Dr. David Ardell



S&E 1 Bldg., RM 228
School of Natural Sciences
University of California, Merced
5200 N. Lake Road
Merced, California 95348



Ph.D., Stanford University

A.B., Harvard University

Current Position: 
Assistant Professor, School of Natural Sciences, University of California, Merced
Research Interests: 

Computational biology of gene expression systems, including:

  • Structure, function, evolution and coevolution with genomes
  • Functional and evolutionary bioinformatics of RNA and proteins
  • Evolutionary and comparative genomics

 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. To appear.

P. Holloway, K. Swenson, D. Ardell, N. El-Mabrouk (2013). Ancestral genome organization: an alignment approach. J Comput Biol. 20(4):280-95
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

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

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
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

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

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

Drosophila Comparative Genome Sequencing and Analysis Consortium (2007).

Evolution of genes and genomes in the context of the Drosophila phylogeny

E. Freyhult, Y. Cui, O. Nilsson and D.H. Ardell (2007). New computational methods reveal tRNA identity element divergence between Proteobacteria and Cyanobacteria