Search Results - "Monteiro, Pedro T."

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods by Francisco, Alexandre P, Vaz, Cátia, Monteiro, Pedro T, Melo-Cristino, José, Ramirez, Mário, Carriço, Joäo A

“…With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods…”
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YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts by Monteiro, Pedro T, Oliveira, Jorge, Pais, Pedro, Antunes, Miguel, Palma, Margarida, Cavalheiro, Mafalda, Galocha, Mónica, Godinho, Cláudia P, Martins, Luís C, Bourbon, Nuno, Mota, Marta N, Ribeiro, Ricardo A, Viana, Romeu, Sá-Correia, Isabel, Teixeira, Miguel C

“…Abstract The YEASTRACT+ information system (http://YEASTRACT-PLUS.org/) is a wide-scope tool for the analysis and prediction of transcription regulatory…”
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YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae by Teixeira, Miguel C, Monteiro, Pedro T, Palma, Margarida, Costa, Catarina, Godinho, Cláudia P, Pais, Pedro, Cavalheiro, Mafalda, Antunes, Miguel, Lemos, Alexandre, Pedreira, Tiago, Sá-Correia, Isabel

“…Abstract The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT-www.yeastract.com) information system has been, for 11 years, a key…”
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Logical Modeling and Dynamical Analysis of Cellular Networks by Abou-Jaoudé, Wassim, Traynard, Pauline, Monteiro, Pedro T, Saez-Rodriguez, Julio, Helikar, Tomáš, Thieffry, Denis, Chaouiya, Claudine

“…The logical (or logic) formalism is increasingly used to model regulatory and signaling networks. Complementing these applications, several groups contributed…”
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Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0 by Naldi, Aurélien, Hernandez, Céline, Abou-Jaoudé, Wassim, Monteiro, Pedro T, Chaouiya, Claudine, Thieffry, Denis

“…The logical formalism is well adapted to model large cellular networks, in particular when detailed kinetic data are scarce. This tutorial focuses on this…”
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The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks by Naldi, Aurélien, Hernandez, Céline, Levy, Nicolas, Stoll, Gautier, Monteiro, Pedro T, Chaouiya, Claudine, Helikar, Tomáš, Zinovyev, Andrei, Calzone, Laurence, Cohen-Boulakia, Sarah, Thieffry, Denis, Paulevé, Loïc

“…Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many…”
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From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon by Oliveira, Jorge, Antunes, Miguel, Godinho, Claudia P, Teixeira, Miguel C, Sá-Correia, Isabel, Monteiro, Pedro T

“…Abstract Numerous genomes are sequenced and made available to the community through the NCBI portal. However, and, unlike what happens for gene function…”
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Estimating Attractor Reachability in Asynchronous Logical Models by Mendes, Nuno D, Henriques, Rui, Remy, Elisabeth, Carneiro, Jorge, Monteiro, Pedro T, Chaouiya, Claudine

“…Logical models are well-suited to capture salient dynamical properties of regulatory networks. For networks controlling cell fate decisions, cell fates are…”
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Repairing Boolean logical models from time-series data using Answer Set Programming by Lemos, Alexandre, Lynce, Inês, Monteiro, Pedro T

“…Boolean models of biological signalling-regulatory networks are increasingly used to formally describe and understand complex biological processes. These…”
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Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis by Teixeira, Andreia Sofia, Monteiro, Pedro, Carrico, Joao, Ramos de Almeida Ramirez, Mário Nuno, Francisco, Alexandre P.

“…Copyright: © 2015 Teixeira et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits…”
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Room usage optimization in timetabling: A case study at Universidade de Lisboa by Lemos, Alexandre, Melo, Francisco S, Monteiro, Pedro T, Lynce, Inês

“…This paper discusses the problem of room usage optimization for university timetables: given a timetable, we want to optimize the room occupation by…”
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Model checking to assess T-helper cell plasticity by Abou-Jaoudé, Wassim, Monteiro, Pedro T, Naldi, Aurélien, Grandclaudon, Maximilien, Soumelis, Vassili, Chaouiya, Claudine, Thieffry, Denis

“…Computational modeling constitutes a crucial step toward the functional understanding of complex cellular networks. In particular, logical modeling has proven…”
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EpiLog: A software for the logical modelling of epithelial dynamics [version 2; peer review: 3 approved] by Varela, Pedro L, Ramos, Camila V, Monteiro, Pedro T, Chaouiya, Claudine

“…Cellular responses are governed by regulatory networks subject to external signals from surrounding cells and to other micro-environmental cues. The logical…”
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EpiLog: A software for the logical modelling of epithelial dynamics by Varela, Pedro L, Ramos, Camila V, Monteiro, Pedro T, Chaouiya, Claudine

“…Cellular responses are governed by regulatory networks subject to external signals from surrounding cells and to other micro-environmental cues. The logical…”
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Boolean function metrics can assist modelers to check and choose logical rules by Zobolas, John, Monteiro, Pedro T., Kuiper, Martin, Flobak, Åsmund

“…•A framework of Boolean function metrics for logical modeling.•Truth density reveals different output patterns for various Boolean functions.•Commonly used…”
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Transcriptome-wide differences between Saccharomyces cerevisiae and Saccharomyces cerevisiae var. boulardii: Clues on host survival and probiotic activity based on promoter sequence variability by Pais, Pedro, Oliveira, Jorge, Almeida, Vanda, Yilmaz, Melike, Monteiro, Pedro T., Teixeira, Miguel C.

“…Although Saccharomyces cerevisiae and S. cerevisiae var. boulardii share more than 95% genome sequence homology, only S. cerevisiae var. boulardii displays…”
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Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors by Selvaggio, Gianluca, Canato, Sara, Pawar, Archana, Monteiro, Pedro T, Guerreiro, Patrícia S, Brás, M Manuela, Janody, Florence, Chaouiya, Claudine

“…Epithelial-to-mesenchymal transition (EMT) has been associated with cancer cell heterogeneity, plasticity, and metastasis. However, the extrinsic signals…”
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On logical bifurcation diagrams by Abou-Jaoudé, Wassim, Monteiro, Pedro T.

“…Bifurcation theory provides a powerful framework to analyze the dynamics of differential systems as a function of specific parameters. Abou-Jaoudé et al…”
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Introducing UniCorT: an iterative university course timetabling tool with MaxSAT by Lemos, Alexandre, Monteiro, Pedro T., Lynce, Inês

“…This paper describes the UniCorT tool designed to solve uni versity co u r se t imetabling problems specifically tailored for the 2019 International…”
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A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks by Monteiro, Pedro T, Dumas, Estelle, Besson, Bruno, Mateescu, Radu, Page, Michel, Freitas, Ana T, de Jong, Hidde

“…The study of biological networks has led to the development of increasingly large and detailed models. Computer tools are essential for the simulation of the…”
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