Arlin Stoltzfus

Summary

Affiliation: National Institute of Standards and Technology
Country: USA

Publications

  1. ncbi request reprint Amino acid exchangeability and the adaptive code hypothesis
    Arlin Stoltzfus
    Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
    J Mol Evol 65:456-62. 2007
  2. doi request reprint Evidence for a predominant role of oxidative damage in germline mutation in mammals
    Arlin Stoltzfus
    Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, United States
    Mutat Res 644:71-3. 2008
  3. ncbi request reprint Mutation-biased adaptation in a protein NK model
    Arlin Stoltzfus
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Gaithersburg, Maryland, USA
    Mol Biol Evol 23:1852-62. 2006
  4. pmc Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data
    Thomas Hladish
    Center for Advanced Research in Biotechnology, Rockville, MD 20850, USA
    BMC Bioinformatics 8:191. 2007
  5. ncbi request reprint A sequence-based model accounts largely for the relationship of intron positions to protein structural features
    Danny W De Kee
    Center for Advanced Research in Biotechnology, Rockville, MD, USA
    Mol Biol Evol 24:2158-68. 2007
  6. pmc Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
    Arlin Stoltzfus
    Institute for Bioscience and Biotechnology Research, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
    BMC Bioinformatics 14:158. 2013
  7. doi request reprint Climbing mount probable: mutation as a cause of nonrandomness in evolution
    Arlin Stoltzfus
    Center for Advanced Research in Biotechnology, Rockville, MD 20850, USA
    J Hered 100:637-47. 2009
  8. pmc Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis
    Arlin Stoltzfus
    Biochemical Science Division, NIST, Gaithersburg, MD, USA
    BMC Res Notes 5:574. 2012
  9. ncbi request reprint The evolutionary gain of spliceosomal introns: sequence and phase preferences
    Wei Gang Qiu
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland, USA
    Mol Biol Evol 21:1252-63. 2004
  10. pmc Constructive neutral evolution: exploring evolutionary theory's curious disconnect
    Arlin Stoltzfus
    Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
    Biol Direct 7:35. 2012

Detail Information

Publications16

  1. ncbi request reprint Amino acid exchangeability and the adaptive code hypothesis
    Arlin Stoltzfus
    Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
    J Mol Evol 65:456-62. 2007
    ..The results reported here indicate that most of the nonrandomness in the amino acids to codon assignments can be explained by incremental code evolution, with a small residue of orderliness that may reflect code adaptation...
  2. doi request reprint Evidence for a predominant role of oxidative damage in germline mutation in mammals
    Arlin Stoltzfus
    Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, United States
    Mutat Res 644:71-3. 2008
    ..Analysis of damage susceptibility holds promise for improving models of mutational specificity...
  3. ncbi request reprint Mutation-biased adaptation in a protein NK model
    Arlin Stoltzfus
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Gaithersburg, Maryland, USA
    Mol Biol Evol 23:1852-62. 2006
    ..Thus, mutational explanations for evolved patterns need not presuppose neutral evolution...
  4. pmc Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data
    Thomas Hladish
    Center for Advanced Research in Biotechnology, Rockville, MD 20850, USA
    BMC Bioinformatics 8:191. 2007
    ..However, due to its complexity, NEXUS is not well supported by software and is not easily accessible to bioinformatics users and developers...
  5. ncbi request reprint A sequence-based model accounts largely for the relationship of intron positions to protein structural features
    Danny W De Kee
    Center for Advanced Research in Biotechnology, Rockville, MD, USA
    Mol Biol Evol 24:2158-68. 2007
    ..Phase-dependent correlations with secondary structure and side-chain surface accessibility are particularly strong. However, these phase-dependent correlations are explained largely by the sequence-based disruptive model...
  6. pmc Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
    Arlin Stoltzfus
    Institute for Bioscience and Biotechnology Research, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
    BMC Bioinformatics 14:158. 2013
    ..Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces...
  7. doi request reprint Climbing mount probable: mutation as a cause of nonrandomness in evolution
    Arlin Stoltzfus
    Center for Advanced Research in Biotechnology, Rockville, MD 20850, USA
    J Hered 100:637-47. 2009
    ..To meet this challenge requires developing knowledge of mutation as a biological process, understanding how mutation imposes propensities on evolution, and applying methods of analysis that incorporate mutational effects...
  8. pmc Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis
    Arlin Stoltzfus
    Biochemical Science Division, NIST, Gaithersburg, MD, USA
    BMC Res Notes 5:574. 2012
    ..Nevertheless, little is known about current practices, or best practices, for publishing trees and associated data so as to promote re-use...
  9. ncbi request reprint The evolutionary gain of spliceosomal introns: sequence and phase preferences
    Wei Gang Qiu
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland, USA
    Mol Biol Evol 21:1252-63. 2004
    ..Thus, intron gain accounts for the vast majority of extant introns and for the bias toward phase 0 introns that previously was interpreted as evidence for ancient formative introns...
  10. pmc Constructive neutral evolution: exploring evolutionary theory's curious disconnect
    Arlin Stoltzfus
    Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
    Biol Direct 7:35. 2012
    ..This view, which now lays claim to important theoretical, experimental, and practical results, demands our attention. CNE provides a way to explore its most significant implications about the role of variation in evolution...
  11. ncbi request reprint Mutationism and the dual causation of evolutionary change
    Arlin Stoltzfus
    Center for Advanced Research in Biotechnology, Rockville, MD 20850, USA
    Evol Dev 8:304-17. 2006
    ....
  12. pmc Nexplorer: phylogeny-based exploration of sequence family data
    Vivek Gopalan
    Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
    Bioinformatics 22:120-1. 2006
    ..Nexplorer provides a flexible means to develop customized views that combine a tree and a data matrix or alignment, to create subsets of data, and to output data files or publication-quality graphics...
  13. ncbi request reprint Molecular evolution: introns fall into place
    Arlin Stoltzfus
    Center for Advanced Research in Biotechnology CARB, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
    Curr Biol 14:R351-2. 2004
    ..The evolutionary origin of spliceosomal introns remains elusive. The startling success of a new way of predicting intron sites suggests that the splicing machinery determines where introns are added to genes...
  14. doi request reprint Gene identification in black cohosh (Actaea racemosa L.): expressed sequence tag profiling and genetic screening yields candidate genes for production of bioactive secondary metabolites
    Martin J Spiering
    Fischell Department of Bioengineering, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
    Plant Cell Rep 30:613-29. 2011
    ....
  15. pmc The exchangeability of amino acids in proteins
    Lev Y Yampolsky
    Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee 37614 1710, USA
    Genetics 170:1459-72. 2005
    ..EX not only captures useful information on exchangeability while remaining free of other effects, but also outperforms all measures tested except for the best-performing alignment scoring matrix, which is comparable in performance...