DENNIS PAUL WALL

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. ncbi request reprint Origin and rapid diversification of a tropical moss
    Dennis P Wall
    Department of Integrative Biology, University of California, Berkeley, California 94720, USA
    Evolution 59:1413-24. 2005
  2. pmc Autworks: a cross-disease network biology application for Autism and related disorders
    Tristan H Nelson
    The Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    BMC Med Genomics 5:56. 2012
  3. pmc Cross-pollination of research findings, although uncommon, may accelerate discovery of human disease genes
    Marlena Duda
    The Center for Biomedical Informatics, Harvard Medical School, Boston, MA, USA
    BMC Med Genet 13:114. 2012
  4. pmc Use of artificial intelligence to shorten the behavioral diagnosis of autism
    Dennis P Wall
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 7:e43855. 2012
  5. pmc Use of machine learning to shorten observation-based screening and diagnosis of autism
    D P Wall
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115 6030, USA
    Transl Psychiatry 2:e100. 2012
  6. pmc Systems analysis of inflammatory bowel disease based on comprehensive gene information
    Satoru 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
  7. pmc Cloud computing for comparative genomics
    Dennis P Wall
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    BMC Bioinformatics 11:259. 2010
  8. pmc Genotator: a disease-agnostic tool for genetic annotation of disease
    Dennis P Wall
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    BMC Med Genomics 3:50. 2010
  9. pmc Functional genomic analysis of the rates of protein evolution
    Dennis 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
  10. pmc Phylogenetically informed logic relationships improve detection of biological network organization
    Jike Cui
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    BMC Bioinformatics 12:476. 2011

Research Grants

Collaborators

Detail Information

Publications21

  1. ncbi request reprint Origin and rapid diversification of a tropical moss
    Dennis 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...
  2. pmc Autworks: a cross-disease network biology application for Autism and related disorders
    Tristan 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...
  3. pmc Cross-pollination of research findings, although uncommon, may accelerate discovery of human disease genes
    Marlena 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...
  4. pmc Use of artificial intelligence to shorten the behavioral diagnosis of autism
    Dennis 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...
  5. pmc Use of machine learning to shorten observation-based screening and diagnosis of autism
    D P Wall
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115 6030, USA
    Transl Psychiatry 2:e100. 2012
    ....
  6. pmc Systems analysis of inflammatory bowel disease based on comprehensive gene information
    Satoru 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...
  7. pmc Cloud computing for comparative genomics
    Dennis 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...
  8. pmc Genotator: a disease-agnostic tool for genetic annotation of disease
    Dennis 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...
  9. pmc Functional genomic analysis of the rates of protein evolution
    Dennis 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
    ....
  10. pmc Phylogenetically informed logic relationships improve detection of biological network organization
    Jike 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...
  11. doi request reprint Comparative analysis of neurological disorders focuses genome-wide search for autism genes
    D P Wall
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Genomics 93:120-9. 2009
    ....
  12. ncbi request reprint Roundup: a multi-genome repository of orthologs and evolutionary distances
    Todd 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...
  13. pmc Coevolution of gene expression among interacting proteins
    Hunter 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...
  14. ncbi request reprint 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...
  15. ncbi request reprint Evolutionary patterns of codon usage in the chloroplast gene rbcL
    Dennis 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...
  16. pmc A simple dependence between protein evolution rate and the number of protein-protein interactions
    Hunter 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...
  17. ncbi request reprint Adjusting for selection on synonymous sites in estimates of evolutionary distance
    Aaron 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...
  18. ncbi request reprint Conservation of the RB1 gene in human and primates
    Theru A Sivakumaran
    Division of Genetics, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
    Hum Mutat 25:396-409. 2005
    ....
  19. ncbi request reprint Converging on a general model of protein evolution
    Joshua 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...
  20. pmc The role of selection in the evolution of human mitochondrial genomes
    Toomas 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...
  21. ncbi request reprint Ortholog detection using the reciprocal smallest distance algorithm
    Dennis 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 Grants1