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Vanderbilt-Ingram Cancer CenterVanderbilt-Ingram Cancer Center

 
Andrew J.  Link

Andrew J. Link, Ph.D.

Associate Professor of Pathology, Microbiology and Immunology
Assistant Professor of Biochemistry
Researcher

Contact Information:

Vanderbilt University Medical Center
AA4210A MCN
Nashville, TN 37232-8575
615-343-6823
Fax: 615-343-7392

Research Description

My laboratory focuses on the human immune response and protein synthesis using functional genomics and systems biology approaches. In one area of research, we are using systems biology to analyze the human immune response after vaccination. Using global transcriptomics and proteomics, we are profiling and modeling immune cell responses following influenza vaccination. The goals are to develop safer vaccines and to predict individual responses following vaccination. In a second area, we apply mass spectrometry-based proteomics, genetics, and molecular biology to answer fundamental questions of protein synthesis and translational control. To better understand this essential process, we are comprehensively identifying the protein interactions in the translation machinery. Several unexpected translation factors and posttranslational modifications are currently being evaluated for roles in cell growth and translation fidelity. A third area of research focuses on the function of the human gene ZNF9. The genetic cause of human myotonic dystrophy type 2 is the expansion CCTG repeats in the first intron of the znf9 gene. Our data show that ZNF9 is a positive regulator of cap-independent translation and that it interacts with the ribosome. We are working to identify the functional mechanisms of ZNF9 and (CCTG/CCUG)n expansion in translation and muscles using DM2 mouse models and human patient samples. A fourth area of interest is the development of bioinformatics methods to process, analyze, and interpret large-scale functional genomics and mass spectrometry-based proteomics data sets. While generating large amounts of genomics and proteomics data has become routine, no comprehensive set of integrative tools for rigorous analysis and annotation of this type of data is currently available. The laboratory has been developing an innovative open-source database schema and comprehensive suite of analysis applications for interpreting and visualizing proteomics data in a biologically intuitive format. Our functional genomics and mass spectrometry-based approaches has been the enabling technology responsible for a large number successful collaborations at Vanderbilt University and at other universities.

Publications
  • 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. Discovering naturally processed antigenic determinants that confer protective T cell immunity. J. Clin. Invest [print-electronic]. 2013 May; 123(5): 1976-87. PMID: 23543059, PMCID: PMC3635741, PII: 67388, DOI: 10.1172/JCI67388, ISSN: 1558-8238.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/23543059.
  • 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. Sculpting MHC class II-restricted self and non-self peptidome by the class I Ag-processing machinery and its impact on Th-cell responses. Eur. J. Immunol [print-electronic]. 2013 May; 43(5): 1162-72. PMID: 23386199, PMCID: PMC3798073, DOI: 10.1002/eji.201243087, ISSN: 1521-4141.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/23386199.
  • 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. A novel algorithm for validating peptide identification from a shotgun proteomics search engine. J. Proteome Res [print-electronic]. 2013 Mar 3/1/2013; 12(3): 1108-19. PMID: 23402659, PMCID: PMC3608465, DOI: 10.1021/pr300631t, ISSN: 1535-3907.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/23402659.
  • Browne CM, Samir P, Fites JS, Villarreal SA, Link AJ. 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 [print-electronic]. 2013 Mar; 33(5): 1041-56. PMID: 23263984, PMCID: PMC3623073, PII: MCB.00811-12, DOI: 10.1128/MCB.00811-12, ISSN: 1098-5549.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/23263984.
  • Mushrush DJ, Koteiche HA, Sammons MA, Link AJ, McHaourab HS, Lacy DB. Studies of the mechanistic details of the pH-dependent association of botulinum neurotoxin with membranes. J. Biol. Chem [print-electronic]. 2011 Jul 7/29/2011; 286(30): 27011-8. PMID: 21652698, PMCID: PMC3143659, PII: M111.256982, DOI: 10.1074/jbc.M111.256982, ISSN: 1083-351X.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21652698.
  • Samir P, Link AJ. Analyzing the cryptome: uncovering secret sequences. AAPS J [print-electronic]. 2011 Jun; 13(2): 152-8. PMID: 21327597, PMCID: PMC3085711, DOI: 10.1208/s12248-011-9252-2, ISSN: 1550-7416.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21327597.
  • Farley AR, Powell DW, Weaver CM, Jennings JL, Link AJ. Assessing the components of the eIF3 complex and their phosphorylation status. J. Proteome Res [print-electronic]. 2011 Apr 4/1/2011; 10(4): 1481-94. PMID: 21280672, PMCID: PMC3446855, DOI: 10.1021/pr100877m, ISSN: 1535-3907.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21280672.
  • Sammons MA, Samir P, Link AJ. Saccharomyces cerevisiae Gis2 interacts with the translation machinery and is orthogonal to myotonic dystrophy type 2 protein ZNF9. Biochem. Biophys. Res. Commun [print-electronic]. 2011 Mar 3/4/2011; 406(1): 13-9. PMID: 21277287, PII: S0006-291X(11)00129-X, DOI: 10.1016/j.bbrc.2011.01.086, ISSN: 1090-2104.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21277287.
  • Xu BJ, Yan W, Jovanovic B, An AQ, Cheng N, Aakre ME, Yi Y, Eng J, Link AJ, Moses HL. Quantitative analysis of the secretome of TGF-beta signaling-deficient mammary fibroblasts. Proteomics. 2010 Jul; 10(13): 2458-70. PMID: 20405477, PMCID: PMC4156855, DOI: 10.1002/pmic.200900701, ISSN: 1615-9861.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/20405477.
  • Sammons MA, Antons AK, Bendjennat M, Udd B, Krahe R, Link AJ. ZNF9 activation of IRES-mediated translation of the human ODC mRNA is decreased in myotonic dystrophy type 2. PLoS ONE. 2010; 5(2): e9301. PMID: 20174632, PMCID: PMC2823779, DOI: 10.1371/journal.pone.0009301, ISSN: 1932-6203.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/20174632.
  • Link AJ, Labaer J. In-gel trypsin digest of gel-fractionated proteins. Cold Spring Harb Protoc. 2009 Feb; 2009(2): pdb.prot5110. PMID: 20147065, PII: 2009/2/pdb.prot5110, DOI: 10.1101/pdb.prot5110, ISSN: 1559-6095.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/20147065.
  • Farley AR, Link AJ. Identification and quantification of protein posttranslational modifications. Meth. Enzymol. 2009; 463: 725-63. PMID: 19892200, PII: S0076-6879(09)63040-8, DOI: 10.1016/S0076-6879(09)63040-8, ISSN: 1557-7988.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/19892200.
  • Arnett DR, Jennings JL, Tabb DL, Link AJ, Weil PA. A proteomics analysis of yeast Mot1p protein-protein associations: insights into mechanism. Mol. Cell Proteomics [print-electronic]. 2008 Nov; 7(11): 2090-106. PMID: 18596064, PMCID: PMC2577210, PII: M800221-MCP200, DOI: 10.1074/mcp.M800221-MCP200, ISSN: 1535-9484.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/18596064.
  • Osipovich AB, Jennings JL, Lin Q, Link AJ, Ruley HE. Dyggve-Melchior-Clausen syndrome: chondrodysplasia resulting from defects in intracellular vesicle traffic. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2008 Oct 10/21/2008; 105(42): 16171-6. PMID: 18852472, PMCID: PMC2571016, PII: 0804259105, DOI: 10.1073/pnas.0804259105, ISSN: 1091-6490.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/18852472.
  • Yang Z, Browning CF, Hallaq H, Yermalitskaya L, Esker J, Hall MR, Link AJ, Ham AJ, McGrath MJ, Mitchell CA, Murray KT. Four and a half LIM protein 1: a partner for KCNA5 in human atrium. Cardiovasc. Res [print-electronic]. 2008 Jun 6/1/2008; 78(3): 449-57. PMID: 18281375, PII: cvn038, DOI: 10.1093/cvr/cvn038, ISSN: 0008-6363.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/18281375.
  • Link AJ, Labaer J. Construction of Nucleic Acid Programmable Protein Arrays (NAPPA) 2: Preparing Bacterial Cultures in a 96-Well Format. CSH Protoc. 2008; 2008: pdb.prot5057. PMID: 21356712.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21356712.
  • Link AJ, Labaer J. Construction of Nucleic Acid Programmable Protein Arrays (NAPPA) 3: Isolating DNA Plasmids in a 96-Well Plate Format. CSH Protoc. 2008; 2008: pdb.prot5058. PMID: 21356713.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21356713.
  • Link AJ, Labaer J. Construction of Nucleic Acid Programmable Protein Arrays (NAPPA) 4: DNA Biotinylation, Precipitation, and Arraying of Samples. CSH Protoc. 2008; 2008: pdb.prot5059. PMID: 21356714.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21356714.
  • Link AJ, Labaer J. Construction of Nucleic Acid Programmable Protein Arrays (NAPPA) 5: Expressing Proteins on NAPPA Slides. CSH Protoc. 2008; 2008: pdb.prot5060. PMID: 21356715.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21356715.
  • Link AJ, Labaer J. Construction of Nucleic Acid Programmable Protein Arrays (NAPPA) 6: Detecting Proteins on NAPPA Slides. CSH Protoc. 2008; 2008: pdb.prot5061. PMID: 21356716.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21356716.
  • Link AJ, Labaer J. Construction of Nucleic Acid Programmable Protein Arrays (NAPPA) 7: Detecting DNA on NAPPA Slides. CSH Protoc. 2008; 2008: pdb.prot5062. PMID: 21356717.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21356717.
  • Link AJ, Labaer J. Using the Nucleic Acid Programmable Protein Array (NAPPA) for Identifying Protein-Protein Interactions. Protocol 1: Coexpression of Query Protein on NAPPA Slides. CSH Protoc. 2008; 2008: pdb.prot5108. PMID: 21356754.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21356754.
  • Link AJ, Labaer J. Using the Nucleic Acid Programmable Protein Array (NAPPA) for Identifying Protein-Protein Interactions. Protocol 2: Detection of Query Proteins on NAPPA Slides. CSH Protoc. 2008; 2008: pdb.prot5109. PMID: 21356755.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21356755.
  • Link AJ, Labaer J. Using the Nucleic Acid Programmable Protein Array (NAPPA) for Identifying Protein-Protein Interactions: General Guidelines. CSH Protoc. 2008; 2008: pdb.ip62. PMID: 21356738.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/21356738.
  • Gerbasi VR, Link AJ. The myotonic dystrophy type 2 protein ZNF9 is part of an ITAF complex that promotes cap-independent translation. Mol. Cell Proteomics [print-electronic]. 2007 Jun; 6(6): 1049-58. PMID: 17327219, PII: M600384-MCP200, DOI: 10.1074/mcp.M600384-MCP200, ISSN: 1535-9476.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/17327219.
  • Venkov CD, Link AJ, Jennings JL, Plieth D, Inoue T, Nagai K, Xu C, Dimitrova YN, Rauscher FJ, Neilson EG. A proximal activator of transcription in epithelial-mesenchymal transition. J. Clin. Invest. 2007 Feb; 117(2): 482-91. PMID: 17273560, PMCID: PMC1783826, DOI: 10.1172/JCI29544, ISSN: 0021-9738.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/17273560.
  • Yoon HJ, Feoktistova A, Chen JS, Jennings JL, Link AJ, Gould KL. Role of Hcn1 and its phosphorylation in fission yeast anaphase-promoting complex/cyclosome function. J. Biol. Chem [print-electronic]. 2006 Oct 10/27/2006; 281(43): 32284-93. PMID: 16950791, PII: M603867200, DOI: 10.1074/jbc.M603867200, ISSN: 0021-9258.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/16950791.
  • McAfee KJ, Duncan DT, Assink M, Link AJ. Analyzing proteomes and protein function using graphical comparative analysis of tandem mass spectrometry results. Mol. Cell Proteomics [print-electronic]. 2006 Aug; 5(8): 1497-513. PMID: 16707483, PII: T500027-MCP200, DOI: 10.1074/mcp.T500027-MCP200, ISSN: 1535-9476.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/16707483.
  • Fleischer TC, Weaver CM, McAfee KJ, Jennings JL, Link AJ. Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Genes Dev. 2006 May 5/15/2006; 20(10): 1294-307. PMID: 16702403, PMCID: PMC1472904, PII: 20/10/1294, DOI: 10.1101/gad.1422006, ISSN: 0890-9369.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/16702403.
  • Peng R, Hawkins I, Link AJ, Patton JG. The splicing factor PSF is part of a large complex that assembles in the absence of pre-mRNA and contains all five snRNPs. RNA Biol [print-electronic]. 2006 Apr; 3(2): 69-76. PMID: 17114945, PII: 3017, ISSN: 1555-8584.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/17114945.
  • Duncan DT, Craig R, Link AJ. Parallel tandem: a program for parallel processing of tandem mass spectra using PVM or MPI and X!Tandem. J. Proteome Res. 2005 Sep; 4(5): 1842-7. PMID: 16212440, DOI: 10.1021/pr050058i, ISSN: 1535-3893.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/16212440.
  • Sung U, Jennings JL, Link AJ, Blakely RD. Proteomic analysis of human norepinephrine transporter complexes reveals associations with protein phosphatase 2A anchoring subunit and 14-3-3 proteins. Biochem. Biophys. Res. Commun. 2005 Aug 8/5/2005; 333(3): 671-8. PMID: 15963952, PII: S0006-291X(05)01166-6, DOI: 10.1016/j.bbrc.2005.05.165, ISSN: 0006-291X.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/15963952.
  • Link AJ, Fleischer TC, Weaver CM, Gerbasi VR, Jennings JL. Purifying protein complexes for mass spectrometry: applications to protein translation. Methods [print-electronic]. 2005 Mar; 35(3): 274-90. PMID: 15722224, PII: S1046-2023(04)00209-9, DOI: 10.1016/j.ymeth.2004.08.019, ISSN: 1046-2023.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/15722224.
  • Gerbasi VR, Weaver CM, Hill S, Friedman DB, Link AJ. Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that repress gene expression. Mol. Cell. Biol. 2004 Sep; 24(18): 8276-87. PMID: 15340087, PMCID: PMC515043, PII: 24/18/8276, DOI: 10.1128/MCB.24.18.8276-8287.2004, ISSN: 0270-7306.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/15340087.
  • Powell DW, Weaver CM, Jennings JL, McAfee KJ, He Y, Weil PA, Link AJ. Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol. Cell. Biol. 2004 Aug; 24(16): 7249-59. PMID: 15282323, PMCID: PMC479721, PII: 24/16/7249, DOI: 10.1128/MCB.24.16.7249-7259.2004, ISSN: 0270-7306.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/15282323.
  • Gould KL, Ren L, Feoktistova AS, Jennings JL, Link AJ. Tandem affinity purification and identification of protein complex components. Methods. 2004 Jul; 33(3): 239-44. PMID: 15157891, PII: S1046202303003189, DOI: 10.1016/j.ymeth.2003.11.019, ISSN: 1046-2023.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/15157891.
  • Venkatram S, Tasto JJ, Feoktistova A, Jennings JL, Link AJ, Gould KL. Identification and characterization of two novel proteins affecting fission yeast gamma-tubulin complex function. Mol. Biol. Cell [print-electronic]. 2004 May; 15(5): 2287-301. PMID: 15004232, PMCID: PMC404023, PII: E03-10-0728, DOI: 10.1091/mbc.E03-10-0728, ISSN: 1059-1524.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/15004232.
  • Link AJ, Jennings JL, Washburn MP. Analysis of protein composition using multidimensional chromatography and mass spectrometry. Curr Protoc Protein Sci. 2004 Feb; Chapter 23: Unit 23.1. PMID: 18429262, DOI: 10.1002/0471140864.ps2301s34, ISSN: 1934-3663.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/18429262.
  • Gould, K.L., Ren, L., Feoktistova, A.S., Jennings, J.L., Link, A.J.. Tandem affinity purification and identification of protein complex components. Methods. 2004; 33: 239-44.
  • Kobor, M.S., Venkatasubrahmanyam, S., Meneghini, M.D., Gin, J.W., Jennings, J.L., Link, A.J. Madhani, H.D., Rine, J.. A protein complex complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biology. 2004; 23: 587-99.
  • Lewis, P.W., Beall, E.L., Fleischer, T.C., Georlette, D., Link, A.J., Botchan, M.R.. Identification of a Drosophila Myb-E2F2/RBF complex that represses transcription. Genes and Development. in press. M.R. 2004.
  • Link, A.J., Fleischer, T.C., Weaver, C.M., Gerbasi, V.R., Jennings, J.L.. Purifying protein complexes for mass spectrometry: applications to protein translation. in press. Methods. 2004.
  • Link, A.J.. Complex Mixture Analysis . The Encyclopedia of Mass Spectrometry. Elsevier Science. 2004; 23: 274-89.
  • Morrell, J.L., Tomlin, G.C. , Venkatram, S., Rajagopalan, S. Feoktistova, A.S., Tasto, J.J., Mehta, S., Jennings, J.L., Link, A.J., Balasubramanian, M.K., Gould, K.L.. Sid4p-Cdc11p assemble the septation initiation network and its regulators a the S. pombe SPB. Curr, Biol. 2004; 12: 579-84.
  • Powell, D.W., Weaver, C.M., Jennings, J.L., Mcafee, K.J., He, Y., Weil, P.A., Link, A.J.. Cluster analysis of mass spectrometry data reveals a novel component of SAGA. MCB. 2004; 24: 7249-59.
  • Sattlegger, E., Swanson, M.J., Ashcraft, E.A., Jennings, J.L., Fekete, R. A., Link, A.J., Hinnebusch, A.G.. Y1H1 is an actin-binding protein that inhibits protein kinase GCN2 and impairs general amino acid control when overexpressed. JBC. 2004; ((279)): 29952-62.
  • Venkatram, S., Tasto, J.J., Feoktistova, A.S., Jennings, J.L., Link, A.J., Gould, K.L.. Identification and characterization of two novel proteins affecting fission yeast gamma-tubulin complex function. MCB. 2004; 15: 22870-2301.
  • Li J, Hawkins IC, Harvey CD, Jennings JL, Link AJ, Patton JG. Regulation of alternative splicing by SRrp86 and its interacting proteins. Mol. Cell. Biol. 2003 Nov; 23(21): 7437-47. PMID: 14559993, PMCID: PMC207616, ISSN: 0270-7306.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/14559993.
  • Li, J., Jennings, J.J., Link, A.J., Patton J.G.. Regulation of alternative splicing by SRrp86 and its interacting proteins. MCB. 2003; 23: 7437-47.
  • Yik, J.H., Chen, R., Nishimura, R., Jennings, J.L., Link, A.J. Zhou, Q.. Inhibition of P-TEFb (CDC9/Cyclin T) kinase and RNA polymerase II transcription by the coordinated actions of HEXIM1 and 7SK snRNA. Mol. Cell. 2003; 12: 971-82.
  • Yoon HJ, Feoktistova A, Wolfe BA, Jennings JL, Link AJ, Gould KL. Proteomics analysis identifies new components of the fission and budding yeast anaphase-promoting complexes. Curr. Biol. 2002 Dec 12/10/2002; 12(23): 2048-54. PMID: 12477395, PII: S0960982202013313, ISSN: 0960-9822.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/12477395.
  • Link AJ. Multidimensional peptide separations in proteomics. Trends Biotechnol. 2002 Dec; 20(12 Suppl): S8-13. PMID: 12570153, PII: S1471-1931(02)00202-1, ISSN: 0167-7799.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/12570153.
  • Sanders SL, Jennings J, Canutescu A, Link AJ, Weil PA. Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol. Cell. Biol. 2002 Jul; 22(13): 4723-38. PMID: 12052880, PMCID: PMC133885, ISSN: 0270-7306.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/12052880.
  • Ohi MD, Link AJ, Ren L, Jennings JL, McDonald WH, Gould KL. Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Mol. Cell. Biol. 2002 Apr; 22(7): 2011-24. PMID: 11884590, PMCID: PMC133674, ISSN: 0270-7306.
    Available from: http://www.ncbi.nlm.nih.gov/pubmed/11884590.
  • Andrew J. Link. Multidimensional peptide separations in proteomics. Trends Guide to Proteomics. 2002; in press.
  • Link, A.J.. Multidimensional peptide separations in proteomics. Trends in Biochemistry. 2002; ((20)): S8-S13.
  • Ohi, M. D., Link, A. J., Ren, L., Jennings, J. J., McDonald, W. H., Gould, K. L. Proteomics analysis reveals stable multi-protein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNPs. Mol. Cell. Bio. 2002; 22: 2011-24.
  • Sanders, S. L., Jennings, J. J., Canutescu, A., Link, A. J., Weil, P. A. Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of the general transcription factor TFIID. Mol. Cell. Biol. 2002; 22: 4723-38.
  • Squazzo, S. L., Costa, P. J., Lindstrom, D., Kumer, K. E., Simic, R., Jennings, J. L., Link, A. J., Arndt, K. M., Hartzog, G. The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO. 2002; 21: 1764.
  • Yoon, H.J., Feoktistova, A., Wolfe, B.A., Jennings, J. L., Link, A.J., Gould, K.L.. Proteomics analysis identifies new components of the fission and budding yeast anaphase-promoting complexes. Curr, Biol. 2002; 12: 2048-54.
  • Yates III, J.R., Link, A. J. and Schieltz, D. Direct analysis of proteins in mixtures. Application to protein complexes. Methods Molecular Biology. 2000; 146: 17-26.
  • Link AJ. Autoradiography of 2-D gels. Methods in Molecular Biology. 1999; 112: 285-90.
  • Link AJ. Bizios N. Measuring the radioactivity of 2-D protein extracts. Methods in Molecular Biology. 1999; 112: 105-7.
  • Link AJ. Internal standards for 2-D. Methods in Molecular Biology. 1999; 112: 281-4.
  • Link, A. J., Eng, J., Schieltz, D., Carmack, E., Mize, G., Morris, G., Garvik, B, Yates III, J. R. Direct analysis of protein complexes by mass spectrometry. Nature Biotechnology. 1999; 17: 676-82.
  • Tong, W., Link, A.J. and Yates III, J.R. Identification of protein complexes by solid-phase microextraction/multistep elution/capillary electrophoresis/tandem mass spectrometry. Anal. Chem. 1999; 71: 2270-8.
  • Yates JR 3rd. Carmack E. Hays L. Link AJ. Eng JK. Automated protein identification using microcolumn liquid chromatography-tandem mass spectrometry. Methods in Molecular Biology. 1999; 112: 553-69.
  • Gatlin, C. L., Kleeman, G. R., Hays, L. G., Link, A. J., Yates III, J. R. 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. Anal. Biochem. 1998; 263: 93-101.
  • Link, A. J., Carmack, E., and Yate III, J. R.. A strategy for the identification of proteins localized to subcellular spaces: Application to E. coli periplasmic proteins. Inter. J. of Mass Spectrometry and Ion Processes. 1997; 160: 303-16.
  • Link, A. J., Phillips, D. R. and Church, G. M. Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: Application to open reading frame characterization. J. Bacteriol. 1997; 179: 6228-37.
  • Link, A.J. Robison, K., and Church, G.M. Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli. Electrophoresis. 1997; 18: 1259-313.
  • Link, A.J., Hays, L. G., Carmack, E. B., and Yates III, J. R. Identifying the major proteome components of Haemophilus influenzae type-strain NCTC 8143. Electrophoresis. 1997; 18: 1324-34.
  • Yates III, J. R., McCormack, A. L., Schieltz, D., Carmack, E., and Link, A. J. Direct analysis of protein mixtures by tandem mass spectrometry. J. Protein Chemistry. 1997; 16: 495-7.
  • Link, A. J., Eng, J., and Yates III, J. R. Analyzing complex biological systems by using Micro-LC/ESI/MS/MS. American Laboratory. 1996; 28: 27-30.
  • Yates III, J. R., McCormack, A. L., Link, A. J., Schieltz, D., Eng, J., Hays, L. Future prospects for the analysis of complex biological systems using micro-column liquid chromatography-electrospray tandem mass spectrometry. Analyst. 1996; 121: 65R-76R.
  • Almiron, M., Link, A.J., Furlong, D., and Kolter, R. A novel DNA binding protein with regulatory and protective roles in starved E. coli. Genes & Development. 1992; 6: 2646-54.
  • Carlone, R.L., Boulianne, R.P., and Link, A.J. Identification of proteins potentially involved in proximal-distal pattern formation in the regenerating forelimb of the newt. Biochem. Cell Biol. 1992; 70: 285-90.
  • Ajioka, J.W., Smoller, D. A., Jones, R.W., Carulli, J. P., Vellek, A. E., Garza, D., Link, A.J., Duncan, I.W., and Hartl, D.L. Drosophila genome project: one-hit coverage in yeast artificial chromosomes. Chromosoma. 1991; 100: 495-509.
  • Danilevskaya, O.N., Kurenova, E.V., Pavlova, M.N., Bebebov, D.V., Link, A.J., Koga, A., Vellek, A., and Hartl, D.L. HeT-A family of DNA sequences in the Y chromosome of Drosophila melanogaster share homology with the X-linked stellate genes. Chromosoma. 1991; 100: 118-24.
  • Kafatos, F.C., Louis, C., Savakis, C., Glover, D.M., Ashburner, M., Link, A.J., Siden-Kiamos, I., and Saunders, R. D. Integrated maps of the Drosophila genome: progress and prospects. Trends in Genetics. 1991; 7: 155-61.
  • Link,A.J. and Olson, M.V. Physical map of the Saccharomyces cerevisiae genome at the 110-kilobase resolution. 127. 1991; 681-698: Genetics.
  • Tempst, P., Link, A.J., Riviere, L.R., Fleming, M., and Elicone, C. Internal sequence analysis of proteins separated on polyacrylamide gels at the sub-microgram level: Improved methods, applications, and gene cloning strategies. Electrophoresis. 1990; 11: 537-53.