Publications

Preprints

  1. Sloutsky, Roman and Kristen M. Naegle. “Accuracy through Subsampling of Protein EvolutioN: Analyzing and reconstructing protein divergence using an ensemble approach”. 

Publications

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  1. Sloutsky, Roman and Kristen M. Naegle. Proteome-Level Analysis Indicates Global Mechanisms for Post-Translational Regulation of RRM Domains. J Mol Biol. 2017 Nov 14. pii: S0022-2836(17)30539-9. doi: 10.1016/j.jmb.2017.11.001. [Epub ahead of print] PubMed PMID: 29146174. Read.
  2. Mooradian, A. D., Held, J. M., & Naegle, K. M. (2017). Using ProteomeScout: A resource of post-translational modifications, their experiments, and the proteins that they annotate. Current Protocols in Bioinformatics, 59, 13.32.1–13.32.27. doi: 10.1002/cpbi.31. Read
  3. Schaberg, Katherine E., Venktesh S Shirure, Elizabeth A Worley, Steven C George, and Kristen M Naegle. “Ensemble Clustering of Phosphoproteomic Data Identifies Differences in Protein Interactions and Cell-Cell Junction Integrity of HER2-Overexpressing Cells.” Integr. Biol., 2017. doi:10.1039/C7IB00054E. Read

  4. Sloutsky, Roman, and Kristen M. Naegle. “High-Resolution Identification of Specificity Determining Positions in the LacI Protein Family Using Ensembles of Sub-Sampled Alignments.” PLOS ONE 11, no. 9 (2016): e0162579. Read

  5. Noren, David P., Byron L. Long, Raquel Norel, Kahn Rrhissorrakrai, Kenneth Hess, Chenyue Wendy Hu, Alex J. Bisberg, et al. “A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis.” PLOS Computational Biology 12, no. 6 (2016). Read *Naegle lab members Tom Ronan, Jennifer Flynn and Kristen Naegle contributed as part of the DREAM 9 AML-OPC Consortium

  6. Ronan, Tom, Zhijie Qi, and Kristen M. Naegle. “Avoiding Common Pitfalls When Clustering Biological Data.” Sci. Signal 9, no. 432 (2016): re6. doi 10.1126/scisignal.aad1932. Abstract Reprint Full Text.

    Screen Shot 2016-06-16 at 1.47.29 PM

    • One of the top 5 most accessed Science journal articles and made the home page of Science.
    • Most tweeted article in history of Science Signaling.
  7. Ronan T, Macdonald-Obermann JL, Huelsmann L, Bessman NJ, Naegle KM*, L.J. Pike* Different EGF Receptor Agonists Produce Unique Signatures for the Recruitment of Downstream Signaling Protein. The Journal of biological chemistry. 2016; PMID: 26786109 *co-corresponding authors  Read
    Tom's talented wife Sarah made this for possible cover art as Article of the week. Although it wasn't chosen, it's one of our favorites!

    Tom’s talented wife Sarah made this for possible cover art as Article of the week. Although it wasn’t chosen, it’s one of our favorites!

  8. Naegle K*, Gough NR, Yaffe MB*. Criteria for biological reproducibility: what does “n” mean? Science signaling. 2015; 8(371):fs7. PMID: 25852186 *co-corresponding authors Read
  9.  Holehouse AS, Naegle KM. Reproducible Analysis of Post-Translational
    Modifications in Proteomes-Application to Human Mutations. PloS one. 2015;
    10(12):e0144692. PMID: 26659599, PMCID: PMC4685989 Read
  10. Matlock MK, Holehouse AS, Naegle KM. ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. Nucleic acids research. 2015; 43(Database issue):D521-30. PMID: 25414335, PMCID: PMC4383955. Read
  11. Cho Y, Sloutsky R, Naegle KM, Cavalli V. Injury-induced HDAC5 nuclear export is essential for axon regeneration. Cell. 2013; 155(4):894-908. NIHMSID: NIHMS570481, PMID: 24209626, PMCID: PMC3987749 Read
  12. Iwai LK, Payne LS, Luczynski MT, Chang F, Xu H, Clinton RW, Paul A, Esposito EA, Gridley S, Leitinger B, Naegle KM, and PH Huang. Phosphoproteomics of
    collagen receptor networks reveals SHP-2 phosphorylation downstream of wild-type DDR2 and its lung cancer mutants. The Biochemical journal. 2013; 454(3):501-13. PMID: 23822953, PMCID: PMC3893797 Read
  13. Sloutsky R, Jimenez N, Swamidass SJ, Naegle KM. Accounting for noise when
    clustering biological data. Briefings in bioinformatics. 2013; 14(4):423-36. PMID: 23063929 Read
  14. Naegle KM, White FM, Lauffenburger DA, Yaffe MB. Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions. Molecular BioSystems. 2012; 8(10):2771-82. NIHMSID: NIHMS402706 PMID:
    22851037, PMCID: PMC3501258 Read
  15. Naegle KM, Welsch RE, Yaffe MB, White FM, Lauffenburger DA. MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets. PLoS computational biology. 2011;
    7(7):e1002119.PMID: 21799663, PMCID: PMC3140961 Read
  16. Naegle KM*, Gymrek M*, Joughin BA, Wagner JP, Welsch RE, et al. PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. Molecular and cellular proteomics : MCP. 2010; 9(11):2558-70. PMID: 20631208, PMCID: PMC2984232 *authors contributed equally Read
  17. Joughin BA*, Naegle KM*, Huang PH*, Yaffe MB, Lauffenburger DA, and FM White. An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells. Molecular BioSystems. 2009; 5(1):59-67. NIHMSID: NIHMS105339 PMID: 19081932, PMCID: PMC2701618 *authors contributed equally Read