Research Papers

Environmental Interactions and Epistasis Are Revealed in the Proteomic Responses to Complex Stimuli. (2015) Samir P., Rahul, JC Slaughter, AJ Link – PloS one, DOI: 10.1371/journal.pone.0134099

Hoek K.L., Samir P., Howard L.M., Niu X., Prasad N., Galassie A., Liu Q., Allos T.M., Floyd K.A., Guo Y., Shyr Y., Levy S.E., Joyce S., Edwards K.M., Link A.J. (2015). A cell-based systems biology assessment of human blood to monitor immune responses after influenza vaccination.  PloS one,  e0118528, DOI: 10.1371/journal.pone.0118528

Spencer, C. T., Dragovic, S. M., Conant, S. B., Gray, J. J., Zheng, M., Samir, P., Niu, X., Moutaftsi, M., Van Kaer, L., Sette, A., et al. (2013). Sculpting MHC class II-restricted self and non-self peptidome by the class I antigen-processing machinery and its consequences on Th-cell responses. Eur J Immunol. Volume 43, Issue 5, pages 1162–1172, May 2013. DOI: 10.1002/eji.201243087

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­Browne, C. M., Samir, P., Fites, J. S., Villarreal, S. A., and Link, A. J. (2013). The Yeast Eukaryotic Translation Initiation Factor 2B Translation Initiation Complex Interacts with the Fatty Acid Synthesis Enzyme YBR159W and Endoplasmic Reticulum Membranes. Mol Cell Biol 33, 1041-1056. DOI: 10.1128/MCB.00811-12

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­Jian, L., Niu, X., Xia, Z., Samir, P., Sumanasekera, C., Mu, Z., Jennings, J. L., Hoek, K. L., Allos, T., Howard, L. M., et al. (2013). A Novel Algorithm for Validating Peptide Identification from a Shotgun Proteomics Search Engine. J Proteome Res. 12 (3), 1108-1119. DOI: 10.1021/pr300631t

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­Samir, P., and Link, A. J. (2011). Analyzing the cryptome: uncovering secret sequences. AAPS J 13, 152-158. DOI: 10.1208/s12248-011-9252-2

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­Sammons, M. A., Samir, P., and Link, A. J. (2011). Saccharomyces cerevisiae Gis2 interacts with the translation machinery and is orthogonal to myotonic dystrophy type 2 protein ZNF9. Biochem Biophys Res Commun 406, 13-19. DOI:10.1016/j.bbrc.2011.01.086

Posters and Talks

Galassie, A. C., Samir, P., Hoek K.L., Niu, X., Link, A. J. (2014) Poster: Quantitative Proteomic and Systems Analysis of Cells in Response to External Stimuli. 62nd ASMS Conference on Mass Spectrometry and Allied Topics, Baltimore, MD.

Samir, P., Hoek K.L., Howard, L. M., Allos, T., Galassie, A. C., Niu, X., Creech, C. B., Joyce, S., Edwards, K. M., Link, A. J. (2013) Poster: Optimizing the iTRAQ Multiplexing Strategy for Quantitative Proteomics Analysis of Immune Cell Subsets Fractionated from Whole Blood of Human Subjects. 61st ASMS Conference on Mass Spectrometry and Allied Topics, Minneapolis, MN.

Howard, L. M.,  Link, A. J. ,Hoek, K. L., Allos, T., Samir, P., Diggins, K. E., Liu, Q., Prasad, N., Shuey, M., Niu, X., Creech, C. B., Levy, S., Joyce, S., Edwards, K. M (2013) Poster: Systems Analysis of Inactivated Influenza Vaccine Responses in Distinct Immune Cell Types. IDWeek 2013 Meeting, San Francisco, CA.

Levy, S. E., Prasad, N.,  Samir, P.,  Link, A. J.,  DeAngelis, T.,  Hendrickson,  C. L., Jones, A. L., Patel, K., Boone, B. E., Robinson, M. P., Pointer, S.,  Wimbish, J. (2013) Poster: ZNF9 splicing patterns as potential prognostic markers for severity of Myotonic Dystrophy Type 2, Advances in Genome Biology and Technology Meeting, Marco Island, FL.

Howard, L. M., Hoek, K. L., Allos, T., Samir, P., Niu, X., Creech, C. B., Edwards, K. M., Link, A. J. (2013) Poster: Systems Biology Assessment of Human Immune Responses after Seasonal Trivalent Inactivated Influenza Vaccine. Pediatric Academic Societies annual meeting. Washington, DC.

Hoek, K. L., Howard, L. M., Allos, T., Samir, P., Niu, X., Creech, C. B., Edwards, K. M., Link, A. J. (2013 Poster: Systems Biology Assessment of Human Immune Responses after Seasonal Trivalent Inactivated Influenza Vaccine. American Association of Immunologists Meeting, Honolulu, HI

Howard, L. M., Hoek, K. L., Allos, T., Samir, P., Diggins, K. E., Liu, Q., Prasad, N., Shuey, M., Niu, X., Creech, C. B., Levy, S., Joyce, S., Edwards, K. M., Link, A. J. (2012) Poster: Optimized Human Immune Cell Isolation for Application in Systems Vaccinology, IDWeek 2012 Meeting, San Diego, CA.

Samir, P., Browne, C., Link, A. J. (2012). Poster: Carbon Source Alters the Protein Composition of Yeast Ribosomes. Translational Control Meeting, Cold Spring Harbor Lab, Cold Spring Harbor, NY.

Samir, P., Browne, C., Link, A. J. (2012). Poster: Environmental Cues Alter the Protein Composition of Yeast Ribosomes. Vanderbilt Institute of Chemical Biology Symposium, Vanderbilt University School of Medicine, Nashville, TN.

Browne, C., Samir, P., Weaver, C., Link, A. J. (2012). Poster: YBR159W, A fatty Acid Synthesis Enzyme, Targets EIF2B to the ER Membrane and Increases the Efficiency of ER Protein Translation. Translational Control Meeting, Heidelberg, Germany.