Andrew J Link, B.S., B.A., M.A., Ph.D.

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Publications

The following timeline graph is generated from all co-authored publications.

1. Cell-Based Systems Biology Analysis of Human AS03-Adjuvanted H5N1 Avian Influenza Vaccine Responses: A Phase I Randomized Controlled Trial. Howard LM, Hoek KL, Goll JB, Samir P, Galassie A, Allos TM, Niu X, Gordy LE, Creech CB, Prasad N, Jensen TL, Hill H, Levy SE, Joyce S, Link AJ, Edwards KM (2017) PLoS One 12(1): e0167488
   › Primary publication · 28099485 (PubMed) · PMC5242433 (PubMed Central)
2. Viral infection causes a shift in the self peptide repertoire presented by human MHC class I molecules. Spencer CT, Bezbradica JS, Ramos MG, Arico CD, Conant SB, Gilchuk P, Gray JJ, Zheng M, Niu X, Hildebrand W, Link AJ, Joyce S (2015) Proteomics Clin Appl 9(11-12): 1035-52
   › Primary publication · 26768311 (PubMed) · PMC4920078 (PubMed Central)
3. Focus on Immunology and Proteomics. Link AJ (2015) Proteomics Clin Appl 9(11-12): 965-6
   › Primary publication · 26768310 (PubMed)
4. An adaptive classification model for peptide identification. Liang X, Xia Z, Jian L, Niu X, Link A (2015) BMC Genomics : S1
   › Primary publication · 26578406 (PubMed) · PMC4652454 (PubMed Central)
5. l2 Multiple Kernel Fuzzy SVM-Based Data Fusion for Improving Peptide Identification. Jian L, Xia Z, Niu X, Liang X, Samir P, Link AJ (2016) IEEE/ACM Trans Comput Biol Bioinform 13(4): 804-9
   › Primary publication · 26394437 (PubMed)
6. Environmental Interactions and Epistasis Are Revealed in the Proteomic Responses to Complex Stimuli. Samir P, Rahul , Slaughter JC, Link AJ (2015) PLoS One 10(8): e0134099
   › Primary publication · 26247773 (PubMed) · PMC4527715 (PubMed Central)
7. Proteomic contributions to our understanding of vaccine and immune responses. Galassie AC, Link AJ (2015) Proteomics Clin Appl 9(11-12): 972-89
   › Primary publication · 26172619 (PubMed) · PMC4713355 (PubMed Central)
8. A cell-based systems biology assessment of human blood to monitor immune responses after influenza vaccination. Hoek KL, Samir P, Howard LM, Niu X, Prasad N, Galassie A, Liu Q, Allos TM, Floyd KA, Guo Y, Shyr Y, Levy SE, Joyce S, Edwards KM, Link AJ (2015) PLoS One 10(2): e0118528
   › Primary publication · 25706537 (PubMed) · PMC4338067 (PubMed Central)
9. Analysis of protein composition using multidimensional chromatography and mass spectrometry. Link AJ, Washburn MP (2014) Curr Protoc Protein Sci : 23.1.1-23.1.25
   › Primary publication · 25367006 (PubMed)
10. Peptide identification based on fuzzy classification and clustering. Liang X, Xia Z, Niu X, Link AJ, Pang L, Wu FX, Zhang H (2013) Proteome Sci 11(Suppl 1): S10
    › Primary publication · 24564935 (PubMed) · PMC3908838 (PubMed Central)
11. Discovering naturally processed antigenic determinants that confer protective T cell immunity. Gilchuk P, Spencer CT, Conant SB, Hill T, Gray JJ, Niu X, Zheng M, Erickson JJ, Boyd KL, McAfee KJ, Oseroff C, Hadrup SR, Bennink JR, Hildebrand W, Edwards KM, Crowe JE, Williams JV, Buus S, Sette A, Schumacher TN, Link AJ, Joyce S (2013) J Clin Invest 123(5): 1976-87
    › Primary publication · 23543059 (PubMed) · PMC3635741 (PubMed Central)
12. A novel algorithm for validating peptide identification from a shotgun proteomics search engine. Jian L, Niu X, Xia Z, Samir P, Sumanasekera C, Mu Z, Jennings JL, Hoek KL, Allos T, Howard LM, Edwards KM, Weil PA, Link AJ (2013) J Proteome Res 12(3): 1108-19
    › Primary publication · 23402659 (PubMed) · PMC3608465 (PubMed Central)
13. Sculpting MHC class II-restricted self and non-self peptidome by the class I Ag-processing machinery and its impact on Th-cell responses. Spencer CT, Dragovic SM, Conant SB, Gray JJ, Zheng M, Samir P, Niu X, Moutaftsi M, Van Kaer L, Sette A, Link AJ, Joyce S (2013) Eur J Immunol 43(5): 1162-72
    › Primary publication · 23386199 (PubMed) · PMC3798073 (PubMed Central)
14. The yeast eukaryotic translation initiation factor 2B translation initiation complex interacts with the fatty acid synthesis enzyme YBR159W and endoplasmic reticulum membranes. Browne CM, Samir P, Fites JS, Villarreal SA, Link AJ (2013) Mol Cell Biol 33(5): 1041-56
    › Primary publication · 23263984 (PubMed) · PMC3623073 (PubMed Central)
15. The sodium channel accessory subunit Navβ1 regulates neuronal excitability through modulation of repolarizing voltage-gated K⁺ channels. Marionneau C, Carrasquillo Y, Norris AJ, Townsend RR, Isom LL, Link AJ, Nerbonne JM (2012) J Neurosci 32(17): 5716-27
    › Primary publication · 22539834 (PubMed) · PMC3347704 (PubMed Central)
16. Trichloroacetic acid (TCA) precipitation of proteins. Link AJ, LaBaer J (2011) Cold Spring Harb Protoc 2011(8): 993-4
    › Primary publication · 21807853 (PubMed)
17. Setup and demonstration of a nanoelectrospray ionization source and tandem mass spectrometry. Link AJ, LaBaer J (2011) Cold Spring Harb Protoc 2011(7): 888-91
    › Primary publication · 21724816 (PubMed)
18. Studies of the mechanistic details of the pH-dependent association of botulinum neurotoxin with membranes. Mushrush DJ, Koteiche HA, Sammons MA, Link AJ, McHaourab HS, Lacy DB (2011) J Biol Chem 286(30): 27011-8
    › Primary publication · 21652698 (PubMed) · PMC3143659 (PubMed Central)
19. Microdialysis combined with proteomics for protein identification in breast tumor microenvironment in vivo. Xu BJ, Yan W, Jovanovic B, Shaw AK, An QA, Eng J, Chytil A, Link AJ, Moses HL (2010) Cancer Microenviron 4(1): 61-71
    › Primary publication · 21505562 (PubMed) · PMC3047629 (PubMed Central)
20. Affinity capture of TAP-tagged protein complexes: affinity purification step 2. Link AJ, Weaver C, Farley A (2011) Cold Spring Harb Protoc 2011(4): pdb.prot5607
    › Primary publication · 21460056 (PubMed)
21. IgG affinity capture of TAP-tagged protein complexes from cell extracts: affinity purification step 1. Link AJ, Weaver C, Farley A (2011) Cold Spring Harb Protoc 2011(4): pdb.prot5606
    › Primary publication · 21460055 (PubMed)
22. Making yeast cell extracts for purifying TAP-tagged protein complexes. Link AJ, Weaver C, Farley A (2011) Cold Spring Harb Protoc 2011(4): pdb.prot5605
    › Primary publication · 21460054 (PubMed)
23. Growing and harvesting TAP-tagged yeast cells. Link AJ, Weaver C, Farley A (2011) Cold Spring Harb Protoc 2011(4): pdb.prot5604
    › Primary publication · 21460053 (PubMed)
24. Analyzing the cryptome: uncovering secret sequences. Samir P, Link AJ (2011) AAPS J 13(2): 152-8
    › Primary publication · 21327597 (PubMed) · PMC3085711 (PubMed Central)
25. Solution protein digest. Link AJ, LaBaer J (2011) Cold Spring Harb Protoc 2011(2): pdb.prot5569
    › Primary publication · 21285269 (PubMed)
26. Assessing the components of the eIF3 complex and their phosphorylation status. Farley AR, Powell DW, Weaver CM, Jennings JL, Link AJ (2011) J Proteome Res 10(4): 1481-94
    › Primary publication · 21280672 (PubMed) · PMC3446855 (PubMed Central)
27. Saccharomyces cerevisiae Gis2 interacts with the translation machinery and is orthogonal to myotonic dystrophy type 2 protein ZNF9. Sammons MA, Samir P, Link AJ (2011) Biochem Biophys Res Commun 406(1): 13-9
    › Primary publication · 21277287 (PubMed)
28. Identification of residue-to-residue contact between a peptide ligand and its G protein-coupled receptor using periodate-mediated dihydroxyphenylalanine cross-linking and mass spectrometry. Umanah GK, Huang L, Ding FX, Arshava B, Farley AR, Link AJ, Naider F, Becker JM (2010) J Biol Chem 285(50): 39425-36
    › Primary publication · 20923758 (PubMed) · PMC2998077 (PubMed Central)
29. Quantitative analysis of the secretome of TGF-beta signaling-deficient mammary fibroblasts. Xu BJ, Yan W, Jovanovic B, An AQ, Cheng N, Aakre ME, Yi Y, Eng J, Link AJ, Moses HL (2010) Proteomics 10(13): 2458-70
    › Primary publication · 20405477 (PubMed) · PMC4156855 (PubMed Central)
30. ZNF9 activation of IRES-mediated translation of the human ODC mRNA is decreased in myotonic dystrophy type 2. Sammons MA, Antons AK, Bendjennat M, Udd B, Krahe R, Link AJ (2010) PLoS One 5(2): e9301
    › Primary publication · 20174632 (PubMed) · PMC2823779 (PubMed Central)
31. Identification and quantification of protein posttranslational modifications. Farley AR, Link AJ (2009) Methods Enzymol : 725-63
    › Primary publication · 19892200 (PubMed)
32. Proteomic analyses of native brain K(V)4.2 channel complexes. Marionneau C, LeDuc RD, Rohrs HW, Link AJ, Townsend RR, Nerbonne JM (2009) Channels (Austin) 3(4): 284-94
    › Primary publication · 19713751 (PubMed) · PMC2826169 (PubMed Central)
33. Dyggve-Melchior-Clausen syndrome: chondrodysplasia resulting from defects in intracellular vesicle traffic. Osipovich AB, Jennings JL, Lin Q, Link AJ, Ruley HE (2008) Proc Natl Acad Sci U S A 105(42): 16171-6
    › Primary publication · 18852472 (PubMed) · PMC2571016 (PubMed Central)
34. A proteomics analysis of yeast Mot1p protein-protein associations: insights into mechanism. Arnett DR, Jennings JL, Tabb DL, Link AJ, Weil PA (2008) Mol Cell Proteomics 7(11): 2090-106
    › Primary publication · 18596064 (PubMed) · PMC2577210 (PubMed Central)
35. Four and a half LIM protein 1: a partner for KCNA5 in human atrium. Yang Z, Browning CF, Hallaq H, Yermalitskaya L, Esker J, Hall MR, Link AJ, Ham AJ, McGrath MJ, Mitchell CA, Murray KT (2008) Cardiovasc Res 78(3): 449-57
    › Primary publication · 18281375 (PubMed)
36. Plasma membrane Ca(2+) -ATPase associates with CLP36, alpha-actinin and actin in human platelets. Bozulic LD, Malik MT, Powell DW, Nanez A, Link AJ, Ramos KS, Dean WL (2007) Thromb Haemost 97(4): 587-97
    › Primary publication · 17393022 (PubMed)
37. The myotonic dystrophy type 2 protein ZNF9 is part of an ITAF complex that promotes cap-independent translation. Gerbasi VR, Link AJ (2007) Mol Cell Proteomics 6(6): 1049-58
    › Primary publication · 17327219 (PubMed)
38. Dap1/PGRMC1 binds and regulates cytochrome P450 enzymes. Hughes AL, Powell DW, Bard M, Eckstein J, Barbuch R, Link AJ, Espenshade PJ (2007) Cell Metab 5(2): 143-9
    › Primary publication · 17276356 (PubMed)
39. A proximal activator of transcription in epithelial-mesenchymal transition. Venkov CD, Link AJ, Jennings JL, Plieth D, Inoue T, Nagai K, Xu C, Dimitrova YN, Rauscher FJ, Neilson EG (2007) J Clin Invest 117(2): 482-91
    › Primary publication · 17273560 (PubMed) · PMC1783826 (PubMed Central)
40. The splicing factor PSF is part of a large complex that assembles in the absence of pre-mRNA and contains all five snRNPs. Peng R, Hawkins I, Link AJ, Patton JG (2006) RNA Biol 3(2): 69-76
    › Primary publication · 17114945 (PubMed)
41. Role of Hcn1 and its phosphorylation in fission yeast anaphase-promoting complex/cyclosome function. Yoon HJ, Feoktistova A, Chen JS, Jennings JL, Link AJ, Gould KL (2006) J Biol Chem 281(43): 32284-93
    › Primary publication · 16950791 (PubMed)
42. Analyzing proteomes and protein function using graphical comparative analysis of tandem mass spectrometry results. McAfee KJ, Duncan DT, Assink M, Link AJ (2006) Mol Cell Proteomics 5(8): 1497-513
    › Primary publication · 16707483 (PubMed)
43. Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Fleischer TC, Weaver CM, McAfee KJ, Jennings JL, Link AJ (2006) Genes Dev 20(10): 1294-307
    › Primary publication · 16702403 (PubMed) · PMC1472904 (PubMed Central)
44. Discovery of regulatory molecular events and biomarkers using 2D capillary chromatography and mass spectrometry. Powell DW, Merchant ML, Link AJ (2006) Expert Rev Proteomics 3(1): 63-74
    › Primary publication · 16445351 (PubMed)
45. Guidelines for the next 10 years of proteomics. Wilkins MR, Appel RD, Van Eyk JE, Chung MC, Görg A, Hecker M, Huber LA, Langen H, Link AJ, Paik YK, Patterson SD, Pennington SR, Rabilloud T, Simpson RJ, Weiss W, Dunn MJ (2006) Proteomics 6(1): 4-8
    › Primary publication · 16400714 (PubMed)
46. The novel ATP-binding cassette protein ARB1 is a shuttling factor that stimulates 40S and 60S ribosome biogenesis. Dong J, Lai R, Jennings JL, Link AJ, Hinnebusch AG (2005) Mol Cell Biol 25(22): 9859-73
    › Primary publication · 16260602 (PubMed) · PMC1280274 (PubMed Central)
47. Parallel tandem: a program for parallel processing of tandem mass spectra using PVM or MPI and X!Tandem. Duncan DT, Craig R, Link AJ (2005) J Proteome Res 4(5): 1842-7
    › Primary publication · 16212440 (PubMed)
48. Proteomic analysis of human neutrophil granules. Lominadze G, Powell DW, Luerman GC, Link AJ, Ward RA, McLeish KR (2005) Mol Cell Proteomics 4(10): 1503-21
    › Primary publication · 15985654 (PubMed)
49. Proteomic analysis of human norepinephrine transporter complexes reveals associations with protein phosphatase 2A anchoring subunit and 14-3-3 proteins. Sung U, Jennings JL, Link AJ, Blakely RD (2005) Biochem Biophys Res Commun 333(3): 671-8
    › Primary publication · 15963952 (PubMed)
50. Mto2p, a novel fission yeast protein required for cytoplasmic microtubule organization and anchoring of the cytokinetic actin ring. Venkatram S, Jennings JL, Link A, Gould KL (2005) Mol Biol Cell 16(6): 3052-63
    › Primary publication · 15800064 (PubMed) · PMC1142447 (PubMed Central)
51. Purifying protein complexes for mass spectrometry: applications to protein translation. Link AJ, Fleischer TC, Weaver CM, Gerbasi VR, Jennings JL (2005) Methods 35(3): 274-90
    › Primary publication · 15722224 (PubMed)
52. Identification of a Drosophila Myb-E2F2/RBF transcriptional repressor complex. Lewis PW, Beall EL, Fleischer TC, Georlette D, Link AJ, Botchan MR (2004) Genes Dev 18(23): 2929-40
    › Primary publication · 15545624 (PubMed) · PMC534653 (PubMed Central)
53. Requirements of fission yeast septins for complex formation, localization, and function. An H, Morrell JL, Jennings JL, Link AJ, Gould KL (2004) Mol Biol Cell 15(12): 5551-64
    › Primary publication · 15385632 (PubMed) · PMC532033 (PubMed Central)
54. Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that repress gene expression. Gerbasi VR, Weaver CM, Hill S, Friedman DB, Link AJ (2004) Mol Cell Biol 24(18): 8276-87
    › Primary publication · 15340087 (PubMed) · PMC515043 (PubMed Central)
55. Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Powell DW, Weaver CM, Jennings JL, McAfee KJ, He Y, Weil PA, Link AJ (2004) Mol Cell Biol 24(16): 7249-59
    › Primary publication · 15282323 (PubMed) · PMC479721 (PubMed Central)
56. Tandem affinity purification and identification of protein complex components. Gould KL, Ren L, Feoktistova AS, Jennings JL, Link AJ (2004) Methods 33(3): 239-44
    › Primary publication · 15157891 (PubMed)
57. Sid4p-Cdc11p assembles the septation initiation network and its regulators at the S. pombe SPB. Morrell JL, Tomlin GC, Rajagopalan S, Venkatram S, Feoktistova AS, Tasto JJ, Mehta S, Jennings JL, Link A, Balasubramanian MK, Gould KL (2004) Curr Biol 14(7): 579-84
    › Primary publication · 15062098 (PubMed)
58. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. Kobor MS, Venkatasubrahmanyam S, Meneghini MD, Gin JW, Jennings JL, Link AJ, Madhani HD, Rine J (2004) PLoS Biol 2(5): E131
    › Primary publication · 15045029 (PubMed) · PMC374244 (PubMed Central)
59. Identification and characterization of two novel proteins affecting fission yeast gamma-tubulin complex function. Venkatram S, Tasto JJ, Feoktistova A, Jennings JL, Link AJ, Gould KL (2004) Mol Biol Cell 15(5): 2287-301
    › Primary publication · 15004232 (PubMed) · PMC404023 (PubMed Central)
60. Inhibition of P-TEFb (CDK9/Cyclin T) kinase and RNA polymerase II transcription by the coordinated actions of HEXIM1 and 7SK snRNA. Yik JH, Chen R, Nishimura R, Jennings JL, Link AJ, Zhou Q (2003) Mol Cell 12(4): 971-82
    › Primary publication · 14580347 (PubMed)
61. Regulation of alternative splicing by SRrp86 and its interacting proteins. Li J, Hawkins IC, Harvey CD, Jennings JL, Link AJ, Patton JG (2003) Mol Cell Biol 23(21): 7437-47
    › Primary publication · 14559993 (PubMed) · PMC207616 (PubMed Central)
62. Multidimensional peptide separations in proteomics. Link AJ (2002) Trends Biotechnol 20(12 Suppl): S8-13
    › Primary publication · 12570153 (PubMed)
63. Proteomics analysis identifies new components of the fission and budding yeast anaphase-promoting complexes. Yoon HJ, Feoktistova A, Wolfe BA, Jennings JL, Link AJ, Gould KL (2002) Curr Biol 12(23): 2048-54
    › Primary publication · 12477395 (PubMed)
64. Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Sanders SL, Jennings J, Canutescu A, Link AJ, Weil PA (2002) Mol Cell Biol 22(13): 4723-38
    › Primary publication · 12052880 (PubMed) · PMC133885 (PubMed Central)
65. The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. Squazzo SL, Costa PJ, Lindstrom DL, Kumer KE, Simic R, Jennings JL, Link AJ, Arndt KM, Hartzog GA (2002) EMBO J 21(7): 1764-74
    › Primary publication · 11927560 (PubMed) · PMC125365 (PubMed Central)
66. Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Ohi MD, Link AJ, Ren L, Jennings JL, McDonald WH, Gould KL (2002) Mol Cell Biol 22(7): 2011-24
    › Primary publication · 11884590 (PubMed) · PMC133674 (PubMed Central)
67. Direct analysis of proteins in mixtures. Application to protein complexes. Yates JR, Link AJ, Schieltz D (2000) Methods Mol Biol : 17-26
    › Primary publication · 10948494 (PubMed)
68. Identification of proteins in complexes by solid-phase microextraction/multistep elution/capillary electrophoresis/tandem mass spectrometry. Tong W, Link A, Eng JK, Yates JR (1999) Anal Chem 71(13): 2270-8
    › Primary publication · 10405597 (PubMed)
69. Direct analysis of protein complexes using mass spectrometry. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JR (1999) Nat Biotechnol 17(7): 676-82
    › Primary publication · 10404161 (PubMed)
70. Automated protein identification using microcolumn liquid chromatography-tandem mass spectrometry. Yates JR, Carmack E, Hays L, Link AJ, Eng JK (1999) Methods Mol Biol : 553-69
    › Primary publication · 10027276 (PubMed)
71. Autoradiography of 2-D gels. Link AJ (1999) Methods Mol Biol : 285-90
    › Primary publication · 10027253 (PubMed)
72. Internal standards for 2-D. Link AJ (1999) Methods Mol Biol : 281-4
    › Primary publication · 10027252 (PubMed)
73. Measuring the radioactivity of 2-D protein extracts. Link AJ, Bizios N (1999) Methods Mol Biol : 105-7
    › Primary publication · 10027234 (PubMed)
74. Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry. Gatlin CL, Kleemann GR, Hays LG, Link AJ, Yates JR (1998) Anal Biochem 263(1): 93-101
    › Primary publication · 9750149 (PubMed)
75. Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization. Link AJ, Phillips D, Church GM (1997) J Bacteriol 179(20): 6228-37
    › Primary publication · 9335267 (PubMed) · PMC179534 (PubMed Central)
76. Identifying the major proteome components of Haemophilus influenzae type-strain NCTC 8143. Link AJ, Hays LG, Carmack EB, Yates JR (1997) Electrophoresis 18(8): 1314-34
    › Primary publication · 9298647 (PubMed)
77. Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Link AJ, Robison K, Church GM (1997) Electrophoresis 18(8): 1259-313
    › Primary publication · 9298646 (PubMed)
78. Direct analysis of protein mixtures by tandem mass spectrometry. Yates JR, McCormack AL, Schieltz D, Carmack E, Link A (1997) J Protein Chem 16(5): 495-7
    › Primary publication · 9246634 (PubMed)

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