Synthetic lethality and the minimal genome size problem.

Gene knockout studies suggest that ~300 genes in a bacterial genome and ~1,100 genes in a yeast genome cannot be deleted without loss of viability. These single-gene knockout experiments do not account for negative genetic interactions, when two or more genes can each be deleted without effect, but their joint deletion is lethal. Thus, large-scale single-gene deletion studies underestimate the size of a minimal gene set compatible with cell survival.

Single-cell transcriptomics reveals stage- and side-specificity of gene modules in colorectal cancer.

Background: An understanding of mechanisms underlying colorectal cancer (CRC) development and progression is yet to be fully elucidated. This study aims to employ network theoretic approaches to analyse single cell transcriptomic data from CRC to better characterize its progression and sided-ness.

Methods: We utilized a recently published single-cell RNA sequencing data (GEO-GSE178341) and parsed the cell X gene data by stage and side (right and left colon).

Modular and mechanistic changes across stages of colorectal cancer.

Background: While mechanisms contributing to the progression and metastasis of colorectal cancer (CRC) are well studied, cancer stage-specific mechanisms have been less comprehensively explored. This is the focus of this manuscript.

Methods: Using previously published data for CRC (Gene Expression Omnibus ID GSE21510), we identified differentially expressed genes (DEGs) across four stages of the disease.

Topological and functional comparison of community detection algorithms in biological networks.

Background: Community detection algorithms are fundamental tools to uncover important features in networks. There are several studies focused on social networks but only a few deal with biological networks. Directly or indirectly, most of the methods maximize modularity, a measure of the density of links within communities as compared to links between communities.