Ruedi Aebersold

Publication Activity (10 Years)

Years Active: 2006-2023
Publications (10 Years): 6

Top Topics

Molecular Dynamics

Mass Spectrometry

Spectral Features

Top Venues

Briefings Bioinform.

Publications

Fang Wang, Fan Yang, Longkai Huang, Wei Li, Jiangning Song, Robin B. Gasser, Ruedi Aebersold, Guohua Wang, Jianhua Yao
Deep domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profiling. Nat. Mac. Intell. 5 (11) (2023)
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
PCfun: a hybrid computational framework for systematic characterization of protein complex function. Briefings Bioinform. 23 (4) (2022)
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. Bioinform. 37 (Supplement) (2021)
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
Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach. PLoS Comput. Biol. 14 (6) (2018)
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
The SysteMHC Atlas project. Nucleic Acids Res. 46 (Database-Issue) (2018)
Ruedi Aebersold, Matthias Mann
Mass-spectrometric exploration of proteome structure and function. Nat. 537 (7620) (2016)
Lin-Yang Cheng, Yansheng Liu, Ching-Yun Chang, Hannes L. Röst, Ruedi Aebersold, Olga Vitek
Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition. BMC Bioinform. 16 (S-2) (2015)
Hannes L. Röst, George Rosenberger, Ruedi Aebersold, Lars Malmström
Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Bioinform. 31 (14) (2015)
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
Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation. Nat. 524 (7564) (2015)
George Rosenberger, Christina Ludwig, Hannes L. Röst, Ruedi Aebersold, Lars Malmström
aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Bioinform. 30 (17) (2014)
Ruedi Aebersold, Oliver Kohlbacher, Olga Vitek
Computational Mass Spectrometry (Dagstuhl Seminar 13491). Dagstuhl Reports 3 (12) (2013)
Timothy Clough, Safia Thaminy, Susanne Ragg, Ruedi Aebersold, Olga Vitek
Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs. BMC Bioinform. 13 (S-16) (2012)
Abdullah Kahraman, Lars Malmström, Ruedi Aebersold
Xwalk: computing and visualizing distances in cross-linking experiments. Bioinform. 27 (15) (2011)
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
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. BMC Bioinform. 12 (2011)
Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann
Proteome Coverage Prediction for Integrated Proteomics Datasets. J. Comput. Biol. 18 (3) (2011)
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
openBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinform. 12 (2011)
Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann
Proteome Coverage Prediction for Integrated Proteomics Datasets. RECOMB (2010)
Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann
Proteome coverage prediction with infinite Markov models. Bioinform. 25 (12) (2009)
Sandra N. Loevenich, Erich Brunner, Nichole L. King, Eric W. Deutsch, Stephen E. Stein, Ruedi Aebersold, Ernst Hafen
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. BMC Bioinform. 10 (2009)
Nils Gehlenborg, Wei Yan, Inyoul Y. Lee, Hyuntae Yoo, Kay Nieselt, Daehee Hwang, Ruedi Aebersold, Leroy Hood
Prequips - an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. Bioinform. 25 (5) (2009)
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
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinform. 9 (2008)
Hector Ramos, P. Shannon, Ruedi Aebersold
The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data. Bioinform. 24 (18) (2008)
Daehee Hwang, Ning Zhang, Hookeun Lee, Eugene Yi, Hui Zhang, Inyoul Y. Lee, Leroy Hood, Ruedi Aebersold
MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis. Bioinform. 24 (22) (2008)
Dominique Zosso, Michael Podvinec, Markus Müller, Ruedi Aebersold, Manuel C. Peitsch, Torsten Schwede
Tandem Mass Spectrometry Protein Identification on a PC Grid. HealthGrid (2007)
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
The PeptideAtlas project. Nucleic Acids Res. 34 (Database-Issue) (2006)