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. doi request reprint A literature search tool for intelligent extraction of disease-associated genes
    Jae Yoon Jung
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
    J Am Med Inform Assoc 21:399-405. 2014
  3. pmc Detecting biological network organization and functional gene orthologs
    Jike Cui
    The Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 27:2919-20. 2011
  4. pmc Roundup 2.0: enabling comparative genomics for over 1800 genomes
    Todd F Deluca
    The Center for Biomedical Informatics, Harvard Medical School and Department of Pathology, Beth Israel Deaconess Medical Center, Boston MA 02115, USA
    Bioinformatics 28:715-6. 2012
  5. pmc Identification of autoimmune gene signatures in autism
    J Y Jung
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Transl Psychiatry 1:e63. 2011
  6. pmc Cloud computing for comparative genomics with windows azure platform
    Insik Kim
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA, USA School of Electrical and Computer Engineering, Ulsan National Institute of Technology, Ulsan, Korea
    Evol Bioinform Online 8:527-34. 2012
  7. pmc Haplotype structure enables prioritization of common markers and candidate genes in autism spectrum disorder
    B N Vardarajan
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA, USA
    Transl Psychiatry 3:e262. 2013
  8. pmc Cost-effective cloud computing: a case study using the comparative genomics tool, roundup
    Parul Kudtarkar
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115
    Evol Bioinform Online 6:197-203. 2010
  9. 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
  10. 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

Research Grants

Collaborators

Detail Information

Publications30

  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. doi request reprint A literature search tool for intelligent extraction of disease-associated genes
    Jae Yoon Jung
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
    J Am Med Inform Assoc 21:399-405. 2014
    ..To extract disorder-associated genes from the scientific literature in PubMed with greater sensitivity for literature-based support than existing methods...
  3. pmc Detecting biological network organization and functional gene orthologs
    Jike Cui
    The Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 27:2919-20. 2011
    ..To run the computation, users need to provide the GI IDs of the genes of interest...
  4. pmc Roundup 2.0: enabling comparative genomics for over 1800 genomes
    Todd F Deluca
    The Center for Biomedical Informatics, Harvard Medical School and Department of Pathology, Beth Israel Deaconess Medical Center, Boston MA 02115, USA
    Bioinformatics 28:715-6. 2012
    ..In addition, gene IDs can be retrieved using FASTA sequence search. All source code and orthologs are freely available...
  5. pmc Identification of autoimmune gene signatures in autism
    J Y Jung
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Transl Psychiatry 1:e63. 2011
    ..Significant associations between ASD and two autoimmune disorders were identified. This genetic association supports the idea that specific immunological abnormalities may underlie the etiology of autism, at least in a number of cases...
  6. pmc Cloud computing for comparative genomics with windows azure platform
    Insik Kim
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA, USA School of Electrical and Computer Engineering, Ulsan National Institute of Technology, Ulsan, Korea
    Evol Bioinform Online 8:527-34. 2012
    ..Here we introduce the Microsoft Azure platform with detailed execution steps and a cost comparison with Amazon Web Services...
  7. pmc Haplotype structure enables prioritization of common markers and candidate genes in autism spectrum disorder
    B N Vardarajan
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA, USA
    Transl Psychiatry 3:e262. 2013
    ....
  8. pmc Cost-effective cloud computing: a case study using the comparative genomics tool, roundup
    Parul Kudtarkar
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115
    Evol Bioinform Online 6:197-203. 2010
    ....
  9. 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...
  10. 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...
  11. 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...
  12. 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
    ....
  13. 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...
  14. 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...
  15. 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...
  16. 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...
  17. 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
    ....
  18. 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
    ....
  19. 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...
  20. 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...
  21. 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...
  22. 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...
  23. 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...
  24. 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...
  25. 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...
  26. 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...
  27. 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...
  28. 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
    ....

Research Grants1