Publications

An updated list of publications is also available from Google Scholar.

1. Lukas Käll and Olga VitekComputational mass spectrometry-based proteomics. PLoS Computational Biology, 7(12): e1002277.
2. Viktor Granholm, William S Noble and Lukas KällSamples of Known Protein Content to Assess the Statistical Calibration of Scores Assigned to Peptide-Spectrum Matches in Shotgun Proteomics.Journal of Proteome Research, 10(5):2671-2678, 2011
3. Viktor Granholm and Lukas KällQuality assessments of peptide-spectrum matches in shotgun proteomics.Proteomics, 11(6):1086-1093, 2011
4. Lukas KällPrediction of transmembrane topology and signal peptide given a protein’s amino acid sequence.Methods Mol Biol 673: 53-62, 2010.
5. Luminita Moruz, Daniela Tomazela and Lukas KällTraining, selection and robust calibration of retention time models for targeted proteomicsJournal of Proteome Research, 9(10):5209-5216, 2010
6. Marina Spivak, Jason Weston, Léon Bottou, Lukas Käll and William Stafford NobleImprovements to the Percolator algorithm for peptide identification from
   shotgun proteomics data setsJournal of Proteome Research, 8(7):3737-3745, August 2009
   
7. Lukas Käll, John D. Storey and William
   Stafford Nobleqvality: Nonparametric estimation of q values and posterior error
   probabilities
   Bioinformatics, 25(7):964-966, February 2009
8. Nir Yosef and Lukas KällFrom sequence to structure to networksGenome Biology, 9(11):3022-7, November 2008
9. Sheila M. Reynolds, Lukas Käll, Michael E. Riffle, Jeff A. Bilmes and William Stafford NobleTransmembrane topology and signal peptide prediction using dynamic
   Bayesian networksPLoS Computational Biology, 4(11):e1000213, November 2008
10. Gennifer E. Merrihew, Colleen Davis, Brent Ewing, Garry Williams,
    Lukas Käll, Barbara E. Frewen, William Stafford Noble, Phil Green, James H. Thomas and Michael
    J. MacCossUse of Shotgun Proteomoics for the Identification, Confirmation,
    and
    Correction of C. elegans Gene AnnotationsGenome Research, 18(10):1660-9 October 2008
11. Lukas Käll, John D. Storey and William
    Stafford NobleNonparametric estimation of posterior error probabilities associated
    with peptides identified by tandem mass spectrometryBioinformatics, 24(16):i42-i48, August 2008
12. Lukas Käll, John D. Storey, Michael J. MacCoss and William Stafford NoblePosterior error probabilities and false discovery rates: two sides of the
    same coinJournal of Proteome Research, 7(1):40-44, January 2008
13. Lukas Käll, John D. Storey, Michael J. MacCoss and William Stafford Noble
    Assigning confidence measures to peptides identified by tandem mass
    spectrometryJournal of Proteome Research, 7(1):29-34, January 2008
14. Carolina Lundin, Lukas Käll, Scott Kreher, Erik Sonnhammer, John Carlson, Gunnar von Heijne and IngMarie Nilsson,Membrane topology of the Drosophila OR83b odorant receptorFEBS Letters, 581:5601-4, December 2007
15. Lukas Käll, Jesse Canterbury, Jason Weston, William Stafford Noble and Michael MacCoss.Semi-supervised learning for peptide identification from shotgun proteomics datasetsNature Methods 4:923 – 925, November 2007
16. Lukas Käll, Anders Krogh and Erik Sonnhammer.Advantages of combined transmembrane topology and signal peptide prediction–the Phobius web serverNucleic Acids Research, 35(Suppl 2):W429-W432Web, May 2007.
17. Lukas Käll.Predicting transmembrane topology and signal peptides with hidden Markov modelsPhD Thesis(abstract)
18. Markus Wistrand*, Lukas Käll* and Erik L.L. Sonnhammer.A general model of G protein-coupled receptor sequences and its application to detect remote homologs.Protein Science, 15(3):509-21, Mars 2006.
    

    *These authors contributed equally to this work.

19. Lukas Käll, Anders Krogh and Erik Sonnhammer.An HMM posterior decoder for sequence feature prediction that includes
    homology informationBioinformatics, 21 (Suppl 1):i251-i257, June 2005.
20. Anna Henricson, Lukas Käll and Erik Sonnhammer.Transmembrane topology of presenilin by reconciling experimental and
    computational approaches.FEBS Journal, 272 (11):2727-2733, June 2005.
21. Lukas Käll, Anders Krogh and Erik L. L.
    Sonnhammer.A Combined Transmembrane Topology and Signal Peptide Prediction Method.Journal of Molecular Biology,
    338(5):1027-1036, May 2004.
22. Lukas Käll and Erik L.L.Sonnhammer.Reliability of transmembrane predictions in whole-genome data.FEBS Letters, 532:415-418, Dec 2002.