EcoCyc is a bioinformatics database available online at EcoCyc. org that describes the
genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term …

Transcription regulation networks control the expression of genes. The transcription
networks of well-studied microorganisms appear to be made up of a small set of recurring …

Praise for the first edition:… superb, beautifully written and organized work that takes an
engineering approach to systems biology. Alon provides nicely written appendices to …

The transcription factors OCT4, SOX2, and NANOG have essential roles in early
development and are required for the propagation of undifferentiated embryonic stem (ES) …

For more than a decade, numerous studies have suggested that the c-Myc oncogenic
protein is likely to broadly influence the composition of the transcriptome. However, the …

Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The
software provides genome-informatics tools such as a genome browser, sequence …

The inability of neurons to regenerate long axons within the CNS is a major impediment to
improving outcome after spinal cord injury, stroke, and other CNS insults. Recent advances …

Pathway Tools is a production-quality software environment for creating a type of model-
organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc …

EcoCyc is a bioinformatics database available at EcoCyc. org that describes the genome
and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the …

Regulatory circuits controlling gene expression constantly rewire to adapt to environmental
stimuli, differentiation cues, and disease. We review our current understanding of the …