Dr. Scient., University of Oslo,
Siv. Ing. NTH, Trondheim, Norway
The Bioinformatics Group
Department of Microbiology
Oslo University Hospital - Rikshospitalet
PO Box 4950 Nydalen, NO-0424 Oslo, NORWAY
Phone: +47 22 84 47 84
Fields of interest:
Structural and applied bioinformatics
Protein modeling and structural biology
Bioinformatics and Computational Life Science teaching
Ab initio quantum chemical methods
Physical organic chemistry
Relativistic and parity violating effects in chemistry
Bioinformatics: I am working as a research scientist within the field of
structural and applied bioinformatics in the
bioinformatics group at the Department of Microbiology,
Rikshospitalet - Oslo University Hospital. Our group
was one of eleven research groups at the Centre for Molecular Biology
and Neuroscience until December 2012. 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. I am bioinformatics teaching coordinator
at the University of Oslo Computational Life Science initiative,
July 2013 and responsible for the course
Bioinformatics for Molecular Biology.
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
quantum chemistry package . This is a fully relativistic program code
that has been used in a number of relativistic 4-component studies of chemical
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.
Bioinformatics and molecular biology
- M. Alexeeva, P. Guragain, A. N. Tesfahun, M. Tomkuviene, A. Arshad,
R. Gerasimaite, A. Ruksenaite, G. Urbanaviciute, M. Bjørås,
J. K. Laerdahl, A. Klungland, S. Klimasauskas, and S. Bjelland,
"Excision of the doubly methylated base N4,5-dimethylcytosine
from DNA by Escherichia coli Nei and Fpg proteins",
Phil. Trans. R. Soc. Lond. B 373, 20170337 (2018).
- K. Søberg, L. V. Moen, B. S. Skålhegg,
and J. K. Laerdahl, "Evolution of the cAMP-dependent protein kinase (PKA)
catalytic subunit isoforms",
PLoS ONE 12, e0181091 (2017).
- T. B. Strøm, J. K. Laerdahl, and T. P. Leren,
"Mutations affecting the transmembrane domain of the LDL receptor:
impact of charged residues on the membrane insertion",
Hum. Mol. Genet. 26, 1634 (2017).
- M. N. Moen, R. Fjær, E. H. Hamdani, J. K. Laerdahl, R. J. Menchini,
M. D. Vigeland, Y. Sheng, D. Undlien, B. Hassel, M. A. Salih, H. Y. El Khashab,
K. K. Selmer, and F. A. Chaudhry,
"Pathogenic variants in KCTD7 perturb neuronal K+ fluxes and glutamine
Brain 139, 3109 (2016).
- T. B. Strøm, J. K. Laerdahl, and T. P. Leren,
"Mutation p.L799R in the LDLR, which affects the transmembrane domain of the LDLR,
prevents membrane insertion and causes secretion of the mutant LDLR",
Hum. Mol. Genet. 24, 5836 (2015).
- S. Zeissig, B.-S. Petersen, M. Tomczak, E. Melum, E. Huc-Claustre, S. K. Dougan,
J. K. Laerdahl, B. Stade, M. Forster, S. Schreiber, D. Weir, A. M. Leichtner,
A. Franke, and R. S. Blumberg, "Early-onset Crohn's disease and autoimmunity
associated with a variant in CTLA-4",
Gut 64, 1889 (2015).
- T. B. Strøm, K. Tveten, J. K. Laerdahl, and T. P. Leren,
"Mutation G805R in the transmembrane domain of the LDL receptor gene causes
familial hypercholesterolemia by inducing ectodomain cleavage of the LDL
receptor in the endoplasmic reticulum",
FEBS Open Bio. 4, 321 (2014).
- E. D. Zegeye, S. V. Balasingham, J. K. Laerdahl, H. Homberset,
P. E. Kristiansen, and T. Tønjum, "Effects of conserved residues
and naturally occurring mutations on Mycobacterium tuberculosis
RecG helicase activity",
Microbiology 160, 217 (2014).
- S. Z. Krokeide, J. K. Laerdahl, M. Salah, L. Luna, F. H. Cederkvist,
A. M. Fleming, C. J Burrows, B. Dalhus, and M. Bjørås,
"Human NEIL3 is mainly a monofunctional DNA glycosylase removing
spiroiminodihydantoin and guanidinohydantoin",
DNA Repair 12, 1159 (2013).
- 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. 183, 66 (2013).
- K. Søberg, T. Jahnsen, T. Rognes, B. S. Skålhegg,
and J. K. Laerdahl, "Evolutionary paths of the cAMP-dependent protein kinase (PKA)
PLoS ONE 8, e60935 (2013).
- 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
PLoS ONE 7, e47466 (2012).
- 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 58, 1074 (2013).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
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).
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).
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).
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).
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).
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).
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).
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).
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
Nucleic Acids Res. 35, 2451 (2007).
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).
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).
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).
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).
A. A. Adzhubei, J. K. Laerdahl, and A. V. Vlasova,
"preAssemble: a tool for automatic sequencer trace data processing",
BMC Bioinformatics 7, 22 (2006).
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
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).
J. K. Laerdahl and E. Uggerud, "Nucleophilic identity substitution
reactions. The reaction between water and protonated alcohols",
Org. Biomol. Chem. 1, 2935 (2003).
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).
J. K. Laerdahl and E. Uggerud, "Gas phase nucleophilic substitution",
Int. J. Mass. Spectrom. 214, 277 (2002).
Molecular physics and theoretical chemistry
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).
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).
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).
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).
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).
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).
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).
J. K. Laerdahl, R. Wesendrup, and P. Schwerdtfeger, "D- or L-alanine:
That is the question", ChemPhysChem 1, 60 (2000).
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,
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,
J. Thyssen, J. K. Laerdahl, and P. Schwerdtfeger, "Fully relativistic
coupled cluster treatment for parity-violating energy differences in molecules",
Rev. Lett. 85, 3105 (2000).
I. S. Lim, J. K. Laerdahl, and P. Schwerdtfeger,"The static electric
dipole polarizability of Rb+", J. Phys. B 33, L91 (2000).
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).
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).
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).
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).
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
J. Chem. Phys. 109, 10806 (1998).
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).
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).
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).
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).
J. K. Laerdahl,
"Development and applications of relativistic quantum chemical methods",
Ph.D. thesis, University of Oslo (1997).
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).
"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).
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,
Last modified: May 03, 2018