Ruedi Aebersold

According to our database, Ruedi Aebersold authored at least 26 papers between 2006 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

Deep domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profiling.

Fang Wang, Fan Yang, Longkai Huang, Wei Li, Jiangning Song, Robin B. Gasser, Ruedi Aebersold, Guohua Wang, Jianhua Yao

Nat. Mac. Intell., October, 2023

2022

PCfun: a hybrid computational framework for systematic characterization of protein complex function.

Varun S. Sharma, Andrea Fossati, Rodolfo Ciuffa, Marija Buljan, Evan G. Williams, Zhen Chen, Wenguang Shao, Patrick G. A. Pedrioli, Anthony W. Purcell, María Rodríguez Martínez, Jiangning Song, Matteo Manica, Ruedi Aebersold, Chen Li

Briefings Bioinform., 2022

2021

On the feasibility of deep learning applications using raw mass spectrometry data.

Joris Cadow, Matteo Manica, Roland Mathis, Tiannan Guo, Ruedi Aebersold, María Rodríguez Martínez

Bioinform., 2021

2018

Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach.

Nicolas Henry, Eva-Maria Krammer, Florian Stengel, Quentin Adams, François Van Liefferinge, Ellen Hubin, Rui Chaves, Rouslan Efremov, Ruedi Aebersold, Guy Vandenbussche, Martine Prévost, Vincent Raussens, Stéphanie Deroo

PLoS Comput. Biol., 2018

The SysteMHC Atlas project.

Wenguang Shao, Patrick G. A. Pedrioli, Witold Wolski, Christian Scurtescu, Emanuel Schmid, Juan Antonio Vizcaíno, Mathieu Courcelles, Heiko Schuster, Daniel Kowalewski, Fabio Marino, Cecilia S. Lindestam 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 Nielsen, Eric W. Deutsch, David S. Campbell, Robert L. Moritz, Roman A. Zubarev, Anders Jimmy Ytterberg, Anthony W. Purcell, Miguel Marcilla, Alberto Paradela, Qi Wang, Catherine E. Costello, Nicola Ternette, Peter A. van Veelen, Cécile A. C. M. van Els, Albert J. R. Heck, Gustavo A. de Souza, Ludvig M. Sollid, Arie Admon, Stefan Stevanovic, Hans-Georg Rammensee, Pierre Thibault, Claude Perreault, Michal Bassani-Sternberg, Ruedi Aebersold, Etienne Caron

Nucleic Acids Res., 2018

2016

Mass-spectrometric exploration of proteome structure and function.

Ruedi Aebersold, Matthias Mann

Nat., 2016

2015

Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation.

Nadinath B. Nillegoda, Janine Kirstein, Anna Szlachcic, Mykhaylo Berynskyy, Antonia Stank, Florian Stengel, Kristin Arnsburg, Xuechao Gao, Annika Scior, Ruedi Aebersold, D. Lys Guilbride, Rebecca C. Wade, Richard I. Morimoto, Matthias P. Mayer, Bernd Bukau

Nat., 2015

Computational Mass Spectrometry (Dagstuhl Seminar 15351).

Rudolf Aebersold, Oliver Kohlbacher, Olga Vitek

Dagstuhl Reports, 2015

Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition.

Lin-Yang Cheng, Yansheng Liu, Ching-Yun Chang, Hannes L. Röst, Ruedi Aebersold, Olga Vitek

BMC Bioinform., 2015

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

Hannes L. Röst, George Rosenberger, Ruedi Aebersold, Lars Malmström

Bioinform., 2015

2014

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.

George Rosenberger, Christina Ludwig, Hannes L. Röst, Ruedi Aebersold, Lars Malmström

Bioinform., 2014

2013

Computational Mass Spectrometry (Dagstuhl Seminar 13491).

Ruedi Aebersold, Oliver Kohlbacher, Olga Vitek

Dagstuhl Reports, 2013

2012

Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs.

Timothy Clough, Safia Thaminy, Susanne Ragg, Ruedi Aebersold, Olga Vitek

BMC Bioinform., 2012

2011

Proteome Coverage Prediction for Integrated Proteomics Datasets.

Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann

J. Comput. Biol., 2011

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry.

Mi-Youn K. Brusniak, Sung-Tat Kwok, Mark Christiansen, David S. Campbell, Lukas Reiter, Paola Picotti, Ulrike Kusebauch, Hector Ramos, Eric W. Deutsch, Jingchun Chen, Robert L. Moritz, Ruedi Aebersold

BMC Bioinform., 2011

openBIS: a flexible framework for managing and analyzing complex data in biology research.

Angela Bauch, Izabela Adamczyk, Piotr Buczek, Franz-Josef Elmer, Kaloyan Enimanev, Pawel Glyzewski, Manuel Kohler, Tomasz Pylak, Andreas Quandt, Chandrasekhar Ramakrishnan, Christian Beisel, Lars Malmström, Ruedi Aebersold, Bernd Rinn

BMC Bioinform., 2011

Xwalk: computing and visualizing distances in cross-linking experiments.

Abdullah Kahraman, Lars Malmström, Ruedi Aebersold

Bioinform., 2011

2010

Spectral Library Searching for Peptide Identification via Tandem MS.

Henry Lam, Ruedi Aebersold

Proceedings of the Proteome Bioinformatics, 2010

2009

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.

Sandra N. Loevenich, Erich Brunner, Nichole L. King, Eric W. Deutsch, Stephen E. Stein, Ruedi Aebersold, Ernst Hafen

BMC Bioinform., 2009

Prequips - an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data.

Nils Gehlenborg, Wei Yan, Inyoul Y. Lee, Hyuntae Yoo, Kay Nieselt, Daehee Hwang, Ruedi Aebersold, Leroy Hood

Bioinform., 2009

Proteome coverage prediction with infinite Markov models.

Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann

Bioinform., 2009

2008

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.

Mi-Youn K. Brusniak, Bernd Bodenmiller, David S. Campbell, Kelly Cooke, James Eddes, Andrew Garbutt, Hollis Lau, Simon Letarte, Lukas N. Mueller, Vagisha Sharma, Olga Vitek, Ning Zhang, Ruedi Aebersold, Julian D. Watts

BMC Bioinform., 2008

The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data.

Hector Ramos, P. Shannon, Ruedi Aebersold

Bioinform., 2008

MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis.

Daehee Hwang, Ning Zhang, Hookeun Lee, Eugene Yi, Hui Zhang, Inyoul Y. Lee, Leroy Hood, Ruedi Aebersold

Bioinform., 2008

2007

Tandem Mass Spectrometry Protein Identification on a PC Grid.

Dominique Zosso, Michael Podvinec, Markus Müller, Ruedi Aebersold, Manuel C. Peitsch, Torsten Schwede

Proceedings of the From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences, 2007

2006

The PeptideAtlas project.

Frank Desiere, Eric W. Deutsch, Nichole L. King, Alexey I. Nesvizhskii, Parag Mallick, Jimmy K. Eng, Sharon Chen, James Eddes, Sandra N. Loevenich, Ruedi Aebersold

Nucleic Acids Res., 2006