Publications
2013
Vardarajan BN, Eran A, Jung JY, Kunkel LM, Wall DP. Haplotype structure enables prioritization of common markers and candidate genes in autism spectrum disorder. Nature, Translational Psychiatry e262. Full text available.
Wall DP, Tonellato PJ. Genomics-informed pathology. The Scientist. 2013. Link
Diaz-Beltran L, Cano C, Wall DP, and Esteban, FJ. Systems biology as a comparative approach to understand complex gene expression in neurological diseases. Behavioral Sciences 3: 253-272. Abstract
Issa S A, Kienzler R, El-Kalioby M, Tonellato P J, Wall D, Bruggmann R & Abouelhoda M. Streaming support for data intensive cloud-based sequence analysis. BioMed Research International 2013, 791051, doi:10.1155/2013/791051 (2013). Abstract
2012
Nelson TH, Jung JY, Deluca TF, Hinebaugh BK, St Gabriel KC, Wall DP. Autworks: a cross-disease network biology application for Autism and related disorders. BMC Med Genomics. 2012 Nov 28;5(1):56. Full text available.
Marlena Duda, Tristan Nelson and Dennis P Wall. Cross-pollination of research findings, although uncommon, may accelerate discovery of human disease genes. BMC Medical Genetics 2012, 13:114. Abstract.
Insik Kim, Jung JY, DeLuca TF, Nelson TH, Wall DP. Cloud Computing for Comparative Genomics with Windows Azure Platform. Evolutionary Bioinformatics. 2012 Aug 30. Abstract. PDF.
DP Wall, Dally R, Luyster R, Jung JY, DeLuca TF. Use of Artificial Intelligence to Shorten the Behavioral Diagnosis of Autism. PLoS ONE. 2012 Aug 27. Full-text link.
DP Wall, Tonellato PJ. The future of genomics in pathology. F1000 Med Rep. 2012 Jul 2. Full-text link.
DP Wall, Kosmicki J, DeLuca TF, Harstad E, Fusaro VA. Use of machine learning to shorten observation-based screening and diagnosis of autism. Transl Psychiatry. 2012 Apr 10. Full-text link. PDF.
Satoru Suzuki, Takako Takai-Igarashi, Yutaka Fukuoka, DP Wall, Hiroshi Tanaka, Peter J Tonellato. Systems analysis of inflammatory bowel disease based on comprehensive gene information. BMC Med Genet. 2012; 13: 25. Full-text link.
DeLuca TF, Cui J, Jung JY, St. Gabriel KC, Wall DP. Roundup 2.0: Enabling comparative genomics for over 1800 genomes. Bioinformatics. 2012 Jan 13.
2011
Cui J, Deluca TF, Jung JY, Wall DP. Phylogenetically informed logic relationships improve detection of biological network organization. BMC Bioinformatics. 2011 Dec 15;12(1):476.
Jung JY, Kohane IS, Wall DP. Identification of autoimmune gene signatures in autism. Transl Psychiatry. 2011 Dec 13. Full-text link
Fusaro VA, Patil P, Gafni E, Wall DP, Tonellato PJ. Biomedical cloud computing with Amazon Web Services. PLoS Comput Biol. 2011 Aug.
Cui J, DeLuca TF, Jung JY, Wall DP. Detecting biological network organization and functional gene orthologs. Bioinformatics. 2011 Oct 15;27(20):2919-20.
2010
Wall DP, Pivovarov R, Tong M, Jung JY, Fusaro VA, DeLuca TF, Tonellato PJ. Genotator: a disease-agnostic tool for genetic annotation of disease. BMC Med Genomics. 2010 pdf
Wall D, Kudtarkar P, Fusaro V, Pivovarov R, Patil P, Tonellato P. Cloud computing for comparative genomics. BMC Bioinformatics 2010;11:259. pdf
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