Keywords
Last Name

William Evan Johnson, PhD

TitleAssociate Professor
InstitutionBoston University School of Medicine
DepartmentMedicine
DivisionComputational Biomedicine
Address72 E. Concord St Evans Building
Boston MA 02118
Phone(617) 638-2541
ORCID ORCID Icon0000-0002-6247-6595
Other Positions
TitleAssociate Professor
InstitutionBoston University School of Public Health
DepartmentBiostatistics

TitleMember
InstitutionBoston University
DepartmentBioinformatics Graduate Program

 Research Expertise & Professional Interests
William Johnson specializes in computational biology and biostatistics, developing new tools to investigate disease prognoses and causes and to help determine effective regimens based on individual patients’ risk factors. He has published in the journals Cell, Proceedings of the National Academy of Sciences, Biometrics, Nature Reviews Genetics, Annals of Applied Statistics, and Biostatistics. His work has been funded by the NIH.

The focus of his group's research is to develop computational and statistical tools to investigate core components that contribute to disease prognosis and etiology, and for the accurate determination of optimal diagnostic, prognostic, and therapeutic regimens for individual patients. They are actively developing methods and software tools for data preprocessing, integration, and downstream analysis, and applying these tools in a variety of clinical and biomedical applications. Their work includes a balance between statistical methods development, algorithm optimization, and clinical application. Statistical innovation focuses on the development of clinically motivated tools that integrate linear modeling, Bayesian methods, factor analysis and structural equations models, Hidden Markov models, mixture models, dynamic programming, and high-performance parallel computing. This work has resulted in widely used tools and algorithms for profiling transcription factors (MAT, MA2C), preprocessing and integrating of genomic data (ComBat, BatchQC, SCAN-UPC), aligning sequencing reads (GNUMAP), developing multi-gene biomarker signatures (ASSIGN), and metagenomic profiling (PathoScope). They have successfully applied their tools in several biomedical and clinical scenarios, ranging from mechanistic studies and to precision genomics.

 Self-Described Keywords
  • Computational biology
  • Bayesian biostatistics
  • genomic medicine
  • tumor heterogeneity
  • metagenomics
  • infectious disease diagnostics
  • single cell sequencing
  • batch effects
 Publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
List All   |   Timeline
  1. Yazdani N, Shen Y, Johnson WE, Bryant CD. Striatal transcriptome analysis of a congenic mouse line (chromosome 11: 50-60Mb) exhibiting reduced methamphetamine sensitivity. Genom Data. 2016 Jun; 8:77-80. PMID: 27222804.
    View in: PubMed
  2. Hilton SK, Castro-Nallar E, Pérez-Losada M, Toma I, McCaffrey TA, Hoffman EP, Siegel MO, Simon GL, Johnson WE, Crandall KA. Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology. Front Microbiol. 2016; 7:484. PMID: 27092134.
    View in: PubMed
  3. 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. PMID: 26969729.
    View in: PubMed
  4. Yazdani N, Parker CC, Shen Y, Reed ER, Guido MA, Kole LA, Kirkpatrick SL, Lim JE, Sokoloff G, Cheng R, Johnson WE, Palmer AA, Bryant CD. Hnrnph1 Is A Quantitative Trait Gene for Methamphetamine Sensitivity. PLoS Genet. 2015 Dec; 11(12):e1005713. PMID: 26658939.
    View in: PubMed
  5. 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; 8:72. PMID: 26538066.
    View in: PubMed
  6. 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; 8:50. PMID: 26277095.
    View in: PubMed
  7. Rahman M, Jackson LK, Johnson WE, Li DY, Bild AH, Piccolo SR. Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results. Bioinformatics. 2015 Nov 15; 31(22):3666-72. PMID: 26209429.
    View in: PubMed
  8. MacNeil SM, Johnson WE, Li DY, Piccolo SR, Bild AH. Inferring pathway dysregulation in cancers from multiple types of omic data. Genome Med. 2015; 7(1):61. PMID: 26170901.
    View in: PubMed
  9. Hong C, Manimaran S, Johnson WE. PathoQC: Computationally Efficient Read Preprocessing and Quality Control for High-Throughput Sequencing Data Sets. Cancer Inform. 2014; 13(Suppl 1):167-76. PMID: 25983538.
    View in: PubMed
  10. Whipple JM, Youssef OA, Aruscavage PJ, Nix DA, Hong C, Johnson WE, Bass BL. Genome-wide profiling of the C. elegans dsRNAome. RNA. 2015 May; 21(5):786-800. PMID: 25805852.
    View in: PubMed
  11. Grubaugh ND, Sharma S, Krajacich BJ, Fakoli Iii LS, Bolay FK, Diclaro Ii JW, Johnson WE, Ebel GD, Foy BD, Brackney DE. Xenosurveillance: a novel mosquito-based approach for examining the human-pathogen landscape. PLoS Negl Trop Dis. 2015 Mar; 9(3):e0003628. PMID: 25775236.
    View in: PubMed
  12. Mortenson JB, Heppler LN, Banks CJ, Weerasekara VK, Whited MD, Piccolo SR, Johnson WE, Thompson JW, Andersen JL. Histone deacetylase 6 (HDAC6) promotes the pro-survival activity of 14-3-3? via deacetylation of lysines within the 14-3-3? binding pocket. J Biol Chem. 2015 May 15; 290(20):12487-96. PMID: 25770209.
    View in: PubMed
  13. Castro-Nallar E, Hasan NA, Cebula TA, Colwell RR, Robison RA, Johnson WE, Crandall KA. Concordance and discordance of sequence survey methods for molecular epidemiology. PeerJ. 2015; 3:e761. PMID: 25737810.
    View in: PubMed
  14. 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. PMID: 25617415.
    View in: PubMed
  15. Anand S, Bench Alvarez TM, Johnson WE, Esplin MS, Merrell K, Porter TF, Graves SW. Serum biomarkers predictive of pre-eclampsia. Biomark Med. 2015; 9(6):563-75. PMID: 26079961.
    View in: PubMed
  16. Shah DJ, Rohlfing F, Anand S, Johnson WE, Alvarez MT, Cobell J, King J, Young SA, Kauwe JS, Graves SW. Discovery and Subsequent Confirmation of Novel Serum Biomarkers Diagnosing Alzheimer's Disease. J Alzheimers Dis. 2015; 49(2):317-27. PMID: 26484917.
    View in: PubMed
  17. Campbell JD, Liu G, Luo L, Xiao J, Gerrein J, Juan-Guardela B, Tedrow J, Alekseyev YO, Yang IV, Correll M, Geraci M, Quackenbush J, Sciurba F, Schwartz DA, Kaminski N, Johnson WE, Monti S, Spira A, Beane J, Lenburg ME. Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data. RNA. 2015 Feb; 21(2):164-71. PMID: 25519487.
    View in: PubMed
  18. Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, Mazumder R. Census-based rapid and accurate metagenome taxonomic profiling. BMC Genomics. 2014; 15:918. PMID: 25336203.
    View in: PubMed
  19. 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. PMID: 25225611.
    View in: PubMed
  20. 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; 15:262. PMID: 25091138.
    View in: PubMed
  21. Bild AH, Chang JT, Johnson WE, Piccolo SR. A field guide to genomics research. PLoS Biol. 2014 Jan; 12(1):e1001744. PMID: 24409093.
    View in: PubMed
  22. 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; 14:337. PMID: 24261665.
    View in: PubMed
  23. 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. PMID: 24128763.
    View in: PubMed
  24. Cohen AL, Piccolo SR, Cheng L, Soldi R, Han B, Johnson WE, Bild AH. Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers. BMC Med Genomics. 2013; 6:35. PMID: 24079712.
    View in: PubMed
  25. 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. PMID: 23843222.
    View in: PubMed
  26. O'Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013; 5(3):28. PMID: 23537139.
    View in: PubMed
  27. Woolstenhulme CJ, Parajuli S, Healey DW, Valverde DP, Petersen EN, Starosta AL, Guydosh NR, Johnson WE, Wilson DN, Buskirk AR. Nascent peptides that block protein synthesis in bacteria. Proc Natl Acad Sci U S A. 2013 Mar 5; 110(10):E878-87. PMID: 23431150.
    View in: PubMed
  28. 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. PMID: 22959562.
    View in: PubMed
  29. Warf MB, Shepherd BA, Johnson WE, Bass BL. Effects of ADARs on small RNA processing pathways in C. elegans. Genome Res. 2012 Aug; 22(8):1488-98. PMID: 22673872.
    View in: PubMed
  30. 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. PMID: 22257669.
    View in: PubMed
  31. 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; 7:513. PMID: 21772261.
    View in: PubMed
  32. Lyon GJ, Jiang T, Van Wijk R, Wang W, Bodily PM, Xing J, Tian L, Robison RJ, Clement M, Lin Y, Zhang P, Liu Y, Moore B, Glessner JT, Elia J, Reimherr F, van Solinge WW, Yandell M, Hakonarson H, Wang J, Johnson WE, Wei Z, Wang K. Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Discov Med. 2011 Jul; 12(62):41-55. PMID: 21794208.
    View in: PubMed
  33. Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen 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 ST, Pysher TJ, Jorde LB, Hakonarson H, Lillehaug JR, Biesecker LG, Yandell M, Arnesen T, Lyon GJ. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet. 2011 Jul 15; 89(1):28-43. PMID: 21700266.
    View in: PubMed
  34. Evan Johnson W, Welker NC, Bass BL. Dynamic linear model for the identification of miRNAs in next-generation sequencing data. Biometrics. 2011 Dec; 67(4):1206-14. PMID: 21385162.
    View in: PubMed
  35. Warf MB, Johnson WE, Bass BL. Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer. RNA. 2011 Apr; 17(4):563-77. PMID: 21307183.
    View in: PubMed
  36. Clement NL, Clement MJ, Snell Q, Johnson WE. Parallel Mapping Approaches for GNUMAP. IPDPS. 2011; 435-443. PMID: 23396612.
    View in: PubMed
  37. Rai K, Sarkar S, Broadbent TJ, Voas M, Grossmann KF, Nadauld LD, Dehghanizadeh S, Hagos FT, Li Y, Toth RK, Chidester S, Bahr TM, Johnson WE, Sklow B, Burt R, Cairns BR, Jones DA. DNA demethylase activity maintains intestinal cells in an undifferentiated state following loss of APC. Cell. 2010 Sep 17; 142(6):930-42. PMID: 20850014.
    View in: PubMed
  38. Thyagarajan B, Blaszczak AG, Chandler KJ, Watts JL, Johnson WE, Graves BJ. ETS-4 is a transcriptional regulator of life span in Caenorhabditis elegans. PLoS Genet. 2010 Sep; 6(9):e1001125. PMID: 20862312.
    View in: PubMed
  39. 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. PMID: 20838408.
    View in: PubMed
  40. Hollenhorst PC, Chandler KJ, Poulsen RL, Johnson WE, Speck NA, Graves BJ. DNA specificity determinants associate with distinct transcription factor functions. PLoS Genet. 2009 Dec; 5(12):e1000778. PMID: 20019798.
    View in: PubMed
  41. 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. PMID: 19861355.
    View in: PubMed
  42. Gottardo R, Li W, Johnson WE, Liu XS. A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments. Biometrics. 2008 Jun; 64(2):468-78. PMID: 17888037.
    View in: PubMed
  43. 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. PMID: 17727723.
    View in: PubMed
  44. 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. PMID: 16895995.
    View in: PubMed
  45. Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007 Jan; 8(1):118-27. PMID: 16632515.
    View in: PubMed
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