Network biology: understanding the cell's functional organization

AL Barabasi, ZN Oltvai - Nature reviews genetics, 2004 - nature.com
A key aim of postgenomic biomedical research is to systematically catalogue all molecules
and their interactions within a living cell. There is a clear need to understand how these …

A census of human transcription factors: function, expression and evolution

JM Vaquerizas, SK Kummerfeld, SA Teichmann… - Nature Reviews …, 2009 - nature.com
Transcription factors are key cellular components that control gene expression: their
activities determine how cells function and respond to the environment. Currently, there is …

Studying and modelling dynamic biological processes using time-series gene expression data

Z Bar-Joseph, A Gitter, I Simon - Nature Reviews Genetics, 2012 - nature.com
Biological processes are often dynamic, thus researchers must monitor their activity at
multiple time points. The most abundant source of information regarding such dynamic …

Transcriptional Regulatory Networks in Saccharomyces cerevisiae

TI Lee, NJ Rinaldi, F Robert, DT Odom, Z Bar-Joseph… - science, 2002 - science.org
We have determined how most of the transcriptional regulators encoded in the eukaryote
Saccharomyces cerevisiae associate with genes across the genome in living cells. Just as …

Transcriptional Regulation in Saccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and …

S Hahn, ET Young - Genetics, 2011 - academic.oup.com
Here we review recent advances in understanding the regulation of mRNA synthesis in
Saccharomyces cerevisiae. Many fundamental gene regulatory mechanisms have been …

Genomic targets of the human c-Myc protein

PC Fernandez, SR Frank, L Wang… - Genes & …, 2003 - genesdev.cshlp.org
The transcription factor Myc is induced by mitogenic signals and regulates downstream
cellular responses. If overexpressed, Myc promotes malignant transformation. Myc …

E2F integrates cell cycle progression with DNA repair, replication, and G2/M checkpoints

B Ren, H Cam, Y Takahashi, T Volkert… - Genes & …, 2002 - genesdev.cshlp.org
The E2F transcription factor family is known to play a key role in the timely expression of
genes required for cell cycle progression and proliferation, but only a few E2F target genes …

[HTML][HTML] A unified theory of gene expression

G Orphanides, D Reinberg - Cell, 2002 - cell.com
The human genome has been called" the blueprint for life." This master plan is realized
through the process of gene expression. Recent progress has revealed that many of the …

Genomic analysis of regulatory network dynamics reveals large topological changes

NM Luscombe, M Madan Babu, H Yu, M Snyder… - Nature, 2004 - nature.com
Network analysis has been applied widely, providing a unifying language to describe
disparate systems ranging from social interactions to power grids. It has recently been used …

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs

S Cawley, S Bekiranov, HH Ng, P Kapranov… - Cell, 2004 - cell.com
Using high-density oligonucleotide arrays representing essentially all nonrepetitive
sequences on human chromosomes 21 and 22, we map the binding sites in vivo for three …