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List of works by Pedro Monteiro

A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks

scientific article

Cooperative development of logical modelling standards and tools with CoLoMoTo

scientific article published on 25 January 2015

Dynamical modeling and analysis of large cellular regulatory networks.

scientific article published on June 2013

Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control

article by Aurélien Nald et al published 2012 in Lecture Notes in Computer Science

Efficient Verification for Logical Models of Regulatory Networks

article

Efficient parameter search for qualitative models of regulatory networks using symbolic model checking

scientific article published on September 2010

EpiLog: A software for the logical modelling of epithelial dynamics

article

Estimating Attractor Reachability in Asynchronous Logical Models

article

From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon

scientific article published on 10 August 2021

Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks.

scientific article published in January 2012

Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors

scientific article published on 26 March 2020

Large-Scale Simulations of Bacterial Populations Over Complex Networks

scientific article published on 09 July 2018

Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0.

scientific article

Logical Modeling and Dynamical Analysis of Cellular Networks

scientific article

Model checking to assess T-helper cell plasticity

scientific article

Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis

scientific article published on 23 March 2015

On logical bifurcation diagrams

scientific article published on 15 January 2019

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods.

scientific article

Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step-by-Step Guided Analysis

scientific article published on January 2016

Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae.

scientific article published in September 2011

Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches

scientific article published on 11 October 2010

Repairing Boolean logical models from time-series data using Answer Set Programming

article

Revision of Boolean Models of Regulatory Networks Using Stable State Observations

scientific article published on 03 December 2019

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

scientific article

Temporal logic patterns for querying dynamic models of cellular interaction networks

scientific article

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.

scientific article

The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts.

scientific article

The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae

scientific article

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae ⬇️

scientific article published on 28 October 2013

YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts

scientific article published on 01 January 2020

YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae

scientific article

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae.

scientific article published on 25 September 2017

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface

scientific article published on 23 October 2010

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