Marek Kimmel

Publication Activity (10 Years)

Years Active: 1993-2022
Publications (10 Years): 10

Top Topics

Sensitivity Analysis

Ionizing Radiation

Top Venues

PLoS Comput. Biol.

J. Appl. Probab.

Publications

Jaroslaw Smieja, Andrzej Swierniak, Marek Kimmel
A Minimal Model of Cancer Growth, Metastasis and Treatment. ACIIDS (Companion) (2022)
Emilia Kozlowska, Rafal Suwinski, Monika Giglok, Andrzej Swierniak, Marek Kimmel
Mathematical model predicts response to chemotherapy in advanced non-resectable non-small cell lung cancer patients treated with platinum-based doublet. PLoS Comput. Biol. 16 (10) (2020)
Tomasz Wojdyla, Hrishikesh Mehta, Taly Glaubach, Roberto Bertolusso, Marta Iwanaszko, Rosemary Braun, Seth J. Corey, Marek Kimmel
Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia. PLoS Comput. Biol. 15 (1) (2019)
Marzena Mura, Céline Feillet, Roberto Bertolusso, Franck Delaunay, Marek Kimmel
Mathematical modelling reveals unexpected inheritance and variability patterns of cell cycle parameters in mammalian cells. PLoS Comput. Biol. 15 (6) (2019)
Malgorzata Kardynska, Anna Paszek, Jaroslaw Smieja, David G. Spiller, Wieslawa Widlak, Michael R. H. White, Pawel Paszek, Marek Kimmel
Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level. PLoS Comput. Biol. 14 (4) (2018)
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
Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples. BMC Bioinform. 19 (1) (2018)
Biao Li, Amanda Sierra, Juan Jose Deudero, Fatih Semerci, Andrew Laitman, Marek Kimmel, Mirjana Maletic-Savatic
Multitype Bellman-Harris branching model provides biological predictors of early stages of adult hippocampal neurogenesis. BMC Syst. Biol. 11 (S-5) (2017)
Thomas O. McDonald, Marek Kimmel
Multitype infinite-allele branching processes in continuous time. J. Appl. Probab. 54 (2) (2017)
Navin Rustagi, Oliver A. Hampton, Jie Li, Liu Xi, Richard A. Gibbs, Sharon E. Plon, Marek Kimmel, David A. Wheeler
ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data. BMC Bioinform. 17 (2016)
Malgorzata Kardynska, Jaroslaw Smieja, Anna Naumowicz, Patryk Janus, Piotr Widlak, Marek Kimmel
Sloppy/Stiff Parameters Rankings in Sensitivity Analysis of Signaling Pathways. BIOINFORMATICS (2016)
Jaroslaw Smieja, Malgorzata Kardynska, Anna Naumowicz, Patryk Janus, Piotr Widlak, Marek Kimmel
In Silico Analysis of Interactions Between NFkB and HSF Pathways. BIOINFORMATICS (2015)
Thomas O. McDonald, Marek Kimmel
A multitype infinite-allele branching process with applications to cancer evolution. J. Appl. Probab. 52 (3) (2015)
Marcin Pacholczyk, Karolina Smolinska, Marta Iwanaszko, Marek Kimmel
Computational approach for modeling and testing NF-kB binding sites. IWBBIO (2014)
Marta Iwanaszko, Patryk Janus, Tomasz Stokowy, Piotr Widlak, Marek Kimmel
Changes in heat shock duration influence regulatory schemes of HSF1 activity. IWBBIO (2014)
Krzysztof A. Cyran, Marek Kimmel
Comparison of Connectionist and Rough Set Based Knowledge Discovery Methods in Search for Selection in Genes Implicated in Human Familial Cancer. ICMMI (2013)
Marcin Pacholczyk, Damian Borys, Marek Kimmel
Finite absorbing Markov chain as a model of small-ligand binding process. IWBBIO (2013)
Roberto Bertolusso, Marek Kimmel
Spatial and Stochastic Effects in a Model of Viral Infection. Fundam. Informaticae 118 (4) (2012)
Marcin Pacholczyk, Marek Kimmel
Exploring the Landscape of Protein-Ligand Interaction Energy Using Probabilistic Approach. J. Comput. Biol. 18 (6) (2011)
Marek Kimmel
Stochastic Effects in Signaling Pathways in Cells: Interaction between Visualization and Modeling. ICMMI (2009)
Andrzej Polanski, Rafal Pokrzywa, Marek Kimmel
A Survey of Text Processing Tools for the Automatic Analysis of Molecular Sequences. Aspects of Natural Language Processing (2009)
David M. Kristensen, R. Matthew Ward, Andreas Martin Lisewski, Serkan Erdin, Brian Y. Chen, Viacheslav Fofanov, Marek Kimmel, Lydia E. Kavraki, Olivier Lichtarge
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinform. 9 (2008)
Jaroslaw Smieja, Mohammad Jamaluddin, Allan R. Brasier, Marek Kimmel
Model-based analysis of interferon-beta induced signaling pathway. Bioinform. 24 (20) (2008)
Brian Y. Chen, Drew H. Bryant, Viacheslav Fofanov, David M. Kristensen, Amanda E. Cruess, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction. J. Bioinform. Comput. Biol. 5 (2a) (2007)
Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs. J. Comput. Biol. 14 (6) (2007)
Krzysztof Fujarewicz, Marek Kimmel, Tomasz Lipniacki, Andrzej Swierniak
Adjoint Systems for Models of Cell Signaling Pathways and their Application to Parameter Fitting. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (3) (2007)
Tomasz Lipniacki, Krzysztof Puszynski, Pawel Paszek, Allan R. Brasier, Marek Kimmel
B signaling. BMC Bioinform. 8 (2007)
Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. RECOMB (2006)
Brian Y. Chen, Viacheslav Fofanov, David M. Kristensen, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs. Pacific Symposium on Biocomputing (2005)
Anna K. Marciniak-Czochra, Marek Kimmel
Mathematical model of tumor invasion along linear or tubular structures. Math. Comput. Model. 41 (10) (2005)
Bo Peng, Marek Kimmel
simuPOP: a forward-time population genetics simulation environment. Bioinform. 21 (18) (2005)
Krzysztof Simek, Krzysztof Fujarewicz, Andrzej Swierniak, Marek Kimmel, Barbara Jarzab, Malgorzata Wiench, Joanna Rzeszowska
Using SVD and SVM methods for selection, classification, clustering and modeling of DNA microarray data. Eng. Appl. Artif. Intell. 17 (4) (2004)
Andrzej Polanski, Marek Kimmel
Methods for estimation of demographic parameters from DNA sequence samples. ACC (2002)
Marek Kimmel, Olga Y. Gorlova
Stochastic models of progression of cancer and their use in controlling cancer-related mortality. ACC (2002)
Andrzej Swierniak, Andrzej Polanski, Jaroslaw Smieja, Marek Kimmel, Joanna Rzeszowska-Wolny
Control theoretic approach to random branching walk models arising in molecular biology. ACC (2002)
Ovide Arino, Marek Kimmel
Comparison of Approaches to Modeling of Cell Population Dynamics. SIAM J. Appl. Math. 53 (5) (1993)