Publications (50) Publications de Francisco Javier Planes Pedreño

2024

  1. BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities

    Bioinformatics, Vol. 40, Núm. 5

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

    npj Systems Biology and Applications, Vol. 10, Núm. 1

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

    Briefings in Bioinformatics, Vol. 25, Núm. 3

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

    Bioinformatics, Vol. 40, Núm. 6

2023

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

    NPJ systems biology and applications, Vol. 9, Núm. 1, pp. 32

2022

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

    PLoS Computational Biology, Vol. 18, Núm. 3

  2. ALAD Inhibition by Porphobilinogen Rationalizes the Accumulation of δ-Aminolevulinate in Acute Porphyrias

    Biochemistry, Vol. 61, Núm. 21, pp. 2409-2416

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

    PLoS Computational Biology, Vol. 18, Núm. 5

  4. Landscape and clinical significance of long noncoding RNAs involved in multiple myeloma expressed fusion transcripts

    American Journal of Hematology

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

    npj Systems Biology and Applications, Vol. 8, Núm. 1

  6. The bone marrow niche regulates redox and energy balance in MLL::AF9 leukemia stem cells

    Leukemia, Vol. 36, Núm. 8, pp. 1969-1979

2021

  1. An extended reconstruction of human gut microbiota metabolism of dietary compounds

    Nature Communications, Vol. 12, Núm. 1

  2. Characterization of complete lncRNAs transcriptome reveals the functional and clinical impact of lncRNAs in multiple myeloma

    Leukemia, Vol. 35, Núm. 5, pp. 1438-1450

  3. Effect of freezing on gut microbiota composition and functionality for in vitro fermentation experiments

    Nutrients, Vol. 13, Núm. 7

  4. Gene expression derived from alternative promoters improves prognostic stratification in multiple myeloma

    Leukemia, Vol. 35, Núm. 10, pp. 3012-3016

2020

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

    Reproductive toxicology (Elmsford, N.Y.), Vol. 94, pp. 55-64

  2. Drugsniper, a tool to exploit loss-of-function screens, identifies CREBBP as a predictive biomarker of VOLASERTIB in small cell lung carcinoma (SCLC)

    Cancers, Vol. 12, Núm. 7, pp. 1-18

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

    Bioinformatics, Vol. 36, Núm. 6, pp. 1986-1988

2019

  1. Adaptation of the human gut microbiota metabolic network during the first year after birth

    Frontiers in Microbiology, Vol. 10, Núm. APR

  2. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

    Nature Protocols, Vol. 14, Núm. 3, pp. 639-702