phylogeny

Summary

Summary: The relationships of groups of organisms as reflected by their genetic makeup.

Top Publications

  1. ncbi PAML 4: phylogenetic analysis by maximum likelihood
    Ziheng Yang
    Department of Biology, Galton Laboratory, University College London, London, UK
    Mol Biol Evol 24:1586-91. 2007
  2. 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
  3. pmc MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    Koichiro Tamura
    Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
    Mol Biol Evol 28:2731-9. 2011
  4. 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
  5. 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
  6. ncbi New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    Stephane Guindon
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, Centre National de la Recherche Scientifique, Universite de Montpellier, Montpellier Cedex 5, France
    Syst Biol 59:307-21. 2010
  7. 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
  8. doi jModelTest: phylogenetic model averaging
    David Posada
    Mol Biol Evol 25:1253-6. 2008
  9. pmc Bayesian phylogenetics with BEAUti and the BEAST 1.7
    Alexei J Drummond
    Department of Computer Science, University of Auckland, Auckland, New Zealand
    Mol Biol Evol 29:1969-73. 2012
  10. pmc MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
    Fredrik Ronquist
    Department of Biodiversity Informatics, Swedish Museum of Natural History, SE 10405 Stockholm, Sweden
    Syst Biol 61:539-42. 2012

Detail Information

Publications304 found, 100 shown here

  1. ncbi PAML 4: phylogenetic analysis by maximum likelihood
    Ziheng Yang
    Department of Biology, Galton Laboratory, University College London, London, UK
    Mol Biol Evol 24:1586-91. 2007
    ..The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html)...
  2. 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)...
  3. pmc MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    Koichiro Tamura
    Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
    Mol Biol Evol 28:2731-9. 2011
    ..This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net...
  4. 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...
  5. 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...
  6. ncbi New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    Stephane Guindon
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, Centre National de la Recherche Scientifique, Universite de Montpellier, Montpellier Cedex 5, France
    Syst Biol 59:307-21. 2010
    PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology...
  7. 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...
  8. doi jModelTest: phylogenetic model averaging
    David Posada
    Mol Biol Evol 25:1253-6. 2008
    ..importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment ..
  9. pmc Bayesian phylogenetics with BEAUti and the BEAST 1.7
    Alexei J Drummond
    Department of Computer Science, University of Auckland, Auckland, New Zealand
    Mol Biol Evol 29:1969-73. 2012
    ..BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk...
  10. pmc MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
    Fredrik Ronquist
    Department of Biodiversity Informatics, Swedish Museum of Natural History, SE 10405 Stockholm, Sweden
    Syst Biol 61:539-42. 2012
    ..A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software...
  11. ncbi MRBAYES: Bayesian inference of phylogenetic trees
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Bioinformatics 17:754-5. 2001
    The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo.
  12. pmc Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    Qiong Wang
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Appl Environ Microbiol 73:5261-7. 2007
    ..It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/...
  13. 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
    ..data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods...
  14. 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
    ..APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes...
  15. pmc The RAST Server: rapid annotations using subsystems technology
    Ramy K Aziz
    Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA
    BMC Genomics 9:75. 2008
    ..The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them...
  16. ncbi Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    J Castresana
    European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biol Evol 17:540-52. 2000
    ....
  17. pmc FastTree 2--approximately maximum-likelihood trees for large alignments
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
    PLoS ONE 5:e9490. 2010
    ..We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability...
  18. 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...
  19. pmc MUSCLE: a multiple sequence alignment method with reduced time and space complexity
    Robert C Edgar
    Department of Plant and Microbial Biology, 461 Koshland Hall, University of California, Berkeley, CA 94720 3102, USA
    BMC Bioinformatics 5:113. 2004
    ..We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles...
  20. 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...
  21. 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...
  22. pmc SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    Elmar Pruesse
    Microbial Genomics Group, Max Planck Institute for Marine Microbiology
    Nucleic Acids Res 35:7188-96. 2007
    ..The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs...
  23. pmc Diversity of the human intestinal microbial flora
    Paul B Eckburg
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S 169, 300 Pasteur Drive, Stanford CA 94305 5107, USA
    Science 308:1635-8. 2005
    ..We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease...
  24. pmc Enterotypes of the human gut microbiome
    Manimozhiyan Arumugam
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 473:174-80. 2011
    ..For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers...
  25. ncbi Genome sequence of the palaeopolyploid soybean
    Jeremy Schmutz
    HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, Alabama 35806, USA
    Nature 463:178-83. 2010
    ..An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties...
  26. pmc Relaxed phylogenetics and dating with confidence
    Alexei J Drummond
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS Biol 4:e88. 2006
    In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum...
  27. ncbi ProtTest 3: fast selection of best-fit models of protein evolution
    Diego Darriba
    Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
    Bioinformatics 27:1164-5. 2011
    ..We have implemented a high-performance computing (HPC) version of ProtTest that can be executed in parallel in multicore desktops and clusters. This version, called ProtTest 3, includes new features and extended capabilities...
  28. pmc RDP3: a flexible and fast computer program for analyzing recombination
    Darren P Martin
    Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Centre for High Performance Computing, Rosebank, Cape Town, South Africa
    Bioinformatics 26:2462-3. 2010
    ..The new RDP3 can accommodate large datasets and is capable of analyzing alignments ranging in size from 1000 × 10 kilobase sequences to 20 × 2 megabase sequences within 48 h on a desktop PC...
  29. pmc UniFrac: a new phylogenetic method for comparing microbial communities
    Catherine Lozupone
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Appl Environ Microbiol 71:8228-35. 2005
    ....
  30. ncbi Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    Gerard Talavera
    Department of Physiology, Institute of Molecular Biology of Barcelona, Barcelona, Spain
    Syst Biol 56:564-77. 2007
    ..This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies...
  31. pmc Phylogeny.fr: robust phylogenetic analysis for the non-specialist
    A Dereeper
    Information Génomique et Structurale IGS, CNRS UPR2589, IFR 88, Marseille, France
    Nucleic Acids Res 36:W465-9. 2008
    ..The Phylogeny.fr platform transparently chains programs to automatically perform these tasks...
  32. pmc Evolution and classification of the CRISPR-Cas systems
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
    Nat Rev Microbiol 9:467-77. 2011
    ..Accordingly, we propose a 'polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR-cas loci...
  33. pmc ARB: a software environment for sequence data
    Wolfgang Ludwig
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 853530 Freising, Germany
    Nucleic Acids Res 32:1363-71. 2004
    ..Currently, the package is used by numerous working groups worldwide...
  34. pmc EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
    Albert J Vilella
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 19:327-35. 2009
    ..All data are made available in a number of formats and will be kept up to date with the Ensembl project...
  35. 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
    ..They are used to compute substitution probabilities along phylogeny branches and thus the likelihood of the data. They are also essential in protein alignment...
  36. pmc Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans
    Rebecca J Garten
    WHO Collaborating Center for Influenza, Centers for Disease Control and Prevention CDC, Atlanta, GA 30333, USA
    Science 325:197-201. 2009
    ..Antigenically the viruses are homogeneous and similar to North American swine A(H1N1) viruses but distinct from seasonal human A(H1N1)...
  37. pmc trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
    Salvador Capella-Gutierrez
    Comparative Genomics Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 88 08003 Barcelona, Spain
    Bioinformatics 25:1972-3. 2009
    ..Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized...
  38. pmc An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    Daniel McDonald
    Department of Chemistry and Biochemistry and Biofrontiers Institute, University of Colorado, Boulder, CO, USA
    ISME J 6:610-8. 2012
    ..The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/...
  39. pmc Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 39:W475-8. 2011
    ..Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services...
  40. pmc The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
    F Meyer
    Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S Cass Avenue, Argonne, IL 60439, USA
    BMC Bioinformatics 9:386. 2008
    ..High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers...
  41. pmc Microbial diversity in the deep sea and the underexplored "rare biosphere"
    Mitchell L Sogin
    Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, 7 MBL Street, Woods Hole, MA 02543, USA
    Proc Natl Acad Sci U S A 103:12115-20. 2006
    ..Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes...
  42. ncbi Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses
    Robert Lanfear
    Centre for Macroevolution and Macroecology, Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
    Mol Biol Evol 29:1695-701. 2012
    ..PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from www.robertlanfear.com/partitionfinder...
  43. pmc MEGAN analysis of metagenomic data
    Daniel H Huson
    Center for Bioinformatics, Tubingen University, Sand 14, 72076 Tubingen, Germany
    Genome Res 17:377-86. 2007
    ..Also, simulations that evaluate the performance of the approach for different read lengths are presented...
  44. 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...
  45. pmc Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology
    Wayne Delport
    Department of Pathology, Antiviral Research Center, University of California, San Diego, CA, USA
    Bioinformatics 26:2455-7. 2010
    ..Here, we summarize the analyses options currently available on Datamonkey, and provide guidelines for their use in evolutionary biology. Availability and documentation: http://www.datamonkey.org...
  46. pmc Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
    Patrick D Schloss
    Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS ONE 6:e27310. 2011
    ....
  47. pmc Bacterial community variation in human body habitats across space and time
    Elizabeth K Costello
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Science 326:1694-7. 2009
    ..These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease...
  48. 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
    ....
  49. pmc Evolution of MRSA during hospital transmission and intercontinental spread
    Simon R Harris
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 15A, UK
    Science 327:469-74. 2010
    ..The ability to interrogate and resolve bacterial populations is applicable to a range of infectious diseases, as well as microbial ecology...
  50. ncbi PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
    Nicolas Lartillot
    Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    Bioinformatics 25:2286-8. 2009
    ..However, there still lacks a common implementation allowing one to freely combine these independent features, so as to test their ability to jointly improve phylogenetic and dating accuracy...
  51. ncbi Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
    Maria Anisimova
    Equipe Méthodes et Algorithmes pour la Bioinformatique LIRMM CNRS, Universite Montpellier II, Montpellier 34392, France
    Syst Biol 55:539-52. 2006
    ..The aLRT is implemented within the algorithm used by the recent fast maximum likelihood tree estimation program PHYML (Guindon and Gascuel, 2003)...
  52. pmc FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
    Morgan N Price
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, CA, USA
    Mol Biol Evol 26:1641-50. 2009
    ..In simulations, FastTree was slightly more accurate than Neighbor-Joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree...
  53. pmc Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases
    Daniel N Frank
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309 0347, USA
    Proc Natl Acad Sci U S A 104:13780-5. 2007
    ..Patient stratification by GI microbiota provides further evidence that CD represents a spectrum of disease states and suggests that treatment of some forms of IBD may be facilitated by redress of the detected microbiological imbalances...
  54. 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...
  55. ncbi CONSEL: for assessing the confidence of phylogenetic tree selection
    H Shimodaira
    The Institute of Statistical Mathematics, 4 6 7 Minami Azabu, Minatoku, Tokyo 106 8569, Japan
    Bioinformatics 17:1246-7. 2001
    ..CONSEL calculates all these p-values from the output of the phylogeny program packages such as Molphy, PAML, and PAUP*...
  56. ncbi The genome of the domesticated apple (Malus × domestica Borkh.)
    Riccardo Velasco
    Istituto Agrario San Michele all Adige Research and Innovation Centre, Foundation Edmund Mach, Trento, Italy
    Nat Genet 42:833-9. 2010
    ....
  57. ncbi RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
    A Stamatakis
    Department of Computer Science, Technical University of Munich Boltzmannstrasse 3, D 85748 München, Germany
    Bioinformatics 21:456-63. 2005
    ..Due to the combinatorial and computational complexity the size of trees which can be computed on a Biologist's PC workstation within reasonable time is limited to trees containing approximately 100 taxa...
  58. pmc Rapid pneumococcal evolution in response to clinical interventions
    Nicholas J Croucher
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Science 331:430-4. 2011
    ..This study details how genomic plasticity within lineages of recombinogenic bacteria can permit adaptation to clinical interventions over remarkably short time scales...
  59. pmc Detection of nonneutral substitution rates on mammalian phylogenies
    Katherine S Pollard
    Gladstone Institutes, University of California, San Francisco, San Francisco, California 94158, USA
    Genome Res 20:110-21. 2010
    ..increases (acceleration) in rate but not both, or assume that selection acts uniformly across the branches of a phylogeny. Here we examine the more general problem of detecting departures from the neutral rate of substitution in ..
  60. pmc Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus
    M C Enright
    Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, Oxford University, Oxford OX1 3FY
    J Clin Microbiol 38:1008-15. 2000
    ..MLST provides an unambiguous method for assigning MRSA and MSSA isolates to known clones or assigning them as novel clones via the Internet...
  61. ncbi Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation
    Mannis van Oven
    Department of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, The Netherlands
    Hum Mutat 30:E386-94. 2009
    ..In order to facilitate a better use of known mtDNA variation, we have constructed an updated comprehensive phylogeny of global human mtDNA variation, based on both coding- and control region mutations...
  62. ncbi MYB transcription factors in Arabidopsis
    Christian Dubos
    Institut Jean Pierre Bourgin, UMR1318 INRA AgroParisTech, 78026 Versailles Cedex, France
    Trends Plant Sci 15:573-81. 2010
    ..The elucidation of MYB protein function and regulation that is possible in Arabidopsis will provide the foundation for predicting the contributions of MYB proteins to the biology of plants in general...
  63. ncbi Insights into the phylogeny and coding potential of microbial dark matter
    Christian Rinke
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 499:431-7. 2013
    ..This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet...
  64. pmc Bayesian inference of species trees from multilocus data
    Joseph Heled
    Department of Computer Science, University of Auckland, New Zealand
    Mol Biol Evol 27:570-80. 2010
    ..We demonstrate that both BEST and our method have much better estimation accuracy for species tree topology than concatenation, and our method outperforms BEST in divergence time and population size estimation...
  65. pmc Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
    Conrad L Schoch
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 109:6241-6. 2012
    ....
  66. pmc Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    Marie Touchon
    Atelier de BioInformatique, Universite Pierre et Marie Curie Paris 6, Paris, France
    PLoS Genet 5:e1000344. 2009
    ..Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite ..
  67. 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
    ..individual transmitted or founder viruses generally exhibited a Poisson distribution of mutations and star-like phylogeny, which coalesced to an inferred consensus sequence at or near the estimated time of virus transmission...
  68. pmc A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    Dongying Wu
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 462:1056-60. 2009
    ..Our results strongly support the need for systematic 'phylogenomic' efforts to compile a phylogeny-driven 'Genomic Encyclopedia of Bacteria and Archaea' in order to derive maximum knowledge from existing ..
  69. ncbi An approximately unbiased test of phylogenetic tree selection
    Hidetoshi Shimodaira
    Institute of Statistical Mathematics, 4 6 7 Minami Azabu, Minatoku, Tokyo 106 8569, Japan
    Syst Biol 51:492-508. 2002
    ..A practical suggestion is provided as to which test should be used under particular circumstances...
  70. pmc The ecoresponsive genome of Daphnia pulex
    John K Colbourne
    Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
    Science 331:555-61. 2011
    ..Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges...
  71. ncbi Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification
    Robert W Meredith
    Department of Biology, University of California, Riverside, CA 92521, USA
    Science 334:521-4. 2011
    ..Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods...
  72. pmc Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
    Micah Hamady
    Department of Computer Science, University of Colorado, Boulder, CO, USA
    ISME J 4:17-27. 2010
    ..Together, these case studies point the way toward a broad range of applications and show some of the new features of Fast UniFrac...
  73. 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..
  74. ncbi Ancestral polyploidy in seed plants and angiosperms
    Yuannian Jiao
    Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nature 473:97-100. 2011
    ....
  75. ncbi Genetic history of an archaic hominin group from Denisova Cave in Siberia
    David Reich
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 468:1053-60. 2010
    ..This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans...
  76. 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...
  77. pmc Evolution of mammals and their gut microbes
    Ruth E Ley
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA
    Science 320:1647-51. 2008
    ..The results indicate that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial ..
  78. pmc Dendroscope: An interactive viewer for large phylogenetic trees
    Daniel H Huson
    Center for Bioinformatics Tübingen ZBIT, Eberhard Karls Universitat Tubingen, Sand 14, 72076 Tubingen, Germany
    BMC Bioinformatics 8:460. 2007
    ..Moreover, many programs are difficult to install or are not available for all common operating systems...
  79. ncbi The protein kinase complement of the human genome
    G Manning
    SUGEN Inc, 230 East Grand Avenue, South San Francisco, CA 94080, USA
    Science 298:1912-34. 2002
    ..We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons...
  80. pmc Population genomics of domestic and wild yeasts
    Gianni Liti
    Institute of Genetics, Queen s Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
    Nature 458:337-41. 2009
    ....
  81. 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...
  82. 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
    ..Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of ..
  83. pmc PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium
    Huaiyu Mi
    Evolutionary Systems Biology Group, SRI International, Lawrence Berkeley National Laboratory, USA
    Nucleic Acids Res 38:D204-10. 2010
    ..In addition, PANTHER trees are being annotated with gene function as part of the Gene Ontology Reference Genome project, resulting in an increasing number of curated functional annotations...
  84. pmc Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection
    Jesus F Salazar-Gonzalez
    University of Alabama at Birmingham, Birmingham, AL 35294, USA
    J Exp Med 206:1273-89. 2009
    ..These findings reveal viral properties associated with mucosal HIV-1 transmission and a limited set of rapidly evolving adaptive mutations driven primarily, but not exclusively, by early cytotoxic T cell responses...
  85. pmc Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics
    Peter Arensburger
    Center for Disease Vector Research, University of California Riverside, Riverside, CA 92521, USA
    Science 330:86-8. 2010
    ....
  86. 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
    ....
  87. 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
    ..These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions...
  88. pmc Bayesian phylogeography finds its roots
    Philippe Lemey
    Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium
    PLoS Comput Biol 5:e1000520. 2009
    ..From these analyses, we conclude that our phylogeographic framework will make an important asset in molecular epidemiology that can be easily generalized to infer biogeogeography from genetic data for many organisms...
  89. ncbi Classification of papillomaviruses
    Ethel Michele de Villiers
    Reference Center for Papillomaviruses, Division for the Characterization of Tumorviruses, Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany
    Virology 324:17-27. 2004
    ..The taxonomic status of PV types, subtypes, and variants remains unchanged and is based on the traditional criteria that the sequence of their L1 genes should be at least 10%, 2-10%, and maximally 2% dissimilar from one another...
  90. pmc Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    Arthur Brady
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    Nat Methods 6:673-6. 2009
    ..We also describe how combining Phymm with sequence alignment algorithms improves accuracy...
  91. pmc Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
    Ken Kurokawa
    Laboratory of Comparative Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
    DNA Res 14:169-81. 2007
    ..In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes...
  92. pmc Origin of the human malaria parasite Plasmodium falciparum in gorillas
    Weimin Liu
    Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
    Nature 467:420-5. 2010
    ..falciparum formed a monophyletic lineage within the gorilla parasite radiation. These findings indicate that P. falciparum is of gorilla origin and not of chimpanzee, bonobo or ancient human origin...
  93. ncbi The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    R C Lee
    Harvard University, Department of Cellular and Developmental Biology, Cambridge, Massachusetts 02138
    Cell 75:843-54. 1993
    ..elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin-4 regulates lin-14 translation via an antisense RNA-RNA interaction...
  94. ncbi A phylogenomic study of birds reveals their evolutionary history
    Shannon J Hackett
    Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
    Science 320:1763-8. 2008
    ..sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods...
  95. 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...
  96. pmc phyloXML: XML for evolutionary biology and comparative genomics
    Mira V Han
    School of Informatics, Indiana University, Bloomington, IN 47408, USA
    BMC Bioinformatics 10:356. 2009
    ..The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types...
  97. pmc Phylogenetic and functional assessment of orthologs inference projects and methods
    Adrian M Altenhoff
    Institute of Computational Science, ETH Zurich, and Swiss Institute of Bioinformatics, Zurich, Switzerland
    PLoS Comput Biol 5:e1000262. 2009
    ..Furthermore, orthology is typically only assessed in terms of function conservation, despite the phylogeny-based original definition of Fitch...
  98. pmc A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids
    Jan Janouskovec
    Department of Botany, University of British Columbia, Vancouver, BC, Canada
    Proc Natl Acad Sci U S A 107:10949-54. 2010
    ..g., ciliates, Cryptosporidium, and Phytophthora)...
  99. pmc Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator
    Paul D N Hebert
    Department of Zoology, University of Guelph, Guelph, ON, N1G 2W1, Canada
    Proc Natl Acad Sci U S A 101:14812-7. 2004
    ..They also illustrate the value of DNA barcoding, especially when coupled with traditional taxonomic tools, in disclosing hidden diversity...
  100. pmc Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"
    Vladimir Hampl
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5
    Proc Natl Acad Sci U S A 106:3859-64. 2009
    ..However, molecular phylogeny has not provided clear evidence that either Chromalveolata or Excavata is monophyletic, nor has it resolved the ..
  101. pmc Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths
    Thorsten Kloesges
    Institute of Botany III, Heinrich Heine University Dusseldorf, Dusseldorf, Germany
    Mol Biol Evol 28:1057-74. 2011
    ..Moreover, the nature of the transferred genes suggests that gene transfer in proteobacteria is frequently mediated by conjugation...

Research Grants69

  1. Systematics of medically important Dermacentor tick vectors
    Dmitry A Apanaskevich; Fiscal Year: 2011
    ..To develop a DNA barcode system for Dermacentor species;and Aim 4. To reconstruct a phylogeny for Dermacentor species using mitochondrial and nuclear genes. Impact...
  2. A XENOPUS LAEVIS RESEARCH RESOURCE FOR IMMUNOBIOLOGY
    Jacques Robert; Fiscal Year: 2013
    ..provided by applicant): Xenopus laevis is one of the best ectothermic vertebrate models for studying the phylogeny and ontogeny of the immune system. The evolutionary distance of X...
  3. Presynaptic Mechanisms Regulating the Dopamine Transporter
    JAMES A HARDAWAY; Fiscal Year: 2013
    ..provided by applicant): The catecholamine neurotransmitter dopamine (DA) functions in neural circuits across phylogeny to modulate both simple and complex behaviors...
  4. Evolutionary Analysis of the Histone Deacetylase Family: Biomedical Research
    JOSEPH LEWIS GRAVES; Fiscal Year: 2011
    ..addition, I shall need to further develop my understanding of the theory behind computational methods applied to phylogeny and elucidating adaptive evolution at the molecular level...
  5. EVOLUTIONARY ORIGINS OF IMMUNE-TYPE GENES
    GARY WILLIAM LITMAN; Fiscal Year: 2013
    ..Acquisition of complete genome sequences in species that represent key points in phylogeny not only permit in-depth analysis of immune mediators but also represent an invaluable resource for ..
  6. Retinal Cell-Fate Determination and Pattern Formation
    Graeme Mardon; Fiscal Year: 2012
    ..Since genetic pathways are often conserved and reiteratively used during organ formation across phylogeny, studying the development of simpler organisms can provide rapid and significant insight into human disease...
  7. The population genetics of antibiotic resistance in multi-drug environments
    Roy Kishony; Fiscal Year: 2013
    ..Whole-genome sequencing allows reconstruction of the phylogeny of strains isolated from patients over time, and permits the identification of individual mutation events and ..
  8. The Role of Plasmids in Rickettsia Biology
    ULRIKE GERTRUD MUNDERLOH; Fiscal Year: 2013
    ..We propose a comprehensive analysis of the distribution, phylogeny and role of plasmids in the biology of rickettsiae associated with blood-feeding arthropods...
  9. Chemical Biodiversity: Investigating the Phylogeny and Functional Toxins of Venom
    MANDE N HOLFORD; Fiscal Year: 2010
    ..biochemists and neurologists, but very little is known about toxins from terebrids and other Toxoglossa, and the phylogeny of these families is largely in doubt...
  10. Statistical Models in Epigenomics
    Kimberly D Siegmund; Fiscal Year: 2011
    ..used to reconstruct the genealogy of species and individuals, and we propose to translate this general molecular phylogeny approach to human cancers...
  11. Molecular Evolution of Drosophila Y Chromosome
    Andrew G Clark; Fiscal Year: 2012
    ..There are now 12 complete genome sequences for species of Drosophila whose well-known phylogeny provides a rich resource for analysis of Y chromosome dynamics...
  12. Integrated Desktop Software for Management of Hepatitic C Data
    Johanna C Craig; Fiscal Year: 2010
    ..We will also develop a phylogeny tool for assembling alignments into evolutionary trees that will color-code and time-stamp the input sequences (..
  13. Presynaptic Regulation of C.elegans Dopamine Transporter
    Randy D Blakely; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Dopamine (DA) is a neurotransmitter used throughout phylogeny to modulate circuits controlling movement, attention, reward and cognition...
  14. ONTOGENY AND PHYLOGENY OF THE MHC
    Martin Flajnik; Fiscal Year: 2009
    ..tropicalis), we will begin to analyze the modes of silencing in the tetraploids and eventually the higher order octo- and dodecaploid individuals. ..
  15. Viral and Microbial RNA Modifying Enzymes
    STEWART H SHUMAN; Fiscal Year: 2013
    ..They also provide instructive clues to eukaryal phylogeny and evolution of large DNA viruses...
  16. Signaling pathways and expansion of hematopoietic stem cells in zebrafish
    JILL L DE JONG; Fiscal Year: 2010
    ..cells (HSCs) are formed during embryogenesis by a complex process that is largely conserved across vertebrate phylogeny. The zebrafish mutant kugelig (kgg) has a severe defect in hematopoiesis, as well as altered anterior-posterior ..
  17. Structure and Function of DNA Repair Enzymes
    Susan S Wallace; Fiscal Year: 2013
    ..germ line and somatic DNA sequence variants of the oxidative DNA glycosylases and RAD51 based on structure and phylogeny. Project 1 will demonstrate whether these repair variants Induce cellular transformation, are mutagenic in mouse ..
  18. The Population Genetics of Divergence
    EMANUEL HEY; Fiscal Year: 2013
    ..This will be the first such method that does not assume a given phylogeny;that does not assume that gene flow has not occurred;and that makes no assumptions about the relative population ..
  19. Identification of transcriptional determinants of dendritic patterning
    David M Miller; Fiscal Year: 2010
    ..and are thus likely to depend on conserved genetic programs that control nociceptor morphogenesis throughout phylogeny. The mechanisms that govern the creation of these complex structures are poorly understood but recent studies in ..
  20. EVOLUTIONARY ORIGINS OF IMMUNE-TYPE GENES
    GARY LITMAN; Fiscal Year: 2009
    ..Acquisition of complete genome sequences in species that represent key points in phylogeny not only permit in-depth analysis of immune mediators but also represent an invaluable resource for ..
  21. International Conference on the Cell and Molecular Biology of Chlamydomonas
    David R Mitchell; Fiscal Year: 2013
    ..Because of the recent explosion of genomic sequencing and its consequent revelation of eukaryotic phylogeny, it is important for the Chlamydomonas community to understand both the uniqueness of this organism and its ..
  22. Modeling evolution of functional context in proteins
    David D Pollock; Fiscal Year: 2012
    ..information in protein sequence biodiversity is to use parametric statistical inference with realistic phylogeny-based models...
  23. Phylogeny, Structure and Virulence Contributions of NMEC's Virulence Plasmids
    Lisa K Nolan; Fiscal Year: 2013
    ..we will generate sequences of interesting NMEC plasmids, compare them to other plasmids, determine their phylogeny and evolution, and define their core and pan-genome...
  24. Genome Variability and Population Processes of Lyme Disease Pathogens
    Weigang Qiu; Fiscal Year: 2013
    ..The SC3 support during 1998- 2012 is behind the PI's leading roles in the phylogeny-based selection of strains for whole-genome sequencing, the discovery of widespread recombination and estimation ..
  25. MECHANOTRANSDUCTION IN C ELEGANS
    Joshua M Kaplan; Fiscal Year: 2013
    ..Given the strong conservation of these pathways across phylogeny, it is likely that our experiments will provide new insights into the general mechanisms underlying these ..
  26. Modeling Microtubule Dynamics in Mitosis
    David J Odde; Fiscal Year: 2013
    ..2) Are plus-end directed molecular motors the main controllers of kMT assembly and chromosome congression across phylogeny and in human cells? 3) What are the nanoscale-kHz dynamics of kMT plus-ends at the kinetochore? In each case we ..
  27. BIOCHEMICAL AND GENETIC ANALYSIS OF YEAST KINETOCHORES
    PETER KARL SORGER; Fiscal Year: 2010
    ..Aim 5. An on-line resource will be created to disseminate information on kinetochore functions, assays and phylogeny (a data sharing resource)...
  28. Identification of Novel Denitrosylases
    Jonathan S Stamler; Fiscal Year: 2013
    ..previously that denitrosylating activates discovered in microorganisms are likely to be highly conserved through phylogeny, and our analysis is thus likely to reveal novel enzymatic activities of broad purview in the analysis of ..
  29. Mining a collection of soil amoebae for antibacteria agents
    Marcin S Filutowicz; Fiscal Year: 2012
    ..The late Dr. Kenneth Raper, an authority on the ecology and phylogeny of social amoebae, amassed this resource...
  30. Neurotoxic Effects of Volatile Anesthetics in C. elegans
    Philip G Morgan; Fiscal Year: 2012
    ..support the belief that interactions leading to apoptosis will be maintained at a high level when studied across phylogeny. We hypothesize that identification of the genes which control anesthetic induced neurotoxicity will target ..
  31. Virtual Machines and Cloud Computing for automated and portable sequence analysis
    W Florian Fricke; Fiscal Year: 2010
    ..Supported applications will include 16S rRNA-based phylogeny and community comparison, and identification, assembly, annotation and functional characterization of viral, ..
  32. The Transporter Classification Database (TCDB)
    Milton H Saier; Fiscal Year: 2013
    ..This last effort will derive reliable new biological knowledge from a variety of sources, including phylogeny, motif, domain, operon and regulon analyses. Our Specific Aims are as follows: 1...
  33. Predictive Structure-Based Models of Malaria Resistance
    David Hecht; Fiscal Year: 2013
    ..These models will be tested and validated by using the first 70% of the phylogeny in order to predict the remaining 30%...
  34. Lymphoproliferative Disorders in Primary Immunodeficiencies
    JOHN MICHAEL ROUTES; Fiscal Year: 2012
    ..family members and household contacts of infected and uninfected patients with CVID and determine the molecular phylogeny of HHV8 in infected cohorts by amplifying the highly polymorphic HHV8 K1 ORF by PCR and performing DNA ..
  35. Identifying Genome Wide SINE Retrotransposons Contributing to Dog Size Variation
    Nathan B Sutter; Fiscal Year: 2012
    ..SINEs that disrupt gene expression and splicing will also be identified and a SINE-based breed phylogeny will be built...
  36. Genetic Mechanisms of Survivorship Disparities after Unrelated HCT
    Effie W Petersdorf; Fiscal Year: 2013
    ..and its organization on haplotypes in individuals of AFA, API, CAU ancestry as defined by AIMs;2) define the phylogeny of ILIA, ILIB, IL1RN, IL6, IL6R, IL15 and IL15FiA haplotypes in cades;3) define SNP, haplotype, and clad-based ..
  37. Molecular patterning and specification of the fovea during retinal development.
    Nathan A Mundell; Fiscal Year: 2013
    ..Specific Aim 2: Determine if A-P, D-V and RFZ gene expression patterns are shared across phylogeny. Specific Aim 3: Determine if reciprocal inhibitory interactions between patterned transcription factors are ..
  38. Determining piwi function using in vivo imaging of stem cells in Hydra.
    Celina Juliano; Fiscal Year: 2012
    ..of Hydra as a model system to further understand piwi functions in stem cells that are conserved across phylogeny. The Hydra, a basal metazoan, has a well-characterized stem cell lineage, the 1-cell lineage, in which two piwi ..
  39. Detection of Distribution of New Genes in Drosophila Phylogeny
    MANYUAN NO LONG; Fiscal Year: 2010
    ..We will estimate the rate of new gene origination and its variation along branches of the phylogeny, using related statistical analyses including maximum likelihood approach...
  40. Molelcular determinants of synaptic plasticity
    Janet E Richmond; Fiscal Year: 2013
    ..This phenomenon has been observed throughout animal phylogeny which suggests that the underlying pathways are conserved...
  41. Predoctoral Training Program in Bioinformatics and Computational Biology
    Timothy C Elston; Fiscal Year: 2013
    ..of bioinformatics and computational biology, such as information theory, machine learning, sequence comparison, phylogeny, data management, ontology, data mining, biostatistics, biomolecular structure/function prediction, and modeling ..
  42. ENTAMOEBA HISTOLYTICA GENOME PROJECT
    Brendan Loftus; Fiscal Year: 2002
    ..The study of the E. histolytica genome serves as a model organism for reconstructing the phylogeny of early branching eukaryotes and will also provide insights into the history of anaerobic lumenal parasites...
  43. Detect small and very small in-space inversions and improve alignment quality
    Minmei Hou; Fiscal Year: 2010
    ..We will use phylogeny information and evolutionary properties of the species, together with probability analysis, to verify very small ..
  44. Genetics 2012: Model Organism to Human Cancer
    PAUL WARREN STERNBERG; Fiscal Year: 2012
    ..However, we still need to learn how best to apply model organisms across the entire spectrum of phylogeny to aspects of cancer biology for which evolution has suited them...
  45. Phylogeography and Spatial Dynamics of Epidemic Rabies
    Leslie A Real; Fiscal Year: 2013
    ..different types and phases of SEIR dynamics on the residual signature of demographic change within the molecular phylogeny, based on predicted variation in the structure of the coalescent...
  46. PHYLOGENETIC ANALYSIS OF CHLOROPLAST DNA POLYMORPHISMS I
    Steven Strauss; Fiscal Year: 1990
    The goals of the proposed research are to study chloroplast genetics and phylogeny in two genera of conifers, Pinus and Pseudotsuga...
  47. TRP Channel Function and Regulation
    X Z Shawn Xu; Fiscal Year: 2010
    ..Given the high conservation of TRP family channels throughout phylogeny and the fact that mutations in TRP family channels lead to a number of human diseases such as polycystic kidney ..
  48. Phylogeny of Fairness: Roles of Number Representation and Social Cognition
    ELLEN ELIZABETH FURLONG; Fiscal Year: 2012
    ..e., autists who cannot reason about intentions, or patients with Down syndrome who have deficits in mathematical cognition). ..
  49. Global Analysis of Proteolysis in Apoptosis
    James A Wells; Fiscal Year: 2013
    ..doubles the number of known caspase targets and tells us what can be cut, but not how fast or how conserved in phylogeny. In Specific Aim 1, we will use quantitative selected reaction monitoring (SRM) approaches to determine for the ..
  50. Sequence alignment fidelity in genomics and bioinformatics
    Michael S Rosenberg; Fiscal Year: 2010
    ..approach for determining the composition of gene families which makes use of evolutionary principles, including phylogeny and ancestral sequence reconstruction;and (4) to improve a sequence simulation program to include (a) better ..
  51. Bayesian Joint Estimation of Alignment and Phylogeny
    Marc A Suchard; Fiscal Year: 2012
    ..not directly observed;they are inferred properties of the raw sequence data and must be estimated along with the phylogeny. Current tools handle this inference sequentially, first determining a sometimes poor estimate of the alignment ..
  52. CARBONATOAPATITE FORMATION IN ENAMEL MINERALIZATION
    Takaaki Aoba; Fiscal Year: 1993
    ..Fish enameloid provides a unique model, since the fluoride incorporation into the mineral is related to the phylogeny of fishes...
  53. Genetics 2010: Model Organisms to Human Biology
    FRED M WINSTON; Fiscal Year: 2010
    ..However, we still need to learn how best to apply model organisms across the entire spectrum of phylogeny to those problems of human biology for which evolution has suited them...
  54. HOST GENETIC DETERMINANTS OF HIV PATHOGENESIS
    Sunil Ahuja; Fiscal Year: 1999
    ..For example, reconstructing the phylogeny of chemokine system gene variants provides the biological framework for designing studies of disease association ..
  55. Population Genetics of M. Tuberculosis During Disease Epidemics
    CAITLIN S PEPPERELL; Fiscal Year: 2010
    ..The candidate proposes to use TB genotyping techniques to create a micro-phylogeny of TB isolates from these communities...
  56. The temporal reconfiguration of regulatory networks: From yeast to cancer
    Aviv Regev; Fiscal Year: 2011
    ..transcriptional states in the hematopoiesis ontogeny and the evolution of regulatory networks in the Ascomycota phylogeny. The work will unify disparate problems - including how cell adapts to changing growth conditions, how cancer ..
  57. Urethral Microbiome of Adolescent Males
    J Dennis Fortenberry; Fiscal Year: 2012
    ..and up to 36 1-month follow-up samples for characterization of microflora using high-throughput 16s rRNA phylogeny, Q-PCR and metagenomic sequencing...
  58. The temporal reconfiguration of regulatory networks: From yeast to cancer
    Aviv Regev; Fiscal Year: 2012
    ..transcriptional states in the hematopoiesis ontogeny and the evolution of regulatory networks in the Ascomycota phylogeny. The work will unify disparate problems - including how cell adapts to changing growth conditions, how cancer ..
  59. Mechanisms of Risk and Resilience in ASD: Ontogeny, Phylogeny and Gene Disruption
    Ami Klin; Fiscal Year: 2013
    ..abstract_text> ..
  60. Applying Molecular Phylogeny to Predict Clinical Outcomes in Cancer
    Kimberly D Siegmund; Fiscal Year: 2011
    DESCRIPTION (provided by applicant): Our goal is to investigate the utility of cancer molecular phylogeny, a novel technological concept, to predict clinical outcomes...
  61. Genetic mechanisms that regulate left/right asymmetric neuron size
    Oliver Hobert; Fiscal Year: 2010
    ..elegans as a model system. Lateral differences in neuron cell size are conserved across phylogeny, can be observed in humans and are disrupted in psychiatric disorders, illustrating the overall importance of ..
  62. Extending Bayesian Phylogenetic Analysis
    John P Huelsenbeck; Fiscal Year: 2013
    ..I plan to develop methods for estimating bacterial species phylogeny in the face of this horizontal gene transfer...
  63. Phylogeography of Verrucarum sand fly disease vectors
    Leonard Munstermann; Fiscal Year: 2006
    ..serrana) using total evidence approaches--DNA sequences, hybridization and isoenzymes. (3) To infer a molecular phylogeny for species of the Verrucarum group and related subgenera, and genera, based on comparison of mitochondrial (..
  64. PHYLOGENY AND ONTOGENY OF AN AUDITORY SYSTEM
    DAVID YAGER; Fiscal Year: 2004
    ..This line of research will lead to a clearer understanding of the neural and non-neural characteristics that define a hot spot for auditory system evolution. ..
  65. WHIPPLE BACILLUS AND THE ETIOLOGY OF SARCOIDOSIS
    David Fredricks; Fiscal Year: 1999
    ..The proposed research will help to elucidate the causative role, natural ecology, detailed phylogeny, and physiological characteristics of the Whipple bacillus, as well as the spectrum of disease with which it is ..
  66. POPULATION BIOLOGY OF SURFACE POLYSACCHARIDES IN CHOLERA
    John Morris; Fiscal Year: 2004
    ..Initial phylogenetic studies suggest that serotype and/or capsule type are independent of phylogeny. We hypothesize that there is frequent horizontal/sexual transfer and rearrangement of surface polysaccharide ..
  67. Micro RNA Expression and Cancer
    Thomas Schmittgen; Fiscal Year: 2005
    ..To date over 200 miRNAs have been discovered across all multicellular phylogeny including C. elegans, Drosophila, plants, mice and humans...
  68. ONTOGENY AND PHYLOGENY OF HUMAN PEROXISOMAL FUNCTION
    Golder Wilson; Fiscal Year: 1993
    ....
  69. CELLULAR INTERACTIONS WITH COMPLEMENT AND PROPERDIN
    SHAUN RUDDY; Fiscal Year: 1990
    Because of its precedence in phylogeny and its freedom from the requirement for an adaptive immune response (i.e., specific antibody), the alternative pathway for complement activation must be an important mechanism for host defense...