Käll Lab

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• Members
  • Lukas Käll
  • Jesper Lind
  • Luminita Moruz
  • Alexey Moiseenko
• News
• Publications
• Software and servers
  • Percolator
  • mimic
  • qvality
  • Phobius
  • GPCRHMM
• Positions

Publications:

• Marina Spivak, Jason Weston, Léon Bottou, Lukas Käll, William Stafford Noble
  Improvements to the Percolator algorithm for peptide identification from shotgun proteomics data sets
  Journal of Proteome Research, in press
• 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
  
• Nir Yosef and Lukas Käll
  From sequence to structure to networks
  Genome Biology, 9(11):3022-7, November 2008
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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.
  
• Lukas Käll.
  Predicting transmembrane topology and signal peptides with hidden Markov models
  PhD Thesis
  (abstract)
• 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.
  
• 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.
  
• 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.
  
• 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.
  
• Lukas Käll and Erik L.L.Sonnhammer.
  Reliability of transmembrane predictions in whole-genome data.
  FEBS Letters, 532:415-418, Dec 2002.