Kris Laukens

Summary

Affiliation: University of Antwerp
Country: Belgium

Publications

  1. ncbi Flexible network reconstruction from relational databases with Cytoscape and CytoSQL
    Kris Laukens
    Department of Mathematics and Computer Science, University of Antwerp, Antwerpen, Belgium
    BMC Bioinformatics 11:360. 2010
  2. ncbi Cytokinin affinity purification and identification of a tobacco BY-2 adenosine kinase
    Kris Laukens
    Laboratorium voor Plantenbiochemie en fysiologie, Department of Biology, University of Antwerp UIA, Universiteitsplein 1, B 2610, Antwerp, Belgium
    FEBS Lett 533:63-6. 2003
  3. ncbi Construction of a two-dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow-2 cell suspension culture
    Kris Laukens
    Laboratorium voor Planten biochemie en fysiologie, Department of Biology, University of Antwerp, Belgium
    Proteomics 4:720-7. 2004
  4. ncbi Integration of gel-based proteome data with pProRep
    Kris Laukens
    Laboratory of Plant Physiology and Plant Biochemistry, University of Antwerp Groenenborgerlaan 171, B 2020 Antwerp, Belgium
    Bioinformatics 22:2838-40. 2006
  5. ncbi Unraveling tobacco BY-2 protein complexes with BN PAGE/LC-MS/MS and clustering methods
    Noor Remmerie
    Center for Proteomics CFP, Groenenborgerlaan 171, B 2020 Antwerp, Belgium
    J Proteomics 74:1201-17. 2011
  6. ncbi Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications
    Noor Remmerie
    Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, B 2020 Antwerp, Belgium
    Phytochemistry 72:1192-218. 2011
  7. ncbi Fast liquid chromatography coupled to electrospray tandem mass spectrometry peptide sequencing for cross-species protein identification
    Erwin Witters
    Universiteit Antwerpen, UIA, dept Biologie, Laboratorium voor plantenbiochemie, Universiteitsplein 1, B 2610 Antwerpen, Belgium
    Rapid Commun Mass Spectrom 17:2188-94. 2003
  8. ncbi Prediction of kinase-specific phosphorylation sites using conditional random fields
    Thanh Hai Dang
    Intelligent Systems Laboratory and Advanced Database Research and Modelling, Department of Mathematics and Computer Science, Middelheimlaan 1, B 2020 Antwerpen, Belgium
    Bioinformatics 24:2857-64. 2008
  9. ncbi A hormone and proteome approach to picturing the initial metabolic events during Plasmodiophora brassicae infection on Arabidopsis
    Sylvie Devos
    Laboratory of Plant Physiology and Plant Biochemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
    Mol Plant Microbe Interact 19:1431-43. 2006
  10. ncbi An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data
    Trung N Vu
    Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
    BMC Bioinformatics 12:405. 2011

Collaborators

Detail Information

Publications18

  1. ncbi Flexible network reconstruction from relational databases with Cytoscape and CytoSQL
    Kris Laukens
    Department of Mathematics and Computer Science, University of Antwerp, Antwerpen, Belgium
    BMC Bioinformatics 11:360. 2010
    ..However, molecular data are often stored in relational databases with their own specific structure, for which dedicated plugins do not exist. Therefore, a more generic solution is presented...
  2. ncbi Cytokinin affinity purification and identification of a tobacco BY-2 adenosine kinase
    Kris Laukens
    Laboratorium voor Plantenbiochemie en fysiologie, Department of Biology, University of Antwerp UIA, Universiteitsplein 1, B 2610, Antwerp, Belgium
    FEBS Lett 533:63-6. 2003
    ..The presented results show for the first time a plant adenosine kinase affinity-purified to homogeneity that was identified by primary structure analysis...
  3. ncbi Construction of a two-dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow-2 cell suspension culture
    Kris Laukens
    Laboratorium voor Planten biochemie en fysiologie, Department of Biology, University of Antwerp, Belgium
    Proteomics 4:720-7. 2004
    ..This publicly accessible database provides a solid basis for tobacco BY-2 proteomics in the future...
  4. ncbi Integration of gel-based proteome data with pProRep
    Kris Laukens
    Laboratory of Plant Physiology and Plant Biochemistry, University of Antwerp Groenenborgerlaan 171, B 2020 Antwerp, Belgium
    Bioinformatics 22:2838-40. 2006
    ..ua.ac.be/pProRep. The application requires a web server that runs PHP 5 (http://www.php.net) and MySQL. Some (non-essential) extensions need additional freely available libraries: details are described in the installation instructions...
  5. ncbi Unraveling tobacco BY-2 protein complexes with BN PAGE/LC-MS/MS and clustering methods
    Noor Remmerie
    Center for Proteomics CFP, Groenenborgerlaan 171, B 2020 Antwerp, Belgium
    J Proteomics 74:1201-17. 2011
    ..Both well characterized long-lived protein complexes as well as potential temporary sequential multi-enzyme complexes were characterized...
  6. ncbi Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications
    Noor Remmerie
    Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, B 2020 Antwerp, Belgium
    Phytochemistry 72:1192-218. 2011
    ..In this review an overview is given of the current status of these aspects in plant studies with special attention to non-genomic model plants...
  7. ncbi Fast liquid chromatography coupled to electrospray tandem mass spectrometry peptide sequencing for cross-species protein identification
    Erwin Witters
    Universiteit Antwerpen, UIA, dept Biologie, Laboratorium voor plantenbiochemie, Universiteitsplein 1, B 2610 Antwerpen, Belgium
    Rapid Commun Mass Spectrom 17:2188-94. 2003
    ..The method was evaluated and put into force to generate data for a tobacco cell culture protein database...
  8. ncbi Prediction of kinase-specific phosphorylation sites using conditional random fields
    Thanh Hai Dang
    Intelligent Systems Laboratory and Advanced Database Research and Modelling, Department of Mathematics and Computer Science, Middelheimlaan 1, B 2020 Antwerpen, Belgium
    Bioinformatics 24:2857-64. 2008
    ..All of these models suffer from certain limitations, such as the fact that they do not take into account the dependencies between amino acid motifs within protein sequences in a global fashion...
  9. ncbi A hormone and proteome approach to picturing the initial metabolic events during Plasmodiophora brassicae infection on Arabidopsis
    Sylvie Devos
    Laboratory of Plant Physiology and Plant Biochemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
    Mol Plant Microbe Interact 19:1431-43. 2006
    ..Consequently, a de novo meristematic area is established that acts as a sink for host-derived indole-3-acetic acid, carbohydrates, nitrogen, and energy to maintain the pathogen and to trigger gall development...
  10. ncbi An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data
    Trung N Vu
    Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
    BMC Bioinformatics 12:405. 2011
    ..abstract:..
  11. ncbi A bioanalytical method for the proteome wide display and analysis of protein complexes from whole plant cell lysates
    Noor Remmerie
    Center for Proteome Analysis and Mass Spectrometry, University of Antwerp, Antwerp, Belgium
    Proteomics 9:598-609. 2009
    ..Furthermore practical issues concerning the use of this 2-D BN/SDS-PAGE display method for the analysis of protein-protein interactions are discussed...
  12. ncbi Best practices for hybridization design in two-colour microarray analysis
    Dries Knapen
    Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
    Trends Biotechnol 27:406-14. 2009
    ....
  13. ncbi A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics
    Ellen Van Damme
    Laboratory of Protein Chemistry, Proteomics and Signal Transduction, Department of Biomedical Sciences, University of Antwerp Campus Drie Eiken, Universiteitsplein 1 Building T, Wilrijk, Belgium
    Int J Biol Sci 6:51-67. 2010
    ..Additionally, we show an enrichment of SUMOylatable proteins in the PML-NBs through an in-house prediction algorithm. Therefore, based on the PML network, we hypothesize that PML-NBs may function as a nuclear SUMOylation hotspot...
  14. ncbi Functional genomics in a non-model crop: transcriptomics or proteomics?
    Sebastien Christian Carpentier
    Laboratory of Tropical Crop Improvement, Katholieke Universiteit, 3001 Leuven, Belgium
    Physiol Plant 133:117-30. 2008
    ..The information on the abundance of transcripts was obtained by serial analysis of gene expression (SAGE), while information on the abundance of proteins was obtained via two-dimensional gel electrophoresis...
  15. ncbi Organization of proteomics data with YassDB
    Allan L Thomsen
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense
    Methods Mol Biol 367:271-87. 2007
    ..The setup and use of the YassDB database application with two client programs "pProRep" and "VEMS" will be outlined...
  16. ncbi Banana (Musa spp.) as a model to study the meristem proteome: acclimation to osmotic stress
    Sebastien C Carpentier
    Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit Leuven, Leuven, Belgium
    Proteomics 7:92-105. 2007
    ..This work shows that proteome analysis can be used successfully to perform quantitative difference analysis and to characterize genetic variations in a recalcitrant crop...
  17. ncbi A novel cell division factor from tobacco 2B-13 cells that induced cell division in auxin-starved tobacco BY-2 cells
    Takashi Shimizu
    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Naturwissenschaften 93:278-85. 2006
    ..The significance of CDF as a possible ABC-transporter is discussed in relationship to auxin-autotrophic growth and auxin-signaling pathway...
  18. ncbi Proteome analysis of non-model plants: a challenging but powerful approach
    Sebastien Christian Carpentier
    Division of Crop Biotechnics, K U Leuven, Leuven, Belgium
    Mass Spectrom Rev 27:354-77. 2008
    ..We will illustrate the power of 2DE for non-model plants in combination with multivariate data analysis and MS/MS identification and will evaluate possible alternatives...