Research Topics
| DENNIS PAUL WALLSummaryAffiliation: Harvard University Country: USA Publications
Research Grants
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Detail Information
Publications
Origin and rapid diversification of a tropical mossDennis P Wall
Department of Integrative Biology, University of California, Berkeley, California 94720, USA
Evolution 59:1413-24. 2005..Identifying the cause for this rapid diversification requires further testing, but it appears to be related to a general shift in reproductive strategy from sexual to asexual, which may be a key innovation for this young group...
Autworks: a cross-disease network biology application for Autism and related disordersTristan H Nelson
The Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
BMC Med Genomics 5:56. 2012..Network based cross-disorder analysis can aid in the understanding and characterization of the molecular pathology of autism, but there are few tools that enable us to conduct cross-disorder analysis and to visualize the results...- Cross-pollination of research findings, although uncommon, may accelerate discovery of human disease genesMarlena Duda
The Center for Biomedical Informatics, Harvard Medical School, Boston, MA, USA
BMC Med Genet 13:114. 2012..In light of this large genetic overlap, we tested whether cross-disease research approaches lead to faster, more impactful discoveries... - Use of artificial intelligence to shorten the behavioral diagnosis of autismDennis P Wall
Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
PLoS ONE 7:e43855. 2012..Such a tool could assist in streamlining the clinical diagnostic process overall, leading to faster screening and earlier treatment of individuals with autism... - Use of machine learning to shorten observation-based screening and diagnosis of autismD P Wall
Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115 6030, USA
Transl Psychiatry 2:e100. 2012.... - Systems analysis of inflammatory bowel disease based on comprehensive gene informationSatoru Suzuki
Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1 5 45 Yushima, Bunkyo ku, Tokyo 113 8510, Japan
BMC Med Genet 13:25. 2012..We employ a new knowledge driven HDN gene and molecular database systems approach to analyze Inflammatory Bowel Disease (IBD), whose pathogenesis remains largely unknown... - Cloud computing for comparative genomicsDennis P Wall
Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
BMC Bioinformatics 11:259. 2010..We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes... - Genotator: a disease-agnostic tool for genetic annotation of diseaseDennis P Wall
Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
BMC Med Genomics 3:50. 2010..With few exceptions, researchers must manually search a variety of sites to assemble a complete set of genetic evidence for a particular disease of interest, a process that is both time-consuming and error-prone... - Functional genomic analysis of the rates of protein evolutionDennis P Wall
Department of Biological Sciences, and Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 102:5483-8. 2005.... - Phylogenetically informed logic relationships improve detection of biological network organizationJike Cui
Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
BMC Bioinformatics 12:476. 2011..Despite this success, few studies have attempted to search beyond just pairwise relationships among genes. Here we search for logic relationships involving three genes, and explore its potential application in gene network analyses... 
Comparative analysis of neurological disorders focuses genome-wide search for autism genesD P Wall
Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
Genomics 93:120-9. 2009....- Roundup: a multi-genome repository of orthologs and evolutionary distancesTodd F Deluca
The Center for Biomedical Informatics and Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
Bioinformatics 22:2044-6. 2006..Results may be downloaded as phylogenetic matrices for subsequent analysis, including the construction of whole-genome phylogenies based on gene-content data. AVAILABILITY: http://rodeo.med.harvard.edu/tools/roundup... - Coevolution of gene expression among interacting proteinsHunter B Fraser
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 101:9033-8. 2004..Our results also suggest that expression coevolution can be used for computational prediction of protein-protein interactions... - Use of the nuclear gene glyceraldehyde 3-phosphate dehydrogenase for phylogeny reconstruction of recently diverged lineages in Mitthyridium (Musci: Calymperaceae)Dennis P Wall
Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, USA
Mol Phylogenet Evol 25:10-26. 2002..In general, gpd was found to hold great promise not only for improving resolution of chloroplast-derived phylogenies, but also for phylogenetic reconstruction of recent, diversifying lineages... - Evolutionary patterns of codon usage in the chloroplast gene rbcLDennis P Wall
Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
J Mol Evol 56:673-88; discussion 689-90. 2003..This suggests that codon usage bias may be constrained by particular amino acids and, thus, may serve as a good predictor of what residues are most important for protein fitness... 
A simple dependence between protein evolution rate and the number of protein-protein interactionsHunter B Fraser
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
BMC Evol Biol 3:11. 2003..However, the generality of this observation has recently been challenged. Here we examine the problem using protein-protein interaction data from the yeast Saccharomyces cerevisiae and genome sequences from two other yeast species...- Adjusting for selection on synonymous sites in estimates of evolutionary distanceAaron E Hirsh
Department of Biological Sciences, Stanford University, Stanford, California, USA
Mol Biol Evol 22:174-7. 2005..Here, we use the relationship between codon bias and synonymous divergence observed in four species of the genus Saccharomyces to provide a simple correction for selection on silent sites... - Conservation of the RB1 gene in human and primatesTheru A Sivakumaran
Division of Genetics, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
Hum Mutat 25:396-409. 2005.... - Converging on a general model of protein evolutionJoshua T Herbeck
Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98103, USA
Trends Biotechnol 23:485-7. 2005..These results indicate that a general model of protein evolution will emerge as more functional genomic data from a diversity of organisms accumulate... - The role of selection in the evolution of human mitochondrial genomesToomas Kivisild
Department of Human and Clinical Genetics, Leiden University Medical Center, 2333 AL Leiden, The Netherlands
Genetics 172:373-87. 2006..We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups... - Ortholog detection using the reciprocal smallest distance algorithmDennis P Wall
Methods Mol Biol 396:95-110. 2007..The flexibility of this tool makes it a unique and powerful addition to other available approaches for ortholog detection...
Research Grants
- Characterizing the genetic systems of autism through multi-disease analysisDENNIS PAUL WALL; Fiscal Year: 2010....