The Yeast Resource Center Public Data Repository. - Michael Riffle; Lars Malmström; Trisha N. Davis (Nucleic Acids Res., 2005)

2DDB - a bioinformatics solution for analysis of quantitative proteomics data. - Lars Malmström; György Marko-Varga; Gunilla Westergren-Thorsson; Thomas Laurell; Johan Malmström (BMC Bioinform., 2006)

Accelerating 3D Protein Modeling Using Cloud Computing: Using Rosetta as a Service on the IBM SmartCloud. - Peter Z. Kunszt; Lars Malmström; Nicola Fantini; Wibke Sudholt; Marcel Lautenschlager; Roland Reifler; Stefan Ruckstuhl (e-Science Workshops, 2011)

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)

Improving the Swiss Grid Proteomics Portal: Requirements and new Features based on Experience and Usability Considerations. - Peter Z. Kunszt; Lorenz Blum; Béla Hullár; Emanuel Schmid; Adam Srebniak; Witold Wolski; Bernd Rinn; Franz-Josef Elmer; Chandrasekhar Ramakrishnan; Andreas Quandt; Lars Malmström (IWSG, 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)

DIANA - algorithmic improvements for analysis of data-independent acquisition MS data. - Johan Teleman; Hannes L. Röst; George Rosenberger; Uwe Schmitt; Lars Malmström; Johan Malmström; Fredrik Levander (Bioinform., 2015)

iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations. - Peter Z. Kunszt; Lorenz Blum; Béla Hullár; Emanuel Schmid; Adam Srebniak; Witold Wolski; Bernd Rinn; Franz-Josef Elmer; Chandrasekhar Ramakrishnan; Andreas Quandt; Lars Malmström (Concurr. Comput. Pract. Exp., 2015)

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. - Katherine Wolstencroft; Olga Krebs; Jacky L. Snoep; Natalie J. Stanford; Finn Bacall; Martin Golebiewski; Rostyk Kuzyakiv; Quyen Nguyen; Stuart Owen; Stian Soiland-Reyes; Jakub Straszewski; David D. van Niekerk; et al. (Nucleic Acids Res., 2017)

Greedy de novo motif discovery to construct motif repositories for bacterial proteomes. - Hamed Khakzad; Johan Malmström; Lars Malmström (BMC Bioinform., 2019)

Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data. - Hamed Khakzad; Lotta Happonen; Johan Malmström; Lars Malmström (Bioinform., 2021)

Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology. - Hamed Khakzad; Lotta Happonen; Yasaman Karami; Sounak Chowdhury; Gizem Ertürk Bergdahl; Michael Nilges; Guy Tran Van Nhieu; Johan Malmström; Lars Malmström (PLoS Comput. Biol., 2021)

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics. - Carlos Gueto-Tettay; Di Tang; Lotta Happonen; Moritz Heusel; Hamed Khakzad; Johan Malmström; Lars Malmström (PLoS Comput. Biol., 2023)