The microbiome is a complex and dynamic community of microorganisms that co-exist
interdependently within an ecosystem, and interact with its host or environment. Longitudinal …

Regulation of gene expression is central to many biological processes. Although
reconstruction of regulatory circuits from genomic data alone is therefore desirable, this …

16S ribosomal RNA (rRNA) gene and other environmental sequencing techniques provide
snapshots of microbial communities, revealing phylogeny and the abundances of microbial …

Transcriptional and post-transcriptional regulation of gene expression is of fundamental
importance to numerous biological processes. Nowadays, an increasing amount of gene …

Understanding how gene expression programs are controlled requires identifying regulatory
relationships between transcription factors and target genes. Gene regulatory networks are …

The elucidation of gene regulatory networks is one of the major challenges of systems
biology. Measurements about genes that are exploited by network inference methods are …

Environmental gene regulatory influence networks (EGRINs) coordinate the timing and rate
of gene expression in response to environmental signals. EGRINs encompass many layers …

Organisms from all domains of life use gene regulation networks to control cell growth,
identity, function, and responses to environmental challenges. Although accurate global …

Transcriptional regulatory networks (TRNs) provide insight into cellular behavior by
describing interactions between transcription factors (TFs) and their gene targets. The assay …

Motivation: Reconstructing the topology of gene regulatory networks (GRNs) from time
series of gene expression data remains an important open problem in computational …