Applied Statistics, 3:1183-1203.

Gottardo R, Li W, Johnson WE, Liu XS (2008). A flexible and powerful Bayesian hierarchical model for ChIP-chip experiments. Biometrics , 64 : 468-478

Song JS, Johnson WE, Zhu X, Zhang X, Jiang N, Liu XS (2007). Model-based analysis of two-color tiling arrays. Genome Biology , 8 : R178. (Joint first author)

Johnson WE, Rabinovic A, Li C (2007). Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics , 8  (1):118-127.

Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS (2006). Model-based analysis of tiling-arrays for ChIP-chip. Proceedings of the National Academy of Sciences 103  (33):12457-12462