Genomes and Genes
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.
Publications334 found, 100 shown here
- Protein homology detection by HMM-HMM comparisonJohannes 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...
- Predicting transmembrane protein topology with a hidden Markov model: application to complete genomesA 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/...
- The HHpred interactive server for protein homology detection and structure predictionJohannes 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...
- Improved prediction of signal peptides: SignalP 3.0Jannick 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..
- Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structureJ 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...
- Profile hidden Markov modelsS 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...
- Gene prediction with a hidden Markov model and a new intron submodelMario 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...
- TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-findersW 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...
- Bayesian selection of continuous-time Markov chain evolutionary modelsM A Suchard
Department of Biomathematics, UCLA School of Medicine, Los Angeles, CA 90095-7088, USA
Mol Biol Evol 18:1001-13. 2001....
- GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regionsJ 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...
- The TIGRFAMs database of protein familiesDaniel 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...
- PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping dataKai 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...
- Improved microbial gene identification with GLIMMERA 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...
- Bayesian coalescent inference of past population dynamics from molecular sequencesA J Drummond
Department of Zoology, University of Oxford, Oxford, United Kingdom
Mol Biol Evol 22:1185-92. 2005....
- PANTHER: a library of protein families and subfamilies indexed by functionPaul 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...
- Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence dataAlexei 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...
- Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple lociBruce 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...
- Hidden Markov model speed heuristic and iterative HMM search procedureL 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...
- An introduction to Markov modelling for economic evaluationA 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...
- The HMMTOP transmembrane topology prediction serverG 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...
- Using Bayesian networks to analyze expression dataN 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)...
- Improved splice site detection in GenieM 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...
- Discovery and characterization of chromatin states for systematic annotation of the human genomeJason 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...
- AUGUSTUS: a web server for gene finding in eukaryotesMario 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...
- Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVsJoshua 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...
- Strong association of de novo copy number mutations with autismJonathan 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...
- Relaxed phylogenetics and dating with confidenceAlexei 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...
- Principles of good practice for decision analytic modeling in health-care evaluation: report of the ISPOR Task Force on Good Research Practices--Modeling StudiesMilton 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...
- Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sourcesMario 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...
- Analysis of single-molecule FRET trajectories using hidden Markov modelingSean 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...
- Modeling compositional heterogeneityPeter 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...
- A Markov random field model for network-based analysis of genomic dataZhi 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...
- Counting labeled transitions in continuous-time Markov models of evolutionVladimir 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...
- MrBayes on a graphics processing unitJianfu 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...
- Identifying dispersed epigenomic domains from ChIP-Seq dataQiang 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...
- An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq dataHan 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...
- Improving marginal likelihood estimation for Bayesian phylogenetic model selectionWangang 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...
- Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inferenceGautam 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...
- HMM Logos for visualization of protein familiesBenjamin 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...
- Hidden Markov modelsS 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...
- Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamicsVladimir 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...
- Bayesian phylogenetic model selection using reversible jump Markov chain Monte CarloJohn 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....
- The MAPPER database: a multi-genome catalog of putative transcription factor binding sitesVoichita 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...
- Integrated study of copy number states and genotype calls using high-density SNP arraysWei 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...
- Markov chain Monte Carlo without likelihoodsPaul 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...
- The fine-scale structure of recombination rate variation in the human genomeGilean 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...
- Bayesian estimation of ancestral character states on phylogeniesMark 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...
- A combined empirical and mechanistic codon modelAdi 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...
- JIGSAW: integration of multiple sources of evidence for gene predictionJonathan 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...
- Bayesian spiking neurons I: inferenceSophie 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...
- Broad phylogenomic sampling improves resolution of the animal tree of lifeCasey 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...
- Microbial gene identification using interpolated Markov modelsS 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...
- Cost effectiveness of screening for hepatitis C virus in asymptomatic, average-risk adultsM 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...
- Large-scale copy number polymorphism in the human genomeJonathan 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...
- QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping dataStefano 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...
- Economic analysis of targeting chemotherapy using a 21-gene RT-PCR assay in lymph-node-negative, estrogen-receptor-positive, early-stage breast cancerJohn Hornberger
The SPHERE Institute Acumen, LLC, Burlingame, CA 94010, USA
Am J Manag Care 11:313-24. 2005....
- Estimation of stage-specific fibrosis progression rates in chronic hepatitis C virus infection: a meta-analysis and meta-regressionHla 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...
- Assessing the impact of secondary structure and solvent accessibility on protein evolutionN Goldman
Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
Genetics 149:445-58. 1998....
- Multilocus association mapping using variable-length Markov chainsSharon 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...
- AUGUSTUS: ab initio prediction of alternative transcriptsMario 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...
- A hidden Markov model for predicting transmembrane helices in protein sequencesE 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...
- Widespread genomic signatures of natural selection in hominid evolutionGraham 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...
- 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
- Bayesian phylogenetic analysis of combined dataJohan 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...
- Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroESChakra 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...
- Neural dynamics as sampling: a model for stochastic computation in recurrent networks of spiking neuronsLars 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 ..
- Evaluation of clustering algorithms for protein-protein interaction networksSylvain 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)...
- Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov modelThomas 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...
- Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov modelsArthur 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...
- Accurate splice site prediction using support vector machinesSören Sonnenburg
Fraunhofer Institute FIRST, Kekuléstr, 7, 12489 Berlin, Germany
BMC Bioinformatics 8:S7. 2007For 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.
- Economic evaluation of sunitinib malate for the first-line treatment of metastatic renal cell carcinomaEdit 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...
- Cost-utility of the 21-gene recurrence score assay in node-negative and node-positive breast cancerNathan 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...
- Maximum entropy modeling of short sequence motifs with applications to RNA splicing signalsGene 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...
- An algorithm to estimate the importance of bacterial acquisition routes in hospital settingsM 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...
- Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximationDaniele Linaro
Biophysical and Electronic Engineering Department, University of Genoa, Genoa, Italy
PLoS Comput Biol 7:e1001102. 2011....
- Effective identification of conserved pathways in biological networks using hidden Markov modelsXiaoning Qian
Department of Computer Science and Engineering, University of South Florida, Tampa, Florida, United States of America
PLoS ONE 4:e8070. 2009....
- A neural network model for generating complex birdsong syntaxKentaro 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...
- Bayesian phylogenetic inference via Markov chain Monte Carlo methodsB 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...
- A taxonomy of model structures for economic evaluation of health technologiesAlan 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...
- Genomic DNA k-mer spectra: models and modalitiesBenny Chor
School of Computer Science, Tel Aviv University, Klausner St, Ramat Aviv, Tel Aviv 39040, Israel
Genome Biol 10:R108. 2009....
- The PANTHER database of protein families, subfamilies, functions and pathwaysHuaiyu 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...
- A compound poisson process for relaxing the molecular clockJ 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...
- Prediction of regulatory elements in mammalian genomes using chromatin signaturesKyoung 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....
- Using generalized ensemble simulations and Markov state models to identify conformational statesGregory 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...
- Gene identification in novel eukaryotic genomes by self-training algorithmAlexandre 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...
- 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...
- Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET dataJonathan 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...
- Choosing among partition models in Bayesian phylogeneticsYu 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...
- A computational model of the human left-ventricular epicardial myocyteVivek 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...
- An accurate sequentially Markov conditional sampling distribution for the coalescent with recombinationJoshua 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...
- Divergence time and evolutionary rate estimation with multilocus dataJeffrey 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...
- Cost effectiveness of facility-based care, home-based care and mobile clinics for provision of antiretroviral therapy in UgandaJoseph 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...
- The cost-utility of maintenance treatment with venlafaxine in patients with recurrent major depressive disorderP 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...
- Learning to count: robust estimates for labeled distances between molecular sequencesJohn 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...
- A direct optimization approach to hidden Markov modeling for single channel kineticsF Qin
Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA
Biophys J 79:1915-27. 2000....
- New protease inhibitors for the treatment of chronic hepatitis C: a cost-effectiveness analysisShan 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...
- Recognition of beta-structural motifs using hidden Markov models trained with simulated evolutionAnoop 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...
- Breast cancer screening in BRCA1 mutation carriers: effectiveness of MR imaging--Markov Monte Carlo decision analysisJanie 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...
- Bayesian inference of biochemical kinetic parameters using the linear noise approximationMichał 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...
- A fuzzy locally adaptive Bayesian segmentation approach for volume determination in PETMathieu 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...
- NRPSsp: non-ribosomal peptide synthase substrate predictorCarlos 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...
- Markov Chain Monte Carlo and Exact Logistic RegressionCyrus Mehta; Fiscal Year: 2004..The Phase 2 effort aims to incorporate this new generation of computing algorithms into future versions of LogXact. ..
- Statistical models to investigate long-distance QTL transcription regulationBARBARA 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. ..
- Statistical models to investigate long-distance QTL transcription regulationBARBARA ELIZABETH ENGELHARDT; Fiscal Year: 2013..We will make all of our methods and results publicly available. ..
- Methods for modeling air pollution effects on exhaled biomarkersSANDRAH 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. ..
- The Population Genetics of DivergenceEMANUEL 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 ..
- Discovery of exon, microRNA and clinical prognostic markers of glioblastoma surviSANDRA L RODRIGUEZ ZAS; Fiscal Year: 2010....
- Evaluation of Tritium: Relative Biological Effectiveness and Cancer MortalityDavid 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. ..
- Inferring Multiple-SNP Disease Association with DNA Resequence DataRasmus 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. ..
- Modeling Transcriptional Reprogramming by Markov Chain Monte Carlo SamplingMichael 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. ..
- Methods for Reducing Spatial Uncertainty and Bias in Disease SurveillanceJustin Lessler; Fiscal Year: 2013....
- Support for the Fourth International Joint IMS-ISBA ConferenceMontserrat Fuentes; Fiscal Year: 2010....
- Mathematical and Statistical Modeling of Mycobacterial Disease ControlREBECCA 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. ..
- Sex, Drugs and Consequences of Dropout on HIV Outcomes in WIHS, MACS, and AIEDRPSAMANTHA MAWHINNEY-DELSON; Fiscal Year: 2012..abstract_text> ..
- Meta-analysis of CAM therapies for HIVHenry 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. ..
- Bayesian hierarchical nonlinear models for pharmacogenomic cytotoxicity studiesBrooke L Fridley; Fiscal Year: 2012....
- Integrative genomic models for analysis of pharmacogenomic studiesBrooke 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. ..
- Geographic modeling of very low birth weights around and near Texas federal superJames 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. ..
- BAYESIAN MODELING AND DATA INTEGRATION IN INFECTIOUS DISEASE PHYLODYNAMICSVladimir 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 ..
- A New Approach to Phylogenetic Analysis Using Structural InformationAbel Rodriguez; Fiscal Year: 2013..4] To train interdisciplinary scientists capable of using sophisticated statistical methods to solve complex problems in evolutionary biology. ..
- An Open-Source Algorithm Isolating Overlapping Signatures in Microarray DataMichael Ochs; Fiscal Year: 2009..Such information is vital to understanding human disease and the response to therapy, especially with new molecularly targeted therapeutics. ..
- Fathering Practices and Positive Development among African American AdolescentsSHAUNA MICHELLE COOPER; Fiscal Year: 2013....
- METHODS FOR THE GENETIC EPIDEMIOLOGY OF COMPLEX TRAITSELIZABETH ALISON THOMPSON; Fiscal Year: 2013..Finally, software implementing these methods will be developed, documented and released. ..
- Statistical &Computational Tools for Reconstruction of Gene Regulatory NetworksPeter 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. ..
- A Novel Bayesian Model Averaging Approach for Genome Wide Association StudiesMichael D Swartz; Fiscal Year: 2010....
- A Computational Genotyping System for Improved Influenza SurveillanceGuoqing 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. ..
- Interval Timing and Motor Programming by Cortico-Striatal EnsemblesMiguel 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 ..
- Bayesian Variable Selection in Generalized Linear Models with Missing VariblesXiaowei 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. ..
- Integrating Social, Behavioral &Preventive Sciences to Reduce Children's CariesThomas W Valente; Fiscal Year: 2012..The proposed program therefore coalesces an environment with high need, and investigators from institutions with extraordinary depth. ..
- Statistical Algorithms for Valid Inferences in Genomic DataGeorge 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. ..
- Integrated Prediction of Protein Struture at 1D, 2D and 3D LevelsJianlin 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. ..
- Population genetics of deleterious polymorphism in human populationsKirk 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. ..
- Software for cost-benefit analysis of LBP interventionsNancy Nelson; Fiscal Year: 2006..The software will encourage adoption of methods for preventing occupational low back disorders. [unreadable] [unreadable] [unreadable] [unreadable]..
- GENETIC EPIDEMIOLOGY OF ELEVATED APOB LEVELGAIL 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. ..
- Causal Dynamic Predictive Models for Cross Sectional Observational DataSiamak Noorbaloochi; Fiscal Year: 2013..Over the course of numerous such research studies the cumulative impact of this research could be substantial. ..
- Mimimal-Perturbation Dynamic Control of the Melanoma Gene Regulatory NetworkDan 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...
- Combined-survey estimation and Markov-chain simulation of childhood obesityMichael 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. ..
- Combined-survey estimation and Markov-chain simulation of childhood obesityMichael 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. ..
- Mathematical and Statistical Models for NucleosomeJi Ping Wang; Fiscal Year: 2010..5) Automate the developed tools and algorithms. ..
- Modifier Genes of Familial Hypertrophic CardiomyopathyALI 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. ..
- Accurate Models for Predicting Radiation-Induced InjuryShiva 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. ..
- MODELING THE NATURAL HISTORY OF DIABETIC RETINOPATHYBruce Craig; Fiscal Year: 1999..We will investigate several difference screening and treatment programs for each type of diabetes. ..
- Active Life Expectancy by Sex, Race-Ethnicity, EducationApril 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. ..
- Modeling Human Exposure-Dose Relationships:1,3-ButadieneThomas 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...
- MCMSki II: Markov Chain Monte Carlo in Theory and PracticeBradley Carlin; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- The use of recombining genetic markers for demographic inferenceJohn Pool; Fiscal Year: 2009....
- A Scoring Method for MCMC Linkage AnalysisEDWARD 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. ..
- NONPARAMETRIC ANALYSIS OF CENSORED DATAMartin 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. ..
- Modeling HIV and STD in Drug User and Social NetworksWANDA 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. ..
- Computational Statistics for Model-Based Genomic Data IntegrationMichael 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. ..
- Quantifying HIV Transmission Risk in Sex/Drug NetworksW 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. ..
- EFFECTS OF RETIREMENT AND LIFE CHANGES ON HEALTHTHOMAS 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. ..
- MAPPING COMPLEX DISEASES USING MARKOV CHAIN MONTE CARLOSimon Heath; Fiscal Year: 2001..Methods for checking the fit of models to data will also be investigated. ..
- Markov Chain Monte Carlo and Exact Logistic RegressionCyrus 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. ..
- STATISTICAL METHODS IN AIDS RESEARCHJeremy 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. ..
- Building a Latino admixture map & pilot study to find Type 2 Diabetes riskDavid 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]..
- NONPARAMETRIC ANALYSIS OF MULTIPLE CURVES IN CANCERMARY 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. ..
- Selection and Association in Coalescent GenealogiesMARY KUHNER; Fiscal Year: 2006..We will create freely distributed software implementing these methods and will test them using real and simulated data. ..
- STATISTICAL ANALYSIS OF HUMAN CIRCADIAN RHYTHMSEmery Brown; Fiscal Year: 2001....
- Bayesian Methods for Sample Size CalculationKELLY 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. ..
- SOFTWARE FOR MISSING DATA IN CANCER CLINICAL TRIALSCyrus Mehta; Fiscal Year: 1999..abstract_text> ..
- Predicting bone formation induced by mechanical loading using agent based modelsSundar Srinivasan; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- STATISTICAL METHODS FOR MOLECULAR CANCER DATAMichael 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. ..
- MODELS FOR THE GENETIC EPIDEMIOLOGY OF CHRONIC DISEASESANDRA 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. ..
- Statistical & Computational Tools for Reconstruction of Gene Regulatory NetworksPeter Salzman; Fiscal Year: 2007..These advances will have direct effect on identification of targets for cancer cure. ..