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A network-based approach to integrate nutrient microenvironment in the prediction of synthetic lethality in cancer metabolism

PLoS computational biology, 2022-03, Vol.18 (3), p.e1009395-e1009395

2022

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BOSO: A novel feature selection algorithm for linear regression with high-dimensional data

PLoS computational biology, 2022-05, Vol.18 (5), p.e1010180-e1010180

2022

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An in-silico approach to predict and exploit synthetic lethality in cancer metabolism

Nature communications, 2017-09, Vol.8 (1), p.459-9, Article 459

2017

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gMCS: fast computation of genetic minimal cut sets in large networks

Bioinformatics, 2019-02, Vol.35 (3), p.535-537

2019

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An automated network-based tool to search for metabolic vulnerabilities in cancer

Nature communications, 2024-10, Vol.15 (1), p.8685-15, Article 8685

2024

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An extended reconstruction of human gut microbiota metabolism of dietary compounds

Nature communications, 2021-08, Vol.12 (1), p.4728-4728, Article 4728

2021

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Computing the shortest elementary flux modes in genome-scale metabolic networks

Bioinformatics, 2009-12, Vol.25 (23), p.3158-3165

2009

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Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast Context-Specific Network Reconstruction Method

PloS one, 2016-05, Vol.11 (5), p.e0154583-e0154583

2016

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Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells

NPJ systems biology and applications, 2023-07, Vol.9 (1), p.32-32, Article 32

2023

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In-silico prediction of key metabolic differences between two non-small cell lung cancer subtypes

PloS one, 2014-08, Vol.9 (8), p.e103998-e103998

2014

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Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota

NPJ systems biology and applications, 2024-05, Vol.10 (1), p.56-56, Article 56

2024

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Path finding methods accounting for stoichiometry in metabolic networks

Genome biology, 2011-05, Vol.12 (5), p.R49-R49, Article R49

2011

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Adaptation of the Human Gut Microbiota Metabolic Network During the First Year After Birth

Frontiers in microbiology, 2019-04, Vol.10, p.848-848

2019

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Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments

Nutrients, 2021-06, Vol.13 (7), p.2207

2021

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Prediction of degradation pathways of phenolic compounds in the human gut microbiota through enzyme promiscuity methods

NPJ systems biology and applications, 2022-07, Vol.8 (1), p.24-24, Article 24

2022

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Direct calculation of minimal cut sets involving a specific reaction knock-out

Bioinformatics, 2016-07, Vol.32 (13), p.2001-2007

2016

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Recovering metabolic pathways via optimization

Bioinformatics, 2007-01, Vol.23 (1), p.92-98

2007

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Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks

Bioinformatics (Oxford, England), 2014-08, Vol.30 (15), p.2197-2203

2014

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gMCSpy: efficient and accurate computation of genetic minimal cut sets in Python

Bioinformatics (Oxford, England), 2024-06, Vol.40 (6)

2024

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Computational approach for collection and prediction of molecular initiating events in developmental toxicity

Reproductive toxicology (Elmsford, N.Y.), 2020-06, Vol.94, p.55-64

2020

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On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models

Bioinformatics, 2020-03, Vol.36 (6), p.1986-1988

2020

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CANCERTOOL: a visualization and representation interface to exploit cancer datasets

Cancer research (Chicago, Ill.), 2018-11, Vol.78 (21), p.6320-6328

2018

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Joint analysis of miRNA and mRNA expression data

Briefings in bioinformatics, 2013-05, Vol.14 (3), p.263-278

2013

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Review and meta-analysis of the genetic Minimal Cut Set approach for gene essentiality prediction in cancer metabolism

Briefings in bioinformatics, 2024-03, Vol.25 (3)

2024

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A network-based approach to integrate nutrient microenvironment in the prediction of synthetic lethality in cancer metabolism

BOSO: A novel feature selection algorithm for linear regression with high-dimensional data

An in-silico approach to predict and exploit synthetic lethality in cancer metabolism

gMCS: fast computation of genetic minimal cut sets in large networks

An automated network-based tool to search for metabolic vulnerabilities in cancer

An extended reconstruction of human gut microbiota metabolism of dietary compounds

Computing the shortest elementary flux modes in genome-scale metabolic networks

BET inhibitors down-regulate the expression of the essential lncRNA SMILO in multiple myeloma through regulation of the transcription factor FLI1

Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast Context-Specific Network Reconstruction Method

Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells

In-silico prediction of key metabolic differences between two non-small cell lung cancer subtypes

Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota

Path finding methods accounting for stoichiometry in metabolic networks

Adaptation of the Human Gut Microbiota Metabolic Network During the First Year After Birth

Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments

Prediction of degradation pathways of phenolic compounds in the human gut microbiota through enzyme promiscuity methods

Direct calculation of minimal cut sets involving a specific reaction knock-out

Recovering metabolic pathways via optimization

Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks

gMCSpy: efficient and accurate computation of genetic minimal cut sets in Python

Computational approach for collection and prediction of molecular initiating events in developmental toxicity

On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models

CANCERTOOL: a visualization and representation interface to exploit cancer datasets

Joint analysis of miRNA and mRNA expression data

Review and meta-analysis of the genetic Minimal Cut Set approach for gene essentiality prediction in cancer metabolism

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