Dr. Jon K. Lærdahl

Dr. Scient., University of Oslo,
Siv. Ing. NTH, Trondheim, Norway

Jon K. Laerdahl Address:
The Bioinformatics Group
Centre for Molecular Biology and Neuroscience (CMBN)
Department of Medical Microbiology
Oslo University Hospital - Rikshospitalet
PO Box 4950 Nydalen, NO-0424 Oslo, NORWAY
Phone: +47 22 84 47 84         Fax: +47 22 84 47 82
mail-address

Fields of interest:

     Structural and applied bioinformatics
     Protein modeling and structural biology
     Molecular modeling
     Theoretical Chemistry
     Ab initio quantum chemical methods
     Physical organic chemistry
     Relativistic and parity violating effects in chemistry

ballResearch Interests
ballPublications
ballPersonal stuff

Research interests

Bioinformatics: I am working as a research scientist within the field of structural and applied bioinformatics in the bioinformatics group at the Centre for Molecular Biology and Neuroscience at Rikshospitalet/Oslo University Hospital. I am actively collaborating with a number of groups at the hospital and at the University of Oslo on projects involving topics as diverse as DNA repair and genome maintenance, low density lipoprotein homeostasis, amino acid transporters, and G-protein coupled receptors. Lately, I have each year given several courses in computational biology and structural bioinformatics at the University of Oslo.

Since the spring 2011 I have also been employed by the Oslo University Hospital and University of Oslo Bioinformatics Core Facility.

Prior to May 2004, I was working for the Norwegian Salmon Genome Project (SGP) in the bioinformatics group at the Biotechnology Center of the University of Oslo where we developed a sequence processing pipeline and database for salmon sequence data. I was also working in the group for scientific computing at the University of Oslo Computer Center.

Theoretical Chemistry: I did my Ph.D. at the University of Oslo supervised by Professor Knut Fægri jr. and a postdoc at the University of Auckland, New Zealand, in the group of Professor Peter Schwerdtfeger (now at Massey University) within the fields of quantum chemistry and theoretical molecular physics. Particularly I worked on relativistic effects in chemistry and the influence of weak interactions giving rise to parity-odd effects (P-odd and P- and T-odd). I am one of the authors of the Dirac quantum chemistry package . This is a fully relativistic program code that has been used in a number of relativistic 4-component studies of chemical properties.

I also did a postdoc at the University of Oslo in the group of Professor Einar Uggerud, within the field of gas phase ion chemistry and processes. In particular I worked on nucleophilic substitution reactions studied by high level ab initio methods.

Selected publications

Bioinformatics and molecular biology

  1. P. H. Backe, R. Simm, J. K. Laerdahl, B. Dalhus, A. Fagerlund, O. A. Økstad, T. Rognes, I. Alseth, A.-B. Kolstø, and M. Bjørås, "A new family of proteins related to the HEAT-like repeat DNA glycosylases with affinity for branched DNA structures", J. Struct. Biol. (in press).
  2. K. Søberg, T. Jahnsen, T. Rognes, B. S. Skålhegg, and J. K. Laerdahl, "Evolutionary paths of the cAMP-dependent protein kinase (PKA) catalytic subunits", PLoS ONE 8, e60935 (2013).
  3. C. Fladeby, E. S. Vik, J. K. Laerdahl, C. Gran Neurauter, J. E. Heggelund, E. Thorgaard, P. Strøm-Andersen, M. Bjørås, B. Dalhus, and I. Alseth, "The human homolog of Escherichia coli endonuclease V is a nucleolar protein with affinity for branched DNA structures", PLoS ONE 7, e47466 (2012).
  4. D. Ellinghaus, T. Folseraas, K. Holm, E. Ellinghaus, E. Melum, T. Balschun, J. K. Laerdahl, A. Shiryaev, et al., "Genome-wide association analysis in sclerosing cholangitis and ulcerative colitis identifies risk loci at GPR35 and TCF4", Hepatology (in press).
  5. E. D. Zegeye, S. V. Balasingham, J. K. Laerdahl, H. Homberset, and T. Tønjum, "Mycobacterium tuberculosis RecG binds and unwinds model DNA substrates with a preference for Holliday Junctions", Microbiology 158, 1982 (2012).
  6. S. V. Balasingham, E. D. Zegeye, H. Homberset, M. L. Rossi, J. K. Laerdahl, V. A. Bohr, and T. Tønjum, "Enzymatic activities and DNA substrate specificity of Mycobacterium tuberculosis DNA helicase XPB", PLoS One 7: e36960 (2012).
  7. T. Folseraas, E. Melum, P. Rausch, B. D. Juran, E. Ellinghaus, A. Shiryaev, J. K. Laerdahl, D. Ellinghaus, et al., "Extended analysis of a genome-wide association study in primary sclerosing cholangitis detects multiple novel risk loci", J. Hepatol. 57, 366 (2012).
  8. K. Søberg, A. C. V. Larsen, M. Diskar, P. H. Backe, M Bjørås, T. Jahnsen, J. K. Laerdahl, T. Rognes, F. W. Herberg, and B. S. Skålhegg, "Identification and characterization of novel mutations in the human gene encoding the catalytic subunit Calpha of Protein Kinase A (PKA)", PLoS One 7: e34838 (2012).
  9. H. Korvald, P. Ø. Falnes, J. K. Laerdahl, M. Bjørås, and I. Alseth, "The Schizosaccharomyces pombe AlkB homolog Abh1 exhibits AP lyase activity but no demethylase activity", DNA Repair 11, 453 (2012).
  10. K. Tveten, Ø. L. Holla, J. Cameron, T. B. Strøm, K. E. Berge, J. K. Laerdahl, and T. P. Leren, "Interaction between the ligand-binding domain of the LDL receptor and the C-terminal domain of PCSK9 is required for PCSK9 to remain bound to the LDL receptor during endosomal acidification", Hum. Mol. Genet. 21, 1402 (2012).
  11. H. Korvald, A. M. Mølstad Moe, F. H. Cederkvist, B. Thiede, J. K. Laerdahl, M. Bjørås, and I. Alseth, "Schizosaccharomyces pombe Ofd2 is a nuclear 2-oxoglutarate and iron dependent dioxygenase interacting with histones", PLoS One 6: e25188 (2011).
  12. Ø. L. Holla, J. Cameron, K. Tveten, T. B. Strøm, K. E. Berge, J. K. Laerdahl, and T. P. Leren, "Role of the C-terminal domain of PCSK9 in degradation of the LDL receptors", J. Lipid Res. 52, 1787 (2011).
  13. Ø. L. Holla, J. K. Laerdahl, T. B. Strøm, K. Tveten, J. Cameron, K. E. Berge, and T. P. Leren, "Removal of acidic residues of the prodomain of PCSK9 increases its activity towards the LDL receptor", Biochem. Biophys. Res. Commun. 406, 234 (2011).
  14. J. K. Laerdahl, H. Korvald, L. Nilsen, K. Dahl-Michelsen, T. Rognes, M. Bjørås, and I. Alseth, "Schizosaccharomyces pombe encodes a mutated AP endonuclease 1", DNA Repair 10, 296 (2011).
  15. E. Melum, A. Franke, C. Schramm, T. J.Weismüller, D. N. Gotthardt, F. A. Offner, B. D. Juran, J. K. Laerdahl, et al., "Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci", Nat. Genet. 43, 17 (2011).
  16. J. R. Hov, V. Keitel, J. K. Laerdahl, L. Spomer, E. Ellinghaus, A. ElSharawy, E. Melum, K. M. Boberg, et al., "Mutational characterization of the bile acid receptor TGR5 in primary sclerosing cholangitis", PLoS One 5: e12403 (2010).
  17. M. S. Nordlund, D. J. Warren, J. K. Laerdahl, and E. Paus, "Studies on multiple forms of proGRP in serum from small cell lung cancer patients", Tumor Biol. 30, 265 (2009).
  18. B. Dalhus, J. K. Laerdahl, P. H. Backe, and M. Bjørås, "DNA base repair - recognition and initiation of catalysis", FEMS Microbiol. Rev. 33, 1044 (2009).
  19. S. Z. Krokeide, N. Bolstad, J. K. Laerdahl, M. Bjørås, and Luisa Luna, "Expression and purification of NEIL3, a human DNA glycosylase homolog", Protein Expr. Purif. 65, 160 (2009).
  20. J. Cameron, Ø. L. Holla, J. K. Laerdahl, M. A. Kulseth, K. E. Berge, and T. P. Leren, "Mutation S462P in the PCSK9 gene reduces secretion of mutant PCSK9 without affecting the autocatalytic cleavage", Atherosclerosis 203, 161 (2009).
  21. J. Cameron, Ø. L. Holla, K. E. Berge, M. A. Kulseth, T. Ranheim, T. P. Leren, and J. K. Laerdahl, "Investigations on the evolutionary conservation of PCSK9 reveal a functionally important protrusion", FEBS J. 275, 4121 (2008).
  22. E. Larsen, L. Kleppa, T. J. Meza, L. A. Meza-Zepeda, C. Rada, C. G. Castellanos, G. F. Lien, G. J. Nesse, M. S. Neuberger, J. K. Laerdahl, R. W. Doughty,
    and A. Klungland, "Early-onset lymphoma and extensive embryonic apoptosis in two domain-specific Fen1 mice mutants", Cancer Res. 68, 4571 (2008).
  23. J. Cameron, Ø. L. Holla, J. K. Laerdahl, M. A. Kulseth, T. Ranheim, T. Rognes,
    K. E. Berge, and T. P. Leren, "Characterization of novel mutations in the catalytic domain of the PCSK9 gene", J. Intern. Med. 263, 420 (2008).
  24. B. Dalhus, I. Høydal Helle, P. H. Backe, I. Alseth, T. Rognes, M. Bjørås, and
    J. K. Laerdahl, "Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats",
    Nucleic Acids Res. 35, 2451 (2007). [pdf] [Suppl. movies 1 and 2]
  25. A. Klungland, J. K. Laerdahl, and T. Rognes, "OGG1: from structural analysis to the knockout mouse", in "Oxidative Damage to Nucleic Acids", Eds. M. D. Evans and M. S. Cooke, Landes Bioscience (2007).
  26. A. A. Adzhubei, A. V. Vlasova, H. Hagen-Larsen, T. A. Ruden, J. K. Laerdahl, and B. Høyheim, "Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource", BMC Genomics 8, 209 (2007).
  27. B. Hayes, J. K. Laerdahl, S. Lien, T. Moen, P. Berg, K. Hindar, W. S. Davidson,
    B. F. Koop, A. Adzhubei, and B. Høyheim, "An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences", Aquaculture 265, 82 (2007).
  28. H. Hagen-Larsen, J. K. Laerdahl, F. Panitz, A. Adzhubei, and B. Høyheim, "An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar)", BMC Genomics 6, 171 (2005).
  29. A. A. Adzhubei, J. K. Laerdahl, and A. V. Vlasova, "preAssemble: a tool for automatic sequencer trace data processing", BMC Bioinformatics 7, 22 (2006).
  30. P. E. Sæbø, S. M. Andersen, J. Myrseth, J. K. Laerdahl, and T. Rognes, "PARALIGN: rapid and sensitive sequencing similarity searches powered by parallel computing technology", Nucleic Acids Res. 33, W535 (2005).

Physical Organic Chemistry

  1. J. K. Laerdahl, P. U. Civcir, L. Bache-Andreassen, and E. Uggerud, "Nucleophilic identity substitution reactions. The reaction between hydrogen fluoride and protonated alkyl fluorides", Org. Biomol. Chem. 4, 135 (2006).
  2. J. K. Laerdahl and E. Uggerud, "Nucleophilic identity substitution reactions. The reaction between water and protonated alcohols", Org. Biomol. Chem. 1, 2935 (2003).
  3. J. K. Laerdahl, L. Bache-Andreassen, and E. Uggerud, "Nucleophilic identity substitution reactions. The reaction between ammonia and protonated amines", Org. Biomol. Chem. 1, 2943 (2003).
  4. J. K. Laerdahl and E. Uggerud, "Gas phase nucleophilic substitution", Int. J. Mass. Spectrom. 214, 277 (2002).

Molecular physics and theoretical chemistry

  1. P. Schwerdtfeger, A. Kuhn, R. Bast, J, K. Laerdahl, F. Faglioni, and P. Lazzeretti, "The vibrational spectrum of camphor from ab initio and density functional theory and parity violation in the C-C*-CO bending mode", Chem. Phys. Lett. 383, 496 (2004).
  2. H. Heiberg, O. Gropen, J, K. Laerdahl, O. Swang, and U. Wahlgren, "The performance of density functional theory for LnF (Ln = Nd, Eu, Gd, Yb) and YbH", Theor. Chem. Acc. 110, 118 (2003).
  3. R. Wesendrup, J. K. Laerdahl, B. Compton, and P. Schwerdtfeger, "Biomolecular homochirality and electroweak interactions. I. The Yamagata hypthesis", J. Phys. Chem. A107, 6668 (2003).
  4. P. Schwerdtfeger, J. K. Laerdahl, and Ch. Chardonnet, "Calculation of parity-violation effects for the C-F stretching mode of chiral methyl fluorides", Phys. Rev. A 65, 042508 (2002).
  5. I. S. Lim, J. K. Laerdahl, and P. Schwerdtfeger, "Fully relativistic coupled-cluster static dipole polarizabilities of the positively charged alkali atoms from Li+ to 119+", J. Chem. Phys. 116, 172 (2001).
  6. P. Schwerdtfeger, T. Söhnel, M. Pernpointner, J. K. Laerdahl, and F. E. Wagner, "Comparison of ab initio and density functional calculations of electric fieøld gradients: The 57Fe nuclear quadropole moment from Mossbauer data", J. Chem. Phys. 115, 5913 (2001).
  7. J. K. Laerdahl, P. Schwerdtfeger, and H. M. Quiney, "Theoretical analysis of parity-violating energy differences between the enantiomers of chiral molecules", Phys. Rev. Lett. 84, 3811 (2000).
  8. J. K. Laerdahl, R. Wesendrup, and P. Schwerdtfeger, "D- or L-alanine: That is the question", ChemPhysChem 1, 60 (2000).
  9. A. S. Lahamer, S. M. Mahurin, R. N. Compton, D. House, J. K. Laerdahl, M. Lein, and P. Schwerdtfeger, "Search for a parity-violating energy difference between enantiomers of a chiral iron complex", Phys. Rev. Lett. 85, 4470 (2000).
  10. P. Schwerdtfeger, J. R. Brown, J. K. Laerdahl, and H. Stoll, "The accuracy of the pseudopotential approximation. III. A comparison between pseudopotential and all-electron methods for Au and AuH", J. Chem. Phys. 113, 7110 (2000).
  11. J. Thyssen, J. K. Laerdahl, and P. Schwerdtfeger, "Fully relativistic coupled cluster treatment for parity-violating energy differences in molecules", Phys. Rev. Lett. 85, 3105 (2000).
  12. I. S. Lim, J. K. Laerdahl, and P. Schwerdtfeger,"The static electric dipole polarizability of Rb+", J. Phys. B 33, L91 (2000).
  13. J. K. Laerdahl and P. Schwerdtfeger, "Fully relativistic ab initio calculations of the energies of chiral molecules including parity-violating weak interactions", Phys. Rev. A 60, 4439 (1999).
  14. I. S. Lim, M. Pernpointner, M. Seth, J. K. Laerdahl, P. Schwerdtfeger, P. Neogrady, and M. Urban, "Relativistic coupled-cluster static dipole polarizabilities of the alkali metals from Li to element 119", Phys. Rev. A 60, 2822 (1999).
  15. P. Schwerdtfeger, M. Pernpointner, and J. K. Laerdahl, "The accuracy of current density functionals for the calculation of electric field gradients: A comparison with ab initio methods for HCl and CuCl", J. Chem. Phys. 111, 3357 (1999).
  16. R. Wesendrup, J. K. Laerdahl, and P. Schwerdtfeger,"Relativistic effects in gold chemistry. VI. Coupled cluster calculations for the isoelectronic series AuPt-, Au2, and AuHg+", J. Chem. Phys. 110, 9457 (1999).
  17. J. K. Laerdahl, K. Fægri jr, L. Visscher, and T. Saue, "A fully relativistic Dirac-Hartree-Fock and MP2 study of the lanthanide and actinide contraction", J. Chem. Phys. 109, 10806 (1998).
  18. H. M. Quiney, J. K. Laerdahl, K. Fægri jr, and T. Saue, "Ab initio Dirac-Hartree-Fock calculations of chemical properties and PT-odd effects in thallium fluoride", Phys. Rev. A 57, 920 (1998).
  19. J. K. Laerdahl, K. Fægri jr, C. Rømming, O. Swang, K. Schöffel, and T. Midtgård, "Substituent crowding in nitrobenzenes", J. Mol. Struct. 445, 89 (1998).
  20. J. K. Laerdahl, T. Saue, K. Fægri jr, and H. M. Quiney, " Ab initio study of PT-odd interactions in thallium fluoride", Phys. Rev. Lett. 79, 1642 (1997).
  21. J. K. Laerdahl, T. Saue, and K. Fægri jr, "Direct relativistic MP2: Properties of ground state CuF, AgF and AuF", Theor. Chem. Acc. 97, 177 (1997).

Additional:

  1. J. K. Laerdahl, "Development and applications of relativistic quantum chemical methods", Ph.D. thesis, University of Oslo (1997).
  2. J. K. Laerdahl, "Contrast agents for medical imaging diagnostics by magnetic resonance (MRI) (Polyamines for complexation of paramagnetic ions, testing of different sythestic methods)", Diploma thesis, Norwegian Institute of Technology (1992).
  3. "Dirac, a relativistic ab initio electronic structure program, Release 3.2 (2000)", written by T. Saue, V. Bakken, T. Enevoldsen, T. Helgaker, H. J. Aa. Jensen, J. K. Laerdahl, K. Ruud, J. Thyssen, and L. Visscher (Dirac Program Wiki).

Protein structure visualization and modeling

A simple example of protein structure visualization for a DNA repair enzyme.

Some personal stuff

A panorama from Bjørgovarden, Nord-Aurdal, Norway.

Last modified: April 18, 2013