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Items: 18


ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models.

Sloutsky R, Naegle KM.

Elife. 2019 Oct 17;8. pii: e47676. doi: 10.7554/eLife.47676.


Predicting Patient Response to the Antiarrhythmic Mexiletine Based on Genetic Variation.

Zhu W, Mazzanti A, Voelker TL, Hou P, Moreno JD, Angsutararux P, Naegle KM, Priori SG, Silva JR.

Circ Res. 2019 Feb 15;124(4):539-552. doi: 10.1161/CIRCRESAHA.118.314050.


Proteome-Level Analysis Indicates Global Mechanisms for Post-Translational Regulation of RRM Domains.

Sloutsky R, Naegle KM.

J Mol Biol. 2018 Jan 5;430(1):41-44. doi: 10.1016/j.jmb.2017.11.001. Epub 2017 Nov 14.


Using ProteomeScout: A Resource of Post-Translational Modifications, Their Experiments, and the Proteins That They Annotate.

Mooradian AD, Held JM, Naegle KM.

Curr Protoc Bioinformatics. 2017 Sep 13;59:13.32.1-13.32.27. doi: 10.1002/cpbi.31.


Ensemble clustering of phosphoproteomic data identifies differences in protein interactions and cell-cell junction integrity of HER2-overexpressing cells.

Schaberg KE, Shirure VS, Worley EA, George SC, Naegle KM.

Integr Biol (Camb). 2017 Jun 19;9(6):539-547. doi: 10.1039/c7ib00054e.


High-Resolution Identification of Specificity Determining Positions in the LacI Protein Family Using Ensembles of Sub-Sampled Alignments.

Sloutsky R, Naegle KM.

PLoS One. 2016 Sep 28;11(9):e0162579. doi: 10.1371/journal.pone.0162579. eCollection 2016.


Avoiding common pitfalls when clustering biological data.

Ronan T, Qi Z, Naegle KM.

Sci Signal. 2016 Jun 14;9(432):re6. doi: 10.1126/scisignal.aad1932. Review.


Different Epidermal Growth Factor Receptor (EGFR) Agonists Produce Unique Signatures for the Recruitment of Downstream Signaling Proteins.

Ronan T, Macdonald-Obermann JL, Huelsmann L, Bessman NJ, Naegle KM, Pike LJ.

J Biol Chem. 2016 Mar 11;291(11):5528-40. doi: 10.1074/jbc.M115.710087. Epub 2016 Jan 19.


Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations.

Holehouse AS, Naegle KM.

PLoS One. 2015 Dec 14;10(12):e0144692. doi: 10.1371/journal.pone.0144692. eCollection 2015.


Injury-Induced HDAC5 Nuclear Export Is Essential for Axon Regeneration.

Cho Y, Sloutsky R, Naegle KM, Cavalli V.

Cell. 2015 Apr 23;161(3):691. doi: 10.1016/j.cell.2015.04.019. Epub 2015 Apr 23. No abstract available.


ProteomeScout: a repository and analysis resource for post-translational modifications and proteins.

Matlock MK, Holehouse AS, Naegle KM.

Nucleic Acids Res. 2015 Jan;43(Database issue):D521-30. doi: 10.1093/nar/gku1154. Epub 2014 Nov 20.


Injury-induced HDAC5 nuclear export is essential for axon regeneration.

Cho Y, Sloutsky R, Naegle KM, Cavalli V.

Cell. 2013 Nov 7;155(4):894-908. doi: 10.1016/j.cell.2013.10.004. Erratum in: Cell. 2015 Apr 23;161(3):691.


Phosphoproteomics of collagen receptor networks reveals SHP-2 phosphorylation downstream of wild-type DDR2 and its lung cancer mutants.

Iwai LK, Payne LS, Luczynski MT, Chang F, Xu H, Clinton RW, Paul A, Esposito EA, Gridley S, Leitinger B, Naegle KM, Huang PH.

Biochem J. 2013 Sep 15;454(3):501-13. doi: 10.1042/BJ20121750.


Accounting for noise when clustering biological data.

Sloutsky R, Jimenez N, Swamidass SJ, Naegle KM.

Brief Bioinform. 2013 Jul;14(4):423-36. doi: 10.1093/bib/bbs057. Epub 2012 Oct 14.


Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions.

Naegle KM, White FM, Lauffenburger DA, Yaffe MB.

Mol Biosyst. 2012 Oct;8(10):2771-82. doi: 10.1039/c2mb25200g.


MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets.

Naegle KM, Welsch RE, Yaffe MB, White FM, Lauffenburger DA.

PLoS Comput Biol. 2011 Jul;7(7):e1002119. doi: 10.1371/journal.pcbi.1002119. Epub 2011 Jul 21.


PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies.

Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM.

Mol Cell Proteomics. 2010 Nov;9(11):2558-70. doi: 10.1074/mcp.M110.001206. Epub 2010 Jul 14.


An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells.

Joughin BA, Naegle KM, Huang PH, Yaffe MB, Lauffenburger DA, White FM.

Mol Biosyst. 2009 Jan;5(1):59-67. doi: 10.1039/b815075c. Epub 2008 Oct 30.

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