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Items: 14

1.

QIIME allows analysis of high-throughput community sequencing data.

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R.

Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. Epub 2010 Apr 11. No abstract available.

2.

Proteomic analysis reveals virus-specific Hsp25 modulation in cardiac myocytes.

Li L, Sevinsky JR, Rowland MD, Bundy JL, Stephenson JL, Sherry B.

J Proteome Res. 2010 May 7;9(5):2460-71. doi: 10.1021/pr901151k.

3.

Systematic comparison of the human saliva and plasma proteomes.

Yan W, Apweiler R, Balgley BM, Boontheung P, Bundy JL, Cargile BJ, Cole S, Fang X, Gonzalez-Begne M, Griffin TJ, Hagen F, Hu S, Wolinsky LE, Lee CS, Malamud D, Melvin JE, Menon R, Mueller M, Qiao R, Rhodus NL, Sevinsky JR, States D, Stephenson JL, Than S, Yates JR, Yu W, Xie H, Xie Y, Omenn GS, Loo JA, Wong DT.

Proteomics Clin Appl. 2009 Jan 1;3(1):116-134.

4.

Proteomics of Pyrococcus furiosus, a hyperthermophilic archaeon refractory to traditional methods.

Lee AM, Sevinsky JR, Bundy JL, Grunden AM, Stephenson JL Jr.

J Proteome Res. 2009 Aug;8(8):3844-51. doi: 10.1021/pr801119h.

PMID:
19425607
5.

Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects.

Cargile BJ, Sevinsky JR, Essader AS, Eu JP, Stephenson JL Jr.

Electrophoresis. 2008 Jul;29(13):2768-78. doi: 10.1002/elps.200700701.

PMID:
18615785
6.

Whole genome searching with shotgun proteomic data: applications for genome annotation.

Sevinsky JR, Cargile BJ, Bunger MK, Meng F, Yates NA, Hendrickson RC, Stephenson JL Jr.

J Proteome Res. 2008 Jan;7(1):80-8. Epub 2007 Dec 7.

PMID:
18062665
7.

Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data.

Bunger MK, Cargile BJ, Sevinsky JR, Deyanova E, Yates NA, Hendrickson RC, Stephenson JL Jr.

J Proteome Res. 2007 Jun;6(6):2331-40. Epub 2007 May 9.

PMID:
17488105
8.

Minimizing back exchange in 18O/16O quantitative proteomics experiments by incorporation of immobilized trypsin into the initial digestion step.

Sevinsky JR, Brown KJ, Cargile BJ, Bundy JL, Stephenson JL Jr.

Anal Chem. 2007 Mar 1;79(5):2158-62. Epub 2007 Jan 24.

9.

Analysis of membrane proteins from human chronic myelogenous leukemia cells: comparison of extraction methods for multidimensional LC-MS/MS.

Ruth MC, Old WM, Emrick MA, Meyer-Arendt K, Aveline-Wolf LD, Pierce KG, Mendoza AM, Sevinsky JR, Hamady M, Knight RD, Resing KA, Ahn NG.

J Proteome Res. 2006 Mar;5(3):709-19.

PMID:
16512687
10.

Immobilized pH gradient isoelectric focusing as a first-dimension separation in shotgun proteomics.

Cargile BJ, Sevinsky JR, Essader AS, Stephenson JL Jr, Bundy JL.

J Biomol Tech. 2005 Sep;16(3):181-9. Review.

11.

Incorporating expression data in metabolic modeling: a case study of lactate dehydrogenase.

Downer J, Sevinsky JR, Ahn NG, Resing KA, Betterton MD.

J Theor Biol. 2006 Jun 7;240(3):464-74. Epub 2005 Dec 2.

PMID:
16325864
12.

Comparison of label-free methods for quantifying human proteins by shotgun proteomics.

Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, Ahn NG.

Mol Cell Proteomics. 2005 Oct;4(10):1487-502. Epub 2005 Jun 23.

13.
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