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List of works by Marek Kimmel

A general calculus of fitness landscapes finds genes under selection in cancers

scientific article published in 2022

A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes

scientific article published on 06 February 2019

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

scientific article published in April 2003

A random evolution related to a Fisher-Wright-Moran model with mutation, recombination and drift

article

A robust estimator of mutation rates

scientific article

A simple model of linkage disequilibrium and genetic drift in human genomic SNPs: importance of demography and SNP age.

scientific article published in January 2005

A smoking-based carcinogenesis model for lung cancer risk prediction

scientific article

Adjoint systems for models of cell signaling pathways and their application to parameter fitting.

scientific article published in July 2007

Adjusting a cancer mortality-prediction model for disease status-related eligibility criteria

scientific article

Algorithms for structural comparison and statistical analysis of 3D protein motifs.

scientific article

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

scientific article

An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures

scientific article published on 01 February 2003

An Operator Semigroup in Mathematical Genetics

article

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

scientific article published on 07 April 2005

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

scientific article published on 09 September 2020

Application of the Moran Model in Estimating Selection Coefficient of Mutated CSF3R Clones in the Evolution of Severe Congenital Neutropenia to Myeloid Neoplasia

scientific article published on 17 September 2020

Assessment of Luminal and Basal Phenotypes in Bladder Cancer

scientific article published on 16 June 2020

Association of smoking with tumor size at diagnosis in non-small cell lung cancer

scientific article

Asymptotic behavior of a Moran model with mutations, drift and recombination among multiple loci.

scientific article published on 11 November 2009

Asymptotic behavior of joint distributions of characteristics of a pair of randomly chosen individuals in discrete-time Fisher-Wright models with mutations and drift.

scientific article published in December 2004

Bernoulli mixture models in application to the evaluation of algorithms estimating functionality of missense mutations

scientific article published in October 2012

CT screening for lung cancer: the first ten years

scientific article

Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction

scientific article published on April 2007

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

scientific article published in January 2006

Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways

scientific article

Chapter 11: Rice-MD Anderson lung cancer model

scientific article published in July 2012

Chapter 13: CISNET lung models: comparison of model assumptions and model structures

scientific article

Chronic Infection Depletes Hematopoietic Stem Cells through Stress-Induced Terminal Differentiation

scientific article

Coalescence computations for large samples drawn from populations of time-varying sizes

scientific article

Complex SNP-based haplotypes in three human helicases: implications for cancer association studies

scientific article published on April 2002

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

scientific article

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

scientific article published on 6 May 2015

Deterministic and stochastic models of NFkappaB pathway

scientific article published on 18 October 2007

Different rates of DNA replication at early versus late S-phase sections: multiscale modeling of stochastic events related to DNA content/EdU (5-ethynyl-2'deoxyuridine) incorporation distributions

scientific article

Dynamic cross talk model of the epithelial innate immune response to double-stranded RNA stimulation: coordinated dynamics emerging from cell-level noise.

scientific article

Estimating the growth rates of primary lung tumours from samples with missing measurements.

scientific article published in April 2005

Estimation of the effects of smoking and DNA repair capacity on coefficients of a carcinogenesis model for lung cancer

scientific article

Evolution and cancer: a mathematical biology approach

scientific article published on 20 April 2010

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

scientific article

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

scientific article

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

scientific article published on 18 December 2017

Exploring the landscape of protein-ligand interaction energy using probabilistic approach

scientific article

Factors influencing ascertainment bias of microsatellite allele sizes: impact on estimates of mutation rates

scientific article published on 14 August 2013

Forward-time simulations of human populations with complex diseases

scientific article

Gaussian Mixture Decomposition of Time-Course DNA Microarray Data

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

article

Genetic Susceptibility for Lung Cancer: Interactions with Gender and Smoking History and Impact on Early Detection Policies ⬇️

scientific article published on January 1, 2003

Genetic demographic networks: Mathematical model and applications

scientific article published on July 2016

Haplotype and linkage disequilibrium architecture for human cancer-associated genes

scientific article published on December 2002

Heat shock factor 1 (HSF1) cooperates with estrogen receptor α (ERα) in the regulation of estrogen action in breast cancer cells

scientific article published on 16 November 2021

Heat shock response regulates stimulus-specificity and sensitivity of the pro-inflammatory NF-κB signalling

scientific article published on 24 May 2020

Hematopoiesis and its disorders: a systems biology approach

scientific article

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

scientific article

Heterozygous screen in Saccharomyces cerevisiae identifies dosage-sensitive genes that affect chromosome stability

scientific article published on February 2008

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

scientific article

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

scientific article published on November 2011

Impact of reduced tobacco smoking on lung cancer mortality in the United States during 1975-2000.

scientific article published on 14 March 2012

Initial medical attention on patients with early-stage non-small cell lung cancer

scientific article

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

scientific article published in July 2005

Interferon Gamma Mediates Hematopoietic Stem Cell Activation and Niche Relocalization through BST2

scientific article published on 01 December 2020

Irradiation with UV-C inhibits TNF-α-dependent activation of the NF-κB pathway in a mechanism potentially mediated by reactive oxygen species

scientific article

Mathematical model of NF-kappaB regulatory module

scientific article

Mathematical model predicts response to chemotherapy in advanced non-resectable non-small cell lung cancer patients treated with platinum-based doublet

scientific article published on 05 October 2020

Mathematical modeling as a tool for planning anticancer therapy.

scientific article published on 13 October 2009

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

scientific article published on 03 June 2019

Microarray experiments and factors which affect their reliability

scientific article

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

scientific article published on 19 August 2008

Modeling Neutral Evolution Using an Infinite-Allele Markov Branching Process

Modeling epigenetic regulation of PRC1 protein accumulation in the cell cycle.

scientific article

Modeling excess lung cancer risk among screened arm participants in the Mayo Lung Project

scientific article

Modeling neutral evolution of Alu elements using a branching process

scientific article

Modeling the mortality reduction due to computed tomography screening for lung cancer

scientific article

Modeling the natural history and detection of lung cancer based on smoking behavior

scientific article

Molecular mechanisms of autosomal recessive hypercholesterolemia.

scientific article

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

scientific article published on 3 October 2017

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

scientific article published on 07 January 2019

NF-κB and IRF pathways: cross-regulation on target genes promoter level

scientific article published on 17 April 2015

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

scientific article

Non-homogeneous infinite sites model under demographic change: mathematical description and asymptotic behavior of pairwise distributions

scientific article published in February 2002

Non-homogeneous infinitely many sites discrete-time model with exact coalescent

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

scientific article published on 01 July 2005

Pharmacogenetic characterization of naturally occurring germline NT5C1A variants to chemotherapeutic nucleoside analogs

scientific article published on 22 February 2016

Pooled analysis suggests benefit of catheter-based hematoma removal for intracerebral hemorrhage

scientific article published on 20 March 2019

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

scientific article

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

scientific article

Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes.

scientific article published on 21 February 2018

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

scientific article published on 30 April 2018

RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation

article

Reaction-diffusion approach to modeling of the spread of early tumors along linear or tubular structures

scientific article published on 14 September 2006

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

scientific article published on 2 May 2006

Replication Stress Leading to Apoptosis within the S-phase Contributes to Synergism between Vorinostat and AZD1775 in HNSCC Harboring High-Risk TP53 Mutation.

scientific article published on 8 August 2017

Role of stem-cell divisions in cancer risk

scientific article published on August 2017

Simulations provide support for the common disease-common variant hypothesis

scientific article published on 6 December 2006

Single TNFalpha trimers mediating NF-kappaB activation: stochastic robustness of NF-kappaB signaling.

scientific article

Small median tumor diameter at cure threshold (<20 mm) among aggressive non-small cell lung cancers in male smokers predicts both chest X-ray and CT screening outcomes in a novel simulation framework

scientific article published on 21 May 2012

Stability of bacterial toggle switches is enhanced by cell-cycle lengthening by several orders of magnitude.

scientific article published on 11 February 2014

Stathmokinetic analysis of human epidermal cells in vitro.

scientific article published on May 1986

Stationary Distribution of Telomere Lengths in Cells with Telomere Length Maintenance and its Parametric Inference

scientific article published on 20 November 2020

Statistical analysis of missense mutation classifiers

scientific article published on 31 December 2012

Stochastic Hypothesis of Transition from Inborn Neutropenia to AML: Interactions of Cell Population Dynamics and Population Genetics

scientific article published on 29 April 2013

Stochastic effects of multiple regulators on expression profiles in eukaryotes.

scientific article published on 8 December 2004

Stochastic models of stem cells and their descendants under different criticality assumptions

scientific article published in 2022

Stochastic regulation in early immune response

scientific article

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

scientific article published in June 2006

Stochasticity and determinism in models of hematopoiesis

scientific article

Strength of the purifying selection against different categories of the point mutations in the coding regions of the human genome

scientific article published on 24 February 2006

Systems hematology: an introduction

scientific article published in January 2014

TNFalpha-induced activation of NFkappaB protects against UV-induced apoptosis specifically in p53-proficient cells.

scientific article

The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs.

scientific article published in July 2007

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

scientific article

Thick distribution tails in models of cancer secondary tumors ⬇️

scientific article published on 3 January 2018

Time to the MRCA of a sample in a Wright-Fisher model with variable population size

scientific article published on 6 October 2011

Transcriptional stochasticity in gene expression.

scientific article published on 21 July 2005

Urothelial-to-Neural Plasticity Drives Progression to Small Cell Bladder Cancer

scientific article published on 27 May 2020

Wee-1 kinase inhibition overcomes cisplatin resistance associated with high-risk TP53 mutations in head and neck cancer through mitotic arrest followed by senescence

scientific article

simuPOP: a forward-time population genetics simulation environment

scientific article

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