ProSpect: An R Package for Analyzing SELDI Measurements Identifying Protein Biomarkers. - Andreas Quandt; Alexander Ploner; Chuen Seng Tan; Janne Lehtiö; Yudi Pawitan (CompLife, 2005)

Finding regions of significance in SELDI measurements for identifying protein biomarkers. - Chuen Seng Tan; Alexander Ploner; Andreas Quandt; Janne Lehtiö; Yudi Pawitan (Bioinform., 2006)

Correlating gene and protein expression data using Correlated Factor Analysis. - Chuen Seng Tan; Agus Salim; Alexander Ploner; Janne Lehtiö; Kee Seng Chia; Yudi Pawitan (BMC Bioinform., 2009)

Multivariate meta-analysis of proteomics data from human prostate and colon tumours. - Lina Hultin Rosenberg; Bo Franzén; Gert Auer; Janne Lehtiö; Jenny Forshed (BMC Bioinform., 2010)

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks. - Andrey Alexeyenko; Woojoo Lee; Maria Pernemalm; Justin Guegan; Philippe Dessen; Vladimir Lazar; Janne Lehtiö; Yudi Pawitan (BMC Bioinform., 2012)

Optimizing analytical depth and cost efficiency of IEF-LC/MS proteomics. - Ilona Kifer; Amir Ben-Dor; Zohar Yakhini; Rui Mamede Branca; Janne Lehtiö; Ping Xu (BIBM, 2014)

Optimizing Analytical Depth and Cost Efficiency of IEF-LC/MS Proteomics. - Ilona Kifer; Rui Mamede Branca; Amir Ben-Dor; Linhui Zhai; Ping Xu; Janne Lehtiö; Zohar Yakhini (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides. - Husen M. Umer; Enrique Audain; Yafeng Zhu; Julianus Pfeuffer; Timo Sachsenberg; Janne Lehtiö; Rui Mamede Branca; Yasset Pérez-Riverol (Bioinform., 2022)