SCANMS: adjusting for multiple comparisons in sliding window neutrality tests. - David H. Ardell (Bioinform., 2004)

Informatic Approaches to Molecular Translation. - David H. Ardell (Intelligent Information Systems, 2005)

The Genomic Pattern of tDNA Operon Expression in E. coli. - David H. Ardell; Leif A. Kirsebom (PLoS Comput. Biol., 2005)

TFAM 1.0: an online tRNA function classifier. - Helena Tåquist; Yuanyuan Cui; David H. Ardell (Nucleic Acids Res., 2007)

An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis sigma66 promoters. - Ronna R. Mallios; David M. Ojcius; David H. Ardell (BMC Bioinform., 2009)

Evolution of Genome Organization by Duplication and Loss: An Alignment Approach. - Patrick Holloway; Krister M. Swenson; David H. Ardell; Nadia El-Mabrouk (RECOMB, 2012)

Ancestral Genome Organization: An Alignment Approach. - Patrick Holloway; Krister M. Swenson; David H. Ardell; Nadia El-Mabrouk (J. Comput. Biol., 2013)

tRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria. - Katherine C. H. Amrine; Wesley D. Swingley; David H. Ardell (PLoS Comput. Biol., 2014)

Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line. - Claus Weinholdt; Henri Wichmann; Johanna Kotrba; David H. Ardell; Matthias Kappler; Alexander W. Eckert; Dirk Vordermark; Ivo Grosse (BMC Bioinform., 2019)

tSFM 1.0: tRNA Structure-Function Mapper. - Travis J. Lawrence; Fatemeh Hadi-Nezhad; Ivo Grosse; David H. Ardell (Bioinform., 2021)