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Three-dimensional dynamic views of proteomes as a novel readout for physiological and pathological alterations


Systematic detection of functional proteoform groups from bottom-up proteomic datasets

Author(s): Bludau, Isabell Frank, Max Dörig, Christian Cai, Yujia Heusel, Moritz Rosenberger, George Picotti, Paola Collins, Ben C. Röst, Hannes Aebersold, Ruedi
Published in: Nature Communications, Issue 20411723, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-24030-x

Comparative analysis of the intracellular responses to disease-related aggregation-prone proteins

Author(s): Melnik, Andre Cappelletti, Valentina Vaggi, Federico Piazza, Ilaria Tognetti, Marco Schwarz, Carmen Cereghetti, Gea Ahmed, Mennat A. Soste, Martin Matlack, Kent de Souza, Natalie Csikasz-Nagy, Attila Picotti, Paola
Published in: Journal of Proteomics, Issue 18743919, 2020, ISSN 1874-3919
Publisher: Elsevier BV
DOI: 10.1016/j.jprot.2020.103862

USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit

Author(s): Montellese, Christian van den Heuvel, Jasmin Ashiono, Caroline Dörner, Kerstin Melnik, André Jonas, Stefanie Zemp, Ivo Picotti, Paola Gillet, Ludovic C. Kutay, Ulrike
Published in: eLife, Issue 2050084X, 2020, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.54435

Combining data integration and molecular dynamics for target identification in α-Synuclein-aggregating neurodegenerative diseases: Structural insights on Synaptojanin-1 (Synj1).

Author(s): Kirsten Jenkins; Teodora Mateeva; István Szabó; Andre Melnik; Paola Picotti; Attila Csikász-Nagy; Attila Csikász-Nagy; Edina Rosta
Published in: Computational and Structural Biotechnology Journal, Vol 18, Iss , Pp 1032-1042 (2020), Issue 20010370, 2020, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.3929/ethz-b-000465810

Comparative analysis of cancer cell responses to targeted radionuclide therapy (TRT) and external beam radiotherapy (EBRT)

Author(s): Grzmil, Michal Boersema, Paul Sharma, Ashish Blanc, Alain Imobersteg, Stefan Pruschy, Martin Picotti, Paola Schibli, Roger Behe, Martin
Published in: Journal of Hematology & Oncology, Issue 17568722, 2022, ISSN 1756-8722
Publisher: BioMed Central
DOI: 10.1186/s13045-022-01343-y

Combining CRISPRi and metabolomics for functional annotation of compound libraries

Author(s): Miquel Anglada-Girotto; Gabriel Handschin; Karin Ortmayr; Adrian I. Campos; Ludovic Gillet; Pablo Manfredi; Claire V. Mulholland; Michael Berney; Urs Jenal; Paola Picotti; Mattia Zampieri
Published in: Nature Chemical Biology, 18 (5), Issue 15524469, 2022, ISSN 1552-4469
Publisher: Springer Nature
DOI: 10.1038/s41589-022-00970-3

Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ

Author(s): Valentina Cappelletti, Thomas Hauser, Ilaria Piazza, Monika Pepelnjak, Liliana Malinovska, Tobias Fuhrer, Yaozong Li, Christian Dörig, Paul Boersema, Ludovic Gillet, Jan Grossbach, Aurelien Dugourd, Julio Saez-Rodriguez, Andreas Beyer, Nicola Zamboni, Amedeo Caflisch, Natalie de Souza, Paola Picotti
Published in: Cell, Issue 184/2, 2021, Page(s) 545-559.e22, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2020.12.021

Systematic detection of functional proteoform groups from bottom-up proteomic datasets

Author(s): Isabell Bludau; Isabell Bludau; Max Frank; Christian Dörig; Yujia Cai; Moritz Heusel; Moritz Heusel; George Rosenberger; George Rosenberger; Paola Picotti; Ben C. Collins; Ben C. Collins; Hannes L. Röst; Ruedi Aebersold; Ruedi Aebersold
Published in: Nature Communications, 12 (1), Issue 5, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.3929/ethz-b-000491987

Detecting Protein-Small Molecule Interactions Using Limited Proteolysis-Mass Spectrometry (LiP-MS).

Author(s): Monika Pepelnjak; Natalie de Souza; Natalie de Souza; Paola Picotti
Published in: Trends in Biochemical Sciences, Issue 3, 2020, ISSN 0968-0004
Publisher: Elsevier BV
DOI: 10.3929/ethz-b-000441347

A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes

Author(s): Ilaria Piazza, Nigel Beaton, Roland Bruderer, Thomas Knobloch, Crystel Barbisan, Lucie Chandat, Alexander Sudau, Isabella Siepe, Oliver Rinner, Natalie de Souza, Paola Picotti, Lukas Reiter
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-18071-x

Global, in situ analysis of the structural proteome in individuals with Parkinson’s disease to identify a new class of biomarker

Author(s): Mackmull, Marie-Therese Nagel, Luise Sesterhenn, Fabian Muntel, Jan Grossbach, Jan Stalder, Patrick Bruderer, Roland Reiter, Lukas van de Berg, Wilma D.J. de Souza, Natalie Beyer, Andreas Picotti, Paola
Published in: Nature Structural & Molecular Biology, Issue 14764687, 2022, ISSN 1476-4687
Publisher: Springer Nature
DOI: 10.1038/s41594-022-00837-0

Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance

Author(s): Kamrad, Stephan Grossbach, Jan Rodríguez-López, Maria Mülleder, Michael Townsend, StJohn Cappelletti, Valentina Stojanovski, Gorjan Correia-Melo, Clara Picotti, Paola Beyer, Andreas Ralser, Markus Bähler, Jürg
Published in: Molecular Systems Biology, Issue 17444292, 2020, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20199270

Deciphering the signaling network of breast cancer improves drug sensitivity prediction.

Author(s): Marco Tognetti; Attila Gábor; Attila Gábor; Mi Yang; Mi Yang; Valentina Cappelletti; Jonas Windhager; Oscar M. Rueda; Konstantina Charmpi; Elham Esmaeilishirazifard; Elham Esmaeilishirazifard; Alejandra Bruna; Natalie de Souza; Natalie de Souza; Carlos Caldas; Carlos Caldas; Andreas Beyer; Paola Picotti; Julio Saez-Rodriguez; Julio Saez-Rodriguez; Bernd Bodenmiller
Published in: Cell Systems, 12 (5), Issue 24054720, 2021, ISSN 2405-4720
Publisher: CellPress
DOI: 10.3929/ethz-b-000485506

Structure of Mycobacterium tuberculosis Cya, an evolutionary ancestor of the mammalian membrane adenylyl cyclases

Author(s): Mehta, Ved Khanppnavar, Basavraj Schuster, Dina Kantarci, Ilayda Vercellino, Irene Kosturanova, Angela Iype, Tarun Stefanic, Sasa Picotti, Paola Korkhov, Volodymyr M.
Published in: eLife, Issue 2050084X, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.77032

Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule disassembly

Author(s): Gea Cereghetti, Caroline Wilson-Zbinden, Vera M. Kissling, Maren Diether, Alexandra Arm, Haneul Yoo, Ilaria Piazza, Shady Saad, Paola Picotti, D. Allan Drummond, Uwe Sauer, Reinhard Dechant, Matthias Peter
Published in: Nature Cell Biology, Issue 23/10, 2021, Page(s) 1085-1094, ISSN 1465-7392
Publisher: Nature Publishing Group
DOI: 10.1038/s41556-021-00760-4

Limited Proteolysis-Mass Spectrometry to Identify Metabolite-Protein Interactions

Author(s): Aleš Holfeld, Jan-Philipp Quast, Roland Bruderer, Lukas Reiter, Natalie de Souza & Paola Picotti
Published in: Cell-Wide Identification of Metabolite-Protein Interactions, 2022, ISBN 978-1-0716-2624-5
Publisher: Springer Nature

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