The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

It is well established that the vast majority of human RNA transcripts do not encode for
proteins and that non-coding RNAs regulate cell physiology and shape cellular functions. A …

The transcription regulatory network inside a eukaryotic cell is defined by the combinatorial
actions of transcription factors (TFs). However, TF binding studies in plants are too few in …

Transcription factors bind in a combinatorial fashion to specify the on-and-off states of
genes; the ensemble of these binding events forms a regulatory network, constituting the …

Complex biological systems and cellular networks may underlie most genotype to
phenotype relationships. Here, we review basic concepts in network biology, discussing …

Abstract TOR (T arget O f R apamycin) is a highly conserved protein kinase that is important
in both fundamental and clinical biology. In fundamental biology, TOR is a nutrient-sensitive …

The induction of pluripotency or trans-differentiation of one cell type to another can be
accomplished with cell-lineage-specific transcription factors. Here, we report that repression …

Cytoscape is an open source software project for integrating biomolecular interaction
networks with high-throughput expression data and other molecular states into a unified …

With the increase in genomewide experiments and the sequencing of multiple genomes, the
analysis of large data sets has become commonplace in biology. It is often the case that …

This book addresses some theoretical aspects of semisupervised learning (SSL). The book
is organized as a collection of different contributions of authors who are experts on this topic …