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Scholarly Interest Report
         
Marek Kimmel
Professor
Professor of Statistics
 
e-mail:kimmel@rice.edu
 
  • M.S. Control Engineering (1977) Silesian Technical University, Gliwice, Poland
  • Ph.D. Technical Sciences (1980) Silesian Technical University, Gliwice, Poland
  • Dr. hab. Math. Sci. Mathematical Sciences (1997) Jagiellonian University, Krakow, Poland
 
Primary Department
   Department of Statistics
Picture
 
Department Affiliations
 
  • Institute of Biosciences and Bioengineering
  • Keck Center for Quantitative Biomedical Sciences
  • Ken Kennedy Institute for Information Technology
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    Research Areas
     Population Dynamics, Branching Processes, Statistical Genetics, Molecular Evolution, Bioinformatics
     
    Teaching Areas
     Stochastic Processes, Bioinformatics
     
    Selected Publications
     Abstracts
     

    Kristensen, D.M., Chen, B.Y., Fofanov, V.Y., Ward, R.M., Lisewski, A.M., Kimmel, M., Kavraki, L.E. and Lichtarge, O. "Recurrent Use of Evolutionary Importance for Functional Annotation of Proteins Based on Local Structural Similarity." Protein Science (2006) : 1530-6.

     
     

    Kimmel, M. and Polanski, A. "On Detection of Population Growth Based on SNP Data." American Journal Human Genetics, 61 (2002) : A2352.

     
     

    Kimmel, M., Bonnen, P.E., Wang, P., Chakraborty, R. and Nelson, D.L. "Haplotype and Linkage Disequilibrium Architecture for Human Cancer-Associated Genes." American Journal Human Genetics, 61 (2002) : A1629.

     
     

    Kimmel, M., Fu, Y.X., Zu, H., Renwick, A. and Chakraborty, R. "Effects if Additive Selection and Recombination on Homozygosity Test at Micorsatellie Loci Under Generalized Stepwise Mutation Model." American Journal Human Genetics: A1142.

     
     

    Kimmel, M., Gorlova, O., Amos, C., Spitz, M. and Henschke, C. "Modeling of Periodic Screening of Smokers with Increased Genetic Susceptibility to Lung Cancer: Impact on Population -Based Mortality." American Journal Human Genetics, 61 (2002) : A1263.

     
     

    Kimmel, M., Renwick, A., Zu, H., Fu, Y.X. and Chakraborty, R. "Relative Heterozygosity Contributed by Alleles of Different Frequency Class is Not Invariant at Micorsatellite Loci." American Journal Human Genetics, 61 (2002) : A1150.

     
     

    Kimmel, M., Xu, H., Fu, X.Y., Renwick, A. and Chakraborty, R. "Microsatellite Variation: Effects of Natural Selection, Population Structure, and Demographic Changes of Population Size." American Journal Human Genetics, 61 (2002) : A2392.

     
     

    Kimmel, M., Chakraborty, R., Jin, L. and Deka, R. "Extent and Pattern of Gene Diversity at Microsatellite Loci: Implications for Disease-Gene Association Studies." American Journal Human Genetics, 69 (2001) : A262.

     
     

    Kimmel, M., Renwick, A., Bonnen, P., Trikka, D., Nelson, D. and Chakraborty, R. "Single-Nucleotide Polymorphisms at Several Cancer Susceptibility Genes Do Not Conform to the Infinite Site Model of Mutation." American Journal Human Genetics, 69: A1380.

     
     

    Kimmel, M., Renwick, A., Deka, R. and Chakraborty, R. "Evolution of Microsatellite Loci and Past Demography of Modern Humans." American Journal of Human Genetics: A1418.

     
     

    Kimmel, M., Xu, H., Renwick, A. and Chakraborty, R. "Effects of Population Substructure on the Homozygosity Test of Neutrality Under the Stepwise Mutation Model." American Journal Human Genetics (2001) : A1393.

     
     Refereed articles
     

    Kristensen, D., Ward, R., Lisewski, A., Erdin, S., Chen, B., Fofanov, V., Kimmel, M., Kavraki, L. and Lichtarge, O. "Prediction of Enzyme Function Based on 3D Templates of Evolutionarily Important Amino Acids." BMC Bioinformatics, 9(1) (2008 Jan 11) : 17.

     
     

    Chen, B., Bryant, D., Cruess, A., Bylund, J., Fofanov, V., Kristensen, D., Kimmel, M., Lichtarge, O. and Kavraki, L. "Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity for Function Prediction." Comput Syst Bioinformatics Conf., 6 (2007) : 343-55.

     
     

    Chen, B., Bryant, D., Fofanov, V., Kristensen, D., Cruess, A., Kimmel, M., Lichtarge, O. and Kavraki, L. "Cavity Scaling: Automated Refinement of Cavity-Aware Motifs in Protein Function Prediction." J Bioinform Comput Biol, 5(2a) (2007 Apr) : 353-82.

     
     

    Chen, B., Fofanov, V., Bryant, D., Dodson, B., Kristensen, D., Lisewski, A., Kimmel, M., Lichtarge, O. and Kavraki, L. "The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs." J Comput Biol, 14(6) (2007 Jul-Aug) : 791-816.

     
     

    Fujarewicz, K., Kimmel, M., Lipniacki, T. and Swierniak, A. "Adjoint Systems for Models of Cell Signaling Pathways and Their Application to Parameter Fitting." IEEE/ACM Trans Comput Biol Bioinform, 4 (3) (2007 Jul-Sep) : 322-35.

     
     

    Lipniacki, T. and Kimmel, M. "Deterministic and Stochastic Models of NFkappaB Pathway." Cardiovasc Toxicol, 7 (4) (2007) : 215-34.

     
     

    Lipniacki, T., Puszynski, K., Paszek, P., Brasier, A. and Kimmel, M. "Single TNFalpha Trimers Mediating NF-kappaB Activation: Stochastic Robustness of NF-kappaB Signaling ." BMC Bioinformatics, 8 (1) (2007 Oct 9) : 376.

     
     

    Marciniak-Czochra, A. and Kimmel, M. "Reaction-Diffusion Approach to Modeling of the Spread of Early Tumors Along Linear or Tubular Structures." J Theor Biol, 244(3) (2007 Feb 7) : 375-87.

     
     

    Peng, B. and Kimmel, M. "Simulations Provide Support for the Common Disease-Common Variant Hypothesis." Genetics, 175(2) (2007 Feb) : 763-76.

     
     

    Peng, B., Amos, C. and Kimmel, M. "Forward-Time Simulations of Human Populations with Complex Diseases." PLoS Genet, 3(3) (2007 Mar) : e47.

     
     Articles
     

    Jaruszewicz, Joanna, Marek Kimmel, and Tomasz Lipniacki "Stability of bacterial toggle switches is enhanced by cell-cycle lengthening by several orders of magnitude." Physical Review E, 89 no. 2 (2014)

     
     

    Kimmel, Marek, and Seth Corey "Stochastic hypothesis of transition from inborn neutropenia to AML: interactions of cell population dynamics and population genetics." Frontiers in oncology 3 (2013)

     
     

    Li, Biao, and Marek Kimmel "Factors influencing ascertainment bias of microsatellite allele sizes: impact on estimates of mutation rates." Genetics, 195, No. 2 (2013) : 563-572.

     
     

    Statistical Analysis of Missense Mutation Classifiers. "Kimmel, M., and Hicks, S.." Hum Mut. (2012)


    http://onlinelibrary.wiley.com/doi/10.1002/humu.22243/abstract
     
     

    Wu, Xiaowei and Kimmel, Marek "Modeling Neutral Evolution Using an Infinite-Allele Markov Branching Process." International Journal of Stochastic Analysis (2013)

     
     

    Bertolusso, R. and Kimmel, M. "Modeling spatial effects in early carcinogenesis: Stochastic versus deterministic reaction-diffusion systems. To appear in the journal of Mathematical Modeling of Natural Phenomena."  (2012) In Press

     
     

    Chen, X., Gorlov, I.P., Ying, J., Merriman, K.W., Kimmel, M., et al. "Initial Medical Attention on Patients with Early-Stage Non-Small Cell Lung Cancer." PLoS One, 7 (3): e32644.

     
     

    Cited (Hicks, S., Wheeler, D. A., Plon, S. E. & Kimmel, M. Hum. Mutat. 32, 661–668 (2011))

     
     

    Foy, M., Yip, R., Chen, X., Kimmel, M., Gorlova, O.Y., Henschke, C.I. "Modeling the mortality reduction due to computed tomography screening for lung cancer." Cancer [ePub ahead of print] (2011)

     
     

    Hicks, S. and Kimmel, M. "Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed." Human Mutation (2011) In Press

     
     

    Cyran, K.A. and Kimmel, M. "Alternatives to the Wright-Fisher model: the robustness of mitochondrial Eve dating." Theor Popul Biol, 78(3) (2010) : 165-72.

     
     

    Foy, M., Spitz, M.R., Kimmel, M. and Gorlova, O.Y. "A smoking-based carcinogenesis model for lung cancer risk prediction." Int J Cancer (2010)

     
     

    Foy, M., Yip, R., Chen, X., Kimmel, M., Gorlova, O.Y., and Henschke, C.I. "Modeling the mortality reduction due to computed tomography screening for lung cancer." Cancer (2010)

     
     

    Goldwasser, D. and Kimmel, M. "Modeling excess lung cancer risk among screened arm participants in the Mayo Lung Project." Cancer, 116(1) (2010) : 122-31.

     
     

    Kimmel, M. "Evolution and cancer: a mathematical biology approach." Biol Direct, 5:29

     
     

    Kimmel, M. and Mathaes, M. "Modeling neutral evolution of Alu elements using a branching process.." BMC Genomics (2010)

     
     

    Pacholczyk, M. and Kimmel, M. "Exploring the Landscape of Protein-Ligand Interaction Energy Using Probabilistic Approach." J Comput Biol (2010)

     
     

    Whichard, Z.L., Sarkar, C.A., Kimmel, M., and Corey, S.J. "Hematopoiesis and its disorders: a systems biology approach." Blood, 115(12) (2010) : 2339-47.

     
     

    Wu, X. and Kimmel, M. "A note on the path to extinction of critical Markov branching processes.." Statistics & Probability Letters, 80 (5-6) (2010) : 263-269.

     
     

    Gorlov, I.P., Kimmel, M. and Amos, C.I. "Strength of the Purifying Selection Against Different Categories of the Point Mutations in the Coding Regions of the Human Genome." Human Molecular Genetics, 15 (2006) : 1143-50.

     
     

    Lipniacki, T., Paszek P., Brasier, A.R., Luxon, B. and Kimmel, M. "Stochastic Regulation in Early Immune Response." Biophysical Journal, 90 (2006) : 725-42.

     
     

    Lipniacki, T., Paszek, P., Marciniak-Czochra, A., Brasier, A.R. and Kimmel, M. "Transcriptional Stochasticity in Gene Expression." Journal of Theoretical Biology, 238 (2006) : 348-67.

     
     

    Marciniak-Czochra, A. and Kimmel, M. "Reaction-Diffusion Approach to Modeling of the Spread of Early Tumors Along Linear or Tubular Structures." Journal Theoretical Biology (09/14/2006) Submitted

     
     

    Peng, B. and Kimmel, M. "Simulations Provide Support For the Common Disease Common Variant Hypothesis." Genetics (12/06/2006) Submitted

     
     

    Swartz, M.D., Kimmel, M., Mueller, P. and Amos, C.I. "Stochastic Search Gene Suggestion: a Bayesian Hierarchical Model for Gene Mapping." Biometrics, 62 (2006) : 495-503.

     
     

    Chen, B.Y., Fofanov, V.Y., Kristensen, D.M., Kimmel, M., Lichtarge, O. and Kavraki, L.E. "Algorithms for Structural Comparision and Statistical Analysis of 3D Protein Motifs." Pacific Symposium on Biocomputing (2005) : 334-45.

     
     

    Fujarewicz, K., Kimmel, M. and Swierniak, A. "On Fitting of Mathematical Models of Cell Signaling Pathways Using Adjoint Systems." Mathematical Biosciences and Engineering, 2 (2005) : 527-534.

     
     

    Gorlova, O., Peng, B., Yankelevitz, D., Henschke, C. and Kimmel, M. "Estimating the Growth Rates of Primary Lung Tumors From Samples with Missing Measurements." Statistics in Medicine, 24 (Apr 15, 2005) : 1117-34.

     
     

    Krzysztof, A., Cyran and Kimmel, M. "Interactions of Neanderthals and Modern Humans: What Can Be Inferred from Mitochondrial DNA?." Mathematical Biosciences and Engineering, 2 (2005) : 487-498.

     
     

    Lipniacki, T., Paszek, P., Marciniak-Czochra, A., Brasier, A.R. and Kimmel, M. "Transcriptional Stochasticity in Gene Expression." Journal of Theoretical Biology (Jul 20, 2005)

     
     

    Marciniak-Czochra, A. and Kimmel, M. "Mathematical Model of Tumor Invasion Along Linear or Tubular Structures." Mathematical and Computer Modelling, 41 (2005) : 1097-1108.

     
     

    Pacholczyk, M. and Kimmel, M. "Analysis of Differences in Amino Acid Substitution Patterns, Using Multilevel G-Tests." Comptes Redus Biologies, 7 (Jul 2005) : 632-41.

     
     

    Paszek, P., Lipniacki, T., Brasier, A.R., Tian, B., Nowak, D.E. and Kimmel, M. "Stochastic Effects of Multiple Regulators on Expression Profiles in Eukaryotes." Journal of Theoretical Biology, 233 (Apr 7, 2005) : 423-33.

     
     

    Peng, B. and Kimmel, M. "simuPOP: A Forward-Time Population Genetics Simulation Environment." Bioinformatics, 18 (Jul 14, 2005) : 3686-7.

     
     

    Polanska, J. and Kimmel, M. "A Simple Model of Linkage Disequilibrium and Genetic Drift in Human Genomic SNPs: Importance of Demography and SNP Age." Human Heredity (2005) In Press

     
     

    Lipniacki, T., Paszek, P., Brasier, A.R., Luxon, B. and Kimmel, M. "Mathematical Model of NF-kappaB Regulatory Module." Journal of Theoretical Biology, 228(2) (2004) : 195-215.

     
     

    Kimmel, M. and Simek, K. "A Computer Algorithm of Estimation of Dynamics of Multiple Gene Expression Based on Singular Value Decomposition." Mathematical Biosciences (2002) In Press

     
     

    Kimmel, M., Bobrowski, A., Wang, N. and Chakraborty, R. "Non-Homogeneous Infinite Sites Model Under Demographic Change: Mathematical Description and Asymptotic Behavior of Pairwise Distrbutions." Math Biosciences, 175 (2002) : 83-115.

     
     

    Kimmel, M., Henschke, C.I., Yankelevitz, D.F. and Libby, D. "CT Screening for Lung Cancer: The First Ten Years." Cancer Journal, 1 (2002) : S47-54.

     
     

    Kimmel, M., Polanski, A. and Bobrowski, A. "A Note on Distributions of Times to Coalescence, Under Time-Dependent Population Size." Theoretical Population BiologyIn Press

     
     

    Kimmel, M., Trikka, D., Fang, Z., Renwick, A., Jones, S.H., Chakraborty, R. and Nelson, D. "Complex SNP-Based Haplotypes in Three Human Helicases: Implications for Cancer Association Studies." Genome Research, 12 (2002) : 627-639.

     
     

    Kimmel, M., Yao, H., Kristensen, D.M., Mihalek, I., Sowa, M.E., Shaw, C., Kavraki, L. and Lichtarge, O. "An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Stuctures." Journal of Molecular Biology

     
     

    Kimmel, M. "An Application of a General Branching Process in The Study of The Genetics of Aging." Journal of Theoretical Biology, 213 (2001) : 547-557.

     
     Books
     

    Kimmel M and Axelrod DE. "Branching Processes in Biology, 2nd Ed..." Springer, New York (2014) In Press

     
     

    Peng, B., Amos, C., and Kimmel, M. "Forward-time Population Genetics Simulations."  (2012)

     
     

    Marek Kimmel and Andrzej Polanski "The Bioinformatics Book." Springer (2010)

     
     

    Andrzej Polanski, Marek Kimmel "Bioinformatics."  (2007)

     
     

    Kimmel, M. and Axelrod, D. "Branching Processes in Biology."  (2002)

     
     

    Arino, O., Axelrod, D.E. and Kimmel, M. "Advances In Mathematical Population Dynamics - Molecules, Cells, and Man. (Mathematical Biology and Medicine, Vol. 6)." : 1-839.

     
     Book chapters
     

    Kimmel, M., Gorlova, O. and Henschke, C. "Modeling Lung Cancer Screening." General Biostatistics: Recent Advances in Quantitative Methods in Cancer and Human Health Risk Assessment (May 2005) : 161-173.

     
     Book reviews
     

    Yakovlev, A.Y. and Zorin, A.V. "Computer Simulation in Cell Raiobiology." Springer-Verlag (2004) In Press

     
     Refereed conference papers
     

    Bobrowski, A. and Kimmel, M. "A Random Evolution Related to a Fisher-Wright-Moran Model With Mutation, Recombination and Drift." Mathematical Methods in the Applied Sciences (2003) In Press

     
     

    Fujarewicz, K., Kimmel, M., Rzeszowska-Wolny, J. and Swierniak, A. "A Note on Classification of Gene Expression Data Using Support Vector Machines." Journal of Biological Systems, 11 (2003) : 43-56.

     
     

    Kimmel, M. and Gorlova, O. "Stochastic Models of Progression of Cancer and Their Use in Controlling Cancer-Related Mortality." International Journal of Applied Mathematics and Computer Science, 13 (2003) : 279-287.

     
     

    Kimmel, M. and Polanski, A. "Population Genetics Models for The Statistics of DNA Samples Under Different Demographic Scenarios-Maximum Likelihood Versus Approximate Methods." International Journal of Applied Mathematics and Computer Science, 13 (2003) : 347-355.

     
     

    Polanski, A., Bobrowski, A. and Kimmel, M. "A Note on Distributions of Times to Coalescence, Under Time-Dependent Population Size." Theoretical Population Biology, 63 (2003) : 33-44.

     
     

    Renwick, A., Bonnen, P., Trikka, D., Nelson, R., Chakraborty, R. and Kimmel, M. "Sampling Properties of Estimator of Nucleotide Diversity at Discovered SNP Sites." International Journal of Applied Mathematics and Computer Science, 13 (2003) : 385-394.

     
     

    Simek, K. and Kimmel, M. "A Note on Estimation of Dynamics of Multiple Gene Expression Based on Singular Value Decomposition." Mathematical Biosciences, 182 (2003) : 183-199.

     
     

    Yao, H., Kristensen, D.M., Mihalek, I., Sowa, M.E., Shaw, C., Kimmel, M., Kavraki, L. and Lichtarge, O. "An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures." Journal of Molecular Biology, 326 (2003) : 255-261.

     
     Other
     

    Marek Kimmel and Andrzej Polanski "The Bioinformatics Book." Published in Japanese (2011)

     
     

    Kimmel, M. and Swierniak, A. "Control Theory Approach to Cancer Chemotherapy: Benefiting from Phase Dependence and Overcoming Drug Resistance." Tutorials in Mathematical Biosciences (2006) : 185-221.

     
     

    Kimmel, M. "g401210 Genome Signals and Assembly." Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, 8 (Sept 2005)

     
     

    Bobrowski, A. and Kimmel, M. "Dynamics of Life History of a DNA Repeat Sequences." Archives of Control Sciences, 9 (2001) : 57-68.

     
     

    Bobrowski, A., Kimmel, M., Arino, O. and Chakraborty, R. "A Semigroup Representation and Asymptotic Behavior of Certain Statistics of the Fisher-Wright-Moran Coalescent. In Stochastic Processes." Handbook of Statistics series (2001)

     
     

    Fujarewicz, K., Kimmel, M., Rzeszowska-Wolny, J. and Swierniak, A. "Improved Classification of Microarray Gene Expression Data Using Support Vector Machines." Journal of Medical Informatics and Technologies, 2 (2001) : MI9-MI19.

     
     

    Gorlova, O., Kimmel, M. and Henschke, C. "Modeling of Long Term Screening for Lung Cancer." Cancer, 92 (2001) : 1531-1540.

     
     

    Polanska, J. and Kimmel, M. "A Model of Dynamics of Mutation, Genetic Drift and Recombination in DNA -Repeat Genetic Loci." Archives of Control Sciences, 9 (2001) : 143-158.

     
     

    Renwick, A., Davison, L., Spratt, H., King, JP. and Kimmel, M. "DNA Dinucleotide Evolution in Humans: Fitting Theory to Facts." Genetics, 159 (Oct 2001) : 737-47.

     
     

    Swierniak, A., Kimmel, M., Smieja, J. and Rzeszowska-Wolny, J. "Modeling of Aging-System Theoretic Approach." Journal of Medical Informatics and Technologies., 2 (2001) : MI3-MI8.

     
     

    Trikka, D., Fang, Z., Renwick, A., Jones, S.H., Chakraborty, R., Kimmel, M. and Nelson, D. "Complex SNP-Based Haplotypes in Three Human Helicases Demostrate the Need for Ethnically Matched Control Populations in Association Studies." Genome Research

     
     

    Bat, O., Kimmel, M. and Axelrod, D.E. "Computer Simulation of Expansions of CGG DNA Triplet Repeats in the Fragile X Syndrome."  (1998) : 47-67.

     
     

    Bobrowski, A. and Kimmel, M. "Asymptotic Behavior of an Operator Exponential Related to Branching Random Walk Models of DNA Repeats." Journal of Biological Systems, 6 (1998, in press)

     
     

    Bobrowski, A., Kimmel, M., Arino, O. and Chakraborty, R. "A Semigroup Representation and Asymptotic Behavior of Fisher-Wright-Moran Coalescent."  (1999, under review)

     
     

    Chakraborty, R. and Kimmel, M. "Statistics of Microsatellite Loci: Estimation of Mutation Rate and Pattern of Population Expansion."  (1999, in press)

     
     

    Deka, R., Guangyun, S., Smelser, D., Zhong, Y., Kimmel, M. and Chakraborty, R. "Rate and Directionality of Mutations, and Effects of Allele-Size Constraints at Anonymous, Gene-Associated and Disease-Causing Loci." Molecular Biology and Evolution (1999, under review)

     
     

    Kimmel, M. and Swierniak, A. "Infinite-Dimensional Model of Evolution of Drug Resistance of Cancer Cells." Journal of Mathematical Systems, Estimation and Control, 8 (1998) : 1-16.

     
     

    Kimmel, M., Chakraborty, R., King, J.P., Bamshad, M., Watkins, W.S., Jorde, L.B. "Signature of Population Expansion in Microsatellite Repeat Data." Genetics, 148 (1998) : 1921-1930.

     
     

    Olofsson, P. and Kimmel, M. "Stochastic Models of Telomere Shortening." Mathematical Biosciences (1998, in press)

     
     

    Polanski, A., Chakraborty, R., Kimmel, M. and Deka, R. "Dynamic Balance of Segregation Distortion and Selection Maintains Normal Allele Sizes at The Myotonic Dystrophy Locus." Mathematical Biosciences, 147 (1998) : 93-112.

     
     

    Polanski, A., Kimmel, M. and Chakraborty, R. "Application of a Time-Dependent Coalescence Process for Inferring the History of Population Size Changes From DNA Sequence Data." Proceedings of the National Academy of Sciences USA, 95 (1998) : 5456-5461.

     
     

    Swierniak, A., Polanski, A. and Kimmel, M. "Qualitative Analysis of The Infinite Model of Drug Resistance Evolution."  (1998) : 595-612.

     
    Presentations
     Invited Talks
     

    Speaker.  "Stochastic and Deterministic Population Processes: From Branching to the Transport Equation." Department of Statistics, Rice University, Houston, TX. (February 8, 2010)

     
     

    "Modeling the Mortality Reduction Due to CT Screening for Lung Cancer." 21st International Conference on Screening for Lung Cancer , Zhuhai, China. (October 24-25, 2009) With Millennia Foy, Olga Gorlova, Claudia Henschke, Rowena Yip, and David Yankelevitz

     
     

    "Levels of Mathematical description of stochastic transcription and translation networks." Stochastic Models in Biological Sciences, Warsaw, Poland. (May 30, 2006)

     
     

    "Modeling Lung Cancer: Risks, Progression, and Screening." Annual CISNET Meeting, Bethesda, Maryland. (July 12, 2006)

     
     

    "Application of mixture models to gene expression profiles and cellular stress analysis." ECMTB 2005, Dresden, Germany. (July 18-22, 2005) With Polanska J., Rzeszowska-Wolny J., Polanski A.

     
     

    "Ascertainment bias of allele sizes at microsat loci." University of London, London, UK. (November 30 - December 2, 2005)

     
     

    "Demographic history of modern humans and complex genetic diseases: A forward-time modeling study.." Continuous and Discrete Modelling in Mechanics, Warsaw, Poland. (September 5-9, 2005)

     
     

    "Deterministic and stochastic effects in metabolic pathways." CITI Luncheon, Rice University. (February 2004)

     
     

    "Distributions of time to coalesce under stochastic population growths: application to MRCA dating." World Congress of Nonlinear Analysts, Orlando, FL. (July 2004) With Cyran, K., Kimmel, M.

     
     

    "Growth rates of screen-detected lung tumors." Weill Medical College of Cornell University, New York. (April 2004)

     
     

    "Mathematical model of linear or tubular tumor growth with diffusion of growth factor molecules." Vanderbilt University Math Department, Tennessee. (November 2004)

     
     

    "Modeling Deterministic and Stochastic Effects in the NFkB Regulatory Module." Los Alamos National Laboratory, New Mexico. (May 2004) With Kimmel, M., Lipniacki, T., Paszek, P.

     
     

    "A Semigroup Representation and Asymptotic Behavior of the Fisher-Wright-Moran Coalescent." University of Rochester, Rochester,NY.. (March 2003)

     
     

    "Modeling of progression and detection of lung cancer, implications of genetic susceptibility." Meeting of Medical Statistics-Current Development in Statistical Methodology for Genetic Architecture of Complex Diseases, Oberwolfach, Germany. (February 2-8, 2003)

     
     

    "Ascertatinment Bias in Inter-Species Genetic Studies or do Humans Mutate Faster Than Chimps?." Conference on Mathematical Modeling of Population Dynamics, Bedlewo, Polans. (June 24-28, 2002)

     
     

    Contributed talk.  "Control Theoretic Approach to Random Branching Walk Models Arising in Molecular Biology." 2002 American Control Conference, Anchorage, Alaska. (May 8-10, 2002) With A. Swierniak, A. Polanski, J. Smieja, M. Kimmel, J. Rzeszowska-Wolny

     
     

    "Implications of Measures of Usefulness for Lung Cancer Screening RCT's." The Sixth International Conference on Screening for Lung Cancer, The American Hospital of Paris, International Affiliate of Cornell Medical College and New York-Presbyterian Hospital, France. (April 5-7, 2002)

     
     

    "Incorporation of Gene Expression and Proteome Information in Modeling of Lung Cancer Progression." Program of Polish-Japanese Bilateral Seminar on Bioinformatics,, Science Center, Academy of Sciences, Poznan. (June 24, 2002)

     
     

    Contributed talk.  "Methods for Estimation of Demographic Parameters from DNA Sequence Samples." 2002 American Control Conference, Anchorage, Alaska. (May 8-10, 2002) With A. Polanski, M. Kimmel,

     
     

    "Positive Feedbacks in Two Models of Molecular Biology." European Society of the Mathematical and Theoretical Biology 5th Conference, Milano, Italy. (July 2-6, 2002) With Andrzej Swierniak, Jaroslaw Smieja

     
     

    Co-Authored abstract.  "Selection and Classification of Microarray Gene Expression Data." School on Population Dynamics, Bedlewo, Poland. (June 17-21, 2002) With K. Fujarewicz, M. Kimmel, J. Rzeszowska, A. Swierniak

     
     

    Co-Authored abstract.  "Singular Value Decomposition Based Dynamics of Gene Expression Data." School on Population Dynamics, Bedlewo, Poland. (June 17-21, 2002) With K. Simek, M. Kimmel,

     
     

    Contributed talk.  "Stochastic Models of Progression of Cancer and Their Use In Controlling Cancer-Related Mortality." 2002 American Control Conference, Anchorage, Alaska. (May 8-10, 2002) With M. Kimmel, O. Gorlova

     
     

    "Why Mathematics is Needed to Understand Disease-Gene Associations." European Society of the Mathematical and Theoretical Biology 5th Conference, Milano, Italy. (July 2-6, 2002)

     
     

    "Amino Acid Substitution Matrices for Compositionally Biased Bacterial Genomes." DIMACS Special Focus on Computational Molecular Biology, DIMACS Workshop on Whole Genome Comparison, Rutgers University, Piscataway, NJ. (February 28-March 2, 2001) With Susan Abramski

     
     

    "Overdiagnosis and Curabililty of Lung Cancer." The Fourth International Conference on Screening for Lung Cancer, Weill Cornell Medical College of Cornell University, New York. (February 23, 2001)

     
     

    "SNP Haplotypes and Cancer." Gliwice Science Encounters 2001, Department of Experimental and Clinical Radiobiology Center of Oncology, M. Sklodowska-Curie Memorial Institute Branch in Gliwice. (November 23-24, 2001)

     
     Lectures
     

    "Alternatives to the Wright-Fisher Model and Robustness of Mitochondrial Eve Dating." Rice University, (March 2004)

     
     

    "Branching Processes in Biology." Series of Lectures, Summer School of Statistics and Probablity, Switzerland. (September-October 2004)

     
     

    "Why Mathematics is Needed to Understand Complex Genetic Diseases." School on Population Dynamics, Bedlewo, Poland. (June 17-21, 2002)

     
     Other
     

    "Mitochondrial Eve - Mother of All Humans Lived 200,000 Years Ago." The research is available online in the journal Theoretical Population Biology., (08/17/2010)

     
     

    "Deterministic and stochastic models of metabolic pathways in the immune response." ECMTB 2005, Dresden, Germany. (July 18-22, 2005) With Marciniak-Czochra A.

     
     

    Presentation.  "Modeling of Lung Cancer: Progression and Detection." CISNET Annual Meeting, Rockville, Maryland. (November 12-15, 2002)

     
     

    Invited Instructor.  "The Promise of Genetic Research:Prevention and Treating Disease." School of Continuing Studies, Rice University, Houston, Texas. (April 16, 2002)

     
     

    "Extent and Pattern of Gene Diversity at Microsatellite Loci: Implications for Disease-Gene Association Study." Annual Meeting of the American Society of Human Genetics, San Diego, CA. (October 12-16, 2002) With R. Chakraborty, L. Jin, R. Deka, M. Kimmel,

     
     

    "Branching Processes, Coalescence and Genetic Mapping." 22nd European Meeting of Statisticians, Vilnius, Lithuania. (August 12-18, 1998) With V. Shane Pankratz

     
     

    "Mathematical Models in Population Genetics, Lyapunov Differential Equation and Migrations of Early Modern Humans." Seminar Talk, Department of Mathematics, Arizona State University, Tempe, Arizona. (October 16, 1998)

     
     

    "Population Dynamics Coded in DNA." Seminar Talk, Department of Statistics, Oxford University. (June, 1998)

     
     

    "Population Dynamics Coded in DNA: History of Growth and Migrations of Modern Humans." Department of Mathematics, Gotheborg University, Sweden. (April 14, 1998)

     
     

    "Population Dynamics of Genetic Diseases and Disequilibrium Mapping." Fifth International Conference in Mathematical Population Dynamics, Zakopane, Poland. (June 21-26, 1998) With V. Shane Pankratz

     
     

    "Semigroup Representation and Asymptotic Behavior of the Fisher-Wright-Moran Coalescent with Applications in Genetics." Asymptotic Properties of Evolution Equations and Their Applications, Banach Center, Warsaw, Poland. (June28 - July3, 1998) With Adam Bobrowski

     
     

    "Signatures of Population Expansion in Microsatellite Repeat Data." Seminar Talk, Department of Zoology, Oxford University. (April, 1998)

     
     

    "The Coalescent, Fisher-Wright-Moran model, and Lyapunov Equation." Workshop in Population Dynamics, Gotheborg University, Sweden. (May 13, 1998)

     
     Posters
     

    "An Accurate, Sensitive and Scalable Method to Identify Functional Sites in Protein Structures." 2002 Bioinformatics Symposium, Houston , Texas. (October 15-16, 2002) With H. Yao, D.M. Kristensen, I. Mihalek, M.E. Sowa, C. Shaw, M. Kimmel, L. Kavraki, O. Lichtarge

     
     

    "Clustering Analysis on SAGE Data." Bioinformatics Symposium, Houston, Texas. (October 14-15, 2002) With K. Baggerly, L. Deng, M. Kimmel,

     
     

    "Effects of Population Substructure on the Homozygosity Test of Neurality Under the Stepwise Mutation Model." Annual Meeting of the American Society of Human Genetics, San Diego, CA. (October 12-16, 2002) With H. Xu, A. Renwick, M. Kimmel, R. Chakraborty

     
     

    "Single-Nucleotide Polymorphisms at Several Cancer Susceptibility Genes Do Not Conform to the Infinite Site Model of Mutation." Annual Meeting of The American Society of Human Genetics, San Diego, CA. (October 12-16, 2001) With A. Renwick, P. Bonnen, D. Trikka, D. Nelson, R. Chakraborty, M. Kimmel,

     
     Seminar Speaker
     

    "Stochasticity in Signaling Pathways and Gene Regulation: The NFkB Example and the Principle of Stochastic Robustness." Keck Seminar Series, Rice University, Houston, Texas. (November 3, 2006)

     
     Workshops
     

    "Networks flux regulating gene expression pathways." EMBO Workshop, Gosau, Austria. (October 12-15, 2006) With Fell, D., White, M.

     
     

    "Modeling of Transcriptional Stochasticity in Eukaryotes and Its Consequences for NF-kB Regulation." Stochastic Phenomena in Gene Regulation, Rice University. (October 20-22, 2005) With Tomasz Lipniacki

     
     

    "Integration of gene expression and protein activity data to estimate structure of a metabolic pathway." Institute for Mathematical Sciences National University of Singapore, Singapore. (January 2004)

     
     

    "Mathematical model of NF-kappaB regulatory module." Mathematical Biosciences Institute, Ohio State University. (Sept. 29-Oct. 3, 2003) With Brasier A., Lipniacki T., Luxon B., Paszek Pawel

     
     

    "Modeling Progression of Lung Cancer: From Genetic Susceptibility to Tumor Growth and Metasis." Mathematical Biosciences Institute, Ohio State University. (November 10-14, 2003) With Gorlova O.

     
     

    "Stochastic Models of Repeat DNA Motifs and Amplified Genes.." Mathematical Biosciences Institute, Ohio State University. (November 17-19, 2003)

     
     

    Workshop Chair.  "RCT Design Issues in Screening for Lung Cancer." The Sixth International Conference on Screening for Lung Cancer, The American Hospital of Paris, International Affiliate of Cornell Medical College and New York-Presbyterian Hospital. (April 5-7, 2002) With J. Cuzick

     
     

    Invited Instructor.  "Using Mathematical Modeling and Computer Simulation to Improve Cancer Therapy." II Summer School and Scientific Workshop, Propriano, France. (September 2-6, 2002)

     
     

    Workshop Chair.  "Research on Overdiagnosis and Curability of Lung Cancer." The Fourth International Conference on Screening for Lung Cancer, Weill Cornell Medical College of Cornell University, New York. (February 24, 2001)

     
    Editorial Positions
     Editor, Mathematical Biosciences (1995 - present). (2013 - 2013)

     Member of the Editorial Board, Journal of the National Cancer Institute. (2010 - 2010)

     Editor, Mathematical Biology Editor, Biology Direct . (2013 - 2013)

     Member of the Editorial Board, Journal of Theoretical Biology. (2006 - 2006)

     Member of the Editorial Board, Journal of Theoretical Biology. (2003 - 2003)

     Member of the Editorial Board, Journal of the National Cancer Institute. (2005 - 2005)

     Member of the Editorial Board, Mathematical Biosciences. (2006 - 2006)

     Member of the Editorial Board, Mathematical Biosciences. (2003 - 2003)

     Member of the Editorial Board, Mathmatical Biosciences. (2005 - 2005)

     Member of the Editorial Board, Journal of Biological Systems. (2006 - 2006)

     Member of the Editorial Board, Journal of Biological Systems. (2003 - 2003)

     Member of the Editorial Board, Journal of Theoretical Biology. (2005 - 2005)

     Member of the Editorial Board, Journal of the National Cancer Institute. (2006 - 2006)

     Member of the Editorial Board, Journal of the National Cancer Institute. (2003 - 2003)

     Member of the Editorial Board, Journal of Biological Systems. (2005 - 2005)

    Supervised Theses & Dissertations
     Heidi Marie Spratt, PhD A Comparison of Three Methods Used to Determine Functionally Important Protein Residues. (2002) (Thesis or Dissertation Director)

     Deepa Rajan, Master of Art Analysis of Regulatory Mechanisms of Genes Controlled by the Transcription Factor NF-KappaB. (2004) (Thesis or Dissertation Director)

     Michael Swartz, Ph.D Stochastic Search Gene Suggestion: Hierarchical Bayesian Model Selection Meets Gene Mapping. (2004) (Thesis or Dissertation Director)

     Li Deng, Ph.D Modeling the Carcinogenesis in Lung Cancer: Taking the Interaction between Genetic Factors and Smoking into Account. (2005) (Thesis or Dissertation Director)

     Deepa Rajan, M.A. Analysis of Regulatory Mechanisms of Genes Controlled by the Transcription Factor NF-kappaB. (2005) (Thesis or Dissertation Director)

     Bo Peng, Ph.D. Forward-time population genetics simulation and its applications in the mapping of complex human diseases. (2006) (Thesis or Dissertation Director)

     Pawel Paszek, Ph.D. Modeling stochasticity in gene regulation. (2006) (Thesis or Dissertation Director)

     Jose-Miguel Yamal, Ph.D. Multilevel Plytomous Classification. (2006) (Thesis or Dissertation Director)

     Pawel Paszek, Ph.D. Modeling Stochasticity in Gene Regulation. (2007) (Thesis or Dissertation Director)

     Biao Li, Ph.D. TBA. (2013) (Thesis or Dissertation Director)

    Awards, Prizes, & Fellowships
     State Professorship, Republic of Poland (2002)

     Organizer, ESMTB School, Biology and Mathematics of Cells (June 2001)

    Positions Held
     Member, Institute of Mathematical Statistics. (2006 - 2006)

     Head Organizer, Mathematical Methods and Models in Biology and Medicine. (2005 - 2005)

     Chair of Organizing Committee, Stochasitc Phenomena in Gene Regulation. (2005 - 2005)

     Member, Cell Kinetics Society. (2006 - 2006)

     Member, American Statistical Association. (2006 - 2006)

     Member, Society for Mathematical Biology. (2006 - 2006)

     Member, Genetics Society of America. (2006 - 2006)