Proteomics 4D: The proteome in context

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Publikacje

Reproducible Tissue Homogenization and Protein Extraction for Quantitative Proteomics Using MicroPestle-Assisted Pressure-Cycling Technology

Autorzy: Shiying Shao, Tiannan Guo, Vera Gross, Alexander Lazarev, Ching Chiek Koh, Silke Gillessen, Markus Joerger, Wolfram Jochum, Ruedi Aebersold
Opublikowane w: Journal of Proteome Research, Numer 15/6, 2016, Strona(/y) 1821-1829, ISSN 1535-3893
Wydawca: American Chemical Society
DOI: 10.1021/acs.jproteome.5b01136

Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex

Autorzy: Marcello Clerici, Marco Faini, Lena M. Muckenfuss, Ruedi Aebersold, Martin Jinek
Opublikowane w: Nature Structural & Molecular Biology, Numer 25/2, 2018, Strona(/y) 135-138, ISSN 1545-9993
Wydawca: Nature Publishing Group
DOI: 10.1038/s41594-017-0020-6

SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools

Autorzy: Peter Blattmann, Moritz Heusel, Ruedi Aebersold
Opublikowane w: PLOS ONE, Numer 11/4, 2016, Strona(/y) e0153160, ISSN 1932-6203
Wydawca: Public Library of Science
DOI: 10.1371/journal.pone.0153160

Orthogonal Proteomic Platforms and Their Implications for the Stable Classification of High-Grade Serous Ovarian Cancer Subtypes

Autorzy: Stefani N. Thomas, Betty Friedrich, Michael Schnaubelt, Daniel W. Chan, Hui Zhang, Ruedi Aebersold
Opublikowane w: iScience, Numer 23/6, 2020, Strona(/y) 101079, ISSN 2589-0042
Wydawca: ScienceDirect
DOI: 10.1016/j.isci.2020.101079

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry

Autorzy: Thomas Walzthoeni, Lukasz A Joachimiak, George Rosenberger, Hannes L Röst, Lars Malmström, Alexander Leitner, Judith Frydman, Ruedi Aebersold
Opublikowane w: Nature Methods, Numer 12/12, 2015, Strona(/y) 1185-1190, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/nmeth.3631

The SysteMHC Atlas project

Autorzy: Wenguang Shao, Patrick G A Pedrioli, Witold Wolski, Cristian Scurtescu, Emanuel Schmid, Juan A Vizcaíno, Mathieu Courcelles, Heiko Schuster, Daniel Kowalewski, Fabio Marino, Cecilia S L Arlehamn, Kerrie Vaughan, Bjoern Peters, Alessandro Sette, Tom H M Ottenhoff, Krista E Meijgaarden, Natalie Nieuwenhuizen, Stefan H E Kaufmann, Ralph Schlapbach, John C Castle, Alexey I Nesvizhskii, Morten Niel
Opublikowane w: Nucleic Acids Research, Numer 46/D1, 2017, Strona(/y) D1237-D1247, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkx664

Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes

Autorzy: Isabell Bludau, Moritz Heusel, Max Frank, George Rosenberger, Robin Hafen, Amir Banaei-Esfahani, Audrey van Drogen, Ben C. Collins, Matthias Gstaiger, Ruedi Aebersold
Opublikowane w: Nature Protocols, Numer 15/8, 2020, Strona(/y) 2341-2386, ISSN 1754-2189
Wydawca: Nature Publishing Group
DOI: 10.1038/s41596-020-0332-6

Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases

Autorzy: Marija Buljan, Rodolfo Ciuffa, Audrey van Drogen, Anton Vichalkovski, Martin Mehnert, George Rosenberger, Sohyon Lee, Markku Varjosalo, Lucia Espona Pernas, Vincent Spegg, Berend Snijder, Ruedi Aebersold, Matthias Gstaiger
Opublikowane w: Molecular Cell, Numer 79/3, 2020, Strona(/y) 504-520.e9, ISSN 1097-2765
Wydawca: Cell Press
DOI: 10.1016/j.molcel.2020.07.001

Systematic characterization of pan‐cancer mutation clusters

Autorzy: Buljan, Marija; Blattmann, Peter; Aebersold, Ruedi; Boutros, Michael
Opublikowane w: Molecular Systems Biology, Numer 1, 2018, ISSN 1744-4292
Wydawca: Nature Publishing Group
DOI: 10.3929/ethz-b-000256182

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS

Autorzy: George Rosenberger, Yansheng Liu, Hannes L Röst, Christina Ludwig, Alfonso Buil, Ariel Bensimon, Martin Soste, Tim D Spector, Emmanouil T Dermitzakis, Ben C Collins, Lars Malmström, Ruedi Aebersold
Opublikowane w: Nature Biotechnology, Numer 35/8, 2017, Strona(/y) 781-788, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/nbt.3908

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines

Autorzy: Blattmann, Peter; Henriques, David; Zimmermann, Michael; Frommelt, Fabian; Sauer, Uwe; Saez-Rodriguez, Julio; Aebersold, Ruedi
Opublikowane w: Cell Systems, Numer 11, 2017, ISSN 2405-4712
Wydawca: Cell Systems
DOI: 10.3929/ethz-b-000228208

A Proteomic Connectivity Map

Autorzy: Christian Feller, Ruedi Aebersold
Opublikowane w: Cell Systems, Numer 6/4, 2018, Strona(/y) 403-405, ISSN 2405-4712
Wydawca: Cell Systems
DOI: 10.1016/j.cels.2018.04.007

Structures of human PRC2 with its cofactors AEBP2 and JARID2

Autorzy: Vignesh Kasinath, Marco Faini, Simon Poepsel, Dvir Reif, Xinyu Ashlee Feng, Goran Stjepanovic, Ruedi Aebersold, Eva Nogales
Opublikowane w: Science, Numer 359/6378, 2018, Strona(/y) 940-944, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.aar5700

Molecular basis for disassembly of an importin:ribosomal protein complex by the escortin Tsr2

Autorzy: Sabina Schütz, Erich Michel, Fred F. Damberger, Michaela Oplová, Cohue Peña, Alexander Leitner, Ruedi Aebersold, Frederic H.-T. Allain, Vikram Govind Panse
Opublikowane w: Nature Communications, Numer 9/1, 2018, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-018-06160-x

AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation

Autorzy: Julia Hülsmann, Bojana Kravic, Matthias Weith, Matthias Gstaiger, Ruedi Aebersold, Ben C. Collins, Hemmo Meyer
Opublikowane w: Molecular & Cellular Proteomics, Numer 17/7, 2018, Strona(/y) 1295-1307, ISSN 1535-9476
Wydawca: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.RA117.000471

Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals

Autorzy: Simon Schwörer, Friedrich Becker, Christian Feller, Ali H. Baig, Ute Köber, Henriette Henze, Johann M. Kraus, Beibei Xin, André Lechel, Daniel B. Lipka, Christy S. Varghese, Manuel Schmidt, Remo Rohs, Ruedi Aebersold, Kay L. Medina, Hans A. Kestler, Francesco Neri, Julia von Maltzahn, Stefan Tümpel, K. Lenhard Rudolph
Opublikowane w: Nature, Numer 540/7633, 2016, Strona(/y) 428-432, ISSN 0028-0836
Wydawca: Nature Publishing Group
DOI: 10.1038/nature20603

Structure of a human cap-dependent 48S translation pre-initiation complex

Autorzy: Boris Eliseev, Lahari Yeramala, Alexander Leitner, Manikandan Karuppasamy, Etienne Raimondeau, Karine Huard, Elena Alkalaeva, Ruedi Aebersold, Christiane Schaffitzel
Opublikowane w: Nucleic Acids Research, Numer 46/5, 2018, Strona(/y) 2678-2689, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gky054

Author Correction: Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex

Autorzy: Marcello Clerici, Marco Faini, Lena M. Muckenfuss, Ruedi Aebersold, Martin Jinek
Opublikowane w: Nature Structural & Molecular Biology, Numer 25/4, 2018, Strona(/y) 355-355, ISSN 1545-9993
Wydawca: Nature Publishing Group
DOI: 10.1038/s41594-018-0044-6

System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects

Autorzy: Camille Terfve, Eduard Sabidó, Yibo Wu, Emanuel Gonçalves, Meena Choi, Stefania Vaga, Olga Vitek, Julio Saez-Rodriguez, Ruedi Aebersold
Opublikowane w: Journal of Proteome Research, Numer 16/2, 2017, Strona(/y) 831-841, ISSN 1535-3893
Wydawca: American Chemical Society
DOI: 10.1021/acs.jproteome.6b00815

Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

Autorzy: Christina Ludwig, Ludovic Gillet, George Rosenberger, Sabine Amon, Ben C Collins, Ruedi Aebersold
Opublikowane w: Molecular Systems Biology, Numer 14/8, 2018, Strona(/y) e8126, ISSN 1744-4292
Wydawca: Nature Publishing Group
DOI: 10.15252/msb.20178126

Integrative Structural Investigation on the Architecture of Human Importin4_Histone H3/H4_Asf1a Complex and Its Histone H3 Tail Binding

Autorzy: Jungmin Yoon, Seung Joong Kim, Sojin An, Saehyun Cho, Alexander Leitner, Taeyang Jung, Ruedi Aebersold, Hans Hebert, Uhn-Soo Cho, Ji-Joon Song
Opublikowane w: Journal of Molecular Biology, Numer 430/6, 2018, Strona(/y) 822-841, ISSN 0022-2836
Wydawca: Academic Press
DOI: 10.1016/j.jmb.2018.01.015

Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population

Autorzy: Evan G. Williams, Yibo Wu, Witold Wolski, Jun Yong Kim, Jiayi Lan, Moaraj Hasan, Christian Halter, Pooja Jha, Dongryeol Ryu, Johan Auwerx, Ruedi Aebersold
Opublikowane w: Molecular & Cellular Proteomics, Numer 17/9, 2018, Strona(/y) 1766-1777, ISSN 1535-9476
Wydawca: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.RA118.000554

Tandem mass spectral libraries of peptides and their roles in proteomics research

Autorzy: Wenguang Shao, Henry Lam
Opublikowane w: Mass Spectrometry Reviews, Numer 36/5, 2017, Strona(/y) 634-648, ISSN 0277-7037
Wydawca: John Wiley & Sons Inc.
DOI: 10.1002/mas.21512

Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells

Autorzy: Yansheng Liu, Christelle Borel, Li Li, Torsten Müller, Evan G. Williams, Pierre-Luc Germain, Marija Buljan, Tatjana Sajic, Paul J. Boersema, Wenguang Shao, Marco Faini, Giuseppe Testa, Andreas Beyer, Stylianos E. Antonarakis, Ruedi Aebersold
Opublikowane w: Nature Communications, Numer 8/1, 2017, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-017-01422-6

Molecular basis of AKAP79 regulation by calmodulin

Autorzy: Neha Patel, Florian Stengel, Ruedi Aebersold, Matthew G. Gold
Opublikowane w: Nature Communications, Numer 8/1, 2017, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-017-01715-w

Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex

Autorzy: Marcello Clerici, Marco Faini, Ruedi Aebersold, Martin Jinek
Opublikowane w: eLife, Numer 6, 2017, ISSN 2050-084X
Wydawca: eLife Sciences Publications
DOI: 10.7554/eLife.33111

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

Autorzy: George Rosenberger, Isabell Bludau, Uwe Schmitt, Moritz Heusel, Christie L Hunter, Yansheng Liu, Michael J MacCoss, Brendan X MacLean, Alexey I Nesvizhskii, Patrick G A Pedrioli, Lukas Reiter, Hannes L Röst, Stephen Tate, Ying S Ting, Ben C Collins, Ruedi Aebersold
Opublikowane w: Nature Methods, Numer 14/9, 2017, Strona(/y) 921-927, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/NMETH.4398

Impact of Alternative Splicing on the Human Proteome

Autorzy: Yansheng Liu, Mar Gonzàlez-Porta, Sergio Santos, Alvis Brazma, John C. Marioni, Ruedi Aebersold, Ashok R. Venkitaraman, Vihandha O. Wickramasinghe
Opublikowane w: Cell Reports, Numer 20/5, 2017, Strona(/y) 1229-1241, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2017.07.025

Quantitative proteomics: challenges and opportunities in basic and applied research

Autorzy: Olga T Schubert, Hannes L Röst, Ben C Collins, George Rosenberger, Ruedi Aebersold
Opublikowane w: Nature Protocols, Numer 12/7, 2017, Strona(/y) 1289-1294, ISSN 1754-2189
Wydawca: Nature Publishing Group
DOI: 10.1038/nprot.2017.040

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

Autorzy: Ben C. Collins, Christie L. Hunter, Yansheng Liu, Birgit Schilling, George Rosenberger, Samuel L. Bader, Daniel W. Chan, Bradford W. Gibson, Anne-Claude Gingras, Jason M. Held, Mio Hirayama-Kurogi, Guixue Hou, Christoph Krisp, Brett Larsen, Liang Lin, Siqi Liu, Mark P. Molloy, Robert L. Moritz, Sumio Ohtsuki, Ralph Schlapbach, Nathalie Selevsek, Stefani N. Thomas, Shin-Cheng Tzeng, Hui Zhang, Rued
Opublikowane w: Nature Communications, Numer 8/1, 2017, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-017-00249-5

Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry

Autorzy: Etienne Caron, Romain Roncagalli, Takeshi Hase, Witold E. Wolski, Meena Choi, Marisa G. Menoita, Stephane Durand, Antonio García-Blesa, Ivo Fierro-Monti, Tatjana Sajic, Moritz Heusel, Tobias Weiss, Marie Malissen, Ralph Schlapbach, Ben C. Collins, Samik Ghosh, Hiroaki Kitano, Ruedi Aebersold, Bernard Malissen, Matthias Gstaiger
Opublikowane w: Cell Reports, Numer 18/13, 2017, Strona(/y) 3219-3226, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2017.03.019

Structural modeling of protein–RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS

Autorzy: Georg Dorn, Alexander Leitner, Julien Boudet, Sébastien Campagne, Christine von Schroetter, Ahmed Moursy, Ruedi Aebersold, Frédéric H-T Allain
Opublikowane w: Nature Methods, Numer 14/5, 2017, Strona(/y) 487-490, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/NMETH.4235

Building ProteomeTools based on a complete synthetic human proteome

Autorzy: Daniel P Zolg, Mathias Wilhelm, Karsten Schnatbaum, Johannes Zerweck, Tobias Knaute, Bernard Delanghe, Derek J Bailey, Siegfried Gessulat, Hans-Christian Ehrlich, Maximilian Weininger, Peng Yu, Judith Schlegl, Karl Kramer, Tobias Schmidt, Ulrike Kusebauch, Eric W Deutsch, Ruedi Aebersold, Robert L Moritz, Holger Wenschuh, Thomas Moehring, Stephan Aiche, Andreas Huhmer, Ulf Reimer, Bernhard Kuster
Opublikowane w: Nature Methods, Numer 14/3, 2017, Strona(/y) 259-262, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/NMETH.4153

On the Dependency of Cellular Protein Levels on mRNA Abundance

Autorzy: Yansheng Liu, Andreas Beyer, Ruedi Aebersold
Opublikowane w: Cell, Numer 165/3, 2016, Strona(/y) 535-550, ISSN 0092-8674
Wydawca: Cell Press
DOI: 10.1016/j.cell.2016.03.014

A multicenter study benchmarks software tools for label-free proteome quantification

Autorzy: Pedro Navarro, Jörg Kuharev, Ludovic C Gillet, Oliver M Bernhardt, Brendan MacLean, Hannes L Röst, Stephen A Tate, Chih-Chiang Tsou, Lukas Reiter, Ute Distler, George Rosenberger, Yasset Perez-Riverol, Alexey I Nesvizhskii, Ruedi Aebersold, Stefan Tenzer
Opublikowane w: Nature Biotechnology, Numer 34/11, 2016, Strona(/y) 1130-1136, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/nbt.3685

Systems proteomics of liver mitochondria function

Autorzy: E. G. Williams, Y. Wu, P. Jha, S. Dubuis, P. Blattmann, C. A. Argmann, S. M. Houten, T. Amariuta, W. Wolski, N. Zamboni, R. Aebersold, J. Auwerx
Opublikowane w: Science, Numer 352/6291, 2016, Strona(/y) aad0189-aad0189, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.aad0189

Proteome-wide association studies identify biochemical modules associated with a wing-size phenotype in Drosophila melanogaster

Autorzy: Hirokazu Okada, H. Alexander Ebhardt, Sibylle Chantal Vonesch, Ruedi Aebersold, Ernst Hafen
Opublikowane w: Nature Communications, Numer 7, 2016, Strona(/y) 12649, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/ncomms12649

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

Autorzy: Ulrike Kusebauch, David S. Campbell, Eric W. Deutsch, Caroline S. Chu, Douglas A. Spicer, Mi-Youn Brusniak, Joseph Slagel, Zhi Sun, Jeffrey Stevens, Barbara Grimes, David Shteynberg, Michael R. Hoopmann, Peter Blattmann, Alexander V. Ratushny, Oliver Rinner, Paola Picotti, Christine Carapito, Chung-Ying Huang, Meghan Kapousouz, Henry Lam, Tommy Tran, Emek Demir, John D. Aitchison, Chris Sander, Le
Opublikowane w: Cell, Numer 166/3, 2016, Strona(/y) 766-778, ISSN 0092-8674
Wydawca: Cell Press
DOI: 10.1016/j.cell.2016.06.041

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

Autorzy: Hannes L Röst, Yansheng Liu, Giuseppe D'Agostino, Matteo Zanella, Pedro Navarro, George Rosenberger, Ben C Collins, Ludovic Gillet, Giuseppe Testa, Lars Malmström, Ruedi Aebersold
Opublikowane w: Nature Methods, Numer 13/9, 2016, Strona(/y) 777-783, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/nmeth.3954

Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome

Autorzy: Xiaorong Wang, Peter Cimermancic, Clinton Yu, Andreas Schweitzer, Nikita Chopra, James L. Engel, Charles H Greenberg, Alexander S Huszagh, Florian Beck, Eri Sakata, Yingying Yang, Eric J Novitsky, Alexander Leitner, Paolo Nanni, Abdullah Kahraman, Xing Guo, Jack E Dixon, Scott D Rychnovsky, Ruedi Aebersold, Wolfgang Baumeister, Andrej Sali, Lan Huang
Opublikowane w: Molecular & Cellular Proteomics, 2017, Strona(/y) mcp.M116.065326, ISSN 1535-9476
Wydawca: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.M116.065326

Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry

Autorzy: Pavel Bouchal, Olga T. Schubert, Jakub Faktor, Lenka Capkova, Hana Imrichova, Karolina Zoufalova, Vendula Paralova, Roman Hrstka, Yansheng Liu, Holger Alexander Ebhardt, Eva Budinska, Rudolf Nenutil, Ruedi Aebersold
Opublikowane w: Cell Reports, Numer 28/3, 2019, Strona(/y) 832-843.e7, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2019.06.046

Complex‐centric proteome profiling by SEC ‐ SWATH ‐ MS

Autorzy: Moritz Heusel, Isabell Bludau, George Rosenberger, Robin Hafen, Max Frank, Amir Banaei‐Esfahani, Audrey Drogen, Ben C Collins, Matthias Gstaiger, Ruedi Aebersold
Opublikowane w: Molecular Systems Biology, Numer 15/1, 2019, ISSN 1744-4292
Wydawca: Nature Publishing Group
DOI: 10.15252/msb.20188438

Mass Spectrometric Exploration of the Biochemical Basis of Living Systems

Autorzy: Ruedi Aebersold, Peter Blattmann
Opublikowane w: CHIMIA International Journal for Chemistry, Numer 73/7, 2019, Strona(/y) 540-548, ISSN 0009-4293
Wydawca: Schweizerische Chemische Gedellschaft
DOI: 10.2533/chimia.2019.540

Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry

Autorzy: Sabine Amon, Fabienne Meier-Abt, Ludovic C. Gillet, Slavica Dimitrieva, Alexandre P. A. Theocharides, Markus G. Manz, Ruedi Aebersold
Opublikowane w: Molecular & Cellular Proteomics, Numer 18/7, 2019, Strona(/y) 1454-1467, ISSN 1535-9476
Wydawca: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.TIR119.001431

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

Autorzy: Alexander Schäfer, Enio Gjerga, Richard WD Welford, Imke Renz, Francois Lehembre, Peter MA Groenen, Julio Saez‐Rodriguez, Ruedi Aebersold, Matthias Gstaiger
Opublikowane w: Molecular Systems Biology, Numer 15/8, 2019, ISSN 1744-4292
Wydawca: Nature Publishing Group
DOI: 10.15252/msb.20198828

Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins

Autorzy: Shao, Wenguang; Guo, Tiannan; Toussaint, Nora C.; Xue, Peng; Wagner, Ulrich; Li, Li; Charmpi, Konstantina; Zhu, Yi; Wu, Jianmin; Buljan, Marija; Sun, Rui; Rutishauser, Dorothea; Hermanns, Thomas; Fankhauser, Christian Daniel; Poyet, Cedric; Ljubicic, Jelena; Rupp, Niels; Rüschoff, Jan H.; Zhong, Qing; Beyer, Andreas; Ji, Jiafu; Collins, Ben C.; Liu, Yansheng; Rätsch, Gunnar; Wild, Peter J.; Aebe
Opublikowane w: Shao, Wenguang <javascript:contributorCitation( 'Shao, Wenguang' );>; Guo, Tiannan <javascript:contributorCitation( 'Guo, Tiannan' );>; Toussaint, Nora C <javascript:contributorCitation( 'Toussaint, Nora C' );>; Xue, Peng <javascript:contributorCitation( 'Xue, Peng' );>; Wagner, Ulrich <javascript:contributorCitation( 'Wagner, Ulrich' );>; Li, Li <javascript:contri, Numer 8, 2019, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.5167/uzh-171764

Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals

Autorzy: Natalie Romanov, Michael Kuhn, Ruedi Aebersold, Alessandro Ori, Martin Beck, Peer Bork
Opublikowane w: Cell, Numer 177/5, 2019, Strona(/y) 1308-1318.e10, ISSN 0092-8674
Wydawca: Cell Press
DOI: 10.1016/j.cell.2019.03.015

The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification

Autorzy: Helleboid, Pierre-Yves; Heusel, Moritz; Duc, Julien; Piot, Cecile; Thorball, Christian W.; Coluccio, Andrea; Pontis, Julien; Turelli, Priscilla; Aebersold, Ruedi; Trono, Didier
Opublikowane w: The EMBO Journal, 38 (18), Numer 2, 2019, ISSN 0261-4189
Wydawca: Nature Publishing Group
DOI: 10.3929/ethz-b-000360670

Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines

Autorzy: Guo, T.; Luna, A.; Rajapakse, V.N.; Koh, C.C.; Wu, Z.; Liu, W.; Sun, Y.; Gao, H.; Menden, M.P.; Xu, C.; Calzone, L.; Martignetti, L.; Auwerx, C.; Buljan, M.; Banaei-Esfahani, A.; Ori, A.; Iskar, M.; Gillet, L.; Bi, R.; Zhang, J.; Zhang, H.; Yu, C.; Zhong, Q.; Varma, S.; Schmitt, U.; Qiu, P.; Zhang, Q.; Zhu, Y.; Wild, P.J.; Garnett, M.J.; Bork, P.; Beck, M.; Liu, K.; Saez-Rodriguez, J.; Elloumi, F.
Opublikowane w: iScience, 21, Numer 5, 2019, ISSN 1538-8514
Wydawca: iScience
DOI: 10.3929/ethz-b-000378057

Identification of Protein Abundance Changes in Hepatocellular Carcinoma Tissues Using PCT–SWATH

Autorzy: Yi Zhu, Jiang Zhu, Cong Lu, Qiushi Zhang, Wei Xie, Ping Sun, Xiaochuan Dong, Liang Yue, Yaoting Sun, Xiao Yi, Tiansheng Zhu, Guan Ruan, Ruedi Aebersold, Shi'ang Huang, Tiannan Guo
Opublikowane w: PROTEOMICS – Clinical Applications, Numer 13/1, 2018, Strona(/y) 1700179, ISSN 1862-8346
Wydawca: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/prca.201700179

Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex

Autorzy: Saikat Chowdhury, Chinatsu Otomo, Alexander Leitner, Kazuto Ohashi, Ruedi Aebersold, Gabriel C. Lander, Takanori Otomo
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 115/42, 2018, Strona(/y) E9792-E9801, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1811874115

Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins

Autorzy: Peter Blattmann, Vivienne Stutz, Giulia Lizzo, Joy Richard, Philipp Gut, Ruedi Aebersold
Opublikowane w: Scientific Data, Numer 6/1, 2019, ISSN 2052-4463
Wydawca: Sci Data
DOI: 10.1038/sdata.2019.11

Multi-omic measurements of heterogeneity in HeLa cells across laboratories

Autorzy: Yansheng Liu, Yang Mi, Torsten Mueller, Saskia Kreibich, Evan G. Williams, Audrey Van Drogen, Christelle Borel, Max Frank, Pierre-Luc Germain, Isabell Bludau, Martin Mehnert, Michael Seifert, Mario Emmenlauer, Isabel Sorg, Fedor Bezrukov, Frederique Sloan Bena, Hu Zhou, Christoph Dehio, Giuseppe Testa, Julio Saez-Rodriguez, Stylianos E. Antonarakis, Wolf-Dietrich Hardt, Ruedi Aebersold
Opublikowane w: Nature Biotechnology, Numer 37/3, 2019, Strona(/y) 314-322, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/s41587-019-0037-y

The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis

Autorzy: Daniel Gestaut, Soung Hun Roh, Boxue Ma, Grigore Pintilie, Lukasz A. Joachimiak, Alexander Leitner, Thomas Walzthoeni, Ruedi Aebersold, Wah Chiu, Judith Frydman
Opublikowane w: Cell, Numer 177/3, 2019, Strona(/y) 751-765.e15, ISSN 0092-8674
Wydawca: Cell Press
DOI: 10.1016/j.cell.2019.03.012

The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions

Autorzy: Lilia Kaustov, Alexander Lemak, Hong Wu, Marco Faini, Lixin Fan, Xianyang Fang, Hong Zeng, Shili Duan, Abdellah Allali-Hassani, Fengling Li, Yong Wei, Masoud Vedadi, Ruedi Aebersold, Yunxing Wang, Scott Houliston, Cheryl H Arrowsmith
Opublikowane w: Nucleic Acids Research, 2019, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkz697

Quantitative Interactomics in Primary T Cells Provides a Rationale for Concomitant PD-1 and BTLA Coinhibitor Blockade in Cancer Immunotherapy

Autorzy: Javier Celis-Gutierrez, Peter Blattmann, Yunhao Zhai, Nicolas Jarmuzynski, Kilian Ruminski, Claude Grégoire, Youcef Ounoughene, Frédéric Fiore, Ruedi Aebersold, Romain Roncagalli, Matthias Gstaiger, Bernard Malissen
Opublikowane w: Cell Reports, Numer 27/11, 2019, Strona(/y) 3315-3330.e7, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2019.05.041

A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS

Autorzy: Moritz Heusel, Max Frank, Mario Köhler, Sabine Amon, Fabian Frommelt, George Rosenberger, Isabell Bludau, Simran Aulakh, Monika I. Linder, Yansheng Liu, Ben C. Collins, Matthias Gstaiger, Ulrike Kutay, Ruedi Aebersold
Opublikowane w: Cell Systems, Numer 10/2, 2020, Strona(/y) 133-155.e6, ISSN 2405-4712
Wydawca: Cell Syst.
DOI: 10.1016/j.cels.2020.01.001

ChromID identifies the protein interactome at chromatin marks

Autorzy: Rodrigo Villaseñor, Ramon Pfaendler, Christina Ambrosi, Stefan Butz, Sara Giuliani, Elana Bryan, Thomas W. Sheahan, Annika L. Gable, Nina Schmolka, Massimiliano Manzo, Joël Wirz, Christian Feller, Christian von Mering, Ruedi Aebersold, Philipp Voigt, Tuncay Baubec
Opublikowane w: Nature Biotechnology, 2020, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/s41587-020-0434-2

A Conserved Mito-Cytosolic Translational Balance Links Two Longevity Pathways

Autorzy: Marte Molenaars, Georges E. Janssens, Evan G. Williams, Aldo Jongejan, Jiayi Lan, Sylvie Rabot, Fatima Joly, Perry D. Moerland, Bauke V. Schomakers, Marco Lezzerini, Yasmine J. Liu, Mark A. McCormick, Brian K. Kennedy, Michel van Weeghel, Antoine H.C. van Kampen, Ruedi Aebersold, Alyson W. MacInnes, Riekelt H. Houtkooper
Opublikowane w: Cell Metabolism, Numer 31/3, 2020, Strona(/y) 549-563.e7, ISSN 1550-4131
Wydawca: Cell Press
DOI: 10.1016/j.cmet.2020.01.011

The Polyglutamine Expansion at the N-Terminal of Huntingtin Protein Modulates the Dynamic Configuration and Phosphorylation of the C-Terminal HEAT Domain

Autorzy: Taeyang Jung, Baehyun Shin, Giorgio Tamo, Hyeongju Kim, Ravi Vijayvargia, Alexander Leitner, Maria J. Marcaida, Juan Astorga-Wells, Roy Jung, Ruedi Aebersold, Matteo Dal Peraro, Hans Hebert, Ihn Sik Seong, Ji-Joon Song
Opublikowane w: Structure, Numer 28/9, 2020, Strona(/y) 1035-1050.e8, ISSN 0969-2126
Wydawca: ScienceDirect
DOI: 10.1016/j.str.2020.06.008

The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

Autorzy: Marco Faini, Florian Stengel, Ruedi Aebersold
Opublikowane w: Journal of The American Society for Mass Spectrometry, Numer 27/6, 2016, Strona(/y) 966-974, ISSN 1044-0305
Wydawca: Elsevier BV
DOI: 10.1007/s13361-016-1382-4

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry

Autorzy: Etienne Caron, Daniel J. Kowalewski, Ching Chiek Koh, Theo Sturm, Heiko Schuster and Ruedi Aebersold
Opublikowane w: Molecular & Cellular Proteomics, Numer 12, 2015, Strona(/y) 3105-17, ISSN 1535-9476
Wydawca: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.m115.052431

Author Correction: Proteomic and interactomic insights into the molecular basis of cell functional diversity

Autorzy: Isabell Bludau, Ruedi Aebersold
Opublikowane w: Nature Reviews Molecular Cell Biology, Numer 21/6, 2020, Strona(/y) 353-353, ISSN 1471-0072
Wydawca: Nature Publishing Group
DOI: 10.1038/s41580-020-0249-5

Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines

Autorzy: Alexander Leitner, Marco Faini, Florian Stengel, Ruedi Aebersold
Opublikowane w: Trends in Biochemical Sciences, Numer 41/1, 2016, Strona(/y) 20-32, ISSN 0968-0004
Wydawca: Elsevier BV
DOI: 10.1016/j.tibs.2015.10.008

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

Autorzy: Martin Mehnert, Rodolfo Ciuffa, Fabian Frommelt, Federico Uliana, Audrey van Drogen, Kilian Ruminski, Matthias Gstaiger, Ruedi Aebersold
Opublikowane w: Nature Communications, Numer 11/1, 2020, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-020-17387-y

Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms

Autorzy: Hannes L. Röst, Ruedi Aebersold, Olga T. Schubert
Opublikowane w: Proteomics: Methods and Protocols, 2017, Strona(/y) 289-307
Wydawca: Springer New York
DOI: 10.1007/978-1-4939-6747-6_20

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