Mathias Uhlén – universalgeni och min handledare, som peppat och pressat vid rätt tillfällen. Kanon! Som de säger i kören.
Hela HPR – för fantastiskt data! Och för platsen i badtunnan.
Åsa Sivertsson – för alla ord. Intressanta, många och klarsynta.
Linn Fagerberg – för hjälp i kritiska lägen. Och för goda äppeldrinkar.
Jorge Andrade – Grid-kungen. Oj, vad snabbt det blev.
Jacob Odeberg – att skriva pek live tillsammans är en alldeles ypperlig idé.
HPR IT – Kalle Jonasson, Per Oksvold, Mattias Forsberg, Martin Zwahlen och Janne Lund – för givande diskussioner och hjälp med PRESTIGE och allt möjligt LIMS-relaterat.
Marcus Gry – för fina heatmaps och korrelationer.
Erik Sonnhammer – för värdefull expertgranskning.
Cristina Al-Khalili Szigyarto – en av de riktigt goda på vår planet.
HPR LG – för professionalism men ändå avspändhet, och för trevliga och nyttiga sammankomster, både i mötesrum och på mer kontorsavlägsna platser.
Professorerna - Sophia Hober, Joakim Lundeberg, Stefan Ståhl, Per-Åke Nygren – för en alldeles sällsynt positiv attityd.
DNA-klubb-workshopgänget – intensivt men ack så lärorikt.
Johan Rockberg, Basia Hjelm, Pawel Zajac, Carl Hamsten, Lotta Agaton, Mats Lindskog och Maria Malmqvist – sköna nuvarande och dåvarande rumskamrater!
Marica Hamsten, Cecilia Eriksson, Johanna Steen, Caroline Asplund och Anna Sköllermo – för fina pratstunder.
Malin Andersen – AZ och sen KTH, med lite CSHL som krydda.
Sara Gunnerås – för fina bilder på antikropp och kolonn.
Fredrik Sterky – för att du tog hand om mig så bra där i början när allting var nytt.
Alla på plan 3 – tänk om alla arbetsplatser vore så trevliga.
Niclas Jareborg – för att du öppnade porten till bioinformatikens underbara värld, och visade att det går att göra en massa med nåt som heter Perl.
Kodaporna och ni andra på gamla Visual – för all kunskap, om allt från hashar till ironi.
Peter Sigurdson – för att du hjälpte mig att vara lite besvärlig.
Pia Dosenovic – världens finaste vän, i alla väder.
Ina Berglund – a k a Rollan, C2, collekt, bk... Jenkins är en härlig typ.
Mamman och Pappan Berglund – bättre görs inte.
Erik Björling – min främste kritiker, men också mitt största stöd. Jag är såååå övertygad om att all good things inte come to an end.
REFERENCES
Agaton, C., Falk, R., Höiden Guthenberg, I., Göstring, L., Uhlén, M., and Hober, S. (2004). Selective enrichment of monospecific polyclonal antibodies for antibody-based proteomics efforts. J Chromatogr A 1043: 33-40.
Agaton, C., Galli, J., Höiden Guthenberg, I., Janzon, L., Hansson, M., Asplund, A., Brundell, E., Lindberg, S., Ruthberg, I., Wester, K., et al. (2003). Affinity proteomics for systematic protein profiling of chromosome 21 gene products in human tissues. Mol Cell Proteomics 2: 405-414.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. J Mol Biol 215: 403-410.
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. Anderson, L., and Seilhamer, J. (1997). A comparison of selected mRNA and
protein abundances in human liver. Electrophoresis 18: 533-537.
Anderson, N.L., and Anderson, N.G. (2002). The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 1: 845-867. Andrade, J., Berglund, L., Uhlén, M., and Odeberg, J. (2006). Using Grid
technology for computationally intensive applied bioinformatics analyses. In Silico Biol 6: 495-504.
Atassi, M.Z., and Smith, J.A. (1978). A proposal for the nomenclature of antigenic sites in peptides and proteins. Immunochemistry 15: 609-610.
Attwood, T.K., Bradley, P., Flower, D.R., Gaulton, A., Maudling, N., Mitchell, A.L., Moulton, G., Nordle, A., Paine, K., Taylor, P., et al. (2003). PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res 31: 400-402. Avery, O.T., MacLeod, C.M., and McCarty, M. (1944). Studies on the chemical
nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. Journal of Experimental Medicine 79: 137-158. Barbe, L., Lundberg, E., Oksvold, P., Stenius, A., Lewin, E., Björling, E., Asplund,
A., Pontén, F., Brismar, H., Uhlén, M., et al. (2008). Toward a confocal subcellular atlas of the human proteome. Mol Cell Proteomics 7: 499-508. Bendtsen, J.D., Nielsen, H., von Heijne, G., and Brunak, S. (2004). Improved
prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783-795.
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Wheeler, D.L. (2008). GenBank. Nucleic Acids Res 36: D25-30.
Berman, H., Henrick, K., and Nakamura, H. (2003). Announcing the worldwide Protein Data Bank. Nat Struct Biol 10: 980.
Bertone, P., Stolc, V., Royce, T.E., Rozowsky, J.S., Urban, A.E., Zhu, X., Rinn, J.L., Tongprasit, W., Samanta, M., Weissman, S., et al. (2004). Global identification of human transcribed sequences with genome tiling arrays. Science 306: 2242-2246.
Beste, G., Schmidt, F.S., Stibora, T., and Skerra, A. (1999). Small antibody-like proteins with prescribed ligand specificities derived from the lipocalin fold. Proc Natl Acad Sci U S A 96: 1898-1903.
Better, M., Chang, C.P., Robinson, R.R., and Horwitz, A.H. (1988). Escherichia coli secretion of an active chimeric antibody fragment. Science 240: 1041-1043.
Binz, H.K., Amstutz, P., Kohl, A., Stumpp, M.T., Briand, C., Forrer, P., Grutter, M.G., and Pluckthun, A. (2004). High-affinity binders selected from designed ankyrin repeat protein libraries. Nat Biotechnol 22: 575-582.
Bird, R.E., Hardman, K.D., Jacobson, J.W., Johnson, S., Kaufman, B.M., Lee, S.M., Lee, T., Pope, S.H., Riordan, G.S., and Whitlow, M. (1988). Single-chain antigen-binding proteins. Science 242: 423-426.
Birney, E., Andrews, T.D., Bevan, P., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cuff, J., Curwen, V., Cutts, T., et al. (2004). An overview of Ensembl. Genome Res 14: 925-928.
Birney, E., Stamatoyannopoulos, J.A., Dutta, A., Guigo, R., Gingeras, T.R., Margulies, E.H., Weng, Z., Snyder, M., Dermitzakis, E.T., Thurman, R.E., et al. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816. Björling, E., Lindskog, C., Oksvold, P., Linné, J., Kampf, C., Hober, S., Uhlén, M.,
and Pontén, F. (2007). A web-based tool for in silico biomarker discovery based on tissue-specific protein profiles in normal and cancer tissues. Mol Cell Proteomics.
Blom, N., Sicheritz-Pontén, T., Gupta, R., Gammeltoft, S., and Brunak, S. (2004). Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4: 1633-1649.
Blythe, M.J., and Flower, D.R. (2005). Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci 14: 246-248.
Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D.H., Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M., et al. (2000). Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18: 630-634.
Bru, C., Courcelle, E., Carrere, S., Beausse, Y., Dalmar, S., and Kahn, D. (2005). The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res 33: D212-215.
Casadio, R., Martelli, P.L., and Pierleoni, A. (2008). The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation. Brief Funct Genomic Proteomic.
Chou, K.C., and Shen, H.B. (2006). Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-Nearest Neighbor classifiers. J Proteome Res 5: 1888-1897.
Clamp, M., Fry, B., Kamal, M., Xie, X., Cuff, J., Lin, M.F., Kellis, M., Lindblad-Toh, K., and Lander, E.S. (2007). Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci U S A 104:
Colinge, J., and Bennett, K.L. (2007). Introduction to computational proteomics. PLoS Comput Biol 3: e114.
Collins, F.S., Green, E.D., Guttmacher, A.E., and Guyer, M.S. (2003). A vision for the future of genomics research. Nature 422: 835-847.
Coons, A. (1941). Immunological properties of an antibody containing a fluorescent group. Proc Soc Exp Biol Med 47: 200-202.
Crick, F. (1970). Central dogma of molecular biology. Nature 227: 561-563.
Crick, F.H. (1958). On protein synthesis. The Symposia of the Society for Experimental Biology 12: 138-163.
Crick, F.H., Barnett, L., Brenner, S., and Watts-Tobin, R.J. (1961). General nature of the genetic code for proteins. Nature 192: 1227-1232.
Cunningham, F., and Deber, C.M. (2007). Optimizing synthesis and expression of transmembrane peptides and proteins. Methods 41: 370-380.
Curwen, V., Eyras, E., Andrews, T.D., Clarke, L., Mongin, E., Searle, S.M., and Clamp, M. (2004). The Ensembl automatic gene annotation system. Genome Res 14: 942-950.
Dahm, R. (2005). Friedrich Miescher and the discovery of DNA. Dev Biol 278: 274-288.
Diehn, M., Sherlock, G., Binkley, G., Jin, H., Matese, J.C., Hernandez-Boussard, T., Rees, C.A., Cherry, J.M., Botstein, D., Brown, P.O., et al. (2003). SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res 31: 219-223.
Dunn, C., O'Dowd, A., and Randall, R.E. (1999). Fine mapping of the binding sites of monoclonal antibodies raised against the Pk tag. J Immunol Methods
224: 141-150.
Eddy, S.R. (2004). Where did the BLOSUM62 alignment score matrix come from? Nat Biotechnol 22: 1035-1036.
Edgar, R., Domrachev, M., and Lash, A.E. (2002). Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
Edman, P. (1949). A method for the determination of amino acid sequence in peptides. Arch Biochem 22: 475.
Ellington, A.D., and Szostak, J.W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822.
Emanuelsson, O., Brunak, S., von Heijne, G., and Nielsen, H. (2007). Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2: 953-971.
Emini, E.A., Hughes, J.V., Perlow, D.S., and Boger, J. (1985). Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol 55: 836-839.
Engvall, E., and Perlman, P. (1971). Enzyme-linked immunosorbent assay (ELISA). Quantitative assay of immunoglobulin G. Immunochemistry 8: 871-874.
Erni, F., and Frei, R.W. (1978). Two-dimensional column liquid chromatographic technique for resolution of complex mixtures. Journal of Chromatography 149: 561-569.
Evans, D.M., Williams, K.P., McGuinness, B., Tarr, G., Regnier, F., Afeyan, N., and Jindal, S. (1996). Affinity-based screening of combinatorial libraries using automated, serial-column chromatography. Nat Biotechnol 14: 504-507.
Falk, R., Ramström, M., Ståhl, S., and Hober, S. (2007). Approaches for systematic proteome exploration. Biomol Eng 24: 155-168.
Fields, S., and Song, O. (1989). A novel genetic system to detect protein-protein interactions. Nature 340: 245-246.
Finn, R.D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Moxon, S., Marshall, M., Khanna, A., Durbin, R., et al. (2006). Pfam: clans, web tools and services. Nucleic Acids Res 34: D247-251.
Fleury, D., Daniels, R.S., Skehel, J.J., Knossow, M., and Bizebard, T. (2000). Structural evidence for recognition of a single epitope by two distinct antibodies. Proteins 40: 572-578.
Flicek, P., Aken, B.L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., et al. (2008). Ensembl 2008. Nucleic Acids Res 36: D707-714.
Garnier, J., Osguthorpe, D.J., and Robson, B. (1978). Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 120: 97-120.
GeneOntology Consortium. (2008). The Gene Ontology project in 2008. Nucleic Acids Res 36: D440-444.
Green, N., Alexander, H., Olson, A., Alexander, S., Shinnick, T.M., Sutcliffe, J.G., and Lerner, R.A. (1982). Immunogenic structure of the influenza virus hemagglutinin. Cell 28: 477-487.
Greenbaum, J.A., Andersen, P.H., Blythe, M., Bui, H.H., Cachau, R.E., Crowe, J., Davies, M., Kolaskar, A.S., Lund, O., Morrison, S., et al. (2007). Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit 20: 75-82.
Haab, B.B., Dunham, M.J., and Brown, P.O. (2001). Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol 2: RESEARCH0004.
Hancock, D.C., and O'Reilly, N.J. (2005). Immunochemical Protocols, 3 ed. Humana Press, Totowa.
Harris, C.L., Lublin, D.M., and Morgan, B.P. (2002). Efficient generation of monoclonal antibodies for specific protein domains using recombinant immunoglobulin fusion proteins: pitfalls and solutions. J Immunol Methods
268: 245-258.
Haste Andersen, P., Nielsen, M., and Lund, O. (2006). Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci 15: 2558-2567.
Hattori, M., Fujiyama, A., Taylor, T.D., Watanabe, H., Yada, T., Park, H.S., Toyoda, A., Ishii, K., Totoki, Y., Choi, D.K., et al. (2000). The DNA sequence of human chromosome 21. Nature 405: 311-319.
Hopp, T.P., and Woods, K.R. (1981). Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A 78: 3824-3828. Hulett, H.R., Bonner, W.A., Barrett, J., and Herzenberg, L.A. (1969). Cell sorting:
automated separation of mammalian cells as a function of intracellular fluorescence. Science 166: 747-749.
Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., Cuche, B.A., de Castro, E., Lachaize, C., Langendijk-Genevaux, P.S., and Sigrist, C.J. (2008). The 20 years of PROSITE. Nucleic Acids Res 36: D245-249.
Humphery-Smith, I. (2004). A human proteome project with a beginning and an end. Proteomics 4: 2519-2521.
Huston, J.S., Levinson, D., Mudgett-Hunter, M., Tai, M.S., Novotny, J., Margolies, M.N., Ridge, R.J., Bruccoleri, R.E., Haber, E., Crea, R., et al. (1988). Protein engineering of antibody binding sites: recovery of specific activity in an anti-digoxin single-chain Fv analogue produced in Escherichia coli. Proc Natl Acad Sci U S A 85: 5879-5883.
Iyer, R., Jenkinson, C.P., Vockley, J.G., Kern, R.M., Grody, W.W., and Cederbaum, S. (1998). The human arginases and arginase deficiency. J Inherit Metab Dis
21 Suppl 1: 86-100.
Jones, D.T. (2007). Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23: 538-544. Käll, L., Krogh, A., and Sonnhammer, E.L. (2005). An HMM posterior decoder
for sequence feature prediction that includes homology information. Bioinformatics 21 Suppl 1: i251-257.
Käll, L., Krogh, A., and Sonnhammer, E.L. (2007). Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res 35: W429-432.
Käll, L., and Sonnhammer, E.L. (2002). Reliability of transmembrane predictions in whole-genome data. FEBS Lett 532: 415-418.
Kampf, C., Andersson, A.C., Wester, K., Björling, E., Uhlén, M., and Pontén, F. (2004). Antibody-based tissue profiling as a tool for clinical proteomics. Clin. Proteomics 1: 285-299.
Karplus, P.A., and Schulz, G.E. (1985). Prediction of chain flexibility in proteins. A tool for the selection of peptide antigens. Naturwissenschaften 72: 212-213. Kendrew, J.C., Dickerson, R.E., Strandberg, B.E., Hart, R.G., Davies, D.R.,
Phillips, D.C., and Shore, V.C. (1960). Structure of Myoglobin: A Three-Dimensional Fourier Synthesis at 2 Å. Resolution. Nature 185: 422-427. Klabunde, T., and Hessler, G. (2002). Drug design strategies for targeting
Köhler, G., and Milstein, C. (1975). Continuous cultures of fused cells secreting antibody of predefined specificity. Nature 256: 495-497.
Kononen, J., Bubendorf, L., Kallioniemi, A., Barlund, M., Schraml, P., Leighton, S., Torhorst, J., Mihatsch, M.J., Sauter, G., and Kallioniemi, O.P. (1998). Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med 4: 844-847.
Kulikova, T., Akhtar, R., Aldebert, P., Althorpe, N., Andersson, M., Baldwin, A., Bates, K., Bhattacharyya, S., Bower, L., Browne, P., et al. (2007). EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res 35: D16-20. Kulkarni-Kale, U., Bhosle, S., and Kolaskar, A.S. (2005). CEP: a conformational
epitope prediction server. Nucleic Acids Res 33: W168-171.
Kyte, J., and Doolittle, R.F. (1982). A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. (2001). Initial sequencing and analysis of the human genome. Nature 409: 860-921. Larsen, J.E., Lund, O., and Nielsen, M. (2006). Improved method for predicting
linear B-cell epitopes. Immunome Res 2: 2.
Larsson, M., Gräslund, S., Yuan, L., Brundell, E., Uhlén, M., Höög, C., and Ståhl, S. (2000). High-throughput protein expression of cDNA products as a tool in functional genomics. J Biotechnol 80: 143-157.
Laver, W.G., Air, G.M., Webster, R.G., and Smith-Gill, S.J. (1990). Epitopes on protein antigens: misconceptions and realities. Cell 61: 553-556.
Lazarides, E., and Weber, K. (1974). Actin antibody: the specific visualization of actin filaments in non-muscle cells. Proc Natl Acad Sci U S A 71: 2268-2272.
Lerner, R.A., Green, N., Alexander, H., Liu, F.T., Sutcliffe, J.G., and Shinnick, T.M. (1981). Chemically synthesized peptides predicted from the nucleotide sequence of the hepatitis B virus genome elicit antibodies reactive with the native envelope protein of Dane particles. Proc Natl Acad Sci U S A 78: 3403-3407.
Letunic, I., Copley, R.R., Pils, B., Pinkert, S., Schultz, J., and Bork, P. (2006). SMART 5: domains in the context of genomes and networks. Nucleic Acids Res 34: D257-260.
Lindskog, M., Rockberg, J., Uhlén, M., and Sterky, F. (2005). Selection of protein epitopes for antibody production. Biotechniques 38: 723-727.
Lisowska, E. (2001). Antigenic properties of human glycophorins--an update. Adv Exp Med Biol 491: 155-169.
Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H., et al. (1996). Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14: 1675-1680.
Luscombe, N.M., Greenbaum, D., and Gerstein, M. (2001). What is bioinformatics? A proposed definition and overview of the field. Methods
Mann, M., and Jensen, O.N. (2003). Proteomic analysis of post-translational modifications. Nat Biotechnol 21: 255-261.
Markham, K., Bai, Y., and Schmitt-Ulms, G. (2007). Co-immunoprecipitations revisited: an update on experimental concepts and their implementation for sensitive interactome investigations of endogenous proteins. Anal Bioanal Chem 389: 461-473.
Maxam, A.M., and Gilbert, W. (1977). A new method for sequencing DNA. Proc Natl Acad Sci U S A 74: 560-564.
McGinnis, S., and Madden, T.L. (2004). BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 32: W20-25.
Mi, H., Lazareva-Ulitsky, B., Loo, R., Kejariwal, A., Vandergriff, J., Rabkin, S., Guo, N., Muruganujan, A., Doremieux, O., Campbell, M.J., et al. (2005). The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res 33: D284-288.
Miescher, F. (1871). Ueber die chemische Zusammensetzung der Eiterzellen. Med.-Chem. Unters. 4: 441-460.
Miklos, G.L., and Maleszka, R. (2001). Protein functions and biological contexts. Proteomics 1: 169-178.
Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Buillard, V., Cerutti, L., Copley, R., et al. (2007). New developments in the InterPro database. Nucleic Acids Res 35: D224-228. Naaby-Hansen, S., Waterfield, M.D., and Cramer, R. (2001).
Proteomics--post-genomic cartography to understand gene function. Trends Pharmacol Sci 22: 376-384.
Nair, R., and Rost, B. (2002). Sequence conserved for subcellular localization. Protein Sci 11: 2836-2847.
Nilsson, P., Paavilainen, L., Larsson, K., Ödling, J., Sundberg, M., Andersson, A.C., Kampf, C., Persson, A., Al-Khalili Szigyarto, C., Ottosson, J., et al. (2005). Towards a human proteome atlas: high-throughput generation of mono-specific antibodies for tissue profiling. Proteomics 5: 4327-4337. Nirenberg, M.W. (1963). The genetic code. II. Sci Am 208: 80-94.
Nord, K., Gunneriusson, E., Ringdahl, J., Ståhl, S., Uhlén, M., and Nygren, P.Å. (1997). Binding proteins selected from combinatorial libraries of an alpha-helical bacterial receptor domain. Nat Biotechnol 15: 772-777.
O'Farrell, P.H. (1975). High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250: 4007-4021.
Odorico, M., and Pellequer, J.L. (2003). BEPITOPE: predicting the location of continuous epitopes and patterns in proteins. J Mol Recognit 16: 20-22. Olive, C., Toth, I., and Jackson, D. (2001). Technological advances in antigen
delivery and synthetic peptide vaccine developmental strategies. Mini Rev Med Chem 1: 429-438.
Parker, J.M., Guo, D., and Hodges, R.S. (1986). New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry 25: 5425-5432.
Perutz, M.F., Rossmann, M.G., Cullis, A.F., Muirhead, H., Will, G., and North, A.C.T. (1960). Structure of Haemoglobin: A Three-Dimensional Fourier Sythesis at 5.5-Å. Resolution, Obtained by X-ray Analysis. Nature 185: 416-422.
Ponomarenko, J.V., and Bourne, P.E. (2007). Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol 7: 64. Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., and
Lopez, R. (2005). InterProScan: protein domains identifier. Nucleic Acids Res 33: W116-120.
Rebhan, M., Chalifa-Caspi, V., Prilusky, J., and Lancet, D. (1997). GeneCards: integrating information about genes, proteins and diseases. Trends Genet 13: 163.
Renart, J., Reiser, J., and Stark, G.R. (1979). Transfer of proteins from gels to diazobenzyloxymethyl-paper and detection with antisera: a method for studying antibody specificity and antigen structure. Proc Natl Acad Sci U S A 76: 3116-3120.
Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M., and Seraphin, B. (1999). A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17: 1030-1032. Rodda, S.J., Geysen, H.M., Mason, T.J., and Schoofs, P.G. (1986). The antibody
response to myoglobin--I. Systematic synthesis of myoglobin peptides reveals location and substructure of species-dependent continuous antigenic determinants. Mol Immunol 23: 603-610.
Sanger, F., Nicklen, S., and Coulson, A.R. (1977). DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74: 5463-5467.
Sanger, F., and Tuppy, H. (1951a). The amino-acid sequence in the phenylalanyl chain of insulin. 2. The investigation of peptides from enzymic hydrolysates. Biochem J 49: 481-490.
Sanger, F., and Tuppy, H. (1951b). The amino-acid sequence in the phenylalanyl chain of insulin. I. The identification of lower peptides from partial hydrolysates. Biochem J 49: 463-481.
Schena, M., Shalon, D., Davis, R.W., and Brown, P.O. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
Scott, M.S., Thomas, D.Y., and Hallett, M.T. (2004). Predicting subcellular localization via protein motif co-occurrence. Genome Res 14: 1957-1966. Selengut, J.D., Haft, D.H., Davidsen, T., Ganapathy, A., Gwinn-Giglio, M.,
Nelson, W.C., Richter, A.R., and White, O. (2007). TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res 35: D260-264. Shiraki, T., Kondo, S., Katayama, S., Waki, K., Kasukawa, T., Kawaji, H., Kodzius,
R., Watahiki, A., Nakamura, M., Arakawa, T., et al. (2003). Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A 100:
Sjölander, A., Nygren, P.Å., Ståhl, S., Berzins, K., Uhlén, M., Perlmann, P., and Andersson, R. (1997). The serum albumin-binding region of streptococcal protein G: a bacterial fusion partner with carrier-related properties. J Immunol Methods 201: 115-123.
Sollner, J. (2006). Selection and combination of machine learning classifiers for prediction of linear B-cell epitopes on proteins. J Mol Recognit 19: 209-214. Sollner, J., and Mayer, B. (2006). Machine learning approaches for prediction of
linear B-cell epitopes on proteins. J Mol Recognit 19: 200-208.
Sonnhammer, E.L., von Heijne, G., and Krogh, A. (1998). A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 6: 175-182.
Sprenger, J., Fink, J.L., and Teasdale, R.D. (2006). Evaluation and comparison of mammalian subcellular localization prediction methods. BMC Bioinformatics
7 Suppl 5: S3.
Stabenau, A., McVicker, G., Melsopp, C., Proctor, G., Clamp, M., and Birney, E. (2004). The Ensembl core software libraries. Genome Res 14: 929-933. Steen, J., Uhlén, M., Hober, S., and Ottosson, J. (2006). High-throughput protein
purification using an automated set-up for high-yield affinity chromatography. Protein Expr Purif 46: 173-178.
Strömberg, S., Björklund, M.G., Asplund, C., Sköllermo, A., Persson, A., Wester, K., Kampf, C., Nilsson, P., Andersson, A.C., Uhlén, M., et al. (2007). A high-throughput strategy for protein profiling in cell microarrays using automated image analysis. Proteomics 7: 2142-2150.
Sugawara, H., Abe, T., Gojobori, T., and Tateno, Y. (2007). DDBJ working on evaluation and classification of bacterial genes in INSDC. Nucleic Acids Res
35: D13-15.
Sutcliffe, J.G., Shinnick, T.M., Green, N., Liu, F.T., Niman, H.L., and Lerner, R.A. (1980). Chemical synthesis of a polypeptide predicted from nucleotide sequence allows detection of a new retroviral gene product. Nature 287: 801-805.
Tanaka, K., Waki, H., Ido, Y., Akita, S., Yoshida, Y., and Yoshida, T. (1988). Protein and polymer analysis up to m/z 100.000 by laser ionisation time-of-flight mass spectrometry. Commun. Mass Spectrom. 2: 151-153.
Tanford, C., and Reynolds, J. (2001). Nature's Robots: A History of Proteins, 1 ed. Oxford University Press, Oxford.
Taussig, M.J., Stoevesandt, O., Borrebaeck, C.A., Bradbury, A.R., Cahill, D., Cambillau, C., de Daruvar, A., Dubel, S., Eichler, J., Frank, R., et al. (2007). ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat Methods 4: 13-17.
Terpe, K. (2003). Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol
60: 523-533.
Travers, P., Walport, M., and Kenneth, M. (2007). Janeway's Immunobiology, 7 ed. Garland Publishing, New York.
Tusnady, G.E., and Simon, I. (2001). The HMMTOP transmembrane topology prediction server. Bioinformatics 17: 849-850.
Uhlén, M. (2007). Mapping the human proteome using antibodies. Mol Cell Proteomics 6: 1455-1456.
Uhlén, M., Björling, E., Agaton, C., Szigyarto, C.A., Amini, B., Andersen, E., Andersson, A.C., Angelidou, P., Asplund, A., Asplund, C., et al. (2005). A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol Cell Proteomics 4: 1920-1932.
Uhlén, M., and Pontén, F. (2005). Antibody-based proteomics for human tissue profiling. Mol Cell Proteomics 4: 384-393.
UniProt Consortium. (2008). The universal protein resource (UniProt). Nucleic Acids Res 36: D190-195.
Van Regenmortel, M.H. (2006). Immunoinformatics may lead to a reappraisal of the nature of B cell epitopes and of the feasibility of synthetic peptide vaccines. J Mol Recognit 19: 183-187.
Van Regenmortel, M.H., and Pellequer, J.L. (1994). Predicting antigenic determinants in proteins: looking for unidimensional solutions to a