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ABSTRACT. Boolean network models have gained popularity in computational systems biology over the last dozen years. Many of these networks use canalizing Boolean functions, which has led to increased interest in the study of these functions. The canalizing depth of a function describes how many canalizing variables can be recursively "picked off", until a non-canalizing function remains. In this paper, we show how every Boolean function has a unique algebraic form involving extended monomial layers and a well-defined core polynomial. This generalizes recent work on the algebraic structure of nested canalizing functions, and it yields a stratification of all Boolean functions by their canalizing depth. As a result, we obtain closed formulas for the number of n-variable Boolean functions with depth k, which simultaneously generalizes enumeration formulas for canalizing, and nested canalizing functions.

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An RNA bi-structure is a pair of RNA secondary structures that are considered as arc-diagrams. We present a novel weighted homology theory for RNA bi-structures, which was obtained through the intersections of loops. The weighted homology of the intersection complex X features a new boundary operator and is formulated over a discrete valuation ring, R. We establish basic properties of the weighted complex and show how to deform it in order to eliminate any 3-simplices. We connect the simplicial homology, Hi(X), and weighted homology, Hi,R(X), in two ways: first, via chain maps, and second, via the relative homology. We compute H0,R(X) by means of a recursive contraction procedure on a weighted spanning tree and H1,R(X) via an inflation map, by which the simplicial homology of the 1-skeleton allows us to determine the weighted homology H1,R(X). The homology module H2,R(X) is naturally obtained from H2(X) via chain maps. Furthermore, we show that all weighted homology modules Hi,R(X) are trivial for i>2. The invariant factors of our structure theorems, as well as the weighted Whitehead moves facilitating the removal of filled tetrahedra, are given a combinatorial interpretation. The weighted homology of bi-structures augments the simplicial counterpart by introducing novel torsion submodules and preserving the free submodules that appear in the simplicial homology.