Computational scientists have developed algorithms inspired by natural evolution for at least
50 years. These algorithms solve optimization and design problems by building solutions …

Abstract Interpretation of high-throughput biological data requires a knowledge of the design
principles underlying the networks that sustain cellular functions. Of particular importance is …

The cilium is an essential organelle at the surface of mammalian cells whose dysfunction
causes a wide range of genetic diseases collectively called ciliopathies. The current rate at …

We hypothesize that life began not with the first self‐reproducing molecule or metabolic
network, but as a prebiotic ecology of co‐evolving populations of macromolecular aggregates (…

The organization of transcription within the prokaryotic nucleoid may be expected to both
depend on and determine the structure of the chromosome. Indeed, immunofluorescence …

Transcriptional activity has been shown to relate to the organization of chromosomes in the
eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA …

… Képès has postulated the existence of a positive feedback loop connecting periodic genome
layout to the cellular conformation of chromosomes onto transcriptional control [71]. This …

We propose a simple algorithm to detect dominating synonymous codon usage bias in
genomes. The algorithm is based on a precise mathematical formulation of the problem that lead …

… a linear discriminant function f such that the set of k's with f(k) … f, the largest positive (smallest
negative) values α i defining f … ) the linear discriminant function f and tested prediction …

… by Képès, protein networks in Chapter 5 by Ideker and coworker, metabolic networks in
Chapter 6 by Fell, and mixed molecular networks in Chapter 7 by Schächter. At the cellular level, …