Gavin GroupPublications
Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding.
Iskar, M., Zeller, G., Blattmann, P., Campillos, M., Kuhn, M., Kaminska, K.H., Runz, H., Gavin, A.C., Pepperkok, R., van Noort, V. & Bork, P.
Mol Syst Biol. 2013 Apr 30;9:662. doi: 10.1038/msb.2013.20. PubMed
Structural and functional characterization of a phosphatase domain within yeast general transcription factor TFIIIC.
Taylor, N.M., Glatt, S., Hennrich, M.L., von Scheven, G., Grotsch, H., Fernandez-Tornero, C., Rybin, V., Gavin, A.C., Kolb, P. & Muller, C.W.
J Biol Chem. 2013 Apr 8. PubMed
In Vivo profiling and visualization of cellular protein-lipid interactions using bifunctional Fatty acids.
Haberkant, P., Raijmakers, R., Wildwater, M., Sachsenheimer, T., Brugger, B., Maeda, K., Houweling, M., Gavin, A.C., Schultz, C., van Meer, G., Heck, A.J. & Holthuis, J.C.
Angew Chem Int Ed Engl. 2013 Apr 2;52(14):4033-8. doi: 10.1002/anie.201210178.Epub 2013 Feb 28. PubMed
Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP.
Bonn, S., Zinzen, R.P., Perez-Gonzalez, A., Riddell, A., Gavin, A.C. & Furlong, E.E.
Nat Protoc. 2012 Apr 26;7(5):978-94. doi: 10.1038/nprot.2012.049. PubMed
Transcription start site associated RNAs in bacteria.
Yus, E., Guell, M., Vivancos, A.P., Chen, W.H., Lluch-Senar, M., Delgado, J., Gavin, A.C., Bork, P. & Serrano, L.
Mol Syst Biol. 2012 May 22;8:585. doi: 10.1038/msb.2012.16. PubMed
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium.
van Noort, V., Seebacher, J., Bader, S., Mohammed, S., Vonkova, I., Betts, M.J., Kuhner, S., Kumar, R., Maier, T., O'Flaherty, M., Rybin, V., Schmeisky, A., Yus, E., Stulke, J., Serrano, L., Russell, R.B., Heck, A.J., Bork, P. & Gavin, A.C.
Mol Syst Biol. 2012 Feb 28;8:571. doi: 10.1038/msb.2012.4. PubMed
Deciphering a global network of functionally associated post-translational modifications.
Minguez, P., Parca, L., Diella, F., Mende, D.R., Kumar, R., Helmer-Citterich, M., Gavin, A.C., van Noort, V. & Bork, P.
Mol Syst Biol. 2012 Jul 17;8:599. doi: 10.1038/msb.2012.31. PubMed
Structural analyses of the Slm1-PH domain demonstrate ligand binding in the non-canonical site.
Anand, K., Maeda, K. & Gavin, A.C.
PLoS One. 2012;7(5):e36526. Epub 2012 May 4. PubMed
Quantification of mRNA and protein and integration with protein turnover in a bacterium.
Maier, T., Schmidt, A., Guell, M., Kuhner, S., Gavin, A.C., Aebersold, R. & Serrano, L.
Mol Syst Biol. 2011 Jul 19;7:511. doi: 10.1038/msb.2011.38. PubMed
SnapShot: Protein-Protein Interaction Networks.
Seebacher, J. & Gavin, A.C.
Cell. 2011 Mar 18;144(6):1000-1000.e1. PubMed
Mass Spectrometry Reveals Stable Modules in holo and apo RNA Polymerases I and III.
Lane, L.A., Fernandez-Tornero, C., Zhou, M., Morgner, N., Ptchelkine, D., Steuerwald, U., Politis, A., Lindner, D., Gvozdenovic, J., Gavin, A.C., Muller, C.W. & Robinson, C.V.
Structure. 2011 Jan 12;19(1):90-100. PubMed
A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae.
Gallego, O., Betts, M.J., Gvozdenovic-Jeremic, J., Maeda, K., Matetzki, C., Aguilar-Gurrieri, C., Beltran-Alvarez, P., Bonn, S., Fernandez-Tornero, C., Jensen, L.J., Kuhn, M., Trott, J., Rybin, V., Muller, C.W., Bork, P., Kaksonen, M., Russell, R.B. & Gavin, A.C.
Mol Syst Biol. 2010 Nov 30;6:430. doi: 10.1038/msb.2010.87. PubMed
Recent advances in charting protein-protein interaction: mass spectrometry-based approaches.
Gavin, A.C., Maeda, K. & Kuhner, S.
Curr Opin Biotechnol. 2010 Oct 8. PubMed
3rd US-EU workshop: systems level understanding of DNA damage responses.
Sander, M., Begley, T.J., Desaintes, C., Gavin, A.C., Pelroy, R., Pothof, J., Shiloh, Y., van Gent, D., Van Houten, B., Yaffe, M. & Mullenders, L.
Mutat Res. 2010 Oct 13;692(1-2):53-60. Epub 2010 Aug 19. PubMed
Visualizing biological data - now and in the future.
O'Donoghue, S.I., Gavin, A.C., Gehlenborg, N., Goodsell, D.S., Heriche, J.K., Nielsen, C.B., North, C., Olson, A.J., Procter, J.B., Shattuck, D.W., Walter, T. & Wong, B.
Nat Methods. 2010 Mar;7(3 Suppl):S2-4. PubMed
Visualization of omics data for systems biology.
Gehlenborg, N., O'Donoghue, S.I., Baliga, N.S., Goesmann, A., Hibbs, M.A., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D. & Gavin, A.C.
Nat Methods. 2010 Mar;7(3 Suppl):S56-68. PubMed
Impact of genome reduction on bacterial metabolism and its regulation.
Yus, E., Maier, T., Michalodimitrakis, K., van Noort, V., Yamada, T., Chen, W.H., Wodke, J.A., Guell, M., Martinez, S., Bourgeois, R., Kuhner, S., Raineri, E., Letunic, I., Kalinina, O.V., Rode, M., Herrmann, R., Gutierrez-Gallego, R., Russell, R.B., Gavin, A.C., Bork, P. & Serrano, L.
Science. 2009 Nov 27;326(5957):1263-8. PubMed
Transcriptome complexity in a genome-reduced bacterium.
Guell, M., van Noort, V., Yus, E., Chen, W.H., Leigh-Bell, J., Michalodimitrakis, K., Yamada, T., Arumugam, M., Doerks, T., Kuhner, S., Rode, M., Suyama, M., Schmidt, S., Gavin, A.C., Bork, P. & Serrano, L.
Science. 2009 Nov 27;326(5957):1268-71. PubMed
Proteome organization in a genome-reduced bacterium.
Kühner S., van Noort V., Betts M.J., Leo-Macias A., Batisse C., Rode M., Yamada T., Maier T., Bader S., Beltran-Alvarez P., Castaño-Diez D., Chen W.H., Devos D., Güell Cargol M., Norambuena T., Racke I., Rybin V., Schmidt A., Yus E., Aebersold R., Herrmann R., Böttcher B., Frangakis A.S., Russell R.B., Serrano L., Bork, P. and Gavin, A.C.
Science, 2009, 326, 1235-1240
Full text
Meeting report on the 7th World Congress of the Human Proteome Organization (HUPO) in Amsterdam: Proteome Biology.
Gavin, A.C., Aebersold, R. & Heck, A.J.
Mol Cell Proteomics. 2008 Nov;7(11):2288-91. PubMed
Drug target identification using side-effect similarity.
Campillos, M., Kuhn, M., Gavin, A.C., Jensen, L.J. & Bork, P.
Science. 2008 Jul 11;321(5886):263-6. PubMed
Interaction networks for systems biology.
Bader, S., Kuhner, S. & Gavin, A.C.
FEBS Lett. 2008 Apr 9;582(8):1220-4. Epub 2008 Feb 20. PubMed
The social network of a cell: Recent advances in interactome mapping.
Charbonnier, S., Gallego, O. & Gavin, A.C.
Biotechnol Annu Rev. 2008;14:1-28. PubMed
The minimum information required for reporting a molecular interaction experiment (MIMIx).
Orchard, S., Salwinski, L., Kerrien, S., Montecchi-Palazzi, L., Oesterheld, M., Stumpflen, V., Ceol, A., Chatr-Aryamontri, A., Armstrong, J., Woollard, P., Salama, J.J., Moore, S., Wojcik, J., Bader, G.D., Vidal, M., Cusick, M.E., Gerstein, M., Gavin, A.C., Superti-Furga, G., Greenblatt, J., Bader, J., Uetz, P., Tyers, M., Legrain, P., Fields, S., Mulder, N., Gilson, M., Niepmann, M., Burgoon, L., Rivas Jde, L., Prieto, C., Perreau, V.M., Hogue, C., Mewes, H.W., Apweiler, R., Xenarios, I., Eisenberg, D., Cesareni, G. & Hermjakob, H.
Nat Biotechnol. 2007 Aug;25(8):894-8. PubMed
New perspectives on an old disease: proteomics in cancer research.
Gallego, O. & Gavin, A.C.
Genome Biol. 2007 Apr 30;8(4):303. PubMed
Towards quantitative analysis of proteome dynamics.
Kuhner, S. & Gavin, A.C.
Nat Biotechnol. 2007 Mar;25(3):298-300. PubMed
Casein kinase 2-dependent serine phosphorylation of MuSK regulates acetylcholine receptor aggregation at the neuromuscular junction.
Cheusova, T., Khan, M.A., Schubert, S.W., Gavin, A.C., Buchou, T., Jacob, G., Sticht, H., Allende, J., Boldyreff, B., Brenner, H.R. & Hashemolhosseini, S.
Genes Dev. 2006 Jul 1;20(13):1800-16. PubMed
Proteome survey reveals modularity of the yeast cell machinery.
Gavin, A.C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L.J., Bastuck, S., Dumpelfeld, B., Edelmann, A., Heurtier, M.A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A.M., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J.M., Kuster, B., Bork, P., Russell, R.B. & Superti-Furga, G.
Nature. 2006 Mar 30;440(7084):631-6. Epub 2006 Jan 22. PubMed
Protein co-membership and biochemical affinity purifications.
Gavin, A.C. & Hopf, C.
Drug Discovery Today: Technology 2006
Expanding the frontiers of proteomics.
Gavin, A.C. & Heck, A.
Drug Discovery Today: Technology 2006
Keystone symposia: proteomics and bioinformatics and systems and biology.
Gavin, A.C.
Expert Rev. Proteomics 2005;2:291-3.
Structure-based assembly of protein complexes in yeast.
Aloy, P., Böttcher, B., Ceulemans, H., Leutwein, C., Mellwig, C., Fischer, S., Gavin, A.C., Bork, P., Superti-Furga, G., Serrano, L. & Russell, R.B.
Science 2004 Mar 26;303(5666):2026-9. PubMed
A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway.
Bouwmeester, T., Bauch, A., Ruffner, H., Angrand, P.O., Bergamini, G., Croughton, K., Cruciat, C., Eberhard, D., Gagneur, J., Ghidelli, S., Hopf, C., Huhse, B., Mangano, R., Michon, A.M., Schirle, M., Schlegl, J., Schwab, M., Stein, M.A., Bauer, A., Casari, G., Drewes, G., Gavin, A.C., Jackson, D.B., Joberty, G., Neubauer, G., Rick, J., Kuster, B. & Superti-Furga, G.
Nat Cell Biol 2004 Feb;6(2):97-105. Epub 2004 Jan 25. PubMed
Protein complexes and proteome organization from yeast to man.
Gavin, A.C. & Superti-Furga, G.
Curr Opin Chem Biol 2003 Feb;7(1):21-7. PubMed
90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors.
Grandi, P., Rybin, V., Bassler, J., Petfalski, E., Strauss, D., Marzioch, M., Schafer, T., Kuster, B., Tschochner, H., Tollervey, D., Gavin, A.C. & Hurt, E.
Mol Cell 2002 Jul;10(1):105-15. PubMed
A complex prediction: three-dimensional model of the yeast exosome.
Aloy, P., Ciccarelli, F.D., Leutwein, C., Gavin, A.C., Superti-Furga, G., Bork, P., Böttcher, B. & Russell, R.B.
EMBO Rep 2002 Jul;3(7):628-35. PubMed
Functional organization of the yeast proteome by systematic analysis of protein complexes.
Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G. & Superti-Furga, G.
Nature 2002 Jan 10;415(6868):141-7. PubMed
Perspectives: signal transduction. Cell survival demands some Rsk.
Nebreda, A.R. & Gavin, A.C.
Science 1999 Nov 12;286(5443):1309-10 PubMed
A p90(rsk) mutant constitutively interacting with MAP kinase uncouples MAP kinase from p34(cdc2)/cyclin B activation in Xenopus oocytes.
Gavin, A.C., Ni Ainle, A., Chierici, E., Jones, M. & Nebreda, A.R.
Mol Biol Cell 1999 Sep;10(9):2971-86. PubMed
A MAP kinase docking site is required for phosphorylation and activation of p90(rsk)/MAPKAP kinase-1.
Gavin, A.C. & Nebreda, A.R.
Curr Biol 1999 Mar 11;9(5):281-4. PubMed
Cell survival demands some Rsk.
Nebreda A.R. & Gavin A.C.
Science 1999;286:309-1310.
Regulation and G2/M transition promoting activity of the human Abl tyrosine kinase in Xenopus oocytes.
Dorey K., Barilà D., Gavin A.C., Nebreda A.R. & Superti-Furga G.
Biol. Chem. 1999;380:223-230.
A link between MAP kinase and p34(cdc2)/cyclin B during oocyte maturation: p90(rsk) phosphorylates and inactivates the p34(cdc2) inhibitory kinase Myt1.
Palmer, A., Gavin, A.C. & Nebreda, A.R.
EMBO J 1998 Sep 1;17(17):5037-47. PubMed
Ribosomal S6 kinase p90rsk and mRNA cap-binding protein eIF4E phosphorylations correlate with MAP kinase activation during meiotic reinitiation of mouse oocytes.
Gavin, A.C. & Schorderet-Slatkine, S.
Mol Reprod Dev 1997 Mar;46(3):383-91. PubMed
An accumulation of p34cdc2 at the end of mouse oocyte growth correlates with the acquisition of meiotic competence.
de Vant'ery, C., Gavin, A.C., Vassalli, J.D. & Schorderet-Slatkine, S.
Dev Biol 1996 Mar 15;174(2):335-44. PubMed
Histone H1 kinase activity, germinal vesicle breakdown and M phase entry in mouse oocytes.
Gavin, A.C., Cavadore, J.C. & Schorderet-Slatkine, S.
J Cell Sci 1994 Jan;107 ( Pt 1):275-83. PubMed
Okadaic acid and p13suc1 modulate the reinitiation of meiosis in mouse oocytes.
Gavin, A.C., Vassalli, J.D., Cavadore, J.C. & Schorderet-Slatkine, S.
Mol Reprod Dev 1992 Nov;33(3):287-96. PubMed
Induction of M-phase entry of prophase-blocked mouse oocytes through microinjection of okadaic acid, a specific phosphatase inhibitor.
Gavin, A.C., Tsukitani, Y. & Schorderet-Slatkine, S.
Exp Cell Res 1991 Jan;192(1):75-81. PubMed
The interaction of lithium with forskolin-inhibited meiotic maturation of denuded mouse oocytes.
Gavin, A.C. & Schorderet-Slatkine, S.
Exp Cell Res 1988 Nov;179(1):298-302. PubMed