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The early fly embryo offers a relatively pure version of the problem of spatial scaling in biological pattern formation. Within three hours, a blueprint for the final segmented body plan of the animal is visible in striped patterns of gene expression. We measure the positions of these stripes in an ensemble of 100+ embryos from a laboratory strain of Drosophila melanogaster, under controlled conditions. These embryos vary in length by only 4% (rms), yet stripes are positioned with 1% accuracy; precision and scaling of the pattern are intertwined. We can see directly the variation of absolute stripe positions with length, and the precision is so high as to exclude alternatives, such as combinations of unscaled signals from the two ends of the embryo.
Motivated by recent experimental work, we define and study a deterministic model of the complex miRNA-based regulatory circuit that putatively controls the early stage of myogenesis in human. We aim in particular at a quantitative understanding of (i
In biochemical networks, reactions often occur on disparate timescales and can be characterized as either fast or slow. The quasi-steady state approximation (QSSA) utilizes timescale separation to project models of biochemical networks onto lower-dim
A wide range of organisms features molecular machines, circadian clocks, which generate endogenous oscillations with ~24 h periodicity and thereby synchronize biological processes to diurnal environmental fluctuations. Recently, it has become clear t
In mammals, most cells in the brain and peripheral tissues generate circadian (~24hr) rhythms autonomously. These self-sustained rhythms are coordinated and entrained by a master circadian clock in the suprachiasmatic nucleus (SCN). Within the SCN, t
Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction networks that p