The complex and hierarchical vascular network of arteries, veins, capillaries features considerable endothelial heterogeneity, yet the regulatory pathways directing arteriovenous specification, differentiation identity are still not fully understood. Recent advances in analysis endothelial-specific gene elements, single cell RNA sequencing (scRNA-seq) lineage tracing has both emphasized importa...

In an effort to understand the dynamic organization of the protein interaction network and its role in the regulation of cell behavior, positioning of proteins into specific network localities was studied with respect to their expression dynamics. First, we find that constitutively expressed and dynamically co-regulated proteins cluster in distinct functionally specialized network neighborhoods...

Inference of gene regulatory network is a useful approach to understand the control systems in living cells. To obtain the better insights into the gene regulation, we developed statistical approach, based on Structural Equation Modeling (SEM) in combination with factor analysis and improved four-step procedure. This approach allowed us to reconstruct a model of transcriptional regulation that ...

Reductionist treatments of the epigenetic regulation of gene expression suffer the same mereological and sufficiency fallacies that haunt both contemporary systems biology and neural network models of high order cognition. Shifting perspective from the massively parallel space of gene matrix interactions to the grammar/syntax of the time series of developmentally expressed phenotypes using a co...

If fragments of DNA are transcribed (expressed), they deserve to be called (parts of) a gene. Whether transcription takes place depends on the 'gene regulatory network'. This network is defined as the complex interplay of the sequence, biochemical modifications and structure of the chromosomal DNA with the regulatory proteins/RNA (transcription factors, co-factors, regulating RNA and the transc...

Extinction reduces fear to stimuli that were once associated with an aversive event by no longer coupling the stimulus with the aversive event. Extinction learning is supported by a network comprising the amygdala, hippocampus, and prefrontal cortex. Previous studies implicate a critical role of GABA in extinction learning, specifically the GAD65 isoform of the GABA synthesizing enzyme glutamic...

We consider the problem of network completion, which is to make the minimum amount of modifications to a given network so that the resulting network is most consistent with the observed data. We employ here a certain type of differential equations as gene regulation rules in a genetic network, gene expression time series data as observed data, and deletions and additions of edges as basic modif...