Search Results - "Planes, J"

A network-based approach to integrate nutrient microenvironment in the prediction of synthetic lethality in cancer metabolism by Apaolaza, Iñigo, San José-Enériz, Edurne, Valcarcel, Luis V, Agirre, Xabier, Prosper, Felipe, Planes, Francisco J

“…Synthetic Lethality (SL) is currently defined as a type of genetic interaction in which the loss of function of either of two genes individually has limited…”
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BOSO: A novel feature selection algorithm for linear regression with high-dimensional data by Valcárcel, Luis V, San José-Enériz, Edurne, Cendoya, Xabier, Rubio, Ángel, Agirre, Xabier, Prósper, Felipe, Planes, Francisco J

“…With the frenetic growth of high-dimensional datasets in different biomedical domains, there is an urgent need to develop predictive methods able to deal with…”
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An in-silico approach to predict and exploit synthetic lethality in cancer metabolism by Apaolaza, Iñigo, San José-Eneriz, Edurne, Tobalina, Luis, Miranda, Estíbaliz, Garate, Leire, Agirre, Xabier, Prósper, Felipe, Planes, Francisco J.

“…Synthetic lethality is a promising concept in cancer research, potentially opening new possibilities for the development of more effective and selective…”
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gMCS: fast computation of genetic minimal cut sets in large networks by Apaolaza, Iñigo, Valcarcel, Luis Vitores, Planes, Francisco J

“…Abstract Motivation The identification of minimal gene knockout strategies to engineer metabolic systems constitutes one of the most relevant applications of…”
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An automated network-based tool to search for metabolic vulnerabilities in cancer by Valcárcel, Luis V., San José-Enériz, Edurne, Ordoñez, Raquel, Apaolaza, Iñigo, Olaverri-Mendizabal, Danel, Barrena, Naroa, Valcárcel, Ana, Garate, Leire, San Miguel, Jesús, Pineda-Lucena, Antonio, Agirre, Xabier, Prósper, Felipe, Planes, Francisco J.

“…The development of computational tools for the systematic prediction of metabolic vulnerabilities of cancer cells constitutes a central question in systems…”
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An extended reconstruction of human gut microbiota metabolism of dietary compounds by Blasco, Telmo, Pérez-Burillo, Sergio, Balzerani, Francesco, Hinojosa-Nogueira, Daniel, Lerma-Aguilera, Alberto, Pastoriza, Silvia, Cendoya, Xabier, Rubio, Ángel, Gosalbes, María José, Jiménez-Hernández, Nuria, Pilar Francino, M., Apaolaza, Iñigo, Rufián-Henares, José Ángel, Planes, Francisco J.

“…Understanding how diet and gut microbiota interact in the context of human health is a key question in personalized nutrition. Genome-scale metabolic networks…”
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Joint analysis of miRNA and mRNA expression data by Muniategui, Ander, Pey, Jon, Planes, Francisco J, Rubio, Angel

“…miRNAs are small RNA molecules ('22 nt) that interact with their target mRNAs inhibiting translation or/and cleavaging the target mRNA. This interaction is…”
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Computing the shortest elementary flux modes in genome-scale metabolic networks by de Figueiredo, Luis F., Podhorski, Adam, Rubio, Angel, Kaleta, Christoph, Beasley, John E., Schuster, Stefan, Planes, Francisco J.

“…Motivation: Elementary flux modes (EFMs) represent a key concept to analyze metabolic networks from a pathway-oriented perspective. In spite of considerable…”
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BET inhibitors down-regulate the expression of the essential lncRNA SMILO in multiple myeloma through regulation of the transcription factor FLI1 by Gómez-Echarte, Nahia, José-Enériz, Edurne San, Carrasco-León, Arantxa, Barrena, Naroa, Miranda, Estibaliz, Garate, Leire, García-Torre, Beatriz, Alonso-Moreno, Sandra, Gimenez-Camino, Naroa, Urizar-Compains, Estibaliz, Olaverri-Mendizabal, Danel, Aguirre-Ruiz, Paula, Ariceta, Beñat, Tamariz-Amador, Luis-Esteban, Rodriguez-Otero, Paula, Planes, Francisco J, Belver, Laura, Martín-Subero, José Ignacio, Prosper, Felipe, Agirre, Xabier

“…Not available.Not available…”
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New Inference Rules for Max-SAT by Li, C. M., Manya, F., Planes, J.

“…Exact Max-SAT solvers, compared with SAT solvers, apply little inference at each node of the proof tree. Commonly used SAT inference rules like unit…”
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Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast Context-Specific Network Reconstruction Method by Tobalina, Luis, Pey, Jon, Rezola, Alberto, Planes, Francisco J

“…Gene Essentiality Analysis based on Flux Balance Analysis (FBA-based GEA) is a promising tool for the identification of novel metabolic therapeutic targets in…”
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Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells by Barrena, Naroa, Valcárcel, Luis V., Olaverri-Mendizabal, Danel, Apaolaza, Iñigo, Planes, Francisco J.

“…Synthetic lethality (SL) is a promising concept in cancer research. A wide array of computational tools has been developed to predict and exploit synthetic…”
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Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota by Balzerani, Francesco, Blasco, Telmo, Pérez-Burillo, Sergio, Valcarcel, Luis V., Hassoun, Soha, Planes, Francisco J.

“…Despite significant advances in reconstructing genome-scale metabolic networks, the understanding of cellular metabolism remains incomplete for many organisms…”
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In-silico prediction of key metabolic differences between two non-small cell lung cancer subtypes by Rezola, Alberto, Pey, Jon, Rubio, Ángel, Planes, Francisco J

“…Metabolism expresses the phenotype of living cells and understanding it is crucial for different applications in biotechnology and health. With the increasing…”
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Adaptation of the Human Gut Microbiota Metabolic Network During the First Year After Birth by Fuertes, Alvaro, Pérez-Burillo, Sergio, Apaolaza, Iñigo, Vallès, Yvonne, Francino, M Pilar, Rufián-Henares, José Ángel, Planes, Francisco J

“…Predicting the metabolic behavior of the human gut microbiota in different contexts is one of the most promising areas of constraint-based modeling. Recently,…”
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Path finding methods accounting for stoichiometry in metabolic networks by Pey, Jon, Prada, Joaquín, Beasley, John E, Planes, Francisco J

“…Graph-based methods have been widely used for the analysis of biological networks. Their application to metabolic networks has been much discussed, in…”
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Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments by Pérez-Burillo, Sergio, Hinojosa-Nogueira, Daniel, Navajas-Porras, Beatriz, Blasco, Telmo, Balzerani, Francesco, Lerma-Aguilera, Alberto, León, Daniel, Pastoriza, Silvia, Apaolaza, Iñigo, Planes, Francisco J., Francino, Maria Pilar, Rufián-Henares, José Ángel

“…The gut microbiota has a profound effect on human health and is modulated by food and bioactive compounds. To study such interaction, in vitro batch…”
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Prediction of degradation pathways of phenolic compounds in the human gut microbiota through enzyme promiscuity methods by Balzerani, Francesco, Hinojosa-Nogueira, Daniel, Cendoya, Xabier, Blasco, Telmo, Pérez-Burillo, Sergio, Apaolaza, Iñigo, Francino, M. Pilar, Rufián-Henares, José Ángel, Planes, Francisco J.

“…The relevance of phenolic compounds in the human diet has increased in recent years, particularly due to their role as natural antioxidants and chemopreventive…”
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Advances in network-based metabolic pathway analysis and gene expression data integration by Rezola, Alberto, Pey, Jon, Tobalina, Luis, Rubio, Ángel, Beasley, John E, Planes, Francisco J

“…With the emergence of metabolic networks, novel mathematical pathway concepts were introduced in the past decade, aiming to go beyond canonical maps. However,…”
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Exploring metabolic pathways in genome-scale networks via generating flux modes by REZOLA, A, DE FIGUEIREDO, L. F, BROCK, M, PEY, J, PODHORSKI, A, WITTMANN, C, SCHUSTER, S, BOCKMAYR, A, PLANES, F. J

“…The reconstruction of metabolic networks at the genome scale has allowed the analysis of metabolic pathways at an unprecedented level of complexity. Elementary…”
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