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ORCIDRuedi Aebersold
Person information
- affiliation: ETH Zurich, Institute for Systems Biology, Switzerland
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2020 – today
- 2025
[i3]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:
Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. CoRR abs/2502.15867 (2025)- 2023
- [j22]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): 1236-1249 (2023) - 2022
- [j21]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) - 2021
- [j20]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): 245-253 (2021)
2010 – 2019
- 2018
- [j19]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:
The SysteMHC Atlas project. Nucleic Acids Res. 46(Database-Issue): D1237-D1247 (2018) - [j18]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) - 2016
- [j17]Ruedi Aebersold, Matthias Mann:
Mass-spectrometric exploration of proteome structure and function. Nat. 537(7620): 347-355 (2016) - 2015
- [j16]Hannes L. Röst, George Rosenberger, Ruedi Aebersold, Lars Malmström:
Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Bioinform. 31(14): 2415-2417 (2015) - [j15]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): A4 (2015) - [j14]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): 247-251 (2015) - [i2]Rudolf Aebersold, Oliver Kohlbacher, Olga Vitek:
Computational Mass Spectrometry (Dagstuhl Seminar 15351). Dagstuhl Reports 5(8): 9-33 (2015) - 2014
- [j13]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): 2511-2513 (2014) - 2013
- [i1]Ruedi Aebersold, Oliver Kohlbacher, Olga Vitek:
Computational Mass Spectrometry (Dagstuhl Seminar 13491). Dagstuhl Reports 3(12): 1-16 (2013) - 2012
- [j12]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): S6 (2012) - 2011
- [j11]Abdullah Kahraman, Lars Malmström, Ruedi Aebersold:
Xwalk: computing and visualizing distances in cross-linking experiments. Bioinform. 27(15): 2163-2164 (2011) - [j10]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: 78 (2011) - [j9]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: 468 (2011) - [j8]Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann:
Proteome Coverage Prediction for Integrated Proteomics Datasets. J. Comput. Biol. 18(3): 283-293 (2011) - 2010
- [c2]Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann:
Proteome Coverage Prediction for Integrated Proteomics Datasets. RECOMB 2010: 96-109 - [p1]Henry Lam, Ruedi Aebersold:
Spectral Library Searching for Peptide Identification via Tandem MS. Proteome Bioinformatics 2010: 95-103
2000 – 2009
- 2009
- [j7]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): 682-683 (2009) - [j6]Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann:
Proteome coverage prediction with infinite Markov models. Bioinform. 25(12) (2009) - [j5]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) - 2008
- [j4]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): 2110-2111 (2008) - [j3]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): 2641-2642 (2008) - [j2]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) - 2007
- [c1]Dominique Zosso, Michael Podvinec, Markus Müller, Ruedi Aebersold, Manuel C. Peitsch, Torsten Schwede:
Tandem Mass Spectrometry Protein Identification on a PC Grid. HealthGrid 2007: 3-12 - 2006
- [j1]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): 655-658 (2006)
Coauthor Index
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