Johnson JE - Search Results

1

Integrative meta-omics in Galaxy and beyond.

Schiml VC, Delogu F, Kumar P, Kunath B, Batut B, Mehta S, Johnson JE, Grüning B, Pope PB, Jagtap PD, Griffin TJ, Arntzen MØ. Schiml VC, et al. Among authors: johnson je. Environ Microbiome. 2023 Jul 7;18(1):56. doi: 10.1186/s40793-023-00514-9. Environ Microbiome. 2023. PMID: 37420292 Free PMC article.

2

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.

Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, Onsongo G, Frey BL, Griffin TJ, Smith LM. Sheynkman GM, et al. Among authors: johnson je. BMC Genomics. 2014 Aug 22;15(1):703. doi: 10.1186/1471-2164-15-703. BMC Genomics. 2014. PMID: 25149441 Free PMC article.

3

Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.

Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, Shenykman GM, Bandhakavi S, Smith LM, Griffin TJ. Jagtap PD, et al. Among authors: johnson je. J Proteome Res. 2014 Dec 5;13(12):5898-908. doi: 10.1021/pr500812t. Epub 2014 Oct 23. J Proteome Res. 2014. PMID: 25301683 Free PMC article.

4

Metaproteomic analysis using the Galaxy framework.

Jagtap PD, Blakely A, Murray K, Stewart S, Kooren J, Johnson JE, Rhodus NL, Rudney J, Griffin TJ. Jagtap PD, et al. Among authors: johnson je. Proteomics. 2015 Oct;15(20):3553-65. doi: 10.1002/pmic.201500074. Epub 2015 Jul 24. Proteomics. 2015. PMID: 26058579

5

NCBI BLAST+ integrated into Galaxy.

Cock PJ, Chilton JM, Grüning B, Johnson JE, Soranzo N. Cock PJ, et al. Among authors: johnson je. Gigascience. 2015 Aug 25;4:39. doi: 10.1186/s13742-015-0080-7. eCollection 2015. Gigascience. 2015. PMID: 26336600 Free PMC article.

6

Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics.

Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT. Vermillion KL, et al. Among authors: johnson je. J Proteome Res. 2015 Nov 6;14(11):4792-804. doi: 10.1021/acs.jproteome.5b00575. Epub 2015 Oct 23. J Proteome Res. 2015. PMID: 26435507

7

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.

Rudney JD, Jagtap PD, Reilly CS, Chen R, Markowski TW, Higgins L, Johnson JE, Griffin TJ. Rudney JD, et al. Among authors: johnson je. Microbiome. 2015 Dec 19;3:69. doi: 10.1186/s40168-015-0136-z. Microbiome. 2015. PMID: 26684897 Free PMC article.

8

Proteogenomic Analysis of a Hibernating Mammal Indicates Contribution of Skeletal Muscle Physiology to the Hibernation Phenotype.

Anderson KJ, Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT. Anderson KJ, et al. Among authors: johnson je. J Proteome Res. 2016 Apr 1;15(4):1253-61. doi: 10.1021/acs.jproteome.5b01138. Epub 2016 Mar 3. J Proteome Res. 2016. PMID: 26903422

9

An Accessible Proteogenomics Informatics Resource for Cancer Researchers.

Chambers MC, Jagtap PD, Johnson JE, McGowan T, Kumar P, Onsongo G, Guerrero CR, Barsnes H, Vaudel M, Martens L, Grüning B, Cooke IR, Heydarian M, Reddy KL, Griffin TJ. Chambers MC, et al. Among authors: johnson je. Cancer Res. 2017 Nov 1;77(21):e43-e46. doi: 10.1158/0008-5472.CAN-17-0331. Cancer Res. 2017. PMID: 29092937 Free PMC article.

10

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.

Blank C, Easterly C, Gruening B, Johnson J, Kolmeder CA, Kumar P, May D, Mehta S, Mesuere B, Brown Z, Elias JE, Hervey WJ, McGowan T, Muth T, Nunn B, Rudney J, Tanca A, Griffin TJ, Jagtap PD. Blank C, et al. Among authors: johnson j. Proteomes. 2018 Jan 31;6(1):7. doi: 10.3390/proteomes6010007. Proteomes. 2018. PMID: 29385081 Free PMC article.

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