monte carlo method

Summary

Summary: In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)

Top Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. pmc Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    Bruce Rannala
    Department of Medical Genetics, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
    Genetics 164:1645-56. 2003
  6. pmc Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
    Alexei J Drummond
    School of Biological Sciences, University of Auckland 1001, Auckland, New Zealand
    Genetics 161:1307-20. 2002
  7. pmc Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems
    Tina Toni
    Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
    J R Soc Interface 6:187-202. 2009
  8. ncbi Design of a novel globular protein fold with atomic-level accuracy
    Brian Kuhlman
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Science 302:1364-8. 2003
  9. ncbi Toward high-resolution de novo structure prediction for small proteins
    Philip Bradley
    University of Washington, Department of Biochemistry, and Howard Hughes Medical Institute, Box 357350, Seattle, WA 98195, USA
    Science 309:1868-71. 2005
  10. pmc Relaxed phylogenetics and dating with confidence
    Alexei J Drummond
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS Biol 4:e88. 2006

Detail Information

Publications359 found, 100 shown here

  1. 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...
  2. 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...
  3. 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
    ....
  4. 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
    ....
  5. pmc Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    Bruce Rannala
    Department of Medical Genetics, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
    Genetics 164:1645-56. 2003
    ..Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models...
  6. pmc Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
    Alexei J Drummond
    School of Biological Sciences, University of Auckland 1001, Auckland, New Zealand
    Genetics 161:1307-20. 2002
    ..We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences...
  7. pmc Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems
    Tina Toni
    Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
    J R Soc Interface 6:187-202. 2009
    ..Moreover, we develop ABC SMC as a tool for model selection; given a range of different mathematical descriptions, ABC SMC is able to choose the best model using the standard Bayesian model selection apparatus...
  8. ncbi Design of a novel globular protein fold with atomic-level accuracy
    Brian Kuhlman
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Science 302:1364-8. 2003
    ..2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature...
  9. ncbi Toward high-resolution de novo structure prediction for small proteins
    Philip Bradley
    University of Washington, Department of Biochemistry, and Howard Hughes Medical Institute, Box 357350, Seattle, WA 98195, USA
    Science 309:1868-71. 2005
    ..5 angstroms) can be achieved for small protein domains (<85 residues). The primary bottleneck to consistent high-resolution prediction appears to be conformational sampling...
  10. pmc Relaxed phylogenetics and dating with confidence
    Alexei J Drummond
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS Biol 4:e88. 2006
    ..From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution...
  11. ncbi A comparison of the ability of different propensity score models to balance measured variables between treated and untreated subjects: a Monte Carlo study
    Peter C Austin
    Institute for Clinical Evaluative Sciences, Toronto, Ont, Canada
    Stat Med 26:734-53. 2007
    ..Finally, the mean squared error for estimating a null treatment effect was lower when either of the first two propensity scores was used compared to when either of the last two propensity score models was used...
  12. 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...
  13. ncbi MrBayes on a graphics processing unit
    Jianfu Zhou
    Nankai Baidu Joint Laboratory, College of Information Technical Science, Nankai University, Tianjin, China
    Bioinformatics 27:1255-61. 2011
    ..The GPU has been used as a cost-effective means for computational research in many fields. However, until now, some limitations have prevented the GPU from being used to run MrBayes MC³ effectively...
  14. 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...
  15. ncbi Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites
    Remo Rohs
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Structure 13:1499-509. 2005
    ..Contributions of specific base pair steps to the overall bending are shown in terms of local structural parameters. The analysis of conformational substates provides new insights into the energetic origins of intrinsic DNA bending...
  16. ncbi A simple model for complex dynamical transitions in epidemics
    D J Earn
    Department of Mathematics and Statistics, McMaster University, Hamilton, Ontario L8S 4K1, Canada
    Science 287:667-70. 2000
    ..Measles is a natural ecological system that exhibits different dynamical transitions at different times and places, yet all of these transitions can be predicted as bifurcations of a single nonlinear model...
  17. ncbi Sub-angstrom modeling of complexes between flexible peptides and globular proteins
    Barak Raveh
    Department of Microbiology and Molecular Genetics, Insitute for Medical Research Israel Canada, Hadassah Medical School, The Hebrew University, Jerusalem, 91120 Israel
    Proteins 78:2029-40. 2010
    ....
  18. 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
    ....
  19. 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
    ..Here we propose a sequential Monte Carlo sampler that convincingly overcomes these inefficiencies. We demonstrate its implementation through an epidemiological study of the transmission rate of tuberculosis...
  20. ncbi The fine-scale structure of recombination rate variation in the human genome
    Gilean A T McVean
    Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
    Science 304:581-4. 2004
    ..We demonstrate that recombination hotspots are a ubiquitous feature of the human genome, occurring on average every 200 kilobases or less, but recombination occurs preferentially outside genes...
  21. 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
    ..Here we present a Markov chain Monte Carlo method for generating observations from a posterior distribution without the use of likelihoods...
  22. ncbi Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, USA
    Mol Biol Evol 21:1123-33. 2004
    ....
  23. ncbi SPICKER: a clustering approach to identify near-native protein folds
    Yang Zhang
    Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington St, Buffalo, New York 14203, USA
    J Comput Chem 25:865-71. 2004
    ..Although native fold identification from divergent decoy structures remains a challenge, our overall results show significant improvement over our previous clustering algorithms...
  24. pmc Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
    Jody Hey
    Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08846, USA
    Proc Natl Acad Sci U S A 104:2785-90. 2007
    ..Several examples, including an application to the divergence of chimpanzee subspecies, are provided...
  25. ncbi Stratification and weighting via the propensity score in estimation of causal treatment effects: a comparative study
    Jared K Lunceford
    Merck Research Laboratories, Ry34 A316, P O Box 2000, Rahway, NJ 07065 0900, USA
    Stat Med 23:2937-60. 2004
    ....
  26. pmc A modified sleeping beauty transposon system that can be used to model a wide variety of human cancers in mice
    Adam J Dupuy
    Department of Anatomy and Cell Biology, Center for Bioinformatics, Computational Biology and Biomedical Engineering, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
    Cancer Res 69:8150-6. 2009
    ..These novel alleles provide additional tools for the SB system and provide some insight into how this mutagenesis system can be manipulated to model cancer in mice...
  27. pmc The role of non-native interactions in the folding of knotted proteins
    Tatjana Skrbic
    ECT European Centre for Theoretical Studies in Nuclear Physics and Related Areas, Villazzano Trento, Italy
    PLoS Comput Biol 8:e1002504. 2012
    ....
  28. pmc Epistatic association mapping in homozygous crop cultivars
    Hai Yan Lu
    Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
    PLoS ONE 6:e17773. 2011
    ..As a result, 19 main-effect QTLs and 3 epistatic QTLs were identified, more than 10 novel alleles were mined and 3 elite parental combinations, such as Daqingdou and Zhengzhou790034, were predicted...
  29. pmc An efficient Monte Carlo method for estimating Ne from temporally spaced samples using a coalescent-based likelihood
    Eric C Anderson
    Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, California 95060, USA
    Genetics 170:955-67. 2005
    ..User-friendly software implementing the algorithm for Mac, Windows, and Unix/Linux is available for download. Applications of this computational framework to other problems are discussed...
  30. pmc Performance metrics of an optical spectral imaging system for intra-operative assessment of breast tumor margins
    Torre M Bydlon
    Department of Biomedical Engineering, Duke University, 136 Hudson Hall, Box 90281, Durham, NC, 27708, USA
    Opt Express 18:8058-76. 2010
    ..The manuscript includes a discussion of how the speed of the system can be improved to work within the time constraints of an intra-operative setting...
  31. ncbi Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    Jeffrey J Gray
    Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, J 567 Health Sciences, Box 357350, Seattle, WA 98195, USA
    J Mol Biol 331:281-99. 2003
    ....
  32. ncbi Convergence and parameter choice for Monte-Carlo simulations of diffusion MRI
    Matt G Hall
    Centre for Medical Image Computing CMIC, University College London, London, UK
    IEEE Trans Med Imaging 28:1354-64. 2009
    ..This swelling-induced restriction may be an important mechanism in explaining the changes in apparent diffusion constant observed in the aftermath of acute ischemic stroke...
  33. pmc Cooperativity between trans and cis interactions in cadherin-mediated junction formation
    Yinghao Wu
    Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
    Proc Natl Acad Sci U S A 107:17592-7. 2010
    ..We discuss these results in light of available experimental information on cadherin binding free energies that are transformed from their bulk solution values to interaction energies on a 2D lattice...
  34. pmc Computational thermostabilization of an enzyme
    Aaron Korkegian
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center FHCRC, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    Science 308:857-60. 2005
    ..The redesigned enzyme induced an increased, temperature-dependent bacterial growth rate under conditions that required its activity, thereby coupling molecular and metabolic engineering...
  35. pmc A compound poisson process for relaxing the molecular clock
    J P Huelsenbeck
    Department of Biology, University of Rochester, New York 14627, USA
    Genetics 154:1879-92. 2000
    ..This model should prove useful for estimating divergence times when substitution rates vary across lineages...
  36. ncbi Bayesian phylogenetic inference via Markov chain Monte Carlo methods
    B Mau
    Department of Statistics, University of Wisconsin Madison, 53706 1685, USA
    Biometrics 55:1-12. 1999
    ..The algorithm mixes well in both examples from random starting trees, generating reproducible estimates and credible sets for the path of evolution...
  37. pmc Choosing among partition models in Bayesian phylogenetics
    Yu Fan
    Department of Ecology and Evolutionary Biology, University of Connecticut
    Mol Biol Evol 28:523-32. 2011
    ..Such dedicated path-based Markov chain Monte Carlo analyses appear to be a cost of estimating marginal likelihoods accurately...
  38. ncbi On the dosimetric behaviour of photon dose calculation algorithms in the presence of simple geometric heterogeneities: comparison with Monte Carlo calculations
    Antonella Fogliata
    Oncology Institute of Southern Switzerland, Medical Physics Unit, Bellinzona, Switzerland
    Phys Med Biol 52:1363-85. 2007
    ..035 g cm(-3)), enhanced for the most energetic beam. For denser, and more clinical, densities a better agreement among the sophisticated algorithms with respect to MC was observed...
  39. pmc Construct-level predictive validity of educational attainment and intellectual aptitude tests in medical student selection: meta-regression of six UK longitudinal studies
    I C McManus
    UCL Medical School, University College London, Gower Street, London WC1E 6BT, UK
    BMC Med 11:243. 2013
    ..That problem of interpretation can be solved by calculating construct-level predictive validity, an estimate of true predictor-outcome correlation across the range of applicant abilities...
  40. pmc Robust, tunable biological oscillations from interlinked positive and negative feedback loops
    Tony Yu Chen Tsai
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 5174, USA
    Science 321:126-9. 2008
    ..Positive-plus-negative oscillators also appear to be more robust and easier to evolve, rationalizing why they are found in contexts where an adjustable frequency is unimportant...
  41. pmc Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation
    Oliver F Lange
    Department Chemie, Biomolecular NMR and Munich Center for Integrated Protein Science, Technische Universitat Munchen, Garching, Germany
    Proteins 80:884-95. 2012
    ....
  42. ncbi Monte Carlo simulations to support start-up and treatment planning of scanned proton and carbon ion therapy at a synchrotron-based facility
    K Parodi
    Heidelberg Ion Beam Therapy Center and Department of Radiation Oncology, Heidelberg University Clinic, Heidelberg, Germany
    Phys Med Biol 57:3759-84. 2012
    ..This paper can thus provide useful information and guidelines for the start-up and clinical operation of forthcoming ion beam therapy facilities similar to HIT...
  43. pmc An efficient hierarchical generalized linear mixed model for mapping QTL of ordinal traits in crop cultivars
    Jian Ying Feng
    Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China
    PLoS ONE 8:e59541. 2013
    ..As a result, 6 main-effect QTL and 3 QTL-by-environment interactions were identified...
  44. pmc The optimal height of the synaptic cleft
    Leonid P Savtchenko
    Institute of Neurology, University College London, Queen Square, London, United Kingdom
    Proc Natl Acad Sci U S A 104:1823-8. 2007
    ..Therefore, our results suggest that a simple fundamental principle may underlie the synaptic cleft architecture: to maximize synaptic strength...
  45. pmc Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and molecular dynamics study
    Iskra Staneva
    Department of Astronomy and Theoretical Physics, Computational Biology and Biological Physics Group, Lund University, Lund, Sweden
    PLoS Comput Biol 8:e1002682. 2012
    ..Our results highlight the importance of overall physical properties of IDP segments, such as net charge or presence of strongly hydrophobic amino acids, for molecular recognition via coupled folding-binding...
  46. ncbi Monte Carlo prediction of near-infrared light propagation in realistic adult and neonatal head models
    Yuich Fukui
    Department of Electronics and Electrical Engineering, Keio University, 3 141, Hyoshi, Kohoku Ku, Yokohama 223 8522, Japan
    Appl Opt 42:2881-7. 2003
    ..The intensely sensitive region in the neonatal brain is confined to the gray matter; however, the spatial sensitivity profile penetrates into the deeper region of the white matter...
  47. pmc Monte Carlo study of a two-compartment exchange model of diffusion
    Els Fieremans
    Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY 10016, USA
    NMR Biomed 23:711-24. 2010
    ..For larger permeabilities, the exchange time obtained from fitting to the Kärger model overestimates the actual exchange time, leading to an underestimated value of cell membrane permeability...
  48. pmc Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations
    T B Kepler
    Santa Fe Institute, Santa Fe, New Mexico 87501, USA
    Biophys J 81:3116-36. 2001
    ..We find stochastic bistability where the deterministic equations predict monostability and vice-versa. We derive and solve equations for the mean waiting times for spontaneous transitions between quasistable states in these switches...
  49. pmc Method for depth-resolved quantitation of optical properties in layered media using spatially modulated quantitative spectroscopy
    Rolf B Saager
    University of California Irvine, Beckman Laser Institute, 1002 Health Sciences Road, Irvine, California 92612, USA
    J Biomed Opt 16:077002. 2011
    ....
  50. pmc Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone
    Kateri H DuBay
    Department of Chemistry, University of California at Berkeley, Berkeley, California, United States of America
    PLoS Comput Biol 7:e1002168. 2011
    ..These robust correlations persist across the entire protein (up to 60 Å in the case of calmodulin) and can propagate long-range changes in side-chain variability in response to single residue perturbations...
  51. ncbi Theoretical and computational protein design
    Ilan Samish
    Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Annu Rev Phys Chem 62:129-49. 2011
    ..Developments in such computational protein design are discussed, along with recent accomplishments, ranging from the redesign of existing proteins to the design of new functionalities and nonbiological applications...
  52. pmc Measurement of the spatial backscattering impulse-response at short length scales with polarized enhanced backscattering
    Andrew J Radosevich
    Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
    Opt Lett 36:4737-9. 2011
    ..We conclude by demonstrating the extraordinary sensitivity of our technique to the shape of the scattering phase function, including higher order shape parameters than the anisotropy factor (or first moment)...
  53. pmc Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling
    Jan Schellenberger
    Bioinformatics and Systems Biology Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0419, USA
    BMC Syst Biol 6:9. 2012
    ..Unlike previous work, this method does not require assumption of the flux distribution beforehand...
  54. pmc Online tool to guide decisions for BRCA1/2 mutation carriers
    Allison W Kurian
    Stanford University School of Medicine, Stanford, CA, USA
    J Clin Oncol 30:497-506. 2012
    ..A clinical decision tool could guide these complex choices...
  55. ncbi Optical properties of selected native and coagulated human brain tissues in vitro in the visible and near infrared spectral range
    A N Yaroslavsky
    Wellman Laboratories of Photomedicine, Department of Dermatology, Boston, MA 02114, USA
    Phys Med Biol 47:2059-73. 2002
    ..A comparison with data from the literature revealed the importance of the employed tissue preparation technique and the impact of the theoretical model used to extract the optical coefficients from the measured quantities...
  56. ncbi Geometrical and Monte Carlo projectors in 3D PET reconstruction
    Pablo Aguiar
    Fundación IDICHUS IDIS, Complexo Hospitalario Universitario de Santiago de Compostela, Departamento de Física de Partículas, Universidade de Santiago de Compostela, Spain
    Med Phys 37:5691-702. 2010
    ..The Monte Carlo-based method under consideration involves an extensive model of the system response matrix based on Monte Carlo simulations and is computed off-line and stored on disk...
  57. ncbi Monte Carlo simulations of protein amyloid formation reveal origin of sigmoidal aggregation kinetics
    Björn Linse
    Lund University, Chemical Centre, Department of Biochemistry, P O Box 124, SE 221 00 Lund, Sweden
    Mol Biosyst 7:2296-303. 2011
    ....
  58. pmc Simulation of near-infrared light absorption considering individual head and prefrontal cortex anatomy: implications for optical neuroimaging
    Florian B Haeussinger
    Department of Psychiatry and Psychotherapy, University of Tuebingen, Tuebingen, Germany
    PLoS ONE 6:e26377. 2011
    ..Our findings suggest to consider individual SCD and frontal sinus volume as anatomical factors impacting fNIRS sensitivity. Head circumference may represent a practical measure to partly control for these sources of error variance...
  59. pmc Dynamic causal modeling of subcortical connectivity of language
    Olivier David
    Grenoble Institut des Neuroscience, INSERM U 836, 38042 Grenoble, France
    J Neurosci 31:2712-7. 2011
    ..This study is the first demonstration in cognitive neuroscience that subcortical-cortical loops can be empirically investigated using noninvasive electrophysiological recordings...
  60. pmc Monte Carlo radiotherapy simulations of accelerated repopulation and reoxygenation for hypoxic head and neck cancer
    W M Harriss-Phillips
    Department of Medical Physics, Royal Adelaide Hospital Cancer Centre, Adelaide, SA, Australia
    Br J Radiol 84:903-18. 2011
    ..The model was designed to simulate individual cell division up to 10(8) cells, while incorporating radiobiological effects, including accelerated repopulation and reoxygenation during treatment...
  61. pmc Binding free energy landscape of domain-peptide interactions
    Iskra Staneva
    Department of Astronomy and Theoretical Physics, Computational Biology and Biological Physics Group, Lund University, Lund, Sweden
    PLoS Comput Biol 7:e1002131. 2011
    ..Our combined results are consistent with a binding mechanism in which the peptide C terminal residue binds in an initial, rate-limiting step...
  62. pmc Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins
    Luke Czapla
    1 Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
    J Mol Biol 409:278-89. 2011
    ..This combination of experiment and simulation provides a powerful new approach to resolve a long-standing problem in the biophysics of protein/DNA interactions...
  63. ncbi Guided tree topology proposals for Bayesian phylogenetic inference
    Sebastian Höhna
    Department of Mathematics, Stockholm University, SE 10691 Stockholm, Sweden
    Syst Biol 61:1-11. 2012
    ..We also introduce conditional clade probabilities and demonstrate that they provide a superior means of approximating tree topology posterior probabilities from samples recorded during MCMC...
  64. ncbi PBPK modelling of inter-individual variability in the pharmacokinetics of environmental chemicals
    Frederic Y Bois
    UTC, Technological University of Compiegne, Chair of Mathematical Modelling for Systems Toxicology, Royallieu Research Centre, BP 20529, 60205 Compiegne Cedex, France
    Toxicology 278:256-67. 2010
    ..This article reviews those developments and illustrates them with recent applications to environmentally relevant questions...
  65. ncbi The annual impact of seasonal influenza in the US: measuring disease burden and costs
    Noelle Angelique M Molinari
    Immunization Service Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Mail Stop E 88, Atlanta, GA 30333, USA
    Vaccine 25:5086-96. 2007
    ..However, no previous studies have systematically estimated the annual economic burden of influenza epidemics, an estimate necessary to guide policy makers effectively...
  66. ncbi Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
    Gautam Altekar
    Department of Computer Science, University of Rochester, USA
    Bioinformatics 20:407-15. 2004
    ..Metropolis coupled MCMC [(MC)(3)], a variant of MCMC, allows multiple peaks in the landscape of trees to be more readily explored, but at the cost of increased execution time...
  67. ncbi Conformational transitions of adsorbed proteins on surfaces of varying polarity
    Gaurav Anand
    Howard P Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180 3590, USA
    Langmuir 26:10803-11. 2010
    ..Thus, increasing the nonpolar nature of the surfaces resulted in a more rigid adsorbed layer, in good agreement with the experiments...
  68. pmc Complex geometric models of diffusion and relaxation in healthy and damaged white matter
    Bennett A Landman
    Department of Biomedical Engineering, John Hopkins University, Baltimore, MD 21218, USA
    NMR Biomed 23:152-62. 2010
    ..g. mesh-based) geometries. Three-dimensional diffusion displacement probability functions are mapped with high reproducibility, and thus can be readily used to assess reproducibility of diffusion-derived contrasts...
  69. pmc Bayesian methods for instrumental variable analysis with genetic instruments ('Mendelian randomization'): example with urate transporter SLC2A9 as an instrumental variable for effect of urate levels on metabolic syndrome
    Paul M McKeigue
    Public Health Sciences Section, Division of Community Health Sciences, University of Edinburgh Medical School, Edinburgh, UK
    Int J Epidemiol 39:907-18. 2010
    ....
  70. ncbi Grand canonical Monte Carlo simulations of water in protein environments
    Hyung June Woo
    Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA
    J Chem Phys 121:6392-400. 2004
    ..Im, S. Berneche, and B. Roux, J. Chem. Phys. 114, 2924 (2001)]. As a last illustration of water confined in the interior of a protein, the hydration of the central cavity of the KcsA potassium channel is simulated...
  71. pmc Probing the mechanisms of fibril formation using lattice models
    Mai Suan Li
    Institute of Physics, Polish Academy of Sciences, Al Lotnikow 32 46, 02 668 Warsaw, Poland
    J Chem Phys 129:175101. 2008
    ..The detailed analysis shows that elements of the three popular models, namely, nucleation and growth, templated assembly, and nucleated conformational conversion are present at various stages of fibril assembly...
  72. ncbi Adaptive filtering for global interference cancellation and real-time recovery of evoked brain activity: a Monte Carlo simulation study
    Quan Zhang
    Harvard Medical School, Massachusetts General Hospital, Neural Systems Group, 13th Street, Building 149, Room 2651, Charlestown, Massachusetts 02129, USA
    J Biomed Opt 12:044014. 2007
    ..The technique can be performed in real time, an important feature required for applications such as brain activity localization, biofeedback, and potential neuroprosthetic devices...
  73. ncbi Dosimetric validation of Acuros XB with Monte Carlo methods for photon dose calculations
    K Bush
    Department of Medical Physics, British Columbia Cancer Agency Vancouver Island Center, Victoria, British Columbia V8R 6V5, Canada
    Med Phys 38:2208-21. 2011
    ....
  74. pmc Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations
    Luke Czapla
    Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Wright Rieman Laboratories, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA
    J Mol Biol 382:353-70. 2008
    ..The local bending and undertwisting of DNA by HU, in combination with the number of bound proteins, provide a structural rationale for the condensation of DNA and the observed expression levels of reporter genes in vivo...
  75. pmc Control of confounding of genetic associations in stratified populations
    Clive J Hoggart
    Epidemiology Unit, London School of Hygiene and Tropical Medicine, Umited Kingdom
    Am J Hum Genet 72:1492-1504. 2003
    ..With only 32 markers informative for ancestry, the efficiency of the analysis is 70%. These methods can deal with both confounding and selection bias in genetic-association studies, making family-based designs unnecessary...
  76. ncbi Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny
    Stephane Aris-Brosou
    Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, England
    Syst Biol 51:703-14. 2002
    ..Estimates of the rates were in accordance with the Cambrian explosion hypothesis and suggested some more recent lineage-specific bursts of evolution...
  77. ncbi Diffusion-weighted MRI measurements on stroke patients reveal water-exchange mechanisms in sub-acute ischaemic lesions
    J Latt
    Department of Medical Radiation Physics, Lund University, Lund, Sweden
    NMR Biomed 22:619-28. 2009
    ..The information can improve the understanding of the relationship between the DW-MRI signal intensity and the microstructural properties of the lesions...
  78. ncbi Use of randomized sampling for analysis of metabolic networks
    Jan Schellenberger
    Bioinformatics Program, University of California, San Diego, La Jolla, CA 92093 0412, USA
    J Biol Chem 284:5457-61. 2009
    ..We present an overview of this emerging area of research in systems biology...
  79. pmc Possible cooperation of differential adhesion and chemotaxis in mound formation of Dictyostelium
    Y Jiang
    Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
    Biophys J 75:2615-25. 1998
    ..The simulations provide a method to determine the processes necessary for patterning and suggest a series of further experiments...
  80. ncbi Analyzing survival curves at a fixed point in time
    John P Klein
    Division of Biostatistics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
    Stat Med 26:4505-19. 2007
    ..The methods are illustrated on a study comparing survival for autologous and allogeneic bone marrow transplants...
  81. ncbi CONV--convolution for responses to a finite diameter photon beam incident on multi-layered tissues
    L Wang
    Bioengineering Program, Texas A and M University, College Station 77843 3120, USA
    Comput Methods Programs Biomed 54:141-50. 1997
    ..The program, including the source code, has been in the public domain since 1992 and can be downloaded from the web site at http:(/)/biomed.tamu.edu/-lw...
  82. ncbi Efficient Monte Carlo modelling of individual tumour cell propagation for hypoxic head and neck cancer
    W Tuckwell
    School of Chemistry and Physics, University of Adelaide, South Australia, Australia
    Phys Med Biol 53:4489-507. 2008
    ....
  83. ncbi Modeling tumor growth and irradiation response in vitro--a combination of high-performance computing and web-based technologies including VRML visualization
    G S Stamatakos
    Department of Electrical and Computer Engineering, Biomedical Simulations and Medical Imaging Unit, National Technical University of Athens, GR 157 80 Zografos, Greece
    IEEE Trans Inf Technol Biomed 5:279-89. 2001
    ..Currently, our group is investigating extensions of the presented algorithms so that efficient descriptions of the corresponding clinical (in vivo) cases are achieved...
  84. ncbi Experimental characterization and physical modelling of the dose distribution of scanned proton pencil beams
    E Pedroni
    Paul Scherrer Institute, CH 5232 Villigen PSI, Switzerland
    Phys Med Biol 50:541-61. 2005
    ..This applies also to the complex non-homogeneous dose distributions required for the delivery of range-intensity-modulated proton therapy, a novel therapy technique developed at PSI...
  85. ncbi Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    A Rambaut
    Department of Zoology, University of Oxford, UK
    Comput Appl Biosci 13:235-8. 1997
    ..Thus, large sets of replicate simulations can be easily created. This can be used to test phylogenetic hypotheses using the parametric bootstrap...
  86. ncbi Bayesian inference of the demographic history of chimpanzees
    Daniel Wegmann
    Department of Biology, Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
    Mol Biol Evol 27:1425-35. 2010
    ....
  87. ncbi Monte Carlo and TLD dosimetry of an 192Ir high dose-rate brachytherapy source
    P Karaiskos
    Physics Department, University of Athens, Greece
    Med Phys 25:1975-84. 1998
    ..However, these functions depend on radial distance at angles close to the longitudinal axis of the source, where deviations of up to 20% are observed...
  88. pmc Previous estimates of mitochondrial DNA mutation level variance did not account for sampling error: comparing the mtDNA genetic bottleneck in mice and humans
    Passorn Wonnapinij
    Center of Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
    Am J Hum Genet 86:540-50. 2010
    ..Our results show that variance measurements based on fewer than 20 measurements are generally unreliable and ideally more than 50 measurements are required to reliably compare variances with less than a 2-fold difference...
  89. ncbi EGSnrc Monte Carlo calculated dosimetry parameters for 192Ir and 169Yb brachytherapy sources
    R E P Taylor
    Carleton Laboratory for Radiotherapy Physics, Ottawa Carleton Institute of Physics, Carleton University Campus Ottawa, Ontario KIS 5B6, Canada
    Med Phys 35:4933-44. 2008
    ..physics.carleton.ca/clrp/seed_database/)...
  90. ncbi Multidistance probe arrangement to eliminate artifacts in functional near-infrared spectroscopy
    Toru Yamada
    National Institute of Advanced Industrial Science and Technology, Neuroscience Research Institute, 1 1 1 Umezono Central 2, Tsukuba, Ibaraki 305 8568, Japan
    J Biomed Opt 14:064034. 2009
    ..A statistically significant increase in oxygenated hemoglobin and decrease in deoxygenated hemoglobin are simultaneously observed at the contralateral primary motor area...
  91. pmc Bayesian inference of biochemical kinetic parameters using the linear noise approximation
    Michał Komorowski
    Department of Statistics, University of Warwick, Coventry, UK
    BMC Bioinformatics 10:343. 2009
    ..In this paper we present a simple and computationally efficient algorithm for the estimation of biochemical kinetic parameters from gene reporter data...
  92. ncbi Belief propagation in networks of spiking neurons
    Andreas Steimer
    Institute of Neuroinformatics, University of Zurich, and ETH Zurich, Zurich, 8057 Switzerland
    Neural Comput 21:2502-23. 2009
    ..These two examples, and also a statistical analysis, demonstrate good agreement between the performance of our networks and the direct numerical evaluation of belief propagation...
  93. ncbi Factors affecting the accuracy of near-infrared spectroscopy concentration calculations for focal changes in oxygenation parameters
    Gary Strangman
    Neural Systems Group, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
    Neuroimage 18:865-79. 2003
    ....
  94. pmc Clonal interference, multiple mutations and adaptation in large asexual populations
    Craig A Fogle
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Genetics 180:2163-73. 2008
    ..Using our simulations, we are able to explore the limits of validity of both of these approaches, and we explore the complex dynamics in the regimes where neither one is fully applicable...
  95. pmc Permutation tests for multiple loci affecting a quantitative character
    R W Doerge
    Biometrics Unit, Cornell University, Ithaca, New York 14853, USA
    Genetics 142:285-94. 1996
    ..The search space for minor QTL is unrestricted, and RET-based tests may be more powerful than the CET-based test when the structural model is approximately true...
  96. pmc Stochastic gene expression in fluctuating environments
    Mukund Thattai
    Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genetics 167:523-30. 2004
    ..However, this heterogeneity is beneficial only if the bacterial response rate is sufficiently low. Our results could be useful in the design of artificial evolution experiments and in the optimization of fermentation processes...
  97. ncbi Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees
    David C Marshall
    Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N Eagleville Road, U 3043, Storrs, CT 06269, USA
    Syst Biol 59:108-17. 2010
    ..In more difficult situations, accurate branch length estimation may not be possible with Bayesian methods because of dependence of the solution on the branch length prior...
  98. ncbi Bayesian variable and model selection methods for genetic association studies
    Brooke L Fridley
    Division of Biostatistics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
    Genet Epidemiol 33:27-37. 2009
    ....
  99. ncbi Accommodating phylogenetic uncertainty in evolutionary studies
    J P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Science 288:2349-50. 2000
    ..We describe methods for accommodating phylogenetic uncertainty in evolutionary studies by means of Bayesian inference. The methods are computationally intensive but general enough to be applied in most comparative evolutionary studies...
  100. ncbi Some methods of propensity-score matching had superior performance to others: results of an empirical investigation and Monte Carlo simulations
    Peter C Austin
    Institute for Clinical Evaluative Sciences, Toronto, ON, Canada
    Biom J 51:171-84. 2009
    ..2 of the standard deviation of the logit of the propensity score and the use of calipers of width 0.02 and 0.03 tended to have superior performance for estimating treatment effects...
  101. ncbi Comparing impact and cost-effectiveness of primary prevention strategies for lipid-lowering
    Mark J Pletcher
    University of California, San Francisco, San Francisco, California 94107, USA
    Ann Intern Med 150:243-54. 2009
    ..Lipid-lowering therapy is costly but effective at reducing coronary heart disease (CHD) risk...

Research Grants77

  1. Prediction of Second Cancer Risks for Children Treated with Proton - vs. - Photon
    Wayne D Newhauser; Fiscal Year: 2010
    ..In the future, we expect that the lower-risk treatments will result in fewer second cancers and this will translate into longer, higher-quality lives for survivors of childhood cancer (presently 270,000 persons in the United States). ..
  2. Logical Analysis of Data and Cardiac Surgery Risk
    Eugene Blackstone; Fiscal Year: 2006
    ..3. Develop predictive instruments using relative risk forests, a new Monte Carlo method for estimating risk values in large survival data settings with large numbers of correlated variables...
  3. Heterogeneity Among Unobserved Subpopulations
    Booil Jo; Fiscal Year: 2006
    ..Statistical modeling features demonstrated in empirical examples will have implications not on y in outcomes analysis, but also in study design strategies for mental health research. ..
  4. Improved Protein Mapping for Fragment-Based Drug Design
    Sandor Vajda; Fiscal Year: 2005
    ..Preliminary results suggest that mapping with fragments from well designed libraries will provide very useful information for drug design. ..
  5. Accelerated x-ray therapy planning system PEREGRINE
    PAUL NIZIN; Fiscal Year: 2004
    ..Among currently available computational methods, the Monte Carlo method of calculating dose distributionsis most universal and accurate...
  6. Cloud-Based Bioinformatics for Immune Repertoire Analysis
    David Scott Johnson; Fiscal Year: 2013
    ..of comparisons of multiple data sets, and (iv) statistical significance testing of findings via a Monte Carlo method. We tested the computational modules with actual immune repertoire data generated in-house for internal ..
  7. Image-Based Modeling of Ca2+ Signaling in Ventricular Myocytes
    Zeyun Yu; Fiscal Year: 2010
    ..e. calcium sparks) are formed within/around a single CRU using the Monte Carlo method. Anatomical models extracted from 3D EM images will be used to specify the simulation domains...
  8. NOVEL APPROACHES TO RADIO-IMMUNOCONJUGATE DOSIMETRY
    Lee Chin; Fiscal Year: 1991
    ..The dosimetric tools developed here will be appropriate for later application to clinical radio-immunotherapy...
  9. Multispectral Fluorescence Molecular Tomography with Structured Light
    Xavier Intes; Fiscal Year: 2013
    ..by employing structured light illumination strategies and by using reconstruction algorithms based on the Monte Carlo method, the inverse optical molecular imaging problem can be solved accurately to provide quantitative spatial maps ..
  10. DISTANCE MEASUREMENTS IN METALLOPROTEINS
    GARY BRUDVIG; Fiscal Year: 2002
    ..to determine the surface accessibility of paramagnetic centers in proteins will be extended by using a Monte Carlo method to model the excluded protein volume and the distribution of Dy3+-chelate complexes in the solution ..
  11. RESOLUTION LIMITS FOR FLUORESCENCE TOMOGRAPHIC MOLECULAR IMAGING
    XIAOFENG STEVE ZHANG; Fiscal Year: 2012
    ..The effects of anatomical prior information from micro-CT will also be studied. Image reconstruction will be based on a Monte Carlo method using parallel computing on supercomputers.
  12. RESOLUTION LIMITS FOR FLUORESCENCE TOMOGRAPHIC MOLECULAR IMAGING
    XIAOFENG STEVE ZHANG; Fiscal Year: 2011
    ..The effects of anatomical prior information from micro-CT will also be studied. Image reconstruction will be based on a Monte Carlo method using parallel computing on supercomputers.
  13. Better correlation of outcomes with MC dose calculation
    Indrin Chetty; Fiscal Year: 2007
    ..for non-small cell lung cancer) to investigate whether dose distributions calculated with the more accurate Monte Carlo method will improve the correlation between the clinical patient outcomes and the calculated dose distributions...
  14. Accurate, easy-to-commission radiotherapy beam models
    Bruce Faddegon; Fiscal Year: 2008
    ..This will allow clinics around the country to take advantage of the computational accuracy of this state-of-the-art clinical tool. [unreadable] [unreadable]..
  15. Diffuse optical brain imaging for stroke rehabilitation
    Gary Strangman; Fiscal Year: 2007
    ..Importantly, use of the DOT technology in such a research program is expected to enable the investigation of tasks and populations that are otherwise beyond the reach of existing brain imaging technologies. [unreadable] [unreadable]..
  16. Bi-Plane Correlation Imaging: Detection of Lung Cancer
    Ehsan Samei; Fiscal Year: 2007
    ..The findings will be used to substantiate the capability of BCI for improving the early detection of lung nodules and to optimize its performance on actual clinical cases. ..
  17. Early Detection of Lung Cancer via Bi Plane Correlation
    Ehsan Samei; Fiscal Year: 2002
    ..The findings will be used to demonstrate the capability of the approach for improving the detection of lung nodules, and thus the prognosis of lung cancer. ..
  18. Diffuse optical imaging of intracranial pressure changes
    Gary Strangman; Fiscal Year: 2004
    ....
  19. Visualization of Multi-Resolution Reconstructions Using Interactive Stereoscopy
    Arkadiusz Sitek; Fiscal Year: 2008
    ..The work involves design and creation of software for reconstruction and stereoscopic display of tetrahedron based images and evaluation against human observers for the lesion detection task. ..
  20. Resolution requirements for mammographic displays
    Ehsan Samei; Fiscal Year: 2004
    ..The results will be used to formulate recommendations to the breast imaging community concerning display resolution criteria for safe and optimized soft-copy display of digital mammograms. ..
  21. 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. ..
  22. Investigation of Monte Carlo Tools for IMRT
    Chang Ming Ma; Fiscal Year: 2005
    ..The results will be used as reference materials in retrospective studies as well as ongoing clinical trials. ..
  23. Statistical Analysis of RIX for Complex Traits
    Fei Zou; Fiscal Year: 2005
    ..abstract_text> ..
  24. Public Use Samples of 1910 & 1920 Puerto Rican Censuses
    Alberto Palloni; Fiscal Year: 2004
    ..These comparisons will shed light on the nature and importance of assimilation processes. ..
  25. Biologically Based Reaction Network Modeling of P4502E1
    Brad Reisfeld; Fiscal Year: 2005
    ....
  26. PREVENTION OF SUICIDE IN THE ELDERLY
    George Alexopoulos; Fiscal Year: 2002
    ..Data will also be collected to document the impact of intervention on patient care, and on physician knowledge, attitudes, and satisfaction and test hypotheses derived from preliminary studies of the three IRCs. ..
  27. Treatment Effectiveness in Depressed Patients with COPD
    George Alexopoulos; Fiscal Year: 2006
    ..Finally, we believe that our approach to the care of depressed, medically ill patients can generate a practice model that has the ability to rapidly incorporate advances made in clinical science. ..
  28. Cornell ACISR for Late Life Depression
    George Alexopoulos; Fiscal Year: 2007
    ..We are confident that our work will both advance scientific knowledge and have a broad impact on the care of depressed, disabled elders. ..
  29. Electron Transport in Tissue-Like Material
    LARRY TOBUREN; Fiscal Year: 2008
    ..The results will enhance our effort to establish clinically relevant radiation treatment with a better understanding of potential damage to healthy tissue. [unreadable] [unreadable] [unreadable]..
  30. 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. ..
  31. Structural Models to Bridge Observational and Randomized Evidence: HAART and AIDS
    Stephen Cole; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  32. Admixture Mapping of Sarcoidosis Genes in African American
    Benjamin Rybicki; Fiscal Year: 2007
    ..Our proposed study has the potential to uncover genes of modest effect not easily detectable by linkage and may in some instances actually be more statistically powerful than traditional case-control association methods. ..
  33. MISSING DATA, MEASUREMENT ERROR AND APPLICATIONS
    Ching Yun Wang; Fiscal Year: 2002
    ..The investigator states that the proposed methods will also accommodate two-stage designs which are becoming popular in epidemiologic research and particular in genetic epidemiology. ..
  34. Novel Statistical Methods for Data with Missing Values
    Hua Yun Chen; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  35. Nonparametric Inference for Neuroimaging Data
    Timothy Johnson; Fiscal Year: 2008
    ..abstract_text> ..
  36. ADAPTATION OF NEW STATISTICAL IDEAS FOR MEDICINE
    Bradley Efron; Fiscal Year: 2002
    ....
  37. 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. ..
  38. GENETICS OF SPECIATION IN DROSOPHILA
    EMANUEL HEY; Fiscal Year: 2001
    ....
  39. Using Clinically-Enhanced Claims Data to Guide Treatment of Acute Heart Failure
    Mark Sonneborn; Fiscal Year: 2010
    ..The database will be used to conduct a study of the comparative effectiveness of different drug treatments of patients hospitalized with acute worsening of congestive heart failure. ..
  40. Using Clinically-Enhanced Claims Data to Guide Selection of Coronary Procedures
    HAROLD KILBURN; Fiscal Year: 2010
    ....
  41. 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. ..
  42. Biological Models of Influenza A Virus
    Gilles Clermont; Fiscal Year: 2010
    ....
  43. A Multivariate Probit Model for Health Services Research
    Hua Yun Chen; Fiscal Year: 2006
    ..uic.edu/labs/biostat. No general multivariate probit regression software is currently available. [unreadable] [unreadable]..
  44. Four-dimensional IMAT planning using graph algorithms
    Cedric X Yu; Fiscal Year: 2010
    ..Successful achievement of the aforementioned project aims will provide planning and practical image guidance for the safe and efficient delivery of IMAT, and significantly improve cancer treatments. ..
  45. Predicting common protein mechanisms by the light of evolution
    ANDREW NEUWALD; Fiscal Year: 2009
    ..And (v) propose molecular mechanisms based on these analyses. ..
  46. HEALTH CONDITIONS OF ELDERLY PUERTO RICANS
    Alberto Palloni; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  47. Decisionmaking in Pediatric Palliative Care
    JOHN FEUDTNER; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  48. Conference on Aging in Developing Countries: Building Integrated Research Agendas
    Alberto Palloni; Fiscal Year: 2007
    ..As a consequence, this meeting is highly relevant for policy design not just for public health but also for policies related to labor force, income distribution, and pensions systems. [unreadable] [unreadable] [unreadable]..
  49. NATURAL HISTORY OF HEPATITIS C INFECTION IN HIV DISEASE
    C Horsburgh; Fiscal Year: 2003
    ..These studies are expected to improve our understanding of the natural history and pathogenesis of HCV in immunosuppressed hosts. ..
  50. Three Methods for Costing Methadone Treatment Services
    GARY ZARKIN; Fiscal Year: 2006
    ..abstract_text> ..
  51. Self-Focused Attention and Nonconscious Self-Evaluation
    PAUL SILVIA; Fiscal Year: 2005
    ..Examining the cognitive processes that give rise to automatic self-evaluation will enhance psychology's understanding of how to prevent, treat, and regulate maladaptive and self-defeating patterns of thought. ..
  52. Mixed Model Approach to Gene Mapping for Complex Traits
    Shizhong Xu; Fiscal Year: 2005
    ..The number, map positions and effects of QTL responsible for ethological divergence between species will be determined by associating mating behavior with polymorphic molecular markers in interspecific backcross hybrids. ..
  53. 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. ..
  54. Advanced Sequence-Based Prediction of Protein Function
    ANDREW NEUWALD; Fiscal Year: 2005
    ..abstract_text> ..
  55. ADAPTATION OF NEW STATISTICAL IDEAS FOR MEDICINE
    Bradley Efron; Fiscal Year: 2005
    ..g. genes), among hundreds or thousands of possibilities and identifying groups of cases that work together to influence disease etiology. ..
  56. A Dynamic Disability Specific Physical Activity Scale
    Barth Riley; Fiscal Year: 2006
    ..abstract_text> ..
  57. ATHEROGENESIS AND THE BONE MARROW ANGIOTENSIN SYSTEM
    Carlos Ferrario; Fiscal Year: 2004
    ..The proposed research will uncover novel mechanisms of atherogenesis that may have significant impact in the development of new therapeutic modalities applicable to cardiovascular and blood vessel diseases. ..
  58. BALANCING SURVIVAL AND OTOTOXICITY IN CISPLATIN THERAPY
    Yuelin Li; Fiscal Year: 2003
    ....
  59. The formation of visual objects
    Jacob Feldman; Fiscal Year: 2007
    ..This research may lead to technological advancement in the area of computer vision, as well as to better understanding of disorders of perceptual organization such as visual agnosia and dyslexia. [unreadable] [unreadable]..
  60. COST EFFECTIVENESS OF ALCOHOL TREATMENT
    GARY ZARKIN; Fiscal Year: 2004
    ..abstract_text> ..
  61. Behavioral Health Effects of September 11th, 2001
    Charles DiMaggio; Fiscal Year: 2006
    ..abstract_text> ..
  62. New Methods for Improved Image-based Dosimetry
    Michael Stabin; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  63. PSA BASED EARLY DETECTION OF PROSTATE CANCER RECURRENCE
    Jeremy Taylor; Fiscal Year: 2008
    ..abstract_text> ..
  64. Microbial Fingerprinting Chip and Automated Analysis
    DON DALY; Fiscal Year: 2003
    ..Because the method and DNA chip is "universal", it may be applicable for the identification of other microorganism, as demonstrated in our preliminary studies with Salmonella, Xanthomonas and E. coli pathogens. ..
  65. Do Statins Ameliorate Periodontal Disease?
    Barry Saver; Fiscal Year: 2005
    ....
  66. PREVENTION OF GERATRIC DEPRESSION
    George Alexopoulos; Fiscal Year: 2003
    ..Accordingly, we are well positioned to meet the challenges inherent in this difficult but important area of research. ..
  67. Molecular mechanisms of voltage-gated ion channels
    Hans Peter Larsson; Fiscal Year: 2006
    ..These measurements will be used to determine how S4 moves in the different channels and will further our understanding of the different mechanisms of opening of these two classes of channels. ..
  68. REMOTE SENSING AND GIS FOR SCHISTOSOMIASIS CONTROL
    Robert Spear; Fiscal Year: 2002
    ..Subsequently, efforts will be made to make the classification more precise by supplementing these data with ecological and landscape data and to evaluate alternative remotely sensed data for their ability to predict risk areas. ..
  69. Decoupling Dynamics of the Autonomic Nervous System
    Ki Chon; Fiscal Year: 2005
    ..abstract_text> ..
  70. 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. ..
  71. MOLECULAR ANGLE TRANSITIONS IN MUSCLE
    THOMAS BURGHARDT; Fiscal Year: 2001
    ....
  72. Mechanisms of DNA Polymerases
    Tamar Schlick; Fiscal Year: 2007
    ..Such studies have immediate applications to the diagnostics, and eventually treatment via polymerase inhibitors, of human diseases caused by defective repair of DNA, like various cancers and premature aging. ..
  73. Breast CT scanner for earlier cancer detection
    John Boone; Fiscal Year: 2002
    ..that particularly warrant screening using breast CT. The Phase II trial will shed more light on this issue. ..
  74. Data Evaluation for Early Disease Outbreak Detection
    Kenneth Kleinman; Fiscal Year: 2007
    ..abstract_text> ..