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1

An integrated mass spectrometric and computational framework for the analysis of protein interaction networks

Rinner, Oliver, Mueller, Lukas N., Hubálek, Martin, Müller, Markus, Gstaiger, Matthias, Aebersold, Ruedi

Journal:

Nature Biotechnology

Year:

2007

Language:

english

File:

PDF, 337 KB

english, 2007

2

Quantitative interaction proteomics using mass spectrometry

Wepf, Alexander, Glatter, Timo, Schmidt, Alexander, Aebersold, Ruedi, Gstaiger, Matthias

Journal:

Year:

2009

Language:

english

File:

PDF, 177 KB

english, 2009

3

Analysis of protein complexes using mass spectrometry

Gingras, Anne-Claude, Gstaiger, Matthias, Raught, Brian, Aebersold, Ruedi

Journal:

Nature Reviews Molecular Cell Biology

Year:

2007

Language:

english

File:

PDF, 592 KB

english, 2007

4

Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS

Varjosalo, Markku, Sacco, Roberto, Stukalov, Alexey, van Drogen, Audrey, Planyavsky, Melanie, Hauri, Simon, Aebersold, Ruedi, Bennett, Keiryn L, Colinge, Jacques, Gstaiger, Matthias, Superti-Furga, Gi

Journal:

Year:

2013

Language:

english

File:

PDF, 766 KB

english, 2013

5

10.1038/13886

Johnson, Randall S., Dealy, Marian J., Nguyen, Khanh V.T., Lo, Jessica, Gstaiger, Matthias, Krek, Wilhelm, Elson, David, Arbeit, Jeffrey, Kipreos, Edward T.

Journal:

Nature Genetics

Year:

1999

Language:

english

File:

PDF, 2.36 MB

english, 1999

6

A B-cell coactivator of octamer-binding transcription factors

Gstaiger, Matthias, Knoepfel, Lea, Georgiev, Oleg, Schaffner, Walter, Hovens, Christopher M.

Journal:

Year:

1995

File:

PDF, 464 KB

1995

7

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

Gstaiger, Matthias, Aebersold, Ruedi

Journal:

Nature Reviews Genetics

Year:

2009

Language:

english

File:

PDF, 456 KB

english, 2009

8

An integrated workflow for charting the human interaction proteome: insights into the PP2A system

Glatter, Timo, Wepf, Alexander, Aebersold, Ruedi, Gstaiger, Matthias

Journal:

Molecular Systems Biology

Year:

2009

Language:

english

File:

PDF, 4.52 MB

english, 2009

9

The dASPP-dRASSF8 Complex Regulates Cell-Cell Adhesion during Drosophila Retinal Morphogenesis

Paul F. Langton, Julien Colombani, Eunice H.Y. Chan, Alexander Wepf, Matthias Gstaiger, Nicolas Tapon

Journal:

Current Biology

Year:

2009

Language:

english

File:

PDF, 2.40 MB

english, 2009

10

Fine mapping of protein interaction surfaces with a PCR-based mutagenesis screen in yeast

Matthias Gstaiger, Oleg Georgiev, Walter Schaffner

Journal:

Trends in Genetics

Year:

1996

Language:

english

File:

PDF, 244 KB

english, 1996

11

SAINT-MS1: Protein–Protein Interaction Scoring Using Label-free Intensity Data in Affinity Purification-Mass Spectrometry Experiments

Choi, Hyungwon, Glatter, Timo, Gstaiger, Mathias, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Year:

2012

Language:

english

File:

PDF, 753 KB

english, 2012

12

Association of Human SCFSKP2Subunit p19SKP1with Interphase Centrosomes and Mitotic Spindle Poles

Matthias Gstaiger, Alain Marti, Wilhelm Krek

Journal:

Experimental Cell Research

Year:

1999

Language:

english

File:

PDF, 288 KB

english, 1999

13

Oct-1 POU and octamer DNA co-operate to recognise the Bob-1 transcription co-activator via induced folding

Ju-Fang Chang, Kathryn Phillips, Thomas Lundbäck, Matthias Gstaiger, John E. Ladbury, Ben Luisi

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 719 KB

english, 1999

14

Two versatile eukaryotic expression vectors permitting epitope tagging, radiolabelling and nuclear localisation of expressed proteins

Oleg Georgiev, Jean-Pierre Bourquin, Matthias Gstaiger, Lea Knoepfel, Walter Schaffner, Christopher Hovens

Journal:

Year:

1996

Language:

english

File:

PDF, 254 KB

english, 1996

15

S6K1-Mediated Disassembly of Mitochondrial URI/PP1γ Complexes Activates a Negative Feedback Program that Counters S6K1 Survival Signaling

Nabil Djouder, Stefan Christian Metzler, Alexander Schmidt, Christiane Wirbelauer, Matthias Gstaiger, Ruedi Aebersold, Daniel Hess, Wilhelm Krek

Journal:

Year:

2007

Language:

english

File:

PDF, 1.70 MB

english, 2007

16

Combined Functional Genomic and Proteomic Approaches Identify a PP2A Complex as a Negative Regulator of Hippo Signaling

Paulo S. Ribeiro, Filipe Josué, Alexander Wepf, Michael C. Wehr, Oliver Rinner, Gavin Kelly, Nicolas Tapon, Matthias Gstaiger

Journal:

Year:

2010

Language:

english

File:

PDF, 2.39 MB

english, 2010

17

Regulation of PTEN activity by p38 -PKD1 signaling in neutrophils confers inflammatory responses in the lung

Ittner, A., Block, H., Reichel, C. A., Varjosalo, M., Gehart, H., Sumara, G., Gstaiger, M., Krombach, F., Zarbock, A., Ricci, R.

Journal:

Journal of Experimental Medicine

Year:

2012

Language:

english

File:

PDF, 3.91 MB

english, 2012

18

A method to resolve the composition of heterogeneous affinity-purified protein complexes assembled around a common protein by chemical cross-linking, gel electrophoresis and mass spectrometry

Rudashevskaya, Elena L, Sacco, Roberto, Kratochwill, Klaus, Huber, Marie L, Gstaiger, Matthias, Superti-Furga, Giulio, Bennett, Keiryn L

Journal:

Bioentrepreneur

Year:

2012

Language:

english

File:

PDF, 333 KB

english, 2012

19

NSs Protein of Rift Valley Fever Virus Induces the Specific Degradation of the Double-Stranded RNA-Dependent Protein Kinase

Habjan, M., Pichlmair, A., Elliott, R. M., Overby, A. K., Glatter, T., Gstaiger, M., Superti-Furga, G., Unger, H., Weber, F.

Journal:

Journal of Virology

Year:

2009

Language:

english

File:

PDF, 1.84 MB

english, 2009

20

PIMS Modulates Immune Tolerance by Negatively Regulating Drosophila Innate Immune Signaling

Nouara Lhocine, Paulo S. Ribeiro, Nicolas Buchon, Alexander Wepf, Rebecca Wilson, Tencho Tenev, Bruno Lemaitre, Matthias Gstaiger, Pascal Meier, François Leulier

Journal:

Cell Host & Microbe

Year:

2008

Language:

english

File:

PDF, 1.24 MB

english, 2008

21

Genotype–phenotype relationships in light of a modular protein interaction landscape

Gstaiger, Matthias, Aebersold, Ruedi

Journal:

Molecular BioSystems

Year:

2013

Language:

english

File:

PDF, 1.34 MB

english, 2013

22

The Protein Interaction Landscape of the Human CMGC Kinase Group

Varjosalo, Markku, Keskitalo, Salla, Van Drogen, Audrey, Nurkkala, Helka, Vichalkovski, Anton, Aebersold, Ruedi, Gstaiger, Matthias

Journal:

Year:

2013

Language:

english

File:

PDF, 4.09 MB

english, 2013

23

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

Collins, Ben C, Gillet, Ludovic C, Rosenberger, George, Röst, Hannes L, Vichalkovski, Anton, Gstaiger, Matthias, Aebersold, Ruedi

Journal:

Year:

2013

Language:

english

File:

PDF, 1.39 MB

english, 2013

24

Multi-sensoral and automated derivation of inundated areas using TerraSAR-X and ENVISAT ASAR data

Gstaiger, Veronika, Huth, Juliane, Gebhardt, Steffen, Wehrmann, Thilo, Kuenzer, Claudia

Journal:

International Journal of Remote Sensing

Year:

2012

Language:

english

File:

PDF, 1.16 MB

english, 2012

25

Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1

Hauri, Simon, Wepf, Alexander, van Drogen, Audrey, Varjosalo, Markku, Tapon, Nic, Aebersold, Ruedi, Gstaiger, Matthias

Journal:

Molecular Systems Biology

Year:

2013

Language:

english

File:

PDF, 915 KB

english, 2013

26

Endolysosomal sorting of ubiquitylated caveolin-1 is regulated by VCP and UBXD1 and impaired by VCP disease mutations

Ritz, Danilo, Vuk, Maja, Kirchner, Philipp, Bug, Monika, Schütz, Sabina, Hayer, Arnold, Bremer, Sebastian, Lusk, Caleb, Baloh, Robert H., Lee, Houkeun, Glatter, Timo, Gstaiger, Matthias, Aebersold, Ru

Journal:

Nature Cell Biology

Year:

2011

Language:

english

File:

PDF, 2.06 MB

english, 2011

27

Strong transcriptional activators isolated from viral DNA by the ‘activator trap’, a novel selection system in mammalian cells

Gstaiger, Matthias, Schaffner, Walter

Journal:

Nucleic Acids Research

Year:

1994

Language:

english

File:

PDF, 2.50 MB

english, 1994

28

Control of Nutrient-Sensitive Transcription Programs by the Unconventional Prefoldin URI

Journal:

Year:

2003

Language:

english

File:

PDF, 479 KB

english, 2003

29

Skp2 is oncogenic and overexpressed in human cancers

Gstaiger, M., Jordan, R., Lim, M., Catzavelos, C., Mestan, J., Slingerland, J., Krek, W.

Journal:

Proceedings of the National Academy of Sciences

Year:

2001

Language:

english

File:

PDF, 937 KB

english, 2001

30

Bacterial effector binds host cell adenylyl cyclase to potentiate G s-dependent cAMP production

Pulliainen, A. T., Pieles, K., Brand, C. S., Hauert, B., Bohm, A., Quebatte, M., Wepf, A., Gstaiger, M., Aebersold, R., Dessauer, C. W., Dehio, C.

Journal:

Proceedings of the National Academy of Sciences

Year:

2012

Language:

english

File:

PDF, 592 KB

english, 2012

31

EphA2 cleavage by MT1-MMP triggers single cancer cell invasion via homotypic cell repulsion

Sugiyama, N., Gucciardo, E., Tatti, O., Varjosalo, M., Hyytiainen, M., Gstaiger, M., Lehti, K.

Journal:

The Journal of Cell Biology

Year:

2013

Language:

english

File:

PDF, 7.04 MB

english, 2013

32

The HRPT2 Tumor Suppressor Gene Product Parafibromin Associates with Human PAF1 and RNA Polymerase II

Yart, A., Gstaiger, M., Wirbelauer, C., Pecnik, M., Anastasiou, D., Hess, D., Krek, W.

Journal:

Molecular and Cellular Biology

Year:

2005

Language:

english

File:

PDF, 524 KB

english, 2005

33

Open Reading Frame UL26 of Human Cytomegalovirus Encodes a Novel Tegument Protein That Contains a Strong Transcriptional Activation Domain

Stamminger, T., Gstaiger, M., Weinzierl, K., Lorz, K., Winkler, M., Schaffner, W.

Journal:

Journal of Virology

Year:

2002

Language:

english

File:

PDF, 1.17 MB

english, 2002

34

Quantitative Proteomic Analysis of Protein Complexes: Concurrent Identification of Interactors and Their State of Phosphorylation

Pflieger, D., Junger, M. A., Muller, M., Rinner, O., Lee, H., Gehrig, P. M., Gstaiger, M., Aebersold, R.

Journal:

Molecular & Cellular Proteomics

Year:

2007

Language:

english

File:

PDF, 1.07 MB

english, 2007

35

The oxygen sensor PHD3 limits glycolysis under hypoxia via direct binding to pyruvate kinase

Chen, Nan, Rinner, Oliver, Czernik, Dominika, Nytko, Katarzyna J, Zheng, Dan, Stiehl, Daniel P, Zamboni, Nicola, Gstaiger, Matthias, Frei, Christian

Journal:

Year:

2011

Language:

english

File:

PDF, 539 KB

english, 2011

36

An Inducible Retroviral Expression System for Tandem Affinity Purification Mass-Spectrometry-Based Proteomics Identifies Mixed Lineage Kinase Domain-like Protein (MLKL) as an Heat Shock Protein 90 (HSP90) Client

Bigenzahn, Johannes W., Fauster, Astrid, Rebsamen, Manuele, Kandasamy, Richard K., Scorzoni, Stefania, Vladimer, Gregory I., Müller, André C., Gstaiger, Matthias, Zuber, Johannes, Bennett, Keiryn L.,

Journal:

Molecular & Cellular Proteomics

Year:

2016

Language:

english

File:

PDF, 2.01 MB

english, 2016

37

Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome

Glatter, T., Schittenhelm, R. B., Rinner, O., Roguska, K., Wepf, A., Junger, M. A., Kohler, K., Jevtov, I., Choi, H., Schmidt, A., Nesvizhskii, A. I., Stocker, H., Hafen, E., Aebersold, R., Gstaiger,

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.04 MB

english, 2014

38

An Inducible Retroviral Expression System for Tandem Affinity Purification Mass-Spectrometry-Based Proteomics Identifies Mixed Lineage Kinase Domain-like Protein (MLKL) as an Heat Shock Protein 90 (HSP90) Client

Bigenzahn, Johannes W., Fauster, Astrid, Rebsamen, Manuele, Kandasamy, Richard K., Scorzoni, Stefania, Vladimer, Gregory I., Müller, André C., Gstaiger, Matthias, Zuber, Johannes, Bennett, Keiryn L.,

Journal:

Molecular & Cellular Proteomics

Year:

2016

Language:

english

File:

PDF, 2.01 MB

english, 2016

39

Tandem affinity purification combined with inducible shRNA expression as a tool to study the maturation of macromolecular assemblies

Wyler, E., Zimmermann, M., Widmann, B., Gstaiger, M., Pfannstiel, J., Kutay, U., Zemp, I.

Journal:

Year:

2011

Language:

english

File:

PDF, 1.27 MB

english, 2011

40

A High-Density Map for Navigating the Human Polycomb Complexome

Hauri, Simon, Comoglio, Federico, Seimiya, Makiko, Gerstung, Moritz, Glatter, Timo, Hansen, Klaus, Aebersold, Ruedi, Paro, Renato, Gstaiger, Matthias, Beisel, Christian

Journal:

Year:

2016

Language:

english

File:

PDF, 2.91 MB

english, 2016

41

Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF-α Signaling

Ciuffa, Rodolfo, Caron, Etienne, Leitner, Alexander, Uliana, Federico, Gstaiger, Matthias, Aebersold, Ruedi

Journal:

Journal of Proteome Research

Year:

2017

Language:

english

File:

PDF, 3.99 MB

english, 2017

42

SPIE Proceedings [SPIE SPIE LASE - San Francisco, California, United States (Saturday 28 January 2017)] Free-Space Laser Communication and Atmospheric Propagation XXIX - DLR's free space experimental laser terminal for optical aircraft downlinks

Hemmati, Hamid, Boroson, Don M., Fuchs, Christian, Schmidt, Christopher, Rödiger, Benjamin, Shrestha, Amita, Brechtelsbauer, Martin, Ramirez Molina, Julio, Pacheco, Jorge, Gstaiger, Veronika

Year:

2017

Language:

english

File:

PDF, 1.44 MB

english, 2017

43

Systematic Analysis of Human Protein Phosphatase Interactions and Dynamics

Yadav, Leena, Tamene, Fitsum, Göös, Helka, van Drogen, Audrey, Katainen, Riku, Aebersold, Ruedi, Gstaiger, Matthias, Varjosalo, Markku

Journal:

Year:

2017

Language:

english

File:

PDF, 2.51 MB

english, 2017

44

The von Hippel-Lindau tumor suppressor protein is a component of an E3 ubiquitin-protein ligase activity

Lisztwan, J., Imbert, G., Wirbelauer, C., Gstaiger, M., Krek, W.

Journal:

Genes & Development

Year:

1999

Language:

english

File:

PDF, 1.52 MB

english, 1999

45

AP-SWATH reveals direct involvement of VCP/p97 in integrated stress response signaling through facilitating CReP/PPP1R15B degradation

Hülsmann, Julia, Kravic, Bojana, Weith, Matthias, Gstaiger, Matthias, Aebersold, Ruedi H., Collins, Ben C, Meyer, Hemmo

Journal:

Molecular & Cellular Proteomics

Year:

2018

Language:

english

File:

PDF, 6.00 MB

english, 2018

46

2D vs. 3D Change Detection Using Aerial Imagery to Support Crisis Management of Large-Scale Events

Gstaiger, Veronika, Tian, Jiaojiao, Kiefl, Ralph, Kurz, Franz

Journal:

Year:

2018

Language:

english

File:

PDF, 28.27 MB

english, 2018

47

Complex‐centric proteome profiling by SEC‐SWATH‐MS

Heusel, Moritz, Bludau, Isabell, Rosenberger, George, Hafen, Robin, Frank, Max, Banaei‐Esfahani, Amir, van Drogen, Audrey, Collins, Ben C, Gstaiger, Matthias, Aebersold, Ruedi

Journal:

Molecular Systems Biology

Year:

2019

Language:

english

File:

PDF, 3.18 MB

english, 2019

48

BRAF inhibition sensitizes melanoma cells to α-amanitin via decreased RNA polymerase II assembly

Frischknecht, Lukas, Britschgi, Christian, Galliker, Patricia, Christinat, Yann, Vichalkovski, Anton, Gstaiger, Matthias, Kovacs, Werner J., Krek, Wilhelm

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 2.52 MB

english, 2019

49

Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data

Schäfer, Alexander, Gjerga, Enio, Welford, Richard WD, Renz, Imke, Lehembre, Francois, Groenen, Peter MA, Saez‐Rodriguez, Julio, Aebersold, Ruedi, Gstaiger, Matthias

Journal:

Molecular Systems Biology

Year:

2019

File:

PDF, 4.45 MB

2019

50

Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes

Mehnert, Martin, Ciuffa, Rodolfo, Frommelt, Fabian, Uliana, Federico, van Drogen, Audrey, Ruminski, Kilian, Gstaiger, Matthias, Aebersold, Ruedi

Journal:

Nature Communications

Year:

2020

File:

PDF, 1.95 MB

2020

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