Studying how genomes express themselves

2016

  1. D.H. Ardell and Ya-Ming Hou (2016). Initiator tRNA Genes Template the 3′ CCA End at High Frequencies in Bacteria. BMC Genomics 17:1003.
  2. Winter B. and Ardell D.[H.] (2016). Rethinking Zipf’s Frequency-meaning Relationship: Implications For The Evolution Of Word Meaning. In S.G. Roberts, C. Cuskley, L. McCrohon, L. Barceló-Coblijn, O. Fehér & T. Verhoef (eds.) The Evolution of Language: Proceedings of the 11th International Conference (EVOLANG11). Available online: http://evolang.org/neworleans/papers/58.html
  3. Ardell D.[H.], Anderson N. and Winter B. (2016). Noise In Phonology Affects Encoding Strategies In Morphology. In S.G. Roberts, C. Cuskley, L. McCrohon, L. Barceló-Coblijn, O. Fehér & T. Verhoef (eds.) The Evolution of Language: Proceedings of the 11th International Conference (EVOLANG11). Available online: http://evolang.org/neworleans/papers/165.html

2015

  1. T.J. Lawrence, K.T. Kauffman, K.C.H. Amrine, D.L. Carper, R.S. Lee, P.J. Becich, C.J. Canales and D.H. Ardell (2015). FAST: FAST Analysis of Sequences Toolbox. Front. Genet.6:172.
  2. D.A Burow, M.C. Umeh-Garcia, M.B. True, C.D. Bakhaj, D.H. Ardell and M.D. Cleary (2015). Dynamic regulation of mRNA decay during neural development. Neural Development 10:11.

2014

  1. S. Huette, B. Winter, T. Matlock, D.H. Ardell and M. Spivey (2014). Eye movements during listening reveal spontaneous grammatical processing. Front. Psychol. 5:410.
  2. K.C.H. Amrine, W.D. Swingley, and D.H. Ardell (2014). tRNA signatures reveal a polyphyletic origin of SAR11 strains among Alphaproteobacteria. PLoS Comp. Biol. 10(2): e1003454.

2013

  1. P. Holloway, K. Swenson, D. Ardell, N. El-Mabrouk (2013). Ancestral genome organization: an alignment approach. J Comput Biol. 20(4):280-95.
  2. P.J. Becich, B.P. Stark, H.S. Bhat and D.H. Ardell (2013). CMCpy: Genetic Code-Message Coevolution Models in Python. Evolutionary Bioinformatics 9:111-125

2012

  1. P. Holloway, K.M. Swenson, D.H. Ardell, and N. El-Mabrouk (2012). Evolution of Genome Organization by Duplication and Loss: An Alignment Approach. RECOMB 2012 7262/2012:94-112

2010

  1. D.H. Ardell (2010). Computational analysis of tRNA identity. FEBS Lett., 584(2):325-333

    Download the codebase to reproduce the tRNA structure figures in this review.

2009

  1. R.M. Mallios, D.M. Ojcius, D.H. Ardell (2009). An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis sigma66 promoters. BMC Bioinformatics, 10:271.
  2. K. Illergård, D.H. Ardell, A. Elofsson (2009). Structure is three to ten times more conserved than sequence–a study of structural response in protein cores. Proteins 77(3):499-508.

2008

  1. 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.

2007

  1. 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.
  2. 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
  3. 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.
  4. H. Tåquist, Y. Cui, and D.H. Ardell (2007). TFAM 1.0: an online tRNA function classifier. Nucl. Acids Res. 35:W350-W353
  5. 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.

2006

  1. 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
  2. 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
  3. 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.

  4. 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.

2005

  1. D.H. Ardell and L.A. Kirsebom (2005). The genomic pattern of tDNA operon expression in E. coli. PLoS Comp. Biol. 1(1):e12
  2. 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.

2004

  1. 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.

  2. D.H. Ardell (2004). SCANMS: Adjusting for multiple comparisons in sliding window neutrality tests.Bioinformatics 20(12):1986-1988.

2003

  1. D.H. Ardell, C.A. Lozupone and L.F. Landweber (2003). Polymorphism, recombination, and alternative unscrambling in the DNA polymerase α gene of the ciliate Stylonychia lemnae (alveolata; class Spirotrichea). Genetics 165(4):1761-1777.
  2. 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.

2002

  1. 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.
  2. 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]

2001

  1. 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]
  2. 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]

1998

  1. 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]