List of works - Alex Graudenzi

A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development

scientific article published on 08 May 2012

A stochastic model of autocatalytic reaction networks

scientific article published on 7 October 2011

A stochastic model of catalytic reaction networks in protocells ⬇️

article

A stochastic model of the emergence of autocatalytic cycles

article

Algorithmic methods to infer the evolutionary trajectories in cancer progression ⬇️

scientific article published on 28 June 2016

CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks

scientific article published on 4 February 2016

CAPRI: efficient inference of cancer progression models from cross-sectional data ⬇️

scientific article

CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer

scientific article published on September 2015

Distributed delays in a hybrid model of tumor-immune system interplay.

scientific article published on February 2013

Dynamical properties of a boolean model of gene regulatory network with memory

scientific article

GESTODIFFERENT: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process

scientific article published on 3 January 2013

Growth and division in a dynamic protocell model

scientific article published on 3 December 2014

Inferring tree causal models of cancer progression with probability raising

scientific article

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism

scientific article published on 28 February 2019

Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power

scientific article published on 20 September 2018

Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model

Investigating the relation between stochastic differentiation, homeostasis and clonal expansion in intestinal crypts via multiscale modeling

scientific article

Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data

scientific article published on 25 April 2019

Modeling Cumulative Biological Phenomena with Suppes-Bayes Causal Networks.

scientific article published on 4 July 2018

On RAF Sets and Autocatalytic Cycles in Random Reaction Networks ⬇️

article published in 2014

Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks

scientific article

Preface

Robustness analysis of a Boolean model of gene regulatory network with memory

scientific article published on 21 March 2011

SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data

scientific article

TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. ⬇️

scientific article

The Diffusion of Perturbations in a Model of Coupled Random Boolean Networks

article

VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples

scientific article published on 28 January 2021

List of works by Alex Graudenzi

A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development

A stochastic model of autocatalytic reaction networks

A stochastic model of catalytic reaction networks in protocells ⬇️

A stochastic model of the emergence of autocatalytic cycles

Algorithmic methods to infer the evolutionary trajectories in cancer progression ⬇️

CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks

CAPRI: efficient inference of cancer progression models from cross-sectional data ⬇️

CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer

Distributed delays in a hybrid model of tumor-immune system interplay.

Dynamical properties of a boolean model of gene regulatory network with memory

GESTODIFFERENT: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process

Growth and division in a dynamic protocell model

Inferring tree causal models of cancer progression with probability raising

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism

Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power

Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model

Investigating the relation between stochastic differentiation, homeostasis and clonal expansion in intestinal crypts via multiscale modeling

Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data

Modeling Cumulative Biological Phenomena with Suppes-Bayes Causal Networks.

On RAF Sets and Autocatalytic Cycles in Random Reaction Networks ⬇️

Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks

Preface

Robustness analysis of a Boolean model of gene regulatory network with memory

SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data

TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. ⬇️

The Diffusion of Perturbations in a Model of Coupled Random Boolean Networks

VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples