Toussaint, NC, Dönnes, P, and Kohlbacher, O (2008).
A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-based Vaccines
PLoS Comput. Biol. 4(12):e1000246.

Shatkay, H, Höglund, A, Brady, S, Blum, T, Dönnes, P, and Kohlbacher, O (2007).
SherLoc : High-Accuracy Prediction of Protein Subcellular Localization by Integrating Text and Protein Sequence Data.
Bioinformatics 23(11):1410-1417.

Höglund, A, Dönnes, P, Blum, T, Adolph, H, and Kohlbacher, O (2006).
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid composition
Bioinformatics 22(10):1158-65.

Höglund, A, Blum, T, Brady, S, Dönnes, P, Miguel, JS, Rocheford, M, Kohlbacher, O, and Shatkay, H (2006).
Significantly improved prediction of subcellular localization by integrating text and protein sequence data
In: Proceedings of the Pacific Symposium on Biocomputing (PSB 2006). PSB.

Dönnes, P, and Kohlbacher, O (2006).
SVMHC: a server for prediction of MHC-binding peptides
Nucleic Acids Res. 34:W194-W197.

Supper, J, Dönnes, P, and Kohlbacher, O (2005).
Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules
Springer Lecture Notes in Computer Science (LNCS) 3686:446-453.

Höglund, A, Dönnes, P, Adolph, H, and Kohlbacher, O (2005).
From prediction of subcellular localization to functional classification: Discrimination of DNA-packing and other nuclear proteins
Online Journal of Bioinformatics 6(1):51-64.

Dönnes, P, and Kohlbacher, O (2005).
Integrated modelling of the major events in the MHC class I antigen processing pathway
Protein Sci. 14(8):2132--2140.

Höglund, A, Dönnes, P, Blum, T, Adolph, H, and Kohlbacher, O (2005).
Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localization
In: Proceedings of the German Conference on Bioinformatics (GCB 2005), edited by Andrew Torda, Stefan Kurtz, Matthias Rarey. GI, pages 45--59.

Schuler, MM, Dönnes, P, Nastke, M, Kohlbacher, O, Rammensee, H, and Stevanovic, S (2005).
SNEP: SNP-derived Epitope Prediction program for minor H antigens.
Immunogenetics 57(11):816-820.

Schuler, M, Dönnes, P, Nastke, M, Kohlbacher, O, Rammensee, H, and Stevanovic, S (2005).
SNEP: SNP-derived Epitope Prediction program for minor H antigens
In: Joint Annual Meeting of the German and Scandinavian Societies of Immunology, 21-24 September 2005, Kiel, Germany, edited by Dietrich Kabelitz. Immunobiology 210(6-8), pages 361-622.

Dönnes, P, Höglund, A, Sturm, M, Comtesse, N, Backes, C, Meese, E, Kohlbacher, O, and Lenhof, H (2004).
Integrative analysis of cancer-related data using CAP
FASEB Journal 18(12):1465-1467.

Dönnes, P, and Höglund, A (2004).
Predicting Protein Subcellular Localization: Past, Present, and Future
Genomics Proteomics Bioinformatics 2(4):209--215.

Dönnes, P, and Elofsson, A (2002).
Prediction of MHC class I binding peptides, using SVMHC
BMC Bioinformatics 3(25).