Research Topics
| Temple SmithSummaryAffiliation: Boston University Country: USA Publications
Research Grants
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Detail Information
Publications
Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case studyArjun 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...- GTPases and the origin of the ribosomeHyman 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... 
Current limitations to protein threading approachesT 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...
Diversity of WD-repeat proteinsTemple 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...- The origin and evolution of the ribosomeTemple 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... - The WD repeat: a common architecture for diverse functionsT 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... - Survey of human mitochondrial diseases using new genomic/proteomic toolsT 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... - Protein fold recognition by total alignment probabilityJ 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... - Filtered neighbors threadingJ 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... - Performance of threading scoring functions designed using new optimization methodJ R Bienkowska
BioMolecular Engineering Research Center, College of Engineering, Boston University, Massachusetts 02215, USA
J Comput Biol 6:299-311. 1999..94... - Genomic detection of new yeast pre-mRNA 3'-end-processing signalsJ H Graber
Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA
Nucleic Acids Res 27:888-94. 1999.... - Homology model for the ligand-binding domain of the human estrogen receptorG 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... - 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 evolutionJ 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... - Phylogenetic relationship of the complete Rauscher murine leukemia virus genome with other murine leukemia virus genomesA 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... - Functional conservation between members of an ancient duplicated transcription factor family, LSF/GrainyheadKavitha 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... - Evolutionary changes in gene regulation from a comparative analysis of multiple Drosophila speciesLan 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... - Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sitesJoel 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... - Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomesArjun 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... - Evolution of genes and genomes on the Drosophila phylogenyAndrew 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... - Genome-scale analysis of positionally relocated genesArjun Bhutkar
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Genome Res 17:1880-7. 2007.... - Techniques for multi-genome synteny analysis to overcome assembly limitationsArjun 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... - Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotesPrashanth 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... - Triage protein fold predictionHongxian 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... - Gene expansion in Trichomonas vaginalis: a case study on transmembrane cyclasesJike 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... - Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical mapsStephen 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... - Information-theoretic dissection of pairwise contact potentialsMelissa 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... - The archaeal origins of the eukaryotic translational systemHyman 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... - Transcription factor map alignment of promoter regionsEnrique Blanco
Research Group in Biomedical Informatics, , Barcelona, Catalonia, Spain
PLoS Comput Biol 2:e49. 2006.... - 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 Grants
- AUTOMATED PROTEIN FOLD MODEL GENERATIONTemple 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. ..