Priyotosh Sil

An integrated resource for systems-level analysis of aging hallmarks and associated genes

This paper introduces AgingHallmarksDB, a resource for systems-level analysis of aging hallmarks and associated genes, demonstrating its utility through various analyses of disease and transcriptome data.

Simple threshold-based Boolean rules fall short in capturing biological regulatory network dynamics

This study evaluates threshold majority rules in gene regulatory network modeling, finding they lack biological realism and fail to capture key dynamics observed in empirical data.

Choices of regulatory logic class modulate the dynamical regime in random Boolean networks

This study shows that biologically meaningful Boolean functions stabilize random Boolean network dynamics more than random functions, across varying network sizes and connectivities.

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.

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.