A general computational approach to predicting synergistic transcriptional cores that determine cell subpopulation identities

in Nucleic Acids Research (2019)

An integrative method to predict signallingperturbations for cellular transitions

in Nucleic Acids Research (2019)

A complex of the ubiquitin ligase TRIM32 and the deubiquitinase USP7 balances the level of c-Myc ubiquitination and thereby determines neural stem cell fate specification

in Cell Death and Differentiation (2018)

Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift

in Nature Communications (2018)

A systems biology approach to identify niche determinants of cellular phenotypes

in Stem Cell Research (2016)

Recent reports indicate a dominant role for cellular microenvironment or niche for stably maintaining cellular phenotypic states. Identification of key niche mediated signaling that maintains stem cells ... [more ▼]

Recent reports indicate a dominant role for cellular microenvironment or niche for stably maintaining cellular phenotypic states. Identification of key niche mediated signaling that maintains stem cells in specific phenotypic states remains a challenge, mainly due to the complex and dynamic nature of stem cell-niche interactions. In order to overcome this, we consider that stem cells maintain their phenotypic state by experiencing a constant effect created by the niche by integrating its signals via signaling pathways. Such a constant niche effect should induce sustained activation/inhibition of specific stem cell signaling pathways that controls the gene regulatory program defining the cellular phenotypic state. Based on this view, we propose a computational approach to identify the most likely receptor mediated signaling responsible for transmitting niche signals to the transcriptional regulatory network that maintain cell-specific gene expression patterns, termed as niche determinants. We demonstrate the utility of our method in different stem cell systems by identifying several known and novel niche determinants. Given the key role of niche in several degenerative diseases, identification of niche determinants can aid in developing strategies for potential applications in regenerative medicine. [less ▲]

A computational strategy for predicting lineage specifiers in stem cell subpopulations

in Stem Cell Research (2015)

The RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAs

in Nucleic Acids Research (2015)

Gene regulatory network analysis reveals differences in site-specific cell fate determination in mammalian brain

in Frontiers in Cellular Neuroscience (2014)