Marek Kimmel

According to our database, Marek Kimmel authored at least 37 papers between 1993 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

A Minimal Model of Cancer Growth, Metastasis and Treatment.

Jaroslaw Smieja, Andrzej Swierniak, Marek Kimmel

Proceedings of the Recent Challenges in Intelligent Information and Database Systems, 2022

2020

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

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 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

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

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

2017

Multitype infinite-allele branching processes in continuous time.

Thomas O. McDonald, Marek Kimmel

J. Appl. Probab., 2017

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

2016

On Things Not Seen.

Marek Kimmel

Proceedings of the Challenges in Computational Statistics and Data Mining, 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

Sloppy/Stiff Parameters Rankings in Sensitivity Analysis of Signaling Pathways.

Malgorzata Kardynska, Jaroslaw Smieja, Anna Naumowicz, Patryk Janus, Piotr Widlak, Marek Kimmel

Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016), 2016

2015

A multitype infinite-allele branching process with applications to cancer evolution.

Thomas O. McDonald, Marek Kimmel

J. Appl. Probab., 2015

In Silico Analysis of Interactions Between NFkB and HSF Pathways.

Jaroslaw Smieja, Malgorzata Kardynska, Anna Naumowicz, Patryk Janus, Piotr Widlak, Marek Kimmel

Proceedings of the BIOINFORMATICS 2015, 2015

2014

Computational approach for modeling and testing NF-kB binding sites.

Marcin Pacholczyk, Karolina Smolinska, Marta Iwanaszko, Marek Kimmel

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

Changes in heat shock duration influence regulatory schemes of HSF1 activity.

Marta Iwanaszko, Patryk Janus, Tomasz Stokowy, Piotr Widlak, Marek Kimmel

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

2013

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

Marcin Pacholczyk, Damian Borys, Marek Kimmel

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2013

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

Proceedings of the Man-Machine Interactions 3, 2013

2012

Spatial and Stochastic Effects in a Model of Viral Infection.

Roberto Bertolusso, Marek Kimmel

Fundam. Informaticae, 2012

2011

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

Marcin Pacholczyk, Marek Kimmel

J. Comput. Biol., 2011

2009

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

Marek Kimmel

Proceedings of the Man-Machine Interactions, 2009

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

Andrzej Polanski, Rafal Pokrzywa, Marek Kimmel

Proceedings of the Aspects of Natural Language Processing, 2009

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

Model-based analysis of interferon-beta induced signaling pathway.

Jaroslaw Smieja, Mohammad Jamaluddin, Allan R. Brasier, Marek Kimmel

Bioinform., 2008

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

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

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

Single TNF<i>alpha </i>trimers mediating NF-<i>kappa</i>B activation: stochastic robustness of NF-<i>kappa</i>B signaling.

Tomasz Lipniacki, Krzysztof Puszynski, Pawel Paszek, Allan R. Brasier, Marek Kimmel

BMC Bioinform., 2007

Bioinformatics.

Andrzej Polanski, Marek Kimmel

Springer, 2007

2006

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

Proceedings of the Research in Computational Molecular Biology, 2006

2005

Mathematical model of tumor invasion along linear or tubular structures.

Anna K. Marciniak-Czochra, Marek Kimmel

Math. Comput. Model., 2005

simuPOP: a forward-time population genetics simulation environment.

Bo Peng, Marek Kimmel

Bioinform., 2005

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

Proceedings of the Biocomputing 2005, 2005

2004

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

2002

Control theoretic approach to random branching walk models arising in molecular biology.

Andrzej Swierniak, Andrzej Polanski, Jaroslaw Smieja, Marek Kimmel, Joanna Rzeszowska-Wolny

Proceedings of the American Control Conference, 2002

Methods for estimation of demographic parameters from DNA sequence samples.

Andrzej Polanski, Marek Kimmel

Proceedings of the American Control Conference, 2002

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

Marek Kimmel, Olga Y. Gorlova

Proceedings of the American Control Conference, 2002

1993

Comparison of Approaches to Modeling of Cell Population Dynamics.

Ovide Arino, Marek Kimmel

SIAM J. Appl. Math., 1993