Marek Kimmel

Summary

Affiliation: Rice University
Country: USA

Publications

  1. pmc The dependence of expression of NF-κB-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3' UTR
    Marta Iwanaszko
    Institute of Automatic Control, Silesian University of Technology, Akademicka 16, Gliwice, Poland
    BMC Genomics 13:182. 2012
  2. pmc Adjusting a cancer mortality-prediction model for disease status-related eligibility criteria
    Millennia Foy
    Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 1825 Pressler St, Houston, TX 77030, USA
    BMC Med Res Methodol 11:64. 2011
  3. pmc Single TNFalpha trimers mediating NF-kappaB activation: stochastic robustness of NF-kappaB signaling
    Tomasz Lipniacki
    Institute of Fundamental Technological Research, Swietokrzyska 21, 00 049 Warsaw, Poland
    BMC Bioinformatics 8:376. 2007
  4. pmc Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
    David M Kristensen
    Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Bioinformatics 9:17. 2008
  5. pmc Modeling neutral evolution of Alu elements using a branching process
    Marek Kimmel
    Department of Statistics, Rice University, Houston, TX 77005, USA
    BMC Genomics 11:S11. 2010
  6. ncbi request reprint Stochastic search gene suggestion: a Bayesian hierarchical model for gene mapping
    Michael D Swartz
    Department of Statistics, Texas A and M University, 3143 TAMU, College Station, Texas 77843, USA
    Biometrics 62:495-503. 2006
  7. ncbi request reprint Deterministic and stochastic models of NFkappaB pathway
    Tomasz Lipniacki
    Polish Academy of Sciences, Institute of Fundamental Technological Research, Swietokrzyska 21, 00 049, Warsaw, Poland
    Cardiovasc Toxicol 7:215-34. 2007
  8. doi request reprint A robust estimator of mutation rates
    Xiaowei Wu
    Department of Statistics, Rice University, Houston, TX 77005, USA
    Mutat Res 661:101-9. 2009
  9. pmc Modeling excess lung cancer risk among screened arm participants in the Mayo Lung Project
    Deborah L Goldwasser
    Department of Statistics, Rice University, Houston, TX 77005, USA
    Cancer 116:122-31. 2010
  10. ncbi request reprint A simple model of linkage disequilibrium and genetic drift in human genomic SNPs: importance of demography and SNP age
    Joanna Polanska
    System Engineering Group, Silesian University of Technology, Gliwice, Poland
    Hum Hered 60:181-95. 2005

Collaborators

Detail Information

Publications36

  1. pmc The dependence of expression of NF-κB-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3' UTR
    Marta Iwanaszko
    Institute of Automatic Control, Silesian University of Technology, Akademicka 16, Gliwice, Poland
    BMC Genomics 13:182. 2012
    ..It is not obvious what mechanism is responsible for segregation of the genes' timing of transcriptional response...
  2. pmc Adjusting a cancer mortality-prediction model for disease status-related eligibility criteria
    Millennia Foy
    Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 1825 Pressler St, Houston, TX 77030, USA
    BMC Med Res Methodol 11:64. 2011
    ....
  3. pmc Single TNFalpha trimers mediating NF-kappaB activation: stochastic robustness of NF-kappaB signaling
    Tomasz Lipniacki
    Institute of Fundamental Technological Research, Swietokrzyska 21, 00 049 Warsaw, Poland
    BMC Bioinformatics 8:376. 2007
    ..The NF-kappaB regulatory network controls innate immune response by transducing variety of pathogen-derived and cytokine stimuli into well defined single-cell gene regulatory events...
  4. pmc Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
    David M Kristensen
    Department of Molecular and Human Genetics, Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Bioinformatics 9:17. 2008
    ..Since experimentally determined functional sites are not common enough to define 3D templates on a large scale, this work tests a computational strategy to select relevant residues for 3D templates...
  5. pmc Modeling neutral evolution of Alu elements using a branching process
    Marek Kimmel
    Department of Statistics, Rice University, Houston, TX 77005, USA
    BMC Genomics 11:S11. 2010
    ..Since Alu elements substantially impact the shape of our genome, there is a need for modeling the amplification, mutation and selection forces of these elements...
  6. ncbi request reprint Stochastic search gene suggestion: a Bayesian hierarchical model for gene mapping
    Michael D Swartz
    Department of Statistics, Texas A and M University, 3143 TAMU, College Station, Texas 77843, USA
    Biometrics 62:495-503. 2006
    ..Our software is available on the website http://www.epigenetic.org/Linkage/ssgs-public/...
  7. ncbi request reprint Deterministic and stochastic models of NFkappaB pathway
    Tomasz Lipniacki
    Polish Academy of Sciences, Institute of Fundamental Technological Research, Swietokrzyska 21, 00 049, Warsaw, Poland
    Cardiovasc Toxicol 7:215-34. 2007
    ..This high cell-to-cell variability can be one of the weapons of the immune defense. Such non-deterministic defense may be harder to overcome by relatively simple programs coded in viruses and other pathogens...
  8. doi request reprint A robust estimator of mutation rates
    Xiaowei Wu
    Department of Statistics, Rice University, Houston, TX 77005, USA
    Mutat Res 661:101-9. 2009
    ..The impact of these effects on the practice of fluctuation analysis is discussed...
  9. pmc Modeling excess lung cancer risk among screened arm participants in the Mayo Lung Project
    Deborah L Goldwasser
    Department of Statistics, Rice University, Houston, TX 77005, USA
    Cancer 116:122-31. 2010
    ..The authors of this report examined the consistency of the MLP data with a modified 2-stage clonal expansion (TSCE) model of excess LC risk...
  10. ncbi request reprint A simple model of linkage disequilibrium and genetic drift in human genomic SNPs: importance of demography and SNP age
    Joanna Polanska
    System Engineering Group, Silesian University of Technology, Gliwice, Poland
    Hum Hered 60:181-95. 2005
    ..Polymorphisms at loci implicated in human disease, seem to be younger than average. Our results supplement the conclusions originally obtained by Reich and co-workers for the same set of data...
  11. pmc Haplotype and linkage disequilibrium architecture for human cancer-associated genes
    Penelope E Bonnen
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Genome Res 12:1846-53. 2002
    ..As a result, a low marker density should be adequate to identify haplotypes that represent the common variation at a locus, thereby decreasing costs and increasing efficacy of association studies...
  12. ncbi request reprint Transcriptional stochasticity in gene expression
    Tomasz Lipniacki
    Institute of Fundamental Technological Research, Swietokrzyska 21, 00 049 Warsaw, Poland
    J Theor Biol 238:348-67. 2006
    ..The resulting PDEs are approximated by a system of many ordinary equations, which are then numerically solved...
  13. ncbi request reprint simuPOP: a forward-time population genetics simulation environment
    Bo Peng
    Department of Statistics, Rice University, Houston, TX 77005, USA
    Bioinformatics 21:3686-7. 2005
    ....
  14. ncbi request reprint Interactions of neanderthals and modern humans: what can be inferred from mitochondrial DNA?
    Krzysztof A Cyran
    Institute of Informatics, Silesian University of Technology, Akademicka 16, 44 100 Gliwice, Poland
    Math Biosci Eng 2:487-98. 2005
    ..sapiens fossils. As a result, a maximum value of 15% admixture is obtained. This estimate is discussed in the context of its consequences for the two competing theories of modern human origin...
  15. ncbi request reprint Stochastic effects of multiple regulators on expression profiles in eukaryotes
    Pawel Paszek
    Department of Statistics, Rice University, 6100 Main Street, MS 138, Houston, TX 77005, USA
    J Theor Biol 233:423-33. 2005
    ..Comparison between these two modes of description reveals that single cells behave qualitatively different from the cell population. This analysis provides insights useful for understanding of microarray experiments...
  16. ncbi request reprint Mathematical model of NF-kappaB regulatory module
    Tomasz Lipniacki
    Institute of Fundamental Technological Research, Warsaw, Poland
    J Theor Biol 228:195-215. 2004
    ..The model allows detailed analysis of kinetics of the involved proteins and their complexes and gives the predictions of the possible responses of whole kinetics to the change in the level of a given activator or inhibitor...
  17. ncbi request reprint A note on estimation of dynamics of multiple gene expression based on singular value decomposition
    Krzysztof Simek
    Department of Statistics, Rice University, Mail Stop 138, 6100 Main Street, P O 1892, Houston, TX 77005, USA
    Math Biosci 182:183-99. 2003
    ..Summarizing we point out that approximation of multiple gene expression data preceded by SVD provides some insight into the dynamics but may also lead to unexpected difficulties, like overfitting problems...
  18. ncbi request reprint The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs
    Brian Y Chen
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    J Comput Biol 14:791-816. 2007
    ..In exhaustive comparison of all possible motifs based on the active sites of 10 well-studied proteins, we observed that optimized motifs were among the most sensitive and specific...
  19. pmc Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity
    David M Kristensen
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
    Protein Sci 15:1530-6. 2006
    ....
  20. pmc Complex SNP-based haplotypes in three human helicases: implications for cancer association studies
    Dimitra Trikka
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Genome Res 12:627-39. 2002
    ....
  21. pmc Simulations provide support for the common disease-common variant hypothesis
    Bo Peng
    Department of Statistics, Rice University, Houston, Texas 77005, USA
    Genetics 175:763-76. 2007
    ..We discuss the implications for mapping of complex diseases...
  22. ncbi request reprint An accurate, sensitive, and scalable method to identify functional sites in protein structures
    Hui Yao
    Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza T921, Houston, TX 77030, USA
    J Mol Biol 326:255-61. 2003
    ..This should help focus structure-function studies, rational drug design, protein engineering, and functional annotation to the relevant regions of a protein...
  23. ncbi request reprint Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction
    Brian Y Chen
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    J Bioinform Comput Biol 5:353-82. 2007
    ..While the optimal placement of C-spheres remains a difficult open problem, we compared two logical placement strategies to better understand C-sphere placement...
  24. ncbi request reprint Strength of the purifying selection against different categories of the point mutations in the coding regions of the human genome
    Ivan P Gorlov
    Department of Epidemiology, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Hum Mol Genet 15:1143-50. 2006
    ....
  25. ncbi request reprint Estimating the growth rates of primary lung tumours from samples with missing measurements
    Olga Gorlova
    Department of Epidemiology, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Stat Med 24:1117-34. 2005
    ..The relative error of the best estimates, as assessed by simulation, rarely exceeds 20 per cent. We found that the results of application of our estimation procedures to chest X-ray screening data agree well with the expectations...
  26. pmc Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis
    Wei Zhang
    The University of Texas Houston Medical School, Department of Biochemistry and Molecular Biology, Houston, TX 77030, USA
    Structure 16:1770-6. 2008
    ....
  27. ncbi request reprint Genetic susceptibility for lung cancer: interactions with gender and smoking history and impact on early detection policies
    Olga Y Gorlova
    University of Texas M D Anderson Cancer Center, Houston, Tex, USA
    Hum Hered 56:139-45. 2003
    ....
  28. ncbi request reprint Composite motifs integrating multiple protein structures increase sensitivity for function prediction
    Brian Y Chen
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    Comput Syst Bioinformatics Conf 6:343-55. 2007
    ..On our data set, we observed that composite motifs simultaneously capture variations in active site conformation, diminish the problem of selecting motif structures, and enable the fusion of protein structures from diverse data sources...
  29. ncbi request reprint Non-homogeneous infinite sites model under demographic change: mathematical description and asymptotic behavior of pairwise distributions
    Adam Bobrowski
    Department of Mathematics, University of Houston, Houston, TX, USA
    Math Biosci 175:83-115. 2002
    ..The patterns of bivariate distributions from the HV1 and HV2 data in these data are consistent with those generated by the model involving a stepwise change in population size...
  30. ncbi request reprint Adjoint systems for models of cell signaling pathways and their application to parameter fitting
    Krzysztof Fujarewicz
    Institute of Automatic Control, Silesian University of Technology, Poland
    IEEE/ACM Trans Comput Biol Bioinform 4:322-35. 2007
    ..The method is especially suited for hybrid, continuous-discrete time systems. As an example we use the mathematical model of the NF-kB regulatory module, which plays a major role in the innate immune response in animals...
  31. pmc Stochastic regulation in early immune response
    Tomasz Lipniacki
    Institute of Fundamental Technological Research, Warsaw, Poland
    Biophys J 90:725-42. 2006
    ..Our theoretical predictions of single cell kinetics are supported by recent experimental studies of oscillations in NF-kappaB signaling made on single cells...
  32. ncbi request reprint Analysis of differences in amino acid substitution patterns, using multilevel G-tests
    Marcin Pacholczyk
    Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44 100 Gliwice, Poland
    C R Biol 328:632-41. 2005
    ....
  33. pmc Forward-time simulations of human populations with complex diseases
    Bo Peng
    Department of Epidemiology, The University of Texas M D Anderson Cancer Center, Houston, Texas, United States of America
    PLoS Genet 3:e47. 2007
    ..Nonadditive fitness models, population structure, and gene-gene interactions are simulated. Case-control, sibpair, and large pedigree samples are drawn from the simulated populations and are examined by a variety of gene-mapping methods...
  34. ncbi request reprint Reaction-diffusion approach to modeling of the spread of early tumors along linear or tubular structures
    Anna Marciniak-Czochra
    Institute of Applied Mathematics, University of Heidelberg, Im Neuenheimer Feld 294, 69120 Heidelberg, Germany
    J Theor Biol 244:375-87. 2007
    ..This phenomenon may serve as a mathematical explanation of "unexpected" rapid growth and invasion of temporarily stable structures composed of cancer cells...
  35. ncbi request reprint Molecular mechanisms of autosomal recessive hypercholesterolemia
    Jonathan C Cohen
    McDermott Center for Human Growth and Development, Center for Human Nutrition, Department of Internal Medicine, The Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, USA
    Curr Opin Lipidol 14:121-7. 2003
    ..This review summarizes the findings of new investigations into the pathophysiology and molecular genetics of ARH...
  36. ncbi request reprint Asymptotic behavior of joint distributions of characteristics of a pair of randomly chosen individuals in discrete-time Fisher-Wright models with mutations and drift
    Adam Bobrowski
    Institute of Mathematics, Polish Academy of Sciences, ul Sniadeckich 8, 00 956, Warsaw, Poland
    Theor Popul Biol 66:355-67. 2004
    ..Genetics 148 (1998) 1921) and King et al. (Mol. Biol. Evol. 17(12) (2000) 1895) in the context of continuous-time models, may also be used in discrete-time models to detect past population growth...

Research Grants6

  1. Lung Cancer Model: Risk, Progression and Intervention
    Marek Kimmel; Fiscal Year: 2007
    ..The individual-based approach is also suitable for modeling of interventions, which do not yet exist such as new treatments. ..
  2. Collaborative Research : Stochastic Modeling and Estimation of Gene Transcription
    Marek Kimmel; Fiscal Year: 2010
    ..In our approach, the biological experiments are motivated by data needed for modeling and estimation, and mathematical methods are based on the observed biological model behavior. ..
  3. Collaborative Research : Stochastic Modeling and Estimation of Gene Transcription
    Marek Kimmel; Fiscal Year: 2010
    ..In our approach, the biological experiments are motivated by data needed for modeling and estimation, and mathematical methods are based on the observed biological model behavior. ..