Literature DB >> 23005679

General theory of genotype to phenotype mapping: derivation of epigenetic landscapes from N-node complex gene regulatory networks.

Carlos Villarreal1, Pablo Padilla-Longoria, Elena R Alvarez-Buylla.   

Abstract

We propose a systematic methodology to construct a probabilistic epigenetic landscape of cell-fate attainment associated with N-node Boolean genetic regulatory networks. The general derivation proposed here is exemplified with an Arabidopsis thaliana network underlying floral organ determination grounded on qualitative experimental data.

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Year:  2012        PMID: 23005679     DOI: 10.1103/PhysRevLett.109.118102

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  14 in total

1.  Relative stability of network states in Boolean network models of gene regulation in development.

Authors:  Joseph Xu Zhou; Areejit Samal; Aymeric Fouquier d'Hérouël; Nathan D Price; Sui Huang
Journal:  Biosystems       Date:  2016-03-07       Impact factor: 1.973

2.  Dynamical modeling predicts an inflammation-inducible CXCR7+ B cell precursor with potential implications in lymphoid blockage pathologies.

Authors:  Jennifer Enciso; Luis Mendoza; Elena R Álvarez-Buylla; Rosana Pelayo
Journal:  PeerJ       Date:  2020-09-29       Impact factor: 2.984

3.  A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity.

Authors:  Mariana Esther Martinez-Sanchez; Luis Mendoza; Carlos Villarreal; Elena R Alvarez-Buylla
Journal:  PLoS Comput Biol       Date:  2015-06-19       Impact factor: 4.475

Review 4.  Modeling the epigenetic attractors landscape: toward a post-genomic mechanistic understanding of development.

Authors:  Jose Davila-Velderrain; Juan C Martinez-Garcia; Elena R Alvarez-Buylla
Journal:  Front Genet       Date:  2015-04-23       Impact factor: 4.599

5.  Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates.

Authors:  Jose Davila-Velderrain; Carlos Villarreal; Elena R Alvarez-Buylla
Journal:  BMC Syst Biol       Date:  2015-05-13

6.  An extended gene protein/products Boolean network model including post-transcriptional regulation.

Authors:  Alfredo Benso; Stefano Di Carlo; Gianfranco Politano; Alessandro Savino; Alessandro Vasciaveo
Journal:  Theor Biol Med Model       Date:  2014-05-07       Impact factor: 2.432

7.  Role of Cytokine Combinations on CD4+ T Cell Differentiation, Partial Polarization, and Plasticity: Continuous Network Modeling Approach.

Authors:  Mariana E Martinez-Sanchez; Leonor Huerta; Elena R Alvarez-Buylla; Carlos Villarreal Luján
Journal:  Front Physiol       Date:  2018-08-02       Impact factor: 4.566

Review 8.  From Discrete to Continuous Modeling of Lymphocyte Development and Plasticity in Chronic Diseases.

Authors:  Jennifer Enciso; Rosana Pelayo; Carlos Villarreal
Journal:  Front Immunol       Date:  2019-08-20       Impact factor: 7.561

9.  A system-level mechanistic explanation for asymmetric stem cell fates: Arabidopsis thaliana root niche as a study system.

Authors:  Mónica L García-Gómez; Diego Ornelas-Ayala; Adriana Garay-Arroyo; Berenice García-Ponce; María de la Paz Sánchez; Elena R Álvarez-Buylla
Journal:  Sci Rep       Date:  2020-02-26       Impact factor: 4.379

10.  On the role of sparseness in the evolution of modularity in gene regulatory networks.

Authors:  Carlos Espinosa-Soto
Journal:  PLoS Comput Biol       Date:  2018-05-18       Impact factor: 4.475

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