Temple Smith

Summary

Affiliation: Boston University
Country: USA

Publications

  1. pmc Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study
    Arjun Bhutkar
    BioMolecular Engineering Research Center, Boston University, Cummington St, Boston, MA 02215, USA
    Genome Biol 8:R236. 2007
  2. pmc GTPases and the origin of the ribosome
    Hyman Hartman
    BioMolecular Engineering Research Center, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Biol Direct 5:36. 2010
  3. ncbi request reprint Current limitations to protein threading approaches
    T F Smith
    BioMolecular Engineering Research Center, College of Engineering, Boston University, Massachusetts 02215, USA
    J Comput Biol 4:217-25. 1997
  4. doi request reprint Diversity of WD-repeat proteins
    Temple F Smith
    BioMolecular Engineering Research Center, College of Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Subcell Biochem 48:20-30. 2008
  5. pmc The origin and evolution of the ribosome
    Temple F Smith
    BioMolecular Engineering Research Center, 36 Cummington Street, Boston University, Boston, MA 02215, USA
    Biol Direct 3:16. 2008
  6. ncbi request reprint The WD repeat: a common architecture for diverse functions
    T F Smith
    Boston University, BioMolecular Engineering Research Center, Boston, MA 02215, USA
    Trends Biochem Sci 24:181-5. 1999
  7. pmc Survey of human mitochondrial diseases using new genomic/proteomic tools
    T N Plasterer
    BioMolecular Engineering Research Center and Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
    Genome Biol 2:RESEARCH0021. 2001
  8. ncbi request reprint Protein fold recognition by total alignment probability
    J R Bienkowska
    BioMolecular Engineering Research Center, College of Engineering, Boston University, Boston, Massachusetts 02215, USA
    Proteins 40:451-62. 2000
  9. ncbi request reprint Filtered neighbors threading
    J R Bienkowska
    BioMolecular Engineering Research Center, College of Engineering, Boston University, MA 02215, USA
    Proteins 37:346-59. 1999
  10. ncbi request reprint Performance of threading scoring functions designed using new optimization method
    J R Bienkowska
    BioMolecular Engineering Research Center, College of Engineering, Boston University, Massachusetts 02215, USA
    J Comput Biol 6:299-311. 1999

Research Grants

  1. AUTOMATED PROTEIN FOLD MODEL GENERATION
    Temple Smith; Fiscal Year: 2003

Detail Information

Publications29

  1. pmc Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study
    Arjun Bhutkar
    BioMolecular Engineering Research Center, Boston University, Cummington St, Boston, MA 02215, USA
    Genome Biol 8:R236. 2007
    ..The results provide insight into evolutionary chromosomal dynamics and synteny analysis, and inform speciation studies...
  2. pmc GTPases and the origin of the ribosome
    Hyman Hartman
    BioMolecular Engineering Research Center, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Biol Direct 5:36. 2010
    ..All of these GTPases also contain the OB fold also found in the non GTPase IF1 involved in initiation. The GTPase involved in the signal recognition particle in most Bacteria and Archaea is SRP54...
  3. ncbi request reprint Current limitations to protein threading approaches
    T F Smith
    BioMolecular Engineering Research Center, College of Engineering, Boston University, Massachusetts 02215, USA
    J Comput Biol 4:217-25. 1997
    ..Also discussed is one of the likely sources of the current limited success, that being the form of the pairwise potentials used in most threading approaches...
  4. doi request reprint Diversity of WD-repeat proteins
    Temple F Smith
    BioMolecular Engineering Research Center, College of Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Subcell Biochem 48:20-30. 2008
    ..It supports both their ancient and proto eukaryotic origins and supports a likely association with many genetic diseases...
  5. pmc The origin and evolution of the ribosome
    Temple F Smith
    BioMolecular Engineering Research Center, 36 Cummington Street, Boston University, Boston, MA 02215, USA
    Biol Direct 3:16. 2008
    ..Comparison between the two subunits, exploiting the detailed three-dimensional structures of the bacterial and archaeal ribosomes, is especially informative...
  6. ncbi request reprint The WD repeat: a common architecture for diverse functions
    T F Smith
    Boston University, BioMolecular Engineering Research Center, Boston, MA 02215, USA
    Trends Biochem Sci 24:181-5. 1999
    ..Proteins that have very similar surfaces are likely to have common binding partners and similar functions...
  7. pmc Survey of human mitochondrial diseases using new genomic/proteomic tools
    T N Plasterer
    BioMolecular Engineering Research Center and Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
    Genome Biol 2:RESEARCH0021. 2001
    ..These profiles can also find distant homologs with determined three-dimensional structures that aid in the interpretation of effects of missense mutations...
  8. ncbi request reprint Protein fold recognition by total alignment probability
    J R Bienkowska
    BioMolecular Engineering Research Center, College of Engineering, Boston University, Boston, Massachusetts 02215, USA
    Proteins 40:451-62. 2000
    ..Fold recognition by total probability was 40% more accurate than fold recognition by the optimal alignment probability. Proteins 2000;40:451-462...
  9. ncbi request reprint Filtered neighbors threading
    J R Bienkowska
    BioMolecular Engineering Research Center, College of Engineering, Boston University, MA 02215, USA
    Proteins 37:346-59. 1999
    ..These results show that reduction of noise from the observed neighbor pair preferences by filtering leads to noticeable improvements in the predicted sequence-to-structure alignments...
  10. ncbi request reprint Performance of threading scoring functions designed using new optimization method
    J R Bienkowska
    BioMolecular Engineering Research Center, College of Engineering, Boston University, Massachusetts 02215, USA
    J Comput Biol 6:299-311. 1999
    ..94...
  11. pmc Genomic detection of new yeast pre-mRNA 3'-end-processing signals
    J H Graber
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 27:888-94. 1999
    ....
  12. ncbi request reprint Homology model for the ligand-binding domain of the human estrogen receptor
    G J Maalouf
    Boston University, BioMolecular Engineering Research Center, MA 02215, USA
    J Biomol Struct Dyn 15:841-51. 1998
    ..It also provides a possible explanation for how hER discriminates between estradiol and testosterone...
  13. ncbi request reprint Structural analysis of the CD11b gene and phylogenetic analysis of the alpha-integrin gene family demonstrate remarkable conservation of genomic organization and suggest early diversification during evolution
    J C Fleming
    Hematology Oncology Division, Beth Israel Hospital, Boston, MA 02215
    J Immunol 150:480-90. 1993
    ..Furthermore, comparison of the CD11b gene structure with that of platelet glycoprotein IIb and Drosophila PS2 suggest how the human leukocyte integrins evolved and dispersed during the course of evolution...
  14. ncbi request reprint Phylogenetic relationship of the complete Rauscher murine leukemia virus genome with other murine leukemia virus genomes
    A H Khimani
    Laboratory of Viral Pathogenesis, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Virology 238:64-7. 1997
    ..In summary, a phylogenetic analysis involving various MuLVs has been performed, in which the postulated close relationship between R-MuLV and F-MuLV has been confirmed, consistent with the pathobiology of the two viruses...
  15. pmc Functional conservation between members of an ancient duplicated transcription factor family, LSF/Grainyhead
    Kavitha Venkatesan
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 31:4304-16. 2003
    ..e. to the time when the first multicellular organisms are thought to have arisen...
  16. ncbi request reprint Evolutionary changes in gene regulation from a comparative analysis of multiple Drosophila species
    Lan Hu
    Boston University, Boston MA 02215, U S A
    Genome Inform 18:12-21. 2007
    ..Extensions of our approach could be used to shed light on the role of gene regulation in the evolutionary adaptation to different environmental conditions...
  17. pmc Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites
    Joel H Graber
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 30:1851-8. 2002
    ..The lack of an apparent 3'-processing site calls into question the validity of some predicted genes. This is specifically investigated for predicted genes with overlapping coding sequences...
  18. pmc Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes
    Arjun Bhutkar
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 179:1657-80. 2008
    ..On the other hand, an analysis of the disruption of syntenic blocks between species allowed the identification of fixed inversion breakpoints and estimates of breakpoint reuse and lineage-specific breakpoint event segregation...
  19. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  20. pmc Genome-scale analysis of positionally relocated genes
    Arjun Bhutkar
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genome Res 17:1880-7. 2007
    ....
  21. ncbi request reprint Techniques for multi-genome synteny analysis to overcome assembly limitations
    Arjun Bhutkar
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
    Genome Inform 17:152-61. 2006
    ..This approach was applied to a comparative study involving Drosophila.melanogaster and Drosophila.pseudoobscura genomes, as an example, and has been useful in analyzing inter-species syntenic relationships...
  22. ncbi request reprint Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes
    Prashanth Vishwanath
    BioMolecular Engineering Research Center, Boston University, 36 Cummington St, Boston, MA 02215, USA
    Mol Phylogenet Evol 33:615-25. 2004
    ..Interestingly, phylogenetic analysis places the origin of eukaryotes at about the same time and shows a closer relationship of the eukaryotic ribosome-associated proteins to crenarchaeal rather than euryarchaeal counterparts...
  23. ncbi request reprint Triage protein fold prediction
    Hongxian He
    BioMolecular Engineering Research Center, Biomedical Engineering Department, Boston University, Boston, Massachusetts 02215, USA
    Proteins 48:654-63. 2002
    ..Two different schemes of assigning Bayesian model priors are presented and discussed...
  24. ncbi request reprint Gene expansion in Trichomonas vaginalis: a case study on transmembrane cyclases
    Jike Cui
    Boston University, Boston, MA 02215, U S A
    Genome Inform 18:35-43. 2007
    ..We gave three possible hypotheses for that observation: a) Sequencing error or stop-codon read-through; b) Recency of duplication and mutation; c) The likelihood of functional pseudogene...
  25. pmc Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps
    Stephen W Schaeffer
    Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Genetics 179:1601-55. 2008
    ..Despite the conservation of genes within homologous chromosome arms across species, the karyotypes of these species have changed through the fusion of chromosomal arms followed by subsequent rearrangement events...
  26. ncbi request reprint Information-theoretic dissection of pairwise contact potentials
    Melissa S Cline
    Center for Biomolecular Science and Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA
    Proteins 49:7-14. 2002
    ..We found the information in amino acid contacts to be modest: 0.04 bits per contact. Of that, only 0.01 bits of information could not be attributed to hydropathy, charge, disulfide bonding, or burial...
  27. pmc The archaeal origins of the eukaryotic translational system
    Hyman Hartman
    Biological Engineering Division, Building 56, Room 354, Massachusetts Institute of Technology, Cambridge MA 02139, USA
    Archaea 2:1-9. 2006
    ..Phylogenetic analyses provide support for the timing of this acquisition coinciding with an ancient bottleneck in prokaryotic diversity...
  28. pmc Transcription factor map alignment of promoter regions
    Enrique Blanco
    Research Group in Biomedical Informatics, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
    PLoS Comput Biol 2:e49. 2006
    ....
  29. ncbi request reprint A search method for homologs of small proteins. Ubiquitin-like proteins in prokaryotic cells?
    Jadwiga R Bienkowska
    Serono Reproductive Biology Institute, One Technology Place, Rockland, MA 02370, USA
    Protein Eng 16:897-904. 2003
    ..This approach results in the identification of 90 probable ubiquitin-related proteins, including examples from the two prokaryotic domains of life, Archaea and Bacteria...

Research Grants3

  1. AUTOMATED PROTEIN FOLD MODEL GENERATION
    Temple Smith; Fiscal Year: 2003
    ..In addition, these libraries and their associated analysis tools will provide valuable data to aid in the experimental design to test predictions about the cellular roles of such proteins. ..