Ajay Subbaroyan

Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph

The paper evaluates how different regulatory logic rules affect the structural features of Boolean network state transition graphs, finding that biologically meaningful rules improve bushiness and convergence.

Preponderance of generalized chain functions in reconstructed Boolean models of biological networks

The paper analyzes Boolean functions in biological networks and finds generalized chain functions are significantly enriched in NCFs across multiple datasets.

ViCEKb: Vitiligo-linked Chemical Exposome Knowledgebase

ViCEKb compiles 113 unique chemical triggers of vitiligo from literature, standardizes chemical data, and highlights their biological impacts and regulatory status.

Leveraging Developmental Landscapes for Model Selection in Boolean Gene Regulatory Networks

The paper develops a method to select Boolean gene regulatory network models by leveraging developmental landscapes and attractor stability, finding that a recent model fails to respect expected cell state hierarchies and proposing an algorithm to correct this.

Composition structures and biologically meaningful logics: plausibility and relevance in bipartite models of gene regulation

The paper investigates composition structures in bipartite Boolean network models of gene regulation, finding they are enriched in real biological networks but likely driven by nested canalyzing and read-once functions.

Minimum complexity drives regulatory logic in Boolean models of living systems

The paper analyzes Boolean functions in gene regulatory networks, finding that odd-biased and read-once functions are enriched due to their minimal Boolean complexity and average sensitivity.