Teufel A, Grahnen JA, Liberles DA. (2012) "Modeling proteins at the interface of structure, evolution and population genetics". In "Computational Modeling of Biological Systems: From Molecules to Pathways", ed. Dokholyan NV. 2012 edition, Springer, NY, NY.
Grahnen JA, Nandakumar P, Kubelka J, Liberles DA. (2011) "Biophysical and Structural Considerations for Protein Sequence Evolution" BMC Evolutionary Biology, 11:361
Siltberg-Liberles J, Grahnen JA, Liberles DA. (2011) "The Evolution of Protein Structures and Structural Ensembles Under Functional Constraint" Genes, 2:4.
Konrad A, Teufel A, Grahnen JA, Liberles DA (2011) "Towards a General Model for the Evolutionary Dynamics of Gene Duplicates" Genome Biology and Evolution, 3:1197-1209.
Grahnen JA, Kubelka J, Liberles DA. (2011) "Fast Side Chain Replacement in Proteins Using a Coarse-Grained Approach for Evaluating the Effects of Mutation During Evolution" Journal of Molecular Evolution, 73:1.
Liberles DA, Tisdell MDM, Grahnen JA. (2011) "Binding constraints on the evolution of enzymes and signaling proteins" Proceedings of the Royal Society B: Biological Sciences, 278:1714.
Grahnen JA, Amunson KE, Kubelka J. (2010) "DFT-based simulation of IR amide I' spectra for a small protein in solution, comparison of explicit and empirical solvent models" Journal of Physical Chemistry B, 144:40.
Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA. (2010) "Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery" BMC Genomics, 11:180.
Grahnen J (2007) "Computer-aided prediction of residue-residue contacts in transmembrane proteins". Umea University, Umea, Sweden. (Masters thesis)
Grahnen JA. (2011) "Coarse-grained structure-based models of sequence evolution". Presented at the NESCent Catalysis Meeting "Modeling Protein Structural and Energietic Constraints On Sequence Evoluation".
Grahnen J, Rastogi S, Liberles DA. (2009) Evaluating the dosage balance hypothesis of gene duplicate evolution after whole genome duplication: patterns of gene loss and amino acid substitutions. Presented at the 2009 Annual Meeting of the Society for Molecular Biology and Evolution.
Parchman TL, Buerkle CA, Grahnen J, Benkman CW. (2009) Characterization of gene-based markers and population structure as a basis for dissecting the genetics of serotiny in lodgepole pine. Presented at Evolution 2009.
Hennerdal A, Grahnen J, Elofsson A. (2007) Contact prediction for transmembrane proteins. Presented at the 15th International Conference on Intelligent Systems for Molecular Biology.