Marek Kimmel

发表

Identification and identifiability of models of cell signalling pathways

Krzysztof Fujarewicz, Marek Kimmel, Andrzej Świerniak, 2008 .

Appendix: Forward‐Time Simulations Using simuPOP

Marek Kimmel, Bo Peng, Christopher I. Amos, 2012 .

Using SVD and SVM methods for selection, classification, clustering and modeling of DNA microarray data

Krzysztof Fujarewicz, Marek Kimmel, Andrzej Swierniak, 2004, Eng. Appl. Artif. Intell..

Geometry-inspired Optimization Methods for Structural Motifs for Protein Function Prediction

Lydia E. Kavraki, Mark Moll, Olivier Lichtarge, 2007 .

Modelling of cell aging - system theoretic approach

Andrzej Świerniak, Marek Kimmel, Jarosław Śmieja, 2001 .

Adjoint Systems for Models of Cell Signaling Pathways and their Application to Parameter Fitting

Krzysztof Fujarewicz, Marek Kimmel, Andrzej Swierniak, 2007, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

In Silico Analysis of Interactions Between NFkB and HSF Pathways

Jaroslaw Smieja, Marek Kimmel, Malgorzata Kardynska, 2015, BIOINFORMATICS.

On Things Not Seen

Marek Kimmel, 2016, Challenges in Computational Statistics and Data Mining.

Single TNFα trimers mediating NF-κB activation: stochastic robustness of NF-κB signaling

Marek Kimmel, Krzysztof Puszynski, Tomasz Lipniacki, 2007, BMC Bioinformatics.

Computational approach for modeling and testing NF-kB binding sites

Marek Kimmel, Marcin Pacholczyk, Karolina Smolinska, 2014, IWBBIO.

Finite absorbing Markov chain as a model of small-ligand binding process

Damian Borys, Marek Kimmel, Marcin Pacholczyk, 2013, IWBBIO.

Multi-null hypotheses method as an expert knowledge generator for AI-based detection of selection operating at molecular level

Marek Kimmel, Krzysztof A. Cyran, 2013 .

Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples

Marek Kimmel, Christopher I. Amos, Ivan P. Gorlov, 2018, BMC Bioinformatics.

Exploring the Landscape of Protein-Ligand Interaction Energy Using Probabilistic Approach

Marek Kimmel, Marcin Pacholczyk, M. Kimmel, 2011, J. Comput. Biol..

Composite motifs integrating multiple protein structures increase sensitivity for function prediction.

Olivier Lichtarge, Lydia E Kavraki, Marek Kimmel, 2007, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction

Lydia E. Kavraki, Andreas Martin Lisewski, Olivier Lichtarge, 2006, RECOMB.

Stochastic search gene suggestion: a Bayesian hierarchical model for gene mapping.

Marek Kimmel, Michael D Swartz, Christopher I Amos, 2006, Biometrics.

Branching processes in biology

Marek Kimmel, David E. Axelrod, M. Kimmel, 2002 .

Mathematical modelling reveals unexpected inheritance and variability patterns of cell cycle parameters in mammalian cells

Marek Kimmel, Céline Feillet, Franck Delaunay, 2019, PLoS Comput. Biol..

Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction

Lydia E. Kavraki, Olivier Lichtarge, Marek Kimmel, 2007, J. Bioinform. Comput. Biol..

Sloppy/Stiff Parameters Rankings in Sensitivity Analysis of Signaling Pathways

Jaroslaw Smieja, Marek Kimmel, Malgorzata Kardynska, 2016, BIOINFORMATICS.

Comparison of Approaches to Modeling of Cell Population Dynamics

Marek Kimmel, Ovide Arino, M. Kimmel, 1993, SIAM J. Appl. Math..

Multitype Bellman-Harris branching model provides biological predictors of early stages of adult hippocampal neurogenesis

Biao Li, Marek Kimmel, Fatih Semerci, 2017, BMC Systems Biology.

Model-based analysis of interferon-beta induced signaling pathway

Marek Kimmel, Jaroslaw Smieja, Allan R. Brasier, 2008, Bioinform..

A Survey of Text Processing Tools for the Automatic Analysis of Molecular Sequences

Andrzej Polanski, Marek Kimmel, Rafal Pokrzywa, 2009, Aspects of Natural Language Processing.

TESTING FOR SIGNATURES OF NATURAL SELECTION AT MOLECULAR GENES LEVEL

Joanna Polanska, Marek Kimmel, Krzysztof A. Cyran, 2004 .

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs

Lydia E. Kavraki, Andreas Martin Lisewski, Olivier Lichtarge, 2007, J. Comput. Biol..

Cavity-aware motifs reduce false positives in protein function prediction.

Olivier Lichtarge, Lydia E Kavraki, Marek Kimmel, 2006, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

Pre-selective and selective phase in tumor development

Marek Kimmel, Tomasz Wojdyla, M. Kimmel, 2016 .

Simulating Populations with Complex Human Diseases

Marek Kimmel, Bo Peng, Christopher I. Amos, 2012 .

On fitting of mathematical models of cell signaling pathways using adjoint systems.

Krzysztof Fujarewicz, Marek Kimmel, Andrzej Swierniak, 2005, Mathematical biosciences and engineering : MBE.

Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs

Lydia E. Kavraki, Olivier Lichtarge, Marek Kimmel, 2004, Pacific Symposium on Biocomputing.

Forward-Time Population Genetics Simulations: Methods, Implementation, and Applications

Marek Kimmel, Bo Peng, Christopher I. Amos, 2012 .

Changes in heat shock duration influence regulatory schemes of HSF1 activity

Tomasz Stokowy, Marek Kimmel, Patryk Janus, 2014, IWBBIO.

Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia

Rosemary Braun, Marek Kimmel, Marta Iwanaszko, 2019, PLoS Comput. Biol..

Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level

Jaroslaw Smieja, Marek Kimmel, Malgorzata Kardynska, 2018, PLoS Comput. Biol..

Stochasticity and determinism in models of hematopoiesis.

Marek Kimmel, M. Kimmel, 2014, Advances in experimental medicine and biology.

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

Lydia E. Kavraki, Andreas Martin Lisewski, Olivier Lichtarge, 2008, BMC Bioinformatics.

Stochastic Effects in Signaling Pathways in Cells: Interaction between Visualization and Modeling

Marek Kimmel, M. Kimmel, 2009, ICMMI.

Spatial and Stochastic Effects in a Model of Viral Infection

Marek Kimmel, Roberto Bertolusso, M. Kimmel, 2012, Fundam. Informaticae.

ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data

Jie Li, Marek Kimmel, Navin Rustagi, 2016, BMC Bioinformatics.

System Engineering Approach to Planning Anticancer Therapies.

Jaroslaw Smieja, Andrzej Świerniak, Marek Kimmel, 2016, Anticancer research.

simuPOP: a forward-time population genetics simulation environment

Marek Kimmel, Bo Peng, M. Kimmel, 2005, Bioinform..

Deterministic modeling of interferon-beta signaling pathway

Jaroslaw Smieja, Marek Kimmel, Allan R. Brasier, 2006 .

Comparison of Connectionist and Rough Set Based Knowledge Discovery Methods in Search for Selection in Genes Implicated in Human Familial Cancer

Marek Kimmel, Krzysztof A. Cyran, M. Kimmel, 2013, ICMMI.

Mathematical model of tumor invasion along linear or tubular structures

Marek Kimmel, Anna K. Marciniak-Czochra, M. Kimmel, 2005, Math. Comput. Model..

Error Analysis of Genetic Linkage Data

Robert W. Cottingham, Marek Kimmel, Margaret Gelder Ehm, 1997 .

Statistical Inference From Stem Cell Barcoding Data Using Adaptive Approximate Bayesian Computation

Marek Kimmel, Siyi Chen, Katherine Y. King, 2021 .

The dependence of expression of NF-κB-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3′ UTR

Marek Kimmel, Allan R Brasier, Marta Iwanaszko, 2012, BMC Genomics.

Stochastic regulation in early immune response.

Marek Kimmel, Tomasz Lipniacki, Pawel Paszek, 2006, Biophysical journal.

Adjoint Systems for Models of Cell Signaling Pathways and their Application to Parameter Fitting

Krzysztof Fujarewicz, Marek Kimmel, Andrzej Swierniak, 2007, TCBB.

Modeling epigenetic regulation of PRC1 protein accumulation in the cell cycle

Jaroslaw Smieja, Marek Kimmel, Marzena Dolbniak, 2015, Biology Direct.

Modelling growth of drug resistant cancer populations as the system with positive feedback

Jaroslaw Smieja, Andrzej Polanski, Marek Kimmel, 2003 .

Modelling and analysis of dynamics of viral infection of cells and of interferon resistance

Marek Kimmel, Philipp Getto, Anna Marciniak-Czochra, 2008 .

Stochastic models of progression of cancer and their use in controlling cancer-related mortality

Marek Kimmel, Olga Y. Gorlova, M. Kimmel, 2002, Proceedings of the 2002 American Control Conference (IEEE Cat. No.CH37301).

Mathematical model of NF- κB regulatory module

Marek Kimmel, Tomasz Lipniacki, Allan R. Brasier, 2004 .

Analysis of differences in amino acid substitution patterns, using multilevel G-tests.

Marek Kimmel, Marcin Pacholczyk, M. Kimmel, 2005, Comptes rendus biologies.

Microarray experiments and factors which affect their reliability

Roman Jaksik, Marek Kimmel, Joanna Rzeszowska-Wolny, 2015, Biology Direct.

Stochastic effects of multiple regulators on expression profiles in eukaryotes.

Marek Kimmel, Tomasz Lipniacki, Pawel Paszek, 2005, Journal of theoretical biology.

The point-process approach to age- and time-dependent branching processes

Marek Kimmel, M. Kimmel, 1983, Advances in Applied Probability.

Asymptotic analysis of a cell cycle model based on unequal division

Marek Kimmel, Ovide Arino, 1987 .

Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity

Olivier Lichtarge, Marek Kimmel, L. Kavraki, 2006, Protein science : a publication of the Protein Society.

Assay of Cell Cycle Kinetics by Multivariate Flow Cytometry Using the Principle of Stathmokinesis

Marek Kimmel, Zbigniew Darzynkiewicz, M. Kimmel, 1987 .

Reaction-Difusion Model of Early Carcinogenesis: The Effects of Influx of Mutated Cells

Marek Kimmel, Anna Marciniak-Czochra, M. Kimmel, 2008 .

Mathematical model of NF-kappaB regulatory module.

Marek Kimmel, Tomasz Lipniacki, Pawel Paszek, 2004, Journal of theoretical biology.

NF‐κB signaling pathway is inhibited by heat shock independently of active transcription factor HSF1 and increased levels of inducible heat shock proteins

Katarzyna Szołtysek, Marek Kimmel, Patryk Janus, 2011, Genes to cells : devoted to molecular & cellular mechanisms.

A NOTE ON CLASSIFICATION OF GENE EXPRESSION DATA USING SUPPORT VECTOR MACHINES

Krzysztof Fujarewicz, Marek Kimmel, Andrzej Swierniak, 2003 .

Nonparametric analysis of stathmokinesis

Marek Kimmel, 1985 .

CT screening for lung cancer: the first ten years.

Marek Kimmel, David F Yankelevitz, Claudia I Henschke, 2002, Cancer journal.

Transcriptional stochasticity in gene expression.

Marek Kimmel, Tomasz Lipniacki, Pawel Paszek, 2006, Journal of theoretical biology.

Simulations Provide Support for the Common Disease–Common Variant Hypothesis

Marek Kimmel, Bo Peng, M. Kimmel, 2007, Genetics.

THE ITERATED GALTON-WATSON PROCESS

Marek Kimmel, Boleslaw Gawel, 1996 .

Parameter estimation for models of cell signaling pathways based on semi-quantitative data

Krzysztof Fujarewicz, Andrzej Świerniak, Marek Kimmel, 2006 .

Time-continuous branching walk models of unstable gene amplification

Marek Kimmel, David N. Stivers, 1994 .

Interactions of neanderthals and modern humans: what can be inferred from mitochondrial DNA?

Marek Kimmel, Krzysztof A Cyran, 2005, Mathematical biosciences and engineering : MBE.

Haplotype and linkage disequilibrium architecture for human cancer-associated genes.

Marek Kimmel, Ranajit Chakraborty, David L Nelson, 2002, Genome research.

An equivalence result for integral equations with application to branching processes

Marek Kimmel, 1982 .

ASYMPTOTIC BEHAVIOUR OF AN OPERATOR EXPONENTIAL RELATED TO BRANCHING RANDOM WALK MODELS OF DNA REPEATS

Marek Kimmel, Adam Bobrowski, 1999 .

Alternatives to the Wright-Fisher model: the robustness of mitochondrial Eve dating.

Marek Kimmel, M. Kimmel, K. Cyran, 2010, Theoretical population biology.

Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed

Marek Kimmel, David A Wheeler, D. Wheeler, 2011, Human mutation.

Mathematical Model of Leukemic-Cell Circulation in the Mouse

Marek Kimmel, Barbara Kimmel, Janusz Skierski, 1983 .

Quantitative Biology: Theory, Computational Methods, and Models

Terrence J. Sejnowski, Alan S. Perelson, Marco S. Nobile, 2018 .

Deterministic and Stochastic Models of NFκB Pathway

Marek Kimmel, Tomasz Lipniacki, M. Kimmel, 2007, Cardiovascular Toxicology.

Dynamic Cross Talk Model of the Epithelial Innate Immune Response to Double-Stranded RNA Stimulation: Coordinated Dynamics Emerging from Cell-Level Noise

Marek Kimmel, Tomasz Lipniacki, Allan R. Brasier, 2014, PloS one.

Using control theory to make cancer chemotherapy beneficial from phase dependence and resistant to drug resistance

Andrzej Świerniak, Marek Kimmel, A. Świerniak, 2004 .

Quasistationarity in a Branching Model of Division-Within-Division

Marek Kimmel, M. Kimmel, 1997 .

Analysis of two mechanisms of telomere maintenance based on the theory of g-Networks and stochastic automata networks

Marek Kimmel, M. Kimmel, Kyung Hyun Lee, 2020, BMC Genomics.

Evolutionary action and structural basis of the allosteric switch controlling β2AR functional selectivity

Angela D. Wilkins, Olivier Lichtarge, Michel Bouvier, 2017, Nature Communications.

Model-based analysis of interferon-beta induced signaling pathway

Jaroslaw Smieja, Marek Kimmel, Allan R. Brasier, 2008, Bioinform..

Noncompact semigroups of operators generated by cell kinetics models

Marek Kimmel, Ovide Arino, Eva Sánchez, 1991, Differential and Integral Equations.

Stability analysis of models of cell production systems

Marek Kimmel, Ovide Arino, M. Kimmel, 1986 .

Estimation and prediction of cell cycle specific effects of anticancer drugs

Marek Kimmel, M. Kimmel, F. Traganos, 1986 .

Identifying conformational states of macromolecules by eigen-analysis of resampled cryo-EM images.

Marek Kimmel, Pawel A Penczek, Christian M T Spahn, 2011, Structure.

On the clonal inheritance model of cell proliferation

Marek Kimmel, David N. Stivers, 1995 .

Gaussian Mixture Decomposition of Time-Course DNA Microarray Data

Joanna Polanska, Andrzej Polanski, Marek Kimmel, 2007 .

Evolutionary Action Score of TP53 Coding Variants Is Predictive of Platinum Response in Head and Neck Cancer Patients.

Olivier Lichtarge, Marek Kimmel, Thomas O McDonald, 2015, Cancer research.

Evolutionary Action Score of TP53 Identifies High-Risk Mutations Associated with Decreased Survival and Increased Distant Metastases in Head and Neck Cancer.

Olivier Lichtarge, Marek Kimmel, Beth M Beadle, 2015, Cancer research.

Deterministic and stochastic models of NFkappaB pathway.

Marek Kimmel, Tomasz Lipniacki, 2007, Cardiovascular toxicology.

Forward-Time Simulations of Human Populations with Complex Diseases

Marek Kimmel, Bo Peng, Christopher I Amos, 2007, PLoS genetics.

Modeling Spatial Effects in Early Carcinogenesis : Stochastic Versus Deterministic Reaction-Diffusion Systems

Marek Kimmel, M. Kimmel, R. Bertolusso, 2012 .

Hematopoiesis and its disorders: a systems biology approach.

Marek Kimmel, Casim A Sarkar, Seth J Corey, 2010, Blood.

Cross talk between cytokine and hyperthermia-induced pathways: identification of different subsets of NF-κB-dependent genes regulated by TNFα and heat shock

Roman Jaksik, Tomasz Stokowy, Marek Kimmel, 2015, Molecular Genetics and Genomics.

Qualitative analysis of controlled drug resistance model - inverse Laplace and and semigroup approach

Jaroslaw Smieja, Marek Kimmel, Andrzej Swierniak, 1999 .

Emergence of stable DNA repeats from random sequences under unequal sister chromatid exchange

Marek Kimmel, Keith A. Baggerly, 1995 .

Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis.

Wei Zhang, Marek Kimmel, Pawel A Penczek, 2008, Structure.

A note on estimation of dynamics of multiple gene expression based on singular value decomposition.

Marek Kimmel, Krzysztof Simek, M. Kimmel, 2003, Mathematical biosciences.

Predicting Minimal Residual Disease in Acute Myeloid Leukemia through Stochastic Modeling of Clonality

Roman Jaksik, Marek Kimmel, S. Corey, 2019, bioRxiv.

Control Problems Arising in Chemotherapy Under Evolving Drug Resistance

Andrzej Polanski, Andrzej Świerniak, Marek Kimmel, 1996 .