L Holm

Summary

Affiliation: University of Helsinki
Country: Finland

Publications

  1. ncbi BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    BMC Bioinformatics 13:33. 2012
  2. ncbi Comprehensive comparison of graph based multiple protein sequence alignment strategies
    Ilya Plyusnin
    Institute of Biotechnology, University of Helsinki, P, O, Box 56, Viikinkaari 5, Helsinki, Finland
    BMC Bioinformatics 13:64. 2012
  3. ncbi Oligomerization of Uukuniemi virus nucleocapsid protein
    Anna Katz
    Department of Virology, Infection Biology Research Program, Haartman Institute, PO Box 21, University of Helsinki, Helsinki, Finland
    Virol J 7:187. 2010
  4. ncbi Inferring the physical connectivity of complex networks from their functional dynamics
    Hung Xuan Ta
    Institute of Biotechnology, PO Box 56, 00014 University of Helsinki, Finland
    BMC Syst Biol 4:70. 2010
  5. ncbi Towards structured output prediction of enzyme function
    Katja Astikainen
    Department of Computer Science, PO Box 68, FI 00014 University of Helsinki, Finland
    BMC Proc 2:S2. 2008
  6. ncbi Adhesive polypeptides of Staphylococcus aureus identified using a novel secretion library technique in Escherichia coli
    Riikka Kylväjä
    Division of General Microbiology, Department of Biosciences, University of Helsinki, Viikinkaari 9C, University of Helsinki, Finland
    BMC Microbiol 11:117. 2011
  7. ncbi Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function
    Petri Toronen
    The Holm Group, Biocenter II, Institute of Biotechnology, PO Box 56, 00014 University of Helsinki, Finland
    BMC Bioinformatics 10:307. 2009
  8. ncbi Generation of Gene Ontology benchmark datasets with various types of positive signal
    Petri Toronen
    The Holm Group, Biocenter II, Institute of Biotechnology, PO Box 56, 00014 University of Helsinki, Finland
    BMC Bioinformatics 10:319. 2009
  9. ncbi Dali server: conservation mapping in 3D
    Liisa Holm
    Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, Finland
    Nucleic Acids Res 38:W545-9. 2010
  10. ncbi Searching protein structure databases with DaliLite v.3
    L Holm
    Department of Biological and Environmental Sciences, and Institute of Biotechnology, P O Box 56 Viikinkaari 5, 00014 University of Helsinki, Finland
    Bioinformatics 24:2780-1. 2008

Collaborators

  • A Heger
  • Petri Toronen
  • Matti Kankainen
  • Ilya Plyusnin
  • Riikka Kylväjä
  • Hung Xuan Ta
  • Anna Katz
  • Katja Astikainen
  • Teija Ojala
  • Benita Westerlund-Wikström
  • Chang No Yoon
  • Alexander N Freiberg
  • Alexander Plyusnin
  • Seung Kee Han
  • Ramon Flick
  • Ralf F Pettersson
  • Antti Vaheri
  • Vera Backström
  • Axel R Schulz
  • Angelo Mateos
  • Pauli J Ojala
  • Petri Pehkonen
  • Pekka Marttinen
  • Sandor Szedmak
  • Juho Rousu

Detail Information

Publications11

  1. ncbi BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    BMC Bioinformatics 13:33. 2012
    ..This problem has created a pressing need for improvements in homology-based annotation...
  2. ncbi Comprehensive comparison of graph based multiple protein sequence alignment strategies
    Ilya Plyusnin
    Institute of Biotechnology, University of Helsinki, P, O, Box 56, Viikinkaari 5, Helsinki, Finland
    BMC Bioinformatics 13:64. 2012
    ..We systematically varied information sources, guiding trees, score transformations and iterative refinement options, and evaluated the resulting alignments on BAliBASE and SABmark...
  3. ncbi Oligomerization of Uukuniemi virus nucleocapsid protein
    Anna Katz
    Department of Virology, Infection Biology Research Program, Haartman Institute, PO Box 21, University of Helsinki, Helsinki, Finland
    Virol J 7:187. 2010
    ..The aim was to locate the domains involved in the N protein oligomerization and study the process in detail...
  4. ncbi Inferring the physical connectivity of complex networks from their functional dynamics
    Hung Xuan Ta
    Institute of Biotechnology, PO Box 56, 00014 University of Helsinki, Finland
    BMC Syst Biol 4:70. 2010
    ..Given observations of a network system's behaviours or measurements of its functional dynamics, what can we conclude of the details of physical connectivity of the underlying structure?..
  5. ncbi Towards structured output prediction of enzyme function
    Katja Astikainen
    Department of Computer Science, PO Box 68, FI 00014 University of Helsinki, Finland
    BMC Proc 2:S2. 2008
    ..CONCLUSION : Structured output prediction with GTG features is shown to be computationally feasible and to have accuracy on par with state-of-the-art approaches in enzyme function prediction...
  6. ncbi Adhesive polypeptides of Staphylococcus aureus identified using a novel secretion library technique in Escherichia coli
    Riikka Kylväjä
    Division of General Microbiology, Department of Biosciences, University of Helsinki, Viikinkaari 9C, University of Helsinki, Finland
    BMC Microbiol 11:117. 2011
    ....
  7. ncbi Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function
    Petri Toronen
    The Holm Group, Biocenter II, Institute of Biotechnology, PO Box 56, 00014 University of Helsinki, Finland
    BMC Bioinformatics 10:307. 2009
    ..Alternatively, one monitors the average differential expression level of genes belonging to a given functional class. So far these two types of method have not been combined...
  8. ncbi Generation of Gene Ontology benchmark datasets with various types of positive signal
    Petri Toronen
    The Holm Group, Biocenter II, Institute of Biotechnology, PO Box 56, 00014 University of Helsinki, Finland
    BMC Bioinformatics 10:319. 2009
    ..Despite the importance of this procedure, there is a little work on consistent evaluation of various GO analysis methods. Especially, there is no literature on creating benchmark datasets for GO analysis tools...
  9. ncbi Dali server: conservation mapping in 3D
    Liisa Holm
    Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, Finland
    Nucleic Acids Res 38:W545-9. 2010
    ..In favourable cases, protein structure comparison can lead to evolutionary discoveries not detected by sequence analysis...
  10. ncbi Searching protein structure databases with DaliLite v.3
    L Holm
    Department of Biological and Environmental Sciences, and Institute of Biotechnology, P O Box 56 Viikinkaari 5, 00014 University of Helsinki, Finland
    Bioinformatics 24:2780-1. 2008
    ..biocenter.helsinki.fi/dali_server is running DaliLite v.3. The software can be downloaded for academic use from http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads/v3...
  11. ncbi More for less in structural genomics
    A Heger
    Institute of Biotechnology, PO Box 56, 00014 University of Helsinki, Finland
    J Struct Funct Genomics 4:57-66. 2003
    ..Our results support an increase in the granularity of covering protein space that has potentially enormous economic implications for planning the transition to the full production phase of structural genomics...