Ruedi Aebersold

27 papers B 1Journal 24Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence.
CoRR
Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Samuel H. Payne, Wout Bittremieux, Markus Ralser, Chen Li, Yi Chen, Zhen Dong, Yasset Pérez-Riverol, Asif Khan, Chris Sander, Ruedi Aebersold, Juan Antonio Vizcaíno, Jonathan R. Krieger, Jianhua Yao, Han Wen, Linfeng Zhang, Yunping Zhu, Yue Xuan, Benjamin Boyang Sun, Liang Qiao, Henning Hermjakob, Haixu Tang, Huanhuan Gao, Yamin Deng, Qing Zhong, Cheng Chang, Nuno Bandeira, Ming Li, Weinan E, Siqi Sun, Yuedong Yang, Gilbert S. Omenn, Yue Zhang, Ping Xu, Yan Fu, Xiaowen Liu, Christopher M. Overall, Yu Wang, Eric W. Deutsch, Luonan Chen, Jürgen Cox, Vadim Demichev, Fuchu He, Jiaxing Huang, Huilin Jin, Chao Liu, Nan Li, Zhongzhi Luan, Jiangning Song, Kaicheng Yu, Wanggen Wan, Tai Wang, Kang Zhang, Le Zhang, Peter A. Bell, Matthias Mann, Bing Zhang, Tiannan Guo
2023 J jnl
Deep domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profiling.
Nat. Mac. Intell.
Fang Wang, Fan Yang, Longkai Huang, Wei Li, Jiangning Song, Robin B. Gasser, Ruedi Aebersold, Guohua Wang, Jianhua Yao
2022 J jnl
PCfun: a hybrid computational framework for systematic characterization of protein complex function.
Briefings Bioinform.
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
2021 J jnl
On the feasibility of deep learning applications using raw mass spectrometry data.
Bioinform.
Joris Cadow, Matteo Manica, Roland Mathis, Tiannan Guo, Ruedi Aebersold, María Rodríguez Martínez
2018 J jnl
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.
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
2018 J jnl
The SysteMHC Atlas project.
Nucleic Acids Res.
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 Magne Sollid, Arie Admon, Stefan Stevanovic, Hans-Georg Rammensee, Pierre Thibault, Claude Perreault, Michal Bassani-Sternberg, Ruedi Aebersold, Etienne Caron
2016 J jnl
Mass-spectrometric exploration of proteome structure and function.
Nat.
Ruedi Aebersold, Matthias Mann
2015 J jnl
Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation.
Nat.
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
2015 J jnl
Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.
Bioinform.
Hannes L. Röst, George Rosenberger, Ruedi Aebersold, Lars Malmström
2015 J jnl
Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition.
BMC Bioinform.
Lin-Yang Cheng, Yansheng Liu, Ching-Yun Chang, Hannes L. Röst, Ruedi Aebersold, Olga Vitek
2014 J jnl
aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.
Bioinform.
George Rosenberger, Christina Ludwig, Hannes L. Röst, Ruedi Aebersold, Lars Malmström
2013 J jnl
Computational Mass Spectrometry (Dagstuhl Seminar 13491).
Dagstuhl Reports
Ruedi Aebersold, Oliver Kohlbacher, Olga Vitek
2012 J jnl
Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs.
BMC Bioinform.
Timothy Clough, Safia Thaminy, Susanne Ragg, Ruedi Aebersold, Olga Vitek
2011 J jnl
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry.
BMC Bioinform.
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
2011 J jnl
Proteome Coverage Prediction for Integrated Proteomics Datasets.
J. Comput. Biol.
Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann
2011 J jnl
Xwalk: computing and visualizing distances in cross-linking experiments.
Bioinform.
Abdullah Kahraman, Lars Malmström, Ruedi Aebersold
2011 J jnl
openBIS: a flexible framework for managing and analyzing complex data in biology research.
BMC Bioinform.
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
2010 B conf
Proteome Coverage Prediction for Integrated Proteomics Datasets.
RECOMB
Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann
2010 — ch.
Spectral Library Searching for Peptide Identification via Tandem MS.
Proteome Bioinformatics
Henry Lam, Ruedi Aebersold
2009 J jnl
Prequips - an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data.
Bioinform.
Nils Gehlenborg, Wei Yan, Inyoul Y. Lee, Hyuntae Yoo, Kay Nieselt, Daehee Hwang, Ruedi Aebersold, Leroy Hood
2009 J jnl
Proteome coverage prediction with infinite Markov models.
Bioinform.
Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann
2009 J jnl
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
BMC Bioinform.
Sandra N. Loevenich, Erich Brunner, Nichole L. King, Eric W. Deutsch, Stephen E. Stein, Ruedi Aebersold, Ernst Hafen
2008 J jnl
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.
BMC Bioinform.
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
2008 J jnl
MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis.
Bioinform.
Daehee Hwang, Ning Zhang, Hookeun Lee, Eugene Yi, Hui Zhang, Inyoul Y. Lee, Leroy Hood, Ruedi Aebersold
2008 J jnl
The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data.
Bioinform.
Hector Ramos, P. Shannon, Ruedi Aebersold
2007 — conf
Tandem Mass Spectrometry Protein Identification on a PC Grid.
HealthGrid
Dominique Zosso, Michael Podvinec, Markus Müller, Ruedi Aebersold, Manuel C. Peitsch, Torsten Schwede
2006 J jnl
The PeptideAtlas project.
Nucleic Acids Res.
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