2007
Willyard, A., Syring, J., Gernandt, D.S., Liston, A. & Cronn, R. 2007. Fossil calibration of molecular divergence inferences a moderate mutation rate and recent radiations for Pinus. Molecular Biology and Evolution. 24: 90-101.

2005
Gernandt, D.S., Geada López, G., Ortiz García, S. & A. Liston. 2005. Phylogeny and classification of Pinus. Taxon. 54: 29-42.

Stone, J.K. & D.S. Gernandt. 2005. A reassessment of Hemiphacidium, Rhabdocline, and Sarcotrochila (Hemiphacidiaceae). Mycotaxon 91: 115-126.

2003
Gernandt, D.S., Liston, A. & D. Piñero. 2003. Phylogenetics of Pinus subsections Cembroides and Nelsoniae inferred from cpDNA sequences. Systematic Botany. 28: 657-673.

Johnston, P.R., Park, D., Dick, M.A., Ortiz-García, S. & D.S. Gernandt. 2003. Identifying pine-inhabiting Lophodermium species using PCR-RFLP. New Zealand Journal of Forestry Science 33: 10-24.

Ortiz-García, S., Gernandt, D.S., Stone, J.K., Johnston, P.R., Chapela, I.H., Salas-Lizano, R. & E.R. Alvarez-Buylla. 2003. Phylogenetics of Lophodermium from pine. Mycologia. 95: 846-859.

2002
Fay, M.F., Gernandt, D.S., Cowan, R.S., Kitchen, M.A.R. & C. Kitchen. 2002. Parentage of an unknown member of the Sorbus latifolia (Lam.) Pers. group (Rosaceae). Watsonia 24: 91-100.

2001
Gernandt, D.S., Liston, A. & D. Piñero. 2001. Variation in the nrDNA ITS of Pinus subsection Cembroides: implications for molecular systematic studies of pine species complexes. Molecular Phylogenetics and Evolution. 21: 449-467.

Gernandt, D.S., Platt, J.L., Stone, J.K. Spatafora, J.W., Holst-Jensen, A., Hamelin, R.C & L.M. Kohn. 2001. Phylogenetics of Helotiales and Rhytismatales based on partial small subunit nuclear ribosomal DNA sequences. Mycologia 93: 915-933.

1999
Gernandt, D.S. & A. Liston. 1999. Internal transcribed spacer region evolution in Larix and Pseudotsuga (Pinaceae). American Journal of Botany 86: 711-723.
Gernandt, D.S. & J.K. Stone. 1999. Phylogenetic analysis of nuclear ribosomal DNA places the nematode parasite, Drechmeria coniospora, in Clavicipitaceae. Mycologia 91: 993-1000.

1997
Camacho, F.J., Gernandt, D.S., Liston, A., Stone, J.K. & A.S. Klein. 1997. Endophytic fungal DNA, the source of contamination in spruce needle DNA. Molecular Ecology 6: 983-987.
Gernandt, D.S., Camacho, F.J. & J.K. Stone. 1997. Meria laricis, an anamorph of Rhabdocline. Mycologia 89: 735-744.