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Publications:
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P. Larsson, A. Hinas, D.H. Ardell, L.A. Kirsebom, A.
Virtanen, F. Söderbom (2008).De novo search for
non-coding RNA genes in the AT-rich genome of
Dictyostelium discoideum: Performance of
Markov-dependent genome feature scoring. Genome Res.
18(6)888-899.
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M. Mačvanin, E.I. Gonzalez de Valdivia, D.H. Ardell, and L.A. Isaksson (2007). Transient erythromycin resistance phenotype associated with peptidyl-tRNA drop-off on early UGG and GGG codons.
J. Bacteriology, 189(24):8993-9000.
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Drosophila Comparative Genome Sequencing and Analysis Consortium (2007). Evolution of genes and genomes in the context of
the Drosophila phylogeny. Nature 450(7167):203-218
- E. Freyhult, Y. Cui, O. Nilsson and D.H. Ardell (2007). New computational methods reveal tRNA
identity element divergence between Proteobacteria
and Cyanobacteria. Biochimie 89(10):1276-1288.
- H. Tåquist, Y. Cui, and D.H. Ardell (2007). TFAM 1.0: an online tRNA function
classifier. Nucl.
Acids Res. 35:W350-W353
- W.-J. Chang, V.M. Addis, A.J. Li, E. Axelsson, D.H. Ardell,
L.F. Landweber (2007). Intron Evolution and Information processing in the DNA polymerase alpha gene in spirotrichous ciliates: A hypothesis for interconversion between DNA and RNA
deletion. Biology Direct 2:6.
- G. Sella and D.H. Ardell (2006).
The coevolution of genes and genetic codes:
Crick's frozen accident revisited.
J. Mol. Evol. 63(3):297-313
- H. Jin, Q. Zhao, E.I. Gonzalez de
Valdivia, D.H. Ardell, M. Stenström, and L.A. Isaksson (2006).
Influences on gene expression in vivo by a Shine-Dalgarno sequence.
Mol. Microbiol. 60:480
- E. Freyhult, V. Moulton and D.H. Ardell (2006).
Visualizing Bacterial tRNA Identity Determinants and
Antideterminants Using Function Logos and Inverse Function
Logos.
Nucl. Acids Res. 34(3):905-916.
- D.H. Ardell and S.G.E. Andersson (2006).
TFAM detects co-evolution of tRNA identity rules after lateral
transfer of Histidyl-tRNA synthetase.
Nucl. Acids Res. 34(3):893-904.
- D.H. Ardell and L.A. Kirsebom (2005).
The genomic pattern of tDNA operon
expression in E. coli.
PLoS Comp. Biol. 1(1):e12
- B.M.F. Pettersson, D.H. Ardell and L.A. Kirsebom (2005). The
5’ leader of Escherichia coli tRNA precursors gives a
growth advantage.
J. Mol. Biol. 351(1):9-15.
- C.M. Alsmark, A.C. Frank, E. O. Karlberg, B. Legault,
D.H. Ardell, B. Canback, A.-S. Eriksson, A.K. Naslund,
S.A. Handley, M. Huvet, B. La Scola, M. Holmberg, and S.G.E. Andersson
(2004) The louse-borne human pathogen Bartonella quintana is a genomic
derivative of the zoonotic agent Bartonella
henselae. Proc. Natl. Acad. Sci. USA. 101(26):9716-9721.
- D.H. Ardell (2004).
SCANMS: Adjusting for multiple comparisons in
sliding window neutrality tests.
Bioinformatics 20(12):1986-1988.
- D.H. Ardell, C.A. Lozupone and L.F. Landweber (2003). Polymorphism,
recombination, and alternative unscrambling in the DNA polymerase
gene of the ciliate Stylonychia lemnae
(alveolata; class Spirotrichea). Genetics
165(4):1761-1777.
- E. Salaneck, D.H. Ardell, E.T. Larson and D. Larhammar (2003). Three
neuropeptide Y receptors in the spiny dogfish Squalus acanthias
support en bloc duplications in early vertebrate
evolution.
Molecular Biology and Evolution. 20(8):1271-1280.
- D.H. Ardell and G. Sella (2002). No accident: genetic codes freeze in
error-correcting patterns of the standard genetic code.
Philosophical Transactions of the Royal Society of London B 3571625-1642.[PDF]
- G. Sella and D.H. Ardell (2002). The impact of message mutation on the
fitness of a genetic code. Journal of Molecular Evolution 54(5):638-651.[PDF]
- D.H. Ardell and G. Sella (2001). On the evolution of redundancy in
genetic codes. Journal of Molecular Evolution 53(4/5):269-281.[PDF]
- D.H. Ardell and S.O. Andersen (2001). Tentative identification of a
proresilin gene in Drosophila melanogaster. Insect
Biochemistry and Molecular Biology 31:965-970. [PDF]
- D.H. Ardell (1998). On error-minimization in a sequential origin of
the Standard Genetic Code. Journal of Molecular Evolution 47(1):1-13.[PDF]