Anne-Claude Gavin

Publications

2018

Boulter E., Estrach S., Tissot F.S., Hennrich M.L., Tosello L., Cailleteau L., de la Ballina L.R., Pisano S., Gavin A.C. and Féral C.C. (2018). Cell metabolism regulates integrin mechanosensing via an SLC3A2-dependent sphingolipid biosynthesis pathway. Nat. Commun. 9, 4862.

Kastritis P.L. and Gavin A.C. (2018). Enzymatic complexes across scales. Essays Biochem. 62, 501-514.

Šoštarić N., O’Reilly F.J., Giansanti P., Heck A.J.R., Gavin A.C. and van Noort V. (2018). Effects of acetylation and phosphorylation on subunit interactions in three large eukaryotic complexes. Mol. Cell. Proteomics 17, 2387-2401.

Hennrich M.L.‡, Romanov N.‡, Horn P. ‡, Jaeger S., Eckstein V., Steeples V., Ye F., Ding X., Poisa-Beiro L., Lai M.C., Lang B., Boultwood J., Luft T., Zaugg J.B., Pellagatti A., Bork P., Aloy P., Gavin A.C. # and Ho A.D.# (2018). Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline. Nat. Commun. 9, 4004.

Pellagatti A., Armstrong R.N., Steeples V., Sharma E., Repapi E., Singh S., Sanchi A., Radujkovic A., Horn P., Dolatshad H., Roy S., Broxholme J., Lockstone H., Taylor S., Giagounidis A., Vyas P., Schuh A., Hamblin A., Papaemmanuil E., Killick S., Malcovati L., Hennrich M.L., Gavin A.C., Ho A.D., Luft T., Hellström-Lindberg E., Cazzola M., Smith C.W.J., Smith S. and Boultwood J. (2018). Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations. Blood 132, 1225-1240.

2017

Reckel S., Gehin C., Tardivon D., Georgeon S., Kükenshöner T., Löhr F., Koide A., Buchner L., Panjkovich A., Reynaud A., Pinho S., Gerig B., Svergun D., Pojer F., Güntert P., Dötsch V., Koide S., Gavin A.C. and Hantschel O. (2017). Structural and functional dissection of the DH and PH domains of oncogenic Bcr-Abl tyrosine kinase. Nat. Commun. 8, 2101.

Kastritis P.L. ‡, O'Reilly F.J. ‡, Bock T. ‡, Li Y., Rogon M.Z., Buczak K., Romanov N., Betts M.J., Bui K.H., Hagen W.J., Hennrich M.L., Mackmull M.T., Rappsilber J., Russell R.B., Bork P., Beck M. # and Gavin A.C. # (2017). Capturing protein communities by structural proteomics in a thermophilic eukaryote. Mol. Syst. Biol. 13, 936.

Betts M.J., Wichmann O., Utz M., Andre T., Petsalaki E., Minguez P., Parca L., Roth F.P., Gavin A.C., Bork P. and Russell R.B. (2017). Systematic identification of phosphorylation-mediated protein interaction switches. PLoS Comput Biol. 13, e1005462.

2016

Lujan P., Varsano G., Rubio T., Hennrich M.L., Sachsenheimer T., Galvez-Santisteban M., Martin-Belmonte F., Gavin A.C., Brügger B. and Koehn M. (2016). PRL-3 disrupts epithelial architecture by altering the post-mitotic midbody position. J. Cell Sci. 129, 4130-4142.

Andrews B.J., Walhout A.J.M., Iyengar R. and The Human Cells Project Working Group (2016). Quantitative human cell encyclopedia. Sci. Signal. 9, mr1.

Saliba A.E. ‡, Vonkova I. ‡, Deghou S. ‡, Ceschia S., Tischer C., Kugler K.G., Bork P., Ellenberg J., Gavin A.C. (2016). A protocol for the systematic and quantitative measurement of protein–lipid interactions using the liposome microarray-based assay. Nat. Protoc. 11, 1021-1038.

Chen W.H., van Noort V., Lluch-Senar M., Hennrich M.L., Wodke J.A., Yus E., Alibés A., Roma G., Mende D.R., Pesavento C., Typas A., Gavin A.C., Serrano L. and Bork P. (2016).  Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances. Nucleic Acids Res. 44, 1192-1202.

Chiapparino A., Maeda K, Turei D., Saez-Rodriguez J. and Gavin A.C. (2016). The orchestra of lipid-transfer proteins at the crossroads between metabolism and signalling. Prog. Lipid Res. 61, 30-39.

Haberkant P., Stein F., Höglinger D., Gerl M., Brügger B., Van Veldhoven P.P.,  Krijgsveld J., Gavin A.C. and Schultz C. (2016). Bifunctional sphingosine for cell-based analysis of protein-sphingolipid interactions. ACS Chem. Biol. 11, 222-230.

2015

Saliba A.E., Vonkova I., Gavin A.C. (2015). The systematic analysis of protein–lipid interactions comes of age. Nat. Rev. Mol. Cell Biol. 16, 753-761.

VonkovaI. ‡, Saliba A.E. ‡,DeghouS. ‡, Anand K., Ceschia S., Doerks T., Galih A., Kugler K.G., Maeda K, Rybin V., van Noort V.,  Ellenberg J., Bork P.#and Gavin A.C.# (2015).  Lipid cooperativity as a general membrane-recruitment principle of PH domains. Cell Rep. 12, 1519-1530.

Paul V.D., Mühlenhoff U., Stümpfig M., Seebacher J., Kugler K.G., Renicke C., Taxis C., Gavin A.C., Pierik A.J. and Lill R. (2015). The deca-GX3 proteins Yae1-Lto1 function as adaptors recruiting the ABC protein Rli1 for iron-sulfur cluster insertion. eLife 4, e08231.

Köberlin M.S. ‡, Snijder B. ‡, Heinz L.X., Baumann C.L., Fauster A., Vladimer G.I., Gavin A.C. and Superti-Furga G. (2015). A conserved circular network of coregulated lipids modulates innate immune responses. Cell 162, 170-183.

Hennrich M.L. and Gavin A.C. (2015). Quantitative mass spectrometry of posttranslational modifications: keys to confidence. Sci. Signal. 8, 5-6.

Lluch-Senar M., Delgado J., Chen W.H., Lloréns-Rico V., O’Reilly F.J., Wodke J.A., Unal E.B., Yus E., Martinez S., Nichols R.J., Ferrar T., Vivancos A., Schmeisky A., Stülke J., van Noort V., Gavin A.C., Bork P. and Luis Serrano L. (2015).  Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Mol. Syst. Biol. 11, 780.

Betts M.J., Lu Q., Jiang Y., Drusko A., Wichmann O., Utz M., Valtierra-Gutiérrez I.A., Schlesner M., Jaeger N., Jones D.T., Pfister S., Lichter P., Eils R., Siebert R., Bork P., Apic G., Gavin A.C. and Russell R.B. (2015).  Mechismo: predicting mechanistic impact of mutations and modifications on molecular interactions. Nucleic Acids Res. 43, e10.

Glatt S., Zabel R., Vonkova I., Kumar A., Netz D.J., Pierik A.J., Rybin V., Lill R., Gavin A.C., Balbach J., Breunig K.D. and Müller C.W. (2015).  Structure of the Kti11/Kti13 heterodimer and its double role in modifications of tRNA and eukaryotic elongation factor 2. Structure 23, 149-60.

2014

Gustafsson M., Nestor C.E., Zhang H., Barabási A.L., Baranzini S., Brunak S., Chung K.F., Federoff H.F., Gavin A.C., Meehan R.R., Picotti P., Pujana M., Rajewsky N., Smith K.G., Sterk P.J., Villoslada P. and Benson M. (2014).  Modules, networks and systems medicine for understanding disease and aiding diagnosis. Genome Med. 6, 82.

Bock T., Chen W.H., Ori A., Malik N., Silva-Martin N., Huerta-Cepas J., Powell S.T., Kastritis P.L., Smyshlyaev G., Vonkova I., Kirkpatrick J., Doerks T., Nesme L., Bassler J., Kos M., Hurt E., Carlomagno T., Gavin A.C., Barabas O., Muller C.W., van Noort V., Beck M. and Bork P. (2014).  An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum. Nucleic Acids Res. 42, 13525-33.

Maeda K., Poletto M., Chiapparino A. and Gavin A.C. (2014).  A generic protocol for the purification and characterization of water-soluble complexes of affinity-tagged proteins and lipids. Nat. Protoc. 9, 2256-2266.

Saliba A.E. ‡, Vonkova I. ‡, Ceschia S., Findlay G.M., Maeda K., Tischer C., Deghou S., van Noort V., Bork P., Pawson T., Ellenberg J. and Gavin A.C. (2014).  A quantitative liposome microarray to systematically characterize protein-lipid interactions. Nat. Methods 11, 47-50.

2013

Maeda K., Anand K., Chiapparino A., Kumar A., Poletto M., Kaksonen M. and Gavin A.C. (2013).  Interactome map uncovers phosphatidylserine transport by oxysterol-binding proteins. Nature 501, 257-261.

Marcotte E., Boone C., Babu M.M. and Gavin A.C. (2013).  Network biology editorial 2013. Mol. Biosyst. 9, 1557-1558.

Iskar M., Zeller G., Blattmann P., Campillos M., Kuhn M., Kaminska K.H., Runz H., Gavin A.C., Pepperkok R., van Noort V. and Bork P. (2013).  Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Mol. Syst. Biol. 9, 662.

Taylor N.M., Glatt S., Hennrich M.L., von Scheven G., Grötsch H., Fernández-Tornero C., Rybin V., Gavin A.C., Kolb P. and Müller C.W. (2013).  Structural and functional characterization of a phosphatase domain within yeast general transcription factor IIIC. J. Biol. Chem. 288, 15110-15120.

Gallego O., Specht T, Brach T., Kumar A., Gavin A.C. and Kaksonen M. (2013).  Detection and characterization of protein interactions in vivo by a simple live-cell imaging method. PLoS One 8: e62195.

Kuhn M., Al Banchaabouchi M., Campillos M., Jensen L.J., Gross C., Gavin A.C. and Bork P. (2013).  Systematic identification of proteins that elicit drug side effects. Mol. Syst. Biol. 9, 663.

Haberkant P., Raijmakers R., Wildwater M., Sachsenheimer T., Brügger B., Maeda K., Houweling M., Gavin A.C., Schultz C., van Meer G., Heck A.J. and Holthuis J.C. (2013).  In vivo profiling and visualization of cellular protein-lipid interactions using bifunctional fatty acids. Angew Chem Int Ed Engl, 52, 4033-4038.

2012

Minguez P., Parca L., Diella F., Mende D.R., Kumar R., Helmer-Citterich M., Gavin A.C., van Noort V. and Bork P. (2012).  Deciphering a global network of functionally associated post-translational modifications. Mol. Syst. Biol.8, 599.

Yus E., Güell M., Vivancos A.P., Chen W.H., Lluch-Senar M., Delgado J., Gavin A.C., Bork P. and Serrano L. (2012).  Transcription start site associated RNAs in bacteria. Mol. Syst. Biol. 8, 585.

Anand K., Maeda K. and Gavin A.C. (2012).  Structural analyses of Slm1-PH domain demonstrate ligand binding in the non-canonical site. PLoS One 7, e36526.

Bonn S., Zinzen R.P., Perez-Gonzalez A., Riddell A., Gavin A.C. and Furlong E.E (2012).  Cell type–specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nat. Protoc. 7, 978-994.

van Noort V. ‡, Seebacher J. ‡, Bader S. ‡, Mohammed S., Vonkova I., Betts M.J., Kühner S., Kumar R., Maier T., O’Flaherty M., Rybin V., Schmeisky A., Yus E., Stülke J., Serrano L., Russell R.B., Heck A.J., Bork P.# and Gavin A.C.# (2012).  Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol. Syst. Biol. 8, 571.

2011

Maier T., Schmidt A., Güell M., Kühner S., Gavin A.C., Aebersold R. and Serrano L. (2011).  Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol. Syst. Biol. 7, 511.

Seebacher J. and Gavin A.C. (2011).  SnapShot: protein-protein interaction networks. Cell 144, 1000.

Lane L.A.,  Fernández-Tornero C., Zhou M., Morgner N., Ptchelkine D., Steuerwald U., Politis A., Lindner D., Gvozdenovic J., Gavin A.C.,. Müller C.W. and Robinson C.V. (2011).  Mass spectrometry reveals stable modules in holo and apo RNA polymerases I and III. Structure 19, 90-100.

Gavin A.C., Maeda K. and Kühner S. (2011).  Recent advances in charting protein-protein interaction: mass spectrometry-based approaches. Curr. Opin. Biotechnol. 22, 42-49.

2010

Gallego O., Betts M.J., Gvozdenovic-Jeremic J., Maeda K., Matetzki C., Aguilar-Gurrieri C., Beltran-Alvarez P., Bonn S., Fernández-Tornero C., Jensen L.J., Kuhn M, Trott J., Rybin V., Müller C.W., Bork P., Kaksonen M., Russell R.B. and Gavin A.C. (2010).  A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae. Mol. Syst. Biol. 6, 430.

Sander M., Begley T.J., Desaintes C., Gavin A.C., Pelroy R., Pothof J., Shiloh Y., van Gent D., Van Houten B., Yaffe M. and Mullenders L. (2010).  3rd US-EU Workshop: Systems level understanding of DNA damage responses. Mutat Res. 692, 53-60.

O’Donoghue S.I., Gavin A.C., Gehlenborg N., Goodsell D.S., Hériché J.K., Nielsen C.B., North C., Olson A.J., Procter J.B., Shattuck D.W., Walter T., Wong B. (2010).  Visualizing biological data - now and in the future. Nat. Methods 7, S2-S4.

Gehlenborg N., O’Donoghue S.I., Baliga N.S., Goesmann A., Hibbs M.A., Kitano H., Kohlbacher O., Neuweger H., Schneider R., Tenenbaum D. and Gavin A.C. (2010).  Visualization of Omics Data for Systems Biology. Nat. Methods 7, S56-S68.

2009

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.# (2009).  Proteome organization in a genome-reduced bacterium. Science 326, 1235-1240.

Yus E., Maier T., Michalodimitrakis K., van Noort V., Yamada T., Chen W.-H., Wodke J.A.H., Güell M., Martínez S., Bourgeois R., Kühner S., Raineri E., Letunic I., Kalinina O.V., Rode M., Herrmann R., Gutiérrez-Gallego R., Russell R.B., Gavin A.C., Bork P. and Serrano L. (2009).  Impact of genome reduction on bacterial metabolism and its regulation. Science 326, 1263-1268.

Güell M., van Noort V., Yus E., Chen W.-H., Leigh-Bell J., Michalodimitrakis K., Yamada T., Arumugam M., Doerks T., Kühner S., Rode M., Suyama M., Gavin A.C., Bork P. and Serrano L. (2009).  Transcriptome complexity in a genome-reduced bacterium. Science 326, 1268-1271.

2008

Gavin A.C., Aebersold R. and Heck A.J. (2008).  Meeting report on the 7th World Congress of the Human Proteome Organization (HUPO) in Amsterdam: Proteome Biology. Mol. Cell. Proteomics 7, 2288-2291.

Campillos M., Kuhn M., Gavin A.C., Jensen L.J. and Bork P. (2008).  Drug target identification using side-effect similarity. Science 321, 263-266.

Charbonnier S., Gallego O. and Gavin A.C. (2008).  The social network of a cell: recent advances in interactome mapping. Biotechnol. Annu. Rev. 14, 1-28.

Bader S., Kühner S. and Gavin A.C. (2008).  Interaction networks for systems biology. FEBS Letters 582, 1220-1224.

2007

Orchard S., Salwinski L., Kerrien s., Montecchi-Palazzi L., Oesterheld M., Stümpflen V., Ceol A., Chatr-aryamontri A., Armstrong J., Woollard P., Salama J., Moore S., Wojcik J., Bader G.D., Vidal M., Cusick M., Gerstein M., Gavin A.C., Superti-Furga G., Greenblatt J., Bader J., Uetz P., Tyers M., Legrain P., Fields S., The GO Consortium, Gilson M.,  Hogue C., Mewes H.W., Apweiler R., XenarioS I., Eisenberg D., Cesareni G. and Hermjakob H. (2007).  The minimum information required for reporting a molecular interaction experiment (MIMIx). Nature Biotech. 25, 894-898.

Gallego, O. and Gavin A.C. (2007).  New perspectives on an old disease: proteomics in cancer research. Genome Biol. 8, 303-306.

Kühner, S. and Gavin A.C. (2007).  Towards quantitative analysis of proteome dynamics. Nature Biotech. 25, 298-300.

2006

Gavin A.C. and Heck A. (2006).  Expanding the frontiers of proteomics. Drug Discovery Today: Technology doi:10.1016/j.ddtec.2006.09.016.

Gavin A.C. and Hopf C. (2006).  Protein co-membership and biochemical affinity purifications. Drug Discovery Today: Technology doi:10.1016/j.ddtec.2006.07.001.

Cheusova T., Khan M.A., Schubert S.W., Gavin A.C., Buchou T., Jacob G., Sticht H., Allende J., Boldyreff B., Brenner H.R. and Hashemolhosseini S. (2006).  Casein kinase 2-dependent serine phosphorylation of MuSK regulates acetylcholine receptor aggregation at the neuromuscular junction. Genes Dev. 13, 1800-1816.

Gavin A.C.‡, Aloy P. ‡, Grandi P., Krause R., Boesche M., Marzioch M., Rau C., Jensen L.J., Bastuck S., Dümpelfeld 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. and Superti-Furga G. (2006).  Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636.

2005

Gavin A.C. (2005).  Keystone symposia: proteomics and bioinformatics and systems and biology. Expert Rev. Proteomics 2, 291-293.

2004

Aloy P., Böttcher B., Ceulemans H., Leutwein C., Mellwig C., Fischer S., Gavin A.C., Bork P., Superti-Furga G., Serrano L. and Russell R.B. (2004).  Structure-based assembly of protein complexes in yeast. Science 303, 2026-2029.

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. and Superti-Furga G. (2004).  A physical and functional map of the human TNFa/NF-kB signal transduction pathway. Nat. Cell Biol. 6, 97-105.

2003

Gavin A.C. and Superti-Furga G. (2003).  Protein complexes and proteome organization from yeast to man. Curr. Opin. Chem. Biol. 7, 21-27.

Grandi P., Rybin V., Bassler J., Petfalski E., Strauss D., Marzioch M., Schafer T., Kuster B., Tschochner H., Tollervey D., Gavin A.C. and Hurt E. (2002).  90S Pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors. Mol. Cell 10, 105-115.

2002

Aloy P., Ciccarelli F.D., Leutwein C., Gavin A.C., Superti-Furga G., Bork P., Böttcher B. and Russell R.B. (2002).  A complex prediction: three-dimensional model of the yeast exosome. EMBO rep. 3, 628-635.

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. and Superti-Furga G. (2002).  Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147.

1999-1988

Nebreda A.R. and Gavin A.C. (1999).  Cell survival demands some Rsk. Science 286, 1309-1310.

Gavin A.C., Ni Ainle A., Chierici E., Jones M. and Nebreda A.R. (1999).  A p90rsk mutant constitutively interacting with MAP kinase uncouples MAP kinase from MPF activation in Xenopus oocytes. Mol. Biol. Cell 10, 2971-2986.

Gavin A.C. and Nebreda A.R. (1999).  A MAP kinase docking site is required for phosphorylation and activation of p90rsk/MAPKAP kinase-1. Curr. Biol. 9, 281-284.

Dorey K., Barilà D., Gavin A.C., Nebreda A.R. and Superti-Furga G. (1999).  Regulation and G2/M transition promoting activity of the human Abl tyrosine kinase in Xenopus oocytes. Biol. Chem. 380, 223-230.

Palmer A., Gavin A.C. and Nebreda A.R. (1998).  A link between MAP kinase and p34cdc2/cyclin B during oocyte maturation: p90rsk phosphorylates and inactivates the p34cdc2 inhibitory kinase Myt1. EMBO J. 17, 5037-5047.

Gavin A.C. and Schorderet-Slatkine, S. (1997).  Ribosomal S6 kinase p90rsk and mRNA cap binding protein eIF4E phosphorylation correlate with MAP kinase activation during meiotic reinitiation of mouse oocytes. Mol. Reprod. Dev. 46, 383-391.

De Vantery C., Gavin A.C., Vassalli J.-D. and Schorderet-Slatkine S. (1996).  An accumulation of p34cdc2 at the end of mouse oocyte growth correlates with the acquisition of meiotic competence. Dev. Biol. 174, 335-344.

Gavin A.C., Cavadore J.-C. and Schorderet-Slatkine S. (1994).  Histone H1 kinase activity, germinal vesicle breakdown and M phase entry in mouse oocytes. J. Cell Sci. 107, 275-283.

Gavin A.C. Vassalli J.-D., Cavadore J.-C. and Schorderet-Slatkine S. (1992).  Okadaic acid and p13suc1 modulate the reinitiation of meiosis in the mouse oocyte. Mol. Reprod. Dev. 33, 287-296.

Gavin A.C., Tsukitani Y. and Schorderet-Slatkine S. (1991).  Induction of M-phase entry of prophase-blocked mouse oocytes through micro-injection of okadaic acid, a specific phosphatase inhibitor. Exp. Cell Res. 192, 75-81.

Gavin A.C. and Schorderet-Slatkine, S. (1988).  The interaction of lithium with forskolin-inhibited meiotic maturation of denuded mouse oocytes. Exp. Cell Res. 179, 298-302.

Book chapter:  “Protein-Protein Interactions”. (2007). In: Wilkins MR, Appel RD, Williams KL, Hochstrasser DF, eds. Second edition. Proteome research: Concepts, Technology and Application. Berlin Heidelberg: Springer Verlag; 2007:pp 169-192.