Käll Lab

Publications:

  1. Lukas Käll and Olga Vitek
    Computational mass spectrometry-based proteomics.
    PLoS Computational Biology, 7(12): e1002277.
  2. Viktor Granholm, William S Noble and Lukas Käll
    Samples 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 Käll
    Quality assessments of peptide-spectrum matches in shotgun proteomics.
    Proteomics, 11(6):1086-1093, 2011
  4. Lukas Käll
    Prediction 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 Käll
    Training, selection and robust calibration of retention time models for targeted proteomics
    Journal of Proteome Research, 9(10):5209-5216, 2010
  6. Marina Spivak, Jason Weston, Léon Bottou, Lukas Käll and William Stafford Noble
    Improvements to the Percolator algorithm for peptide identification from shotgun proteomics data sets
    Journal of Proteome Research, 8(7):3737-3745, August 2009
  7. Lukas Käll, John D. Storey and William Stafford Noble
    qvality: Nonparametric estimation of q values and posterior error probabilities
    Bioinformatics, 25(7):964-966, February 2009
  8. Nir Yosef and Lukas Käll
    From sequence to structure to networks
    Genome Biology, 9(11):3022-7, November 2008
  9. Sheila M. Reynolds, Lukas Käll, Michael E. Riffle, Jeff A. Bilmes and William Stafford Noble
    Transmembrane topology and signal peptide prediction using dynamic Bayesian networks
    PLoS 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. MacCoss
    Use of Shotgun Proteomoics for the Identification, Confirmation, and Correction of C. elegans Gene Annotations
    Genome Research, 18(10):1660-9 October 2008
  11. Lukas Käll, John D. Storey and William Stafford Noble
    Nonparametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry
    Bioinformatics, 24(16):i42-i48, August 2008
  12. Lukas Käll, John D. Storey, Michael J. MacCoss and William Stafford Noble
    Posterior error probabilities and false discovery rates: two sides of the same coin
    Journal 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 spectrometry
    Journal 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 receptor
    FEBS 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 datasets
    Nature 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 server
    Nucleic Acids Research, 35(Suppl 2):W429-W432Web, May 2007.
  17. Lukas Käll.
    Predicting transmembrane topology and signal peptides with hidden Markov models
    PhD 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 information
    Bioinformatics, 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.