Adkins JN - Search Results

1

In silico method for modelling metabolism and gene product expression at genome scale.

Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. Lerman JA, et al. Among authors: adkins jn. Nat Commun. 2012 Jul 3;3:929. doi: 10.1038/ncomms1928. Nat Commun. 2012. PMID: 22760628 Free PMC article.

2

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.

Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Gupta N, et al. Among authors: adkins jn. Genome Res. 2007 Sep;17(9):1362-77. doi: 10.1101/gr.6427907. Epub 2007 Aug 9. Genome Res. 2007. PMID: 17690205 Free PMC article.

3

Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition.

Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, Smith RD, Dabney AR. Karpievitch YV, et al. Among authors: adkins jn. Bioinformatics. 2009 Oct 1;25(19):2573-80. doi: 10.1093/bioinformatics/btp426. Epub 2009 Jul 14. Bioinformatics. 2009. PMID: 19602524 Free PMC article.

4

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.

Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D, Weitz KK, Eils R, König R, Smith RD, Palsson BØ. Lewis NE, et al. Among authors: adkins jn. Mol Syst Biol. 2010 Jul;6:390. doi: 10.1038/msb.2010.47. Mol Syst Biol. 2010. PMID: 20664636 Free PMC article.

5

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.

Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Özdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjörnsdóttir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, Bumann D. Thiele I, et al. Among authors: adkins jn. BMC Syst Biol. 2011 Jan 18;5:8. doi: 10.1186/1752-0509-5-8. BMC Syst Biol. 2011. PMID: 21244678 Free PMC article.

6

Technologies and approaches to elucidate and model the virulence program of salmonella.

McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F. McDermott JE, et al. Among authors: adkins jn. Front Microbiol. 2011 Jun 2;2:121. doi: 10.3389/fmicb.2011.00121. eCollection 2011. Front Microbiol. 2011. PMID: 21687430 Free PMC article.

7

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.

Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO. Charusanti P, et al. Among authors: adkins jn. BMC Syst Biol. 2011 Oct 13;5:163. doi: 10.1186/1752-0509-5-163. BMC Syst Biol. 2011. PMID: 21995956 Free PMC article.

8

Comparative omics-driven genome annotation refinement: application across Yersiniae.

Schrimpe-Rutledge AC, Jones MB, Chauhan S, Purvine SO, Sanford JA, Monroe ME, Brewer HM, Payne SH, Ansong C, Frank BC, Smith RD, Peterson SN, Motin VL, Adkins JN. Schrimpe-Rutledge AC, et al. Among authors: adkins jn. PLoS One. 2012;7(3):e33903. doi: 10.1371/journal.pone.0033903. Epub 2012 Mar 27. PLoS One. 2012. PMID: 22479471 Free PMC article.

9

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ. Peterson ES, et al. Among authors: adkins jn. BMC Genomics. 2012 Apr 5;13:131. doi: 10.1186/1471-2164-13-131. BMC Genomics. 2012. PMID: 22480257 Free PMC article.

10

Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics.

Schrimpe-Rutledge AC, Fontès G, Gritsenko MA, Norbeck AD, Anderson DJ, Waters KM, Adkins JN, Smith RD, Poitout V, Metz TO. Schrimpe-Rutledge AC, et al. Among authors: adkins jn. J Proteome Res. 2012 Jul 6;11(7):3520-32. doi: 10.1021/pr3002996. Epub 2012 May 29. J Proteome Res. 2012. PMID: 22578083 Free PMC article.

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