D P Wall

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. doi request reprint The Potential of Accelerating Early Detection of Autism through Content Analysis of YouTube Videos
    Vincent A Fusaro
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 9:e93533. 2014
  2. 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
  3. 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
  4. ncbi request reprint Detecting putative orthologs
    D P Wall
    Department of Biological Sciences, Stanford University, CA 94305, USA
    Bioinformatics 19:1710-1. 2003
  5. 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
  6. 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
  7. 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
  8. 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
  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. ncbi request reprint Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia
    Joshua T Herbeck
    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
    Microbiology 149:2585-96. 2003

Collaborators

Detail Information

Publications15

  1. doi request reprint The Potential of Accelerating Early Detection of Autism through Content Analysis of YouTube Videos
    Vincent A Fusaro
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 9:e93533. 2014
    ....
  2. 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...
  3. 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...
  4. ncbi request reprint Detecting putative orthologs
    D P Wall
    Department of Biological Sciences, Stanford University, CA 94305, USA
    Bioinformatics 19:1710-1. 2003
    ..rsd finds many putative orthologs missed by rbh because it is less likely than rbh to be misled by the presence of a close paralog...
  5. 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...
  6. 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...
  7. 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...
  8. 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...
  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. ncbi request reprint Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia
    Joshua T Herbeck
    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
    Microbiology 149:2585-96. 2003
    ..However, these impacts of mutation and drift are apparently attenuated by selection on amino acid composition at high-expression genes...
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. 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
    ....