Lista de obras -

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

artículo científico publicado en 2022

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

artículo científico publicado en 2019

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

artículo científico publicado en 2003

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

article

A robust estimator of mutation rates

artículo científico publicado en 2008

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

artículo científico publicado en 2005

A smoking‐based carcinogenesis model for lung cancer risk prediction ⬇️

artículo científico publicado el 29 de marzo de 2011

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

artículo científico publicado en 2007

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

artículo científico publicado el 11 de mayo de 2011

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

artículo científico publicado en 2005

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

artículo científico publicado en 2010

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

artículo científico publicado en 2003

An Operator Semigroup in Mathematical Genetics

article

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

artículo científico publicado en 2005

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

artículo científico publicado en 2020

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

artículo científico publicado en 2020

Assessment of Luminal and Basal Phenotypes in Bladder Cancer

artículo científico publicado en 2020

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

artículo científico publicado el 8 de junio de 2011

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

artículo científico publicado en 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.

artículo científico publicado en 2004

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

artículo científico publicado en 2012

CT screening for lung cancer: the first ten years

artículo científico publicado en 2002

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

artículo científico publicado en 2007

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

artículo científico publicado en 2006

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

artículo científico publicado en 2018

Chapter 11: Rice-MD Anderson lung cancer model

artículo científico publicado en 2012

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

artículo científico publicado en 2012

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

artículo científico publicado en 2016

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

artículo científico publicado en 2017

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

artículo científico publicado en 2002

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

artículo científico publicado en 2007

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

artículo científico publicado en 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

artículo científico publicado en 2014

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

artículo científico publicado en 2014

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

artículo científico publicado en 2005

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

artículo científico publicado en 2009

Evolution and cancer: a mathematical biology approach

artículo científico publicado en 2010

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

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 2017

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

artículo científico publicado en 2011

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

artículo científico publicado en 2007

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 ⬇️

artículo científico publicado el 1 de enero de 2003

Genetic demographic networks: Mathematical model and applications

artículo científico publicado en 2016

Haplotype and linkage disequilibrium architecture for human cancer-associated genes

artículo científico publicado en 2002

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

artículo científico publicado en 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

artículo científico publicado en 2010

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

artículo científico publicado en 2008

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

artículo científico publicado en 2008

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

artículo científico publicado en 2016

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

artículo científico publicado en 2011

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

artículo científico publicado en 2012

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

artículo científico publicado en 2012

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

artículo científico publicado en 2005

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

artículo científico publicado en 2020

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

artículo científico publicado en 2016

Mathematical model of NF-kappaB regulatory module

artículo científico publicado en 2004

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

artículo científico publicado en 2020

Mathematical modeling as a tool for planning anticancer therapy.

artículo científico publicado en 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

artículo científico publicado en 2015

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.

artículo científico publicado en 2015

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

artículo científico publicado en 2010

Modeling neutral evolution of Alu elements using a branching process

artículo científico publicado en 2010

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

artículo científico publicado el 10 de enero de 2011

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

artículo científico publicado en 2014

Molecular mechanisms of autosomal recessive hypercholesterolemia.

artículo científico publicado en 2003

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

artículo científico publicado en 2017

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

artículo científico publicado en 2019

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

artículo científico publicado en 2015

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

artículo científico publicado en 2011

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

artículo científico publicado en 2002

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

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

artículo científico publicado en 2005

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

artículo científico publicado en 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.

artículo científico publicado en 2008

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

artículo científico publicado en 2011

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

artículo científico publicado en 2018

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

artículo científico publicado en 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

artículo científico publicado en 2006

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

artículo científico publicado en 2006

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

artículo científico publicado en 2017

Role of stem-cell divisions in cancer risk

artículo científico publicado en 2017

Simulations provide support for the common disease-common variant hypothesis

artículo científico publicado en 2006

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

artículo científico publicado en 2007

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

artículo científico publicado en 2012

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

artículo científico publicado en 2014

Stathmokinetic analysis of human epidermal cells in vitro.

artículo científico publicado en 1986

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

artículo científico publicado en 2020

Statistical analysis of missense mutation classifiers

artículo científico publicado en 2012

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

artículo científico publicado en 2013

Stochastic effects of multiple regulators on expression profiles in eukaryotes.

artículo científico publicado en 2004

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

artículo científico publicado en 2022

Stochastic regulation in early immune response

artículo científico publicado en 2005

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

artículo científico publicado en 2006

Stochasticity and determinism in models of hematopoiesis

artículo científico publicado en 2014

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

artículo científico publicado en 2014

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

artículo científico publicado en 2008

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

artículo científico publicado en 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

artículo científico publicado en 2012

Thick distribution tails in models of cancer secondary tumors ⬇️

artículo científico publicado en 2018

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

artículo científico publicado en 2011

Transcriptional stochasticity in gene expression.

artículo científico publicado en 2005

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

artículo científico publicado en 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

artículo científico publicado en 2014

simuPOP: a forward-time population genetics simulation environment

artículo científico publicado en 2005

Lista de obras de

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

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

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

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

A robust estimator of mutation rates

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

A smoking‐based carcinogenesis model for lung cancer risk prediction ⬇️

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

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

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

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

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

An Operator Semigroup in Mathematical Genetics

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

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

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

Assessment of Luminal and Basal Phenotypes in Bladder Cancer

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

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

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

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

CT screening for lung cancer: the first ten years

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

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

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

Chapter 11: Rice-MD Anderson lung cancer model

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

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

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

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

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

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

Deterministic and stochastic models of NFkappaB pathway

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

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

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

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

Evolution and cancer: a mathematical biology approach

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

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

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

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

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

Forward-time simulations of human populations with complex diseases

Gaussian Mixture Decomposition of Time-Course DNA Microarray Data

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

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

Genetic demographic networks: Mathematical model and applications

Haplotype and linkage disequilibrium architecture for human cancer-associated genes

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

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

Hematopoiesis and its disorders: a systems biology approach

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

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

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

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

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

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

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

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

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

Mathematical model of NF-kappaB regulatory module

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

Mathematical modeling as a tool for planning anticancer therapy.

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

Microarray experiments and factors which affect their reliability

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

Modeling Neutral Evolution Using an Infinite-Allele Markov Branching Process

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

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

Modeling neutral evolution of Alu elements using a branching process

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

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

Molecular mechanisms of autosomal recessive hypercholesterolemia.

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

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

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

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

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