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)

Tandem Mass Spectrometry Protein Identification on a PC Grid. - Dominique Zosso; Michael Podvinec; Markus Müller; Ruedi Aebersold; Manuel C. Peitsch; Torsten Schwede (HealthGrid, 2007)

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)

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)

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; et al. (BMC Bioinform., 2008)

Proteome coverage prediction with infinite Markov models. - Manfred Claassen; Ruedi Aebersold; Joachim M. Buhmann (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)

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)

Spectral Library Searching for Peptide Identification via Tandem MS. - Henry Lam; Ruedi Aebersold (Proteome Bioinformatics, 2010)

Xwalk: computing and visualizing distances in cross-linking experiments. - Abdullah Kahraman; Lars Malmström; Ruedi Aebersold (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; et al. (BMC Bioinform., 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)

Proteome Coverage Prediction for Integrated Proteomics Datasets. - Manfred Claassen; Ruedi Aebersold; Joachim M. Buhmann (J. Comput. Biol., 2011)

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)

Computational Mass Spectrometry (Dagstuhl Seminar 13491). - Ruedi Aebersold; Oliver Kohlbacher; Olga Vitek (Dagstuhl Reports, 2013)

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)

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. - Hannes L. Röst; George Rosenberger; Ruedi Aebersold; Lars Malmström (Bioinform., 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)

Computational Mass Spectrometry (Dagstuhl Seminar 15351). - Rudolf Aebersold; Oliver Kohlbacher; Olga Vitek (Dagstuhl Reports, 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; et al. (Nat., 2015)

Mass-spectrometric exploration of proteome structure and function. - Ruedi Aebersold; Matthias Mann (Nat., 2016)

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; et al. (Nucleic Acids Res., 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; et al. (PLoS Comput. Biol., 2018)

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)

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 009; Wenguang Shao; Patrick G. A. Pedrioli; Anthony W. Purcell; María Rodríguez Martínez; Jiangning Song; Matteo Manica; et al. (Briefings Bioinform., 2022)

Deep domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profiling. - Fang Wang 028; Fan Yang 081; Longkai Huang; Wei Li 184; Jiangning Song; Robin B. Gasser; Ruedi Aebersold; Guohua Wang; Jianhua Yao 001 (Nat. Mac. Intell., 2023)

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. - Yingying Sun; Jun A; Zhiwei Liu; Rui Sun; Liujia Qian; Samuel H. Payne; Wout Bittremieux; Markus Ralser; Chen Li 021; Yi Chen; Zhen Dong; Yasset Pérez-Riverol; et al. (CoRR, 2025)