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

Similarities and differences in the associations of biological entities among species can
provide us with a better understanding of evolutionary relationships. Often the evolution of …

Module network inference is an established statistical method to reconstruct co-expression
modules and their upstream regulatory programs from integrated multi-omics datasets …

Transcriptional regulatory networks specify regulatory proteins controlling the context-
specific expression levels of genes. Inference of genome-wide regulatory networks is central …

Divergence in gene regulation can play a major role in evolution. Here, we used a
phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum …

Global warming poses major challenges for plant survival and agricultural productivity. Thus,
efforts to enhance stress resilience in plants are key strategies for protecting food security …

Induced pluripotent stem cells (iPSCs) are regarded as a central tool to understand human
biology in health and disease. Similarly, iPSCs from non-human primates should be a …

Changes in gene expression have been hypothesized to play an important role in the
evolution of divergent morphologies. To test this hypothesis in a model system, we …

Understanding gene regulatory networks is critical to understanding cellular differentiation
and response to external stimuli. Methods for global network inference have been …

Measuring allele-specific expression in interspecies hybrids is a powerful way to detect cis-
regulatory changes underlying adaptation. However, it remains difficult to identify genes …