L Holm

Summary

Affiliation: University of Helsinki
Country: Finland

Publications

  1. pmc SANS: high-throughput retrieval of protein sequences allowing 50% mismatches
    J Patrik Koskinen
    Department of Biosciences, Division of Genetics University of Helsinki, 00014 Helsinki, Finland
    Bioinformatics 28:i438-i443. 2012
  2. pmc POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, PO Box 56 Viikinkaari 5, FIN 00014, Helsinki, Finland
    Nucleic Acids Res 33:W427-31. 2005
  3. pmc POXO: a web-enabled tool series to discover transcription factor binding sites
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, PO Box 56 Viikinkaari 5, FIN 00014 Helsinki, Finland
    Nucleic Acids Res 34:W534-40. 2006
  4. pmc Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana
    Matti Kankainen
    Institute of Biotechnology, PO Box 56 Viikinkaari 5, FIN 00014, Helsinki, Finland
    Nucleic Acids Res 34:e124. 2006
  5. pmc PairsDB atlas of protein sequence space
    Andreas Heger
    MRC Functional Genetics Unit, University of Oxford, UK
    Nucleic Acids Res 36:D276-80. 2008
  6. pmc GOParGenPy: a high throughput method to generate gene ontology data matrices
    Ajay Anand Kumar
    Institute of Biotechnology, University of Helsinki, PO Box 56, Viikinkaari 5, Helsinki 00014, Finland
    BMC Bioinformatics 14:242. 2013
  7. pmc BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    BMC Bioinformatics 13:33. 2012
  8. pmc 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
  9. pmc 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
  10. pmc 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

Collaborators

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

Detail Information

Publications17

  1. pmc SANS: high-throughput retrieval of protein sequences allowing 50% mismatches
    J Patrik Koskinen
    Department of Biosciences, Division of Genetics University of Helsinki, 00014 Helsinki, Finland
    Bioinformatics 28:i438-i443. 2012
    ..Sequence similarity searching followed by k-nearest neighbor classification is the most widely used tool to predict the function or structure of anonymous gene products that come out of genome sequencing projects...
  2. pmc POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, PO Box 56 Viikinkaari 5, FIN 00014, Helsinki, Finland
    Nucleic Acids Res 33:W427-31. 2005
    ..The program is freely available at http://ekhidna.biocenter.helsinki.fi/poco...
  3. pmc POXO: a web-enabled tool series to discover transcription factor binding sites
    Matti Kankainen
    Institute of Biotechnology, University of Helsinki, PO Box 56 Viikinkaari 5, FIN 00014 Helsinki, Finland
    Nucleic Acids Res 34:W534-40. 2006
    ..The performance of POXO is demonstrated by analysing expression data from pathogen treated Arabidopsis thaliana. In this example, POXO detected activated gene sets and suggested transcription factors responsible for their regulation...
  4. pmc Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana
    Matti Kankainen
    Institute of Biotechnology, PO Box 56 Viikinkaari 5, FIN 00014, Helsinki, Finland
    Nucleic Acids Res 34:e124. 2006
    ..Thus, in comparison to analyses of manually selected gene lists, the systematic analysis of every cluster can reveal unexpected biological phenomena and produce much more comprehensive biological insights to the experiment of interest...
  5. pmc PairsDB atlas of protein sequence space
    Andreas Heger
    MRC Functional Genetics Unit, University of Oxford, UK
    Nucleic Acids Res 36:D276-80. 2008
    ..Moreover, query-anchored stacked sequence alignments, profiles and consensus sequences are useful in studies of sequence conservation patterns for clues about possible functional sites...
  6. pmc GOParGenPy: a high throughput method to generate gene ontology data matrices
    Ajay Anand Kumar
    Institute of Biotechnology, University of Helsinki, PO Box 56, Viikinkaari 5, Helsinki 00014, Finland
    BMC Bioinformatics 14:242. 2013
    ..The structure of GO is dynamic and is updated on a daily basis. However, the popular existing methods use outdated versions of GO. Moreover, these tools are slow to process large datasets consisting of more than 20,000 genes...
  7. pmc 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...
  8. pmc 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...
  9. pmc 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...
  10. pmc 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?..
  11. pmc 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...
  12. pmc 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
    ....
  13. pmc 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...
  14. pmc 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...
  15. pmc 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...
  16. pmc 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
    ..The Red Queen said, 'It takes all the running you can do, to keep in the same place.' Lewis Carrol..
  17. ncbi request reprint 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...