Arjun Bhutkar, Susan Russo, Temple F. Smith, William M. Gelbart
Genome scale synteny analysis, the analysis of relative gene-order conservation between species, can provide key insights into evolutionary chromosomal dynamics, rearrangement rates between species,...
Lan Hu, Daniel Segrè, Temple F. Smith
Exploiting the ortholog/homolog information now available from the complete genomic sequences of twelve species of Drosophila, we have investigated the ability of regulatory site recognition methods...
35 GENE EXPANSION IN TRICHOMONAS VAGINALIS: A CASE STUDY ON TRANSMEMBRANE CYCLASES (2010)
Temple F. Smith, John Samuelson
The draft genome of Trichomonas vaginalis was recently published, but not much is known on why it has such a large genome. In part this size is due to many gene family expansions. For example we...
GTPases and the origin of the ribosome (2010)
Hartman, Hyman, Smith, Temple F
Abstract Background This paper is an attempt to trace the evolution of the ribosome through the evolution of the universal P-loop GTPases that are involved with the ribosome in translation and with...
The origin and evolution of the ribosome (2008)
Smith, Temple F, Lee, Jung C, Gutell, Robin R, Hartman, Hyman
Abstract Background The origin and early evolution of the active site of the ribosome can be elucidated through an analysis of the ribosomal proteins' taxonomic block structures and their RNA...
EVOLUTIONARY CONSTRAINT NETWORKS IN LIGAND-BINDING DOMAINS: AN INFORMATION-THEORETIC APPROACH (2008)
Sylvia B. Nagl, James Freeman, Temple F. Smith
Ligand-binding sites in homologous protein domains can diverge greatly during evolution. This poses a particularly interesting problem in those cases where the ligand-binding site is situated in, or...
Comprehensive statistical method for protein fold recognition (2008)
Jadwiga R. Biefikowska, Lihua Yu, Sophia Zarakhovich Robert, G. Rogers, Temple F. Smith
We present a protein fold recognition method that uses a comprehensive statistical interpretation of structural Hid-den Markov Models (HMMs). The structure/fi)ld recogni-tion is done by summing the...
Michael S. Waterman, Los Angeles, Culiforniu I I, Temple F. Smith
important mathematical problem in molecular biology. Dynamic programming methods are currently the most useful computer technique but are frequently very expensive in running time. In this paper new...
The Continuing Case of the:-- Florida Dentist (2008)
S. Res, Temple F. Smith, Michael S. Waterman
the free atmosphere, away from the influ- 2. S. M. et a/.. J. Geophys. Res. 92. 1977 ences of the earth's surface. From all of these measurements will come an understanding of the processes that...
Protein Constraints Induced by Multiframe Encoding (2007)
Temple F. Smith, Michael S. Waterman
INTRODUCTION The recent sequencing of the viral genomes SV40, X174 [1-3] strongly supports the existence of multiframe codon reading. This overlapping of protein sequence information within the...
Bhutkar, Arjun, Gelbart, William M, Smith, Temple F
Abstract A simple, fast, and biologically inspired computational approach for inferring genome-scale rearrangement phylogeny and ancestral gene order has been developed. This has been applied to...
Genome-scale analysis of positionally relocated genes (2007)
Bhutkar, Arjun, Russo, Susan M., Smith, Temple F., Gelbart, William M.
During evolution, genome reorganization includes large-scale events such as inversions, translocations, and segmental or even whole-genome duplications, as well as fine-scale events such as the...
Transcription Factor Map Alignment of Promoter Regions (2006)
Enrique Blanco, Xavier Messeguer, Temple F. Smith, Roderic Guigó
We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the...
The archaeal origins of the eukaryotic translational system (2006)
Hyman Hartman, Paola Favaretto, Temple F. Smith
Among the 78 eukaryotic ribosomal proteins, eleven are specific to Eukarya, 33 are common only to Archaea and Eukarya and 34 are homologous (at least in part) to those of both Bacteria and Archaea....
Constraining ribosomal RNA conformational space (2005)
Favaretto, Paola, Bhutkar, Arjun, Smith, Temple F.
Despite the potential for many possible secondary-structure conformations, the native sequence of ribosomal RNA (rRNA) is able to find the correct and universally conserved core fold. This study...
A search method for homologs of small proteins. Ubiquitin-like proteins in prokaryotic cells? (2003)
Bienkowska, Jadwiga R., Hartman, Hyman, Smith, Temple F.
The question of protein homology versus analogy arises when proteins share a common function or a common structural fold without any statistically significant amino acid sequence similarity. Even...
Venkatesan, Kavitha, McManus, Heather R., Mello, Craig C., Smith, Temple F., Hansen, Ulla
The LSF/Grainyhead transcription factor family is involved in many important biological processes, including cell cycle, cell growth and development. In order to investigate the evolutionary...
Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites (2002)
Graber, Joel H., McAllister, Gregory D., Smith, Temple F.
We present a tool for the prediction of mRNA 3′‐processing (cleavage and polyadenylation) sites in the yeast Saccharomyces cerevisiae, based on a discrete state-space model or hidden Markov...
Survey of human mitochondrial diseases using new genomic/proteomic tools (2001)
Plasterer, Thomas N, Smith, Temple F, Mohr, Scott C
Abstract Background We have constructed Bayesian prior-based, amino-acid sequence profiles for the complete yeast mitochondrial proteome and used them to develop methods for identifying and...
Hisbergues, Michael, Gaitatzes, Chrysanthe G., Joset, Françoise, Bedu, Sylvie, Smith, Temple F.
Synechocystis PCC6803 possesses several open reading frames encoding putative WD-repeat proteins. One, the Hat protein, is involved in the control of a high-affinity transport system for inorganic...
Global optimum protein threading with gapped alignment and empirical pair score functions (1996)
Richard H. Lathrop, Temple F. Smith
We describe a branch-and-bound search algorithm for finding the exact global optimum gapped sequencestructure alignment ("threading") between a protein sequence and a protein core...
Global optimum protein threading with gapped alignment and empirical pair score functions (1996)
Richard H. Lathrop, Temple F. Smith
We describe a branch-and-bound search algorithm for finding the exact global optimum gapped sequencestructure alignment ("threading") between a protein sequence and a protein core...
A Biologically Meaningful Model for Comparing Molecular Phylogenies (1995)
Boris Mirkin, Ilya Muchnik, Temple F. Smith
In the framework of the problem of combining different gene trees into a unique species phylogeny, a model for duplication/speciation/loss events along the evolutionary tree is introduced. The model...
The ancient regulatory-protein family of WD-repeat proteins (1994)
Eva J. Neer, Carl J. Schmidt, Raman Nambudripad, Temple F. Smith
Randall F. Smith, Temple F. Smith
A multiple sequence alignment algorithm is described that uses a dynamic programming-based pattern construction method to align a set of homologous sequences based on their common pattern of...
Corruption of genomic databases with anomalous sequence (1992)
Lamperti, Edward D., Kittelberger, J.Matthew, Smith, Temple F., VillaKomaroff, Lydia
We describe evidence that DNA sequences from vectors used for cloning and sequencing have been incorporated accidentally into eukaryotic entries in the GenBank database. These incorporations were not...
Automatic evaluation of protein sequence functional patterns (1991)
Guigó, Roderic, Johanson, Ann, Smith, Temple F.
A procedure that automatically provides an evaluation of the diagnostic ability of a protein sequence functional pattern is described. The procedure relies on the identification of the closest...
Fischel-Ghodsian, Fariba, Mathiowitz, George, Smith, Temple F.
A method for comparison of protein sequences based on their primary and secondary structure is described. Protein sequences are annotated with predicted secondary structures (using a modified Chou...
New analytical tool for analysis of splice site sequence determinants (1989)
Mengeritsky, Galina, Smith, Temple F.
A new analytical method has been used to examine the set of 40 exon/intron boundaries within the rat embryonic myosin heavy chain (MHCemb) gene. It has also been applied to an additional set of...
Lathrop, Richard H., Webster, Teresa A., Smith, Temple F.
There are many situations in which a very detailed low-level description encodes, through a hierarchical organization, a recognizable higher-order pattern. The macro-molecular structural...
Lathrop, Richard H., Webster, Teresa A., Smith, Temple F.
There are many situations in which a very detailed low-level description encodes, through a hierarchical organization, a recognizable higher-order pattern. The macro-molecular structural...
Molecular genetics and computer analyses (1987)
Gruskin, Karen D., Smith, Temple F.
This issue of CABIOS contains a set of reviewed papers which relate to the recent Macromolecules, Genes and Computers International Workshop and Symposium held August 12–17, 1986 in Waterville...
A modified Chou and Fasman protein structure algorithm (1987)
Ralph, William W., Webster, Teresa, Smith, Temple F.
A FORTRAN program PRSTRC has been developed for protein secondary structure prediction, which is a modified Chou and Fasman (1978) analysis. This implementation carries out a running average of amino...
Recognition of characteristic patterns in sets of functionally equivalent DNA sequences (1987)
Mengeritsky, Galina, Smith, Temple F.
An algorithm has been developed for the identification of unknown patterns which are distinctive for a set of short DNA sequences believed to be functionally equivalent. A pattern is defined as being...
The statistical distribution of nucleic acid similarities (1985)
Smith, Temple F., Waterman, Michael S., Burks, Christian
All pairs of a large set of known vertebrate DNA sequences were searched by computer for most similar segments. Analysis of this data shows that the computed similarity scores are distributed...
Algorithms for Restriction Map Comparisons (1984)
Michael S. Waterman, Temple F. Smith, Harold L. Katcher
An algorithm is presented which compares two restriction ~ ~ lating maps, yielding a measure of distance between the maps and re-the maps by an alignment. This new algorithm finds the minimum...
Algorithms for restriction map comparisons (1984)
Waterman, Michael S., Smith, Temple F., Katcher, Harold L.
An algorithm is presented which compares two restriction maps, yielding a measure of distance between the maps and relating the maps by an alignment. This new algorithm finds the minimum weighted sum...
Hierarchical analysis of influenza A hemagglutinin gene sequences (1982)
Lipman, David J., Smith, Temple F., Beckman, Richard J., Waterman, Michael S.
Five recently sequenced hemagglutinin genes from Influenza A virus strains are studied for similarities in a hierarchical fashion. The sequences are compared for similarity, first on the level of...
The deuteron amplitudes from a composite particle nuclear scattering theory / (1969)
Thesis (Ph. D.)--University of Colorado, 1969.
Operons in Escherichia coli: Genomic analyses and predictions
Salgado, Heladia, Moreno-Hagelsieb, Gabriel, Smith, Temple F., Collado-Vides, Julio
The rich knowledge of operon organization in Escherichia coli, together with the completed chromosomal sequence of this bacterium, enabled us to perform an analysis of distances between genes and of...
In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species
Graber, Joel H., Cantor, Charles R., Mohr, Scott C., Smith, Temple F.
We have investigated mRNA 3′-end-processing signals in each of six eukaryotic species (yeast, rice, arabidopsis, fruitfly, mouse, and human) through the analysis of more than 20,000 3′-expressed...
Probabilistic prediction of Saccharomyces cerevisiae mRNA 3′-processing sites
Graber, Joel H., McAllister, Gregory D., Smith, Temple F.
We present a tool for the prediction of mRNA 3′-processing (cleavage and polyadenylation) sites in the yeast Saccharomyces cerevisiae, based on a discrete state-space model or hidden Markov model....
Venkatesan, Kavitha, McManus, Heather R., Mello, Craig C., Smith, Temple F., Hansen, Ulla
The LSF/Grainyhead transcription factor family is involved in many important biological processes, including cell cycle, cell growth and development. In order to investigate the evolutionary...
Fitch, Walter M., Smith, Temple F.
Current theory is adequate to the task of finding an optimal alignment between two character strings such as nucleic acids. Most algorithms currently in use must fail to find the homologous alignment...
Constraining ribosomal RNA conformational space
Favaretto, Paola, Bhutkar, Arjun, Smith, Temple F.
Despite the potential for many possible secondary-structure conformations, the native sequence of ribosomal RNA (rRNA) is able to find the correct and universally conserved core fold. This study...
Transcription Factor Map Alignment of Promoter Regions
Blanco, Enrique, Messeguer, Xavier, Smith, Temple F, Guigó, Roderic
We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the...
Operons in Escherichia coli: Genomic analyses and predictions
Salgado, Heladia, Moreno-Hagelsieb, Gabriel, Smith, Temple F., Collado-Vides, Julio
The rich knowledge of operon organization in Escherichia coli, together with the completed chromosomal sequence of this bacterium, enabled us to perform an analysis of distances between genes and of...
In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species
Graber, Joel H., Cantor, Charles R., Mohr, Scott C., Smith, Temple F.
We have investigated mRNA 3′-end-processing signals in each of six eukaryotic species (yeast, rice, arabidopsis, fruitfly, mouse, and human) through the analysis of more than 20,000 3′-expressed...
Probabilistic prediction of Saccharomyces cerevisiae mRNA 3′-processing sites
Graber, Joel H., McAllister, Gregory D., Smith, Temple F.
We present a tool for the prediction of mRNA 3′-processing (cleavage and polyadenylation) sites in the yeast Saccharomyces cerevisiae, based on a discrete state-space model or hidden Markov model....
Venkatesan, Kavitha, McManus, Heather R., Mello, Craig C., Smith, Temple F., Hansen, Ulla
The LSF/Grainyhead transcription factor family is involved in many important biological processes, including cell cycle, cell growth and development. In order to investigate the evolutionary...
Fitch, Walter M., Smith, Temple F.
Current theory is adequate to the task of finding an optimal alignment between two character strings such as nucleic acids. Most algorithms currently in use must fail to find the homologous alignment...
Constraining ribosomal RNA conformational space
Favaretto, Paola, Bhutkar, Arjun, Smith, Temple F.
Despite the potential for many possible secondary-structure conformations, the native sequence of ribosomal RNA (rRNA) is able to find the correct and universally conserved core fold. This study...
Transcription Factor Map Alignment of Promoter Regions
Blanco, Enrique, Messeguer, Xavier, Smith, Temple F, Guigó, Roderic
We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the...
Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study
Bhutkar, Arjun, Gelbart, William M, Smith, Temple F
A simple, fast, and biologically-inspired computational approach to infer genome-scale rearrangement phylogeny and ancestral gene order has been developed and applied to eight Drosophila genomes,...
Hisbergues, Michael, Gaitatzes, Chrysanthe G., Joset, Françoise, Bedu, Sylvie, Smith, Temple F.
Synechocystis PCC6803 possesses several open reading frames encoding putative WD-repeat proteins. One, the Hat protein, is involved in the control of a high-affinity transport system for inorganic...
The origin and evolution of the ribosome
Smith, Temple F, Lee, Jung C, Gutell, Robin R, Hartman, Hyman
Genome-scale analysis of positionally relocated genes
Bhutkar, Arjun, Russo, Susan M., Smith, Temple F., Gelbart, William M.
During evolution, genome reorganization includes large-scale events such as inversions, translocations, and segmental or even whole-genome duplications, as well as fine-scale events such as the...
Schaeffer, Stephen W., Bhutkar, Arjun, McAllister, Bryant F., Matsuda, Muneo, Matzkin, Luciano M., O'Grady, Patrick M., ...
The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of...
Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes
Bhutkar, Arjun, Schaeffer, Stephen W., Russo, Susan M., Xu, Mu, Smith, Temple F., Gelbart, William M.
The availability of 12 complete genomes of various species of genus Drosophila provides a unique opportunity to analyze genome-scale chromosomal rearrangements among a group of closely related...
The archaeal origins of the eukaryotic translational system
Hartman, Hyman, Favaretto, Paola, Smith, Temple F.
Among the 78 eukaryotic ribosomal proteins, eleven are specific to Eukarya, 33 are common only to Archaea and Eukarya and 34 are homologous (at least in part) to those of both Bacteria and Archaea....