Ruedi Aebersold (R Aebersold)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 86

Top Topics

Escherichia Coli

Mass Spectrometry

Artificial Intelligence

Top Venues

Nature communications

Molecular systems biology

The Journal of cell biology

This page only lists publications with an associated author ORCID identifier.

Publications

Fabian Frommelt, Andrea Fossati, Federico Uliana, Fabian Wendt, Peng Xue, Moritz Heusel, Bernd Wollscheid, Ruedi Aebersold, Rodolfo Ciuffa, Matthias Gstaiger
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes. Nature methods 21 (4) (2024)
Fabian Frommelt, Andrea Fossati, Federico Uliana, Fabian Wendt, Peng Xue, Moritz Heusel, Bernd Wollscheid, Ruedi Aebersold, Rodolfo Ciuffa, Matthias Gstaiger
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes. Nature methods 21 (4) (2024)
Alina C Teuscher, Cyril Statzer, Anita Goyala, Seraina A Domenig, Ingmar Schoen, Max Hess, Alexander M Hofer, Andrea Fossati, Viola Vogel, Orcun Goksel, Ruedi Aebersold, Collin Yvès Ewald
Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans. Nature communications 15 (1) (2024)
Alina C Teuscher, Cyril Statzer, Anita Goyala, Seraina A Domenig, Ingmar Schoen, Max Hess, Alexander M Hofer, Andrea Fossati, Viola Vogel, Orcun Goksel, Ruedi Aebersold, Collin Yvès Ewald
Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans. Nature communications 15 (1) (2024)
Alina C Teuscher, Cyril Statzer, Anita Goyala, Seraina A Domenig, Ingmar Schoen, Max Hess, Alexander M Hofer, Andrea Fossati, Viola Vogel, Orcun Goksel, Ruedi Aebersold, Collin Yvès Ewald
Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans. Nature communications 15 (1) (2024)
Fabian Frommelt, Andrea Fossati, Federico Uliana, Fabian Wendt, Peng Xue, Moritz Heusel, Bernd Wollscheid, Ruedi Aebersold, Rodolfo Ciuffa, Matthias Gstaiger
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes. Nature methods 21 (4) (2024)
Alina C Teuscher, Cyril Statzer, Anita Goyala, Seraina A Domenig, Ingmar Schoen, Max Hess, Alexander M Hofer, Andrea Fossati, Viola Vogel, Orcun Goksel, Ruedi Aebersold, Collin Yvès Ewald
Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans. Nature communications 15 (1) (2024)
Fabian Frommelt, Andrea Fossati, Federico Uliana, Fabian Wendt, Peng Xue, Moritz Heusel, Bernd Wollscheid, Ruedi Aebersold, Rodolfo Ciuffa, Matthias Gstaiger
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes. Nature methods (2024)
Fabian Frommelt, Andrea Fossati, Federico Uliana, Fabian Wendt, Peng Xue, Moritz Heusel, Bernd Wollscheid, Ruedi Aebersold, Rodolfo Ciuffa, Matthias Gstaiger
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes. Nature methods 21 (4) (2024)
Alina C Teuscher, Cyril Statzer, Anita Goyala, Seraina A Domenig, Ingmar Schoen, Max Hess, Alexander M Hofer, Andrea Fossati, Viola Vogel, Orcun Goksel, Ruedi Aebersold, Collin Yvès Ewald
Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans. Nature communications 15 (1) (2024)
Fabian Frommelt, Andrea Fossati, Federico Uliana, Fabian Wendt, Peng Xue, Moritz Heusel, Bernd Wollscheid, Ruedi Aebersold, Rodolfo Ciuffa, Matthias Gstaiger
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes. Nature methods 21 (4) (2024)
Fabian Frommelt, Andrea Fossati, Federico Uliana, Fabian Wendt, Peng Xue, Moritz Heusel, Bernd Wollscheid, Ruedi Aebersold, Rodolfo Ciuffa, Matthias Gstaiger
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes. Nature methods 21 (4) (2024)
Chenhao Wu, Matteo Mori, Miriam Abele, Amir Banaei-Esfahani, Zhongge Zhang, Hiroyuki Okano, Ruedi Aebersold, Christina Ludwig, Terence Hwa
Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves. Nature microbiology 8 (2) (2023)
Federico Uliana, Rodolfo Ciuffa, Ranjan Mishra, Andrea Fossati, Fabian Frommelt, Sabrina Keller, Martin Mehnert, Eivind Salmorin Birkeland, Frank van Drogen, Nevena Srejić, Matthias Peter, Nicolas Tapon, Ruedi Aebersold, Matthias Gstaiger
Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration. Molecular systems biology (2023)
Laurent Gatto, Ruedi Aebersold, Juergen Cox, Vadim Demichev, Jason Derks, Edward Emmott, Alexander M Franks, Alexander R Ivanov, Ryan T Kelly, Luke Khoury, Andrew Leduc, Michael J MacCoss, Peter Nemes, David H Perlman, Aleksandra A Petelski, Christopher M Rose, Erwin M Schoof, Jennifer E Van Eyk, Christophe Vanderaa, John Yates Iii, Nikolai Slavov
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nature methods 20 (3) (2023)
Laurent Gatto, Ruedi Aebersold, Juergen Cox, Vadim Demichev, Jason Derks, Edward Emmott, Alexander M Franks, Alexander R Ivanov, Ryan T Kelly, Luke Khoury, Andrew Leduc, Michael J MacCoss, Peter Nemes, David H Perlman, Aleksandra A Petelski, Christopher M Rose, Erwin M Schoof, Jennifer E Van Eyk, Christophe Vanderaa, John Yates Iii, Nikolai Slavov
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nature methods 20 (3) (2023)
Chenhao Wu, Matteo Mori, Miriam Abele, Amir Banaei-Esfahani, Zhongge Zhang, Hiroyuki Okano, Ruedi Aebersold, Christina Ludwig, Terence Hwa
Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves. Nature microbiology 8 (2) (2023)
Nina Zila, Ossia M Eichhoff, Irene Steiner, Thomas Mohr, Andrea Bileck, Phil Fang Cheng, Alexander Leitner, Ludovic C J Gillet, Tatjana Sajic, Sandra Goetze, Betty Friedrich, Patricia Bortel, Johanna Strobl, René Reitermaier, Sabrina A Hogan, Julia Martínez Gómez, Ramon Staeger, Felix Tuchmann, Sophie Peters, Georg Stary, Mario Kuttke, Adelheid Elbe-Buerger, Christoph Hoeller, Rainer Kunstfeld, Wolfgang Weninger, Bernd Wollscheid, Reinhard Dummer, Lars Einar French, Christopher Gerner, Ruedi Aebersold, Mitchell Paul Levesque, Verena Paulitschke
Proteomic profiling of advanced melanoma patients to predict therapeutic response to anti-PD-1 therapy. Clinical cancer research : an official journal of the American Association for Cancer Research (2023)
Laurent Gatto, Ruedi Aebersold, Juergen Cox, Vadim Demichev, Jason Derks, Edward Emmott, Alexander M Franks, Alexander R Ivanov, Ryan T Kelly, Luke Khoury, Andrew Leduc, Michael J MacCoss, Peter Nemes, David H Perlman, Aleksandra A Petelski, Christopher M Rose, Erwin M Schoof, Jennifer E Van Eyk, Christophe Vanderaa, John Yates Iii, Nikolai Slavov
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nature methods 20 (3) (2023)
Chenhao Wu, Matteo Mori, Miriam Abele, Amir Banaei-Esfahani, Zhongge Zhang, Hiroyuki Okano, Ruedi Aebersold, Christina Ludwig, Terence Hwa
Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves. Nature microbiology 8 (2) (2023)
Chenhao Wu, Matteo Mori, Miriam Abele, Amir Banaei-Esfahani, Zhongge Zhang, Hiroyuki Okano, Ruedi Aebersold, Christina Ludwig, Terence Hwa
Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves. Nature microbiology 8 (2) (2023)
Marija Buljan, Amir Banaei-Esfahani, Peter Blattmann, Fabienne Meier-Abt, Wenguang Shao, Olga Vitek, Hua Tang, Ruedi Aebersold
A computational framework for the inference of protein complex remodeling from whole-proteome measurements. Nature methods (2023)
Laurent Gatto, Ruedi Aebersold, Juergen Cox, Vadim Demichev, Jason Derks, Edward Emmott, Alexander M Franks, Alexander R Ivanov, Ryan T Kelly, Luke Khoury, Andrew Leduc, Michael J MacCoss, Peter Nemes, David H Perlman, Aleksandra A Petelski, Christopher M Rose, Erwin M Schoof, Jennifer E Van Eyk, Christophe Vanderaa, John Yates Iii, Nikolai Slavov
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nature methods 20 (3) (2023)
Laurent Gatto, Ruedi Aebersold, Juergen Cox, Vadim Demichev, Jason Derks, Edward Emmott, Alexander M Franks, Alexander R Ivanov, Ryan T Kelly, Luke Khoury, Andrew Leduc, Michael J MacCoss, Peter Nemes, David H Perlman, Aleksandra A Petelski, Christopher M Rose, Erwin M Schoof, Jennifer E Van Eyk, Christophe Vanderaa, John Yates Iii, Nikolai Slavov
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nature methods (2023)
Chenhao Wu, Matteo Mori, Miriam Abele, Amir Banaei-Esfahani, Zhongge Zhang, Hiroyuki Okano, Ruedi Aebersold, Christina Ludwig, Terence Hwa
Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves. Nature microbiology 8 (2) (2023)
Qing Zhong, Rui Sun, Adel T Aref, Zainab Noor, Asim Anees, Yi Zhu, Natasha Lucas, Rebecca C Poulos, Mengge Lyu, Tiansheng Zhu, Guo-Bo Chen, Yingrui Wang, Xuan Ding, Dorothea Rutishauser, Niels J Rupp, Jan H Rueschoff, Cédric Poyet, Thomas Hermanns, Christian Fankhauser, María Rodríguez Martínez, Wenguang Shao, Marija Buljan, Janis Frederick Neumann, Andreas Beyer, Peter G Hains, Roger R Reddel, Phillip J Robinson, Ruedi Aebersold, Tiannan Guo, Peter J Wild
Proteomic-based stratification of intermediate-risk prostate cancer patients. Life science alliance 7 (2) (2023)
Chenhao Wu, Matteo Mori, Miriam Abele, Amir Banaei-Esfahani, Zhongge Zhang, Hiroyuki Okano, Ruedi Aebersold, Christina Ludwig, Terence Hwa
Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves. Nature microbiology 8 (2) (2023)
Georg Dorn, Christoph Gmeiner, Tebbe de Vries, Emil Dedic, Mihajlo Novakovic, Fred F Damberger, Christophe Maris, Esteban Finol, Chris P Sarnowski, Joachim Kohlbrecher, Timothy J Welsh, Sreenath Bolisetty, Raffaele Mezzenga, Ruedi Aebersold, Alexander Leitner, Maxim Yulikov, Gunnar Jeschke, Frédéric Hai-Trieu Allain
Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility. Nature communications 14 (1) (2023)
Laurent Gatto, Ruedi Aebersold, Juergen Cox, Vadim Demichev, Jason Derks, Edward Emmott, Alexander M Franks, Alexander R Ivanov, Ryan T Kelly, Luke Khoury, Andrew Leduc, Michael J MacCoss, Peter Nemes, David H Perlman, Aleksandra A Petelski, Christopher M Rose, Erwin M Schoof, Jennifer E Van Eyk, Christophe Vanderaa, John Yates Iii, Nikolai Slavov
Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. Nature methods 20 (3) (2023)
Grant A King, Rahel Wettstein, Joseph M Varberg, Keerthana Chetlapalli, Madison E Walsh, Ludovic C J Gillet, Claudia Hernández-Armenta, Pedro Beltrao, Ruedi Aebersold, Sue L Jaspersen, Joao Matos, Elçin Ünal
Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization. The Journal of cell biology 222 (2) (2022)
Grant A King, Rahel Wettstein, Joseph M Varberg, Keerthana Chetlapalli, Madison E Walsh, Ludovic C J Gillet, Claudia Hernández-Armenta, Pedro Beltrao, Ruedi Aebersold, Sue L Jaspersen, Joao Matos, Elçin Ünal
Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization. The Journal of cell biology 222 (2) (2022)
Grant A King, Rahel Wettstein, Joseph M Varberg, Keerthana Chetlapalli, Madison E Walsh, Ludovic C J Gillet, Claudia Hernández-Armenta, Pedro Beltrao, Ruedi Aebersold, Sue L Jaspersen, Joao Matos, Elçin Ünal
Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization. The Journal of cell biology 222 (2) (2022)
Moritz Schaefer, Amena Nabih, Daniel Spies, Victoria Hermes, Maxime Bodak, Harry Wischnewski, Patrick Stalder, Richard Patryk Ngondo, Luz Angelica Liechti, Tatjana Sajic, Ruedi Aebersold, David Gatfield, Constance Ciaudo
Global and precise identification of functional miRNA targets in mESCs by integrative analysis. EMBO reports 23 (9) (2022)
Rodolfo Ciuffa, Federico Uliana, Jonathan Mannion, Martin Mehnert, Tencho Tenev, Cathy Marulli, Ari Satanowski, Lena Maria Leone Keller, Pilar Natalia Rodilla Ramirez, Alessandro Ori, Matthias Gstaiger, Pascal Meier, Ruedi Aebersold
Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics. Proceedings of the National Academy of Sciences of the United States of America 119 (40) (2022)
Yaoting Sun, Sathiyamoorthy Selvarajan, Zelin Zang, Wei Liu, Yi Zhu, Hao Zhang, Wanyuan Chen, Hao Chen, Lu Li, Xue Cai, Huanhuan Gao, Zhicheng Wu, Yongfu Zhao, Lirong Chen, Xiaodong Teng, Sangeeta Mantoo, Tony Kiat-Hon Lim, Bhuvaneswari Hariraman, Serene Yeow, Syed Muhammad Fahmy Alkaff, Sze Sing Lee, Guan Ruan, Qiushi Zhang, Tiansheng Zhu, Yifan Hu, Zhen Dong, Weigang Ge, Qi Xiao, Weibin Wang, Guangzhi Wang, Junhong Xiao, Yi He, Zhihong Wang, Wei Sun, Yuan Qin, Jiang Zhu, Xu Zheng, Linyan Wang, Xi Zheng, Kailun Xu, Yingkuan Shao, Shu Zheng, Kexin Liu, Ruedi Aebersold, Haixia Guan, Xiaohong Wu, Dingcun Luo, Wen Tian, Stan Ziqing Li, Oi Lian Kon, Narayanan Gopalakrishna Iyer, Tiannan Guo
Artificial intelligence defines protein-based classification of thyroid nodules. Cell discovery 8 (1) (2022)
Grant A King, Rahel Wettstein, Joseph M Varberg, Keerthana Chetlapalli, Madison E Walsh, Ludovic C J Gillet, Claudia Hernández-Armenta, Pedro Beltrao, Ruedi Aebersold, Sue L Jaspersen, Joao Matos, Elçin Ünal
Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization. The Journal of cell biology 222 (2) (2022)
Anna Knörlein, Chris P Sarnowski, Tebbe de Vries, Moritz Stoltz, Michael Götze, Ruedi Aebersold, Frédéric Hai-Trieu Allain, Alexander Leitner, Jonathan Hall
Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes. Nature communications 13 (1) (2022)
Grant A King, Rahel Wettstein, Joseph M Varberg, Keerthana Chetlapalli, Madison E Walsh, Ludovic C J Gillet, Claudia Hernández-Armenta, Pedro Beltrao, Ruedi Aebersold, Sue L Jaspersen, Joao Matos, Elçin Ünal
Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization. The Journal of cell biology 222 (2) (2022)
Yaoting Sun, Sathiyamoorthy Selvarajan, Zelin Zang, Wei Liu, Yi Zhu, Hao Zhang, Wanyuan Chen, Hao Chen, Lu Li, Xue Cai, Huanhuan Gao, Zhicheng Wu, Yongfu Zhao, Lirong Chen, Xiaodong Teng, Sangeeta Mantoo, Tony Kiat-Hon Lim, Bhuvaneswari Hariraman, Serene Yeow, Syed Muhammad Fahmy Alkaff, Sze Sing Lee, Guan Ruan, Qiushi Zhang, Tiansheng Zhu, Yifan Hu, Zhen Dong, Weigang Ge, Qi Xiao, Weibin Wang, Guangzhi Wang, Junhong Xiao, Yi He, Zhihong Wang, Wei Sun, Yuan Qin, Jiang Zhu, Xu Zheng, Linyan Wang, Xi Zheng, Kailun Xu, Yingkuan Shao, Shu Zheng, Kexin Liu, Ruedi Aebersold, Haixia Guan, Xiaohong Wu, Dingcun Luo, Wen Tian, Stan Ziqing Li, Oi Lian Kon, Narayanan Gopalakrishna Iyer, Tiannan Guo
Author Correction: Artificial intelligence defines protein-based classification of thyroid nodules. Cell discovery 8 (1) (2022)
Seyed Babak Loghmani, Eric Zitzow, Gene Ching Chiek Koh, Andreas Ulmer, Nadine Veith, Ruth Großeholz, Madlen Rossnagel, Maren Loesch, Ruedi Aebersold, Bernd Kreikemeyer, Tomas Fiedler, Ursula Kummer
All Driven by Energy Demand? Integrative Comparison of Metabolism of Enterococcus faecalis Wildtype and a Glutamine Synthase Mutant. Microbiology spectrum 10 (2) (2022)
Matteo Mori, Zhongge Zhang, Amir Banaei-Esfahani, Jean-Beno Æt Lalanne, Hiroyuki Okano, Ben C Collins, Alexander Schmidt, Olga T Schubert, Deok-Sun Lee, Gene-Wei Li, Ruedi Aebersold, Terence Hwa, Christina Ludwig
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions. Molecular systems biology 17 (5) (2022)
Jelena Čuklina, Chloe H Lee, Evan Graehl Williams, Tatjana Sajic, Ben C Collins, María Rodríguez Martínez, Varun S Sharma, Fabian Wendt, Sandra Goetze, Gregory R Keele, Bernd Wollscheid, Ruedi Aebersold, Patrick G A Pedrioli
Diagnostics and correction of batch effects in large-scale proteomic studies: a tutorial. Molecular systems biology 17 (8) (2022)
Rohan Balakrishnan, Matteo Mori, Igor Segota, Zhongge Zhang, Ruedi Aebersold, Christina Ludwig, Terence Hwa
Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria. Science (New York, N.Y.) 378 (6624) (2022)
Jean-David Morel, Lucie Sauzéat, Ludger J E Goeminne, Pooja Jha, Evan Graehl Williams, Riekelt H Houtkooper, Ruedi Aebersold, Johan Auwerx, Vincent Balter
The mouse metallomic landscape of aging and metabolism. Nature communications 13 (1) (2022)
Jan Großbach, Ludovic C J Gillet, Mathieu Clément-Ziza, Corinna L Schmalohr, Olga T Schubert, Maximilian Schütter, Julia S P Mawer, Christopher A Barnes, Isabell Bludau, Matthias Weith, Peter Tessarz, Martin Graef, Ruedi Aebersold, Andreas Beyer
The impact of genomic variation on protein phosphorylation states and regulatory networks. Molecular systems biology 18 (5) (2022)
Grant A King, Rahel Wettstein, Joseph M Varberg, Keerthana Chetlapalli, Madison E Walsh, Ludovic C J Gillet, Claudia Hernández-Armenta, Pedro Beltrao, Ruedi Aebersold, Sue L Jaspersen, Joao Matos, Elçin Ünal
Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization. The Journal of cell biology 222 (2) (2022)
Grant A King, Rahel Wettstein, Joseph M Varberg, Keerthana Chetlapalli, Madison E Walsh, Ludovic C J Gillet, Claudia Hernández-Armenta, Pedro Beltrao, Ruedi Aebersold, Sue L Jaspersen, Joao Matos, Elçin Ünal
Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization. The Journal of cell biology 222 (2) (2022)
Isabell Bludau, Max Frank, Christian Dörig, Yujia Cai, Moritz Heusel, George A Rosenberger, Paola Picotti, Ben C Collins, Hannes L Röst, Ruedi Aebersold
Systematic detection of functional proteoform groups from bottom-up proteomic datasets. Nature communications 12 (1) (2021)
Federico Uliana, Matej Vizovišek, Laura Acquasaliente, Rodolfo Ciuffa, Andrea Fossati, Fabian Frommelt, Sandra Goetze, Bernd Wollscheid, Matthias Gstaiger, Vincenzo De Filippis, Ulrich Auf dem Keller, Ruedi Aebersold
Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. Nature communications 12 (1) (2021)
Jonathan J Knowlton, Daniel Gestaut, Boxue Ma, Gwen M Taylor, Alpay Burak Seven, Alexander Leitner, Gregory J Wilson, Sreejesh Shanker, Nathan A Yates, B V Venkataram Prasad, Ruedi Aebersold, Wah Chiu, Judith Frydman, Terence S Dermody
Structural and functional dissection of reovirus capsid folding and assembly by the prefoldin-TRiC/CCT chaperone network. Proceedings of the National Academy of Sciences of the United States of America 118 (11) (2021)
Stefan Gerhardy, Michaela Oborská-Oplová, Ludovic C J Gillet, Richard Börner, Rob W van Nues, Alexander Leitner, Erich Michel, Janusz Jurand Petkowski, Sander Granneman, Roland K O Sigel, Ruedi Aebersold, Vikram Govind Panse
Puf6 primes 60S pre-ribosome nuclear export at low temperature. Nature communications 12 (1) (2021)
Vignesh Kasinath, Curtis Beck, Paul Victor Sauer, Simon Poepsel, Jennifer Kosmatka, Marco Faini, Daniel Toso, Ruedi Aebersold, Eva Nogales
JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications. Science (New York, N.Y.) 371 (6527) (2021)
Joris Cadow, Matteo Manica, Roland Mathis, Tiannan Guo, Ruedi Aebersold, María Rodríguez Martínez
On the feasibility of deep learning applications using raw mass spectrometry data. Bioinformatics (Oxford, England) 37 (Suppl_1) (2021)
Andrea Fossati, Chen Li, Federico Uliana, Fabian Wendt, Fabian Frommelt, Peter Sykacek, Moritz Heusel, Mahmoud Hallal, Isabell Bludau, Tümay Capraz, Peng Xue, Jiangning Song, Bernd Wollscheid, Anthony Wayne Purcell, Matthias Gstaiger, Ruedi Aebersold
PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. Nature methods 18 (5) (2021)
Huoming Zhang, Pei Liu, Tiannan Guo, Huayan Zhao, Dalila Bensaddek, Ruedi Aebersold, Liming Xiong
Author Correction: Arabidopsis proteome and the mass spectral assay library. Scientific data 8 (1) (2021)
Isabell Bludau, Moritz Heusel, Max Frank, George A Rosenberger, Robin Hafen, Amir Banaei-Esfahani, Audrey van Drogen, Ben C Collins, Matthias Gstaiger, Ruedi Aebersold
Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes. Nature protocols 15 (8) (2020)
Florian Meier, Andreas-David Brunner, Max Frank, Annie Ha, Isabell Bludau, Eugenia Voytik, Stephanie Kaspar-Schoenefeld, Markus Lubeck, Oliver Raether, Nicolai Bache, Ruedi Aebersold, Ben C Collins, Hannes L Röst, Matthias Mann
diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition. Nature methods 17 (12) (2020)
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
ChromID identifies the protein interactome at chromatin marks. Nature biotechnology 38 (6) (2020)
Subash Adhikari, Edouard C Nice, Eric W Deutsch, Lydie Lane, Gilbert S Omenn, Stephen R Pennington, Young-Ki Paik, Christopher M Overall, Fernando J Corrales, Ileana M Cristea, Jennifer E Van Eyk, Mathias Uhlen, Cecilia Lindskog, Daniel W Chan, Amos Bairoch, James C Waddington, Joshua L Justice, Joshua LaBaer, Henry Rodriguez, Fuchu He, Markus Kostrzewa, Peipei Ping, Rebekah L Gundry, Peter Stewart, Sanjeeva Srivastava, Sudhir Srivastava, Fabio C S Nogueira, Gilberto B Domont, Yves Vandenbrouck, Maggie P Y Lam, Sara Wennersten, Juan Antonio Vizcaino, Marc R Wilkins, Jochen M Schwenk, Emma Lundberg, Nuno Bandeira, Gyorgy Marko-Varga, Susan T Weintraub, Charles Pineau, Ulrike Kusebauch, Robert L Moritz, Seong Beom Ahn, Magnus Palmblad, Michael Paul Snyder, Ruedi Aebersold, Mark S Baker
A high-stringency blueprint of the human proteome. Nature communications 11 (1) (2020)
Rebecca C Poulos, Peter G Hains, Rohan Shah, Natasha Lucas, Dylan Xavier, Srikanth S Manda, Asim Anees, Jennifer M S Koh, Sadia Mahboob, Max Wittman, Steven G Williams, Erin K Sykes, Michael Hecker, Michael Dausmann, Merridee A Wouters, Keith Ashman, Jean Yee Hwa Yang, Peter J Wild, Anna De Fazio, Rosemary L Balleine, Brett J Tully, Ruedi Aebersold, Terence P Speed, Yansheng Liu, Roger R Reddel, Phillip J Robinson, Qing Zhong
Strategies to enable large-scale proteomics for reproducible research. Nature communications 11 (1) (2020)
Emiliya Poghosyan, Ioan Iacovache, Lenka Faltova, Alexander Leitner, Pinfen Yang, Dennis R Diener, Ruedi Aebersold, Benoit Zuber, Takashi Ishikawa
The structure and symmetry of the radial spoke protein complex in Chlamydomonas flagella. Journal of cell science 133 (16) (2020)
Sapir Schlam-Babayov, Ariel Bensimon, Michal Harel, Tamar Geiger, Ruedi Aebersold, Yael Ziv, Yosef Shiloh
Phosphoproteomics reveals novel modes of function and inter-relationships among PIKKs in response to genotoxic stress. The EMBO journal 40 (2) (2020)
Martin Mehnert, Rodolfo Ciuffa, Fabian Frommelt, Federico Uliana, Audrey van Drogen, Kilian Ruminski, Matthias Gstaiger, Ruedi Aebersold
Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes. Nature communications 11 (1) (2020)
Isabell Bludau, Ruedi Aebersold
Proteomic and interactomic insights into the molecular basis of cell functional diversity. Nature reviews. Molecular cell biology 21 (6) (2020)
Alexander Schäfer, Enio Gjerga, Richard Wd Welford, Imke Renz, Francois Lehembre, Peter Ma Groenen, Julio Saez-Rodriguez, Ruedi Aebersold, Matthias Gstaiger
Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data. Molecular systems biology 15 (8) (2020)
Somsakul Pop Wongpalee, Shiheng Liu, Javier Gallego-Bartolomé, Alexander Leitner, Ruedi Aebersold, Wanlu Liu, Linda Yen, Maria A Nohales, Peggy Hsuanyu Kuo, Ajay A Vashisht, James A Wohlschlegel, Suhua Feng, Steve A Kay, Z Hong Zhou, Steven E Jacobsen
CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation. Nature communications 10 (1) (2019)
Tatjana Sajic, Rodolfo Ciuffa, Vera Lemos, Pan Xu, Valentina Leone, Chen Li, Evan G Williams, Georgios Makris, Amir Banaei-Esfahani, Mathias F Heikenwälder, Kristina Schoonjans, Ruedi Aebersold
A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model. Scientific reports 9 (1) (2019)
Wenguang Shao, Tiannan Guo, Nora C Toussaint, Peng Xue, Ulrich Wagner, Li Li, Konstantina Charmpi, Yi Zhu, Jianmin Wu, Marija Buljan, Rui Sun, Dorothea Rutishauser, Thomas Hermanns, Christian Daniel Fankhauser, Cedric Poyet, Jelena Ljubicic, Niels Rupp, Jan H Rüschoff, Qing Zhong, Andreas Beyer, Jiafu Ji, Ben C Collins, Yansheng Liu, Gunnar Rätsch, Peter J Wild, Ruedi Aebersold
Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nature communications 10 (1) (2019)
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
Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nature biotechnology 37 (3) (2019)
Moritz Heusel, Isabell Bludau, George A Rosenberger, Robin Hafen, Max Frank, Amir Banaei-Esfahani, Audrey van Drogen, Ben C Collins, Matthias Gstaiger, Ruedi Aebersold
Complex-centric proteome profiling by SEC-SWATH-MS. Molecular systems biology 15 (1) (2019)
Pierre-Yves Helleboid, Moritz Heusel, Julien Duc, Cécile Piot, Christian W Thorball, Andrea Coluccio, Julien Pontis, Michaël Imbeault, Priscilla Turelli, Ruedi Aebersold, Didier Trono
The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification. The EMBO journal 38 (18) (2019)
Verena Paulitschke, Ossia Eichhoff, Christopher Gerner, Philipp Paulitschke, Andrea Bileck, Thomas Mohr, Phil F Cheng, Alexander Leitner, Emmanuella Guenova, Ieva Saulite, Sandra N Freiberger, Anja Irmisch, Bernhard Knapp, Nina Zila, Theodora-Pagona Chatziisaak, Jürgen Stephan, Joanna Mangana, Rainer Kunstfeld, Hubert Pehamberger, Ruedi Aebersold, Reinhard Dummer, Mitchell Paul Levesque
Proteomic identification of a marker signature for MAPKi resistance in melanoma. The EMBO journal 38 (15) (2019)
Ben C Collins, Ruedi Aebersold
Proteomics goes parallel. Nature biotechnology 36 (11) (2019)
Huoming Zhang, Pei Liu, Tiannan Guo, Huayan Zhao, Dalila Bensaddek, Ruedi Aebersold, Liming Xiong
Arabidopsis proteome and the mass spectral assay library. Scientific data 6 (1) (2019)
Peter Blattmann, Vivienne Stutz, Giulia Lizzo, Joy Richard, Philipp Gut, Ruedi Aebersold
Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins. Scientific data 6 (2019)
D Forchelet, S Béguin, T Sajic, N Bararpour, Z Pataky, M Frias, S Grabherr, M Augsburger, Y Liu, M Charnley, J Déglon, Ruedi Aebersold, Aurelien Thomas, P Renaud
Separation of blood microsamples by exploiting sedimentation at the microscale. Scientific reports 8 (1) (2018)
Marija Buljan, Peter Blattmann, Ruedi Aebersold, Michael Boutros
Systematic characterization of pan-cancer mutation clusters. Molecular systems biology 14 (3) (2018)
Marcello Clerici, Marco Faini, Lena M Muckenfuss, Ruedi Aebersold, Martin Jinek
Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Nature structural & molecular biology 25 (2) (2018)
Evan Graehl Williams, Yibo Wu, Witold E Wolski, Jun Yong Kim, Jiayi Lan, Moaraj Hasan, Christian Halter, Pooja Jha, Dongryeol Ryu, Johan Auwerx, Ruedi Aebersold
Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population. Molecular & cellular proteomics : MCP 17 (9) (2018)
Sabina Schütz, Erich Michel, Fred F Damberger, Michaela Oplová, Cohue Peña, Alexander Leitner, Ruedi Aebersold, Frederic H-T Allain, Vikram Govind Panse
Molecular basis for disassembly of an importin:ribosomal protein complex by the escortin Tsr2. Nature communications 9 (1) (2018)
Heiko Schuster, Wenguang Shao, Tobias Weiss, Patrick G A Pedrioli, Patrick Roth, Michael Weller, David S Campbell, Eric W Deutsch, Robert L Moritz, Oliver Planz, Hans-Georg Rammensee, Ruedi Aebersold, Etienne Caron
A tissue-based draft map of the murine MHC class I immunopeptidome. Scientific data 5 (2018)
Saikat Chowdhury, Chinatsu Otomo, Alexander Leitner, Kazuto Ohashi, Ruedi Aebersold, Gabriel C Lander, Takanori Otomo
Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex. Proceedings of the National Academy of Sciences of the United States of America 115 (42) (2018)
Teresa Cortes, Olga T Schubert, Amir Banaei-Esfahani, Ben C Collins, Ruedi Aebersold, Douglas B Young
Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival. Scientific reports 7 (1) (2017)
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
Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells. Nature communications 8 (1) (2017)
Neha Patel, Florian Stengel, Ruedi Aebersold, Matthew G Gold
Molecular basis of AKAP79 regulation by calmodulin. Nature communications 8 (1) (2017)
George A 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 Sonia Ting, Ben C Collins, Ruedi Aebersold
Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nature methods 14 (9) (2017)