molecular evolution

Summary

Summary: Evolution at the molecular level of DNA sequences and proteins. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)

Top Publications

  1. pmc The impact of recombination on nucleotide substitutions in the human genome
    Laurent Duret
    Laboratoire de Biometrie et Biologie Evolutive, Universite de Lyon, Universite Lyon 1, CNRS, UMR 5558, Villeurbanne, France
    PLoS Genet 4:e1000071. 2008
  2. pmc BEAST: Bayesian evolutionary analysis by sampling trees
    Alexei J Drummond
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    BMC Evol Biol 7:214. 2007
  3. pmc Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools
    Paul D Thomas
    Evolutionary Systems Biology Group, SRI International 333 Ravenswood Ave, Menlo Park CA 94025, USA
    Nucleic Acids Res 34:W645-50. 2006
  4. ncbi MrBayes 3: Bayesian phylogenetic inference under mixed models
    Fredrik Ronquist
    Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Norbyv 18D, SE 752 36 Uppsala, Sweden
    Bioinformatics 19:1572-4. 2003
  5. pmc RNA-based gene duplication: mechanistic and evolutionary insights
    Henrik Kaessmann
    Center for Integrative Genomics, University of Lausanne, Genopode, CH 1015 Lausanne, Switzerland
    Nat Rev Genet 10:19-31. 2009
  6. ncbi RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    Alexandros Stamatakis
    Swiss Federal Institute of Technology Lausanne, School of Computer and Communication Sciences Lab Prof Moret, Station 14, CH 1015 Lausanne, Switzerland
    Bioinformatics 22:2688-90. 2006
  7. ncbi MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    Koichiro Tamura
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA
    Mol Biol Evol 24:1596-9. 2007
  8. ncbi A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    Stephane Guindon
    LIRMM, CNRS, 161 rue Ada, 34392, Montpellier Cedex 5, France
    Syst Biol 52:696-704. 2003
  9. pmc Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    Daniel Falush
    Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
    Genetics 164:1567-87. 2003
  10. ncbi A rapid bootstrap algorithm for the RAxML Web servers
    Alexandros Stamatakis
    Exelixis Lab, Teaching and Research Unit Bioinformatics, Department of Computer Science, Ludwig Maximilians University Munich, Munich, Germany
    Syst Biol 57:758-71. 2008

Detail Information

Publications312 found, 100 shown here

  1. pmc The impact of recombination on nucleotide substitutions in the human genome
    Laurent Duret
    Laboratoire de Biometrie et Biologie Evolutive, Universite de Lyon, Universite Lyon 1, CNRS, UMR 5558, Villeurbanne, France
    PLoS Genet 4:e1000071. 2008
    ..Our results also shed light on variations in the rate of crossover relative to non-crossover events, along chromosomes and according to sex, and also on the conservation of hotspot density between human and chimp...
  2. pmc BEAST: Bayesian evolutionary analysis by sampling trees
    Alexei J Drummond
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    BMC Evol Biol 7:214. 2007
    ..A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented...
  3. pmc Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools
    Paul D Thomas
    Evolutionary Systems Biology Group, SRI International 333 Ravenswood Ave, Menlo Park CA 94025, USA
    Nucleic Acids Res 34:W645-50. 2006
    ..All three web services are available at http://www.pantherdb.org/tools...
  4. ncbi MrBayes 3: Bayesian phylogenetic inference under mixed models
    Fredrik Ronquist
    Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Norbyv 18D, SE 752 36 Uppsala, Sweden
    Bioinformatics 19:1572-4. 2003
    ..g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters...
  5. pmc RNA-based gene duplication: mechanistic and evolutionary insights
    Henrik Kaessmann
    Center for Integrative Genomics, University of Lausanne, Genopode, CH 1015 Lausanne, Switzerland
    Nat Rev Genet 10:19-31. 2009
    ..For example, analyses of chromosomal gene movement patterns via RNA-based gene duplication have shed fresh light on the evolutionary origin and biology of our sex chromosomes...
  6. ncbi RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    Alexandros Stamatakis
    Swiss Federal Institute of Technology Lausanne, School of Computer and Communication Sciences Lab Prof Moret, Station 14, CH 1015 Lausanne, Switzerland
    Bioinformatics 22:2688-90. 2006
    ..The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively...
  7. ncbi MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    Koichiro Tamura
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA
    Mol Biol Evol 24:1596-9. 2007
    ..The current version of MEGA is available free of charge at (http://www.megasoftware.net)...
  8. ncbi A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    Stephane Guindon
    LIRMM, CNRS, 161 rue Ada, 34392, Montpellier Cedex 5, France
    Syst Biol 52:696-704. 2003
    ..This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/...
  9. pmc Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    Daniel Falush
    Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
    Genetics 164:1567-87. 2003
    ..The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu...
  10. ncbi A rapid bootstrap algorithm for the RAxML Web servers
    Alexandros Stamatakis
    Exelixis Lab, Teaching and Research Unit Bioinformatics, Department of Computer Science, Ludwig Maximilians University Munich, Munich, Germany
    Syst Biol 57:758-71. 2008
    ..These Web servers offer the possibility to conduct large-scale phylogenetic inferences to a large part of the community that does not have access to, or the expertise to use, high-performance computing resources...
  11. ncbi ProtTest: selection of best-fit models of protein evolution
    Federico Abascal
    Department of Biochemistry, Genetics and Immunology, Universidad de Vigo, Spain
    Bioinformatics 21:2104-5. 2005
    ..We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment...
  12. ncbi Application of phylogenetic networks in evolutionary studies
    Daniel H Huson
    Center for Bioinformatics ZBIT, Tubingen University, Tubingen, Germany
    Mol Biol Evol 23:254-67. 2006
    ..Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees...
  13. ncbi Repbase Update, a database of eukaryotic repetitive elements
    J Jurka
    Genetic Information Research Institute, Mountain View, CA 94043, USA
    Cytogenet Genome Res 110:462-7. 2005
    ..Sequences from Repbase Update are used to screen and annotate repetitive elements using programs such as Censor and RepeatMasker. Repbase Update is available on the worldwide web at http://www.girinst.org/Repbase_Update.html...
  14. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
    ..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
  15. ncbi APE: Analyses of Phylogenetics and Evolution in R language
    Emmanuel Paradis
    Laboratoire de Paléontologie, Paléobiologie and Phylogénie, Institut des Sciences de l Evolution, Universite Montpellier II, F 34095 Montpellier cedex 05, France
    Bioinformatics 20:289-90. 2004
    Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics...
  16. ncbi MODELTEST: testing the model of DNA substitution
    D Posada
    Department of Zoology, Brigham Young University, 574 WIDB, Provo, UT 84602 5255, USA
    Bioinformatics 14:817-8. 1998
    ..The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data...
  17. ncbi Bayesian coalescent inference of past population dynamics from molecular sequences
    A J Drummond
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 22:1185-92. 2005
    ....
  18. ncbi HyPhy: hypothesis testing using phylogenies
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego San Diego, CA 92103, USA
    Bioinformatics 21:676-9. 2005
    ..AVAILABILITY: http://www.hyphy.org CONTACT: muse@stat.ncsu.edu SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org...
  19. ncbi A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    S Whelan
    Department of Zoology, University of Cambridge, Cambridge, England
    Mol Biol Evol 18:691-9. 2001
    ....
  20. ncbi CRISPR provides acquired resistance against viruses in prokaryotes
    Rodolphe Barrangou
    Danisco USA Inc, 3329 Agriculture Drive, Madison, WI 53716, USA
    Science 315:1709-12. 2007
    ..Thus, CRISPR, together with associated cas genes, provided resistance against phages, and resistance specificity is determined by spacer-phage sequence similarity...
  21. ncbi Not so different after all: a comparison of methods for detecting amino acid sites under selection
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego, USA
    Mol Biol Evol 22:1208-22. 2005
    ..We demonstrate our methods on sequence data from the human immunodeficiency virus type 1 env and pol genes and simulated alignments...
  22. ncbi The genetic legacy of the Quaternary ice ages
    G Hewitt
    School of Biological Sciences, University of East Anglia, Norwich, UK
    Nature 405:907-13. 2000
    ..The present genetic structure of populations, species and communities has been mainly formed by Quaternary ice ages, and genetic, fossil and physical data combined can greatly help our understanding of how organisms were so affected...
  23. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  24. ncbi Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
    Mol Biol Evol 22:2472-9. 2005
    ..Bayes empirical Bayes identification of amino acid sites under positive selection along the foreground branches was found to be reliable, but lacked power...
  25. pmc The COG database: a tool for genome-scale analysis of protein functions and evolution
    R L Tatusov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 28:33-6. 2000
    ..The COG database is accompanied by the COGNITOR program that is used to fit new proteins into the COGs and can be applied to functional and phylogenetic annotation of newly sequenced genomes...
  26. pmc Prospects for inferring very large phylogenies by using the neighbor-joining method
    Koichiro Tamura
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, 85287 4501, USA
    Proc Natl Acad Sci U S A 101:11030-5. 2004
    ..Our results encourage the use of complex models of nucleotide substitution for estimating evolutionary distances and hint at bright prospects for the application of the NJ and related methods in inferring large phylogenies...
  27. ncbi Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 23:127-8. 2007
    ..Various types of data such as genome sizes or protein domain repertoires can be mapped onto the tree. Export to several bitmap and vector graphics formats is supported. AVAILABILITY: iTOL is available at http://itol.embl.de..
  28. pmc The COG database: an updated version includes eukaryotes
    Roman L Tatusov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    BMC Bioinformatics 4:41. 2003
    ..Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies...
  29. pmc Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
    Brandon F Keele
    Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, AL 35223, USA
    Proc Natl Acad Sci U S A 105:7552-7. 2008
    ....
  30. pmc Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 15:1034-50. 2005
    ..Noncoding HCEs also show strong statistical evidence of an enrichment for RNA secondary structure...
  31. ncbi An improved general amino acid replacement matrix
    Si Quang Le
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS, Universite Montpellier II, Montpellier, France
    Mol Biol Evol 25:1307-20. 2008
    ..Results with the test alignments from Pfam are analogous. LG and a PHYML implementation can be downloaded from http://atgc.lirmm.fr/LG...
  32. ncbi The evolutionary fate and consequences of duplicate genes
    M Lynch
    Department of Biology, University of Oregon, Eugene, OR 97403, USA
    Science 290:1151-5. 2000
    ..Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species...
  33. ncbi Detecting recent positive selection in the human genome from haplotype structure
    Pardis C Sabeti
    Whitehead Institute MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 419:832-7. 2002
    ..More generally, the method could be used to scan the entire genome for evidence of recent positive selection...
  34. ncbi Prediction of mammalian microRNA targets
    Benjamin P Lewis
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 115:787-98. 2003
    ..The predicted regulatory targets of mammalian miRNAs were enriched for genes involved in transcriptional regulation but also encompassed an unexpectedly broad range of other functions...
  35. ncbi TimeTree: a public knowledge-base of divergence times among organisms
    S Blair Hedges
    Department of Biology, Pennsylvania State University, University Park, PA 16802 5301, USA
    Bioinformatics 22:2971-2. 2006
    ..Results are presented and summarized, allowing users to quickly determine the range and robustness of time estimates and the degree of consensus from the published literature...
  36. pmc Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    D Allan Drummond
    FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Cell 134:341-52. 2008
    ..The mechanistic model of molecular evolution that emerges yields testable biochemical predictions, calls into question the use of nonsynonymous-to-..
  37. ncbi The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    Olivier Jaillon
    Genoscope CEA and UMR 8030 CNRS Genoscope Université d Evry, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France
    Nature 449:463-7. 2007
    ..Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants...
  38. pmc eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data
    Edward J Feil
    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
    J Bacteriol 186:1518-30. 2004
    ..pneumoniae and Staphylococcus aureus MLST databases, and the more complicated clonal complexes observed for Campylobacter jejuni and Neisseria meningitidis...
  39. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  40. ncbi Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    Z Yang
    Department of Biology, University College, London, United Kingdom
    Mol Biol Evol 15:568-73. 1998
    ..The likelihood analysis thus confirmed most, but not all, conclusions Messier and Stewart reached using reconstructed ancestral sequences to estimate synonymous and nonsynonymous rates for different lineages...
  41. ncbi Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California, San Diego, CA 92103, USA
    Bioinformatics 21:2531-3. 2005
    ..The methods range from very fast data exploration to the some of the most complex models available in public domain software, and are implemented to run in parallel on a cluster of computers...
  42. pmc Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    R Nielsen
    Department of Integrative Biology, University of California, Berkeley 94720 3140, USA
    Genetics 148:929-36. 1998
    ..Positively selected sites are found in both the V3 region and the flanking regions...
  43. ncbi A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    Nicolas Lartillot
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Montreal, Quebec Canada
    Mol Biol Evol 21:1095-109. 2004
    ....
  44. ncbi Automated phylogenetic detection of recombination using a genetic algorithm
    Sergei L Kosakovsky Pond
    Department of Pathology, University of California San Diego, USA
    Mol Biol Evol 23:1891-901. 2006
    ..Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection...
  45. ncbi Neighbor-net: an agglomerative method for the construction of phylogenetic networks
    David Bryant
    McGill Centre for Bioinformatics, Montreal, Quebec, Canada
    Mol Biol Evol 21:255-65. 2004
    ..and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. Neighbor-Net is available as part of the SplitsTree4 software package...
  46. ncbi Mobile elements: drivers of genome evolution
    Haig H Kazazian
    Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Science 303:1626-32. 2004
    ..Although the host can often control their numbers, massive expansions of retrotransposons have been tolerated during evolution. Now mobile elements are becoming useful tools for learning more about genome evolution and gene function...
  47. ncbi Systematic functional analysis of the Caenorhabditis elegans genome using RNAi
    Ravi S Kamath
    Wellcome Trust Cancer Research UK Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
    Nature 421:231-7. 2003
    ..Our resulting data set and reusable RNAi library of 16,757 bacterial clones will facilitate systematic analyses of the connections among gene sequence, chromosomal location and gene function in C. elegans...
  48. ncbi Identification of novel genes coding for small expressed RNAs
    M Lagos-Quintana
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, , Germany
    Science 294:853-8. 2001
    ..This suggests that sequence-specific, posttranscriptional regulatory mechanisms mediated by small RNAs are more general than previously appreciated...
  49. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
    ..Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport...
  50. pmc The genomic and epidemiological dynamics of human influenza A virus
    Andrew Rambaut
    Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK
    Nature 453:615-9. 2008
    ..system, manifest as 'antigenic drift' of the viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the genome-scale evolutionary dynamics of this pathogen...
  51. ncbi Microsatellites: simple sequences with complex evolution
    Hans Ellegren
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE 752 36 Uppsala, Sweden
    Nat Rev Genet 5:435-45. 2004
  52. pmc Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
    Thomas M Keane
    Department of Biology, National University of Ireland, Maynooth, Co Kildare, Ireland
    BMC Evol Biol 6:29. 2006
    ..These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner...
  53. pmc Evolution of pathogenicity and sexual reproduction in eight Candida genomes
    Geraldine Butler
    UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
    Nature 459:657-62. 2009
    ..Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes...
  54. pmc The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana
    Steven B Cannon
    Plant Biology Department, University of Minnesota, St, Paul, MN 55108, USA
    BMC Plant Biol 4:10. 2004
    ....
  55. pmc Distribution and intensity of constraint in mammalian genomic sequence
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 15:901-13. 2005
    ..We anticipate that GERP and the types of analyses it facilitates will provide further insights and improved annotation for the human genome as mammalian genome sequence data become richer...
  56. ncbi The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization
    Christina A Cuomo
    Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
    Science 317:1400-2. 2007
    ..These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts...
  57. ncbi The genome sequence of the filamentous fungus Neurospora crassa
    James E Galagan
    Whitehead Institute Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 422:859-68. 2003
    ..Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes...
  58. pmc Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
    J Graham Ruby
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genome Res 17:1850-64. 2007
    ....
  59. ncbi Bayesian inference of phylogeny and its impact on evolutionary biology
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Science 294:2310-4. 2001
    ....
  60. ncbi The incomplete natural history of mitochondria
    J William O Ballard
    Department of Biological Sciences, University of Iowa, Iowa City, Iowa 52242, USA
    Mol Ecol 13:729-44. 2004
    ..Here we limelight mitochondrial ecology, sexually antagonistic selection, life-history evolution including ageing and disease, and the evolution of mitochondrial inheritance...
  61. ncbi Mechanisms of, and barriers to, horizontal gene transfer between bacteria
    Christopher M Thomas
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Nat Rev Microbiol 3:711-21. 2005
    ..However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition...
  62. ncbi The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes
    Helen Skaletsky
    Howard Hughes Medical Institute, Whitehead Institute, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 423:825-37. 2003
    ..9% identity, which is maintained by frequent gene conversion (non-reciprocal transfer). The most prominent features here are eight massive palindromes, at least six of which contain testis genes...
  63. pmc Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
    Robert K Jansen
    Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 104:19369-74. 2007
    ..Moreover, a lineage-specific correlation was detected between rates of nucleotide substitutions, indels, and genomic rearrangements...
  64. pmc An algorithm for progressive multiple alignment of sequences with insertions
    Ari Löytynoja
    European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom
    Proc Natl Acad Sci U S A 102:10557-62. 2005
    ..Our results suggest that some insertion/deletion "hot spots" may actually be artifacts of traditional alignment algorithms...
  65. pmc MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences
    Sudhir Kumar
    Biodesign Institute, A240, Arizona State University, Tempe, AZ 85287 5301, USA
    Brief Bioinform 9:299-306. 2008
    ..We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods...
  66. pmc Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
    Wendy S W Wong
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
    Genetics 168:1041-51. 2004
    ..The parsimony method has a very low rate of false positives but very little power for detecting positive selection or identifying positively selected sites...
  67. pmc Biological identifications through DNA barcodes
    Paul D N Hebert
    Department of Zoology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
    Proc Biol Sci 270:313-21. 2003
    ..Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
  68. ncbi Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
    James E Galagan
    The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
    Nature 438:1105-15. 2005
    ..These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation...
  69. ncbi Bayesian selection of continuous-time Markov chain evolutionary models
    M A Suchard
    Department of Biomathematics, UCLA School of Medicine, Los Angeles, CA 90095-7088, USA
    Mol Biol Evol 18:1001-13. 2001
    ....
  70. ncbi Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum
    T J Anderson
    Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, Oxford, England
    Mol Biol Evol 17:1467-82. 2000
    ..These data reveal a range of population structures within a single pathogen species and suggest intimate links between patterns of epidemiology and genetic structure in this organism...
  71. pmc Genome sequence of the human malaria parasite Plasmodium falciparum
    Malcolm J Gardner
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:498-511. 2002
    ..The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria...
  72. ncbi The Phaeodactylum genome reveals the evolutionary history of diatom genomes
    Chris Bowler
    CNRS UMR8186, Department of Biology, Ecole Normale Superieure, 46 rue d Ulm, 75005 Paris, France
    Nature 456:239-44. 2008
    ..These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans...
  73. ncbi A molecular evolutionary framework for the phylum Nematoda
    M L Blaxter
    Institute of Cell, Animal and Population Biology, University of Edinburgh, UK
    Nature 392:71-5. 1998
    ..We clarify the relationship of C. elegans to major parasitic groups; this will allow more effective exploitation of our genetic and biological knowledge of this model species...
  74. ncbi GARD: a genetic algorithm for recombination detection
    Sergei L Kosakovsky Pond
    Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 22:3096-8. 2006
    ..The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments...
  75. pmc Estimate of the mutation rate per nucleotide in humans
    M W Nachman
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
    Genetics 156:297-304. 2000
    ..This high rate is difficult to reconcile with multiplicative fitness effects of individual mutations and suggests that synergistic epistasis among harmful mutations may be common...
  76. pmc Data growth and its impact on the SCOP database: new developments
    Antonina Andreeva
    MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK
    Nucleic Acids Res 36:D419-25. 2008
    ..SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop...
  77. pmc Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion
    Harald Brussow
    Nestle, Research Center, Vers chez les Blanc, CH 1000 Lausanne, Switzerland
    Microbiol Mol Biol Rev 68:560-602, table of contents. 2004
    ..In addition, they can serve as anchoring points for genome inversions. The current review presents the available genomics and biological data on prophages from bacterial pathogens in an evolutionary framework...
  78. ncbi Darwinian evolution can follow only very few mutational paths to fitter proteins
    Daniel M Weinreich
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Science 312:111-4. 2006
    ..This implies that the protein tape of life may be largely reproducible and even predictable...
  79. ncbi Rates of evolutionary change in viruses: patterns and determinants
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 9:267-76. 2008
    ....
  80. pmc Identification of Birds through DNA Barcodes
    Paul D N Hebert
    Department of Zoology, University of Guelph, Guelph, Ontario, Canada
    PLoS Biol 2:e312. 2004
    ..The growing evidence for the effectiveness of DNA barcodes as a basis for species identification supports an international exercise that has recently begun to assemble a comprehensive library of COI sequences linked to named specimens...
  81. pmc Assessing the evolutionary impact of amino acid mutations in the human genome
    Adam R Boyko
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    PLoS Genet 4:e1000083. 2008
    ....
  82. ncbi Integrins: bidirectional, allosteric signaling machines
    Richard O Hynes
    Howard Hughes Medical Institute, Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 110:673-87. 2002
    ..Long-range conformational changes couple these functions via allosteric equilibria...
  83. ncbi Rates of molecular evolution are linked to life history in flowering plants
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, 21 Sachem Street, Post Office Box 208105, Yale University, New Haven, CT 06520 8105, USA
    Science 322:86-9. 2008
    Variable rates of molecular evolution have been documented across the tree of life, but the cause of this observed variation within and among clades remains uncertain...
  84. pmc Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis
    Blake C Meyers
    Department of Vegetable Crops, University of California, Davis, California 95616, USA
    Plant Cell 15:809-34. 2003
    ..The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges...
  85. ncbi The Sorghum bicolor genome and the diversification of grasses
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 457:551-6. 2009
    ..About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance...
  86. ncbi Genome evolution and adaptation in a long-term experiment with Escherichia coli
    Jeffrey E Barrick
    Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
    Nature 461:1243-7. 2009
    ..In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable...
  87. ncbi The evolution of gene regulation by transcription factors and microRNAs
    Kevin Chen
    Center for Comparative Functional Genomics, Department of Biology, New York University, New York, New York 10003, USA
    Nat Rev Genet 8:93-103. 2007
    ..As an initial step towards integrating these mechanisms into a unified framework, we propose a simple model that describes the transcriptional regulation of new microRNA genes...
  88. ncbi The evolution of gene duplications: classifying and distinguishing between models
    Hideki Innan
    Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Nat Rev Genet 11:97-108. 2010
    ..Setting out these predictions is an important step towards identifying the main mechanisms that are involved in the evolution of gene duplications...
  89. ncbi Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
    Gavin J D Smith
    State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
    Nature 459:1122-5. 2009
    ..Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans...
  90. pmc Soft sweeps: molecular population genetics of adaptation from standing genetic variation
    Joachim Hermisson
    Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians University Munich, Germany
    Genetics 169:2335-52. 2005
    ..We find that soft sweeps with weaker selective footprints are likely under both scenarios if the mutation rate and/or the selection coefficient is high...
  91. ncbi Orthologs, paralogs, and evolutionary genomics
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Annu Rev Genet 39:309-38. 2005
    ....
  92. ncbi Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization
    Nicholas H Putnam
    Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
    Science 317:86-94. 2007
    ..Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor...
  93. ncbi Bayesian estimation of ancestral character states on phylogenies
    Mark Pagel
    School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading, England
    Syst Biol 53:673-84. 2004
    ..We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods (BayesMultiState) is available from the authors...
  94. ncbi Biased gene conversion and the evolution of mammalian genomic landscapes
    Laurent Duret
    Universite de Lyon 1, CNRS, UMR5558, Laboratoire de Biometrie et Biologie Evolutive, F 69622, Villeurbanne, France
    Annu Rev Genomics Hum Genet 10:285-311. 2009
    ..Here we review the recent evidence for a GC-biased gene conversion process in mammals, and its consequences for genomic landscapes, molecular evolution, and human functional genomics.
  95. ncbi Cancer as an evolutionary and ecological process
    Lauren M F Merlo
    Cellular and Molecular Oncology Program, The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
    Nat Rev Cancer 6:924-35. 2006
    ..The tools of evolutionary biology and ecology are providing new insights into neoplastic progression and the clinical control of cancer...
  96. pmc The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection
    Nilu Goonetilleke
    Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, England, UK
    J Exp Med 206:1253-72. 2009
    ..These included clusters of mutations in envelope that were targeted by NAbs, a few isolated sites that reverted to the consensus sequence, and bystander mutations in linkage with T cell-driven escape...
  97. pmc The tree of one percent
    Tal Dagan
    Institute of Botany, University of Dusseldorf, D 40225 Dusseldorf, Germany
    Genome Biol 7:118. 2006
    ..To incorporate such processes into the bigger picture of early evolution, biologists need to depart from the preconceived notion that all genomes are related by a single bifurcating tree...
  98. pmc Search for a 'Tree of Life' in the thicket of the phylogenetic forest
    Pere Puigbò
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Biol 8:59. 2009
    ..However, the possibility remains that a statistical central trend still exists in the phylogenetic 'forest of life'...
  99. ncbi Evolution of protein kinase signaling from yeast to man
    Gerard Manning
    Sugen Inc 230 East Grand Ave, South San Francisco, CA 94080, USA
    Trends Biochem Sci 27:514-20. 2002
    ....
  100. ncbi Mapping the antigenic and genetic evolution of influenza virus
    Derek J Smith
    Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
    Science 305:371-6. 2004
    ..Further, this approach offers a route to predicting the relative success of emerging strains, which could be achieved by quantifying the combined effects of population level immune escape and viral fitness on strain evolution...
  101. ncbi Predicting the evolution of human influenza A
    R M Bush
    Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
    Science 286:1921-5. 1999
    ..However, not all codons in these sites had predictive value. Monitoring new H3 isolates for additional changes in positively selected codons might help identify the most fit extant viral strains that arise during antigenic drift...

Research Grants73

  1. Enterovirus RNA Translation and Replication
    David J Barton; Fiscal Year: 2013
    ..if substantiated by the proposed investigation, will have significant impact on our understanding of molecular evolution, drawing attention to the common features and mechanisms of a viral RNA-dependent RNA polymerase and ..
  2. Defining evolutionary trajectories: Molecular adaptation to antibiotic resistance
    ADIL YOUSIF SHAMOO; Fiscal Year: 2012
    ..The proposed work is an important step in the transition of molecular evolution from a retroactive posture that analyzes past events to one in which evolution research is used pro-..
  3. Novel Therapeutic Vaccines for Chronic HBV
    ROBERT GERALD WHALEN; Fiscal Year: 2013
    ..HBsAg variants containing xenogeneic sequences with novel T epitopes have been identified using a directed molecular evolution approach...
  4. Discovery of Critical Host Genes Enabling Resistance to HIV-1 Infection as Therap
    Leyla S Diaz; Fiscal Year: 2012
    ..These leading scFv candidates will be built out into full- length human IgG1 antibodies and using molecular evolution approach, the binding affinities of lead antibody candidates will be enhanced by several orders of ..
  5. Phylogenomics and functional diversification of the Heterochromatin Protein 1 gen
    MIA TAUNA LEVINE; Fiscal Year: 2012
    ..Using population genetic and molecular evolution analyses, I will rigorously determine if patterns of sequence evolution are consistent with an ongoing ..
  6. SELF-SPLICING INTEINS: FUNCTION, EVOLUTION, APPLICATION
    Marlene Belfort; Fiscal Year: 2013
    ..Inteins exist at the crossroads of the disparate disciplines of protein chemistry, biotechnology and molecular evolution. Their autocatalytic peptide cleavage and ligation reactions make them useful tools in modern chemical ..
  7. Optimized Adaptation of Simian-tropic R5 HIV Clade C to Pig-tailed Macaques
    RUTH MARGRIT RUPRECHT; Fiscal Year: 2013
    ..3. Perform an intrarectal titration and assess viral pathogenicity 4. Assess the molecular evolution of stHIV-C in the absence and presence of adaptive immunity and during disease progression...
  8. Functional genetic evolution of human brain and behavior
    Eric J Vallender; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): This proposal is focused on integrating comparative genetics and molecular evolution with functional neurobiology as a means of generating a better understanding of human neuropsychiatric and ..
  9. Infectious Disease Genomics and Bioinformatics Training in Brazil
    Jessica C Kissinger; Fiscal Year: 2013
    ..establish a sustainable core infrastructure at the CPqRR in the areas of bioinformatics, epidemiology and molecular evolution that will complement existing NIH-funded research and facilitate research conducted in other laboratories...
  10. Molecular Evolution Strategies to Derive New Recombinant AAV Vectors
    Mark A Kay; Fiscal Year: 2012
    ..We have shown proof-of-principle studies using 8 diverse naturally isolated capsids in DNA shuffling (or molecular evolution) reactions to make a library of capsid genes...
  11. Using a cyclotide-based molecular scaffold to select specific protein-protein inh
    Mark W Nowak; Fiscal Year: 2010
    ..inhibitors of NEMO/IKK[unreadable] binding would be facilitated (as proposed here) through the power of molecular evolution strategies and high throughput cell based screening using fluorescence-activated cell sorting (FACS) to ..
  12. Novel Vaccine Immunogens for Pandemic H5 Influenza
    ROBERT GERALD WHALEN; Fiscal Year: 2009
    ..We propose here a novel way to approach this problem, using the power of directed molecular evolution. This technology encompasses a method for creating novel protein sequences coupled with a means of ..
  13. Sexual conflict and relocation of genes by duplication
    ESTHER BETRAN; Fiscal Year: 2013
    ..Whole genome polymorphism data from D. melanogaster and comparative genomics will be exploited using the most current bioinformatics tools and molecular evolution software to achieve these objectives.
  14. Mechanisms of Hemoglobin Adaptation to Hypoxia in High-altitude Rodents
    Jay F Storz; Fiscal Year: 2012
    ..This highly interdisciplinary study will integrate the tools and theory of molecular population genetics, molecular evolution, structural biology, and protein biochemistry...
  15. Gene Therapy for Neurodegenerative Lysosomal Storage Diseases
    Douglas R Martin; Fiscal Year: 2013
    ..Finally, Aim 3 will test the principle of in vivo selection of an AAV capsid library (molecular evolution) to identify AAV vectors with tropism for the GM1 mouse central nervous system (CNS) after intravascular (..
  16. Biotechnology Training in Biomedical Sciences and Engineering
    Yi Tang; Fiscal Year: 2013
    ..vaults (protein nanocapsules), nanobiotechnology, bioinformatics, genomics, proteomics, protein molecular evolution, and incorporation of unnatural amino acids in recombinant proteins...
  17. Structural Studies and Char. of Neurotoxic Venom Peptides from Sicariidae Spiders
    NIKOLAUS MARTIN LOENING; Fiscal Year: 2012
    ..These have helped us begin to understand the patterns of molecular evolution of these toxins and identify peptides for further study...
  18. Cell Biology, Genetics, and Biochemistry Training Program
    DAVID OWEN MORGAN; Fiscal Year: 2013
    ..DNA replication, RNA splicing, transcriptional control, infectious disease, and various problems in molecular evolution. These studies use the tools of cell biology, genetics and biochemistry to exploit a wide range of systems, ..
  19. Molecular Evolution of Drosophila Y Chromosome
    Andrew G Clark; Fiscal Year: 2012
    ..The proposed study entails primary discovery of most of the Y- linked genes across a group of 12 species and a detailed study of their evolutionary divergence. ..
  20. High Performance Validation and Classification of Metagenomic Ribosomal-RNA Seque
    Daniel Frank; Fiscal Year: 2011
    ..1 ..
  21. Molecular Evolution of Multifunctional DNA Nanoparticles
    Bradley T Messmer; Fiscal Year: 2013
    ..g., farnesylated proteins). ..
  22. Chk1 signaling in the G2 DNA damage checkpoint
    MATTHEW O CONNELL; Fiscal Year: 2009
    ..to maintain genome stability, and when they fail, the ensuing instability allows for a heightened rate of molecular evolution that is a hallmark of cancer initiation and progression...
  23. Molecular Evolution and Life Cycle of Wolbachia Bacteriohage
    Seth R Bordenstein; Fiscal Year: 2012
    ..Based on these observations, the experimental focus of this proposal is on the molecular evolution and predation of Wolbachia phage WO-B. The specific aims are to: 1...
  24. Germline-Specific Immunogens for the Induction of Neutralizing Antibodies to HIV-
    ROBERT GERALD WHALEN; Fiscal Year: 2013
    ..We propose therefore to use a directed molecular evolution approach to identify germline-specific immunogens...
  25. Vaccination against mucosal HIV clade C transmission
    RUTH MARGRIT RUPRECHT; Fiscal Year: 2011
    ..the virulence of R5 SHIVenvC's, generating a fully heterologous SHIVenvC, and by comparing the molecular evolution of HIV clade C env in infected African mother/infant pairs and in rhesus monkeys infected with SHIV's ..
  26. Germline-Specific Immunogens for the Induction of Neutralizing Antibodies to HIV-
    ROBERT GERALD WHALEN; Fiscal Year: 2013
    ..We propose therefore to employ a directed molecular evolution approach to the problem of identifying germline-specific immunogens...
  27. MOLECULAR BASIS OF BORRELIA PATHOGENESIS
    Alan G Barbour; Fiscal Year: 2010
    ..We will test this by molecular evolution analyses of the expressed and archival variable genes in different strains of B...
  28. Elucidation and Evolutionary Potential of a Latent Pathway for PLP Synthesis
    Shelley D Copley; Fiscal Year: 2013
    ..This work has important implications for molecular evolution, both in the past, and in the present in response to selective pressures exerted by anthropogenic compounds ..
  29. Molecular evolution of AAV vectors for anti-HIV gene therapy
    KATHERINE JULIE EXCOFFON; Fiscal Year: 2012
    ..The proposed research also provides an opportunity to investigate the complex consequences of viral co-infection and may lead to novel insights into viral interactions, pathogenicity, and therapeutic strategies. ..
  30. A Unified Model of Gene Regulatory Circuit Evolution
    Victor Hanson-Smith; Fiscal Year: 2013
    ..The goal of this project is to combine multiple approaches - genomics, biochemistry, molecular evolution, ancestral reconstruction, and computational modeling - to learn the evolutionary mechanisms underlying ..
  31. High-specificity affinity reagents for N-glycosylation site mapping and glycomics
    Robert J Woods; Fiscal Year: 2013
    ..Using computational methods to guide molecular evolution, carbohydrate-processing enzymes will be converted into high affinity receptor proteins that retain the ..
  32. The Role of CyclophilinA in the Evolution of Retroviral Restriction
    RAYMOND MALFAVON BORJA; Fiscal Year: 2010
    ..Along with coursework in genomics and molecular evolution, I will be attending classes in virology and career development classes (ran by the student-post-doc ..
  33. Molecular evolution of odorant receptor specificities in Drosophila
    STEPHANIE MARIE ROLLMANN; Fiscal Year: 2013
    ..abstract_text> ..
  34. Structural Relay Methods for Functional Peptide Discovery
    PHILLIP TODD ORDOUKHANIAN; Fiscal Year: 2013
    ..We propose to bring powerful tools of molecular evolution to bear on the delivery of agents that do not carry genetic information...
  35. Deciphering how tropomyosin regulates the actin filament
    SARAH ELLEN HITCHCOCK-DEGREGORI; Fiscal Year: 2013
    ..The four aims are: Aim 1. Analysis of the molecular evolution of genes encoding tropomyosin...
  36. A Model System For Host-Pathogen Interactions: Drosophila And Its Parasitic Wasps
    TODD ALEXANDER SCHLENKE; Fiscal Year: 2012
    ..genes, and by inferring the past selection pressures on these genes using standard population genetics and molecular evolution techniques...
  37. Epistasis: its role in complex tratis, gene expression and speciation
    Michael J Wade; Fiscal Year: 2012
    ..reduction of hybrid fitness when brought together in a common genetic background;(2) characterizing the molecular evolution of these genes through their patterns of expression and sequence diversity within and among species;(3) ..
  38. CSHL Course on Advanced Sequencing Technologies &Applications
    David J Stewart; Fiscal Year: 2013
    ..Applications are anticipated from a diversity of scientific backgrounds including molecular evolution, development, neuroscience, cancer, plant biology and microbiology...
  39. CSHL Statistical Methods for Functional Genomics
    David J Stewart; Fiscal Year: 2013
    ..Applications are anticipated from scientists with a variety of scientific backgrounds, including molecular evolution, development, neuroscience, cancer, plant biology, and immunology...
  40. Re-engineering the arylomycins for antibiotic activity
    Floyd E Romesberg; Fiscal Year: 2010
    ..Our project will provide a detailed understanding of the molecular evolution of resistance, and importantly, should elucidate how the arylomycins might re-engineer for potency...
  41. Genetics Cellular and Molecular Sciences Training Grant
    Justin P Kumar; Fiscal Year: 2013
    ..biochemistry, development, cell biology, microbiology, molecular genetics, structural biology, and molecular evolution. Trainees have the opportunity to engage in the highly collaborative and stimulating intellectual ..
  42. Molecular Fluorescent Toolkit
    VLADISLAV VERKHUSHA; Fiscal Year: 2013
    ..We will apply directed molecular evolution techniques consisting of rational structure-based design and random mutagenesis of candidate proteins, ..
  43. Evolution of codon usage bias in the genus Drosophila
    Jeffrey Powell; Fiscal Year: 2009
    ..Thus, most studies of such slightly deleterious mutations, a major feature of molecular evolution, are confined to analytical statistical scrutiny (as opposed to empirical experimental manipulations)...
  44. Engineering Morphogenetic Factors for Enhanced Genetic Reprogramming
    Charles A Gersbach; Fiscal Year: 2011
    ..limitations, we propose to enhance the intrinsic properties of the reprogramming factors through directed molecular evolution. This represents a new conceptual direction in the area of genetic reprogramming and capitalizes on the ..
  45. The National Neurotrauma Society 30th Annual Conference (Phoenix July 22-25,2012)
    KEVIN KA WANG WANG; Fiscal Year: 2012
    ..research and clinical tools in neuro-rehabilitation will be the key, as is the understanding of the molecular evolution from TBI to chronic neurodegenerative diseases such as Alzheimer's and Chronic Traumatic ..
  46. Structure, Function and Inhibition of Beta-lactamases
    Brian K Shoichet; Fiscal Year: 2013
    ..These enzymes are a pressing medical problem and a fascinating example of molecular evolution. One goal of this research program is to understand the molecular bases of this evolving activity...
  47. The Ninth International Congress of Neuroethology Proposal
    George D Pollak; Fiscal Year: 2010
    ..on topics such as bird song learning, neural networks for olfactory behavior, acoustic communication, molecular evolution of vision, behaviors guided by pheromones, among others...
  48. SUMMER INSTITUTE IN STATISTICAL GENETICS
    Bruce S Weir; Fiscal Year: 2013
    ..Inferences of Relationships and Relatedness;12. Comparative Genomics and Molecular Evolution;13. QTL Mapping;14. Mixed Models;15. Human Association Mapping;16. Coalescent Theory;17...
  49. Quantitavie and Computational Biology Graduate Program
    David Botstein; Fiscal Year: 2013
    ..bacteria, eukaryotic models and mammalian systems;computational projects ranging from bio-informatics and molecular evolution to high-throughput data visualization and systems biology projects ranging from microbial metabolism to ..
  50. A High-throughput Strategy to Identify HIV Intra-subtype Recombinant Sequences
    Ming Zhang; Fiscal Year: 2013
    ..a great degree of sequence diversity that we have overlooked in many aspects of studies, including viral molecular evolution and molecular epidemiology studies...
  51. Detection of Distribution of New Genes in Drosophila Phylogeny
    MANYUAN NO LONG; Fiscal Year: 2010
    ..b>Molecular evolution and population genetic analyses will be also conducted to detect adaptive evolution of new functional genes...
  52. Promotion of Plasmodium Research and Training in India
    Jane M Carlton; Fiscal Year: 2012
    ..The topics of training will include: population diversity and genetics, molecular evolution, genetic association studies, in vitro culture, bioinformatics, genomics, mosquito transmission studies, ..
  53. Training in Population Biology of Infectious Diseases
    Leslie A Real; Fiscal Year: 2013
    ..The training is complemented by core courses in population biology, evolutionary biology, ecology, molecular evolution, and statistics and mathematical modeling...
  54. Treponomics: enhanced tools for genetic manipulation in spirochetes
    J Christopher Fenno; Fiscal Year: 2013
    ..tissue, offers a range of targets for research into microbe-host interactions, microbial physiology and molecular evolution. While pathogenic behaviors and disease associations of oral spirochetes are clearly distinct from those of ..
  55. The genetics of Crohn's disease in the Ashkenazi Jewish population
    Ken Hui; Fiscal Year: 2013
    ..This will extend the disease-oriented analysis from Aim 2 to include compound heterozygosity and the molecular evolution of each variant...
  56. Protein function prediction by statistical phylogenomics
    Steven E Brenner; Fiscal Year: 2010
    ..We will improve the key internal parameters of the molecular evolution model, and improve interpretability of the results...
  57. Rapid evolution of genes critical for genome integrity
    SARA SAWYER; Fiscal Year: 2013
    The molecular evolution of primate DNA double-strand break repair genes will be studied. These genes are important for genome stability, and many cancer syndromes have been linked to mutations in these genes...
  58. Exploiting Molecular Evolution to Expand Synthetic Biology
    MEGAN FRANCES COLE; Fiscal Year: 2012
    ..I will exploit evolutionary analyses to advance the creation of peptide libraries that can be used in drug screens for therapeutic compounds. ..
  59. Development of a Computational Framework for TCR Engineering
    Zhiping Weng; Fiscal Year: 2013
    ..Efforts to improve TCR affinity via in vitro molecular evolution can impact antigen specificity, and attempts to improve chain pairing have yet to yield an effective ..
  60. Molecular study of genes and pathways in late stages of urinary tract infection
    Swaine L Chen; Fiscal Year: 2010
    ..for positive selection in pathogenic bacteria;and (3) establish the power, accuracy, and relevance of molecular evolution theory and algorithms for in vivo studies...
  61. A New Approach to Phylogenetic Analysis Using Structural Information
    Abel Rodriguez; Fiscal Year: 2013
    ..among multiple species, as well as to provide insights into the mechanisms driving the process of molecular evolution. This proposal is informed by two recent trends in phylogenetic analysis...
  62. HGV2012/2013 Int'l Meetings on Human Genome Variation &Complex Genome Analysis
    Pui Yan Kwok; Fiscal Year: 2013
    ..genome sequencing era that take into account copy number variations and de novo mutations, to the study of molecular evolution based on comparative genome variation analysis, and to the social and ethical implications of human ..
  63. TEST OF NEUTRAL MOLECULAR EVOLUTION
    Martin Kreitman; Fiscal Year: 1999
    ..Rates of synonymous and amino acid substitutions will be determined for these species pairs, and examined for consistency with the patterns observed for D. melanogaster and D. simulans. ..
  64. Convergent Molecular Evolution of Moth and Spider Silks
    NADIA AYOUB; Fiscal Year: 2009
    ..of silk production in multiple arthropod lineages provides an ideal model system to examine convergent molecular evolution. With an initial focus on spiders and moths, the databases and analytical methods developed here will lay ..
  65. MOLECULAR EVOLUTION IN MAMMALS
    CHARLES SIBLEY; Fiscal Year: 1992
    ..5. To reconstruct the branching pattern and measure median genomic rates of evolution of the major mammalian lineages...
  66. Molecular Evolution of flavivirus-resistance in mice
    Stephane Boissinot; Fiscal Year: 2005
    ..In our third aim we will analyze the molecular evolution of flavivirus-resistance...
  67. Molecular evolution of latrotoxins: neurotoxins from black widow spider venom
    JESSICA GARB; Fiscal Year: 2009
    ..a-latrotoxins on vertebrate cells;and (3) to investigate the global phylogenetic distribution and molecular evolution of latrotoxins with bioinformatic analyses to pinpoint the timing and circumstances surrounding the origin ..
  68. MECHANISTIC STUDIES OF PROKARYOTIC MANNOSYLTRANSFERASES
    JON THORSON; Fiscal Year: 2002
    ..analogs; and Man Talpha4/Man Tbeta4 structural probes including site-directed mutagenesis; in vitro molecular evolution; differential labeling and/or active site-directed affinity labeling), the proposed work should help define ..
  69. CODING & NONCODING REGIONS IN DNA SEQUENCES
    THOMAS JUKES; Fiscal Year: 1991
    ..It therefore seems that studies of molecular evolution must be included in analyzing the human genome...
  70. EVOLUTIONARY DYNAMICS OF GENE-FOR-GENE SYSTEMS
    Joy Bergelson; Fiscal Year: 2004
    ..about how the population biology influences the frequencies of host and pathogen alleles and the pattern of molecular evolution at the cloned loci...
  71. Characterization of cougar lentiviruses
    Mary Poss; Fiscal Year: 2003
    ..order to develop an understanding of endemic feline lentiviruses, we have investigated the epidemiology and molecular evolution of a species-specific feline lentivirus (FIVFco) in wild cougars (Fells concolor) in the western United ..
  72. Molecular Evolution of Viral Epitopes: Adaptive Evolution of Evasion
    Helen Piontkivska; Fiscal Year: 2010
    ..These results can be used in the development of novel vaccines and treatments and will lead to better understating of host- pathogen interactions. ..
  73. Molecular Evolution of Resistance in Strep. pyogenes
    DEBRA BESSEN; Fiscal Year: 2005
    ..GAS provide a sound model system for understanding the molecular evolution underlying the early stages of the emergence and global spread of antibiotic resistance.