Comparison of Approaches to Modeling of Cell Population Dynamics. - Ovide Arino; Marek Kimmel (SIAM J. Appl. Math., 1993)

Stochastic models of progression of cancer and their use in controlling cancer-related mortality. - Marek Kimmel; Olga Y. Gorlova (ACC, 2002)

Methods for estimation of demographic parameters from DNA sequence samples. - Andrzej Polanski; Marek Kimmel (ACC, 2002)

Control theoretic approach to random branching walk models arising in molecular biology. - Andrzej Swierniak; Andrzej Polanski; Jaroslaw Smieja; Marek Kimmel; Joanna Rzeszowska-Wolny (ACC, 2002)

Using SVD and SVM methods for selection, classification, clustering and modeling of DNA microarray data. - Krzysztof Simek; Krzysztof Fujarewicz; Andrzej Swierniak; Marek Kimmel; Barbara Jarzab; Malgorzata Wiench; Joanna Rzeszowska (Eng. Appl. Artif. Intell., 2004)

Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs. - Brian Y. Chen; Viacheslav Fofanov; David M. Kristensen; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (Pacific Symposium on Biocomputing, 2005)

simuPOP: a forward-time population genetics simulation environment. - Bo Peng 001; Marek Kimmel (Bioinform., 2005)

Mathematical model of tumor invasion along linear or tubular structures. - Anna K. Marciniak-Czochra; Marek Kimmel (Math. Comput. Model., 2005)

Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. - Brian Y. Chen; Viacheslav Fofanov; Drew H. Bryant; Bradley D. Dodson; David M. Kristensen; Andreas Martin Lisewski; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (RECOMB, 2006)

Bioinformatics. - Andrzej Polanski; Marek Kimmel (Springer, 2007)

Single TNFalpha trimers mediating NF-kappaB activation: stochastic robustness of NF-kappaB signaling. - Tomasz Lipniacki; Krzysztof Puszynski; Pawel Paszek; Allan R. Brasier; Marek Kimmel (BMC Bioinform., 2007)

Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction. - Brian Y. Chen; Drew H. Bryant; Viacheslav Fofanov; David M. Kristensen; Amanda E. Cruess; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (J. Bioinform. Comput. Biol., 2007)

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs. - Brian Y. Chen; Viacheslav Fofanov; Drew H. Bryant; Bradley D. Dodson; David M. Kristensen; Andreas Martin Lisewski; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (J. Comput. Biol., 2007)

Adjoint Systems for Models of Cell Signaling Pathways and their Application to Parameter Fitting. - Krzysztof Fujarewicz; Marek Kimmel; Tomasz Lipniacki; Andrzej Swierniak (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

Model-based analysis of interferon-beta induced signaling pathway. - Jaroslaw Smieja; Mohammad Jamaluddin; Allan R. Brasier; Marek Kimmel (Bioinform., 2008)

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. - David M. Kristensen; R. Matthew Ward; Andreas Martin Lisewski; Serkan Erdin; Brian Y. Chen; Viacheslav Fofanov; Marek Kimmel; Lydia E. Kavraki; Olivier Lichtarge (BMC Bioinform., 2008)

A Survey of Text Processing Tools for the Automatic Analysis of Molecular Sequences. - Andrzej Polanski; Rafal Pokrzywa; Marek Kimmel (Aspects of Natural Language Processing, 2009)

Stochastic Effects in Signaling Pathways in Cells: Interaction between Visualization and Modeling. - Marek Kimmel (ICMMI, 2009)

Exploring the Landscape of Protein-Ligand Interaction Energy Using Probabilistic Approach. - Marcin Pacholczyk; Marek Kimmel (J. Comput. Biol., 2011)

Spatial and Stochastic Effects in a Model of Viral Infection. - Roberto Bertolusso; Marek Kimmel (Fundam. Informaticae, 2012)

Comparison of Connectionist and Rough Set Based Knowledge Discovery Methods in Search for Selection in Genes Implicated in Human Familial Cancer. - Krzysztof A. Cyran; Marek Kimmel (ICMMI, 2013)

Finite absorbing Markov chain as a model of small-ligand binding process. - Marcin Pacholczyk; Damian Borys; Marek Kimmel (IWBBIO, 2013)

Changes in heat shock duration influence regulatory schemes of HSF1 activity. - Marta Iwanaszko; Patryk Janus; Tomasz Stokowy; Piotr Widlak; Marek Kimmel (IWBBIO, 2014)

Computational approach for modeling and testing NF-kB binding sites. - Marcin Pacholczyk; Karolina Smolinska; Marta Iwanaszko; Marek Kimmel (IWBBIO, 2014)

In Silico Analysis of Interactions Between NFkB and HSF Pathways. - Jaroslaw Smieja; Malgorzata Kardynska; Anna Naumowicz; Patryk Janus; Piotr Widlak; Marek Kimmel (BIOINFORMATICS, 2015)

A multitype infinite-allele branching process with applications to cancer evolution. - Thomas O. McDonald; Marek Kimmel (J. Appl. Probab., 2015)

Sloppy/Stiff Parameters Rankings in Sensitivity Analysis of Signaling Pathways. - Malgorzata Kardynska; Jaroslaw Smieja; Anna Naumowicz; Patryk Janus; Piotr Widlak; Marek Kimmel (BIOINFORMATICS, 2016)

ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data. - Navin Rustagi; Oliver A. Hampton; Jie Li; Liu Xi; Richard A. Gibbs; Sharon E. Plon; Marek Kimmel; David A. Wheeler (BMC Bioinform., 2016)

On Things Not Seen. - Marek Kimmel (Challenges in Computational Statistics and Data Mining, 2016)

Multitype Bellman-Harris branching model provides biological predictors of early stages of adult hippocampal neurogenesis. - Biao Li; Amanda Sierra; Juan Jose Deudero; Fatih Semerci; Andrew Laitman; Marek Kimmel; Mirjana Maletic-Savatic (BMC Syst. Biol., 2017)

Multitype infinite-allele branching processes in continuous time. - Thomas O. McDonald; Marek Kimmel (J. Appl. Probab., 2017)

Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples. - Ivan P. Gorlov; Claudio W. Pikielny; Hildreth R. Frost; Stephanie C. Her; Michael D. Cole; Samuel D. Strohbehn; David Wallace-Bradley; Marek Kimmel; Olga Y. Gorlova; Christopher I. Amos (BMC Bioinform., 2018)

Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level. - Malgorzata Kardynska; Anna Paszek; Jaroslaw Smieja; David G. Spiller; Wieslawa Widlak; Michael R. H. White; Pawel Paszek; Marek Kimmel (PLoS Comput. Biol., 2018)

Mathematical modelling reveals unexpected inheritance and variability patterns of cell cycle parameters in mammalian cells. - Marzena Mura; Céline Feillet; Roberto Bertolusso; Franck Delaunay; Marek Kimmel (PLoS Comput. Biol., 2019)

Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia. - Tomasz Wojdyla; Hrishikesh Mehta; Taly Glaubach; Roberto Bertolusso; Marta Iwanaszko; Rosemary Braun; Seth J. Corey; Marek Kimmel (PLoS Comput. Biol., 2019)

Mathematical model predicts response to chemotherapy in advanced non-resectable non-small cell lung cancer patients treated with platinum-based doublet. - Emilia Kozlowska; Rafal Suwinski; Monika Giglok; Andrzej Swierniak; Marek Kimmel (PLoS Comput. Biol., 2020)

A Minimal Model of Cancer Growth, Metastasis and Treatment. - Jaroslaw Smieja; Andrzej Swierniak; Marek Kimmel (ACIIDS (Companion), 2022)