markov chains

Summary

Summary: A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.

Top Publications

  1. ncbi Protein homology detection by HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, D 72076 Tubingen, Germany
    Bioinformatics 21:951-60. 2005
  2. ncbi Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    J Mol Biol 305:567-80. 2001
  3. pmc The HHpred interactive server for protein homology detection and structure prediction
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W244-8. 2005
  4. ncbi Improved prediction of signal peptides: SignalP 3.0
    Jannick Dyrløv Bendtsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    J Mol Biol 340:783-95. 2004
  5. ncbi Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    J Gough
    Laboratory of Molecular Biology, MRC, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 313:903-19. 2001
  6. ncbi Profile hidden Markov models
    S R Eddy
    Department of Genetics, Washington University School of Medicine, 4566 Scott Avenue, St Louis, MO 63110, USA
    Bioinformatics 14:755-63. 1998
  7. 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
  8. ncbi TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
    W H Majoros
    Bioinformatics Department, The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 20:2878-9. 2004
  9. 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
  10. pmc GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
    J Besemer
    School of Biology and School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
    Nucleic Acids Res 29:2607-18. 2001

Detail Information

Publications334 found, 100 shown here

  1. ncbi Protein homology detection by HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, D 72076 Tubingen, Germany
    Bioinformatics 21:951-60. 2005
    ..Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution...
  2. ncbi Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    A Krogh
    Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    J Mol Biol 305:567-80. 2001
    ..We discuss the possible relevance of this finding for our understanding of membrane protein assembly mechanisms. A TMHMM prediction service is available at http://www.cbs.dtu.dk/services/TMHMM/...
  3. pmc The HHpred interactive server for protein homology detection and structure prediction
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W244-8. 2005
    ..A detailed help facility is available. As a demonstration, we analyze the sequence of SpoVT, a transcriptional regulator from Bacillus subtilis. HHpred can be accessed at http://protevo.eb.tuebingen.mpg.de/hhpred...
  4. ncbi Improved prediction of signal peptides: SignalP 3.0
    Jannick Dyrløv Bendtsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    J Mol Biol 340:783-95. 2004
    ..The new method has been benchmarked against other available methods. Predictions can be made at the publicly available web server..
  5. ncbi Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    J Gough
    Laboratory of Molecular Biology, MRC, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 313:903-19. 2001
    ..The annotations derived from these matches are available from a public web server at: http://stash.mrc-lmb.cam.ac.uk/SUPERFAMILY. This server also enables users to match their own sequences against the SUPERFAMILY model library...
  6. ncbi Profile hidden Markov models
    S R Eddy
    Department of Genetics, Washington University School of Medicine, 4566 Scott Avenue, St Louis, MO 63110, USA
    Bioinformatics 14:755-63. 1998
    ..Several software implementations and two large libraries of profile HMMs of common protein domains are available. HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise...
  7. 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...
  8. ncbi TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
    W H Majoros
    Bioinformatics Department, The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 20:2878-9. 2004
    ..Both programs have been used at TIGR for the annotation of the Aspergillus fumigatus and Toxoplasma gondii genomes...
  9. 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
    ....
  10. pmc GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
    J Besemer
    School of Biology and School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
    Nucleic Acids Res 29:2607-18. 2001
    ..These motifs were shown to possess a significant variability, the functional and evolutionary connections of which are discussed...
  11. pmc The TIGRFAMs database of protein families
    Daniel H Haft
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:371-3. 2003
    ..The database currently contains over 1600 protein families. TIGRFAMs is available for searching or downloading at www.tigr.org/TIGRFAMs...
  12. pmc PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    Kai Wang
    Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 17:1665-74. 2007
    ..3%. Our results demonstrate the feasibility of whole-genome fine-mapping of CNVs via high-density SNP genotyping...
  13. 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...
  14. 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
    ....
  15. pmc PANTHER: a library of protein families and subfamilies indexed by function
    Paul D Thomas
    Protein Informatics, Celera Genomics, Foster City, California 94404, USA
    Genome Res 13:2129-41. 2003
    ..Third, we use the family HMMs to rank missense single nucleotide polymorphisms (SNPs), on a database-wide scale, according to their likelihood of affecting protein function...
  16. 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...
  17. 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...
  18. pmc Hidden Markov model speed heuristic and iterative HMM search procedure
    L Steven Johnson
    Department of Immunology and Pathology, Washington University School of Medicine, St Louis, Missouri, USA
    BMC Bioinformatics 11:431. 2010
    ..Profile hidden Markov models (profile-HMMs) are sensitive tools for remote protein homology detection, but the main scoring algorithms, Viterbi or Forward, require considerable time to search large sequence databases...
  19. ncbi An introduction to Markov modelling for economic evaluation
    A Briggs
    Health Economics Research Centre, Institute of Health Sciences, University of Oxford, England
    Pharmacoeconomics 13:397-409. 1998
    ..Analysts should be aware of the limitations of Markov models, particularly the Markovian assumption, although the adept modeller will often find ways around this problem...
  20. ncbi The HMMTOP transmembrane topology prediction server
    G E Tusnády
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, H 1518 Budapest, PO Box 7, Hungary
    Bioinformatics 17:849-50. 2001
    ..This option improves the prediction accuracy as well as helps the interpretation of experimental results, i.e. in epitope insertion experiments...
  21. 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)...
  22. ncbi Improved splice site detection in Genie
    M G Reese
    Human Genome Informatics Group, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    J Comput Biol 4:311-23. 1997
    ..In further splice site experiments, we also looked at correlations between splice site scores and intron and exon lengths, as well as at the effect of distance to the nearest splice site on false positive rates...
  23. pmc Discovery and characterization of chromatin states for systematic annotation of the human genome
    Jason Ernst
    MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:817-25. 2010
    ..This approach provides a complementary functional annotation of the human genome that reveals the genome-wide locations of diverse classes of epigenetic function...
  24. pmc AUGUSTUS: a web server for gene finding in eukaryotes
    Mario Stanke
    University of Gottingen, Institut fur Mikrobiologie und Genetik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Nucleic Acids Res 32:W309-12. 2004
    ..The advantage of our program becomes apparent especially for larger input sequences containing more than one gene. The server is available at http://augustus.gobics.de...
  25. pmc Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs
    Joshua M Korn
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:1253-60. 2008
    ..The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype...
  26. pmc Strong association of de novo copy number mutations with autism
    Jonathan Sebat
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Science 316:445-9. 2007
    ..Affected genomic regions were highly heterogeneous and included mutations of single genes. These findings establish de novo germline mutation as a more significant risk factor for ASD than previously recognized...
  27. 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...
  28. ncbi Principles of good practice for decision analytic modeling in health-care evaluation: report of the ISPOR Task Force on Good Research Practices--Modeling Studies
    Milton C Weinstein
    Center for Risk Analysis, Harvard School of Public Health, Boston, MA 02115, USA
    Value Health 6:9-17. 2003
    ..This report describes the consensus of a task force convened to provide modelers with guidelines for conducting and reporting modeling studies...
  29. pmc Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
    Mario Stanke
    lnstitut für Mikrobiologie und Genetik, Universitat Gottingen, Gottingen, Germany
    BMC Bioinformatics 7:62. 2006
    ..Therefore extrinsic evidence is most valuable when it is balanced with sequence-intrinsic evidence...
  30. pmc Analysis of single-molecule FRET trajectories using hidden Markov modeling
    Sean A McKinney
    Department of Physics and Howard Hughes Medical Institute, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Biophys J 91:1941-51. 2006
    ..The algorithm is then applied to the analysis of the binding and dissociation of three RecA monomers on a DNA construct...
  31. 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...
  32. ncbi A Markov random field model for network-based analysis of genomic data
    Zhi Wei
    Genomics and Computational Biology Graduate Group, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Bioinformatics 23:1537-44. 2007
    ..Such a procedure models the dependency of the DE patterns of genes on the networks using a local discrete MRF model...
  33. ncbi Counting labeled transitions in continuous-time Markov models of evolution
    Vladimir N Minin
    Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
    J Math Biol 56:391-412. 2008
    ..We conclude with two examples that demonstrate the utility of our results...
  34. 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...
  35. pmc Identifying dispersed epigenomic domains from ChIP-Seq data
    Qiang Song
    Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    Bioinformatics 27:870-1. 2011
    ..While high-throughput methods like ChIP-Seq have led to a flood of high-quality data about these epigenomic domains, there remain important analysis problems that are not adequately solved by current analysis tools...
  36. ncbi An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
    Han Xu
    Computational and Mathematical Biology Group, Genome Institute of Singapore, 138672 Singapore
    Bioinformatics 24:2344-9. 2008
    ..Thus the DHMSs are potentially identifiable by comparing two ChIP-seq libraries. However, little has been addressed on this issue in literature...
  37. 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...
  38. 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...
  39. pmc HMM Logos for visualization of protein families
    Benjamin Schuster-Böckler
    Department of Mathematics and Computer Science, Freie Universitat Berlin, Germany
    BMC Bioinformatics 5:7. 2004
    ..Profile Hidden Markov Models (pHMMs) are a widely used tool for protein family research. Up to now, however, there exists no method to visualize all of their central aspects graphically in an intuitively understandable way...
  40. ncbi Hidden Markov models
    S R Eddy
    Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
    Curr Opin Struct Biol 6:361-5. 1996
    ..During the past year, applications of these powerful new HMM-based profiles have begun to appear in the fields of protein-structure prediction and large-scale genome-sequence analysis...
  41. pmc Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics
    Vladimir N Minin
    Department of Statistics, University of Washington, USA
    Mol Biol Evol 25:1459-71. 2008
    ..Next, we estimate the demographic histories of human influenza A hemagglutinin sequences, serially sampled throughout 3 flu seasons...
  42. 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
    ....
  43. pmc The MAPPER database: a multi-genome catalog of putative transcription factor binding sites
    Voichita D Marinescu
    Children s Hospital Informatics Program, Children s Hospital Boston, Harvard Medical School, Enders Research Building EN 150 9, 300 Longwood Avenue, Boston, MA 02115, USA
    Nucleic Acids Res 33:D91-7. 2005
    ..Alternatively, the interface allows the user to retrieve binding sites for a single transcription factor of interest in a single gene or in all genes of the human, mouse or fruit fly genomes...
  44. pmc Integrated study of copy number states and genotype calls using high-density SNP arrays
    Wei Sun
    Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
    Nucleic Acids Res 37:5365-77. 2009
    ..We evaluated genoCN by applications to 162 HapMap individuals and a brain tumor (glioblastoma) dataset and showed that our method can successfully identify both types of copy number differences and produce high-quality genotype calls...
  45. pmc Markov chain Monte Carlo without likelihoods
    Paul Marjoram
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Proc Natl Acad Sci U S A 100:15324-8. 2003
    ..The approach is illustrated by an example of ancestral inference in population genetics. A number of open problems are highlighted in the discussion...
  46. 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...
  47. ncbi Bayesian estimation of ancestral character states on phylogenies
    Mark Pagel
    School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading, England
    Syst Biol 53:673-84. 2004
    ..We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods (BayesMultiState) is available from the authors...
  48. ncbi A combined empirical and mechanistic codon model
    Adi Doron-Faigenboim
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
    Mol Biol Evol 24:388-97. 2007
    ..Using the suggested model, we further analyze human immunodeficiency virus type 1 protease sequences obtained from drug-treated patients and reveal positive selection in sites that are known to confer drug resistance to the virus...
  49. ncbi JIGSAW: integration of multiple sources of evidence for gene prediction
    Jonathan E Allen
    Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, College Park, MD 20742, USA
    Bioinformatics 21:3596-603. 2005
    ..Genome annotation pipelines collect a variety of types of evidence about gene structure and synthesize the results, which can then be refined further through manual, expert curation of gene models...
  50. ncbi Bayesian spiking neurons I: inference
    Sophie Deneve
    Departement d Etudes Cognitives, Ecole Normale Superieure, College de France, 75005 Paris, France
    Neural Comput 20:91-117. 2008
    ..Spikes signal the occurrence of new information-what cannot be predicted from the past activity. As a result, firing statistics are close to Poisson, albeit providing a deterministic representation of probabilities...
  51. ncbi Broad phylogenomic sampling improves resolution of the animal tree of life
    Casey W Dunn
    Kewalo Marine Laboratory, PBRC, University of Hawaii, 41 Ahui Street, Honolulu, Hawaii 96813, USA
    Nature 452:745-9. 2008
    ..Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree...
  52. pmc Microbial gene identification using interpolated Markov models
    S L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 26:544-8. 1998
    ..As a result, GLIMMER is more flexible and more powerful than fixed-order Markov methods, which have previously been the primary content-based technique for finding genes in microbial DNA...
  53. ncbi Cost effectiveness of screening for hepatitis C virus in asymptomatic, average-risk adults
    M E Singer
    Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
    Am J Med 111:614-21. 2001
    ..5%. Screening with PCR only was never cost effective. CONCLUSIONS: This analysis does not support the widespread screening for hepatitis C among asymptomatic, average-risk adults...
  54. ncbi Large-scale copy number polymorphism in the human genome
    Jonathan Sebat
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Science 305:525-8. 2004
    ..We observed copy number variation of 70 different genes within CNP intervals, including genes involved in neurological function, regulation of cell growth, regulation of metabolism, and several genes known to be associated with disease...
  55. pmc QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data
    Stefano Colella
    Genomics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, UK
    Nucleic Acids Res 35:2013-25. 2007
    ..In conclusion, QuantiSNP is a novel algorithm for high-resolution CNV/aneuploidy detection with application to clinical genetics, cancer and disease association studies...
  56. ncbi Economic analysis of targeting chemotherapy using a 21-gene RT-PCR assay in lymph-node-negative, estrogen-receptor-positive, early-stage breast cancer
    John Hornberger
    The SPHERE Institute Acumen, LLC, Burlingame, CA 94010, USA
    Am J Manag Care 11:313-24. 2005
    ....
  57. ncbi Estimation of stage-specific fibrosis progression rates in chronic hepatitis C virus infection: a meta-analysis and meta-regression
    Hla Hla Thein
    University Health Network, Division of Clinical Decision Making and Health Care Research, Toronto, Ontario, Canada
    Hepatology 48:418-31. 2008
    ..Duration of infection was the most consistent factor significantly associated with progression of fibrosis...
  58. pmc Assessing the impact of secondary structure and solvent accessibility on protein evolution
    N Goldman
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
    Genetics 149:445-58. 1998
    ....
  59. pmc Multilocus association mapping using variable-length Markov chains
    Sharon R Browning
    Department of Statistics, The University of Auckland, Auckland 92019, New Zealand
    Am J Hum Genet 78:903-13. 2006
    ..I present analyses of two published data sets that show that this approach can have better power than single-marker tests or sliding-window haplotypic tests...
  60. pmc AUGUSTUS: ab initio prediction of alternative transcripts
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Nucleic Acids Res 34:W435-9. 2006
    ..The AUGUSTUS web interface and the downloadable open-source stand-alone program are freely available from http://augustus.gobics.de...
  61. ncbi A hidden Markov model for predicting transmembrane helices in protein sequences
    E L Sonnhammer
    National Center for Biotechnology Information, NLM NIH, Bethesda, Maryland 20894, USA
    Proc Int Conf Intell Syst Mol Biol 6:175-82. 1998
    ..The same accuracy was achieved on a larger dataset of 160 proteins. These results compare favourably with existing methods...
  62. pmc Widespread genomic signatures of natural selection in hominid evolution
    Graham McVicker
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    PLoS Genet 5:e1000471. 2009
    ..Our analyses reveal a dominant role for selection in shaping genomic diversity and divergence patterns, clarify hominid evolution, and provide a baseline for investigating specific selective events...
  63. ncbi What is a hidden Markov model?
    Sean R Eddy
    Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd, Box 8510, Saint Louis, Missouri 63108, USA
    Nat Biotechnol 22:1315-6. 2004
  64. 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...
  65. pmc Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES
    Chakra Chennubhotla
    Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
    Mol Syst Biol 2:36. 2006
    ..Comparison with collective modes deduced from normal mode analysis reveals the propensity of global hinge regions to act as messengers in the transmission of allosteric signals...
  66. pmc Neural dynamics as sampling: a model for stochastic computation in recurrent networks of spiking neurons
    Lars Buesing
    Institute for Theoretical Computer Science, Graz University of Technology, Graz, Austria
    PLoS Comput Biol 7:e1002211. 2011
    ..inconsistent with the dynamics of spiking neurons, we introduce a different approach based on non-reversible Markov chains that is able to reflect inherent temporal processes of spiking neuronal activity through a suitable choice of ..
  67. pmc Evaluation of clustering algorithms for protein-protein interaction networks
    Sylvain Brohée
    Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Universite Libre de Bruxelles, CP 263, Campus Plaine, Bd, du Triomphe, B 1050 Bruxelles, Belgium
    BMC Bioinformatics 7:488. 2006
    ..In this paper we present a comparative assessment of four algorithms: Markov Clustering (MCL), Restricted Neighborhood Search Clustering (RNSC), Super Paramagnetic Clustering (SPC), and Molecular Complex Detection (MCODE)...
  68. pmc Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model
    Thomas Mailund
    Bioinformatics Research Centre, Aarhus University, Denmark
    PLoS Genet 7:e1001319. 2011
    ..We also report a negative correlation between chromosome size and ancestral effective population size, which we interpret as a signature of recombination increasing the efficacy of selection...
  69. pmc Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    Arthur Brady
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    Nat Methods 6:673-6. 2009
    ..We also describe how combining Phymm with sequence alignment algorithms improves accuracy...
  70. pmc Accurate splice site prediction using support vector machines
    Sören Sonnenburg
    Fraunhofer Institute FIRST, Kekuléstr, 7, 12489 Berlin, Germany
    BMC Bioinformatics 8:S7. 2007
    For splice site recognition, one has to solve two classification problems: discriminating true from decoy splice sites for both acceptor and donor sites. Gene finding systems typically rely on Markov Chains to solve these tasks.
  71. ncbi Economic evaluation of sunitinib malate for the first-line treatment of metastatic renal cell carcinoma
    Edit Remak
    Health Care Analytics, United BioSource Corp, 20 Bloomsbury Square, London WC1A 2NS, United Kingdom
    J Clin Oncol 26:3995-4000. 2008
    ..To assess the cost effectiveness and cost utility of sunitinib malate as a first-line treatment in metastatic renal cell carcinoma (mRCC) compared with interferon-alfa (IFN-alpha) and interleukin-2 (IL-2) from a US societal perspective...
  72. ncbi Cost-utility of the 21-gene recurrence score assay in node-negative and node-positive breast cancer
    Nathan W D Lamond
    Department of Medicine, Dalhousie University, 454 Bethune Building 1276 South Park Street, Halifax NS, B3H 2Y9, Canada
    Breast Cancer Res Treat 133:1115-23. 2012
    ..RS-guided adjuvant therapy appears to be a cost-effective strategy in both N- and N+, endocrine-sensitive breast cancer with resultant CU ratios well below commonly quoted thresholds...
  73. ncbi Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    Gene Yeo
    Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue Building 68 223, Cambridge, MA 02319, USA
    J Comput Biol 11:377-94. 2004
    ..Our best models out-perform previous probabilistic models in the discrimination of human 5' (donor) and 3' (acceptor) splice sites from decoys. Finally, we discuss mechanistically motivated ways of comparing models...
  74. ncbi An algorithm to estimate the importance of bacterial acquisition routes in hospital settings
    M C J Bootsma
    Department of Mathematics, Utrecht University, Utrecht, Kingdom of the Netherlands
    Am J Epidemiol 166:841-51. 2007
    ..6% and 17.6% for ICU-1 and ICU-2, respectively. By use of longitudinal colonization data only, the algorithm determines the relative importance of acquisition routes taking patient dependency into account...
  75. pmc Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximation
    Daniele Linaro
    Biophysical and Electronic Engineering Department, University of Genoa, Genoa, Italy
    PLoS Comput Biol 7:e1001102. 2011
    ....
  76. pmc Effective identification of conserved pathways in biological networks using hidden Markov models
    Xiaoning Qian
    Department of Computer Science and Engineering, University of South Florida, Tampa, Florida, United States of America
    PLoS ONE 4:e8070. 2009
    ....
  77. ncbi A neural network model for generating complex birdsong syntax
    Kentaro Katahira
    Graduate School of Frontier Sciences, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8561, Japan
    Biol Cybern 97:441-8. 2007
    ..Numerical simulation showed that this model can generate first-order Markov process song sequences...
  78. 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...
  79. ncbi A taxonomy of model structures for economic evaluation of health technologies
    Alan Brennan
    School of Health and Related Research ScHARR, University of Sheffield, Sheffield, UK
    Health Econ 15:1295-310. 2006
    ..The paper provides guidance for choosing a model, based on key requirements, including output requirements, the population size, and system complexity...
  80. pmc Genomic DNA k-mer spectra: models and modalities
    Benny Chor
    School of Computer Science, Tel Aviv University, Klausner St, Ramat Aviv, Tel Aviv 39040, Israel
    Genome Biol 10:R108. 2009
    ....
  81. pmc The PANTHER database of protein families, subfamilies, functions and pathways
    Huaiyu Mi
    Computational Biology, Applied Biosystems, 850 Lincoln Center Drive, Foster City, CA 94404, USA
    Nucleic Acids Res 33:D284-8. 2005
    ..Efforts are underway to add PANTHER to the InterPro suite of databases, and to make PANTHER consistent with the PIRSF database. PANTHER is now publicly available without restriction at http://panther.appliedbiosystems.com...
  82. 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...
  83. pmc Prediction of regulatory elements in mammalian genomes using chromatin signatures
    Kyoung Jae Won
    Dept of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0359, USA
    BMC Bioinformatics 9:547. 2008
    ....
  84. pmc Using generalized ensemble simulations and Markov state models to identify conformational states
    Gregory R Bowman
    Biophysics Program, Stanford University, Stanford, CA 94305, USA
    Methods 49:197-201. 2009
    ..Besides building MSMs, the code also includes tools for model evaluation and visualization...
  85. pmc Gene identification in novel eukaryotic genomes by self-training algorithm
    Alexandre Lomsadze
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332 0230, USA
    Nucleic Acids Res 33:6494-506. 2005
    ..Thus, a self-training algorithm that had been assumed feasible only for prokaryotic genomes has now been developed for ab initio eukaryotic gene identification...
  86. pmc Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)
    Vincent A Voelz
    Department of Chemistry, Stanford University, Stanford, California 94305, USA
    J Am Chem Soc 132:1526-8. 2010
    ..We believe that using simulation data such as these to seed adaptive resampling simulations will be a promising new method for achieving statistically converged descriptions of folding landscapes at longer time scales than ever before...
  87. pmc Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data
    Jonathan E Bronson
    Department of Chemistry, Columbia University, New York, New York, USA
    Biophys J 97:3196-205. 2009
    ..Source code used in this analysis, including a graphical user interface, is available open source via http://vbFRET.sourceforge.net...
  88. 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...
  89. pmc A computational model of the human left-ventricular epicardial myocyte
    Vivek Iyer
    The Center for Cardiovascular Bioinformatics and Modeling and The Whitaker Biomedical Engineering Institute, The Johns Hopkins University School of Medicine and Whiting School of Engineering, Baltimore, Maryland 21093, USA
    Biophys J 87:1507-25. 2004
    ..The model therefore serves as a useful tool for investigating mechanisms of arrhythmia and consequences of drug-channel interactions in the human left-ventricular myocyte...
  90. pmc An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination
    Joshua S Paul
    Computer Science Division, University of California, Berkeley, California 94720, USA
    Genetics 187:1115-28. 2011
    ..The framework presented here can be adopted in a wide range of applications in population genetics, including imputing missing sequence data, estimating recombination rates, and inferring human colonization history...
  91. ncbi Divergence time and evolutionary rate estimation with multilocus data
    Jeffrey L Thorne
    Bioinformatics Research Center, Box 7566, North Carolina State University, Raleigh, North Carolina 27695 7566, USA
    Syst Biol 51:689-702. 2002
    ..The fact that evolutionary rates and times are confounded when sequence data are compared is emphasized and the importance of fossil information for disentangling rates and times is stressed...
  92. pmc Cost effectiveness of facility-based care, home-based care and mobile clinics for provision of antiretroviral therapy in Uganda
    Joseph B Babigumira
    Pharmaceutical Outcomes Research and Policy Program, Department of Pharmacy, University of Washington, Seattle, WA 98195 7630, USA
    Pharmacoeconomics 27:963-73. 2009
    ..This analysis supports the implementation of FBC for scale-up and sustainability of ART in Uganda. HBC and MCC would be competitive only if there is increased access, increased adherence or reduced cost...
  93. pmc The cost-utility of maintenance treatment with venlafaxine in patients with recurrent major depressive disorder
    P Sobocki
    Department of Learning, Informatics, Management and Ethics, Medical Management Centre, Karolinska Institutet, Stockholm, Sweden
    Int J Clin Pract 62:623-32. 2008
    ..The aim of this study was to assess the cost-utility of maintenance treatment with venlafaxine in patients with recurrent major depressive disorder, based on a recent clinical trial...
  94. pmc Learning to count: robust estimates for labeled distances between molecular sequences
    John D O'Brien
    Department of Biomathematics, University of California, Los Angeles, USA
    Mol Biol Evol 26:801-14. 2009
    ..In the final example, we demonstrate the advantages of using robust synonymous distances to alleviate the effect of convergent evolution on phylogenetic analysis of an HIV transmission network...
  95. pmc A direct optimization approach to hidden Markov modeling for single channel kinetics
    F Qin
    Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA
    Biophys J 79:1915-27. 2000
    ....
  96. pmc New protease inhibitors for the treatment of chronic hepatitis C: a cost-effectiveness analysis
    Shan Liu
    Center for Health Policy, Stanford University, CA, USA
    Ann Intern Med 156:279-90. 2012
    ..Protease inhibitors increase the effectiveness of standard therapy, but they are costly. A genetic assay may identify patients most likely to benefit from this treatment advance...
  97. pmc Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution
    Anoop Kumar
    Department of Computer Science, Tufts University, Medford, MA, USA
    Bioinformatics 26:i287-93. 2010
    ..However, these models do not capture pairwise statistical preferences of residues that are hydrogen bonded in beta-sheets. We thus explore methods for incorporating pairwise dependencies into these models...
  98. ncbi Breast cancer screening in BRCA1 mutation carriers: effectiveness of MR imaging--Markov Monte Carlo decision analysis
    Janie M Lee
    Department of Radiology, Institute for Technology Assessment, Division of Hematology Oncology, Department of Medicine, Massachusetts General Hospital, 101 Merrimac St, 10th Floor, Boston, MA 02114, USA
    Radiology 246:763-71. 2008
    ..To project intermediate and long-term clinical outcomes of magnetic resonance (MR) imaging screening for breast cancer in women with BRCA1 gene mutations...
  99. 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...
  100. pmc A fuzzy locally adaptive Bayesian segmentation approach for volume determination in PET
    Mathieu Hatt
    LATIM, INSERM, U650, 29609 Brest, France
    IEEE Trans Med Imaging 28:881-93. 2009
    ..FLAB was compared with a threshold approach as well as the previously proposed fuzzy hidden Markov chains (FHMC) and the fuzzy C-Means (FCM) algorithms...
  101. ncbi NRPSsp: non-ribosomal peptide synthase substrate predictor
    Carlos Prieto
    Institute of Biotechnology of León, INBIOTEC, Parque Cientifico de Leon, 24006 Leon, Spain
    Bioinformatics 28:426-7. 2012
    ..We have applied computational mining methods in order to build a database of NRPSs modules that bind to specific substrates. We have used this database to build a hidden Markov model predictor of substrates that bind to a given NRPS...

Research Grants64

  1. Markov Chain Monte Carlo and Exact Logistic Regression
    Cyrus Mehta; Fiscal Year: 2004
    ..The Phase 2 effort aims to incorporate this new generation of computing algorithms into future versions of LogXact. ..
  2. Statistical models to investigate long-distance QTL transcription regulation
    BARBARA ELIZABETH ENGELHARDT; Fiscal Year: 2011
    ..With the role of thousands of possibly disease-related mutations in hand, researchers can begin to piece together the mechanism of a disease and translate their findings into treatments for the disease much more quickly. ..
  3. Statistical models to investigate long-distance QTL transcription regulation
    BARBARA ELIZABETH ENGELHARDT; Fiscal Year: 2013
    ..We will make all of our methods and results publicly available. ..
  4. Methods for modeling air pollution effects on exhaled biomarkers
    SANDRAH PROCTOR ECKEL; Fiscal Year: 2013
    ..This methodological work will be generalizable to the study of determinants of a broad class of non-invasive exhaled breath biomarkers and other processes involving deterministic systems. ..
  5. The Population Genetics of Divergence
    EMANUEL HEY; Fiscal Year: 2013
    ..NopagenumberingnecessaryforAppendix.) Appendix is Included Number of publications and manuscripts accepted for publication (not to exceed 10) Other items (list): PHS 398 (Rev. 04/06) Page 4 Form Page 3 ..
  6. Discovery of exon, microRNA and clinical prognostic markers of glioblastoma survi
    SANDRA L RODRIGUEZ ZAS; Fiscal Year: 2010
    ....
  7. Evaluation of Tritium: Relative Biological Effectiveness and Cancer Mortality
    David B Richardson; Fiscal Year: 2011
    ..In addition, we will use Markov Chain Monte Carlo methods to combine current information on the RBE for tritium with our epidemiological data in order to estimate a (posterior) distribution of the RBE for tritium. ..
  8. Inferring Multiple-SNP Disease Association with DNA Resequence Data
    Rasmus Nielsen; Fiscal Year: 2010
    ..These methods will also be extended to include prior information about molecular mechanisms of gene function, where available, as well as environmental contributions to disease risk. ..
  9. Modeling Transcriptional Reprogramming by Markov Chain Monte Carlo Sampling
    Michael F Ochs; Fiscal Year: 2013
    ..This will substantially improve inference of the specific changes that drive systems out of homeostasis and of treatment response in individual cases. ..
  10. Methods for Reducing Spatial Uncertainty and Bias in Disease Surveillance
    Justin Lessler; Fiscal Year: 2013
    ....
  11. Support for the Fourth International Joint IMS-ISBA Conference
    Montserrat Fuentes; Fiscal Year: 2010
    ....
  12. Mathematical and Statistical Modeling of Mycobacterial Disease Control
    REBECCA LEE SMITH; Fiscal Year: 2013
    ..Optimal control methods will be determined using the new techniques developed, improving public health strategies for these globally important diseases. ..
  13. Sex, Drugs and Consequences of Dropout on HIV Outcomes in WIHS, MACS, and AIEDRP
    SAMANTHA MAWHINNEY-DELSON; Fiscal Year: 2012
    ..abstract_text> ..
  14. Meta-analysis of CAM therapies for HIV
    Henry S Sacks; Fiscal Year: 2013
    ..This proposal will use modern mathematical techniques to summarize the evidence about the usefulness of a variety of CAM therapies for problems common in people with HIV. ..
  15. Bayesian hierarchical nonlinear models for pharmacogenomic cytotoxicity studies
    Brooke L Fridley; Fiscal Year: 2012
    ....
  16. Integrative genomic models for analysis of pharmacogenomic studies
    Brooke L Fridley; Fiscal Year: 2010
    ..These models will also be applicable to the study of complex diseases where multiple types of genomic data are collected. ..
  17. Geographic modeling of very low birth weights around and near Texas federal super
    James A Thompson; Fiscal Year: 2010
    ..These advances include both Multivariate and hierarchical modeling. The results will be crucial for designing and justifying the locations and diseases to evaluate in a forthcoming application. ..
  18. BAYESIAN MODELING AND DATA INTEGRATION IN INFECTIOUS DISEASE PHYLODYNAMICS
    Vladimir Minin; Fiscal Year: 2013
    ..One of the main deliverables of this research will be open source software, implementing the proposed new Bayesian phylodynamic methods for integration of infectious disease sequence data with other sources of information. 1 ..
  19. A New Approach to Phylogenetic Analysis Using Structural Information
    Abel Rodriguez; Fiscal Year: 2013
    ..4] To train interdisciplinary scientists capable of using sophisticated statistical methods to solve complex problems in evolutionary biology. ..
  20. An Open-Source Algorithm Isolating Overlapping Signatures in Microarray Data
    Michael Ochs; Fiscal Year: 2009
    ..Such information is vital to understanding human disease and the response to therapy, especially with new molecularly targeted therapeutics. ..
  21. Fathering Practices and Positive Development among African American Adolescents
    SHAUNA MICHELLE COOPER; Fiscal Year: 2013
    ....
  22. METHODS FOR THE GENETIC EPIDEMIOLOGY OF COMPLEX TRAITS
    ELIZABETH ALISON THOMPSON; Fiscal Year: 2013
    ..Finally, software implementing these methods will be developed, documented and released. ..
  23. Statistical &Computational Tools for Reconstruction of Gene Regulatory Networks
    Peter Salzman; Fiscal Year: 2012
    ..The ultimate long term goal of this research is directed at understanding the basis of oncogenes cooperation and identification of malignant pathways. These advances will have direct effect on identification of targets for cancer cure. ..
  24. A Novel Bayesian Model Averaging Approach for Genome Wide Association Studies
    Michael D Swartz; Fiscal Year: 2010
    ....
  25. A Computational Genotyping System for Improved Influenza Surveillance
    Guoqing Lu; Fiscal Year: 2010
    ..With the genotyping database system, newly emerging influenza A viral genotypes can be identified in a timely and cost-effective manner. ..
  26. Interval Timing and Motor Programming by Cortico-Striatal Ensembles
    Miguel A L Nicolelis; Fiscal Year: 2013
    ..We will use neural decoding algorithms (Wiener filter, Kalman filter, discriminant analysis and Markov chains) to extract both temporal and spatial characteristics of motor patterns from large populations of cortical and ..
  27. Bayesian Variable Selection in Generalized Linear Models with Missing Varibles
    Xiaowei Yang; Fiscal Year: 2013
    ..Development of these procedures and contribution of the software to statisticians and researchers in medical research would significantly improve the quality of evaluation of important and clinically relevant data. ..
  28. Integrating Social, Behavioral &Preventive Sciences to Reduce Children's Caries
    Thomas W Valente; Fiscal Year: 2012
    ..The proposed program therefore coalesces an environment with high need, and investigators from institutions with extraordinary depth. ..
  29. Statistical Algorithms for Valid Inferences in Genomic Data
    George Casella; Fiscal Year: 2010
    ..The proposed cluster test can provide a screening tool to identify data with possible genetic associations, again leading to information on genetic associations. ..
  30. Integrated Prediction of Protein Struture at 1D, 2D and 3D Levels
    Jianlin Cheng; Fiscal Year: 2013
    ..These tools and web services will be useful for protein structure prediction, structure determination, functional analysis, protein engineering, protein mutagenesis analysis, and protein design. ..
  31. Population genetics of deleterious polymorphism in human populations
    Kirk Lohmueller; Fiscal Year: 2009
    ..This research will provide novel insights regarding human evolutionary history which are critical to the design and interpretation studies of genetic variation and risk to common disease. ..
  32. Software for cost-benefit analysis of LBP interventions
    Nancy Nelson; Fiscal Year: 2006
    ..The software will encourage adoption of methods for preventing occupational low back disorders. [unreadable] [unreadable] [unreadable] [unreadable]..
  33. GENETIC EPIDEMIOLOGY OF ELEVATED APOB LEVEL
    GAIL JARVIK; Fiscal Year: 1999
    ..Aim 5. To refine the position of the apolipoprotein B elevating level gene(s). Aim 6. Subsequent work to identify the locus if positive evidence of linkage to a strong candidate gene region is obtained. ..
  34. Causal Dynamic Predictive Models for Cross Sectional Observational Data
    Siamak Noorbaloochi; Fiscal Year: 2013
    ..Over the course of numerous such research studies the cumulative impact of this research could be substantial. ..
  35. Mimimal-Perturbation Dynamic Control of the Melanoma Gene Regulatory Network
    Dan Schonfeld; Fiscal Year: 2013
    ..a new mathematical framework for the solution of the inverse perturbation problem for ergodic and non-ergodic Markov chains;i.e...
  36. Combined-survey estimation and Markov-chain simulation of childhood obesity
    Michael S Rendall; Fiscal Year: 2012
    ..Estimates of the impacts on childhood obesity of biological, behavioral, and socio-economic variables, and of potential policy interventions, are derived from simulated childhood life paths. ..
  37. Combined-survey estimation and Markov-chain simulation of childhood obesity
    Michael S Rendall; Fiscal Year: 2010
    ..Estimates of the impacts on childhood obesity of biological, behavioral, and socio-economic variables, and of potential policy interventions, are derived from simulated childhood life paths. ..
  38. Mathematical and Statistical Models for Nucleosome
    Ji Ping Wang; Fiscal Year: 2010
    ..5) Automate the developed tools and algorithms. ..
  39. Modifier Genes of Familial Hypertrophic Cardiomyopathy
    ALI MARIAN; Fiscal Year: 2005
    ..Treatment found to induce regression of hypertrophy in the rabbit with FHCM will most likely also induce regression of hypertrophy in human FHCM and hypertrophy due to other cardiac causes. ..
  40. Accurate Models for Predicting Radiation-Induced Injury
    Shiva Das; Fiscal Year: 2009
    ..They will be made publicly available via the Internet. The overall impact of this work will be to facilitate significant reduction in thoracic radiotherapy-induced injury via accurate prediction. ..
  41. MODELING THE NATURAL HISTORY OF DIABETIC RETINOPATHY
    Bruce Craig; Fiscal Year: 1999
    ..We will investigate several difference screening and treatment programs for each type of diabetes. ..
  42. Active Life Expectancy by Sex, Race-Ethnicity, Education
    April Greek; Fiscal Year: 2004
    ..With the sample including data for individuals at the tip of the Baby Boom generation (born 1947 and earlier), the information derived from the proposed study will help to plan for the pending increases in the older population. ..
  43. Modeling Human Exposure-Dose Relationships:1,3-Butadiene
    Thomas Smith; Fiscal Year: 2005
    ..Similarly differences in the formation and detoxification rates will be tested for associations with subject characteristics, such as genotypes and dietary antioxidants. Findings will be important for US risk assessments...
  44. MCMSki II: Markov Chain Monte Carlo in Theory and Practice
    Bradley Carlin; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  45. The use of recombining genetic markers for demographic inference
    John Pool; Fiscal Year: 2009
    ....
  46. A Scoring Method for MCMC Linkage Analysis
    EDWARD DAW; Fiscal Year: 2004
    ..These guidelines will be used in future studies, which we believe will lead to the identification of additional disease-related genes. ..
  47. NONPARAMETRIC ANALYSIS OF CENSORED DATA
    Martin Tanner; Fiscal Year: 2000
    ..This methodology will also be applied to a variety of models in the generalized linear model family for which no competing exact or higher-order methods are available. ..
  48. Modeling HIV and STD in Drug User and Social Networks
    WANDA MORRIS; Fiscal Year: 2005
    ..It will enable public health professionals to identify population-level prevention strategies that make a network less vulnerable to spread. And it will identify the type of network data needed to inform such efforts. ..
  49. Computational Statistics for Model-Based Genomic Data Integration
    Michael A Newton; Fiscal Year: 2013
    ..If successful, the project will enable biomedical scientists to more effectively express the functional content of their experimental results, and it will further the information science of genomic data integration. ..
  50. Quantifying HIV Transmission Risk in Sex/Drug Networks
    W Morris; Fiscal Year: 2006
    ..It will enable public health professionals to identify population-level prevention strategies that make a network less vulnerable to spread. Moreover, it will identify the type of network data needed to inform such efforts. ..
  51. EFFECTS OF RETIREMENT AND LIFE CHANGES ON HEALTH
    THOMAS WAN; Fiscal Year: 1980
    ..Finally, we will use a Markov Chain model to construct transition probabilities of the changes in functional capacities in order to estimate the need for care. ..
  52. MAPPING COMPLEX DISEASES USING MARKOV CHAIN MONTE CARLO
    Simon Heath; Fiscal Year: 2001
    ..Methods for checking the fit of models to data will also be investigated. ..
  53. Markov Chain Monte Carlo and Exact Logistic Regression
    Cyrus Mehta; Fiscal Year: 2001
    ..The new generation of hybrid network-MCMC algorithms will handle substantially larger problems that nevertheless need exact inference. The commercial potential is considerable since such data sets are common in scientific studies. ..
  54. STATISTICAL METHODS IN AIDS RESEARCH
    Jeremy Taylor; Fiscal Year: 1999
    ..The methods in both projects will be evaluated and compared to other approaches on simulated, clinical trial and Multicenter AIDS Cohort Study (MACS) data. The methodology has wide applicability to both AIDS and non-AIDS studies. ..
  55. Building a Latino admixture map & pilot study to find Type 2 Diabetes risk
    David Reich; Fiscal Year: 2007
    ..The study will also enable larger admixture mapping studies with many thousands of patients with Type 2 Diabetes, which we would like to pursue both in U.S. Latino and in Latin American populations. [unreadable] [unreadable] [unreadable]..
  56. NONPARAMETRIC ANALYSIS OF MULTIPLE CURVES IN CANCER
    MARY LINDSTROM; Fiscal Year: 2000
    ..The applicability of theoretical results to small samples will be checked by simulation and all successful algorithms will be implemented in the S statistical language and made publicly available. ..
  57. Selection and Association in Coalescent Genealogies
    MARY KUHNER; Fiscal Year: 2006
    ..We will create freely distributed software implementing these methods and will test them using real and simulated data. ..
  58. STATISTICAL ANALYSIS OF HUMAN CIRCADIAN RHYTHMS
    Emery Brown; Fiscal Year: 2001
    ....
  59. Bayesian Methods for Sample Size Calculation
    KELLY ZOU; Fiscal Year: 2003
    ..Our approach may allow for better evaluation of outcomes (e.g., effectiveness, quality, access, cost of health services). The methodology is applicable to the design of similar health care quality studies. ..
  60. SOFTWARE FOR MISSING DATA IN CANCER CLINICAL TRIALS
    Cyrus Mehta; Fiscal Year: 1999
    ..abstract_text> ..
  61. Predicting bone formation induced by mechanical loading using agent based models
    Sundar Srinivasan; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  62. STATISTICAL METHODS FOR MOLECULAR CANCER DATA
    Michael Newton; Fiscal Year: 1999
    ..Computer simulation of the model will be useful both to study bias and variance properties of the proposed methods and as the basis for power calculations to design marker studies. ..
  63. MODELS FOR THE GENETIC EPIDEMIOLOGY OF CHRONIC DISEASE
    SANDRA HASSTEDT; Fiscal Year: 2009
    ..In addition, this application proposes to implement changes to increase computational speed, allow data exploration, and facilitate data handling and analysis, while continuing to distribute and support PAP. ..
  64. Statistical & Computational Tools for Reconstruction of Gene Regulatory Networks
    Peter Salzman; Fiscal Year: 2007
    ..These advances will have direct effect on identification of targets for cancer cure. ..