genetic models

Summary

Summary: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.

Top Publications

  1. 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
  2. pmc Inference of population structure using multilocus genotype data
    J K Pritchard
    Department of Statistics, University of Oxford, United Kingdom
    Genetics 155:945-59. 2000
  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 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
  5. ncbi A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    B M Bolstad
    Group in Biostatistics, University of California, Berkeley, CA 94720, USA
    Bioinformatics 19:185-93. 2003
  6. pmc Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    Daniel Falush
    Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
    Genetics 164:1567-87. 2003
  7. pmc Prediction of total genetic value using genome-wide dense marker maps
    T H Meuwissen
    Research Institute of Animal Science and Health, 8200 AB Lelystad, The Netherlands
    Genetics 157:1819-29. 2001
  8. 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
  9. 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
  10. ncbi R/qtl: QTL mapping in experimental crosses
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
    Bioinformatics 19:889-90. 2003

Detail Information

Publications297 found, 100 shown here

  1. 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...
  2. pmc Inference of population structure using multilocus genotype data
    J K Pritchard
    Department of Statistics, University of Oxford, United Kingdom
    Genetics 155:945-59. 2000
    ..g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html...
  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 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)...
  5. ncbi A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    B M Bolstad
    Group in Biostatistics, University of California, Berkeley, CA 94720, USA
    Bioinformatics 19:185-93. 2003
    ..Normalization is a process for reducing this variation. It is common to see non-linear relations between arrays and the standard normalization provided by Affymetrix does not perform well in these situations...
  6. pmc Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    Daniel Falush
    Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
    Genetics 164:1567-87. 2003
    ..The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu...
  7. pmc Prediction of total genetic value using genome-wide dense marker maps
    T H Meuwissen
    Research Institute of Animal Science and Health, 8200 AB Lelystad, The Netherlands
    Genetics 157:1819-29. 2001
    ..It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval...
  8. 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...
  9. 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...
  10. ncbi R/qtl: QTL mapping in experimental crosses
    Karl W Broman
    Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
    Bioinformatics 19:889-90. 2003
    ....
  11. ncbi A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
    Jianming Yu
    Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
    Nat Genet 38:203-8. 2006
    ..As this new method crosses the boundary between family-based and structured association samples, it provides a powerful complement to currently available methods for association mapping...
  12. ncbi Bayesian coalescent inference of past population dynamics from molecular sequences
    A J Drummond
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 22:1185-92. 2005
    ....
  13. pmc CAP3: A DNA sequence assembly program
    X Huang
    Department of Computer Science, Michigan Technological University, Houghton, Michigan 49931 USA
    Genome Res 9:868-77. 1999
    ..PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints...
  14. ncbi The structure of haplotype blocks in the human genome
    Stacey B Gabriel
    Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
    Science 296:2225-9. 2002
    ..Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease...
  15. ncbi Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
    Nathaniel D Heintzman
    Ludwig Institute for Cancer Research, University of California San Diego UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653 USA
    Nat Genet 39:311-8. 2007
    ..Our results give insight into the connections between chromatin modifications and transcriptional regulatory activity and provide a new tool for the functional annotation of the human genome...
  16. 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...
  17. ncbi A new multipoint method for genome-wide association studies by imputation of genotypes
    Jonathan Marchini
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Nat Genet 39:906-13. 2007
    ..A notable future use of our method will be to boost power by combining data from genome-wide scans that use different SNP sets...
  18. 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...
  19. 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...
  20. pmc Human MicroRNA targets
    Bino John
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    PLoS Biol 2:e363. 2004
    ..microrna.org. Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes...
  21. ncbi Microsatellites: simple sequences with complex evolution
    Hans Ellegren
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE 752 36 Uppsala, Sweden
    Nat Rev Genet 5:435-45. 2004
  22. pmc JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
    Jan Christian Bryne
    Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N 5008 Bergen, Norway
    Nucleic Acids Res 36:D102-6. 2008
    ..JASPAR is available at http://jaspar.genereg.net...
  23. pmc Approximate Bayesian computation in population genetics
    Mark A Beaumont
    School of Animal and Microbial Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, United Kingdom
    Genetics 162:2025-35. 2002
    ..We also compare the relative efficiency of inferences obtained using methods based on summary statistics with those obtained directly from the data using MCMC...
  24. pmc A comparison of bayesian methods for haplotype reconstruction from population genotype data
    Matthew Stephens
    Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
    Am J Hum Genet 73:1162-9. 2003
    ..The new algorithm is included in the software package PHASE, version 2.0, available online (http://www.stat.washington.edu/stephens/software.html)...
  25. ncbi A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    Nicolas Lartillot
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Montreal, Quebec Canada
    Mol Biol Evol 21:1095-109. 2004
    ....
  26. ncbi Efficient methods to compute genomic predictions
    P M Vanraden
    Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 2350, USA
    J Dairy Sci 91:4414-23. 2008
    ..Actual gains may differ because the simulation did not account for linkage disequilibrium in the base population or selection in subsequent generations...
  27. ncbi The evolutionary fate and consequences of duplicate genes
    M Lynch
    Department of Biology, University of Oregon, Eugene, OR 97403, USA
    Science 290:1151-5. 2000
    ..Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species...
  28. pmc Improved microbial gene identification with GLIMMER
    A L Delcher
    Department of Computer Science, Loyola College in Maryland, Baltimore, MD 21210, USA
    Nucleic Acids Res 27:4636-41. 1999
    ..When the analysis is restricted to genes that have significant homology to genes in other organisms, GLIMMER misses <1% of known genes...
  29. ncbi Generating samples under a Wright-Fisher neutral model of genetic variation
    Richard R Hudson
    Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA
    Bioinformatics 18:337-8. 2002
    ..The samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models...
  30. 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...
  31. pmc Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering
    Sharon R Browning
    Department of Statistics, The University of Auckland, Auckland, New Zealand
    Am J Hum Genet 81:1084-97. 2007
    ..1 days of computing time, with 99% of masked alleles imputed correctly. Our method is implemented in the Beagle software package, which is freely available...
  32. ncbi Statistical properties of new neutrality tests against population growth
    Sebastian E Ramos-Onsins
    Departament de Genetica, Universitat de Barcelona, E 08071 Barcelona, Spain
    Mol Biol Evol 19:2092-100. 2002
    ..The behavior of the R(2) test is superior for small sample sizes, whereas F(S) is better for large sample sizes. We also show that some popular statistics based on the mismatch distribution are very conservative...
  33. ncbi Genomic selection: prediction of accuracy and maximisation of long term response
    Mike Goddard
    Department of Primary Industries, University of Melbourne, Victoria, Australia
    Genetica 136:245-57. 2009
    ..This index varies the weight given to a marker according to its frequency such that markers where the favourable allele has low frequency receive more weight in the index...
  34. ncbi Hsp90 as a capacitor for morphological evolution
    S L Rutherford
    Howard Hughes Medical Institute, University of Chicago, Illinois 60637, USA
    Nature 396:336-42. 1998
    ..This provides a plausible mechanism for promoting evolutionary change in otherwise entrenched developmental processes...
  35. ncbi Darwinian evolution can follow only very few mutational paths to fitter proteins
    Daniel M Weinreich
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Science 312:111-4. 2006
    ..This implies that the protein tape of life may be largely reproducible and even predictable...
  36. pmc Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection
    Y X Fu
    Human Genetics Center, University of Texas, Houston 77225, USA
    Genetics 147:915-25. 1997
    ..We show that Fu and Li's tests are among the most powerful tests against background selection. Implications of these results are discussed...
  37. pmc Preservation of duplicate genes by complementary, degenerative mutations
    A Force
    Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
    Genetics 151:1531-45. 1999
    ..Cooke et al. 1997 (p. 362)..
  38. pmc MicroRNA targeting specificity in mammals: determinants beyond seed pairing
    Andrew Grimson
    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Cell 27:91-105. 2007
    ..Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets...
  39. pmc MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals
    John Tsang
    Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Cell 26:753-67. 2007
    ..Our results strongly suggest that coordinated transcriptional and miRNA-mediated regulation is a recurrent motif to enhance the robustness of gene regulation in mammalian genomes...
  40. ncbi Bayesian phylogenetic analysis of combined data
    Johan A A Nylander
    Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18 D, SE 752 36 Uppsala, Sweden
    Syst Biol 53:47-67. 2004
    ..Thus, Bayes factors appear to be useful for selecting among complex models, but it is still unclear whether their use strikes a reasonable balance between model complexity and error in parameter estimates...
  41. ncbi Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits
    S Purcell
    Social, Genetics and Developmental Psychiatry Research Centre, Institute of Psychiatry, King s College London, De Crespigny Park, UK
    Bioinformatics 19:149-50. 2003
    ..A website for performing power calculations for the design of linkage and association genetic mapping studies of complex traits...
  42. 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...
  43. ncbi Efficiency and power in genetic association studies
    Paul I W de Bakker
    Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6818, Boston, Massachusetts 02114 2790, USA
    Nat Genet 37:1217-23. 2005
    ..Power is robust to the completeness of the reference panel from which tags are selected. These findings have implications for prioritizing tag SNPs and interpreting association studies...
  44. pmc An algorithm for progressive multiple alignment of sequences with insertions
    Ari Löytynoja
    European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom
    Proc Natl Acad Sci U S A 102:10557-62. 2005
    ..Our results suggest that some insertion/deletion "hot spots" may actually be artifacts of traditional alignment algorithms...
  45. ncbi GARD: a genetic algorithm for recombination detection
    Sergei L Kosakovsky Pond
    Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 22:3096-8. 2006
    ..The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments...
  46. pmc RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
    Socorro Gama-Castro
    Program of Computational Genomics, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, A P 565 A, Cuernavaca, Morelos 62100, Mexico
    Nucleic Acids Res 36:D120-4. 2008
    ..The data can be accessed through overviews of correlations about gene regulation. RegulonDB associated original literature, together with more than 4000 curation notes, can now be searched with the Textpresso text mining engine...
  47. ncbi Is a new and general theory of molecular systematics emerging?
    Scott V Edwards
    Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Evolution 63:1-19. 2009
    ....
  48. ncbi Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
    Beth Shapiro
    Mol Biol Evol 23:7-9. 2006
    ....
  49. ncbi Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions
    Christian Lanctôt
    Department Biologie II, Ludwig Maximilians Universitat, Grosshadernerstr 2, Planegg Martinsried, Germany
    Nat Rev Genet 8:104-15. 2007
    ..Understanding how the dynamic nature of the positioning of genetic material in the nuclear space and the higher-order architecture of the nucleus are integrated is therefore essential to our overall understanding of gene regulation...
  50. ncbi MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years?
    L Bernatchez
    Department de Biologie, Universite Laval, Ste Foy, Quebec, Canada
    J Evol Biol 16:363-77. 2003
    ..We conclude this review by proposing several directions where future research is needed...
  51. ncbi Use of within-array replicate spots for assessing differential expression in microarray experiments
    Gordon K Smyth
    Walter and Eliza Hall Institute of Medical Research, Melbourne, Vic, Australia
    Bioinformatics 21:2067-75. 2005
    ..The usual practice is to average the duplicate or triplicate results for each probe before assessing differential expression. This results in the loss of valuable information about genewise variability...
  52. pmc Bayesian inference of recent migration rates using multilocus genotypes
    Gregory A Wilson
    Department of Medical Genetics, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
    Genetics 163:1177-91. 2003
    ....
  53. pmc A model-based method for identifying species hybrids using multilocus genetic data
    E C Anderson
    Department of Statistics, University of Washington, Seattle, Washington 98195, USA
    Genetics 160:1217-29. 2002
    ..We demonstrate the method on allozyme data from two species of hybridizing trout, as well as on two simulated data sets...
  54. pmc Solving the riddle of codon usage preferences: a test for translational selection
    Mario dos Reis
    School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
    Nucleic Acids Res 32:5036-44. 2004
    ..Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model...
  55. ncbi Engineering stability in gene networks by autoregulation
    A Becskei
    EMBL, Structures and Biocomputing, Heidelberg, Germany
    Nature 405:590-3. 2000
    ..Here we have designed and constructed simple gene circuits consisting of a regulator and transcriptional repressor modules in Escherichia coli and we show the gain of stability produced by negative feedback...
  56. ncbi Gene prediction with a hidden Markov model and a new intron submodel
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Universitat Gottingen, Gottingen, Germany
    Bioinformatics 19:ii215-25. 2003
    ..Gene finding programs have achieved relatively high accuracy on short genomic sequences but do not perform well on longer sequences with an unknown number of genes in them. Here existing programs tend to predict many false exons...
  57. ncbi A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility
    Jason H Moore
    Computational Genetics Laboratory, Department of Genetics, Dartmouth Hitchcock Medical Center, One Medical Center Dr, 706 Rubin Bldg, HB7937, Lebanon, NH 03756, USA
    J Theor Biol 241:252-61. 2006
    ..We then apply this strategy to detecting, characterizing, and interpreting epistatic models in a genetic study (n = 500) of atrial fibrillation and show that both classification and model interpretation are significantly improved...
  58. ncbi A fine-scale map of recombination rates and hotspots across the human genome
    Simon Myers
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Science 310:321-4. 2005
    ....
  59. pmc Chromosome inversions, local adaptation and speciation
    Mark Kirkpatrick
    Section of Integrative Biology, University of Texas, Austin 78712, USA
    Genetics 173:419-34. 2006
    ..We discuss data that support the hypothesis, review other mechanisms for inversion evolution, and suggest possible tests...
  60. pmc An integrative genomics approach to infer causal associations between gene expression and disease
    Eric E Schadt
    Rosetta Inpharmatics, Seattle, Washington 98109, USA
    Nat Genet 37:710-7. 2005
    ..We also demonstrate the utility of this approach by identifying and experimentally validating the involvement of three new genes in susceptibility to obesity...
  61. ncbi Network motifs: theory and experimental approaches
    Uri Alon
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Rev Genet 8:450-61. 2007
    ..Here I review network motifs and their functions, with an emphasis on experimental studies. Network motifs in other biological networks are also mentioned, including signalling and neuronal networks...
  62. ncbi Neighbor-net: an agglomerative method for the construction of phylogenetic networks
    David Bryant
    McGill Centre for Bioinformatics, Montreal, Quebec, Canada
    Mol Biol Evol 21:255-65. 2004
    ..and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. Neighbor-Net is available as part of the SplitsTree4 software package...
  63. pmc TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics
    Gangolf Jobb
    Department of Statistics, University of Munich, Ludwigstr, 33, D 80539 Munich, Germany
    BMC Evol Biol 4:18. 2004
    ..Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience...
  64. 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
    ....
  65. ncbi Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
    Peter Beerli
    School of Computational Science and Department of Biological Sciences, Florida State University, Tallahassee, FL 32306 4120, USA
    Bioinformatics 22:341-5. 2006
    ..Using simulated datasets, the Bayesian method generally fares better than the ML approach in accuracy and coverage, although for some values the two approaches are equal in performance...
  66. pmc Using genomic data to unravel the root of the placental mammal phylogeny
    William J Murphy
    Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A and M University, College Station, TX 77843, USA
    Genome Res 17:413-21. 2007
    ..We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny...
  67. pmc The impact of recombination on nucleotide substitutions in the human genome
    Laurent Duret
    Laboratoire de Biometrie et Biologie Evolutive, Universite de Lyon, Universite Lyon 1, CNRS, UMR 5558, Villeurbanne, France
    PLoS Genet 4:e1000071. 2008
    ..Our results also shed light on variations in the rate of crossover relative to non-crossover events, along chromosomes and according to sex, and also on the conservation of hotspot density between human and chimp...
  68. ncbi Identifying differentially expressed genes using false discovery rate controlling procedures
    Anat Reiner
    Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Bioinformatics 19:368-75. 2003
    ..The procedures are studied using simulated microarray data, and their performance is examined relative to their ease of implementation...
  69. ncbi Bayesian inference of epistatic interactions in case-control studies
    Yu Zhang
    Department of Statistics, The Pennsylvania State University, Thomas Building 422A, University Park, Pennsylvania 16802, USA
    Nat Genet 39:1167-73. 2007
    ....
  70. pmc BioGRID: a general repository for interaction datasets
    Chris Stark
    Ontario Cancer Institute, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9
    Nucleic Acids Res 34:D535-9. 2006
    ..User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID...
  71. pmc Trends between gene content and genome size in prokaryotic species with larger genomes
    Konstantinos T Konstantinidis
    Center for Microbial Ecology and Departments of Crop and Soil Sciences, Michigan State University, East Lansing, MI 48824 1325, USA
    Proc Natl Acad Sci U S A 101:3160-5. 2004
    ..These trends suggest that larger genome-sized species may dominate in environments where resources are scarce but diverse and where there is little penalty for slow growth, such as soil...
  72. ncbi Recombination and linkage disequilibrium in Arabidopsis thaliana
    Sung Kim
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nat Genet 39:1151-5. 2007
    ..LD also reflects the action of selection, and it is more extensive between nonsynonymous polymorphisms than between synonymous polymorphisms...
  73. ncbi An evolutionary view of human recombination
    Graham Coop
    Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
    Nat Rev Genet 8:23-34. 2007
    ....
  74. ncbi Mechanisms of, and barriers to, horizontal gene transfer between bacteria
    Christopher M Thomas
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Nat Rev Microbiol 3:711-21. 2005
    ..However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition...
  75. ncbi Using Bayesian networks to analyze expression data
    N Friedman
    School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
    J Comput Biol 7:601-20. 2000
    ..We then describe a method for recovering gene interactions from microarray data using tools for learning Bayesian networks. Finally, we demonstrate this method on the S. cerevisiae cell-cycle measurements of Spellman et al. (1998)...
  76. pmc OGG1 initiates age-dependent CAG trinucleotide expansion in somatic cells
    Irina V Kovtun
    Department of Pharmacology and Experimental Therapeutics, Mayo Clinic and Foundation, 200 First Street SW, Rochester, Minnesota 55905, USA
    Nature 447:447-52. 2007
    ..Age-dependent CAG expansion provides a direct molecular link between oxidative damage and toxicity in post-mitotic neurons through a DNA damage response, and error-prone repair of single-strand breaks...
  77. pmc Stochastic mRNA synthesis in mammalian cells
    Arjun Raj
    Courant Institute of Mathematical Sciences, New York University, New York, New York, USA
    PLoS Biol 4:e309. 2006
    ..These results demonstrate that gene expression in mammalian cells is subject to large, intrinsically random fluctuations and raise questions about how cells are able to function in the face of such noise...
  78. 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)...
  79. ncbi Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level
    A L Hughes
    Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
    Heredity (Edinb) 99:364-73. 2007
    ..Rather adaptive phenotypes are much more likely to result from other causes, including single amino-acid changes; deletion or silencing of genes or changes in the pattern of gene expression...
  80. pmc A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
    Travis N Mavrich
    Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Genome Res 18:1073-83. 2008
    ..3' NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3' NFRs in gene looping...
  81. ncbi Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix
    J Li
    The Ministry of Education MOE Key Laboratory of Bioinformatics, Department of Automation, Tsinghua University, Beijing, People s Republic of China
    Heredity (Edinb) 95:221-7. 2005
    ..With its efficiency and accuracy, the M(eff) method provides an alternative to computationally intensive methods such as the permutation test...
  82. ncbi A synthetic oscillatory network of transcriptional regulators
    M B Elowitz
    Department of Molecular Biology and Physics, Princeton University, New Jersey 08544, USA
    Nature 403:335-8. 2000
    ..Such 'rational network design may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networks...
  83. pmc Genomic scans for selective sweeps using SNP data
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 15:1566-75. 2005
    ..Evidence for selective sweeps is also found in many other regions, including genes known to be associated with disease risk such as DPP10 and COL4A3...
  84. ncbi A slow RNA polymerase II affects alternative splicing in vivo
    Manuel De la Mata
    Laboratorio de Fisiologia y Biologia Molecular, Departamento de Fisiologia, Biologia Molecular y Celular, IFIBYNE CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon 2, Buenos Aires, Argentina
    Mol Cell 12:525-32. 2003
    ..These results provide a direct proof for the elongation control of alternative splicing in vivo...
  85. ncbi A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders
    Jennifer A Lee
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, 77030, USA
    Cell 131:1235-47. 2007
    ..We propose that complex duplication and deletion rearrangements associated with PMD, and potentially other nonrecurrent rearrangements, may be explained by this replication-based mechanism...
  86. ncbi The distribution of fitness effects of new mutations
    Adam Eyre-Walker
    Centre for the Study of Evolution, University of Sussex, Brighton, BN1 9QG, UK
    Nat Rev Genet 8:610-8. 2007
    ....
  87. ncbi Hybrid speciation
    James Mallet
    Galton Laboratory, Department of Biology, University College London, 4 Stephenson Way, London NW1 2HE, UK
    Nature 446:279-83. 2007
    ..Now, new genetic evidence suggests that hybrid speciation, even without polyploidy, is more common in plants and also animals than we thought...
  88. ncbi A relationship matrix including full pedigree and genomic information
    A Legarra
    INRA, UR631 SAGA, BP 52627, 32326 Castanet Tolosan, France
    J Dairy Sci 92:4656-63. 2009
    ..Numerical examples and alternative expressions are discussed. Matrix H is suitable for iteration on data algorithms that multiply a vector times a matrix, such as preconditioned conjugated gradients...
  89. ncbi A microRNA in a multiple-turnover RNAi enzyme complex
    Gyorgy Hutvagner
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, Room 825, 364 Plantation Street, Worcester, MA 01605, USA
    Science 297:2056-60. 2002
    ..Each let-7-containing complex directs multiple rounds of RNA cleavage, which explains the remarkable efficiency of the RNAi pathway in human cells...
  90. ncbi Active genes dynamically colocalize to shared sites of ongoing transcription
    Cameron S Osborne
    Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, CB2 4AT, UK
    Nat Genet 36:1065-71. 2004
    ..Thus, rather than recruiting and assembling transcription complexes, active genes migrate to preassembled transcription sites...
  91. ncbi Comparisons of dN/dS are time dependent for closely related bacterial genomes
    Eduardo P C Rocha
    Atelier de BioInformatique, Universite Paris VI, 75005 Paris, France
    J Theor Biol 239:226-35. 2006
    ..We conclude that, because of the critical effect of time since divergence, inter-taxa comparisons are only possible by comparing trajectories of dN/dS over time and it is not valid to compare taxa on the basis of single time points...
  92. pmc Defining genetic interaction
    Ramamurthy Mani
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 105:3461-6. 2008
    ..Additionally, we show that the Additive and Log definitions, each commonly used in population genetics, lead to differing conclusions related to the selective advantages of sexual reproduction...
  93. ncbi Bayesian estimation of concordance among gene trees
    Cecile Ane
    Department of Statistics, University of Wisconsin, USA
    Mol Biol Evol 24:412-26. 2007
    ..We demonstrate the method on a set of 106 genes from 8 yeast species...
  94. ncbi Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation
    Zhixin Xie
    Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331, USA
    Curr Biol 13:784-9. 2003
    ..These results indicate that DCL1 mRNA is subject to negative feedback regulation through the activity of a miRNA...
  95. ncbi Transcriptional regulation in constraints-based metabolic models of Escherichia coli
    Markus W Covert
    Department of Bioengineering, University of California, San Diego, La Jolla, California 92093 0412, USA
    J Biol Chem 277:28058-64. 2002
    ..This combined metabolic/regulatory model is thus an important step toward the goal of synthesizing genome-scale models that accurately represent E. coli behavior...
  96. ncbi Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals
    Rudolf Jaenisch
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Nat Genet 33:245-54. 2003
    ..The extent to which environmental effects can provoke epigenetic responses represents an exciting area of future research...
  97. ncbi Selection on codon bias
    Ruth Hershberg
    Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
    Annu Rev Genet 42:287-99. 2008
    ....
  98. 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
    ....
  99. ncbi Heritability in the genomics era--concepts and misconceptions
    Peter M Visscher
    Queensland Institute of Medical Research, Royal Brisbane Hospital Post Office, Brisbane 4029, Queensland, Australia
    Nat Rev Genet 9:255-66. 2008
    ..Recent reports of substantial heritability for gene expression and new estimation methods using marker data highlight the relevance of heritability in the genomics era...
  100. 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...
  101. pmc Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon
    S L Martin
    Department of Cellular and Structural Biology, University of Colorado School of Medicine, Denver, Colorado 80262, USA
    Mol Cell Biol 21:467-75. 2001
    ..These findings suggest a role for L1 ORF1p in mediating nucleic acid strand transfer steps during L1 reverse transcription...

Research Grants8

  1. Discovery metabolite profiling of the prolyl peptidases
    Alan Saghatelian; Fiscal Year: 2009
    ..Furthermore, the application of DMP to peptidases will demonstrate the generality of this approach for the future characterization of medically relevant enzymes and signaling pathways. ..
  2. STARTLE GATING AND LOCOMOTION IN D2-FAMILY KNOCKOUT MICE
    Mark Geyer; Fiscal Year: 2004
    ..Strains of gene knockout mice that lack either the D2, D3, or D4 receptors have been generated as genetic models to understand the functions, at a systems level, of these multiple independent genes...
  3. UPPER GI TRACT MEDIATION OF THE SATIETY EFFECTS OF FATS
    James Gibbs; Fiscal Year: 1999
    ..This proposal is to identify these mechanisms in Sprague Dawley rats, and in three genetic models of obesity characterized by abnormal fat intake: Zucker fa/fa, Osborne Mendel and S 5B/PI rats...
  4. Sunlight Exposure & Vitamin D Metabolic Gene Variations in Parkinson's Disease
    Beate R Ritz; Fiscal Year: 2010
    ..number of laboratory studies demonstrates that vitamin D acts as a neuroprotective agent in toxin-induced and genetic models of PD, and studies in humans suggest geographic differences in PD rates exist with north-south gradients...
  5. Nutritional mechanisms and intestinal tumorigenesis
    Leonard Augenlicht; Fiscal Year: 2009
    ..We will use two mouse genetic models: the p27+/+, +/- and -/- mice;and a conditional knockout of Pofutl(F/F), the locus that encodes the ..
  6. Neurodegeneration in Aging Retarded Mice
    Roger Albin; Fiscal Year: 2009
    ..The development of murine genetic models of polyglutamine (polyQ) diseases with varying phenotypes and the existence of mouse lines with retarded aging ..
  7. Inferring Multiple-SNP Disease Association with DNA Resequence Data
    Rasmus Nielsen; Fiscal Year: 2010
    ..sample will no longer suffer from problems of ascertainment bias, and the full spectrum of population genetic models may be fitted to the data...
  8. REGULATION/INSULIN SECRETION BY PROTEIN PHOSPHORYLATION
    John Hutton; Fiscal Year: 2003
    ..of such molecules has however been impeded by their low abundance in mammalian tissues and lack of tractable Genetic models in lower organisms. We have identified an insulin granule membrane protein tyrosine phosphatase (P.T..P...