Lars Snipen

Summary

Affiliation: Norwegian University of Life Sciences
Country: Norway

Publications

  1. pmc Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli
    Lars Snipen
    Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
    Microb Inform Exp 2:8. 2012
  2. pmc Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands
    Jon Bohlin
    Norwegian School of Veterinary Science, Epicentre, Department of Food Safety and Infection Biology, Ullevålsveien 72, Oslo, Norway
    BMC Genomics 13:66. 2012
  3. pmc Comparative genomic analysis reveals significant enrichment of mobile genetic elements and genes encoding surface structure-proteins in hospital-associated clonal complex 2 Enterococcus faecalis
    Margrete Solheim
    Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, N 1432 As, Norway
    BMC Microbiol 11:3. 2011
  4. pmc Analysis of intra-genomic GC content homogeneity within prokaryotes
    Jon Bohlin
    Norwegian School of Veterinary Science, Department of Food Safety and Infection Biology, Ullevålsveien 72, P, O, Box 8146 Dep, NO 0033 Oslo, Norway
    BMC Genomics 11:464. 2010
  5. pmc Comparative genomics of Enterococcus faecalis from healthy Norwegian infants
    Margrete Solheim
    Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, As, Norway
    BMC Genomics 10:194. 2009
  6. pmc Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods
    Jon Bohlin
    Norwegian School of Veterinary Science, Department of Food Safety and Infection Biology, EpiCenter, Ullevålsveien 72, PO Box 8146 Dep, NO 0033 Oslo, Norway
    BMC Evol Biol 10:249. 2010
  7. pmc Detection of divergent genes in microbial aCGH experiments
    Lars Snipen
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, N 1432 As, Norway
    BMC Bioinformatics 7:181. 2006
  8. pmc Microbial comparative pan-genomics using binomial mixture models
    Lars Snipen
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
    BMC Genomics 10:385. 2009
  9. pmc Improved analysis of bacterial CGH data beyond the log-ratio paradigm
    Lars Snipen
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
    BMC Bioinformatics 10:91. 2009
  10. ncbi request reprint Mixture models as a method to find present and divergent genes in comparative genomic hybridization studies on bacteria
    Guri Feten
    Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P O Box 5003, N 1432 As, Norway
    Biom J 49:242-58. 2007

Detail Information

Publications30

  1. pmc Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli
    Lars Snipen
    Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
    Microb Inform Exp 2:8. 2012
    ..abstract:..
  2. pmc Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands
    Jon Bohlin
    Norwegian School of Veterinary Science, Epicentre, Department of Food Safety and Infection Biology, Ullevålsveien 72, Oslo, Norway
    BMC Genomics 13:66. 2012
    ..We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure...
  3. pmc Comparative genomic analysis reveals significant enrichment of mobile genetic elements and genes encoding surface structure-proteins in hospital-associated clonal complex 2 Enterococcus faecalis
    Margrete Solheim
    Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, N 1432 As, Norway
    BMC Microbiol 11:3. 2011
    ..Population structure studies by multilocus sequence typing have defined distinct clonal complexes (CC) of E. faecalis enriched in hospitalized patients (CC2, CC9, CC28 and CC40)...
  4. pmc Analysis of intra-genomic GC content homogeneity within prokaryotes
    Jon Bohlin
    Norwegian School of Veterinary Science, Department of Food Safety and Infection Biology, Ullevålsveien 72, P, O, Box 8146 Dep, NO 0033 Oslo, Norway
    BMC Genomics 11:464. 2010
    ..We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content of the total genome. A low GCVAR indicates intra-genomic GC homogeneity and high GCVAR heterogeneity...
  5. pmc Comparative genomics of Enterococcus faecalis from healthy Norwegian infants
    Margrete Solheim
    Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, As, Norway
    BMC Genomics 10:194. 2009
    ..In an attempt to gain insight into the genetic make-up of commensal E. faecalis, we have studied genomic variation in a collection of community-derived E. faecalis isolated from the feces of Norwegian infants...
  6. pmc Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods
    Jon Bohlin
    Norwegian School of Veterinary Science, Department of Food Safety and Infection Biology, EpiCenter, Ullevålsveien 72, PO Box 8146 Dep, NO 0033 Oslo, Norway
    BMC Evol Biol 10:249. 2010
    ....
  7. pmc Detection of divergent genes in microbial aCGH experiments
    Lars Snipen
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, N 1432 As, Norway
    BMC Bioinformatics 7:181. 2006
    ..As experimental settings vary considerably, it is not possible to develop a classical discriminant or statistical learning approach...
  8. pmc Microbial comparative pan-genomics using binomial mixture models
    Lars Snipen
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
    BMC Genomics 10:385. 2009
    ..Attempts to estimate these quantities have been made, using regression methods or mixture models. We extend the latter approach by using statistical ideas developed for capture-recapture problems in ecology and epidemiology...
  9. pmc Improved analysis of bacterial CGH data beyond the log-ratio paradigm
    Lars Snipen
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
    BMC Bioinformatics 10:91. 2009
    ..We propose an alternative approach, where microarray signals are used in a different way and sequence identity is predicted using a supervised learning approach...
  10. ncbi request reprint Mixture models as a method to find present and divergent genes in comparative genomic hybridization studies on bacteria
    Guri Feten
    Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P O Box 5003, N 1432 As, Norway
    Biom J 49:242-58. 2007
    ..Some summaries of the data sets are proposed as a guide for the choice of model and the choice of number of components. The models are applied on data from CGH experiments with the bacteria Staphylococcus aureus and..
  11. pmc Comparative genomic analysis of pathogenic and probiotic Enterococcus faecalis isolates, and their transcriptional responses to growth in human urine
    Heidi C Vebø
    Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, As, Norway
    PLoS ONE 5:e12489. 2010
    ..faecalis strain may to a great extent be determined by presence of fitness and virulence factors, rather than the level of expression of such traits...
  12. pmc The transcriptome of the nosocomial pathogen Enterococcus faecalis V583 reveals adaptive responses to growth in blood
    Heidi C Vebø
    Laboratory of Microbial Gene Technology and Food Microbiology, Biotechnology and Food Science, The Norwegian University of Life Sciences, As, Norway
    PLoS ONE 4:e7660. 2009
    ..faecalis have been established. However, the process in which E. faecalis gains access to the bloodstream and establishes a persistent infection is not well understood...
  13. pmc Transcriptional responses of Enterococcus faecalis V583 to bovine bile and sodium dodecyl sulfate
    Margrete Solheim
    Laboratory of Microbial Gene Technology and Food Microbiology, The Norwegian University of Life Sciences, PO Box 5003, N 1432 As, Norway
    Appl Environ Microbiol 73:5767-74. 2007
    ..The overall results presented here indicate that different mechanisms are involved in detergent resistance in E. faecalis...
  14. doi request reprint Comparative genomics of Lactobacillus sakei with emphasis on strains from meat
    O Ludvig Nyquist
    Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P O Box 5003, 1432 As, Norway
    Mol Genet Genomics 285:297-311. 2011
    ..We have demonstrated a highly conserved organization of the L. sakei genomes investigated, and the 23K strain is a suitable model organism to study core features of the L. sakei species...
  15. pmc Improving stability and understandability of genotype-phenotype mapping in Saccharomyces using regularized variable selection in L-PLS regression
    Tahir Mehmood
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
    BMC Bioinformatics 13:327. 2012
    ..Results were compared to PLS-based procedures, where no background information was used...
  16. pmc Exploration of multivariate analysis in microbial coding sequence modeling
    Tahir Mehmood
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
    BMC Bioinformatics 13:97. 2012
    ..Comparisons between the methods were performed on DNA, codon and protein sequences with highly conserved genes taken from several species with different genomic properties...
  17. doi request reprint Microarray-based transcriptome of Listeria monocytogenes adapted to sublethal concentrations of acetic acid, lactic acid, and hydrochloric acid
    Girum Tadesse Tessema
    Nofima Norwegian Institute of Food, Fisheries and Aquaculture Research, As, Norway
    Can J Microbiol 58:1112-23. 2012
    ..The present study revealed the complex transcriptional responses of L. monocytogenes towards food-related acidulants and opens the roadmap for more specific and in-depth future studies...
  18. doi request reprint Target recognition, resistance, immunity and genome mining of class II bacteriocins from Gram-positive bacteria
    Morten Kjos
    Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, As, Norway
    Microbiology 157:3256-67. 2011
    ..We also discuss some examples of how the current wealth of genome sequences provides an invaluable source in the search for novel class II bacteriocins...
  19. ncbi request reprint Regression as a method to predict copy numbers in comparative genomic hybridization studies on bacteria
    Guri Feten
    Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P O Box 5003, N 1432 As, Norway
    Biom J 48:255-70. 2006
    ..The predictors were applied on CGH data obtained from experiments with Enterococcus faecalis strains in order to determine copy number of relevant genes in five different strains...
  20. pmc Survey of genomic diversity among Enterococcus faecalis strains by microarray-based comparative genomic hybridization
    Agot Aakra
    Laboratory of Microbial Gene Technology, Department of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, P O Box 5003, N 1432 As, Norway
    Appl Environ Microbiol 73:2207-17. 2007
    ..The contents of genes related to stress tolerance appeared similar in V583 and the nine test strains, supporting the view of E. faecalis as an organism able to resist harsh conditions...
  21. pmc Growth rate-dependent control in Enterococcus faecalis: effects on the transcriptome and proteome, and strong regulation of lactate dehydrogenase
    Ibrahim Mehmeti
    Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Science, As, Norway
    Appl Environ Microbiol 78:170-6. 2012
    ..e., 0.15 h⁻¹). For many gene products, a discrepancy between transcriptomic and proteomic data were seen, indicating posttranscriptional regulation of expression...
  22. pmc Global transcriptome response in Lactobacillus sakei during growth on ribose
    Anette McLeod
    Nofima Mat AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, As, NO 1430, Norway
    BMC Microbiol 11:145. 2011
    ..We used a whole-genome microarray based on the genome sequence of L. sakei strain 23K to investigate the global transcriptome response of three L. sakei strains when grown on ribose compared with glucose...
  23. pmc Transcriptional response of Enterococcus faecalis V583 to erythromycin
    Agot Aakra
    Laboratory of Microbial Gene Technology, Norwegian University of Life Sciences, P O Box 5003, N 1432 As, Norway
    Antimicrob Agents Chemother 49:2246-59. 2005
    ..Other specific genes that were found to be up-regulated were genes encoding ABC transporters and two-component regulatory systems, and these may be genes that are important for the specific response of V583 to erythromycin...
  24. ncbi request reprint Rotation testing in gene set enrichment analysis for small direct comparison experiments
    Guro Dørum
    Norwegian University of Life Sciences
    Stat Appl Genet Mol Biol 8:Article34. 2009
    ..The rotation test is a generalisation of the permutation test, and can in addition be used on indirect comparison data and for testing significance of other types of test statistics outside the GSEA framework...
  25. pmc A Partial Least Squares based algorithm for parsimonious variable selection
    Tahir Mehmood
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Norway
    Algorithms Mol Biol 6:27. 2011
    ..abstract:..
  26. pmc The Response of Enterococcus faecalis V583 to Chloramphenicol Treatment
    Agot Aakra
    Department of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, P O Box 5003, 1432 As, Norway
    Int J Microbiol 2010:483048. 2010
    ..Among the upregulated genes were EF1732 and EF1733, which code for potential chloramphenicol transporters. Efflux of drug out of the cells may be one mechanism used by V583 to overcome the effect of chloramphenicol...
  27. pmc Global transcriptional analysis of spontaneous sakacin P-resistant mutant strains of Listeria monocytogenes during growth on different sugars
    Girum Tadesse Tessema
    Nofima Mat AS, As, Norway
    PLoS ONE 6:e16192. 2011
    ..Taken together, the present study showed that a single time exposure to the class IIa bacteriocin sakacin P may elicit contrasting phenotypic and transcriptome responses in L. monocytogenes possibly through regulation of the mpt...
  28. pmc The abi proteins and their involvement in bacteriocin self-immunity
    Morten Kjos
    Laboratory of Microbial Gene Technology and Food Microbiology, Norwegian University of Life Sciences, P O Box 5003, N 1432 As, Norway
    J Bacteriol 192:2068-76. 2010
    ....
  29. pmc Mining for genotype-phenotype relations in Saccharomyces using partial least squares
    Tahir Mehmood
    Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Norway
    BMC Bioinformatics 12:318. 2011
    ..We introduce a methodology based on a BLAST approach for extracting information from genomic sequences and Soft- Thresholding Partial Least Squares (ST-PLS) for mapping genotype-phenotype relations...