likelihood functions

Summary

Summary: Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.

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. doi jModelTest: phylogenetic model averaging
    David Posada
    Mol Biol Evol 25:1253-6. 2008
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Detail Information

Publications262 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. doi jModelTest: phylogenetic model averaging
    David Posada
    Mol Biol Evol 25:1253-6. 2008
    ..The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es...
  3. 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/...
  4. 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
    ....
  5. 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...
  6. 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
    ....
  7. 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)...
  8. 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...
  9. 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*. Furthermore, CONSEL is applicable to a wide class of problems where the BPs are available...
  10. 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...
  11. 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...
  12. 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...
  13. ncbi Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests
    David Posada
    Departamento de Bioquimica, Genética e Inmunología, Facultad de Biologia, Universidad de Vigo, Vigo 36200, Spain
    Syst Biol 53:793-808. 2004
    ..To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus(genus Carabus) ground beetles described by Sota and Vogler (2001)...
  14. 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...
  15. ncbi Sequence-based species delimitation for the DNA taxonomy of undescribed insects
    Joan Pons
    Department of Entomology, The Natural History Museum, London SW7 5BD, United Kingdom
    Syst Biol 55:595-609. 2006
    ....
  16. 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...
  17. 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
    ....
  18. ncbi TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
    Heiko A Schmidt
    Max Planck Institut fur Molekulare Genetik, Ihnestr 73, D 14195 Berlin, Germany
    Bioinformatics 18:502-4. 2002
    ..To reduce waiting time for larger datasets the tree reconstruction part of the software has been parallelized using message passing that runs on clusters of workstations as well as parallel computers...
  19. ncbi Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences
    Jerome C Regier
    Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA
    Nature 463:1079-83. 2010
    ..These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships...
  20. ncbi Merlin--rapid analysis of dense genetic maps using sparse gene flow trees
    Goncalo R Abecasis
    The Wellcome Trust Center for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
    Nat Genet 30:97-101. 2002
    ....
  21. ncbi Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis
    Richard H Ree
    Department of Botany, Field Museum of Natural History, Chicago, Illinois 60605, USA
    Syst Biol 57:4-14. 2008
    ..The DEC model is thus an incremental advance that highlights considerable potential in the nascent field of model-based historical biogeographic inference...
  22. pmc Distinguishing migration from isolation: a Markov chain Monte Carlo approach
    R Nielsen
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Genetics 158:885-96. 2001
    ..The use of the method is illustrated in an application to mitochondrial DNA sequence data from a fish species: the threespine stickleback (Gasterosteus aculeatus)...
  23. ncbi A phylogenomic approach to resolve the arthropod tree of life
    Karen Meusemann
    Zoologisches Forschungsmuseum Alexander Koenig, Molecular Biology Unit, Bonn, Germany
    Mol Biol Evol 27:2451-64. 2010
    ..However, our analyses also showed for few deep splits that were recently thought to be resolved, for example, the position of myriapods, a remarkable sensitivity to methods of analyses...
  24. ncbi Estimating maximum likelihood phylogenies with PhyML
    Stephane Guindon
    Laboratoire d Informatique, de Robotique et de Microélectronique de Montpellier LIRMM, UMR 5506 CNRS, Universite Montpellier II, Montpellier, France
    Methods Mol Biol 537:113-37. 2009
    ..We illustrate the strengths and pitfalls of this program through the analysis of a real data set. PhyML v3.0 is available from (http://atgc_montpellier.fr/phyml/)...
  25. pmc A coalescent-based method for detecting and estimating recombination from gene sequences
    Gil McVean
    Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
    Genetics 160:1231-41. 2002
    ..The extremely high level of recombination detected in both HIV1 and HIV2 sequences demonstrates that recombination cannot be ignored in the analysis of viral population genetic data...
  26. ncbi A likelihood approach to estimating phylogeny from discrete morphological character data
    P O Lewis
    Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 3043, USA
    Syst Biol 50:913-25. 2001
    ....
  27. ncbi Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish
    Simone Hoegg
    Department of Biology, University of Konstanz, 78457 Konstanz, Germany
    J Mol Evol 59:190-203. 2004
    ..The additional number of genes resulting from this event might have facilitated the evolutionary radiation and the phenotypic diversification of the teleost fish...
  28. ncbi Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
    M Anisimova
    Department of Biology, Galton Laboratory, University College London, London, England
    Mol Biol Evol 18:1585-92. 2001
    ..The exact distribution assumed for the omega ratio over sites was found not to affect the effectiveness of the LRT...
  29. pmc Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood
    Simon A Berger
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss Wolfsbrunnenweg 35, D 69118 Heidelberg, Germany
    Syst Biol 60:291-302. 2011
    ..We are also actively developing a Web server that offers a freely available service for computing read placements on trees using the EPA...
  30. ncbi Inconsistency of phylogenetic estimates from concatenated data under coalescence
    Laura Salter Kubatko
    Department of Statistics and Evolution, The Ohio State University, Columbus, Ohio 43210, USA
    Syst Biol 56:17-24. 2007
    ..These results highlight the importance of incorporating variation in gene histories into multilocus phylogenetics...
  31. pmc PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference
    Stephane Guindon
    Bioinformatics Institute and Allan Wilson Centre, University of Auckland Private Bag 92019, Auckland, New Zealand
    Nucleic Acids Res 33:W557-9. 2005
    ..The server and its documentation are available at http://atgc.lirmm.fr/phyml...
  32. ncbi Variance stabilization applied to microarray data calibration and to the quantification of differential expression
    Wolfgang Huber
    Department of Molecular Genome Analysis, German Cancer Research Center, INF 280, Heidelberg, 69120, Germany
    Bioinformatics 18:S96-104. 2002
    ..We demonstrate our approach on data sets from different experimental platforms, including two-colour cDNA arrays and a series of Affymetrix oligonucleotide arrays...
  33. pmc PyEvolve: a toolkit for statistical modelling of molecular evolution
    Andrew Butterfield
    Centre for Bioinformation Science, John Curtin School of Medical Research and Mathematical Sciences Institute, Australian National University, Canberra, ACT 0200, Australia
    BMC Bioinformatics 5:1. 2004
    ..Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation...
  34. pmc Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings
    Peter M Visscher
    Genetic Epidemiology Group, Queensland Institute of Medical Research, Brisbane, Australia
    PLoS Genet 2:e41. 2006
    ....
  35. ncbi How many bootstrap replicates are necessary?
    Nicholas D Pattengale
    Department of Computer Science, University of New Mexico, Albuquerque, New Mexico 87123, USA
    J Comput Biol 17:337-54. 2010
    ..The complete test suite is available at http://lcbb.epfl.ch/BS.tar.bz2, and BS with our stopping criteria is included in the latest release of RAxML v7.2.5, available at http://wwwkramer.in.tum.de/exelixis/software.html...
  36. pmc Diagnostic tests 4: likelihood ratios
    Jonathan J Deeks
    Screening and Test Evaluation Program, School of Public Health, University of Sydney, NSW 2006, Australia
    BMJ 329:168-9. 2004
  37. ncbi Estimation of individual admixture: analytical and study design considerations
    Hua Tang
    Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genet Epidemiol 28:289-301. 2005
    ..g., simulations) not possible by Bayesian methods. Our simulation results demonstrate that inclusion of ancestral populations or their surrogates in the analysis is required by any method of IA estimation to obtain reasonable results...
  38. pmc A new method of inference of ancestral nucleotide and amino acid sequences
    Z Yang
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA
    Genetics 141:1641-50. 1995
    ..84, 0.76, and 0.51, respectively. The probability that an amino acid in an ancestral sequence is correctly reconstructed by the likelihood analysis ranged from 91.3 to 98.7% for the four ancestral sequences...
  39. ncbi An empirical codon model for protein sequence evolution
    Carolin Kosiol
    EMBL European corrected Bioinformatics Institute, Hinxton, United Kingdom
    Mol Biol Evol 24:1464-79. 2007
    ..We point out the biological interpretation of our ECM and possible consequences for studies of selection...
  40. pmc Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates
    Michael E Alfaro
    Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 106:13410-4. 2009
    ....
  41. ncbi Estimating a binary character's effect on speciation and extinction
    Wayne P Maddison
    Department of Zoology, University of British Columbia, Vancouver, Canada
    Syst Biol 56:701-10. 2007
    ..g., is the rate of speciation elevated for one character state over the other?). We demonstrate the application of the method using simulated data with known parameter values...
  42. pmc Improving marginal likelihood estimation for Bayesian phylogenetic model selection
    Wangang Xie
    Abbott, 100 Abbott Park, R436 AP9A 2, Abbott Park, IL 60064, USA
    Syst Biol 60:150-60. 2011
    ..We conclude that the greatly increased accuracy of the SS and TI methods argues for their use instead of the HM method, despite the extra computation needed...
  43. ncbi A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli
    Patricia Escobar-Paramo
    INSERM E0339, Faculte de Medecine Xavier Bichat, Paris, France
    Mol Biol Evol 21:1085-94. 2004
    ..Thus, the E. coli genome seems to be formed by an "ancestral" and a "derived" background, each one responsible for the acquisition and expression of different virulence factors...
  44. ncbi Modeling compositional heterogeneity
    Peter G Foster
    Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
    Syst Biol 53:485-95. 2004
    ..It is shown that when composition is not accommodated, then the model does not fit, and incorrect trees are found; but when composition is accommodated, the model then fits, and the known correct phylogenies are obtained...
  45. pmc Estimating genetic parameters in natural populations using the "animal model"
    Loeske E B Kruuk
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland, UK
    Philos Trans R Soc Lond B Biol Sci 359:873-90. 2004
    ....
  46. ncbi Testing for phylogenetic signal in comparative data: behavioral traits are more labile
    Simon P Blomberg
    Department of Biology, University of California, Riverside, California 92521, USA
    Evolution 57:717-45. 2003
    ....
  47. pmc Gene duplication and fragmentation in the zebra finch major histocompatibility complex
    Christopher N Balakrishnan
    Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
    BMC Biol 8:29. 2010
    ....
  48. pmc Sequential Monte Carlo without likelihoods
    S A Sisson
    School of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052, Australia
    Proc Natl Acad Sci U S A 104:1760-5. 2007
    ..ways of evaluating posterior distributions in the presence of analytically or computationally intractable likelihood functions. Despite representing a substantial methodological advance, existing methods based on rejection sampling or ..
  49. ncbi Testing congruence in phylogenomic analysis
    Jessica W Leigh
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
    Syst Biol 57:104-15. 2008
    ..Investigating phylogenomic data sets for conflicting signals has the potential to both improve phylogenetic accuracy and inform our understanding of genome evolution...
  50. ncbi STEM: species tree estimation using maximum likelihood for gene trees under coalescence
    Laura S Kubatko
    Departments of Statistics and Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
    Bioinformatics 25:971-3. 2009
    ..It includes options to compute the ML species tree, search the space of all species trees for the k trees of highest likelihood and compute ML branch lengths for a user-input species tree...
  51. ncbi Assessing the probability that a positive report is false: an approach for molecular epidemiology studies
    Sholom Wacholder
    Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 7244, USA
    J Natl Cancer Inst 96:434-42. 2004
    ..An FPRP-based criterion for deciding whether to call a finding noteworthy formalizes the process already used informally by investigators--that is, tempering enthusiasm for remarkable study findings with considerations of plausibility...
  52. pmc An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants
    Stephen A Smith
    National Evolutionary Synthesis Center, Durham, NC 27705, USA
    Proc Natl Acad Sci U S A 107:5897-902. 2010
    ..g., the early radiation of herbaceous clades within angiosperms) may still be biasing our inferences...
  53. ncbi The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference
    Alan R Lemmon
    Section of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA
    Syst Biol 58:130-45. 2009
    ....
  54. pmc A scan for positively selected genes in the genomes of humans and chimpanzees
    Rasmus Nielsen
    Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    PLoS Biol 3:e170. 2005
    ..The polymorphism analysis further supports the presence of positive selection in these genes by showing an excess of high-frequency derived nonsynonymous mutations...
  55. pmc Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets
    Arong Luo
    Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    BMC Evol Biol 10:242. 2010
    ....
  56. ncbi Coalescent methods for estimating phylogenetic trees
    Liang Liu
    Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
    Mol Phylogenet Evol 53:320-8. 2009
    ..Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide ..
  57. pmc Mammalian phylogeny reveals recent diversification rate shifts
    Tanja Stadler
    Institut für Integrative Biologie, Eidgenössiche Technische Hochschule Zurich, 8092 Zurich, Switzerland
    Proc Natl Acad Sci U S A 108:6187-92. 2011
    ..g., present-day species or virus data. In particular, the method is very robust toward noise and uncertainty in the phylogeny and can account for incomplete taxon sampling...
  58. pmc Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates
    Lars Hendrich
    Department of Entomology, Zoological State Collection, Munich, Germany
    PLoS ONE 5:e14448. 2010
    ..Then, we contrasted phylogenetic subsampling with the hitherto more commonly applied geographical subsampling, where sister species are not necessarily captured...
  59. pmc MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
    Manuel Stark
    Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland
    BMC Genomics 11:461. 2010
    ..Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem...
  60. pmc Patterns of positive selection in six Mammalian genomes
    Carolin Kosiol
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 4:e1000144. 2008
    ..This study provides additional evidence for widespread positive selection in mammalian evolution and new genome-wide insights into the functional implications of positive selection...
  61. ncbi Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission
    Cynthia A Derdeyn
    Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
    Science 303:2019-22. 2004
    ..This reveals characteristics of the envelope glycoprotein that influence HIV-1 transmission and may have implications for vaccine design...
  62. ncbi Selecting the best-fit model of nucleotide substitution
    D Posada
    Department of Zoology, Brigham Young University, Provo, Utah 84602 5255, USA
    Syst Biol 50:580-601. 2001
    ..We show here that a best-fit model can be readily identified. Consequently, given the relevance of models, model fitting should be routine in any phylogenetic analysis that uses models of evolution...
  63. ncbi A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
    Joseph P Bielawski
    Department of Biology, University College London, London, WC1E 6BT, UK
    J Mol Evol 59:121-32. 2004
    ..Limitations of the new method are discussed...
  64. ncbi The epidemic behavior of the hepatitis C virus
    O G Pybus
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Science 292:2323-5. 2001
    ..Our model builds a bridge between the disciplines of population genetics and mathematical epidemiology by using pathogen gene sequences to infer the population dynamic history of an infectious disease...
  65. ncbi Likelihood methods for detecting temporal shifts in diversification rates
    Daniel L Rabosky
    Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853 2701, USA
    Evolution 60:1152-64. 2006
    ..I illustrate use of the method by analyzing a published phylogeny for Australian agamid lizards...
  66. pmc Markov chain Monte Carlo without likelihoods
    Paul Marjoram
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Proc Natl Acad Sci U S A 100:15324-8. 2003
    ..The approach is illustrated by an example of ancestral inference in population genetics. A number of open problems are highlighted in the discussion...
  67. ncbi Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees
    Kevin Liu
    Department of Computer Sciences, University of Texas at Austin, One University Station C0500, Austin, TX 78712, USA
    Science 324:1561-4. 2009
    ..In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies...
  68. ncbi rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny
    Matthew W Dimmic
    Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109 1055, USA
    J Mol Evol 55:65-73. 2002
    ..We provide evidence that rtREV is a more realistic evolutionary model for analyses of the pol gene, although it is inapplicable to analyses involving the gag gene...
  69. pmc Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
    Yee Hwa Yang
    Department of Statistics, Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720 3860, USA
    Nucleic Acids Res 30:e15. 2002
    ..Lastly, to allow for comparisons of expression levels across slides, a robust method based on maximum likelihood estimation is proposed to adjust for scale differences among slides...
  70. ncbi Different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures
    Jacco Wallinga
    National Institute for Public Health and the Environment, Bilthoven, The Netherlands
    Am J Epidemiol 160:509-16. 2004
    ..In controlling SARS outbreaks, timely alerts have been essential: Delaying the institution of control measures by 1 week would have nearly tripled the epidemic size and would have increased the expected epidemic duration by 4 weeks...
  71. pmc Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
    Maria Anisimova
    Department of Biology, University College London, London WC1E 6BT, United Kingdom
    Genetics 164:1229-36. 2003
    ..Identification of sites under positive selection by the empirical Bayes method appears to be less affected than the LRT by recombination...
  72. ncbi Coalescent genealogy samplers: windows into population history
    Mary K Kuhner
    Department of Genome Sciences, University of Washington, Seattle, WA 98195 5065, USA
    Trends Ecol Evol 24:86-93. 2009
    ..This review summarizes available genealogy-sampler software, including data requirements and limitations on the use of each program...
  73. pmc Detecting positive selection within genomes: the problem of biased gene conversion
    Abhirami Ratnakumar
    Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
    Philos Trans R Soc Lond B Biol Sci 365:2571-80. 2010
    ..Our results indicate that gBGC significantly affects the evolution of coding sequences in primates, often leading to patterns of evolution that can be mistaken for positive selection...
  74. pmc High-resolution species trees without concatenation
    Scott V Edwards
    Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 104:5936-41. 2007
    ..These results make accessible an alternative paradigm for combining data in phylogenomics that focuses attention on the singularity of species histories and away from the idiosyncrasies and multiplicities of individual gene histories...
  75. ncbi Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics
    Per Erixon
    Department of Systematic Botany, Evolutionary Biology Centre, Uppsala University, Norbyv 18D, SE 75236 Uppsala, Sweden
    Syst Biol 52:665-73. 2003
    ..When data are analyzed under the correct model, nonparametric bootstrapping is conservative. Bayesian posterior probabilities are also conservative in this respect, but less so...
  76. ncbi LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
    Mary K Kuhner
    Department of Genome Sciences Box 357730 University of Washington Seattle, 98195 7730, USA
    Bioinformatics 22:768-70. 2006
    ..It is available as portable source code and executables for all three major platforms...
  77. ncbi A molecular timeline for the origin of photosynthetic eukaryotes
    Hwan Su Yoon
    Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, Iowa, USA
    Mol Biol Evol 21:809-18. 2004
    ..e., acritarchs) from the early Mesoproterozoic (1,500 MYA) and with a major eukaryotic diversification in the very late Mesoproterozoic and Neoproterozoic, provide a molecular timeline for understanding algal evolution...
  78. ncbi Increased taxon sampling greatly reduces phylogenetic error
    Derrick J Zwickl
    Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas, Austin, Texas 78712, USA
    Syst Biol 51:588-98. 2002
    ..Taking each of these results into account re-enforces the conclusion that increased sampling of taxa is one of the most important ways to increase overall phylogenetic accuracy...
  79. pmc Unifying vertical and nonvertical evolution: a stochastic ARG-based framework
    Erik W Bloomquist
    Department of Biostatistics, UCLA School of Public Health, Los Angeles, CA 90095, USA
    Syst Biol 59:27-41. 2010
    ..To demonstrate SMARTIE, we explore 2 separate phylogenetic applications, one involving pathogenic Leptospirochete and the other Saccharomyces...
  80. ncbi Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy
    Jimmy A McGuire
    Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA 94720 3160, USA
    Syst Biol 56:837-56. 2007
    ....
  81. pmc Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
    Guy Baele
    Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
    Mol Biol Evol 29:2157-67. 2012
    ..The methods used in this article are now available in BEAST, a powerful user-friendly software package to perform Bayesian evolutionary analyses...
  82. ncbi Maximum likelihood methods for detecting adaptive evolution after gene duplication
    Joseph P Bielawski
    Department of Biology, University College London, Darwin Building, Gower Street, London WCIE 6BT, United Kingdom
    J Struct Funct Genomics 3:201-12. 2003
    ..We also comment on the limitations of these methods and discuss directions for further improvements...
  83. ncbi Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies
    Richard G FitzJohn
    Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
    Syst Biol 58:595-611. 2009
    ..Our methods allow for the direct estimation of the effect of a trait on speciation and extinction rates using incompletely resolved phylogenies...
  84. ncbi Empirical and hierarchical Bayesian estimation of ancestral states
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Syst Biol 50:351-66. 2001
    ..We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis...
  85. ncbi Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power
    David Paetkau
    Department of Zoology and Entomology, University of Queensland, St Lucia, QLD 4072, Australia
    Mol Ecol 13:55-65. 2004
    ....
  86. pmc A simple and robust statistical test for detecting the presence of recombination
    Trevor C Bruen
    McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
    Genetics 172:2665-81. 2006
    ..The results suggest that phi(w) is one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances...
  87. ncbi Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model
    Chen Meng
    Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM 87131, USA
    Theor Popul Biol 75:35-45. 2009
    ..Using our model, we propose methods for estimating the extent of the role of hybridization in both a likelihood and a Bayesian framework. The performance of our methods is examined using both simulated and empirical data...
  88. ncbi Asynchronous colonization of Madagascar by the four endemic clades of primates, tenrecs, carnivores, and rodents as inferred from nuclear genes
    Celine Poux
    Department of Biochemistry 161, Radboud University Nijmegen, 6500 HB, Nijmegen, PO Box 9101, The Netherlands
    Syst Biol 54:719-30. 2005
    ....
  89. ncbi morePhyML: improving the phylogenetic tree space exploration with PhyML 3
    Alexis Criscuolo
    Unite de Biologie Moleculaire du Gene chez les Extremophiles, Departement de Microbiologie, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
    Mol Phylogenet Evol 61:944-8. 2011
    ..Based on the analysis of a large number of amino acid and nucleotide data, I show that morePhyML allows inferring more accurate phylogenetic trees than several other recently developed ML tree inference softwares in many cases...
  90. pmc Towards a global barcode library for Lymantria (Lepidoptera: Lymantriinae) tussock moths of biosecurity concern
    Jeremy R deWaard
    Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 5:e14280. 2010
    ....
  91. pmc Familial identification: population structure and relationship distinguishability
    Rori V Rohlfs
    Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
    PLoS Genet 8:e1002469. 2012
    ..All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States...
  92. pmc Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages
    Christine N Shulse
    Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 6:e20146. 2011
    ....
  93. ncbi False phylogenies on wood mice due to cryptic cytochrome-b pseudogene
    Sylvain Dubey
    School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
    Mol Phylogenet Evol 50:633-41. 2009
    ..The presence of this cryptic pseudogene in published sequences is supported by different pathways. This has led to important errors in previous molecular trees and hence to partial misinterpretations in the phylogeny of Apodemus...
  94. pmc A new general biomarker-based incidence estimator
    Reshma Kassanjee
    DST NRF Centre of Excellence in Epidemiological Modelling and Analysis SACEMA, University of Stellenbosch, Stellenbosch, South Africa
    Epidemiology 23:721-8. 2012
    ..Despite widespread applications to HIV, there is currently no consensus on the correct handling of biomarker results classifying persons as "recently" infected long after the infections occurred...
  95. pmc Hotspots of biased nucleotide substitutions in human genes
    Jonas Berglund
    Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    PLoS Biol 7:e26. 2009
    ..This process can lead to accelerated evolution in coding sequences and excess amino acid replacement substitutions, thereby generating significant results for tests of positive selection...
  96. ncbi Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species
    Rongling Wu
    Department of Statistics, University of Florida, Gainesville, Florida 32611, USA
    Theor Popul Biol 61:349-63. 2002
    ..A numerical example is presented to demonstrate the statistical properties of the model for characterizing the linkage phase between markers...
  97. ncbi Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial
    Si Quang Le
    Méthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS Universite Montpellier II, 161 rue Ada, Montpellier Cedex 5, France
    Syst Biol 59:277-87. 2010
    ..Our data, models, and software are available for download from http://atgc.lirmm.fr/phyml-structure/...
  98. pmc Identification of Plasmodium malariae, a human malaria parasite, in imported chimpanzees
    Toshiyuki Hayakawa
    Laboratory of Malariology, International Research Center of Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
    PLoS ONE 4:e7412. 2009
    ..malariae infection in humans. To our knowledge, this is the first to report P. malariae infection in chimpanzees and a human malaria parasite from nonhuman primates imported to a nonendemic country...
  99. ncbi Identification of distant family relationships
    Øivind Skare
    Norwegian Institute of Public Health, 0403 Oslo, Norway
    Bioinformatics 25:2376-82. 2009
    ..Throughout, we will view the problem of relationship estimation as one of pedigree identification rather than identity-by-descent, and thus focus on applications where determination of the exact relationship is important...
  100. pmc Mixture models and exploratory analysis in networks
    M E J Newman
    Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA
    Proc Natl Acad Sci U S A 104:9564-9. 2007
    ..We give a number of examples demonstrating how the method can be used to shed light on the properties of real-world networks, including social and information networks...
  101. ncbi PAL: an object-oriented programming library for molecular evolution and phylogenetics
    A Drummond
    School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, New Zealand
    Bioinformatics 17:662-3. 2001
    ..AVAILIABILTY: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License...

Research Grants81

  1. Analyzing Complex Stochastic Models using Approximate Bayesian Computation
    BRANDON TURNER; Fiscal Year: 2013
    ..are capable of enjoying the benefits of Bayesian analyses has been limited to models that possess tractable likelihood functions. These models are typically referred to as "simulation-based" models, and as a result of their complicated ..
  2. STATISTICAL METHODS FOR QUANTITATIVE PET
    Richard Leahy; Fiscal Year: 2001
    ..pair-wise smoothing, anatomically-based priors, spatially variant weightings for uniform resolution) and likelihood functions (e.g...
  3. Synergism of Gene and Environment in Cancer Studies: A New Bayesian Approach
    Bhramar Mukherjee; Fiscal Year: 2008
    ..The methods developed may be routinely applied to various epidemiological studies of gene-environment interaction. [unreadable] [unreadable] [unreadable] [unreadable]..
  4. ADVANCED ANALYSIS OF THE DEVELOPMENT OF ALCOHOL PROBLEMS
    Bengt Muthen; Fiscal Year: 2005
    ..The central part of the substantive training will occur through collaboration with a few key experts in alcohol and related fields. ..
  5. Semiparametric Regression Analysis of Censored Data
    Danyu Lin; Fiscal Year: 2004
    ..Applications to real medical studies will be provided. The research results will be disseminated to practicing statisticians and medical investigators via publications, lectures and software distributions. ..
  6. Structural models and direct and indirect effects of alcohol use on HIV infection
    Stephen R Cole; Fiscal Year: 2010
    ..Second, it will provide innovations and detailed worked examples in quantitative methods for complex observational data analysis. ..
  7. STATISTICAL METHODS FOR OUTCOME-DEPENDENT SAMPLING
    Haibo Zhou; Fiscal Year: 2010
    ..These include the Cancer Risk in Uranium Miners Study, the Magnetic Fields and Breast Cancer Risk Study, the Collaborative Perinatal Project, the Family Heart Study, and the DDE-antiandrogen Study. ..
  8. ALCOHOL & CRASH FATALITIES: ETHNIC GROUPS AT RISK
    Eduardo Romano; Fiscal Year: 2003
    ..The results from the project will be useful to policymakers and program managers and will inform the design and delivery of traffic safety interventions tailored to minority populations. ..
  9. Structural Models to Bridge Observational and Randomized Evidence: HAART and AIDS
    Stephen Cole; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  10. A partially Linear Tree-based Regression Model for Assessing Complex Joint Gene-g
    Jinbo Chen; Fiscal Year: 2008
    ..The second specific aim is to apply the developed method in analyses of several cancer genetic epidemiology studies to explore joint gene-gene or gene-environment interactions. [unreadable] [unreadable] [unreadable]..
  11. Impact of Depression & Function on Healthcare Use & Cost
    Bruce Friedman; Fiscal Year: 2006
    ....
  12. Neural mechanisms of risk aversion
    Joshua Brown; Fiscal Year: 2007
    ..Once we know how certain parts of the brain avoid risky behavior, then we will figure out how to help these parts of the brain to keep people from taking drugs. [unreadable] [unreadable] [unreadable]..
  13. Neural mechanisms of risky behavior avoidance
    Joshua W Brown; Fiscal Year: 2010
    ..Impairments in these mechanisms are associated with substance use and abuse. Knowledge of such mechanisms can inform the prevention and treatment of substance abuse problems. ..
  14. Statistical Methods in HIV Vaccine Efficacy Trials
    Peter Gilbert; Fiscal Year: 2009
    ..By improving the design and analysis of efficacy and NHP trials for addressing these areas, the project will benefit public health. ..
  15. Data Evaluation for Early Disease Outbreak Detection
    Kenneth Kleinman; Fiscal Year: 2007
    ..abstract_text> ..
  16. Pretest probability assesment and D-dimer testing for pulmonary embolism
    D Courtney; Fiscal Year: 2008
    ..He has significant experience in mentoring junior investigators and an emphasis in disease detection and outcome prediction to ensure development of the PI toward that of an independently funded investigator. ..
  17. Economic Consequences of Alcohol Use Disorders
    Michael French; Fiscal Year: 2008
    ..Finally, the research significance is high because few studies have used contemporary research methods and data to estimate the economic effects of alcohol use and abuse. ..
  18. Neurobiology of a Simple Oculomotor System: Circuitry
    NICHOLAS STRAUSFELD; Fiscal Year: 2008
    ..It will also lead to the implementation of silicon-based circuits that enable motion detection and shape discrimination and potentially provide the basis for a visual prosthetic device. [unreadable] [unreadable]..
  19. Microevolution of conserved developmental genes
    PAUL HOHENLOHE; Fiscal Year: 2007
    ..Conversely, lack of variation and a negative selection result would suggest that other loci or regulatory pathways are involved in vertebral development. [unreadable] [unreadable] [unreadable]..
  20. Treatment and Costs of Neonatal Jaundice in a Large HMO
    Thomas Newman; Fiscal Year: 2007
    ..The results of this study will help make neonatal jaundice guidelines and treatment decisions more evidence based. [unreadable] [unreadable] [unreadable]..
  21. Robust Hierarchical Finite Mixture Modeling of Collagen Fibril Diameters
    Inna Chervoneva; Fiscal Year: 2008
    ..This project focuses on developing novel statistical methods for analyses of such decompositions. [unreadable] [unreadable] [unreadable]..
  22. Phylogeny and Genomic Inference for Quantitative Traits
    Joseph Felsenstein; Fiscal Year: 2008
    ..In this way the testing framework will begin to unify population biology inferences with genomic methods, as genomic methods are increasingly applied to the biology of natural populations. ..
  23. Neurobehavioral Regulation of Cigarette Cravings
    Brian Hitsman; Fiscal Year: 2008
    ..abstract_text> ..
  24. Health and Well-Being Among Older-Old in U.S. and Japan
    Jersey Liang; Fiscal Year: 2008
    ..As all three institutions are strongly committed to this research initiative, the responsibility of financing will be shared, making it an extremely attractive investment for the National Institutes of Health. ..
  25. SaTScan: Spatial Scan Statistic Surveillance Software
    Martin Kulldorff; Fiscal Year: 2008
    ..In this project, we propose to further develop and maintain the SaTScan software to fulfill many of these needs. ..
  26. INFERENCE IN REGRESSION MODELS WITH MISSING COVARIATES
    Joseph G Ibrahim; Fiscal Year: 2010
    ..The proposed methodologies in Aims 1-2 are primarily motivated from several studies in the PI's collaborative work. ..
  27. Estimating Cancer Risks of Rare Genetic Variants
    MARINELA contact CAPANU; Fiscal Year: 2010
    ..The research will involve hierarchical statistical modeling, a technique that aggregates the evidence about lots of rare mutations to increase the ability to predict the effects of each mutation individually. ..
  28. Pathways into Services for Alcohol and Drug Disorders
    Mark J Edlund; Fiscal Year: 2010
    ..The results of the study will inform policy to increase rates of utilization of effective substance abuse services among those with substance use disorders. ..
  29. Genomic analysis of pediatric SIRS and septic shock
    Hector Wong; Fiscal Year: 2009
    ..Child health will be positively impacted by developing the capability of conducting zinc supplementation trials in a safe and rigorous manner. ..
  30. Design and analysis of adaptive multistage genetic association studies
    Edwin van den Oord; Fiscal Year: 2010
    ..The goal of this project is to develop a flexible framework for designing these studies in a cost-effective way and optimize subsequent replication efforts. ..
  31. Trajectories of Subjective Well-being and Ethnicity in Old Age
    Jersey Liang; Fiscal Year: 2010
    ..The analytical strategies will include a combination of multi-level analysis, cluster analysis, multinomial logit analysis, and structural equation modeling. ..
  32. Alcoholism Susceptibility Genes in High Density Families
    Shirley Hill; Fiscal Year: 2009
    ..4 cm intervals for all three generations would be combined and linkage analyses performed using the well validated alcoholism phenotype and the well validated childhood diagnoses obtained from the K-SADS. ..
  33. FAMILIAL COLORECTAL NEOPLASIA COLLABORATIVE GROUP
    Noralane Lindor; Fiscal Year: 2007
    ..fs20\par \par } ..
  34. Childhood Predictors and Consequences of Adult Smoking
    Judith Brook; Fiscal Year: 2008
    ..Identification of childhood and adolescent factors that can lessen or compensate for the impact of tobacco use on later functioning would provide additional aids for effective prevention and treatment efforts. ..
  35. Pharmacogenetics of the Antidepressant Response in Geriatric Major Depression
    Greer M Murphy; Fiscal Year: 2010
    ..Many patients are resistant to antidepressant medication treatment. A method for identifying patients likely to benefit from antidepressant treatment would decrease patient distress and save health care dollars. ..
  36. Psychiatric Treatment and Violence Risk Management
    Jeffrey Swanson; Fiscal Year: 2008
    ..Through additional R01-fundable projects to be developed, this work will lead eventually to better-targeted interventions and policies for reducing violence risk and improving quality of life for persons with SMI. ..
  37. Clinically enhanced multi-purpose administrative dataset for comparative effectiv
    Hamisu Salihu; Fiscal Year: 2010
    ....
  38. Microglial Neuroprotection and Neurotoxicity
    Greer Murphy; Fiscal Year: 2007
    ..Although microglial neurotoxicity undoubtedly occurs in many disease states, it is important to understand how microglia might be induced to clear abnormal proteins from the brain or provide neuroprotection. ..
  39. QUANTITATIVE ASSOCIATION METHODS FOR GENE MAPPING
    Daniel Schaid; Fiscal Year: 2001
    ..The advantages of this proposed research, over those currently used to identify and characterize genes of complex diseases, are that it will offer a more powerful and flexible method to find these types of genes. ..
  40. Model-Based Methods for the Analyses of Weighted Data
    Michael Elliott; Fiscal Year: 2005
    ..abstract_text> ..
  41. COSTS AND BENEFITS OF ALCOHOL SERVICES & INTERVENTIONS
    Michael French; Fiscal Year: 2005
    ..S. as well as abroad, the proposed study holds important potential to assist researchers, policymakers, and program directors with economic evaluation guidelines and "real world" applications. ..
  42. Genetic Influence on Personality Disorder
    Jeanette Taylor; Fiscal Year: 2004
    ..abstract_text> ..
  43. Transition Model for Incomplete Longitudinal Binary Data
    Xiaowei Yang; Fiscal Year: 2003
    ..appropriate modeling strategy than other longitudinal modeling choices such as marginal models using quasi-likelihood functions and generalized linear mixed models...
  44. Impact of Poverty, LBW, and Obesity Across the Lifespan
    Patricia Reagan; Fiscal Year: 2004
    ....
  45. Cross-species gene finding and annotation
    Lior Pachter; Fiscal Year: 2004
    ..The computational complexity of the problem is greatly reduced by the use of something we call an approximate alignment. ..
  46. Radio-Immunotherapy (RIT) Planning Using SPECT
    LAWRENCE ZENG; Fiscal Year: 2004
    ..Novel image reconstruction algorithms will be developed to provided quantitative SPECT images. Our hypothesis will be verified through human observer studies and Channelized Hotelling observer studies. ..
  47. ORGANIZATIONAL FACTORS IN YOUTH MENTAL HEALTH SERVICES
    GREGORY AARONS; Fiscal Year: 2004
    ..The research project will include agencies serving adolescents (ages 12-18) representing those most commonly used by youth with co-morbid disorders. ..
  48. POPULATION-BASED MANAGEMENT OF DEPRESSION
    Gregory Simon; Fiscal Year: 2003
    ..e. 12-18 mos) Incremental cost and cost-effectiveness of each intervention program compared to care as usual. ..
  49. LINKAGE DISEQUILIBRIUM MAPPING USING THE COALESCENT
    Joseph Felsenstein; Fiscal Year: 2001
    ..We will make available computer programs in C++ to compute the likelihoods, and distribute them, free, over the Internet as source code, documentation, and executables. ..
  50. ADOLESCENT SMOKING CESSATION
    John Roll; Fiscal Year: 2002
    ..Secondarily, the proposed study will provide valuable information on the nicotine withdrawal syndrome in adolescents, a topic about which relatively little is known. ..
  51. Prognostic Significance of Altered DNA Methylation
    Chandrika Piyathilake; Fiscal Year: 2002
    ..A newly developed and tested immunohistochemical technique, which measures the degree of global methylation in intact and specific types of cells, will be used to evaluate global DNA methylation in the proposed study. ..
  52. MEASURING THE QUALITY OF CARE FOR HIGH RISK INFANTS
    Jeannette Rogowski; Fiscal Year: 2001
    ..abstract_text> ..
  53. Breast Cancer Imaging Using a Solid-State SPECT Camera
    G Zeng; Fiscal Year: 2005
    ..abstract_text> ..
  54. PREDICTORS OF RELAPSE TO SMOKING IN LUNG CANCER
    Mario Schootman; Fiscal Year: 2005
    ..abstract_text> ..
  55. Geography of Amputations Among African Americans
    Mario Schootman; Fiscal Year: 2005
    ..abstract_text> ..
  56. Coping and Social Comparison in Elderly Cardiac Patients
    Jerry Suls; Fiscal Year: 2006
    ..Although the present research focuses on adaptation to cardiac disease, results should also be relevant and exportable to older adults that are coping with other chronic illnesses. ..
  57. TIME RELATED FACTORS IN CANCER EPIDEMIOLOGY
    Bryan Langholz; Fiscal Year: 2006
    ..The impact of these projects is to expand the design and analysis "tools"' available to epidemiologic research in a way that will improve validity and cost-efficiency. [unreadable] [unreadable]..
  58. Effectively Implementing Psychiatric Advance Directives
    Jeffrey Swanson; Fiscal Year: 2006
    ..The proposed study will provide information about a state's experience with PADs so that policymakers may be guided in implementing PADs elsewhere. ..
  59. COGNITIVE/PERSONALITY FACTORS IN RELATIVES OF ALCOHOLICS
    Shirley Hill; Fiscal Year: 2006
    ..New measures will be added to explore non-shared environmental effects in these families where sibling pairs are available for study (N=346 sib pairs). ..
  60. Regulation of CSF-1 in Ovarian Cancer
    SETSUKO CHAMBERS; Fiscal Year: 2006
    ..Moreover, the results of these studies will provide the scientific basis for a future trial of anti-androgen therapy as a chemopreventative agent in patients at high risk for the development of ovarian cancer. ..
  61. Behavior Change: Reinforcemnt Schedule Effects
    John Roll; Fiscal Year: 2006
    ..Based on the widespread success of contingency management across many different applications, we believe that the results of the proposed study will have 9enerality beyond the field of substance abuse treatment. ..
  62. An Exploratory Center for Obesity Research (RMI)
    Adam Drewnowski; Fiscal Year: 2006
    ..By promoting interagency collaborations, these efforts will help the NIH develop a roadmap on how to effectively translate research findings into national, state, and local health policy. [unreadable] [unreadable]..
  63. YOUTH-FOCUSED MEDIA TO PREVENT SUBSTANCE USE
    Brian Flynn; Fiscal Year: 2003
    ..Indicators of social climate for substance user use and exposure to school and community programs and mass media campaigns with similar objectives will be assessed in the process evaluation. ..
  64. ASSORTMENT AND TRANSMISSION OF ALCOHOL AND TOBACCO USE
    Chandra Reynolds; Fiscal Year: 2001
    ..abstract_text> ..
  65. Latent Growth Curve Paths to Longevity: The Terman Study
    Chandra Reynolds; Fiscal Year: 2008
    ..abstract_text> ..
  66. Multivariate Analysis of the Total Fertility Rate and Its Components
    Robert D Retherford; Fiscal Year: 2010
    ..The new methodology involves major extensions of methodology developed during an earlier R03 grant ("Components of Nuptiality and Fertility Change," 5R03HD45508-2, PI: Retherford) that expired November 30, 2007. ..
  67. OCULAR HYPERTENSION TREATMENT STUDY (OHTS)
    Robert Weinreb; Fiscal Year: 2008
    ....
  68. Components of nuptiality and fertility change
    Robert Retherford; Fiscal Year: 2006
    ..abstract_text> ..
  69. Cholesterol metabolism pathway: Cognitive change and Alzheimer's disease risk
    Chandra A Reynolds; Fiscal Year: 2010
    ....
  70. BIOLOGICAL EXPLANATIONS OF SES DIFFERENCES IN HEALTH
    Eileen Crimmins; Fiscal Year: 2001
    ....
  71. PHYSICIAN INTERVENTION TO IMPROVE DIABETES CARE
    PATRICK O CONNOR; Fiscal Year: 2002
    ..The study will have substantial impact on clinical practice and policy whether the results are positive or negative. If successful, the interventions will be easily disseminated to other primary care practice settings. ..
  72. Reducing Clinical Inertia in Diabetes Care
    PATRICK O CONNOR; Fiscal Year: 2007
    ..Results of this project will have significant clinical and policy implications. ..
  73. Prostate cancer in Blacks: Role of poverty and diet
    MOHAMMED OLIVER; Fiscal Year: 2007
    ..K07 project findings will be used to help develop culturally appropriate interventions in African-American communities to decrease dietary fat intake and increase physical activity. ..
  74. Preparation and Distribution of the NUJLSOA
    Eileen Crimmins; Fiscal Year: 2003
    ..In order to acquire use of the data, researchers must agree to use the data only for research purposes and not to use data to describe or identify individuals. ..
  75. Methods for Selecting Among Mathematical Models of Cognition
    JAY MYUNG; Fiscal Year: 2009
    ..The proposed work will contribute to this understanding. The fruits of this research will extend into other areas of psychology and the broader behavioral sciences and health sciences. ..
  76. ORGANIZATIONAL CHARACTERISTICS AND CHRONIC DISEASE CARE
    PATRICK O CONNOR; Fiscal Year: 2001
    ..Results will be relevant to policy makers, purchasers, health plans, medical groups, and clinics that are seeking to improve chronic disease care, and may suggest new intervention strategies worth further investigation. ..
  77. Female Juvenile Offenders: Differentiating Mechanisms of Violence Risk by Race
    Preeti Chauhan; Fiscal Year: 2006
    ..The[unreadable] implications of these findings are particularly pertinent to the public health system which serves these high-risk[unreadable] females. ..
  78. Biological Risk Underlying Education Health Differences
    Eileen Crimmins; Fiscal Year: 2006
    ..4) Examine changes over time in the patterning of biological risk by education. ..
  79. Risk and Protective Mechanisms in Child Maltreatment
    Jungmeen Kim; Fiscal Year: 2007
    ..Furthermore, the proposed research will provide critical information for the development of effective preventive interventions for child abuse and neglect. ..
  80. Comparative Bioinformatics and TP53 Expression
    PETER WADDELL; Fiscal Year: 2009
    ..abstract_text> ..