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Items: 1 to 20 of 79

1.

Proteome profiling outperforms transcriptome profiling for co-expression 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. 2016 Nov 11. pii: mcp.M116.060301. [Epub ahead of print]

2.

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 Oct 31. [Epub ahead of print]

PMID:
27788331
3.

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.

4.

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.

5.

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.

6.

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.

7.

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 IeM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD; CPTAC Investigators..

Cell. 2016 Jul 28;166(3):755-65. doi: 10.1016/j.cell.2016.05.069.

PMID:
27372738
8.

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.

PMID:
27133506
9.

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.

10.

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.

11.

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.

12.

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.

13.

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. Review.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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]

19.

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. No abstract available.

20.

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. No abstract available.

PMID:
24878722
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