Coordinated regulation of gene expression relies on transcription factors (TFs) binding to
specific DNA sites. Our large-scale information–theoretical analysis of> 950 TF-binding …

MITF governs multiple steps in the development of melanocytes, including specification from
neural crest, growth, survival, and terminal differentiation. In addition, the level of MITF …

One goal of human genetics is to understand how the information for precise and dynamic
gene expression programs is encoded in the genome. The interactions of transcription …

Charting a temporal path in gene networks requires linking early transcription factor (TF)-
triggered events to downstream effects. We scale-up a cell-based TF-perturbation assay to …

The transcriptome, as the pool of all transcribed elements in a given cell, is regulated by the
interaction between different molecular levels, involving epigenetic, transcriptional, and post …

Distributed information processing in biological and computational systems Page 1 94
COMMUNICATIONS OF THE ACM | JANUARY 2015 | VOL. 58 | NO. 1 review articles DOI:10.1145/2678280 …

Computer science and biology have enjoyed a long and fruitful relationship for decades.
Biologists rely on computational methods to analyze and integrate large data sets, while …

Cellular gene expression changes throughout a dynamic biological process, such as
differentiation. Pseudotimes estimate cells' progress along a dynamic process based on …

Expression reprogramming directed by transcription factors is a primary gene regulation
underlying most aspects of the biology of any organism. Our views of how gene regulation is …

Deciphering gene regulatory networks (GRNs) is both a promise and challenge of systems
biology. The promise lies in identifying key transcription factors (TFs) that enable an …