An HMM posterior decoder for sequence feature prediction that includes homology information. - Lukas Käll; Anders Krogh; Erik L. L. Sonnhammer (ISMB (Supplement of Bioinformatics), 2005)

Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. - Lukas Käll; Anders Krogh; Erik L. L. Sonnhammer (Nucleic Acids Res., 2007)

Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. - Lukas Käll; John D. Storey; William Stafford Noble (ECCB, 2008)

Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks. - Sheila M. Reynolds; Lukas Käll; Michael Riffle; Jeff A. Bilmes; William Stafford Noble (PLoS Comput. Biol., 2008)

QVALITY: non-parametric estimation of q-values and posterior error probabilities. - Lukas Käll; John D. Storey; William Stafford Noble (Bioinform., 2009)

Computational Mass Spectrometry-Based Proteomics. - Lukas Käll; Olga Vitek (PLoS Comput. Biol., 2011)

A cross-validation scheme for machine learning algorithms in shotgun proteomics. - Viktor Granholm; William Stafford Noble; Lukas Käll (BMC Bioinform., 2012)

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. - Konstantinos D. Tsirigos; Christoph Peters; Nanjiang Shu; Lukas Käll; Arne Elofsson (Nucleic Acids Res., 2015)

Uncertainty estimation of predictions of peptides' chromatographic retention times in shotgun proteomics. - Heydar Maboudi Afkham; Xuanbin Qiu; Matthew The; Lukas Käll (Bioinform., 2017)

CoExpresso: assess the quantitative behavior of protein complexes in human cells. - Morteza Chalabi Hajkarim; Vasileios Tsiamis; Lukas Käll; Fabio Vandin; Veit Schwämmle (BMC Bioinform., 2019)

Parallelized calculation of permutation tests. - Markus Ekvall; Michael Höhle; Lukas Käll (Bioinform., 2021)

Survival analysis of pathway activity as a prognostic determinant in breast cancer. - Gustavo S. Jeuken; Nicholas P. Tobin; Lukas Käll (PLoS Comput. Biol., 2022)

Semi-supervised Learning While Controlling the FDR with an Application to Tandem Mass Spectrometry Analysis. - Jack Freestone; Lukas Käll; William Stafford Noble; Uri Keich (RECOMB, 2024)

ECCB2024: The 23rd European Conference on Computational Biology. - Anu Kukkonen-Macchi; Sampsa Hautaniemi; Katharina F. Heil; Merja Heinäniemi; Lars Juhl Jensen; Sini Junttila; Lukas Käll; Asta Laiho; Peter Maccallum; Matti Nykter; Bengt Persson; Tomi Suomi; et al. (Bioinform., 2024)

ProHap Explorer: Visualizing Haplotypes in Proteogenomic Datasets. - Jakub Vasícek; Dafni Skiadopoulou; Ksenia Kuznetsova; Lukas Käll; Marc Vaudel; Stefan Bruckner (CoRR, 2025)