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ChIP-Seq Analysis of the σE Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response.

Li J, Overall CC, Johnson RC, Jones MB, McDermott JE, Heffron F, Adkins JN, Cambronne ED.

PLoS One. 2015 Sep 21;10(9):e0138466. doi: 10.1371/journal.pone.0138466. eCollection 2015.


Mio acts in the Drosophila brain to control nutrient storage and feeding.

Docherty JE, Manno JE, McDermott JE, DiAngelo JR.

Gene. 2015 Sep 1;568(2):190-5. doi: 10.1016/j.gene.2015.05.055. Epub 2015 May 27.


Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics.

Webb-Robertson BJ, Wiberg HK, Matzke MM, Brown JN, Wang J, McDermott JE, Smith RD, Rodland KD, Metz TO, Pounds JG, Waters KM.

J Proteome Res. 2015 May 1;14(5):1993-2001. doi: 10.1021/pr501138h. Epub 2015 Apr 22.


Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in σ(E)-regulated SPI-2 gene expression.

Li J, Overall CC, Nakayasu ES, Kidwai AS, Jones MB, Johnson RC, Nguyen NT, McDermott JE, Ansong C, Heffron F, Cambronne ED, Adkins JN.

Front Microbiol. 2015 Feb 10;6:27. doi: 10.3389/fmicb.2015.00027. eCollection 2015.


Global analysis of Salmonella alternative sigma factor E on protein translation.

Li J, Nakayasu ES, Overall CC, Johnson RC, Kidwai AS, McDermott JE, Ansong C, Heffron F, Cambronne ED, Adkins JN.

J Proteome Res. 2015 Apr 3;14(4):1716-26. doi: 10.1021/pr5010423. Epub 2015 Feb 27.


Bayesian proteoform modeling improves protein quantification of global proteomic measurements.

Webb-Robertson BJ, Matzke MM, Datta S, Payne SH, Kang J, Bramer LM, Nicora CD, Shukla AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM.

Mol Cell Proteomics. 2014 Dec;13(12):3639-46. doi: 10.1074/mcp.M113.030932.


CpG preconditioning regulates miRNA expression that modulates genomic reprogramming associated with neuroprotection against ischemic injury.

Vartanian KB, Mitchell HD, Stevens SL, Conrad VK, McDermott JE, Stenzel-Poore MP.

J Cereb Blood Flow Metab. 2015 Feb;35(2):257-66. doi: 10.1038/jcbfm.2014.193. Epub 2014 Nov 12.


Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements.

Webb-Robertson BJ, Matzke MM, Datta S, Payne SH, Kang J, Bramer LM, Nicora CD, Shukla AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM.

Mol Cell Proteomics. 2014 Aug 16. pii: mcp.O113.030932. [Epub ahead of print]


Integrative genomics and computational systems medicine.

McDermott JE, Huang Y, Zhang B, Xu H, Zhao Z.

Biomed Res Int. 2014;2014:945253. doi: 10.1155/2014/945253. Epub 2014 Jun 15. No abstract available.


Computational methods for omics data.

Zhao Z, Zhang B, Huang Y, Xu H, McDermott JE.

Int J Comput Biol Drug Des. 2014;7(2-3):97-101. doi: 10.1504/IJCBDD.2014. Epub 2014 May 28. No abstract available.


Interdisciplinary dialogue for education, collaboration, and innovation: intelligent Biology and Medicine in and beyond 2013.

Zhang B, Huang Y, McDermott JE, Posey RH, Xu H, Zhao Z.

BMC Genomics. 2013;14 Suppl 8:S1. doi: 10.1186/1471-2164-14-S8-S1. Epub 2013 Dec 9.


A semiautomated framework for integrating expert knowledge into disease marker identification.

Wang J, Webb-Robertson BJ, Matzke MM, Varnum SM, Brown JN, Riensche RM, Adkins JN, Jacobs JM, Hoidal JR, Scholand MB, Pounds JG, Blackburn MR, Rodland KD, McDermott JE.

Dis Markers. 2013;35(5):513-23. doi: 10.1155/2013/613529. Epub 2013 Oct 10.


A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses.

Mitchell HD, Eisfeld AJ, Sims AC, McDermott JE, Matzke MM, Webb-Robertson BJ, Tilton SC, Tchitchek N, Josset L, Li C, Ellis AL, Chang JH, Heegel RA, Luna ML, Schepmoes AA, Shukla AK, Metz TO, Neumann G, Benecke AG, Smith RD, Baric RS, Kawaoka Y, Katze MG, Waters KM.

PLoS One. 2013 Jul 25;8(7):e69374. doi: 10.1371/journal.pone.0069374. Print 2013.


Genus-optimized strategy for the identification of chlamydial type III secretion substrates.

Hovis KM, Mojica S, McDermott JE, Pedersen L, Simhi C, Rank RG, Myers GS, Ravel J, Hsia RC, Bavoil PM.

Pathog Dis. 2013 Dec;69(3):213-22. doi: 10.1111/2049-632X.12070. Epub 2013 Aug 14.


Reproducibility: two more red flags for suspect work.

McDermott JE.

Nature. 2013 Jul 18;499(7458):284. doi: 10.1038/499284b. No abstract available.


Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes.

Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F, Smith RD, Peterson SN, Ansong C, Hyduke DR, Metz TO, Adkins JN.

Mol Biosyst. 2013 Jun;9(6):1522-34. doi: 10.1039/c3mb25598k. Epub 2013 Apr 5.


Sequential projection pursuit principal component analysis--dealing with missing data associated with new -omics technologies.

Webb-Robertson BJ, Matzke MM, Metz TO, McDermott JE, Walker H, Rodland KD, Pounds JG, Waters KM.

Biotechniques. 2013 Mar;54(3):165-8. doi: 10.2144/000113978.


RNA type III secretion signals that require Hfq.

Niemann GS, Brown RN, Mushamiri IT, Nguyen NT, Taiwo R, Stufkens A, Smith RD, Adkins JN, McDermott JE, Heffron F.

J Bacteriol. 2013 May;195(10):2119-25. doi: 10.1128/JB.00024-13. Epub 2013 Feb 8.


Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data.

McDermott JE, Wang J, Mitchell H, Webb-Robertson BJ, Hafen R, Ramey J, Rodland KD.

Expert Opin Med Diagn. 2013 Jan;7(1):37-51.


A multi-omic systems approach to elucidating Yersinia virulence mechanisms.

Ansong C, Schrimpe-Rutledge AC, Mitchell HD, Chauhan S, Jones MB, Kim YM, McAteer K, Deatherage Kaiser BL, Dubois JL, Brewer HM, Frank BC, McDermott JE, Metz TO, Peterson SN, Smith RD, Motin VL, Adkins JN.

Mol Biosyst. 2013 Jan 27;9(1):44-54. doi: 10.1039/c2mb25287b. Epub 2012 Nov 13.

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