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Items: 1 to 50 of 88

1.

Improving network inference algorithms using resampling methods.

Colby SM, McClure RS, Overall CC, Renslow RS, McDermott JE.

BMC Bioinformatics. 2018 Oct 12;19(1):376. doi: 10.1186/s12859-018-2402-0.

2.

Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma.

Sharpnack MF, Ranbaduge N, Srivastava A, Cerciello F, Codreanu SG, Liebler DC, Mascaux C, Miles WO, Morris R, McDermott JE, Sharpnack JL, Amann J, Maher CA, Machiraju R, Wysocki VH, Govindan R, Mallick P, Coombes KR, Huang K, Carbone DP.

J Thorac Oncol. 2018 Oct;13(10):1519-1529. doi: 10.1016/j.jtho.2018.06.025. Epub 2018 Jul 11.

PMID:
30017829
3.

Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors.

Duhen T, Duhen R, Montler R, Moses J, Moudgil T, de Miranda NF, Goodall CP, Blair TC, Fox BA, McDermott JE, Chang SC, Grunkemeier G, Leidner R, Bell RB, Weinberg AD.

Nat Commun. 2018 Jul 13;9(1):2724. doi: 10.1038/s41467-018-05072-0.

4.

Class 4 Semaphorins and Plexin-B receptors regulate GABAergic and glutamatergic synapse development in the mammalian hippocampus.

McDermott JE, Goldblatt D, Paradis S.

Mol Cell Neurosci. 2018 Oct;92:50-66. doi: 10.1016/j.mcn.2018.06.008. Epub 2018 Jul 4.

PMID:
29981480
5.

Species-specific transcriptomic network inference of interspecies interactions.

McClure RS, Overall CC, Hill EA, Song HS, Charania M, Bernstein HC, McDermott JE, Beliaev AS.

ISME J. 2018 Aug;12(8):2011-2023. doi: 10.1038/s41396-018-0145-6. Epub 2018 May 24.

PMID:
29795448
6.

Inhibition of interleukin-1 receptor-associated kinase-1 is a therapeutic strategy for acute myeloid leukemia subtypes.

Hosseini MM, Kurtz SE, Abdelhamed S, Mahmood S, Davare MA, Kaempf A, Elferich J, McDermott JE, Liu T, Payne SH, Shinde U, Rodland KD, Mori M, Druker BJ, Singer JW, Agarwal A.

Leukemia. 2018 Nov;32(11):2374-2387. doi: 10.1038/s41375-018-0112-2. Epub 2018 Mar 29.

PMID:
29743719
7.

Time-resolved proteome profiling of normal lung development.

Moghieb A, Clair G, Mitchell HD, Kitzmiller J, Zink EM, Kim YM, Petyuk V, Shukla A, Moore RJ, Metz TO, Carson J, McDermott JE, Corley RA, Whitsett JA, Ansong C.

Am J Physiol Lung Cell Mol Physiol. 2018 Jul 1;315(1):L11-L24. doi: 10.1152/ajplung.00316.2017. Epub 2018 Mar 8.

PMID:
29516783
8.

Ten simple rules for drawing scientific comics.

McDermott JE, Partridge M, Bromberg Y.

PLoS Comput Biol. 2018 Jan 4;14(1):e1005845. doi: 10.1371/journal.pcbi.1005845. eCollection 2018 Jan. No abstract available.

9.

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome.

Maier TV, Lucio M, Lee LH, VerBerkmoes NC, Brislawn CJ, Bernhardt J, Lamendella R, McDermott JE, Bergeron N, Heinzmann SS, Morton JT, González A, Ackermann G, Knight R, Riedel K, Krauss RM, Schmitt-Kopplin P, Jansson JK.

MBio. 2017 Oct 17;8(5). pii: e01343-17. doi: 10.1128/mBio.01343-17.

10.

Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction.

Wang J, Ma Z, Carr SA, Mertins P, Zhang H, Zhang Z, Chan DW, Ellis MJ, Townsend RR, Smith RD, McDermott JE, Chen X, Paulovich AG, Boja ES, Mesri M, Kinsinger CR, Rodriguez H, Rodland KD, Liebler DC, Zhang B.

Mol Cell Proteomics. 2017 Jan;16(1):121-134. doi: 10.1074/mcp.M116.060301. Epub 2016 Nov 11.

11.

Cells Respond to Distinct Nanoparticle Properties with Multiple Strategies As Revealed by Single-Cell RNA-Seq.

Mitchell HD, Markillie LM, Chrisler WB, Gaffrey MJ, Hu D, Szymanski CJ, Xie Y, Melby ES, Dohnalkova A, Taylor RC, Grate EK, Cooley SK, McDermott JE, Heredia-Langner A, Orr G.

ACS Nano. 2016 Nov 22;10(11):10173-10185. Epub 2016 Oct 31.

PMID:
27788331
12.

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus.

McDermott JE, Mitchell HD, Gralinski LE, Eisfeld AJ, Josset L, Bankhead A 3rd, Neumann G, Tilton SC, Schäfer A, Li C, Fan S, McWeeney S, Baric RS, Katze MG, Waters KM.

BMC Syst Biol. 2016 Sep 23;10(1):93.

13.

Network analysis of transcriptomics expands regulatory landscapes in Synechococcus sp. PCC 7002.

McClure RS, Overall CC, McDermott JE, Hill EA, Markillie LM, McCue LA, Taylor RC, Ludwig M, Bryant DA, Beliaev AS.

Nucleic Acids Res. 2016 Oct 14;44(18):8810-8825. Epub 2016 Aug 27.

14.

Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth.

Bernstein HC, McClure RS, Hill EA, Markillie LM, Chrisler WB, Romine MF, McDermott JE, Posewitz MC, Bryant DA, Konopka AE, Fredrickson JK, Beliaev AS.

MBio. 2016 Jul 26;7(4). pii: e00949-16. doi: 10.1128/mBio.00949-16.

15.

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway.

Shi T, Niepel M, McDermott JE, Gao Y, Nicora CD, Chrisler WB, Markillie LM, Petyuk VA, Smith RD, Rodland KD, Sorger PK, Qian WJ, Wiley HS.

Sci Signal. 2016 Jul 12;9(436):rs6. doi: 10.1126/scisignal.aaf0891.

16.

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD; CPTAC Investigators.

Cell. 2016 Jul 28;166(3):755-765. doi: 10.1016/j.cell.2016.05.069. Epub 2016 Jun 29.

17.

The landscape of viral proteomics and its potential to impact human health.

Oxford KL, Wendler JP, McDermott JE, White Iii RA, Powell JD, Jacobs JM, Adkins JN, Waters KM.

Expert Rev Proteomics. 2016 Jun;13(6):579-91. doi: 10.1080/14789450.2016.1184091. Epub 2016 May 26. Review.

PMID:
27133506
18.

Prediction of multi-drug resistance transporters using a novel sequence analysis method.

McDermott JE, Bruillard P, Overall CC, Gosink L, Lindemann SR.

Version 2. F1000Res. 2015 Mar 9 [revised 2015 Jan 1];4:60. doi: 10.12688/f1000research.6200.2. eCollection 2015.

19.

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts.

Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJ, Li S, Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Liu T, Kim S, McDermott JE, Payne SH, Petyuk VA, Rodland KD, Smith RD, Yang F, Chan DW, Zhang B, Zhang H, Zhang Z, Zhou JY, Liebler DC.

J Proteome Res. 2016 Mar 4;15(3):691-706. doi: 10.1021/acs.jproteome.5b00859. Epub 2015 Dec 22.

20.

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.

21.

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.

22.

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. Review.

23.

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.

24.

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.

25.

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.

26.

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.

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 Aug 16. pii: mcp.O113.030932. [Epub ahead of print]

28.

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.

29.

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.

PMID:
24878722
30.

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.

31.

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.

32.

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.

33.

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.

34.

Reproducibility: two more red flags for suspect work.

McDermott JE.

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

PMID:
23868253
35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

Modeling dynamic regulatory processes in stroke.

McDermott JE, Jarman K, Taylor R, Lancaster M, Shankaran H, Vartanian KB, Stevens SL, Stenzel-Poore MP, Sanfilippo A.

PLoS Comput Biol. 2012;8(10):e1002722. doi: 10.1371/journal.pcbi.1002722. Epub 2012 Oct 11.

41.

A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments.

Matzke MM, Brown JN, Gritsenko MA, Metz TO, Pounds JG, Rodland KD, Shukla AK, Smith RD, Waters KM, McDermott JE, Webb-Robertson BJ.

Proteomics. 2013 Feb;13(3-4):493-503. doi: 10.1002/pmic.201200269. Epub 2012 Nov 8. Review.

42.

Mio/dChREBP coordinately increases fat mass by regulating lipid synthesis and feeding behavior in Drosophila.

Sassu ED, McDermott JE, Keys BJ, Esmaeili M, Keene AC, Birnbaum MJ, DiAngelo JR.

Biochem Biophys Res Commun. 2012 Sep 14;426(1):43-8. doi: 10.1016/j.bbrc.2012.08.028. Epub 2012 Aug 12.

43.

Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling.

Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim YM, Nakayasu ES, Li J, Kidwai A, Niemann G, Brown RN, Metz TO, McAteer K, Heffron F, Peterson SN, Motin V, Palsson BO, Smith RD, Adkins JN.

Curr Top Microbiol Immunol. 2013;363:21-41. doi: 10.1007/82_2012_247. Review.

44.

Suppressed expression of T-box transcription factors is involved in senescence in chronic obstructive pulmonary disease.

Acquaah-Mensah GK, Malhotra D, Vulimiri M, McDermott JE, Biswal S.

PLoS Comput Biol. 2012;8(7):e1002597. doi: 10.1371/journal.pcbi.1002597. Epub 2012 Jul 19. Erratum in: PLoS Comput Biol. 2017 Jan 27;13(1):e1005263.

45.

Identification and validation of Ifit1 as an important innate immune bottleneck.

McDermott JE, Vartanian KB, Mitchell H, Stevens SL, Sanfilippo A, Stenzel-Poore MP.

PLoS One. 2012;7(6):e36465. doi: 10.1371/journal.pone.0036465. Epub 2012 Jun 20.

46.

Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis.

McDermott JE, Diamond DL, Corley C, Rasmussen AL, Katze MG, Waters KM.

BMC Syst Biol. 2012 Apr 30;6:28. doi: 10.1186/1752-0509-6-28.

47.

HPV genotypes in high grade cervical lesions and invasive cervical carcinoma as detected by two commercial DNA assays, North Carolina, 2001-2006.

Hariri S, Steinau M, Rinas A, Gargano JW, Ludema C, Unger ER, Carter AL, Grant KL, Bamberg M, McDermott JE, Markowitz LE, Brewer NT, Smith JS.

PLoS One. 2012;7(3):e34044. doi: 10.1371/journal.pone.0034044. Epub 2012 Mar 29.

48.

Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation.

Diamond DL, Krasnoselsky AL, Burnum KE, Monroe ME, Webb-Robertson BJ, McDermott JE, Yeh MM, Dzib JF, Susnow N, Strom S, Proll SC, Belisle SE, Purdy DE, Rasmussen AL, Walters KA, Jacobs JM, Gritsenko MA, Camp DG, Bhattacharya R, Perkins JD, Carithers RL Jr, Liou IW, Larson AM, Benecke A, Waters KM, Smith RD, Katze MG.

Hepatology. 2012 Jul;56(1):28-38. doi: 10.1002/hep.25649. Epub 2012 Apr 24.

49.

An adaptive coarse graining method for signal transduction in three dimensions.

Archuleta MN, McDermott JE, Edwards JS, Resat H.

Fundam Inform. 2012;118(4). doi: 10.3233/FI-2012-720.

50.

Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems.

McDermott JE, Shankaran H, Eisfeld AJ, Belisle SE, Neuman G, Li C, McWeeney S, Sabourin C, Kawaoka Y, Katze MG, Waters KM.

BMC Syst Biol. 2011 Nov 11;5:190. doi: 10.1186/1752-0509-5-190.

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