Publications


Johnson Lab Publications:

  1. Lam S, Mandrekar SJ, Gesthalter Y, Allen Ziegler KL, Seisler DK, Midthun DE, Mao JT, Aubry MC, McWilliams A, Sin DD, Shaipanich T, Liu G, Johnson E, Bild A, Lenburg ME, Ionescu DN, Mayo J, Yi JE, Tazelaar H, Harmsen WS, Smith J, Spira AE, Beane J, Limburg PJ, Szabo E; Cancer Prevention Network.. A Randomized Phase IIb Trial of myo-Inositol in Smokers with Bronchial Dysplasia. Cancer Prev Res (Phila). 2016 Dec;9(12):906-914. PubMed PMID: 27658890; PubMed Central PMCID: PMC5136333.
  2. Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE. BatchQC: interactive software for evaluating sample and batch effects in genomic data. Bioinformatics. 2016 Aug 18. pii: btw538. [Epub ahead of print] PubMed PMID: 27540268.
  3. 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 Apr 11;8:77-80. doi: 10.1016/j.gdata.2016.03.009. PubMed PMID: 27222804; PubMed Central PMCID: PMC4856813.
  4. 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 Apr 7;7:484. doi: 10.3389/fmicb.2016.00484. PubMed PMID: 27092134; PubMed Central PMCID: PMC4823605.
  5. 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. doi: 10.15252/msb.20156506. PubMed PMID: 26969729; PubMed Central PMCID: PMC4812528.
  6. 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. 2016;49(2):317-27. doi: 10.3233/JAD-150498. PubMed PMID: 26484917.
  7. 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 10;11(12):e1005713. doi: 10.1371/journal.pgen.1005713. PubMed PMID: 26658939; PubMed Central PMCID: PMC4675533.
  8. 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. doi: 10.1093/bioinformatics/btv377. PubMed PMID: 26209429; PubMed Central PMCID: PMC4804769.
  9. 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.
  10. 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. doi: 10.1186/s12920-015-0121-1. PubMed PMID: 26277095; PubMed Central PMCID: PMC4537781.
  11. MacNeil SM, Johnson WE, Li DY, Piccolo SR, Bild AH. Inferring pathway dysregulation in cancers from multiple types of omic data. Genome Med. 2015 Jun 26;7(1):61. doi: 10.1186/s13073-015-0189-4. PubMed PMID: 26170901; PubMed Central PMCID: PMC4499940.
  12. 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. doi: 10.1093/bioinformatics/btv031. PubMed PMID: 25617415; PubMed Central PMCID: PMC4443674.
  13. 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 14-3-3ζ via deacetylation of lysines within the 14-3-3ζ binding pocket. J Biol Chem. 2015 May 15;290(20):12487-96. doi: 10.1074/jbc.M114.607580. PubMed PMID: 25770209; PubMed Central PMCID: PMC4432270.
  14. Hong C, Manimaran S, Johnson WE. PathoQC: Computationally Efficient Read Preprocessing and Quality Control for High-Throughput Sequencing Data Sets. Cancer Inform. 2015 May 12;13(Suppl 1):167-76. doi: 10.4137/CIN.S13890. Review. PubMed PMID: 25983538; PubMed Central PMCID: PMC4429651.
  15. 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. doi: 10.1261/rna.048801.114. PubMed PMID: 25805852; PubMed Central PMCID: PMC4408787.
  16. 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 16;9(3):e0003628. doi: 10.1371/journal.pntd.0003628. PubMed PMID: 25775236; PubMed Central PMCID: PMC4361501.
  17. 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 Feb 17;3:e761. doi: 10.7717/peerj.761. PubMed PMID: 25737810; PubMed Central PMCID: PMC4338773.
  18. 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. doi: 10.1261/rna.046060.114. PubMed PMID: 25519487; PubMed Central PMCID: PMC4338344.
  19. 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. doi: 10.2217/bmm.15.21. PubMed PMID: 26079961.
  20. 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 Oct 21;15:918. doi: 10.1186/1471-2164-15-918. PubMed PMID: 25336203; PubMed Central PMCID: PMC4218995.
  21. 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 Sep 5;2:33. doi: 10.1186/2049-2618-2-33. PubMed PMID: 25225611; PubMed Central PMCID: PMC4164323.
  22. 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. doi: 10.1186/1471-2105-15-262. PubMed PMID: 25091138; PubMed Central PMCID: PMC4131054.
  23. 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.

  24. 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.

  25. 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.

  26. 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.

  27. 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 Sep 30;6:35. PubMed PMID: 24079712; PubMed Central PMCID: PMC3850967.

  28. 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. PubMed PMID: 23431150; PubMed Central PMCID: PMC3593848.

  29. 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. PubMed PMID: 23537139; PubMed Central PMCID: PMC3706896.

  30. 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.

  31. 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. PubMed PMID: 22673872; PubMed Central PMCID: PMC3409262.

  32. 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.

  33. 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.

  34. 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.

  35. 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. PubMed PMID: 21700266; PubMed Central PMCID: PMC3135802.

  36. 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. PubMed PMID: 21794208; PubMed Central PMCID: PMC3544941.

  37. 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. PubMed PMID: 21307183; PubMed Central PMCID: PMC3062169.

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

  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. PubMed PMID: 20838408; PubMed Central PMCID: PMC3880143.

  40. 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. PubMed PMID: 20850014; PubMed Central PMCID: PMC2943938.

  41. 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 16;6(9):e1001125. PubMed PMID: 20862312; PubMed Central PMCID: PMC2940738.

  42. 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.

  43. 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. PubMed PMID: 20019798; PubMed Central PMCID: PMC2787013.

  44. 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.

  45. 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. PubMed PMID: 17888037.

  46. 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.

  47. 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.

  48. 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.