Publications
2009
Esteban FJ and Wall DP. Using game theory to detect genes involved in Autism Spectrum Disorder. TOP. 2009. pdf
Abu-Elneel K, Liu T, Gazzaniga FS, Nishimura Y, Wall DP, Geschwind DH, Lao K, Kosik KS. Reply to the "Letter to the Editors" by Steven Buyske. Neurogenetics. 2009 Feb 24. pdf
Cano C, Monaghan T, Blanco A, Wall DP, Peshkin L. Collaborative text-annotation resource for disease-centered relation extraction from biomedical text. J Biomed Inform. 2009 Feb 14. pdf
Wall DP, Esteban FJ, Deluca TF, Huyck M, Monaghan T, Velez de Mendizabal N, Goñí J, Kohane IS. Comparative analysis of neurological disorders focuses genome-wide search for autism genes. Genomics. 2009 Feb;93(2):120-9. pdf
2008
Abu-Elneel K, Liu T, Gazzaniga FS, Nishimura Y, Wall DP, Geschwind DH, Lao K, Kosik KS. Heterogeneous dysregulation of microRNAs across the autism spectrum. Neurogenetics. 2008 Jul;9(3):153-61. pdf
Singh S, Wall DP. Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function. Evol Bioinform Online. 2008;4:217-23. pdf
2007
Wall DP, Deluca T. Ortholog detection using the reciprocal smallest distance algorithm. Methods Mol Biol. 2007;396:95-110. pdf
2006
Deluca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP. Roundup: a multi-genome repository of orthologs and evolutionary distances. Bioinformatics. 2006 Aug 15;22(16):2044-6. pdf
Van Vactor D, Wall DP, Johnson KG. Heparan sulfate proteoglycans and the emergence of neuronal connectivity. Curr Opin Neurobiol. 2006 Feb;16(1):40-51. pdf
Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K, Passarino G, Underhill PA, Scharfe C, Torroni A, Scozzari R, Modiano D, Coppa A, de Knijff P, Feldman M, Cavalli-Sforza LL, Oefner PJ. The role of selection in the evolution of human mitochondrial genomes. Genetics. 2006 Jan;172(1):373-87. pdf
2005
Herbeck JT, Wall DP. Converging on a general model of protein evolution. Trends Biotechnol. 2005 Oct;23(10):485-7. pdf
Wall DP. Origin and rapid diversification of a tropical moss. Evolution. 2005 Jul;59(7):1413-24. pdf
Sivakumaran TA, Shen P, Wall DP, Do BH, Kucheria K, Oefner PJ. Conservation of the RB1 gene in human and primates. Hum Mutat. 2005 Apr;25(4):396-409. pdf
Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, Eisen MB, Feldman MW. Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5483-8. pdf
Hirsh AE, Fraser HB, Wall DP. Adjusting for selection on synonymous sites in estimates of evolutionary distance. Mol Biol Evol. 2005 Jan;22(1):174-7. pdf
2004
Fraser HB, Hirsh AE, Wall DP, Eisen MB. Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):9033-8. pdf
2003
Herbeck JT, Wall DP, Wernegreen JJ. Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia. Microbiology. 2003 Sep;149(Pt 9):2585-96. pdf
Wall DP, Fraser HB, Hirsh AE. Detecting putative orthologs. Bioinformatics. 2003 Sep 1;19(13):1710-1. pdf
Wall DP, Herbeck JT. Evolutionary patterns of codon usage in the chloroplast gene rbcL. J Mol Evol. 2003 Jun;56(6):673-88; discussion 689-90. pdf
Fraser HB, Wall DP, Hirsh AE. A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol Biol. 2003 May 23;3:11. pdf
2002
Wall DP. Use of the nuclear gene glyceraldehyde 3-phosphate dehydrogenase for phylogeny reconstruction of recently diverged lineages in Mitthyridium (Musci: Calymperaceae). Mol Phylogenet Evol. 2002 Oct;25(1):10-26. pdf