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

Genome modularity and synthetic biology: Engineering systems

(2018) Milsee Mol et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Testing the hypothesis that biological modularity is shaped by adaptation: Xylem in the Bursera simaruba clade of tropical trees

(2017) Claudia Gabriela Montes-Cartas et al.   EVOLUTION & DEVELOPMENT

Logical modeling of lymphoid and myeloid cell specification and transdifferentiation

(2017) Samuel Collombet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of network modularity on the spread of perturbation impact in experimental metapopulations

(2017) Luis J. Gilarranz et al.   SCIENCE

Perspectives on Gene Regulatory Network Evolution

(2017) Marc S. Halfon   TRENDS IN GENETICS

Intelligence is associated with the modular structure of intrinsic brain networks

(2017) Kirsten Hilger et al.   Scientific Reports

Complex modular architecture around a simple toolkit of wing pattern genes

(2017) Steven M. Van Belleghem et al.   Nature Ecology & Evolution

Habitat variability does not generally promote metabolic network modularity in flies and mammals

(2016) Kazuhiro Takemoto   BIOSYSTEMS

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

(2016) Joseph Xu Zhou et al.   BIOSYSTEMS

Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells

(2016) Lucas Sánchez et al.   BMC Systems Biology

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

Community detection in networks: A user guide

(2016) Santo Fortunato et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Model-Based Characterization of Inflammatory Gene Expression Patterns of Activated Macrophages

(2016) Julia Rex et al.   PLoS Computational Biology

The Evolutionary Origins of Hierarchy

(2016) Henok Mengistu et al.   PLoS Computational Biology

A Network Model to Describe the Terminal Differentiation of B Cells

(2016) Akram Méndez et al.   PLoS Computational Biology

Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes

(2016) Abibatou Mbodj et al.   PLoS Computational Biology

The evolutionary origin of bilaterian smooth and striated myocytes

(2016) Thibaut Brunet et al.   eLife

A model of the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva

(2015) Nathan Weinstein et al.   BMC BIOINFORMATICS

Neural Modularity Helps Organisms Evolve to Learn New Skills without Forgetting Old Skills

(2015) Kai Olav Ellefsen et al.   PLoS Computational Biology

Dynamics of Transcription Factor Binding Site Evolution

(2015) Murat Tuğrul et al.   PLoS Genetics

Modeling the evolution of complex genetic systems: The gene network family tree

(2014) Janna L. Fierst et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Dynamics of Cell-Fate Determination and Patterning in the Vascular Bundles of Arabidopsis thaliana

(2013) Mariana Benítez et al.   PLoS One

Mutation Rules and the Evolution of Sparseness and Modularity in Biological Systems

(2013) Tamar Friedlander et al.   PLoS One

The evolutionary origins of modularity

(2013) J. Clune et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Finding Missing Interactions of the Arabidopsis thaliana Root Stem Cell Niche Gene Regulatory Network

(2013) Eugenio Azpeitia et al.   Frontiers in Plant Science

Modular gene-circuit design takes two steps forward

(2012) Jeffrey J Tabor   NATURE METHODS

General Theory of Genotype to Phenotype Mapping: Derivation of Epigenetic Landscapes from N-Node Complex Gene Regulatory Networks

(2012) Carlos Villarreal et al.   PHYSICAL REVIEW LETTERS

Predictive computation of genomic logic processing functions in embryonic development

(2012) I. S. Peter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post-Darwinian biology?

(2011) Sui Huang   BIOESSAYS

Protein Structural Modularity and Robustness Are Associated with Evolvability

(2011) Mary M. Rorick et al.   Genome Biology and Evolution

Two developmental modules establish 3D beak-shape variation in Darwin's finches

(2011) R. Mallarino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability

(2011) Kirsten H. ten Tusscher et al.   PLoS Computational Biology

Specialization Can Drive the Evolution of Modularity

(2010) Carlos Espinosa-Soto et al.   PLoS Computational Biology

Survival of the sparsest: robust gene networks are parsimonious

(2008) Robert D Leclerc   Molecular Systems Biology

The evolution of cell types in animals: emerging principles from molecular studies

(2008) Detlev Arendt   NATURE REVIEWS GENETICS

Community Structure in Directed Networks

(2008) E. A. Leicht et al.   PHYSICAL REVIEW LETTERS

Is evolvability evolvable?

(2007) Massimo Pigliucci   NATURE REVIEWS GENETICS